Multiple sequence alignment - TraesCS3B01G471000

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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 TraesCS3B01G471000 chr3B 100.000 2680 0 0 1 2680 719425926 719428605 0.000000e+00 4950.0
1 TraesCS3B01G471000 chr3B 95.455 814 37 0 1867 2680 663418673 663419486 0.000000e+00 1299.0
2 TraesCS3B01G471000 chr3B 98.837 86 1 0 434 519 693084094 693084009 1.280000e-33 154.0
3 TraesCS3B01G471000 chr1B 97.041 811 23 1 1870 2680 436208873 436209682 0.000000e+00 1363.0
4 TraesCS3B01G471000 chr1B 96.415 809 29 0 1872 2680 532658493 532659301 0.000000e+00 1334.0
5 TraesCS3B01G471000 chr1B 96.512 86 3 0 434 519 112863576 112863661 2.780000e-30 143.0
6 TraesCS3B01G471000 chr6B 96.786 809 26 0 1872 2680 659253491 659252683 0.000000e+00 1351.0
7 TraesCS3B01G471000 chr6B 96.663 809 27 0 1872 2680 274217066 274216258 0.000000e+00 1345.0
8 TraesCS3B01G471000 chr6B 97.674 86 2 0 434 519 252820857 252820942 5.980000e-32 148.0
9 TraesCS3B01G471000 chr6B 96.591 88 3 0 435 522 630850568 630850481 2.150000e-31 147.0
10 TraesCS3B01G471000 chr5B 96.415 809 27 2 1872 2680 654765592 654764786 0.000000e+00 1332.0
11 TraesCS3B01G471000 chr5B 85.714 49 7 0 19 67 609891597 609891645 5.000000e-03 52.8
12 TraesCS3B01G471000 chr3D 93.841 893 40 3 842 1720 543771875 543772766 0.000000e+00 1330.0
13 TraesCS3B01G471000 chr3D 81.281 406 34 16 70 435 543768618 543769021 9.390000e-75 291.0
14 TraesCS3B01G471000 chr3D 79.050 358 44 21 517 847 543769020 543769373 1.620000e-52 217.0
15 TraesCS3B01G471000 chr7B 96.159 807 31 0 1874 2680 134503410 134504216 0.000000e+00 1319.0
16 TraesCS3B01G471000 chr4B 95.946 814 29 3 1869 2680 82302597 82303408 0.000000e+00 1317.0
17 TraesCS3B01G471000 chr4B 95.808 811 34 0 1870 2680 600240629 600239819 0.000000e+00 1310.0
18 TraesCS3B01G471000 chr4B 93.684 95 5 1 429 523 454519344 454519251 1.000000e-29 141.0
19 TraesCS3B01G471000 chr3A 95.586 657 20 1 1064 1720 680737476 680738123 0.000000e+00 1044.0
20 TraesCS3B01G471000 chr3A 93.427 213 13 1 808 1019 680736734 680736946 5.570000e-82 315.0
21 TraesCS3B01G471000 chr7A 95.506 89 4 0 434 522 10086062 10085974 2.780000e-30 143.0
22 TraesCS3B01G471000 chr7D 94.505 91 5 0 434 524 195280221 195280131 1.000000e-29 141.0
23 TraesCS3B01G471000 chr4A 93.548 93 6 0 434 526 14814646 14814738 3.600000e-29 139.0
24 TraesCS3B01G471000 chr2D 92.708 96 6 1 428 523 131465395 131465301 1.290000e-28 137.0
25 TraesCS3B01G471000 chr1A 100.000 30 0 0 395 424 545025921 545025892 3.730000e-04 56.5


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 TraesCS3B01G471000 chr3B 719425926 719428605 2679 False 4950.000000 4950 100.0000 1 2680 1 chr3B.!!$F2 2679
1 TraesCS3B01G471000 chr3B 663418673 663419486 813 False 1299.000000 1299 95.4550 1867 2680 1 chr3B.!!$F1 813
2 TraesCS3B01G471000 chr1B 436208873 436209682 809 False 1363.000000 1363 97.0410 1870 2680 1 chr1B.!!$F2 810
3 TraesCS3B01G471000 chr1B 532658493 532659301 808 False 1334.000000 1334 96.4150 1872 2680 1 chr1B.!!$F3 808
4 TraesCS3B01G471000 chr6B 659252683 659253491 808 True 1351.000000 1351 96.7860 1872 2680 1 chr6B.!!$R3 808
5 TraesCS3B01G471000 chr6B 274216258 274217066 808 True 1345.000000 1345 96.6630 1872 2680 1 chr6B.!!$R1 808
6 TraesCS3B01G471000 chr5B 654764786 654765592 806 True 1332.000000 1332 96.4150 1872 2680 1 chr5B.!!$R1 808
7 TraesCS3B01G471000 chr3D 543768618 543772766 4148 False 612.666667 1330 84.7240 70 1720 3 chr3D.!!$F1 1650
8 TraesCS3B01G471000 chr7B 134503410 134504216 806 False 1319.000000 1319 96.1590 1874 2680 1 chr7B.!!$F1 806
9 TraesCS3B01G471000 chr4B 82302597 82303408 811 False 1317.000000 1317 95.9460 1869 2680 1 chr4B.!!$F1 811
10 TraesCS3B01G471000 chr4B 600239819 600240629 810 True 1310.000000 1310 95.8080 1870 2680 1 chr4B.!!$R2 810
11 TraesCS3B01G471000 chr3A 680736734 680738123 1389 False 679.500000 1044 94.5065 808 1720 2 chr3A.!!$F1 912

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
682 725 0.039888 TGCATTGACGAAGACGACGA 60.04 50.0 0.0 0.0 42.66 4.2 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1804 4885 0.031857 CATCACTGCAAACCCGCAAA 59.968 50.0 0.0 0.0 42.45 3.68 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
27 28 4.890158 AAATCAAACAGGGGTCAAATCC 57.110 40.909 0.00 0.00 0.00 3.01
28 29 2.302587 TCAAACAGGGGTCAAATCCC 57.697 50.000 0.00 0.00 46.31 3.85
38 39 4.895224 GGGTCAAATCCCGAATTTAGAC 57.105 45.455 12.14 12.14 35.77 2.59
39 40 3.630769 GGGTCAAATCCCGAATTTAGACC 59.369 47.826 20.73 20.73 44.44 3.85
40 41 4.266714 GGTCAAATCCCGAATTTAGACCA 58.733 43.478 22.13 1.00 44.49 4.02
41 42 4.095932 GGTCAAATCCCGAATTTAGACCAC 59.904 45.833 22.13 9.82 44.49 4.16
42 43 4.698304 GTCAAATCCCGAATTTAGACCACA 59.302 41.667 0.00 0.00 35.77 4.17
43 44 5.182380 GTCAAATCCCGAATTTAGACCACAA 59.818 40.000 0.00 0.00 35.77 3.33
44 45 5.770663 TCAAATCCCGAATTTAGACCACAAA 59.229 36.000 0.00 0.00 35.77 2.83
45 46 6.265649 TCAAATCCCGAATTTAGACCACAAAA 59.734 34.615 0.00 0.00 35.77 2.44
46 47 6.658188 AATCCCGAATTTAGACCACAAAAA 57.342 33.333 0.00 0.00 0.00 1.94
47 48 5.699097 TCCCGAATTTAGACCACAAAAAG 57.301 39.130 0.00 0.00 0.00 2.27
48 49 4.521256 TCCCGAATTTAGACCACAAAAAGG 59.479 41.667 0.00 0.00 0.00 3.11
49 50 4.279922 CCCGAATTTAGACCACAAAAAGGT 59.720 41.667 0.00 0.00 43.46 3.50
58 59 3.580731 ACCACAAAAAGGTCAAAACACG 58.419 40.909 0.00 0.00 32.90 4.49
59 60 3.256136 ACCACAAAAAGGTCAAAACACGA 59.744 39.130 0.00 0.00 32.90 4.35
60 61 4.238514 CCACAAAAAGGTCAAAACACGAA 58.761 39.130 0.00 0.00 0.00 3.85
61 62 4.686554 CCACAAAAAGGTCAAAACACGAAA 59.313 37.500 0.00 0.00 0.00 3.46
62 63 5.350091 CCACAAAAAGGTCAAAACACGAAAT 59.650 36.000 0.00 0.00 0.00 2.17
63 64 6.128418 CCACAAAAAGGTCAAAACACGAAATT 60.128 34.615 0.00 0.00 0.00 1.82
64 65 7.294473 CACAAAAAGGTCAAAACACGAAATTT 58.706 30.769 0.00 0.00 0.00 1.82
65 66 7.800847 CACAAAAAGGTCAAAACACGAAATTTT 59.199 29.630 0.00 0.00 0.00 1.82
66 67 7.800847 ACAAAAAGGTCAAAACACGAAATTTTG 59.199 29.630 3.73 3.73 44.74 2.44
67 68 7.428282 AAAAGGTCAAAACACGAAATTTTGT 57.572 28.000 5.16 5.16 44.08 2.83
68 69 6.641176 AAGGTCAAAACACGAAATTTTGTC 57.359 33.333 8.17 13.44 44.08 3.18
82 83 6.510478 CGAAATTTTGTCAAACCTCGTCTACA 60.510 38.462 0.00 0.00 30.14 2.74
111 113 4.518249 CCAAAGAGGATTGTAGAGGGTTC 58.482 47.826 0.00 0.00 41.22 3.62
114 116 4.338795 AGAGGATTGTAGAGGGTTCTGA 57.661 45.455 0.00 0.00 34.79 3.27
125 127 2.355837 GTTCTGAGCCACGCGTGA 60.356 61.111 39.10 19.17 0.00 4.35
126 128 1.954146 GTTCTGAGCCACGCGTGAA 60.954 57.895 39.10 21.67 0.00 3.18
153 155 4.180817 CTCACTCAAAAACCACCAAAACC 58.819 43.478 0.00 0.00 0.00 3.27
161 163 0.818040 ACCACCAAAACCTCTCGTGC 60.818 55.000 0.00 0.00 0.00 5.34
167 169 1.403679 CAAAACCTCTCGTGCCAAACA 59.596 47.619 0.00 0.00 0.00 2.83
169 171 1.308998 AACCTCTCGTGCCAAACAAG 58.691 50.000 0.00 0.00 0.00 3.16
194 196 6.073327 GCCTTAAGCAGTCAACTAACTTTT 57.927 37.500 0.00 0.00 42.97 2.27
195 197 6.504398 GCCTTAAGCAGTCAACTAACTTTTT 58.496 36.000 0.00 0.00 42.97 1.94
196 198 6.637254 GCCTTAAGCAGTCAACTAACTTTTTC 59.363 38.462 0.00 0.00 42.97 2.29
327 358 7.966246 ATAAAATGAAATTGACAAGCTGCAA 57.034 28.000 1.02 0.00 36.10 4.08
332 363 4.038282 TGAAATTGACAAGCTGCAACATCT 59.962 37.500 1.02 0.00 0.00 2.90
344 375 0.107508 CAACATCTGGGATGAGCGGT 60.108 55.000 13.51 0.00 0.00 5.68
351 394 4.148825 GGATGAGCGGTGGCGAGT 62.149 66.667 0.00 0.00 46.35 4.18
362 405 2.049802 GGCGAGTTTCGGTCGTCA 60.050 61.111 0.34 0.00 41.70 4.35
379 422 1.116536 TCACCACCGGAGCTACAACA 61.117 55.000 9.46 0.00 0.00 3.33
384 427 0.602905 ACCGGAGCTACAACAGTTGC 60.603 55.000 9.46 0.00 34.82 4.17
386 429 1.626654 CGGAGCTACAACAGTTGCCG 61.627 60.000 13.56 13.20 35.11 5.69
443 486 3.742983 CGAAGCAGGTACTTCCTCC 57.257 57.895 0.00 0.00 46.24 4.30
444 487 0.179134 CGAAGCAGGTACTTCCTCCG 60.179 60.000 0.00 0.00 46.24 4.63
445 488 0.896226 GAAGCAGGTACTTCCTCCGT 59.104 55.000 0.00 0.00 46.24 4.69
446 489 2.097825 GAAGCAGGTACTTCCTCCGTA 58.902 52.381 0.00 0.00 46.24 4.02
447 490 2.226962 AGCAGGTACTTCCTCCGTAA 57.773 50.000 0.00 0.00 46.24 3.18
448 491 2.532843 AGCAGGTACTTCCTCCGTAAA 58.467 47.619 0.00 0.00 46.24 2.01
449 492 2.496470 AGCAGGTACTTCCTCCGTAAAG 59.504 50.000 0.00 0.00 46.24 1.85
450 493 2.233186 GCAGGTACTTCCTCCGTAAAGT 59.767 50.000 0.00 0.00 46.24 2.66
451 494 3.445096 GCAGGTACTTCCTCCGTAAAGTA 59.555 47.826 0.00 0.00 46.24 2.24
452 495 4.082026 GCAGGTACTTCCTCCGTAAAGTAA 60.082 45.833 0.00 0.00 46.24 2.24
453 496 5.394993 GCAGGTACTTCCTCCGTAAAGTAAT 60.395 44.000 0.00 0.00 46.24 1.89
454 497 6.183360 GCAGGTACTTCCTCCGTAAAGTAATA 60.183 42.308 0.00 0.00 46.24 0.98
455 498 7.471120 GCAGGTACTTCCTCCGTAAAGTAATAT 60.471 40.741 0.00 0.00 46.24 1.28
456 499 9.071276 CAGGTACTTCCTCCGTAAAGTAATATA 57.929 37.037 0.00 0.00 46.24 0.86
457 500 9.646522 AGGTACTTCCTCCGTAAAGTAATATAA 57.353 33.333 0.00 0.00 44.42 0.98
458 501 9.905171 GGTACTTCCTCCGTAAAGTAATATAAG 57.095 37.037 0.00 0.00 39.11 1.73
461 504 8.358895 ACTTCCTCCGTAAAGTAATATAAGAGC 58.641 37.037 0.00 0.00 34.05 4.09
462 505 6.906659 TCCTCCGTAAAGTAATATAAGAGCG 58.093 40.000 0.00 0.00 0.00 5.03
463 506 6.488006 TCCTCCGTAAAGTAATATAAGAGCGT 59.512 38.462 0.00 0.00 0.00 5.07
464 507 7.013655 TCCTCCGTAAAGTAATATAAGAGCGTT 59.986 37.037 0.00 0.00 0.00 4.84
465 508 7.650903 CCTCCGTAAAGTAATATAAGAGCGTTT 59.349 37.037 0.00 0.00 0.00 3.60
466 509 9.669353 CTCCGTAAAGTAATATAAGAGCGTTTA 57.331 33.333 0.00 0.00 0.00 2.01
467 510 9.669353 TCCGTAAAGTAATATAAGAGCGTTTAG 57.331 33.333 0.00 0.00 0.00 1.85
468 511 9.669353 CCGTAAAGTAATATAAGAGCGTTTAGA 57.331 33.333 0.00 0.00 0.00 2.10
513 556 9.530633 AAACGCTCTTATATTAGTTTACAGAGG 57.469 33.333 0.00 0.00 31.14 3.69
514 557 7.659186 ACGCTCTTATATTAGTTTACAGAGGG 58.341 38.462 8.36 8.36 42.53 4.30
515 558 7.504911 ACGCTCTTATATTAGTTTACAGAGGGA 59.495 37.037 14.96 0.00 40.49 4.20
516 559 8.024285 CGCTCTTATATTAGTTTACAGAGGGAG 58.976 40.741 4.76 0.00 40.49 4.30
517 560 8.862085 GCTCTTATATTAGTTTACAGAGGGAGT 58.138 37.037 0.00 0.00 0.00 3.85
526 569 5.785940 AGTTTACAGAGGGAGTAACAAGGAT 59.214 40.000 0.00 0.00 31.67 3.24
548 591 3.155167 GGTGAGGGCTAGGACCGG 61.155 72.222 0.00 0.00 34.63 5.28
557 600 1.897615 CTAGGACCGGCGAGTAGGG 60.898 68.421 9.30 0.00 0.00 3.53
558 601 3.426309 TAGGACCGGCGAGTAGGGG 62.426 68.421 9.30 0.00 0.00 4.79
628 671 3.691342 GGCGGCAAAGGGGGAAAC 61.691 66.667 3.07 0.00 0.00 2.78
634 677 2.190841 CAAAGGGGGAAACGCGTGT 61.191 57.895 14.98 7.31 45.87 4.49
655 698 1.305201 GCGCCGATGGGATTTTCTTA 58.695 50.000 0.00 0.00 34.06 2.10
671 714 2.256174 TCTTAGTACGCGTGCATTGAC 58.744 47.619 28.70 14.62 0.00 3.18
676 719 0.387494 TACGCGTGCATTGACGAAGA 60.387 50.000 24.59 0.00 42.10 2.87
678 721 1.225475 GCGTGCATTGACGAAGACG 60.225 57.895 11.20 0.00 42.10 4.18
679 722 1.614227 GCGTGCATTGACGAAGACGA 61.614 55.000 11.20 0.00 42.10 4.20
680 723 0.091344 CGTGCATTGACGAAGACGAC 59.909 55.000 0.00 0.00 42.10 4.34
681 724 0.091344 GTGCATTGACGAAGACGACG 59.909 55.000 0.00 0.00 42.66 5.12
682 725 0.039888 TGCATTGACGAAGACGACGA 60.040 50.000 0.00 0.00 42.66 4.20
683 726 0.362512 GCATTGACGAAGACGACGAC 59.637 55.000 0.00 0.00 42.66 4.34
684 727 0.628781 CATTGACGAAGACGACGACG 59.371 55.000 5.58 5.58 42.66 5.12
689 732 3.222323 GAAGACGACGACGACGCG 61.222 66.667 18.98 17.96 43.96 6.01
722 765 1.229428 CCATCATCCCCAATCGAACG 58.771 55.000 0.00 0.00 0.00 3.95
723 766 0.588252 CATCATCCCCAATCGAACGC 59.412 55.000 0.00 0.00 0.00 4.84
725 768 2.203015 ATCCCCAATCGAACGCCG 60.203 61.111 0.00 0.00 40.25 6.46
737 804 4.570663 ACGCCGACGCCTAGCATC 62.571 66.667 0.00 0.00 45.53 3.91
741 808 4.569023 CGACGCCTAGCATCGCCA 62.569 66.667 0.00 0.00 37.45 5.69
743 810 1.289066 GACGCCTAGCATCGCCATA 59.711 57.895 0.00 0.00 0.00 2.74
745 812 1.290324 CGCCTAGCATCGCCATACT 59.710 57.895 0.00 0.00 0.00 2.12
836 912 4.346730 TCAGTATTACCCTCCTCGTTTGA 58.653 43.478 0.00 0.00 0.00 2.69
882 3464 2.439156 GCTGAATCAAGCCGGCCT 60.439 61.111 26.15 7.54 37.20 5.19
895 3477 2.537560 CGGCCTGCATCGATCAACC 61.538 63.158 0.00 1.40 0.00 3.77
916 3498 3.064408 CCATCAGGTGAATCATCAACACG 59.936 47.826 0.00 0.00 46.21 4.49
923 3505 3.125316 GTGAATCATCAACACGTCCCTTC 59.875 47.826 0.00 0.00 37.30 3.46
1047 3670 1.305219 TACGCACAGGAATGGCTTGC 61.305 55.000 0.00 0.00 0.00 4.01
1072 4148 2.159819 GAGACGCCTTCTGACCTGCA 62.160 60.000 0.00 0.00 33.22 4.41
1655 4731 4.814294 GTGTTCGGCCCGCGAGAT 62.814 66.667 8.23 0.00 0.00 2.75
1680 4756 2.941415 GCCAGGTGTGGTCTCCAATAAG 60.941 54.545 0.00 0.00 46.96 1.73
1720 4801 5.762218 CCTCTTGAACTGGATGAATATGACC 59.238 44.000 0.00 0.00 0.00 4.02
1721 4802 5.684704 TCTTGAACTGGATGAATATGACCC 58.315 41.667 0.00 0.00 0.00 4.46
1722 4803 4.437682 TGAACTGGATGAATATGACCCC 57.562 45.455 0.00 0.00 0.00 4.95
1723 4804 3.181455 TGAACTGGATGAATATGACCCCG 60.181 47.826 0.00 0.00 0.00 5.73
1724 4805 1.072331 ACTGGATGAATATGACCCCGC 59.928 52.381 0.00 0.00 0.00 6.13
1725 4806 0.400213 TGGATGAATATGACCCCGCC 59.600 55.000 0.00 0.00 0.00 6.13
1726 4807 0.400213 GGATGAATATGACCCCGCCA 59.600 55.000 0.00 0.00 0.00 5.69
1727 4808 1.202879 GGATGAATATGACCCCGCCAA 60.203 52.381 0.00 0.00 0.00 4.52
1728 4809 2.154462 GATGAATATGACCCCGCCAAG 58.846 52.381 0.00 0.00 0.00 3.61
1729 4810 0.916086 TGAATATGACCCCGCCAAGT 59.084 50.000 0.00 0.00 0.00 3.16
1730 4811 1.134220 TGAATATGACCCCGCCAAGTC 60.134 52.381 0.00 0.00 0.00 3.01
1731 4812 1.141053 GAATATGACCCCGCCAAGTCT 59.859 52.381 0.00 0.00 34.02 3.24
1732 4813 0.759346 ATATGACCCCGCCAAGTCTC 59.241 55.000 0.00 0.00 34.02 3.36
1733 4814 0.325296 TATGACCCCGCCAAGTCTCT 60.325 55.000 0.00 0.00 34.02 3.10
1734 4815 1.903877 ATGACCCCGCCAAGTCTCTG 61.904 60.000 0.00 0.00 34.02 3.35
1735 4816 2.526873 ACCCCGCCAAGTCTCTGT 60.527 61.111 0.00 0.00 0.00 3.41
1736 4817 2.113243 GACCCCGCCAAGTCTCTGTT 62.113 60.000 0.00 0.00 0.00 3.16
1737 4818 1.376037 CCCCGCCAAGTCTCTGTTC 60.376 63.158 0.00 0.00 0.00 3.18
1738 4819 1.371183 CCCGCCAAGTCTCTGTTCA 59.629 57.895 0.00 0.00 0.00 3.18
1739 4820 0.036010 CCCGCCAAGTCTCTGTTCAT 60.036 55.000 0.00 0.00 0.00 2.57
1740 4821 1.611673 CCCGCCAAGTCTCTGTTCATT 60.612 52.381 0.00 0.00 0.00 2.57
1741 4822 1.734465 CCGCCAAGTCTCTGTTCATTC 59.266 52.381 0.00 0.00 0.00 2.67
1742 4823 1.391485 CGCCAAGTCTCTGTTCATTCG 59.609 52.381 0.00 0.00 0.00 3.34
1743 4824 1.734465 GCCAAGTCTCTGTTCATTCGG 59.266 52.381 0.00 0.00 0.00 4.30
1744 4825 2.350522 CCAAGTCTCTGTTCATTCGGG 58.649 52.381 0.00 0.00 0.00 5.14
1745 4826 2.289694 CCAAGTCTCTGTTCATTCGGGT 60.290 50.000 0.00 0.00 0.00 5.28
1746 4827 2.738846 CAAGTCTCTGTTCATTCGGGTG 59.261 50.000 0.00 0.00 0.00 4.61
1747 4828 1.276421 AGTCTCTGTTCATTCGGGTGG 59.724 52.381 0.00 0.00 0.00 4.61
1748 4829 1.002087 GTCTCTGTTCATTCGGGTGGT 59.998 52.381 0.00 0.00 0.00 4.16
1749 4830 2.232941 GTCTCTGTTCATTCGGGTGGTA 59.767 50.000 0.00 0.00 0.00 3.25
1750 4831 3.104512 TCTCTGTTCATTCGGGTGGTAT 58.895 45.455 0.00 0.00 0.00 2.73
1751 4832 4.098960 GTCTCTGTTCATTCGGGTGGTATA 59.901 45.833 0.00 0.00 0.00 1.47
1752 4833 4.341235 TCTCTGTTCATTCGGGTGGTATAG 59.659 45.833 0.00 0.00 0.00 1.31
1753 4834 4.283337 TCTGTTCATTCGGGTGGTATAGA 58.717 43.478 0.00 0.00 0.00 1.98
1754 4835 4.098960 TCTGTTCATTCGGGTGGTATAGAC 59.901 45.833 0.00 0.00 0.00 2.59
1755 4836 3.181484 TGTTCATTCGGGTGGTATAGACG 60.181 47.826 0.00 0.00 0.00 4.18
1756 4837 2.934887 TCATTCGGGTGGTATAGACGA 58.065 47.619 0.00 0.00 0.00 4.20
1757 4838 3.289836 TCATTCGGGTGGTATAGACGAA 58.710 45.455 0.00 0.00 45.83 3.85
1759 4840 3.720949 TTCGGGTGGTATAGACGAATG 57.279 47.619 0.00 0.00 38.46 2.67
1760 4841 1.338973 TCGGGTGGTATAGACGAATGC 59.661 52.381 0.00 0.00 0.00 3.56
1761 4842 1.067974 CGGGTGGTATAGACGAATGCA 59.932 52.381 0.00 0.00 0.00 3.96
1762 4843 2.755650 GGGTGGTATAGACGAATGCAG 58.244 52.381 0.00 0.00 0.00 4.41
1763 4844 2.364324 GGGTGGTATAGACGAATGCAGA 59.636 50.000 0.00 0.00 0.00 4.26
1764 4845 3.006967 GGGTGGTATAGACGAATGCAGAT 59.993 47.826 0.00 0.00 0.00 2.90
1765 4846 3.990469 GGTGGTATAGACGAATGCAGATG 59.010 47.826 0.00 0.00 0.00 2.90
1766 4847 4.501571 GGTGGTATAGACGAATGCAGATGT 60.502 45.833 0.00 0.00 0.00 3.06
1767 4848 5.278808 GGTGGTATAGACGAATGCAGATGTA 60.279 44.000 0.00 0.00 0.00 2.29
1768 4849 5.859114 GTGGTATAGACGAATGCAGATGTAG 59.141 44.000 0.00 0.00 0.00 2.74
1769 4850 5.535030 TGGTATAGACGAATGCAGATGTAGT 59.465 40.000 0.00 0.00 0.00 2.73
1770 4851 6.713450 TGGTATAGACGAATGCAGATGTAGTA 59.287 38.462 0.00 0.00 0.00 1.82
1771 4852 7.393515 TGGTATAGACGAATGCAGATGTAGTAT 59.606 37.037 0.00 0.00 0.00 2.12
1772 4853 7.698550 GGTATAGACGAATGCAGATGTAGTATG 59.301 40.741 0.00 0.00 0.00 2.39
1773 4854 5.521906 AGACGAATGCAGATGTAGTATGT 57.478 39.130 0.00 0.00 0.00 2.29
1774 4855 6.635030 AGACGAATGCAGATGTAGTATGTA 57.365 37.500 0.00 0.00 0.00 2.29
1775 4856 6.439599 AGACGAATGCAGATGTAGTATGTAC 58.560 40.000 0.00 0.00 0.00 2.90
1776 4857 5.212934 ACGAATGCAGATGTAGTATGTACG 58.787 41.667 0.00 0.00 0.00 3.67
1777 4858 4.617223 CGAATGCAGATGTAGTATGTACGG 59.383 45.833 0.00 0.00 0.00 4.02
1778 4859 5.529791 GAATGCAGATGTAGTATGTACGGT 58.470 41.667 0.00 0.00 0.00 4.83
1779 4860 4.994907 TGCAGATGTAGTATGTACGGTT 57.005 40.909 0.00 0.00 0.00 4.44
1780 4861 5.333299 TGCAGATGTAGTATGTACGGTTT 57.667 39.130 0.00 0.00 0.00 3.27
1781 4862 5.345702 TGCAGATGTAGTATGTACGGTTTC 58.654 41.667 0.00 0.00 0.00 2.78
1782 4863 5.126545 TGCAGATGTAGTATGTACGGTTTCT 59.873 40.000 0.00 0.00 0.00 2.52
1783 4864 5.686397 GCAGATGTAGTATGTACGGTTTCTC 59.314 44.000 0.00 0.00 0.00 2.87
1784 4865 5.907945 CAGATGTAGTATGTACGGTTTCTCG 59.092 44.000 0.00 0.00 0.00 4.04
1785 4866 5.587844 AGATGTAGTATGTACGGTTTCTCGT 59.412 40.000 0.00 0.00 45.88 4.18
1786 4867 5.221891 TGTAGTATGTACGGTTTCTCGTC 57.778 43.478 0.00 0.00 42.82 4.20
1787 4868 3.772060 AGTATGTACGGTTTCTCGTCC 57.228 47.619 0.00 0.00 42.82 4.79
1788 4869 3.084039 AGTATGTACGGTTTCTCGTCCA 58.916 45.455 0.00 0.00 42.82 4.02
1789 4870 2.649331 ATGTACGGTTTCTCGTCCAG 57.351 50.000 0.00 0.00 42.82 3.86
1790 4871 1.321474 TGTACGGTTTCTCGTCCAGT 58.679 50.000 0.00 0.00 42.82 4.00
1791 4872 1.682854 TGTACGGTTTCTCGTCCAGTT 59.317 47.619 0.00 0.00 42.82 3.16
1792 4873 2.101249 TGTACGGTTTCTCGTCCAGTTT 59.899 45.455 0.00 0.00 42.82 2.66
1793 4874 1.861971 ACGGTTTCTCGTCCAGTTTC 58.138 50.000 0.00 0.00 39.34 2.78
1794 4875 1.145803 CGGTTTCTCGTCCAGTTTCC 58.854 55.000 0.00 0.00 0.00 3.13
1795 4876 1.145803 GGTTTCTCGTCCAGTTTCCG 58.854 55.000 0.00 0.00 0.00 4.30
1796 4877 1.145803 GTTTCTCGTCCAGTTTCCGG 58.854 55.000 0.00 0.00 0.00 5.14
1797 4878 0.034337 TTTCTCGTCCAGTTTCCGGG 59.966 55.000 0.00 0.00 0.00 5.73
1798 4879 1.117142 TTCTCGTCCAGTTTCCGGGT 61.117 55.000 0.00 0.00 0.00 5.28
1799 4880 0.251297 TCTCGTCCAGTTTCCGGGTA 60.251 55.000 0.00 0.00 0.00 3.69
1800 4881 0.604578 CTCGTCCAGTTTCCGGGTAA 59.395 55.000 0.00 0.00 0.00 2.85
1801 4882 0.318120 TCGTCCAGTTTCCGGGTAAC 59.682 55.000 8.34 8.34 0.00 2.50
1802 4883 0.033781 CGTCCAGTTTCCGGGTAACA 59.966 55.000 17.30 0.00 39.74 2.41
1803 4884 1.338389 CGTCCAGTTTCCGGGTAACAT 60.338 52.381 17.30 1.89 39.74 2.71
1804 4885 2.786777 GTCCAGTTTCCGGGTAACATT 58.213 47.619 17.30 0.00 39.74 2.71
1805 4886 3.151554 GTCCAGTTTCCGGGTAACATTT 58.848 45.455 17.30 0.00 39.74 2.32
1806 4887 3.570975 GTCCAGTTTCCGGGTAACATTTT 59.429 43.478 17.30 0.00 39.74 1.82
1807 4888 3.570550 TCCAGTTTCCGGGTAACATTTTG 59.429 43.478 17.30 7.66 39.74 2.44
1808 4889 3.313690 CAGTTTCCGGGTAACATTTTGC 58.686 45.455 17.30 0.00 39.74 3.68
1809 4890 2.030628 AGTTTCCGGGTAACATTTTGCG 60.031 45.455 17.30 0.00 39.74 4.85
1810 4891 0.882474 TTCCGGGTAACATTTTGCGG 59.118 50.000 0.00 0.00 35.56 5.69
1811 4892 0.961358 TCCGGGTAACATTTTGCGGG 60.961 55.000 0.00 0.00 35.06 6.13
1812 4893 1.245376 CCGGGTAACATTTTGCGGGT 61.245 55.000 0.00 0.00 39.74 5.28
1813 4894 0.599060 CGGGTAACATTTTGCGGGTT 59.401 50.000 0.00 0.00 39.74 4.11
1814 4895 1.000052 CGGGTAACATTTTGCGGGTTT 60.000 47.619 0.00 0.00 39.74 3.27
1815 4896 2.409012 GGGTAACATTTTGCGGGTTTG 58.591 47.619 0.00 0.00 39.74 2.93
1816 4897 1.795872 GGTAACATTTTGCGGGTTTGC 59.204 47.619 0.00 0.00 0.00 3.68
1817 4898 2.474816 GTAACATTTTGCGGGTTTGCA 58.525 42.857 0.00 0.00 44.61 4.08
1823 4904 3.353600 TGCGGGTTTGCAGTGATG 58.646 55.556 0.00 0.00 40.62 3.07
1824 4905 1.528076 TGCGGGTTTGCAGTGATGT 60.528 52.632 0.00 0.00 40.62 3.06
1825 4906 1.081242 GCGGGTTTGCAGTGATGTG 60.081 57.895 0.00 0.00 34.15 3.21
1826 4907 1.795170 GCGGGTTTGCAGTGATGTGT 61.795 55.000 0.00 0.00 34.15 3.72
1827 4908 1.518325 CGGGTTTGCAGTGATGTGTA 58.482 50.000 0.00 0.00 0.00 2.90
1828 4909 1.196808 CGGGTTTGCAGTGATGTGTAC 59.803 52.381 0.00 0.00 0.00 2.90
1829 4910 2.504367 GGGTTTGCAGTGATGTGTACT 58.496 47.619 0.00 0.00 0.00 2.73
1830 4911 3.670625 GGGTTTGCAGTGATGTGTACTA 58.329 45.455 0.00 0.00 0.00 1.82
1831 4912 3.435671 GGGTTTGCAGTGATGTGTACTAC 59.564 47.826 0.00 0.00 0.00 2.73
1832 4913 4.062293 GGTTTGCAGTGATGTGTACTACA 58.938 43.478 0.00 0.00 44.87 2.74
2100 5181 1.352083 CTTCCTCTCCCACTTCCACA 58.648 55.000 0.00 0.00 0.00 4.17
2202 5285 4.431524 TTCCGCCCCATCCCCTCT 62.432 66.667 0.00 0.00 0.00 3.69
2254 5337 4.070552 GAGGAACAGCGCCCGAGT 62.071 66.667 2.29 0.00 0.00 4.18
2433 5516 8.329346 AGAAGAATTTGATATGGAAGAGGAGA 57.671 34.615 0.00 0.00 0.00 3.71
2435 5518 9.571816 GAAGAATTTGATATGGAAGAGGAGAAT 57.428 33.333 0.00 0.00 0.00 2.40
2650 5733 1.734465 GCGCATTGCAGAGAAACTAGT 59.266 47.619 9.69 0.00 45.45 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 5.456042 GGGATTTGACCCCTGTTTGATTTTT 60.456 40.000 0.00 0.00 43.81 1.94
5 6 4.041567 GGGATTTGACCCCTGTTTGATTTT 59.958 41.667 0.00 0.00 43.81 1.82
6 7 3.582647 GGGATTTGACCCCTGTTTGATTT 59.417 43.478 0.00 0.00 43.81 2.17
7 8 3.173151 GGGATTTGACCCCTGTTTGATT 58.827 45.455 0.00 0.00 43.81 2.57
8 9 2.820178 GGGATTTGACCCCTGTTTGAT 58.180 47.619 0.00 0.00 43.81 2.57
9 10 1.546773 CGGGATTTGACCCCTGTTTGA 60.547 52.381 0.00 0.00 46.62 2.69
10 11 0.887933 CGGGATTTGACCCCTGTTTG 59.112 55.000 0.00 0.00 46.62 2.93
11 12 0.774908 TCGGGATTTGACCCCTGTTT 59.225 50.000 0.00 0.00 46.62 2.83
12 13 0.774908 TTCGGGATTTGACCCCTGTT 59.225 50.000 0.00 0.00 46.62 3.16
13 14 0.999712 ATTCGGGATTTGACCCCTGT 59.000 50.000 0.00 0.00 46.62 4.00
14 15 2.143876 AATTCGGGATTTGACCCCTG 57.856 50.000 0.00 0.00 46.62 4.45
15 16 2.919772 AAATTCGGGATTTGACCCCT 57.080 45.000 0.00 0.00 46.62 4.79
16 17 3.630769 GTCTAAATTCGGGATTTGACCCC 59.369 47.826 4.47 0.00 46.62 4.95
17 18 3.630769 GGTCTAAATTCGGGATTTGACCC 59.369 47.826 21.00 9.39 42.47 4.46
18 19 4.095932 GTGGTCTAAATTCGGGATTTGACC 59.904 45.833 22.93 22.93 44.88 4.02
19 20 4.698304 TGTGGTCTAAATTCGGGATTTGAC 59.302 41.667 4.47 9.32 38.40 3.18
20 21 4.912586 TGTGGTCTAAATTCGGGATTTGA 58.087 39.130 4.47 0.00 38.40 2.69
21 22 5.637006 TTGTGGTCTAAATTCGGGATTTG 57.363 39.130 4.47 0.00 38.40 2.32
22 23 6.658188 TTTTGTGGTCTAAATTCGGGATTT 57.342 33.333 0.00 0.00 40.88 2.17
23 24 6.295067 CCTTTTTGTGGTCTAAATTCGGGATT 60.295 38.462 0.00 0.00 0.00 3.01
24 25 5.185056 CCTTTTTGTGGTCTAAATTCGGGAT 59.815 40.000 0.00 0.00 0.00 3.85
25 26 4.521256 CCTTTTTGTGGTCTAAATTCGGGA 59.479 41.667 0.00 0.00 0.00 5.14
26 27 4.279922 ACCTTTTTGTGGTCTAAATTCGGG 59.720 41.667 0.00 0.00 31.03 5.14
27 28 5.447624 ACCTTTTTGTGGTCTAAATTCGG 57.552 39.130 0.00 0.00 31.03 4.30
37 38 3.256136 TCGTGTTTTGACCTTTTTGTGGT 59.744 39.130 0.00 0.00 41.07 4.16
38 39 3.839293 TCGTGTTTTGACCTTTTTGTGG 58.161 40.909 0.00 0.00 0.00 4.17
39 40 5.830900 TTTCGTGTTTTGACCTTTTTGTG 57.169 34.783 0.00 0.00 0.00 3.33
40 41 7.428282 AAATTTCGTGTTTTGACCTTTTTGT 57.572 28.000 0.00 0.00 0.00 2.83
41 42 7.800847 ACAAAATTTCGTGTTTTGACCTTTTTG 59.199 29.630 20.71 0.00 45.02 2.44
42 43 7.866729 ACAAAATTTCGTGTTTTGACCTTTTT 58.133 26.923 20.71 3.46 45.02 1.94
43 44 7.171678 TGACAAAATTTCGTGTTTTGACCTTTT 59.828 29.630 20.71 5.75 45.02 2.27
44 45 6.647067 TGACAAAATTTCGTGTTTTGACCTTT 59.353 30.769 20.71 6.24 45.02 3.11
45 46 6.159988 TGACAAAATTTCGTGTTTTGACCTT 58.840 32.000 20.71 6.50 45.02 3.50
46 47 5.715070 TGACAAAATTTCGTGTTTTGACCT 58.285 33.333 20.71 6.74 45.02 3.85
47 48 6.396459 TTGACAAAATTTCGTGTTTTGACC 57.604 33.333 20.71 14.71 45.02 4.02
48 49 6.734617 GGTTTGACAAAATTTCGTGTTTTGAC 59.265 34.615 20.71 16.85 45.02 3.18
49 50 6.647067 AGGTTTGACAAAATTTCGTGTTTTGA 59.353 30.769 20.71 5.43 45.02 2.69
50 51 6.826612 AGGTTTGACAAAATTTCGTGTTTTG 58.173 32.000 1.27 15.66 46.64 2.44
51 52 6.183360 CGAGGTTTGACAAAATTTCGTGTTTT 60.183 34.615 15.97 0.00 33.20 2.43
52 53 5.287513 CGAGGTTTGACAAAATTTCGTGTTT 59.712 36.000 15.97 0.00 33.20 2.83
53 54 4.796312 CGAGGTTTGACAAAATTTCGTGTT 59.204 37.500 15.97 0.00 33.20 3.32
54 55 4.142556 ACGAGGTTTGACAAAATTTCGTGT 60.143 37.500 23.40 9.41 41.50 4.49
55 56 4.347813 ACGAGGTTTGACAAAATTTCGTG 58.652 39.130 23.40 7.55 41.50 4.35
56 57 4.334481 AGACGAGGTTTGACAAAATTTCGT 59.666 37.500 23.87 23.87 43.60 3.85
57 58 4.844267 AGACGAGGTTTGACAAAATTTCG 58.156 39.130 19.77 19.77 38.68 3.46
58 59 6.721321 TGTAGACGAGGTTTGACAAAATTTC 58.279 36.000 1.27 0.47 0.00 2.17
59 60 6.687081 TGTAGACGAGGTTTGACAAAATTT 57.313 33.333 1.27 0.00 0.00 1.82
60 61 6.687081 TTGTAGACGAGGTTTGACAAAATT 57.313 33.333 1.27 0.00 0.00 1.82
61 62 6.687081 TTTGTAGACGAGGTTTGACAAAAT 57.313 33.333 1.27 0.00 34.74 1.82
62 63 6.459024 CCATTTGTAGACGAGGTTTGACAAAA 60.459 38.462 1.27 0.00 39.45 2.44
63 64 5.008217 CCATTTGTAGACGAGGTTTGACAAA 59.992 40.000 0.00 0.00 40.08 2.83
64 65 4.513692 CCATTTGTAGACGAGGTTTGACAA 59.486 41.667 0.00 0.00 0.00 3.18
65 66 4.062293 CCATTTGTAGACGAGGTTTGACA 58.938 43.478 0.00 0.00 0.00 3.58
66 67 3.435671 CCCATTTGTAGACGAGGTTTGAC 59.564 47.826 0.00 0.00 0.00 3.18
67 68 3.670625 CCCATTTGTAGACGAGGTTTGA 58.329 45.455 0.00 0.00 0.00 2.69
68 69 2.161609 GCCCATTTGTAGACGAGGTTTG 59.838 50.000 0.00 0.00 0.00 2.93
82 83 2.906568 ACAATCCTCTTTGGCCCATTT 58.093 42.857 0.00 0.00 35.26 2.32
111 113 1.646540 TTTTTCACGCGTGGCTCAG 59.353 52.632 36.41 12.69 0.00 3.35
126 128 5.476091 TGGTGGTTTTTGAGTGAGTTTTT 57.524 34.783 0.00 0.00 0.00 1.94
131 133 4.081697 AGGTTTTGGTGGTTTTTGAGTGAG 60.082 41.667 0.00 0.00 0.00 3.51
132 134 3.835395 AGGTTTTGGTGGTTTTTGAGTGA 59.165 39.130 0.00 0.00 0.00 3.41
135 137 4.682787 GAGAGGTTTTGGTGGTTTTTGAG 58.317 43.478 0.00 0.00 0.00 3.02
142 144 0.818040 GCACGAGAGGTTTTGGTGGT 60.818 55.000 0.00 0.00 0.00 4.16
145 147 0.106918 TTGGCACGAGAGGTTTTGGT 60.107 50.000 0.00 0.00 0.00 3.67
161 163 2.887152 ACTGCTTAAGGCTCTTGTTTGG 59.113 45.455 4.29 0.00 42.39 3.28
167 169 3.778954 AGTTGACTGCTTAAGGCTCTT 57.221 42.857 4.29 0.00 42.39 2.85
169 171 4.570930 AGTTAGTTGACTGCTTAAGGCTC 58.429 43.478 4.29 0.00 42.39 4.70
301 330 9.656040 TTGCAGCTTGTCAATTTCATTTTATAT 57.344 25.926 0.00 0.00 0.00 0.86
304 333 6.760298 TGTTGCAGCTTGTCAATTTCATTTTA 59.240 30.769 1.17 0.00 0.00 1.52
318 349 1.134367 CATCCCAGATGTTGCAGCTTG 59.866 52.381 1.17 0.00 0.00 4.01
326 357 0.107508 CACCGCTCATCCCAGATGTT 60.108 55.000 4.60 0.00 0.00 2.71
327 358 1.524002 CACCGCTCATCCCAGATGT 59.476 57.895 4.60 0.00 0.00 3.06
344 375 2.049802 GACGACCGAAACTCGCCA 60.050 61.111 0.00 0.00 38.82 5.69
362 405 1.119574 ACTGTTGTAGCTCCGGTGGT 61.120 55.000 13.38 13.38 0.00 4.16
410 453 3.866379 TTCGCCCCATGCAACAGCT 62.866 57.895 0.00 0.00 41.33 4.24
435 478 8.358895 GCTCTTATATTACTTTACGGAGGAAGT 58.641 37.037 0.00 0.00 40.22 3.01
436 479 7.537991 CGCTCTTATATTACTTTACGGAGGAAG 59.462 40.741 0.00 0.00 0.00 3.46
437 480 7.013655 ACGCTCTTATATTACTTTACGGAGGAA 59.986 37.037 0.00 0.00 0.00 3.36
438 481 6.488006 ACGCTCTTATATTACTTTACGGAGGA 59.512 38.462 0.00 0.00 0.00 3.71
439 482 6.675987 ACGCTCTTATATTACTTTACGGAGG 58.324 40.000 0.00 0.00 0.00 4.30
440 483 8.571461 AAACGCTCTTATATTACTTTACGGAG 57.429 34.615 0.00 0.00 0.00 4.63
441 484 9.669353 CTAAACGCTCTTATATTACTTTACGGA 57.331 33.333 0.00 0.00 0.00 4.69
442 485 9.669353 TCTAAACGCTCTTATATTACTTTACGG 57.331 33.333 0.00 0.00 0.00 4.02
487 530 9.530633 CCTCTGTAAACTAATATAAGAGCGTTT 57.469 33.333 0.00 0.00 0.00 3.60
488 531 8.142551 CCCTCTGTAAACTAATATAAGAGCGTT 58.857 37.037 0.00 0.00 0.00 4.84
489 532 7.504911 TCCCTCTGTAAACTAATATAAGAGCGT 59.495 37.037 0.00 0.00 0.00 5.07
490 533 7.883217 TCCCTCTGTAAACTAATATAAGAGCG 58.117 38.462 0.00 0.00 0.00 5.03
491 534 8.862085 ACTCCCTCTGTAAACTAATATAAGAGC 58.138 37.037 0.00 0.00 0.00 4.09
498 541 8.755977 CCTTGTTACTCCCTCTGTAAACTAATA 58.244 37.037 0.00 0.00 32.58 0.98
499 542 7.456902 TCCTTGTTACTCCCTCTGTAAACTAAT 59.543 37.037 0.00 0.00 32.58 1.73
500 543 6.783977 TCCTTGTTACTCCCTCTGTAAACTAA 59.216 38.462 0.00 0.00 32.58 2.24
501 544 6.317312 TCCTTGTTACTCCCTCTGTAAACTA 58.683 40.000 0.00 0.00 32.58 2.24
502 545 5.152934 TCCTTGTTACTCCCTCTGTAAACT 58.847 41.667 0.00 0.00 32.58 2.66
503 546 5.479124 TCCTTGTTACTCCCTCTGTAAAC 57.521 43.478 0.00 0.00 32.58 2.01
504 547 5.045869 CCATCCTTGTTACTCCCTCTGTAAA 60.046 44.000 0.00 0.00 32.58 2.01
505 548 4.469945 CCATCCTTGTTACTCCCTCTGTAA 59.530 45.833 0.00 0.00 0.00 2.41
506 549 4.030913 CCATCCTTGTTACTCCCTCTGTA 58.969 47.826 0.00 0.00 0.00 2.74
507 550 2.840651 CCATCCTTGTTACTCCCTCTGT 59.159 50.000 0.00 0.00 0.00 3.41
508 551 2.420687 GCCATCCTTGTTACTCCCTCTG 60.421 54.545 0.00 0.00 0.00 3.35
509 552 1.840635 GCCATCCTTGTTACTCCCTCT 59.159 52.381 0.00 0.00 0.00 3.69
510 553 1.134068 GGCCATCCTTGTTACTCCCTC 60.134 57.143 0.00 0.00 0.00 4.30
511 554 0.919710 GGCCATCCTTGTTACTCCCT 59.080 55.000 0.00 0.00 0.00 4.20
512 555 0.463833 CGGCCATCCTTGTTACTCCC 60.464 60.000 2.24 0.00 0.00 4.30
513 556 0.463833 CCGGCCATCCTTGTTACTCC 60.464 60.000 2.24 0.00 0.00 3.85
514 557 0.252197 ACCGGCCATCCTTGTTACTC 59.748 55.000 0.00 0.00 0.00 2.59
515 558 0.035439 CACCGGCCATCCTTGTTACT 60.035 55.000 0.00 0.00 0.00 2.24
516 559 0.035820 TCACCGGCCATCCTTGTTAC 60.036 55.000 0.00 0.00 0.00 2.50
517 560 0.251916 CTCACCGGCCATCCTTGTTA 59.748 55.000 0.00 0.00 0.00 2.41
518 561 1.002134 CTCACCGGCCATCCTTGTT 60.002 57.895 0.00 0.00 0.00 2.83
521 564 3.411517 CCCTCACCGGCCATCCTT 61.412 66.667 0.00 0.00 0.00 3.36
541 584 4.835891 CCCCTACTCGCCGGTCCT 62.836 72.222 1.90 0.00 0.00 3.85
548 591 4.208686 CTGGTCGCCCCTACTCGC 62.209 72.222 0.00 0.00 0.00 5.03
575 618 4.814294 ACGCGTTCTCCCCATCGC 62.814 66.667 5.58 0.00 44.23 4.58
617 660 2.190841 CACACGCGTTTCCCCCTTT 61.191 57.895 10.22 0.00 0.00 3.11
634 677 2.044451 AAAATCCCATCGGCGCCA 60.044 55.556 28.98 14.46 0.00 5.69
637 680 2.561569 ACTAAGAAAATCCCATCGGCG 58.438 47.619 0.00 0.00 0.00 6.46
640 683 3.181774 CGCGTACTAAGAAAATCCCATCG 59.818 47.826 0.00 0.00 0.00 3.84
642 685 3.869246 CACGCGTACTAAGAAAATCCCAT 59.131 43.478 13.44 0.00 0.00 4.00
655 698 0.665068 TTCGTCAATGCACGCGTACT 60.665 50.000 13.44 0.00 39.74 2.73
671 714 3.222323 GCGTCGTCGTCGTCTTCG 61.222 66.667 13.09 4.98 39.49 3.79
725 768 1.009389 GTATGGCGATGCTAGGCGTC 61.009 60.000 2.03 2.03 40.75 5.19
728 795 2.832931 CAGTATGGCGATGCTAGGC 58.167 57.895 0.00 0.00 0.00 3.93
741 808 7.620880 TGCTGATTAGTGTTTTACTCCAGTAT 58.379 34.615 0.00 0.00 40.89 2.12
743 810 5.865085 TGCTGATTAGTGTTTTACTCCAGT 58.135 37.500 0.00 0.00 40.89 4.00
745 812 8.892723 CATAATGCTGATTAGTGTTTTACTCCA 58.107 33.333 0.00 0.00 40.89 3.86
818 893 4.100498 GGACATCAAACGAGGAGGGTAATA 59.900 45.833 0.00 0.00 0.00 0.98
836 912 7.939588 AGTGTTAGCTTCTTTTTCTTAGGACAT 59.060 33.333 0.00 0.00 0.00 3.06
882 3464 1.210234 ACCTGATGGTTGATCGATGCA 59.790 47.619 0.54 0.00 46.05 3.96
895 3477 3.686241 ACGTGTTGATGATTCACCTGATG 59.314 43.478 0.00 0.00 0.00 3.07
923 3505 2.866510 CAAAGTGATGTGCGCGCG 60.867 61.111 28.44 28.44 0.00 6.86
1019 3610 0.173481 TCCTGTGCGTACTGATGAGC 59.827 55.000 11.95 0.00 0.00 4.26
1342 4418 1.135431 CGAGCACAGAGAGAACAGAGG 60.135 57.143 0.00 0.00 0.00 3.69
1655 4731 4.954118 AGACCACACCTGGCGGGA 62.954 66.667 21.81 0.00 42.08 5.14
1680 4756 3.680786 GGCCAAACCGCTGGTTCC 61.681 66.667 12.33 7.05 46.20 3.62
1720 4801 0.036010 ATGAACAGAGACTTGGCGGG 60.036 55.000 0.00 0.00 0.00 6.13
1721 4802 1.734465 GAATGAACAGAGACTTGGCGG 59.266 52.381 0.00 0.00 0.00 6.13
1722 4803 1.391485 CGAATGAACAGAGACTTGGCG 59.609 52.381 0.00 0.00 0.00 5.69
1723 4804 1.734465 CCGAATGAACAGAGACTTGGC 59.266 52.381 0.00 0.00 0.00 4.52
1724 4805 2.289694 ACCCGAATGAACAGAGACTTGG 60.290 50.000 0.00 0.00 0.00 3.61
1725 4806 2.738846 CACCCGAATGAACAGAGACTTG 59.261 50.000 0.00 0.00 0.00 3.16
1726 4807 2.289694 CCACCCGAATGAACAGAGACTT 60.290 50.000 0.00 0.00 0.00 3.01
1727 4808 1.276421 CCACCCGAATGAACAGAGACT 59.724 52.381 0.00 0.00 0.00 3.24
1728 4809 1.002087 ACCACCCGAATGAACAGAGAC 59.998 52.381 0.00 0.00 0.00 3.36
1729 4810 1.348064 ACCACCCGAATGAACAGAGA 58.652 50.000 0.00 0.00 0.00 3.10
1730 4811 3.543680 ATACCACCCGAATGAACAGAG 57.456 47.619 0.00 0.00 0.00 3.35
1731 4812 4.098960 GTCTATACCACCCGAATGAACAGA 59.901 45.833 0.00 0.00 0.00 3.41
1732 4813 4.369182 GTCTATACCACCCGAATGAACAG 58.631 47.826 0.00 0.00 0.00 3.16
1733 4814 3.181484 CGTCTATACCACCCGAATGAACA 60.181 47.826 0.00 0.00 0.00 3.18
1734 4815 3.067180 TCGTCTATACCACCCGAATGAAC 59.933 47.826 0.00 0.00 0.00 3.18
1735 4816 3.289836 TCGTCTATACCACCCGAATGAA 58.710 45.455 0.00 0.00 0.00 2.57
1736 4817 2.934887 TCGTCTATACCACCCGAATGA 58.065 47.619 0.00 0.00 0.00 2.57
1737 4818 3.720949 TTCGTCTATACCACCCGAATG 57.279 47.619 0.00 0.00 33.13 2.67
1738 4819 3.554337 GCATTCGTCTATACCACCCGAAT 60.554 47.826 0.00 0.00 45.88 3.34
1739 4820 2.223876 GCATTCGTCTATACCACCCGAA 60.224 50.000 0.00 0.00 41.16 4.30
1740 4821 1.338973 GCATTCGTCTATACCACCCGA 59.661 52.381 0.00 0.00 0.00 5.14
1741 4822 1.067974 TGCATTCGTCTATACCACCCG 59.932 52.381 0.00 0.00 0.00 5.28
1742 4823 2.364324 TCTGCATTCGTCTATACCACCC 59.636 50.000 0.00 0.00 0.00 4.61
1743 4824 3.728076 TCTGCATTCGTCTATACCACC 57.272 47.619 0.00 0.00 0.00 4.61
1744 4825 4.621991 ACATCTGCATTCGTCTATACCAC 58.378 43.478 0.00 0.00 0.00 4.16
1745 4826 4.937201 ACATCTGCATTCGTCTATACCA 57.063 40.909 0.00 0.00 0.00 3.25
1746 4827 6.015027 ACTACATCTGCATTCGTCTATACC 57.985 41.667 0.00 0.00 0.00 2.73
1747 4828 8.237949 ACATACTACATCTGCATTCGTCTATAC 58.762 37.037 0.00 0.00 0.00 1.47
1748 4829 8.336801 ACATACTACATCTGCATTCGTCTATA 57.663 34.615 0.00 0.00 0.00 1.31
1749 4830 7.220741 ACATACTACATCTGCATTCGTCTAT 57.779 36.000 0.00 0.00 0.00 1.98
1750 4831 6.635030 ACATACTACATCTGCATTCGTCTA 57.365 37.500 0.00 0.00 0.00 2.59
1751 4832 5.521906 ACATACTACATCTGCATTCGTCT 57.478 39.130 0.00 0.00 0.00 4.18
1752 4833 5.339875 CGTACATACTACATCTGCATTCGTC 59.660 44.000 0.00 0.00 0.00 4.20
1753 4834 5.212934 CGTACATACTACATCTGCATTCGT 58.787 41.667 0.00 0.00 0.00 3.85
1754 4835 4.617223 CCGTACATACTACATCTGCATTCG 59.383 45.833 0.00 0.00 0.00 3.34
1755 4836 5.529791 ACCGTACATACTACATCTGCATTC 58.470 41.667 0.00 0.00 0.00 2.67
1756 4837 5.531122 ACCGTACATACTACATCTGCATT 57.469 39.130 0.00 0.00 0.00 3.56
1757 4838 5.531122 AACCGTACATACTACATCTGCAT 57.469 39.130 0.00 0.00 0.00 3.96
1758 4839 4.994907 AACCGTACATACTACATCTGCA 57.005 40.909 0.00 0.00 0.00 4.41
1759 4840 5.589192 AGAAACCGTACATACTACATCTGC 58.411 41.667 0.00 0.00 0.00 4.26
1760 4841 5.907945 CGAGAAACCGTACATACTACATCTG 59.092 44.000 0.00 0.00 0.00 2.90
1761 4842 5.587844 ACGAGAAACCGTACATACTACATCT 59.412 40.000 0.00 0.00 41.44 2.90
1762 4843 5.814783 ACGAGAAACCGTACATACTACATC 58.185 41.667 0.00 0.00 41.44 3.06
1763 4844 5.220931 GGACGAGAAACCGTACATACTACAT 60.221 44.000 0.00 0.00 42.63 2.29
1764 4845 4.094887 GGACGAGAAACCGTACATACTACA 59.905 45.833 0.00 0.00 42.63 2.74
1765 4846 4.592179 GGACGAGAAACCGTACATACTAC 58.408 47.826 0.00 0.00 42.63 2.73
1766 4847 4.882671 GGACGAGAAACCGTACATACTA 57.117 45.455 0.00 0.00 42.63 1.82
1767 4848 3.772060 GGACGAGAAACCGTACATACT 57.228 47.619 0.00 0.00 42.63 2.12
1772 4853 2.428888 AACTGGACGAGAAACCGTAC 57.571 50.000 0.00 0.00 43.49 3.67
1773 4854 2.288395 GGAAACTGGACGAGAAACCGTA 60.288 50.000 0.00 0.00 43.49 4.02
1774 4855 1.539712 GGAAACTGGACGAGAAACCGT 60.540 52.381 0.00 0.00 46.43 4.83
1775 4856 1.145803 GGAAACTGGACGAGAAACCG 58.854 55.000 0.00 0.00 0.00 4.44
1776 4857 1.145803 CGGAAACTGGACGAGAAACC 58.854 55.000 0.00 0.00 0.00 3.27
1777 4858 1.145803 CCGGAAACTGGACGAGAAAC 58.854 55.000 0.00 0.00 0.00 2.78
1778 4859 0.034337 CCCGGAAACTGGACGAGAAA 59.966 55.000 0.73 0.00 36.72 2.52
1779 4860 1.117142 ACCCGGAAACTGGACGAGAA 61.117 55.000 0.73 0.00 38.25 2.87
1780 4861 0.251297 TACCCGGAAACTGGACGAGA 60.251 55.000 0.73 0.00 38.25 4.04
1781 4862 0.604578 TTACCCGGAAACTGGACGAG 59.395 55.000 0.73 0.00 38.25 4.18
1782 4863 0.318120 GTTACCCGGAAACTGGACGA 59.682 55.000 0.73 0.00 38.25 4.20
1783 4864 0.033781 TGTTACCCGGAAACTGGACG 59.966 55.000 17.23 0.00 38.25 4.79
1784 4865 2.484742 ATGTTACCCGGAAACTGGAC 57.515 50.000 17.23 2.30 38.25 4.02
1785 4866 3.512219 AAATGTTACCCGGAAACTGGA 57.488 42.857 17.23 2.13 38.25 3.86
1786 4867 3.859252 GCAAAATGTTACCCGGAAACTGG 60.859 47.826 17.23 0.00 41.18 4.00
1787 4868 3.313690 GCAAAATGTTACCCGGAAACTG 58.686 45.455 17.23 10.19 0.00 3.16
1788 4869 2.030628 CGCAAAATGTTACCCGGAAACT 60.031 45.455 17.23 4.33 0.00 2.66
1789 4870 2.321263 CGCAAAATGTTACCCGGAAAC 58.679 47.619 0.73 7.96 0.00 2.78
1790 4871 1.269998 CCGCAAAATGTTACCCGGAAA 59.730 47.619 0.73 0.00 38.04 3.13
1791 4872 0.882474 CCGCAAAATGTTACCCGGAA 59.118 50.000 0.73 0.00 38.04 4.30
1792 4873 0.961358 CCCGCAAAATGTTACCCGGA 60.961 55.000 0.73 0.00 38.04 5.14
1793 4874 1.245376 ACCCGCAAAATGTTACCCGG 61.245 55.000 0.00 0.00 35.74 5.73
1794 4875 0.599060 AACCCGCAAAATGTTACCCG 59.401 50.000 0.00 0.00 0.00 5.28
1795 4876 2.409012 CAAACCCGCAAAATGTTACCC 58.591 47.619 0.00 0.00 0.00 3.69
1796 4877 1.795872 GCAAACCCGCAAAATGTTACC 59.204 47.619 0.00 0.00 0.00 2.85
1797 4878 2.474735 CTGCAAACCCGCAAAATGTTAC 59.525 45.455 0.00 0.00 42.45 2.50
1798 4879 2.101582 ACTGCAAACCCGCAAAATGTTA 59.898 40.909 0.00 0.00 42.45 2.41
1799 4880 1.134551 ACTGCAAACCCGCAAAATGTT 60.135 42.857 0.00 0.00 42.45 2.71
1800 4881 0.463620 ACTGCAAACCCGCAAAATGT 59.536 45.000 0.00 0.00 42.45 2.71
1801 4882 0.860533 CACTGCAAACCCGCAAAATG 59.139 50.000 0.00 0.00 42.45 2.32
1802 4883 0.749649 TCACTGCAAACCCGCAAAAT 59.250 45.000 0.00 0.00 42.45 1.82
1803 4884 0.749649 ATCACTGCAAACCCGCAAAA 59.250 45.000 0.00 0.00 42.45 2.44
1804 4885 0.031857 CATCACTGCAAACCCGCAAA 59.968 50.000 0.00 0.00 42.45 3.68
1805 4886 1.106351 ACATCACTGCAAACCCGCAA 61.106 50.000 0.00 0.00 42.45 4.85
1806 4887 1.528076 ACATCACTGCAAACCCGCA 60.528 52.632 0.00 0.00 40.32 5.69
1807 4888 1.081242 CACATCACTGCAAACCCGC 60.081 57.895 0.00 0.00 0.00 6.13
1808 4889 1.196808 GTACACATCACTGCAAACCCG 59.803 52.381 0.00 0.00 0.00 5.28
1809 4890 2.504367 AGTACACATCACTGCAAACCC 58.496 47.619 0.00 0.00 0.00 4.11
1810 4891 4.062293 TGTAGTACACATCACTGCAAACC 58.938 43.478 0.00 0.00 35.97 3.27
1811 4892 5.862924 ATGTAGTACACATCACTGCAAAC 57.137 39.130 4.80 0.00 44.99 2.93
1847 4928 9.613428 TCTAACGATCATGACCAAAATTCTATT 57.387 29.630 0.00 0.00 0.00 1.73
1848 4929 9.265901 CTCTAACGATCATGACCAAAATTCTAT 57.734 33.333 0.00 0.00 0.00 1.98
1849 4930 7.224753 GCTCTAACGATCATGACCAAAATTCTA 59.775 37.037 0.00 0.00 0.00 2.10
1850 4931 6.037610 GCTCTAACGATCATGACCAAAATTCT 59.962 38.462 0.00 0.00 0.00 2.40
1851 4932 6.183360 TGCTCTAACGATCATGACCAAAATTC 60.183 38.462 0.00 0.00 0.00 2.17
1852 4933 5.647658 TGCTCTAACGATCATGACCAAAATT 59.352 36.000 0.00 0.00 0.00 1.82
1853 4934 5.185454 TGCTCTAACGATCATGACCAAAAT 58.815 37.500 0.00 0.00 0.00 1.82
1854 4935 4.574892 TGCTCTAACGATCATGACCAAAA 58.425 39.130 0.00 0.00 0.00 2.44
1855 4936 4.200838 TGCTCTAACGATCATGACCAAA 57.799 40.909 0.00 0.00 0.00 3.28
1856 4937 3.885724 TGCTCTAACGATCATGACCAA 57.114 42.857 0.00 0.00 0.00 3.67
1857 4938 3.638627 AGATGCTCTAACGATCATGACCA 59.361 43.478 0.00 0.00 0.00 4.02
1858 4939 4.233789 GAGATGCTCTAACGATCATGACC 58.766 47.826 0.00 0.00 0.00 4.02
1859 4940 4.233789 GGAGATGCTCTAACGATCATGAC 58.766 47.826 0.00 0.00 0.00 3.06
1860 4941 3.891366 TGGAGATGCTCTAACGATCATGA 59.109 43.478 0.00 0.00 0.00 3.07
1861 4942 4.248691 TGGAGATGCTCTAACGATCATG 57.751 45.455 0.00 0.00 0.00 3.07
1862 4943 4.626042 GTTGGAGATGCTCTAACGATCAT 58.374 43.478 7.71 0.00 40.83 2.45
1863 4944 4.046938 GTTGGAGATGCTCTAACGATCA 57.953 45.455 7.71 0.00 40.83 2.92
2433 5516 5.632118 AGCTAGGATCATTGCAAGATCATT 58.368 37.500 26.21 19.80 42.84 2.57
2435 5518 4.701651 AGCTAGGATCATTGCAAGATCA 57.298 40.909 26.21 14.53 42.84 2.92
2650 5733 1.243902 GAAAAACCGGTCATGGCTCA 58.756 50.000 8.04 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.