Multiple sequence alignment - TraesCS3B01G441100

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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 TraesCS3B01G441100 chr3B 100.000 4143 0 0 1 4143 680479237 680475095 0.000000e+00 7651.0
1 TraesCS3B01G441100 chr3B 91.782 1947 108 30 973 2898 680677203 680675288 0.000000e+00 2662.0
2 TraesCS3B01G441100 chr3B 90.423 1984 124 27 941 2898 680733107 680731164 0.000000e+00 2551.0
3 TraesCS3B01G441100 chr3A 90.558 2044 113 34 872 2898 651961880 651963860 0.000000e+00 2632.0
4 TraesCS3B01G441100 chr3A 93.388 1694 84 11 1446 3130 651996504 651998178 0.000000e+00 2483.0
5 TraesCS3B01G441100 chr3A 93.046 1510 88 11 1399 2898 651648923 651650425 0.000000e+00 2191.0
6 TraesCS3B01G441100 chr3A 83.043 690 73 28 731 1394 651648288 651648959 1.660000e-163 586.0
7 TraesCS3B01G441100 chr3A 86.667 405 22 7 949 1341 651996052 651996436 1.780000e-113 420.0
8 TraesCS3B01G441100 chr3A 86.544 379 39 10 3768 4143 652015394 652015763 1.390000e-109 407.0
9 TraesCS3B01G441100 chr3A 89.963 269 11 7 3167 3425 651998180 651998442 2.390000e-87 333.0
10 TraesCS3B01G441100 chr3A 86.391 169 6 2 3477 3645 651998463 651998614 7.120000e-38 169.0
11 TraesCS3B01G441100 chr3A 77.574 272 40 16 702 955 651994927 651995195 1.200000e-30 145.0
12 TraesCS3B01G441100 chr3D 90.960 1969 114 39 959 2895 516670994 516672930 0.000000e+00 2591.0
13 TraesCS3B01G441100 chr3D 92.153 1096 58 11 2051 3127 516856627 516857713 0.000000e+00 1522.0
14 TraesCS3B01G441100 chr3D 88.132 1306 93 30 715 2007 516855192 516856448 0.000000e+00 1496.0
15 TraesCS3B01G441100 chr3D 90.909 517 34 8 3119 3634 516857873 516858377 0.000000e+00 682.0
16 TraesCS3B01G441100 chr3D 93.103 203 13 1 3928 4130 516864103 516864304 3.130000e-76 296.0
17 TraesCS3B01G441100 chr3D 86.611 239 14 5 3643 3881 516860074 516860294 8.890000e-62 248.0
18 TraesCS3B01G441100 chr7D 91.034 1606 115 19 1400 2994 502231584 502233171 0.000000e+00 2141.0
19 TraesCS3B01G441100 chr7D 81.695 590 84 16 1 583 42648461 42649033 1.740000e-128 470.0
20 TraesCS3B01G441100 chr7D 88.725 204 15 5 1205 1402 502231425 502231626 4.140000e-60 243.0
21 TraesCS3B01G441100 chr1A 85.881 772 104 4 2096 2863 460281706 460282476 0.000000e+00 817.0
22 TraesCS3B01G441100 chr1A 82.459 553 77 17 3 549 133990309 133989771 2.260000e-127 466.0
23 TraesCS3B01G441100 chr7B 86.453 561 65 9 2 557 504770976 504770422 4.580000e-169 604.0
24 TraesCS3B01G441100 chr7B 82.609 506 77 11 3 504 94184029 94183531 1.770000e-118 436.0
25 TraesCS3B01G441100 chr2A 81.905 630 86 18 1 614 591741844 591741227 1.330000e-139 507.0
26 TraesCS3B01G441100 chr2A 82.250 569 80 13 1 556 678067619 678068179 4.850000e-129 472.0
27 TraesCS3B01G441100 chr2A 84.828 435 59 6 2 436 746681410 746680983 8.230000e-117 431.0
28 TraesCS3B01G441100 chr5A 82.529 601 76 18 9 603 170859798 170859221 6.180000e-138 501.0
29 TraesCS3B01G441100 chr5A 95.745 47 2 0 3766 3812 4050806 4050852 4.440000e-10 76.8
30 TraesCS3B01G441100 chr5D 82.143 532 93 2 1458 1988 192537909 192538439 4.880000e-124 455.0
31 TraesCS3B01G441100 chr2B 82.779 511 70 11 2 505 751312564 751312065 1.370000e-119 440.0
32 TraesCS3B01G441100 chr2B 82.422 512 70 14 2 505 751289920 751289421 2.960000e-116 429.0
33 TraesCS3B01G441100 chr2B 95.455 44 2 0 3770 3813 401070573 401070616 2.070000e-08 71.3
34 TraesCS3B01G441100 chr2D 81.748 515 74 15 2 505 159863085 159863590 2.980000e-111 412.0
35 TraesCS3B01G441100 chr2D 81.061 528 66 19 7 517 278069187 278068677 1.400000e-104 390.0
36 TraesCS3B01G441100 chr2D 78.988 257 43 9 263 516 534726100 534726348 9.210000e-37 165.0
37 TraesCS3B01G441100 chr5B 92.000 50 2 2 3772 3821 386528149 386528196 7.430000e-08 69.4


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 TraesCS3B01G441100 chr3B 680475095 680479237 4142 True 7651.0 7651 100.0000 1 4143 1 chr3B.!!$R1 4142
1 TraesCS3B01G441100 chr3B 680675288 680677203 1915 True 2662.0 2662 91.7820 973 2898 1 chr3B.!!$R2 1925
2 TraesCS3B01G441100 chr3B 680731164 680733107 1943 True 2551.0 2551 90.4230 941 2898 1 chr3B.!!$R3 1957
3 TraesCS3B01G441100 chr3A 651961880 651963860 1980 False 2632.0 2632 90.5580 872 2898 1 chr3A.!!$F1 2026
4 TraesCS3B01G441100 chr3A 651648288 651650425 2137 False 1388.5 2191 88.0445 731 2898 2 chr3A.!!$F3 2167
5 TraesCS3B01G441100 chr3A 651994927 651998614 3687 False 710.0 2483 86.7966 702 3645 5 chr3A.!!$F4 2943
6 TraesCS3B01G441100 chr3D 516670994 516672930 1936 False 2591.0 2591 90.9600 959 2895 1 chr3D.!!$F1 1936
7 TraesCS3B01G441100 chr3D 516855192 516864304 9112 False 848.8 1522 90.1816 715 4130 5 chr3D.!!$F2 3415
8 TraesCS3B01G441100 chr7D 502231425 502233171 1746 False 1192.0 2141 89.8795 1205 2994 2 chr7D.!!$F2 1789
9 TraesCS3B01G441100 chr7D 42648461 42649033 572 False 470.0 470 81.6950 1 583 1 chr7D.!!$F1 582
10 TraesCS3B01G441100 chr1A 460281706 460282476 770 False 817.0 817 85.8810 2096 2863 1 chr1A.!!$F1 767
11 TraesCS3B01G441100 chr1A 133989771 133990309 538 True 466.0 466 82.4590 3 549 1 chr1A.!!$R1 546
12 TraesCS3B01G441100 chr7B 504770422 504770976 554 True 604.0 604 86.4530 2 557 1 chr7B.!!$R2 555
13 TraesCS3B01G441100 chr2A 591741227 591741844 617 True 507.0 507 81.9050 1 614 1 chr2A.!!$R1 613
14 TraesCS3B01G441100 chr2A 678067619 678068179 560 False 472.0 472 82.2500 1 556 1 chr2A.!!$F1 555
15 TraesCS3B01G441100 chr5A 170859221 170859798 577 True 501.0 501 82.5290 9 603 1 chr5A.!!$R1 594
16 TraesCS3B01G441100 chr5D 192537909 192538439 530 False 455.0 455 82.1430 1458 1988 1 chr5D.!!$F1 530
17 TraesCS3B01G441100 chr2D 159863085 159863590 505 False 412.0 412 81.7480 2 505 1 chr2D.!!$F1 503
18 TraesCS3B01G441100 chr2D 278068677 278069187 510 True 390.0 390 81.0610 7 517 1 chr2D.!!$R1 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
658 702 0.032952 TGTCCGTCTGGTGTTAGTGC 59.967 55.0 0.00 0.0 36.30 4.40 F
672 716 0.036164 TAGTGCGTTGGAGTTGGCAT 59.964 50.0 0.00 0.0 37.77 4.40 F
1169 2149 0.037326 TAGTTCTCACCTGCAAGCGG 60.037 55.0 0.00 0.0 0.00 5.52 F
2529 3753 0.390735 GGCCGGAGTCAACGTATGTT 60.391 55.0 5.05 0.0 39.43 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1747 2810 1.000607 GCGATGGTGTAGCCGATAGAA 60.001 52.381 0.00 0.00 41.21 2.10 R
2022 3228 3.247886 TCAGAATTACTCCTCGATCGACG 59.752 47.826 15.15 10.92 44.09 5.12 R
2946 4182 1.341482 TGACCCAGTTTGGCTTTCACA 60.341 47.619 0.00 0.00 35.79 3.58 R
4069 10958 1.340405 ACCACATGTCATTGGGAGAGC 60.340 52.381 6.18 0.00 37.18 4.09 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
52 53 2.440409 CCAGATGGGTGTTCTTCAAGG 58.560 52.381 0.00 0.00 0.00 3.61
86 90 8.164070 AGACCTGGTATGTACTTCTTTTGATTT 58.836 33.333 0.00 0.00 0.00 2.17
94 98 7.164230 TGTACTTCTTTTGATTTGGTTGTGT 57.836 32.000 0.00 0.00 0.00 3.72
181 188 5.129485 TGCAAGTTTTGGTATTGGGAAGAAA 59.871 36.000 0.00 0.00 0.00 2.52
182 189 6.052360 GCAAGTTTTGGTATTGGGAAGAAAA 58.948 36.000 0.00 0.00 0.00 2.29
221 228 8.892723 TGTTGATAGCACGAAATTTGATAGATT 58.107 29.630 0.00 0.00 0.00 2.40
223 230 8.661352 TGATAGCACGAAATTTGATAGATTCA 57.339 30.769 0.00 0.00 0.00 2.57
232 239 6.500684 AATTTGATAGATTCACGTGCACTT 57.499 33.333 16.19 1.59 32.84 3.16
245 252 3.874543 ACGTGCACTTGTTGTTAGAATGA 59.125 39.130 16.19 0.00 0.00 2.57
250 257 5.008613 TGCACTTGTTGTTAGAATGAAGACC 59.991 40.000 0.00 0.00 0.00 3.85
281 311 4.867047 AGATTAGATGTGAAGCAACGTCTG 59.133 41.667 15.39 0.00 44.35 3.51
352 388 7.094677 CCACAGATCAACAATGAAGACATACAA 60.095 37.037 0.00 0.00 39.49 2.41
354 390 9.017509 ACAGATCAACAATGAAGACATACAAAT 57.982 29.630 0.00 0.00 39.49 2.32
489 528 8.836268 AATGTACTCAAATGCATCAAAATGTT 57.164 26.923 0.00 0.00 35.18 2.71
490 529 8.836268 ATGTACTCAAATGCATCAAAATGTTT 57.164 26.923 0.00 0.00 35.18 2.83
491 530 8.074474 TGTACTCAAATGCATCAAAATGTTTG 57.926 30.769 0.00 0.00 33.41 2.93
494 533 7.411274 ACTCAAATGCATCAAAATGTTTGTTG 58.589 30.769 0.00 7.21 33.66 3.33
497 537 9.269453 TCAAATGCATCAAAATGTTTGTTGATA 57.731 25.926 0.00 4.67 41.44 2.15
576 620 1.270826 CTATGGATCAGATGCGTCCGT 59.729 52.381 1.23 0.00 34.72 4.69
603 647 2.441532 GCATGGCCAGCACATCCT 60.442 61.111 13.05 0.00 0.00 3.24
604 648 1.152902 GCATGGCCAGCACATCCTA 60.153 57.895 13.05 0.00 0.00 2.94
605 649 1.450531 GCATGGCCAGCACATCCTAC 61.451 60.000 13.05 0.00 0.00 3.18
606 650 0.107066 CATGGCCAGCACATCCTACA 60.107 55.000 13.05 0.00 0.00 2.74
607 651 0.848735 ATGGCCAGCACATCCTACAT 59.151 50.000 13.05 0.00 0.00 2.29
608 652 1.506025 TGGCCAGCACATCCTACATA 58.494 50.000 0.00 0.00 0.00 2.29
609 653 1.843206 TGGCCAGCACATCCTACATAA 59.157 47.619 0.00 0.00 0.00 1.90
610 654 2.240921 TGGCCAGCACATCCTACATAAA 59.759 45.455 0.00 0.00 0.00 1.40
611 655 3.117550 TGGCCAGCACATCCTACATAAAT 60.118 43.478 0.00 0.00 0.00 1.40
612 656 3.254166 GGCCAGCACATCCTACATAAATG 59.746 47.826 0.00 0.00 0.00 2.32
613 657 3.254166 GCCAGCACATCCTACATAAATGG 59.746 47.826 0.00 0.00 0.00 3.16
614 658 4.717877 CCAGCACATCCTACATAAATGGA 58.282 43.478 0.00 0.00 0.00 3.41
615 659 4.516698 CCAGCACATCCTACATAAATGGAC 59.483 45.833 0.00 0.00 32.16 4.02
616 660 5.125356 CAGCACATCCTACATAAATGGACA 58.875 41.667 0.00 0.00 32.16 4.02
617 661 5.589855 CAGCACATCCTACATAAATGGACAA 59.410 40.000 0.00 0.00 32.16 3.18
618 662 6.095300 CAGCACATCCTACATAAATGGACAAA 59.905 38.462 0.00 0.00 32.16 2.83
619 663 6.663093 AGCACATCCTACATAAATGGACAAAA 59.337 34.615 0.00 0.00 32.16 2.44
620 664 7.342799 AGCACATCCTACATAAATGGACAAAAT 59.657 33.333 0.00 0.00 32.16 1.82
621 665 7.981225 GCACATCCTACATAAATGGACAAAATT 59.019 33.333 0.00 0.00 32.16 1.82
622 666 9.520204 CACATCCTACATAAATGGACAAAATTC 57.480 33.333 0.00 0.00 32.16 2.17
623 667 9.253832 ACATCCTACATAAATGGACAAAATTCA 57.746 29.630 0.00 0.00 32.16 2.57
624 668 9.740239 CATCCTACATAAATGGACAAAATTCAG 57.260 33.333 0.00 0.00 32.16 3.02
625 669 9.699410 ATCCTACATAAATGGACAAAATTCAGA 57.301 29.630 0.00 0.00 32.16 3.27
626 670 9.527157 TCCTACATAAATGGACAAAATTCAGAA 57.473 29.630 0.00 0.00 0.00 3.02
627 671 9.793252 CCTACATAAATGGACAAAATTCAGAAG 57.207 33.333 0.00 0.00 0.00 2.85
655 699 2.295253 GGATGTCCGTCTGGTGTTAG 57.705 55.000 0.00 0.00 36.30 2.34
656 700 1.549170 GGATGTCCGTCTGGTGTTAGT 59.451 52.381 0.00 0.00 36.30 2.24
657 701 2.607187 GATGTCCGTCTGGTGTTAGTG 58.393 52.381 0.00 0.00 36.30 2.74
658 702 0.032952 TGTCCGTCTGGTGTTAGTGC 59.967 55.000 0.00 0.00 36.30 4.40
659 703 1.007336 GTCCGTCTGGTGTTAGTGCG 61.007 60.000 0.00 0.00 36.30 5.34
660 704 1.006571 CCGTCTGGTGTTAGTGCGT 60.007 57.895 0.00 0.00 0.00 5.24
661 705 0.599204 CCGTCTGGTGTTAGTGCGTT 60.599 55.000 0.00 0.00 0.00 4.84
662 706 0.506932 CGTCTGGTGTTAGTGCGTTG 59.493 55.000 0.00 0.00 0.00 4.10
663 707 0.865769 GTCTGGTGTTAGTGCGTTGG 59.134 55.000 0.00 0.00 0.00 3.77
664 708 0.753867 TCTGGTGTTAGTGCGTTGGA 59.246 50.000 0.00 0.00 0.00 3.53
665 709 1.148310 CTGGTGTTAGTGCGTTGGAG 58.852 55.000 0.00 0.00 0.00 3.86
666 710 0.466543 TGGTGTTAGTGCGTTGGAGT 59.533 50.000 0.00 0.00 0.00 3.85
667 711 1.134340 TGGTGTTAGTGCGTTGGAGTT 60.134 47.619 0.00 0.00 0.00 3.01
668 712 1.263217 GGTGTTAGTGCGTTGGAGTTG 59.737 52.381 0.00 0.00 0.00 3.16
669 713 1.263217 GTGTTAGTGCGTTGGAGTTGG 59.737 52.381 0.00 0.00 0.00 3.77
670 714 0.237498 GTTAGTGCGTTGGAGTTGGC 59.763 55.000 0.00 0.00 0.00 4.52
671 715 0.179043 TTAGTGCGTTGGAGTTGGCA 60.179 50.000 0.00 0.00 0.00 4.92
672 716 0.036164 TAGTGCGTTGGAGTTGGCAT 59.964 50.000 0.00 0.00 37.77 4.40
673 717 0.823356 AGTGCGTTGGAGTTGGCATT 60.823 50.000 0.00 0.00 37.77 3.56
674 718 0.878416 GTGCGTTGGAGTTGGCATTA 59.122 50.000 0.00 0.00 37.77 1.90
675 719 1.472480 GTGCGTTGGAGTTGGCATTAT 59.528 47.619 0.00 0.00 37.77 1.28
676 720 1.742831 TGCGTTGGAGTTGGCATTATC 59.257 47.619 0.00 0.00 0.00 1.75
677 721 1.268032 GCGTTGGAGTTGGCATTATCG 60.268 52.381 0.00 0.00 0.00 2.92
678 722 1.268032 CGTTGGAGTTGGCATTATCGC 60.268 52.381 0.00 0.00 0.00 4.58
679 723 1.742831 GTTGGAGTTGGCATTATCGCA 59.257 47.619 0.00 0.00 0.00 5.10
680 724 2.346766 TGGAGTTGGCATTATCGCAT 57.653 45.000 0.00 0.00 0.00 4.73
681 725 1.948834 TGGAGTTGGCATTATCGCATG 59.051 47.619 0.00 0.00 0.00 4.06
682 726 1.267806 GGAGTTGGCATTATCGCATGG 59.732 52.381 0.00 0.00 0.00 3.66
683 727 1.949525 GAGTTGGCATTATCGCATGGT 59.050 47.619 0.00 0.00 0.00 3.55
684 728 1.677576 AGTTGGCATTATCGCATGGTG 59.322 47.619 0.00 0.00 0.00 4.17
685 729 1.675483 GTTGGCATTATCGCATGGTGA 59.325 47.619 0.00 0.00 0.00 4.02
686 730 2.275134 TGGCATTATCGCATGGTGAT 57.725 45.000 0.00 0.00 36.67 3.06
687 731 2.153645 TGGCATTATCGCATGGTGATC 58.846 47.619 0.00 0.00 34.45 2.92
688 732 2.224597 TGGCATTATCGCATGGTGATCT 60.225 45.455 0.00 0.00 34.45 2.75
689 733 2.161012 GGCATTATCGCATGGTGATCTG 59.839 50.000 0.00 0.00 34.45 2.90
690 734 2.413765 GCATTATCGCATGGTGATCTGC 60.414 50.000 0.00 9.82 35.68 4.26
691 735 2.618442 TTATCGCATGGTGATCTGCA 57.382 45.000 5.62 0.00 38.30 4.41
692 736 2.845363 TATCGCATGGTGATCTGCAT 57.155 45.000 5.62 1.73 38.30 3.96
693 737 1.977056 ATCGCATGGTGATCTGCATT 58.023 45.000 5.62 0.00 38.30 3.56
694 738 1.753930 TCGCATGGTGATCTGCATTT 58.246 45.000 5.62 0.00 38.30 2.32
695 739 1.672363 TCGCATGGTGATCTGCATTTC 59.328 47.619 5.62 0.00 38.30 2.17
696 740 1.596220 CGCATGGTGATCTGCATTTCG 60.596 52.381 5.62 0.00 38.30 3.46
697 741 1.862815 GCATGGTGATCTGCATTTCGC 60.863 52.381 0.00 0.00 38.28 4.70
698 742 1.674441 CATGGTGATCTGCATTTCGCT 59.326 47.619 8.84 0.00 43.06 4.93
699 743 1.089112 TGGTGATCTGCATTTCGCTG 58.911 50.000 8.84 0.00 43.06 5.18
700 744 0.379669 GGTGATCTGCATTTCGCTGG 59.620 55.000 8.84 0.00 43.06 4.85
701 745 1.089920 GTGATCTGCATTTCGCTGGT 58.910 50.000 0.00 0.00 43.06 4.00
702 746 1.063174 GTGATCTGCATTTCGCTGGTC 59.937 52.381 0.00 0.00 46.85 4.02
703 747 1.065926 TGATCTGCATTTCGCTGGTCT 60.066 47.619 5.91 0.00 46.81 3.85
704 748 1.596727 GATCTGCATTTCGCTGGTCTC 59.403 52.381 0.00 0.00 44.16 3.36
705 749 0.610174 TCTGCATTTCGCTGGTCTCT 59.390 50.000 0.00 0.00 43.06 3.10
706 750 0.725686 CTGCATTTCGCTGGTCTCTG 59.274 55.000 0.00 0.00 43.06 3.35
713 757 2.673523 GCTGGTCTCTGGTGCCAT 59.326 61.111 0.00 0.00 0.00 4.40
755 799 2.354343 GCTGGCTGGCTCCTTCTT 59.646 61.111 2.00 0.00 0.00 2.52
786 831 4.429212 CCGGCCGTGTCGATGTCA 62.429 66.667 26.12 0.00 29.41 3.58
792 837 0.598942 CCGTGTCGATGTCAACCACA 60.599 55.000 0.00 0.00 40.18 4.17
899 981 4.918060 CGCACACACGCACACACG 62.918 66.667 0.00 0.00 39.50 4.49
903 985 4.297891 CACACGCACACACGCAGG 62.298 66.667 0.00 0.00 36.19 4.85
904 986 4.522689 ACACGCACACACGCAGGA 62.523 61.111 0.00 0.00 36.19 3.86
905 987 3.705638 CACGCACACACGCAGGAG 61.706 66.667 0.00 0.00 36.19 3.69
906 988 3.911698 ACGCACACACGCAGGAGA 61.912 61.111 0.00 0.00 36.19 3.71
1165 2145 6.013725 TCCTCTTAATTAGTTCTCACCTGCAA 60.014 38.462 0.00 0.00 0.00 4.08
1169 2149 0.037326 TAGTTCTCACCTGCAAGCGG 60.037 55.000 0.00 0.00 0.00 5.52
1174 2154 2.031012 CACCTGCAAGCGGACTCA 59.969 61.111 1.69 0.00 0.00 3.41
1175 2155 1.597854 CACCTGCAAGCGGACTCAA 60.598 57.895 1.69 0.00 0.00 3.02
1192 2177 3.076621 CTCAATCTGTTGGCAGCAGTTA 58.923 45.455 27.15 12.54 42.29 2.24
1368 2405 1.132453 TCTCGTCTCATGGCGTACTTG 59.868 52.381 0.00 0.00 0.00 3.16
1378 2415 2.577700 TGGCGTACTTGATTGTTGGTT 58.422 42.857 0.00 0.00 0.00 3.67
1382 2419 4.219033 GCGTACTTGATTGTTGGTTTCTG 58.781 43.478 0.00 0.00 0.00 3.02
1383 2420 4.024387 GCGTACTTGATTGTTGGTTTCTGA 60.024 41.667 0.00 0.00 0.00 3.27
1384 2421 5.440685 CGTACTTGATTGTTGGTTTCTGAC 58.559 41.667 0.00 0.00 0.00 3.51
1385 2422 5.236478 CGTACTTGATTGTTGGTTTCTGACT 59.764 40.000 0.00 0.00 0.00 3.41
1386 2423 5.757850 ACTTGATTGTTGGTTTCTGACTC 57.242 39.130 0.00 0.00 0.00 3.36
1387 2424 5.440610 ACTTGATTGTTGGTTTCTGACTCT 58.559 37.500 0.00 0.00 0.00 3.24
1388 2425 5.297776 ACTTGATTGTTGGTTTCTGACTCTG 59.702 40.000 0.00 0.00 0.00 3.35
1389 2426 5.034852 TGATTGTTGGTTTCTGACTCTGA 57.965 39.130 0.00 0.00 0.00 3.27
1390 2427 4.816385 TGATTGTTGGTTTCTGACTCTGAC 59.184 41.667 0.00 0.00 0.00 3.51
1391 2428 2.821546 TGTTGGTTTCTGACTCTGACG 58.178 47.619 0.00 0.00 0.00 4.35
1392 2429 2.167693 TGTTGGTTTCTGACTCTGACGT 59.832 45.455 0.00 0.00 0.00 4.34
1393 2430 3.382227 TGTTGGTTTCTGACTCTGACGTA 59.618 43.478 0.00 0.00 0.00 3.57
1394 2431 4.038763 TGTTGGTTTCTGACTCTGACGTAT 59.961 41.667 0.00 0.00 0.00 3.06
1395 2432 5.242171 TGTTGGTTTCTGACTCTGACGTATA 59.758 40.000 0.00 0.00 0.00 1.47
1396 2433 5.562506 TGGTTTCTGACTCTGACGTATAG 57.437 43.478 0.00 0.00 0.00 1.31
1397 2434 4.142447 TGGTTTCTGACTCTGACGTATAGC 60.142 45.833 0.00 0.00 0.00 2.97
1436 2499 1.267806 GGTTTCTCACTCGGACGTACA 59.732 52.381 0.00 0.00 0.00 2.90
1437 2500 2.094854 GGTTTCTCACTCGGACGTACAT 60.095 50.000 0.00 0.00 0.00 2.29
1438 2501 3.127548 GGTTTCTCACTCGGACGTACATA 59.872 47.826 0.00 0.00 0.00 2.29
1439 2502 4.201990 GGTTTCTCACTCGGACGTACATAT 60.202 45.833 0.00 0.00 0.00 1.78
1440 2503 5.338365 GTTTCTCACTCGGACGTACATATT 58.662 41.667 0.00 0.00 0.00 1.28
1747 2810 0.539986 ATGCTAACATCGTCGGGGTT 59.460 50.000 7.42 7.42 0.00 4.11
2015 3221 6.464322 CCAAGTCATAGGTAGGTGATTATGCA 60.464 42.308 0.00 0.00 0.00 3.96
2016 3222 6.102897 AGTCATAGGTAGGTGATTATGCAC 57.897 41.667 0.00 0.00 38.05 4.57
2019 3225 5.602561 TCATAGGTAGGTGATTATGCACACT 59.397 40.000 5.30 0.00 40.52 3.55
2022 3228 4.100189 AGGTAGGTGATTATGCACACTCTC 59.900 45.833 5.30 0.00 40.52 3.20
2023 3236 3.170791 AGGTGATTATGCACACTCTCG 57.829 47.619 5.30 0.00 40.52 4.04
2041 3254 3.874400 TCGTCGATCGAGGAGTAATTC 57.126 47.619 30.62 10.84 44.01 2.17
2232 3456 2.027385 CTCATCGAGATCCAGGACACA 58.973 52.381 0.00 0.00 0.00 3.72
2325 3549 1.134965 GTCTTCTACATGCTCTGCGGT 60.135 52.381 0.00 0.00 0.00 5.68
2529 3753 0.390735 GGCCGGAGTCAACGTATGTT 60.391 55.000 5.05 0.00 39.43 2.71
2587 3814 2.359354 TGAACATGTTCCGGGCGG 60.359 61.111 30.66 0.00 38.77 6.13
2673 3900 3.580319 GTGGGGTTCCTGGGTGCT 61.580 66.667 0.00 0.00 0.00 4.40
2790 4017 2.502492 GCTCAGCCTCGGATGCCTA 61.502 63.158 1.44 0.00 0.00 3.93
2912 4139 2.092211 CACGCACCGAAGAACATTCTAC 59.908 50.000 0.00 0.00 36.28 2.59
2946 4182 2.736670 AAGTTCACTTTGGCTGGAGT 57.263 45.000 0.00 0.00 30.82 3.85
3033 4270 0.596859 GGCTAATGACCGCCGTAGTC 60.597 60.000 0.00 0.00 36.45 2.59
3052 4289 5.153950 AGTCGCCTCAAAGAAAAGATACT 57.846 39.130 0.00 0.00 0.00 2.12
3053 4290 6.282199 AGTCGCCTCAAAGAAAAGATACTA 57.718 37.500 0.00 0.00 0.00 1.82
3054 4291 6.100668 AGTCGCCTCAAAGAAAAGATACTAC 58.899 40.000 0.00 0.00 0.00 2.73
3055 4292 6.071278 AGTCGCCTCAAAGAAAAGATACTACT 60.071 38.462 0.00 0.00 0.00 2.57
3056 4293 7.122353 AGTCGCCTCAAAGAAAAGATACTACTA 59.878 37.037 0.00 0.00 0.00 1.82
3057 4294 7.220491 GTCGCCTCAAAGAAAAGATACTACTAC 59.780 40.741 0.00 0.00 0.00 2.73
3102 4346 6.019881 GTCACCAACTAATGTTCTTGTTTTGC 60.020 38.462 0.00 0.00 33.52 3.68
3108 4352 2.270275 TGTTCTTGTTTTGCGTGGTG 57.730 45.000 0.00 0.00 0.00 4.17
3165 4577 8.450578 TGAAAAGAATATTGAAGTGTGTCTGT 57.549 30.769 0.00 0.00 0.00 3.41
3169 4581 6.223852 AGAATATTGAAGTGTGTCTGTCGTT 58.776 36.000 0.00 0.00 0.00 3.85
3188 4600 0.836606 TTGTTGTCACCCTGAGCTCA 59.163 50.000 17.19 17.19 0.00 4.26
3193 4605 0.246086 GTCACCCTGAGCTCAGACTG 59.754 60.000 39.34 30.82 46.59 3.51
3254 4676 6.524586 CGATTTTGAAGCTAAAGTTGATCCAC 59.475 38.462 0.00 0.00 0.00 4.02
3307 4729 3.046390 CGAATCCTCGGAAGAATCTTCG 58.954 50.000 15.88 11.53 41.57 3.79
3314 4736 4.691216 CCTCGGAAGAATCTTCGTTTTCTT 59.309 41.667 15.88 0.69 43.12 2.52
3315 4737 5.179555 CCTCGGAAGAATCTTCGTTTTCTTT 59.820 40.000 15.88 0.00 41.12 2.52
3316 4738 5.985781 TCGGAAGAATCTTCGTTTTCTTTG 58.014 37.500 15.88 0.00 41.12 2.77
3421 4843 3.394635 GATCCCGGCCGGCACTTTA 62.395 63.158 39.46 18.37 0.00 1.85
3463 4885 0.467384 CGGTGAGATTCCAGATGCCT 59.533 55.000 0.00 0.00 0.00 4.75
3472 4894 3.292492 TTCCAGATGCCTAGTCTCGTA 57.708 47.619 0.00 0.00 0.00 3.43
3569 4997 0.396435 TCGCAGATTCTGTGGTTGGT 59.604 50.000 23.32 0.00 41.68 3.67
3570 4998 1.202758 TCGCAGATTCTGTGGTTGGTT 60.203 47.619 23.32 0.00 41.68 3.67
3571 4999 1.069022 CGCAGATTCTGTGGTTGGTTG 60.069 52.381 17.66 0.00 38.21 3.77
3572 5000 1.270550 GCAGATTCTGTGGTTGGTTGG 59.729 52.381 14.90 0.00 33.43 3.77
3652 6768 9.698309 AAAATACATAGAGGAATACGATGACAG 57.302 33.333 0.00 0.00 0.00 3.51
3662 6778 5.398711 GGAATACGATGACAGTTAGCTAACG 59.601 44.000 26.66 22.86 40.96 3.18
3682 6798 2.223249 CGTGGCCCTTTTATCGATGTTG 60.223 50.000 8.54 0.00 0.00 3.33
3688 6804 4.496507 GCCCTTTTATCGATGTTGAAGAGC 60.497 45.833 8.54 5.55 0.00 4.09
3689 6805 4.878397 CCCTTTTATCGATGTTGAAGAGCT 59.122 41.667 8.54 0.00 0.00 4.09
3716 6832 1.014564 CCGAACTTCTCCTCAACGGC 61.015 60.000 0.00 0.00 33.03 5.68
3727 6843 4.020928 TCTCCTCAACGGCTGTTATTACAA 60.021 41.667 11.38 0.00 36.28 2.41
3729 6845 5.064558 TCCTCAACGGCTGTTATTACAAAA 58.935 37.500 11.38 0.00 36.28 2.44
3730 6846 5.049267 TCCTCAACGGCTGTTATTACAAAAC 60.049 40.000 11.38 0.00 36.28 2.43
3731 6847 5.048991 CCTCAACGGCTGTTATTACAAAACT 60.049 40.000 11.38 0.00 36.28 2.66
3732 6848 5.753744 TCAACGGCTGTTATTACAAAACTG 58.246 37.500 11.38 0.00 36.28 3.16
3733 6849 5.297278 TCAACGGCTGTTATTACAAAACTGT 59.703 36.000 11.38 0.00 36.28 3.55
3735 6851 7.173562 TCAACGGCTGTTATTACAAAACTGTAT 59.826 33.333 11.38 0.00 36.28 2.29
3736 6852 7.443259 ACGGCTGTTATTACAAAACTGTATT 57.557 32.000 0.00 0.00 32.92 1.89
3737 6853 8.550710 ACGGCTGTTATTACAAAACTGTATTA 57.449 30.769 0.00 0.00 32.92 0.98
3738 6854 8.445493 ACGGCTGTTATTACAAAACTGTATTAC 58.555 33.333 0.00 0.00 32.92 1.89
3739 6855 8.444715 CGGCTGTTATTACAAAACTGTATTACA 58.555 33.333 0.00 0.00 32.92 2.41
3770 6886 7.331934 CAGAAAACGATTGAAGATACTCTTGGA 59.668 37.037 0.00 0.00 36.73 3.53
3803 6919 7.606456 TGACTAAGTTAGATGGGTGTTTGATTC 59.394 37.037 16.89 0.00 0.00 2.52
3808 6924 3.891049 AGATGGGTGTTTGATTCTAGCC 58.109 45.455 0.00 0.00 0.00 3.93
3809 6925 3.266772 AGATGGGTGTTTGATTCTAGCCA 59.733 43.478 0.00 0.00 43.87 4.75
3823 6939 1.482593 CTAGCCACACACCTAAGGGAG 59.517 57.143 0.00 0.00 36.25 4.30
3865 6981 3.493873 GCTCATCTGCTCATGGATGTACA 60.494 47.826 0.00 0.00 39.93 2.90
3868 6984 4.162888 TCATCTGCTCATGGATGTACAGTT 59.837 41.667 0.33 0.00 39.93 3.16
3874 6990 5.822519 TGCTCATGGATGTACAGTTAAATCC 59.177 40.000 0.33 2.68 41.25 3.01
3965 10854 4.826733 TGTGTATGCAAAGTTTCATGACCT 59.173 37.500 0.00 0.00 0.00 3.85
3977 10866 6.118170 AGTTTCATGACCTTATGACATCCTG 58.882 40.000 0.00 0.00 36.84 3.86
3984 10873 3.852578 ACCTTATGACATCCTGGGAGTTT 59.147 43.478 0.00 0.00 0.00 2.66
3988 10877 0.991920 GACATCCTGGGAGTTTGGGA 59.008 55.000 0.00 0.00 0.00 4.37
4022 10911 2.978156 ATCAGGGCTCCAAAACAAGA 57.022 45.000 0.00 0.00 0.00 3.02
4060 10949 9.824534 TTCTCAAAGCTTTGATTTTTGTTTTTC 57.175 25.926 35.40 0.00 45.26 2.29
4072 10961 8.345565 TGATTTTTGTTTTTCTGTCTAGAGCTC 58.654 33.333 5.27 5.27 33.70 4.09
4087 10976 2.093075 AGAGCTCTCCCAATGACATGTG 60.093 50.000 11.45 0.00 0.00 3.21
4130 11019 8.987890 GGGCGCATATAATTTTTGTTCATATTT 58.012 29.630 10.83 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
63 64 7.176690 ACCAAATCAAAAGAAGTACATACCAGG 59.823 37.037 0.00 0.00 0.00 4.45
64 65 8.110860 ACCAAATCAAAAGAAGTACATACCAG 57.889 34.615 0.00 0.00 0.00 4.00
65 66 8.356657 CAACCAAATCAAAAGAAGTACATACCA 58.643 33.333 0.00 0.00 0.00 3.25
86 90 0.604243 CGAATCCGGGAACACAACCA 60.604 55.000 0.00 0.00 0.00 3.67
181 188 6.037172 GTGCTATCAACAGATCGGTGTATTTT 59.963 38.462 0.00 0.00 0.00 1.82
182 189 5.523916 GTGCTATCAACAGATCGGTGTATTT 59.476 40.000 0.00 0.00 0.00 1.40
189 196 2.492019 TCGTGCTATCAACAGATCGG 57.508 50.000 0.00 0.00 0.00 4.18
196 203 9.374960 GAATCTATCAAATTTCGTGCTATCAAC 57.625 33.333 0.00 0.00 0.00 3.18
221 228 2.894902 TCTAACAACAAGTGCACGTGA 58.105 42.857 34.48 14.25 0.00 4.35
223 230 3.874543 TCATTCTAACAACAAGTGCACGT 59.125 39.130 12.01 5.01 0.00 4.49
232 239 6.419484 TCTCTGGTCTTCATTCTAACAACA 57.581 37.500 0.00 0.00 0.00 3.33
245 252 8.774546 TCACATCTAATCTTATCTCTGGTCTT 57.225 34.615 0.00 0.00 0.00 3.01
250 257 8.763356 GTTGCTTCACATCTAATCTTATCTCTG 58.237 37.037 0.00 0.00 0.00 3.35
305 335 3.550842 GGCTTCTCGATTTTGCACACTTT 60.551 43.478 0.00 0.00 0.00 2.66
316 346 3.265791 GTTGATCTGTGGCTTCTCGATT 58.734 45.455 0.00 0.00 0.00 3.34
352 388 9.717942 GCTCTCACTAGTTGGATTAATATCATT 57.282 33.333 0.00 0.00 32.09 2.57
354 390 8.250143 TGCTCTCACTAGTTGGATTAATATCA 57.750 34.615 0.00 0.00 32.09 2.15
413 449 8.093927 AGACCAAAGAAAACAAAGAATCACAAA 58.906 29.630 0.00 0.00 0.00 2.83
425 461 7.390718 GCTAGGAGAATAAGACCAAAGAAAACA 59.609 37.037 0.00 0.00 0.00 2.83
528 569 3.128349 GGTGCCCGTATGTATACACTTG 58.872 50.000 7.96 0.42 32.87 3.16
531 572 2.750948 CTGGTGCCCGTATGTATACAC 58.249 52.381 7.96 0.00 32.87 2.90
557 598 1.000274 CACGGACGCATCTGATCCATA 60.000 52.381 0.00 0.00 34.98 2.74
589 633 1.506025 TATGTAGGATGTGCTGGCCA 58.494 50.000 4.71 4.71 0.00 5.36
597 641 9.253832 TGAATTTTGTCCATTTATGTAGGATGT 57.746 29.630 0.00 0.00 33.33 3.06
636 680 1.549170 ACTAACACCAGACGGACATCC 59.451 52.381 0.00 0.00 35.59 3.51
637 681 2.607187 CACTAACACCAGACGGACATC 58.393 52.381 0.00 0.00 35.59 3.06
638 682 1.337823 GCACTAACACCAGACGGACAT 60.338 52.381 0.00 0.00 35.59 3.06
639 683 0.032952 GCACTAACACCAGACGGACA 59.967 55.000 0.00 0.00 35.59 4.02
640 684 1.007336 CGCACTAACACCAGACGGAC 61.007 60.000 0.00 0.00 35.59 4.79
641 685 1.287815 CGCACTAACACCAGACGGA 59.712 57.895 0.00 0.00 35.59 4.69
642 686 0.599204 AACGCACTAACACCAGACGG 60.599 55.000 0.00 0.00 38.77 4.79
643 687 0.506932 CAACGCACTAACACCAGACG 59.493 55.000 0.00 0.00 0.00 4.18
644 688 0.865769 CCAACGCACTAACACCAGAC 59.134 55.000 0.00 0.00 0.00 3.51
645 689 0.753867 TCCAACGCACTAACACCAGA 59.246 50.000 0.00 0.00 0.00 3.86
646 690 1.148310 CTCCAACGCACTAACACCAG 58.852 55.000 0.00 0.00 0.00 4.00
647 691 0.466543 ACTCCAACGCACTAACACCA 59.533 50.000 0.00 0.00 0.00 4.17
648 692 1.263217 CAACTCCAACGCACTAACACC 59.737 52.381 0.00 0.00 0.00 4.16
649 693 1.263217 CCAACTCCAACGCACTAACAC 59.737 52.381 0.00 0.00 0.00 3.32
650 694 1.588674 CCAACTCCAACGCACTAACA 58.411 50.000 0.00 0.00 0.00 2.41
651 695 0.237498 GCCAACTCCAACGCACTAAC 59.763 55.000 0.00 0.00 0.00 2.34
652 696 0.179043 TGCCAACTCCAACGCACTAA 60.179 50.000 0.00 0.00 0.00 2.24
653 697 0.036164 ATGCCAACTCCAACGCACTA 59.964 50.000 0.00 0.00 33.31 2.74
654 698 0.823356 AATGCCAACTCCAACGCACT 60.823 50.000 0.00 0.00 33.31 4.40
655 699 0.878416 TAATGCCAACTCCAACGCAC 59.122 50.000 0.00 0.00 33.31 5.34
656 700 1.742831 GATAATGCCAACTCCAACGCA 59.257 47.619 0.00 0.00 35.35 5.24
657 701 1.268032 CGATAATGCCAACTCCAACGC 60.268 52.381 0.00 0.00 0.00 4.84
658 702 1.268032 GCGATAATGCCAACTCCAACG 60.268 52.381 0.00 0.00 0.00 4.10
659 703 1.742831 TGCGATAATGCCAACTCCAAC 59.257 47.619 0.00 0.00 0.00 3.77
660 704 2.121291 TGCGATAATGCCAACTCCAA 57.879 45.000 0.00 0.00 0.00 3.53
661 705 1.948834 CATGCGATAATGCCAACTCCA 59.051 47.619 0.00 0.00 0.00 3.86
662 706 1.267806 CCATGCGATAATGCCAACTCC 59.732 52.381 0.00 0.00 0.00 3.85
663 707 1.949525 ACCATGCGATAATGCCAACTC 59.050 47.619 0.00 0.00 0.00 3.01
664 708 1.677576 CACCATGCGATAATGCCAACT 59.322 47.619 0.00 0.00 0.00 3.16
665 709 1.675483 TCACCATGCGATAATGCCAAC 59.325 47.619 0.00 0.00 0.00 3.77
666 710 2.049888 TCACCATGCGATAATGCCAA 57.950 45.000 0.00 0.00 0.00 4.52
667 711 2.153645 GATCACCATGCGATAATGCCA 58.846 47.619 0.00 0.00 0.00 4.92
668 712 2.161012 CAGATCACCATGCGATAATGCC 59.839 50.000 0.00 0.00 0.00 4.40
669 713 2.413765 GCAGATCACCATGCGATAATGC 60.414 50.000 12.96 12.96 32.06 3.56
670 714 2.809696 TGCAGATCACCATGCGATAATG 59.190 45.455 0.00 0.00 45.54 1.90
671 715 3.130280 TGCAGATCACCATGCGATAAT 57.870 42.857 0.00 0.00 45.54 1.28
672 716 2.618442 TGCAGATCACCATGCGATAA 57.382 45.000 0.00 0.00 45.54 1.75
673 717 2.845363 ATGCAGATCACCATGCGATA 57.155 45.000 0.00 0.00 45.54 2.92
674 718 1.977056 AATGCAGATCACCATGCGAT 58.023 45.000 0.00 0.00 45.54 4.58
675 719 1.672363 GAAATGCAGATCACCATGCGA 59.328 47.619 0.00 0.00 45.54 5.10
676 720 1.596220 CGAAATGCAGATCACCATGCG 60.596 52.381 0.00 1.80 45.54 4.73
677 721 1.862815 GCGAAATGCAGATCACCATGC 60.863 52.381 0.00 0.00 45.45 4.06
678 722 2.115348 GCGAAATGCAGATCACCATG 57.885 50.000 0.00 0.00 45.45 3.66
689 733 0.674895 ACCAGAGACCAGCGAAATGC 60.675 55.000 0.00 0.00 46.98 3.56
690 734 1.081892 CACCAGAGACCAGCGAAATG 58.918 55.000 0.00 0.00 0.00 2.32
691 735 0.674895 GCACCAGAGACCAGCGAAAT 60.675 55.000 0.00 0.00 0.00 2.17
692 736 1.301716 GCACCAGAGACCAGCGAAA 60.302 57.895 0.00 0.00 0.00 3.46
693 737 2.343758 GCACCAGAGACCAGCGAA 59.656 61.111 0.00 0.00 0.00 4.70
694 738 3.695606 GGCACCAGAGACCAGCGA 61.696 66.667 0.00 0.00 0.00 4.93
695 739 3.320879 ATGGCACCAGAGACCAGCG 62.321 63.158 0.00 0.00 36.78 5.18
696 740 1.748122 CATGGCACCAGAGACCAGC 60.748 63.158 0.00 0.00 36.78 4.85
697 741 0.107800 CTCATGGCACCAGAGACCAG 60.108 60.000 7.45 0.00 36.78 4.00
698 742 1.556373 CCTCATGGCACCAGAGACCA 61.556 60.000 13.21 0.00 37.99 4.02
699 743 1.222936 CCTCATGGCACCAGAGACC 59.777 63.158 13.21 0.00 0.00 3.85
700 744 4.950479 CCTCATGGCACCAGAGAC 57.050 61.111 13.21 0.00 0.00 3.36
887 969 4.522689 TCCTGCGTGTGTGCGTGT 62.523 61.111 0.00 0.00 37.81 4.49
891 973 2.280119 TGTCTCCTGCGTGTGTGC 60.280 61.111 0.00 0.00 0.00 4.57
895 977 3.231889 CTGCCTGTCTCCTGCGTGT 62.232 63.158 0.00 0.00 0.00 4.49
898 980 3.655810 GACCTGCCTGTCTCCTGCG 62.656 68.421 0.00 0.00 32.39 5.18
899 981 2.267324 GACCTGCCTGTCTCCTGC 59.733 66.667 0.00 0.00 32.39 4.85
903 985 1.194781 TTCAGGGACCTGCCTGTCTC 61.195 60.000 13.51 0.00 43.31 3.36
904 986 0.548682 ATTCAGGGACCTGCCTGTCT 60.549 55.000 13.51 0.00 43.31 3.41
905 987 0.393537 CATTCAGGGACCTGCCTGTC 60.394 60.000 13.51 0.00 43.31 3.51
906 988 1.687612 CATTCAGGGACCTGCCTGT 59.312 57.895 13.51 0.00 43.31 4.00
1165 2145 0.674895 GCCAACAGATTGAGTCCGCT 60.675 55.000 0.00 0.00 38.15 5.52
1368 2405 4.084328 CGTCAGAGTCAGAAACCAACAATC 60.084 45.833 0.00 0.00 0.00 2.67
1378 2415 5.820947 TGTATGCTATACGTCAGAGTCAGAA 59.179 40.000 0.00 0.00 0.00 3.02
1382 2419 5.676532 ACTGTATGCTATACGTCAGAGTC 57.323 43.478 0.00 0.00 0.00 3.36
1383 2420 7.747155 ATTACTGTATGCTATACGTCAGAGT 57.253 36.000 0.00 0.00 0.00 3.24
1384 2421 8.290325 TCAATTACTGTATGCTATACGTCAGAG 58.710 37.037 0.00 0.00 0.00 3.35
1385 2422 8.161699 TCAATTACTGTATGCTATACGTCAGA 57.838 34.615 0.00 0.00 0.00 3.27
1386 2423 8.972262 ATCAATTACTGTATGCTATACGTCAG 57.028 34.615 0.00 0.00 0.00 3.51
1387 2424 9.191995 CAATCAATTACTGTATGCTATACGTCA 57.808 33.333 0.00 0.00 0.00 4.35
1388 2425 9.193133 ACAATCAATTACTGTATGCTATACGTC 57.807 33.333 0.00 0.00 0.00 4.34
1389 2426 9.542462 AACAATCAATTACTGTATGCTATACGT 57.458 29.630 0.00 0.00 0.00 3.57
1390 2427 9.797473 CAACAATCAATTACTGTATGCTATACG 57.203 33.333 0.00 0.00 0.00 3.06
1392 2429 9.845740 ACCAACAATCAATTACTGTATGCTATA 57.154 29.630 0.00 0.00 0.00 1.31
1393 2430 8.752005 ACCAACAATCAATTACTGTATGCTAT 57.248 30.769 0.00 0.00 0.00 2.97
1394 2431 8.574251 AACCAACAATCAATTACTGTATGCTA 57.426 30.769 0.00 0.00 0.00 3.49
1395 2432 7.466746 AACCAACAATCAATTACTGTATGCT 57.533 32.000 0.00 0.00 0.00 3.79
1396 2433 8.028938 AGAAACCAACAATCAATTACTGTATGC 58.971 33.333 0.00 0.00 0.00 3.14
1397 2434 9.559958 GAGAAACCAACAATCAATTACTGTATG 57.440 33.333 0.00 0.00 0.00 2.39
1436 2499 2.551032 CTGCACACATCGGCATCAATAT 59.449 45.455 0.00 0.00 39.65 1.28
1437 2500 1.941975 CTGCACACATCGGCATCAATA 59.058 47.619 0.00 0.00 39.65 1.90
1438 2501 0.736636 CTGCACACATCGGCATCAAT 59.263 50.000 0.00 0.00 39.65 2.57
1439 2502 1.307355 CCTGCACACATCGGCATCAA 61.307 55.000 0.00 0.00 39.65 2.57
1440 2503 1.746239 CCTGCACACATCGGCATCA 60.746 57.895 0.00 0.00 39.65 3.07
1747 2810 1.000607 GCGATGGTGTAGCCGATAGAA 60.001 52.381 0.00 0.00 41.21 2.10
2022 3228 3.247886 TCAGAATTACTCCTCGATCGACG 59.752 47.826 15.15 10.92 44.09 5.12
2023 3236 4.815040 TCAGAATTACTCCTCGATCGAC 57.185 45.455 15.15 0.70 0.00 4.20
2032 3245 7.661968 TGCTGACTATGTATCAGAATTACTCC 58.338 38.462 6.19 0.00 45.46 3.85
2037 3250 7.772292 ACACATTGCTGACTATGTATCAGAATT 59.228 33.333 6.19 0.00 45.46 2.17
2041 3254 6.915544 AACACATTGCTGACTATGTATCAG 57.084 37.500 0.00 0.00 45.40 2.90
2790 4017 4.496336 GCGGCAAGGGAGATGGCT 62.496 66.667 0.00 0.00 40.88 4.75
2912 4139 2.114825 GAACTTTACCGGACGCTATCG 58.885 52.381 9.46 0.00 42.43 2.92
2946 4182 1.341482 TGACCCAGTTTGGCTTTCACA 60.341 47.619 0.00 0.00 35.79 3.58
3033 4270 6.476053 GGTAGTAGTATCTTTTCTTTGAGGCG 59.524 42.308 0.00 0.00 0.00 5.52
3052 4289 6.016527 CACACACTCTTGACACTTAGGTAGTA 60.017 42.308 0.00 0.00 34.56 1.82
3053 4290 4.894114 ACACACTCTTGACACTTAGGTAGT 59.106 41.667 0.00 0.00 37.68 2.73
3054 4291 5.221263 ACACACACTCTTGACACTTAGGTAG 60.221 44.000 0.00 0.00 0.00 3.18
3055 4292 4.647853 ACACACACTCTTGACACTTAGGTA 59.352 41.667 0.00 0.00 0.00 3.08
3056 4293 3.451178 ACACACACTCTTGACACTTAGGT 59.549 43.478 0.00 0.00 0.00 3.08
3057 4294 4.051922 GACACACACTCTTGACACTTAGG 58.948 47.826 0.00 0.00 0.00 2.69
3069 4310 5.277345 GAACATTAGTTGGTGACACACACTC 60.277 44.000 8.08 0.39 42.55 3.51
3102 4346 6.920569 ATTAAATTAGCTTCTACCACCACG 57.079 37.500 0.00 0.00 0.00 4.94
3150 4562 3.938963 ACAAACGACAGACACACTTCAAT 59.061 39.130 0.00 0.00 0.00 2.57
3165 4577 1.948104 CTCAGGGTGACAACAAACGA 58.052 50.000 0.00 0.00 0.00 3.85
3169 4581 0.836606 TGAGCTCAGGGTGACAACAA 59.163 50.000 13.74 0.00 0.00 2.83
3193 4605 4.383649 GTGATTTGAACATGCATGACACAC 59.616 41.667 32.75 25.14 0.00 3.82
3269 4691 2.746277 GACGCTTCGCCAACCCAT 60.746 61.111 0.00 0.00 0.00 4.00
3307 4729 5.978934 TCCACTCGTAGAACAAAGAAAAC 57.021 39.130 0.00 0.00 34.09 2.43
3314 4736 4.628074 CTTCCTTTCCACTCGTAGAACAA 58.372 43.478 0.00 0.00 34.09 2.83
3315 4737 3.554337 GCTTCCTTTCCACTCGTAGAACA 60.554 47.826 0.00 0.00 34.09 3.18
3316 4738 2.994578 GCTTCCTTTCCACTCGTAGAAC 59.005 50.000 0.00 0.00 34.09 3.01
3463 4885 5.149973 ACTCAAGAGTGTCTACGAGACTA 57.850 43.478 1.20 1.81 45.27 2.59
3540 4968 1.493950 GAATCTGCGATGGCGACTGG 61.494 60.000 0.00 0.00 44.10 4.00
3569 4997 2.949909 ATGCTACCGTCGGCACCAA 61.950 57.895 12.28 0.00 41.39 3.67
3570 4998 3.387091 ATGCTACCGTCGGCACCA 61.387 61.111 12.28 5.98 41.39 4.17
3571 4999 2.890474 CATGCTACCGTCGGCACC 60.890 66.667 12.28 0.00 41.39 5.01
3572 5000 3.564027 GCATGCTACCGTCGGCAC 61.564 66.667 12.28 1.03 41.39 5.01
3652 6768 1.817357 AAAGGGCCACGTTAGCTAAC 58.183 50.000 24.05 24.05 0.00 2.34
3662 6778 3.013921 TCAACATCGATAAAAGGGCCAC 58.986 45.455 6.18 0.00 0.00 5.01
3702 6818 2.743636 TAACAGCCGTTGAGGAGAAG 57.256 50.000 0.00 0.00 45.00 2.85
3759 6875 7.873505 ACTTAGTCAAACTTGTCCAAGAGTATC 59.126 37.037 13.69 2.23 40.79 2.24
3760 6876 7.736893 ACTTAGTCAAACTTGTCCAAGAGTAT 58.263 34.615 13.69 0.00 40.79 2.12
3761 6877 7.120923 ACTTAGTCAAACTTGTCCAAGAGTA 57.879 36.000 13.69 0.00 40.79 2.59
3762 6878 5.990668 ACTTAGTCAAACTTGTCCAAGAGT 58.009 37.500 13.69 1.70 40.79 3.24
3770 6886 6.710744 CACCCATCTAACTTAGTCAAACTTGT 59.289 38.462 0.00 0.00 0.00 3.16
3803 6919 1.482593 CTCCCTTAGGTGTGTGGCTAG 59.517 57.143 0.00 0.00 0.00 3.42
3808 6924 2.779506 GGTTTCTCCCTTAGGTGTGTG 58.220 52.381 0.00 0.00 0.00 3.82
3809 6925 1.346722 CGGTTTCTCCCTTAGGTGTGT 59.653 52.381 0.00 0.00 0.00 3.72
3823 6939 2.474032 GCTCGTGATTAGCAACGGTTTC 60.474 50.000 0.00 0.00 39.83 2.78
3924 10813 9.793252 GCATACACATGAAGAATTTGTTTATCT 57.207 29.630 0.00 0.00 31.59 1.98
3925 10814 9.571810 TGCATACACATGAAGAATTTGTTTATC 57.428 29.630 0.00 0.00 31.59 1.75
3926 10815 9.926158 TTGCATACACATGAAGAATTTGTTTAT 57.074 25.926 0.00 0.00 31.59 1.40
3965 10854 3.053693 CCCAAACTCCCAGGATGTCATAA 60.054 47.826 0.00 0.00 0.00 1.90
4000 10889 4.735369 TCTTGTTTTGGAGCCCTGATTTA 58.265 39.130 0.00 0.00 0.00 1.40
4005 10894 4.341366 AAATTCTTGTTTTGGAGCCCTG 57.659 40.909 0.00 0.00 0.00 4.45
4022 10911 5.876651 AGCTTTGAGAAAGGGTCAAAATT 57.123 34.783 0.00 0.00 42.03 1.82
4060 10949 3.068024 GTCATTGGGAGAGCTCTAGACAG 59.932 52.174 18.25 5.74 0.00 3.51
4069 10958 1.340405 ACCACATGTCATTGGGAGAGC 60.340 52.381 6.18 0.00 37.18 4.09
4087 10976 2.606108 GCCCGACAAAATTTCATGACC 58.394 47.619 0.00 0.00 0.00 4.02
4102 10991 4.096532 TGAACAAAAATTATATGCGCCCGA 59.903 37.500 4.18 0.00 0.00 5.14
4103 10992 4.355437 TGAACAAAAATTATATGCGCCCG 58.645 39.130 4.18 0.00 0.00 6.13
4104 10993 8.532977 AATATGAACAAAAATTATATGCGCCC 57.467 30.769 4.18 0.00 0.00 6.13


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

AutoCloner maintained by Alex Coulton.