Multiple sequence alignment - TraesCS2D01G313100

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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 TraesCS2D01G313100 chr2D 100.000 3866 0 0 1 3866 402713075 402716940 0.000000e+00 7140.0
1 TraesCS2D01G313100 chr2B 95.461 2930 100 19 757 3664 476561309 476564227 0.000000e+00 4643.0
2 TraesCS2D01G313100 chr2B 85.366 492 39 14 1 477 476560698 476561171 2.700000e-131 479.0
3 TraesCS2D01G313100 chr2B 95.376 173 7 1 3655 3826 797534648 797534820 1.370000e-69 274.0
4 TraesCS2D01G313100 chr2B 93.578 109 5 2 468 576 458623247 458623141 1.110000e-35 161.0
5 TraesCS2D01G313100 chr2A 94.139 2218 73 21 777 2984 539970408 539972578 0.000000e+00 3323.0
6 TraesCS2D01G313100 chr2A 90.727 399 20 7 1 390 539967944 539968334 2.060000e-142 516.0
7 TraesCS2D01G313100 chr2A 93.023 86 6 0 571 656 539968391 539968476 4.050000e-25 126.0
8 TraesCS2D01G313100 chr1D 98.171 164 3 0 3661 3824 126223505 126223342 1.760000e-73 287.0
9 TraesCS2D01G313100 chr1D 98.171 164 3 0 3661 3824 160451658 160451495 1.760000e-73 287.0
10 TraesCS2D01G313100 chr3D 98.160 163 3 0 3662 3824 53385679 53385517 6.320000e-73 285.0
11 TraesCS2D01G313100 chr6A 96.951 164 5 0 3661 3824 33015648 33015811 3.800000e-70 276.0
12 TraesCS2D01G313100 chr5B 96.407 167 6 0 3658 3824 105528175 105528009 3.800000e-70 276.0
13 TraesCS2D01G313100 chr1B 95.349 172 7 1 3657 3828 387195506 387195676 4.920000e-69 272.0
14 TraesCS2D01G313100 chr1B 90.000 120 9 3 467 585 328139793 328139676 6.690000e-33 152.0
15 TraesCS2D01G313100 chr5D 94.350 177 9 1 3654 3829 498722078 498721902 1.770000e-68 270.0
16 TraesCS2D01G313100 chr5D 94.231 104 5 1 471 574 299412218 299412320 1.440000e-34 158.0
17 TraesCS2D01G313100 chr6D 93.333 180 11 1 3660 3839 90890446 90890268 8.240000e-67 265.0
18 TraesCS2D01G313100 chr7B 93.103 116 6 2 469 584 747370736 747370623 6.640000e-38 169.0
19 TraesCS2D01G313100 chr7D 96.939 98 2 1 477 574 80971195 80971099 3.090000e-36 163.0
20 TraesCS2D01G313100 chr3B 95.146 103 3 2 477 578 674424194 674424295 1.110000e-35 161.0
21 TraesCS2D01G313100 chr7A 95.000 100 4 1 475 574 628008476 628008574 5.170000e-34 156.0
22 TraesCS2D01G313100 chr4B 90.435 115 7 4 472 585 538218850 538218739 8.650000e-32 148.0
23 TraesCS2D01G313100 chr6B 85.315 143 13 8 466 605 179356669 179356806 1.450000e-29 141.0
24 TraesCS2D01G313100 chr6B 82.090 67 9 2 3800 3865 709022533 709022469 2.000000e-03 54.7


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 TraesCS2D01G313100 chr2D 402713075 402716940 3865 False 7140.000000 7140 100.000000 1 3866 1 chr2D.!!$F1 3865
1 TraesCS2D01G313100 chr2B 476560698 476564227 3529 False 2561.000000 4643 90.413500 1 3664 2 chr2B.!!$F2 3663
2 TraesCS2D01G313100 chr2A 539967944 539972578 4634 False 1321.666667 3323 92.629667 1 2984 3 chr2A.!!$F1 2983

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
413 432 0.175760 GACGCTTCCCAGCTGTATGA 59.824 55.0 13.81 3.25 44.85 2.15 F
1035 2913 0.465705 CCCACATACACGGCTCATCT 59.534 55.0 0.00 0.00 0.00 2.90 F
2232 4113 0.518636 CTTTGTGCAGTGGTGATCGG 59.481 55.0 0.00 0.00 0.00 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1653 3534 0.041047 TGTTGTAGGTGACGACGTCG 60.041 55.0 34.58 34.58 44.54 5.12 R
2244 4125 0.385751 TCTTCGGCATTAGCTCCTCG 59.614 55.0 0.00 0.00 41.70 4.63 R
3809 5706 0.108281 GCTTGTACTCCCTCCGTTCC 60.108 60.0 0.00 0.00 0.00 3.62 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
34 35 3.088532 TGTGCAAGTTCAAGAAACACCT 58.911 40.909 0.00 0.00 40.56 4.00
43 44 5.952347 AGTTCAAGAAACACCTTTTTCCTCT 59.048 36.000 0.00 0.00 40.56 3.69
53 54 1.394917 CTTTTTCCTCTGTCATCGCCG 59.605 52.381 0.00 0.00 0.00 6.46
97 102 7.533426 TCCTACAGTCGTCTTTATGTACTTTC 58.467 38.462 0.00 0.00 0.00 2.62
114 119 7.261325 TGTACTTTCTTCATCAGCTCTACATC 58.739 38.462 0.00 0.00 0.00 3.06
142 148 3.602104 CCATCTGGGCTTTGTGGAT 57.398 52.632 0.00 0.00 31.59 3.41
146 154 3.346631 CTGGGCTTTGTGGATGCGC 62.347 63.158 0.00 0.00 40.44 6.09
223 231 6.513230 CGTTTTGACATTCTTCTGGAATCACA 60.513 38.462 0.00 0.00 42.20 3.58
226 234 4.999311 TGACATTCTTCTGGAATCACACTG 59.001 41.667 0.00 0.00 42.20 3.66
302 318 3.157087 AGTTGCTCCATTTTCCGTTCAT 58.843 40.909 0.00 0.00 0.00 2.57
367 383 3.966665 TCTGATTTTCCACCTTTTGGCTT 59.033 39.130 0.00 0.00 46.47 4.35
404 423 2.355716 CCAAATCTAAGGACGCTTCCCA 60.356 50.000 5.45 0.00 44.10 4.37
406 425 0.466124 ATCTAAGGACGCTTCCCAGC 59.534 55.000 5.45 0.00 44.10 4.85
413 432 0.175760 GACGCTTCCCAGCTGTATGA 59.824 55.000 13.81 3.25 44.85 2.15
442 461 5.512232 GCAGGAGAAAATATCCGGAGAGAAT 60.512 44.000 11.34 0.00 42.02 2.40
454 473 3.628942 CCGGAGAGAATCATGCAATTTCA 59.371 43.478 0.00 0.00 37.82 2.69
455 474 4.277672 CCGGAGAGAATCATGCAATTTCAT 59.722 41.667 0.00 0.00 37.82 2.57
489 508 9.896263 CTAAATAATTTAGTACTCTCTCCGTCC 57.104 37.037 0.00 0.00 38.21 4.79
490 509 6.897706 ATAATTTAGTACTCTCTCCGTCCC 57.102 41.667 0.00 0.00 0.00 4.46
493 512 2.599408 AGTACTCTCTCCGTCCCAAA 57.401 50.000 0.00 0.00 0.00 3.28
494 513 2.885616 AGTACTCTCTCCGTCCCAAAA 58.114 47.619 0.00 0.00 0.00 2.44
495 514 3.442076 AGTACTCTCTCCGTCCCAAAAT 58.558 45.455 0.00 0.00 0.00 1.82
497 516 5.021458 AGTACTCTCTCCGTCCCAAAATAA 58.979 41.667 0.00 0.00 0.00 1.40
498 517 4.903045 ACTCTCTCCGTCCCAAAATAAA 57.097 40.909 0.00 0.00 0.00 1.40
499 518 5.437191 ACTCTCTCCGTCCCAAAATAAAT 57.563 39.130 0.00 0.00 0.00 1.40
501 520 5.174037 TCTCTCCGTCCCAAAATAAATGT 57.826 39.130 0.00 0.00 0.00 2.71
502 521 5.183228 TCTCTCCGTCCCAAAATAAATGTC 58.817 41.667 0.00 0.00 0.00 3.06
503 522 5.045869 TCTCTCCGTCCCAAAATAAATGTCT 60.046 40.000 0.00 0.00 0.00 3.41
504 523 5.183228 TCTCCGTCCCAAAATAAATGTCTC 58.817 41.667 0.00 0.00 0.00 3.36
505 524 4.912586 TCCGTCCCAAAATAAATGTCTCA 58.087 39.130 0.00 0.00 0.00 3.27
506 525 5.317808 TCCGTCCCAAAATAAATGTCTCAA 58.682 37.500 0.00 0.00 0.00 3.02
507 526 5.414454 TCCGTCCCAAAATAAATGTCTCAAG 59.586 40.000 0.00 0.00 0.00 3.02
508 527 5.095490 CGTCCCAAAATAAATGTCTCAAGC 58.905 41.667 0.00 0.00 0.00 4.01
509 528 5.106157 CGTCCCAAAATAAATGTCTCAAGCT 60.106 40.000 0.00 0.00 0.00 3.74
510 529 6.570378 CGTCCCAAAATAAATGTCTCAAGCTT 60.570 38.462 0.00 0.00 0.00 3.74
511 530 7.361713 CGTCCCAAAATAAATGTCTCAAGCTTA 60.362 37.037 0.00 0.00 0.00 3.09
512 531 7.970614 GTCCCAAAATAAATGTCTCAAGCTTAG 59.029 37.037 0.00 0.00 0.00 2.18
513 532 7.669722 TCCCAAAATAAATGTCTCAAGCTTAGT 59.330 33.333 0.00 0.00 0.00 2.24
514 533 8.956426 CCCAAAATAAATGTCTCAAGCTTAGTA 58.044 33.333 0.00 0.00 0.00 1.82
515 534 9.774742 CCAAAATAAATGTCTCAAGCTTAGTAC 57.225 33.333 0.00 0.00 0.00 2.73
519 538 9.726438 AATAAATGTCTCAAGCTTAGTACAACT 57.274 29.630 0.00 0.00 0.00 3.16
520 539 9.726438 ATAAATGTCTCAAGCTTAGTACAACTT 57.274 29.630 0.00 4.81 0.00 2.66
521 540 8.451908 AAATGTCTCAAGCTTAGTACAACTTT 57.548 30.769 0.00 0.08 0.00 2.66
522 541 6.844696 TGTCTCAAGCTTAGTACAACTTTG 57.155 37.500 0.00 0.00 0.00 2.77
523 542 6.346096 TGTCTCAAGCTTAGTACAACTTTGT 58.654 36.000 0.00 0.00 44.86 2.83
524 543 7.494211 TGTCTCAAGCTTAGTACAACTTTGTA 58.506 34.615 0.00 0.00 42.35 2.41
539 558 8.174733 ACAACTTTGTACTAGAGCTAAGTACA 57.825 34.615 26.36 26.36 44.25 2.90
546 565 8.400184 TGTACTAGAGCTAAGTACAAAGTTGA 57.600 34.615 27.28 11.49 43.37 3.18
547 566 8.512956 TGTACTAGAGCTAAGTACAAAGTTGAG 58.487 37.037 27.28 0.00 43.37 3.02
548 567 7.762588 ACTAGAGCTAAGTACAAAGTTGAGA 57.237 36.000 0.00 0.00 0.00 3.27
549 568 7.595604 ACTAGAGCTAAGTACAAAGTTGAGAC 58.404 38.462 0.00 0.00 0.00 3.36
550 569 6.406692 AGAGCTAAGTACAAAGTTGAGACA 57.593 37.500 0.00 0.00 0.00 3.41
551 570 6.217294 AGAGCTAAGTACAAAGTTGAGACAC 58.783 40.000 0.00 0.00 0.00 3.67
552 571 6.041069 AGAGCTAAGTACAAAGTTGAGACACT 59.959 38.462 0.00 0.00 0.00 3.55
553 572 6.583562 AGCTAAGTACAAAGTTGAGACACTT 58.416 36.000 0.00 4.72 38.74 3.16
554 573 7.723324 AGCTAAGTACAAAGTTGAGACACTTA 58.277 34.615 0.00 5.48 35.87 2.24
555 574 8.368668 AGCTAAGTACAAAGTTGAGACACTTAT 58.631 33.333 0.00 0.00 35.87 1.73
556 575 8.989980 GCTAAGTACAAAGTTGAGACACTTATT 58.010 33.333 0.00 0.00 35.87 1.40
560 579 8.621286 AGTACAAAGTTGAGACACTTATTTTGG 58.379 33.333 0.00 0.00 35.87 3.28
561 580 6.805713 ACAAAGTTGAGACACTTATTTTGGG 58.194 36.000 0.00 0.00 35.87 4.12
562 581 6.605594 ACAAAGTTGAGACACTTATTTTGGGA 59.394 34.615 0.00 0.00 35.87 4.37
563 582 7.287696 ACAAAGTTGAGACACTTATTTTGGGAT 59.712 33.333 0.00 0.00 35.87 3.85
564 583 6.824305 AGTTGAGACACTTATTTTGGGATG 57.176 37.500 0.00 0.00 0.00 3.51
565 584 5.711976 AGTTGAGACACTTATTTTGGGATGG 59.288 40.000 0.00 0.00 0.00 3.51
566 585 5.512942 TGAGACACTTATTTTGGGATGGA 57.487 39.130 0.00 0.00 0.00 3.41
567 586 5.500234 TGAGACACTTATTTTGGGATGGAG 58.500 41.667 0.00 0.00 0.00 3.86
568 587 4.860022 AGACACTTATTTTGGGATGGAGG 58.140 43.478 0.00 0.00 0.00 4.30
569 588 3.954258 GACACTTATTTTGGGATGGAGGG 59.046 47.826 0.00 0.00 0.00 4.30
570 589 3.596046 ACACTTATTTTGGGATGGAGGGA 59.404 43.478 0.00 0.00 0.00 4.20
571 590 4.210331 CACTTATTTTGGGATGGAGGGAG 58.790 47.826 0.00 0.00 0.00 4.30
572 591 3.858638 ACTTATTTTGGGATGGAGGGAGT 59.141 43.478 0.00 0.00 0.00 3.85
577 596 4.569676 TTTGGGATGGAGGGAGTAGATA 57.430 45.455 0.00 0.00 0.00 1.98
642 661 5.997732 AGCGAAAATGAAAACAATCATCG 57.002 34.783 0.00 0.00 39.08 3.84
663 682 8.458052 TCATCGTTATACATTGCTGAATTTGTT 58.542 29.630 0.00 0.00 0.00 2.83
664 683 9.075519 CATCGTTATACATTGCTGAATTTGTTT 57.924 29.630 0.00 0.00 0.00 2.83
665 684 9.638239 ATCGTTATACATTGCTGAATTTGTTTT 57.362 25.926 0.00 0.00 0.00 2.43
666 685 9.123709 TCGTTATACATTGCTGAATTTGTTTTC 57.876 29.630 0.00 0.00 0.00 2.29
667 686 9.128107 CGTTATACATTGCTGAATTTGTTTTCT 57.872 29.630 0.00 0.00 0.00 2.52
669 688 5.662211 ACATTGCTGAATTTGTTTTCTGC 57.338 34.783 8.54 8.54 45.46 4.26
687 706 6.599356 TTCTGCATACCTTGAACTAGTACA 57.401 37.500 0.00 0.00 0.00 2.90
793 2660 3.672808 AGAAGAGAACATCACCTGCTTG 58.327 45.455 0.00 0.00 0.00 4.01
794 2661 1.818642 AGAGAACATCACCTGCTTGC 58.181 50.000 0.00 0.00 0.00 4.01
859 2727 4.780815 TGAGTTTTCACTGTGATCTGGTT 58.219 39.130 11.86 0.00 31.22 3.67
862 2730 6.152661 TGAGTTTTCACTGTGATCTGGTTTTT 59.847 34.615 11.86 0.00 31.22 1.94
866 2734 4.973168 TCACTGTGATCTGGTTTTTAGCT 58.027 39.130 6.36 0.00 0.00 3.32
928 2796 3.563808 TGCGTACTTGCAGAAATTTCAGT 59.436 39.130 19.99 15.56 40.62 3.41
929 2797 4.752604 TGCGTACTTGCAGAAATTTCAGTA 59.247 37.500 19.99 14.64 40.62 2.74
931 2799 6.072728 TGCGTACTTGCAGAAATTTCAGTAAT 60.073 34.615 19.99 10.04 40.62 1.89
935 2803 9.463443 GTACTTGCAGAAATTTCAGTAATTTGT 57.537 29.630 19.99 13.30 44.46 2.83
1035 2913 0.465705 CCCACATACACGGCTCATCT 59.534 55.000 0.00 0.00 0.00 2.90
1647 3528 1.306654 TATGCTCTCCCGGGGTTGT 60.307 57.895 23.50 4.92 0.00 3.32
2126 4007 1.228675 CCCTTTGTGAGCAAGGCCT 60.229 57.895 0.00 0.00 35.82 5.19
2232 4113 0.518636 CTTTGTGCAGTGGTGATCGG 59.481 55.000 0.00 0.00 0.00 4.18
2455 4336 0.040058 TGGCAACATGGAGCAATCCT 59.960 50.000 12.74 0.00 46.17 3.24
2704 4585 1.281577 TGTCTGATGGTTGCATGCCTA 59.718 47.619 16.68 0.00 0.00 3.93
2806 4687 4.769488 AGTTGAGCTCTAGAGATGTTGTCA 59.231 41.667 24.24 8.07 0.00 3.58
3034 4921 8.322906 TCCATCTTAAGATTGTTGTGTAACAG 57.677 34.615 15.49 0.00 46.63 3.16
3068 4955 2.633967 TCTTGCAATTTTGGCTGGTCAT 59.366 40.909 0.00 0.00 0.00 3.06
3069 4956 3.831333 TCTTGCAATTTTGGCTGGTCATA 59.169 39.130 0.00 0.00 0.00 2.15
3070 4957 4.282957 TCTTGCAATTTTGGCTGGTCATAA 59.717 37.500 0.00 0.00 0.00 1.90
3071 4958 4.822685 TGCAATTTTGGCTGGTCATAAT 57.177 36.364 0.00 0.00 0.00 1.28
3072 4959 4.757594 TGCAATTTTGGCTGGTCATAATC 58.242 39.130 0.00 0.00 0.00 1.75
3073 4960 3.798337 GCAATTTTGGCTGGTCATAATCG 59.202 43.478 0.00 0.00 0.00 3.34
3183 5070 5.818136 TTTGACCTTGAGTCTGAAACTTG 57.182 39.130 0.00 0.00 46.46 3.16
3283 5170 2.772515 CTGGGACTAAAACTAGGGAGGG 59.227 54.545 0.00 0.00 0.00 4.30
3321 5208 7.686438 ATGTTGTATGTCTGCTGATGTTTTA 57.314 32.000 0.00 0.00 0.00 1.52
3323 5210 7.529158 TGTTGTATGTCTGCTGATGTTTTATG 58.471 34.615 0.00 0.00 0.00 1.90
3407 5300 3.193691 GTGCCTAGACAAACTGCTAGAGA 59.806 47.826 0.00 0.00 36.97 3.10
3450 5347 2.992124 TCGTGTTCAACCTTCTCCAA 57.008 45.000 0.00 0.00 0.00 3.53
3520 5417 7.581011 TTCTCTTTTCTCTTTGCACAAAAAC 57.419 32.000 0.00 0.00 0.00 2.43
3521 5418 6.924111 TCTCTTTTCTCTTTGCACAAAAACT 58.076 32.000 0.00 0.00 0.00 2.66
3522 5419 6.808212 TCTCTTTTCTCTTTGCACAAAAACTG 59.192 34.615 0.00 0.00 0.00 3.16
3524 5421 3.865011 TCTCTTTGCACAAAAACTGCA 57.135 38.095 0.00 0.00 42.95 4.41
3525 5422 4.389890 TCTCTTTGCACAAAAACTGCAT 57.610 36.364 0.00 0.00 44.04 3.96
3572 5469 2.505407 TCATGTAGGCACCATACAAGCT 59.495 45.455 0.00 0.00 36.75 3.74
3664 5561 8.596781 ACAGAACAGAGGACTTTACATATACT 57.403 34.615 0.00 0.00 0.00 2.12
3665 5562 8.688151 ACAGAACAGAGGACTTTACATATACTC 58.312 37.037 0.00 0.00 0.00 2.59
3666 5563 8.138712 CAGAACAGAGGACTTTACATATACTCC 58.861 40.741 0.00 0.00 0.00 3.85
3667 5564 6.980416 ACAGAGGACTTTACATATACTCCC 57.020 41.667 0.00 0.00 0.00 4.30
3668 5565 6.684538 ACAGAGGACTTTACATATACTCCCT 58.315 40.000 0.00 0.00 0.00 4.20
3669 5566 6.778559 ACAGAGGACTTTACATATACTCCCTC 59.221 42.308 0.00 0.00 38.27 4.30
3670 5567 6.209788 CAGAGGACTTTACATATACTCCCTCC 59.790 46.154 0.00 0.00 38.65 4.30
3671 5568 5.078256 AGGACTTTACATATACTCCCTCCG 58.922 45.833 0.00 0.00 0.00 4.63
3672 5569 4.831710 GGACTTTACATATACTCCCTCCGT 59.168 45.833 0.00 0.00 0.00 4.69
3673 5570 5.303845 GGACTTTACATATACTCCCTCCGTT 59.696 44.000 0.00 0.00 0.00 4.44
3674 5571 6.402456 ACTTTACATATACTCCCTCCGTTC 57.598 41.667 0.00 0.00 0.00 3.95
3675 5572 5.303845 ACTTTACATATACTCCCTCCGTTCC 59.696 44.000 0.00 0.00 0.00 3.62
3676 5573 3.614568 ACATATACTCCCTCCGTTCCT 57.385 47.619 0.00 0.00 0.00 3.36
3677 5574 4.736611 ACATATACTCCCTCCGTTCCTA 57.263 45.455 0.00 0.00 0.00 2.94
3678 5575 5.070823 ACATATACTCCCTCCGTTCCTAA 57.929 43.478 0.00 0.00 0.00 2.69
3679 5576 5.461327 ACATATACTCCCTCCGTTCCTAAA 58.539 41.667 0.00 0.00 0.00 1.85
3680 5577 6.082707 ACATATACTCCCTCCGTTCCTAAAT 58.917 40.000 0.00 0.00 0.00 1.40
3681 5578 7.243824 ACATATACTCCCTCCGTTCCTAAATA 58.756 38.462 0.00 0.00 0.00 1.40
3682 5579 7.899709 ACATATACTCCCTCCGTTCCTAAATAT 59.100 37.037 0.00 0.00 0.00 1.28
3683 5580 9.417561 CATATACTCCCTCCGTTCCTAAATATA 57.582 37.037 0.00 0.00 0.00 0.86
3685 5582 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
3686 5583 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
3687 5584 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
3688 5585 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
3689 5586 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
3690 5587 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
3691 5588 8.645110 CCCTCCGTTCCTAAATATAAGTCTTTA 58.355 37.037 0.00 0.00 0.00 1.85
3711 5608 9.699703 GTCTTTATAGAGATTCCACTATGAACC 57.300 37.037 0.00 0.00 32.57 3.62
3712 5609 9.434275 TCTTTATAGAGATTCCACTATGAACCA 57.566 33.333 9.70 0.00 32.57 3.67
3713 5610 9.482627 CTTTATAGAGATTCCACTATGAACCAC 57.517 37.037 9.70 0.00 32.57 4.16
3714 5611 8.547481 TTATAGAGATTCCACTATGAACCACA 57.453 34.615 9.70 0.00 32.57 4.17
3715 5612 5.965033 AGAGATTCCACTATGAACCACAT 57.035 39.130 0.00 0.00 42.39 3.21
3716 5613 8.727100 ATAGAGATTCCACTATGAACCACATA 57.273 34.615 0.00 0.00 40.07 2.29
3717 5614 6.821388 AGAGATTCCACTATGAACCACATAC 58.179 40.000 0.00 0.00 40.07 2.39
3718 5615 5.601662 AGATTCCACTATGAACCACATACG 58.398 41.667 0.00 0.00 40.07 3.06
3719 5616 5.362717 AGATTCCACTATGAACCACATACGA 59.637 40.000 0.00 0.00 40.07 3.43
3720 5617 5.408880 TTCCACTATGAACCACATACGAA 57.591 39.130 0.00 0.00 40.07 3.85
3721 5618 5.607939 TCCACTATGAACCACATACGAAT 57.392 39.130 0.00 0.00 40.07 3.34
3722 5619 5.356426 TCCACTATGAACCACATACGAATG 58.644 41.667 0.00 0.00 40.07 2.67
3724 5621 6.097129 TCCACTATGAACCACATACGAATGTA 59.903 38.462 0.00 0.00 44.70 2.29
3725 5622 6.929049 CCACTATGAACCACATACGAATGTAT 59.071 38.462 0.00 0.00 44.70 2.29
3726 5623 8.085909 CCACTATGAACCACATACGAATGTATA 58.914 37.037 0.00 0.00 44.70 1.47
3727 5624 9.639601 CACTATGAACCACATACGAATGTATAT 57.360 33.333 0.00 0.00 44.70 0.86
3732 5629 9.855021 TGAACCACATACGAATGTATATAGATG 57.145 33.333 0.00 0.00 44.70 2.90
3733 5630 8.703604 AACCACATACGAATGTATATAGATGC 57.296 34.615 0.00 0.00 44.70 3.91
3734 5631 7.836842 ACCACATACGAATGTATATAGATGCA 58.163 34.615 0.00 0.00 44.70 3.96
3735 5632 8.478066 ACCACATACGAATGTATATAGATGCAT 58.522 33.333 0.00 0.00 44.70 3.96
3754 5651 8.844244 AGATGCATTTTAAGTGTAGATTCATCC 58.156 33.333 0.00 0.00 0.00 3.51
3755 5652 7.936496 TGCATTTTAAGTGTAGATTCATCCA 57.064 32.000 0.00 0.00 0.00 3.41
3756 5653 8.523915 TGCATTTTAAGTGTAGATTCATCCAT 57.476 30.769 0.00 0.00 0.00 3.41
3757 5654 8.970020 TGCATTTTAAGTGTAGATTCATCCATT 58.030 29.630 0.00 0.00 0.00 3.16
3758 5655 9.807649 GCATTTTAAGTGTAGATTCATCCATTT 57.192 29.630 0.00 0.00 0.00 2.32
3761 5658 9.638239 TTTTAAGTGTAGATTCATCCATTTTGC 57.362 29.630 0.00 0.00 0.00 3.68
3762 5659 8.579850 TTAAGTGTAGATTCATCCATTTTGCT 57.420 30.769 0.00 0.00 0.00 3.91
3763 5660 6.690194 AGTGTAGATTCATCCATTTTGCTC 57.310 37.500 0.00 0.00 0.00 4.26
3764 5661 6.421485 AGTGTAGATTCATCCATTTTGCTCT 58.579 36.000 0.00 0.00 0.00 4.09
3765 5662 6.318144 AGTGTAGATTCATCCATTTTGCTCTG 59.682 38.462 0.00 0.00 0.00 3.35
3766 5663 6.094603 GTGTAGATTCATCCATTTTGCTCTGT 59.905 38.462 0.00 0.00 0.00 3.41
3767 5664 7.280876 GTGTAGATTCATCCATTTTGCTCTGTA 59.719 37.037 0.00 0.00 0.00 2.74
3768 5665 7.994911 TGTAGATTCATCCATTTTGCTCTGTAT 59.005 33.333 0.00 0.00 0.00 2.29
3769 5666 7.273320 AGATTCATCCATTTTGCTCTGTATG 57.727 36.000 0.00 0.00 0.00 2.39
3770 5667 6.832384 AGATTCATCCATTTTGCTCTGTATGT 59.168 34.615 0.00 0.00 0.00 2.29
3771 5668 7.994911 AGATTCATCCATTTTGCTCTGTATGTA 59.005 33.333 0.00 0.00 0.00 2.29
3772 5669 7.558161 TTCATCCATTTTGCTCTGTATGTAG 57.442 36.000 0.00 0.00 0.00 2.74
3773 5670 6.653020 TCATCCATTTTGCTCTGTATGTAGT 58.347 36.000 0.00 0.00 0.00 2.73
3774 5671 6.763135 TCATCCATTTTGCTCTGTATGTAGTC 59.237 38.462 0.00 0.00 0.00 2.59
3775 5672 5.428253 TCCATTTTGCTCTGTATGTAGTCC 58.572 41.667 0.00 0.00 0.00 3.85
3776 5673 5.045942 TCCATTTTGCTCTGTATGTAGTCCA 60.046 40.000 0.00 0.00 0.00 4.02
3777 5674 5.065218 CCATTTTGCTCTGTATGTAGTCCAC 59.935 44.000 0.00 0.00 0.00 4.02
3778 5675 3.887621 TTGCTCTGTATGTAGTCCACC 57.112 47.619 0.00 0.00 0.00 4.61
3779 5676 3.101643 TGCTCTGTATGTAGTCCACCT 57.898 47.619 0.00 0.00 0.00 4.00
3780 5677 4.245251 TGCTCTGTATGTAGTCCACCTA 57.755 45.455 0.00 0.00 0.00 3.08
3781 5678 4.207955 TGCTCTGTATGTAGTCCACCTAG 58.792 47.826 0.00 0.00 0.00 3.02
3782 5679 4.208746 GCTCTGTATGTAGTCCACCTAGT 58.791 47.826 0.00 0.00 0.00 2.57
3783 5680 5.104235 TGCTCTGTATGTAGTCCACCTAGTA 60.104 44.000 0.00 0.00 0.00 1.82
3784 5681 5.470777 GCTCTGTATGTAGTCCACCTAGTAG 59.529 48.000 0.00 0.00 0.00 2.57
3785 5682 6.688411 GCTCTGTATGTAGTCCACCTAGTAGA 60.688 46.154 0.00 0.00 0.00 2.59
3786 5683 7.204243 TCTGTATGTAGTCCACCTAGTAGAA 57.796 40.000 0.00 0.00 0.00 2.10
3787 5684 7.813331 TCTGTATGTAGTCCACCTAGTAGAAT 58.187 38.462 0.00 0.00 0.00 2.40
3788 5685 7.937942 TCTGTATGTAGTCCACCTAGTAGAATC 59.062 40.741 0.00 0.00 0.00 2.52
3789 5686 7.813331 TGTATGTAGTCCACCTAGTAGAATCT 58.187 38.462 0.00 0.00 0.00 2.40
3790 5687 7.937942 TGTATGTAGTCCACCTAGTAGAATCTC 59.062 40.741 0.00 0.00 0.00 2.75
3791 5688 6.578313 TGTAGTCCACCTAGTAGAATCTCT 57.422 41.667 0.00 0.00 0.00 3.10
3792 5689 7.687383 TGTAGTCCACCTAGTAGAATCTCTA 57.313 40.000 0.00 0.00 0.00 2.43
3817 5714 8.943909 ACAAAGACTTATATTTAGGAACGGAG 57.056 34.615 0.00 0.00 0.00 4.63
3818 5715 7.985752 ACAAAGACTTATATTTAGGAACGGAGG 59.014 37.037 0.00 0.00 0.00 4.30
3819 5716 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
3820 5717 6.379579 AGACTTATATTTAGGAACGGAGGGA 58.620 40.000 0.00 0.00 0.00 4.20
3821 5718 6.494146 AGACTTATATTTAGGAACGGAGGGAG 59.506 42.308 0.00 0.00 0.00 4.30
3822 5719 6.141790 ACTTATATTTAGGAACGGAGGGAGT 58.858 40.000 0.00 0.00 0.00 3.85
3823 5720 7.300658 ACTTATATTTAGGAACGGAGGGAGTA 58.699 38.462 0.00 0.00 0.00 2.59
3824 5721 7.232330 ACTTATATTTAGGAACGGAGGGAGTAC 59.768 40.741 0.00 0.00 0.00 2.73
3825 5722 2.905415 TTAGGAACGGAGGGAGTACA 57.095 50.000 0.00 0.00 0.00 2.90
3826 5723 2.905415 TAGGAACGGAGGGAGTACAA 57.095 50.000 0.00 0.00 0.00 2.41
3827 5724 1.558233 AGGAACGGAGGGAGTACAAG 58.442 55.000 0.00 0.00 0.00 3.16
3828 5725 0.108281 GGAACGGAGGGAGTACAAGC 60.108 60.000 0.00 0.00 0.00 4.01
3829 5726 0.896226 GAACGGAGGGAGTACAAGCT 59.104 55.000 0.00 0.00 0.00 3.74
3830 5727 1.275573 GAACGGAGGGAGTACAAGCTT 59.724 52.381 0.00 0.00 0.00 3.74
3831 5728 2.226962 ACGGAGGGAGTACAAGCTTA 57.773 50.000 0.00 0.00 0.00 3.09
3832 5729 2.532843 ACGGAGGGAGTACAAGCTTAA 58.467 47.619 0.00 0.00 0.00 1.85
3833 5730 3.105283 ACGGAGGGAGTACAAGCTTAAT 58.895 45.455 0.00 0.00 0.00 1.40
3834 5731 3.118738 ACGGAGGGAGTACAAGCTTAATG 60.119 47.826 0.00 0.00 0.00 1.90
3835 5732 3.206964 GGAGGGAGTACAAGCTTAATGC 58.793 50.000 0.00 0.00 43.29 3.56
3836 5733 3.370527 GGAGGGAGTACAAGCTTAATGCA 60.371 47.826 0.00 0.00 45.94 3.96
3837 5734 4.455606 GAGGGAGTACAAGCTTAATGCAT 58.544 43.478 0.00 0.00 45.94 3.96
3838 5735 4.202441 AGGGAGTACAAGCTTAATGCATG 58.798 43.478 0.00 0.00 44.94 4.06
3839 5736 4.080356 AGGGAGTACAAGCTTAATGCATGA 60.080 41.667 0.00 0.00 42.37 3.07
3840 5737 4.640201 GGGAGTACAAGCTTAATGCATGAA 59.360 41.667 0.00 0.00 42.37 2.57
3841 5738 5.300286 GGGAGTACAAGCTTAATGCATGAAT 59.700 40.000 0.00 0.00 42.37 2.57
3842 5739 6.183360 GGGAGTACAAGCTTAATGCATGAATT 60.183 38.462 3.88 3.88 42.37 2.17
3843 5740 7.013274 GGGAGTACAAGCTTAATGCATGAATTA 59.987 37.037 0.00 1.62 42.37 1.40
3844 5741 8.571336 GGAGTACAAGCTTAATGCATGAATTAT 58.429 33.333 6.97 0.00 42.37 1.28
3849 5746 8.571336 ACAAGCTTAATGCATGAATTATACTCC 58.429 33.333 6.97 0.00 42.37 3.85
3850 5747 7.693969 AGCTTAATGCATGAATTATACTCCC 57.306 36.000 6.97 0.00 45.94 4.30
3851 5748 7.465116 AGCTTAATGCATGAATTATACTCCCT 58.535 34.615 6.97 0.00 45.94 4.20
3852 5749 7.609532 AGCTTAATGCATGAATTATACTCCCTC 59.390 37.037 6.97 0.00 45.94 4.30
3853 5750 7.148171 GCTTAATGCATGAATTATACTCCCTCC 60.148 40.741 6.97 0.00 42.31 4.30
3854 5751 4.271696 TGCATGAATTATACTCCCTCCG 57.728 45.455 0.00 0.00 0.00 4.63
3855 5752 3.646162 TGCATGAATTATACTCCCTCCGT 59.354 43.478 0.00 0.00 0.00 4.69
3856 5753 4.102524 TGCATGAATTATACTCCCTCCGTT 59.897 41.667 0.00 0.00 0.00 4.44
3857 5754 4.691216 GCATGAATTATACTCCCTCCGTTC 59.309 45.833 0.00 0.00 0.00 3.95
3858 5755 5.511545 GCATGAATTATACTCCCTCCGTTCT 60.512 44.000 0.00 0.00 0.00 3.01
3859 5756 5.531122 TGAATTATACTCCCTCCGTTCTG 57.469 43.478 0.00 0.00 0.00 3.02
3860 5757 5.205821 TGAATTATACTCCCTCCGTTCTGA 58.794 41.667 0.00 0.00 0.00 3.27
3861 5758 5.659525 TGAATTATACTCCCTCCGTTCTGAA 59.340 40.000 0.00 0.00 0.00 3.02
3862 5759 6.326583 TGAATTATACTCCCTCCGTTCTGAAT 59.673 38.462 0.00 0.00 0.00 2.57
3863 5760 6.749036 ATTATACTCCCTCCGTTCTGAATT 57.251 37.500 0.00 0.00 0.00 2.17
3864 5761 7.850935 ATTATACTCCCTCCGTTCTGAATTA 57.149 36.000 0.00 0.00 0.00 1.40
3865 5762 3.889520 ACTCCCTCCGTTCTGAATTAC 57.110 47.619 0.00 0.00 0.00 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 1.270625 ACGGCGATGACAGAGGAAAAA 60.271 47.619 16.62 0.00 0.00 1.94
43 44 0.179137 CTGAAGCTACGGCGATGACA 60.179 55.000 16.62 5.04 44.37 3.58
53 54 4.319177 AGGATGTTGTTGACTGAAGCTAC 58.681 43.478 0.00 0.00 0.00 3.58
97 102 5.904941 AGTTGAGATGTAGAGCTGATGAAG 58.095 41.667 0.00 0.00 0.00 3.02
137 143 1.806758 GCCAATGTTGCGCATCCAC 60.807 57.895 12.75 7.47 36.67 4.02
140 146 1.517694 CAGGCCAATGTTGCGCATC 60.518 57.895 12.75 12.06 36.67 3.91
141 147 2.574929 CAGGCCAATGTTGCGCAT 59.425 55.556 12.75 0.00 40.03 4.73
142 148 3.682885 CCAGGCCAATGTTGCGCA 61.683 61.111 5.66 5.66 0.00 6.09
146 154 2.975536 CAGCCCAGGCCAATGTTG 59.024 61.111 5.01 0.00 43.17 3.33
223 231 6.013379 TCCATTCCTTCATAACAAGTCTCAGT 60.013 38.462 0.00 0.00 0.00 3.41
226 234 5.819901 CCTCCATTCCTTCATAACAAGTCTC 59.180 44.000 0.00 0.00 0.00 3.36
302 318 4.299586 TCCAACCAAGATACAGAATGCA 57.700 40.909 0.00 0.00 42.53 3.96
367 383 0.759959 TTGGGGCAACAGTCGACTTA 59.240 50.000 17.26 0.00 39.74 2.24
404 423 0.250234 TCCTGCGCTTTCATACAGCT 59.750 50.000 9.73 0.00 34.88 4.24
406 425 2.299993 TCTCCTGCGCTTTCATACAG 57.700 50.000 9.73 0.00 0.00 2.74
413 432 2.614057 CGGATATTTTCTCCTGCGCTTT 59.386 45.455 9.73 0.00 0.00 3.51
477 496 4.903045 TTTATTTTGGGACGGAGAGAGT 57.097 40.909 0.00 0.00 0.00 3.24
478 497 5.186198 ACATTTATTTTGGGACGGAGAGAG 58.814 41.667 0.00 0.00 0.00 3.20
479 498 5.045869 AGACATTTATTTTGGGACGGAGAGA 60.046 40.000 0.00 0.00 0.00 3.10
480 499 5.186198 AGACATTTATTTTGGGACGGAGAG 58.814 41.667 0.00 0.00 0.00 3.20
481 500 5.174037 AGACATTTATTTTGGGACGGAGA 57.826 39.130 0.00 0.00 0.00 3.71
482 501 4.941263 TGAGACATTTATTTTGGGACGGAG 59.059 41.667 0.00 0.00 0.00 4.63
483 502 4.912586 TGAGACATTTATTTTGGGACGGA 58.087 39.130 0.00 0.00 0.00 4.69
484 503 5.637006 TTGAGACATTTATTTTGGGACGG 57.363 39.130 0.00 0.00 0.00 4.79
486 505 6.272822 AGCTTGAGACATTTATTTTGGGAC 57.727 37.500 0.00 0.00 0.00 4.46
488 507 7.830739 ACTAAGCTTGAGACATTTATTTTGGG 58.169 34.615 9.86 0.00 0.00 4.12
489 508 9.774742 GTACTAAGCTTGAGACATTTATTTTGG 57.225 33.333 9.86 0.00 0.00 3.28
493 512 9.726438 AGTTGTACTAAGCTTGAGACATTTATT 57.274 29.630 9.86 0.00 0.00 1.40
494 513 9.726438 AAGTTGTACTAAGCTTGAGACATTTAT 57.274 29.630 9.86 0.00 0.00 1.40
495 514 9.555727 AAAGTTGTACTAAGCTTGAGACATTTA 57.444 29.630 9.86 0.00 0.00 1.40
497 516 7.499232 ACAAAGTTGTACTAAGCTTGAGACATT 59.501 33.333 9.86 0.05 40.16 2.71
498 517 6.992715 ACAAAGTTGTACTAAGCTTGAGACAT 59.007 34.615 9.86 0.00 40.16 3.06
499 518 6.346096 ACAAAGTTGTACTAAGCTTGAGACA 58.654 36.000 9.86 7.12 40.16 3.41
513 532 9.288576 TGTACTTAGCTCTAGTACAAAGTTGTA 57.711 33.333 26.95 11.00 43.37 2.41
514 533 8.174733 TGTACTTAGCTCTAGTACAAAGTTGT 57.825 34.615 26.95 1.75 43.37 3.32
521 540 8.400184 TCAACTTTGTACTTAGCTCTAGTACA 57.600 34.615 26.05 26.05 44.25 2.90
522 541 8.728833 TCTCAACTTTGTACTTAGCTCTAGTAC 58.271 37.037 22.81 22.81 38.93 2.73
523 542 8.728833 GTCTCAACTTTGTACTTAGCTCTAGTA 58.271 37.037 0.00 0.00 0.00 1.82
524 543 7.230913 TGTCTCAACTTTGTACTTAGCTCTAGT 59.769 37.037 6.64 6.64 0.00 2.57
525 544 7.539366 GTGTCTCAACTTTGTACTTAGCTCTAG 59.461 40.741 0.00 0.00 0.00 2.43
526 545 7.230913 AGTGTCTCAACTTTGTACTTAGCTCTA 59.769 37.037 0.00 0.00 0.00 2.43
527 546 6.041069 AGTGTCTCAACTTTGTACTTAGCTCT 59.959 38.462 0.00 0.00 0.00 4.09
528 547 6.217294 AGTGTCTCAACTTTGTACTTAGCTC 58.783 40.000 0.00 0.00 0.00 4.09
529 548 6.163135 AGTGTCTCAACTTTGTACTTAGCT 57.837 37.500 0.00 0.00 0.00 3.32
530 549 6.846325 AAGTGTCTCAACTTTGTACTTAGC 57.154 37.500 0.00 0.00 37.05 3.09
534 553 8.621286 CCAAAATAAGTGTCTCAACTTTGTACT 58.379 33.333 0.00 0.00 40.77 2.73
535 554 7.860872 CCCAAAATAAGTGTCTCAACTTTGTAC 59.139 37.037 0.00 0.00 40.77 2.90
536 555 7.776030 TCCCAAAATAAGTGTCTCAACTTTGTA 59.224 33.333 0.00 0.00 40.77 2.41
537 556 6.605594 TCCCAAAATAAGTGTCTCAACTTTGT 59.394 34.615 0.00 0.00 40.77 2.83
538 557 7.038154 TCCCAAAATAAGTGTCTCAACTTTG 57.962 36.000 0.00 0.00 40.77 2.77
539 558 7.255942 CCATCCCAAAATAAGTGTCTCAACTTT 60.256 37.037 0.00 0.00 40.77 2.66
540 559 6.209391 CCATCCCAAAATAAGTGTCTCAACTT 59.791 38.462 0.00 0.00 42.89 2.66
541 560 5.711976 CCATCCCAAAATAAGTGTCTCAACT 59.288 40.000 0.00 0.00 0.00 3.16
542 561 5.710099 TCCATCCCAAAATAAGTGTCTCAAC 59.290 40.000 0.00 0.00 0.00 3.18
543 562 5.886609 TCCATCCCAAAATAAGTGTCTCAA 58.113 37.500 0.00 0.00 0.00 3.02
544 563 5.500234 CTCCATCCCAAAATAAGTGTCTCA 58.500 41.667 0.00 0.00 0.00 3.27
545 564 4.884164 CCTCCATCCCAAAATAAGTGTCTC 59.116 45.833 0.00 0.00 0.00 3.36
546 565 4.325344 CCCTCCATCCCAAAATAAGTGTCT 60.325 45.833 0.00 0.00 0.00 3.41
547 566 3.954258 CCCTCCATCCCAAAATAAGTGTC 59.046 47.826 0.00 0.00 0.00 3.67
548 567 3.596046 TCCCTCCATCCCAAAATAAGTGT 59.404 43.478 0.00 0.00 0.00 3.55
549 568 4.210331 CTCCCTCCATCCCAAAATAAGTG 58.790 47.826 0.00 0.00 0.00 3.16
550 569 3.858638 ACTCCCTCCATCCCAAAATAAGT 59.141 43.478 0.00 0.00 0.00 2.24
551 570 4.526438 ACTCCCTCCATCCCAAAATAAG 57.474 45.455 0.00 0.00 0.00 1.73
552 571 5.293643 TCTACTCCCTCCATCCCAAAATAA 58.706 41.667 0.00 0.00 0.00 1.40
553 572 4.903149 TCTACTCCCTCCATCCCAAAATA 58.097 43.478 0.00 0.00 0.00 1.40
554 573 3.747852 TCTACTCCCTCCATCCCAAAAT 58.252 45.455 0.00 0.00 0.00 1.82
555 574 3.214694 TCTACTCCCTCCATCCCAAAA 57.785 47.619 0.00 0.00 0.00 2.44
556 575 2.961536 TCTACTCCCTCCATCCCAAA 57.038 50.000 0.00 0.00 0.00 3.28
557 576 3.471306 ACTATCTACTCCCTCCATCCCAA 59.529 47.826 0.00 0.00 0.00 4.12
558 577 3.072086 ACTATCTACTCCCTCCATCCCA 58.928 50.000 0.00 0.00 0.00 4.37
559 578 3.837399 ACTATCTACTCCCTCCATCCC 57.163 52.381 0.00 0.00 0.00 3.85
634 653 9.454585 AAATTCAGCAATGTATAACGATGATTG 57.545 29.630 0.00 0.00 0.00 2.67
663 682 6.999950 TGTACTAGTTCAAGGTATGCAGAAA 58.000 36.000 0.00 0.00 0.00 2.52
664 683 6.599356 TGTACTAGTTCAAGGTATGCAGAA 57.401 37.500 0.00 0.00 0.00 3.02
665 684 6.599356 TTGTACTAGTTCAAGGTATGCAGA 57.401 37.500 10.55 0.00 0.00 4.26
666 685 7.849804 AATTGTACTAGTTCAAGGTATGCAG 57.150 36.000 18.21 0.00 0.00 4.41
667 686 9.378551 CTAAATTGTACTAGTTCAAGGTATGCA 57.621 33.333 18.21 0.00 0.00 3.96
668 687 9.595823 TCTAAATTGTACTAGTTCAAGGTATGC 57.404 33.333 18.21 0.00 0.00 3.14
758 2625 6.616947 TGTTCTCTTCTCGCAAAAAGAAAAA 58.383 32.000 0.00 0.00 32.60 1.94
759 2626 6.189677 TGTTCTCTTCTCGCAAAAAGAAAA 57.810 33.333 0.00 0.00 32.60 2.29
760 2627 5.811399 TGTTCTCTTCTCGCAAAAAGAAA 57.189 34.783 0.00 0.00 32.60 2.52
761 2628 5.527214 TGATGTTCTCTTCTCGCAAAAAGAA 59.473 36.000 0.00 0.00 31.45 2.52
762 2629 5.050091 GTGATGTTCTCTTCTCGCAAAAAGA 60.050 40.000 0.00 0.00 0.00 2.52
763 2630 5.142962 GTGATGTTCTCTTCTCGCAAAAAG 58.857 41.667 0.00 0.00 0.00 2.27
764 2631 4.024048 GGTGATGTTCTCTTCTCGCAAAAA 60.024 41.667 0.00 0.00 0.00 1.94
765 2632 3.498397 GGTGATGTTCTCTTCTCGCAAAA 59.502 43.478 0.00 0.00 0.00 2.44
766 2633 3.067106 GGTGATGTTCTCTTCTCGCAAA 58.933 45.455 0.00 0.00 0.00 3.68
767 2634 2.300152 AGGTGATGTTCTCTTCTCGCAA 59.700 45.455 0.00 0.00 0.00 4.85
768 2635 1.895798 AGGTGATGTTCTCTTCTCGCA 59.104 47.619 0.00 0.00 0.00 5.10
769 2636 2.266554 CAGGTGATGTTCTCTTCTCGC 58.733 52.381 0.00 0.00 0.00 5.03
770 2637 2.094286 AGCAGGTGATGTTCTCTTCTCG 60.094 50.000 0.00 0.00 0.00 4.04
771 2638 3.608316 AGCAGGTGATGTTCTCTTCTC 57.392 47.619 0.00 0.00 0.00 2.87
772 2639 3.672808 CAAGCAGGTGATGTTCTCTTCT 58.327 45.455 0.00 0.00 0.00 2.85
773 2640 2.161211 GCAAGCAGGTGATGTTCTCTTC 59.839 50.000 0.00 0.00 0.00 2.87
774 2641 2.157738 GCAAGCAGGTGATGTTCTCTT 58.842 47.619 0.00 0.00 0.00 2.85
775 2642 1.612726 GGCAAGCAGGTGATGTTCTCT 60.613 52.381 0.00 0.00 0.00 3.10
862 2730 8.771920 TCTATTTTTCGAGAAAATGTCAGCTA 57.228 30.769 19.57 2.84 39.69 3.32
928 2796 9.469807 ACAATTGCACTTCGAAAATACAAATTA 57.530 25.926 5.05 0.00 0.00 1.40
929 2797 8.364129 ACAATTGCACTTCGAAAATACAAATT 57.636 26.923 5.05 0.00 0.00 1.82
931 2799 7.763172 AACAATTGCACTTCGAAAATACAAA 57.237 28.000 5.05 0.00 0.00 2.83
935 2803 7.763172 ACAAAACAATTGCACTTCGAAAATA 57.237 28.000 5.05 0.00 0.00 1.40
936 2804 6.660887 ACAAAACAATTGCACTTCGAAAAT 57.339 29.167 5.05 0.00 0.00 1.82
1035 2913 0.183971 TTTCCTTGTTTCGGGCAGGA 59.816 50.000 0.00 0.00 0.00 3.86
1551 3432 2.262292 GGGTTGTAGGCGTACGCA 59.738 61.111 37.99 19.20 44.11 5.24
1653 3534 0.041047 TGTTGTAGGTGACGACGTCG 60.041 55.000 34.58 34.58 44.54 5.12
2232 4113 2.764128 TCCTCGGCATCCTCCCAC 60.764 66.667 0.00 0.00 0.00 4.61
2244 4125 0.385751 TCTTCGGCATTAGCTCCTCG 59.614 55.000 0.00 0.00 41.70 4.63
2455 4336 5.055812 GCCCATTTCATTCAACAACTCAAA 58.944 37.500 0.00 0.00 0.00 2.69
2806 4687 5.850557 TCACTGTTGGTCAAATTGTCAAT 57.149 34.783 7.46 0.00 0.00 2.57
2897 4783 8.280497 CCCATCGCTATAACATAACAAAGTTAC 58.720 37.037 0.00 0.00 33.49 2.50
3034 4921 7.489113 CCAAAATTGCAAGATAATGGAGTACAC 59.511 37.037 4.94 0.00 0.00 2.90
3042 4929 5.180271 ACCAGCCAAAATTGCAAGATAATG 58.820 37.500 4.94 0.00 0.00 1.90
3068 4955 5.196341 ACTATCCACGAAGATTGCGATTA 57.804 39.130 0.00 0.00 0.00 1.75
3069 4956 4.060038 ACTATCCACGAAGATTGCGATT 57.940 40.909 0.00 0.00 0.00 3.34
3070 4957 3.735237 ACTATCCACGAAGATTGCGAT 57.265 42.857 0.00 0.00 0.00 4.58
3071 4958 3.520290 AACTATCCACGAAGATTGCGA 57.480 42.857 0.00 0.00 0.00 5.10
3072 4959 5.062934 TGTTAAACTATCCACGAAGATTGCG 59.937 40.000 0.00 0.00 0.00 4.85
3073 4960 6.417191 TGTTAAACTATCCACGAAGATTGC 57.583 37.500 0.00 0.00 0.00 3.56
3183 5070 4.470334 AAATTACCAACCATCCATGCAC 57.530 40.909 0.00 0.00 0.00 4.57
3262 5149 2.772515 CCCTCCCTAGTTTTAGTCCCAG 59.227 54.545 0.00 0.00 0.00 4.45
3283 5170 5.643777 ACATACAACATTCCAGCTACTTGAC 59.356 40.000 0.00 0.00 0.00 3.18
3356 5243 1.073284 GGCTCCACCCTTGTAAGACAA 59.927 52.381 0.00 0.00 36.54 3.18
3359 5246 0.984230 CTGGCTCCACCCTTGTAAGA 59.016 55.000 0.00 0.00 37.83 2.10
3450 5347 6.231211 AGTCTCCGAAATTTTGTATGTGTCT 58.769 36.000 4.72 0.00 0.00 3.41
3521 5418 9.612066 TGTTCATCACAGTAAATTATAGATGCA 57.388 29.630 0.00 0.00 33.34 3.96
3572 5469 9.295825 CAATAGGCCATACTGGTTTCATTATTA 57.704 33.333 5.01 0.00 40.46 0.98
3597 5494 8.394121 GCCATACTTTGTTTTTCATTTTCAACA 58.606 29.630 0.00 0.00 0.00 3.33
3664 5561 6.379579 AGACTTATATTTAGGAACGGAGGGA 58.620 40.000 0.00 0.00 0.00 4.20
3665 5562 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
3685 5582 9.699703 GGTTCATAGTGGAATCTCTATAAAGAC 57.300 37.037 0.00 0.00 30.97 3.01
3686 5583 9.434275 TGGTTCATAGTGGAATCTCTATAAAGA 57.566 33.333 0.00 0.00 30.97 2.52
3687 5584 9.482627 GTGGTTCATAGTGGAATCTCTATAAAG 57.517 37.037 0.00 0.00 30.97 1.85
3688 5585 8.988060 TGTGGTTCATAGTGGAATCTCTATAAA 58.012 33.333 0.00 0.00 30.97 1.40
3689 5586 8.547481 TGTGGTTCATAGTGGAATCTCTATAA 57.453 34.615 0.00 0.00 30.97 0.98
3690 5587 8.727100 ATGTGGTTCATAGTGGAATCTCTATA 57.273 34.615 0.00 0.00 34.67 1.31
3691 5588 7.623999 ATGTGGTTCATAGTGGAATCTCTAT 57.376 36.000 0.00 0.00 34.67 1.98
3692 5589 7.255486 CGTATGTGGTTCATAGTGGAATCTCTA 60.255 40.741 0.00 0.00 39.36 2.43
3693 5590 5.965033 ATGTGGTTCATAGTGGAATCTCT 57.035 39.130 0.00 0.00 34.67 3.10
3694 5591 5.692204 CGTATGTGGTTCATAGTGGAATCTC 59.308 44.000 0.00 0.00 39.36 2.75
3695 5592 5.362717 TCGTATGTGGTTCATAGTGGAATCT 59.637 40.000 0.00 0.00 39.36 2.40
3696 5593 5.597806 TCGTATGTGGTTCATAGTGGAATC 58.402 41.667 0.00 0.00 39.36 2.52
3697 5594 5.607939 TCGTATGTGGTTCATAGTGGAAT 57.392 39.130 0.00 0.00 39.36 3.01
3698 5595 5.408880 TTCGTATGTGGTTCATAGTGGAA 57.591 39.130 0.00 0.00 39.36 3.53
3699 5596 5.105106 ACATTCGTATGTGGTTCATAGTGGA 60.105 40.000 6.89 0.00 43.29 4.02
3700 5597 5.116180 ACATTCGTATGTGGTTCATAGTGG 58.884 41.667 6.89 0.00 43.29 4.00
3701 5598 7.946655 ATACATTCGTATGTGGTTCATAGTG 57.053 36.000 16.91 0.00 44.56 2.74
3706 5603 9.855021 CATCTATATACATTCGTATGTGGTTCA 57.145 33.333 16.91 0.00 44.56 3.18
3707 5604 8.808529 GCATCTATATACATTCGTATGTGGTTC 58.191 37.037 16.91 0.00 44.56 3.62
3708 5605 8.311109 TGCATCTATATACATTCGTATGTGGTT 58.689 33.333 16.91 5.39 44.56 3.67
3709 5606 7.836842 TGCATCTATATACATTCGTATGTGGT 58.163 34.615 16.91 8.59 44.56 4.16
3710 5607 8.877808 ATGCATCTATATACATTCGTATGTGG 57.122 34.615 16.91 3.59 44.56 4.17
3728 5625 8.844244 GGATGAATCTACACTTAAAATGCATCT 58.156 33.333 0.00 0.00 0.00 2.90
3729 5626 8.623903 TGGATGAATCTACACTTAAAATGCATC 58.376 33.333 0.00 0.00 0.00 3.91
3730 5627 8.523915 TGGATGAATCTACACTTAAAATGCAT 57.476 30.769 0.00 0.00 0.00 3.96
3731 5628 7.936496 TGGATGAATCTACACTTAAAATGCA 57.064 32.000 0.00 0.00 0.00 3.96
3732 5629 9.807649 AAATGGATGAATCTACACTTAAAATGC 57.192 29.630 0.00 0.00 0.00 3.56
3735 5632 9.638239 GCAAAATGGATGAATCTACACTTAAAA 57.362 29.630 0.00 0.00 0.00 1.52
3736 5633 9.023962 AGCAAAATGGATGAATCTACACTTAAA 57.976 29.630 0.00 0.00 0.00 1.52
3737 5634 8.579850 AGCAAAATGGATGAATCTACACTTAA 57.420 30.769 0.00 0.00 0.00 1.85
3738 5635 8.049117 AGAGCAAAATGGATGAATCTACACTTA 58.951 33.333 0.00 0.00 0.00 2.24
3739 5636 6.888632 AGAGCAAAATGGATGAATCTACACTT 59.111 34.615 0.00 0.00 0.00 3.16
3740 5637 6.318144 CAGAGCAAAATGGATGAATCTACACT 59.682 38.462 0.00 0.00 0.00 3.55
3741 5638 6.094603 ACAGAGCAAAATGGATGAATCTACAC 59.905 38.462 0.00 0.00 0.00 2.90
3742 5639 6.182627 ACAGAGCAAAATGGATGAATCTACA 58.817 36.000 0.00 0.00 0.00 2.74
3743 5640 6.690194 ACAGAGCAAAATGGATGAATCTAC 57.310 37.500 0.00 0.00 0.00 2.59
3744 5641 7.994911 ACATACAGAGCAAAATGGATGAATCTA 59.005 33.333 4.46 0.00 39.69 1.98
3745 5642 6.832384 ACATACAGAGCAAAATGGATGAATCT 59.168 34.615 4.46 0.00 39.69 2.40
3746 5643 7.035840 ACATACAGAGCAAAATGGATGAATC 57.964 36.000 4.46 0.00 39.69 2.52
3747 5644 7.776969 ACTACATACAGAGCAAAATGGATGAAT 59.223 33.333 4.46 0.00 39.69 2.57
3748 5645 7.112122 ACTACATACAGAGCAAAATGGATGAA 58.888 34.615 4.46 0.00 39.69 2.57
3749 5646 6.653020 ACTACATACAGAGCAAAATGGATGA 58.347 36.000 4.46 0.00 39.69 2.92
3750 5647 6.017605 GGACTACATACAGAGCAAAATGGATG 60.018 42.308 0.00 0.00 42.46 3.51
3751 5648 6.058183 GGACTACATACAGAGCAAAATGGAT 58.942 40.000 0.00 0.00 0.00 3.41
3752 5649 5.045942 TGGACTACATACAGAGCAAAATGGA 60.046 40.000 0.00 0.00 0.00 3.41
3753 5650 5.065218 GTGGACTACATACAGAGCAAAATGG 59.935 44.000 0.00 0.00 0.00 3.16
3754 5651 5.065218 GGTGGACTACATACAGAGCAAAATG 59.935 44.000 0.00 0.00 0.00 2.32
3755 5652 5.045578 AGGTGGACTACATACAGAGCAAAAT 60.046 40.000 0.00 0.00 0.00 1.82
3756 5653 4.286032 AGGTGGACTACATACAGAGCAAAA 59.714 41.667 0.00 0.00 0.00 2.44
3757 5654 3.838317 AGGTGGACTACATACAGAGCAAA 59.162 43.478 0.00 0.00 0.00 3.68
3758 5655 3.441101 AGGTGGACTACATACAGAGCAA 58.559 45.455 0.00 0.00 0.00 3.91
3759 5656 3.101643 AGGTGGACTACATACAGAGCA 57.898 47.619 0.00 0.00 0.00 4.26
3760 5657 4.208746 ACTAGGTGGACTACATACAGAGC 58.791 47.826 0.00 0.00 0.00 4.09
3761 5658 6.828788 TCTACTAGGTGGACTACATACAGAG 58.171 44.000 0.00 0.00 0.00 3.35
3762 5659 6.819947 TCTACTAGGTGGACTACATACAGA 57.180 41.667 0.00 0.00 0.00 3.41
3763 5660 7.940137 AGATTCTACTAGGTGGACTACATACAG 59.060 40.741 0.00 0.00 0.00 2.74
3764 5661 7.813331 AGATTCTACTAGGTGGACTACATACA 58.187 38.462 0.00 0.00 0.00 2.29
3765 5662 8.158789 AGAGATTCTACTAGGTGGACTACATAC 58.841 40.741 0.00 0.00 0.00 2.39
3766 5663 8.277720 AGAGATTCTACTAGGTGGACTACATA 57.722 38.462 0.00 0.00 0.00 2.29
3767 5664 7.156694 AGAGATTCTACTAGGTGGACTACAT 57.843 40.000 0.00 0.00 0.00 2.29
3768 5665 6.578313 AGAGATTCTACTAGGTGGACTACA 57.422 41.667 0.00 0.00 0.00 2.74
3769 5666 7.967890 GTAGAGATTCTACTAGGTGGACTAC 57.032 44.000 8.60 0.00 44.45 2.73
3792 5689 7.985752 CCTCCGTTCCTAAATATAAGTCTTTGT 59.014 37.037 0.00 0.00 0.00 2.83
3793 5690 7.441458 CCCTCCGTTCCTAAATATAAGTCTTTG 59.559 40.741 0.00 0.00 0.00 2.77
3794 5691 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
3795 5692 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
3796 5693 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
3797 5694 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
3798 5695 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
3799 5696 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
3800 5697 7.068702 TGTACTCCCTCCGTTCCTAAATATAA 58.931 38.462 0.00 0.00 0.00 0.98
3801 5698 6.613699 TGTACTCCCTCCGTTCCTAAATATA 58.386 40.000 0.00 0.00 0.00 0.86
3802 5699 5.461327 TGTACTCCCTCCGTTCCTAAATAT 58.539 41.667 0.00 0.00 0.00 1.28
3803 5700 4.870636 TGTACTCCCTCCGTTCCTAAATA 58.129 43.478 0.00 0.00 0.00 1.40
3804 5701 3.716431 TGTACTCCCTCCGTTCCTAAAT 58.284 45.455 0.00 0.00 0.00 1.40
3805 5702 3.173953 TGTACTCCCTCCGTTCCTAAA 57.826 47.619 0.00 0.00 0.00 1.85
3806 5703 2.905415 TGTACTCCCTCCGTTCCTAA 57.095 50.000 0.00 0.00 0.00 2.69
3807 5704 2.731572 CTTGTACTCCCTCCGTTCCTA 58.268 52.381 0.00 0.00 0.00 2.94
3808 5705 1.558233 CTTGTACTCCCTCCGTTCCT 58.442 55.000 0.00 0.00 0.00 3.36
3809 5706 0.108281 GCTTGTACTCCCTCCGTTCC 60.108 60.000 0.00 0.00 0.00 3.62
3810 5707 0.896226 AGCTTGTACTCCCTCCGTTC 59.104 55.000 0.00 0.00 0.00 3.95
3811 5708 1.349067 AAGCTTGTACTCCCTCCGTT 58.651 50.000 0.00 0.00 0.00 4.44
3812 5709 2.226962 TAAGCTTGTACTCCCTCCGT 57.773 50.000 9.86 0.00 0.00 4.69
3813 5710 3.458189 CATTAAGCTTGTACTCCCTCCG 58.542 50.000 9.86 0.00 0.00 4.63
3814 5711 3.206964 GCATTAAGCTTGTACTCCCTCC 58.793 50.000 9.86 0.00 41.15 4.30
3815 5712 3.873910 TGCATTAAGCTTGTACTCCCTC 58.126 45.455 9.86 0.00 45.94 4.30
3816 5713 4.080356 TCATGCATTAAGCTTGTACTCCCT 60.080 41.667 9.86 0.00 45.70 4.20
3817 5714 4.199310 TCATGCATTAAGCTTGTACTCCC 58.801 43.478 9.86 0.00 45.70 4.30
3818 5715 5.818136 TTCATGCATTAAGCTTGTACTCC 57.182 39.130 9.86 0.00 45.70 3.85
3823 5720 8.571336 GGAGTATAATTCATGCATTAAGCTTGT 58.429 33.333 9.86 0.00 45.70 3.16
3824 5721 8.025445 GGGAGTATAATTCATGCATTAAGCTTG 58.975 37.037 9.86 0.00 46.60 4.01
3825 5722 7.946776 AGGGAGTATAATTCATGCATTAAGCTT 59.053 33.333 3.48 3.48 45.94 3.74
3826 5723 7.465116 AGGGAGTATAATTCATGCATTAAGCT 58.535 34.615 0.00 3.77 45.94 3.74
3827 5724 7.148171 GGAGGGAGTATAATTCATGCATTAAGC 60.148 40.741 0.00 0.00 45.96 3.09
3828 5725 7.065085 CGGAGGGAGTATAATTCATGCATTAAG 59.935 40.741 0.00 0.00 0.00 1.85
3829 5726 6.878923 CGGAGGGAGTATAATTCATGCATTAA 59.121 38.462 0.00 0.00 0.00 1.40
3830 5727 6.013725 ACGGAGGGAGTATAATTCATGCATTA 60.014 38.462 0.00 0.14 0.00 1.90
3831 5728 5.221925 ACGGAGGGAGTATAATTCATGCATT 60.222 40.000 0.00 0.00 0.00 3.56
3832 5729 4.287067 ACGGAGGGAGTATAATTCATGCAT 59.713 41.667 0.00 0.00 0.00 3.96
3833 5730 3.646162 ACGGAGGGAGTATAATTCATGCA 59.354 43.478 0.00 0.00 0.00 3.96
3834 5731 4.273148 ACGGAGGGAGTATAATTCATGC 57.727 45.455 0.00 0.00 0.00 4.06
3835 5732 5.928839 CAGAACGGAGGGAGTATAATTCATG 59.071 44.000 0.00 0.00 0.00 3.07
3836 5733 5.839063 TCAGAACGGAGGGAGTATAATTCAT 59.161 40.000 0.00 0.00 0.00 2.57
3837 5734 5.205821 TCAGAACGGAGGGAGTATAATTCA 58.794 41.667 0.00 0.00 0.00 2.57
3838 5735 5.786264 TCAGAACGGAGGGAGTATAATTC 57.214 43.478 0.00 0.00 0.00 2.17
3839 5736 6.749036 ATTCAGAACGGAGGGAGTATAATT 57.251 37.500 0.00 0.00 0.00 1.40
3840 5737 6.749036 AATTCAGAACGGAGGGAGTATAAT 57.251 37.500 0.00 0.00 0.00 1.28
3841 5738 7.047460 GTAATTCAGAACGGAGGGAGTATAA 57.953 40.000 0.00 0.00 0.00 0.98
3842 5739 6.645790 GTAATTCAGAACGGAGGGAGTATA 57.354 41.667 0.00 0.00 0.00 1.47
3843 5740 5.532664 GTAATTCAGAACGGAGGGAGTAT 57.467 43.478 0.00 0.00 0.00 2.12
3844 5741 4.996788 GTAATTCAGAACGGAGGGAGTA 57.003 45.455 0.00 0.00 0.00 2.59
3845 5742 3.889520 GTAATTCAGAACGGAGGGAGT 57.110 47.619 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.