Multiple sequence alignment - TraesCS4B01G059400

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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 TraesCS4B01G059400 chr4B 100.000 4820 0 0 1 4820 50724324 50729143 0.000000e+00 8901.0
1 TraesCS4B01G059400 chr4B 81.720 465 69 10 1 453 458983711 458984171 1.640000e-99 374.0
2 TraesCS4B01G059400 chr4B 85.845 219 15 12 511 716 413123383 413123598 8.120000e-53 219.0
3 TraesCS4B01G059400 chr4A 95.925 1546 57 6 2524 4067 567490859 567492400 0.000000e+00 2501.0
4 TraesCS4B01G059400 chr4A 92.016 1741 84 24 811 2523 567489096 567490809 0.000000e+00 2394.0
5 TraesCS4B01G059400 chr4A 87.121 660 44 8 4188 4820 567492474 567493119 0.000000e+00 710.0
6 TraesCS4B01G059400 chr4A 80.300 533 83 9 1 511 698809647 698810179 2.720000e-102 383.0
7 TraesCS4B01G059400 chr4A 88.809 277 26 3 1461 1735 37900429 37900702 7.730000e-88 335.0
8 TraesCS4B01G059400 chr4D 94.816 1524 53 9 749 2255 35126720 35125206 0.000000e+00 2353.0
9 TraesCS4B01G059400 chr4D 94.172 1510 52 9 2862 4345 35123716 35122217 0.000000e+00 2268.0
10 TraesCS4B01G059400 chr4D 90.838 513 36 5 4 507 35127322 35126812 0.000000e+00 676.0
11 TraesCS4B01G059400 chr4D 96.286 350 12 1 2525 2873 35125060 35124711 1.500000e-159 573.0
12 TraesCS4B01G059400 chr4D 87.500 352 18 4 4343 4671 35121901 35121553 2.720000e-102 383.0
13 TraesCS4B01G059400 chr4D 100.000 98 0 0 2426 2523 35125208 35125111 1.070000e-41 182.0
14 TraesCS4B01G059400 chr5B 82.168 572 51 24 1180 1749 311075882 311076404 1.230000e-120 444.0
15 TraesCS4B01G059400 chr3A 81.203 532 79 8 1 511 79459391 79459922 4.490000e-110 409.0
16 TraesCS4B01G059400 chr3A 85.714 210 17 7 519 716 478701470 478701262 4.890000e-50 209.0
17 TraesCS4B01G059400 chr5A 83.991 431 51 10 1105 1535 28603845 28604257 9.720000e-107 398.0
18 TraesCS4B01G059400 chr5A 80.183 545 82 13 1 520 78177966 78177423 7.570000e-103 385.0
19 TraesCS4B01G059400 chr5A 81.857 463 74 7 1 455 414419798 414420258 9.790000e-102 381.0
20 TraesCS4B01G059400 chr5A 88.325 197 16 5 522 716 426301505 426301696 3.750000e-56 230.0
21 TraesCS4B01G059400 chr2B 80.488 533 82 9 1 511 763373286 763373818 5.850000e-104 388.0
22 TraesCS4B01G059400 chr2B 88.945 199 15 3 521 717 210009143 210009336 6.230000e-59 239.0
23 TraesCS4B01G059400 chr6A 80.337 534 81 11 1 511 495444339 495444871 2.720000e-102 383.0
24 TraesCS4B01G059400 chr6A 81.356 118 15 5 2367 2482 2723381 2723269 6.640000e-14 89.8
25 TraesCS4B01G059400 chr1A 80.337 534 81 11 1 511 494740811 494741343 2.720000e-102 383.0
26 TraesCS4B01G059400 chr1D 89.492 295 29 2 1241 1535 22041105 22040813 5.890000e-99 372.0
27 TraesCS4B01G059400 chr1D 90.374 187 17 1 1557 1743 258387852 258388037 1.340000e-60 244.0
28 TraesCS4B01G059400 chr6D 86.301 219 14 11 514 719 450269581 450269366 1.750000e-54 224.0
29 TraesCS4B01G059400 chr3B 88.172 186 20 2 531 716 733901188 733901005 2.260000e-53 220.0
30 TraesCS4B01G059400 chr3B 83.830 235 19 13 511 730 810594212 810593982 6.320000e-49 206.0
31 TraesCS4B01G059400 chr3B 85.427 199 23 5 521 717 526279250 526279444 8.180000e-48 202.0
32 TraesCS4B01G059400 chr2A 86.598 194 22 3 526 717 165862674 165862865 1.360000e-50 211.0
33 TraesCS4B01G059400 chr2D 83.886 211 19 10 1156 1366 565857638 565857833 2.290000e-43 187.0
34 TraesCS4B01G059400 chr1B 81.557 244 28 11 511 738 268803695 268803937 8.240000e-43 185.0
35 TraesCS4B01G059400 chr6B 100.000 28 0 0 484 511 20031648 20031675 9.000000e-03 52.8


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 TraesCS4B01G059400 chr4B 50724324 50729143 4819 False 8901.000000 8901 100.000000 1 4820 1 chr4B.!!$F1 4819
1 TraesCS4B01G059400 chr4A 567489096 567493119 4023 False 1868.333333 2501 91.687333 811 4820 3 chr4A.!!$F3 4009
2 TraesCS4B01G059400 chr4A 698809647 698810179 532 False 383.000000 383 80.300000 1 511 1 chr4A.!!$F2 510
3 TraesCS4B01G059400 chr4D 35121553 35127322 5769 True 1072.500000 2353 93.935333 4 4671 6 chr4D.!!$R1 4667
4 TraesCS4B01G059400 chr5B 311075882 311076404 522 False 444.000000 444 82.168000 1180 1749 1 chr5B.!!$F1 569
5 TraesCS4B01G059400 chr3A 79459391 79459922 531 False 409.000000 409 81.203000 1 511 1 chr3A.!!$F1 510
6 TraesCS4B01G059400 chr5A 78177423 78177966 543 True 385.000000 385 80.183000 1 520 1 chr5A.!!$R1 519
7 TraesCS4B01G059400 chr2B 763373286 763373818 532 False 388.000000 388 80.488000 1 511 1 chr2B.!!$F2 510
8 TraesCS4B01G059400 chr6A 495444339 495444871 532 False 383.000000 383 80.337000 1 511 1 chr6A.!!$F1 510
9 TraesCS4B01G059400 chr1A 494740811 494741343 532 False 383.000000 383 80.337000 1 511 1 chr1A.!!$F1 510

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
633 656 0.091344 CGAGCGCTCAACACGTTTAG 59.909 55.0 34.69 12.34 0.00 1.85 F
634 657 0.179248 GAGCGCTCAACACGTTTAGC 60.179 55.0 31.91 6.11 36.68 3.09 F
1647 1702 0.323957 GGACGAAGGGGTTGCTAACT 59.676 55.0 0.00 0.00 0.00 2.24 F
2408 2469 0.179078 GAGAGGCTCCTGCAGTCATG 60.179 60.0 13.81 0.00 41.91 3.07 F
2923 4040 1.490621 GCATTCTTTTGTGCTTGCGT 58.509 45.0 0.00 0.00 38.30 5.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1647 1702 0.250234 CCTGCAGAAGACCCGATTCA 59.750 55.000 17.39 0.00 0.00 2.57 R
2391 2452 0.826715 TACATGACTGCAGGAGCCTC 59.173 55.000 19.93 6.49 41.13 4.70 R
3375 4494 1.270826 TCAGAAGACTGACCAAGCTCG 59.729 52.381 0.00 0.00 46.55 5.03 R
3612 4731 1.818674 ACTGAACGAATGGCAATTCCC 59.181 47.619 8.28 0.00 39.29 3.97 R
4555 6040 0.674895 ATTGCCTCTGTCTGCGAACC 60.675 55.000 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
27 29 2.938798 GGTGGGTGGGTGGGATGA 60.939 66.667 0.00 0.00 0.00 2.92
49 51 1.213926 GTCCTCCATCCAGATTGGCTT 59.786 52.381 0.00 0.00 37.47 4.35
67 69 2.841988 GGGATCTCTCCGGCAGCT 60.842 66.667 0.00 0.00 43.11 4.24
87 89 1.302832 CGCCAAGGGATAGGGATGC 60.303 63.158 0.00 0.00 0.00 3.91
215 218 2.057137 ACACACACTGCAACTGGAAT 57.943 45.000 0.00 0.00 0.00 3.01
249 252 5.360714 CACATTTGGGGAAGTAAGCACATAT 59.639 40.000 0.00 0.00 0.00 1.78
324 327 5.179555 GGACTGGAGATGAACAAACTTACAC 59.820 44.000 0.00 0.00 0.00 2.90
328 331 4.455877 GGAGATGAACAAACTTACACAGGG 59.544 45.833 0.00 0.00 0.00 4.45
389 397 6.294361 TGGCACAGCTCTTATAGTTTTAGA 57.706 37.500 0.00 0.00 0.00 2.10
458 466 8.575649 TCTCTGATAATTTTAGGACCCAAAAC 57.424 34.615 0.00 0.00 0.00 2.43
568 591 6.936335 CCAAAGGGGCATATCCAATTAATTTC 59.064 38.462 0.00 0.00 36.21 2.17
569 592 5.982890 AGGGGCATATCCAATTAATTTCG 57.017 39.130 0.00 0.00 36.21 3.46
570 593 4.772100 AGGGGCATATCCAATTAATTTCGG 59.228 41.667 0.00 0.00 36.21 4.30
571 594 4.526650 GGGGCATATCCAATTAATTTCGGT 59.473 41.667 0.00 0.00 36.21 4.69
572 595 5.336451 GGGGCATATCCAATTAATTTCGGTC 60.336 44.000 0.00 0.00 36.21 4.79
573 596 5.242838 GGGCATATCCAATTAATTTCGGTCA 59.757 40.000 0.00 0.00 36.21 4.02
574 597 6.071391 GGGCATATCCAATTAATTTCGGTCAT 60.071 38.462 0.00 0.00 36.21 3.06
575 598 7.029563 GGCATATCCAATTAATTTCGGTCATC 58.970 38.462 0.00 0.00 34.01 2.92
576 599 7.029563 GCATATCCAATTAATTTCGGTCATCC 58.970 38.462 0.00 0.00 0.00 3.51
577 600 7.309133 GCATATCCAATTAATTTCGGTCATCCA 60.309 37.037 0.00 0.00 0.00 3.41
578 601 8.575589 CATATCCAATTAATTTCGGTCATCCAA 58.424 33.333 0.00 0.00 0.00 3.53
579 602 7.601705 ATCCAATTAATTTCGGTCATCCAAT 57.398 32.000 0.00 0.00 0.00 3.16
580 603 7.416964 TCCAATTAATTTCGGTCATCCAATT 57.583 32.000 0.00 0.00 0.00 2.32
581 604 8.526667 TCCAATTAATTTCGGTCATCCAATTA 57.473 30.769 0.00 0.00 0.00 1.40
582 605 9.142014 TCCAATTAATTTCGGTCATCCAATTAT 57.858 29.630 0.00 0.00 28.53 1.28
584 607 9.748708 CAATTAATTTCGGTCATCCAATTATGT 57.251 29.630 0.00 0.00 28.53 2.29
585 608 9.965824 AATTAATTTCGGTCATCCAATTATGTC 57.034 29.630 0.00 0.00 28.53 3.06
586 609 8.512966 TTAATTTCGGTCATCCAATTATGTCA 57.487 30.769 0.00 0.00 28.53 3.58
589 612 6.618287 TTCGGTCATCCAATTATGTCAATC 57.382 37.500 0.00 0.00 0.00 2.67
590 613 5.063204 TCGGTCATCCAATTATGTCAATCC 58.937 41.667 0.00 0.00 0.00 3.01
591 614 4.821260 CGGTCATCCAATTATGTCAATCCA 59.179 41.667 0.00 0.00 0.00 3.41
592 615 5.299028 CGGTCATCCAATTATGTCAATCCAA 59.701 40.000 0.00 0.00 0.00 3.53
593 616 6.507023 GGTCATCCAATTATGTCAATCCAAC 58.493 40.000 0.00 0.00 0.00 3.77
594 617 6.201517 GTCATCCAATTATGTCAATCCAACG 58.798 40.000 0.00 0.00 0.00 4.10
595 618 6.038161 GTCATCCAATTATGTCAATCCAACGA 59.962 38.462 0.00 0.00 0.00 3.85
596 619 5.811399 TCCAATTATGTCAATCCAACGAC 57.189 39.130 0.00 0.00 0.00 4.34
597 620 4.638421 TCCAATTATGTCAATCCAACGACC 59.362 41.667 0.00 0.00 0.00 4.79
598 621 4.640201 CCAATTATGTCAATCCAACGACCT 59.360 41.667 0.00 0.00 0.00 3.85
599 622 5.820423 CCAATTATGTCAATCCAACGACCTA 59.180 40.000 0.00 0.00 0.00 3.08
600 623 6.317642 CCAATTATGTCAATCCAACGACCTAA 59.682 38.462 0.00 0.00 30.32 2.69
601 624 7.148154 CCAATTATGTCAATCCAACGACCTAAA 60.148 37.037 0.00 0.00 29.81 1.85
602 625 8.405531 CAATTATGTCAATCCAACGACCTAAAT 58.594 33.333 0.00 0.00 29.81 1.40
603 626 7.931578 TTATGTCAATCCAACGACCTAAATT 57.068 32.000 0.00 0.00 0.00 1.82
604 627 5.621197 TGTCAATCCAACGACCTAAATTG 57.379 39.130 0.00 0.00 0.00 2.32
605 628 4.083003 TGTCAATCCAACGACCTAAATTGC 60.083 41.667 0.00 0.00 0.00 3.56
606 629 4.156008 GTCAATCCAACGACCTAAATTGCT 59.844 41.667 0.00 0.00 0.00 3.91
607 630 4.764823 TCAATCCAACGACCTAAATTGCTT 59.235 37.500 0.00 0.00 0.00 3.91
608 631 5.242838 TCAATCCAACGACCTAAATTGCTTT 59.757 36.000 0.00 0.00 0.00 3.51
609 632 6.431543 TCAATCCAACGACCTAAATTGCTTTA 59.568 34.615 0.00 0.00 0.00 1.85
610 633 6.827586 ATCCAACGACCTAAATTGCTTTAA 57.172 33.333 0.00 0.00 0.00 1.52
611 634 6.827586 TCCAACGACCTAAATTGCTTTAAT 57.172 33.333 0.00 0.00 0.00 1.40
612 635 6.616947 TCCAACGACCTAAATTGCTTTAATG 58.383 36.000 0.00 0.00 0.00 1.90
613 636 6.207810 TCCAACGACCTAAATTGCTTTAATGT 59.792 34.615 0.00 0.00 0.00 2.71
614 637 6.526674 CCAACGACCTAAATTGCTTTAATGTC 59.473 38.462 0.00 0.00 31.56 3.06
615 638 5.864986 ACGACCTAAATTGCTTTAATGTCG 58.135 37.500 18.48 18.48 45.72 4.35
616 639 5.640357 ACGACCTAAATTGCTTTAATGTCGA 59.360 36.000 22.79 0.00 44.64 4.20
617 640 6.183360 ACGACCTAAATTGCTTTAATGTCGAG 60.183 38.462 22.79 8.03 44.64 4.04
618 641 5.880341 ACCTAAATTGCTTTAATGTCGAGC 58.120 37.500 0.00 0.00 36.95 5.03
619 642 4.963953 CCTAAATTGCTTTAATGTCGAGCG 59.036 41.667 0.00 0.00 39.23 5.03
620 643 2.458592 ATTGCTTTAATGTCGAGCGC 57.541 45.000 0.00 0.00 39.23 5.92
621 644 1.438651 TTGCTTTAATGTCGAGCGCT 58.561 45.000 11.27 11.27 39.23 5.92
622 645 0.999406 TGCTTTAATGTCGAGCGCTC 59.001 50.000 27.64 27.64 39.23 5.03
623 646 0.999406 GCTTTAATGTCGAGCGCTCA 59.001 50.000 34.69 18.66 0.00 4.26
624 647 1.393539 GCTTTAATGTCGAGCGCTCAA 59.606 47.619 34.69 17.41 0.00 3.02
625 648 2.784665 GCTTTAATGTCGAGCGCTCAAC 60.785 50.000 34.69 28.50 0.00 3.18
626 649 2.073117 TTAATGTCGAGCGCTCAACA 57.927 45.000 31.47 31.47 0.00 3.33
627 650 1.346365 TAATGTCGAGCGCTCAACAC 58.654 50.000 31.93 24.81 0.00 3.32
628 651 1.617755 AATGTCGAGCGCTCAACACG 61.618 55.000 31.93 20.44 0.00 4.49
629 652 2.729862 GTCGAGCGCTCAACACGT 60.730 61.111 34.69 0.00 0.00 4.49
630 653 2.027024 TCGAGCGCTCAACACGTT 59.973 55.556 34.69 0.00 0.00 3.99
631 654 1.590525 TCGAGCGCTCAACACGTTT 60.591 52.632 34.69 0.00 0.00 3.60
632 655 0.318022 TCGAGCGCTCAACACGTTTA 60.318 50.000 34.69 4.78 0.00 2.01
633 656 0.091344 CGAGCGCTCAACACGTTTAG 59.909 55.000 34.69 12.34 0.00 1.85
634 657 0.179248 GAGCGCTCAACACGTTTAGC 60.179 55.000 31.91 6.11 36.68 3.09
652 675 8.729262 CGTTTAGCGTGTAGTTAATTTCATAC 57.271 34.615 0.00 0.00 35.54 2.39
653 676 7.842721 CGTTTAGCGTGTAGTTAATTTCATACC 59.157 37.037 0.00 0.00 35.54 2.73
654 677 8.658609 GTTTAGCGTGTAGTTAATTTCATACCA 58.341 33.333 0.00 0.00 0.00 3.25
655 678 8.774890 TTAGCGTGTAGTTAATTTCATACCAA 57.225 30.769 0.00 0.00 0.00 3.67
656 679 7.675962 AGCGTGTAGTTAATTTCATACCAAA 57.324 32.000 0.00 0.00 0.00 3.28
657 680 8.276252 AGCGTGTAGTTAATTTCATACCAAAT 57.724 30.769 0.00 0.00 0.00 2.32
658 681 9.386010 AGCGTGTAGTTAATTTCATACCAAATA 57.614 29.630 0.00 0.00 0.00 1.40
672 695 9.771534 TTCATACCAAATATAACGATGATCACA 57.228 29.630 0.00 0.00 0.00 3.58
673 696 9.423061 TCATACCAAATATAACGATGATCACAG 57.577 33.333 0.00 0.00 0.00 3.66
674 697 9.423061 CATACCAAATATAACGATGATCACAGA 57.577 33.333 0.00 0.00 0.00 3.41
675 698 9.996554 ATACCAAATATAACGATGATCACAGAA 57.003 29.630 0.00 0.00 0.00 3.02
676 699 8.731275 ACCAAATATAACGATGATCACAGAAA 57.269 30.769 0.00 0.00 0.00 2.52
677 700 9.342308 ACCAAATATAACGATGATCACAGAAAT 57.658 29.630 0.00 0.00 0.00 2.17
687 710 9.862371 ACGATGATCACAGAAATAATATCCTAC 57.138 33.333 0.00 0.00 0.00 3.18
688 711 9.860898 CGATGATCACAGAAATAATATCCTACA 57.139 33.333 0.00 0.00 0.00 2.74
704 727 9.982651 AATATCCTACATAATATCCGCATACAC 57.017 33.333 0.00 0.00 0.00 2.90
705 728 7.661536 ATCCTACATAATATCCGCATACACT 57.338 36.000 0.00 0.00 0.00 3.55
706 729 7.476540 TCCTACATAATATCCGCATACACTT 57.523 36.000 0.00 0.00 0.00 3.16
707 730 8.584063 TCCTACATAATATCCGCATACACTTA 57.416 34.615 0.00 0.00 0.00 2.24
708 731 9.027202 TCCTACATAATATCCGCATACACTTAA 57.973 33.333 0.00 0.00 0.00 1.85
709 732 9.817809 CCTACATAATATCCGCATACACTTAAT 57.182 33.333 0.00 0.00 0.00 1.40
734 757 9.929722 ATATACTTTAATTGCACGTACACATTG 57.070 29.630 0.00 0.00 0.00 2.82
735 758 6.307031 ACTTTAATTGCACGTACACATTGA 57.693 33.333 0.00 0.00 0.00 2.57
736 759 6.140110 ACTTTAATTGCACGTACACATTGAC 58.860 36.000 0.00 0.00 0.00 3.18
737 760 5.933187 TTAATTGCACGTACACATTGACT 57.067 34.783 0.00 0.00 0.00 3.41
738 761 3.811722 ATTGCACGTACACATTGACTG 57.188 42.857 0.00 0.00 0.00 3.51
739 762 0.865111 TGCACGTACACATTGACTGC 59.135 50.000 0.00 0.00 0.00 4.40
740 763 1.148310 GCACGTACACATTGACTGCT 58.852 50.000 0.00 0.00 0.00 4.24
741 764 1.531149 GCACGTACACATTGACTGCTT 59.469 47.619 0.00 0.00 0.00 3.91
742 765 2.411547 GCACGTACACATTGACTGCTTC 60.412 50.000 0.00 0.00 0.00 3.86
743 766 3.059884 CACGTACACATTGACTGCTTCT 58.940 45.455 0.00 0.00 0.00 2.85
744 767 3.494626 CACGTACACATTGACTGCTTCTT 59.505 43.478 0.00 0.00 0.00 2.52
747 770 5.176958 ACGTACACATTGACTGCTTCTTAAC 59.823 40.000 0.00 0.00 0.00 2.01
761 784 5.473504 TGCTTCTTAACAAAATCCTGAGTCC 59.526 40.000 0.00 0.00 0.00 3.85
768 791 3.636764 ACAAAATCCTGAGTCCAAACCAC 59.363 43.478 0.00 0.00 0.00 4.16
796 819 3.039588 GACGAGGCGGCAAAACGA 61.040 61.111 13.08 0.00 33.63 3.85
802 825 2.405594 GCGGCAAAACGACACACA 59.594 55.556 0.00 0.00 35.47 3.72
803 826 1.937362 GCGGCAAAACGACACACAC 60.937 57.895 0.00 0.00 35.47 3.82
827 850 4.337060 CGTGAGTCGTGACCGGCA 62.337 66.667 0.00 0.00 42.41 5.69
830 853 3.681835 GAGTCGTGACCGGCACCT 61.682 66.667 19.09 13.03 44.85 4.00
831 854 3.628280 GAGTCGTGACCGGCACCTC 62.628 68.421 19.09 16.54 44.85 3.85
1107 1146 3.140225 CTACCCTCTCTTCGCCGGC 62.140 68.421 19.07 19.07 0.00 6.13
1307 1346 1.511305 GCGTCATCCAGGTCGAGAA 59.489 57.895 0.00 0.00 0.00 2.87
1397 1441 6.761242 GCCATTCCCCTTTTGTATTTATGTTC 59.239 38.462 0.00 0.00 0.00 3.18
1409 1453 7.145187 TGTATTTATGTTCGTCTTCGATTCG 57.855 36.000 0.00 0.00 45.65 3.34
1486 1538 0.750911 GAGGGGATCTGCTTTGCCTG 60.751 60.000 0.00 0.00 0.00 4.85
1592 1644 1.068588 CTGGTCAGAGAAACGTGTCCA 59.931 52.381 0.95 0.00 32.06 4.02
1595 1647 0.391597 TCAGAGAAACGTGTCCACCC 59.608 55.000 0.95 0.00 0.00 4.61
1598 1650 0.602905 GAGAAACGTGTCCACCCCTG 60.603 60.000 0.95 0.00 0.00 4.45
1647 1702 0.323957 GGACGAAGGGGTTGCTAACT 59.676 55.000 0.00 0.00 0.00 2.24
1795 1850 6.396450 GGATACCGGTAATTTGTCTCCTATC 58.604 44.000 20.22 7.50 0.00 2.08
1872 1927 7.096477 GCAATAAATCCACTGATTTCGTAATGC 60.096 37.037 3.96 5.99 45.87 3.56
1883 1938 9.687210 ACTGATTTCGTAATGCGTATTTATAGA 57.313 29.630 3.47 0.00 42.13 1.98
1927 1982 8.506168 AACATTGTAGAGTGTATACCCATTTG 57.494 34.615 0.00 0.00 0.00 2.32
1945 2000 6.211515 CCATTTGCTTAACAGATAATCAGCC 58.788 40.000 0.00 0.00 0.00 4.85
2012 2067 3.774066 CTGAGCATGTGTTCTATCGTGA 58.226 45.455 0.00 0.00 0.00 4.35
2015 2070 4.805719 TGAGCATGTGTTCTATCGTGAATC 59.194 41.667 0.00 0.00 0.00 2.52
2020 2075 4.421058 TGTGTTCTATCGTGAATCCTTCG 58.579 43.478 0.00 0.00 0.00 3.79
2040 2095 6.980978 CCTTCGTAGTTCATTGTGTCTGATAT 59.019 38.462 0.00 0.00 0.00 1.63
2044 2099 7.275560 TCGTAGTTCATTGTGTCTGATATGTTG 59.724 37.037 0.00 0.00 0.00 3.33
2099 2154 7.804614 TTGGATGCATACGTCAATTTTTAAC 57.195 32.000 4.01 0.00 33.10 2.01
2139 2194 1.017387 CCCTTGTCGGCAAAGATAGC 58.983 55.000 3.10 0.00 33.73 2.97
2196 2251 9.280174 CAAGTTAGGGAGACAGTTTAAACATAA 57.720 33.333 20.06 0.00 0.00 1.90
2329 2389 2.944129 AGGGCACAAGCAAAAAGTAGA 58.056 42.857 0.00 0.00 44.61 2.59
2335 2395 5.288804 GCACAAGCAAAAAGTAGAATGGAA 58.711 37.500 0.00 0.00 41.58 3.53
2408 2469 0.179078 GAGAGGCTCCTGCAGTCATG 60.179 60.000 13.81 0.00 41.91 3.07
2703 2813 7.354025 CAATGAAGATGCATTGCTTTACAAA 57.646 32.000 10.49 0.00 45.80 2.83
2824 2935 7.154656 ACCTCTAAAATTGATTGTTGCCTTTC 58.845 34.615 0.00 0.00 0.00 2.62
2923 4040 1.490621 GCATTCTTTTGTGCTTGCGT 58.509 45.000 0.00 0.00 38.30 5.24
2981 4098 7.552687 TGTGGATATAAAGATGGTGTTCTGTTC 59.447 37.037 0.00 0.00 0.00 3.18
3015 4132 6.207417 ACTTGTGCAATTTACTGCTATGTCTT 59.793 34.615 0.00 0.00 43.07 3.01
3140 4257 6.560253 ACTAAAGAAACAAGCAACGATGAT 57.440 33.333 0.00 0.00 0.00 2.45
3178 4296 6.558771 TGAGTATCTGTGGTTTTTGACATG 57.441 37.500 0.00 0.00 34.92 3.21
3183 4301 2.477375 CTGTGGTTTTTGACATGCATGC 59.523 45.455 26.53 18.59 0.00 4.06
3344 4462 8.547967 TGTTAGATTTCCATGAACAAGACTAC 57.452 34.615 0.00 0.00 0.00 2.73
3359 4478 7.745620 ACAAGACTACGAAATTCAGGAAATT 57.254 32.000 0.00 0.00 39.30 1.82
3570 4689 3.503363 TGATGATGTGTCTGCTGGTTTTC 59.497 43.478 0.00 0.00 0.00 2.29
3612 4731 5.645067 TCAATGTGCTATCTCCTTTCAGTTG 59.355 40.000 0.00 0.00 0.00 3.16
3735 4854 4.764308 GCTCTGATTTCCCAAGTTCTTTCT 59.236 41.667 0.00 0.00 0.00 2.52
3792 4911 5.474578 AGGGAAATCCTTTTGAGCTTTTC 57.525 39.130 0.00 0.00 45.47 2.29
3848 4967 3.507233 ACCACAGCATCGTTGATTTCATT 59.493 39.130 0.00 0.00 0.00 2.57
4110 5229 4.523558 TCTGATGATTGCAAACAACATGGA 59.476 37.500 17.73 11.12 38.99 3.41
4114 5233 5.926214 TGATTGCAAACAACATGGAAATG 57.074 34.783 6.97 0.00 38.99 2.32
4135 5254 9.900264 GAAATGTTTTTCATTATTTCATACGGC 57.100 29.630 0.00 0.00 44.85 5.68
4137 5256 8.633075 ATGTTTTTCATTATTTCATACGGCAG 57.367 30.769 0.00 0.00 32.08 4.85
4151 5270 1.140252 ACGGCAGGTTCTGTTGTAACT 59.860 47.619 0.00 0.00 33.43 2.24
4172 5291 9.361315 GTAACTTTTTCGGTATAATTTGGCATT 57.639 29.630 0.00 0.00 0.00 3.56
4335 5479 1.177401 GTGCTTCTTGGTTCCCATCC 58.823 55.000 0.00 0.00 31.53 3.51
4351 5813 3.758554 CCCATCCAAAGTCATCTTCGTTT 59.241 43.478 0.00 0.00 32.90 3.60
4563 6048 1.864862 CTGCTTGACAGGTTCGCAG 59.135 57.895 0.00 0.00 43.19 5.18
4564 6049 1.445518 TGCTTGACAGGTTCGCAGA 59.554 52.632 0.00 0.00 0.00 4.26
4577 6062 2.036571 CGCAGACAGAGGCAATGCA 61.037 57.895 7.79 0.00 36.70 3.96
4580 6065 1.001641 AGACAGAGGCAATGCACCC 60.002 57.895 7.79 0.00 0.00 4.61
4642 6128 6.775594 TGTATTACTGTATGCAGACTGACT 57.224 37.500 22.95 10.25 45.28 3.41
4676 6162 9.555727 TCTAATACTAATGAATAAACTGTGCCC 57.444 33.333 0.00 0.00 0.00 5.36
4677 6163 6.861065 ATACTAATGAATAAACTGTGCCCG 57.139 37.500 0.00 0.00 0.00 6.13
4682 6168 1.810151 GAATAAACTGTGCCCGCTTGA 59.190 47.619 0.00 0.00 0.00 3.02
4685 6171 0.537143 AAACTGTGCCCGCTTGATCA 60.537 50.000 0.00 0.00 0.00 2.92
4689 6175 0.107066 TGTGCCCGCTTGATCATGAT 60.107 50.000 8.25 8.25 0.00 2.45
4723 6210 5.543714 TCTTCCTACTTTATGCACAAACGA 58.456 37.500 0.00 0.00 0.00 3.85
4727 6214 4.793216 CCTACTTTATGCACAAACGATTGC 59.207 41.667 5.20 0.58 40.34 3.56
4734 6221 1.321016 CACAAACGATTGCTGCTTCG 58.679 50.000 19.04 19.04 40.34 3.79
4735 6222 0.385974 ACAAACGATTGCTGCTTCGC 60.386 50.000 20.07 0.19 40.34 4.70
4738 6227 1.438651 AACGATTGCTGCTTCGCTTA 58.561 45.000 20.07 0.00 38.91 3.09
4744 6233 1.362768 TGCTGCTTCGCTTACAGATG 58.637 50.000 0.00 0.00 33.10 2.90
4757 6246 4.813027 CTTACAGATGCAATTGCCTGTTT 58.187 39.130 32.99 18.21 41.49 2.83
4760 6249 2.158841 CAGATGCAATTGCCTGTTTTGC 59.841 45.455 26.94 4.96 44.59 3.68
4763 6252 0.587768 GCAATTGCCTGTTTTGCACC 59.412 50.000 20.06 0.00 43.95 5.01
4764 6253 0.860533 CAATTGCCTGTTTTGCACCG 59.139 50.000 0.00 0.00 38.72 4.94
4765 6254 0.749649 AATTGCCTGTTTTGCACCGA 59.250 45.000 0.00 0.00 38.72 4.69
4766 6255 0.314935 ATTGCCTGTTTTGCACCGAG 59.685 50.000 0.00 0.00 38.72 4.63
4767 6256 1.034838 TTGCCTGTTTTGCACCGAGT 61.035 50.000 0.00 0.00 38.72 4.18
4768 6257 0.179043 TGCCTGTTTTGCACCGAGTA 60.179 50.000 0.00 0.00 32.85 2.59
4779 6268 1.463444 GCACCGAGTACACCAATGTTC 59.537 52.381 0.00 0.00 40.48 3.18
4787 6276 0.981183 ACACCAATGTTCCCTCGCTA 59.019 50.000 0.00 0.00 34.46 4.26
4789 6278 1.737793 CACCAATGTTCCCTCGCTAAC 59.262 52.381 0.00 0.00 0.00 2.34
4798 6287 1.066858 TCCCTCGCTAACAAAGAGCAG 60.067 52.381 0.00 0.00 40.09 4.24
4799 6288 1.066858 CCCTCGCTAACAAAGAGCAGA 60.067 52.381 0.00 0.00 40.09 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 3.326578 CGTCATCCCACCCACCCA 61.327 66.667 0.00 0.00 0.00 4.51
27 29 0.833287 CCAATCTGGATGGAGGACGT 59.167 55.000 0.00 0.00 40.96 4.34
49 51 3.157252 GCTGCCGGAGAGATCCCA 61.157 66.667 5.05 0.00 0.00 4.37
67 69 1.770110 ATCCCTATCCCTTGGCGCA 60.770 57.895 10.83 0.00 0.00 6.09
87 89 1.811266 CAGTCGGCATGAAGGACGG 60.811 63.158 0.00 0.00 40.50 4.79
151 153 2.594013 GGCTATGAGCTGCAGGGC 60.594 66.667 17.12 6.00 41.99 5.19
176 178 7.148490 TGTGTGTTACAATCTAAATGTCCATCG 60.148 37.037 0.00 0.00 36.06 3.84
215 218 2.855599 TCCCCAAATGTGGTCCATATGA 59.144 45.455 3.65 0.00 44.30 2.15
324 327 1.055040 TTGCAAATTTGGGTCCCCTG 58.945 50.000 19.47 0.00 36.94 4.45
328 331 7.270757 ACTTTAAAATTGCAAATTTGGGTCC 57.729 32.000 20.27 3.64 0.00 4.46
348 355 5.830991 TGTGCCATTTTAGTCCTACAACTTT 59.169 36.000 0.00 0.00 0.00 2.66
368 376 7.495934 TGGATTCTAAAACTATAAGAGCTGTGC 59.504 37.037 0.00 0.00 0.00 4.57
433 441 8.390921 AGTTTTGGGTCCTAAAATTATCAGAGA 58.609 33.333 15.40 0.00 30.62 3.10
543 566 6.438186 AATTAATTGGATATGCCCCTTTGG 57.562 37.500 0.00 0.00 34.97 3.28
544 567 6.646240 CGAAATTAATTGGATATGCCCCTTTG 59.354 38.462 0.39 0.00 34.97 2.77
545 568 6.239572 CCGAAATTAATTGGATATGCCCCTTT 60.240 38.462 0.39 0.00 34.97 3.11
546 569 5.245977 CCGAAATTAATTGGATATGCCCCTT 59.754 40.000 0.39 0.00 34.97 3.95
547 570 4.772100 CCGAAATTAATTGGATATGCCCCT 59.228 41.667 0.39 0.00 34.97 4.79
548 571 4.526650 ACCGAAATTAATTGGATATGCCCC 59.473 41.667 10.69 0.00 34.97 5.80
549 572 5.242838 TGACCGAAATTAATTGGATATGCCC 59.757 40.000 10.69 0.00 34.97 5.36
551 574 7.029563 GGATGACCGAAATTAATTGGATATGC 58.970 38.462 10.69 6.58 0.00 3.14
552 575 8.109705 TGGATGACCGAAATTAATTGGATATG 57.890 34.615 10.69 0.00 39.42 1.78
553 576 8.704849 TTGGATGACCGAAATTAATTGGATAT 57.295 30.769 10.69 5.29 39.42 1.63
554 577 8.704849 ATTGGATGACCGAAATTAATTGGATA 57.295 30.769 10.69 1.43 39.42 2.59
556 579 7.416964 AATTGGATGACCGAAATTAATTGGA 57.583 32.000 10.69 0.00 39.42 3.53
557 580 9.195411 CATAATTGGATGACCGAAATTAATTGG 57.805 33.333 0.39 2.26 39.42 3.16
558 581 9.748708 ACATAATTGGATGACCGAAATTAATTG 57.251 29.630 0.39 0.00 39.42 2.32
560 583 9.130661 TGACATAATTGGATGACCGAAATTAAT 57.869 29.630 0.00 0.00 39.42 1.40
561 584 8.512966 TGACATAATTGGATGACCGAAATTAA 57.487 30.769 0.00 0.00 39.42 1.40
563 586 7.403312 TTGACATAATTGGATGACCGAAATT 57.597 32.000 0.00 0.00 39.42 1.82
564 587 7.255590 GGATTGACATAATTGGATGACCGAAAT 60.256 37.037 0.00 0.00 39.42 2.17
568 591 4.821260 TGGATTGACATAATTGGATGACCG 59.179 41.667 0.00 0.00 39.42 4.79
569 592 6.507023 GTTGGATTGACATAATTGGATGACC 58.493 40.000 0.00 0.00 0.00 4.02
570 593 6.038161 TCGTTGGATTGACATAATTGGATGAC 59.962 38.462 0.00 0.00 0.00 3.06
571 594 6.038161 GTCGTTGGATTGACATAATTGGATGA 59.962 38.462 0.00 0.00 35.20 2.92
572 595 6.201517 GTCGTTGGATTGACATAATTGGATG 58.798 40.000 0.00 0.00 35.20 3.51
573 596 5.299279 GGTCGTTGGATTGACATAATTGGAT 59.701 40.000 0.00 0.00 36.83 3.41
574 597 4.638421 GGTCGTTGGATTGACATAATTGGA 59.362 41.667 0.00 0.00 36.83 3.53
575 598 4.640201 AGGTCGTTGGATTGACATAATTGG 59.360 41.667 0.00 0.00 36.83 3.16
576 599 5.818136 AGGTCGTTGGATTGACATAATTG 57.182 39.130 0.00 0.00 36.83 2.32
577 600 7.931578 TTTAGGTCGTTGGATTGACATAATT 57.068 32.000 1.09 0.00 39.96 1.40
578 601 8.405531 CAATTTAGGTCGTTGGATTGACATAAT 58.594 33.333 1.09 0.00 39.96 1.28
579 602 7.627513 GCAATTTAGGTCGTTGGATTGACATAA 60.628 37.037 0.00 0.00 38.95 1.90
580 603 6.183360 GCAATTTAGGTCGTTGGATTGACATA 60.183 38.462 0.00 0.00 36.83 2.29
581 604 5.393027 GCAATTTAGGTCGTTGGATTGACAT 60.393 40.000 0.00 0.00 36.83 3.06
582 605 4.083003 GCAATTTAGGTCGTTGGATTGACA 60.083 41.667 0.00 0.00 36.83 3.58
584 607 4.331968 AGCAATTTAGGTCGTTGGATTGA 58.668 39.130 0.00 0.00 0.00 2.57
585 608 4.701956 AGCAATTTAGGTCGTTGGATTG 57.298 40.909 0.00 0.00 0.00 2.67
586 609 5.722021 AAAGCAATTTAGGTCGTTGGATT 57.278 34.783 0.00 0.00 0.00 3.01
589 612 6.386654 ACATTAAAGCAATTTAGGTCGTTGG 58.613 36.000 0.00 0.00 0.00 3.77
590 613 6.248420 CGACATTAAAGCAATTTAGGTCGTTG 59.752 38.462 15.46 0.00 39.02 4.10
591 614 6.148150 TCGACATTAAAGCAATTTAGGTCGTT 59.852 34.615 19.87 0.00 41.42 3.85
592 615 5.640357 TCGACATTAAAGCAATTTAGGTCGT 59.360 36.000 19.87 1.84 41.42 4.34
593 616 6.102006 TCGACATTAAAGCAATTTAGGTCG 57.898 37.500 16.76 16.76 41.68 4.79
594 617 5.965918 GCTCGACATTAAAGCAATTTAGGTC 59.034 40.000 0.00 0.00 36.06 3.85
595 618 5.447279 CGCTCGACATTAAAGCAATTTAGGT 60.447 40.000 0.00 0.00 35.76 3.08
596 619 4.963953 CGCTCGACATTAAAGCAATTTAGG 59.036 41.667 0.00 0.00 35.76 2.69
597 620 4.434588 GCGCTCGACATTAAAGCAATTTAG 59.565 41.667 0.00 0.00 35.76 1.85
598 621 4.094294 AGCGCTCGACATTAAAGCAATTTA 59.906 37.500 2.64 0.00 35.76 1.40
599 622 3.119849 AGCGCTCGACATTAAAGCAATTT 60.120 39.130 2.64 0.00 35.76 1.82
600 623 2.420022 AGCGCTCGACATTAAAGCAATT 59.580 40.909 2.64 0.00 35.76 2.32
601 624 2.009774 AGCGCTCGACATTAAAGCAAT 58.990 42.857 2.64 0.00 35.76 3.56
602 625 1.393539 GAGCGCTCGACATTAAAGCAA 59.606 47.619 23.61 0.00 35.76 3.91
603 626 0.999406 GAGCGCTCGACATTAAAGCA 59.001 50.000 23.61 0.00 35.76 3.91
604 627 0.999406 TGAGCGCTCGACATTAAAGC 59.001 50.000 30.75 5.13 0.00 3.51
605 628 2.411748 TGTTGAGCGCTCGACATTAAAG 59.588 45.455 42.95 0.00 46.09 1.85
606 629 2.409012 TGTTGAGCGCTCGACATTAAA 58.591 42.857 42.95 27.49 46.09 1.52
607 630 2.073117 TGTTGAGCGCTCGACATTAA 57.927 45.000 42.95 27.81 46.09 1.40
608 631 3.804601 TGTTGAGCGCTCGACATTA 57.195 47.368 42.95 28.13 46.09 1.90
609 632 4.673403 TGTTGAGCGCTCGACATT 57.327 50.000 42.95 9.77 46.09 2.71
612 635 1.818221 AAACGTGTTGAGCGCTCGAC 61.818 55.000 39.44 39.44 42.86 4.20
613 636 0.318022 TAAACGTGTTGAGCGCTCGA 60.318 50.000 30.75 27.40 0.00 4.04
614 637 0.091344 CTAAACGTGTTGAGCGCTCG 59.909 55.000 30.75 21.89 0.00 5.03
615 638 0.179248 GCTAAACGTGTTGAGCGCTC 60.179 55.000 30.42 30.42 37.32 5.03
616 639 1.860078 GCTAAACGTGTTGAGCGCT 59.140 52.632 11.27 11.27 37.32 5.92
617 640 4.417240 GCTAAACGTGTTGAGCGC 57.583 55.556 6.34 0.00 37.32 5.92
628 651 8.658609 TGGTATGAAATTAACTACACGCTAAAC 58.341 33.333 0.00 0.00 0.00 2.01
629 652 8.774890 TGGTATGAAATTAACTACACGCTAAA 57.225 30.769 0.00 0.00 0.00 1.85
630 653 8.774890 TTGGTATGAAATTAACTACACGCTAA 57.225 30.769 0.00 0.00 0.00 3.09
631 654 8.774890 TTTGGTATGAAATTAACTACACGCTA 57.225 30.769 0.00 0.00 0.00 4.26
632 655 7.675962 TTTGGTATGAAATTAACTACACGCT 57.324 32.000 0.00 0.00 0.00 5.07
646 669 9.771534 TGTGATCATCGTTATATTTGGTATGAA 57.228 29.630 0.00 0.00 0.00 2.57
647 670 9.423061 CTGTGATCATCGTTATATTTGGTATGA 57.577 33.333 0.00 0.00 0.00 2.15
648 671 9.423061 TCTGTGATCATCGTTATATTTGGTATG 57.577 33.333 0.00 0.00 0.00 2.39
649 672 9.996554 TTCTGTGATCATCGTTATATTTGGTAT 57.003 29.630 0.00 0.00 0.00 2.73
650 673 9.825109 TTTCTGTGATCATCGTTATATTTGGTA 57.175 29.630 0.00 0.00 0.00 3.25
651 674 8.731275 TTTCTGTGATCATCGTTATATTTGGT 57.269 30.769 0.00 0.00 0.00 3.67
661 684 9.862371 GTAGGATATTATTTCTGTGATCATCGT 57.138 33.333 0.00 0.00 0.00 3.73
662 685 9.860898 TGTAGGATATTATTTCTGTGATCATCG 57.139 33.333 0.00 0.00 0.00 3.84
678 701 9.982651 GTGTATGCGGATATTATGTAGGATATT 57.017 33.333 0.00 0.00 0.00 1.28
679 702 9.368416 AGTGTATGCGGATATTATGTAGGATAT 57.632 33.333 0.00 0.00 0.00 1.63
680 703 8.762481 AGTGTATGCGGATATTATGTAGGATA 57.238 34.615 0.00 0.00 0.00 2.59
681 704 7.661536 AGTGTATGCGGATATTATGTAGGAT 57.338 36.000 0.00 0.00 0.00 3.24
682 705 7.476540 AAGTGTATGCGGATATTATGTAGGA 57.523 36.000 0.00 0.00 0.00 2.94
683 706 9.817809 ATTAAGTGTATGCGGATATTATGTAGG 57.182 33.333 0.00 0.00 0.00 3.18
708 731 9.929722 CAATGTGTACGTGCAATTAAAGTATAT 57.070 29.630 8.25 0.00 0.00 0.86
709 732 9.152595 TCAATGTGTACGTGCAATTAAAGTATA 57.847 29.630 8.25 0.00 0.00 1.47
710 733 7.960738 GTCAATGTGTACGTGCAATTAAAGTAT 59.039 33.333 8.25 0.00 0.00 2.12
711 734 7.171848 AGTCAATGTGTACGTGCAATTAAAGTA 59.828 33.333 8.25 0.00 0.00 2.24
712 735 6.017440 AGTCAATGTGTACGTGCAATTAAAGT 60.017 34.615 8.25 3.65 0.00 2.66
713 736 6.303022 CAGTCAATGTGTACGTGCAATTAAAG 59.697 38.462 8.25 0.00 0.00 1.85
714 737 6.139435 CAGTCAATGTGTACGTGCAATTAAA 58.861 36.000 8.25 1.02 0.00 1.52
715 738 5.684850 CAGTCAATGTGTACGTGCAATTAA 58.315 37.500 8.25 0.00 0.00 1.40
716 739 4.377943 GCAGTCAATGTGTACGTGCAATTA 60.378 41.667 8.25 0.00 0.00 1.40
717 740 3.609175 GCAGTCAATGTGTACGTGCAATT 60.609 43.478 8.25 7.92 0.00 2.32
718 741 2.095768 GCAGTCAATGTGTACGTGCAAT 60.096 45.455 8.25 1.77 0.00 3.56
719 742 1.262950 GCAGTCAATGTGTACGTGCAA 59.737 47.619 8.25 0.00 0.00 4.08
720 743 0.865111 GCAGTCAATGTGTACGTGCA 59.135 50.000 0.82 0.82 0.00 4.57
721 744 1.148310 AGCAGTCAATGTGTACGTGC 58.852 50.000 0.00 0.00 0.00 5.34
722 745 3.059884 AGAAGCAGTCAATGTGTACGTG 58.940 45.455 0.00 0.00 0.00 4.49
723 746 3.386768 AGAAGCAGTCAATGTGTACGT 57.613 42.857 0.00 0.00 0.00 3.57
724 747 5.176774 TGTTAAGAAGCAGTCAATGTGTACG 59.823 40.000 0.00 0.00 0.00 3.67
725 748 6.539649 TGTTAAGAAGCAGTCAATGTGTAC 57.460 37.500 0.00 0.00 0.00 2.90
726 749 7.561021 TTTGTTAAGAAGCAGTCAATGTGTA 57.439 32.000 0.00 0.00 0.00 2.90
727 750 6.449635 TTTGTTAAGAAGCAGTCAATGTGT 57.550 33.333 0.00 0.00 0.00 3.72
728 751 7.115378 GGATTTTGTTAAGAAGCAGTCAATGTG 59.885 37.037 0.00 0.00 0.00 3.21
729 752 7.014615 AGGATTTTGTTAAGAAGCAGTCAATGT 59.985 33.333 0.00 0.00 0.00 2.71
730 753 7.327761 CAGGATTTTGTTAAGAAGCAGTCAATG 59.672 37.037 0.00 0.00 0.00 2.82
731 754 7.231317 TCAGGATTTTGTTAAGAAGCAGTCAAT 59.769 33.333 0.00 0.00 0.00 2.57
732 755 6.545666 TCAGGATTTTGTTAAGAAGCAGTCAA 59.454 34.615 0.00 0.00 0.00 3.18
733 756 6.061441 TCAGGATTTTGTTAAGAAGCAGTCA 58.939 36.000 0.00 0.00 0.00 3.41
734 757 6.205658 ACTCAGGATTTTGTTAAGAAGCAGTC 59.794 38.462 0.00 0.00 0.00 3.51
735 758 6.064717 ACTCAGGATTTTGTTAAGAAGCAGT 58.935 36.000 0.00 0.00 0.00 4.40
736 759 6.348868 GGACTCAGGATTTTGTTAAGAAGCAG 60.349 42.308 0.00 0.00 0.00 4.24
737 760 5.473504 GGACTCAGGATTTTGTTAAGAAGCA 59.526 40.000 0.00 0.00 0.00 3.91
738 761 5.473504 TGGACTCAGGATTTTGTTAAGAAGC 59.526 40.000 0.00 0.00 0.00 3.86
739 762 7.510549 TTGGACTCAGGATTTTGTTAAGAAG 57.489 36.000 0.00 0.00 0.00 2.85
740 763 7.201875 GGTTTGGACTCAGGATTTTGTTAAGAA 60.202 37.037 0.00 0.00 0.00 2.52
741 764 6.264518 GGTTTGGACTCAGGATTTTGTTAAGA 59.735 38.462 0.00 0.00 0.00 2.10
742 765 6.040391 TGGTTTGGACTCAGGATTTTGTTAAG 59.960 38.462 0.00 0.00 0.00 1.85
743 766 5.894393 TGGTTTGGACTCAGGATTTTGTTAA 59.106 36.000 0.00 0.00 0.00 2.01
744 767 5.300792 GTGGTTTGGACTCAGGATTTTGTTA 59.699 40.000 0.00 0.00 0.00 2.41
747 770 3.304659 CGTGGTTTGGACTCAGGATTTTG 60.305 47.826 0.00 0.00 0.00 2.44
761 784 4.632037 CACATGGCACGTGGTTTG 57.368 55.556 18.88 0.00 0.00 2.93
768 791 2.815211 CCTCGTCCACATGGCACG 60.815 66.667 13.42 13.42 34.44 5.34
780 803 3.343421 GTCGTTTTGCCGCCTCGT 61.343 61.111 0.00 0.00 0.00 4.18
796 819 2.488545 GACTCACGAGATAGGTGTGTGT 59.511 50.000 0.00 0.00 40.85 3.72
802 825 2.008329 GTCACGACTCACGAGATAGGT 58.992 52.381 0.00 0.00 45.77 3.08
803 826 1.331138 GGTCACGACTCACGAGATAGG 59.669 57.143 0.00 0.00 45.77 2.57
837 860 3.127533 AATCGTTGGCTCGGCTGC 61.128 61.111 0.00 0.00 0.00 5.25
838 861 2.753966 CCAATCGTTGGCTCGGCTG 61.754 63.158 4.23 0.00 45.17 4.85
839 862 2.436646 CCAATCGTTGGCTCGGCT 60.437 61.111 4.23 0.00 45.17 5.52
912 944 2.176045 GAACGGGAATGGATGGGTTTT 58.824 47.619 0.00 0.00 0.00 2.43
1397 1441 0.022106 GAACGTGCGAATCGAAGACG 59.978 55.000 6.91 13.27 42.51 4.18
1409 1453 2.166985 CGAACGAACCGAACGTGC 59.833 61.111 0.00 0.00 43.16 5.34
1486 1538 1.153549 AATCGCGGAGAAGACCAGC 60.154 57.895 6.13 0.00 0.00 4.85
1647 1702 0.250234 CCTGCAGAAGACCCGATTCA 59.750 55.000 17.39 0.00 0.00 2.57
1795 1850 2.948979 TGGGTTTTGAGTACAAGTGCTG 59.051 45.455 0.00 0.00 37.32 4.41
1927 1982 4.786609 GCAACGGCTGATTATCTGTTAAGC 60.787 45.833 0.00 0.00 36.96 3.09
1945 2000 3.124921 CCGGGCTAACAGGCAACG 61.125 66.667 0.00 0.00 43.44 4.10
2012 2067 5.639506 CAGACACAATGAACTACGAAGGATT 59.360 40.000 0.00 0.00 0.00 3.01
2015 2070 4.556233 TCAGACACAATGAACTACGAAGG 58.444 43.478 0.00 0.00 0.00 3.46
2020 2075 8.256611 ACAACATATCAGACACAATGAACTAC 57.743 34.615 0.00 0.00 0.00 2.73
2040 2095 0.985760 AGGCCGGGTACAATACAACA 59.014 50.000 2.18 0.00 0.00 3.33
2044 2099 4.075963 TGATAAAGGCCGGGTACAATAC 57.924 45.455 2.18 0.00 0.00 1.89
2099 2154 3.096852 GGTGGTTTTCCCCTATTCCTTG 58.903 50.000 0.00 0.00 39.73 3.61
2109 2164 1.176619 CGACAAGGGGTGGTTTTCCC 61.177 60.000 0.00 0.00 43.90 3.97
2139 2194 2.351350 GCCACGGAACCAAAACAGTATG 60.351 50.000 0.00 0.00 46.00 2.39
2382 2443 2.961741 CTGCAGGAGCCTCTCTACATTA 59.038 50.000 5.57 0.00 41.13 1.90
2384 2445 1.342874 ACTGCAGGAGCCTCTCTACAT 60.343 52.381 19.93 0.00 41.13 2.29
2391 2452 0.826715 TACATGACTGCAGGAGCCTC 59.173 55.000 19.93 6.49 41.13 4.70
2824 2935 1.764723 TCATCACTGCCACAGGATAGG 59.235 52.381 0.00 0.00 35.51 2.57
2857 2968 7.601856 TGCAGAACCATAAAATTTTGACTAGG 58.398 34.615 13.76 9.76 0.00 3.02
2923 4040 4.030216 TGAGGTGAGGCATGTATCAAGTA 58.970 43.478 3.90 0.00 0.00 2.24
2981 4098 7.515059 GCAGTAAATTGCACAAGTTAAACACAG 60.515 37.037 4.99 0.00 43.53 3.66
3015 4132 8.100791 AGAAACTAGCACAACAGATAAACCATA 58.899 33.333 0.00 0.00 0.00 2.74
3068 4185 3.994392 CGTGTTGTGCTTCAGGTATTACT 59.006 43.478 0.00 0.00 0.00 2.24
3156 4273 5.048782 TGCATGTCAAAAACCACAGATACTC 60.049 40.000 0.00 0.00 0.00 2.59
3157 4274 4.826733 TGCATGTCAAAAACCACAGATACT 59.173 37.500 0.00 0.00 0.00 2.12
3158 4275 5.119931 TGCATGTCAAAAACCACAGATAC 57.880 39.130 0.00 0.00 0.00 2.24
3159 4276 5.712004 CATGCATGTCAAAAACCACAGATA 58.288 37.500 18.91 0.00 0.00 1.98
3178 4296 2.154462 AGACTTAACACCACAGCATGC 58.846 47.619 10.51 10.51 42.53 4.06
3183 4301 6.157211 AGAAATCGTAGACTTAACACCACAG 58.843 40.000 0.00 0.00 42.51 3.66
3344 4462 8.812329 TGTTTGTGTAAAATTTCCTGAATTTCG 58.188 29.630 0.00 0.00 44.98 3.46
3359 4478 6.205853 ACCAAGCTCGATTATGTTTGTGTAAA 59.794 34.615 0.00 0.00 0.00 2.01
3375 4494 1.270826 TCAGAAGACTGACCAAGCTCG 59.729 52.381 0.00 0.00 46.55 5.03
3432 4551 5.410746 AGTTCAGAACACACATAGATGCAAG 59.589 40.000 15.85 0.00 0.00 4.01
3570 4689 3.850122 TGAAGTCAGTACCAGACATCG 57.150 47.619 15.85 0.00 36.73 3.84
3593 4712 3.055094 TCCCAACTGAAAGGAGATAGCAC 60.055 47.826 0.00 0.00 39.30 4.40
3612 4731 1.818674 ACTGAACGAATGGCAATTCCC 59.181 47.619 8.28 0.00 39.29 3.97
3822 4941 4.621068 AATCAACGATGCTGTGGTAATG 57.379 40.909 0.00 0.00 0.00 1.90
3823 4942 4.699735 TGAAATCAACGATGCTGTGGTAAT 59.300 37.500 0.00 0.00 0.00 1.89
3824 4943 4.068599 TGAAATCAACGATGCTGTGGTAA 58.931 39.130 0.00 0.00 0.00 2.85
3983 5102 8.958119 ATATCATTTTTCGGACAAACTAGCTA 57.042 30.769 0.00 0.00 0.00 3.32
4110 5229 9.429359 TGCCGTATGAAATAATGAAAAACATTT 57.571 25.926 0.00 0.00 45.60 2.32
4114 5233 7.033185 ACCTGCCGTATGAAATAATGAAAAAC 58.967 34.615 0.00 0.00 0.00 2.43
4132 5251 1.878953 AGTTACAACAGAACCTGCCG 58.121 50.000 0.00 0.00 34.37 5.69
4135 5254 5.163693 ACCGAAAAAGTTACAACAGAACCTG 60.164 40.000 0.00 0.00 37.52 4.00
4137 5256 5.239359 ACCGAAAAAGTTACAACAGAACC 57.761 39.130 0.00 0.00 0.00 3.62
4283 5427 5.230942 GCACAGAGCAAAGTTTCTACTAGA 58.769 41.667 0.00 0.00 44.79 2.43
4335 5479 5.612865 GCAGTAGAAACGAAGATGACTTTG 58.387 41.667 0.00 0.00 41.76 2.77
4351 5813 7.413000 GCTTGAAAGATAACAATTCGCAGTAGA 60.413 37.037 0.00 0.00 0.00 2.59
4555 6040 0.674895 ATTGCCTCTGTCTGCGAACC 60.675 55.000 0.00 0.00 0.00 3.62
4557 6042 1.300971 GCATTGCCTCTGTCTGCGAA 61.301 55.000 0.00 0.00 0.00 4.70
4563 6048 2.401766 CGGGTGCATTGCCTCTGTC 61.402 63.158 6.12 0.00 0.00 3.51
4564 6049 2.360350 CGGGTGCATTGCCTCTGT 60.360 61.111 6.12 0.00 0.00 3.41
4577 6062 8.594550 ACATCTTCTTAATATTAGTATGCGGGT 58.405 33.333 0.00 0.00 0.00 5.28
4611 6096 9.529325 GTCTGCATACAGTAATACAAGTGATTA 57.471 33.333 0.00 0.00 44.77 1.75
4616 6101 7.036220 GTCAGTCTGCATACAGTAATACAAGT 58.964 38.462 4.92 0.00 44.77 3.16
4734 6221 2.165030 ACAGGCAATTGCATCTGTAAGC 59.835 45.455 29.53 13.17 40.21 3.09
4735 6222 4.445452 AACAGGCAATTGCATCTGTAAG 57.555 40.909 30.28 16.43 40.80 2.34
4738 6227 3.395639 CAAAACAGGCAATTGCATCTGT 58.604 40.909 30.32 28.36 42.53 3.41
4757 6246 1.202710 ACATTGGTGTACTCGGTGCAA 60.203 47.619 0.00 0.00 36.63 4.08
4760 6249 2.073816 GGAACATTGGTGTACTCGGTG 58.926 52.381 0.00 0.00 37.67 4.94
4761 6250 1.002773 GGGAACATTGGTGTACTCGGT 59.997 52.381 0.00 0.00 37.67 4.69
4762 6251 1.278127 AGGGAACATTGGTGTACTCGG 59.722 52.381 0.00 0.00 37.67 4.63
4763 6252 2.618053 GAGGGAACATTGGTGTACTCG 58.382 52.381 0.00 0.00 37.67 4.18
4764 6253 2.618053 CGAGGGAACATTGGTGTACTC 58.382 52.381 0.00 0.00 37.67 2.59
4765 6254 1.338769 GCGAGGGAACATTGGTGTACT 60.339 52.381 0.00 0.00 37.67 2.73
4766 6255 1.084289 GCGAGGGAACATTGGTGTAC 58.916 55.000 0.00 0.00 37.67 2.90
4767 6256 0.981183 AGCGAGGGAACATTGGTGTA 59.019 50.000 0.00 0.00 37.67 2.90
4768 6257 0.981183 TAGCGAGGGAACATTGGTGT 59.019 50.000 0.00 0.00 41.28 4.16
4779 6268 1.066858 TCTGCTCTTTGTTAGCGAGGG 60.067 52.381 0.00 0.00 43.11 4.30


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

AutoCloner maintained by Alex Coulton.