Multiple sequence alignment - TraesCS3B01G296600

Loading Multiple Alignment...

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 TraesCS3B01G296600 chr3B 100.000 5223 0 0 1 5223 475826230 475831452 0.000000e+00 9646.0
1 TraesCS3B01G296600 chr3B 89.376 593 56 4 1 588 757716086 757715496 0.000000e+00 739.0
2 TraesCS3B01G296600 chr3B 97.015 67 2 0 585 651 146303245 146303179 4.270000e-21 113.0
3 TraesCS3B01G296600 chr3D 95.358 2736 75 18 1633 4350 365329817 365332518 0.000000e+00 4301.0
4 TraesCS3B01G296600 chr3D 93.447 763 26 8 746 1500 365329029 365329775 0.000000e+00 1110.0
5 TraesCS3B01G296600 chr3D 90.674 579 47 4 1 578 112753862 112754434 0.000000e+00 763.0
6 TraesCS3B01G296600 chr3D 89.483 580 60 1 1 579 439835723 439835144 0.000000e+00 732.0
7 TraesCS3B01G296600 chr3A 94.390 2745 83 22 1633 4350 487432435 487435135 0.000000e+00 4150.0
8 TraesCS3B01G296600 chr3A 91.948 770 31 10 746 1504 487431648 487432397 0.000000e+00 1050.0
9 TraesCS3B01G296600 chr3A 83.000 100 16 1 650 748 142993799 142993700 7.200000e-14 89.8
10 TraesCS3B01G296600 chr6B 94.857 875 45 0 4349 5223 55647383 55646509 0.000000e+00 1367.0
11 TraesCS3B01G296600 chr6B 94.872 78 3 1 1563 1639 22733742 22733665 2.550000e-23 121.0
12 TraesCS3B01G296600 chr2B 91.409 873 74 1 4351 5223 733194970 733195841 0.000000e+00 1195.0
13 TraesCS3B01G296600 chr2B 88.634 871 98 1 4353 5223 589257190 589258059 0.000000e+00 1059.0
14 TraesCS3B01G296600 chr2B 88.262 656 66 7 3 650 150602498 150601846 0.000000e+00 774.0
15 TraesCS3B01G296600 chr2B 93.671 79 4 1 1559 1636 754965251 754965173 3.300000e-22 117.0
16 TraesCS3B01G296600 chr2B 83.168 101 14 3 650 748 673670719 673670620 7.200000e-14 89.8
17 TraesCS3B01G296600 chr4B 90.126 871 86 0 4353 5223 454524509 454525379 0.000000e+00 1133.0
18 TraesCS3B01G296600 chr4B 91.463 82 5 1 1563 1642 612401511 612401592 1.540000e-20 111.0
19 TraesCS3B01G296600 chr7B 88.647 872 98 1 4353 5223 480626804 480627675 0.000000e+00 1061.0
20 TraesCS3B01G296600 chr7B 88.852 610 66 2 4613 5222 392858499 392857892 0.000000e+00 749.0
21 TraesCS3B01G296600 chr7B 89.226 594 53 8 1 586 474483700 474483110 0.000000e+00 732.0
22 TraesCS3B01G296600 chr7B 98.507 67 1 0 585 651 678968194 678968128 9.190000e-23 119.0
23 TraesCS3B01G296600 chr7B 97.015 67 2 0 585 651 7177069 7177135 4.270000e-21 113.0
24 TraesCS3B01G296600 chr4A 85.665 872 121 4 4354 5223 565827155 565828024 0.000000e+00 915.0
25 TraesCS3B01G296600 chr4A 95.946 74 2 1 1563 1635 236541808 236541735 9.190000e-23 119.0
26 TraesCS3B01G296600 chr7D 90.830 578 49 2 1 577 199908664 199909238 0.000000e+00 771.0
27 TraesCS3B01G296600 chr7D 85.000 100 14 1 650 748 107138592 107138691 3.330000e-17 100.0
28 TraesCS3B01G296600 chr7D 90.769 65 5 1 587 651 65540818 65540881 9.320000e-13 86.1
29 TraesCS3B01G296600 chr7D 90.909 55 5 0 693 747 474500541 474500595 2.020000e-09 75.0
30 TraesCS3B01G296600 chr6D 90.767 574 50 3 1 573 372152221 372151650 0.000000e+00 763.0
31 TraesCS3B01G296600 chr5D 90.000 580 55 3 1 578 535148684 535148106 0.000000e+00 747.0
32 TraesCS3B01G296600 chr5D 87.638 542 67 0 1 542 323791611 323792152 9.540000e-177 630.0
33 TraesCS3B01G296600 chr5D 89.000 100 10 1 650 748 66748803 66748902 7.100000e-24 122.0
34 TraesCS3B01G296600 chr5D 93.590 78 3 2 1563 1638 418874060 418873983 1.190000e-21 115.0
35 TraesCS3B01G296600 chr5D 92.500 80 4 1 1562 1639 289038507 289038428 4.270000e-21 113.0
36 TraesCS3B01G296600 chr4D 90.493 568 51 3 1 567 506343174 506343739 0.000000e+00 747.0
37 TraesCS3B01G296600 chr4D 82.111 682 86 24 1 650 82556028 82556705 7.640000e-153 551.0
38 TraesCS3B01G296600 chr4D 93.651 63 3 1 589 651 10101808 10101747 5.570000e-15 93.5
39 TraesCS3B01G296600 chr1D 89.810 579 54 3 1 578 296160611 296160037 0.000000e+00 737.0
40 TraesCS3B01G296600 chr5B 85.799 676 69 18 1 651 491947506 491948179 0.000000e+00 691.0
41 TraesCS3B01G296600 chr1B 82.440 746 125 6 4477 5219 330364618 330365360 0.000000e+00 647.0
42 TraesCS3B01G296600 chr6A 95.946 74 2 1 1563 1635 235083785 235083858 9.190000e-23 119.0
43 TraesCS3B01G296600 chr5A 92.857 84 3 2 1558 1639 702465354 702465272 9.190000e-23 119.0
44 TraesCS3B01G296600 chr2A 92.771 83 2 4 1561 1640 89486241 89486322 3.300000e-22 117.0


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 TraesCS3B01G296600 chr3B 475826230 475831452 5222 False 9646.0 9646 100.0000 1 5223 1 chr3B.!!$F1 5222
1 TraesCS3B01G296600 chr3B 757715496 757716086 590 True 739.0 739 89.3760 1 588 1 chr3B.!!$R2 587
2 TraesCS3B01G296600 chr3D 365329029 365332518 3489 False 2705.5 4301 94.4025 746 4350 2 chr3D.!!$F2 3604
3 TraesCS3B01G296600 chr3D 112753862 112754434 572 False 763.0 763 90.6740 1 578 1 chr3D.!!$F1 577
4 TraesCS3B01G296600 chr3D 439835144 439835723 579 True 732.0 732 89.4830 1 579 1 chr3D.!!$R1 578
5 TraesCS3B01G296600 chr3A 487431648 487435135 3487 False 2600.0 4150 93.1690 746 4350 2 chr3A.!!$F1 3604
6 TraesCS3B01G296600 chr6B 55646509 55647383 874 True 1367.0 1367 94.8570 4349 5223 1 chr6B.!!$R2 874
7 TraesCS3B01G296600 chr2B 733194970 733195841 871 False 1195.0 1195 91.4090 4351 5223 1 chr2B.!!$F2 872
8 TraesCS3B01G296600 chr2B 589257190 589258059 869 False 1059.0 1059 88.6340 4353 5223 1 chr2B.!!$F1 870
9 TraesCS3B01G296600 chr2B 150601846 150602498 652 True 774.0 774 88.2620 3 650 1 chr2B.!!$R1 647
10 TraesCS3B01G296600 chr4B 454524509 454525379 870 False 1133.0 1133 90.1260 4353 5223 1 chr4B.!!$F1 870
11 TraesCS3B01G296600 chr7B 480626804 480627675 871 False 1061.0 1061 88.6470 4353 5223 1 chr7B.!!$F2 870
12 TraesCS3B01G296600 chr7B 392857892 392858499 607 True 749.0 749 88.8520 4613 5222 1 chr7B.!!$R1 609
13 TraesCS3B01G296600 chr7B 474483110 474483700 590 True 732.0 732 89.2260 1 586 1 chr7B.!!$R2 585
14 TraesCS3B01G296600 chr4A 565827155 565828024 869 False 915.0 915 85.6650 4354 5223 1 chr4A.!!$F1 869
15 TraesCS3B01G296600 chr7D 199908664 199909238 574 False 771.0 771 90.8300 1 577 1 chr7D.!!$F3 576
16 TraesCS3B01G296600 chr6D 372151650 372152221 571 True 763.0 763 90.7670 1 573 1 chr6D.!!$R1 572
17 TraesCS3B01G296600 chr5D 535148106 535148684 578 True 747.0 747 90.0000 1 578 1 chr5D.!!$R3 577
18 TraesCS3B01G296600 chr5D 323791611 323792152 541 False 630.0 630 87.6380 1 542 1 chr5D.!!$F2 541
19 TraesCS3B01G296600 chr4D 506343174 506343739 565 False 747.0 747 90.4930 1 567 1 chr4D.!!$F2 566
20 TraesCS3B01G296600 chr4D 82556028 82556705 677 False 551.0 551 82.1110 1 650 1 chr4D.!!$F1 649
21 TraesCS3B01G296600 chr1D 296160037 296160611 574 True 737.0 737 89.8100 1 578 1 chr1D.!!$R1 577
22 TraesCS3B01G296600 chr5B 491947506 491948179 673 False 691.0 691 85.7990 1 651 1 chr5B.!!$F1 650
23 TraesCS3B01G296600 chr1B 330364618 330365360 742 False 647.0 647 82.4400 4477 5219 1 chr1B.!!$F1 742

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
705 750 0.038892 CCATGCACCAAACAGACTGC 60.039 55.000 1.25 0.00 0.00 4.40 F
712 757 0.110056 CCAAACAGACTGCGCACATC 60.110 55.000 5.66 7.50 0.00 3.06 F
1507 1570 0.170561 CGTGTCTAGGTTAGCGCAGT 59.829 55.000 11.47 0.00 0.00 4.40 F
1509 1572 0.815734 TGTCTAGGTTAGCGCAGTCC 59.184 55.000 11.47 8.51 0.00 3.85 F
1513 1576 1.002684 CTAGGTTAGCGCAGTCCTACG 60.003 57.143 11.47 8.15 0.00 3.51 F
2589 2657 1.019673 CAAGCTTCGATGGGATGGTG 58.980 55.000 0.00 0.00 31.67 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2473 2541 0.466124 ATTCTCTTAGCGACCCCTGC 59.534 55.000 0.0 0.0 0.00 4.85 R
2547 2615 3.990469 CGATGTAGCCATGAAGACCATAC 59.010 47.826 0.0 0.0 33.31 2.39 R
2742 2810 2.334977 TGACTGCCCCAAGAGAAAGTA 58.665 47.619 0.0 0.0 0.00 2.24 R
3352 3428 3.077359 GCTCAATGCCTTCAACACTAGT 58.923 45.455 0.0 0.0 35.15 2.57 R
3394 3470 3.196007 TGCGGAAATAACTTTGCTTCG 57.804 42.857 0.0 0.0 31.08 3.79 R
4325 4417 0.033011 AGGCCTCAGACACCGAGTAT 60.033 55.000 0.0 0.0 0.00 2.12 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
111 113 1.076192 GGCGGGAAGGAGAGAGGTA 60.076 63.158 0.00 0.00 0.00 3.08
132 134 0.967887 CAGAGCAGAGGAGGAACCGA 60.968 60.000 0.00 0.00 44.74 4.69
136 138 2.039137 AGAGGAGGAACCGACCCC 59.961 66.667 0.00 0.00 44.74 4.95
220 222 1.235724 CCGACACCAGAAAACCCTTC 58.764 55.000 0.00 0.00 0.00 3.46
237 239 0.249996 TTCGACGGGGGTCAAGAAAC 60.250 55.000 0.00 0.00 0.00 2.78
238 240 1.670083 CGACGGGGGTCAAGAAACC 60.670 63.158 0.00 0.00 38.69 3.27
311 315 2.997897 GAGCCCAGGACCACGAGT 60.998 66.667 0.00 0.00 0.00 4.18
360 364 3.047280 GCACCGCATTGACCGACA 61.047 61.111 0.00 0.00 0.00 4.35
392 396 1.224592 GCAACAGATGGGGGACGAT 59.775 57.895 0.00 0.00 0.00 3.73
573 588 0.832135 AGAGGGAGCGGTGAGAACAA 60.832 55.000 0.00 0.00 0.00 2.83
580 595 2.379634 CGGTGAGAACAATGCGCGA 61.380 57.895 12.10 0.00 0.00 5.87
656 701 4.223964 GCCGCGCCGAGCTTTAAG 62.224 66.667 0.00 0.00 45.59 1.85
657 702 3.564027 CCGCGCCGAGCTTTAAGG 61.564 66.667 0.00 0.00 45.59 2.69
658 703 2.813908 CGCGCCGAGCTTTAAGGT 60.814 61.111 0.00 0.00 45.59 3.50
659 704 2.799540 CGCGCCGAGCTTTAAGGTC 61.800 63.158 13.51 13.51 45.59 3.85
660 705 2.461945 GCGCCGAGCTTTAAGGTCC 61.462 63.158 17.04 4.76 39.44 4.46
661 706 2.165301 CGCCGAGCTTTAAGGTCCG 61.165 63.158 17.04 12.29 39.44 4.79
662 707 1.079336 GCCGAGCTTTAAGGTCCGT 60.079 57.895 17.04 0.00 39.44 4.69
663 708 0.672711 GCCGAGCTTTAAGGTCCGTT 60.673 55.000 17.04 0.00 39.44 4.44
664 709 1.356938 CCGAGCTTTAAGGTCCGTTC 58.643 55.000 17.04 0.00 39.44 3.95
665 710 0.989890 CGAGCTTTAAGGTCCGTTCG 59.010 55.000 17.04 3.52 39.44 3.95
666 711 1.356938 GAGCTTTAAGGTCCGTTCGG 58.643 55.000 12.62 4.74 36.78 4.30
667 712 0.683412 AGCTTTAAGGTCCGTTCGGT 59.317 50.000 11.04 0.00 0.00 4.69
668 713 1.073964 GCTTTAAGGTCCGTTCGGTC 58.926 55.000 11.04 5.58 0.00 4.79
669 714 1.718396 CTTTAAGGTCCGTTCGGTCC 58.282 55.000 17.05 17.05 34.43 4.46
670 715 1.001181 CTTTAAGGTCCGTTCGGTCCA 59.999 52.381 23.95 6.83 36.23 4.02
671 716 0.318120 TTAAGGTCCGTTCGGTCCAC 59.682 55.000 23.95 10.64 36.23 4.02
672 717 0.827089 TAAGGTCCGTTCGGTCCACA 60.827 55.000 23.95 11.83 36.23 4.17
673 718 1.688269 AAGGTCCGTTCGGTCCACAA 61.688 55.000 23.95 0.00 36.23 3.33
674 719 1.227615 GGTCCGTTCGGTCCACAAA 60.228 57.895 19.13 0.00 34.39 2.83
675 720 0.604511 GGTCCGTTCGGTCCACAAAT 60.605 55.000 19.13 0.00 34.39 2.32
676 721 0.794473 GTCCGTTCGGTCCACAAATC 59.206 55.000 11.04 0.00 0.00 2.17
677 722 0.668096 TCCGTTCGGTCCACAAATCG 60.668 55.000 11.04 0.00 0.00 3.34
678 723 1.131826 CGTTCGGTCCACAAATCGC 59.868 57.895 0.00 0.00 0.00 4.58
679 724 1.561717 CGTTCGGTCCACAAATCGCA 61.562 55.000 0.00 0.00 0.00 5.10
680 725 0.802494 GTTCGGTCCACAAATCGCAT 59.198 50.000 0.00 0.00 0.00 4.73
681 726 0.801872 TTCGGTCCACAAATCGCATG 59.198 50.000 0.00 0.00 0.00 4.06
682 727 1.226379 CGGTCCACAAATCGCATGC 60.226 57.895 7.91 7.91 0.00 4.06
683 728 1.882311 GGTCCACAAATCGCATGCA 59.118 52.632 19.57 5.34 0.00 3.96
684 729 0.179156 GGTCCACAAATCGCATGCAG 60.179 55.000 19.57 10.78 0.00 4.41
685 730 0.799534 GTCCACAAATCGCATGCAGC 60.800 55.000 19.57 0.00 40.87 5.25
686 731 1.517694 CCACAAATCGCATGCAGCC 60.518 57.895 19.57 0.00 41.38 4.85
687 732 1.517694 CACAAATCGCATGCAGCCC 60.518 57.895 19.57 0.00 41.38 5.19
688 733 1.978080 ACAAATCGCATGCAGCCCA 60.978 52.632 19.57 0.00 41.38 5.36
689 734 1.324740 ACAAATCGCATGCAGCCCAT 61.325 50.000 19.57 0.00 41.38 4.00
699 744 3.457484 CAGCCCATGCACCAAACA 58.543 55.556 0.00 0.00 41.13 2.83
700 745 1.290955 CAGCCCATGCACCAAACAG 59.709 57.895 0.00 0.00 41.13 3.16
701 746 1.153524 AGCCCATGCACCAAACAGA 59.846 52.632 0.00 0.00 41.13 3.41
702 747 1.181098 AGCCCATGCACCAAACAGAC 61.181 55.000 0.00 0.00 41.13 3.51
703 748 1.181098 GCCCATGCACCAAACAGACT 61.181 55.000 0.00 0.00 37.47 3.24
704 749 0.599558 CCCATGCACCAAACAGACTG 59.400 55.000 0.00 0.00 0.00 3.51
705 750 0.038892 CCATGCACCAAACAGACTGC 60.039 55.000 1.25 0.00 0.00 4.40
706 751 0.386352 CATGCACCAAACAGACTGCG 60.386 55.000 1.25 0.00 31.96 5.18
707 752 2.050985 GCACCAAACAGACTGCGC 60.051 61.111 0.00 0.00 0.00 6.09
708 753 2.833533 GCACCAAACAGACTGCGCA 61.834 57.895 10.98 10.98 0.00 6.09
709 754 1.009675 CACCAAACAGACTGCGCAC 60.010 57.895 5.66 0.00 0.00 5.34
710 755 1.451207 ACCAAACAGACTGCGCACA 60.451 52.632 5.66 0.00 0.00 4.57
711 756 0.819259 ACCAAACAGACTGCGCACAT 60.819 50.000 5.66 0.00 0.00 3.21
712 757 0.110056 CCAAACAGACTGCGCACATC 60.110 55.000 5.66 7.50 0.00 3.06
713 758 0.110056 CAAACAGACTGCGCACATCC 60.110 55.000 5.66 0.00 0.00 3.51
714 759 1.237285 AAACAGACTGCGCACATCCC 61.237 55.000 5.66 0.00 0.00 3.85
715 760 2.046988 CAGACTGCGCACATCCCA 60.047 61.111 5.66 0.00 0.00 4.37
716 761 1.450848 CAGACTGCGCACATCCCAT 60.451 57.895 5.66 0.00 0.00 4.00
717 762 0.179076 CAGACTGCGCACATCCCATA 60.179 55.000 5.66 0.00 0.00 2.74
718 763 0.179073 AGACTGCGCACATCCCATAC 60.179 55.000 5.66 0.00 0.00 2.39
719 764 1.490693 GACTGCGCACATCCCATACG 61.491 60.000 5.66 0.00 0.00 3.06
720 765 2.203001 TGCGCACATCCCATACGG 60.203 61.111 5.66 0.00 0.00 4.02
730 775 3.918544 CCATACGGGCTTGGTTGG 58.081 61.111 0.00 0.00 0.00 3.77
731 776 1.752694 CCATACGGGCTTGGTTGGG 60.753 63.158 0.00 0.00 0.00 4.12
732 777 2.044352 ATACGGGCTTGGTTGGGC 60.044 61.111 0.00 0.00 0.00 5.36
733 778 2.612493 ATACGGGCTTGGTTGGGCT 61.612 57.895 0.00 0.00 0.00 5.19
734 779 2.837031 ATACGGGCTTGGTTGGGCTG 62.837 60.000 0.00 0.00 40.75 4.85
737 782 2.999063 GGCTTGGTTGGGCTGCAT 60.999 61.111 0.50 0.00 0.00 3.96
738 783 2.263540 GCTTGGTTGGGCTGCATG 59.736 61.111 0.50 0.00 0.00 4.06
739 784 2.263540 CTTGGTTGGGCTGCATGC 59.736 61.111 11.82 11.82 41.94 4.06
740 785 3.636313 CTTGGTTGGGCTGCATGCG 62.636 63.158 14.09 9.16 44.05 4.73
785 830 3.117888 TCCAGGTCTAAGCCCATTCAATC 60.118 47.826 0.00 0.00 0.00 2.67
786 831 3.371917 CCAGGTCTAAGCCCATTCAATCA 60.372 47.826 0.00 0.00 0.00 2.57
787 832 3.629398 CAGGTCTAAGCCCATTCAATCAC 59.371 47.826 0.00 0.00 0.00 3.06
788 833 3.266772 AGGTCTAAGCCCATTCAATCACA 59.733 43.478 0.00 0.00 0.00 3.58
789 834 3.378427 GGTCTAAGCCCATTCAATCACAC 59.622 47.826 0.00 0.00 0.00 3.82
790 835 3.063997 GTCTAAGCCCATTCAATCACACG 59.936 47.826 0.00 0.00 0.00 4.49
791 836 0.527565 AAGCCCATTCAATCACACGC 59.472 50.000 0.00 0.00 0.00 5.34
792 837 0.608856 AGCCCATTCAATCACACGCA 60.609 50.000 0.00 0.00 0.00 5.24
793 838 0.457035 GCCCATTCAATCACACGCAT 59.543 50.000 0.00 0.00 0.00 4.73
794 839 1.675483 GCCCATTCAATCACACGCATA 59.325 47.619 0.00 0.00 0.00 3.14
795 840 2.541588 GCCCATTCAATCACACGCATAC 60.542 50.000 0.00 0.00 0.00 2.39
796 841 2.682352 CCCATTCAATCACACGCATACA 59.318 45.455 0.00 0.00 0.00 2.29
802 847 2.162319 ATCACACGCATACACACACA 57.838 45.000 0.00 0.00 0.00 3.72
814 859 0.861185 CACACACACTCACCGTCATG 59.139 55.000 0.00 0.00 0.00 3.07
835 880 1.857364 CACGGCGTAGTGGTCAAAC 59.143 57.895 14.22 0.00 38.40 2.93
1275 1336 1.377856 GCTCCCTGTCCCTTTGCTC 60.378 63.158 0.00 0.00 0.00 4.26
1297 1360 2.467826 GCGGCTGTGCTTGATCCTC 61.468 63.158 0.00 0.00 0.00 3.71
1332 1395 0.875059 GCGCTTGCTTCAGTAAAGGT 59.125 50.000 0.00 0.00 35.37 3.50
1374 1437 2.141122 AACATGTTTCAAGCCGCCGG 62.141 55.000 4.92 0.00 0.00 6.13
1389 1452 2.178890 CCGGGTAGTCGAGACTCGG 61.179 68.421 23.92 20.90 42.54 4.63
1464 1527 4.665645 CGGAGTGTGCGTGTTATTTTGTAG 60.666 45.833 0.00 0.00 0.00 2.74
1481 1544 2.359848 TGTAGAGTTGTACTGCGTGTGT 59.640 45.455 0.00 0.00 0.00 3.72
1500 1563 1.542915 GTGCCACTCGTGTCTAGGTTA 59.457 52.381 0.00 0.00 0.00 2.85
1501 1564 1.816835 TGCCACTCGTGTCTAGGTTAG 59.183 52.381 0.00 0.00 0.00 2.34
1502 1565 1.469423 GCCACTCGTGTCTAGGTTAGC 60.469 57.143 0.00 0.00 0.00 3.09
1503 1566 1.202154 CCACTCGTGTCTAGGTTAGCG 60.202 57.143 0.00 0.00 0.00 4.26
1504 1567 0.450983 ACTCGTGTCTAGGTTAGCGC 59.549 55.000 0.00 0.00 0.00 5.92
1505 1568 0.450583 CTCGTGTCTAGGTTAGCGCA 59.549 55.000 11.47 0.00 0.00 6.09
1506 1569 0.450583 TCGTGTCTAGGTTAGCGCAG 59.549 55.000 11.47 0.00 0.00 5.18
1507 1570 0.170561 CGTGTCTAGGTTAGCGCAGT 59.829 55.000 11.47 0.00 0.00 4.40
1508 1571 1.794437 CGTGTCTAGGTTAGCGCAGTC 60.794 57.143 11.47 0.00 0.00 3.51
1509 1572 0.815734 TGTCTAGGTTAGCGCAGTCC 59.184 55.000 11.47 8.51 0.00 3.85
1510 1573 1.104630 GTCTAGGTTAGCGCAGTCCT 58.895 55.000 11.47 15.86 0.00 3.85
1511 1574 2.295885 GTCTAGGTTAGCGCAGTCCTA 58.704 52.381 11.47 16.14 0.00 2.94
1512 1575 2.033174 GTCTAGGTTAGCGCAGTCCTAC 59.967 54.545 11.47 6.09 0.00 3.18
1513 1576 1.002684 CTAGGTTAGCGCAGTCCTACG 60.003 57.143 11.47 8.15 0.00 3.51
1550 1613 1.628340 ACATGGGCAGCACTACACTTA 59.372 47.619 0.00 0.00 0.00 2.24
1561 1624 5.570206 CAGCACTACACTTAAATGCACATTG 59.430 40.000 0.00 0.00 38.79 2.82
1562 1625 5.241506 AGCACTACACTTAAATGCACATTGT 59.758 36.000 0.00 0.00 38.79 2.71
1563 1626 6.429692 AGCACTACACTTAAATGCACATTGTA 59.570 34.615 0.00 0.00 38.79 2.41
1564 1627 6.523201 GCACTACACTTAAATGCACATTGTAC 59.477 38.462 0.00 0.00 36.30 2.90
1565 1628 7.573096 GCACTACACTTAAATGCACATTGTACT 60.573 37.037 0.00 0.00 36.30 2.73
1566 1629 7.957484 CACTACACTTAAATGCACATTGTACTC 59.043 37.037 0.00 0.00 0.00 2.59
1567 1630 7.878127 ACTACACTTAAATGCACATTGTACTCT 59.122 33.333 0.00 0.00 0.00 3.24
1568 1631 7.133891 ACACTTAAATGCACATTGTACTCTC 57.866 36.000 0.00 0.00 0.00 3.20
1569 1632 6.936900 ACACTTAAATGCACATTGTACTCTCT 59.063 34.615 0.00 0.00 0.00 3.10
1570 1633 7.118390 ACACTTAAATGCACATTGTACTCTCTC 59.882 37.037 0.00 0.00 0.00 3.20
1571 1634 6.595716 ACTTAAATGCACATTGTACTCTCTCC 59.404 38.462 0.00 0.00 0.00 3.71
1572 1635 2.654749 TGCACATTGTACTCTCTCCG 57.345 50.000 0.00 0.00 0.00 4.63
1573 1636 1.893137 TGCACATTGTACTCTCTCCGT 59.107 47.619 0.00 0.00 0.00 4.69
1574 1637 2.299013 TGCACATTGTACTCTCTCCGTT 59.701 45.455 0.00 0.00 0.00 4.44
1575 1638 3.244078 TGCACATTGTACTCTCTCCGTTT 60.244 43.478 0.00 0.00 0.00 3.60
1576 1639 3.368236 GCACATTGTACTCTCTCCGTTTC 59.632 47.826 0.00 0.00 0.00 2.78
1577 1640 4.556233 CACATTGTACTCTCTCCGTTTCA 58.444 43.478 0.00 0.00 0.00 2.69
1578 1641 4.988540 CACATTGTACTCTCTCCGTTTCAA 59.011 41.667 0.00 0.00 0.00 2.69
1579 1642 5.465390 CACATTGTACTCTCTCCGTTTCAAA 59.535 40.000 0.00 0.00 0.00 2.69
1580 1643 6.018262 CACATTGTACTCTCTCCGTTTCAAAA 60.018 38.462 0.00 0.00 0.00 2.44
1581 1644 6.710744 ACATTGTACTCTCTCCGTTTCAAAAT 59.289 34.615 0.00 0.00 0.00 1.82
1582 1645 7.876068 ACATTGTACTCTCTCCGTTTCAAAATA 59.124 33.333 0.00 0.00 0.00 1.40
1583 1646 7.884816 TTGTACTCTCTCCGTTTCAAAATAG 57.115 36.000 0.00 0.00 0.00 1.73
1584 1647 7.223260 TGTACTCTCTCCGTTTCAAAATAGA 57.777 36.000 0.00 0.00 0.00 1.98
1585 1648 7.837863 TGTACTCTCTCCGTTTCAAAATAGAT 58.162 34.615 0.00 0.00 0.00 1.98
1586 1649 7.759886 TGTACTCTCTCCGTTTCAAAATAGATG 59.240 37.037 0.00 0.00 0.00 2.90
1587 1650 6.936279 ACTCTCTCCGTTTCAAAATAGATGA 58.064 36.000 0.00 0.00 0.00 2.92
1588 1651 6.814146 ACTCTCTCCGTTTCAAAATAGATGAC 59.186 38.462 0.00 0.00 0.00 3.06
1589 1652 6.936279 TCTCTCCGTTTCAAAATAGATGACT 58.064 36.000 0.00 0.00 0.00 3.41
1590 1653 7.036220 TCTCTCCGTTTCAAAATAGATGACTC 58.964 38.462 0.00 0.00 0.00 3.36
1591 1654 6.697395 TCTCCGTTTCAAAATAGATGACTCA 58.303 36.000 0.00 0.00 0.00 3.41
1592 1655 7.158697 TCTCCGTTTCAAAATAGATGACTCAA 58.841 34.615 0.00 0.00 0.00 3.02
1593 1656 7.117812 TCTCCGTTTCAAAATAGATGACTCAAC 59.882 37.037 0.00 0.00 0.00 3.18
1594 1657 6.934645 TCCGTTTCAAAATAGATGACTCAACT 59.065 34.615 0.00 0.00 0.00 3.16
1595 1658 7.444183 TCCGTTTCAAAATAGATGACTCAACTT 59.556 33.333 0.00 0.00 0.00 2.66
1596 1659 7.535258 CCGTTTCAAAATAGATGACTCAACTTG 59.465 37.037 0.00 0.00 0.00 3.16
1597 1660 8.070171 CGTTTCAAAATAGATGACTCAACTTGT 58.930 33.333 0.00 0.00 0.00 3.16
1600 1663 9.554395 TTCAAAATAGATGACTCAACTTGTACA 57.446 29.630 0.00 0.00 0.00 2.90
1601 1664 9.554395 TCAAAATAGATGACTCAACTTGTACAA 57.446 29.630 8.28 8.28 0.00 2.41
1604 1667 9.561069 AAATAGATGACTCAACTTGTACAAAGT 57.439 29.630 10.03 9.92 0.00 2.66
1605 1668 9.561069 AATAGATGACTCAACTTGTACAAAGTT 57.439 29.630 10.03 12.51 40.80 2.66
1613 1676 5.767816 AACTTGTACAAAGTTGGGTCATC 57.232 39.130 17.21 0.00 38.88 2.92
1614 1677 5.048846 ACTTGTACAAAGTTGGGTCATCT 57.951 39.130 10.03 0.00 0.00 2.90
1615 1678 6.182507 ACTTGTACAAAGTTGGGTCATCTA 57.817 37.500 10.03 0.00 0.00 1.98
1616 1679 6.779860 ACTTGTACAAAGTTGGGTCATCTAT 58.220 36.000 10.03 0.00 0.00 1.98
1617 1680 7.231467 ACTTGTACAAAGTTGGGTCATCTATT 58.769 34.615 10.03 0.00 0.00 1.73
1618 1681 7.724061 ACTTGTACAAAGTTGGGTCATCTATTT 59.276 33.333 10.03 0.00 0.00 1.40
1619 1682 8.472007 TTGTACAAAGTTGGGTCATCTATTTT 57.528 30.769 5.64 0.00 0.00 1.82
1620 1683 7.881142 TGTACAAAGTTGGGTCATCTATTTTG 58.119 34.615 0.00 0.00 0.00 2.44
1621 1684 6.345096 ACAAAGTTGGGTCATCTATTTTGG 57.655 37.500 0.00 0.00 0.00 3.28
1622 1685 6.074648 ACAAAGTTGGGTCATCTATTTTGGA 58.925 36.000 0.00 0.00 0.00 3.53
1623 1686 6.553100 ACAAAGTTGGGTCATCTATTTTGGAA 59.447 34.615 0.00 0.00 0.00 3.53
1624 1687 6.590234 AAGTTGGGTCATCTATTTTGGAAC 57.410 37.500 0.00 0.00 0.00 3.62
1625 1688 4.700213 AGTTGGGTCATCTATTTTGGAACG 59.300 41.667 0.00 0.00 0.00 3.95
1626 1689 3.616219 TGGGTCATCTATTTTGGAACGG 58.384 45.455 0.00 0.00 0.00 4.44
1627 1690 3.264706 TGGGTCATCTATTTTGGAACGGA 59.735 43.478 0.00 0.00 0.00 4.69
1628 1691 3.877508 GGGTCATCTATTTTGGAACGGAG 59.122 47.826 0.00 0.00 0.00 4.63
1629 1692 3.877508 GGTCATCTATTTTGGAACGGAGG 59.122 47.826 0.00 0.00 0.00 4.30
1630 1693 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
1631 1694 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
1749 1816 5.573282 CGGTATTGTTGATATGATCTCCGAC 59.427 44.000 0.00 0.00 35.94 4.79
1862 1929 2.031097 GCCCAAAGGAATCCAGATGGG 61.031 57.143 24.25 24.25 42.20 4.00
1987 2054 3.902150 ACACAAGTGTATCTGTGAGACG 58.098 45.455 3.64 0.00 42.90 4.18
2009 2076 3.499918 GGTGACACAAACATCTTCTCCTG 59.500 47.826 8.08 0.00 0.00 3.86
2043 2110 5.595542 TGGAAAGATGGCATCTATCAAAAGG 59.404 40.000 29.02 0.00 39.08 3.11
2044 2111 5.595952 GGAAAGATGGCATCTATCAAAAGGT 59.404 40.000 29.02 8.50 39.08 3.50
2098 2165 3.555966 CCCATGGAGTATTGAGGAAACC 58.444 50.000 15.22 0.00 0.00 3.27
2114 2181 2.452600 AACCAAGGAACTGCAAGGAA 57.547 45.000 0.00 0.00 40.86 3.36
2115 2182 2.683211 ACCAAGGAACTGCAAGGAAT 57.317 45.000 0.00 0.00 40.86 3.01
2146 2213 3.197766 TGTGTTACTTGCAGCTAGCCTAT 59.802 43.478 12.13 0.00 44.83 2.57
2147 2214 4.192317 GTGTTACTTGCAGCTAGCCTATT 58.808 43.478 12.13 0.00 44.83 1.73
2148 2215 5.105106 TGTGTTACTTGCAGCTAGCCTATTA 60.105 40.000 12.13 0.00 44.83 0.98
2149 2216 5.234543 GTGTTACTTGCAGCTAGCCTATTAC 59.765 44.000 12.13 0.75 44.83 1.89
2150 2217 5.128827 TGTTACTTGCAGCTAGCCTATTACT 59.871 40.000 12.13 0.00 44.83 2.24
2151 2218 4.762289 ACTTGCAGCTAGCCTATTACTT 57.238 40.909 12.13 0.00 44.83 2.24
2152 2219 4.446371 ACTTGCAGCTAGCCTATTACTTG 58.554 43.478 12.13 1.13 44.83 3.16
2153 2220 2.838736 TGCAGCTAGCCTATTACTTGC 58.161 47.619 12.13 12.56 44.83 4.01
2154 2221 2.170397 TGCAGCTAGCCTATTACTTGCA 59.830 45.455 17.09 17.09 44.83 4.08
2155 2222 2.805099 GCAGCTAGCCTATTACTTGCAG 59.195 50.000 12.13 0.00 38.19 4.41
2156 2223 2.805099 CAGCTAGCCTATTACTTGCAGC 59.195 50.000 12.13 0.00 38.19 5.25
2157 2224 2.703007 AGCTAGCCTATTACTTGCAGCT 59.297 45.455 12.13 0.00 38.19 4.24
2158 2225 3.898123 AGCTAGCCTATTACTTGCAGCTA 59.102 43.478 12.13 0.84 38.19 3.32
2160 2227 3.118905 AGCCTATTACTTGCAGCTAGC 57.881 47.619 6.62 6.62 45.96 3.42
2161 2228 2.147150 GCCTATTACTTGCAGCTAGCC 58.853 52.381 12.13 0.00 44.83 3.93
2162 2229 2.224402 GCCTATTACTTGCAGCTAGCCT 60.224 50.000 12.13 0.00 44.83 4.58
2163 2230 3.006967 GCCTATTACTTGCAGCTAGCCTA 59.993 47.826 12.13 0.00 44.83 3.93
2192 2259 6.472887 AGAAACTAACATTAGCAGGCACTTA 58.527 36.000 0.00 0.00 32.57 2.24
2249 2316 1.484653 TGTGTGACAAGTGGTAGTGCT 59.515 47.619 0.00 0.00 0.00 4.40
2547 2615 6.714810 TGGATTATCCTGGTTTTGGATTATCG 59.285 38.462 12.91 0.00 44.54 2.92
2583 2651 4.131376 ATCGCAAGCTTCGATGGG 57.869 55.556 23.70 11.96 44.00 4.00
2589 2657 1.019673 CAAGCTTCGATGGGATGGTG 58.980 55.000 0.00 0.00 31.67 4.17
2619 2687 6.718388 TGTCATTGAACAATATGCGAGAATC 58.282 36.000 0.00 0.00 0.00 2.52
2742 2810 3.628646 GACGTGCAAGGGCTCCCAT 62.629 63.158 7.82 0.00 41.91 4.00
2889 2957 7.496920 TGATGAAATTCGTCAAATCTAGCATCT 59.503 33.333 14.84 0.00 39.27 2.90
2960 3028 8.969260 AATGTAACTCATCAAATCTAGCATCA 57.031 30.769 0.00 0.00 35.48 3.07
3080 3150 8.902540 TGTTGAGTTAACACTTGATGATACTT 57.097 30.769 8.61 0.00 44.07 2.24
3145 3216 4.497674 GCAATCTGCAGACATCCATCTTTC 60.498 45.833 20.97 0.00 44.26 2.62
3148 3219 2.943690 CTGCAGACATCCATCTTTCCTG 59.056 50.000 8.42 0.00 0.00 3.86
3150 3221 2.942752 GCAGACATCCATCTTTCCTGCA 60.943 50.000 0.00 0.00 43.37 4.41
3183 3254 6.322969 ACAACCAGTTATGATCATGCATGAAT 59.677 34.615 31.79 23.18 40.69 2.57
3352 3428 2.371841 AGAAGATGTAACACCACCAGCA 59.628 45.455 0.00 0.00 0.00 4.41
3394 3470 5.573337 GCATATTATCATGCCTTCTTCCC 57.427 43.478 0.00 0.00 44.55 3.97
3522 3598 3.902881 TGGTTTGTTTCAAGGCAATGT 57.097 38.095 0.00 0.00 0.00 2.71
3590 3678 8.879759 TCTTAGTTGAATATTCCACATTCGTTC 58.120 33.333 18.85 0.00 35.55 3.95
3595 3683 5.872617 TGAATATTCCACATTCGTTCGTTCT 59.127 36.000 12.90 0.00 35.55 3.01
3682 3770 8.468399 TCAGATAATTTATTGCAACAATGAGCA 58.532 29.630 0.00 1.53 39.32 4.26
3683 3771 8.537223 CAGATAATTTATTGCAACAATGAGCAC 58.463 33.333 0.00 0.00 41.05 4.40
3684 3772 8.252417 AGATAATTTATTGCAACAATGAGCACA 58.748 29.630 0.00 0.00 41.05 4.57
3685 3773 6.470557 AATTTATTGCAACAATGAGCACAC 57.529 33.333 0.00 0.00 41.05 3.82
3706 3794 7.381408 GCACACCTCTTTAAAAAGGAATTGTAC 59.619 37.037 14.66 0.06 36.67 2.90
3708 3796 8.410912 ACACCTCTTTAAAAAGGAATTGTACAC 58.589 33.333 14.66 0.00 36.67 2.90
3713 3801 9.137459 TCTTTAAAAAGGAATTGTACACCATGA 57.863 29.630 0.00 0.00 36.67 3.07
3837 3929 4.793028 GCAGTTGAACTTTTGAAGGCTACC 60.793 45.833 0.00 0.00 0.00 3.18
3884 3976 6.655078 AAAAGTCAGTATCATTTGCACCTT 57.345 33.333 0.00 0.00 0.00 3.50
3952 4044 4.590222 ACCTGAATCAAGAAGCAACCATTT 59.410 37.500 0.00 0.00 0.00 2.32
4060 4152 0.321671 GAGCAGCAGACCAGGTAACA 59.678 55.000 0.00 0.00 41.41 2.41
4165 4257 0.553819 TCCTAGAGGGAGAGCCTGAC 59.446 60.000 0.00 0.00 39.58 3.51
4247 4339 3.068024 ACCATTGTGCATTGTCTCGTTTT 59.932 39.130 0.00 0.00 0.00 2.43
4290 4382 1.466856 GCTGATTGGCACCATTCTGA 58.533 50.000 17.52 0.00 31.49 3.27
4325 4417 9.636789 ACATTGGATGAATCAAATAAGAGATGA 57.363 29.630 0.00 0.00 29.48 2.92
4352 4444 1.739562 GTCTGAGGCCTTCACTGCG 60.740 63.158 6.77 0.00 0.00 5.18
4355 4447 0.037326 CTGAGGCCTTCACTGCGTTA 60.037 55.000 6.77 0.00 0.00 3.18
4766 4859 1.762957 GACTGGATTGCCCTACTGCTA 59.237 52.381 0.00 0.00 35.38 3.49
4898 4991 1.460504 TCGATCCGCTACACAGAGTT 58.539 50.000 0.00 0.00 0.00 3.01
5091 5184 1.202302 TCAACGCGGCAAAATCAACAA 60.202 42.857 12.47 0.00 0.00 2.83
5115 5208 0.895530 ACCGATCCGATGTGAACACT 59.104 50.000 6.51 0.00 0.00 3.55
5169 5262 0.178964 TTCTGTTGCCCCTTTCCCAG 60.179 55.000 0.00 0.00 0.00 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 6.332735 TGCTTGCTCGTAGATGTAGATTAT 57.667 37.500 0.00 0.00 33.89 1.28
80 82 4.653888 CCGCCGGGGTTTTCACCT 62.654 66.667 18.27 0.00 43.65 4.00
111 113 1.264045 GGTTCCTCCTCTGCTCTGCT 61.264 60.000 0.00 0.00 0.00 4.24
220 222 1.670083 GGTTTCTTGACCCCCGTCG 60.670 63.158 0.00 0.00 42.37 5.12
354 358 4.295119 GCCACCACGAGTGTCGGT 62.295 66.667 9.00 0.00 45.59 4.69
360 364 3.872603 TTGCTGGCCACCACGAGT 61.873 61.111 0.00 0.00 0.00 4.18
420 424 3.068691 CGGGCTCCAGAACTCGGA 61.069 66.667 0.00 0.00 0.00 4.55
443 447 2.178890 CAGCATCCAGGAGCGCTTC 61.179 63.158 13.26 10.56 35.48 3.86
444 448 2.124819 CAGCATCCAGGAGCGCTT 60.125 61.111 13.26 0.00 35.48 4.68
523 532 0.556380 TCCCTCCCTCTCCTCTCCTT 60.556 60.000 0.00 0.00 0.00 3.36
651 696 3.912899 GGACCGAACGGACCTTAAA 57.087 52.632 22.64 0.00 44.68 1.52
657 702 0.794473 GATTTGTGGACCGAACGGAC 59.206 55.000 20.14 13.36 38.96 4.79
658 703 0.668096 CGATTTGTGGACCGAACGGA 60.668 55.000 20.14 0.00 38.96 4.69
659 704 1.785321 CGATTTGTGGACCGAACGG 59.215 57.895 11.83 11.83 42.03 4.44
660 705 1.131826 GCGATTTGTGGACCGAACG 59.868 57.895 0.00 0.00 0.00 3.95
661 706 0.802494 ATGCGATTTGTGGACCGAAC 59.198 50.000 0.00 0.00 0.00 3.95
662 707 0.801872 CATGCGATTTGTGGACCGAA 59.198 50.000 0.00 0.00 0.00 4.30
663 708 1.643868 GCATGCGATTTGTGGACCGA 61.644 55.000 0.00 0.00 0.00 4.69
664 709 1.226379 GCATGCGATTTGTGGACCG 60.226 57.895 0.00 0.00 0.00 4.79
665 710 0.179156 CTGCATGCGATTTGTGGACC 60.179 55.000 14.09 0.00 0.00 4.46
666 711 0.799534 GCTGCATGCGATTTGTGGAC 60.800 55.000 14.09 0.00 0.00 4.02
667 712 1.507630 GCTGCATGCGATTTGTGGA 59.492 52.632 14.09 0.00 0.00 4.02
668 713 1.517694 GGCTGCATGCGATTTGTGG 60.518 57.895 14.09 0.00 44.05 4.17
669 714 1.517694 GGGCTGCATGCGATTTGTG 60.518 57.895 14.09 0.00 44.05 3.33
670 715 1.324740 ATGGGCTGCATGCGATTTGT 61.325 50.000 14.09 0.00 44.05 2.83
671 716 0.874175 CATGGGCTGCATGCGATTTG 60.874 55.000 14.09 2.09 44.05 2.32
672 717 1.440060 CATGGGCTGCATGCGATTT 59.560 52.632 14.09 0.00 44.05 2.17
673 718 3.125607 CATGGGCTGCATGCGATT 58.874 55.556 14.09 0.00 44.05 3.34
682 727 1.180456 TCTGTTTGGTGCATGGGCTG 61.180 55.000 0.00 0.00 41.91 4.85
683 728 1.153524 TCTGTTTGGTGCATGGGCT 59.846 52.632 0.00 0.00 41.91 5.19
684 729 1.181098 AGTCTGTTTGGTGCATGGGC 61.181 55.000 0.00 0.00 41.68 5.36
685 730 0.599558 CAGTCTGTTTGGTGCATGGG 59.400 55.000 0.00 0.00 0.00 4.00
686 731 0.038892 GCAGTCTGTTTGGTGCATGG 60.039 55.000 0.93 0.00 35.91 3.66
687 732 0.386352 CGCAGTCTGTTTGGTGCATG 60.386 55.000 0.93 0.00 35.57 4.06
688 733 1.951510 CGCAGTCTGTTTGGTGCAT 59.048 52.632 0.93 0.00 35.57 3.96
689 734 2.833533 GCGCAGTCTGTTTGGTGCA 61.834 57.895 0.30 0.00 35.57 4.57
690 735 2.050985 GCGCAGTCTGTTTGGTGC 60.051 61.111 0.30 0.00 0.00 5.01
691 736 1.009675 GTGCGCAGTCTGTTTGGTG 60.010 57.895 12.22 0.00 0.00 4.17
692 737 0.819259 ATGTGCGCAGTCTGTTTGGT 60.819 50.000 12.22 0.00 0.00 3.67
693 738 0.110056 GATGTGCGCAGTCTGTTTGG 60.110 55.000 12.22 0.00 0.00 3.28
694 739 0.110056 GGATGTGCGCAGTCTGTTTG 60.110 55.000 12.22 0.00 0.00 2.93
695 740 1.237285 GGGATGTGCGCAGTCTGTTT 61.237 55.000 12.22 0.00 0.00 2.83
696 741 1.672356 GGGATGTGCGCAGTCTGTT 60.672 57.895 12.22 0.00 0.00 3.16
697 742 2.046892 GGGATGTGCGCAGTCTGT 60.047 61.111 12.22 0.00 0.00 3.41
698 743 0.179076 TATGGGATGTGCGCAGTCTG 60.179 55.000 12.22 0.00 43.18 3.51
699 744 0.179073 GTATGGGATGTGCGCAGTCT 60.179 55.000 12.22 0.00 43.18 3.24
700 745 1.490693 CGTATGGGATGTGCGCAGTC 61.491 60.000 12.22 12.70 43.18 3.51
701 746 1.521457 CGTATGGGATGTGCGCAGT 60.521 57.895 12.22 1.40 43.18 4.40
702 747 2.246739 CCGTATGGGATGTGCGCAG 61.247 63.158 12.22 0.00 43.18 5.18
703 748 2.203001 CCGTATGGGATGTGCGCA 60.203 61.111 5.66 5.66 44.12 6.09
713 758 1.752694 CCCAACCAAGCCCGTATGG 60.753 63.158 0.00 0.00 42.60 2.74
714 759 2.414785 GCCCAACCAAGCCCGTATG 61.415 63.158 0.00 0.00 0.00 2.39
715 760 2.044352 GCCCAACCAAGCCCGTAT 60.044 61.111 0.00 0.00 0.00 3.06
716 761 3.253838 AGCCCAACCAAGCCCGTA 61.254 61.111 0.00 0.00 0.00 4.02
717 762 4.974721 CAGCCCAACCAAGCCCGT 62.975 66.667 0.00 0.00 0.00 5.28
720 765 2.999063 ATGCAGCCCAACCAAGCC 60.999 61.111 0.00 0.00 0.00 4.35
721 766 2.263540 CATGCAGCCCAACCAAGC 59.736 61.111 0.00 0.00 0.00 4.01
722 767 2.263540 GCATGCAGCCCAACCAAG 59.736 61.111 14.21 0.00 37.23 3.61
723 768 3.682885 CGCATGCAGCCCAACCAA 61.683 61.111 19.57 0.00 41.38 3.67
771 816 1.742831 GCGTGTGATTGAATGGGCTTA 59.257 47.619 0.00 0.00 0.00 3.09
785 830 1.192312 GAGTGTGTGTGTATGCGTGTG 59.808 52.381 0.00 0.00 0.00 3.82
786 831 1.202475 TGAGTGTGTGTGTATGCGTGT 60.202 47.619 0.00 0.00 0.00 4.49
787 832 1.192312 GTGAGTGTGTGTGTATGCGTG 59.808 52.381 0.00 0.00 0.00 5.34
788 833 1.497991 GTGAGTGTGTGTGTATGCGT 58.502 50.000 0.00 0.00 0.00 5.24
789 834 0.790207 GGTGAGTGTGTGTGTATGCG 59.210 55.000 0.00 0.00 0.00 4.73
790 835 0.790207 CGGTGAGTGTGTGTGTATGC 59.210 55.000 0.00 0.00 0.00 3.14
791 836 2.058798 GACGGTGAGTGTGTGTGTATG 58.941 52.381 0.00 0.00 0.00 2.39
792 837 1.684450 TGACGGTGAGTGTGTGTGTAT 59.316 47.619 0.00 0.00 0.00 2.29
793 838 1.104630 TGACGGTGAGTGTGTGTGTA 58.895 50.000 0.00 0.00 0.00 2.90
794 839 0.464036 ATGACGGTGAGTGTGTGTGT 59.536 50.000 0.00 0.00 0.00 3.72
795 840 0.861185 CATGACGGTGAGTGTGTGTG 59.139 55.000 0.00 0.00 0.00 3.82
796 841 0.750249 TCATGACGGTGAGTGTGTGT 59.250 50.000 0.00 0.00 0.00 3.72
802 847 1.080501 CGTGCTCATGACGGTGAGT 60.081 57.895 13.76 0.00 45.80 3.41
814 859 2.506438 GACCACTACGCCGTGCTC 60.506 66.667 0.00 0.00 33.60 4.26
822 867 0.040157 TCGACGGTTTGACCACTACG 60.040 55.000 0.00 0.00 38.47 3.51
824 869 1.408340 TGTTCGACGGTTTGACCACTA 59.592 47.619 0.00 0.00 38.47 2.74
835 880 0.237498 GCTTTCCCTTTGTTCGACGG 59.763 55.000 0.00 0.00 0.00 4.79
1288 1349 3.068024 GGTGAGCTAGTGAGAGGATCAAG 59.932 52.174 0.00 0.00 40.43 3.02
1297 1360 1.150567 GCGCATGGTGAGCTAGTGAG 61.151 60.000 0.30 0.00 40.12 3.51
1332 1395 4.963373 TGACTACTTTTGACCATTCGGAA 58.037 39.130 0.00 0.00 35.59 4.30
1374 1437 0.107752 AGTCCCGAGTCTCGACTACC 60.108 60.000 23.74 6.55 43.74 3.18
1389 1452 1.269998 ACTGCGTGTGAGTTCTAGTCC 59.730 52.381 0.00 0.00 0.00 3.85
1464 1527 0.232303 GCACACACGCAGTACAACTC 59.768 55.000 0.00 0.00 41.61 3.01
1481 1544 1.816835 CTAACCTAGACACGAGTGGCA 59.183 52.381 12.04 0.00 42.32 4.92
1502 1565 1.209128 CATTAAGGCGTAGGACTGCG 58.791 55.000 5.44 5.44 41.58 5.18
1503 1566 0.938008 GCATTAAGGCGTAGGACTGC 59.062 55.000 0.00 0.00 0.00 4.40
1527 1590 1.675310 GTAGTGCTGCCCATGTGCA 60.675 57.895 2.03 2.03 39.37 4.57
1531 1594 2.401583 TAAGTGTAGTGCTGCCCATG 57.598 50.000 0.00 0.00 0.00 3.66
1550 1613 3.935203 CGGAGAGAGTACAATGTGCATTT 59.065 43.478 4.00 0.00 0.00 2.32
1561 1624 7.974501 TCATCTATTTTGAAACGGAGAGAGTAC 59.025 37.037 0.00 0.00 0.00 2.73
1562 1625 7.974501 GTCATCTATTTTGAAACGGAGAGAGTA 59.025 37.037 0.00 0.00 0.00 2.59
1563 1626 6.814146 GTCATCTATTTTGAAACGGAGAGAGT 59.186 38.462 0.00 0.00 0.00 3.24
1564 1627 7.038659 AGTCATCTATTTTGAAACGGAGAGAG 58.961 38.462 0.00 0.00 0.00 3.20
1565 1628 6.936279 AGTCATCTATTTTGAAACGGAGAGA 58.064 36.000 0.00 0.00 0.00 3.10
1566 1629 6.813649 TGAGTCATCTATTTTGAAACGGAGAG 59.186 38.462 0.00 0.00 0.00 3.20
1567 1630 6.697395 TGAGTCATCTATTTTGAAACGGAGA 58.303 36.000 0.00 0.00 0.00 3.71
1568 1631 6.968131 TGAGTCATCTATTTTGAAACGGAG 57.032 37.500 0.00 0.00 0.00 4.63
1569 1632 6.934645 AGTTGAGTCATCTATTTTGAAACGGA 59.065 34.615 1.70 0.00 0.00 4.69
1570 1633 7.133891 AGTTGAGTCATCTATTTTGAAACGG 57.866 36.000 1.70 0.00 0.00 4.44
1571 1634 8.070171 ACAAGTTGAGTCATCTATTTTGAAACG 58.930 33.333 10.54 0.00 0.00 3.60
1574 1637 9.554395 TGTACAAGTTGAGTCATCTATTTTGAA 57.446 29.630 10.54 0.00 0.00 2.69
1575 1638 9.554395 TTGTACAAGTTGAGTCATCTATTTTGA 57.446 29.630 10.54 0.00 0.00 2.69
1578 1641 9.561069 ACTTTGTACAAGTTGAGTCATCTATTT 57.439 29.630 10.54 0.00 0.00 1.40
1579 1642 9.561069 AACTTTGTACAAGTTGAGTCATCTATT 57.439 29.630 10.54 0.00 38.88 1.73
1591 1654 5.445964 AGATGACCCAACTTTGTACAAGTT 58.554 37.500 8.56 11.95 40.80 2.66
1592 1655 5.048846 AGATGACCCAACTTTGTACAAGT 57.951 39.130 8.56 6.63 0.00 3.16
1593 1656 7.687941 AATAGATGACCCAACTTTGTACAAG 57.312 36.000 8.56 6.02 0.00 3.16
1594 1657 8.356657 CAAAATAGATGACCCAACTTTGTACAA 58.643 33.333 3.59 3.59 0.00 2.41
1595 1658 7.040062 CCAAAATAGATGACCCAACTTTGTACA 60.040 37.037 0.00 0.00 0.00 2.90
1596 1659 7.175990 TCCAAAATAGATGACCCAACTTTGTAC 59.824 37.037 0.00 0.00 0.00 2.90
1597 1660 7.235079 TCCAAAATAGATGACCCAACTTTGTA 58.765 34.615 0.00 0.00 0.00 2.41
1598 1661 6.074648 TCCAAAATAGATGACCCAACTTTGT 58.925 36.000 0.00 0.00 0.00 2.83
1599 1662 6.588719 TCCAAAATAGATGACCCAACTTTG 57.411 37.500 0.00 0.00 0.00 2.77
1600 1663 6.294508 CGTTCCAAAATAGATGACCCAACTTT 60.295 38.462 0.00 0.00 0.00 2.66
1601 1664 5.183140 CGTTCCAAAATAGATGACCCAACTT 59.817 40.000 0.00 0.00 0.00 2.66
1602 1665 4.700213 CGTTCCAAAATAGATGACCCAACT 59.300 41.667 0.00 0.00 0.00 3.16
1603 1666 4.142469 CCGTTCCAAAATAGATGACCCAAC 60.142 45.833 0.00 0.00 0.00 3.77
1604 1667 4.013728 CCGTTCCAAAATAGATGACCCAA 58.986 43.478 0.00 0.00 0.00 4.12
1605 1668 3.264706 TCCGTTCCAAAATAGATGACCCA 59.735 43.478 0.00 0.00 0.00 4.51
1606 1669 3.877508 CTCCGTTCCAAAATAGATGACCC 59.122 47.826 0.00 0.00 0.00 4.46
1607 1670 3.877508 CCTCCGTTCCAAAATAGATGACC 59.122 47.826 0.00 0.00 0.00 4.02
1608 1671 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
1609 1672 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
1610 1673 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
1611 1674 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
1612 1675 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
1613 1676 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
1614 1677 4.472108 ACATACTCCCTCCGTTCCAAAATA 59.528 41.667 0.00 0.00 0.00 1.40
1615 1678 3.265995 ACATACTCCCTCCGTTCCAAAAT 59.734 43.478 0.00 0.00 0.00 1.82
1616 1679 2.640826 ACATACTCCCTCCGTTCCAAAA 59.359 45.455 0.00 0.00 0.00 2.44
1617 1680 2.262637 ACATACTCCCTCCGTTCCAAA 58.737 47.619 0.00 0.00 0.00 3.28
1618 1681 1.946984 ACATACTCCCTCCGTTCCAA 58.053 50.000 0.00 0.00 0.00 3.53
1619 1682 2.024655 ACTACATACTCCCTCCGTTCCA 60.025 50.000 0.00 0.00 0.00 3.53
1620 1683 2.664015 ACTACATACTCCCTCCGTTCC 58.336 52.381 0.00 0.00 0.00 3.62
1621 1684 3.737355 GCAACTACATACTCCCTCCGTTC 60.737 52.174 0.00 0.00 0.00 3.95
1622 1685 2.167900 GCAACTACATACTCCCTCCGTT 59.832 50.000 0.00 0.00 0.00 4.44
1623 1686 1.755380 GCAACTACATACTCCCTCCGT 59.245 52.381 0.00 0.00 0.00 4.69
1624 1687 2.032620 AGCAACTACATACTCCCTCCG 58.967 52.381 0.00 0.00 0.00 4.63
1625 1688 3.068873 CAGAGCAACTACATACTCCCTCC 59.931 52.174 0.00 0.00 0.00 4.30
1626 1689 3.702045 ACAGAGCAACTACATACTCCCTC 59.298 47.826 0.00 0.00 0.00 4.30
1627 1690 3.714144 ACAGAGCAACTACATACTCCCT 58.286 45.455 0.00 0.00 0.00 4.20
1628 1691 4.184629 CAACAGAGCAACTACATACTCCC 58.815 47.826 0.00 0.00 0.00 4.30
1629 1692 3.619038 GCAACAGAGCAACTACATACTCC 59.381 47.826 0.00 0.00 0.00 3.85
1630 1693 4.499183 AGCAACAGAGCAACTACATACTC 58.501 43.478 0.00 0.00 36.85 2.59
1631 1694 4.543590 AGCAACAGAGCAACTACATACT 57.456 40.909 0.00 0.00 36.85 2.12
1862 1929 1.477558 CCCATCATGTGCTTACCTCCC 60.478 57.143 0.00 0.00 0.00 4.30
1987 2054 3.499918 CAGGAGAAGATGTTTGTGTCACC 59.500 47.826 0.00 0.00 0.00 4.02
2009 2076 3.255642 TGCCATCTTTCCAGCTTTACAAC 59.744 43.478 0.00 0.00 0.00 3.32
2043 2110 9.991388 CTGATATTACTAGCTTAAGATACCGAC 57.009 37.037 6.67 0.00 0.00 4.79
2044 2111 9.175312 CCTGATATTACTAGCTTAAGATACCGA 57.825 37.037 6.67 0.00 0.00 4.69
2098 2165 1.067354 GCCATTCCTTGCAGTTCCTTG 60.067 52.381 0.00 0.00 0.00 3.61
2114 2181 3.510753 TGCAAGTAACACAATCATGCCAT 59.489 39.130 0.00 0.00 0.00 4.40
2115 2182 2.889678 TGCAAGTAACACAATCATGCCA 59.110 40.909 0.00 0.00 0.00 4.92
2192 2259 9.678260 AGCTATAAAACAGTTCATCAAGATTCT 57.322 29.630 0.00 0.00 0.00 2.40
2249 2316 7.873719 TGGTCTCAAAATTCTACAGAAACAA 57.126 32.000 0.00 0.00 37.61 2.83
2473 2541 0.466124 ATTCTCTTAGCGACCCCTGC 59.534 55.000 0.00 0.00 0.00 4.85
2520 2588 9.753674 GATAATCCAAAACCAGGATAATCCATA 57.246 33.333 0.00 0.00 44.94 2.74
2547 2615 3.990469 CGATGTAGCCATGAAGACCATAC 59.010 47.826 0.00 0.00 33.31 2.39
2589 2657 5.284079 GCATATTGTTCAATGACATGGTCC 58.716 41.667 8.11 0.00 0.00 4.46
2742 2810 2.334977 TGACTGCCCCAAGAGAAAGTA 58.665 47.619 0.00 0.00 0.00 2.24
2871 2939 7.264947 TGTAATGAGATGCTAGATTTGACGAA 58.735 34.615 0.00 0.00 0.00 3.85
2889 2957 9.958180 TTATCTCCAAACAAGAGAATGTAATGA 57.042 29.630 0.00 0.00 43.35 2.57
2960 3028 6.006449 AGCTCCAAACAAGAGAATGTAATGT 58.994 36.000 0.00 0.00 32.86 2.71
3065 3135 9.862371 CTTGACTAAGTAAGTATCATCAAGTGT 57.138 33.333 0.00 0.00 39.07 3.55
3145 3216 5.643379 AACTGGTTGTTATAACATGCAGG 57.357 39.130 18.69 10.67 38.95 4.85
3148 3219 8.620416 TGATCATAACTGGTTGTTATAACATGC 58.380 33.333 18.69 13.95 46.69 4.06
3352 3428 3.077359 GCTCAATGCCTTCAACACTAGT 58.923 45.455 0.00 0.00 35.15 2.57
3394 3470 3.196007 TGCGGAAATAACTTTGCTTCG 57.804 42.857 0.00 0.00 31.08 3.79
3590 3678 2.616842 AGTACCTTGCCACAAAAGAACG 59.383 45.455 0.00 0.00 0.00 3.95
3595 3683 2.741145 ACCAAGTACCTTGCCACAAAA 58.259 42.857 0.00 0.00 39.85 2.44
3664 3752 4.039004 AGGTGTGCTCATTGTTGCAATAAA 59.961 37.500 12.87 6.36 41.10 1.40
3682 3770 8.410912 GTGTACAATTCCTTTTTAAAGAGGTGT 58.589 33.333 20.92 19.28 38.28 4.16
3683 3771 7.865889 GGTGTACAATTCCTTTTTAAAGAGGTG 59.134 37.037 20.92 15.43 38.28 4.00
3684 3772 7.562088 TGGTGTACAATTCCTTTTTAAAGAGGT 59.438 33.333 20.92 7.23 38.28 3.85
3685 3773 7.947282 TGGTGTACAATTCCTTTTTAAAGAGG 58.053 34.615 16.89 16.89 38.28 3.69
3706 3794 7.262772 AGCATTTCAGTATTTCAATCATGGTG 58.737 34.615 0.00 0.00 0.00 4.17
3837 3929 3.067180 CCAATTGGGATTCGATGTCCTTG 59.933 47.826 17.36 11.70 40.01 3.61
3884 3976 7.944554 AGAAGGAAATCAGGTACATGAGAAAAA 59.055 33.333 16.18 0.00 31.44 1.94
3952 4044 9.449719 GGTACTTCCAGAATAAGAAGAAATGAA 57.550 33.333 6.75 0.00 41.69 2.57
4060 4152 4.288105 AGAAATTGACTCACATGAGGGTCT 59.712 41.667 21.60 3.76 46.13 3.85
4165 4257 2.746803 GGCGGTTGAAATCCGGTCG 61.747 63.158 0.00 0.00 46.90 4.79
4263 4355 0.387239 GTGCCAATCAGCGAAACCAC 60.387 55.000 0.00 0.00 34.65 4.16
4272 4364 2.621998 GGATCAGAATGGTGCCAATCAG 59.378 50.000 8.77 1.26 36.16 2.90
4277 4369 0.994247 AGTGGATCAGAATGGTGCCA 59.006 50.000 0.00 0.00 36.32 4.92
4319 4411 3.252215 CCTCAGACACCGAGTATCATCTC 59.748 52.174 0.00 0.00 33.17 2.75
4321 4413 2.287909 GCCTCAGACACCGAGTATCATC 60.288 54.545 0.00 0.00 33.17 2.92
4323 4415 1.103803 GCCTCAGACACCGAGTATCA 58.896 55.000 0.00 0.00 33.17 2.15
4324 4416 0.386113 GGCCTCAGACACCGAGTATC 59.614 60.000 0.00 0.00 0.00 2.24
4325 4417 0.033011 AGGCCTCAGACACCGAGTAT 60.033 55.000 0.00 0.00 0.00 2.12
4326 4418 0.251653 AAGGCCTCAGACACCGAGTA 60.252 55.000 5.23 0.00 0.00 2.59
4352 4444 6.217294 GGCTAGATGGTAGAACTGATGTAAC 58.783 44.000 0.00 0.00 0.00 2.50
4355 4447 3.319405 CGGCTAGATGGTAGAACTGATGT 59.681 47.826 0.00 0.00 0.00 3.06
4766 4859 6.558009 CAGAAAATTTGACGATGATGTGGAT 58.442 36.000 0.00 0.00 0.00 3.41
4850 4943 0.756294 TGAAAAGGAGCGGTGACAGA 59.244 50.000 0.00 0.00 0.00 3.41
4898 4991 0.604780 GCTCCACTGCTGCTTTGAGA 60.605 55.000 0.00 0.00 0.00 3.27
5076 5169 1.929836 TGTTGTTGTTGATTTTGCCGC 59.070 42.857 0.00 0.00 0.00 6.53
5169 5262 1.614413 CGGGAGCCCTAAGTATCTGAC 59.386 57.143 3.70 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.