Multiple sequence alignment - TraesCS5A01G379100

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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 TraesCS5A01G379100 chr5A 100.000 2714 0 0 1 2714 576281651 576284364 0.000000e+00 5012
1 TraesCS5A01G379100 chr5A 82.568 740 117 5 905 1642 34716461 34715732 2.280000e-180 641
2 TraesCS5A01G379100 chr5A 94.355 124 7 0 2034 2157 505594138 505594261 9.920000e-45 191
3 TraesCS5A01G379100 chr5A 81.416 226 38 4 351 574 436328128 436327905 5.970000e-42 182
4 TraesCS5A01G379100 chr5D 83.542 960 129 16 715 1669 324754029 324754964 0.000000e+00 870
5 TraesCS5A01G379100 chr5D 93.684 95 6 0 575 669 324753934 324754028 2.820000e-30 143
6 TraesCS5A01G379100 chr7B 82.917 960 135 14 715 1669 506602618 506601683 0.000000e+00 837
7 TraesCS5A01G379100 chr7B 87.006 531 35 13 2185 2710 64480463 64479962 3.920000e-158 568
8 TraesCS5A01G379100 chr7B 91.579 95 8 0 575 669 506602713 506602619 6.100000e-27 132
9 TraesCS5A01G379100 chrUn 92.105 570 33 6 2154 2714 68527636 68527070 0.000000e+00 793
10 TraesCS5A01G379100 chrUn 91.930 570 34 5 2154 2714 98016883 98017449 0.000000e+00 787
11 TraesCS5A01G379100 chrUn 88.798 366 36 4 1659 2022 98016504 98016866 6.900000e-121 444
12 TraesCS5A01G379100 chrUn 87.978 366 31 8 1659 2022 68528007 68527653 1.160000e-113 420
13 TraesCS5A01G379100 chr3B 94.499 509 26 2 1534 2040 795219267 795219775 0.000000e+00 784
14 TraesCS5A01G379100 chr3B 93.200 500 28 3 2153 2648 795219773 795220270 0.000000e+00 730
15 TraesCS5A01G379100 chr6B 93.910 509 29 2 1534 2040 551925750 551926258 0.000000e+00 767
16 TraesCS5A01G379100 chr6B 93.400 500 26 4 2153 2648 551926256 551926752 0.000000e+00 734
17 TraesCS5A01G379100 chr6B 81.938 227 36 4 351 574 714334832 714335056 1.280000e-43 187
18 TraesCS5A01G379100 chr2D 85.616 730 97 6 826 1549 349929478 349930205 0.000000e+00 760
19 TraesCS5A01G379100 chr2D 86.415 530 39 14 2185 2709 131447621 131447120 1.420000e-152 549
20 TraesCS5A01G379100 chr2D 93.846 130 7 1 2027 2156 377306136 377306008 7.670000e-46 195
21 TraesCS5A01G379100 chr2D 82.128 235 30 11 351 581 546220936 546220710 9.920000e-45 191
22 TraesCS5A01G379100 chr5B 84.795 730 102 7 826 1549 483526239 483526965 0.000000e+00 725
23 TraesCS5A01G379100 chr5B 89.649 541 33 5 41 558 698115818 698116358 0.000000e+00 667
24 TraesCS5A01G379100 chr5B 87.121 528 34 13 2185 2707 508813637 508814135 3.920000e-158 568
25 TraesCS5A01G379100 chr5B 87.555 458 56 1 1040 1497 273182742 273183198 1.850000e-146 529
26 TraesCS5A01G379100 chr5B 85.757 337 47 1 1199 1535 273183200 273183535 3.320000e-94 355
27 TraesCS5A01G379100 chr5B 84.647 241 30 7 337 574 407621033 407620797 1.620000e-57 233
28 TraesCS5A01G379100 chr5B 82.379 227 37 3 351 574 691953876 691954102 7.670000e-46 195
29 TraesCS5A01G379100 chr6A 88.028 568 37 13 41 580 466222715 466222151 0.000000e+00 643
30 TraesCS5A01G379100 chr4B 82.415 762 110 10 909 1669 18256910 18257648 0.000000e+00 643
31 TraesCS5A01G379100 chr4B 91.579 95 8 0 575 669 18251849 18251943 6.100000e-27 132
32 TraesCS5A01G379100 chr1D 85.690 594 76 7 962 1549 36392845 36392255 3.840000e-173 617
33 TraesCS5A01G379100 chr4A 87.194 531 34 13 2185 2710 648469787 648470288 8.430000e-160 573
34 TraesCS5A01G379100 chr2B 85.968 563 47 12 43 583 83661943 83662495 8.430000e-160 573
35 TraesCS5A01G379100 chr2B 77.293 458 77 22 132 569 638266505 638266055 7.510000e-61 244
36 TraesCS5A01G379100 chr2B 84.889 225 31 3 351 574 384087874 384087652 9.780000e-55 224
37 TraesCS5A01G379100 chr2B 75.357 560 89 26 40 575 637769606 637769072 9.780000e-55 224
38 TraesCS5A01G379100 chr2B 93.600 125 7 1 2031 2155 387105742 387105619 4.610000e-43 185
39 TraesCS5A01G379100 chr2A 97.041 338 8 2 41 376 733696525 733696862 3.920000e-158 568
40 TraesCS5A01G379100 chr2A 93.651 126 6 2 2030 2155 495957946 495957823 1.280000e-43 187
41 TraesCS5A01G379100 chr3D 86.767 529 36 15 2185 2708 550506782 550507281 2.360000e-155 558
42 TraesCS5A01G379100 chr3D 94.531 128 7 0 2029 2156 607000664 607000537 5.930000e-47 198
43 TraesCS5A01G379100 chr3D 96.581 117 4 0 2039 2155 337959509 337959625 7.670000e-46 195
44 TraesCS5A01G379100 chr6D 95.161 124 6 0 2033 2156 348647332 348647455 2.130000e-46 196
45 TraesCS5A01G379100 chr7D 93.750 128 5 3 2038 2163 241094122 241094248 3.570000e-44 189
46 TraesCS5A01G379100 chr7A 93.077 130 8 1 2029 2158 214220665 214220793 3.570000e-44 189
47 TraesCS5A01G379100 chr1A 93.130 131 6 3 2029 2158 266770372 266770500 3.570000e-44 189


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 TraesCS5A01G379100 chr5A 576281651 576284364 2713 False 5012.0 5012 100.0000 1 2714 1 chr5A.!!$F2 2713
1 TraesCS5A01G379100 chr5A 34715732 34716461 729 True 641.0 641 82.5680 905 1642 1 chr5A.!!$R1 737
2 TraesCS5A01G379100 chr5D 324753934 324754964 1030 False 506.5 870 88.6130 575 1669 2 chr5D.!!$F1 1094
3 TraesCS5A01G379100 chr7B 64479962 64480463 501 True 568.0 568 87.0060 2185 2710 1 chr7B.!!$R1 525
4 TraesCS5A01G379100 chr7B 506601683 506602713 1030 True 484.5 837 87.2480 575 1669 2 chr7B.!!$R2 1094
5 TraesCS5A01G379100 chrUn 98016504 98017449 945 False 615.5 787 90.3640 1659 2714 2 chrUn.!!$F1 1055
6 TraesCS5A01G379100 chrUn 68527070 68528007 937 True 606.5 793 90.0415 1659 2714 2 chrUn.!!$R1 1055
7 TraesCS5A01G379100 chr3B 795219267 795220270 1003 False 757.0 784 93.8495 1534 2648 2 chr3B.!!$F1 1114
8 TraesCS5A01G379100 chr6B 551925750 551926752 1002 False 750.5 767 93.6550 1534 2648 2 chr6B.!!$F2 1114
9 TraesCS5A01G379100 chr2D 349929478 349930205 727 False 760.0 760 85.6160 826 1549 1 chr2D.!!$F1 723
10 TraesCS5A01G379100 chr2D 131447120 131447621 501 True 549.0 549 86.4150 2185 2709 1 chr2D.!!$R1 524
11 TraesCS5A01G379100 chr5B 483526239 483526965 726 False 725.0 725 84.7950 826 1549 1 chr5B.!!$F1 723
12 TraesCS5A01G379100 chr5B 698115818 698116358 540 False 667.0 667 89.6490 41 558 1 chr5B.!!$F4 517
13 TraesCS5A01G379100 chr5B 273182742 273183535 793 False 442.0 529 86.6560 1040 1535 2 chr5B.!!$F5 495
14 TraesCS5A01G379100 chr6A 466222151 466222715 564 True 643.0 643 88.0280 41 580 1 chr6A.!!$R1 539
15 TraesCS5A01G379100 chr4B 18256910 18257648 738 False 643.0 643 82.4150 909 1669 1 chr4B.!!$F2 760
16 TraesCS5A01G379100 chr1D 36392255 36392845 590 True 617.0 617 85.6900 962 1549 1 chr1D.!!$R1 587
17 TraesCS5A01G379100 chr4A 648469787 648470288 501 False 573.0 573 87.1940 2185 2710 1 chr4A.!!$F1 525
18 TraesCS5A01G379100 chr2B 83661943 83662495 552 False 573.0 573 85.9680 43 583 1 chr2B.!!$F1 540
19 TraesCS5A01G379100 chr2B 637769072 637769606 534 True 224.0 224 75.3570 40 575 1 chr2B.!!$R3 535

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
109 112 0.248054 GTGTGTGTGCTGTGTTTCCG 60.248 55.0 0.0 0.0 0.0 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2041 2440 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.0 13.64 4.95 46.06 4.2 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
21 22 1.268625 CCCAAACAAAGGGTTCTACGC 59.731 52.381 0.00 0.00 41.61 4.42
22 23 2.227194 CCAAACAAAGGGTTCTACGCT 58.773 47.619 0.00 0.00 43.70 5.07
27 28 2.768046 AAGGGTTCTACGCTTCCCA 58.232 52.632 3.61 0.00 46.59 4.37
28 29 1.286248 AAGGGTTCTACGCTTCCCAT 58.714 50.000 3.61 0.00 46.59 4.00
29 30 0.831307 AGGGTTCTACGCTTCCCATC 59.169 55.000 0.00 0.00 38.28 3.51
30 31 0.831307 GGGTTCTACGCTTCCCATCT 59.169 55.000 0.00 0.00 39.68 2.90
31 32 1.209747 GGGTTCTACGCTTCCCATCTT 59.790 52.381 0.00 0.00 39.68 2.40
32 33 2.433239 GGGTTCTACGCTTCCCATCTTA 59.567 50.000 0.00 0.00 39.68 2.10
33 34 3.071167 GGGTTCTACGCTTCCCATCTTAT 59.929 47.826 0.00 0.00 39.68 1.73
34 35 4.444449 GGGTTCTACGCTTCCCATCTTATT 60.444 45.833 0.00 0.00 39.68 1.40
35 36 5.123936 GGTTCTACGCTTCCCATCTTATTT 58.876 41.667 0.00 0.00 0.00 1.40
36 37 5.236695 GGTTCTACGCTTCCCATCTTATTTC 59.763 44.000 0.00 0.00 0.00 2.17
37 38 5.607939 TCTACGCTTCCCATCTTATTTCA 57.392 39.130 0.00 0.00 0.00 2.69
38 39 5.357257 TCTACGCTTCCCATCTTATTTCAC 58.643 41.667 0.00 0.00 0.00 3.18
93 96 0.391661 CATAGCCAGCCTTCGTGTGT 60.392 55.000 0.00 0.00 0.00 3.72
98 101 1.643292 CAGCCTTCGTGTGTGTGTG 59.357 57.895 0.00 0.00 0.00 3.82
99 102 2.180204 AGCCTTCGTGTGTGTGTGC 61.180 57.895 0.00 0.00 0.00 4.57
109 112 0.248054 GTGTGTGTGCTGTGTTTCCG 60.248 55.000 0.00 0.00 0.00 4.30
189 199 1.079819 GCTAGCTTCGCACTGGTGA 60.080 57.895 7.70 0.00 0.00 4.02
329 390 2.421739 GAGCAGACACACGTGGGT 59.578 61.111 26.36 26.36 34.19 4.51
364 425 1.065053 CCCGTGGAGAGAGAGAGAGAA 60.065 57.143 0.00 0.00 0.00 2.87
428 496 0.387565 AACGGTCAAAACCATGCCAC 59.612 50.000 0.00 0.00 46.86 5.01
442 510 1.029408 TGCCACGTCAGCACAAAACT 61.029 50.000 5.70 0.00 34.69 2.66
473 541 7.486407 AGCAGTTTGAGGGATGAAAAATATT 57.514 32.000 0.00 0.00 0.00 1.28
511 579 7.086685 TGAGGGACTAGATTTTACTGGTTTT 57.913 36.000 0.00 0.00 41.55 2.43
512 580 8.209802 TGAGGGACTAGATTTTACTGGTTTTA 57.790 34.615 0.00 0.00 41.55 1.52
513 581 8.098912 TGAGGGACTAGATTTTACTGGTTTTAC 58.901 37.037 0.00 0.00 41.55 2.01
514 582 7.981142 AGGGACTAGATTTTACTGGTTTTACA 58.019 34.615 0.00 0.00 36.02 2.41
515 583 8.101419 AGGGACTAGATTTTACTGGTTTTACAG 58.899 37.037 0.00 0.00 40.27 2.74
528 596 7.745620 CTGGTTTTACAGTTGAAGGACTATT 57.254 36.000 0.00 0.00 33.81 1.73
529 597 8.166422 CTGGTTTTACAGTTGAAGGACTATTT 57.834 34.615 0.00 0.00 33.81 1.40
530 598 8.161699 TGGTTTTACAGTTGAAGGACTATTTC 57.838 34.615 0.00 0.00 0.00 2.17
531 599 7.996644 TGGTTTTACAGTTGAAGGACTATTTCT 59.003 33.333 0.00 0.00 0.00 2.52
532 600 9.498176 GGTTTTACAGTTGAAGGACTATTTCTA 57.502 33.333 0.00 0.00 0.00 2.10
558 626 7.893124 ACTATCAGAATAGTTAAGGGACGAA 57.107 36.000 0.00 0.00 44.62 3.85
559 627 8.302515 ACTATCAGAATAGTTAAGGGACGAAA 57.697 34.615 0.00 0.00 44.62 3.46
560 628 8.755977 ACTATCAGAATAGTTAAGGGACGAAAA 58.244 33.333 0.00 0.00 44.62 2.29
561 629 9.595823 CTATCAGAATAGTTAAGGGACGAAAAA 57.404 33.333 0.00 0.00 31.81 1.94
608 676 3.057104 CCTGAACACACGGTGAGTATGTA 60.057 47.826 16.29 0.30 40.02 2.29
609 677 3.904571 TGAACACACGGTGAGTATGTAC 58.095 45.455 16.29 4.44 40.02 2.90
612 680 2.230508 ACACACGGTGAGTATGTACAGG 59.769 50.000 16.29 0.00 38.97 4.00
627 695 1.743252 CAGGGCAAAGCGAGGAGAC 60.743 63.158 0.00 0.00 0.00 3.36
631 699 1.168714 GGCAAAGCGAGGAGACAAAT 58.831 50.000 0.00 0.00 0.00 2.32
648 716 7.417456 GGAGACAAATACAAACCAAAAGGACTT 60.417 37.037 0.00 0.00 0.00 3.01
669 737 1.167851 ACGTGTTGCAATGCTATGCT 58.832 45.000 6.82 0.00 46.54 3.79
670 738 2.355197 ACGTGTTGCAATGCTATGCTA 58.645 42.857 6.82 5.32 46.54 3.49
671 739 2.945008 ACGTGTTGCAATGCTATGCTAT 59.055 40.909 6.82 0.00 46.54 2.97
672 740 4.126437 ACGTGTTGCAATGCTATGCTATA 58.874 39.130 6.82 4.04 46.54 1.31
673 741 4.574421 ACGTGTTGCAATGCTATGCTATAA 59.426 37.500 6.82 0.04 46.54 0.98
674 742 5.065859 ACGTGTTGCAATGCTATGCTATAAA 59.934 36.000 6.82 0.00 46.54 1.40
675 743 5.970612 CGTGTTGCAATGCTATGCTATAAAA 59.029 36.000 6.82 0.00 46.54 1.52
676 744 6.471841 CGTGTTGCAATGCTATGCTATAAAAA 59.528 34.615 6.82 0.00 46.54 1.94
677 745 7.513505 CGTGTTGCAATGCTATGCTATAAAAAC 60.514 37.037 6.82 9.68 46.54 2.43
678 746 7.489113 GTGTTGCAATGCTATGCTATAAAAACT 59.511 33.333 6.82 0.00 46.54 2.66
679 747 7.488792 TGTTGCAATGCTATGCTATAAAAACTG 59.511 33.333 6.82 0.00 46.54 3.16
680 748 7.332213 TGCAATGCTATGCTATAAAAACTGA 57.668 32.000 6.82 0.00 46.54 3.41
681 749 7.770201 TGCAATGCTATGCTATAAAAACTGAA 58.230 30.769 6.82 0.00 46.54 3.02
682 750 8.249638 TGCAATGCTATGCTATAAAAACTGAAA 58.750 29.630 6.82 0.00 46.54 2.69
683 751 9.252962 GCAATGCTATGCTATAAAAACTGAAAT 57.747 29.630 0.00 0.00 43.06 2.17
692 760 9.283768 TGCTATAAAAACTGAAATGAAGTCAGA 57.716 29.630 8.36 0.00 44.44 3.27
703 771 9.713740 CTGAAATGAAGTCAGAAGTAATTATGC 57.286 33.333 0.00 0.00 44.44 3.14
704 772 9.230122 TGAAATGAAGTCAGAAGTAATTATGCA 57.770 29.630 0.00 0.00 0.00 3.96
707 775 7.076842 TGAAGTCAGAAGTAATTATGCAAGC 57.923 36.000 0.00 0.00 0.00 4.01
708 776 6.654582 TGAAGTCAGAAGTAATTATGCAAGCA 59.345 34.615 0.00 0.00 0.00 3.91
709 777 7.174772 TGAAGTCAGAAGTAATTATGCAAGCAA 59.825 33.333 0.00 0.00 0.00 3.91
710 778 7.081526 AGTCAGAAGTAATTATGCAAGCAAG 57.918 36.000 0.00 0.00 0.00 4.01
711 779 6.881065 AGTCAGAAGTAATTATGCAAGCAAGA 59.119 34.615 0.00 0.00 0.00 3.02
712 780 7.065563 AGTCAGAAGTAATTATGCAAGCAAGAG 59.934 37.037 0.00 0.00 0.00 2.85
713 781 7.065085 GTCAGAAGTAATTATGCAAGCAAGAGA 59.935 37.037 0.00 0.00 0.00 3.10
721 789 3.698029 TGCAAGCAAGAGAAAACAGAC 57.302 42.857 0.00 0.00 0.00 3.51
734 802 7.283329 AGAGAAAACAGACACCTTGTAGATTT 58.717 34.615 0.00 0.00 0.00 2.17
747 815 5.067413 CCTTGTAGATTTCATGCTCATGCTT 59.933 40.000 5.04 0.00 38.65 3.91
753 821 1.035385 TCATGCTCATGCTTGCCAGG 61.035 55.000 5.04 0.00 42.07 4.45
768 836 5.070981 GCTTGCCAGGATAGCCTCATATATA 59.929 44.000 0.00 0.00 44.80 0.86
800 868 7.572523 TCTTCCAGGCTAACATTATTTGATG 57.427 36.000 0.00 0.00 0.00 3.07
801 869 6.547141 TCTTCCAGGCTAACATTATTTGATGG 59.453 38.462 0.00 0.00 0.00 3.51
802 870 5.765510 TCCAGGCTAACATTATTTGATGGT 58.234 37.500 0.00 0.00 0.00 3.55
804 872 6.321181 TCCAGGCTAACATTATTTGATGGTTC 59.679 38.462 0.00 0.00 0.00 3.62
806 874 7.201938 CCAGGCTAACATTATTTGATGGTTCAT 60.202 37.037 0.00 0.00 0.00 2.57
807 875 8.199449 CAGGCTAACATTATTTGATGGTTCATT 58.801 33.333 0.00 0.00 0.00 2.57
808 876 8.416329 AGGCTAACATTATTTGATGGTTCATTC 58.584 33.333 0.00 0.00 0.00 2.67
809 877 8.196771 GGCTAACATTATTTGATGGTTCATTCA 58.803 33.333 0.00 0.00 0.00 2.57
841 910 9.612620 GTTGTTCTTTTGGATTCACTACATTAG 57.387 33.333 0.00 0.00 0.00 1.73
875 944 9.382275 ACATCAGTTTCTTTTGTGCTTTAAAAT 57.618 25.926 0.00 0.00 0.00 1.82
991 1062 7.475771 TTTGTTTAATTTCATTTTCAGCGCT 57.524 28.000 2.64 2.64 0.00 5.92
994 1065 6.699204 TGTTTAATTTCATTTTCAGCGCTGAA 59.301 30.769 41.19 41.19 46.72 3.02
1023 1094 1.071385 CCGCTTGAAGATATGGAGGCT 59.929 52.381 0.00 0.00 0.00 4.58
1037 1108 3.114606 TGGAGGCTCCAAATCTATGTCA 58.885 45.455 33.38 5.68 45.00 3.58
1043 1114 3.624707 GCTCCAAATCTATGTCAACCCCA 60.625 47.826 0.00 0.00 0.00 4.96
1061 1132 3.325135 CCCCATCTTGGTGATACCTCTAC 59.675 52.174 0.00 0.00 39.58 2.59
1063 1134 3.325135 CCATCTTGGTGATACCTCTACCC 59.675 52.174 0.00 0.00 39.58 3.69
1067 1138 1.848388 TGGTGATACCTCTACCCGAGA 59.152 52.381 0.00 0.00 42.62 4.04
1076 1147 0.683504 TCTACCCGAGACCCTCTTGC 60.684 60.000 0.00 0.00 0.00 4.01
1154 1225 9.502091 AGGTAATTGCGAGCATAATTTCTTATA 57.498 29.630 0.00 0.00 0.00 0.98
1234 1604 4.568072 TGTAACATTGGTAGCCTCACAT 57.432 40.909 0.00 0.00 0.00 3.21
1254 1624 2.766736 TGACCTTACCCCGTATGGATT 58.233 47.619 1.27 0.00 36.97 3.01
1256 1626 3.524380 TGACCTTACCCCGTATGGATTTT 59.476 43.478 1.27 0.00 36.97 1.82
1262 1632 1.684869 CCCCGTATGGATTTTGCTGGT 60.685 52.381 1.27 0.00 37.49 4.00
1306 1676 3.686016 ACACCGACATAGCAAGGAAAAT 58.314 40.909 0.00 0.00 0.00 1.82
1312 1682 5.335583 CCGACATAGCAAGGAAAATGAAACA 60.336 40.000 0.00 0.00 0.00 2.83
1333 1703 0.867746 TCGATGCGATAAATGCCAGC 59.132 50.000 0.00 0.00 0.00 4.85
1335 1705 0.953727 GATGCGATAAATGCCAGCCA 59.046 50.000 0.00 0.00 0.00 4.75
1337 1707 0.455410 TGCGATAAATGCCAGCCAAC 59.545 50.000 0.00 0.00 0.00 3.77
1338 1708 0.455410 GCGATAAATGCCAGCCAACA 59.545 50.000 0.00 0.00 0.00 3.33
1351 1721 1.677552 CCAACACCCTCTTAGCGGT 59.322 57.895 0.00 0.00 0.00 5.68
1374 1744 6.268847 GGTATCTCCACTATTGATCAACTCCT 59.731 42.308 11.07 0.00 35.97 3.69
1434 1807 6.349280 CGAAAGGGCAATTCTTGATGTCTAAA 60.349 38.462 0.00 0.00 0.00 1.85
1512 1885 2.198827 TTCCACAAGAACCATCGCAT 57.801 45.000 0.00 0.00 0.00 4.73
1517 1890 0.742505 CAAGAACCATCGCATGCCAT 59.257 50.000 13.15 0.78 0.00 4.40
1549 1943 2.933906 CGTAACATGCCAGATACGGTTT 59.066 45.455 0.00 0.00 36.85 3.27
1550 1944 4.114073 CGTAACATGCCAGATACGGTTTA 58.886 43.478 0.00 0.00 36.85 2.01
1551 1945 4.567558 CGTAACATGCCAGATACGGTTTAA 59.432 41.667 0.00 0.00 36.85 1.52
1552 1946 5.276678 CGTAACATGCCAGATACGGTTTAAG 60.277 44.000 0.00 0.00 36.85 1.85
1553 1947 3.541632 ACATGCCAGATACGGTTTAAGG 58.458 45.455 0.00 0.00 0.00 2.69
1554 1948 3.054655 ACATGCCAGATACGGTTTAAGGT 60.055 43.478 0.00 0.00 0.00 3.50
1555 1949 4.162698 ACATGCCAGATACGGTTTAAGGTA 59.837 41.667 0.00 0.00 0.00 3.08
1556 1950 4.127566 TGCCAGATACGGTTTAAGGTAC 57.872 45.455 0.00 0.00 0.00 3.34
1558 1952 4.117685 GCCAGATACGGTTTAAGGTACTG 58.882 47.826 0.00 0.00 40.86 2.74
1559 1953 4.117685 CCAGATACGGTTTAAGGTACTGC 58.882 47.826 0.00 0.00 40.86 4.40
1560 1954 4.142004 CCAGATACGGTTTAAGGTACTGCT 60.142 45.833 0.00 0.00 40.86 4.24
1561 1955 4.804139 CAGATACGGTTTAAGGTACTGCTG 59.196 45.833 0.00 0.00 40.86 4.41
1562 1956 4.708421 AGATACGGTTTAAGGTACTGCTGA 59.292 41.667 0.00 0.00 40.86 4.26
1563 1957 3.975168 ACGGTTTAAGGTACTGCTGAT 57.025 42.857 0.00 0.00 40.86 2.90
1564 1958 6.548622 AGATACGGTTTAAGGTACTGCTGATA 59.451 38.462 0.00 0.00 40.86 2.15
1565 1959 4.752146 ACGGTTTAAGGTACTGCTGATAC 58.248 43.478 0.00 0.00 40.86 2.24
1566 1960 4.221262 ACGGTTTAAGGTACTGCTGATACA 59.779 41.667 0.00 0.00 40.86 2.29
1567 1961 5.172934 CGGTTTAAGGTACTGCTGATACAA 58.827 41.667 0.00 0.00 40.86 2.41
1568 1962 5.815740 CGGTTTAAGGTACTGCTGATACAAT 59.184 40.000 0.00 0.00 40.86 2.71
1569 1963 6.315393 CGGTTTAAGGTACTGCTGATACAATT 59.685 38.462 0.00 0.00 40.86 2.32
1580 1974 6.996282 ACTGCTGATACAATTCATGATGATGA 59.004 34.615 3.32 0.00 36.78 2.92
1716 2112 7.824289 CACAAGAACAAAGGGATAAGATAGACA 59.176 37.037 0.00 0.00 0.00 3.41
1811 2207 8.243426 TCCACTTATTATGTGCATTTTGACTTC 58.757 33.333 0.00 0.00 34.38 3.01
1929 2328 9.015146 AGGAAATTCCCCTCTTTAATAGTACAT 57.985 33.333 8.66 0.00 37.19 2.29
2034 2433 7.454260 AATTTGTGTCCCAGACTTTCTAATC 57.546 36.000 0.00 0.00 33.15 1.75
2040 2439 5.100943 GTCCCAGACTTTCTAATCACGTAC 58.899 45.833 0.00 0.00 0.00 3.67
2041 2440 5.014858 TCCCAGACTTTCTAATCACGTACT 58.985 41.667 0.00 0.00 0.00 2.73
2042 2441 5.125097 TCCCAGACTTTCTAATCACGTACTC 59.875 44.000 0.00 0.00 0.00 2.59
2043 2442 5.341617 CCAGACTTTCTAATCACGTACTCC 58.658 45.833 0.00 0.00 0.00 3.85
2044 2443 5.341617 CAGACTTTCTAATCACGTACTCCC 58.658 45.833 0.00 0.00 0.00 4.30
2045 2444 5.125739 CAGACTTTCTAATCACGTACTCCCT 59.874 44.000 0.00 0.00 0.00 4.20
2046 2445 5.357596 AGACTTTCTAATCACGTACTCCCTC 59.642 44.000 0.00 0.00 0.00 4.30
2047 2446 4.401837 ACTTTCTAATCACGTACTCCCTCC 59.598 45.833 0.00 0.00 0.00 4.30
2048 2447 2.569059 TCTAATCACGTACTCCCTCCG 58.431 52.381 0.00 0.00 0.00 4.63
2049 2448 2.092753 TCTAATCACGTACTCCCTCCGT 60.093 50.000 0.00 0.00 34.71 4.69
2050 2449 1.101331 AATCACGTACTCCCTCCGTC 58.899 55.000 0.00 0.00 31.46 4.79
2051 2450 0.750911 ATCACGTACTCCCTCCGTCC 60.751 60.000 0.00 0.00 31.46 4.79
2052 2451 2.437359 ACGTACTCCCTCCGTCCG 60.437 66.667 0.00 0.00 0.00 4.79
2053 2452 3.207669 CGTACTCCCTCCGTCCGG 61.208 72.222 0.00 0.00 0.00 5.14
2054 2453 2.273449 GTACTCCCTCCGTCCGGA 59.727 66.667 0.00 0.00 42.90 5.14
2055 2454 1.379044 GTACTCCCTCCGTCCGGAA 60.379 63.158 5.23 0.00 44.66 4.30
2056 2455 0.967380 GTACTCCCTCCGTCCGGAAA 60.967 60.000 5.23 0.00 44.66 3.13
2057 2456 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
2058 2457 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
2059 2458 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
2060 2459 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
2061 2460 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
2062 2461 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
2063 2462 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
2064 2463 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
2065 2464 1.205417 TCCGTCCGGAAATACTTGTCC 59.795 52.381 5.23 0.00 42.05 4.02
2074 2473 3.877508 GGAAATACTTGTCCGAGGAATGG 59.122 47.826 0.00 0.00 0.00 3.16
2075 2474 3.560636 AATACTTGTCCGAGGAATGGG 57.439 47.619 0.00 0.00 0.00 4.00
2076 2475 1.946984 TACTTGTCCGAGGAATGGGT 58.053 50.000 0.00 0.00 0.00 4.51
2077 2476 0.324943 ACTTGTCCGAGGAATGGGTG 59.675 55.000 0.00 0.00 0.00 4.61
2078 2477 0.324943 CTTGTCCGAGGAATGGGTGT 59.675 55.000 0.00 0.00 0.00 4.16
2079 2478 1.553248 CTTGTCCGAGGAATGGGTGTA 59.447 52.381 0.00 0.00 0.00 2.90
2080 2479 1.874129 TGTCCGAGGAATGGGTGTAT 58.126 50.000 0.00 0.00 0.00 2.29
2081 2480 1.760613 TGTCCGAGGAATGGGTGTATC 59.239 52.381 0.00 0.00 0.00 2.24
2082 2481 2.040178 GTCCGAGGAATGGGTGTATCT 58.960 52.381 0.00 0.00 0.00 1.98
2083 2482 3.228453 GTCCGAGGAATGGGTGTATCTA 58.772 50.000 0.00 0.00 0.00 1.98
2084 2483 3.256136 GTCCGAGGAATGGGTGTATCTAG 59.744 52.174 0.00 0.00 0.00 2.43
2085 2484 3.139584 TCCGAGGAATGGGTGTATCTAGA 59.860 47.826 0.00 0.00 0.00 2.43
2086 2485 4.090090 CCGAGGAATGGGTGTATCTAGAT 58.910 47.826 10.73 10.73 0.00 1.98
2087 2486 4.081972 CCGAGGAATGGGTGTATCTAGATG 60.082 50.000 15.79 0.00 0.00 2.90
2088 2487 4.524714 CGAGGAATGGGTGTATCTAGATGT 59.475 45.833 15.79 0.00 0.00 3.06
2089 2488 5.710567 CGAGGAATGGGTGTATCTAGATGTA 59.289 44.000 15.79 1.12 0.00 2.29
2090 2489 6.378564 CGAGGAATGGGTGTATCTAGATGTAT 59.621 42.308 15.79 0.00 0.00 2.29
2091 2490 7.093727 CGAGGAATGGGTGTATCTAGATGTATT 60.094 40.741 15.79 6.57 0.00 1.89
2092 2491 8.511748 AGGAATGGGTGTATCTAGATGTATTT 57.488 34.615 15.79 0.42 0.00 1.40
2093 2492 8.949421 AGGAATGGGTGTATCTAGATGTATTTT 58.051 33.333 15.79 0.90 0.00 1.82
2130 2529 9.042008 ACATCTATTTGTATCCATTTGTACGAC 57.958 33.333 0.00 0.00 0.00 4.34
2131 2530 9.040939 CATCTATTTGTATCCATTTGTACGACA 57.959 33.333 0.00 0.00 0.00 4.35
2132 2531 9.607988 ATCTATTTGTATCCATTTGTACGACAA 57.392 29.630 0.00 0.00 36.11 3.18
2133 2532 9.093970 TCTATTTGTATCCATTTGTACGACAAG 57.906 33.333 0.00 0.00 39.53 3.16
2134 2533 7.681939 ATTTGTATCCATTTGTACGACAAGT 57.318 32.000 0.00 0.00 39.53 3.16
2135 2534 8.780846 ATTTGTATCCATTTGTACGACAAGTA 57.219 30.769 0.00 0.00 39.53 2.24
2136 2535 8.780846 TTTGTATCCATTTGTACGACAAGTAT 57.219 30.769 0.00 0.00 39.53 2.12
2137 2536 8.780846 TTGTATCCATTTGTACGACAAGTATT 57.219 30.769 0.00 0.00 39.53 1.89
2138 2537 8.780846 TGTATCCATTTGTACGACAAGTATTT 57.219 30.769 0.00 0.00 39.53 1.40
2139 2538 8.875803 TGTATCCATTTGTACGACAAGTATTTC 58.124 33.333 0.00 0.00 39.53 2.17
2140 2539 6.730960 TCCATTTGTACGACAAGTATTTCC 57.269 37.500 0.00 0.00 39.53 3.13
2141 2540 5.349270 TCCATTTGTACGACAAGTATTTCCG 59.651 40.000 0.00 0.00 39.53 4.30
2142 2541 5.446741 CCATTTGTACGACAAGTATTTCCGG 60.447 44.000 0.00 0.00 39.53 5.14
2143 2542 4.517952 TTGTACGACAAGTATTTCCGGA 57.482 40.909 0.00 0.00 37.69 5.14
2144 2543 3.836949 TGTACGACAAGTATTTCCGGAC 58.163 45.455 1.83 0.00 37.69 4.79
2145 2544 3.255395 TGTACGACAAGTATTTCCGGACA 59.745 43.478 1.83 0.00 41.15 4.02
2146 2545 2.955614 ACGACAAGTATTTCCGGACAG 58.044 47.619 1.83 0.00 0.00 3.51
2147 2546 2.559668 ACGACAAGTATTTCCGGACAGA 59.440 45.455 1.83 0.00 0.00 3.41
2148 2547 3.179830 CGACAAGTATTTCCGGACAGAG 58.820 50.000 1.83 0.00 0.00 3.35
2149 2548 3.522553 GACAAGTATTTCCGGACAGAGG 58.477 50.000 1.83 0.00 0.00 3.69
2150 2549 2.236395 ACAAGTATTTCCGGACAGAGGG 59.764 50.000 1.83 0.00 0.00 4.30
2151 2550 2.500098 CAAGTATTTCCGGACAGAGGGA 59.500 50.000 1.83 0.00 0.00 4.20
2152 2551 2.389715 AGTATTTCCGGACAGAGGGAG 58.610 52.381 1.83 0.00 33.01 4.30
2153 2552 2.108970 GTATTTCCGGACAGAGGGAGT 58.891 52.381 1.83 0.00 33.01 3.85
2154 2553 2.544844 ATTTCCGGACAGAGGGAGTA 57.455 50.000 1.83 0.00 33.01 2.59
2183 2582 8.478066 TGATGCTTTCATACACTTGTATAGACT 58.522 33.333 1.53 0.00 39.06 3.24
2255 2655 9.507329 AGTACAAGACATGAATCACAAAGTAAT 57.493 29.630 0.00 0.00 0.00 1.89
2290 2690 0.178953 AATGTGAAGCTTGGCAGGGT 60.179 50.000 2.10 0.00 0.00 4.34
2350 2750 1.026584 CGCCTGCATCAATCATCCAA 58.973 50.000 0.00 0.00 0.00 3.53
2376 2777 5.827797 TCTGGTCTAACTTCATTTTGCAAGT 59.172 36.000 0.00 0.00 34.16 3.16
2395 2796 6.206438 TGCAAGTTCAGTGTGAGCAATATTTA 59.794 34.615 0.00 0.00 29.40 1.40
2522 2923 4.246458 GAGACAGTAACAGGAATGTCCAC 58.754 47.826 0.79 0.00 42.39 4.02
2534 2935 4.599241 AGGAATGTCCACCTCCATAATAGG 59.401 45.833 0.00 0.00 39.61 2.57
2577 2979 8.682936 ACATTTTGTTGTGGCCAAATTAAATA 57.317 26.923 7.24 0.00 32.28 1.40
2673 3079 3.989056 TCATATGGTGAGTGTAGGACCA 58.011 45.455 2.13 0.00 43.83 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 2.227194 AGCGTAGAACCCTTTGTTTGG 58.773 47.619 0.00 0.00 37.29 3.28
3 4 3.304458 GGAAGCGTAGAACCCTTTGTTTG 60.304 47.826 0.00 0.00 37.29 2.93
4 5 2.882761 GGAAGCGTAGAACCCTTTGTTT 59.117 45.455 0.00 0.00 37.29 2.83
5 6 2.501261 GGAAGCGTAGAACCCTTTGTT 58.499 47.619 0.00 0.00 40.81 2.83
6 7 1.271217 GGGAAGCGTAGAACCCTTTGT 60.271 52.381 0.00 0.00 39.28 2.83
7 8 1.271163 TGGGAAGCGTAGAACCCTTTG 60.271 52.381 0.00 0.00 42.49 2.77
8 9 1.061546 TGGGAAGCGTAGAACCCTTT 58.938 50.000 0.00 0.00 42.49 3.11
9 10 1.209747 GATGGGAAGCGTAGAACCCTT 59.790 52.381 0.00 0.00 42.49 3.95
10 11 0.831307 GATGGGAAGCGTAGAACCCT 59.169 55.000 0.00 0.00 42.49 4.34
11 12 0.831307 AGATGGGAAGCGTAGAACCC 59.169 55.000 0.00 0.00 42.37 4.11
12 13 2.693267 AAGATGGGAAGCGTAGAACC 57.307 50.000 0.00 0.00 0.00 3.62
13 14 5.815740 TGAAATAAGATGGGAAGCGTAGAAC 59.184 40.000 0.00 0.00 0.00 3.01
14 15 5.815740 GTGAAATAAGATGGGAAGCGTAGAA 59.184 40.000 0.00 0.00 0.00 2.10
15 16 5.105106 TGTGAAATAAGATGGGAAGCGTAGA 60.105 40.000 0.00 0.00 0.00 2.59
16 17 5.006746 GTGTGAAATAAGATGGGAAGCGTAG 59.993 44.000 0.00 0.00 0.00 3.51
17 18 4.873827 GTGTGAAATAAGATGGGAAGCGTA 59.126 41.667 0.00 0.00 0.00 4.42
18 19 3.689649 GTGTGAAATAAGATGGGAAGCGT 59.310 43.478 0.00 0.00 0.00 5.07
19 20 3.941483 AGTGTGAAATAAGATGGGAAGCG 59.059 43.478 0.00 0.00 0.00 4.68
20 21 4.943705 TCAGTGTGAAATAAGATGGGAAGC 59.056 41.667 0.00 0.00 0.00 3.86
21 22 5.939883 TGTCAGTGTGAAATAAGATGGGAAG 59.060 40.000 0.00 0.00 0.00 3.46
22 23 5.875224 TGTCAGTGTGAAATAAGATGGGAA 58.125 37.500 0.00 0.00 0.00 3.97
23 24 5.497464 TGTCAGTGTGAAATAAGATGGGA 57.503 39.130 0.00 0.00 0.00 4.37
24 25 5.106157 GGTTGTCAGTGTGAAATAAGATGGG 60.106 44.000 0.00 0.00 0.00 4.00
25 26 5.473162 TGGTTGTCAGTGTGAAATAAGATGG 59.527 40.000 0.00 0.00 0.00 3.51
26 27 6.558771 TGGTTGTCAGTGTGAAATAAGATG 57.441 37.500 0.00 0.00 0.00 2.90
27 28 6.808008 CTGGTTGTCAGTGTGAAATAAGAT 57.192 37.500 0.00 0.00 38.64 2.40
93 96 2.477176 GCCGGAAACACAGCACACA 61.477 57.895 5.05 0.00 0.00 3.72
189 199 3.254166 AGCAGCAATCAACTTGAACGATT 59.746 39.130 0.00 0.00 36.97 3.34
329 390 3.785859 GGGAGCACCTCGCCATGA 61.786 66.667 0.00 0.00 44.04 3.07
364 425 1.631388 TCACCTTCGTCTCTCTCTCCT 59.369 52.381 0.00 0.00 0.00 3.69
428 496 4.466828 CTTTGGATAGTTTTGTGCTGACG 58.533 43.478 0.00 0.00 0.00 4.35
442 510 4.018506 TCATCCCTCAAACTGCTTTGGATA 60.019 41.667 0.00 0.00 37.87 2.59
473 541 2.882137 GTCCCTCAATTGTTGAAACCGA 59.118 45.455 5.13 0.00 39.58 4.69
535 603 9.595823 TTTTTCGTCCCTTAACTATTCTGATAG 57.404 33.333 0.00 0.00 40.91 2.08
549 617 9.649316 TTGGGATAAATATATTTTTCGTCCCTT 57.351 29.630 28.33 7.66 40.68 3.95
550 618 9.649316 TTTGGGATAAATATATTTTTCGTCCCT 57.351 29.630 28.33 8.16 40.68 4.20
567 635 9.928618 TGTTCAGGTGATATTATTTTGGGATAA 57.071 29.630 0.00 0.00 0.00 1.75
568 636 9.349713 GTGTTCAGGTGATATTATTTTGGGATA 57.650 33.333 0.00 0.00 0.00 2.59
569 637 7.838696 TGTGTTCAGGTGATATTATTTTGGGAT 59.161 33.333 0.00 0.00 0.00 3.85
570 638 7.122055 GTGTGTTCAGGTGATATTATTTTGGGA 59.878 37.037 0.00 0.00 0.00 4.37
571 639 7.257722 GTGTGTTCAGGTGATATTATTTTGGG 58.742 38.462 0.00 0.00 0.00 4.12
572 640 6.966632 CGTGTGTTCAGGTGATATTATTTTGG 59.033 38.462 0.00 0.00 0.00 3.28
573 641 6.966632 CCGTGTGTTCAGGTGATATTATTTTG 59.033 38.462 0.00 0.00 0.00 2.44
608 676 2.217038 TCTCCTCGCTTTGCCCTGT 61.217 57.895 0.00 0.00 0.00 4.00
609 677 1.743252 GTCTCCTCGCTTTGCCCTG 60.743 63.158 0.00 0.00 0.00 4.45
612 680 1.168714 ATTTGTCTCCTCGCTTTGCC 58.831 50.000 0.00 0.00 0.00 4.52
627 695 7.703197 ACGTAAAGTCCTTTTGGTTTGTATTTG 59.297 33.333 0.00 0.00 41.38 2.32
631 699 5.647225 ACACGTAAAGTCCTTTTGGTTTGTA 59.353 36.000 0.00 0.00 41.38 2.41
648 716 2.746904 AGCATAGCATTGCAACACGTAA 59.253 40.909 11.91 0.00 45.23 3.18
677 745 9.713740 GCATAATTACTTCTGACTTCATTTCAG 57.286 33.333 0.00 0.00 41.72 3.02
678 746 9.230122 TGCATAATTACTTCTGACTTCATTTCA 57.770 29.630 0.00 0.00 0.00 2.69
681 749 8.186821 GCTTGCATAATTACTTCTGACTTCATT 58.813 33.333 0.00 0.00 0.00 2.57
682 750 7.337689 TGCTTGCATAATTACTTCTGACTTCAT 59.662 33.333 0.00 0.00 0.00 2.57
683 751 6.654582 TGCTTGCATAATTACTTCTGACTTCA 59.345 34.615 0.00 0.00 0.00 3.02
684 752 7.076842 TGCTTGCATAATTACTTCTGACTTC 57.923 36.000 0.00 0.00 0.00 3.01
685 753 7.391554 TCTTGCTTGCATAATTACTTCTGACTT 59.608 33.333 0.00 0.00 0.00 3.01
686 754 6.881065 TCTTGCTTGCATAATTACTTCTGACT 59.119 34.615 0.00 0.00 0.00 3.41
687 755 7.065085 TCTCTTGCTTGCATAATTACTTCTGAC 59.935 37.037 0.00 0.00 0.00 3.51
688 756 7.105588 TCTCTTGCTTGCATAATTACTTCTGA 58.894 34.615 0.00 0.00 0.00 3.27
689 757 7.312657 TCTCTTGCTTGCATAATTACTTCTG 57.687 36.000 0.00 0.00 0.00 3.02
690 758 7.928307 TTCTCTTGCTTGCATAATTACTTCT 57.072 32.000 0.00 0.00 0.00 2.85
691 759 8.854312 GTTTTCTCTTGCTTGCATAATTACTTC 58.146 33.333 0.00 0.00 0.00 3.01
692 760 8.359642 TGTTTTCTCTTGCTTGCATAATTACTT 58.640 29.630 0.00 0.00 0.00 2.24
693 761 7.885297 TGTTTTCTCTTGCTTGCATAATTACT 58.115 30.769 0.00 0.00 0.00 2.24
694 762 8.023128 TCTGTTTTCTCTTGCTTGCATAATTAC 58.977 33.333 0.00 0.00 0.00 1.89
695 763 8.023128 GTCTGTTTTCTCTTGCTTGCATAATTA 58.977 33.333 0.00 0.00 0.00 1.40
696 764 6.865205 GTCTGTTTTCTCTTGCTTGCATAATT 59.135 34.615 0.00 0.00 0.00 1.40
697 765 6.016024 TGTCTGTTTTCTCTTGCTTGCATAAT 60.016 34.615 0.00 0.00 0.00 1.28
698 766 5.299028 TGTCTGTTTTCTCTTGCTTGCATAA 59.701 36.000 0.00 0.00 0.00 1.90
699 767 4.821260 TGTCTGTTTTCTCTTGCTTGCATA 59.179 37.500 0.00 0.00 0.00 3.14
700 768 3.633525 TGTCTGTTTTCTCTTGCTTGCAT 59.366 39.130 0.00 0.00 0.00 3.96
701 769 3.016031 TGTCTGTTTTCTCTTGCTTGCA 58.984 40.909 0.00 0.00 0.00 4.08
702 770 3.366719 GTGTCTGTTTTCTCTTGCTTGC 58.633 45.455 0.00 0.00 0.00 4.01
703 771 3.629398 AGGTGTCTGTTTTCTCTTGCTTG 59.371 43.478 0.00 0.00 0.00 4.01
704 772 3.891049 AGGTGTCTGTTTTCTCTTGCTT 58.109 40.909 0.00 0.00 0.00 3.91
705 773 3.567478 AGGTGTCTGTTTTCTCTTGCT 57.433 42.857 0.00 0.00 0.00 3.91
706 774 3.378427 ACAAGGTGTCTGTTTTCTCTTGC 59.622 43.478 0.00 0.00 35.05 4.01
707 775 6.049149 TCTACAAGGTGTCTGTTTTCTCTTG 58.951 40.000 0.00 0.00 36.96 3.02
708 776 6.235231 TCTACAAGGTGTCTGTTTTCTCTT 57.765 37.500 0.00 0.00 0.00 2.85
709 777 5.871396 TCTACAAGGTGTCTGTTTTCTCT 57.129 39.130 0.00 0.00 0.00 3.10
710 778 7.226720 TGAAATCTACAAGGTGTCTGTTTTCTC 59.773 37.037 13.13 0.00 31.58 2.87
711 779 7.054124 TGAAATCTACAAGGTGTCTGTTTTCT 58.946 34.615 13.13 0.00 31.58 2.52
712 780 7.259290 TGAAATCTACAAGGTGTCTGTTTTC 57.741 36.000 0.00 0.00 31.30 2.29
713 781 7.651808 CATGAAATCTACAAGGTGTCTGTTTT 58.348 34.615 0.00 0.00 0.00 2.43
721 789 5.732528 GCATGAGCATGAAATCTACAAGGTG 60.733 44.000 14.27 0.00 41.20 4.00
734 802 1.035385 CCTGGCAAGCATGAGCATGA 61.035 55.000 14.27 0.00 41.78 3.07
747 815 6.384603 TGATATATATGAGGCTATCCTGGCA 58.615 40.000 0.00 0.00 44.46 4.92
811 879 9.295825 TGTAGTGAATCCAAAAGAACAACATAT 57.704 29.630 0.00 0.00 0.00 1.78
815 883 9.612620 CTAATGTAGTGAATCCAAAAGAACAAC 57.387 33.333 0.00 0.00 0.00 3.32
816 884 9.349713 ACTAATGTAGTGAATCCAAAAGAACAA 57.650 29.630 0.00 0.00 37.69 2.83
841 910 9.922305 GCACAAAAGAAACTGATGTATATCTAC 57.078 33.333 0.89 0.00 34.31 2.59
843 912 8.798859 AGCACAAAAGAAACTGATGTATATCT 57.201 30.769 0.89 0.00 34.31 1.98
844 913 9.846248 AAAGCACAAAAGAAACTGATGTATATC 57.154 29.630 0.00 0.00 0.00 1.63
871 940 8.290325 TGCGTGTTTTTCCAAAACTAAAATTTT 58.710 25.926 8.75 8.75 31.87 1.82
873 942 7.095187 TGTGCGTGTTTTTCCAAAACTAAAATT 60.095 29.630 12.15 0.00 0.00 1.82
875 944 5.694910 TGTGCGTGTTTTTCCAAAACTAAAA 59.305 32.000 12.15 0.00 0.00 1.52
876 945 5.227908 TGTGCGTGTTTTTCCAAAACTAAA 58.772 33.333 12.15 0.00 0.00 1.85
929 999 6.049955 AGTTAGCTTACATAACTGCCTTCA 57.950 37.500 5.55 0.00 40.94 3.02
985 1055 1.136147 GCATGGTCTTTCAGCGCTG 59.864 57.895 31.53 31.53 0.00 5.18
991 1062 0.250684 TCAAGCGGCATGGTCTTTCA 60.251 50.000 5.28 0.00 0.00 2.69
994 1065 0.036732 TCTTCAAGCGGCATGGTCTT 59.963 50.000 5.28 0.00 0.00 3.01
1023 1094 4.478317 AGATGGGGTTGACATAGATTTGGA 59.522 41.667 0.00 0.00 0.00 3.53
1032 1103 1.710244 TCACCAAGATGGGGTTGACAT 59.290 47.619 0.00 0.00 42.97 3.06
1035 1106 2.241176 GGTATCACCAAGATGGGGTTGA 59.759 50.000 0.00 0.00 42.97 3.18
1037 1108 2.509964 GAGGTATCACCAAGATGGGGTT 59.490 50.000 0.00 0.00 42.97 4.11
1043 1114 3.117246 TCGGGTAGAGGTATCACCAAGAT 60.117 47.826 0.00 0.00 41.95 2.40
1061 1132 1.984570 TCAGCAAGAGGGTCTCGGG 60.985 63.158 0.00 0.00 35.36 5.14
1063 1134 0.534412 ATGTCAGCAAGAGGGTCTCG 59.466 55.000 0.00 0.00 35.36 4.04
1067 1138 1.949799 AGAGATGTCAGCAAGAGGGT 58.050 50.000 0.00 0.00 0.00 4.34
1076 1147 8.834749 ATGATGATCAACATTAGAGATGTCAG 57.165 34.615 12.35 0.00 39.56 3.51
1127 1198 6.699575 AGAAATTATGCTCGCAATTACCTT 57.300 33.333 0.00 0.00 0.00 3.50
1197 1268 8.868916 CCAATGTTACAACCATTTAATAACAGC 58.131 33.333 0.00 0.00 38.69 4.40
1234 1604 2.482414 ATCCATACGGGGTAAGGTCA 57.518 50.000 0.00 0.00 37.22 4.02
1254 1624 4.187506 AGGTTTACCCTTTACCAGCAAA 57.812 40.909 0.00 0.00 42.73 3.68
1306 1676 4.969395 GCATTTATCGCATCGATTGTTTCA 59.031 37.500 7.04 0.00 44.59 2.69
1312 1682 2.095567 GCTGGCATTTATCGCATCGATT 60.096 45.455 7.04 0.00 44.59 3.34
1333 1703 0.899720 TACCGCTAAGAGGGTGTTGG 59.100 55.000 0.00 0.00 37.09 3.77
1335 1705 2.694109 GAGATACCGCTAAGAGGGTGTT 59.306 50.000 0.00 0.00 37.09 3.32
1337 1707 1.614413 GGAGATACCGCTAAGAGGGTG 59.386 57.143 0.00 0.00 37.09 4.61
1338 1708 1.217183 TGGAGATACCGCTAAGAGGGT 59.783 52.381 0.00 0.00 42.61 4.34
1351 1721 7.069344 TGAGGAGTTGATCAATAGTGGAGATA 58.931 38.462 12.12 0.00 0.00 1.98
1425 1798 5.889289 AGAGTACCTCCAGACTTTAGACATC 59.111 44.000 0.00 0.00 0.00 3.06
1505 1878 3.063588 GTCAGATATCATGGCATGCGATG 59.936 47.826 30.39 30.39 34.19 3.84
1512 1885 3.386402 TGTTACGGTCAGATATCATGGCA 59.614 43.478 5.32 0.00 0.00 4.92
1517 1890 3.386402 TGGCATGTTACGGTCAGATATCA 59.614 43.478 5.32 0.00 0.00 2.15
1549 1943 7.791029 TCATGAATTGTATCAGCAGTACCTTA 58.209 34.615 0.00 0.00 31.76 2.69
1550 1944 6.653020 TCATGAATTGTATCAGCAGTACCTT 58.347 36.000 0.00 0.00 31.76 3.50
1551 1945 6.239217 TCATGAATTGTATCAGCAGTACCT 57.761 37.500 0.00 0.00 31.76 3.08
1552 1946 6.707608 TCATCATGAATTGTATCAGCAGTACC 59.292 38.462 0.00 0.00 31.76 3.34
1553 1947 7.719778 TCATCATGAATTGTATCAGCAGTAC 57.280 36.000 0.00 0.00 31.76 2.73
1554 1948 8.152246 TCATCATCATGAATTGTATCAGCAGTA 58.848 33.333 0.00 0.00 35.99 2.74
1555 1949 6.996282 TCATCATCATGAATTGTATCAGCAGT 59.004 34.615 0.00 0.00 35.99 4.40
1556 1950 7.435068 TCATCATCATGAATTGTATCAGCAG 57.565 36.000 0.00 0.00 35.99 4.24
1557 1951 7.717875 TCTTCATCATCATGAATTGTATCAGCA 59.282 33.333 0.00 0.00 46.01 4.41
1558 1952 8.095937 TCTTCATCATCATGAATTGTATCAGC 57.904 34.615 0.00 0.00 46.01 4.26
1559 1953 9.880064 GTTCTTCATCATCATGAATTGTATCAG 57.120 33.333 0.00 0.00 46.01 2.90
1560 1954 9.398538 TGTTCTTCATCATCATGAATTGTATCA 57.601 29.630 0.00 0.00 46.01 2.15
1568 1962 9.398538 TCATGTTATGTTCTTCATCATCATGAA 57.601 29.630 0.00 0.00 45.20 2.57
1569 1963 8.833493 GTCATGTTATGTTCTTCATCATCATGA 58.167 33.333 0.00 0.00 40.67 3.07
1580 1974 9.334947 CTATTGATGAGGTCATGTTATGTTCTT 57.665 33.333 0.00 0.00 36.54 2.52
1629 2024 1.789523 TATAAGCTGCCCTTCTCCGT 58.210 50.000 0.00 0.00 34.95 4.69
1662 2058 4.636249 ACATAATCGGAGCATCTTCCTTC 58.364 43.478 0.00 0.00 34.96 3.46
1716 2112 3.941035 CGTTGCCCGTCGTTTAGT 58.059 55.556 0.00 0.00 0.00 2.24
1858 2256 5.422970 GGTATTACCGACCCATACCATGATA 59.577 44.000 0.00 0.00 41.50 2.15
2007 2406 6.884280 AGAAAGTCTGGGACACAAATTAAG 57.116 37.500 0.52 0.00 34.60 1.85
2034 2433 2.758089 CGGACGGAGGGAGTACGTG 61.758 68.421 0.00 0.00 40.75 4.49
2040 2439 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
2041 2440 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
2042 2441 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
2043 2442 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
2044 2443 2.537401 GACAAGTATTTCCGGACGGAG 58.463 52.381 13.64 3.15 46.06 4.63
2045 2444 1.205417 GGACAAGTATTTCCGGACGGA 59.795 52.381 1.83 9.76 43.52 4.69
2046 2445 1.648504 GGACAAGTATTTCCGGACGG 58.351 55.000 1.83 3.96 0.00 4.79
2052 2451 3.877508 CCATTCCTCGGACAAGTATTTCC 59.122 47.826 0.00 0.00 0.00 3.13
2053 2452 3.877508 CCCATTCCTCGGACAAGTATTTC 59.122 47.826 0.00 0.00 0.00 2.17
2054 2453 3.265995 ACCCATTCCTCGGACAAGTATTT 59.734 43.478 0.00 0.00 0.00 1.40
2055 2454 2.844348 ACCCATTCCTCGGACAAGTATT 59.156 45.455 0.00 0.00 0.00 1.89
2056 2455 2.170607 CACCCATTCCTCGGACAAGTAT 59.829 50.000 0.00 0.00 0.00 2.12
2057 2456 1.553248 CACCCATTCCTCGGACAAGTA 59.447 52.381 0.00 0.00 0.00 2.24
2058 2457 0.324943 CACCCATTCCTCGGACAAGT 59.675 55.000 0.00 0.00 0.00 3.16
2059 2458 0.324943 ACACCCATTCCTCGGACAAG 59.675 55.000 0.00 0.00 0.00 3.16
2060 2459 1.646912 TACACCCATTCCTCGGACAA 58.353 50.000 0.00 0.00 0.00 3.18
2061 2460 1.760613 GATACACCCATTCCTCGGACA 59.239 52.381 0.00 0.00 0.00 4.02
2062 2461 2.040178 AGATACACCCATTCCTCGGAC 58.960 52.381 0.00 0.00 0.00 4.79
2063 2462 2.471815 AGATACACCCATTCCTCGGA 57.528 50.000 0.00 0.00 0.00 4.55
2064 2463 3.497332 TCTAGATACACCCATTCCTCGG 58.503 50.000 0.00 0.00 0.00 4.63
2065 2464 4.524714 ACATCTAGATACACCCATTCCTCG 59.475 45.833 4.54 0.00 0.00 4.63
2066 2465 7.726033 ATACATCTAGATACACCCATTCCTC 57.274 40.000 4.54 0.00 0.00 3.71
2067 2466 8.511748 AAATACATCTAGATACACCCATTCCT 57.488 34.615 4.54 0.00 0.00 3.36
2106 2505 9.607988 TTGTCGTACAAATGGATACAAATAGAT 57.392 29.630 0.00 0.00 41.57 1.98
2107 2506 9.093970 CTTGTCGTACAAATGGATACAAATAGA 57.906 33.333 0.00 0.00 41.64 1.98
2108 2507 8.879759 ACTTGTCGTACAAATGGATACAAATAG 58.120 33.333 0.00 0.00 41.64 1.73
2109 2508 8.780846 ACTTGTCGTACAAATGGATACAAATA 57.219 30.769 0.00 0.00 41.64 1.40
2110 2509 7.681939 ACTTGTCGTACAAATGGATACAAAT 57.318 32.000 0.00 0.00 41.64 2.32
2111 2510 8.780846 ATACTTGTCGTACAAATGGATACAAA 57.219 30.769 0.00 0.00 41.64 2.83
2112 2511 8.780846 AATACTTGTCGTACAAATGGATACAA 57.219 30.769 0.00 0.00 41.64 2.41
2113 2512 8.780846 AAATACTTGTCGTACAAATGGATACA 57.219 30.769 0.00 0.00 42.21 2.29
2114 2513 8.333186 GGAAATACTTGTCGTACAAATGGATAC 58.667 37.037 0.00 0.00 37.69 2.24
2115 2514 7.223193 CGGAAATACTTGTCGTACAAATGGATA 59.777 37.037 0.00 0.00 37.69 2.59
2116 2515 6.036735 CGGAAATACTTGTCGTACAAATGGAT 59.963 38.462 0.00 0.00 37.69 3.41
2117 2516 5.349270 CGGAAATACTTGTCGTACAAATGGA 59.651 40.000 0.00 0.00 37.69 3.41
2118 2517 5.446741 CCGGAAATACTTGTCGTACAAATGG 60.447 44.000 0.00 0.00 37.69 3.16
2119 2518 5.349270 TCCGGAAATACTTGTCGTACAAATG 59.651 40.000 0.00 0.00 37.69 2.32
2120 2519 5.349543 GTCCGGAAATACTTGTCGTACAAAT 59.650 40.000 5.23 0.00 37.69 2.32
2121 2520 4.685628 GTCCGGAAATACTTGTCGTACAAA 59.314 41.667 5.23 0.00 37.69 2.83
2122 2521 4.236935 GTCCGGAAATACTTGTCGTACAA 58.763 43.478 5.23 0.00 36.54 2.41
2123 2522 3.255395 TGTCCGGAAATACTTGTCGTACA 59.745 43.478 5.23 0.00 0.00 2.90
2124 2523 3.836949 TGTCCGGAAATACTTGTCGTAC 58.163 45.455 5.23 0.00 0.00 3.67
2125 2524 3.758023 TCTGTCCGGAAATACTTGTCGTA 59.242 43.478 5.23 0.00 0.00 3.43
2126 2525 2.559668 TCTGTCCGGAAATACTTGTCGT 59.440 45.455 5.23 0.00 0.00 4.34
2127 2526 3.179830 CTCTGTCCGGAAATACTTGTCG 58.820 50.000 5.23 0.00 0.00 4.35
2128 2527 3.522553 CCTCTGTCCGGAAATACTTGTC 58.477 50.000 5.23 0.00 0.00 3.18
2129 2528 2.236395 CCCTCTGTCCGGAAATACTTGT 59.764 50.000 5.23 0.00 0.00 3.16
2130 2529 2.500098 TCCCTCTGTCCGGAAATACTTG 59.500 50.000 5.23 0.00 0.00 3.16
2131 2530 2.766828 CTCCCTCTGTCCGGAAATACTT 59.233 50.000 5.23 0.00 0.00 2.24
2132 2531 2.292323 ACTCCCTCTGTCCGGAAATACT 60.292 50.000 5.23 0.00 0.00 2.12
2133 2532 2.108970 ACTCCCTCTGTCCGGAAATAC 58.891 52.381 5.23 0.00 0.00 1.89
2134 2533 2.544844 ACTCCCTCTGTCCGGAAATA 57.455 50.000 5.23 0.00 0.00 1.40
2135 2534 2.544844 TACTCCCTCTGTCCGGAAAT 57.455 50.000 5.23 0.00 0.00 2.17
2136 2535 2.544844 ATACTCCCTCTGTCCGGAAA 57.455 50.000 5.23 0.00 0.00 3.13
2137 2536 3.139584 TCATATACTCCCTCTGTCCGGAA 59.860 47.826 5.23 0.00 0.00 4.30
2138 2537 2.714793 TCATATACTCCCTCTGTCCGGA 59.285 50.000 0.00 0.00 0.00 5.14
2139 2538 3.156288 TCATATACTCCCTCTGTCCGG 57.844 52.381 0.00 0.00 0.00 5.14
2140 2539 3.119316 GCATCATATACTCCCTCTGTCCG 60.119 52.174 0.00 0.00 0.00 4.79
2141 2540 4.093011 AGCATCATATACTCCCTCTGTCC 58.907 47.826 0.00 0.00 0.00 4.02
2142 2541 5.736951 AAGCATCATATACTCCCTCTGTC 57.263 43.478 0.00 0.00 0.00 3.51
2143 2542 5.604231 TGAAAGCATCATATACTCCCTCTGT 59.396 40.000 0.00 0.00 31.50 3.41
2144 2543 6.106648 TGAAAGCATCATATACTCCCTCTG 57.893 41.667 0.00 0.00 31.50 3.35
2215 2614 5.418840 TGTCTTGTACTATCTGACAGATGCA 59.581 40.000 25.26 15.84 35.37 3.96
2290 2690 6.126911 TGAGGTACACATATTTGAGCACCATA 60.127 38.462 5.94 0.00 0.00 2.74
2350 2750 6.899393 TGCAAAATGAAGTTAGACCAGAAT 57.101 33.333 0.00 0.00 0.00 2.40
2376 2777 7.446931 TGGAAAGTAAATATTGCTCACACTGAA 59.553 33.333 0.00 0.00 0.00 3.02
2395 2796 6.282199 AGTTCGTGATATAGTGTGGAAAGT 57.718 37.500 0.00 0.00 0.00 2.66
2534 2935 7.974243 AAAATGTTTTGAATTTTGCTTGCTC 57.026 28.000 0.00 0.00 36.21 4.26
2577 2979 6.017934 GGTCAAGATGTCGCATGTACATTTAT 60.018 38.462 5.37 0.00 37.69 1.40
2673 3079 4.644685 TGAGCTAAAAAGTTGCTGGAGTTT 59.355 37.500 0.00 0.00 37.16 2.66


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

AutoCloner maintained by Alex Coulton.