Multiple sequence alignment - TraesCS6A01G265000

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS6A01G265000 chr6A 100.000 2474 0 0 1 2474 489440530 489443003 0.000000e+00 4569.0
1 TraesCS6A01G265000 chr6A 100.000 51 0 0 3008 3058 489443537 489443587 9.030000e-16 95.3
2 TraesCS6A01G265000 chr6B 93.054 1526 76 15 793 2305 525313395 525314903 0.000000e+00 2204.0
3 TraesCS6A01G265000 chr6B 85.358 601 87 1 1084 1684 79955401 79956000 3.350000e-174 621.0
4 TraesCS6A01G265000 chr6B 85.358 601 87 1 1084 1684 80007920 80008519 3.350000e-174 621.0
5 TraesCS6A01G265000 chr6B 92.742 124 8 1 669 792 525312390 525312512 8.710000e-41 178.0
6 TraesCS6A01G265000 chr6B 76.106 226 37 14 305 516 9311482 9311260 5.390000e-18 102.0
7 TraesCS6A01G265000 chr6D 93.192 1366 73 11 793 2155 353100590 353099242 0.000000e+00 1989.0
8 TraesCS6A01G265000 chr6D 78.970 699 82 27 6 648 353102896 353102207 1.700000e-112 416.0
9 TraesCS6A01G265000 chr6D 75.602 332 53 12 338 645 122988161 122988488 4.110000e-29 139.0
10 TraesCS6A01G265000 chrUn 85.786 598 81 4 1089 1684 27583036 27582441 5.560000e-177 630.0
11 TraesCS6A01G265000 chrUn 85.142 599 83 6 1089 1684 334070582 334069987 2.610000e-170 608.0
12 TraesCS6A01G265000 chrUn 85.640 578 81 2 1108 1684 27567663 27568239 9.380000e-170 606.0
13 TraesCS6A01G265000 chrUn 83.409 663 98 12 1028 1684 27607414 27606758 3.370000e-169 604.0
14 TraesCS6A01G265000 chr7D 80.089 899 125 41 842 1700 22650158 22651042 1.200000e-173 619.0
15 TraesCS6A01G265000 chr7D 75.799 438 73 19 237 645 235695201 235695634 1.120000e-44 191.0
16 TraesCS6A01G265000 chr7D 78.462 130 23 5 386 515 75079018 75078894 2.530000e-11 80.5
17 TraesCS6A01G265000 chr4A 83.845 619 88 11 1089 1700 705628192 705627579 2.040000e-161 579.0
18 TraesCS6A01G265000 chr4B 76.667 390 55 15 296 651 80001558 80001171 1.870000e-42 183.0
19 TraesCS6A01G265000 chr2D 81.522 184 33 1 328 510 612327459 612327642 1.900000e-32 150.0
20 TraesCS6A01G265000 chr7A 75.140 358 57 13 328 662 112689170 112688822 4.110000e-29 139.0
21 TraesCS6A01G265000 chr3B 94.828 58 2 1 2304 2361 71157403 71157347 4.200000e-14 89.8
22 TraesCS6A01G265000 chr3B 79.487 117 19 5 390 506 758733756 758733867 9.090000e-11 78.7
23 TraesCS6A01G265000 chr1D 77.953 127 23 5 390 516 475201233 475201112 1.180000e-09 75.0
24 TraesCS6A01G265000 chr5B 94.595 37 2 0 6 42 321619046 321619010 1.180000e-04 58.4


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6A01G265000 chr6A 489440530 489443587 3057 False 2332.15 4569 100.000 1 3058 2 chr6A.!!$F1 3057
1 TraesCS6A01G265000 chr6B 525312390 525314903 2513 False 1191.00 2204 92.898 669 2305 2 chr6B.!!$F3 1636
2 TraesCS6A01G265000 chr6B 79955401 79956000 599 False 621.00 621 85.358 1084 1684 1 chr6B.!!$F1 600
3 TraesCS6A01G265000 chr6B 80007920 80008519 599 False 621.00 621 85.358 1084 1684 1 chr6B.!!$F2 600
4 TraesCS6A01G265000 chr6D 353099242 353102896 3654 True 1202.50 1989 86.081 6 2155 2 chr6D.!!$R1 2149
5 TraesCS6A01G265000 chrUn 27582441 27583036 595 True 630.00 630 85.786 1089 1684 1 chrUn.!!$R1 595
6 TraesCS6A01G265000 chrUn 334069987 334070582 595 True 608.00 608 85.142 1089 1684 1 chrUn.!!$R3 595
7 TraesCS6A01G265000 chrUn 27567663 27568239 576 False 606.00 606 85.640 1108 1684 1 chrUn.!!$F1 576
8 TraesCS6A01G265000 chrUn 27606758 27607414 656 True 604.00 604 83.409 1028 1684 1 chrUn.!!$R2 656
9 TraesCS6A01G265000 chr7D 22650158 22651042 884 False 619.00 619 80.089 842 1700 1 chr7D.!!$F1 858
10 TraesCS6A01G265000 chr4A 705627579 705628192 613 True 579.00 579 83.845 1089 1700 1 chr4A.!!$R1 611

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
635 692 0.107654 AAATCCTCCAGTACTGCCGC 60.108 55.0 17.86 0.0 0.0 6.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2406 4026 0.039074 GGCTATGATGTAGCGCGAGT 60.039 55.0 12.1 0.0 41.24 4.18 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 9.281371 TCATGGCTCTCTTTATTGATATCAAAG 57.719 33.333 21.50 14.46 39.55 2.77
91 92 7.095523 CGTTAAAGAAAGTTAAGGGTTCATCGA 60.096 37.037 0.00 0.00 0.00 3.59
155 156 3.254060 ACTATGGCATCGTATCATTCGC 58.746 45.455 1.65 0.00 0.00 4.70
157 158 2.238942 TGGCATCGTATCATTCGCTT 57.761 45.000 0.00 0.00 0.00 4.68
184 185 2.171659 TGTTAGGTGCCTCAGTTTGACA 59.828 45.455 0.00 0.00 0.00 3.58
187 188 2.508526 AGGTGCCTCAGTTTGACATTC 58.491 47.619 0.00 0.00 0.00 2.67
223 230 4.741928 AACTTAAGGGGGAATCACACTT 57.258 40.909 4.98 4.98 0.00 3.16
226 233 2.586648 AAGGGGGAATCACACTTGTC 57.413 50.000 0.00 0.00 0.00 3.18
232 239 4.399303 GGGGGAATCACACTTGTCAATAAG 59.601 45.833 0.00 0.00 0.00 1.73
322 343 3.648339 AAACATCCAAGATGCACACAC 57.352 42.857 4.51 0.00 0.00 3.82
323 344 1.538047 ACATCCAAGATGCACACACC 58.462 50.000 4.51 0.00 0.00 4.16
325 346 0.700564 ATCCAAGATGCACACACCCT 59.299 50.000 0.00 0.00 0.00 4.34
326 347 0.250858 TCCAAGATGCACACACCCTG 60.251 55.000 0.00 0.00 0.00 4.45
335 369 2.426738 TGCACACACCCTGAAAAGAAAG 59.573 45.455 0.00 0.00 0.00 2.62
344 378 6.070251 ACACCCTGAAAAGAAAGGAAAACAAT 60.070 34.615 0.00 0.00 35.40 2.71
350 384 9.599866 CTGAAAAGAAAGGAAAACAATAAAGGT 57.400 29.630 0.00 0.00 0.00 3.50
351 385 9.594478 TGAAAAGAAAGGAAAACAATAAAGGTC 57.406 29.630 0.00 0.00 0.00 3.85
358 392 4.157840 GGAAAACAATAAAGGTCTCGCCAT 59.842 41.667 0.00 0.00 40.61 4.40
359 393 4.965119 AAACAATAAAGGTCTCGCCATC 57.035 40.909 0.00 0.00 40.61 3.51
365 399 1.399714 AAGGTCTCGCCATCGTGATA 58.600 50.000 0.00 0.00 39.85 2.15
368 402 2.365617 AGGTCTCGCCATCGTGATAAAT 59.634 45.455 0.00 0.00 39.85 1.40
369 403 2.731976 GGTCTCGCCATCGTGATAAATC 59.268 50.000 0.00 0.00 39.85 2.17
371 405 2.628178 TCTCGCCATCGTGATAAATCCT 59.372 45.455 0.00 0.00 33.88 3.24
372 406 2.989840 CTCGCCATCGTGATAAATCCTC 59.010 50.000 0.00 0.00 36.96 3.71
373 407 2.628178 TCGCCATCGTGATAAATCCTCT 59.372 45.455 0.00 0.00 36.96 3.69
375 409 3.552890 CGCCATCGTGATAAATCCTCTCA 60.553 47.826 0.00 0.00 0.00 3.27
376 410 3.993081 GCCATCGTGATAAATCCTCTCAG 59.007 47.826 0.00 0.00 0.00 3.35
377 411 3.993081 CCATCGTGATAAATCCTCTCAGC 59.007 47.826 0.00 0.00 0.00 4.26
380 415 3.701542 TCGTGATAAATCCTCTCAGCAGT 59.298 43.478 0.00 0.00 0.00 4.40
382 417 5.359860 TCGTGATAAATCCTCTCAGCAGTAA 59.640 40.000 0.00 0.00 0.00 2.24
392 427 4.516698 CCTCTCAGCAGTAACACACAAAAT 59.483 41.667 0.00 0.00 0.00 1.82
394 429 6.347725 CCTCTCAGCAGTAACACACAAAATAC 60.348 42.308 0.00 0.00 0.00 1.89
404 439 8.833493 AGTAACACACAAAATACCACTAAAGAC 58.167 33.333 0.00 0.00 0.00 3.01
412 447 7.994334 ACAAAATACCACTAAAGACAACACCTA 59.006 33.333 0.00 0.00 0.00 3.08
413 448 8.504005 CAAAATACCACTAAAGACAACACCTAG 58.496 37.037 0.00 0.00 0.00 3.02
418 453 6.541278 ACCACTAAAGACAACACCTAGAAAAC 59.459 38.462 0.00 0.00 0.00 2.43
419 454 6.540914 CCACTAAAGACAACACCTAGAAAACA 59.459 38.462 0.00 0.00 0.00 2.83
420 455 7.407337 CACTAAAGACAACACCTAGAAAACAC 58.593 38.462 0.00 0.00 0.00 3.32
421 456 7.065324 CACTAAAGACAACACCTAGAAAACACA 59.935 37.037 0.00 0.00 0.00 3.72
422 457 6.827586 AAAGACAACACCTAGAAAACACAA 57.172 33.333 0.00 0.00 0.00 3.33
423 458 6.827586 AAGACAACACCTAGAAAACACAAA 57.172 33.333 0.00 0.00 0.00 2.83
424 459 6.827586 AGACAACACCTAGAAAACACAAAA 57.172 33.333 0.00 0.00 0.00 2.44
425 460 6.852664 AGACAACACCTAGAAAACACAAAAG 58.147 36.000 0.00 0.00 0.00 2.27
426 461 5.961272 ACAACACCTAGAAAACACAAAAGG 58.039 37.500 0.00 0.00 0.00 3.11
427 462 5.479027 ACAACACCTAGAAAACACAAAAGGT 59.521 36.000 0.00 0.00 37.84 3.50
428 463 5.830000 ACACCTAGAAAACACAAAAGGTC 57.170 39.130 0.00 0.00 35.17 3.85
429 464 5.506708 ACACCTAGAAAACACAAAAGGTCT 58.493 37.500 0.00 0.00 35.17 3.85
430 465 6.655930 ACACCTAGAAAACACAAAAGGTCTA 58.344 36.000 0.00 0.00 35.17 2.59
437 472 7.892609 AGAAAACACAAAAGGTCTACAAAAGT 58.107 30.769 0.00 0.00 0.00 2.66
440 475 7.404671 AACACAAAAGGTCTACAAAAGTGAT 57.595 32.000 0.00 0.00 0.00 3.06
453 488 8.204160 TCTACAAAAGTGATGTCTTCAAGAAGA 58.796 33.333 8.37 8.37 44.47 2.87
492 527 2.878406 CGTCATCGCCCTATCCAAAATT 59.122 45.455 0.00 0.00 0.00 1.82
496 531 6.293955 CGTCATCGCCCTATCCAAAATTTTAT 60.294 38.462 2.44 0.00 0.00 1.40
504 539 8.664798 GCCCTATCCAAAATTTTATGTTTTCAC 58.335 33.333 2.44 0.00 0.00 3.18
506 541 8.868916 CCTATCCAAAATTTTATGTTTTCACCG 58.131 33.333 2.44 0.00 0.00 4.94
509 544 6.480320 TCCAAAATTTTATGTTTTCACCGTGG 59.520 34.615 2.44 0.00 0.00 4.94
510 545 6.293135 CCAAAATTTTATGTTTTCACCGTGGG 60.293 38.462 2.44 0.00 0.00 4.61
533 589 1.335145 AGCTTCAGCAAGGCAATTGT 58.665 45.000 7.40 0.00 45.16 2.71
536 592 2.546373 GCTTCAGCAAGGCAATTGTCAA 60.546 45.455 13.47 0.00 41.29 3.18
574 630 2.781174 TCACACCTTAGGTTTTCACCCT 59.219 45.455 0.00 0.00 45.63 4.34
576 632 1.886542 CACCTTAGGTTTTCACCCTGC 59.113 52.381 0.00 0.00 45.63 4.85
583 639 1.067060 GGTTTTCACCCTGCAAGTCAC 59.933 52.381 0.00 0.00 37.03 3.67
599 656 4.988716 ACGACTGGCACCCGAGGA 62.989 66.667 10.23 0.00 0.00 3.71
601 658 2.997897 GACTGGCACCCGAGGAGT 60.998 66.667 0.00 0.00 0.00 3.85
605 662 3.834799 GGCACCCGAGGAGTACCG 61.835 72.222 0.00 0.00 41.83 4.02
608 665 4.371417 ACCCGAGGAGTACCGCCA 62.371 66.667 5.29 0.00 41.83 5.69
632 689 5.904362 AAAATGAAATCCTCCAGTACTGC 57.096 39.130 17.86 1.71 0.00 4.40
635 692 0.107654 AAATCCTCCAGTACTGCCGC 60.108 55.000 17.86 0.00 0.00 6.53
648 705 4.740822 GCCGCCCCCACTTGTCAT 62.741 66.667 0.00 0.00 0.00 3.06
650 707 2.342650 CCGCCCCCACTTGTCATTG 61.343 63.158 0.00 0.00 0.00 2.82
652 709 2.993471 GCCCCCACTTGTCATTGCG 61.993 63.158 0.00 0.00 0.00 4.85
655 712 2.267351 CCCACTTGTCATTGCGGCA 61.267 57.895 0.00 0.00 0.00 5.69
656 713 1.081242 CCACTTGTCATTGCGGCAC 60.081 57.895 0.05 0.00 0.00 5.01
658 715 2.268076 ACTTGTCATTGCGGCACCC 61.268 57.895 0.05 0.00 0.00 4.61
701 1372 5.812652 TGTAACGTGTTTGAGACATTTTCC 58.187 37.500 0.00 0.00 41.10 3.13
712 1383 2.307686 AGACATTTTCCCCTTTCGCCTA 59.692 45.455 0.00 0.00 0.00 3.93
787 1458 4.931601 CCGACGTGGATATGATTTCATCAT 59.068 41.667 0.00 4.68 46.19 2.45
799 1470 6.312141 TGATTTCATCATGGGAGTAACTGA 57.688 37.500 0.00 0.00 33.59 3.41
801 1472 6.825213 TGATTTCATCATGGGAGTAACTGAAG 59.175 38.462 0.00 0.00 33.59 3.02
802 1473 5.762179 TTCATCATGGGAGTAACTGAAGT 57.238 39.130 0.00 0.00 0.00 3.01
994 2573 4.116328 TCGCGTGAGAGCCTTCCG 62.116 66.667 5.77 0.00 0.00 4.30
1020 2599 1.517257 GGATCGTGTGTGCTCCTCG 60.517 63.158 0.00 0.00 0.00 4.63
1086 2686 1.005748 GATGGATGCATCGAGGCGA 60.006 57.895 20.15 7.11 41.13 5.54
1169 2781 1.874019 CGTGATCTTCGCCGTCCTG 60.874 63.158 0.00 0.00 0.00 3.86
1344 2959 1.307355 CCACAACTGGATCATGCGCA 61.307 55.000 14.96 14.96 40.55 6.09
1643 3258 1.739562 GCTGGAGTTGGCTCTGTCG 60.740 63.158 0.00 0.00 41.38 4.35
1751 3366 2.736995 TCGCCGAGAGCAAAACCG 60.737 61.111 0.00 0.00 44.04 4.44
1820 3435 1.137086 TGCTCGCCTCTAGGATTGTTC 59.863 52.381 0.00 0.00 37.39 3.18
1830 3446 7.336396 GCCTCTAGGATTGTTCTTTTTAGGTA 58.664 38.462 0.00 0.00 37.39 3.08
1872 3488 6.260271 ACTGCAGATCAGAATGTCATTACATG 59.740 38.462 23.35 0.00 44.39 3.21
1941 3558 1.889829 ACGATCAGATGGGCTAGCTAC 59.110 52.381 15.72 8.82 0.00 3.58
1988 3607 7.445402 TCAATTTTTAATTTTGGGGCGAATTGA 59.555 29.630 0.00 0.00 38.14 2.57
2010 3629 5.221581 TGACTCAAACCTAAGTACCCAACTC 60.222 44.000 0.00 0.00 37.50 3.01
2022 3641 3.512219 ACCCAACTCGGATGGTTTTAA 57.488 42.857 0.00 0.00 36.14 1.52
2043 3662 9.887406 TTTTAATTTCTTCACGAGGACAATAAC 57.113 29.630 0.00 0.00 0.00 1.89
2046 3665 4.594123 TCTTCACGAGGACAATAACACA 57.406 40.909 0.00 0.00 0.00 3.72
2076 3695 2.105477 CACATACTCCCTCCATCCCAAG 59.895 54.545 0.00 0.00 0.00 3.61
2213 3833 4.581077 TTGAACATGTGCACATTTAGCA 57.419 36.364 29.48 20.41 40.19 3.49
2216 3836 4.759183 TGAACATGTGCACATTTAGCAGTA 59.241 37.500 29.48 6.83 43.63 2.74
2217 3837 4.952262 ACATGTGCACATTTAGCAGTAG 57.048 40.909 29.48 16.71 43.63 2.57
2239 3859 2.045131 AGTCGCCCTCGTACACCTC 61.045 63.158 0.00 0.00 36.96 3.85
2251 3871 0.389296 TACACCTCGCACATTCCACG 60.389 55.000 0.00 0.00 0.00 4.94
2268 3888 3.818787 GCGTGGAAGCTGGCCATG 61.819 66.667 19.03 19.03 43.70 3.66
2269 3889 3.136123 CGTGGAAGCTGGCCATGG 61.136 66.667 5.51 7.63 38.49 3.66
2305 3925 5.256474 CCCAAGTGAGATGTATGTTCCTTT 58.744 41.667 0.00 0.00 0.00 3.11
2306 3926 5.711976 CCCAAGTGAGATGTATGTTCCTTTT 59.288 40.000 0.00 0.00 0.00 2.27
2307 3927 6.209391 CCCAAGTGAGATGTATGTTCCTTTTT 59.791 38.462 0.00 0.00 0.00 1.94
2327 3947 4.591321 TTTTAGATGAACATGGAGGCCT 57.409 40.909 3.86 3.86 0.00 5.19
2328 3948 3.845781 TTAGATGAACATGGAGGCCTC 57.154 47.619 25.59 25.59 0.00 4.70
2329 3949 1.890552 AGATGAACATGGAGGCCTCT 58.109 50.000 31.36 12.27 0.00 3.69
2330 3950 1.767681 AGATGAACATGGAGGCCTCTC 59.232 52.381 31.36 20.69 39.25 3.20
2338 3958 3.471806 GAGGCCTCTCCCCGGTTC 61.472 72.222 26.25 0.00 34.01 3.62
2341 3961 3.090532 GCCTCTCCCCGGTTCCAT 61.091 66.667 0.00 0.00 0.00 3.41
2342 3962 2.680370 GCCTCTCCCCGGTTCCATT 61.680 63.158 0.00 0.00 0.00 3.16
2343 3963 1.342672 GCCTCTCCCCGGTTCCATTA 61.343 60.000 0.00 0.00 0.00 1.90
2344 3964 0.759346 CCTCTCCCCGGTTCCATTAG 59.241 60.000 0.00 0.00 0.00 1.73
2345 3965 0.106894 CTCTCCCCGGTTCCATTAGC 59.893 60.000 0.00 0.00 0.00 3.09
2346 3966 0.326238 TCTCCCCGGTTCCATTAGCT 60.326 55.000 0.00 0.00 0.00 3.32
2347 3967 0.106894 CTCCCCGGTTCCATTAGCTC 59.893 60.000 0.00 0.00 0.00 4.09
2348 3968 0.619255 TCCCCGGTTCCATTAGCTCA 60.619 55.000 0.00 0.00 0.00 4.26
2349 3969 0.179045 CCCCGGTTCCATTAGCTCAG 60.179 60.000 0.00 0.00 0.00 3.35
2350 3970 0.830648 CCCGGTTCCATTAGCTCAGA 59.169 55.000 0.00 0.00 0.00 3.27
2351 3971 1.209504 CCCGGTTCCATTAGCTCAGAA 59.790 52.381 0.00 0.00 0.00 3.02
2352 3972 2.158755 CCCGGTTCCATTAGCTCAGAAT 60.159 50.000 0.00 0.00 0.00 2.40
2353 3973 2.874701 CCGGTTCCATTAGCTCAGAATG 59.125 50.000 0.00 0.00 34.63 2.67
2369 3989 4.811024 TCAGAATGAAACCATCGATACAGC 59.189 41.667 0.00 0.00 45.97 4.40
2370 3990 4.024556 CAGAATGAAACCATCGATACAGCC 60.025 45.833 0.00 0.00 39.69 4.85
2371 3991 2.325583 TGAAACCATCGATACAGCCC 57.674 50.000 0.00 0.00 0.00 5.19
2372 3992 1.557371 TGAAACCATCGATACAGCCCA 59.443 47.619 0.00 0.00 0.00 5.36
2373 3993 2.213499 GAAACCATCGATACAGCCCAG 58.787 52.381 0.00 0.00 0.00 4.45
2374 3994 0.179045 AACCATCGATACAGCCCAGC 60.179 55.000 0.00 0.00 0.00 4.85
2375 3995 1.050988 ACCATCGATACAGCCCAGCT 61.051 55.000 0.00 0.00 40.77 4.24
2376 3996 0.107456 CCATCGATACAGCCCAGCTT 59.893 55.000 0.00 0.00 36.40 3.74
2377 3997 1.344438 CCATCGATACAGCCCAGCTTA 59.656 52.381 0.00 0.00 36.40 3.09
2378 3998 2.027745 CCATCGATACAGCCCAGCTTAT 60.028 50.000 0.00 0.00 36.40 1.73
2379 3999 2.820059 TCGATACAGCCCAGCTTATG 57.180 50.000 0.00 0.00 36.40 1.90
2380 4000 2.039418 TCGATACAGCCCAGCTTATGT 58.961 47.619 0.00 0.00 36.40 2.29
2381 4001 2.035961 TCGATACAGCCCAGCTTATGTC 59.964 50.000 0.00 0.00 36.40 3.06
2382 4002 2.036475 CGATACAGCCCAGCTTATGTCT 59.964 50.000 0.00 0.00 36.40 3.41
2383 4003 2.988010 TACAGCCCAGCTTATGTCTG 57.012 50.000 0.00 0.00 36.40 3.51
2384 4004 1.279496 ACAGCCCAGCTTATGTCTGA 58.721 50.000 5.55 0.00 36.40 3.27
2385 4005 1.209019 ACAGCCCAGCTTATGTCTGAG 59.791 52.381 5.55 0.00 36.40 3.35
2386 4006 0.835941 AGCCCAGCTTATGTCTGAGG 59.164 55.000 0.00 0.00 33.89 3.86
2387 4007 0.179034 GCCCAGCTTATGTCTGAGGG 60.179 60.000 0.00 0.00 33.54 4.30
2388 4008 1.207791 CCCAGCTTATGTCTGAGGGT 58.792 55.000 0.00 0.00 33.54 4.34
2389 4009 1.139853 CCCAGCTTATGTCTGAGGGTC 59.860 57.143 0.00 0.00 33.54 4.46
2390 4010 2.114616 CCAGCTTATGTCTGAGGGTCT 58.885 52.381 0.00 0.00 33.54 3.85
2391 4011 2.102252 CCAGCTTATGTCTGAGGGTCTC 59.898 54.545 0.00 0.00 33.54 3.36
2392 4012 3.030291 CAGCTTATGTCTGAGGGTCTCT 58.970 50.000 0.00 0.00 33.54 3.10
2393 4013 3.030291 AGCTTATGTCTGAGGGTCTCTG 58.970 50.000 0.00 0.00 0.00 3.35
2394 4014 2.763448 GCTTATGTCTGAGGGTCTCTGT 59.237 50.000 0.00 0.00 32.50 3.41
2395 4015 3.196685 GCTTATGTCTGAGGGTCTCTGTT 59.803 47.826 0.00 0.00 32.50 3.16
2396 4016 4.402793 GCTTATGTCTGAGGGTCTCTGTTA 59.597 45.833 0.00 0.00 32.50 2.41
2397 4017 5.680151 GCTTATGTCTGAGGGTCTCTGTTAC 60.680 48.000 0.00 0.00 32.50 2.50
2398 4018 3.238788 TGTCTGAGGGTCTCTGTTACA 57.761 47.619 0.00 0.00 32.50 2.41
2399 4019 3.572642 TGTCTGAGGGTCTCTGTTACAA 58.427 45.455 0.00 0.00 32.50 2.41
2400 4020 3.574396 TGTCTGAGGGTCTCTGTTACAAG 59.426 47.826 0.00 0.00 32.50 3.16
2401 4021 2.563179 TCTGAGGGTCTCTGTTACAAGC 59.437 50.000 0.00 0.00 32.50 4.01
2402 4022 2.300152 CTGAGGGTCTCTGTTACAAGCA 59.700 50.000 0.00 0.00 0.00 3.91
2403 4023 2.037251 TGAGGGTCTCTGTTACAAGCAC 59.963 50.000 0.00 0.00 0.00 4.40
2404 4024 2.037251 GAGGGTCTCTGTTACAAGCACA 59.963 50.000 0.00 0.00 0.00 4.57
2405 4025 2.438021 AGGGTCTCTGTTACAAGCACAA 59.562 45.455 0.00 0.00 0.00 3.33
2406 4026 3.118038 AGGGTCTCTGTTACAAGCACAAA 60.118 43.478 0.00 0.00 0.00 2.83
2407 4027 3.003378 GGGTCTCTGTTACAAGCACAAAC 59.997 47.826 0.00 0.00 0.00 2.93
2408 4028 3.877508 GGTCTCTGTTACAAGCACAAACT 59.122 43.478 0.00 0.00 0.00 2.66
2409 4029 4.024809 GGTCTCTGTTACAAGCACAAACTC 60.025 45.833 0.00 0.00 0.00 3.01
2410 4030 3.802139 TCTCTGTTACAAGCACAAACTCG 59.198 43.478 0.00 0.00 0.00 4.18
2411 4031 2.286833 TCTGTTACAAGCACAAACTCGC 59.713 45.455 0.00 0.00 0.00 5.03
2412 4032 1.004398 TGTTACAAGCACAAACTCGCG 60.004 47.619 0.00 0.00 0.00 5.87
2413 4033 0.041663 TTACAAGCACAAACTCGCGC 60.042 50.000 0.00 0.00 0.00 6.86
2414 4034 0.878523 TACAAGCACAAACTCGCGCT 60.879 50.000 5.56 0.00 35.90 5.92
2415 4035 0.878523 ACAAGCACAAACTCGCGCTA 60.879 50.000 5.56 0.00 33.45 4.26
2416 4036 0.451135 CAAGCACAAACTCGCGCTAC 60.451 55.000 5.56 0.00 33.45 3.58
2417 4037 0.878523 AAGCACAAACTCGCGCTACA 60.879 50.000 5.56 0.00 33.45 2.74
2418 4038 0.670546 AGCACAAACTCGCGCTACAT 60.671 50.000 5.56 0.00 31.60 2.29
2419 4039 0.247301 GCACAAACTCGCGCTACATC 60.247 55.000 5.56 0.00 0.00 3.06
2420 4040 1.067693 CACAAACTCGCGCTACATCA 58.932 50.000 5.56 0.00 0.00 3.07
2421 4041 1.660607 CACAAACTCGCGCTACATCAT 59.339 47.619 5.56 0.00 0.00 2.45
2422 4042 2.857748 CACAAACTCGCGCTACATCATA 59.142 45.455 5.56 0.00 0.00 2.15
2423 4043 3.060940 CACAAACTCGCGCTACATCATAG 60.061 47.826 5.56 0.00 0.00 2.23
2424 4044 1.772182 AACTCGCGCTACATCATAGC 58.228 50.000 5.56 0.00 37.21 2.97
2425 4045 0.039074 ACTCGCGCTACATCATAGCC 60.039 55.000 5.56 0.00 37.26 3.93
2426 4046 1.067743 CTCGCGCTACATCATAGCCG 61.068 60.000 5.56 5.65 37.26 5.52
2427 4047 1.081442 CGCGCTACATCATAGCCGA 60.081 57.895 5.56 0.00 36.82 5.54
2428 4048 0.456824 CGCGCTACATCATAGCCGAT 60.457 55.000 5.56 0.00 36.82 4.18
2429 4049 0.994995 GCGCTACATCATAGCCGATG 59.005 55.000 0.00 6.79 46.78 3.84
2430 4050 0.994995 CGCTACATCATAGCCGATGC 59.005 55.000 7.98 0.00 45.56 3.91
2446 4066 6.613755 GCCGATGCTAAATAGTAAAAGGAA 57.386 37.500 0.00 0.00 33.53 3.36
2447 4067 7.023197 GCCGATGCTAAATAGTAAAAGGAAA 57.977 36.000 0.00 0.00 33.53 3.13
2448 4068 7.477494 GCCGATGCTAAATAGTAAAAGGAAAA 58.523 34.615 0.00 0.00 33.53 2.29
2449 4069 7.644157 GCCGATGCTAAATAGTAAAAGGAAAAG 59.356 37.037 0.00 0.00 33.53 2.27
2450 4070 8.129211 CCGATGCTAAATAGTAAAAGGAAAAGG 58.871 37.037 0.00 0.00 0.00 3.11
2451 4071 8.674607 CGATGCTAAATAGTAAAAGGAAAAGGT 58.325 33.333 0.00 0.00 0.00 3.50
2460 4080 9.871175 ATAGTAAAAGGAAAAGGTAAAAGGTCA 57.129 29.630 0.00 0.00 0.00 4.02
2461 4081 8.598202 AGTAAAAGGAAAAGGTAAAAGGTCAA 57.402 30.769 0.00 0.00 0.00 3.18
2462 4082 8.692710 AGTAAAAGGAAAAGGTAAAAGGTCAAG 58.307 33.333 0.00 0.00 0.00 3.02
2463 4083 7.490657 AAAAGGAAAAGGTAAAAGGTCAAGT 57.509 32.000 0.00 0.00 0.00 3.16
2464 4084 7.490657 AAAGGAAAAGGTAAAAGGTCAAGTT 57.509 32.000 0.00 0.00 0.00 2.66
2465 4085 7.490657 AAGGAAAAGGTAAAAGGTCAAGTTT 57.509 32.000 0.00 0.00 0.00 2.66
2466 4086 7.490657 AGGAAAAGGTAAAAGGTCAAGTTTT 57.509 32.000 0.00 0.00 0.00 2.43
2467 4087 8.598202 AGGAAAAGGTAAAAGGTCAAGTTTTA 57.402 30.769 0.00 0.00 0.00 1.52
2468 4088 9.038072 AGGAAAAGGTAAAAGGTCAAGTTTTAA 57.962 29.630 0.00 0.00 32.53 1.52
2469 4089 9.090692 GGAAAAGGTAAAAGGTCAAGTTTTAAC 57.909 33.333 0.00 0.00 37.34 2.01
2470 4090 9.090692 GAAAAGGTAAAAGGTCAAGTTTTAACC 57.909 33.333 0.82 0.00 37.65 2.85
2471 4091 6.720112 AGGTAAAAGGTCAAGTTTTAACCC 57.280 37.500 0.82 0.00 37.65 4.11
2472 4092 5.599656 AGGTAAAAGGTCAAGTTTTAACCCC 59.400 40.000 0.82 0.00 37.65 4.95
2473 4093 5.221501 GGTAAAAGGTCAAGTTTTAACCCCC 60.222 44.000 0.00 0.00 32.93 5.40
3026 4646 2.983402 CACATCATGATCATTCGCCC 57.017 50.000 5.16 0.00 0.00 6.13
3027 4647 2.501261 CACATCATGATCATTCGCCCT 58.499 47.619 5.16 0.00 0.00 5.19
3028 4648 2.483106 CACATCATGATCATTCGCCCTC 59.517 50.000 5.16 0.00 0.00 4.30
3029 4649 2.082231 CATCATGATCATTCGCCCTCC 58.918 52.381 5.16 0.00 0.00 4.30
3030 4650 0.397941 TCATGATCATTCGCCCTCCC 59.602 55.000 5.16 0.00 0.00 4.30
3031 4651 0.607489 CATGATCATTCGCCCTCCCC 60.607 60.000 5.16 0.00 0.00 4.81
3032 4652 1.783250 ATGATCATTCGCCCTCCCCC 61.783 60.000 1.18 0.00 0.00 5.40
3048 4668 1.739067 CCCCCTTCTAAACTTGAGCG 58.261 55.000 0.00 0.00 0.00 5.03
3049 4669 1.679032 CCCCCTTCTAAACTTGAGCGG 60.679 57.143 0.00 0.00 0.00 5.52
3050 4670 1.087501 CCCTTCTAAACTTGAGCGGC 58.912 55.000 0.00 0.00 0.00 6.53
3051 4671 0.721718 CCTTCTAAACTTGAGCGGCG 59.278 55.000 0.51 0.51 0.00 6.46
3052 4672 0.721718 CTTCTAAACTTGAGCGGCGG 59.278 55.000 9.78 0.00 0.00 6.13
3053 4673 1.296056 TTCTAAACTTGAGCGGCGGC 61.296 55.000 9.78 8.43 40.37 6.53
3054 4674 3.083600 CTAAACTTGAGCGGCGGCG 62.084 63.158 28.70 28.70 46.35 6.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.896888 AGAGCCATGATGGACTTCTCTAG 59.103 47.826 17.22 0.00 40.96 2.43
1 2 3.894427 GAGAGCCATGATGGACTTCTCTA 59.106 47.826 17.22 0.00 40.96 2.43
2 3 2.699846 GAGAGCCATGATGGACTTCTCT 59.300 50.000 17.22 16.55 40.96 3.10
3 4 2.699846 AGAGAGCCATGATGGACTTCTC 59.300 50.000 22.64 22.64 40.96 2.87
4 5 2.761809 AGAGAGCCATGATGGACTTCT 58.238 47.619 17.22 13.84 40.96 2.85
58 59 9.565090 ACCCTTAACTTTCTTTAACGTAATCTT 57.435 29.630 0.00 0.00 0.00 2.40
65 66 7.013529 CGATGAACCCTTAACTTTCTTTAACG 58.986 38.462 0.00 0.00 0.00 3.18
68 69 6.652062 GGTCGATGAACCCTTAACTTTCTTTA 59.348 38.462 0.00 0.00 32.82 1.85
125 126 8.465273 TGATACGATGCCATAGTTAGCTATAT 57.535 34.615 0.00 0.00 36.24 0.86
126 127 7.875327 TGATACGATGCCATAGTTAGCTATA 57.125 36.000 0.00 0.00 36.24 1.31
127 128 6.775594 TGATACGATGCCATAGTTAGCTAT 57.224 37.500 0.00 0.00 38.38 2.97
130 131 5.004821 CGAATGATACGATGCCATAGTTAGC 59.995 44.000 0.00 0.00 0.00 3.09
134 135 3.056536 AGCGAATGATACGATGCCATAGT 60.057 43.478 0.00 0.00 0.00 2.12
145 146 6.535508 ACCTAACAAAGAGAAGCGAATGATAC 59.464 38.462 0.00 0.00 0.00 2.24
155 156 3.999663 CTGAGGCACCTAACAAAGAGAAG 59.000 47.826 0.00 0.00 0.00 2.85
157 158 2.972713 ACTGAGGCACCTAACAAAGAGA 59.027 45.455 0.00 0.00 0.00 3.10
184 185 9.933723 CCTTAAGTTTTGAAGATCAAATGGAAT 57.066 29.630 6.38 0.00 44.75 3.01
187 188 7.099120 CCCCTTAAGTTTTGAAGATCAAATGG 58.901 38.462 6.38 3.65 44.75 3.16
204 205 4.010349 GACAAGTGTGATTCCCCCTTAAG 58.990 47.826 0.00 0.00 0.00 1.85
208 209 1.444933 TGACAAGTGTGATTCCCCCT 58.555 50.000 0.00 0.00 0.00 4.79
210 211 5.123979 GTCTTATTGACAAGTGTGATTCCCC 59.876 44.000 0.00 0.00 44.73 4.81
294 315 6.433716 TGTGCATCTTGGATGTTTTTGAGATA 59.566 34.615 8.93 0.00 0.00 1.98
295 316 5.244402 TGTGCATCTTGGATGTTTTTGAGAT 59.756 36.000 8.93 0.00 0.00 2.75
303 324 1.888512 GGTGTGTGCATCTTGGATGTT 59.111 47.619 8.93 0.00 0.00 2.71
308 329 0.250858 TCAGGGTGTGTGCATCTTGG 60.251 55.000 0.00 0.00 34.09 3.61
309 330 1.608055 TTCAGGGTGTGTGCATCTTG 58.392 50.000 0.00 0.00 34.54 3.02
311 332 2.158623 TCTTTTCAGGGTGTGTGCATCT 60.159 45.455 0.00 0.00 0.00 2.90
322 343 8.956533 TTTATTGTTTTCCTTTCTTTTCAGGG 57.043 30.769 0.00 0.00 0.00 4.45
323 344 9.045223 CCTTTATTGTTTTCCTTTCTTTTCAGG 57.955 33.333 0.00 0.00 0.00 3.86
325 346 9.594478 GACCTTTATTGTTTTCCTTTCTTTTCA 57.406 29.630 0.00 0.00 0.00 2.69
326 347 9.817809 AGACCTTTATTGTTTTCCTTTCTTTTC 57.182 29.630 0.00 0.00 0.00 2.29
335 369 3.504520 TGGCGAGACCTTTATTGTTTTCC 59.495 43.478 0.00 0.00 40.22 3.13
344 378 1.179152 TCACGATGGCGAGACCTTTA 58.821 50.000 0.00 0.00 41.64 1.85
350 384 2.628178 AGGATTTATCACGATGGCGAGA 59.372 45.455 0.00 0.00 41.16 4.04
351 385 2.989840 GAGGATTTATCACGATGGCGAG 59.010 50.000 0.00 0.00 41.64 5.03
358 392 3.701542 ACTGCTGAGAGGATTTATCACGA 59.298 43.478 0.00 0.00 0.00 4.35
359 393 4.052159 ACTGCTGAGAGGATTTATCACG 57.948 45.455 0.00 0.00 0.00 4.35
365 399 4.202357 TGTGTGTTACTGCTGAGAGGATTT 60.202 41.667 0.00 0.00 0.00 2.17
368 402 2.316108 TGTGTGTTACTGCTGAGAGGA 58.684 47.619 0.00 0.00 0.00 3.71
369 403 2.820059 TGTGTGTTACTGCTGAGAGG 57.180 50.000 0.00 0.00 0.00 3.69
371 405 5.468746 GGTATTTTGTGTGTTACTGCTGAGA 59.531 40.000 0.00 0.00 0.00 3.27
372 406 5.238432 TGGTATTTTGTGTGTTACTGCTGAG 59.762 40.000 0.00 0.00 0.00 3.35
373 407 5.008217 GTGGTATTTTGTGTGTTACTGCTGA 59.992 40.000 0.00 0.00 0.00 4.26
375 409 5.130350 AGTGGTATTTTGTGTGTTACTGCT 58.870 37.500 0.00 0.00 0.00 4.24
376 410 5.432885 AGTGGTATTTTGTGTGTTACTGC 57.567 39.130 0.00 0.00 0.00 4.40
377 411 8.832521 TCTTTAGTGGTATTTTGTGTGTTACTG 58.167 33.333 0.00 0.00 0.00 2.74
380 415 8.734218 TGTCTTTAGTGGTATTTTGTGTGTTA 57.266 30.769 0.00 0.00 0.00 2.41
382 417 7.121463 TGTTGTCTTTAGTGGTATTTTGTGTGT 59.879 33.333 0.00 0.00 0.00 3.72
392 427 6.982160 TTCTAGGTGTTGTCTTTAGTGGTA 57.018 37.500 0.00 0.00 0.00 3.25
394 429 6.540914 TGTTTTCTAGGTGTTGTCTTTAGTGG 59.459 38.462 0.00 0.00 0.00 4.00
404 439 5.961272 ACCTTTTGTGTTTTCTAGGTGTTG 58.039 37.500 0.00 0.00 34.84 3.33
412 447 7.812669 CACTTTTGTAGACCTTTTGTGTTTTCT 59.187 33.333 0.00 0.00 0.00 2.52
413 448 7.810759 TCACTTTTGTAGACCTTTTGTGTTTTC 59.189 33.333 0.00 0.00 0.00 2.29
418 453 6.795399 ACATCACTTTTGTAGACCTTTTGTG 58.205 36.000 0.00 0.00 0.00 3.33
419 454 6.828785 AGACATCACTTTTGTAGACCTTTTGT 59.171 34.615 0.00 0.00 0.00 2.83
420 455 7.264373 AGACATCACTTTTGTAGACCTTTTG 57.736 36.000 0.00 0.00 0.00 2.44
421 456 7.556275 TGAAGACATCACTTTTGTAGACCTTTT 59.444 33.333 0.00 0.00 31.50 2.27
422 457 7.054124 TGAAGACATCACTTTTGTAGACCTTT 58.946 34.615 0.00 0.00 31.50 3.11
423 458 6.591935 TGAAGACATCACTTTTGTAGACCTT 58.408 36.000 0.00 0.00 31.50 3.50
424 459 6.174720 TGAAGACATCACTTTTGTAGACCT 57.825 37.500 0.00 0.00 31.50 3.85
425 460 6.706270 TCTTGAAGACATCACTTTTGTAGACC 59.294 38.462 0.00 0.00 37.92 3.85
426 461 7.715265 TCTTGAAGACATCACTTTTGTAGAC 57.285 36.000 0.00 0.00 37.92 2.59
427 462 8.204160 TCTTCTTGAAGACATCACTTTTGTAGA 58.796 33.333 8.80 0.00 37.92 2.59
428 463 8.370493 TCTTCTTGAAGACATCACTTTTGTAG 57.630 34.615 8.80 0.00 37.92 2.74
429 464 8.731275 TTCTTCTTGAAGACATCACTTTTGTA 57.269 30.769 12.06 0.00 37.92 2.41
430 465 7.630242 TTCTTCTTGAAGACATCACTTTTGT 57.370 32.000 12.06 0.00 37.92 2.83
437 472 6.458751 GCACTGTTTTCTTCTTGAAGACATCA 60.459 38.462 12.06 10.19 44.97 3.07
440 475 4.699735 TGCACTGTTTTCTTCTTGAAGACA 59.300 37.500 12.06 4.07 44.25 3.41
453 488 1.226945 GGCGCTTGTGCACTGTTTT 60.227 52.632 19.41 0.00 39.64 2.43
457 492 4.374702 GACGGCGCTTGTGCACTG 62.375 66.667 19.41 11.95 39.64 3.66
470 505 0.105964 TTTGGATAGGGCGATGACGG 59.894 55.000 0.00 0.00 40.15 4.79
472 507 4.918810 AAATTTTGGATAGGGCGATGAC 57.081 40.909 0.00 0.00 0.00 3.06
475 510 6.976934 ACATAAAATTTTGGATAGGGCGAT 57.023 33.333 13.76 0.00 0.00 4.58
482 517 9.197694 CACGGTGAAAACATAAAATTTTGGATA 57.802 29.630 13.76 0.00 29.44 2.59
492 527 3.225177 TCCCCACGGTGAAAACATAAA 57.775 42.857 10.28 0.00 0.00 1.40
496 531 1.394618 CTTTCCCCACGGTGAAAACA 58.605 50.000 10.28 0.00 30.65 2.83
504 539 2.335712 GCTGAAGCTTTCCCCACGG 61.336 63.158 0.00 0.00 38.21 4.94
506 541 0.600057 CTTGCTGAAGCTTTCCCCAC 59.400 55.000 0.00 0.00 42.66 4.61
509 544 1.181098 TGCCTTGCTGAAGCTTTCCC 61.181 55.000 0.00 0.00 42.66 3.97
510 545 0.675633 TTGCCTTGCTGAAGCTTTCC 59.324 50.000 0.00 0.00 42.66 3.13
533 589 5.419155 TGTGACCTTTATTGGTTGTGTTTGA 59.581 36.000 0.00 0.00 41.00 2.69
536 592 4.098807 GGTGTGACCTTTATTGGTTGTGTT 59.901 41.667 0.00 0.00 41.00 3.32
564 620 1.268539 CGTGACTTGCAGGGTGAAAAC 60.269 52.381 0.00 0.00 0.00 2.43
576 632 1.961277 GGGTGCCAGTCGTGACTTG 60.961 63.158 0.00 0.00 40.20 3.16
583 639 4.135153 CTCCTCGGGTGCCAGTCG 62.135 72.222 0.00 0.00 0.00 4.18
624 681 4.778143 GTGGGGGCGGCAGTACTG 62.778 72.222 18.93 18.93 0.00 2.74
632 689 2.035626 AATGACAAGTGGGGGCGG 59.964 61.111 0.00 0.00 0.00 6.13
635 692 3.277133 CGCAATGACAAGTGGGGG 58.723 61.111 0.00 0.00 31.33 5.40
652 709 2.767505 CATTACTAATCCTCGGGTGCC 58.232 52.381 0.00 0.00 0.00 5.01
655 712 3.454812 ACAAGCATTACTAATCCTCGGGT 59.545 43.478 0.00 0.00 0.00 5.28
656 713 4.073293 ACAAGCATTACTAATCCTCGGG 57.927 45.455 0.00 0.00 0.00 5.14
658 715 7.399523 GTTACAACAAGCATTACTAATCCTCG 58.600 38.462 0.00 0.00 0.00 4.63
661 718 6.959311 CACGTTACAACAAGCATTACTAATCC 59.041 38.462 0.00 0.00 0.00 3.01
662 719 7.515643 ACACGTTACAACAAGCATTACTAATC 58.484 34.615 0.00 0.00 0.00 1.75
663 720 7.429636 ACACGTTACAACAAGCATTACTAAT 57.570 32.000 0.00 0.00 0.00 1.73
667 724 5.966503 TCAAACACGTTACAACAAGCATTAC 59.033 36.000 0.00 0.00 0.00 1.89
712 1383 4.783621 ATGGCCGTGCATCGCTGT 62.784 61.111 0.00 0.00 38.35 4.40
734 1405 3.570975 ACTCCAAAATTAAACGGACCCAC 59.429 43.478 0.00 0.00 0.00 4.61
738 1409 3.822167 TGGGACTCCAAAATTAAACGGAC 59.178 43.478 0.00 0.00 40.73 4.79
787 1458 8.910944 GTTCAGTATATACTTCAGTTACTCCCA 58.089 37.037 12.87 0.00 33.46 4.37
792 1463 9.875675 CGTAGGTTCAGTATATACTTCAGTTAC 57.124 37.037 12.87 11.45 33.46 2.50
994 2573 0.238289 CACACACGATCCAGTTTGGC 59.762 55.000 0.00 0.00 37.47 4.52
1020 2599 2.754552 TCATCCCTGCAAATTGTAGTGC 59.245 45.455 10.05 0.00 41.29 4.40
1023 2602 4.095483 GTCACTCATCCCTGCAAATTGTAG 59.905 45.833 4.03 4.03 0.00 2.74
1544 3159 2.800250 ACCCTGAGCTCCAAATGAAAG 58.200 47.619 12.15 0.00 0.00 2.62
1751 3366 9.928236 GCTACATGAAACTTATTCTTGAAGATC 57.072 33.333 0.00 0.00 0.00 2.75
1820 3435 6.979238 CCAGAATCCTAGACGTACCTAAAAAG 59.021 42.308 0.00 0.00 0.00 2.27
1830 3446 2.688958 GCAGTACCAGAATCCTAGACGT 59.311 50.000 0.00 0.00 0.00 4.34
1912 3529 3.309954 GCCCATCTGATCGTTCTACAAAC 59.690 47.826 0.00 0.00 0.00 2.93
1941 3558 4.991056 TGAAAGAGGAAAAGAGACATGTCG 59.009 41.667 19.85 0.00 34.09 4.35
1988 3607 4.262335 CGAGTTGGGTACTTAGGTTTGAGT 60.262 45.833 0.00 0.00 37.17 3.41
2010 3629 5.933790 TCGTGAAGAAATTAAAACCATCCG 58.066 37.500 0.00 0.00 0.00 4.18
2022 3641 5.995282 TGTGTTATTGTCCTCGTGAAGAAAT 59.005 36.000 0.00 0.00 0.00 2.17
2043 3662 8.156820 TGGAGGGAGTATGTGAATATAAATGTG 58.843 37.037 0.00 0.00 0.00 3.21
2046 3665 8.552296 GGATGGAGGGAGTATGTGAATATAAAT 58.448 37.037 0.00 0.00 0.00 1.40
2058 3677 3.663298 ATCTTGGGATGGAGGGAGTAT 57.337 47.619 0.00 0.00 0.00 2.12
2189 3809 5.814188 TGCTAAATGTGCACATGTTCAAAAA 59.186 32.000 31.98 10.24 36.56 1.94
2194 3814 4.164822 ACTGCTAAATGTGCACATGTTC 57.835 40.909 31.98 20.74 36.56 3.18
2228 3848 1.269166 GAATGTGCGAGGTGTACGAG 58.731 55.000 0.00 0.00 35.72 4.18
2232 3852 0.389296 CGTGGAATGTGCGAGGTGTA 60.389 55.000 0.00 0.00 0.00 2.90
2251 3871 3.818787 CATGGCCAGCTTCCACGC 61.819 66.667 13.05 0.00 36.26 5.34
2274 3894 1.987807 ATCTCACTTGGGCCCCATCG 61.988 60.000 22.27 7.28 31.53 3.84
2305 3925 4.934356 AGGCCTCCATGTTCATCTAAAAA 58.066 39.130 0.00 0.00 0.00 1.94
2306 3926 4.228210 AGAGGCCTCCATGTTCATCTAAAA 59.772 41.667 29.54 0.00 0.00 1.52
2307 3927 3.782523 AGAGGCCTCCATGTTCATCTAAA 59.217 43.478 29.54 0.00 0.00 1.85
2308 3928 3.387962 AGAGGCCTCCATGTTCATCTAA 58.612 45.455 29.54 0.00 0.00 2.10
2309 3929 2.968574 GAGAGGCCTCCATGTTCATCTA 59.031 50.000 29.54 0.00 33.30 1.98
2310 3930 1.767681 GAGAGGCCTCCATGTTCATCT 59.232 52.381 29.54 6.31 33.30 2.90
2311 3931 2.252976 GAGAGGCCTCCATGTTCATC 57.747 55.000 29.54 13.65 33.30 2.92
2321 3941 3.471806 GAACCGGGGAGAGGCCTC 61.472 72.222 26.22 26.22 38.70 4.70
2324 3944 1.342672 TAATGGAACCGGGGAGAGGC 61.343 60.000 6.32 0.00 0.00 4.70
2325 3945 0.759346 CTAATGGAACCGGGGAGAGG 59.241 60.000 6.32 0.00 0.00 3.69
2326 3946 0.106894 GCTAATGGAACCGGGGAGAG 59.893 60.000 6.32 0.00 0.00 3.20
2327 3947 0.326238 AGCTAATGGAACCGGGGAGA 60.326 55.000 6.32 0.00 0.00 3.71
2328 3948 0.106894 GAGCTAATGGAACCGGGGAG 59.893 60.000 6.32 0.00 0.00 4.30
2329 3949 0.619255 TGAGCTAATGGAACCGGGGA 60.619 55.000 6.32 0.00 0.00 4.81
2330 3950 0.179045 CTGAGCTAATGGAACCGGGG 60.179 60.000 6.32 0.00 0.00 5.73
2331 3951 0.830648 TCTGAGCTAATGGAACCGGG 59.169 55.000 6.32 0.00 0.00 5.73
2332 3952 2.691409 TTCTGAGCTAATGGAACCGG 57.309 50.000 0.00 0.00 0.00 5.28
2333 3953 3.797039 TCATTCTGAGCTAATGGAACCG 58.203 45.455 7.65 0.00 35.48 4.44
2334 3954 5.884771 GTTTCATTCTGAGCTAATGGAACC 58.115 41.667 16.42 4.17 42.95 3.62
2335 3955 5.415701 TGGTTTCATTCTGAGCTAATGGAAC 59.584 40.000 18.09 18.09 45.86 3.62
2336 3956 5.569355 TGGTTTCATTCTGAGCTAATGGAA 58.431 37.500 7.65 3.12 35.48 3.53
2337 3957 5.178096 TGGTTTCATTCTGAGCTAATGGA 57.822 39.130 7.65 0.00 35.48 3.41
2338 3958 5.277683 CGATGGTTTCATTCTGAGCTAATGG 60.278 44.000 7.65 0.00 35.48 3.16
2339 3959 5.525012 TCGATGGTTTCATTCTGAGCTAATG 59.475 40.000 1.85 1.85 35.98 1.90
2340 3960 5.674525 TCGATGGTTTCATTCTGAGCTAAT 58.325 37.500 0.00 0.00 32.98 1.73
2341 3961 5.084818 TCGATGGTTTCATTCTGAGCTAA 57.915 39.130 0.00 0.00 32.98 3.09
2342 3962 4.736126 TCGATGGTTTCATTCTGAGCTA 57.264 40.909 0.00 0.00 32.98 3.32
2343 3963 3.616956 TCGATGGTTTCATTCTGAGCT 57.383 42.857 0.00 0.00 32.98 4.09
2344 3964 4.811024 TGTATCGATGGTTTCATTCTGAGC 59.189 41.667 8.54 0.00 32.98 4.26
2345 3965 5.050499 GCTGTATCGATGGTTTCATTCTGAG 60.050 44.000 8.54 0.00 32.98 3.35
2346 3966 4.811024 GCTGTATCGATGGTTTCATTCTGA 59.189 41.667 8.54 0.00 32.98 3.27
2347 3967 4.024556 GGCTGTATCGATGGTTTCATTCTG 60.025 45.833 8.54 0.00 32.98 3.02
2348 3968 4.130118 GGCTGTATCGATGGTTTCATTCT 58.870 43.478 8.54 0.00 32.98 2.40
2349 3969 3.251004 GGGCTGTATCGATGGTTTCATTC 59.749 47.826 8.54 0.00 32.98 2.67
2350 3970 3.214328 GGGCTGTATCGATGGTTTCATT 58.786 45.455 8.54 0.00 32.98 2.57
2351 3971 2.172505 TGGGCTGTATCGATGGTTTCAT 59.827 45.455 8.54 0.00 36.09 2.57
2352 3972 1.557371 TGGGCTGTATCGATGGTTTCA 59.443 47.619 8.54 0.00 0.00 2.69
2353 3973 2.213499 CTGGGCTGTATCGATGGTTTC 58.787 52.381 8.54 0.00 0.00 2.78
2354 3974 1.747206 GCTGGGCTGTATCGATGGTTT 60.747 52.381 8.54 0.00 0.00 3.27
2355 3975 0.179045 GCTGGGCTGTATCGATGGTT 60.179 55.000 8.54 0.00 0.00 3.67
2356 3976 1.050988 AGCTGGGCTGTATCGATGGT 61.051 55.000 8.54 0.00 37.57 3.55
2357 3977 0.107456 AAGCTGGGCTGTATCGATGG 59.893 55.000 8.54 0.00 39.62 3.51
2358 3978 2.820059 TAAGCTGGGCTGTATCGATG 57.180 50.000 8.54 0.00 39.62 3.84
2359 3979 2.634940 ACATAAGCTGGGCTGTATCGAT 59.365 45.455 2.16 2.16 39.62 3.59
2360 3980 2.035961 GACATAAGCTGGGCTGTATCGA 59.964 50.000 0.00 0.00 39.62 3.59
2361 3981 2.036475 AGACATAAGCTGGGCTGTATCG 59.964 50.000 0.00 0.00 39.62 2.92
2362 3982 3.070159 TCAGACATAAGCTGGGCTGTATC 59.930 47.826 13.92 0.00 39.62 2.24
2363 3983 3.041211 TCAGACATAAGCTGGGCTGTAT 58.959 45.455 13.92 0.00 39.62 2.29
2364 3984 2.432146 CTCAGACATAAGCTGGGCTGTA 59.568 50.000 13.92 3.29 39.62 2.74
2365 3985 1.209019 CTCAGACATAAGCTGGGCTGT 59.791 52.381 13.92 3.74 39.62 4.40
2366 3986 1.474677 CCTCAGACATAAGCTGGGCTG 60.475 57.143 9.33 9.33 39.62 4.85
2367 3987 0.835941 CCTCAGACATAAGCTGGGCT 59.164 55.000 0.00 0.00 42.56 5.19
2368 3988 0.179034 CCCTCAGACATAAGCTGGGC 60.179 60.000 0.00 0.00 32.44 5.36
2369 3989 1.139853 GACCCTCAGACATAAGCTGGG 59.860 57.143 0.00 0.00 34.20 4.45
2370 3990 2.102252 GAGACCCTCAGACATAAGCTGG 59.898 54.545 0.00 0.00 34.20 4.85
2371 3991 3.030291 AGAGACCCTCAGACATAAGCTG 58.970 50.000 0.00 0.00 32.06 4.24
2372 3992 3.030291 CAGAGACCCTCAGACATAAGCT 58.970 50.000 0.00 0.00 32.06 3.74
2373 3993 2.763448 ACAGAGACCCTCAGACATAAGC 59.237 50.000 0.00 0.00 32.06 3.09
2374 3994 5.419155 TGTAACAGAGACCCTCAGACATAAG 59.581 44.000 0.00 0.00 32.06 1.73
2375 3995 5.330233 TGTAACAGAGACCCTCAGACATAA 58.670 41.667 0.00 0.00 32.06 1.90
2376 3996 4.930696 TGTAACAGAGACCCTCAGACATA 58.069 43.478 0.00 0.00 32.06 2.29
2377 3997 3.779444 TGTAACAGAGACCCTCAGACAT 58.221 45.455 0.00 0.00 32.06 3.06
2378 3998 3.238788 TGTAACAGAGACCCTCAGACA 57.761 47.619 0.00 0.00 32.06 3.41
2379 3999 3.615351 GCTTGTAACAGAGACCCTCAGAC 60.615 52.174 0.00 0.00 32.06 3.51
2380 4000 2.563179 GCTTGTAACAGAGACCCTCAGA 59.437 50.000 0.00 0.00 32.06 3.27
2381 4001 2.300152 TGCTTGTAACAGAGACCCTCAG 59.700 50.000 0.00 0.00 32.06 3.35
2382 4002 2.037251 GTGCTTGTAACAGAGACCCTCA 59.963 50.000 0.00 0.00 32.06 3.86
2383 4003 2.037251 TGTGCTTGTAACAGAGACCCTC 59.963 50.000 0.00 0.00 0.00 4.30
2384 4004 2.047061 TGTGCTTGTAACAGAGACCCT 58.953 47.619 0.00 0.00 0.00 4.34
2385 4005 2.543777 TGTGCTTGTAACAGAGACCC 57.456 50.000 0.00 0.00 0.00 4.46
2386 4006 3.877508 AGTTTGTGCTTGTAACAGAGACC 59.122 43.478 0.00 0.00 0.00 3.85
2387 4007 4.318121 CGAGTTTGTGCTTGTAACAGAGAC 60.318 45.833 0.00 0.00 0.00 3.36
2388 4008 3.802139 CGAGTTTGTGCTTGTAACAGAGA 59.198 43.478 0.00 0.00 0.00 3.10
2389 4009 3.604772 GCGAGTTTGTGCTTGTAACAGAG 60.605 47.826 0.00 0.00 0.00 3.35
2390 4010 2.286833 GCGAGTTTGTGCTTGTAACAGA 59.713 45.455 0.00 0.00 0.00 3.41
2391 4011 2.639751 GCGAGTTTGTGCTTGTAACAG 58.360 47.619 0.00 0.00 0.00 3.16
2392 4012 1.004398 CGCGAGTTTGTGCTTGTAACA 60.004 47.619 0.00 0.00 0.00 2.41
2393 4013 1.658968 CGCGAGTTTGTGCTTGTAAC 58.341 50.000 0.00 0.00 0.00 2.50
2394 4014 0.041663 GCGCGAGTTTGTGCTTGTAA 60.042 50.000 12.10 0.00 42.01 2.41
2395 4015 1.567537 GCGCGAGTTTGTGCTTGTA 59.432 52.632 12.10 0.00 42.01 2.41
2396 4016 2.327940 GCGCGAGTTTGTGCTTGT 59.672 55.556 12.10 0.00 42.01 3.16
2400 4020 0.247301 GATGTAGCGCGAGTTTGTGC 60.247 55.000 12.10 0.00 45.54 4.57
2401 4021 1.067693 TGATGTAGCGCGAGTTTGTG 58.932 50.000 12.10 0.00 0.00 3.33
2402 4022 2.010145 ATGATGTAGCGCGAGTTTGT 57.990 45.000 12.10 0.00 0.00 2.83
2403 4023 2.097202 GCTATGATGTAGCGCGAGTTTG 60.097 50.000 12.10 0.00 0.00 2.93
2404 4024 2.128035 GCTATGATGTAGCGCGAGTTT 58.872 47.619 12.10 0.00 0.00 2.66
2405 4025 1.603172 GGCTATGATGTAGCGCGAGTT 60.603 52.381 12.10 0.00 41.24 3.01
2406 4026 0.039074 GGCTATGATGTAGCGCGAGT 60.039 55.000 12.10 0.00 41.24 4.18
2407 4027 1.067743 CGGCTATGATGTAGCGCGAG 61.068 60.000 12.10 0.00 41.24 5.03
2408 4028 1.081442 CGGCTATGATGTAGCGCGA 60.081 57.895 12.10 0.00 41.24 5.87
2409 4029 0.456824 ATCGGCTATGATGTAGCGCG 60.457 55.000 0.00 0.00 41.24 6.86
2410 4030 0.994995 CATCGGCTATGATGTAGCGC 59.005 55.000 0.00 0.00 40.67 5.92
2411 4031 0.994995 GCATCGGCTATGATGTAGCG 59.005 55.000 2.78 0.00 45.98 4.26
2423 4043 6.613755 TTCCTTTTACTATTTAGCATCGGC 57.386 37.500 0.00 0.00 41.61 5.54
2424 4044 8.129211 CCTTTTCCTTTTACTATTTAGCATCGG 58.871 37.037 0.00 0.00 0.00 4.18
2425 4045 8.674607 ACCTTTTCCTTTTACTATTTAGCATCG 58.325 33.333 0.00 0.00 0.00 3.84
2434 4054 9.871175 TGACCTTTTACCTTTTCCTTTTACTAT 57.129 29.630 0.00 0.00 0.00 2.12
2435 4055 9.697990 TTGACCTTTTACCTTTTCCTTTTACTA 57.302 29.630 0.00 0.00 0.00 1.82
2436 4056 8.598202 TTGACCTTTTACCTTTTCCTTTTACT 57.402 30.769 0.00 0.00 0.00 2.24
2437 4057 8.472413 ACTTGACCTTTTACCTTTTCCTTTTAC 58.528 33.333 0.00 0.00 0.00 2.01
2438 4058 8.598202 ACTTGACCTTTTACCTTTTCCTTTTA 57.402 30.769 0.00 0.00 0.00 1.52
2439 4059 7.490657 ACTTGACCTTTTACCTTTTCCTTTT 57.509 32.000 0.00 0.00 0.00 2.27
2440 4060 7.490657 AACTTGACCTTTTACCTTTTCCTTT 57.509 32.000 0.00 0.00 0.00 3.11
2441 4061 7.490657 AAACTTGACCTTTTACCTTTTCCTT 57.509 32.000 0.00 0.00 0.00 3.36
2442 4062 7.490657 AAAACTTGACCTTTTACCTTTTCCT 57.509 32.000 0.00 0.00 0.00 3.36
2443 4063 9.090692 GTTAAAACTTGACCTTTTACCTTTTCC 57.909 33.333 0.00 0.00 0.00 3.13
2444 4064 9.090692 GGTTAAAACTTGACCTTTTACCTTTTC 57.909 33.333 0.00 0.00 0.00 2.29
2445 4065 8.042515 GGGTTAAAACTTGACCTTTTACCTTTT 58.957 33.333 0.98 0.00 33.90 2.27
2446 4066 7.364939 GGGGTTAAAACTTGACCTTTTACCTTT 60.365 37.037 0.98 0.00 33.90 3.11
2447 4067 6.098695 GGGGTTAAAACTTGACCTTTTACCTT 59.901 38.462 0.98 0.00 33.90 3.50
2448 4068 5.599656 GGGGTTAAAACTTGACCTTTTACCT 59.400 40.000 0.98 0.00 33.90 3.08
2449 4069 5.221501 GGGGGTTAAAACTTGACCTTTTACC 60.222 44.000 0.98 0.00 33.90 2.85
2450 4070 5.846203 GGGGGTTAAAACTTGACCTTTTAC 58.154 41.667 0.98 0.00 33.90 2.01
3007 4627 2.483106 GAGGGCGAATGATCATGATGTG 59.517 50.000 14.30 0.00 0.00 3.21
3008 4628 2.551721 GGAGGGCGAATGATCATGATGT 60.552 50.000 14.30 0.00 0.00 3.06
3009 4629 2.082231 GGAGGGCGAATGATCATGATG 58.918 52.381 14.30 3.39 0.00 3.07
3010 4630 1.004044 GGGAGGGCGAATGATCATGAT 59.996 52.381 8.25 8.25 0.00 2.45
3011 4631 0.397941 GGGAGGGCGAATGATCATGA 59.602 55.000 9.46 0.00 0.00 3.07
3012 4632 0.607489 GGGGAGGGCGAATGATCATG 60.607 60.000 9.46 0.00 0.00 3.07
3013 4633 1.763770 GGGGAGGGCGAATGATCAT 59.236 57.895 1.18 1.18 0.00 2.45
3014 4634 2.452064 GGGGGAGGGCGAATGATCA 61.452 63.158 0.00 0.00 0.00 2.92
3015 4635 2.432123 GGGGGAGGGCGAATGATC 59.568 66.667 0.00 0.00 0.00 2.92
3029 4649 1.679032 CCGCTCAAGTTTAGAAGGGGG 60.679 57.143 0.00 0.00 0.00 5.40
3030 4650 1.739067 CCGCTCAAGTTTAGAAGGGG 58.261 55.000 0.00 0.00 0.00 4.79
3031 4651 1.087501 GCCGCTCAAGTTTAGAAGGG 58.912 55.000 0.00 0.00 0.00 3.95
3032 4652 0.721718 CGCCGCTCAAGTTTAGAAGG 59.278 55.000 0.00 0.00 0.00 3.46
3033 4653 0.721718 CCGCCGCTCAAGTTTAGAAG 59.278 55.000 0.00 0.00 0.00 2.85
3034 4654 1.296056 GCCGCCGCTCAAGTTTAGAA 61.296 55.000 0.00 0.00 0.00 2.10
3035 4655 1.740296 GCCGCCGCTCAAGTTTAGA 60.740 57.895 0.00 0.00 0.00 2.10
3036 4656 2.785258 GCCGCCGCTCAAGTTTAG 59.215 61.111 0.00 0.00 0.00 1.85
3037 4657 3.115892 CGCCGCCGCTCAAGTTTA 61.116 61.111 0.00 0.00 0.00 2.01


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.