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1 <!DOCTYPE html>
2 <html lang="en">
3 <head>
4 <meta charset="utf-8">
5 <meta http-equiv="X-UA-Compatible" content="IE=edge">
6 <meta name="viewport" content="width=device-width, initial-scale=1">
7 <!-- The above 3 meta tags *must* come first in the head; any other head content must come *after* these tags -->
8 <meta name="description" content="">
9 <meta name="author" content="">
10 <title>Phage QC on AY216660.2 - 76</title>
11 <link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.4/css/bootstrap.min.css">
12 <link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.4/css/bootstrap-theme.min.css">
13
14 <style type="text/css">
15 /*
16 * Base structure
17 */
18
19 /* Move down content because we have a fixed navbar that is 50px tall */
20 body {
21 padding-top: 50px;
22 }
23
24 h3:before {
25 display: block;
26 content: " ";
27 margin-top: -50px;
28 height: 50px;
29 visibility: hidden;
30 }
31
32 /*
33 * Global add-ons
34 */
35
36 .sub-header {
37 padding-bottom: 10px;
38 border-bottom: 1px solid #eee;
39 }
40
41 /*
42 * Top navigation
43 * Hide default border to remove 1px line.
44 */
45 .navbar-fixed-top {
46 border: 0;
47 }
48
49 /*
50 * Sidebar
51 */
52
53 /* Hide for mobile, show later */
54 .sidebar {
55 display: none;
56 }
57 @media (min-width: 768px) {
58 .sidebar {
59 position: fixed;
60 top: 51px;
61 bottom: 0;
62 left: 0;
63 z-index: 1000;
64 display: block;
65 padding: 20px;
66 overflow-x: hidden;
67 overflow-y: auto; /* Scrollable contents if viewport is shorter than content. */
68 background-color: #f5f5f5;
69 border-right: 1px solid #eee;
70 }
71 }
72
73 /* Sidebar navigation */
74 .nav-sidebar {
75 margin-right: -21px; /* 20px padding + 1px border */
76 margin-bottom: 20px;
77 margin-left: -20px;
78 }
79 .nav-sidebar > li > a {
80 padding-right: 20px;
81 padding-left: 20px;
82 }
83 .nav-sidebar > .active > a,
84 .nav-sidebar > .active > a:hover,
85 .nav-sidebar > .active > a:focus {
86 color: #fff;
87 background-color: #428bca;
88 }
89
90
91 /*
92 * Main content
93 */
94
95 .main {
96 padding: 20px;
97 }
98 @media (min-width: 768px) {
99 .main {
100 padding-right: 40px;
101 padding-left: 40px;
102 }
103 }
104 .main .page-header {
105 margin-top: 0;
106 }
107
108
109 /*
110 * Placeholder dashboard ideas
111 */
112
113 .placeholders {
114 margin-bottom: 30px;
115 text-align: center;
116 }
117 .placeholders h4 {
118 margin-bottom: 0;
119 }
120 .placeholder {
121 margin-bottom: 20px;
122 }
123 .placeholder img {
124 display: inline-block;
125 border-radius: 50%;
126 }
127
128 td.moron {
129 font-size: 150%;
130 padding: 0px;
131 color: gray;
132 }
133 .strand_emph {
134 text-decoration: underline;
135 color: black;
136 }
137
138 </style>
139 <!-- HTML5 shim and Respond.js for IE8 support of HTML5 elements and media queries -->
140 <!--[if lt IE 9]>
141 <script src="//oss.maxcdn.com/html5shiv/3.7.2/html5shiv.min.js"></script>
142 <script src="//oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
143 <![endif]-->
144 </head>
145 <body>
146
147 <nav class="navbar navbar-inverse navbar-fixed-top">
148 <div class="container-fluid">
149 <div class="navbar-header">
150 <a class="navbar-brand" href="#">Phage QC on AY216660.2</a>
151 </div>
152 </div>
153 </nav>
154
155 <div class="container-fluid">
156 <div class="row">
157 <div class="col-sm-3 col-md-2 sidebar">
158 <ul class="nav nav-sidebar">
159 <li><a href="#main"><b>Overview</b></a></li>
160 <li><a href="#bad_gene_starts"><b>Bad Gene Starts</b></a></li>
161 <li><a href="#missing_rbs"><small>Missing RBS</small></a></li>
162 <li><a href="#weird_starts"><small>Unusual Start Codons</small></a></li>
163 <li><a href="#excessive_gaps"><small>Excessive Gaps</small></a></li>
164 <li><a href="#excessive_overlap"><small>Excessive Overlaps</small></a></li>
165 <!--<li><a href="#coding_density"><small>Coding Density</small></a></li>-->
166 <li><a href="#antisense"><b>Antisense Genes</b></a></li>
167 <li><a href="#morons"><small>Possible Morons</small></a></li>
168 <li><a href="#annotations"><b>Annotation Issues</b></a></li>
169 <li><a href="#missing_product"><small>Missing Product Tags</small></a></li>
170 </ul>
171 </div>
172 <div class="col-sm-9 col-sm-offset-3 col-md-10 col-md-offset-2 main" id="main">
173 <div class="jumbotron">
174 <div class="row">
175 <div class="col-sm-7">
176 <h1>Phage AY216660.2</h1>
177 <!--<h2>Score: 76/100</h2>-->
178 </div>
179 <!--<div class="col-sm-5">
180 <table class="table table-striped">
181 <thead>
182 <tr>
183 <th>Section</th>
184 <th>Score</th>
185 </tr>
186 </thead>
187 <tbody>
188 <tr><td>Missing RBS</td><td>0%</td></tr>
189 <tr><td>Excessive Gaps</td><td>76%</td></tr>
190 <tr><td>Excessive Overlap</td><td>76%</td></tr>
191 <tr><td>Coding Density Score</td><td>99%</td></tr>
192 <tr><td>Possible Morons</td><td>98%</td></tr>
193 <tr><td>Missing Product Tags</td><td>100%</td></tr>
194 </tbody>
195 </table>
196 </div>-->
197 </div>
198 </div>
199
200 <h2 class="sub-header" id="bad_gene_starts">Gene Starts</h2>
201 <h3 id="missing_rbs">Genes missing RBS <small>0 / 79</small></h3>
202 <p>The following genes have issues with their RBS.</p>
203 <p>
204 Since you have not annotated any possible RBSs, this does not count off from your overall score.
205 </p>
206 <div class="table-responsive">
207 <table class="table table-striped">
208 <thead>
209 <tr>
210 <th>Feature Type</th>
211 <th>ID</th>
212 <th>Location</th>
213 <th>Error</th>
214 <th>Upstream (-15 .. -5)</th>
215 </tr>
216 </thead>
217 <tbody>
218 <tr>
219 <td>gene</td>
220 <td>CPT-T1_001.gene</td>
221 <td>40..576 [1]</td>
222 <td>No RBS annotated, None found</td>
223 <td><span style="font-family:monospace">taaatgttaa</span></td>
224 </tr>
225 <tr>
226 <td>gene</td>
227 <td>CPT-T1_002.gene</td>
228 <td>589..2184 [1]</td>
229 <td>Unannotated but valid RBS</td>
230 <td><span style="font-family:monospace">taacttt AGG </span></td>
231 </tr>
232 <tr>
233 <td>gene</td>
234 <td>CPT-T1_003.gene</td>
235 <td>2230..3522 [1]</td>
236 <td>No RBS annotated, None found</td>
237 <td><span style="font-family:monospace">acggcccttt</span></td>
238 </tr>
239 <tr>
240 <td>gene</td>
241 <td>CPT-T1_004.gene</td>
242 <td>3496..4273 [1]</td>
243 <td>Unannotated but valid RBS</td>
244 <td><span style="font-family:monospace">cc GGAG ccgg</span></td>
245 </tr>
246 <tr>
247 <td>gene</td>
248 <td>CPT-T1_005.gene</td>
249 <td>4264..5388 [1]</td>
250 <td>No RBS annotated, None found</td>
251 <td><span style="font-family:monospace">tccagacttt</span></td>
252 </tr>
253 <tr>
254 <td>gene</td>
255 <td>CPT-T1_006.gene</td>
256 <td>5389..5876 [1]</td>
257 <td>No RBS annotated, None found</td>
258 <td><span style="font-family:monospace">agcaaagtaa</span></td>
259 </tr>
260 <tr>
261 <td>gene</td>
262 <td>CPT-T1_007.gene</td>
263 <td>5926..6705 [1]</td>
264 <td>No RBS annotated, None found</td>
265 <td><span style="font-family:monospace">tagtcctttt</span></td>
266 </tr>
267 <tr>
268 <td>gene</td>
269 <td>CPT-T1_008.gene</td>
270 <td>6784..7755 [1]</td>
271 <td>No RBS annotated, None found</td>
272 <td><span style="font-family:monospace">ttttttatta</span></td>
273 </tr>
274 <tr>
275 <td>gene</td>
276 <td>CPT-T1_009.gene</td>
277 <td>7794..8093 [1]</td>
278 <td>No RBS annotated, None found</td>
279 <td><span style="font-family:monospace">gtcccttttt</span></td>
280 </tr>
281 <tr>
282 <td>gene</td>
283 <td>CPT-T1_010.gene</td>
284 <td>8127..8548 [1]</td>
285 <td>No RBS annotated, None found</td>
286 <td><span style="font-family:monospace">agcgcctttt</span></td>
287 </tr>
288 <tr>
289 <td>gene</td>
290 <td>CPT-T1_011.gene</td>
291 <td>8534..8919 [1]</td>
292 <td>Unannotated but valid RBS</td>
293 <td><span style="font-family:monospace">atgac AGGA c</span></td>
294 </tr>
295 <tr>
296 <td>gene</td>
297 <td>CPT-T1_012.gene</td>
298 <td>8897..9355 [1]</td>
299 <td>No RBS annotated, None found</td>
300 <td><span style="font-family:monospace">atcgtccagt</span></td>
301 </tr>
302 <tr>
303 <td>gene</td>
304 <td>CPT-T1_013.gene</td>
305 <td>9332..9743 [1]</td>
306 <td>No RBS annotated, None found</td>
307 <td><span style="font-family:monospace">gcaatcaagc</span></td>
308 </tr>
309 <tr>
310 <td>gene</td>
311 <td>CPT-T1_014.gene</td>
312 <td>9733..10414 [1]</td>
313 <td>Unannotated but valid RBS</td>
314 <td><span style="font-family:monospace">tac GAG taga</span></td>
315 </tr>
316 <tr>
317 <td>gene</td>
318 <td>CPT-T1_015.gene</td>
319 <td>10516..10845 [1]</td>
320 <td>No RBS annotated, None found</td>
321 <td><span style="font-family:monospace">tgctatcaac</span></td>
322 </tr>
323 <tr>
324 <td>gene</td>
325 <td>CPT-T1_016.gene</td>
326 <td>10516..11162 [1]</td>
327 <td>No RBS annotated, None found</td>
328 <td><span style="font-family:monospace">tgctatcaac</span></td>
329 </tr>
330 <tr>
331 <td>gene</td>
332 <td>CPT-T1_017.gene</td>
333 <td>11192..14076 [1]</td>
334 <td>No RBS annotated, None found</td>
335 <td><span style="font-family:monospace">gttttttcgt</span></td>
336 </tr>
337 <tr>
338 <td>gene</td>
339 <td>CPT-T1_018.gene</td>
340 <td>14067..14432 [1]</td>
341 <td>Unannotated but valid RBS</td>
342 <td><span style="font-family:monospace">cattc AGGA a</span></td>
343 </tr>
344 <tr>
345 <td>gene</td>
346 <td>CPT-T1_019.gene</td>
347 <td>14500..15294 [1]</td>
348 <td>Unannotated but valid RBS</td>
349 <td><span style="font-family:monospace">gttgc AGGT a</span></td>
350 </tr>
351 <tr>
352 <td>gene</td>
353 <td>CPT-T1_020.gene</td>
354 <td>15279..16025 [1]</td>
355 <td>No RBS annotated, None found</td>
356 <td><span style="font-family:monospace">tgtcgcttca</span></td>
357 </tr>
358 <tr>
359 <td>gene</td>
360 <td>CPT-T1_021.gene</td>
361 <td>16009..16621 [1]</td>
362 <td>No RBS annotated, None found</td>
363 <td><span style="font-family:monospace">taatcgttcg</span></td>
364 </tr>
365 <tr>
366 <td>gene</td>
367 <td>CPT-T1_022.gene</td>
368 <td>16688..20217 [1]</td>
369 <td>No RBS annotated, None found</td>
370 <td><span style="font-family:monospace">ataaatagca</span></td>
371 </tr>
372 <tr>
373 <td>gene</td>
374 <td>CPT-T1_023.gene</td>
375 <td>20251..20568 [1]</td>
376 <td>No RBS annotated, None found</td>
377 <td><span style="font-family:monospace">atgccctttt</span></td>
378 </tr>
379 <tr>
380 <td>gene</td>
381 <td>CPT-T1_024.gene</td>
382 <td>20556..21257 [1]</td>
383 <td>No RBS annotated, None found</td>
384 <td><span style="font-family:monospace">cttaatagca</span></td>
385 </tr>
386 <tr>
387 <td>gene</td>
388 <td>CPT-T1_025.gene</td>
389 <td>21279..21518 [-1]</td>
390 <td>No RBS annotated, None found</td>
391 <td><span style="font-family:monospace">aatcacacta</span></td>
392 </tr>
393 <tr>
394 <td>gene</td>
395 <td>CPT-T1_026.gene</td>
396 <td>21755..21906 [1]</td>
397 <td>No RBS annotated, None found</td>
398 <td><span style="font-family:monospace">tgtatatcgt</span></td>
399 </tr>
400 <tr>
401 <td>gene</td>
402 <td>CPT-T1_027.gene</td>
403 <td>22020..23098 [1]</td>
404 <td>No RBS annotated, None found</td>
405 <td><span style="font-family:monospace">attcatcgta</span></td>
406 </tr>
407 <tr>
408 <td>gene</td>
409 <td>CPT-T1_028.gene</td>
410 <td>23129..23820 [1]</td>
411 <td>No RBS annotated, None found</td>
412 <td><span style="font-family:monospace">aaacaaataa</span></td>
413 </tr>
414 <tr>
415 <td>gene</td>
416 <td>CPT-T1_029.gene</td>
417 <td>23854..24289 [1]</td>
418 <td>No RBS annotated, None found</td>
419 <td><span style="font-family:monospace">tcgcccataa</span></td>
420 </tr>
421 <tr>
422 <td>gene</td>
423 <td>CPT-T1_030.gene</td>
424 <td>24351..26550 [-1]</td>
425 <td>No RBS annotated, None found</td>
426 <td><span style="font-family:monospace">cgtgctattt</span></td>
427 </tr>
428 <tr>
429 <td>gene</td>
430 <td>CPT-T1_031.gene</td>
431 <td>26447..26600 [-1]</td>
432 <td>No RBS annotated, None found</td>
433 <td><span style="font-family:monospace">tgcccattgc</span></td>
434 </tr>
435 <tr>
436 <td>gene</td>
437 <td>CPT-T1_032.gene</td>
438 <td>26638..27585 [-1]</td>
439 <td>No RBS annotated, None found</td>
440 <td><span style="font-family:monospace">cgcgtttttt</span></td>
441 </tr>
442 <tr>
443 <td>gene</td>
444 <td>CPT-T1_033.gene</td>
445 <td>27635..28098 [-1]</td>
446 <td>No RBS annotated, None found</td>
447 <td><span style="font-family:monospace">gcaaaaagtg</span></td>
448 </tr>
449 <tr>
450 <td>gene</td>
451 <td>CPT-T1_034.gene</td>
452 <td>28168..30199 [1]</td>
453 <td>No RBS annotated, None found</td>
454 <td><span style="font-family:monospace">gttacaacga</span></td>
455 </tr>
456 <tr>
457 <td>gene</td>
458 <td>CPT-T1_035.gene</td>
459 <td>30181..30612 [1]</td>
460 <td>No RBS annotated, None found</td>
461 <td><span style="font-family:monospace">caaagacttc</span></td>
462 </tr>
463 <tr>
464 <td>gene</td>
465 <td>CPT-T1_036.gene</td>
466 <td>30669..31393 [1]</td>
467 <td>No RBS annotated, None found</td>
468 <td><span style="font-family:monospace">atctcaccaa</span></td>
469 </tr>
470 <tr>
471 <td>gene</td>
472 <td>CPT-T1_037.gene</td>
473 <td>31377..31641 [1]</td>
474 <td>No RBS annotated, None found</td>
475 <td><span style="font-family:monospace">aaaacaaacg</span></td>
476 </tr>
477 <tr>
478 <td>gene</td>
479 <td>CPT-T1_038.gene</td>
480 <td>31695..31917 [1]</td>
481 <td>No RBS annotated, None found</td>
482 <td><span style="font-family:monospace">tcatagaaac</span></td>
483 </tr>
484 <tr>
485 <td>gene</td>
486 <td>CPT-T1_039.gene</td>
487 <td>31881..32167 [1]</td>
488 <td>No RBS annotated, None found</td>
489 <td><span style="font-family:monospace">cttcatctct</span></td>
490 </tr>
491 <tr>
492 <td>gene</td>
493 <td>CPT-T1_040.gene</td>
494 <td>32099..32399 [1]</td>
495 <td>Unannotated but valid RBS</td>
496 <td><span style="font-family:monospace"> GAG ttttacc</span></td>
497 </tr>
498 <tr>
499 <td>gene</td>
500 <td>CPT-T1_041.gene</td>
501 <td>32467..33611 [1]</td>
502 <td>No RBS annotated, None found</td>
503 <td><span style="font-family:monospace">tttcattatc</span></td>
504 </tr>
505 <tr>
506 <td>gene</td>
507 <td>CPT-T1_042.gene</td>
508 <td>33673..34166 [1]</td>
509 <td>No RBS annotated, None found</td>
510 <td><span style="font-family:monospace">ttttatagaa</span></td>
511 </tr>
512 <tr>
513 <td>gene</td>
514 <td>CPT-T1_043.gene</td>
515 <td>34226..34415 [1]</td>
516 <td>No RBS annotated, None found</td>
517 <td><span style="font-family:monospace">accacatcga</span></td>
518 </tr>
519 <tr>
520 <td>gene</td>
521 <td>CPT-T1_044.gene</td>
522 <td>34525..34749 [1]</td>
523 <td>No RBS annotated, None found</td>
524 <td><span style="font-family:monospace">gttcaaaaaa</span></td>
525 </tr>
526 <tr>
527 <td>gene</td>
528 <td>CPT-T1_045.gene</td>
529 <td>34739..35237 [1]</td>
530 <td>Unannotated but valid RBS</td>
531 <td><span style="font-family:monospace"> AGG cgcttaa</span></td>
532 </tr>
533 <tr>
534 <td>gene</td>
535 <td>CPT-T1_046.gene</td>
536 <td>35227..35638 [1]</td>
537 <td>No RBS annotated, None found</td>
538 <td><span style="font-family:monospace">acgcatattg</span></td>
539 </tr>
540 <tr>
541 <td>gene</td>
542 <td>CPT-T1_047.gene</td>
543 <td>35761..36179 [-1]</td>
544 <td>No RBS annotated, None found</td>
545 <td><span style="font-family:monospace">caatcctcga</span></td>
546 </tr>
547 <tr>
548 <td>gene</td>
549 <td>CPT-T1_048.gene</td>
550 <td>36173..37755 [-1]</td>
551 <td>No RBS annotated, None found</td>
552 <td><span style="font-family:monospace">tcacgccgtc</span></td>
553 </tr>
554 <tr>
555 <td>gene</td>
556 <td>CPT-T1_049.gene</td>
557 <td>37741..38294 [-1]</td>
558 <td>No RBS annotated, None found</td>
559 <td><span style="font-family:monospace">gacggcacaa</span></td>
560 </tr>
561 <tr>
562 <td>gene</td>
563 <td>CPT-T1_050.gene</td>
564 <td>38277..38706 [-1]</td>
565 <td>No RBS annotated, None found</td>
566 <td><span style="font-family:monospace">tcaagataac</span></td>
567 </tr>
568 <tr>
569 <td>gene</td>
570 <td>CPT-T1_051.gene</td>
571 <td>38774..38994 [-1]</td>
572 <td>No RBS annotated, None found</td>
573 <td><span style="font-family:monospace">tttacattaa</span></td>
574 </tr>
575 <tr>
576 <td>gene</td>
577 <td>CPT-T1_052.gene</td>
578 <td>38987..39222 [-1]</td>
579 <td>No RBS annotated, None found</td>
580 <td><span style="font-family:monospace">taccaaacaa</span></td>
581 </tr>
582 <tr>
583 <td>gene</td>
584 <td>CPT-T1_053.gene</td>
585 <td>39289..39444 [-1]</td>
586 <td>No RBS annotated, None found</td>
587 <td><span style="font-family:monospace">ggcatatcaa</span></td>
588 </tr>
589 <tr>
590 <td>gene</td>
591 <td>CPT-T1_054.gene</td>
592 <td>39429..39758 [-1]</td>
593 <td>No RBS annotated, None found</td>
594 <td><span style="font-family:monospace">tatcctgact</span></td>
595 </tr>
596 <tr>
597 <td>gene</td>
598 <td>CPT-T1_055.gene</td>
599 <td>39766..39978 [-1]</td>
600 <td>Unannotated but valid RBS</td>
601 <td><span style="font-family:monospace">tagc GGA tcg</span></td>
602 </tr>
603 <tr>
604 <td>gene</td>
605 <td>CPT-T1_056.gene</td>
606 <td>39959..40342 [-1]</td>
607 <td>No RBS annotated, None found</td>
608 <td><span style="font-family:monospace">acatcaacag</span></td>
609 </tr>
610 <tr>
611 <td>gene</td>
612 <td>CPT-T1_057.gene</td>
613 <td>41020..41606 [1]</td>
614 <td>No RBS annotated, None found</td>
615 <td><span style="font-family:monospace">tgtatattga</span></td>
616 </tr>
617 <tr>
618 <td>gene</td>
619 <td>CPT-T1_058.gene</td>
620 <td>41606..41945 [1]</td>
621 <td>Unannotated but valid RBS</td>
622 <td><span style="font-family:monospace">aaaatgt GGA </span></td>
623 </tr>
624 <tr>
625 <td>gene</td>
626 <td>CPT-T1_059.gene</td>
627 <td>42013..42254 [1]</td>
628 <td>Unannotated but valid RBS</td>
629 <td><span style="font-family:monospace">ac GAG atacc</span></td>
630 </tr>
631 <tr>
632 <td>gene</td>
633 <td>CPT-T1_060.gene</td>
634 <td>42247..42487 [1]</td>
635 <td>No RBS annotated, None found</td>
636 <td><span style="font-family:monospace">tcagcacttt</span></td>
637 </tr>
638 <tr>
639 <td>gene</td>
640 <td>CPT-T1_061.gene</td>
641 <td>42473..42594 [1]</td>
642 <td>No RBS annotated, None found</td>
643 <td><span style="font-family:monospace">ggcgacaaca</span></td>
644 </tr>
645 <tr>
646 <td>gene</td>
647 <td>CPT-T1_062.gene</td>
648 <td>42580..42764 [1]</td>
649 <td>No RBS annotated, None found</td>
650 <td><span style="font-family:monospace">ttgctactgt</span></td>
651 </tr>
652 <tr>
653 <td>gene</td>
654 <td>CPT-T1_063.gene</td>
655 <td>42824..43324 [1]</td>
656 <td>No RBS annotated, None found</td>
657 <td><span style="font-family:monospace">ccatcgacaa</span></td>
658 </tr>
659 <tr>
660 <td>gene</td>
661 <td>CPT-T1_064.gene</td>
662 <td>43385..43881 [1]</td>
663 <td>No RBS annotated, None found</td>
664 <td><span style="font-family:monospace">acatcaacca</span></td>
665 </tr>
666 <tr>
667 <td>gene</td>
668 <td>CPT-T1_065.gene</td>
669 <td>43870..44030 [1]</td>
670 <td>No RBS annotated, None found</td>
671 <td><span style="font-family:monospace">actcttgtcc</span></td>
672 </tr>
673 <tr>
674 <td>gene</td>
675 <td>CPT-T1_066.gene</td>
676 <td>44098..44485 [1]</td>
677 <td>No RBS annotated, None found</td>
678 <td><span style="font-family:monospace">gcacgacaac</span></td>
679 </tr>
680 <tr>
681 <td>gene</td>
682 <td>CPT-T1_067.gene</td>
683 <td>44527..44649 [1]</td>
684 <td>No RBS annotated, None found</td>
685 <td><span style="font-family:monospace">gttccccttt</span></td>
686 </tr>
687 <tr>
688 <td>gene</td>
689 <td>CPT-T1_068.gene</td>
690 <td>44625..44852 [1]</td>
691 <td>No RBS annotated, None found</td>
692 <td><span style="font-family:monospace">gacattatct</span></td>
693 </tr>
694 <tr>
695 <td>gene</td>
696 <td>CPT-T1_069.gene</td>
697 <td>44898..45356 [1]</td>
698 <td>No RBS annotated, None found</td>
699 <td><span style="font-family:monospace">cctacaccaa</span></td>
700 </tr>
701 <tr>
702 <td>gene</td>
703 <td>CPT-T1_070.gene</td>
704 <td>45428..45970 [1]</td>
705 <td>No RBS annotated, None found</td>
706 <td><span style="font-family:monospace">ttaagcaacc</span></td>
707 </tr>
708 <tr>
709 <td>gene</td>
710 <td>CPT-T1_071.gene</td>
711 <td>45941..46451 [1]</td>
712 <td>No RBS annotated, None found</td>
713 <td><span style="font-family:monospace">gcctgtgata</span></td>
714 </tr>
715 <tr>
716 <td>gene</td>
717 <td>CPT-T1_072.gene</td>
718 <td>46444..47026 [1]</td>
719 <td>No RBS annotated, None found</td>
720 <td><span style="font-family:monospace">tcacaaaaag</span></td>
721 </tr>
722 <tr>
723 <td>gene</td>
724 <td>CPT-T1_073.gene</td>
725 <td>47085..47308 [1]</td>
726 <td>No RBS annotated, None found</td>
727 <td><span style="font-family:monospace">ctcatcgaca</span></td>
728 </tr>
729 <tr>
730 <td>gene</td>
731 <td>CPT-T1_074.gene</td>
732 <td>47293..47649 [1]</td>
733 <td>No RBS annotated, None found</td>
734 <td><span style="font-family:monospace">cccgatcgaa</span></td>
735 </tr>
736 <tr>
737 <td>gene</td>
738 <td>CPT-T1_075.gene</td>
739 <td>47637..47879 [1]</td>
740 <td>No RBS annotated, None found</td>
741 <td><span style="font-family:monospace">aagtttttca</span></td>
742 </tr>
743 <tr>
744 <td>gene</td>
745 <td>CPT-T1_076.gene</td>
746 <td>47864..48082 [1]</td>
747 <td>Unannotated but valid RBS</td>
748 <td><span style="font-family:monospace">cgt AGGT aac</span></td>
749 </tr>
750 <tr>
751 <td>gene</td>
752 <td>CPT-T1_077.gene</td>
753 <td>48235..48408 [1]</td>
754 <td>No RBS annotated, None found</td>
755 <td><span style="font-family:monospace">gcggcaacaa</span></td>
756 </tr>
757 <tr>
758 <td>gene</td>
759 <td>CPT-T1_078.gene</td>
760 <td>48377..48574 [1]</td>
761 <td>No RBS annotated, None found</td>
762 <td><span style="font-family:monospace">ctggcgttat</span></td>
763 </tr>
764 <tr>
765 <td>gene</td>
766 <td>CPT-T1_079.gene</td>
767 <td>48564..48803 [1]</td>
768 <td>No RBS annotated, None found</td>
769 <td><span style="font-family:monospace">atattgaatt</span></td>
770 </tr>
771 </tbody>
772 </table>
773 </div>
774
775 <h3 id="weird_starts">Start Codon Usage</h3>
776 <p>This section covers genes with unusual start codons</p>
777 <div class="table-responsive">
778 <table class="table table-striped">
779 <thead>
780 <tr>
781 <th>Start Codon</th>
782 <th>Count</th>
783 </tr>
784 </thead>
785 <tbody>
786 <tr><td>ATG</td><td>74</td></tr>
787 <tr><td>GTG</td><td>3</td></tr>
788 <tr><td>TTG</td><td>2</td></tr>
789 </tbody>
790 </table>
791 </div>
792
793 <div class="table-responsive">
794 <table class="table table-striped">
795 <thead>
796 <tr>
797 <th>Feature Type</th>
798 <th>ID</th>
799 <th>Location</th>
800 <th>Error</th>
801 </tr>
802 </thead>
803 <tbody>
804 </tbody>
805 </table>
806 </div>
807
808 <h3 id="excessive_gaps">Intergenic Gaps</h3>
809 <p>Phage genomes are under pressure to maintain high coding density. Large intergenic gaps may be a sign of incorrect gene starts or missing genes.</p>
810 <div class="table-responsive">
811 <table class="table table-striped">
812 <thead>
813 <tr>
814 <th>Region</th>
815 <th>Size</th>
816 <th>Bounding Gene Transcription Direction</th>
817 <th>Message</th>
818 </tr>
819 </thead>
820 <tbody>
821 <tr>
822 <td>2184 .. 2238</td>
823 <td>54</td>
824 <td>→ →</td>
825 <td>
826 </td>
827 </tr>
828 <tr>
829 <td>5876 .. 5937</td>
830 <td>61</td>
831 <td>→ →</td>
832 <td>
833 </td>
834 </tr>
835 <tr>
836 <td>6705 .. 6795</td>
837 <td>90</td>
838 <td>→ →</td>
839 <td>
840 </td>
841 </tr>
842 <tr>
843 <td>10414 .. 10527</td>
844 <td>113</td>
845 <td>→ →</td>
846 <td>
847 </td>
848 </tr>
849 <tr>
850 <td>14432 .. 14511</td>
851 <td>79</td>
852 <td>→ →</td>
853 <td>
854 2 ORFs found in this region
855 </td>
856 </tr>
857 <tr>
858 <td>16621 .. 16698</td>
859 <td>77</td>
860 <td>→ →</td>
861 <td>
862 </td>
863 </tr>
864 <tr>
865 <td>21506 .. 21765</td>
866 <td>259</td>
867 <td>→ →</td>
868 <td>
869 </td>
870 </tr>
871 <tr>
872 <td>21906 .. 22033</td>
873 <td>127</td>
874 <td>→ →</td>
875 <td>
876 </td>
877 </tr>
878 <tr>
879 <td>24289 .. 24350</td>
880 <td>61</td>
881 <td>→ →</td>
882 <td>
883 1 ORFs found in this region
884 </td>
885 </tr>
886 <tr>
887 <td>27573 .. 27634</td>
888 <td>61</td>
889 <td>→ →</td>
890 <td>
891 </td>
892 </tr>
893 <tr>
894 <td>28087 .. 28180</td>
895 <td>93</td>
896 <td>→ →</td>
897 <td>
898 </td>
899 </tr>
900 <tr>
901 <td>30612 .. 30679</td>
902 <td>67</td>
903 <td>→ →</td>
904 <td>
905 1 ORFs found in this region
906 </td>
907 </tr>
908 <tr>
909 <td>31641 .. 31707</td>
910 <td>66</td>
911 <td>→ →</td>
912 <td>
913 </td>
914 </tr>
915 <tr>
916 <td>32399 .. 32477</td>
917 <td>78</td>
918 <td>→ →</td>
919 <td>
920 1 ORFs found in this region
921 </td>
922 </tr>
923 <tr>
924 <td>33611 .. 33683</td>
925 <td>72</td>
926 <td>→ →</td>
927 <td>
928 </td>
929 </tr>
930 <tr>
931 <td>34166 .. 34238</td>
932 <td>72</td>
933 <td>→ →</td>
934 <td>
935 </td>
936 </tr>
937 <tr>
938 <td>34415 .. 34533</td>
939 <td>118</td>
940 <td>→ →</td>
941 <td>
942 </td>
943 </tr>
944 <tr>
945 <td>35638 .. 35760</td>
946 <td>122</td>
947 <td>→ →</td>
948 <td>
949 2 ORFs found in this region
950 </td>
951 </tr>
952 <tr>
953 <td>38693 .. 38773</td>
954 <td>80</td>
955 <td>→ →</td>
956 <td>
957 2 ORFs found in this region
958 </td>
959 </tr>
960 <tr>
961 <td>39211 .. 39288</td>
962 <td>77</td>
963 <td>→ →</td>
964 <td>
965 </td>
966 </tr>
967 <tr>
968 <td>40330 .. 41030</td>
969 <td>700</td>
970 <td>→ →</td>
971 <td>
972 7 ORFs found in this region
973 </td>
974 </tr>
975 <tr>
976 <td>41945 .. 42023</td>
977 <td>78</td>
978 <td>→ →</td>
979 <td>
980 </td>
981 </tr>
982 <tr>
983 <td>42764 .. 42835</td>
984 <td>71</td>
985 <td>→ →</td>
986 <td>
987 </td>
988 </tr>
989 <tr>
990 <td>43324 .. 43395</td>
991 <td>71</td>
992 <td>→ →</td>
993 <td>
994 </td>
995 </tr>
996 <tr>
997 <td>44030 .. 44110</td>
998 <td>80</td>
999 <td>→ →</td>
1000 <td>
1001 </td>
1002 </tr>
1003 <tr>
1004 <td>44485 .. 44538</td>
1005 <td>53</td>
1006 <td>→ →</td>
1007 <td>
1008 </td>
1009 </tr>
1010 <tr>
1011 <td>44852 .. 44909</td>
1012 <td>57</td>
1013 <td>→ →</td>
1014 <td>
1015 </td>
1016 </tr>
1017 <tr>
1018 <td>45356 .. 45439</td>
1019 <td>83</td>
1020 <td>→ →</td>
1021 <td>
1022 6 ORFs found in this region
1023 </td>
1024 </tr>
1025 <tr>
1026 <td>47026 .. 47098</td>
1027 <td>72</td>
1028 <td>→ →</td>
1029 <td>
1030 </td>
1031 </tr>
1032 <tr>
1033 <td>48082 .. 48246</td>
1034 <td>164</td>
1035 <td>→ →</td>
1036 <td>
1037 2 ORFs found in this region
1038 </td>
1039 </tr>
1040 </tbody>
1041 </table>
1042 </div>
1043
1044 <h3 id="excessive_overlap">Overlapping Genes </h3>
1045 <p>Large gene overlaps may indicate an incorrect gene start or miscalled gene.</p>
1046 <div class="table-responsive">
1047 <table class="table table-striped">
1048 <thead>
1049 <tr>
1050 <th>Feature A</th>
1051 <th>Feature B</th>
1052 <th>Shared Region</th>
1053 <th>Overlap Length</th>
1054 </tr>
1055 </thead>
1056 <tbody>
1057 <tr>
1058 <td>CPT-T1_015.gene ([10516:10845](+))</td>
1059 <td>CPT-T1_016.gene ([10516:11162](+))</td>
1060 <td>10527..10844</td>
1061 <td>317 bp</td>
1062 </tr>
1063 <tr>
1064 <td>CPT-T1_030.gene ([24351:26550](-))</td>
1065 <td>CPT-T1_031.gene ([26447:26600](-))</td>
1066 <td>26446..26536</td>
1067 <td>90 bp</td>
1068 </tr>
1069 <tr>
1070 <td>CPT-T1_039.gene ([31881:32167](+))</td>
1071 <td>CPT-T1_040.gene ([32099:32399](+))</td>
1072 <td>32111..32166</td>
1073 <td>55 bp</td>
1074 </tr>
1075 </tbody>
1076 </table>
1077 </div>
1078 <!--<h3 id="coding_density">Coding Density Issues <small>99 / 100</small></h3>
1079 <div class="table-responsive">
1080 <p>
1081 You have a coding density of 93 which scores
1082 99 / 100. Most genomes should be in the 90% to
1083 100% coding density range
1084 </p>
1085 </div>-->
1086
1087 <h2 class="sub-header" id="antisense">Antisense Genes</h2>
1088 <h3 id="morons">Possible Morons <small>78 / 79 (Doesn't count towards score)</small></h3>
1089 <div class="table-responsive">
1090 <table class="table table-striped">
1091 <thead>
1092 <tr>
1093 <th>Feature</th>
1094 <th>RBS</th>
1095 <th>Surrounding Features</th>
1096 </tr>
1097 </thead>
1098 <tbody>
1099 <tr>
1100 <td>CPT-T1_025.gene</td>
1101 <td>No RBS Available</td>
1102 <td class="moron">
1103 →
1104 →
1105 <span class="strand_emph">←</span>
1106 →
1107 →
1108 </div>
1109 </td>
1110 </tr>
1111 </tbody>
1112 </table>
1113 </div>
1114
1115
1116 <h2 class="sub-header" id="annotations">Annotation Issues</h2>
1117 <h3 id="missing_product">Missing Product Tags <small>79 / 79</small></h3>
1118 <div class="table-responsive">
1119 <table class="table table-striped">
1120 <thead>
1121 <tr>
1122 <th>Feature</th>
1123 <th>Qualifiers</th>
1124 </tr>
1125 </thead>
1126 <tbody>
1127 </tbody>
1128 </table>
1129 </div>
1130
1131
1132
1133
1134
1135 </div>
1136 </div>
1137 </div>
1138
1139
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