Multiple sequence alignment - TraesCS6A01G040500

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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 TraesCS6A01G040500 chr6A 100.000 2007 0 0 405 2411 21138349 21136343 0.000000e+00 3707.0
1 TraesCS6A01G040500 chr6A 89.094 541 47 8 958 1488 20871071 20871609 0.000000e+00 662.0
2 TraesCS6A01G040500 chr6A 92.105 418 24 5 1000 1414 54778206 54778617 4.470000e-162 580.0
3 TraesCS6A01G040500 chr6A 100.000 138 0 0 1 138 21138753 21138616 3.080000e-64 255.0
4 TraesCS6A01G040500 chr6D 91.708 1423 74 11 571 1985 20850044 20848658 0.000000e+00 1934.0
5 TraesCS6A01G040500 chr6D 89.496 695 52 12 889 1570 20818759 20818073 0.000000e+00 859.0
6 TraesCS6A01G040500 chr6D 86.053 760 85 16 738 1488 20780357 20781104 0.000000e+00 797.0
7 TraesCS6A01G040500 chr6D 86.747 415 29 8 2005 2411 20848669 20848273 2.850000e-119 438.0
8 TraesCS6A01G040500 chr6D 88.506 261 18 6 2023 2279 20817670 20817418 3.010000e-79 305.0
9 TraesCS6A01G040500 chr6D 89.655 87 8 1 1833 1919 192633518 192633603 2.530000e-20 110.0
10 TraesCS6A01G040500 chr6D 90.278 72 7 0 1740 1811 20782144 20782215 7.100000e-16 95.3
11 TraesCS6A01G040500 chr6D 94.000 50 2 1 1573 1621 20818049 20818000 9.240000e-10 75.0
12 TraesCS6A01G040500 chr7D 94.976 418 15 2 1000 1411 588409310 588409727 0.000000e+00 651.0
13 TraesCS6A01G040500 chr7D 94.133 392 20 3 1013 1404 588541011 588541399 5.740000e-166 593.0
14 TraesCS6A01G040500 chr7A 91.943 422 24 6 1000 1411 689252247 689252668 1.240000e-162 582.0
15 TraesCS6A01G040500 chr3D 91.569 427 24 6 989 1409 50658458 50658038 1.610000e-161 579.0


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 TraesCS6A01G040500 chr6A 21136343 21138753 2410 True 1981.00 3707 100.000000 1 2411 2 chr6A.!!$R1 2410
1 TraesCS6A01G040500 chr6A 20871071 20871609 538 False 662.00 662 89.094000 958 1488 1 chr6A.!!$F1 530
2 TraesCS6A01G040500 chr6D 20848273 20850044 1771 True 1186.00 1934 89.227500 571 2411 2 chr6D.!!$R2 1840
3 TraesCS6A01G040500 chr6D 20780357 20782215 1858 False 446.15 797 88.165500 738 1811 2 chr6D.!!$F2 1073
4 TraesCS6A01G040500 chr6D 20817418 20818759 1341 True 413.00 859 90.667333 889 2279 3 chr6D.!!$R1 1390

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
500 501 0.031917 AAGCCATCATTGCATGGGGA 60.032 50.0 6.21 0.0 43.42 4.81 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1714 2647 0.099613 CAGGTCGATCGTGGAGACAG 59.9 60.0 15.94 0.0 44.46 3.51 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
19 20 2.957491 CCAGCCACAACAAAAACAGA 57.043 45.000 0.00 0.00 0.00 3.41
20 21 2.813061 CCAGCCACAACAAAAACAGAG 58.187 47.619 0.00 0.00 0.00 3.35
21 22 2.426738 CCAGCCACAACAAAAACAGAGA 59.573 45.455 0.00 0.00 0.00 3.10
22 23 3.438360 CAGCCACAACAAAAACAGAGAC 58.562 45.455 0.00 0.00 0.00 3.36
23 24 2.427095 AGCCACAACAAAAACAGAGACC 59.573 45.455 0.00 0.00 0.00 3.85
24 25 2.794631 GCCACAACAAAAACAGAGACCG 60.795 50.000 0.00 0.00 0.00 4.79
25 26 2.450160 CACAACAAAAACAGAGACCGC 58.550 47.619 0.00 0.00 0.00 5.68
26 27 1.404035 ACAACAAAAACAGAGACCGCC 59.596 47.619 0.00 0.00 0.00 6.13
27 28 0.661020 AACAAAAACAGAGACCGCCG 59.339 50.000 0.00 0.00 0.00 6.46
28 29 1.164041 ACAAAAACAGAGACCGCCGG 61.164 55.000 0.00 0.00 0.00 6.13
29 30 1.599797 AAAAACAGAGACCGCCGGG 60.600 57.895 8.57 0.00 40.11 5.73
30 31 3.546714 AAAACAGAGACCGCCGGGG 62.547 63.158 12.43 12.43 43.62 5.73
46 47 3.747976 GGCGCCAACCACCATCAC 61.748 66.667 24.80 0.00 0.00 3.06
47 48 2.983030 GCGCCAACCACCATCACA 60.983 61.111 0.00 0.00 0.00 3.58
48 49 2.981560 GCGCCAACCACCATCACAG 61.982 63.158 0.00 0.00 0.00 3.66
49 50 2.964978 GCCAACCACCATCACAGC 59.035 61.111 0.00 0.00 0.00 4.40
50 51 1.902918 GCCAACCACCATCACAGCA 60.903 57.895 0.00 0.00 0.00 4.41
51 52 1.252904 GCCAACCACCATCACAGCAT 61.253 55.000 0.00 0.00 0.00 3.79
52 53 0.813184 CCAACCACCATCACAGCATC 59.187 55.000 0.00 0.00 0.00 3.91
53 54 1.615116 CCAACCACCATCACAGCATCT 60.615 52.381 0.00 0.00 0.00 2.90
54 55 1.471287 CAACCACCATCACAGCATCTG 59.529 52.381 0.00 0.00 37.52 2.90
55 56 0.679002 ACCACCATCACAGCATCTGC 60.679 55.000 0.00 0.00 42.49 4.26
78 79 4.864334 CCACGCCCTGGCCAGATC 62.864 72.222 34.91 22.24 37.98 2.75
79 80 4.864334 CACGCCCTGGCCAGATCC 62.864 72.222 34.91 19.19 37.98 3.36
81 82 4.864334 CGCCCTGGCCAGATCCAC 62.864 72.222 34.91 16.14 37.98 4.02
82 83 4.512914 GCCCTGGCCAGATCCACC 62.513 72.222 34.91 10.99 34.56 4.61
83 84 3.813724 CCCTGGCCAGATCCACCC 61.814 72.222 34.91 0.00 31.74 4.61
84 85 4.181010 CCTGGCCAGATCCACCCG 62.181 72.222 34.91 10.80 31.74 5.28
85 86 4.181010 CTGGCCAGATCCACCCGG 62.181 72.222 29.88 0.00 31.74 5.73
96 97 4.760047 CACCCGGAACCTCGCCAG 62.760 72.222 0.73 0.00 0.00 4.85
102 103 4.329545 GAACCTCGCCAGCCCACA 62.330 66.667 0.00 0.00 0.00 4.17
103 104 4.643387 AACCTCGCCAGCCCACAC 62.643 66.667 0.00 0.00 0.00 3.82
114 115 4.415150 CCCACACCGGAGCAGCAT 62.415 66.667 9.46 0.00 36.56 3.79
115 116 3.129502 CCACACCGGAGCAGCATG 61.130 66.667 9.46 0.00 36.56 4.06
116 117 3.129502 CACACCGGAGCAGCATGG 61.130 66.667 9.46 0.00 35.86 3.66
117 118 3.321648 ACACCGGAGCAGCATGGA 61.322 61.111 9.46 0.00 35.86 3.41
118 119 2.513204 CACCGGAGCAGCATGGAG 60.513 66.667 9.46 0.00 35.86 3.86
119 120 4.479993 ACCGGAGCAGCATGGAGC 62.480 66.667 9.46 0.00 46.19 4.70
129 130 3.285215 CATGGAGCCAGCCGCATC 61.285 66.667 0.00 0.00 41.38 3.91
130 131 3.800833 ATGGAGCCAGCCGCATCA 61.801 61.111 0.00 0.00 41.38 3.07
131 132 4.783621 TGGAGCCAGCCGCATCAC 62.784 66.667 0.00 0.00 41.38 3.06
133 134 4.783621 GAGCCAGCCGCATCACCA 62.784 66.667 0.00 0.00 41.38 4.17
136 137 4.720902 CCAGCCGCATCACCACCA 62.721 66.667 0.00 0.00 0.00 4.17
137 138 3.434319 CAGCCGCATCACCACCAC 61.434 66.667 0.00 0.00 0.00 4.16
424 425 3.975168 AACCGCTAACACTAACTGGAT 57.025 42.857 0.00 0.00 0.00 3.41
425 426 3.975168 ACCGCTAACACTAACTGGATT 57.025 42.857 0.00 0.00 0.00 3.01
426 427 4.281898 ACCGCTAACACTAACTGGATTT 57.718 40.909 0.00 0.00 0.00 2.17
427 428 4.000988 ACCGCTAACACTAACTGGATTTG 58.999 43.478 0.00 0.00 0.00 2.32
428 429 3.374058 CCGCTAACACTAACTGGATTTGG 59.626 47.826 0.00 0.00 0.00 3.28
429 430 3.374058 CGCTAACACTAACTGGATTTGGG 59.626 47.826 0.00 0.00 0.00 4.12
430 431 4.332828 GCTAACACTAACTGGATTTGGGT 58.667 43.478 0.00 0.00 30.20 4.51
431 432 5.493809 GCTAACACTAACTGGATTTGGGTA 58.506 41.667 0.00 0.00 28.78 3.69
432 433 5.585047 GCTAACACTAACTGGATTTGGGTAG 59.415 44.000 0.00 0.00 28.78 3.18
433 434 4.569719 ACACTAACTGGATTTGGGTAGG 57.430 45.455 0.00 0.00 26.84 3.18
434 435 3.265995 ACACTAACTGGATTTGGGTAGGG 59.734 47.826 0.00 0.00 26.84 3.53
435 436 3.521937 CACTAACTGGATTTGGGTAGGGA 59.478 47.826 0.00 0.00 0.00 4.20
436 437 3.522343 ACTAACTGGATTTGGGTAGGGAC 59.478 47.826 0.00 0.00 0.00 4.46
437 438 2.361085 ACTGGATTTGGGTAGGGACT 57.639 50.000 0.00 0.00 46.37 3.85
438 439 2.197465 ACTGGATTTGGGTAGGGACTC 58.803 52.381 0.00 0.00 41.75 3.36
439 440 1.490910 CTGGATTTGGGTAGGGACTCC 59.509 57.143 0.00 0.00 41.75 3.85
440 441 0.844660 GGATTTGGGTAGGGACTCCC 59.155 60.000 5.90 5.90 45.90 4.30
449 450 3.551407 GGGACTCCCAGATCCGCC 61.551 72.222 9.53 0.00 44.65 6.13
450 451 3.917760 GGACTCCCAGATCCGCCG 61.918 72.222 0.00 0.00 0.00 6.46
451 452 4.593864 GACTCCCAGATCCGCCGC 62.594 72.222 0.00 0.00 0.00 6.53
456 457 4.776322 CCAGATCCGCCGCCAACA 62.776 66.667 0.00 0.00 0.00 3.33
457 458 3.499737 CAGATCCGCCGCCAACAC 61.500 66.667 0.00 0.00 0.00 3.32
466 467 4.351938 CGCCAACACGTCTCGGGA 62.352 66.667 0.00 0.00 32.98 5.14
467 468 2.737376 GCCAACACGTCTCGGGAC 60.737 66.667 4.99 4.99 38.97 4.46
468 469 2.048503 CCAACACGTCTCGGGACC 60.049 66.667 10.50 0.00 39.15 4.46
469 470 2.571216 CCAACACGTCTCGGGACCT 61.571 63.158 10.50 0.00 39.15 3.85
470 471 1.080705 CAACACGTCTCGGGACCTC 60.081 63.158 10.50 0.00 39.15 3.85
471 472 2.623915 AACACGTCTCGGGACCTCG 61.624 63.158 10.50 0.14 39.15 4.63
472 473 3.812019 CACGTCTCGGGACCTCGG 61.812 72.222 10.50 0.00 39.15 4.63
473 474 4.025858 ACGTCTCGGGACCTCGGA 62.026 66.667 10.50 0.00 39.15 4.55
474 475 3.203412 CGTCTCGGGACCTCGGAG 61.203 72.222 10.50 0.00 42.21 4.63
475 476 2.829458 GTCTCGGGACCTCGGAGG 60.829 72.222 22.40 22.40 41.47 4.30
476 477 4.816984 TCTCGGGACCTCGGAGGC 62.817 72.222 23.84 15.66 39.63 4.70
482 483 3.319198 GACCTCGGAGGCCCACAA 61.319 66.667 23.84 0.00 39.63 3.33
483 484 3.316573 GACCTCGGAGGCCCACAAG 62.317 68.421 23.84 0.00 39.63 3.16
484 485 4.785453 CCTCGGAGGCCCACAAGC 62.785 72.222 11.83 0.00 0.00 4.01
493 494 1.153509 GCCCACAAGCCATCATTGC 60.154 57.895 0.00 0.00 0.00 3.56
494 495 1.890625 GCCCACAAGCCATCATTGCA 61.891 55.000 0.00 0.00 0.00 4.08
495 496 0.828022 CCCACAAGCCATCATTGCAT 59.172 50.000 0.00 0.00 0.00 3.96
496 497 1.472552 CCCACAAGCCATCATTGCATG 60.473 52.381 0.00 0.00 33.87 4.06
497 498 1.472552 CCACAAGCCATCATTGCATGG 60.473 52.381 0.00 0.00 45.70 3.66
498 499 0.828022 ACAAGCCATCATTGCATGGG 59.172 50.000 6.21 0.00 43.42 4.00
499 500 0.105964 CAAGCCATCATTGCATGGGG 59.894 55.000 6.21 5.22 43.42 4.96
500 501 0.031917 AAGCCATCATTGCATGGGGA 60.032 50.000 6.21 0.00 43.42 4.81
501 502 0.469331 AGCCATCATTGCATGGGGAG 60.469 55.000 6.21 0.00 43.42 4.30
502 503 1.469335 GCCATCATTGCATGGGGAGG 61.469 60.000 6.21 0.00 43.42 4.30
503 504 0.830444 CCATCATTGCATGGGGAGGG 60.830 60.000 0.00 0.00 39.95 4.30
504 505 0.830444 CATCATTGCATGGGGAGGGG 60.830 60.000 0.00 0.00 0.00 4.79
505 506 2.027434 ATCATTGCATGGGGAGGGGG 62.027 60.000 0.00 0.00 0.00 5.40
506 507 2.287896 ATTGCATGGGGAGGGGGA 60.288 61.111 0.00 0.00 0.00 4.81
507 508 2.397902 ATTGCATGGGGAGGGGGAG 61.398 63.158 0.00 0.00 0.00 4.30
523 524 4.711949 AGGCGGCAGCTTCAGTGG 62.712 66.667 13.08 0.00 44.37 4.00
527 528 4.666253 GGCAGCTTCAGTGGGCCA 62.666 66.667 0.00 0.00 44.01 5.36
528 529 3.368571 GCAGCTTCAGTGGGCCAC 61.369 66.667 29.32 29.32 34.10 5.01
529 530 2.433446 CAGCTTCAGTGGGCCACT 59.567 61.111 33.18 33.18 46.51 4.00
530 531 1.679311 CAGCTTCAGTGGGCCACTA 59.321 57.895 37.13 22.77 43.43 2.74
531 532 0.392193 CAGCTTCAGTGGGCCACTAG 60.392 60.000 37.13 30.74 43.43 2.57
532 533 1.078143 GCTTCAGTGGGCCACTAGG 60.078 63.158 37.13 27.60 43.43 3.02
533 534 1.553690 GCTTCAGTGGGCCACTAGGA 61.554 60.000 37.13 27.74 43.43 2.94
534 535 0.250513 CTTCAGTGGGCCACTAGGAC 59.749 60.000 37.13 10.41 43.43 3.85
540 541 4.913126 GGCCACTAGGACGTTGAG 57.087 61.111 0.00 0.00 36.89 3.02
541 542 2.273908 GGCCACTAGGACGTTGAGA 58.726 57.895 0.00 0.00 36.89 3.27
542 543 0.173708 GGCCACTAGGACGTTGAGAG 59.826 60.000 0.00 0.00 36.89 3.20
543 544 0.173708 GCCACTAGGACGTTGAGAGG 59.826 60.000 0.00 0.00 36.89 3.69
544 545 1.835494 CCACTAGGACGTTGAGAGGA 58.165 55.000 0.00 0.00 36.89 3.71
545 546 1.746220 CCACTAGGACGTTGAGAGGAG 59.254 57.143 0.00 0.00 36.89 3.69
546 547 1.746220 CACTAGGACGTTGAGAGGAGG 59.254 57.143 0.00 0.00 0.00 4.30
547 548 1.341187 ACTAGGACGTTGAGAGGAGGG 60.341 57.143 0.00 0.00 0.00 4.30
548 549 0.033405 TAGGACGTTGAGAGGAGGGG 60.033 60.000 0.00 0.00 0.00 4.79
549 550 2.359967 GGACGTTGAGAGGAGGGGG 61.360 68.421 0.00 0.00 0.00 5.40
550 551 3.003763 ACGTTGAGAGGAGGGGGC 61.004 66.667 0.00 0.00 0.00 5.80
551 552 4.148825 CGTTGAGAGGAGGGGGCG 62.149 72.222 0.00 0.00 0.00 6.13
552 553 3.787001 GTTGAGAGGAGGGGGCGG 61.787 72.222 0.00 0.00 0.00 6.13
553 554 4.005978 TTGAGAGGAGGGGGCGGA 62.006 66.667 0.00 0.00 0.00 5.54
554 555 3.984186 TTGAGAGGAGGGGGCGGAG 62.984 68.421 0.00 0.00 0.00 4.63
590 591 1.153745 CCGCCGAACAGAAGGAGAG 60.154 63.158 0.00 0.00 0.00 3.20
605 606 1.587547 GAGAGGAAATGGGTCATCGC 58.412 55.000 0.00 0.00 33.58 4.58
639 642 9.821240 TGGCCTTAATCCAACATATATGTATTT 57.179 29.630 18.56 11.73 40.80 1.40
748 751 0.251787 AGATTTTGGCCAGGTCACCC 60.252 55.000 5.11 0.00 0.00 4.61
767 770 3.303397 ATCCGCGCCAAAACGAACG 62.303 57.895 0.00 0.00 34.06 3.95
834 837 1.143838 CATCGATCCGGAGCACCAA 59.856 57.895 21.44 1.76 35.59 3.67
858 861 1.376424 CCACCAATCACAGCTCGCT 60.376 57.895 0.00 0.00 0.00 4.93
873 876 0.252284 TCGCTTCCTTCCTCCTTCCT 60.252 55.000 0.00 0.00 0.00 3.36
900 903 0.104304 ATTTAACGATCTCGCCGCCT 59.896 50.000 0.00 0.00 44.43 5.52
929 933 1.444672 CTCCCATCGCAGCATCTGA 59.555 57.895 0.00 0.00 32.44 3.27
961 966 2.870372 GCATCTTGCCGCGAAACT 59.130 55.556 8.23 0.00 37.42 2.66
982 994 2.835431 CCTCTCCGCACCCTCGAT 60.835 66.667 0.00 0.00 0.00 3.59
984 996 1.107538 CCTCTCCGCACCCTCGATTA 61.108 60.000 0.00 0.00 0.00 1.75
985 997 0.312416 CTCTCCGCACCCTCGATTAG 59.688 60.000 0.00 0.00 0.00 1.73
991 1007 1.854227 GCACCCTCGATTAGTAGCAC 58.146 55.000 0.00 0.00 0.00 4.40
1185 1207 2.674380 CTCAAGCAGGTGCACCCC 60.674 66.667 32.29 22.73 45.16 4.95
1531 2273 5.810587 TGTCGGTCTGAAGAAATAGTAATGC 59.189 40.000 0.00 0.00 0.00 3.56
1692 2599 1.004745 TGAATCTTTGACCAGGAGGCC 59.995 52.381 0.00 0.00 39.06 5.19
1698 2631 2.045536 GACCAGGAGGCCTTGCTG 60.046 66.667 6.77 11.69 44.22 4.41
1703 2636 3.353342 AGGAGGCCTTGCTGAAAAG 57.647 52.632 6.77 0.00 0.00 2.27
1714 2647 5.316327 CTTGCTGAAAAGGAAGGGATTAC 57.684 43.478 0.00 0.00 34.27 1.89
1715 2648 4.657814 TGCTGAAAAGGAAGGGATTACT 57.342 40.909 0.00 0.00 0.00 2.24
1716 2649 4.335416 TGCTGAAAAGGAAGGGATTACTG 58.665 43.478 0.00 0.00 0.00 2.74
1717 2650 4.202567 TGCTGAAAAGGAAGGGATTACTGT 60.203 41.667 0.00 0.00 0.00 3.55
1718 2651 4.396478 GCTGAAAAGGAAGGGATTACTGTC 59.604 45.833 0.00 0.00 0.00 3.51
1727 2660 2.959707 AGGGATTACTGTCTCCACGATC 59.040 50.000 10.44 0.00 32.90 3.69
1736 2669 1.037579 TCTCCACGATCGACCTGCAT 61.038 55.000 24.34 0.00 0.00 3.96
1755 2688 6.072286 CCTGCATATTTTGTGTTCTCTGTTCT 60.072 38.462 0.00 0.00 0.00 3.01
1765 2698 5.753438 TGTGTTCTCTGTTCTACAATGTGAC 59.247 40.000 0.00 0.00 0.00 3.67
1776 2709 1.067974 ACAATGTGACCGAGACGTGAA 59.932 47.619 0.00 0.00 0.00 3.18
1834 2768 3.508402 TGATGAGTAGGCACGTGTAGAAA 59.492 43.478 18.38 0.00 0.00 2.52
1835 2769 4.159693 TGATGAGTAGGCACGTGTAGAAAT 59.840 41.667 18.38 2.88 0.00 2.17
1836 2770 4.530710 TGAGTAGGCACGTGTAGAAATT 57.469 40.909 18.38 0.00 0.00 1.82
1837 2771 4.491676 TGAGTAGGCACGTGTAGAAATTC 58.508 43.478 18.38 7.42 0.00 2.17
1838 2772 3.508762 AGTAGGCACGTGTAGAAATTCG 58.491 45.455 18.38 0.00 0.00 3.34
1908 2843 2.376109 CAAGCTCCCTCTGATGCAAAT 58.624 47.619 0.00 0.00 0.00 2.32
1927 2862 2.363306 TGGAGTTTTGGTGAGTGCAT 57.637 45.000 0.00 0.00 0.00 3.96
1940 2875 5.186215 TGGTGAGTGCATTTGATGAATCATT 59.814 36.000 0.00 0.00 36.56 2.57
1952 2887 0.107214 GAATCATTCCGGGTCAGGCA 60.107 55.000 0.00 0.00 0.00 4.75
1968 2903 4.065088 TCAGGCAAGAATGAACACTGTAC 58.935 43.478 0.00 0.00 0.00 2.90
1973 2908 4.083110 GCAAGAATGAACACTGTACATGCT 60.083 41.667 0.00 0.00 32.00 3.79
1974 2909 5.122239 GCAAGAATGAACACTGTACATGCTA 59.878 40.000 0.00 0.00 30.69 3.49
1975 2910 6.183360 GCAAGAATGAACACTGTACATGCTAT 60.183 38.462 0.00 0.00 30.69 2.97
1976 2911 7.627088 GCAAGAATGAACACTGTACATGCTATT 60.627 37.037 0.00 0.28 30.69 1.73
1977 2912 7.928307 AGAATGAACACTGTACATGCTATTT 57.072 32.000 0.00 0.00 29.27 1.40
1978 2913 7.978982 AGAATGAACACTGTACATGCTATTTC 58.021 34.615 0.00 0.00 29.27 2.17
1979 2914 7.826252 AGAATGAACACTGTACATGCTATTTCT 59.174 33.333 0.00 0.00 29.27 2.52
1980 2915 9.098355 GAATGAACACTGTACATGCTATTTCTA 57.902 33.333 0.00 0.00 0.00 2.10
1981 2916 9.618890 AATGAACACTGTACATGCTATTTCTAT 57.381 29.630 0.00 0.00 0.00 1.98
1982 2917 8.648557 TGAACACTGTACATGCTATTTCTATC 57.351 34.615 0.00 0.00 0.00 2.08
1983 2918 8.257306 TGAACACTGTACATGCTATTTCTATCA 58.743 33.333 0.00 0.00 0.00 2.15
1984 2919 8.425577 AACACTGTACATGCTATTTCTATCAC 57.574 34.615 0.00 0.00 0.00 3.06
1985 2920 6.986817 ACACTGTACATGCTATTTCTATCACC 59.013 38.462 0.00 0.00 0.00 4.02
1986 2921 7.147655 ACACTGTACATGCTATTTCTATCACCT 60.148 37.037 0.00 0.00 0.00 4.00
1987 2922 7.712639 CACTGTACATGCTATTTCTATCACCTT 59.287 37.037 0.00 0.00 0.00 3.50
1988 2923 8.267894 ACTGTACATGCTATTTCTATCACCTTT 58.732 33.333 0.00 0.00 0.00 3.11
1989 2924 9.113838 CTGTACATGCTATTTCTATCACCTTTT 57.886 33.333 0.00 0.00 0.00 2.27
1990 2925 9.461312 TGTACATGCTATTTCTATCACCTTTTT 57.539 29.630 0.00 0.00 0.00 1.94
2028 2963 6.747414 ACTCCTATTACTTACCATCATGCA 57.253 37.500 0.00 0.00 0.00 3.96
2120 3057 9.660180 ACTCTTAAACTAATGTTGATCTCTTCC 57.340 33.333 0.00 0.00 36.39 3.46
2121 3058 8.703604 TCTTAAACTAATGTTGATCTCTTCCG 57.296 34.615 0.00 0.00 36.39 4.30
2122 3059 8.528643 TCTTAAACTAATGTTGATCTCTTCCGA 58.471 33.333 0.00 0.00 36.39 4.55
2123 3060 6.969828 AAACTAATGTTGATCTCTTCCGAC 57.030 37.500 0.00 0.00 36.39 4.79
2124 3061 5.923733 ACTAATGTTGATCTCTTCCGACT 57.076 39.130 0.00 0.00 0.00 4.18
2125 3062 6.287589 ACTAATGTTGATCTCTTCCGACTT 57.712 37.500 0.00 0.00 0.00 3.01
2126 3063 6.334202 ACTAATGTTGATCTCTTCCGACTTC 58.666 40.000 0.00 0.00 0.00 3.01
2127 3064 3.594603 TGTTGATCTCTTCCGACTTCC 57.405 47.619 0.00 0.00 0.00 3.46
2156 3093 4.341806 TCCACAAACAAAATGCAGACAGAT 59.658 37.500 0.00 0.00 0.00 2.90
2159 3096 6.364165 CCACAAACAAAATGCAGACAGATAAG 59.636 38.462 0.00 0.00 0.00 1.73
2166 3103 3.887621 TGCAGACAGATAAGTGTACCC 57.112 47.619 0.00 0.00 0.00 3.69
2196 3133 5.455056 AGATCAGAGAACGTACACACTTT 57.545 39.130 0.00 0.00 0.00 2.66
2197 3134 5.462405 AGATCAGAGAACGTACACACTTTC 58.538 41.667 0.00 0.00 34.08 2.62
2279 3222 5.393962 GCGTAGAGTACCGTTTAGAAGAAA 58.606 41.667 0.00 0.00 0.00 2.52
2286 3229 6.536447 AGTACCGTTTAGAAGAAATTTGGGA 58.464 36.000 0.00 0.00 0.00 4.37
2309 3252 4.664688 AAAATGGTCTCCAACAGATCCT 57.335 40.909 0.00 0.00 36.95 3.24
2318 3261 6.351881 GGTCTCCAACAGATCCTGTAAACATA 60.352 42.308 0.00 0.00 44.62 2.29
2355 3298 6.103997 AGGATCATGCAAATTTGACATGAAC 58.896 36.000 35.10 32.80 45.43 3.18
2356 3299 5.870433 GGATCATGCAAATTTGACATGAACA 59.130 36.000 35.10 24.53 45.43 3.18
2365 3308 7.253422 CAAATTTGACATGAACATCCCTCTAC 58.747 38.462 13.08 0.00 0.00 2.59
2367 3310 5.762179 TTGACATGAACATCCCTCTACTT 57.238 39.130 0.00 0.00 0.00 2.24
2368 3311 5.762179 TGACATGAACATCCCTCTACTTT 57.238 39.130 0.00 0.00 0.00 2.66
2406 3349 3.445805 ACCCGTAATATTTTGGCCAACTG 59.554 43.478 20.35 1.40 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.426738 TCTCTGTTTTTGTTGTGGCTGG 59.573 45.455 0.00 0.00 0.00 4.85
1 2 3.438360 GTCTCTGTTTTTGTTGTGGCTG 58.562 45.455 0.00 0.00 0.00 4.85
2 3 2.427095 GGTCTCTGTTTTTGTTGTGGCT 59.573 45.455 0.00 0.00 0.00 4.75
3 4 2.794631 CGGTCTCTGTTTTTGTTGTGGC 60.795 50.000 0.00 0.00 0.00 5.01
4 5 2.794631 GCGGTCTCTGTTTTTGTTGTGG 60.795 50.000 0.00 0.00 0.00 4.17
5 6 2.450160 GCGGTCTCTGTTTTTGTTGTG 58.550 47.619 0.00 0.00 0.00 3.33
6 7 1.404035 GGCGGTCTCTGTTTTTGTTGT 59.596 47.619 0.00 0.00 0.00 3.32
7 8 1.596954 CGGCGGTCTCTGTTTTTGTTG 60.597 52.381 0.00 0.00 0.00 3.33
8 9 0.661020 CGGCGGTCTCTGTTTTTGTT 59.339 50.000 0.00 0.00 0.00 2.83
9 10 1.164041 CCGGCGGTCTCTGTTTTTGT 61.164 55.000 19.97 0.00 0.00 2.83
10 11 1.574428 CCGGCGGTCTCTGTTTTTG 59.426 57.895 19.97 0.00 0.00 2.44
11 12 1.599797 CCCGGCGGTCTCTGTTTTT 60.600 57.895 26.32 0.00 0.00 1.94
12 13 2.032071 CCCGGCGGTCTCTGTTTT 59.968 61.111 26.32 0.00 0.00 2.43
13 14 4.016706 CCCCGGCGGTCTCTGTTT 62.017 66.667 26.32 0.00 0.00 2.83
29 30 3.747976 GTGATGGTGGTTGGCGCC 61.748 66.667 22.73 22.73 0.00 6.53
30 31 2.981560 CTGTGATGGTGGTTGGCGC 61.982 63.158 0.00 0.00 0.00 6.53
31 32 2.981560 GCTGTGATGGTGGTTGGCG 61.982 63.158 0.00 0.00 0.00 5.69
32 33 1.252904 ATGCTGTGATGGTGGTTGGC 61.253 55.000 0.00 0.00 0.00 4.52
33 34 0.813184 GATGCTGTGATGGTGGTTGG 59.187 55.000 0.00 0.00 0.00 3.77
34 35 1.471287 CAGATGCTGTGATGGTGGTTG 59.529 52.381 0.00 0.00 0.00 3.77
35 36 1.830279 CAGATGCTGTGATGGTGGTT 58.170 50.000 0.00 0.00 0.00 3.67
36 37 0.679002 GCAGATGCTGTGATGGTGGT 60.679 55.000 0.00 0.00 38.21 4.16
37 38 1.712018 CGCAGATGCTGTGATGGTGG 61.712 60.000 2.95 0.00 43.78 4.61
38 39 1.022982 ACGCAGATGCTGTGATGGTG 61.023 55.000 14.21 0.00 43.78 4.17
39 40 0.742281 GACGCAGATGCTGTGATGGT 60.742 55.000 14.21 0.00 43.78 3.55
40 41 1.434622 GGACGCAGATGCTGTGATGG 61.435 60.000 14.21 0.00 43.78 3.51
41 42 0.461516 AGGACGCAGATGCTGTGATG 60.462 55.000 14.21 0.00 43.78 3.07
42 43 0.179089 GAGGACGCAGATGCTGTGAT 60.179 55.000 14.21 0.89 43.78 3.06
43 44 1.216444 GAGGACGCAGATGCTGTGA 59.784 57.895 14.21 0.00 43.78 3.58
44 45 1.812922 GGAGGACGCAGATGCTGTG 60.813 63.158 6.45 6.45 46.11 3.66
45 46 2.285773 TGGAGGACGCAGATGCTGT 61.286 57.895 2.95 2.82 39.32 4.40
46 47 1.812922 GTGGAGGACGCAGATGCTG 60.813 63.158 2.95 0.00 39.32 4.41
47 48 2.581354 GTGGAGGACGCAGATGCT 59.419 61.111 2.95 0.00 39.32 3.79
48 49 2.887568 CGTGGAGGACGCAGATGC 60.888 66.667 0.00 0.00 42.21 3.91
62 63 4.864334 GGATCTGGCCAGGGCGTG 62.864 72.222 32.23 7.03 43.06 5.34
64 65 4.864334 GTGGATCTGGCCAGGGCG 62.864 72.222 32.23 8.31 43.06 6.13
65 66 4.512914 GGTGGATCTGGCCAGGGC 62.513 72.222 32.23 22.72 38.95 5.19
66 67 3.813724 GGGTGGATCTGGCCAGGG 61.814 72.222 32.23 9.58 38.95 4.45
67 68 4.181010 CGGGTGGATCTGGCCAGG 62.181 72.222 32.23 14.13 38.95 4.45
68 69 4.181010 CCGGGTGGATCTGGCCAG 62.181 72.222 27.87 27.87 38.95 4.85
69 70 4.731853 TCCGGGTGGATCTGGCCA 62.732 66.667 4.71 4.71 40.17 5.36
70 71 3.407967 TTCCGGGTGGATCTGGCC 61.408 66.667 0.00 0.00 45.91 5.36
71 72 2.124695 GTTCCGGGTGGATCTGGC 60.125 66.667 0.00 0.00 45.91 4.85
72 73 1.972660 GAGGTTCCGGGTGGATCTGG 61.973 65.000 0.00 0.00 45.91 3.86
73 74 1.522569 GAGGTTCCGGGTGGATCTG 59.477 63.158 0.00 0.00 45.91 2.90
74 75 2.058595 CGAGGTTCCGGGTGGATCT 61.059 63.158 0.00 0.00 45.91 2.75
75 76 2.499685 CGAGGTTCCGGGTGGATC 59.500 66.667 0.00 0.00 45.91 3.36
76 77 3.782443 GCGAGGTTCCGGGTGGAT 61.782 66.667 0.00 0.00 45.91 3.41
79 80 4.760047 CTGGCGAGGTTCCGGGTG 62.760 72.222 0.00 0.00 0.00 4.61
85 86 4.329545 TGTGGGCTGGCGAGGTTC 62.330 66.667 0.00 0.00 0.00 3.62
86 87 4.643387 GTGTGGGCTGGCGAGGTT 62.643 66.667 0.00 0.00 0.00 3.50
97 98 4.415150 ATGCTGCTCCGGTGTGGG 62.415 66.667 0.00 0.00 38.76 4.61
98 99 3.129502 CATGCTGCTCCGGTGTGG 61.130 66.667 0.00 0.00 40.09 4.17
99 100 3.129502 CCATGCTGCTCCGGTGTG 61.130 66.667 0.00 0.00 0.00 3.82
100 101 3.320879 CTCCATGCTGCTCCGGTGT 62.321 63.158 0.00 0.00 0.00 4.16
101 102 2.513204 CTCCATGCTGCTCCGGTG 60.513 66.667 0.00 0.00 0.00 4.94
102 103 4.479993 GCTCCATGCTGCTCCGGT 62.480 66.667 0.00 0.00 38.95 5.28
104 105 4.478371 TGGCTCCATGCTGCTCCG 62.478 66.667 0.00 0.00 42.39 4.63
105 106 2.516460 CTGGCTCCATGCTGCTCC 60.516 66.667 0.00 0.00 42.39 4.70
106 107 3.210528 GCTGGCTCCATGCTGCTC 61.211 66.667 0.00 0.79 42.39 4.26
107 108 4.816984 GGCTGGCTCCATGCTGCT 62.817 66.667 0.00 0.00 42.39 4.24
112 113 3.285215 GATGCGGCTGGCTCCATG 61.285 66.667 0.00 0.00 44.05 3.66
113 114 3.800833 TGATGCGGCTGGCTCCAT 61.801 61.111 0.00 1.83 44.05 3.41
114 115 4.783621 GTGATGCGGCTGGCTCCA 62.784 66.667 0.00 0.00 44.05 3.86
116 117 4.783621 TGGTGATGCGGCTGGCTC 62.784 66.667 0.00 0.00 44.05 4.70
119 120 4.720902 TGGTGGTGATGCGGCTGG 62.721 66.667 0.00 0.00 0.00 4.85
120 121 3.434319 GTGGTGGTGATGCGGCTG 61.434 66.667 0.00 0.00 0.00 4.85
404 405 3.975168 ATCCAGTTAGTGTTAGCGGTT 57.025 42.857 0.00 0.00 0.00 4.44
405 406 3.975168 AATCCAGTTAGTGTTAGCGGT 57.025 42.857 0.00 0.00 0.00 5.68
406 407 3.374058 CCAAATCCAGTTAGTGTTAGCGG 59.626 47.826 0.00 0.00 0.00 5.52
407 408 3.374058 CCCAAATCCAGTTAGTGTTAGCG 59.626 47.826 0.00 0.00 0.00 4.26
408 409 4.332828 ACCCAAATCCAGTTAGTGTTAGC 58.667 43.478 0.00 0.00 0.00 3.09
409 410 6.113411 CCTACCCAAATCCAGTTAGTGTTAG 58.887 44.000 0.00 0.00 0.00 2.34
410 411 5.045432 CCCTACCCAAATCCAGTTAGTGTTA 60.045 44.000 0.00 0.00 0.00 2.41
411 412 4.263771 CCCTACCCAAATCCAGTTAGTGTT 60.264 45.833 0.00 0.00 0.00 3.32
412 413 3.265995 CCCTACCCAAATCCAGTTAGTGT 59.734 47.826 0.00 0.00 0.00 3.55
413 414 3.521937 TCCCTACCCAAATCCAGTTAGTG 59.478 47.826 0.00 0.00 0.00 2.74
414 415 3.522343 GTCCCTACCCAAATCCAGTTAGT 59.478 47.826 0.00 0.00 0.00 2.24
415 416 3.780850 AGTCCCTACCCAAATCCAGTTAG 59.219 47.826 0.00 0.00 0.00 2.34
416 417 3.778629 GAGTCCCTACCCAAATCCAGTTA 59.221 47.826 0.00 0.00 0.00 2.24
417 418 2.576648 GAGTCCCTACCCAAATCCAGTT 59.423 50.000 0.00 0.00 0.00 3.16
418 419 2.197465 GAGTCCCTACCCAAATCCAGT 58.803 52.381 0.00 0.00 0.00 4.00
419 420 1.490910 GGAGTCCCTACCCAAATCCAG 59.509 57.143 0.00 0.00 0.00 3.86
420 421 1.591768 GGAGTCCCTACCCAAATCCA 58.408 55.000 0.00 0.00 0.00 3.41
421 422 0.844660 GGGAGTCCCTACCCAAATCC 59.155 60.000 22.04 0.00 44.96 3.01
427 428 0.472161 GGATCTGGGAGTCCCTACCC 60.472 65.000 28.73 19.11 45.70 3.69
428 429 0.828343 CGGATCTGGGAGTCCCTACC 60.828 65.000 28.73 22.00 45.70 3.18
429 430 1.465200 GCGGATCTGGGAGTCCCTAC 61.465 65.000 28.73 15.92 45.70 3.18
430 431 1.152525 GCGGATCTGGGAGTCCCTA 60.153 63.158 28.73 17.21 45.70 3.53
431 432 2.444895 GCGGATCTGGGAGTCCCT 60.445 66.667 28.73 9.17 45.70 4.20
432 433 3.551407 GGCGGATCTGGGAGTCCC 61.551 72.222 22.54 22.54 45.71 4.46
433 434 3.917760 CGGCGGATCTGGGAGTCC 61.918 72.222 0.00 0.00 0.00 3.85
434 435 4.593864 GCGGCGGATCTGGGAGTC 62.594 72.222 9.78 0.00 0.00 3.36
439 440 4.776322 TGTTGGCGGCGGATCTGG 62.776 66.667 9.78 0.00 0.00 3.86
440 441 3.499737 GTGTTGGCGGCGGATCTG 61.500 66.667 9.78 0.00 0.00 2.90
449 450 4.351938 TCCCGAGACGTGTTGGCG 62.352 66.667 13.61 7.22 37.94 5.69
450 451 2.737376 GTCCCGAGACGTGTTGGC 60.737 66.667 13.61 0.00 32.18 4.52
451 452 2.048503 GGTCCCGAGACGTGTTGG 60.049 66.667 12.13 12.13 44.54 3.77
452 453 1.080705 GAGGTCCCGAGACGTGTTG 60.081 63.158 0.00 0.00 44.54 3.33
453 454 2.623915 CGAGGTCCCGAGACGTGTT 61.624 63.158 0.00 0.00 44.54 3.32
454 455 3.054503 CGAGGTCCCGAGACGTGT 61.055 66.667 0.00 0.00 44.54 4.49
455 456 3.812019 CCGAGGTCCCGAGACGTG 61.812 72.222 0.00 0.00 44.54 4.49
456 457 3.972971 CTCCGAGGTCCCGAGACGT 62.973 68.421 0.00 0.00 44.54 4.34
457 458 3.203412 CTCCGAGGTCCCGAGACG 61.203 72.222 1.74 0.00 44.54 4.18
458 459 2.829458 CCTCCGAGGTCCCGAGAC 60.829 72.222 6.24 0.00 42.73 3.36
459 460 4.816984 GCCTCCGAGGTCCCGAGA 62.817 72.222 16.09 0.00 37.80 4.04
465 466 3.316573 CTTGTGGGCCTCCGAGGTC 62.317 68.421 16.09 13.65 39.92 3.85
466 467 3.322466 CTTGTGGGCCTCCGAGGT 61.322 66.667 16.09 0.00 37.80 3.85
467 468 4.785453 GCTTGTGGGCCTCCGAGG 62.785 72.222 10.41 10.41 38.80 4.63
475 476 1.153509 GCAATGATGGCTTGTGGGC 60.154 57.895 0.00 0.00 41.27 5.36
476 477 0.828022 ATGCAATGATGGCTTGTGGG 59.172 50.000 0.00 0.00 0.00 4.61
488 489 2.123164 CCCCCTCCCCATGCAATG 60.123 66.667 0.00 0.00 46.21 2.82
489 490 2.287896 TCCCCCTCCCCATGCAAT 60.288 61.111 0.00 0.00 0.00 3.56
490 491 3.023116 CTCCCCCTCCCCATGCAA 61.023 66.667 0.00 0.00 0.00 4.08
504 505 4.400961 ACTGAAGCTGCCGCCTCC 62.401 66.667 0.00 0.00 36.60 4.30
505 506 3.123620 CACTGAAGCTGCCGCCTC 61.124 66.667 0.00 0.00 36.60 4.70
506 507 4.711949 CCACTGAAGCTGCCGCCT 62.712 66.667 0.00 0.00 36.60 5.52
510 511 4.666253 TGGCCCACTGAAGCTGCC 62.666 66.667 0.00 2.12 42.49 4.85
511 512 2.469465 TAGTGGCCCACTGAAGCTGC 62.469 60.000 26.70 0.00 45.01 5.25
512 513 0.392193 CTAGTGGCCCACTGAAGCTG 60.392 60.000 26.70 5.66 45.01 4.24
513 514 1.557269 CCTAGTGGCCCACTGAAGCT 61.557 60.000 26.70 0.97 45.01 3.74
514 515 1.078143 CCTAGTGGCCCACTGAAGC 60.078 63.158 26.70 0.00 45.01 3.86
515 516 0.250513 GTCCTAGTGGCCCACTGAAG 59.749 60.000 26.70 16.14 45.01 3.02
516 517 1.541310 CGTCCTAGTGGCCCACTGAA 61.541 60.000 26.70 6.40 45.01 3.02
517 518 1.982395 CGTCCTAGTGGCCCACTGA 60.982 63.158 26.70 13.18 45.01 3.41
518 519 1.827399 AACGTCCTAGTGGCCCACTG 61.827 60.000 26.70 15.33 45.01 3.66
520 521 1.375523 CAACGTCCTAGTGGCCCAC 60.376 63.158 5.50 5.50 34.10 4.61
521 522 1.534476 TCAACGTCCTAGTGGCCCA 60.534 57.895 0.00 0.00 0.00 5.36
522 523 1.218316 CTCAACGTCCTAGTGGCCC 59.782 63.158 0.00 0.00 0.00 5.80
523 524 0.173708 CTCTCAACGTCCTAGTGGCC 59.826 60.000 0.00 0.00 0.00 5.36
524 525 0.173708 CCTCTCAACGTCCTAGTGGC 59.826 60.000 0.00 0.00 0.00 5.01
525 526 1.746220 CTCCTCTCAACGTCCTAGTGG 59.254 57.143 0.00 0.00 0.00 4.00
526 527 1.746220 CCTCCTCTCAACGTCCTAGTG 59.254 57.143 0.00 0.00 0.00 2.74
527 528 1.341187 CCCTCCTCTCAACGTCCTAGT 60.341 57.143 0.00 0.00 0.00 2.57
528 529 1.394618 CCCTCCTCTCAACGTCCTAG 58.605 60.000 0.00 0.00 0.00 3.02
529 530 0.033405 CCCCTCCTCTCAACGTCCTA 60.033 60.000 0.00 0.00 0.00 2.94
530 531 1.305381 CCCCTCCTCTCAACGTCCT 60.305 63.158 0.00 0.00 0.00 3.85
531 532 2.359967 CCCCCTCCTCTCAACGTCC 61.360 68.421 0.00 0.00 0.00 4.79
532 533 3.020237 GCCCCCTCCTCTCAACGTC 62.020 68.421 0.00 0.00 0.00 4.34
533 534 3.003763 GCCCCCTCCTCTCAACGT 61.004 66.667 0.00 0.00 0.00 3.99
534 535 4.148825 CGCCCCCTCCTCTCAACG 62.149 72.222 0.00 0.00 0.00 4.10
535 536 3.787001 CCGCCCCCTCCTCTCAAC 61.787 72.222 0.00 0.00 0.00 3.18
536 537 3.984186 CTCCGCCCCCTCCTCTCAA 62.984 68.421 0.00 0.00 0.00 3.02
537 538 4.465446 CTCCGCCCCCTCCTCTCA 62.465 72.222 0.00 0.00 0.00 3.27
543 544 4.168291 CTTCTGCTCCGCCCCCTC 62.168 72.222 0.00 0.00 0.00 4.30
590 591 2.715624 GCGCGATGACCCATTTCC 59.284 61.111 12.10 0.00 0.00 3.13
605 606 2.439519 ATTAAGGCCAACCCCGCG 60.440 61.111 5.01 0.00 36.11 6.46
709 712 3.091545 CTGTTGGGCATTTATCACCAGT 58.908 45.455 0.00 0.00 33.96 4.00
748 751 1.795962 GTTCGTTTTGGCGCGGATG 60.796 57.895 8.83 0.00 0.00 3.51
767 770 1.079503 GTTTGAGATGGACGGACAGC 58.920 55.000 0.00 0.00 0.00 4.40
834 837 2.171448 GAGCTGTGATTGGTGGATAGGT 59.829 50.000 0.00 0.00 0.00 3.08
858 861 2.552367 GAAGGAGGAAGGAGGAAGGAA 58.448 52.381 0.00 0.00 0.00 3.36
873 876 4.261909 GGCGAGATCGTTAAATAGGAAGGA 60.262 45.833 3.94 0.00 42.22 3.36
900 903 3.758133 GATGGGAGGAGGCGGAGGA 62.758 68.421 0.00 0.00 0.00 3.71
914 918 0.376152 GTGTTCAGATGCTGCGATGG 59.624 55.000 0.00 0.00 0.00 3.51
946 951 1.003839 TGGAGTTTCGCGGCAAGAT 60.004 52.632 6.13 0.00 0.00 2.40
953 958 1.446272 GGAGAGGTGGAGTTTCGCG 60.446 63.158 0.00 0.00 0.00 5.87
956 961 0.670854 GTGCGGAGAGGTGGAGTTTC 60.671 60.000 0.00 0.00 0.00 2.78
957 962 1.371558 GTGCGGAGAGGTGGAGTTT 59.628 57.895 0.00 0.00 0.00 2.66
961 966 4.316823 AGGGTGCGGAGAGGTGGA 62.317 66.667 0.00 0.00 0.00 4.02
982 994 2.616960 CATGAACGCTGGTGCTACTAA 58.383 47.619 0.00 0.00 36.97 2.24
984 996 0.391661 CCATGAACGCTGGTGCTACT 60.392 55.000 0.00 0.00 36.97 2.57
985 997 1.982073 GCCATGAACGCTGGTGCTAC 61.982 60.000 0.00 0.00 36.10 3.58
991 1007 3.443045 GGGTGCCATGAACGCTGG 61.443 66.667 0.00 0.00 36.81 4.85
998 1014 4.738998 CCGCCTTGGGTGCCATGA 62.739 66.667 0.00 0.00 31.53 3.07
1099 1121 1.552792 CTTCTTCCCCTTCTTCTCGCT 59.447 52.381 0.00 0.00 0.00 4.93
1185 1207 1.006805 GGAGGAGATGCCGATGTCG 60.007 63.158 0.00 0.00 43.43 4.35
1531 2273 4.261363 GGCAGAAAGTTCCACTGAAAAGAG 60.261 45.833 0.00 0.00 34.07 2.85
1630 2482 6.169557 ACACAATGGACAGTTCTTGTACTA 57.830 37.500 0.00 0.00 41.56 1.82
1631 2483 5.036117 ACACAATGGACAGTTCTTGTACT 57.964 39.130 0.00 0.00 41.56 2.73
1632 2484 5.510671 CAACACAATGGACAGTTCTTGTAC 58.489 41.667 0.00 0.00 41.05 2.90
1692 2599 5.012893 AGTAATCCCTTCCTTTTCAGCAAG 58.987 41.667 0.00 0.00 0.00 4.01
1698 2631 5.186942 GGAGACAGTAATCCCTTCCTTTTC 58.813 45.833 0.00 0.00 0.00 2.29
1699 2632 4.601857 TGGAGACAGTAATCCCTTCCTTTT 59.398 41.667 2.45 0.00 34.47 2.27
1700 2633 4.019231 GTGGAGACAGTAATCCCTTCCTTT 60.019 45.833 2.45 0.00 44.46 3.11
1701 2634 3.519913 GTGGAGACAGTAATCCCTTCCTT 59.480 47.826 2.45 0.00 44.46 3.36
1702 2635 3.108376 GTGGAGACAGTAATCCCTTCCT 58.892 50.000 2.45 0.00 44.46 3.36
1703 2636 2.159085 CGTGGAGACAGTAATCCCTTCC 60.159 54.545 2.45 0.00 44.46 3.46
1704 2637 2.758979 TCGTGGAGACAGTAATCCCTTC 59.241 50.000 2.45 0.00 44.46 3.46
1705 2638 2.816411 TCGTGGAGACAGTAATCCCTT 58.184 47.619 2.45 0.00 44.46 3.95
1706 2639 2.526888 TCGTGGAGACAGTAATCCCT 57.473 50.000 2.45 0.00 44.46 4.20
1707 2640 2.287668 CGATCGTGGAGACAGTAATCCC 60.288 54.545 7.03 0.00 44.46 3.85
1708 2641 2.617308 TCGATCGTGGAGACAGTAATCC 59.383 50.000 15.94 0.00 44.46 3.01
1709 2642 3.548415 GGTCGATCGTGGAGACAGTAATC 60.548 52.174 15.94 0.00 44.46 1.75
1710 2643 2.358267 GGTCGATCGTGGAGACAGTAAT 59.642 50.000 15.94 0.00 44.46 1.89
1711 2644 1.741706 GGTCGATCGTGGAGACAGTAA 59.258 52.381 15.94 0.00 44.46 2.24
1712 2645 1.065636 AGGTCGATCGTGGAGACAGTA 60.066 52.381 15.94 0.00 44.46 2.74
1713 2646 0.322636 AGGTCGATCGTGGAGACAGT 60.323 55.000 15.94 0.00 44.46 3.55
1714 2647 0.099613 CAGGTCGATCGTGGAGACAG 59.900 60.000 15.94 0.00 44.46 3.51
1715 2648 1.934220 GCAGGTCGATCGTGGAGACA 61.934 60.000 15.94 0.00 36.68 3.41
1716 2649 1.226717 GCAGGTCGATCGTGGAGAC 60.227 63.158 15.94 5.12 33.17 3.36
1717 2650 1.037579 ATGCAGGTCGATCGTGGAGA 61.038 55.000 15.94 0.00 35.92 3.71
1718 2651 0.668535 TATGCAGGTCGATCGTGGAG 59.331 55.000 15.94 5.57 35.92 3.86
1727 2660 4.393062 AGAGAACACAAAATATGCAGGTCG 59.607 41.667 0.00 0.00 31.37 4.79
1736 2669 9.337396 ACATTGTAGAACAGAGAACACAAAATA 57.663 29.630 0.00 0.00 30.48 1.40
1755 2688 1.881324 TCACGTCTCGGTCACATTGTA 59.119 47.619 0.00 0.00 0.00 2.41
1765 2698 0.670546 ATGCAACCTTCACGTCTCGG 60.671 55.000 0.00 0.00 0.00 4.63
1817 2750 3.508762 CGAATTTCTACACGTGCCTACT 58.491 45.455 17.22 0.00 0.00 2.57
1834 2768 3.912496 TCATCCATCTTGACACCGAAT 57.088 42.857 0.00 0.00 0.00 3.34
1835 2769 3.912496 ATCATCCATCTTGACACCGAA 57.088 42.857 0.00 0.00 0.00 4.30
1836 2770 5.351948 TTTATCATCCATCTTGACACCGA 57.648 39.130 0.00 0.00 0.00 4.69
1837 2771 6.624352 AATTTATCATCCATCTTGACACCG 57.376 37.500 0.00 0.00 0.00 4.94
1838 2772 7.147846 ACCAAATTTATCATCCATCTTGACACC 60.148 37.037 0.00 0.00 0.00 4.16
1884 2819 0.530211 CATCAGAGGGAGCTTGCTCG 60.530 60.000 15.30 2.88 0.00 5.03
1896 2831 4.021719 ACCAAAACTCCATTTGCATCAGAG 60.022 41.667 0.00 0.00 38.64 3.35
1908 2843 2.363306 ATGCACTCACCAAAACTCCA 57.637 45.000 0.00 0.00 0.00 3.86
1927 2862 3.947196 CTGACCCGGAATGATTCATCAAA 59.053 43.478 0.73 0.00 40.69 2.69
1940 2875 1.198094 TCATTCTTGCCTGACCCGGA 61.198 55.000 0.73 0.00 0.00 5.14
1952 2887 7.928307 AATAGCATGTACAGTGTTCATTCTT 57.072 32.000 17.34 7.68 0.00 2.52
1990 2925 1.133730 AGGAGTAACACCCCGCAAAAA 60.134 47.619 0.00 0.00 0.00 1.94
1991 2926 0.475044 AGGAGTAACACCCCGCAAAA 59.525 50.000 0.00 0.00 0.00 2.44
1992 2927 1.350071 TAGGAGTAACACCCCGCAAA 58.650 50.000 0.00 0.00 0.00 3.68
1993 2928 1.575419 ATAGGAGTAACACCCCGCAA 58.425 50.000 0.00 0.00 0.00 4.85
1994 2929 1.575419 AATAGGAGTAACACCCCGCA 58.425 50.000 0.00 0.00 0.00 5.69
1995 2930 2.697229 AGTAATAGGAGTAACACCCCGC 59.303 50.000 0.00 0.00 0.00 6.13
1996 2931 5.221322 GGTAAGTAATAGGAGTAACACCCCG 60.221 48.000 0.00 0.00 0.00 5.73
1997 2932 5.662657 TGGTAAGTAATAGGAGTAACACCCC 59.337 44.000 0.00 0.00 0.00 4.95
1998 2933 6.796785 TGGTAAGTAATAGGAGTAACACCC 57.203 41.667 0.00 0.00 0.00 4.61
1999 2934 8.015185 TGATGGTAAGTAATAGGAGTAACACC 57.985 38.462 0.00 0.00 0.00 4.16
2000 2935 9.477484 CATGATGGTAAGTAATAGGAGTAACAC 57.523 37.037 0.00 0.00 0.00 3.32
2001 2936 8.148351 GCATGATGGTAAGTAATAGGAGTAACA 58.852 37.037 0.00 0.00 0.00 2.41
2002 2937 8.148351 TGCATGATGGTAAGTAATAGGAGTAAC 58.852 37.037 0.00 0.00 0.00 2.50
2003 2938 8.257602 TGCATGATGGTAAGTAATAGGAGTAA 57.742 34.615 0.00 0.00 0.00 2.24
2028 2963 5.879223 CCATGCTCTGAACTGATACTCTTTT 59.121 40.000 0.00 0.00 0.00 2.27
2156 3093 3.726557 TCTTCCTCTCGGGTACACTTA 57.273 47.619 0.00 0.00 36.25 2.24
2159 3096 2.359531 CTGATCTTCCTCTCGGGTACAC 59.640 54.545 0.00 0.00 36.25 2.90
2166 3103 2.680841 ACGTTCTCTGATCTTCCTCTCG 59.319 50.000 0.00 0.00 0.00 4.04
2255 3197 3.062639 TCTTCTAAACGGTACTCTACGCG 59.937 47.826 3.53 3.53 0.00 6.01
2258 3200 8.654215 CCAAATTTCTTCTAAACGGTACTCTAC 58.346 37.037 0.00 0.00 0.00 2.59
2326 3269 7.465353 TGTCAAATTTGCATGATCCTCTAAA 57.535 32.000 13.54 0.00 0.00 1.85
2336 3279 5.064198 GGGATGTTCATGTCAAATTTGCATG 59.936 40.000 29.78 29.78 40.62 4.06
2340 3283 6.276832 AGAGGGATGTTCATGTCAAATTTG 57.723 37.500 12.15 12.15 0.00 2.32
2365 3308 5.121105 CGGGTTGTAATACTTCCCCTAAAG 58.879 45.833 14.21 0.00 35.11 1.85
2367 3310 4.103342 ACGGGTTGTAATACTTCCCCTAA 58.897 43.478 14.21 0.00 35.11 2.69
2368 3311 3.723325 ACGGGTTGTAATACTTCCCCTA 58.277 45.455 14.21 0.00 35.11 3.53
2384 3327 3.445805 CAGTTGGCCAAAATATTACGGGT 59.554 43.478 22.47 0.00 0.00 5.28


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

AutoCloner maintained by Alex Coulton.