Multiple sequence alignment - TraesCS2D01G203600

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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 TraesCS2D01G203600 chr2D 100.000 3847 0 0 1 3847 155549889 155546043 0.000000e+00 7105
1 TraesCS2D01G203600 chr2D 98.140 1935 33 3 1913 3847 11087787 11085856 0.000000e+00 3371
2 TraesCS2D01G203600 chr2D 96.454 2002 45 10 728 2709 459830858 459832853 0.000000e+00 3280
3 TraesCS2D01G203600 chr2D 93.300 2030 70 30 727 2711 632025042 632023034 0.000000e+00 2935
4 TraesCS2D01G203600 chr2D 96.700 909 26 2 728 1632 11088679 11087771 0.000000e+00 1509
5 TraesCS2D01G203600 chr2D 98.396 748 12 0 2716 3463 632022325 632021578 0.000000e+00 1315
6 TraesCS2D01G203600 chr4D 96.855 2003 37 6 727 2711 414636102 414634108 0.000000e+00 3326
7 TraesCS2D01G203600 chr4D 98.411 1133 14 2 2715 3847 469104560 469105688 0.000000e+00 1989
8 TraesCS2D01G203600 chr4D 98.323 1133 19 0 2715 3847 414633167 414632035 0.000000e+00 1988
9 TraesCS2D01G203600 chr4D 96.237 1063 20 6 727 1772 469101971 469103030 0.000000e+00 1724
10 TraesCS2D01G203600 chr3D 96.798 1999 41 10 715 2693 114397643 114395648 0.000000e+00 3315
11 TraesCS2D01G203600 chr3D 96.368 2010 45 11 725 2709 595953697 595951691 0.000000e+00 3282
12 TraesCS2D01G203600 chr3D 94.118 1105 21 12 2761 3847 114394510 114393432 0.000000e+00 1640
13 TraesCS2D01G203600 chr3D 85.878 262 23 5 448 696 13417681 13417941 2.280000e-67 267
14 TraesCS2D01G203600 chr3D 85.294 204 21 4 283 485 13417474 13417669 6.520000e-48 202
15 TraesCS2D01G203600 chr7D 96.427 1987 47 10 728 2697 370966230 370964251 0.000000e+00 3254
16 TraesCS2D01G203600 chr7D 94.389 1105 17 13 2761 3847 370961802 370960725 0.000000e+00 1655
17 TraesCS2D01G203600 chr6D 95.537 1994 40 12 728 2697 81150542 81148574 0.000000e+00 3144
18 TraesCS2D01G203600 chr6D 94.661 1105 18 11 2761 3847 81147771 81146690 0.000000e+00 1676
19 TraesCS2D01G203600 chr7A 94.734 2013 72 16 719 2709 732102931 732100931 0.000000e+00 3099
20 TraesCS2D01G203600 chr7A 92.209 2028 71 28 728 2709 2773074 2775060 0.000000e+00 2789
21 TraesCS2D01G203600 chr7A 95.725 1731 52 5 1003 2711 652923889 652925619 0.000000e+00 2767
22 TraesCS2D01G203600 chr1A 94.708 2003 63 21 728 2709 1315709 1317689 0.000000e+00 3072
23 TraesCS2D01G203600 chr1A 97.937 727 15 0 1 727 560824619 560825345 0.000000e+00 1260
24 TraesCS2D01G203600 chr5B 92.924 2021 70 29 728 2709 74638685 74640671 0.000000e+00 2872
25 TraesCS2D01G203600 chr5B 95.347 1096 45 3 2752 3847 692285387 692286476 0.000000e+00 1736
26 TraesCS2D01G203600 chr1D 97.440 1133 29 0 2715 3847 414456424 414455292 0.000000e+00 1932
27 TraesCS2D01G203600 chr1D 95.985 1096 27 3 727 1805 276513481 276512386 0.000000e+00 1764
28 TraesCS2D01G203600 chr1D 98.402 751 12 0 2715 3465 276510568 276509818 0.000000e+00 1321
29 TraesCS2D01G203600 chr5D 95.754 1201 30 7 728 1910 58672898 58671701 0.000000e+00 1916
30 TraesCS2D01G203600 chr5D 97.087 1133 11 3 2715 3847 384159640 384160750 0.000000e+00 1890
31 TraesCS2D01G203600 chr5D 93.590 936 50 8 2915 3847 51580399 51581327 0.000000e+00 1387
32 TraesCS2D01G203600 chr7B 94.903 1138 40 5 2712 3847 598646598 598645477 0.000000e+00 1764
33 TraesCS2D01G203600 chr3A 97.802 728 15 1 1 727 28739889 28740616 0.000000e+00 1254
34 TraesCS2D01G203600 chr3A 97.665 728 16 1 1 727 28673841 28674568 0.000000e+00 1249
35 TraesCS2D01G203600 chr3A 97.665 728 16 1 1 727 28745732 28746459 0.000000e+00 1249
36 TraesCS2D01G203600 chr3A 97.665 728 14 2 1 727 28629966 28630691 0.000000e+00 1247
37 TraesCS2D01G203600 chr3A 85.470 234 29 4 466 696 23656597 23656366 4.970000e-59 239
38 TraesCS2D01G203600 chr2B 98.257 631 11 0 97 727 8516841 8517471 0.000000e+00 1105
39 TraesCS2D01G203600 chr2B 97.619 630 15 0 98 727 777641092 777640463 0.000000e+00 1081
40 TraesCS2D01G203600 chr2B 97.468 632 15 1 97 727 198171115 198171746 0.000000e+00 1077
41 TraesCS2D01G203600 chr2B 92.784 97 7 0 1 97 8516709 8516805 1.440000e-29 141
42 TraesCS2D01G203600 chr2B 92.784 97 7 0 1 97 198170983 198171079 1.440000e-29 141
43 TraesCS2D01G203600 chr6A 91.192 193 16 1 93 285 73565827 73566018 1.060000e-65 261


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 TraesCS2D01G203600 chr2D 155546043 155549889 3846 True 7105.0 7105 100.0000 1 3847 1 chr2D.!!$R1 3846
1 TraesCS2D01G203600 chr2D 459830858 459832853 1995 False 3280.0 3280 96.4540 728 2709 1 chr2D.!!$F1 1981
2 TraesCS2D01G203600 chr2D 11085856 11088679 2823 True 2440.0 3371 97.4200 728 3847 2 chr2D.!!$R2 3119
3 TraesCS2D01G203600 chr2D 632021578 632025042 3464 True 2125.0 2935 95.8480 727 3463 2 chr2D.!!$R3 2736
4 TraesCS2D01G203600 chr4D 414632035 414636102 4067 True 2657.0 3326 97.5890 727 3847 2 chr4D.!!$R1 3120
5 TraesCS2D01G203600 chr4D 469101971 469105688 3717 False 1856.5 1989 97.3240 727 3847 2 chr4D.!!$F1 3120
6 TraesCS2D01G203600 chr3D 595951691 595953697 2006 True 3282.0 3282 96.3680 725 2709 1 chr3D.!!$R1 1984
7 TraesCS2D01G203600 chr3D 114393432 114397643 4211 True 2477.5 3315 95.4580 715 3847 2 chr3D.!!$R2 3132
8 TraesCS2D01G203600 chr7D 370960725 370966230 5505 True 2454.5 3254 95.4080 728 3847 2 chr7D.!!$R1 3119
9 TraesCS2D01G203600 chr6D 81146690 81150542 3852 True 2410.0 3144 95.0990 728 3847 2 chr6D.!!$R1 3119
10 TraesCS2D01G203600 chr7A 732100931 732102931 2000 True 3099.0 3099 94.7340 719 2709 1 chr7A.!!$R1 1990
11 TraesCS2D01G203600 chr7A 2773074 2775060 1986 False 2789.0 2789 92.2090 728 2709 1 chr7A.!!$F1 1981
12 TraesCS2D01G203600 chr7A 652923889 652925619 1730 False 2767.0 2767 95.7250 1003 2711 1 chr7A.!!$F2 1708
13 TraesCS2D01G203600 chr1A 1315709 1317689 1980 False 3072.0 3072 94.7080 728 2709 1 chr1A.!!$F1 1981
14 TraesCS2D01G203600 chr1A 560824619 560825345 726 False 1260.0 1260 97.9370 1 727 1 chr1A.!!$F2 726
15 TraesCS2D01G203600 chr5B 74638685 74640671 1986 False 2872.0 2872 92.9240 728 2709 1 chr5B.!!$F1 1981
16 TraesCS2D01G203600 chr5B 692285387 692286476 1089 False 1736.0 1736 95.3470 2752 3847 1 chr5B.!!$F2 1095
17 TraesCS2D01G203600 chr1D 414455292 414456424 1132 True 1932.0 1932 97.4400 2715 3847 1 chr1D.!!$R1 1132
18 TraesCS2D01G203600 chr1D 276509818 276513481 3663 True 1542.5 1764 97.1935 727 3465 2 chr1D.!!$R2 2738
19 TraesCS2D01G203600 chr5D 58671701 58672898 1197 True 1916.0 1916 95.7540 728 1910 1 chr5D.!!$R1 1182
20 TraesCS2D01G203600 chr5D 384159640 384160750 1110 False 1890.0 1890 97.0870 2715 3847 1 chr5D.!!$F2 1132
21 TraesCS2D01G203600 chr5D 51580399 51581327 928 False 1387.0 1387 93.5900 2915 3847 1 chr5D.!!$F1 932
22 TraesCS2D01G203600 chr7B 598645477 598646598 1121 True 1764.0 1764 94.9030 2712 3847 1 chr7B.!!$R1 1135
23 TraesCS2D01G203600 chr3A 28739889 28740616 727 False 1254.0 1254 97.8020 1 727 1 chr3A.!!$F3 726
24 TraesCS2D01G203600 chr3A 28673841 28674568 727 False 1249.0 1249 97.6650 1 727 1 chr3A.!!$F2 726
25 TraesCS2D01G203600 chr3A 28745732 28746459 727 False 1249.0 1249 97.6650 1 727 1 chr3A.!!$F4 726
26 TraesCS2D01G203600 chr3A 28629966 28630691 725 False 1247.0 1247 97.6650 1 727 1 chr3A.!!$F1 726
27 TraesCS2D01G203600 chr2B 777640463 777641092 629 True 1081.0 1081 97.6190 98 727 1 chr2B.!!$R1 629
28 TraesCS2D01G203600 chr2B 8516709 8517471 762 False 623.0 1105 95.5205 1 727 2 chr2B.!!$F1 726
29 TraesCS2D01G203600 chr2B 198170983 198171746 763 False 609.0 1077 95.1260 1 727 2 chr2B.!!$F2 726

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
700 737 0.107017 GTGATGCAGTATGGGGCTGT 60.107 55.0 0.00 0.0 36.42 4.40 F
1294 1357 0.393537 TCGAGGACCCGAACTACTCC 60.394 60.0 2.97 0.0 35.42 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2176 2370 2.759355 TGTCCTGGGTATCAAGTAGGG 58.241 52.381 0.0 0.0 0.00 3.53 R
3095 7260 1.151668 CAACTGTTCTCAAGGGAGCG 58.848 55.000 0.0 0.0 41.13 5.03 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
38 39 3.881952 ATGCAGCAGAACGGCGTCA 62.882 57.895 15.17 5.22 43.16 4.35
59 60 0.820226 CCTGATCTTGTGGAGAGCGA 59.180 55.000 0.00 0.00 43.77 4.93
82 84 9.427127 GCGAGTGAATTATTTCTGTTCTTTATC 57.573 33.333 0.00 0.00 32.78 1.75
426 463 7.067372 GTGTTGGTCAGATCATAAATGGATTCA 59.933 37.037 0.00 0.00 0.00 2.57
427 464 7.781219 TGTTGGTCAGATCATAAATGGATTCAT 59.219 33.333 0.00 0.00 34.56 2.57
428 465 9.288576 GTTGGTCAGATCATAAATGGATTCATA 57.711 33.333 0.00 0.00 32.44 2.15
429 466 9.511272 TTGGTCAGATCATAAATGGATTCATAG 57.489 33.333 0.00 0.00 32.44 2.23
430 467 8.663167 TGGTCAGATCATAAATGGATTCATAGT 58.337 33.333 0.00 0.00 32.44 2.12
431 468 9.512588 GGTCAGATCATAAATGGATTCATAGTT 57.487 33.333 0.00 0.00 32.44 2.24
433 470 9.428097 TCAGATCATAAATGGATTCATAGTTCG 57.572 33.333 0.00 0.00 32.44 3.95
434 471 9.212641 CAGATCATAAATGGATTCATAGTTCGT 57.787 33.333 0.00 0.00 32.44 3.85
435 472 9.784531 AGATCATAAATGGATTCATAGTTCGTT 57.215 29.630 0.00 0.00 32.44 3.85
438 475 9.389755 TCATAAATGGATTCATAGTTCGTTTGA 57.610 29.630 0.00 0.00 32.44 2.69
441 478 5.484173 TGGATTCATAGTTCGTTTGATGC 57.516 39.130 0.00 0.00 0.00 3.91
442 479 4.335315 TGGATTCATAGTTCGTTTGATGCC 59.665 41.667 0.00 0.00 0.00 4.40
443 480 4.335315 GGATTCATAGTTCGTTTGATGCCA 59.665 41.667 0.00 0.00 0.00 4.92
444 481 5.009010 GGATTCATAGTTCGTTTGATGCCAT 59.991 40.000 0.00 0.00 0.00 4.40
445 482 5.484173 TTCATAGTTCGTTTGATGCCATC 57.516 39.130 0.00 0.00 0.00 3.51
446 483 4.769688 TCATAGTTCGTTTGATGCCATCT 58.230 39.130 6.21 0.00 0.00 2.90
447 484 5.185454 TCATAGTTCGTTTGATGCCATCTT 58.815 37.500 6.21 0.00 0.00 2.40
448 485 6.345298 TCATAGTTCGTTTGATGCCATCTTA 58.655 36.000 6.21 0.00 0.00 2.10
449 486 4.946784 AGTTCGTTTGATGCCATCTTAC 57.053 40.909 6.21 3.32 0.00 2.34
450 487 4.579869 AGTTCGTTTGATGCCATCTTACT 58.420 39.130 6.21 0.00 0.00 2.24
451 488 5.003804 AGTTCGTTTGATGCCATCTTACTT 58.996 37.500 6.21 0.00 0.00 2.24
452 489 5.473504 AGTTCGTTTGATGCCATCTTACTTT 59.526 36.000 6.21 0.00 0.00 2.66
453 490 5.957842 TCGTTTGATGCCATCTTACTTTT 57.042 34.783 6.21 0.00 0.00 2.27
454 491 7.174253 AGTTCGTTTGATGCCATCTTACTTTTA 59.826 33.333 6.21 0.00 0.00 1.52
455 492 7.072177 TCGTTTGATGCCATCTTACTTTTAG 57.928 36.000 6.21 0.00 0.00 1.85
456 493 6.653320 TCGTTTGATGCCATCTTACTTTTAGT 59.347 34.615 6.21 0.00 0.00 2.24
457 494 7.820386 TCGTTTGATGCCATCTTACTTTTAGTA 59.180 33.333 6.21 0.00 0.00 1.82
458 495 8.612619 CGTTTGATGCCATCTTACTTTTAGTAT 58.387 33.333 6.21 0.00 29.64 2.12
461 498 8.833231 TGATGCCATCTTACTTTTAGTATAGC 57.167 34.615 6.21 0.00 29.64 2.97
462 499 8.428852 TGATGCCATCTTACTTTTAGTATAGCA 58.571 33.333 6.21 0.00 29.64 3.49
463 500 9.442047 GATGCCATCTTACTTTTAGTATAGCAT 57.558 33.333 0.00 0.00 33.18 3.79
464 501 8.607441 TGCCATCTTACTTTTAGTATAGCATG 57.393 34.615 0.00 0.00 29.64 4.06
465 502 8.210946 TGCCATCTTACTTTTAGTATAGCATGT 58.789 33.333 0.00 0.00 29.64 3.21
466 503 9.706691 GCCATCTTACTTTTAGTATAGCATGTA 57.293 33.333 0.00 0.00 29.64 2.29
483 520 6.236409 AGCATGTATAATGTCTCATCTTGGG 58.764 40.000 0.00 0.00 0.00 4.12
484 521 5.106396 GCATGTATAATGTCTCATCTTGGGC 60.106 44.000 0.00 0.00 0.00 5.36
485 522 5.628797 TGTATAATGTCTCATCTTGGGCA 57.371 39.130 0.00 0.00 0.00 5.36
486 523 6.191657 TGTATAATGTCTCATCTTGGGCAT 57.808 37.500 0.00 0.00 0.00 4.40
487 524 6.604171 TGTATAATGTCTCATCTTGGGCATT 58.396 36.000 0.00 0.00 32.35 3.56
488 525 6.712095 TGTATAATGTCTCATCTTGGGCATTC 59.288 38.462 0.00 0.00 30.94 2.67
489 526 3.657398 ATGTCTCATCTTGGGCATTCA 57.343 42.857 0.00 0.00 0.00 2.57
490 527 2.715046 TGTCTCATCTTGGGCATTCAC 58.285 47.619 0.00 0.00 0.00 3.18
491 528 2.040145 TGTCTCATCTTGGGCATTCACA 59.960 45.455 0.00 0.00 0.00 3.58
492 529 3.285484 GTCTCATCTTGGGCATTCACAT 58.715 45.455 0.00 0.00 0.00 3.21
493 530 3.066342 GTCTCATCTTGGGCATTCACATG 59.934 47.826 0.00 0.00 0.00 3.21
494 531 3.054213 TCTCATCTTGGGCATTCACATGA 60.054 43.478 0.00 0.00 31.07 3.07
495 532 3.889538 CTCATCTTGGGCATTCACATGAT 59.110 43.478 0.00 0.00 33.39 2.45
496 533 5.051409 TCATCTTGGGCATTCACATGATA 57.949 39.130 0.00 0.00 32.35 2.15
497 534 4.823442 TCATCTTGGGCATTCACATGATAC 59.177 41.667 0.00 0.00 32.35 2.24
498 535 4.508551 TCTTGGGCATTCACATGATACT 57.491 40.909 0.00 0.00 31.07 2.12
499 536 4.858850 TCTTGGGCATTCACATGATACTT 58.141 39.130 0.00 0.00 31.07 2.24
500 537 5.263599 TCTTGGGCATTCACATGATACTTT 58.736 37.500 0.00 0.00 31.07 2.66
501 538 4.987408 TGGGCATTCACATGATACTTTG 57.013 40.909 0.00 0.00 31.07 2.77
502 539 4.343231 TGGGCATTCACATGATACTTTGT 58.657 39.130 0.00 0.00 31.07 2.83
503 540 5.504853 TGGGCATTCACATGATACTTTGTA 58.495 37.500 0.00 0.00 31.07 2.41
504 541 5.948758 TGGGCATTCACATGATACTTTGTAA 59.051 36.000 0.00 0.00 31.07 2.41
505 542 6.606796 TGGGCATTCACATGATACTTTGTAAT 59.393 34.615 0.00 0.00 31.07 1.89
506 543 7.123997 TGGGCATTCACATGATACTTTGTAATT 59.876 33.333 0.00 0.00 31.07 1.40
507 544 7.981225 GGGCATTCACATGATACTTTGTAATTT 59.019 33.333 0.00 0.00 31.07 1.82
508 545 9.023967 GGCATTCACATGATACTTTGTAATTTC 57.976 33.333 0.00 0.00 31.07 2.17
509 546 9.793252 GCATTCACATGATACTTTGTAATTTCT 57.207 29.630 0.00 0.00 31.07 2.52
529 566 5.598416 TCTGAAAGAGAAACAGAGTGTGA 57.402 39.130 0.00 0.00 38.67 3.58
530 567 5.977635 TCTGAAAGAGAAACAGAGTGTGAA 58.022 37.500 0.00 0.00 38.67 3.18
531 568 5.812642 TCTGAAAGAGAAACAGAGTGTGAAC 59.187 40.000 0.00 0.00 38.67 3.18
532 569 5.734720 TGAAAGAGAAACAGAGTGTGAACT 58.265 37.500 0.00 0.00 0.00 3.01
533 570 6.873997 TGAAAGAGAAACAGAGTGTGAACTA 58.126 36.000 0.00 0.00 0.00 2.24
534 571 7.500992 TGAAAGAGAAACAGAGTGTGAACTAT 58.499 34.615 0.00 0.00 0.00 2.12
535 572 8.638873 TGAAAGAGAAACAGAGTGTGAACTATA 58.361 33.333 0.00 0.00 0.00 1.31
536 573 9.134734 GAAAGAGAAACAGAGTGTGAACTATAG 57.865 37.037 0.00 0.00 0.00 1.31
537 574 6.626302 AGAGAAACAGAGTGTGAACTATAGC 58.374 40.000 0.00 0.00 0.00 2.97
538 575 6.435904 AGAGAAACAGAGTGTGAACTATAGCT 59.564 38.462 0.00 0.00 0.00 3.32
539 576 6.998802 AGAAACAGAGTGTGAACTATAGCTT 58.001 36.000 0.00 0.00 0.00 3.74
540 577 7.445945 AGAAACAGAGTGTGAACTATAGCTTT 58.554 34.615 0.00 0.00 0.00 3.51
541 578 7.934120 AGAAACAGAGTGTGAACTATAGCTTTT 59.066 33.333 0.00 0.00 0.00 2.27
542 579 8.451908 AAACAGAGTGTGAACTATAGCTTTTT 57.548 30.769 0.00 0.00 0.00 1.94
543 580 9.555727 AAACAGAGTGTGAACTATAGCTTTTTA 57.444 29.630 0.00 0.00 0.00 1.52
544 581 9.726438 AACAGAGTGTGAACTATAGCTTTTTAT 57.274 29.630 0.00 0.00 0.00 1.40
545 582 9.726438 ACAGAGTGTGAACTATAGCTTTTTATT 57.274 29.630 0.00 0.00 0.00 1.40
614 651 6.615088 TGATTTTGAAAGTGAGATTAGCAGC 58.385 36.000 0.00 0.00 0.00 5.25
615 652 6.207221 TGATTTTGAAAGTGAGATTAGCAGCA 59.793 34.615 0.00 0.00 0.00 4.41
616 653 6.389830 TTTTGAAAGTGAGATTAGCAGCAA 57.610 33.333 0.00 0.00 0.00 3.91
617 654 6.389830 TTTGAAAGTGAGATTAGCAGCAAA 57.610 33.333 0.00 0.00 0.00 3.68
618 655 5.362556 TGAAAGTGAGATTAGCAGCAAAC 57.637 39.130 0.00 0.00 0.00 2.93
619 656 4.821260 TGAAAGTGAGATTAGCAGCAAACA 59.179 37.500 0.00 0.00 0.00 2.83
620 657 5.299028 TGAAAGTGAGATTAGCAGCAAACAA 59.701 36.000 0.00 0.00 0.00 2.83
621 658 4.756084 AGTGAGATTAGCAGCAAACAAC 57.244 40.909 0.00 0.00 0.00 3.32
622 659 4.136796 AGTGAGATTAGCAGCAAACAACA 58.863 39.130 0.00 0.00 0.00 3.33
623 660 4.763793 AGTGAGATTAGCAGCAAACAACAT 59.236 37.500 0.00 0.00 0.00 2.71
624 661 5.242393 AGTGAGATTAGCAGCAAACAACATT 59.758 36.000 0.00 0.00 0.00 2.71
625 662 5.922544 GTGAGATTAGCAGCAAACAACATTT 59.077 36.000 0.00 0.00 0.00 2.32
626 663 6.421801 GTGAGATTAGCAGCAAACAACATTTT 59.578 34.615 0.00 0.00 0.00 1.82
627 664 7.594758 GTGAGATTAGCAGCAAACAACATTTTA 59.405 33.333 0.00 0.00 0.00 1.52
628 665 8.306038 TGAGATTAGCAGCAAACAACATTTTAT 58.694 29.630 0.00 0.00 0.00 1.40
629 666 8.693542 AGATTAGCAGCAAACAACATTTTATC 57.306 30.769 0.00 0.00 0.00 1.75
630 667 8.526147 AGATTAGCAGCAAACAACATTTTATCT 58.474 29.630 0.00 0.00 0.00 1.98
631 668 9.787532 GATTAGCAGCAAACAACATTTTATCTA 57.212 29.630 0.00 0.00 0.00 1.98
632 669 9.793252 ATTAGCAGCAAACAACATTTTATCTAG 57.207 29.630 0.00 0.00 0.00 2.43
633 670 6.624423 AGCAGCAAACAACATTTTATCTAGG 58.376 36.000 0.00 0.00 0.00 3.02
634 671 5.289434 GCAGCAAACAACATTTTATCTAGGC 59.711 40.000 0.00 0.00 0.00 3.93
635 672 5.807011 CAGCAAACAACATTTTATCTAGGCC 59.193 40.000 0.00 0.00 0.00 5.19
636 673 5.105351 AGCAAACAACATTTTATCTAGGCCC 60.105 40.000 0.00 0.00 0.00 5.80
637 674 5.660460 CAAACAACATTTTATCTAGGCCCC 58.340 41.667 0.00 0.00 0.00 5.80
638 675 4.881157 ACAACATTTTATCTAGGCCCCT 57.119 40.909 0.00 0.00 0.00 4.79
639 676 5.987019 ACAACATTTTATCTAGGCCCCTA 57.013 39.130 0.00 0.00 0.00 3.53
640 677 6.335781 ACAACATTTTATCTAGGCCCCTAA 57.664 37.500 0.00 0.00 0.00 2.69
641 678 6.922540 ACAACATTTTATCTAGGCCCCTAAT 58.077 36.000 0.00 0.00 0.00 1.73
642 679 6.777580 ACAACATTTTATCTAGGCCCCTAATG 59.222 38.462 0.00 3.09 0.00 1.90
643 680 5.892348 ACATTTTATCTAGGCCCCTAATGG 58.108 41.667 0.00 0.00 0.00 3.16
644 681 5.375655 ACATTTTATCTAGGCCCCTAATGGT 59.624 40.000 0.00 0.00 0.00 3.55
645 682 6.125890 ACATTTTATCTAGGCCCCTAATGGTT 60.126 38.462 0.00 0.00 0.00 3.67
646 683 5.578157 TTTATCTAGGCCCCTAATGGTTC 57.422 43.478 0.00 0.00 0.00 3.62
647 684 1.815757 TCTAGGCCCCTAATGGTTCC 58.184 55.000 0.00 0.00 0.00 3.62
648 685 0.396811 CTAGGCCCCTAATGGTTCCG 59.603 60.000 0.00 0.00 0.00 4.30
649 686 0.326808 TAGGCCCCTAATGGTTCCGT 60.327 55.000 0.00 0.00 0.00 4.69
650 687 1.212250 AGGCCCCTAATGGTTCCGTT 61.212 55.000 0.00 1.84 0.00 4.44
651 688 0.323999 GGCCCCTAATGGTTCCGTTT 60.324 55.000 0.00 0.00 0.00 3.60
652 689 0.815095 GCCCCTAATGGTTCCGTTTG 59.185 55.000 1.49 0.51 0.00 2.93
653 690 1.889262 GCCCCTAATGGTTCCGTTTGT 60.889 52.381 1.49 0.00 0.00 2.83
654 691 2.089201 CCCCTAATGGTTCCGTTTGTC 58.911 52.381 1.49 0.00 0.00 3.18
655 692 2.290705 CCCCTAATGGTTCCGTTTGTCT 60.291 50.000 1.49 0.00 0.00 3.41
656 693 3.418047 CCCTAATGGTTCCGTTTGTCTT 58.582 45.455 1.49 0.00 0.00 3.01
657 694 3.439129 CCCTAATGGTTCCGTTTGTCTTC 59.561 47.826 1.49 0.00 0.00 2.87
658 695 4.324267 CCTAATGGTTCCGTTTGTCTTCT 58.676 43.478 1.49 0.00 0.00 2.85
659 696 4.760204 CCTAATGGTTCCGTTTGTCTTCTT 59.240 41.667 1.49 0.00 0.00 2.52
660 697 5.935789 CCTAATGGTTCCGTTTGTCTTCTTA 59.064 40.000 1.49 0.00 0.00 2.10
661 698 5.941948 AATGGTTCCGTTTGTCTTCTTAG 57.058 39.130 0.00 0.00 0.00 2.18
662 699 4.411256 TGGTTCCGTTTGTCTTCTTAGT 57.589 40.909 0.00 0.00 0.00 2.24
663 700 4.773013 TGGTTCCGTTTGTCTTCTTAGTT 58.227 39.130 0.00 0.00 0.00 2.24
664 701 4.812626 TGGTTCCGTTTGTCTTCTTAGTTC 59.187 41.667 0.00 0.00 0.00 3.01
665 702 5.055144 GGTTCCGTTTGTCTTCTTAGTTCT 58.945 41.667 0.00 0.00 0.00 3.01
666 703 5.177142 GGTTCCGTTTGTCTTCTTAGTTCTC 59.823 44.000 0.00 0.00 0.00 2.87
667 704 5.524971 TCCGTTTGTCTTCTTAGTTCTCA 57.475 39.130 0.00 0.00 0.00 3.27
668 705 5.287226 TCCGTTTGTCTTCTTAGTTCTCAC 58.713 41.667 0.00 0.00 0.00 3.51
669 706 4.448060 CCGTTTGTCTTCTTAGTTCTCACC 59.552 45.833 0.00 0.00 0.00 4.02
670 707 4.448060 CGTTTGTCTTCTTAGTTCTCACCC 59.552 45.833 0.00 0.00 0.00 4.61
671 708 5.612351 GTTTGTCTTCTTAGTTCTCACCCT 58.388 41.667 0.00 0.00 0.00 4.34
672 709 5.888982 TTGTCTTCTTAGTTCTCACCCTT 57.111 39.130 0.00 0.00 0.00 3.95
673 710 5.888982 TGTCTTCTTAGTTCTCACCCTTT 57.111 39.130 0.00 0.00 0.00 3.11
674 711 6.248569 TGTCTTCTTAGTTCTCACCCTTTT 57.751 37.500 0.00 0.00 0.00 2.27
675 712 6.055588 TGTCTTCTTAGTTCTCACCCTTTTG 58.944 40.000 0.00 0.00 0.00 2.44
676 713 6.056236 GTCTTCTTAGTTCTCACCCTTTTGT 58.944 40.000 0.00 0.00 0.00 2.83
677 714 7.147620 TGTCTTCTTAGTTCTCACCCTTTTGTA 60.148 37.037 0.00 0.00 0.00 2.41
678 715 7.878644 GTCTTCTTAGTTCTCACCCTTTTGTAT 59.121 37.037 0.00 0.00 0.00 2.29
679 716 8.095169 TCTTCTTAGTTCTCACCCTTTTGTATC 58.905 37.037 0.00 0.00 0.00 2.24
680 717 6.708285 TCTTAGTTCTCACCCTTTTGTATCC 58.292 40.000 0.00 0.00 0.00 2.59
681 718 3.939066 AGTTCTCACCCTTTTGTATCCG 58.061 45.455 0.00 0.00 0.00 4.18
682 719 3.326880 AGTTCTCACCCTTTTGTATCCGT 59.673 43.478 0.00 0.00 0.00 4.69
683 720 3.328382 TCTCACCCTTTTGTATCCGTG 57.672 47.619 0.00 0.00 0.00 4.94
684 721 2.901192 TCTCACCCTTTTGTATCCGTGA 59.099 45.455 0.00 0.00 0.00 4.35
685 722 3.517901 TCTCACCCTTTTGTATCCGTGAT 59.482 43.478 0.00 0.00 30.46 3.06
686 723 3.605634 TCACCCTTTTGTATCCGTGATG 58.394 45.455 0.00 0.00 0.00 3.07
687 724 2.097466 CACCCTTTTGTATCCGTGATGC 59.903 50.000 0.00 0.00 0.00 3.91
688 725 2.290641 ACCCTTTTGTATCCGTGATGCA 60.291 45.455 0.00 0.00 33.20 3.96
689 726 2.355756 CCCTTTTGTATCCGTGATGCAG 59.644 50.000 0.00 0.00 36.18 4.41
690 727 3.009723 CCTTTTGTATCCGTGATGCAGT 58.990 45.455 0.00 0.00 36.18 4.40
691 728 4.188462 CCTTTTGTATCCGTGATGCAGTA 58.812 43.478 0.00 0.00 36.18 2.74
692 729 4.816385 CCTTTTGTATCCGTGATGCAGTAT 59.184 41.667 0.00 0.00 36.18 2.12
693 730 5.277490 CCTTTTGTATCCGTGATGCAGTATG 60.277 44.000 0.00 0.00 36.18 2.39
694 731 3.385193 TGTATCCGTGATGCAGTATGG 57.615 47.619 5.14 5.14 35.86 2.74
695 732 2.037121 TGTATCCGTGATGCAGTATGGG 59.963 50.000 10.40 0.24 35.86 4.00
696 733 0.397941 ATCCGTGATGCAGTATGGGG 59.602 55.000 10.40 0.00 35.86 4.96
697 734 1.893808 CCGTGATGCAGTATGGGGC 60.894 63.158 0.00 0.00 35.86 5.80
698 735 1.146930 CGTGATGCAGTATGGGGCT 59.853 57.895 0.00 0.00 35.86 5.19
699 736 1.162181 CGTGATGCAGTATGGGGCTG 61.162 60.000 0.00 0.00 35.86 4.85
700 737 0.107017 GTGATGCAGTATGGGGCTGT 60.107 55.000 0.00 0.00 36.42 4.40
701 738 1.140852 GTGATGCAGTATGGGGCTGTA 59.859 52.381 0.00 0.00 36.42 2.74
702 739 1.417517 TGATGCAGTATGGGGCTGTAG 59.582 52.381 0.00 0.00 36.42 2.74
703 740 1.694150 GATGCAGTATGGGGCTGTAGA 59.306 52.381 0.00 0.00 36.42 2.59
704 741 1.578897 TGCAGTATGGGGCTGTAGAA 58.421 50.000 0.00 0.00 36.42 2.10
705 742 1.486310 TGCAGTATGGGGCTGTAGAAG 59.514 52.381 0.00 0.00 36.42 2.85
706 743 1.762957 GCAGTATGGGGCTGTAGAAGA 59.237 52.381 0.00 0.00 36.42 2.87
707 744 2.370189 GCAGTATGGGGCTGTAGAAGAT 59.630 50.000 0.00 0.00 36.42 2.40
708 745 3.181450 GCAGTATGGGGCTGTAGAAGATT 60.181 47.826 0.00 0.00 36.42 2.40
709 746 4.687219 GCAGTATGGGGCTGTAGAAGATTT 60.687 45.833 0.00 0.00 36.42 2.17
710 747 4.818546 CAGTATGGGGCTGTAGAAGATTTG 59.181 45.833 0.00 0.00 0.00 2.32
711 748 4.721776 AGTATGGGGCTGTAGAAGATTTGA 59.278 41.667 0.00 0.00 0.00 2.69
712 749 4.591321 ATGGGGCTGTAGAAGATTTGAA 57.409 40.909 0.00 0.00 0.00 2.69
713 750 3.686016 TGGGGCTGTAGAAGATTTGAAC 58.314 45.455 0.00 0.00 0.00 3.18
714 751 3.073798 TGGGGCTGTAGAAGATTTGAACA 59.926 43.478 0.00 0.00 0.00 3.18
715 752 4.079253 GGGGCTGTAGAAGATTTGAACAA 58.921 43.478 0.00 0.00 0.00 2.83
716 753 4.522789 GGGGCTGTAGAAGATTTGAACAAA 59.477 41.667 2.48 2.48 34.46 2.83
717 754 5.010617 GGGGCTGTAGAAGATTTGAACAAAA 59.989 40.000 4.12 0.00 33.56 2.44
718 755 6.152379 GGGCTGTAGAAGATTTGAACAAAAG 58.848 40.000 4.12 0.00 33.56 2.27
719 756 6.016276 GGGCTGTAGAAGATTTGAACAAAAGA 60.016 38.462 4.12 0.00 33.56 2.52
720 757 7.309438 GGGCTGTAGAAGATTTGAACAAAAGAT 60.309 37.037 4.12 0.00 33.56 2.40
721 758 7.540055 GGCTGTAGAAGATTTGAACAAAAGATG 59.460 37.037 4.12 0.00 33.56 2.90
1030 1075 1.827789 CTCTCTCGCCCCTCTCTGG 60.828 68.421 0.00 0.00 0.00 3.86
1171 1219 3.678056 TCAAGGTCAGTGATGTGTACC 57.322 47.619 0.00 0.00 0.00 3.34
1240 1303 1.463674 ACCCGTGAGATGGATTTTGC 58.536 50.000 0.00 0.00 0.00 3.68
1268 1331 5.414789 TCTTTTGTTGATGTAGATCCCGA 57.585 39.130 0.00 0.00 0.00 5.14
1294 1357 0.393537 TCGAGGACCCGAACTACTCC 60.394 60.000 2.97 0.00 35.42 3.85
1384 1448 1.692762 GGGATTAGCACTGGGAGGAGA 60.693 57.143 0.00 0.00 0.00 3.71
1493 1557 6.513230 GCACTGTTCATTGTTCATGTTCACTA 60.513 38.462 0.00 0.00 34.06 2.74
2176 2370 2.880890 AGCTTGTTGAGGATGTGAACAC 59.119 45.455 0.00 0.00 29.44 3.32
2203 2406 6.575244 ACTTGATACCCAGGACAATATTCA 57.425 37.500 0.00 0.00 0.00 2.57
2520 2723 6.932356 TCAAGGATATTTGTGATGAAGAGC 57.068 37.500 0.00 0.00 0.00 4.09
2779 6894 7.191551 CCACATTCATCACACTTATTAGCAAG 58.808 38.462 0.00 0.00 0.00 4.01
3008 7173 2.086869 CATAGCCCAACAAGTCCACTG 58.913 52.381 0.00 0.00 0.00 3.66
3095 7260 5.047188 CCACAAATTAACACAACTTCACCC 58.953 41.667 0.00 0.00 0.00 4.61
3236 7402 0.179018 GAACTTGGACCAGCACCAGT 60.179 55.000 0.00 0.00 38.70 4.00
3325 7497 0.615331 CCTTGTAGCAGGAGGAGCAA 59.385 55.000 0.00 0.00 35.71 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 0.459063 CTGCATGAGCGACAGTAGCA 60.459 55.000 8.50 0.00 46.23 3.49
38 39 1.066573 CGCTCTCCACAAGATCAGGTT 60.067 52.381 0.00 0.00 32.19 3.50
82 84 7.169158 TGCCAATGTTAAGAATAGGGAAAAG 57.831 36.000 0.00 0.00 0.00 2.27
426 463 6.349300 AGTAAGATGGCATCAAACGAACTAT 58.651 36.000 27.93 6.87 0.00 2.12
427 464 5.730550 AGTAAGATGGCATCAAACGAACTA 58.269 37.500 27.93 4.77 0.00 2.24
428 465 4.579869 AGTAAGATGGCATCAAACGAACT 58.420 39.130 27.93 17.12 0.00 3.01
429 466 4.946784 AGTAAGATGGCATCAAACGAAC 57.053 40.909 27.93 15.43 0.00 3.95
430 467 5.957842 AAAGTAAGATGGCATCAAACGAA 57.042 34.783 27.93 5.00 0.00 3.85
431 468 5.957842 AAAAGTAAGATGGCATCAAACGA 57.042 34.783 27.93 6.49 0.00 3.85
432 469 6.842163 ACTAAAAGTAAGATGGCATCAAACG 58.158 36.000 27.93 13.91 0.00 3.60
435 472 9.273016 GCTATACTAAAAGTAAGATGGCATCAA 57.727 33.333 27.93 13.71 33.89 2.57
436 473 8.428852 TGCTATACTAAAAGTAAGATGGCATCA 58.571 33.333 27.93 6.84 33.89 3.07
437 474 8.833231 TGCTATACTAAAAGTAAGATGGCATC 57.167 34.615 19.78 19.78 33.89 3.91
438 475 9.224267 CATGCTATACTAAAAGTAAGATGGCAT 57.776 33.333 0.00 0.00 33.89 4.40
439 476 8.210946 ACATGCTATACTAAAAGTAAGATGGCA 58.789 33.333 0.00 0.00 33.89 4.92
440 477 8.608844 ACATGCTATACTAAAAGTAAGATGGC 57.391 34.615 0.00 0.00 33.89 4.40
457 494 8.045507 CCCAAGATGAGACATTATACATGCTAT 58.954 37.037 0.00 0.00 0.00 2.97
458 495 7.389232 CCCAAGATGAGACATTATACATGCTA 58.611 38.462 0.00 0.00 0.00 3.49
459 496 6.236409 CCCAAGATGAGACATTATACATGCT 58.764 40.000 0.00 0.00 0.00 3.79
460 497 5.106396 GCCCAAGATGAGACATTATACATGC 60.106 44.000 0.00 0.00 0.00 4.06
461 498 5.999600 TGCCCAAGATGAGACATTATACATG 59.000 40.000 0.00 0.00 0.00 3.21
462 499 6.191657 TGCCCAAGATGAGACATTATACAT 57.808 37.500 0.00 0.00 0.00 2.29
463 500 5.628797 TGCCCAAGATGAGACATTATACA 57.371 39.130 0.00 0.00 0.00 2.29
464 501 6.712095 TGAATGCCCAAGATGAGACATTATAC 59.288 38.462 0.00 0.00 0.00 1.47
465 502 6.712095 GTGAATGCCCAAGATGAGACATTATA 59.288 38.462 0.00 0.00 0.00 0.98
466 503 5.533903 GTGAATGCCCAAGATGAGACATTAT 59.466 40.000 0.00 0.00 0.00 1.28
467 504 4.883585 GTGAATGCCCAAGATGAGACATTA 59.116 41.667 0.00 0.00 0.00 1.90
468 505 3.698040 GTGAATGCCCAAGATGAGACATT 59.302 43.478 0.00 0.00 0.00 2.71
469 506 3.285484 GTGAATGCCCAAGATGAGACAT 58.715 45.455 0.00 0.00 0.00 3.06
470 507 2.040145 TGTGAATGCCCAAGATGAGACA 59.960 45.455 0.00 0.00 0.00 3.41
471 508 2.715046 TGTGAATGCCCAAGATGAGAC 58.285 47.619 0.00 0.00 0.00 3.36
472 509 3.054213 TCATGTGAATGCCCAAGATGAGA 60.054 43.478 0.00 0.00 0.00 3.27
473 510 3.284617 TCATGTGAATGCCCAAGATGAG 58.715 45.455 0.00 0.00 0.00 2.90
474 511 3.369242 TCATGTGAATGCCCAAGATGA 57.631 42.857 0.00 0.00 0.00 2.92
475 512 4.825634 AGTATCATGTGAATGCCCAAGATG 59.174 41.667 0.00 0.00 0.00 2.90
476 513 5.057843 AGTATCATGTGAATGCCCAAGAT 57.942 39.130 0.00 0.00 0.00 2.40
477 514 4.508551 AGTATCATGTGAATGCCCAAGA 57.491 40.909 0.00 0.00 0.00 3.02
478 515 5.105635 ACAAAGTATCATGTGAATGCCCAAG 60.106 40.000 0.00 0.00 0.00 3.61
479 516 4.771577 ACAAAGTATCATGTGAATGCCCAA 59.228 37.500 0.00 0.00 0.00 4.12
480 517 4.343231 ACAAAGTATCATGTGAATGCCCA 58.657 39.130 0.00 0.00 0.00 5.36
481 518 4.989279 ACAAAGTATCATGTGAATGCCC 57.011 40.909 0.00 0.00 0.00 5.36
482 519 8.931385 AAATTACAAAGTATCATGTGAATGCC 57.069 30.769 0.00 0.00 0.00 4.40
483 520 9.793252 AGAAATTACAAAGTATCATGTGAATGC 57.207 29.630 0.00 0.00 0.00 3.56
506 543 5.977635 TCACACTCTGTTTCTCTTTCAGAA 58.022 37.500 0.00 0.00 39.56 3.02
507 544 5.598416 TCACACTCTGTTTCTCTTTCAGA 57.402 39.130 0.00 0.00 36.85 3.27
508 545 5.814705 AGTTCACACTCTGTTTCTCTTTCAG 59.185 40.000 0.00 0.00 0.00 3.02
509 546 5.734720 AGTTCACACTCTGTTTCTCTTTCA 58.265 37.500 0.00 0.00 0.00 2.69
510 547 7.954788 ATAGTTCACACTCTGTTTCTCTTTC 57.045 36.000 0.00 0.00 34.06 2.62
511 548 7.600752 GCTATAGTTCACACTCTGTTTCTCTTT 59.399 37.037 0.84 0.00 34.06 2.52
512 549 7.039363 AGCTATAGTTCACACTCTGTTTCTCTT 60.039 37.037 0.84 0.00 34.06 2.85
513 550 6.435904 AGCTATAGTTCACACTCTGTTTCTCT 59.564 38.462 0.84 0.00 34.06 3.10
514 551 6.626302 AGCTATAGTTCACACTCTGTTTCTC 58.374 40.000 0.84 0.00 34.06 2.87
515 552 6.597832 AGCTATAGTTCACACTCTGTTTCT 57.402 37.500 0.84 0.00 34.06 2.52
516 553 7.659652 AAAGCTATAGTTCACACTCTGTTTC 57.340 36.000 0.84 0.00 34.06 2.78
517 554 8.451908 AAAAAGCTATAGTTCACACTCTGTTT 57.548 30.769 0.84 0.00 34.06 2.83
518 555 9.726438 ATAAAAAGCTATAGTTCACACTCTGTT 57.274 29.630 0.84 0.00 34.06 3.16
519 556 9.726438 AATAAAAAGCTATAGTTCACACTCTGT 57.274 29.630 0.84 0.00 34.06 3.41
588 625 7.758528 GCTGCTAATCTCACTTTCAAAATCATT 59.241 33.333 0.00 0.00 0.00 2.57
589 626 7.094075 TGCTGCTAATCTCACTTTCAAAATCAT 60.094 33.333 0.00 0.00 0.00 2.45
590 627 6.207221 TGCTGCTAATCTCACTTTCAAAATCA 59.793 34.615 0.00 0.00 0.00 2.57
591 628 6.615088 TGCTGCTAATCTCACTTTCAAAATC 58.385 36.000 0.00 0.00 0.00 2.17
592 629 6.579666 TGCTGCTAATCTCACTTTCAAAAT 57.420 33.333 0.00 0.00 0.00 1.82
593 630 6.389830 TTGCTGCTAATCTCACTTTCAAAA 57.610 33.333 0.00 0.00 0.00 2.44
594 631 6.183360 TGTTTGCTGCTAATCTCACTTTCAAA 60.183 34.615 0.00 0.00 0.00 2.69
595 632 5.299028 TGTTTGCTGCTAATCTCACTTTCAA 59.701 36.000 0.00 0.00 0.00 2.69
596 633 4.821260 TGTTTGCTGCTAATCTCACTTTCA 59.179 37.500 0.00 0.00 0.00 2.69
597 634 5.362556 TGTTTGCTGCTAATCTCACTTTC 57.637 39.130 0.00 0.00 0.00 2.62
598 635 5.067674 TGTTGTTTGCTGCTAATCTCACTTT 59.932 36.000 0.00 0.00 0.00 2.66
599 636 4.580167 TGTTGTTTGCTGCTAATCTCACTT 59.420 37.500 0.00 0.00 0.00 3.16
600 637 4.136796 TGTTGTTTGCTGCTAATCTCACT 58.863 39.130 0.00 0.00 0.00 3.41
601 638 4.488126 TGTTGTTTGCTGCTAATCTCAC 57.512 40.909 0.00 0.00 0.00 3.51
602 639 5.710513 AATGTTGTTTGCTGCTAATCTCA 57.289 34.783 0.00 1.34 0.00 3.27
603 640 8.693542 ATAAAATGTTGTTTGCTGCTAATCTC 57.306 30.769 0.00 0.00 0.00 2.75
604 641 8.526147 AGATAAAATGTTGTTTGCTGCTAATCT 58.474 29.630 0.00 0.00 0.00 2.40
605 642 8.693542 AGATAAAATGTTGTTTGCTGCTAATC 57.306 30.769 0.00 0.00 0.00 1.75
606 643 9.793252 CTAGATAAAATGTTGTTTGCTGCTAAT 57.207 29.630 0.00 0.00 0.00 1.73
607 644 8.243426 CCTAGATAAAATGTTGTTTGCTGCTAA 58.757 33.333 0.00 0.00 0.00 3.09
608 645 7.628366 GCCTAGATAAAATGTTGTTTGCTGCTA 60.628 37.037 0.00 0.00 0.00 3.49
609 646 6.624423 CCTAGATAAAATGTTGTTTGCTGCT 58.376 36.000 0.00 0.00 0.00 4.24
610 647 5.289434 GCCTAGATAAAATGTTGTTTGCTGC 59.711 40.000 0.00 0.00 0.00 5.25
611 648 5.807011 GGCCTAGATAAAATGTTGTTTGCTG 59.193 40.000 0.00 0.00 0.00 4.41
612 649 5.105351 GGGCCTAGATAAAATGTTGTTTGCT 60.105 40.000 0.84 0.00 0.00 3.91
613 650 5.109210 GGGCCTAGATAAAATGTTGTTTGC 58.891 41.667 0.84 0.00 0.00 3.68
614 651 5.422012 AGGGGCCTAGATAAAATGTTGTTTG 59.578 40.000 0.84 0.00 0.00 2.93
615 652 5.589831 AGGGGCCTAGATAAAATGTTGTTT 58.410 37.500 0.84 0.00 0.00 2.83
616 653 5.206905 AGGGGCCTAGATAAAATGTTGTT 57.793 39.130 0.84 0.00 0.00 2.83
617 654 4.881157 AGGGGCCTAGATAAAATGTTGT 57.119 40.909 0.84 0.00 0.00 3.32
618 655 6.209391 CCATTAGGGGCCTAGATAAAATGTTG 59.791 42.308 0.84 0.00 0.00 3.33
619 656 6.125890 ACCATTAGGGGCCTAGATAAAATGTT 60.126 38.462 0.84 0.00 42.91 2.71
620 657 5.375655 ACCATTAGGGGCCTAGATAAAATGT 59.624 40.000 0.84 0.00 42.91 2.71
621 658 5.892348 ACCATTAGGGGCCTAGATAAAATG 58.108 41.667 0.84 3.88 42.91 2.32
622 659 6.468798 GGAACCATTAGGGGCCTAGATAAAAT 60.469 42.308 0.84 0.00 42.91 1.82
623 660 5.163023 GGAACCATTAGGGGCCTAGATAAAA 60.163 44.000 0.84 0.00 42.91 1.52
624 661 4.352893 GGAACCATTAGGGGCCTAGATAAA 59.647 45.833 0.84 0.00 42.91 1.40
625 662 3.914435 GGAACCATTAGGGGCCTAGATAA 59.086 47.826 0.84 0.00 42.91 1.75
626 663 3.527937 GGAACCATTAGGGGCCTAGATA 58.472 50.000 0.84 0.00 42.91 1.98
627 664 2.349445 GGAACCATTAGGGGCCTAGAT 58.651 52.381 0.84 0.00 42.91 1.98
628 665 1.815757 GGAACCATTAGGGGCCTAGA 58.184 55.000 0.84 0.00 42.91 2.43
629 666 0.396811 CGGAACCATTAGGGGCCTAG 59.603 60.000 0.84 0.00 42.91 3.02
630 667 0.326808 ACGGAACCATTAGGGGCCTA 60.327 55.000 0.84 0.00 42.91 3.93
631 668 1.212250 AACGGAACCATTAGGGGCCT 61.212 55.000 0.84 0.00 42.91 5.19
632 669 0.323999 AAACGGAACCATTAGGGGCC 60.324 55.000 0.00 0.00 42.91 5.80
633 670 0.815095 CAAACGGAACCATTAGGGGC 59.185 55.000 0.00 0.00 42.91 5.80
634 671 2.089201 GACAAACGGAACCATTAGGGG 58.911 52.381 0.00 0.00 42.91 4.79
635 672 3.067684 AGACAAACGGAACCATTAGGG 57.932 47.619 0.00 0.00 44.81 3.53
636 673 4.324267 AGAAGACAAACGGAACCATTAGG 58.676 43.478 0.00 0.00 42.21 2.69
637 674 5.941948 AAGAAGACAAACGGAACCATTAG 57.058 39.130 0.00 0.00 0.00 1.73
638 675 6.527423 ACTAAGAAGACAAACGGAACCATTA 58.473 36.000 0.00 0.00 0.00 1.90
639 676 5.374071 ACTAAGAAGACAAACGGAACCATT 58.626 37.500 0.00 0.00 0.00 3.16
640 677 4.969484 ACTAAGAAGACAAACGGAACCAT 58.031 39.130 0.00 0.00 0.00 3.55
641 678 4.411256 ACTAAGAAGACAAACGGAACCA 57.589 40.909 0.00 0.00 0.00 3.67
642 679 5.055144 AGAACTAAGAAGACAAACGGAACC 58.945 41.667 0.00 0.00 0.00 3.62
643 680 5.751990 TGAGAACTAAGAAGACAAACGGAAC 59.248 40.000 0.00 0.00 0.00 3.62
644 681 5.751990 GTGAGAACTAAGAAGACAAACGGAA 59.248 40.000 0.00 0.00 0.00 4.30
645 682 5.287226 GTGAGAACTAAGAAGACAAACGGA 58.713 41.667 0.00 0.00 0.00 4.69
646 683 4.448060 GGTGAGAACTAAGAAGACAAACGG 59.552 45.833 0.00 0.00 0.00 4.44
647 684 4.448060 GGGTGAGAACTAAGAAGACAAACG 59.552 45.833 0.00 0.00 0.00 3.60
648 685 5.612351 AGGGTGAGAACTAAGAAGACAAAC 58.388 41.667 0.00 0.00 0.00 2.93
649 686 5.888982 AGGGTGAGAACTAAGAAGACAAA 57.111 39.130 0.00 0.00 0.00 2.83
650 687 5.888982 AAGGGTGAGAACTAAGAAGACAA 57.111 39.130 0.00 0.00 0.00 3.18
651 688 5.888982 AAAGGGTGAGAACTAAGAAGACA 57.111 39.130 0.00 0.00 0.00 3.41
652 689 6.056236 ACAAAAGGGTGAGAACTAAGAAGAC 58.944 40.000 0.00 0.00 0.00 3.01
653 690 6.248569 ACAAAAGGGTGAGAACTAAGAAGA 57.751 37.500 0.00 0.00 0.00 2.87
654 691 7.334671 GGATACAAAAGGGTGAGAACTAAGAAG 59.665 40.741 0.00 0.00 0.00 2.85
655 692 7.166167 GGATACAAAAGGGTGAGAACTAAGAA 58.834 38.462 0.00 0.00 0.00 2.52
656 693 6.573680 CGGATACAAAAGGGTGAGAACTAAGA 60.574 42.308 0.00 0.00 0.00 2.10
657 694 5.581085 CGGATACAAAAGGGTGAGAACTAAG 59.419 44.000 0.00 0.00 0.00 2.18
658 695 5.012354 ACGGATACAAAAGGGTGAGAACTAA 59.988 40.000 0.00 0.00 0.00 2.24
659 696 4.529377 ACGGATACAAAAGGGTGAGAACTA 59.471 41.667 0.00 0.00 0.00 2.24
660 697 3.326880 ACGGATACAAAAGGGTGAGAACT 59.673 43.478 0.00 0.00 0.00 3.01
661 698 3.435671 CACGGATACAAAAGGGTGAGAAC 59.564 47.826 0.00 0.00 0.00 3.01
662 699 3.325425 TCACGGATACAAAAGGGTGAGAA 59.675 43.478 0.00 0.00 31.45 2.87
663 700 2.901192 TCACGGATACAAAAGGGTGAGA 59.099 45.455 0.00 0.00 31.45 3.27
664 701 3.328382 TCACGGATACAAAAGGGTGAG 57.672 47.619 0.00 0.00 31.45 3.51
665 702 3.605634 CATCACGGATACAAAAGGGTGA 58.394 45.455 0.00 0.00 38.59 4.02
666 703 2.097466 GCATCACGGATACAAAAGGGTG 59.903 50.000 0.00 0.00 0.00 4.61
667 704 2.290641 TGCATCACGGATACAAAAGGGT 60.291 45.455 0.00 0.00 0.00 4.34
668 705 2.355756 CTGCATCACGGATACAAAAGGG 59.644 50.000 0.00 0.00 0.00 3.95
669 706 3.009723 ACTGCATCACGGATACAAAAGG 58.990 45.455 0.00 0.00 0.00 3.11
670 707 5.277490 CCATACTGCATCACGGATACAAAAG 60.277 44.000 0.00 0.00 0.00 2.27
671 708 4.574421 CCATACTGCATCACGGATACAAAA 59.426 41.667 0.00 0.00 0.00 2.44
672 709 4.126437 CCATACTGCATCACGGATACAAA 58.874 43.478 0.00 0.00 0.00 2.83
673 710 3.494223 CCCATACTGCATCACGGATACAA 60.494 47.826 0.00 0.00 0.00 2.41
674 711 2.037121 CCCATACTGCATCACGGATACA 59.963 50.000 0.00 0.00 0.00 2.29
675 712 2.612972 CCCCATACTGCATCACGGATAC 60.613 54.545 0.00 0.00 0.00 2.24
676 713 1.623311 CCCCATACTGCATCACGGATA 59.377 52.381 0.00 0.00 0.00 2.59
677 714 0.397941 CCCCATACTGCATCACGGAT 59.602 55.000 0.00 0.00 0.00 4.18
678 715 1.829456 CCCCATACTGCATCACGGA 59.171 57.895 0.00 0.00 0.00 4.69
679 716 1.893808 GCCCCATACTGCATCACGG 60.894 63.158 0.00 0.00 0.00 4.94
680 717 1.146930 AGCCCCATACTGCATCACG 59.853 57.895 0.00 0.00 0.00 4.35
681 718 0.107017 ACAGCCCCATACTGCATCAC 60.107 55.000 0.00 0.00 38.79 3.06
682 719 1.417517 CTACAGCCCCATACTGCATCA 59.582 52.381 0.00 0.00 38.79 3.07
683 720 1.694150 TCTACAGCCCCATACTGCATC 59.306 52.381 0.00 0.00 38.79 3.91
684 721 1.806496 TCTACAGCCCCATACTGCAT 58.194 50.000 0.00 0.00 38.79 3.96
685 722 1.486310 CTTCTACAGCCCCATACTGCA 59.514 52.381 0.00 0.00 38.79 4.41
686 723 1.762957 TCTTCTACAGCCCCATACTGC 59.237 52.381 0.00 0.00 38.79 4.40
687 724 4.696479 AATCTTCTACAGCCCCATACTG 57.304 45.455 0.00 0.00 41.08 2.74
688 725 4.721776 TCAAATCTTCTACAGCCCCATACT 59.278 41.667 0.00 0.00 0.00 2.12
689 726 5.036117 TCAAATCTTCTACAGCCCCATAC 57.964 43.478 0.00 0.00 0.00 2.39
690 727 5.045213 TGTTCAAATCTTCTACAGCCCCATA 60.045 40.000 0.00 0.00 0.00 2.74
691 728 4.263905 TGTTCAAATCTTCTACAGCCCCAT 60.264 41.667 0.00 0.00 0.00 4.00
692 729 3.073798 TGTTCAAATCTTCTACAGCCCCA 59.926 43.478 0.00 0.00 0.00 4.96
693 730 3.686016 TGTTCAAATCTTCTACAGCCCC 58.314 45.455 0.00 0.00 0.00 5.80
694 731 5.705609 TTTGTTCAAATCTTCTACAGCCC 57.294 39.130 0.00 0.00 0.00 5.19
695 732 6.970484 TCTTTTGTTCAAATCTTCTACAGCC 58.030 36.000 0.00 0.00 0.00 4.85
696 733 7.540055 CCATCTTTTGTTCAAATCTTCTACAGC 59.460 37.037 0.00 0.00 0.00 4.40
697 734 8.786898 TCCATCTTTTGTTCAAATCTTCTACAG 58.213 33.333 0.00 0.00 0.00 2.74
698 735 8.690203 TCCATCTTTTGTTCAAATCTTCTACA 57.310 30.769 0.00 0.00 0.00 2.74
699 736 9.617975 CTTCCATCTTTTGTTCAAATCTTCTAC 57.382 33.333 0.00 0.00 0.00 2.59
700 737 8.299570 GCTTCCATCTTTTGTTCAAATCTTCTA 58.700 33.333 0.00 0.00 0.00 2.10
701 738 7.150640 GCTTCCATCTTTTGTTCAAATCTTCT 58.849 34.615 0.00 0.00 0.00 2.85
702 739 6.088616 CGCTTCCATCTTTTGTTCAAATCTTC 59.911 38.462 0.00 0.00 0.00 2.87
703 740 5.922544 CGCTTCCATCTTTTGTTCAAATCTT 59.077 36.000 0.00 0.00 0.00 2.40
704 741 5.241506 TCGCTTCCATCTTTTGTTCAAATCT 59.758 36.000 0.00 0.00 0.00 2.40
705 742 5.460646 TCGCTTCCATCTTTTGTTCAAATC 58.539 37.500 0.00 0.00 0.00 2.17
706 743 5.010012 ACTCGCTTCCATCTTTTGTTCAAAT 59.990 36.000 0.00 0.00 0.00 2.32
707 744 4.338118 ACTCGCTTCCATCTTTTGTTCAAA 59.662 37.500 0.00 0.00 0.00 2.69
708 745 3.882888 ACTCGCTTCCATCTTTTGTTCAA 59.117 39.130 0.00 0.00 0.00 2.69
709 746 3.476552 ACTCGCTTCCATCTTTTGTTCA 58.523 40.909 0.00 0.00 0.00 3.18
710 747 3.498397 TGACTCGCTTCCATCTTTTGTTC 59.502 43.478 0.00 0.00 0.00 3.18
711 748 3.476552 TGACTCGCTTCCATCTTTTGTT 58.523 40.909 0.00 0.00 0.00 2.83
712 749 3.126001 TGACTCGCTTCCATCTTTTGT 57.874 42.857 0.00 0.00 0.00 2.83
713 750 4.691860 ATTGACTCGCTTCCATCTTTTG 57.308 40.909 0.00 0.00 0.00 2.44
714 751 4.616835 GCAATTGACTCGCTTCCATCTTTT 60.617 41.667 10.34 0.00 0.00 2.27
715 752 3.119708 GCAATTGACTCGCTTCCATCTTT 60.120 43.478 10.34 0.00 0.00 2.52
716 753 2.421424 GCAATTGACTCGCTTCCATCTT 59.579 45.455 10.34 0.00 0.00 2.40
717 754 2.012673 GCAATTGACTCGCTTCCATCT 58.987 47.619 10.34 0.00 0.00 2.90
718 755 1.739466 TGCAATTGACTCGCTTCCATC 59.261 47.619 10.34 0.00 0.00 3.51
719 756 1.825090 TGCAATTGACTCGCTTCCAT 58.175 45.000 10.34 0.00 0.00 3.41
720 757 1.536766 CTTGCAATTGACTCGCTTCCA 59.463 47.619 10.34 0.00 0.00 3.53
721 758 1.806542 TCTTGCAATTGACTCGCTTCC 59.193 47.619 10.34 0.00 0.00 3.46
1030 1075 1.394266 CCAGAGCCAGAGAGAGGAGC 61.394 65.000 0.00 0.00 0.00 4.70
1105 1153 1.327690 TAGCCCGATTCCTCGCTGTT 61.328 55.000 0.00 0.00 43.66 3.16
1171 1219 3.332034 CAAACAAGAACCCTACCTACGG 58.668 50.000 0.00 0.00 0.00 4.02
1177 1225 2.963599 TCCCCAAACAAGAACCCTAC 57.036 50.000 0.00 0.00 0.00 3.18
1240 1303 4.768145 TCTACATCAACAAAAGAAACGCG 58.232 39.130 3.53 3.53 0.00 6.01
1268 1331 1.475682 GTTCGGGTCCTCGATTGTAGT 59.524 52.381 3.68 0.00 39.03 2.73
1294 1357 0.038618 TCACCTCATCGTCAACACCG 60.039 55.000 0.00 0.00 0.00 4.94
1384 1448 3.159213 TCAAGTCCACAGGCAATGAAT 57.841 42.857 0.00 0.00 0.00 2.57
1493 1557 5.589855 TGAACAGTGAACATGAACAATGAGT 59.410 36.000 22.38 13.74 38.72 3.41
1603 1674 8.268850 ACTTCATTTATATCACTGTGGTGTTC 57.731 34.615 8.11 0.00 43.41 3.18
1812 2006 9.891828 TTTTAACAGCATACTACACTGAATTTG 57.108 29.630 0.00 0.00 35.38 2.32
2176 2370 2.759355 TGTCCTGGGTATCAAGTAGGG 58.241 52.381 0.00 0.00 0.00 3.53
2203 2406 5.163416 CCTTGTTGGACTTCATTTTCCTTGT 60.163 40.000 0.00 0.00 38.35 3.16
2304 2507 6.101997 CCTTTTGCTTCAGTTCTTTGTTCTT 58.898 36.000 0.00 0.00 0.00 2.52
2520 2723 4.035558 CCCACATGGTCAGATTACAAATCG 59.964 45.833 0.00 0.00 0.00 3.34
2577 2780 5.126779 TGCCACTAGTTCACACATTACAAA 58.873 37.500 0.00 0.00 0.00 2.83
2779 6894 6.207691 TGTGGCTCCTAATTTTCTTATTGC 57.792 37.500 0.00 0.00 0.00 3.56
3095 7260 1.151668 CAACTGTTCTCAAGGGAGCG 58.848 55.000 0.00 0.00 41.13 5.03
3236 7402 4.021368 GTGCTGGTCCAAGTTCTTCTACTA 60.021 45.833 0.00 0.00 0.00 1.82
3325 7497 3.949980 TGCTCCTGCTGCAGCTGT 61.950 61.111 36.61 0.00 42.66 4.40


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

AutoCloner maintained by Alex Coulton.