Multiple sequence alignment - TraesCS4A01G124200

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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 TraesCS4A01G124200 chr4A 100.000 5131 0 0 1 5131 157319655 157324785 0.000000e+00 9476.0
1 TraesCS4A01G124200 chr4A 93.750 48 3 0 4946 4993 15773006 15773053 7.130000e-09 73.1
2 TraesCS4A01G124200 chr4D 97.142 3149 66 12 1433 4574 317539754 317536623 0.000000e+00 5295.0
3 TraesCS4A01G124200 chr4D 92.123 749 30 7 717 1437 317540532 317539785 0.000000e+00 1029.0
4 TraesCS4A01G124200 chr4D 89.109 202 9 1 4747 4948 317536203 317536015 6.640000e-59 239.0
5 TraesCS4A01G124200 chr4D 92.157 51 4 0 4681 4731 317536298 317536248 7.130000e-09 73.1
6 TraesCS4A01G124200 chr4B 96.477 3151 77 15 1433 4574 394604237 394601112 0.000000e+00 5173.0
7 TraesCS4A01G124200 chr4B 91.525 708 33 5 756 1437 394604974 394604268 0.000000e+00 950.0
8 TraesCS4A01G124200 chr4B 82.745 255 28 8 4870 5124 394597793 394597555 4.020000e-51 213.0
9 TraesCS4A01G124200 chr4B 95.935 123 5 0 409 531 644088779 644088657 3.130000e-47 200.0
10 TraesCS4A01G124200 chr4B 96.491 57 2 0 559 615 644088440 644088384 1.520000e-15 95.3
11 TraesCS4A01G124200 chr4B 96.296 54 2 0 4831 4884 394600838 394600785 7.080000e-14 89.8
12 TraesCS4A01G124200 chr3A 91.558 616 51 1 1 615 714216092 714216707 0.000000e+00 848.0
13 TraesCS4A01G124200 chr7D 84.053 602 89 7 10 608 88486573 88485976 1.600000e-159 573.0
14 TraesCS4A01G124200 chr6D 88.235 323 37 1 197 518 17967039 17967361 8.060000e-103 385.0
15 TraesCS4A01G124200 chr6D 97.561 41 1 0 575 615 17967363 17967403 2.560000e-08 71.3
16 TraesCS4A01G124200 chr2D 82.865 356 60 1 1 355 168944453 168944808 8.290000e-83 318.0
17 TraesCS4A01G124200 chr2A 94.681 188 10 0 428 615 203456483 203456670 5.030000e-75 292.0
18 TraesCS4A01G124200 chr1D 75.626 599 137 7 10 603 488701770 488701176 6.500000e-74 289.0
19 TraesCS4A01G124200 chr7A 87.356 174 21 1 10 183 572258043 572257871 1.130000e-46 198.0
20 TraesCS4A01G124200 chr5D 93.056 72 5 0 544 615 482198049 482198120 7.030000e-19 106.0
21 TraesCS4A01G124200 chr6B 95.833 48 2 0 4949 4996 657068579 657068532 1.530000e-10 78.7
22 TraesCS4A01G124200 chr6B 93.878 49 3 0 4946 4994 179987254 179987302 1.980000e-09 75.0
23 TraesCS4A01G124200 chr3B 94.118 51 3 0 4946 4996 498466950 498467000 1.530000e-10 78.7
24 TraesCS4A01G124200 chr2B 95.833 48 2 0 4946 4993 23029091 23029138 1.530000e-10 78.7
25 TraesCS4A01G124200 chr2B 93.750 48 3 0 4946 4993 23029101 23029054 7.130000e-09 73.1
26 TraesCS4A01G124200 chr1B 94.000 50 3 0 4946 4995 118514594 118514643 5.510000e-10 76.8
27 TraesCS4A01G124200 chr5B 93.750 48 3 0 4946 4993 249578634 249578587 7.130000e-09 73.1
28 TraesCS4A01G124200 chr1A 93.750 48 3 0 4946 4993 27400062 27400109 7.130000e-09 73.1


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 TraesCS4A01G124200 chr4A 157319655 157324785 5130 False 9476.000 9476 100.00000 1 5131 1 chr4A.!!$F2 5130
1 TraesCS4A01G124200 chr4D 317536015 317540532 4517 True 1659.025 5295 92.63275 717 4948 4 chr4D.!!$R1 4231
2 TraesCS4A01G124200 chr4B 394597555 394604974 7419 True 1606.450 5173 91.76075 756 5124 4 chr4B.!!$R1 4368
3 TraesCS4A01G124200 chr3A 714216092 714216707 615 False 848.000 848 91.55800 1 615 1 chr3A.!!$F1 614
4 TraesCS4A01G124200 chr7D 88485976 88486573 597 True 573.000 573 84.05300 10 608 1 chr7D.!!$R1 598
5 TraesCS4A01G124200 chr1D 488701176 488701770 594 True 289.000 289 75.62600 10 603 1 chr1D.!!$R1 593

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
669 672 0.036164 TGGCTCTGGCACAACGTAAT 59.964 50.0 0.0 0.0 38.70 1.89 F
688 691 0.246360 TCGAGCCTCATTCGCAGAAA 59.754 50.0 0.0 0.0 45.90 2.52 F
886 897 0.318784 GCCTCACGCCGACCTAATAG 60.319 60.0 0.0 0.0 0.00 1.73 F
1446 1514 0.394565 GCTTGTGAGGTGTCTGTCCT 59.605 55.0 0.0 0.0 38.09 3.85 F
2998 3071 0.179103 GCACTGTTTTGCTTGCACCT 60.179 50.0 0.0 0.0 39.59 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2097 2166 1.821088 AGTCCCTTTCTGGTTCCTGT 58.179 50.000 0.0 0.0 0.0 4.00 R
2613 2682 4.322801 CGAAGAATTTCTGGGTAGGTCTGT 60.323 45.833 0.0 0.0 0.0 3.41 R
2721 2790 1.954927 CCCTCATTAGAGTTTCGGGC 58.045 55.000 0.0 0.0 40.4 6.13 R
3443 3518 1.742308 AGAGTCTGTTAGCCCCCAAA 58.258 50.000 0.0 0.0 0.0 3.28 R
4787 5200 1.074850 GGGGAGAAGGGGAGGAGAG 60.075 68.421 0.0 0.0 0.0 3.20 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
29 30 1.308998 CCTGACAGAACGGCTTTGTT 58.691 50.000 3.32 0.00 34.02 2.83
41 42 7.103299 GAACGGCTTTGTTGATTAGGGTACC 62.103 48.000 2.17 2.17 40.17 3.34
59 60 2.645802 ACCGGCTACAAACTTTGTTCA 58.354 42.857 12.35 0.00 42.22 3.18
60 61 3.219281 ACCGGCTACAAACTTTGTTCAT 58.781 40.909 12.35 0.00 42.22 2.57
62 63 3.004315 CCGGCTACAAACTTTGTTCATGT 59.996 43.478 12.35 0.00 42.22 3.21
93 94 0.609131 ACCAGCCAACCCGAAAGATG 60.609 55.000 0.00 0.00 0.00 2.90
114 115 4.111577 TGGACCAGATATGGAGGAAACTT 58.888 43.478 14.70 0.00 44.43 2.66
171 172 1.206878 TCCATGCTGATACACTGGCT 58.793 50.000 0.00 0.00 0.00 4.75
210 211 3.068732 TGGCGAGAGATGATCAAGGTAAG 59.931 47.826 0.00 0.00 0.00 2.34
218 219 7.628234 AGAGATGATCAAGGTAAGTTCATTGT 58.372 34.615 0.00 0.00 32.13 2.71
248 249 0.842030 TGGGTTCTGCCTCATGTCCT 60.842 55.000 0.00 0.00 37.43 3.85
249 250 0.107459 GGGTTCTGCCTCATGTCCTC 60.107 60.000 0.00 0.00 37.43 3.71
336 339 5.359716 GCACCAAATTGCAATTGAATGAA 57.640 34.783 24.74 0.00 42.49 2.57
437 440 7.229506 GCTACAATATTGGCTATGGAGTTTTCT 59.770 37.037 19.37 0.00 0.00 2.52
438 441 7.961326 ACAATATTGGCTATGGAGTTTTCTT 57.039 32.000 19.37 0.00 0.00 2.52
444 447 8.829373 ATTGGCTATGGAGTTTTCTTCTATTT 57.171 30.769 0.00 0.00 0.00 1.40
476 479 2.477245 TGCTGTAGGGAAGCCAATCTA 58.523 47.619 0.00 0.00 40.06 1.98
477 480 2.435805 TGCTGTAGGGAAGCCAATCTAG 59.564 50.000 0.00 0.00 40.06 2.43
478 481 2.808567 GCTGTAGGGAAGCCAATCTAGC 60.809 54.545 0.00 0.00 34.45 3.42
509 512 2.507339 TGGCAAAACACTGCTTTAGC 57.493 45.000 0.00 0.00 42.25 3.09
526 529 5.929415 GCTTTAGCACTAGAACTTCAGAGTT 59.071 40.000 0.00 0.00 43.94 3.01
527 530 6.425417 GCTTTAGCACTAGAACTTCAGAGTTT 59.575 38.462 0.00 0.00 42.56 2.66
528 531 7.041712 GCTTTAGCACTAGAACTTCAGAGTTTT 60.042 37.037 0.00 0.00 42.56 2.43
529 532 7.715265 TTAGCACTAGAACTTCAGAGTTTTG 57.285 36.000 0.00 0.00 45.88 2.44
530 533 5.059833 AGCACTAGAACTTCAGAGTTTTGG 58.940 41.667 0.00 0.00 45.88 3.28
531 534 4.214332 GCACTAGAACTTCAGAGTTTTGGG 59.786 45.833 0.00 0.00 45.88 4.12
532 535 5.611374 CACTAGAACTTCAGAGTTTTGGGA 58.389 41.667 0.00 0.00 45.88 4.37
533 536 5.467063 CACTAGAACTTCAGAGTTTTGGGAC 59.533 44.000 0.00 0.00 45.88 4.46
534 537 4.779993 AGAACTTCAGAGTTTTGGGACT 57.220 40.909 0.00 0.00 45.88 3.85
535 538 4.709250 AGAACTTCAGAGTTTTGGGACTC 58.291 43.478 0.00 0.00 45.88 3.36
544 547 4.933330 GAGTTTTGGGACTCTTTTTCACC 58.067 43.478 0.00 0.00 42.18 4.02
545 548 4.610333 AGTTTTGGGACTCTTTTTCACCT 58.390 39.130 0.00 0.00 0.00 4.00
546 549 4.402474 AGTTTTGGGACTCTTTTTCACCTG 59.598 41.667 0.00 0.00 0.00 4.00
547 550 3.943671 TTGGGACTCTTTTTCACCTGA 57.056 42.857 0.00 0.00 0.00 3.86
548 551 3.208747 TGGGACTCTTTTTCACCTGAC 57.791 47.619 0.00 0.00 0.00 3.51
549 552 2.777692 TGGGACTCTTTTTCACCTGACT 59.222 45.455 0.00 0.00 0.00 3.41
550 553 3.202151 TGGGACTCTTTTTCACCTGACTT 59.798 43.478 0.00 0.00 0.00 3.01
551 554 4.207955 GGGACTCTTTTTCACCTGACTTT 58.792 43.478 0.00 0.00 0.00 2.66
552 555 5.104277 TGGGACTCTTTTTCACCTGACTTTA 60.104 40.000 0.00 0.00 0.00 1.85
553 556 6.004574 GGGACTCTTTTTCACCTGACTTTAT 58.995 40.000 0.00 0.00 0.00 1.40
554 557 6.490381 GGGACTCTTTTTCACCTGACTTTATT 59.510 38.462 0.00 0.00 0.00 1.40
555 558 7.308649 GGGACTCTTTTTCACCTGACTTTATTC 60.309 40.741 0.00 0.00 0.00 1.75
556 559 7.445707 GGACTCTTTTTCACCTGACTTTATTCT 59.554 37.037 0.00 0.00 0.00 2.40
557 560 8.753497 ACTCTTTTTCACCTGACTTTATTCTT 57.247 30.769 0.00 0.00 0.00 2.52
558 561 8.841300 ACTCTTTTTCACCTGACTTTATTCTTC 58.159 33.333 0.00 0.00 0.00 2.87
559 562 8.166422 TCTTTTTCACCTGACTTTATTCTTCC 57.834 34.615 0.00 0.00 0.00 3.46
560 563 7.777910 TCTTTTTCACCTGACTTTATTCTTCCA 59.222 33.333 0.00 0.00 0.00 3.53
561 564 7.889873 TTTTCACCTGACTTTATTCTTCCAA 57.110 32.000 0.00 0.00 0.00 3.53
562 565 7.889873 TTTCACCTGACTTTATTCTTCCAAA 57.110 32.000 0.00 0.00 0.00 3.28
563 566 8.477419 TTTCACCTGACTTTATTCTTCCAAAT 57.523 30.769 0.00 0.00 0.00 2.32
564 567 9.581289 TTTCACCTGACTTTATTCTTCCAAATA 57.419 29.630 0.00 0.00 0.00 1.40
565 568 9.753674 TTCACCTGACTTTATTCTTCCAAATAT 57.246 29.630 0.00 0.00 0.00 1.28
566 569 9.753674 TCACCTGACTTTATTCTTCCAAATATT 57.246 29.630 0.00 0.00 0.00 1.28
567 570 9.793252 CACCTGACTTTATTCTTCCAAATATTG 57.207 33.333 0.00 0.00 0.00 1.90
568 571 9.533831 ACCTGACTTTATTCTTCCAAATATTGT 57.466 29.630 0.00 0.00 0.00 2.71
579 582 8.902540 TCTTCCAAATATTGTAAGCGATATGT 57.097 30.769 0.00 0.00 33.21 2.29
580 583 8.988934 TCTTCCAAATATTGTAAGCGATATGTC 58.011 33.333 0.00 0.00 33.21 3.06
581 584 8.902540 TTCCAAATATTGTAAGCGATATGTCT 57.097 30.769 0.00 0.00 33.21 3.41
582 585 9.990360 TTCCAAATATTGTAAGCGATATGTCTA 57.010 29.630 0.00 0.00 33.21 2.59
590 593 9.710900 ATTGTAAGCGATATGTCTATCATTTGA 57.289 29.630 0.00 0.00 37.91 2.69
591 594 8.748380 TGTAAGCGATATGTCTATCATTTGAG 57.252 34.615 0.00 0.00 37.91 3.02
592 595 7.814587 TGTAAGCGATATGTCTATCATTTGAGG 59.185 37.037 0.00 0.00 37.91 3.86
593 596 6.596309 AGCGATATGTCTATCATTTGAGGA 57.404 37.500 0.00 0.00 37.91 3.71
594 597 6.997655 AGCGATATGTCTATCATTTGAGGAA 58.002 36.000 0.00 0.00 37.91 3.36
595 598 7.619050 AGCGATATGTCTATCATTTGAGGAAT 58.381 34.615 0.00 0.00 37.91 3.01
596 599 8.753133 AGCGATATGTCTATCATTTGAGGAATA 58.247 33.333 0.00 0.00 37.91 1.75
597 600 9.371136 GCGATATGTCTATCATTTGAGGAATAA 57.629 33.333 0.00 0.00 37.91 1.40
634 637 2.802792 CGGTAATCGAGCCGTGGA 59.197 61.111 15.03 0.00 42.73 4.02
635 638 1.588139 CGGTAATCGAGCCGTGGAC 60.588 63.158 15.03 0.00 42.73 4.02
636 639 1.227176 GGTAATCGAGCCGTGGACC 60.227 63.158 0.00 0.00 0.00 4.46
637 640 1.588139 GTAATCGAGCCGTGGACCG 60.588 63.158 0.00 0.00 0.00 4.79
638 641 1.750018 TAATCGAGCCGTGGACCGA 60.750 57.895 5.72 5.72 39.56 4.69
639 642 1.721664 TAATCGAGCCGTGGACCGAG 61.722 60.000 8.55 0.00 39.56 4.63
642 645 4.070552 GAGCCGTGGACCGAGCTT 62.071 66.667 4.41 0.00 41.23 3.74
643 646 4.379243 AGCCGTGGACCGAGCTTG 62.379 66.667 0.00 0.00 39.14 4.01
644 647 4.373116 GCCGTGGACCGAGCTTGA 62.373 66.667 1.22 0.00 39.56 3.02
645 648 2.125912 CCGTGGACCGAGCTTGAG 60.126 66.667 1.22 0.00 39.56 3.02
646 649 2.651361 CGTGGACCGAGCTTGAGT 59.349 61.111 1.22 0.00 39.56 3.41
647 650 1.734477 CGTGGACCGAGCTTGAGTG 60.734 63.158 1.22 0.00 39.56 3.51
648 651 1.666011 GTGGACCGAGCTTGAGTGA 59.334 57.895 1.22 0.00 0.00 3.41
649 652 0.389166 GTGGACCGAGCTTGAGTGAG 60.389 60.000 1.22 0.00 0.00 3.51
650 653 0.827925 TGGACCGAGCTTGAGTGAGT 60.828 55.000 1.22 0.00 0.00 3.41
651 654 0.389166 GGACCGAGCTTGAGTGAGTG 60.389 60.000 1.22 0.00 0.00 3.51
652 655 0.389166 GACCGAGCTTGAGTGAGTGG 60.389 60.000 1.22 0.00 0.00 4.00
653 656 1.739562 CCGAGCTTGAGTGAGTGGC 60.740 63.158 1.22 0.00 0.00 5.01
654 657 1.291588 CGAGCTTGAGTGAGTGGCT 59.708 57.895 0.00 0.00 35.86 4.75
655 658 0.735632 CGAGCTTGAGTGAGTGGCTC 60.736 60.000 0.00 0.00 43.86 4.70
656 659 0.607620 GAGCTTGAGTGAGTGGCTCT 59.392 55.000 0.00 0.00 43.92 4.09
657 660 0.321021 AGCTTGAGTGAGTGGCTCTG 59.679 55.000 0.00 0.00 34.30 3.35
658 661 0.673022 GCTTGAGTGAGTGGCTCTGG 60.673 60.000 0.00 0.00 34.30 3.86
659 662 0.673022 CTTGAGTGAGTGGCTCTGGC 60.673 60.000 0.00 0.00 34.30 4.85
660 663 1.410050 TTGAGTGAGTGGCTCTGGCA 61.410 55.000 0.00 0.00 40.87 4.92
667 670 3.143338 TGGCTCTGGCACAACGTA 58.857 55.556 0.00 0.00 38.70 3.57
668 671 1.448069 TGGCTCTGGCACAACGTAA 59.552 52.632 0.00 0.00 38.70 3.18
669 672 0.036164 TGGCTCTGGCACAACGTAAT 59.964 50.000 0.00 0.00 38.70 1.89
670 673 0.727398 GGCTCTGGCACAACGTAATC 59.273 55.000 0.00 0.00 38.70 1.75
671 674 0.370273 GCTCTGGCACAACGTAATCG 59.630 55.000 0.00 0.00 38.70 3.34
672 675 1.990799 CTCTGGCACAACGTAATCGA 58.009 50.000 0.00 0.00 38.70 3.59
673 676 1.920574 CTCTGGCACAACGTAATCGAG 59.079 52.381 0.00 0.00 38.70 4.04
674 677 0.370273 CTGGCACAACGTAATCGAGC 59.630 55.000 0.00 0.00 38.70 5.03
675 678 1.017177 TGGCACAACGTAATCGAGCC 61.017 55.000 8.15 8.15 40.89 4.70
676 679 0.739813 GGCACAACGTAATCGAGCCT 60.740 55.000 0.00 0.00 39.21 4.58
677 680 0.645868 GCACAACGTAATCGAGCCTC 59.354 55.000 0.00 0.00 40.62 4.70
678 681 1.990799 CACAACGTAATCGAGCCTCA 58.009 50.000 0.00 0.00 40.62 3.86
679 682 2.540515 CACAACGTAATCGAGCCTCAT 58.459 47.619 0.00 0.00 40.62 2.90
680 683 2.930040 CACAACGTAATCGAGCCTCATT 59.070 45.455 0.00 0.00 40.62 2.57
681 684 3.000322 CACAACGTAATCGAGCCTCATTC 60.000 47.826 0.00 0.00 40.62 2.67
682 685 2.121116 ACGTAATCGAGCCTCATTCG 57.879 50.000 0.00 1.35 40.62 3.34
683 686 0.778815 CGTAATCGAGCCTCATTCGC 59.221 55.000 0.00 0.00 39.71 4.70
684 687 1.852942 GTAATCGAGCCTCATTCGCA 58.147 50.000 0.00 0.00 37.94 5.10
685 688 1.789464 GTAATCGAGCCTCATTCGCAG 59.211 52.381 0.00 0.00 37.94 5.18
686 689 0.461548 AATCGAGCCTCATTCGCAGA 59.538 50.000 0.00 0.00 37.94 4.26
687 690 0.461548 ATCGAGCCTCATTCGCAGAA 59.538 50.000 0.00 0.00 45.90 3.02
688 691 0.246360 TCGAGCCTCATTCGCAGAAA 59.754 50.000 0.00 0.00 45.90 2.52
689 692 1.078709 CGAGCCTCATTCGCAGAAAA 58.921 50.000 0.00 0.00 45.90 2.29
690 693 1.061711 CGAGCCTCATTCGCAGAAAAG 59.938 52.381 0.00 0.00 45.90 2.27
691 694 1.399791 GAGCCTCATTCGCAGAAAAGG 59.600 52.381 13.66 13.66 45.90 3.11
692 695 1.003580 AGCCTCATTCGCAGAAAAGGA 59.996 47.619 18.40 8.00 45.90 3.36
693 696 1.812571 GCCTCATTCGCAGAAAAGGAA 59.187 47.619 18.40 0.48 45.90 3.36
694 697 2.228822 GCCTCATTCGCAGAAAAGGAAA 59.771 45.455 18.40 0.00 45.90 3.13
695 698 3.305335 GCCTCATTCGCAGAAAAGGAAAA 60.305 43.478 18.40 0.00 45.90 2.29
696 699 4.795962 GCCTCATTCGCAGAAAAGGAAAAA 60.796 41.667 18.40 0.00 45.90 1.94
731 734 4.823790 AAAACAAAACGTAATCGAGCCT 57.176 36.364 0.00 0.00 40.62 4.58
733 736 3.034721 ACAAAACGTAATCGAGCCTGA 57.965 42.857 0.00 0.00 40.62 3.86
754 758 4.330620 TGAGACCAAGTTTTACACGTTCAC 59.669 41.667 0.00 0.00 0.00 3.18
756 760 3.260740 ACCAAGTTTTACACGTTCACGA 58.739 40.909 6.30 0.00 43.02 4.35
770 774 0.940519 TCACGAAAACCGAACGCGAT 60.941 50.000 15.93 0.00 41.76 4.58
771 775 0.709467 CACGAAAACCGAACGCGATA 59.291 50.000 15.93 0.00 41.76 2.92
795 799 4.085876 GCAAGTGCAGGGTCACAT 57.914 55.556 0.00 0.00 41.59 3.21
825 830 2.223745 TCCAGGCTGGTAAACGAAAAC 58.776 47.619 31.60 0.00 39.03 2.43
886 897 0.318784 GCCTCACGCCGACCTAATAG 60.319 60.000 0.00 0.00 0.00 1.73
917 928 6.817765 ATTCACAAATATAAATCCGGCGAT 57.182 33.333 9.30 0.00 0.00 4.58
1041 1066 1.444553 GGTGAGCCTCTTCGACGTG 60.445 63.158 0.00 0.00 0.00 4.49
1044 1069 1.289380 GAGCCTCTTCGACGTGGTT 59.711 57.895 11.15 5.55 0.00 3.67
1065 1090 1.892862 CGAGACCTCCGTATCCGCT 60.893 63.158 0.00 0.00 0.00 5.52
1313 1344 3.682696 TGCACCTATATCCGATACGTCT 58.317 45.455 0.00 0.00 0.00 4.18
1336 1367 6.056090 TCCATGTATGTGTTGCTTAGGTTA 57.944 37.500 0.00 0.00 0.00 2.85
1337 1368 5.878116 TCCATGTATGTGTTGCTTAGGTTAC 59.122 40.000 0.00 0.00 0.00 2.50
1358 1389 3.181466 ACTGGTTTGTGCCCTCAATTTTC 60.181 43.478 0.00 0.00 0.00 2.29
1395 1427 3.572255 GGAGGTGTTCTAGAGGCTAGATG 59.428 52.174 5.12 0.00 0.00 2.90
1405 1437 4.137879 GCTAGATGCCTGGTGCTG 57.862 61.111 0.00 0.00 42.00 4.41
1424 1457 5.009210 GTGCTGTGGTGAATTTGTTAGGTTA 59.991 40.000 0.00 0.00 0.00 2.85
1439 1507 3.508845 AGGTTAATGCTTGTGAGGTGT 57.491 42.857 0.00 0.00 0.00 4.16
1444 1512 2.175878 ATGCTTGTGAGGTGTCTGTC 57.824 50.000 0.00 0.00 0.00 3.51
1446 1514 0.394565 GCTTGTGAGGTGTCTGTCCT 59.605 55.000 0.00 0.00 38.09 3.85
1452 1520 3.901222 TGTGAGGTGTCTGTCCTTATTGA 59.099 43.478 0.00 0.00 35.20 2.57
1456 1524 4.848357 AGGTGTCTGTCCTTATTGATTGG 58.152 43.478 0.00 0.00 30.18 3.16
1464 1532 6.208599 TCTGTCCTTATTGATTGGTTTGTTCC 59.791 38.462 0.00 0.00 0.00 3.62
1522 1591 1.446966 GTGCTCGAGGCTGAAGGTC 60.447 63.158 15.58 0.00 42.39 3.85
1647 1716 5.878669 GGAAGTTGGTTACAGTATCCGATTT 59.121 40.000 5.67 5.67 0.00 2.17
1688 1757 8.397906 TCACAAAACTGTTCTCAAGTAAGATTG 58.602 33.333 0.00 0.00 0.00 2.67
1731 1800 3.403038 AGAACAGTATCAGTTGCACCAC 58.597 45.455 0.00 0.00 0.00 4.16
2079 2148 3.108376 GGTTCCTGGTAGACTTCATCCT 58.892 50.000 0.00 0.00 0.00 3.24
2097 2166 8.539117 TTCATCCTGTTGAGATCTTCTATACA 57.461 34.615 0.00 0.00 0.00 2.29
2415 2484 2.846206 TGCTGAGACATCCCTAACCATT 59.154 45.455 0.00 0.00 0.00 3.16
2530 2599 2.986306 AAGGCAAGTGCGCATCAGC 61.986 57.895 15.91 17.68 43.26 4.26
2613 2682 6.719370 AGAGTTTTAATGGTGATTTACAGCCA 59.281 34.615 0.00 0.00 45.18 4.75
2644 2713 3.821033 CCCAGAAATTCTTCGGTCAAACT 59.179 43.478 0.00 0.00 36.61 2.66
2721 2790 0.467384 ACTTCATGGATCCTCCTGCG 59.533 55.000 14.23 5.48 37.46 5.18
2933 3003 7.458397 TCAGGTATGTCAACTAACAATTCCTT 58.542 34.615 0.00 0.00 31.81 3.36
2936 3006 7.393515 AGGTATGTCAACTAACAATTCCTTTCC 59.606 37.037 0.00 0.00 31.81 3.13
2937 3007 7.175990 GGTATGTCAACTAACAATTCCTTTCCA 59.824 37.037 0.00 0.00 31.81 3.53
2938 3008 7.781324 ATGTCAACTAACAATTCCTTTCCAT 57.219 32.000 0.00 0.00 31.81 3.41
2950 3023 5.549742 TTCCTTTCCATTTGCATTTCTGT 57.450 34.783 0.00 0.00 0.00 3.41
2998 3071 0.179103 GCACTGTTTTGCTTGCACCT 60.179 50.000 0.00 0.00 39.59 4.00
3421 3496 6.312426 GCCTATAACCATTCTCATTCGATCTG 59.688 42.308 0.00 0.00 0.00 2.90
3443 3518 1.247567 CCCGGTCAGACTGCAATTTT 58.752 50.000 3.51 0.00 0.00 1.82
3847 3922 0.465460 GCATGGACCATAAGCCGGAA 60.465 55.000 5.05 0.00 0.00 4.30
3931 4006 1.473278 CGTGGAGAGTGGTAAGTCCTC 59.527 57.143 0.00 0.00 37.07 3.71
3997 4072 4.576053 TGACAATGTTGACCTTTCTCTGTG 59.424 41.667 0.00 0.00 0.00 3.66
4159 4234 2.986019 TCATTCTTCTGGTCCCTTGGAA 59.014 45.455 0.00 0.00 31.38 3.53
4160 4235 3.593328 TCATTCTTCTGGTCCCTTGGAAT 59.407 43.478 0.00 0.00 31.38 3.01
4161 4236 3.439857 TTCTTCTGGTCCCTTGGAATG 57.560 47.619 0.00 0.00 31.38 2.67
4162 4237 2.348472 TCTTCTGGTCCCTTGGAATGT 58.652 47.619 0.00 0.00 31.38 2.71
4163 4238 2.040278 TCTTCTGGTCCCTTGGAATGTG 59.960 50.000 0.00 0.00 31.38 3.21
4230 4308 7.662669 CACCATTGTCATGATATCTTCCATGTA 59.337 37.037 0.00 0.00 40.59 2.29
4252 4330 7.913789 TGTAGTAGTTTTCCAGTATTGTGGAT 58.086 34.615 0.00 0.00 46.31 3.41
4269 4347 7.806409 TTGTGGATGGTGAAATCACTATATG 57.194 36.000 11.72 0.00 46.03 1.78
4314 4392 3.814842 TGCTACTGCATTCCGAATTATGG 59.185 43.478 0.00 0.00 45.31 2.74
4315 4393 4.065088 GCTACTGCATTCCGAATTATGGA 58.935 43.478 0.00 0.00 39.41 3.41
4316 4394 4.153117 GCTACTGCATTCCGAATTATGGAG 59.847 45.833 6.04 6.04 43.38 3.86
4479 4557 4.684703 GCTGACATCGTACTGTGTTTACTT 59.315 41.667 2.15 0.00 0.00 2.24
4480 4558 5.164080 GCTGACATCGTACTGTGTTTACTTC 60.164 44.000 2.15 0.00 0.00 3.01
4490 4568 6.679327 ACTGTGTTTACTTCCTTTTGAGAC 57.321 37.500 0.00 0.00 0.00 3.36
4522 4600 5.695424 AACTAGTCAGGAAATTACTCCCC 57.305 43.478 0.00 0.00 35.95 4.81
4586 4664 9.832445 TGAATACAGAAAATATGACTTAGGGTC 57.168 33.333 0.00 0.00 44.70 4.46
4598 4676 5.579564 GACTTAGGGTCACGTCTTAGATT 57.420 43.478 0.00 0.00 43.94 2.40
4599 4677 5.963594 GACTTAGGGTCACGTCTTAGATTT 58.036 41.667 0.00 0.00 43.94 2.17
4600 4678 5.721232 ACTTAGGGTCACGTCTTAGATTTG 58.279 41.667 0.00 0.00 0.00 2.32
4601 4679 5.245526 ACTTAGGGTCACGTCTTAGATTTGT 59.754 40.000 0.00 0.00 0.00 2.83
4673 4799 5.291128 ACTGTTTACTGTGCTATGCGTATTC 59.709 40.000 0.00 0.00 0.00 1.75
4679 4805 0.599991 TGCTATGCGTATTCGGCCTG 60.600 55.000 0.00 0.00 37.56 4.85
4680 4806 0.319555 GCTATGCGTATTCGGCCTGA 60.320 55.000 0.00 0.00 37.56 3.86
4681 4807 1.702886 CTATGCGTATTCGGCCTGAG 58.297 55.000 0.00 0.00 37.56 3.35
4682 4808 1.000163 CTATGCGTATTCGGCCTGAGT 60.000 52.381 0.00 0.00 37.56 3.41
4683 4809 0.530650 ATGCGTATTCGGCCTGAGTG 60.531 55.000 0.00 0.00 37.56 3.51
4684 4810 1.883084 GCGTATTCGGCCTGAGTGG 60.883 63.158 0.00 0.00 37.56 4.00
4685 4811 1.813859 CGTATTCGGCCTGAGTGGA 59.186 57.895 0.00 0.00 38.35 4.02
4686 4812 0.174845 CGTATTCGGCCTGAGTGGAA 59.825 55.000 0.00 0.00 38.35 3.53
4687 4813 1.202533 CGTATTCGGCCTGAGTGGAAT 60.203 52.381 0.00 3.74 38.35 3.01
4689 4815 3.491964 CGTATTCGGCCTGAGTGGAATTA 60.492 47.826 0.00 0.00 38.35 1.40
4690 4816 3.644966 ATTCGGCCTGAGTGGAATTAA 57.355 42.857 0.00 0.00 38.35 1.40
4696 5080 3.381590 GGCCTGAGTGGAATTAATTGACC 59.618 47.826 5.17 2.15 38.35 4.02
4736 5120 5.504392 GCTTTTGCAAAATGAAAAGGTGAG 58.496 37.500 24.06 9.55 46.58 3.51
4737 5121 5.294060 GCTTTTGCAAAATGAAAAGGTGAGA 59.706 36.000 24.06 0.00 46.58 3.27
4738 5122 6.183360 GCTTTTGCAAAATGAAAAGGTGAGAA 60.183 34.615 24.06 0.00 46.58 2.87
4739 5123 7.626028 GCTTTTGCAAAATGAAAAGGTGAGAAA 60.626 33.333 24.06 0.00 46.58 2.52
4740 5124 7.678947 TTTGCAAAATGAAAAGGTGAGAAAA 57.321 28.000 10.02 0.00 0.00 2.29
4741 5125 7.678947 TTGCAAAATGAAAAGGTGAGAAAAA 57.321 28.000 0.00 0.00 0.00 1.94
4790 5203 4.394712 CGCCGGCCACCTTTCTCT 62.395 66.667 23.46 0.00 0.00 3.10
4791 5204 2.436824 GCCGGCCACCTTTCTCTC 60.437 66.667 18.11 0.00 0.00 3.20
4792 5205 2.269241 CCGGCCACCTTTCTCTCC 59.731 66.667 2.24 0.00 0.00 3.71
4793 5206 2.294078 CCGGCCACCTTTCTCTCCT 61.294 63.158 2.24 0.00 0.00 3.69
4794 5207 1.219393 CGGCCACCTTTCTCTCCTC 59.781 63.158 2.24 0.00 0.00 3.71
4795 5208 1.604915 GGCCACCTTTCTCTCCTCC 59.395 63.158 0.00 0.00 0.00 4.30
4796 5209 1.604915 GCCACCTTTCTCTCCTCCC 59.395 63.158 0.00 0.00 0.00 4.30
4797 5210 1.916206 GCCACCTTTCTCTCCTCCCC 61.916 65.000 0.00 0.00 0.00 4.81
4798 5211 0.252927 CCACCTTTCTCTCCTCCCCT 60.253 60.000 0.00 0.00 0.00 4.79
4817 5230 3.721706 CTCCCCTGGTGCTCCCAC 61.722 72.222 1.59 0.00 38.72 4.61
4936 8355 4.371417 CCCATGCCTGGCAGGTGT 62.371 66.667 32.80 19.69 43.65 4.16
4948 8367 2.200370 AGGTGTCCGGTGGTCTGA 59.800 61.111 0.00 0.00 0.00 3.27
4950 8369 1.301479 GGTGTCCGGTGGTCTGAAC 60.301 63.158 0.00 0.00 0.00 3.18
4951 8370 1.746517 GTGTCCGGTGGTCTGAACT 59.253 57.895 0.00 0.00 0.00 3.01
4952 8371 0.106149 GTGTCCGGTGGTCTGAACTT 59.894 55.000 0.00 0.00 0.00 2.66
4954 8373 0.391597 GTCCGGTGGTCTGAACTTCA 59.608 55.000 0.00 0.00 0.00 3.02
4955 8374 0.679505 TCCGGTGGTCTGAACTTCAG 59.320 55.000 12.02 12.02 45.59 3.02
4956 8375 0.951040 CCGGTGGTCTGAACTTCAGC 60.951 60.000 13.24 8.75 43.95 4.26
4958 8377 1.272490 CGGTGGTCTGAACTTCAGCTA 59.728 52.381 13.24 4.92 43.95 3.32
4959 8378 2.689646 GGTGGTCTGAACTTCAGCTAC 58.310 52.381 13.24 14.46 43.95 3.58
4962 8381 2.563179 TGGTCTGAACTTCAGCTACTCC 59.437 50.000 13.24 10.33 43.95 3.85
4963 8382 2.563179 GGTCTGAACTTCAGCTACTCCA 59.437 50.000 13.24 0.00 43.95 3.86
4964 8383 3.367910 GGTCTGAACTTCAGCTACTCCAG 60.368 52.174 13.24 0.00 43.95 3.86
4976 8395 3.458189 GCTACTCCAGCGACATGTATTT 58.542 45.455 0.00 0.00 41.37 1.40
4977 8396 3.491267 GCTACTCCAGCGACATGTATTTC 59.509 47.826 0.00 0.00 41.37 2.17
4978 8397 2.540515 ACTCCAGCGACATGTATTTCG 58.459 47.619 0.00 0.00 38.31 3.46
4981 8400 4.037565 ACTCCAGCGACATGTATTTCGATA 59.962 41.667 8.68 0.00 37.43 2.92
4984 8403 4.148871 CCAGCGACATGTATTTCGATACAG 59.851 45.833 8.68 1.24 39.99 2.74
4985 8404 4.976116 CAGCGACATGTATTTCGATACAGA 59.024 41.667 8.68 0.00 39.99 3.41
4986 8405 5.116225 CAGCGACATGTATTTCGATACAGAG 59.884 44.000 8.68 3.38 39.99 3.35
4987 8406 5.008712 AGCGACATGTATTTCGATACAGAGA 59.991 40.000 8.68 0.00 39.99 3.10
4988 8407 5.340932 GCGACATGTATTTCGATACAGAGAG 59.659 44.000 8.68 0.00 39.99 3.20
4990 8409 6.794636 CGACATGTATTTCGATACAGAGAGAG 59.205 42.308 0.00 0.00 39.99 3.20
4991 8410 7.519168 CGACATGTATTTCGATACAGAGAGAGT 60.519 40.741 0.00 0.00 39.99 3.24
4992 8411 8.678593 ACATGTATTTCGATACAGAGAGAGTA 57.321 34.615 0.00 0.00 39.99 2.59
4993 8412 9.290988 ACATGTATTTCGATACAGAGAGAGTAT 57.709 33.333 0.00 0.00 39.99 2.12
5007 8426 9.877178 ACAGAGAGAGTATAATTGAATTTCGTT 57.123 29.630 0.00 0.00 0.00 3.85
5055 8474 0.320771 TCGAGTTCTTCTGCCAAGGC 60.321 55.000 3.61 3.61 42.35 4.35
5107 8526 6.168270 AGTTGGATCTGACTAAATCTAGGC 57.832 41.667 0.00 0.00 33.18 3.93
5113 8532 7.290014 TGGATCTGACTAAATCTAGGCATTGTA 59.710 37.037 0.00 0.00 42.54 2.41
5114 8533 8.150945 GGATCTGACTAAATCTAGGCATTGTAA 58.849 37.037 0.00 0.00 42.54 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 0.182775 AAGCCGTTCTGTCAGGGTTT 59.817 50.000 0.00 0.00 42.33 3.27
7 8 0.182775 AAAGCCGTTCTGTCAGGGTT 59.817 50.000 0.00 0.00 46.29 4.11
8 9 0.535102 CAAAGCCGTTCTGTCAGGGT 60.535 55.000 0.00 0.00 37.35 4.34
29 30 2.457813 TGTAGCCGGTACCCTAATCA 57.542 50.000 6.25 0.00 0.00 2.57
41 42 4.223320 ACATGAACAAAGTTTGTAGCCG 57.777 40.909 21.14 12.72 44.59 5.52
59 60 3.900601 TGGCTGGTTTGGTGAATTTACAT 59.099 39.130 2.50 0.00 0.00 2.29
60 61 3.300388 TGGCTGGTTTGGTGAATTTACA 58.700 40.909 2.50 0.00 0.00 2.41
62 63 3.070302 GGTTGGCTGGTTTGGTGAATTTA 59.930 43.478 0.00 0.00 0.00 1.40
93 94 4.164221 TCAAGTTTCCTCCATATCTGGTCC 59.836 45.833 0.00 0.00 43.61 4.46
113 114 4.038522 TGATTTTCACAAAGCCCGAATCAA 59.961 37.500 0.00 0.00 31.38 2.57
114 115 3.571828 TGATTTTCACAAAGCCCGAATCA 59.428 39.130 0.00 0.00 31.73 2.57
210 211 2.129607 CAGGTTGCAGCAACAATGAAC 58.870 47.619 33.86 18.55 45.11 3.18
218 219 1.108727 CAGAACCCAGGTTGCAGCAA 61.109 55.000 6.84 2.83 38.60 3.91
248 249 1.604147 TTCCGCAGAATCAGCCGAGA 61.604 55.000 0.00 0.00 0.00 4.04
249 250 0.740868 TTTCCGCAGAATCAGCCGAG 60.741 55.000 0.00 0.00 0.00 4.63
359 362 4.908601 ATACACATCAGGGTCAGAAACA 57.091 40.909 0.00 0.00 0.00 2.83
476 479 1.042229 TTGCCAAACAATCTGCAGCT 58.958 45.000 9.47 0.00 34.81 4.24
477 480 1.868469 TTTGCCAAACAATCTGCAGC 58.132 45.000 9.47 0.00 38.31 5.25
478 481 3.865224 GTTTTGCCAAACAATCTGCAG 57.135 42.857 7.63 7.63 41.85 4.41
509 512 5.467063 GTCCCAAAACTCTGAAGTTCTAGTG 59.533 44.000 10.87 7.26 45.07 2.74
524 527 4.401202 TCAGGTGAAAAAGAGTCCCAAAAC 59.599 41.667 0.00 0.00 0.00 2.43
526 529 3.951680 GTCAGGTGAAAAAGAGTCCCAAA 59.048 43.478 0.00 0.00 0.00 3.28
527 530 3.202151 AGTCAGGTGAAAAAGAGTCCCAA 59.798 43.478 0.00 0.00 0.00 4.12
528 531 2.777692 AGTCAGGTGAAAAAGAGTCCCA 59.222 45.455 0.00 0.00 0.00 4.37
529 532 3.493767 AGTCAGGTGAAAAAGAGTCCC 57.506 47.619 0.00 0.00 0.00 4.46
530 533 7.445707 AGAATAAAGTCAGGTGAAAAAGAGTCC 59.554 37.037 0.00 0.00 0.00 3.85
531 534 8.384607 AGAATAAAGTCAGGTGAAAAAGAGTC 57.615 34.615 0.00 0.00 0.00 3.36
532 535 8.753497 AAGAATAAAGTCAGGTGAAAAAGAGT 57.247 30.769 0.00 0.00 0.00 3.24
533 536 8.293157 GGAAGAATAAAGTCAGGTGAAAAAGAG 58.707 37.037 0.00 0.00 0.00 2.85
534 537 7.777910 TGGAAGAATAAAGTCAGGTGAAAAAGA 59.222 33.333 0.00 0.00 0.00 2.52
535 538 7.940850 TGGAAGAATAAAGTCAGGTGAAAAAG 58.059 34.615 0.00 0.00 0.00 2.27
536 539 7.889873 TGGAAGAATAAAGTCAGGTGAAAAA 57.110 32.000 0.00 0.00 0.00 1.94
537 540 7.889873 TTGGAAGAATAAAGTCAGGTGAAAA 57.110 32.000 0.00 0.00 0.00 2.29
538 541 7.889873 TTTGGAAGAATAAAGTCAGGTGAAA 57.110 32.000 0.00 0.00 0.00 2.69
539 542 9.753674 ATATTTGGAAGAATAAAGTCAGGTGAA 57.246 29.630 0.00 0.00 0.00 3.18
540 543 9.753674 AATATTTGGAAGAATAAAGTCAGGTGA 57.246 29.630 0.00 0.00 0.00 4.02
541 544 9.793252 CAATATTTGGAAGAATAAAGTCAGGTG 57.207 33.333 0.00 0.00 0.00 4.00
542 545 9.533831 ACAATATTTGGAAGAATAAAGTCAGGT 57.466 29.630 0.00 0.00 34.12 4.00
556 559 8.902540 AGACATATCGCTTACAATATTTGGAA 57.097 30.769 0.00 0.00 34.12 3.53
564 567 9.710900 TCAAATGATAGACATATCGCTTACAAT 57.289 29.630 0.00 0.00 40.72 2.71
565 568 9.196552 CTCAAATGATAGACATATCGCTTACAA 57.803 33.333 0.00 0.00 40.72 2.41
566 569 7.814587 CCTCAAATGATAGACATATCGCTTACA 59.185 37.037 0.00 0.00 40.72 2.41
567 570 8.029522 TCCTCAAATGATAGACATATCGCTTAC 58.970 37.037 0.00 0.00 40.72 2.34
568 571 8.122472 TCCTCAAATGATAGACATATCGCTTA 57.878 34.615 0.00 0.00 40.72 3.09
569 572 6.997655 TCCTCAAATGATAGACATATCGCTT 58.002 36.000 0.00 0.00 40.72 4.68
570 573 6.596309 TCCTCAAATGATAGACATATCGCT 57.404 37.500 0.00 0.00 40.72 4.93
571 574 7.840342 ATTCCTCAAATGATAGACATATCGC 57.160 36.000 0.00 0.00 40.72 4.58
610 613 1.461897 CGGCTCGATTACCGTGTTTTT 59.538 47.619 12.15 0.00 44.46 1.94
611 614 1.073177 CGGCTCGATTACCGTGTTTT 58.927 50.000 12.15 0.00 44.46 2.43
612 615 2.745728 CGGCTCGATTACCGTGTTT 58.254 52.632 12.15 0.00 44.46 2.83
613 616 4.489249 CGGCTCGATTACCGTGTT 57.511 55.556 12.15 0.00 44.46 3.32
618 621 1.227176 GGTCCACGGCTCGATTACC 60.227 63.158 1.50 2.49 0.00 2.85
619 622 1.588139 CGGTCCACGGCTCGATTAC 60.588 63.158 1.50 0.00 39.42 1.89
620 623 1.721664 CTCGGTCCACGGCTCGATTA 61.722 60.000 1.50 0.00 44.45 1.75
621 624 3.064987 CTCGGTCCACGGCTCGATT 62.065 63.158 1.50 0.00 44.45 3.34
622 625 3.518998 CTCGGTCCACGGCTCGAT 61.519 66.667 1.50 0.00 44.45 3.59
625 628 4.070552 AAGCTCGGTCCACGGCTC 62.071 66.667 0.00 0.00 44.49 4.70
626 629 4.379243 CAAGCTCGGTCCACGGCT 62.379 66.667 0.00 0.00 46.25 5.52
627 630 4.373116 TCAAGCTCGGTCCACGGC 62.373 66.667 0.00 0.00 44.45 5.68
628 631 2.125912 CTCAAGCTCGGTCCACGG 60.126 66.667 0.00 0.00 44.45 4.94
629 632 1.734477 CACTCAAGCTCGGTCCACG 60.734 63.158 0.00 0.00 46.11 4.94
630 633 0.389166 CTCACTCAAGCTCGGTCCAC 60.389 60.000 0.00 0.00 0.00 4.02
631 634 0.827925 ACTCACTCAAGCTCGGTCCA 60.828 55.000 0.00 0.00 0.00 4.02
632 635 0.389166 CACTCACTCAAGCTCGGTCC 60.389 60.000 0.00 0.00 0.00 4.46
633 636 0.389166 CCACTCACTCAAGCTCGGTC 60.389 60.000 0.00 0.00 0.00 4.79
634 637 1.668294 CCACTCACTCAAGCTCGGT 59.332 57.895 0.00 0.00 0.00 4.69
635 638 1.739562 GCCACTCACTCAAGCTCGG 60.740 63.158 0.00 0.00 0.00 4.63
636 639 0.735632 GAGCCACTCACTCAAGCTCG 60.736 60.000 0.00 0.00 40.43 5.03
637 640 3.135942 GAGCCACTCACTCAAGCTC 57.864 57.895 0.00 0.00 42.74 4.09
638 641 0.321021 CAGAGCCACTCACTCAAGCT 59.679 55.000 0.00 0.00 36.58 3.74
639 642 0.673022 CCAGAGCCACTCACTCAAGC 60.673 60.000 0.00 0.00 36.58 4.01
640 643 0.673022 GCCAGAGCCACTCACTCAAG 60.673 60.000 0.00 0.00 36.58 3.02
641 644 1.372683 GCCAGAGCCACTCACTCAA 59.627 57.895 0.00 0.00 36.58 3.02
642 645 1.838396 TGCCAGAGCCACTCACTCA 60.838 57.895 0.00 0.00 38.69 3.41
643 646 1.375268 GTGCCAGAGCCACTCACTC 60.375 63.158 0.00 0.00 38.69 3.51
644 647 1.699054 TTGTGCCAGAGCCACTCACT 61.699 55.000 0.00 0.00 38.69 3.41
645 648 1.227943 TTGTGCCAGAGCCACTCAC 60.228 57.895 0.00 0.00 38.69 3.51
646 649 1.227943 GTTGTGCCAGAGCCACTCA 60.228 57.895 0.00 0.00 38.69 3.41
647 650 2.320587 CGTTGTGCCAGAGCCACTC 61.321 63.158 0.00 0.00 38.69 3.51
648 651 1.754380 TACGTTGTGCCAGAGCCACT 61.754 55.000 0.00 0.00 38.69 4.00
649 652 0.882927 TTACGTTGTGCCAGAGCCAC 60.883 55.000 0.00 0.00 38.69 5.01
650 653 0.036164 ATTACGTTGTGCCAGAGCCA 59.964 50.000 0.00 0.00 38.69 4.75
651 654 0.727398 GATTACGTTGTGCCAGAGCC 59.273 55.000 0.00 0.00 38.69 4.70
652 655 0.370273 CGATTACGTTGTGCCAGAGC 59.630 55.000 0.00 0.00 35.50 4.09
653 656 1.920574 CTCGATTACGTTGTGCCAGAG 59.079 52.381 0.00 0.00 40.69 3.35
654 657 1.990799 CTCGATTACGTTGTGCCAGA 58.009 50.000 0.00 0.00 40.69 3.86
655 658 0.370273 GCTCGATTACGTTGTGCCAG 59.630 55.000 0.00 0.00 40.69 4.85
656 659 1.017177 GGCTCGATTACGTTGTGCCA 61.017 55.000 14.10 0.00 39.75 4.92
657 660 0.739813 AGGCTCGATTACGTTGTGCC 60.740 55.000 0.00 4.04 39.99 5.01
658 661 0.645868 GAGGCTCGATTACGTTGTGC 59.354 55.000 0.00 0.00 40.69 4.57
659 662 1.990799 TGAGGCTCGATTACGTTGTG 58.009 50.000 10.42 0.00 40.69 3.33
660 663 2.961526 ATGAGGCTCGATTACGTTGT 57.038 45.000 10.42 0.00 40.69 3.32
661 664 2.216488 CGAATGAGGCTCGATTACGTTG 59.784 50.000 10.42 0.00 38.61 4.10
662 665 2.460918 CGAATGAGGCTCGATTACGTT 58.539 47.619 10.42 0.00 38.61 3.99
663 666 1.864435 GCGAATGAGGCTCGATTACGT 60.864 52.381 10.42 0.00 38.61 3.57
664 667 0.778815 GCGAATGAGGCTCGATTACG 59.221 55.000 10.42 14.80 38.61 3.18
665 668 1.789464 CTGCGAATGAGGCTCGATTAC 59.211 52.381 10.42 7.40 38.61 1.89
666 669 1.681264 TCTGCGAATGAGGCTCGATTA 59.319 47.619 10.42 0.00 38.61 1.75
667 670 0.461548 TCTGCGAATGAGGCTCGATT 59.538 50.000 10.42 10.52 38.61 3.34
668 671 0.461548 TTCTGCGAATGAGGCTCGAT 59.538 50.000 10.42 0.11 38.61 3.59
669 672 0.246360 TTTCTGCGAATGAGGCTCGA 59.754 50.000 10.42 0.00 38.61 4.04
670 673 1.061711 CTTTTCTGCGAATGAGGCTCG 59.938 52.381 10.42 0.00 39.33 5.03
671 674 1.399791 CCTTTTCTGCGAATGAGGCTC 59.600 52.381 7.79 7.79 0.00 4.70
672 675 1.003580 TCCTTTTCTGCGAATGAGGCT 59.996 47.619 0.00 0.00 0.00 4.58
673 676 1.453155 TCCTTTTCTGCGAATGAGGC 58.547 50.000 12.25 0.00 0.00 4.70
674 677 4.503741 TTTTCCTTTTCTGCGAATGAGG 57.496 40.909 11.46 11.46 0.00 3.86
709 712 4.973663 CAGGCTCGATTACGTTTTGTTTTT 59.026 37.500 0.00 0.00 40.69 1.94
710 713 4.273969 TCAGGCTCGATTACGTTTTGTTTT 59.726 37.500 0.00 0.00 40.69 2.43
711 714 3.810941 TCAGGCTCGATTACGTTTTGTTT 59.189 39.130 0.00 0.00 40.69 2.83
712 715 3.395639 TCAGGCTCGATTACGTTTTGTT 58.604 40.909 0.00 0.00 40.69 2.83
713 716 2.993899 CTCAGGCTCGATTACGTTTTGT 59.006 45.455 0.00 0.00 40.69 2.83
714 717 3.060895 GTCTCAGGCTCGATTACGTTTTG 59.939 47.826 0.00 0.00 40.69 2.44
715 718 3.251571 GTCTCAGGCTCGATTACGTTTT 58.748 45.455 0.00 0.00 40.69 2.43
722 725 1.270907 ACTTGGTCTCAGGCTCGATT 58.729 50.000 0.00 0.00 0.00 3.34
731 734 4.330620 GTGAACGTGTAAAACTTGGTCTCA 59.669 41.667 0.00 0.00 0.00 3.27
733 736 3.307782 CGTGAACGTGTAAAACTTGGTCT 59.692 43.478 0.00 0.00 34.11 3.85
754 758 0.296642 CCTATCGCGTTCGGTTTTCG 59.703 55.000 5.77 0.00 40.90 3.46
756 760 0.741927 CCCCTATCGCGTTCGGTTTT 60.742 55.000 5.77 0.00 36.13 2.43
787 791 2.942648 GAAGGCGCCCTATGTGACCC 62.943 65.000 26.15 0.00 30.38 4.46
886 897 6.129457 GGATTTATATTTGTGAATTGCGCGAC 60.129 38.462 12.10 0.88 0.00 5.19
1041 1066 1.065251 GATACGGAGGTCTCGTCAACC 59.935 57.143 0.00 0.00 41.38 3.77
1044 1069 3.091318 GGATACGGAGGTCTCGTCA 57.909 57.895 0.00 0.00 41.38 4.35
1191 1222 1.447489 CTCGTCCTTCTGCTGCCAG 60.447 63.158 0.00 0.00 40.54 4.85
1285 1316 7.388224 ACGTATCGGATATAGGTGCAGATATAG 59.612 40.741 0.29 0.00 0.00 1.31
1313 1344 4.568072 ACCTAAGCAACACATACATGGA 57.432 40.909 0.00 0.00 0.00 3.41
1336 1367 2.086610 AATTGAGGGCACAAACCAGT 57.913 45.000 0.00 0.00 33.44 4.00
1337 1368 3.392882 GAAAATTGAGGGCACAAACCAG 58.607 45.455 0.00 0.00 33.44 4.00
1358 1389 3.195825 ACACCTCCTAACTTCTCAATCCG 59.804 47.826 0.00 0.00 0.00 4.18
1366 1397 4.142116 GCCTCTAGAACACCTCCTAACTTC 60.142 50.000 0.00 0.00 0.00 3.01
1395 1427 1.181098 AATTCACCACAGCACCAGGC 61.181 55.000 0.00 0.00 45.30 4.85
1405 1437 6.687604 AGCATTAACCTAACAAATTCACCAC 58.312 36.000 0.00 0.00 0.00 4.16
1424 1457 2.498167 GACAGACACCTCACAAGCATT 58.502 47.619 0.00 0.00 0.00 3.56
1439 1507 6.208599 GGAACAAACCAATCAATAAGGACAGA 59.791 38.462 0.00 0.00 0.00 3.41
1444 1512 5.637006 TCGGAACAAACCAATCAATAAGG 57.363 39.130 0.00 0.00 0.00 2.69
1446 1514 6.825944 TCATCGGAACAAACCAATCAATAA 57.174 33.333 0.00 0.00 0.00 1.40
1452 1520 5.920193 ATCAATCATCGGAACAAACCAAT 57.080 34.783 0.00 0.00 0.00 3.16
1456 1524 6.306356 CAGAACAATCAATCATCGGAACAAAC 59.694 38.462 0.00 0.00 0.00 2.93
1464 1532 4.392754 TCCACACAGAACAATCAATCATCG 59.607 41.667 0.00 0.00 0.00 3.84
1647 1716 2.259266 TGTGACTGCTGCAATCTTCA 57.741 45.000 12.62 8.71 0.00 3.02
1688 1757 5.237779 TCTTCCACGAAATACAAGAACCAAC 59.762 40.000 0.00 0.00 0.00 3.77
1731 1800 5.361857 ACTTCATATCAATCAGCCAAAAGGG 59.638 40.000 0.00 0.00 40.85 3.95
2079 2148 7.363880 GGTTCCTGTGTATAGAAGATCTCAACA 60.364 40.741 0.00 0.00 0.00 3.33
2097 2166 1.821088 AGTCCCTTTCTGGTTCCTGT 58.179 50.000 0.00 0.00 0.00 4.00
2613 2682 4.322801 CGAAGAATTTCTGGGTAGGTCTGT 60.323 45.833 0.00 0.00 0.00 3.41
2644 2713 6.530120 TCAGAGTAAGAACTGTATTTGCCAA 58.470 36.000 0.00 0.00 35.56 4.52
2721 2790 1.954927 CCCTCATTAGAGTTTCGGGC 58.045 55.000 0.00 0.00 40.40 6.13
2933 3003 7.517614 TGTAGTTACAGAAATGCAAATGGAA 57.482 32.000 0.00 0.00 0.00 3.53
2998 3071 3.717775 CAACTTGCTTGCACACACA 57.282 47.368 0.00 0.00 0.00 3.72
3421 3496 3.825160 TTGCAGTCTGACCGGGTGC 62.825 63.158 3.30 11.51 34.62 5.01
3443 3518 1.742308 AGAGTCTGTTAGCCCCCAAA 58.258 50.000 0.00 0.00 0.00 3.28
3560 3635 1.302366 TGAATCTGGTCATGATGCGC 58.698 50.000 0.00 0.00 0.00 6.09
3847 3922 9.425248 AAAACATATTCATTGTAGATGACCCAT 57.575 29.630 5.10 0.00 0.00 4.00
3931 4006 7.630924 ACAAGTTTCATTTCAGACTTTAGACG 58.369 34.615 0.00 0.00 30.41 4.18
4230 4308 6.180472 CCATCCACAATACTGGAAAACTACT 58.820 40.000 0.00 0.00 43.79 2.57
4304 4382 5.300752 ACAAGCATCTACTCCATAATTCGG 58.699 41.667 0.00 0.00 0.00 4.30
4310 4388 5.191722 AGGGAAAACAAGCATCTACTCCATA 59.808 40.000 0.00 0.00 0.00 2.74
4311 4389 4.018050 AGGGAAAACAAGCATCTACTCCAT 60.018 41.667 0.00 0.00 0.00 3.41
4312 4390 3.330701 AGGGAAAACAAGCATCTACTCCA 59.669 43.478 0.00 0.00 0.00 3.86
4313 4391 3.942115 GAGGGAAAACAAGCATCTACTCC 59.058 47.826 0.00 0.00 0.00 3.85
4314 4392 4.633565 CAGAGGGAAAACAAGCATCTACTC 59.366 45.833 0.00 0.00 0.00 2.59
4315 4393 4.042187 ACAGAGGGAAAACAAGCATCTACT 59.958 41.667 0.00 0.00 0.00 2.57
4316 4394 4.327680 ACAGAGGGAAAACAAGCATCTAC 58.672 43.478 0.00 0.00 0.00 2.59
4479 4557 6.177610 AGTTACACAAGTTGTCTCAAAAGGA 58.822 36.000 5.27 0.00 39.91 3.36
4480 4558 6.436843 AGTTACACAAGTTGTCTCAAAAGG 57.563 37.500 5.27 0.00 39.91 3.11
4490 4568 7.730364 ATTTCCTGACTAGTTACACAAGTTG 57.270 36.000 0.00 0.00 0.00 3.16
4522 4600 6.346096 TCTAAGACAAATAATTCAGGACGGG 58.654 40.000 0.00 0.00 0.00 5.28
4560 4638 9.832445 GACCCTAAGTCATATTTTCTGTATTCA 57.168 33.333 0.00 0.00 45.55 2.57
4576 4654 5.579564 AATCTAAGACGTGACCCTAAGTC 57.420 43.478 0.00 0.00 46.51 3.01
4577 4655 5.245526 ACAAATCTAAGACGTGACCCTAAGT 59.754 40.000 0.00 0.00 0.00 2.24
4578 4656 5.721232 ACAAATCTAAGACGTGACCCTAAG 58.279 41.667 0.00 0.00 0.00 2.18
4579 4657 5.733620 ACAAATCTAAGACGTGACCCTAA 57.266 39.130 0.00 0.00 0.00 2.69
4580 4658 5.733620 AACAAATCTAAGACGTGACCCTA 57.266 39.130 0.00 0.00 0.00 3.53
4581 4659 4.618920 AACAAATCTAAGACGTGACCCT 57.381 40.909 0.00 0.00 0.00 4.34
4582 4660 5.717119 TCTAACAAATCTAAGACGTGACCC 58.283 41.667 0.00 0.00 0.00 4.46
4583 4661 7.165483 CGTATCTAACAAATCTAAGACGTGACC 59.835 40.741 0.00 0.00 0.00 4.02
4584 4662 7.165483 CCGTATCTAACAAATCTAAGACGTGAC 59.835 40.741 0.00 0.00 0.00 3.67
4585 4663 7.066163 TCCGTATCTAACAAATCTAAGACGTGA 59.934 37.037 0.00 0.00 0.00 4.35
4586 4664 7.191551 TCCGTATCTAACAAATCTAAGACGTG 58.808 38.462 0.00 0.00 0.00 4.49
4587 4665 7.325660 TCCGTATCTAACAAATCTAAGACGT 57.674 36.000 0.00 0.00 0.00 4.34
4588 4666 9.327529 GTATCCGTATCTAACAAATCTAAGACG 57.672 37.037 0.00 0.00 0.00 4.18
4591 4669 9.627395 CCTGTATCCGTATCTAACAAATCTAAG 57.373 37.037 0.00 0.00 0.00 2.18
4592 4670 9.358406 TCCTGTATCCGTATCTAACAAATCTAA 57.642 33.333 0.00 0.00 0.00 2.10
4593 4671 8.929260 TCCTGTATCCGTATCTAACAAATCTA 57.071 34.615 0.00 0.00 0.00 1.98
4594 4672 7.834881 TCCTGTATCCGTATCTAACAAATCT 57.165 36.000 0.00 0.00 0.00 2.40
4595 4673 8.882415 TTTCCTGTATCCGTATCTAACAAATC 57.118 34.615 0.00 0.00 0.00 2.17
4596 4674 9.273016 CATTTCCTGTATCCGTATCTAACAAAT 57.727 33.333 0.00 0.00 0.00 2.32
4597 4675 8.262227 ACATTTCCTGTATCCGTATCTAACAAA 58.738 33.333 0.00 0.00 35.91 2.83
4598 4676 7.788026 ACATTTCCTGTATCCGTATCTAACAA 58.212 34.615 0.00 0.00 35.91 2.83
4599 4677 7.068962 TGACATTTCCTGTATCCGTATCTAACA 59.931 37.037 0.00 0.00 38.54 2.41
4600 4678 7.381678 GTGACATTTCCTGTATCCGTATCTAAC 59.618 40.741 0.00 0.00 38.54 2.34
4601 4679 7.287005 AGTGACATTTCCTGTATCCGTATCTAA 59.713 37.037 0.00 0.00 38.54 2.10
4673 4799 3.065371 GTCAATTAATTCCACTCAGGCCG 59.935 47.826 0.00 0.00 37.29 6.13
4679 4805 4.258543 TGACCGGTCAATTAATTCCACTC 58.741 43.478 34.60 3.09 36.53 3.51
4680 4806 4.295141 TGACCGGTCAATTAATTCCACT 57.705 40.909 34.60 0.00 36.53 4.00
4696 5080 1.082756 GCACTTCGCAGTTTGACCG 60.083 57.895 0.00 0.00 41.79 4.79
4740 5124 1.303091 CGAGGCCGACGGGAATTTTT 61.303 55.000 17.22 0.00 38.22 1.94
4741 5125 1.743995 CGAGGCCGACGGGAATTTT 60.744 57.895 17.22 0.00 38.22 1.82
4786 5199 1.595058 GGGGAGAAGGGGAGGAGAGA 61.595 65.000 0.00 0.00 0.00 3.10
4787 5200 1.074850 GGGGAGAAGGGGAGGAGAG 60.075 68.421 0.00 0.00 0.00 3.20
4788 5201 1.550374 AGGGGAGAAGGGGAGGAGA 60.550 63.158 0.00 0.00 0.00 3.71
4789 5202 1.383803 CAGGGGAGAAGGGGAGGAG 60.384 68.421 0.00 0.00 0.00 3.69
4790 5203 2.787866 CAGGGGAGAAGGGGAGGA 59.212 66.667 0.00 0.00 0.00 3.71
4791 5204 2.367512 CCAGGGGAGAAGGGGAGG 60.368 72.222 0.00 0.00 0.00 4.30
4792 5205 1.997874 CACCAGGGGAGAAGGGGAG 60.998 68.421 0.00 0.00 0.00 4.30
4793 5206 2.124996 CACCAGGGGAGAAGGGGA 59.875 66.667 0.00 0.00 0.00 4.81
4794 5207 3.732849 GCACCAGGGGAGAAGGGG 61.733 72.222 0.00 0.00 0.00 4.79
4795 5208 2.612115 AGCACCAGGGGAGAAGGG 60.612 66.667 0.00 0.00 0.00 3.95
4796 5209 2.674220 GGAGCACCAGGGGAGAAGG 61.674 68.421 0.00 0.00 35.97 3.46
4797 5210 2.674220 GGGAGCACCAGGGGAGAAG 61.674 68.421 1.58 0.00 39.85 2.85
4798 5211 2.610859 GGGAGCACCAGGGGAGAA 60.611 66.667 1.58 0.00 39.85 2.87
4818 5231 1.528292 GAGGGGAGATCCGACCATCG 61.528 65.000 0.00 0.00 40.07 3.84
4936 8355 2.829094 TGAAGTTCAGACCACCGGA 58.171 52.632 9.46 0.00 0.00 5.14
4956 8375 3.731216 CGAAATACATGTCGCTGGAGTAG 59.269 47.826 0.00 0.00 0.00 2.57
4958 8377 2.165641 TCGAAATACATGTCGCTGGAGT 59.834 45.455 0.00 0.00 37.19 3.85
4959 8378 2.809446 TCGAAATACATGTCGCTGGAG 58.191 47.619 0.00 0.00 37.19 3.86
4962 8381 4.976116 TCTGTATCGAAATACATGTCGCTG 59.024 41.667 0.00 0.00 45.12 5.18
4963 8382 5.008712 TCTCTGTATCGAAATACATGTCGCT 59.991 40.000 0.00 0.00 45.12 4.93
4964 8383 5.212934 TCTCTGTATCGAAATACATGTCGC 58.787 41.667 0.00 0.00 45.12 5.19
4966 8385 7.644490 ACTCTCTCTGTATCGAAATACATGTC 58.356 38.462 0.00 0.00 45.12 3.06
4967 8386 7.575414 ACTCTCTCTGTATCGAAATACATGT 57.425 36.000 2.69 2.69 45.12 3.21
4981 8400 9.877178 AACGAAATTCAATTATACTCTCTCTGT 57.123 29.630 0.00 0.00 0.00 3.41
5085 8504 5.918608 TGCCTAGATTTAGTCAGATCCAAC 58.081 41.667 0.00 0.00 0.00 3.77


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

AutoCloner maintained by Alex Coulton.