Multiple sequence alignment - TraesCS2B01G367800

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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 TraesCS2B01G367800 chr2B 100.000 2705 0 0 1 2705 524065610 524062906 0.000000e+00 4996
1 TraesCS2B01G367800 chr2B 88.198 949 104 4 757 1704 634748127 634747186 0.000000e+00 1125
2 TraesCS2B01G367800 chr2B 87.755 539 63 2 3 539 6811345 6811882 6.360000e-176 627
3 TraesCS2B01G367800 chr2B 87.523 537 64 2 5 539 6898824 6899359 3.830000e-173 617
4 TraesCS2B01G367800 chr4B 97.515 1006 23 2 1702 2705 318374032 318373027 0.000000e+00 1718
5 TraesCS2B01G367800 chr4B 97.512 1005 24 1 1702 2705 300080843 300079839 0.000000e+00 1716
6 TraesCS2B01G367800 chr4B 91.209 91 7 1 636 725 646595135 646595045 3.660000e-24 122
7 TraesCS2B01G367800 chr4B 89.535 86 5 2 643 727 546138242 546138324 3.680000e-19 106
8 TraesCS2B01G367800 chr1A 97.515 1006 23 2 1702 2705 215420649 215421654 0.000000e+00 1718
9 TraesCS2B01G367800 chr1A 89.109 505 35 6 5 492 357419905 357419404 6.400000e-171 610
10 TraesCS2B01G367800 chrUn 97.512 1005 23 2 1703 2705 151745488 151744484 0.000000e+00 1716
11 TraesCS2B01G367800 chrUn 97.233 1012 24 4 1697 2705 133913564 133914574 0.000000e+00 1711
12 TraesCS2B01G367800 chrUn 97.044 1015 28 2 1693 2705 281568361 281567347 0.000000e+00 1707
13 TraesCS2B01G367800 chrUn 96.866 1021 28 4 1688 2705 121018345 121017326 0.000000e+00 1705
14 TraesCS2B01G367800 chr5A 97.329 1011 23 4 1698 2705 251898706 251897697 0.000000e+00 1714
15 TraesCS2B01G367800 chr1B 97.140 1014 26 3 1695 2705 244072409 244071396 0.000000e+00 1709
16 TraesCS2B01G367800 chr4D 86.255 793 102 5 912 1704 315610664 315609879 0.000000e+00 854
17 TraesCS2B01G367800 chr2D 88.748 551 46 6 5 539 565864396 565863846 0.000000e+00 660
18 TraesCS2B01G367800 chr2D 88.468 555 47 4 1 539 223902795 223903348 0.000000e+00 654
19 TraesCS2B01G367800 chr2D 91.009 456 37 3 86 539 484356728 484357181 1.780000e-171 612
20 TraesCS2B01G367800 chr3A 87.748 555 50 4 1 539 439461552 439461000 1.370000e-177 632
21 TraesCS2B01G367800 chr7D 87.500 536 64 3 5 539 632978453 632978986 1.380000e-172 616
22 TraesCS2B01G367800 chr7D 90.610 426 39 1 115 539 416231367 416231792 5.060000e-157 564
23 TraesCS2B01G367800 chr2A 86.827 539 53 7 1 538 15028724 15028203 1.080000e-163 586
24 TraesCS2B01G367800 chr5D 86.207 551 58 4 6 539 398481693 398482242 5.020000e-162 580
25 TraesCS2B01G367800 chr1D 85.946 555 62 2 1 539 253093376 253092822 1.810000e-161 579
26 TraesCS2B01G367800 chr5B 76.456 807 157 22 912 1704 303923855 303923068 9.020000e-110 407
27 TraesCS2B01G367800 chr6A 75.676 666 127 17 906 1557 495260271 495260915 1.570000e-77 300


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 TraesCS2B01G367800 chr2B 524062906 524065610 2704 True 4996 4996 100.000 1 2705 1 chr2B.!!$R1 2704
1 TraesCS2B01G367800 chr2B 634747186 634748127 941 True 1125 1125 88.198 757 1704 1 chr2B.!!$R2 947
2 TraesCS2B01G367800 chr2B 6811345 6811882 537 False 627 627 87.755 3 539 1 chr2B.!!$F1 536
3 TraesCS2B01G367800 chr2B 6898824 6899359 535 False 617 617 87.523 5 539 1 chr2B.!!$F2 534
4 TraesCS2B01G367800 chr4B 318373027 318374032 1005 True 1718 1718 97.515 1702 2705 1 chr4B.!!$R2 1003
5 TraesCS2B01G367800 chr4B 300079839 300080843 1004 True 1716 1716 97.512 1702 2705 1 chr4B.!!$R1 1003
6 TraesCS2B01G367800 chr1A 215420649 215421654 1005 False 1718 1718 97.515 1702 2705 1 chr1A.!!$F1 1003
7 TraesCS2B01G367800 chr1A 357419404 357419905 501 True 610 610 89.109 5 492 1 chr1A.!!$R1 487
8 TraesCS2B01G367800 chrUn 151744484 151745488 1004 True 1716 1716 97.512 1703 2705 1 chrUn.!!$R2 1002
9 TraesCS2B01G367800 chrUn 133913564 133914574 1010 False 1711 1711 97.233 1697 2705 1 chrUn.!!$F1 1008
10 TraesCS2B01G367800 chrUn 281567347 281568361 1014 True 1707 1707 97.044 1693 2705 1 chrUn.!!$R3 1012
11 TraesCS2B01G367800 chrUn 121017326 121018345 1019 True 1705 1705 96.866 1688 2705 1 chrUn.!!$R1 1017
12 TraesCS2B01G367800 chr5A 251897697 251898706 1009 True 1714 1714 97.329 1698 2705 1 chr5A.!!$R1 1007
13 TraesCS2B01G367800 chr1B 244071396 244072409 1013 True 1709 1709 97.140 1695 2705 1 chr1B.!!$R1 1010
14 TraesCS2B01G367800 chr4D 315609879 315610664 785 True 854 854 86.255 912 1704 1 chr4D.!!$R1 792
15 TraesCS2B01G367800 chr2D 565863846 565864396 550 True 660 660 88.748 5 539 1 chr2D.!!$R1 534
16 TraesCS2B01G367800 chr2D 223902795 223903348 553 False 654 654 88.468 1 539 1 chr2D.!!$F1 538
17 TraesCS2B01G367800 chr3A 439461000 439461552 552 True 632 632 87.748 1 539 1 chr3A.!!$R1 538
18 TraesCS2B01G367800 chr7D 632978453 632978986 533 False 616 616 87.500 5 539 1 chr7D.!!$F2 534
19 TraesCS2B01G367800 chr2A 15028203 15028724 521 True 586 586 86.827 1 538 1 chr2A.!!$R1 537
20 TraesCS2B01G367800 chr5D 398481693 398482242 549 False 580 580 86.207 6 539 1 chr5D.!!$F1 533
21 TraesCS2B01G367800 chr1D 253092822 253093376 554 True 579 579 85.946 1 539 1 chr1D.!!$R1 538
22 TraesCS2B01G367800 chr5B 303923068 303923855 787 True 407 407 76.456 912 1704 1 chr5B.!!$R1 792
23 TraesCS2B01G367800 chr6A 495260271 495260915 644 False 300 300 75.676 906 1557 1 chr6A.!!$F1 651

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
532 564 0.108472 TGCATCTCTGGCGACTCTTG 60.108 55.0 0.00 0.0 0.00 3.02 F
1580 1627 0.031010 GATGACCCAGGGGAGGTAGT 60.031 60.0 11.37 0.0 37.88 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1588 1641 0.114364 TTTCCAGCCTTTCCCTTCCC 59.886 55.0 0.0 0.0 0.00 3.97 R
2530 2591 0.923010 GACGATCCGACTACGAACGC 60.923 60.0 0.0 0.0 42.66 4.84 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
131 132 2.029073 CCCAGACACACGACGCTT 59.971 61.111 0.00 0.00 0.00 4.68
173 174 0.465097 CTTGGGCCATCGCTGATCTT 60.465 55.000 7.26 0.00 34.44 2.40
178 180 1.089920 GCCATCGCTGATCTTGTGTT 58.910 50.000 0.00 0.00 0.00 3.32
204 206 2.997897 GACAGCCCACGGTCTCCT 60.998 66.667 0.00 0.00 37.92 3.69
215 217 2.640302 GGTCTCCTGCTCGAGTGCA 61.640 63.158 15.13 6.74 41.05 4.57
374 406 5.050159 CCATCGTCGAATGAAGCATATTGAA 60.050 40.000 0.00 0.00 0.00 2.69
432 464 1.983224 CACATCCGGGTCCTTCACT 59.017 57.895 0.00 0.00 0.00 3.41
484 516 3.517612 TGACTAAGGGACTGCCTACTTT 58.482 45.455 0.00 0.00 40.86 2.66
497 529 4.787551 TGCCTACTTTTGTCTTTGAGGAA 58.212 39.130 0.00 0.00 0.00 3.36
498 530 4.578928 TGCCTACTTTTGTCTTTGAGGAAC 59.421 41.667 0.00 0.00 0.00 3.62
512 544 1.931635 AGGAACTCAGGTCCAGTCTC 58.068 55.000 12.63 0.00 0.00 3.36
528 560 0.682532 TCTCTGCATCTCTGGCGACT 60.683 55.000 0.00 0.00 0.00 4.18
532 564 0.108472 TGCATCTCTGGCGACTCTTG 60.108 55.000 0.00 0.00 0.00 3.02
539 571 2.164865 CTGGCGACTCTTGGACTGCT 62.165 60.000 0.00 0.00 0.00 4.24
540 572 1.739562 GGCGACTCTTGGACTGCTG 60.740 63.158 0.00 0.00 0.00 4.41
541 573 1.290324 GCGACTCTTGGACTGCTGA 59.710 57.895 0.00 0.00 0.00 4.26
542 574 0.735632 GCGACTCTTGGACTGCTGAG 60.736 60.000 0.00 0.00 0.00 3.35
543 575 0.735632 CGACTCTTGGACTGCTGAGC 60.736 60.000 0.00 0.00 0.00 4.26
544 576 0.319728 GACTCTTGGACTGCTGAGCA 59.680 55.000 7.05 7.05 36.92 4.26
580 612 3.844090 GGAGAGCGAGGGCCAGAC 61.844 72.222 6.18 0.00 41.24 3.51
581 613 3.844090 GAGAGCGAGGGCCAGACC 61.844 72.222 6.18 0.00 41.24 3.85
599 631 3.569210 CCCCCTATGCATCGGCCA 61.569 66.667 11.77 0.00 40.13 5.36
600 632 2.281761 CCCCTATGCATCGGCCAC 60.282 66.667 11.77 0.00 40.13 5.01
601 633 2.281761 CCCTATGCATCGGCCACC 60.282 66.667 11.77 0.00 40.13 4.61
602 634 2.281761 CCTATGCATCGGCCACCC 60.282 66.667 0.19 0.00 40.13 4.61
603 635 2.822637 CCTATGCATCGGCCACCCT 61.823 63.158 0.19 0.00 40.13 4.34
604 636 1.302033 CTATGCATCGGCCACCCTC 60.302 63.158 0.19 0.00 40.13 4.30
605 637 2.043604 CTATGCATCGGCCACCCTCA 62.044 60.000 0.19 0.00 40.13 3.86
606 638 1.418097 TATGCATCGGCCACCCTCAT 61.418 55.000 0.19 1.53 40.13 2.90
607 639 2.124151 GCATCGGCCACCCTCATT 60.124 61.111 2.24 0.00 0.00 2.57
608 640 2.484062 GCATCGGCCACCCTCATTG 61.484 63.158 2.24 0.00 0.00 2.82
609 641 1.224315 CATCGGCCACCCTCATTGA 59.776 57.895 2.24 0.00 0.00 2.57
610 642 0.179009 CATCGGCCACCCTCATTGAT 60.179 55.000 2.24 0.00 0.00 2.57
611 643 0.552848 ATCGGCCACCCTCATTGATT 59.447 50.000 2.24 0.00 0.00 2.57
612 644 0.331278 TCGGCCACCCTCATTGATTT 59.669 50.000 2.24 0.00 0.00 2.17
613 645 1.185315 CGGCCACCCTCATTGATTTT 58.815 50.000 2.24 0.00 0.00 1.82
614 646 1.550072 CGGCCACCCTCATTGATTTTT 59.450 47.619 2.24 0.00 0.00 1.94
615 647 2.757868 CGGCCACCCTCATTGATTTTTA 59.242 45.455 2.24 0.00 0.00 1.52
616 648 3.181487 CGGCCACCCTCATTGATTTTTAG 60.181 47.826 2.24 0.00 0.00 1.85
617 649 4.023291 GGCCACCCTCATTGATTTTTAGA 58.977 43.478 0.00 0.00 0.00 2.10
618 650 4.098501 GGCCACCCTCATTGATTTTTAGAG 59.901 45.833 0.00 0.00 0.00 2.43
619 651 4.098501 GCCACCCTCATTGATTTTTAGAGG 59.901 45.833 0.00 0.00 44.26 3.69
623 655 3.638627 CCTCATTGATTTTTAGAGGGGGC 59.361 47.826 0.00 0.00 41.65 5.80
624 656 4.540715 CTCATTGATTTTTAGAGGGGGCT 58.459 43.478 0.00 0.00 0.00 5.19
625 657 5.399038 CCTCATTGATTTTTAGAGGGGGCTA 60.399 44.000 0.00 0.00 41.65 3.93
626 658 5.694995 TCATTGATTTTTAGAGGGGGCTAG 58.305 41.667 0.00 0.00 0.00 3.42
627 659 5.193728 TCATTGATTTTTAGAGGGGGCTAGT 59.806 40.000 0.00 0.00 0.00 2.57
628 660 6.388689 TCATTGATTTTTAGAGGGGGCTAGTA 59.611 38.462 0.00 0.00 0.00 1.82
629 661 5.888982 TGATTTTTAGAGGGGGCTAGTAG 57.111 43.478 0.00 0.00 0.00 2.57
630 662 4.658901 TGATTTTTAGAGGGGGCTAGTAGG 59.341 45.833 0.00 0.00 0.00 3.18
631 663 2.098618 TTTAGAGGGGGCTAGTAGGC 57.901 55.000 15.21 15.21 40.51 3.93
639 671 3.535574 GGCTAGTAGGCCCTGTACT 57.464 57.895 12.66 3.39 45.92 2.73
640 672 2.671896 GGCTAGTAGGCCCTGTACTA 57.328 55.000 12.66 4.56 45.92 1.82
641 673 2.954792 GGCTAGTAGGCCCTGTACTAA 58.045 52.381 12.66 0.00 45.92 2.24
642 674 3.508426 GGCTAGTAGGCCCTGTACTAAT 58.492 50.000 12.66 0.00 45.92 1.73
643 675 3.510753 GGCTAGTAGGCCCTGTACTAATC 59.489 52.174 12.66 6.49 45.92 1.75
644 676 4.409187 GCTAGTAGGCCCTGTACTAATCT 58.591 47.826 10.62 0.00 33.55 2.40
645 677 4.218852 GCTAGTAGGCCCTGTACTAATCTG 59.781 50.000 10.62 2.49 33.55 2.90
646 678 4.267341 AGTAGGCCCTGTACTAATCTGT 57.733 45.455 0.00 0.00 0.00 3.41
647 679 4.621769 AGTAGGCCCTGTACTAATCTGTT 58.378 43.478 0.00 0.00 0.00 3.16
648 680 3.914426 AGGCCCTGTACTAATCTGTTG 57.086 47.619 0.00 0.00 0.00 3.33
649 681 3.182152 AGGCCCTGTACTAATCTGTTGT 58.818 45.455 0.00 0.00 0.00 3.32
650 682 4.359105 AGGCCCTGTACTAATCTGTTGTA 58.641 43.478 0.00 0.00 0.00 2.41
651 683 4.969359 AGGCCCTGTACTAATCTGTTGTAT 59.031 41.667 0.00 0.00 0.00 2.29
652 684 6.141083 AGGCCCTGTACTAATCTGTTGTATA 58.859 40.000 0.00 0.00 0.00 1.47
653 685 6.614087 AGGCCCTGTACTAATCTGTTGTATAA 59.386 38.462 0.00 0.00 0.00 0.98
654 686 6.704937 GGCCCTGTACTAATCTGTTGTATAAC 59.295 42.308 0.00 0.00 37.32 1.89
655 687 6.704937 GCCCTGTACTAATCTGTTGTATAACC 59.295 42.308 0.00 0.00 35.92 2.85
656 688 7.418712 GCCCTGTACTAATCTGTTGTATAACCT 60.419 40.741 0.00 0.00 35.92 3.50
657 689 8.483758 CCCTGTACTAATCTGTTGTATAACCTT 58.516 37.037 0.00 0.00 35.92 3.50
658 690 9.886132 CCTGTACTAATCTGTTGTATAACCTTT 57.114 33.333 0.00 0.00 35.92 3.11
669 701 9.769093 CTGTTGTATAACCTTTCTTTATTTCCG 57.231 33.333 0.00 0.00 35.92 4.30
670 702 8.732531 TGTTGTATAACCTTTCTTTATTTCCGG 58.267 33.333 0.00 0.00 35.92 5.14
671 703 7.324354 TGTATAACCTTTCTTTATTTCCGGC 57.676 36.000 0.00 0.00 0.00 6.13
672 704 7.114095 TGTATAACCTTTCTTTATTTCCGGCT 58.886 34.615 0.00 0.00 0.00 5.52
673 705 8.266473 TGTATAACCTTTCTTTATTTCCGGCTA 58.734 33.333 0.00 0.00 0.00 3.93
674 706 9.281371 GTATAACCTTTCTTTATTTCCGGCTAT 57.719 33.333 0.00 0.00 0.00 2.97
675 707 8.762481 ATAACCTTTCTTTATTTCCGGCTATT 57.238 30.769 0.00 0.00 0.00 1.73
676 708 9.856162 ATAACCTTTCTTTATTTCCGGCTATTA 57.144 29.630 0.00 0.00 0.00 0.98
677 709 7.803279 ACCTTTCTTTATTTCCGGCTATTAG 57.197 36.000 0.00 0.00 0.00 1.73
678 710 6.262496 ACCTTTCTTTATTTCCGGCTATTAGC 59.738 38.462 7.16 7.16 41.46 3.09
679 711 6.262273 CCTTTCTTTATTTCCGGCTATTAGCA 59.738 38.462 17.11 0.00 44.75 3.49
680 712 7.201785 CCTTTCTTTATTTCCGGCTATTAGCAA 60.202 37.037 17.11 3.59 44.75 3.91
681 713 7.633193 TTCTTTATTTCCGGCTATTAGCAAA 57.367 32.000 17.11 9.54 44.75 3.68
682 714 7.259290 TCTTTATTTCCGGCTATTAGCAAAG 57.741 36.000 17.11 14.48 44.75 2.77
683 715 6.262273 TCTTTATTTCCGGCTATTAGCAAAGG 59.738 38.462 17.11 15.48 44.75 3.11
684 716 1.675552 TTCCGGCTATTAGCAAAGGC 58.324 50.000 17.11 0.00 44.75 4.35
685 717 0.544223 TCCGGCTATTAGCAAAGGCA 59.456 50.000 17.11 5.46 44.75 4.75
686 718 1.142870 TCCGGCTATTAGCAAAGGCAT 59.857 47.619 17.11 0.00 44.75 4.40
687 719 2.370519 TCCGGCTATTAGCAAAGGCATA 59.629 45.455 17.11 0.27 44.75 3.14
688 720 2.744202 CCGGCTATTAGCAAAGGCATAG 59.256 50.000 17.11 0.00 44.75 2.23
689 721 2.744202 CGGCTATTAGCAAAGGCATAGG 59.256 50.000 17.11 0.00 44.75 2.57
690 722 2.489722 GGCTATTAGCAAAGGCATAGGC 59.510 50.000 17.11 0.00 44.75 3.93
703 735 3.113260 GCATAGGCCTTGATTCTACGT 57.887 47.619 12.58 0.00 0.00 3.57
704 736 4.252971 GCATAGGCCTTGATTCTACGTA 57.747 45.455 12.58 0.00 0.00 3.57
705 737 4.822026 GCATAGGCCTTGATTCTACGTAT 58.178 43.478 12.58 0.00 0.00 3.06
706 738 4.865365 GCATAGGCCTTGATTCTACGTATC 59.135 45.833 12.58 0.00 0.00 2.24
707 739 5.411781 CATAGGCCTTGATTCTACGTATCC 58.588 45.833 12.58 0.00 0.00 2.59
708 740 3.305720 AGGCCTTGATTCTACGTATCCA 58.694 45.455 0.00 0.00 0.00 3.41
709 741 3.709653 AGGCCTTGATTCTACGTATCCAA 59.290 43.478 0.00 0.00 0.00 3.53
710 742 3.808174 GGCCTTGATTCTACGTATCCAAC 59.192 47.826 0.00 0.00 0.00 3.77
711 743 4.439057 GCCTTGATTCTACGTATCCAACA 58.561 43.478 0.00 0.00 0.00 3.33
712 744 5.057149 GCCTTGATTCTACGTATCCAACAT 58.943 41.667 0.00 0.00 0.00 2.71
713 745 5.527582 GCCTTGATTCTACGTATCCAACATT 59.472 40.000 0.00 0.00 0.00 2.71
714 746 6.511767 GCCTTGATTCTACGTATCCAACATTG 60.512 42.308 0.00 0.00 0.00 2.82
715 747 5.984233 TGATTCTACGTATCCAACATTGC 57.016 39.130 0.00 0.00 0.00 3.56
716 748 5.670485 TGATTCTACGTATCCAACATTGCT 58.330 37.500 0.00 0.00 0.00 3.91
717 749 5.523552 TGATTCTACGTATCCAACATTGCTG 59.476 40.000 0.00 0.00 0.00 4.41
718 750 3.792401 TCTACGTATCCAACATTGCTGG 58.208 45.455 0.00 0.00 35.05 4.85
719 751 1.094785 ACGTATCCAACATTGCTGGC 58.905 50.000 0.96 0.00 33.63 4.85
720 752 1.340017 ACGTATCCAACATTGCTGGCT 60.340 47.619 0.96 0.00 33.63 4.75
721 753 2.093181 ACGTATCCAACATTGCTGGCTA 60.093 45.455 0.96 0.00 33.63 3.93
722 754 2.545526 CGTATCCAACATTGCTGGCTAG 59.454 50.000 0.96 0.00 33.63 3.42
731 763 3.896479 GCTGGCTAGCCAACTCAC 58.104 61.111 35.07 18.87 46.63 3.51
732 764 1.298014 GCTGGCTAGCCAACTCACT 59.702 57.895 35.07 0.00 46.63 3.41
733 765 0.537188 GCTGGCTAGCCAACTCACTA 59.463 55.000 35.07 11.83 46.63 2.74
734 766 1.139853 GCTGGCTAGCCAACTCACTAT 59.860 52.381 35.07 0.00 46.63 2.12
735 767 2.420687 GCTGGCTAGCCAACTCACTATT 60.421 50.000 35.07 0.00 46.63 1.73
736 768 3.201290 CTGGCTAGCCAACTCACTATTG 58.799 50.000 35.07 16.87 46.63 1.90
737 769 3.991291 CTGGCTAGCCAACTCACTATTGG 60.991 52.174 35.07 16.36 46.63 3.16
743 775 2.795329 CCAACTCACTATTGGCCAACT 58.205 47.619 23.27 12.77 40.25 3.16
744 776 2.749621 CCAACTCACTATTGGCCAACTC 59.250 50.000 23.27 0.00 40.25 3.01
745 777 3.560025 CCAACTCACTATTGGCCAACTCT 60.560 47.826 23.27 7.98 40.25 3.24
746 778 3.340814 ACTCACTATTGGCCAACTCTG 57.659 47.619 23.27 15.49 0.00 3.35
747 779 2.012673 CTCACTATTGGCCAACTCTGC 58.987 52.381 23.27 0.00 0.00 4.26
755 787 2.677875 CCAACTCTGCCTTGGCCC 60.678 66.667 9.35 0.00 32.03 5.80
756 788 2.115910 CAACTCTGCCTTGGCCCA 59.884 61.111 9.35 0.00 0.00 5.36
757 789 1.531365 CAACTCTGCCTTGGCCCAA 60.531 57.895 9.35 0.00 0.00 4.12
758 790 1.228675 AACTCTGCCTTGGCCCAAG 60.229 57.895 16.91 16.91 40.75 3.61
759 791 2.011617 AACTCTGCCTTGGCCCAAGT 62.012 55.000 21.65 0.00 39.58 3.16
760 792 1.676967 CTCTGCCTTGGCCCAAGTC 60.677 63.158 21.65 10.36 39.58 3.01
770 802 3.717294 CCCAAGTCCGTCCCCCTG 61.717 72.222 0.00 0.00 0.00 4.45
815 847 0.759346 GATCACAGGGCGATTAGGGT 59.241 55.000 0.00 0.00 0.00 4.34
821 853 0.683179 AGGGCGATTAGGGTTTTGGC 60.683 55.000 0.00 0.00 0.00 4.52
826 858 1.555967 GATTAGGGTTTTGGCAGCCA 58.444 50.000 11.22 11.22 36.72 4.75
845 877 3.834938 CCACCTCTAGTCTAACCCTAGG 58.165 54.545 0.06 0.06 34.06 3.02
863 895 2.046892 GGCGTGGCTGTGATCTGT 60.047 61.111 0.00 0.00 0.00 3.41
865 897 2.103042 GCGTGGCTGTGATCTGTCC 61.103 63.158 0.00 0.00 0.00 4.02
873 905 1.002888 CTGTGATCTGTCCTGGCAAGT 59.997 52.381 0.00 0.00 0.00 3.16
883 915 1.450312 CTGGCAAGTGATCCGTCCC 60.450 63.158 0.00 0.00 0.00 4.46
891 923 0.386113 GTGATCCGTCCCAGTCTAGC 59.614 60.000 0.00 0.00 0.00 3.42
899 931 0.614979 TCCCAGTCTAGCCACCTCAC 60.615 60.000 0.00 0.00 0.00 3.51
900 932 1.617947 CCCAGTCTAGCCACCTCACC 61.618 65.000 0.00 0.00 0.00 4.02
904 936 0.324830 GTCTAGCCACCTCACCCTCT 60.325 60.000 0.00 0.00 0.00 3.69
960 993 1.405243 AAACCCTAGGAGGAGGAGGA 58.595 55.000 11.48 0.00 37.67 3.71
961 994 0.938192 AACCCTAGGAGGAGGAGGAG 59.062 60.000 11.48 0.00 37.67 3.69
962 995 1.002242 ACCCTAGGAGGAGGAGGAGG 61.002 65.000 11.48 0.00 37.67 4.30
963 996 0.703056 CCCTAGGAGGAGGAGGAGGA 60.703 65.000 11.48 0.00 37.67 3.71
964 997 0.777446 CCTAGGAGGAGGAGGAGGAG 59.223 65.000 1.05 0.00 37.67 3.69
965 998 0.777446 CTAGGAGGAGGAGGAGGAGG 59.223 65.000 0.00 0.00 0.00 4.30
966 999 0.350904 TAGGAGGAGGAGGAGGAGGA 59.649 60.000 0.00 0.00 0.00 3.71
986 1019 4.681978 GAGCGGTGGCGTGGAGTT 62.682 66.667 0.00 0.00 46.35 3.01
987 1020 4.681978 AGCGGTGGCGTGGAGTTC 62.682 66.667 0.00 0.00 46.35 3.01
1013 1046 3.333680 AGGTAAACCATGGAGGATGTTGT 59.666 43.478 21.47 0.00 41.22 3.32
1025 1058 4.262808 GGAGGATGTTGTAGGGATGATGAG 60.263 50.000 0.00 0.00 0.00 2.90
1035 1068 1.287739 GGGATGATGAGGGGGTTGAAA 59.712 52.381 0.00 0.00 0.00 2.69
1041 1074 3.117322 TGATGAGGGGGTTGAAACTTTCA 60.117 43.478 0.00 0.00 38.04 2.69
1053 1086 5.630415 TGAAACTTTCAGAGGAGGAGAAA 57.370 39.130 0.00 0.00 34.08 2.52
1074 1107 3.739401 AAAGGGGTGAAGATCCGAATT 57.261 42.857 0.00 0.00 0.00 2.17
1077 1110 1.490910 GGGGTGAAGATCCGAATTCCT 59.509 52.381 0.00 0.00 0.00 3.36
1083 1116 1.403814 AGATCCGAATTCCTGCGAGA 58.596 50.000 0.00 0.00 0.00 4.04
1092 1125 0.972983 TTCCTGCGAGAGAGAAGGGG 60.973 60.000 0.00 0.00 0.00 4.79
1098 1131 1.760029 GCGAGAGAGAAGGGGAAGAAT 59.240 52.381 0.00 0.00 0.00 2.40
1127 1160 3.324108 GGCGGTGGGTAAGGTCCA 61.324 66.667 0.00 0.00 0.00 4.02
1128 1161 2.676265 GGCGGTGGGTAAGGTCCAT 61.676 63.158 0.00 0.00 36.58 3.41
1203 1236 0.179000 GTCCGATCAAGGGCACTGAT 59.821 55.000 0.00 0.00 35.58 2.90
1218 1253 1.271325 ACTGATTGCAATGACGTGGGA 60.271 47.619 18.59 0.00 0.00 4.37
1225 1272 2.499693 TGCAATGACGTGGGAGAGAATA 59.500 45.455 0.00 0.00 0.00 1.75
1238 1285 6.375455 GTGGGAGAGAATATGTTTGTGTTCAT 59.625 38.462 0.00 0.00 0.00 2.57
1305 1352 5.839063 ACCTTGGATGTTCGATAAGGATCTA 59.161 40.000 8.20 0.00 40.18 1.98
1365 1412 9.872684 ATGGAGGATTATGAGTTCAACAATATT 57.127 29.630 0.00 0.00 0.00 1.28
1459 1506 5.467738 ACATCATAGGAAGGTATGTGGAGA 58.532 41.667 0.00 0.00 32.93 3.71
1479 1526 1.536662 AGATACGGGGAGGGATGGC 60.537 63.158 0.00 0.00 0.00 4.40
1506 1553 1.455822 TGGGGAAGTTCATGAGGGTT 58.544 50.000 5.01 0.00 0.00 4.11
1541 1588 3.387699 TGTATCGAGAAGCCCATCATGAA 59.612 43.478 0.00 0.00 0.00 2.57
1542 1589 2.609427 TCGAGAAGCCCATCATGAAG 57.391 50.000 0.00 0.00 0.00 3.02
1560 1607 4.389374 TGAAGGGCTTTACACTTGAGAAG 58.611 43.478 0.00 0.00 0.00 2.85
1566 1613 4.393371 GGCTTTACACTTGAGAAGGATGAC 59.607 45.833 0.00 0.00 0.00 3.06
1568 1615 4.553330 TTACACTTGAGAAGGATGACCC 57.447 45.455 0.00 0.00 36.73 4.46
1577 1624 2.042930 GGATGACCCAGGGGAGGT 59.957 66.667 11.37 0.00 41.50 3.85
1580 1627 0.031010 GATGACCCAGGGGAGGTAGT 60.031 60.000 11.37 0.00 37.88 2.73
1582 1635 2.285442 ACCCAGGGGAGGTAGTGC 60.285 66.667 11.37 0.00 35.24 4.40
1588 1641 2.732619 GGGGAGGTAGTGCGGAAGG 61.733 68.421 0.00 0.00 0.00 3.46
1589 1642 2.732619 GGGAGGTAGTGCGGAAGGG 61.733 68.421 0.00 0.00 0.00 3.95
1606 1659 1.774300 GGGAAGGGAAAGGCTGGAA 59.226 57.895 0.00 0.00 0.00 3.53
1611 1664 0.188342 AGGGAAAGGCTGGAAAGCAA 59.812 50.000 0.00 0.00 36.33 3.91
1616 1669 2.299326 AAGGCTGGAAAGCAAGATGT 57.701 45.000 0.00 0.00 36.33 3.06
1635 1691 3.211963 GATGGGTCATGGTGCCGC 61.212 66.667 0.00 0.00 0.00 6.53
1653 1709 3.877508 GCCGCTTTGAATATGAGTACCTT 59.122 43.478 0.00 0.00 0.00 3.50
1686 1742 1.187974 ACACATGTGGCATCATTGGG 58.812 50.000 28.64 0.23 34.19 4.12
1743 1799 0.541863 CTTACACCCACAGCCCCTAG 59.458 60.000 0.00 0.00 0.00 3.02
1751 1807 0.108138 CACAGCCCCTAGTGCTACAC 60.108 60.000 3.90 0.00 36.81 2.90
1756 1812 2.040178 GCCCCTAGTGCTACACATACT 58.960 52.381 0.00 0.00 36.74 2.12
1770 1826 7.093245 TGCTACACATACTGGACCAATTACTAA 60.093 37.037 0.00 0.00 0.00 2.24
2079 2136 0.969894 CCCGAGGCTATTCTAGGTGG 59.030 60.000 0.00 0.00 0.00 4.61
2442 2502 4.944249 GTTTGCTCGCAGGAAACC 57.056 55.556 16.68 0.00 46.55 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
131 132 1.228769 ACACAGTAGCCCGAGGTGA 60.229 57.895 0.00 0.00 33.82 4.02
204 206 3.292500 CTGCCTCTGCACTCGAGCA 62.293 63.158 13.61 5.66 44.23 4.26
215 217 1.075970 TGCCCGATACTCTGCCTCT 60.076 57.895 0.00 0.00 0.00 3.69
275 277 3.838244 TCACAAAGCAACTCCTGTAGT 57.162 42.857 0.00 0.00 41.49 2.73
278 280 3.004752 ACTTCACAAAGCAACTCCTGT 57.995 42.857 0.00 0.00 35.81 4.00
374 406 3.245284 CACGAACAAAGTGAATGTCGAGT 59.755 43.478 0.00 0.00 41.83 4.18
467 499 3.908103 AGACAAAAGTAGGCAGTCCCTTA 59.092 43.478 0.00 0.00 43.06 2.69
484 516 3.181454 GGACCTGAGTTCCTCAAAGACAA 60.181 47.826 0.00 0.00 40.18 3.18
497 529 0.178950 TGCAGAGACTGGACCTGAGT 60.179 55.000 5.22 0.00 31.21 3.41
498 530 1.136695 GATGCAGAGACTGGACCTGAG 59.863 57.143 5.22 0.00 34.07 3.35
512 544 0.175302 AAGAGTCGCCAGAGATGCAG 59.825 55.000 0.00 0.00 0.00 4.41
540 572 4.537433 CTGCCTACGCCCCTGCTC 62.537 72.222 0.00 0.00 34.43 4.26
543 575 4.473520 CCACTGCCTACGCCCCTG 62.474 72.222 0.00 0.00 0.00 4.45
563 595 3.844090 GTCTGGCCCTCGCTCTCC 61.844 72.222 0.00 0.00 34.44 3.71
564 596 3.844090 GGTCTGGCCCTCGCTCTC 61.844 72.222 0.00 0.00 34.44 3.20
582 614 3.569210 TGGCCGATGCATAGGGGG 61.569 66.667 25.04 13.33 40.13 5.40
583 615 2.281761 GTGGCCGATGCATAGGGG 60.282 66.667 25.04 15.66 40.13 4.79
584 616 2.281761 GGTGGCCGATGCATAGGG 60.282 66.667 25.04 18.03 40.13 3.53
585 617 2.281761 GGGTGGCCGATGCATAGG 60.282 66.667 20.58 20.58 40.13 2.57
586 618 1.302033 GAGGGTGGCCGATGCATAG 60.302 63.158 0.00 0.00 40.13 2.23
587 619 1.418097 ATGAGGGTGGCCGATGCATA 61.418 55.000 0.00 0.00 40.13 3.14
588 620 2.288642 AATGAGGGTGGCCGATGCAT 62.289 55.000 0.00 0.00 40.13 3.96
589 621 2.982643 AATGAGGGTGGCCGATGCA 61.983 57.895 0.00 0.00 40.13 3.96
590 622 2.124151 AATGAGGGTGGCCGATGC 60.124 61.111 0.00 0.00 0.00 3.91
591 623 0.179009 ATCAATGAGGGTGGCCGATG 60.179 55.000 0.00 0.00 0.00 3.84
592 624 0.552848 AATCAATGAGGGTGGCCGAT 59.447 50.000 0.00 0.00 0.00 4.18
593 625 0.331278 AAATCAATGAGGGTGGCCGA 59.669 50.000 0.00 0.00 0.00 5.54
594 626 1.185315 AAAATCAATGAGGGTGGCCG 58.815 50.000 0.00 0.00 0.00 6.13
595 627 4.023291 TCTAAAAATCAATGAGGGTGGCC 58.977 43.478 0.00 0.00 0.00 5.36
596 628 4.098501 CCTCTAAAAATCAATGAGGGTGGC 59.901 45.833 0.00 0.00 40.25 5.01
597 629 5.841957 CCTCTAAAAATCAATGAGGGTGG 57.158 43.478 0.00 0.00 40.25 4.61
601 633 3.638627 GCCCCCTCTAAAAATCAATGAGG 59.361 47.826 0.00 0.00 42.72 3.86
602 634 4.540715 AGCCCCCTCTAAAAATCAATGAG 58.459 43.478 0.00 0.00 0.00 2.90
603 635 4.608170 AGCCCCCTCTAAAAATCAATGA 57.392 40.909 0.00 0.00 0.00 2.57
604 636 5.449553 ACTAGCCCCCTCTAAAAATCAATG 58.550 41.667 0.00 0.00 0.00 2.82
605 637 5.734031 ACTAGCCCCCTCTAAAAATCAAT 57.266 39.130 0.00 0.00 0.00 2.57
606 638 5.132144 CCTACTAGCCCCCTCTAAAAATCAA 59.868 44.000 0.00 0.00 0.00 2.57
607 639 4.658901 CCTACTAGCCCCCTCTAAAAATCA 59.341 45.833 0.00 0.00 0.00 2.57
608 640 4.505215 GCCTACTAGCCCCCTCTAAAAATC 60.505 50.000 0.00 0.00 0.00 2.17
609 641 3.394940 GCCTACTAGCCCCCTCTAAAAAT 59.605 47.826 0.00 0.00 0.00 1.82
610 642 2.775960 GCCTACTAGCCCCCTCTAAAAA 59.224 50.000 0.00 0.00 0.00 1.94
611 643 2.405559 GCCTACTAGCCCCCTCTAAAA 58.594 52.381 0.00 0.00 0.00 1.52
612 644 2.098618 GCCTACTAGCCCCCTCTAAA 57.901 55.000 0.00 0.00 0.00 1.85
613 645 3.865241 GCCTACTAGCCCCCTCTAA 57.135 57.895 0.00 0.00 0.00 2.10
622 654 4.218852 CAGATTAGTACAGGGCCTACTAGC 59.781 50.000 5.28 7.88 30.19 3.42
623 655 5.386924 ACAGATTAGTACAGGGCCTACTAG 58.613 45.833 5.28 2.42 30.19 2.57
624 656 5.399052 ACAGATTAGTACAGGGCCTACTA 57.601 43.478 5.28 9.15 0.00 1.82
625 657 4.267341 ACAGATTAGTACAGGGCCTACT 57.733 45.455 5.28 10.35 0.00 2.57
626 658 4.161754 ACAACAGATTAGTACAGGGCCTAC 59.838 45.833 5.28 0.83 0.00 3.18
627 659 4.359105 ACAACAGATTAGTACAGGGCCTA 58.641 43.478 5.28 0.00 0.00 3.93
628 660 3.182152 ACAACAGATTAGTACAGGGCCT 58.818 45.455 0.00 0.00 0.00 5.19
629 661 3.629142 ACAACAGATTAGTACAGGGCC 57.371 47.619 0.00 0.00 0.00 5.80
630 662 6.704937 GGTTATACAACAGATTAGTACAGGGC 59.295 42.308 0.00 0.00 36.29 5.19
631 663 8.019656 AGGTTATACAACAGATTAGTACAGGG 57.980 38.462 0.00 0.00 36.29 4.45
632 664 9.886132 AAAGGTTATACAACAGATTAGTACAGG 57.114 33.333 0.00 0.00 36.29 4.00
643 675 9.769093 CGGAAATAAAGAAAGGTTATACAACAG 57.231 33.333 0.00 0.00 36.29 3.16
644 676 8.732531 CCGGAAATAAAGAAAGGTTATACAACA 58.267 33.333 0.00 0.00 36.29 3.33
645 677 7.699391 GCCGGAAATAAAGAAAGGTTATACAAC 59.301 37.037 5.05 0.00 0.00 3.32
646 678 7.612633 AGCCGGAAATAAAGAAAGGTTATACAA 59.387 33.333 5.05 0.00 0.00 2.41
647 679 7.114095 AGCCGGAAATAAAGAAAGGTTATACA 58.886 34.615 5.05 0.00 0.00 2.29
648 680 7.563888 AGCCGGAAATAAAGAAAGGTTATAC 57.436 36.000 5.05 0.00 0.00 1.47
649 681 9.856162 AATAGCCGGAAATAAAGAAAGGTTATA 57.144 29.630 5.05 0.00 0.00 0.98
650 682 8.762481 AATAGCCGGAAATAAAGAAAGGTTAT 57.238 30.769 5.05 0.00 0.00 1.89
651 683 9.333724 CTAATAGCCGGAAATAAAGAAAGGTTA 57.666 33.333 5.05 0.00 0.00 2.85
652 684 7.201794 GCTAATAGCCGGAAATAAAGAAAGGTT 60.202 37.037 5.05 0.00 34.48 3.50
653 685 6.262496 GCTAATAGCCGGAAATAAAGAAAGGT 59.738 38.462 5.05 0.00 34.48 3.50
654 686 6.262273 TGCTAATAGCCGGAAATAAAGAAAGG 59.738 38.462 5.05 0.00 41.51 3.11
655 687 7.259290 TGCTAATAGCCGGAAATAAAGAAAG 57.741 36.000 5.05 0.00 41.51 2.62
656 688 7.633193 TTGCTAATAGCCGGAAATAAAGAAA 57.367 32.000 5.05 0.00 41.51 2.52
657 689 7.201785 CCTTTGCTAATAGCCGGAAATAAAGAA 60.202 37.037 5.05 0.00 41.51 2.52
658 690 6.262273 CCTTTGCTAATAGCCGGAAATAAAGA 59.738 38.462 5.05 0.00 41.51 2.52
659 691 6.438763 CCTTTGCTAATAGCCGGAAATAAAG 58.561 40.000 5.05 10.19 41.51 1.85
660 692 5.221165 GCCTTTGCTAATAGCCGGAAATAAA 60.221 40.000 5.05 1.10 41.51 1.40
661 693 4.277423 GCCTTTGCTAATAGCCGGAAATAA 59.723 41.667 5.05 0.00 41.51 1.40
662 694 3.818773 GCCTTTGCTAATAGCCGGAAATA 59.181 43.478 5.05 0.00 41.51 1.40
663 695 2.623416 GCCTTTGCTAATAGCCGGAAAT 59.377 45.455 5.05 0.00 41.51 2.17
664 696 2.021457 GCCTTTGCTAATAGCCGGAAA 58.979 47.619 5.05 3.19 41.51 3.13
665 697 1.065053 TGCCTTTGCTAATAGCCGGAA 60.065 47.619 5.05 0.00 41.51 4.30
666 698 0.544223 TGCCTTTGCTAATAGCCGGA 59.456 50.000 5.05 0.00 41.51 5.14
667 699 1.609208 ATGCCTTTGCTAATAGCCGG 58.391 50.000 10.06 8.64 41.51 6.13
668 700 2.744202 CCTATGCCTTTGCTAATAGCCG 59.256 50.000 10.06 0.00 41.51 5.52
669 701 2.489722 GCCTATGCCTTTGCTAATAGCC 59.510 50.000 10.06 0.00 41.51 3.93
670 702 3.839051 GCCTATGCCTTTGCTAATAGC 57.161 47.619 5.12 5.12 42.82 2.97
683 715 3.113260 ACGTAGAATCAAGGCCTATGC 57.887 47.619 5.16 0.00 0.00 3.14
684 716 5.047306 TGGATACGTAGAATCAAGGCCTATG 60.047 44.000 5.16 7.18 42.51 2.23
685 717 5.084519 TGGATACGTAGAATCAAGGCCTAT 58.915 41.667 5.16 0.00 42.51 2.57
686 718 4.476297 TGGATACGTAGAATCAAGGCCTA 58.524 43.478 5.16 0.00 42.51 3.93
687 719 3.305720 TGGATACGTAGAATCAAGGCCT 58.694 45.455 0.00 0.00 42.51 5.19
688 720 3.746045 TGGATACGTAGAATCAAGGCC 57.254 47.619 0.08 0.00 42.51 5.19
689 721 4.439057 TGTTGGATACGTAGAATCAAGGC 58.561 43.478 0.08 0.00 42.51 4.35
690 722 6.511767 GCAATGTTGGATACGTAGAATCAAGG 60.512 42.308 0.08 0.00 42.51 3.61
691 723 6.258727 AGCAATGTTGGATACGTAGAATCAAG 59.741 38.462 0.08 0.00 42.51 3.02
692 724 6.037062 CAGCAATGTTGGATACGTAGAATCAA 59.963 38.462 0.08 0.41 42.51 2.57
693 725 5.523552 CAGCAATGTTGGATACGTAGAATCA 59.476 40.000 0.08 0.00 42.51 2.57
694 726 5.050091 CCAGCAATGTTGGATACGTAGAATC 60.050 44.000 10.82 0.00 37.96 2.52
695 727 4.816385 CCAGCAATGTTGGATACGTAGAAT 59.184 41.667 10.82 0.00 37.96 2.40
696 728 4.188462 CCAGCAATGTTGGATACGTAGAA 58.812 43.478 10.82 0.00 37.96 2.10
697 729 3.792401 CCAGCAATGTTGGATACGTAGA 58.208 45.455 10.82 0.00 37.96 2.59
698 730 2.287915 GCCAGCAATGTTGGATACGTAG 59.712 50.000 20.45 0.00 37.96 3.51
699 731 2.093181 AGCCAGCAATGTTGGATACGTA 60.093 45.455 20.45 0.00 37.96 3.57
700 732 1.094785 GCCAGCAATGTTGGATACGT 58.905 50.000 20.45 0.00 37.96 3.57
701 733 1.382522 AGCCAGCAATGTTGGATACG 58.617 50.000 20.45 0.00 37.96 3.06
716 748 2.092968 CCAATAGTGAGTTGGCTAGCCA 60.093 50.000 32.88 32.88 45.63 4.75
717 749 2.565841 CCAATAGTGAGTTGGCTAGCC 58.434 52.381 27.71 27.71 39.64 3.93
724 756 3.438087 CAGAGTTGGCCAATAGTGAGTTG 59.562 47.826 23.66 8.17 0.00 3.16
725 757 3.679389 CAGAGTTGGCCAATAGTGAGTT 58.321 45.455 23.66 0.02 0.00 3.01
726 758 2.616510 GCAGAGTTGGCCAATAGTGAGT 60.617 50.000 23.66 0.00 0.00 3.41
727 759 2.012673 GCAGAGTTGGCCAATAGTGAG 58.987 52.381 23.66 10.99 0.00 3.51
728 760 2.113860 GCAGAGTTGGCCAATAGTGA 57.886 50.000 23.66 0.00 0.00 3.41
738 770 2.677875 GGGCCAAGGCAGAGTTGG 60.678 66.667 13.87 0.00 46.36 3.77
739 771 1.530013 CTTGGGCCAAGGCAGAGTTG 61.530 60.000 34.03 10.01 44.11 3.16
740 772 1.228675 CTTGGGCCAAGGCAGAGTT 60.229 57.895 34.03 0.00 44.11 3.01
741 773 2.437897 CTTGGGCCAAGGCAGAGT 59.562 61.111 34.03 0.00 44.11 3.24
742 774 2.437897 ACTTGGGCCAAGGCAGAG 59.562 61.111 40.84 22.73 44.81 3.35
747 779 2.359975 GACGGACTTGGGCCAAGG 60.360 66.667 40.84 28.70 44.81 3.61
748 780 2.359975 GGACGGACTTGGGCCAAG 60.360 66.667 38.15 38.15 45.85 3.61
749 781 3.961414 GGGACGGACTTGGGCCAA 61.961 66.667 19.68 19.68 0.00 4.52
753 785 3.717294 CAGGGGGACGGACTTGGG 61.717 72.222 0.00 0.00 0.00 4.12
754 786 3.717294 CCAGGGGGACGGACTTGG 61.717 72.222 0.00 0.00 35.59 3.61
767 799 0.602905 GACTCAAACCGTCACCCAGG 60.603 60.000 0.00 0.00 0.00 4.45
770 802 1.666872 CGGACTCAAACCGTCACCC 60.667 63.158 0.00 0.00 44.57 4.61
800 832 1.615919 CCAAAACCCTAATCGCCCTGT 60.616 52.381 0.00 0.00 0.00 4.00
801 833 1.102978 CCAAAACCCTAATCGCCCTG 58.897 55.000 0.00 0.00 0.00 4.45
802 834 0.683179 GCCAAAACCCTAATCGCCCT 60.683 55.000 0.00 0.00 0.00 5.19
804 836 0.455815 CTGCCAAAACCCTAATCGCC 59.544 55.000 0.00 0.00 0.00 5.54
815 847 0.771127 ACTAGAGGTGGCTGCCAAAA 59.229 50.000 25.23 6.24 34.18 2.44
821 853 1.757699 GGGTTAGACTAGAGGTGGCTG 59.242 57.143 0.00 0.00 0.00 4.85
826 858 2.790585 CCCCTAGGGTTAGACTAGAGGT 59.209 54.545 26.66 0.00 40.22 3.85
845 877 2.821366 CAGATCACAGCCACGCCC 60.821 66.667 0.00 0.00 0.00 6.13
852 884 0.321919 TTGCCAGGACAGATCACAGC 60.322 55.000 0.00 0.00 0.00 4.40
853 885 1.002888 ACTTGCCAGGACAGATCACAG 59.997 52.381 0.00 0.00 0.00 3.66
863 895 1.596934 GACGGATCACTTGCCAGGA 59.403 57.895 0.00 0.00 0.00 3.86
865 897 1.450312 GGGACGGATCACTTGCCAG 60.450 63.158 0.00 0.00 0.00 4.85
873 905 0.755698 GGCTAGACTGGGACGGATCA 60.756 60.000 0.00 0.00 38.67 2.92
883 915 0.616111 AGGGTGAGGTGGCTAGACTG 60.616 60.000 0.00 0.00 0.00 3.51
900 932 2.759973 TAGGGAGCACGCCAGAGG 60.760 66.667 0.00 0.00 0.00 3.69
960 993 4.787280 CCACCGCTCCCTCCTCCT 62.787 72.222 0.00 0.00 0.00 3.69
980 1013 0.037975 GGTTTACCTCGCGAACTCCA 60.038 55.000 11.33 0.00 0.00 3.86
983 1016 1.674817 CCATGGTTTACCTCGCGAACT 60.675 52.381 11.33 0.00 36.82 3.01
985 1018 0.609151 TCCATGGTTTACCTCGCGAA 59.391 50.000 11.33 0.00 36.82 4.70
986 1019 0.174845 CTCCATGGTTTACCTCGCGA 59.825 55.000 12.58 9.26 36.82 5.87
987 1020 0.810031 CCTCCATGGTTTACCTCGCG 60.810 60.000 12.58 0.00 36.82 5.87
1013 1046 1.296832 TCAACCCCCTCATCATCCCTA 59.703 52.381 0.00 0.00 0.00 3.53
1025 1058 2.158519 TCCTCTGAAAGTTTCAACCCCC 60.159 50.000 18.55 0.00 39.58 5.40
1053 1086 3.739401 ATTCGGATCTTCACCCCTTTT 57.261 42.857 0.00 0.00 0.00 2.27
1056 1089 1.490910 GGAATTCGGATCTTCACCCCT 59.509 52.381 0.00 0.00 0.00 4.79
1074 1107 1.380515 CCCCTTCTCTCTCGCAGGA 60.381 63.158 0.00 0.00 0.00 3.86
1077 1110 0.039764 TCTTCCCCTTCTCTCTCGCA 59.960 55.000 0.00 0.00 0.00 5.10
1083 1116 2.843113 CTCCACATTCTTCCCCTTCTCT 59.157 50.000 0.00 0.00 0.00 3.10
1092 1125 2.570135 GCCTGGATCTCCACATTCTTC 58.430 52.381 0.00 0.00 42.01 2.87
1098 1131 2.284625 ACCGCCTGGATCTCCACA 60.285 61.111 0.00 0.00 42.01 4.17
1127 1160 1.812571 GATGCACCAGTTTGTCCGAAT 59.187 47.619 0.00 0.00 0.00 3.34
1128 1161 1.234821 GATGCACCAGTTTGTCCGAA 58.765 50.000 0.00 0.00 0.00 4.30
1177 1210 0.391661 CCCTTGATCGGACACCACAG 60.392 60.000 0.00 0.00 0.00 3.66
1203 1236 0.684535 TCTCTCCCACGTCATTGCAA 59.315 50.000 0.00 0.00 0.00 4.08
1209 1242 4.020573 ACAAACATATTCTCTCCCACGTCA 60.021 41.667 0.00 0.00 0.00 4.35
1218 1253 8.394971 TGAACATGAACACAAACATATTCTCT 57.605 30.769 0.00 0.00 33.05 3.10
1225 1272 7.490840 TCTTGATTGAACATGAACACAAACAT 58.509 30.769 0.00 0.00 0.00 2.71
1238 1285 6.419484 TCTTACCAGACTCTTGATTGAACA 57.581 37.500 0.00 0.00 0.00 3.18
1305 1352 3.873801 GCACATAATCCTCAACCACCACT 60.874 47.826 0.00 0.00 0.00 4.00
1365 1412 0.396435 ACACTCGCACCCAAATCAGA 59.604 50.000 0.00 0.00 0.00 3.27
1371 1418 1.376683 GCCATACACTCGCACCCAA 60.377 57.895 0.00 0.00 0.00 4.12
1459 1506 0.471971 CCATCCCTCCCCGTATCTGT 60.472 60.000 0.00 0.00 0.00 3.41
1479 1526 2.806945 TGAACTTCCCCATAGCCTTG 57.193 50.000 0.00 0.00 0.00 3.61
1506 1553 5.988310 TCTCGATACAAAACCTCACCTTA 57.012 39.130 0.00 0.00 0.00 2.69
1541 1588 2.979678 TCCTTCTCAAGTGTAAAGCCCT 59.020 45.455 0.00 0.00 0.00 5.19
1542 1589 3.418684 TCCTTCTCAAGTGTAAAGCCC 57.581 47.619 0.00 0.00 0.00 5.19
1545 1592 4.938226 GGGTCATCCTTCTCAAGTGTAAAG 59.062 45.833 0.00 0.00 0.00 1.85
1560 1607 0.764752 CTACCTCCCCTGGGTCATCC 60.765 65.000 12.71 0.00 38.19 3.51
1566 1613 3.470888 CGCACTACCTCCCCTGGG 61.471 72.222 5.50 5.50 0.00 4.45
1568 1615 1.961180 CTTCCGCACTACCTCCCCTG 61.961 65.000 0.00 0.00 0.00 4.45
1577 1624 1.993391 CCCTTCCCCTTCCGCACTA 60.993 63.158 0.00 0.00 0.00 2.74
1580 1627 2.137177 CTTTCCCTTCCCCTTCCGCA 62.137 60.000 0.00 0.00 0.00 5.69
1582 1635 1.303282 CCTTTCCCTTCCCCTTCCG 59.697 63.158 0.00 0.00 0.00 4.30
1588 1641 0.114364 TTTCCAGCCTTTCCCTTCCC 59.886 55.000 0.00 0.00 0.00 3.97
1589 1642 1.550327 CTTTCCAGCCTTTCCCTTCC 58.450 55.000 0.00 0.00 0.00 3.46
1606 1659 1.355381 TGACCCATCCACATCTTGCTT 59.645 47.619 0.00 0.00 0.00 3.91
1611 1664 1.213678 CACCATGACCCATCCACATCT 59.786 52.381 0.00 0.00 0.00 2.90
1616 1669 2.682846 GGCACCATGACCCATCCA 59.317 61.111 0.00 0.00 0.00 3.41
1635 1691 8.970859 AATCAGGAAGGTACTCATATTCAAAG 57.029 34.615 0.00 0.00 38.49 2.77
1686 1742 2.433604 TCATCAGTCCTTCTCTCCATGC 59.566 50.000 0.00 0.00 0.00 4.06
1724 1780 0.541863 CTAGGGGCTGTGGGTGTAAG 59.458 60.000 0.00 0.00 0.00 2.34
1743 1799 3.328382 TTGGTCCAGTATGTGTAGCAC 57.672 47.619 0.00 0.00 34.56 4.40
1751 1807 6.201044 CGAGCTTTAGTAATTGGTCCAGTATG 59.799 42.308 0.00 0.00 0.00 2.39
1756 1812 3.267483 GCGAGCTTTAGTAATTGGTCCA 58.733 45.455 0.00 0.00 0.00 4.02
1837 1893 6.982160 TCCAATTTAGGCAGCATCATATTT 57.018 33.333 0.00 0.00 0.00 1.40
2079 2136 3.311596 GGTCCAATAATAAGGTGACGCAC 59.688 47.826 1.92 1.92 0.00 5.34
2099 2156 1.353022 TCGAAATTACAAGGGCCTGGT 59.647 47.619 19.57 19.57 0.00 4.00
2149 2206 2.369203 TCTTGTTTCCCCACACATACGA 59.631 45.455 0.00 0.00 0.00 3.43
2530 2591 0.923010 GACGATCCGACTACGAACGC 60.923 60.000 0.00 0.00 42.66 4.84


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

AutoCloner maintained by Alex Coulton.