Multiple sequence alignment - TraesCS3B01G213600

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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 TraesCS3B01G213600 chr3B 100.000 4601 0 0 1 4601 252955844 252960444 0.000000e+00 8497.0
1 TraesCS3B01G213600 chr3A 90.734 3378 205 55 810 4119 213256108 213259445 0.000000e+00 4405.0
2 TraesCS3B01G213600 chr3A 85.676 377 47 2 4121 4497 213259619 213259988 1.550000e-104 390.0
3 TraesCS3B01G213600 chr3A 94.375 160 6 1 628 784 213250517 213250676 4.600000e-60 243.0
4 TraesCS3B01G213600 chr3D 93.462 2799 114 32 678 3458 174454971 174457718 0.000000e+00 4091.0
5 TraesCS3B01G213600 chr3D 89.691 679 56 9 3454 4119 174457750 174458427 0.000000e+00 854.0
6 TraesCS3B01G213600 chr3D 86.074 517 63 9 1609 2124 584112475 584111967 8.700000e-152 547.0
7 TraesCS3B01G213600 chr3D 92.523 321 24 0 4281 4601 174474322 174474642 1.170000e-125 460.0
8 TraesCS3B01G213600 chr3D 90.361 166 14 2 4121 4286 174458597 174458760 2.790000e-52 217.0
9 TraesCS3B01G213600 chr3D 100.000 30 0 0 3455 3484 481917075 481917104 6.430000e-04 56.5
10 TraesCS3B01G213600 chr4A 98.726 628 8 0 1 628 743661971 743662598 0.000000e+00 1116.0
11 TraesCS3B01G213600 chr4A 94.277 629 32 3 2 629 608051698 608052323 0.000000e+00 959.0
12 TraesCS3B01G213600 chr1A 98.246 627 11 0 1 627 4527632 4528258 0.000000e+00 1098.0
13 TraesCS3B01G213600 chr4B 97.943 632 9 1 1 628 3844292 3844923 0.000000e+00 1092.0
14 TraesCS3B01G213600 chr7B 97.930 628 13 0 1 628 589703465 589704092 0.000000e+00 1088.0
15 TraesCS3B01G213600 chr5A 97.147 631 14 1 1 627 250565952 250566582 0.000000e+00 1062.0
16 TraesCS3B01G213600 chr5A 81.030 854 128 25 2260 3104 476074046 476074874 0.000000e+00 649.0
17 TraesCS3B01G213600 chr5A 88.350 515 50 7 1609 2121 476073402 476073908 1.090000e-170 610.0
18 TraesCS3B01G213600 chr5A 84.926 471 56 11 1067 1524 476072857 476073325 3.240000e-126 462.0
19 TraesCS3B01G213600 chr5A 82.368 380 62 5 3705 4081 383170276 383169899 4.440000e-85 326.0
20 TraesCS3B01G213600 chr1D 95.548 629 23 5 1 628 297541054 297541678 0.000000e+00 1002.0
21 TraesCS3B01G213600 chr5D 95.397 630 23 5 1 628 245720830 245720205 0.000000e+00 998.0
22 TraesCS3B01G213600 chr5D 83.539 729 106 11 2386 3104 374296772 374297496 0.000000e+00 669.0
23 TraesCS3B01G213600 chr5D 87.810 525 54 8 1602 2125 374295958 374296473 1.420000e-169 606.0
24 TraesCS3B01G213600 chr5D 85.319 470 50 12 1067 1521 374295430 374295895 6.970000e-128 468.0
25 TraesCS3B01G213600 chr5D 94.000 50 3 0 2260 2309 374296641 374296690 4.940000e-10 76.8
26 TraesCS3B01G213600 chr1B 94.913 629 24 7 1 628 603660102 603659481 0.000000e+00 977.0
27 TraesCS3B01G213600 chr1B 74.645 422 91 12 3699 4109 682334969 682335385 6.120000e-39 172.0
28 TraesCS3B01G213600 chr1B 76.892 251 50 6 3699 3944 681959267 681959020 8.030000e-28 135.0
29 TraesCS3B01G213600 chr5B 81.808 874 123 31 2260 3104 446009032 446008166 0.000000e+00 701.0
30 TraesCS3B01G213600 chr5B 84.050 721 92 18 2389 3104 447205425 447204723 0.000000e+00 673.0
31 TraesCS3B01G213600 chr5B 83.657 722 101 16 2389 3104 446413274 446413984 0.000000e+00 664.0
32 TraesCS3B01G213600 chr5B 87.645 518 54 7 1609 2124 446009705 446009196 1.100000e-165 593.0
33 TraesCS3B01G213600 chr5B 87.402 508 56 6 1602 2109 446411986 446412485 1.110000e-160 577.0
34 TraesCS3B01G213600 chr5B 84.109 516 58 6 1609 2124 447206564 447206073 1.160000e-130 477.0
35 TraesCS3B01G213600 chr5B 84.778 473 53 16 1067 1524 446411462 446411930 1.510000e-124 457.0
36 TraesCS3B01G213600 chr5B 84.342 479 60 10 1059 1524 446010246 446009770 5.430000e-124 455.0
37 TraesCS3B01G213600 chr5B 84.435 469 56 12 1067 1521 447207097 447206632 3.270000e-121 446.0
38 TraesCS3B01G213600 chr5B 94.000 50 3 0 2260 2309 447205574 447205525 4.940000e-10 76.8
39 TraesCS3B01G213600 chr7D 79.875 959 164 24 1190 2132 208656645 208655700 0.000000e+00 675.0
40 TraesCS3B01G213600 chr7D 77.886 719 144 13 2393 3104 208655219 208654509 2.540000e-117 433.0
41 TraesCS3B01G213600 chr7A 78.502 721 137 15 2393 3104 221740412 221739701 1.510000e-124 457.0
42 TraesCS3B01G213600 chr7A 80.916 524 93 6 1609 2125 221741288 221740765 1.540000e-109 407.0
43 TraesCS3B01G213600 chr7A 85.329 334 42 6 1190 1518 221741695 221741364 5.700000e-89 339.0
44 TraesCS3B01G213600 chr2B 80.324 432 70 12 3700 4119 13973141 13973569 3.460000e-81 313.0
45 TraesCS3B01G213600 chr2B 80.000 425 74 9 3702 4119 563031054 563031474 2.080000e-78 303.0
46 TraesCS3B01G213600 chr2B 77.958 431 82 11 3699 4119 222594736 222594309 1.640000e-64 257.0
47 TraesCS3B01G213600 chr2A 79.335 421 83 4 3700 4117 10633045 10632626 4.500000e-75 292.0
48 TraesCS3B01G213600 chrUn 92.308 39 1 2 3448 3485 15419765 15419802 2.000000e-03 54.7
49 TraesCS3B01G213600 chrUn 92.308 39 1 2 3448 3485 15577369 15577406 2.000000e-03 54.7
50 TraesCS3B01G213600 chrUn 96.875 32 1 0 3454 3485 15744314 15744283 2.000000e-03 54.7


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 TraesCS3B01G213600 chr3B 252955844 252960444 4600 False 8497.000000 8497 100.000000 1 4601 1 chr3B.!!$F1 4600
1 TraesCS3B01G213600 chr3A 213256108 213259988 3880 False 2397.500000 4405 88.205000 810 4497 2 chr3A.!!$F2 3687
2 TraesCS3B01G213600 chr3D 174454971 174458760 3789 False 1720.666667 4091 91.171333 678 4286 3 chr3D.!!$F3 3608
3 TraesCS3B01G213600 chr3D 584111967 584112475 508 True 547.000000 547 86.074000 1609 2124 1 chr3D.!!$R1 515
4 TraesCS3B01G213600 chr4A 743661971 743662598 627 False 1116.000000 1116 98.726000 1 628 1 chr4A.!!$F2 627
5 TraesCS3B01G213600 chr4A 608051698 608052323 625 False 959.000000 959 94.277000 2 629 1 chr4A.!!$F1 627
6 TraesCS3B01G213600 chr1A 4527632 4528258 626 False 1098.000000 1098 98.246000 1 627 1 chr1A.!!$F1 626
7 TraesCS3B01G213600 chr4B 3844292 3844923 631 False 1092.000000 1092 97.943000 1 628 1 chr4B.!!$F1 627
8 TraesCS3B01G213600 chr7B 589703465 589704092 627 False 1088.000000 1088 97.930000 1 628 1 chr7B.!!$F1 627
9 TraesCS3B01G213600 chr5A 250565952 250566582 630 False 1062.000000 1062 97.147000 1 627 1 chr5A.!!$F1 626
10 TraesCS3B01G213600 chr5A 476072857 476074874 2017 False 573.666667 649 84.768667 1067 3104 3 chr5A.!!$F2 2037
11 TraesCS3B01G213600 chr1D 297541054 297541678 624 False 1002.000000 1002 95.548000 1 628 1 chr1D.!!$F1 627
12 TraesCS3B01G213600 chr5D 245720205 245720830 625 True 998.000000 998 95.397000 1 628 1 chr5D.!!$R1 627
13 TraesCS3B01G213600 chr5D 374295430 374297496 2066 False 454.950000 669 87.667000 1067 3104 4 chr5D.!!$F1 2037
14 TraesCS3B01G213600 chr1B 603659481 603660102 621 True 977.000000 977 94.913000 1 628 1 chr1B.!!$R1 627
15 TraesCS3B01G213600 chr5B 446008166 446010246 2080 True 583.000000 701 84.598333 1059 3104 3 chr5B.!!$R1 2045
16 TraesCS3B01G213600 chr5B 446411462 446413984 2522 False 566.000000 664 85.279000 1067 3104 3 chr5B.!!$F1 2037
17 TraesCS3B01G213600 chr5B 447204723 447207097 2374 True 418.200000 673 86.648500 1067 3104 4 chr5B.!!$R2 2037
18 TraesCS3B01G213600 chr7D 208654509 208656645 2136 True 554.000000 675 78.880500 1190 3104 2 chr7D.!!$R1 1914
19 TraesCS3B01G213600 chr7A 221739701 221741695 1994 True 401.000000 457 81.582333 1190 3104 3 chr7A.!!$R1 1914

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
669 676 0.320374 CAACTGGTAGCGGTCTGGAA 59.680 55.0 6.9 0.0 0.00 3.53 F
1211 1243 0.038526 CTCGCCAACAAGTACCTCGT 60.039 55.0 0.0 0.0 0.00 4.18 F
2167 3133 0.179108 GCTCCGTGTGAGGACCATAC 60.179 60.0 0.0 0.0 41.73 2.39 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2151 3117 0.245539 AACGTATGGTCCTCACACGG 59.754 55.0 2.06 0.0 36.95 4.94 R
2311 3532 0.526662 ACTGGCCGAGAACGTAGAAG 59.473 55.0 8.91 0.0 37.88 2.85 R
3906 5281 0.467844 TCAAACATGCCTGCACCAGT 60.468 50.0 0.00 0.0 0.00 4.00 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
189 190 2.102578 GCAACTGGCTACATGGGATTT 58.897 47.619 0.00 0.00 40.25 2.17
503 505 8.034804 GGATACTGCATGTTTTCCTTGTATTTT 58.965 33.333 0.00 0.00 31.15 1.82
629 636 1.947456 AGCGCCTCTTTTCGAAAAAGT 59.053 42.857 22.67 6.39 0.00 2.66
630 637 3.135994 AGCGCCTCTTTTCGAAAAAGTA 58.864 40.909 22.67 11.23 0.00 2.24
631 638 3.562557 AGCGCCTCTTTTCGAAAAAGTAA 59.437 39.130 22.67 9.05 0.00 2.24
632 639 3.662645 GCGCCTCTTTTCGAAAAAGTAAC 59.337 43.478 22.67 11.26 0.00 2.50
633 640 4.216731 CGCCTCTTTTCGAAAAAGTAACC 58.783 43.478 22.67 9.38 0.00 2.85
634 641 4.216731 GCCTCTTTTCGAAAAAGTAACCG 58.783 43.478 22.67 10.46 0.00 4.44
635 642 4.024641 GCCTCTTTTCGAAAAAGTAACCGA 60.025 41.667 22.67 13.77 0.00 4.69
636 643 5.334646 GCCTCTTTTCGAAAAAGTAACCGAT 60.335 40.000 22.67 0.00 0.00 4.18
637 644 6.304882 CCTCTTTTCGAAAAAGTAACCGATC 58.695 40.000 22.67 0.00 0.00 3.69
638 645 5.908106 TCTTTTCGAAAAAGTAACCGATCG 58.092 37.500 22.67 8.51 0.00 3.69
639 646 3.710437 TTCGAAAAAGTAACCGATCGC 57.290 42.857 10.32 0.00 0.00 4.58
640 647 2.950433 TCGAAAAAGTAACCGATCGCT 58.050 42.857 10.32 0.92 0.00 4.93
641 648 3.319755 TCGAAAAAGTAACCGATCGCTT 58.680 40.909 10.32 5.07 0.00 4.68
642 649 4.484236 TCGAAAAAGTAACCGATCGCTTA 58.516 39.130 10.32 3.90 0.00 3.09
643 650 4.922692 TCGAAAAAGTAACCGATCGCTTAA 59.077 37.500 10.32 0.00 0.00 1.85
644 651 5.011370 CGAAAAAGTAACCGATCGCTTAAC 58.989 41.667 10.32 4.86 0.00 2.01
645 652 5.164022 CGAAAAAGTAACCGATCGCTTAACT 60.164 40.000 10.32 7.17 0.00 2.24
646 653 6.033831 CGAAAAAGTAACCGATCGCTTAACTA 59.966 38.462 10.32 0.00 0.00 2.24
647 654 6.882458 AAAAGTAACCGATCGCTTAACTAG 57.118 37.500 10.32 0.00 0.00 2.57
648 655 5.573337 AAGTAACCGATCGCTTAACTAGT 57.427 39.130 10.32 0.00 0.00 2.57
649 656 5.167218 AGTAACCGATCGCTTAACTAGTC 57.833 43.478 10.32 0.00 0.00 2.59
650 657 3.433513 AACCGATCGCTTAACTAGTCC 57.566 47.619 10.32 0.00 0.00 3.85
651 658 2.372264 ACCGATCGCTTAACTAGTCCA 58.628 47.619 10.32 0.00 0.00 4.02
652 659 2.756760 ACCGATCGCTTAACTAGTCCAA 59.243 45.455 10.32 0.00 0.00 3.53
653 660 3.114065 CCGATCGCTTAACTAGTCCAAC 58.886 50.000 10.32 0.00 0.00 3.77
654 661 3.181489 CCGATCGCTTAACTAGTCCAACT 60.181 47.826 10.32 0.00 0.00 3.16
655 662 3.791887 CGATCGCTTAACTAGTCCAACTG 59.208 47.826 0.26 0.00 0.00 3.16
656 663 3.587797 TCGCTTAACTAGTCCAACTGG 57.412 47.619 0.00 0.00 32.47 4.00
657 664 2.895404 TCGCTTAACTAGTCCAACTGGT 59.105 45.455 0.00 0.00 41.94 4.00
658 665 4.081406 TCGCTTAACTAGTCCAACTGGTA 58.919 43.478 0.00 0.00 39.08 3.25
659 666 4.157289 TCGCTTAACTAGTCCAACTGGTAG 59.843 45.833 0.00 0.00 39.08 3.18
660 667 4.182339 GCTTAACTAGTCCAACTGGTAGC 58.818 47.826 0.00 3.59 39.08 3.58
661 668 4.421948 CTTAACTAGTCCAACTGGTAGCG 58.578 47.826 0.00 0.00 39.08 4.26
662 669 1.183549 ACTAGTCCAACTGGTAGCGG 58.816 55.000 0.00 0.00 38.19 5.52
663 670 1.183549 CTAGTCCAACTGGTAGCGGT 58.816 55.000 0.00 0.00 36.34 5.68
664 671 1.134560 CTAGTCCAACTGGTAGCGGTC 59.865 57.143 6.90 0.00 36.34 4.79
665 672 0.542232 AGTCCAACTGGTAGCGGTCT 60.542 55.000 6.90 0.00 36.34 3.85
666 673 0.389948 GTCCAACTGGTAGCGGTCTG 60.390 60.000 6.90 7.78 36.34 3.51
667 674 1.079127 CCAACTGGTAGCGGTCTGG 60.079 63.158 6.90 12.61 0.00 3.86
668 675 1.541310 CCAACTGGTAGCGGTCTGGA 61.541 60.000 21.07 0.00 0.00 3.86
669 676 0.320374 CAACTGGTAGCGGTCTGGAA 59.680 55.000 6.90 0.00 0.00 3.53
670 677 0.320697 AACTGGTAGCGGTCTGGAAC 59.679 55.000 6.90 0.00 0.00 3.62
671 678 0.542232 ACTGGTAGCGGTCTGGAACT 60.542 55.000 0.00 0.00 0.00 3.01
672 679 0.608640 CTGGTAGCGGTCTGGAACTT 59.391 55.000 0.00 0.00 0.00 2.66
673 680 0.320374 TGGTAGCGGTCTGGAACTTG 59.680 55.000 0.00 0.00 0.00 3.16
674 681 0.391263 GGTAGCGGTCTGGAACTTGG 60.391 60.000 0.00 0.00 0.00 3.61
675 682 0.391263 GTAGCGGTCTGGAACTTGGG 60.391 60.000 0.00 0.00 0.00 4.12
676 683 0.543410 TAGCGGTCTGGAACTTGGGA 60.543 55.000 0.00 0.00 0.00 4.37
701 708 0.663153 GATAGGCGCCAGCGAAAAAT 59.337 50.000 31.54 6.76 46.35 1.82
705 712 1.648467 GGCGCCAGCGAAAAATCTCT 61.648 55.000 24.80 0.00 46.35 3.10
738 745 2.741985 TTGCATCTGACGTGGCGG 60.742 61.111 0.00 0.00 0.00 6.13
804 811 3.785859 CTTGCTAGGCGCCAGGGA 61.786 66.667 31.54 19.04 38.05 4.20
805 812 3.326578 TTGCTAGGCGCCAGGGAA 61.327 61.111 31.54 23.76 38.05 3.97
807 814 2.045340 GCTAGGCGCCAGGGAAAA 60.045 61.111 31.54 3.37 0.00 2.29
808 815 1.453928 GCTAGGCGCCAGGGAAAAT 60.454 57.895 31.54 7.63 0.00 1.82
822 829 3.041946 GGGAAAATGGCTCTCCTCTAGA 58.958 50.000 0.00 0.00 0.00 2.43
837 844 8.001881 TCTCCTCTAGACACTTGAATATTGTC 57.998 38.462 0.00 0.00 40.04 3.18
886 896 1.717194 TCACGGTTACTCGCCATTTC 58.283 50.000 0.00 0.00 0.00 2.17
1007 1027 6.154363 ACTCAAACCTTTTTGGACATCAAGAA 59.846 34.615 0.00 0.00 42.23 2.52
1211 1243 0.038526 CTCGCCAACAAGTACCTCGT 60.039 55.000 0.00 0.00 0.00 4.18
1269 1301 0.893270 CATTCGTGGACTTGGGCCAA 60.893 55.000 19.68 19.68 37.12 4.52
1503 1538 1.813753 CTACAACATCCACCGCCGG 60.814 63.158 0.00 0.00 0.00 6.13
1524 1559 2.434134 CGCTCTCAACGTACGCACC 61.434 63.158 16.72 0.00 0.00 5.01
1551 1594 4.777140 TCGTCGATCGAACGATTACTTA 57.223 40.909 27.10 12.23 45.98 2.24
1552 1595 4.508971 TCGTCGATCGAACGATTACTTAC 58.491 43.478 27.10 5.96 45.98 2.34
1557 1600 6.901887 GTCGATCGAACGATTACTTACAACTA 59.098 38.462 21.31 0.00 43.93 2.24
1558 1601 7.109942 GTCGATCGAACGATTACTTACAACTAG 59.890 40.741 21.31 0.00 43.93 2.57
1559 1602 6.356452 CGATCGAACGATTACTTACAACTAGG 59.644 42.308 10.26 0.00 34.60 3.02
1561 1604 5.097529 CGAACGATTACTTACAACTAGGCA 58.902 41.667 0.00 0.00 0.00 4.75
1562 1605 5.004156 CGAACGATTACTTACAACTAGGCAC 59.996 44.000 0.00 0.00 0.00 5.01
1571 1614 3.876589 AACTAGGCACCCACGCACG 62.877 63.158 0.00 0.00 0.00 5.34
1594 1637 2.159296 GCCCACACGTTGAAGAAAAACT 60.159 45.455 0.00 0.00 0.00 2.66
1899 2007 2.361104 ACGGGCGCCAACATCATT 60.361 55.556 30.85 0.00 0.00 2.57
1926 2034 2.498885 GGGTATGTGGTCGACCTACTTT 59.501 50.000 33.39 21.00 36.82 2.66
2094 2205 0.189574 CCCATCTCAGGAGGGAGCTA 59.810 60.000 0.00 0.00 45.34 3.32
2136 3102 6.205658 GCTCTTTCTTTCTTTTCTAGCTTGGA 59.794 38.462 0.00 0.00 0.00 3.53
2154 3120 0.951558 GACAAACCATGTTGCTCCGT 59.048 50.000 0.00 0.00 44.12 4.69
2155 3121 0.667993 ACAAACCATGTTGCTCCGTG 59.332 50.000 0.00 0.00 40.06 4.94
2165 3131 1.480212 TTGCTCCGTGTGAGGACCAT 61.480 55.000 0.00 0.00 41.66 3.55
2166 3132 0.613572 TGCTCCGTGTGAGGACCATA 60.614 55.000 0.00 0.00 41.73 2.74
2167 3133 0.179108 GCTCCGTGTGAGGACCATAC 60.179 60.000 0.00 0.00 41.73 2.39
2302 3523 4.003648 AGAAGATGGTTCTAGCCGTTTTG 58.996 43.478 0.00 0.00 0.00 2.44
2311 3532 0.394625 TAGCCGTTTTGGGGGTATGC 60.395 55.000 0.00 0.00 38.63 3.14
2324 3556 2.543238 GGGGTATGCTTCTACGTTCTCG 60.543 54.545 0.00 0.00 43.34 4.04
2341 3574 2.230508 TCTCGGCCAGTACAAGTTGTAG 59.769 50.000 16.03 6.22 32.84 2.74
2382 3638 9.897744 TTATTGAGCAAAACTAAATGAAGTGAG 57.102 29.630 0.00 0.00 31.34 3.51
2787 4110 3.797353 GGATTCCTGAGGGGCGCA 61.797 66.667 10.83 0.00 34.39 6.09
3003 4326 2.280321 CCCAACGTCGTCGGGTTT 60.280 61.111 13.61 0.00 41.85 3.27
3202 4526 4.087182 TGCTCCTGTACTTACTACTTGCT 58.913 43.478 0.00 0.00 0.00 3.91
3207 4531 3.102204 TGTACTTACTACTTGCTCCCCC 58.898 50.000 0.00 0.00 0.00 5.40
3265 4589 3.209410 GCATGGATCAGAAGTTGTAGGG 58.791 50.000 0.00 0.00 0.00 3.53
3271 4595 4.142049 GGATCAGAAGTTGTAGGGACTCAG 60.142 50.000 0.00 0.00 41.75 3.35
3272 4596 4.114015 TCAGAAGTTGTAGGGACTCAGA 57.886 45.455 0.00 0.00 41.75 3.27
3273 4597 4.678256 TCAGAAGTTGTAGGGACTCAGAT 58.322 43.478 0.00 0.00 41.75 2.90
3274 4598 5.087323 TCAGAAGTTGTAGGGACTCAGATT 58.913 41.667 0.00 0.00 41.75 2.40
3292 4616 7.663081 ACTCAGATTAAAATTCAAGTGCTCTGA 59.337 33.333 0.00 0.00 36.24 3.27
3293 4617 8.394971 TCAGATTAAAATTCAAGTGCTCTGAA 57.605 30.769 0.00 0.00 35.09 3.02
3324 4650 9.753674 TCAAATTGTAGAATTGGTTATCCTCTT 57.246 29.630 0.00 0.00 31.83 2.85
3368 4694 2.260822 GCCTATTGCTATGAGAGGGGA 58.739 52.381 0.00 0.00 36.87 4.81
3431 4758 7.985752 GCAGTAGGATGTTTAGGTTGTACTATT 59.014 37.037 0.00 0.00 0.00 1.73
3469 4832 8.713271 CCTCTGTCTCAAAATTAGTACAAAGTC 58.287 37.037 0.00 0.00 0.00 3.01
3509 4874 4.736611 TGGGACGGAAGGAGTATAGTAT 57.263 45.455 0.00 0.00 0.00 2.12
3619 4989 2.224670 TGTACACAGTTCCAATCCCACC 60.225 50.000 0.00 0.00 0.00 4.61
3649 5019 7.537596 TTCAACATTTTGTATGGATCACCTT 57.462 32.000 0.00 0.00 34.09 3.50
3671 5042 1.409427 GAGAGGGTCGGGAATGTGTAG 59.591 57.143 0.00 0.00 0.00 2.74
3672 5043 0.179081 GAGGGTCGGGAATGTGTAGC 60.179 60.000 0.00 0.00 0.00 3.58
3756 5128 1.261619 CTCGCCGGTATGATTTTCTGC 59.738 52.381 1.90 0.00 0.00 4.26
3809 5182 0.407139 AGGGATGTCCTGCTTTGCTT 59.593 50.000 0.00 0.00 46.07 3.91
3818 5191 1.327303 CTGCTTTGCTTGGGTGGTTA 58.673 50.000 0.00 0.00 0.00 2.85
3904 5279 2.004583 TGAAAACCATAGACGGCGAG 57.995 50.000 16.62 0.00 0.00 5.03
3906 5281 0.899720 AAAACCATAGACGGCGAGGA 59.100 50.000 16.62 0.00 0.00 3.71
3918 5293 4.007644 CGAGGACTGGTGCAGGCA 62.008 66.667 0.00 0.00 42.18 4.75
3949 5324 2.865551 CACATGTGTGCCCTTGTTTTTC 59.134 45.455 18.03 0.00 39.39 2.29
3965 5340 0.323629 TTTCCGGTGCCGAAGAGAAT 59.676 50.000 12.71 0.00 42.83 2.40
3968 5343 1.551430 TCCGGTGCCGAAGAGAATAAA 59.449 47.619 12.71 0.00 42.83 1.40
3974 5349 2.507886 TGCCGAAGAGAATAAATGGGGA 59.492 45.455 0.00 0.00 0.00 4.81
4016 5391 3.134623 TGCCGTGATTGAATATGAGGACT 59.865 43.478 0.00 0.00 0.00 3.85
4048 5423 5.643664 TCTGAATGCAGATTATTGTGTTGC 58.356 37.500 0.00 0.00 45.88 4.17
4081 5457 2.283298 CAAGGTTCAGGGATGATGACG 58.717 52.381 0.00 0.00 0.00 4.35
4108 5484 3.183775 GCTTCAGAAGTCTTCGCGTTTTA 59.816 43.478 11.94 0.00 34.02 1.52
4109 5485 4.143094 GCTTCAGAAGTCTTCGCGTTTTAT 60.143 41.667 11.94 0.00 34.02 1.40
4119 5495 4.735822 TCTTCGCGTTTTATTGGTTGTTTG 59.264 37.500 5.77 0.00 0.00 2.93
4168 5718 4.696479 ACTTGACATTATCTAGCCCTGG 57.304 45.455 0.00 0.00 33.86 4.45
4185 5735 1.915769 GGCGCTCTCCCCATATCCT 60.916 63.158 7.64 0.00 0.00 3.24
4189 5739 1.188219 GCTCTCCCCATATCCTCGCA 61.188 60.000 0.00 0.00 0.00 5.10
4245 5795 2.754658 CCGCCGTGGTCTACTCCT 60.755 66.667 0.00 0.00 0.00 3.69
4246 5796 2.772691 CCGCCGTGGTCTACTCCTC 61.773 68.421 0.00 0.00 0.00 3.71
4291 5841 2.759560 GGCCATCCCGGTTGCATT 60.760 61.111 0.00 0.00 36.97 3.56
4292 5842 2.358372 GGCCATCCCGGTTGCATTT 61.358 57.895 0.00 0.00 36.97 2.32
4297 5847 1.821753 CATCCCGGTTGCATTTACCAA 59.178 47.619 0.00 0.00 35.31 3.67
4308 5858 5.596836 TGCATTTACCAATCTCCCAAATC 57.403 39.130 0.00 0.00 0.00 2.17
4312 5862 6.407299 GCATTTACCAATCTCCCAAATCATGT 60.407 38.462 0.00 0.00 0.00 3.21
4314 5864 4.598036 ACCAATCTCCCAAATCATGTCT 57.402 40.909 0.00 0.00 0.00 3.41
4324 5874 4.093998 CCCAAATCATGTCTCTTTCTGACG 59.906 45.833 0.00 0.00 37.26 4.35
4326 5876 5.390251 CCAAATCATGTCTCTTTCTGACGTG 60.390 44.000 0.00 9.12 46.82 4.49
4341 5891 0.935196 ACGTGAAGTTCGAACAAGGC 59.065 50.000 28.78 15.11 0.00 4.35
4345 5895 1.946768 TGAAGTTCGAACAAGGCTTGG 59.053 47.619 29.26 13.25 34.12 3.61
4350 5900 0.951558 TCGAACAAGGCTTGGCTTTC 59.048 50.000 29.26 21.57 34.12 2.62
4364 5914 2.303022 TGGCTTTCGAGGACTTGATCTT 59.697 45.455 0.00 0.00 0.00 2.40
4378 5928 5.136105 ACTTGATCTTGAAGAAGTTTGGCT 58.864 37.500 0.00 0.00 0.00 4.75
4382 5932 5.829924 TGATCTTGAAGAAGTTTGGCTTTCT 59.170 36.000 0.00 0.00 37.59 2.52
4383 5933 6.322201 TGATCTTGAAGAAGTTTGGCTTTCTT 59.678 34.615 0.00 0.00 37.59 2.52
4387 5937 6.377327 TGAAGAAGTTTGGCTTTCTTGTAG 57.623 37.500 4.38 0.00 37.59 2.74
4407 5957 5.422331 TGTAGACTTCATCGAAGGAAGGAAT 59.578 40.000 25.04 16.26 44.69 3.01
4413 5963 7.044798 ACTTCATCGAAGGAAGGAATCTAAAG 58.955 38.462 25.04 5.74 44.69 1.85
4421 5971 7.554476 CGAAGGAAGGAATCTAAAGGAATTCTT 59.446 37.037 5.23 0.00 37.28 2.52
4425 5975 9.907229 GGAAGGAATCTAAAGGAATTCTTTCTA 57.093 33.333 15.16 0.00 43.98 2.10
4437 5987 5.125578 GGAATTCTTTCTAGTGGCGGATTTT 59.874 40.000 5.23 0.00 32.16 1.82
4450 6000 4.522405 TGGCGGATTTTTCAAGATCAAAGA 59.478 37.500 0.00 0.00 0.00 2.52
4451 6001 5.185635 TGGCGGATTTTTCAAGATCAAAGAT 59.814 36.000 0.00 0.00 0.00 2.40
4452 6002 5.745769 GGCGGATTTTTCAAGATCAAAGATC 59.254 40.000 0.00 0.00 0.00 2.75
4453 6003 6.324819 GCGGATTTTTCAAGATCAAAGATCA 58.675 36.000 9.43 0.00 29.78 2.92
4454 6004 6.976925 GCGGATTTTTCAAGATCAAAGATCAT 59.023 34.615 9.43 0.00 29.78 2.45
4465 6015 6.796426 AGATCAAAGATCATGCTCAACATTG 58.204 36.000 9.43 0.00 36.64 2.82
4489 6039 4.965532 ACTCAGTAGGGCTCATTCTACAAT 59.034 41.667 0.00 0.00 38.54 2.71
4493 6043 3.185246 AGGGCTCATTCTACAATCGTG 57.815 47.619 0.00 0.00 0.00 4.35
4497 6047 3.375299 GGCTCATTCTACAATCGTGCTTT 59.625 43.478 0.00 0.00 0.00 3.51
4498 6048 4.337763 GCTCATTCTACAATCGTGCTTTG 58.662 43.478 0.00 0.00 0.00 2.77
4499 6049 4.728882 GCTCATTCTACAATCGTGCTTTGG 60.729 45.833 0.00 0.00 0.00 3.28
4500 6050 4.323417 TCATTCTACAATCGTGCTTTGGT 58.677 39.130 0.00 0.00 0.00 3.67
4501 6051 4.154015 TCATTCTACAATCGTGCTTTGGTG 59.846 41.667 0.00 0.00 0.00 4.17
4502 6052 2.422597 TCTACAATCGTGCTTTGGTGG 58.577 47.619 0.00 0.00 0.00 4.61
4503 6053 2.037902 TCTACAATCGTGCTTTGGTGGA 59.962 45.455 0.00 0.00 0.00 4.02
4504 6054 0.951558 ACAATCGTGCTTTGGTGGAC 59.048 50.000 0.00 0.00 0.00 4.02
4505 6055 0.950836 CAATCGTGCTTTGGTGGACA 59.049 50.000 0.00 0.00 0.00 4.02
4506 6056 0.951558 AATCGTGCTTTGGTGGACAC 59.048 50.000 0.00 0.00 0.00 3.67
4508 6058 2.331451 GTGCTTTGGTGGACACGC 59.669 61.111 0.00 0.00 0.00 5.34
4515 6065 2.509336 GGTGGACACGCCTCGATG 60.509 66.667 0.00 0.00 44.06 3.84
4516 6066 2.261671 GTGGACACGCCTCGATGT 59.738 61.111 0.00 0.00 37.63 3.06
4517 6067 1.374252 GTGGACACGCCTCGATGTT 60.374 57.895 0.00 0.00 37.63 2.71
4518 6068 1.080093 TGGACACGCCTCGATGTTC 60.080 57.895 0.00 0.00 37.63 3.18
4519 6069 1.080093 GGACACGCCTCGATGTTCA 60.080 57.895 0.00 0.00 0.00 3.18
4520 6070 0.669318 GGACACGCCTCGATGTTCAA 60.669 55.000 0.00 0.00 0.00 2.69
4521 6071 0.716108 GACACGCCTCGATGTTCAAG 59.284 55.000 0.00 0.00 0.00 3.02
4522 6072 0.670546 ACACGCCTCGATGTTCAAGG 60.671 55.000 0.00 0.00 0.00 3.61
4523 6073 0.670546 CACGCCTCGATGTTCAAGGT 60.671 55.000 0.00 0.00 32.49 3.50
4524 6074 0.034896 ACGCCTCGATGTTCAAGGTT 59.965 50.000 0.00 0.00 32.49 3.50
4525 6075 1.156736 CGCCTCGATGTTCAAGGTTT 58.843 50.000 0.00 0.00 32.49 3.27
4526 6076 1.128692 CGCCTCGATGTTCAAGGTTTC 59.871 52.381 0.00 0.00 32.49 2.78
4527 6077 2.427506 GCCTCGATGTTCAAGGTTTCT 58.572 47.619 0.00 0.00 32.49 2.52
4528 6078 2.814336 GCCTCGATGTTCAAGGTTTCTT 59.186 45.455 0.00 0.00 32.49 2.52
4542 6092 6.774084 CAAGGTTTCTTGTTGTCAAAATTGG 58.226 36.000 0.00 0.00 43.92 3.16
4543 6093 6.048732 AGGTTTCTTGTTGTCAAAATTGGT 57.951 33.333 0.00 0.00 32.87 3.67
4544 6094 6.106003 AGGTTTCTTGTTGTCAAAATTGGTC 58.894 36.000 0.00 0.00 32.87 4.02
4545 6095 6.070824 AGGTTTCTTGTTGTCAAAATTGGTCT 60.071 34.615 0.00 0.00 32.87 3.85
4546 6096 6.593770 GGTTTCTTGTTGTCAAAATTGGTCTT 59.406 34.615 0.00 0.00 32.87 3.01
4547 6097 7.119116 GGTTTCTTGTTGTCAAAATTGGTCTTT 59.881 33.333 0.00 0.00 32.87 2.52
4548 6098 7.826260 TTCTTGTTGTCAAAATTGGTCTTTC 57.174 32.000 0.00 0.00 32.87 2.62
4549 6099 6.929625 TCTTGTTGTCAAAATTGGTCTTTCA 58.070 32.000 0.00 0.00 32.87 2.69
4550 6100 7.382110 TCTTGTTGTCAAAATTGGTCTTTCAA 58.618 30.769 0.00 0.00 32.87 2.69
4551 6101 7.545265 TCTTGTTGTCAAAATTGGTCTTTCAAG 59.455 33.333 0.00 0.00 32.87 3.02
4552 6102 6.696411 TGTTGTCAAAATTGGTCTTTCAAGT 58.304 32.000 0.00 0.00 0.00 3.16
4553 6103 7.158021 TGTTGTCAAAATTGGTCTTTCAAGTT 58.842 30.769 0.00 0.00 36.65 2.66
4554 6104 7.330700 TGTTGTCAAAATTGGTCTTTCAAGTTC 59.669 33.333 0.00 0.00 34.45 3.01
4555 6105 7.169158 TGTCAAAATTGGTCTTTCAAGTTCT 57.831 32.000 0.00 0.00 34.45 3.01
4556 6106 8.287439 TGTCAAAATTGGTCTTTCAAGTTCTA 57.713 30.769 0.00 0.00 34.45 2.10
4557 6107 8.744652 TGTCAAAATTGGTCTTTCAAGTTCTAA 58.255 29.630 0.00 0.00 34.45 2.10
4558 6108 9.237846 GTCAAAATTGGTCTTTCAAGTTCTAAG 57.762 33.333 0.00 0.00 34.45 2.18
4559 6109 8.966868 TCAAAATTGGTCTTTCAAGTTCTAAGT 58.033 29.630 0.00 0.00 34.45 2.24
4560 6110 9.586435 CAAAATTGGTCTTTCAAGTTCTAAGTT 57.414 29.630 0.00 0.00 34.45 2.66
4561 6111 9.586435 AAAATTGGTCTTTCAAGTTCTAAGTTG 57.414 29.630 4.24 4.24 40.00 3.16
4562 6112 5.751243 TGGTCTTTCAAGTTCTAAGTTGC 57.249 39.130 5.56 0.00 38.82 4.17
4563 6113 5.189928 TGGTCTTTCAAGTTCTAAGTTGCA 58.810 37.500 5.56 0.00 38.82 4.08
4564 6114 5.827797 TGGTCTTTCAAGTTCTAAGTTGCAT 59.172 36.000 5.56 0.00 38.82 3.96
4565 6115 6.017109 TGGTCTTTCAAGTTCTAAGTTGCATC 60.017 38.462 5.56 0.00 38.82 3.91
4566 6116 6.017109 GGTCTTTCAAGTTCTAAGTTGCATCA 60.017 38.462 5.56 0.00 38.82 3.07
4567 6117 7.417612 GTCTTTCAAGTTCTAAGTTGCATCAA 58.582 34.615 5.56 0.00 38.82 2.57
4568 6118 7.915397 GTCTTTCAAGTTCTAAGTTGCATCAAA 59.085 33.333 5.56 1.67 38.82 2.69
4569 6119 8.131100 TCTTTCAAGTTCTAAGTTGCATCAAAG 58.869 33.333 5.56 9.39 38.82 2.77
4570 6120 6.317789 TCAAGTTCTAAGTTGCATCAAAGG 57.682 37.500 5.56 0.00 38.82 3.11
4571 6121 6.061441 TCAAGTTCTAAGTTGCATCAAAGGA 58.939 36.000 5.56 0.00 38.82 3.36
4572 6122 6.716628 TCAAGTTCTAAGTTGCATCAAAGGAT 59.283 34.615 5.56 0.00 38.82 3.24
4584 6134 3.857157 TCAAAGGATGTAGGTATGGCC 57.143 47.619 0.00 0.00 37.58 5.36
4585 6135 3.119319 TCAAAGGATGTAGGTATGGCCA 58.881 45.455 8.56 8.56 40.61 5.36
4586 6136 3.721575 TCAAAGGATGTAGGTATGGCCAT 59.278 43.478 24.45 24.45 40.61 4.40
4587 6137 4.167892 TCAAAGGATGTAGGTATGGCCATT 59.832 41.667 26.37 8.85 40.61 3.16
4588 6138 4.814224 AAGGATGTAGGTATGGCCATTT 57.186 40.909 26.37 12.71 40.61 2.32
4589 6139 4.814224 AGGATGTAGGTATGGCCATTTT 57.186 40.909 26.37 12.34 40.61 1.82
4590 6140 4.473444 AGGATGTAGGTATGGCCATTTTG 58.527 43.478 26.37 0.00 40.61 2.44
4591 6141 4.167892 AGGATGTAGGTATGGCCATTTTGA 59.832 41.667 26.37 1.74 40.61 2.69
4592 6142 4.892934 GGATGTAGGTATGGCCATTTTGAA 59.107 41.667 26.37 1.26 40.61 2.69
4593 6143 5.010012 GGATGTAGGTATGGCCATTTTGAAG 59.990 44.000 26.37 0.00 40.61 3.02
4594 6144 4.277476 TGTAGGTATGGCCATTTTGAAGG 58.723 43.478 26.37 0.00 40.61 3.46
4595 6145 2.750814 AGGTATGGCCATTTTGAAGGG 58.249 47.619 26.37 0.00 40.61 3.95
4596 6146 2.314549 AGGTATGGCCATTTTGAAGGGA 59.685 45.455 26.37 0.00 40.61 4.20
4597 6147 2.695147 GGTATGGCCATTTTGAAGGGAG 59.305 50.000 26.37 0.00 33.14 4.30
4598 6148 1.870064 ATGGCCATTTTGAAGGGAGG 58.130 50.000 14.09 0.00 33.14 4.30
4599 6149 0.486879 TGGCCATTTTGAAGGGAGGT 59.513 50.000 0.00 0.00 33.14 3.85
4600 6150 1.713647 TGGCCATTTTGAAGGGAGGTA 59.286 47.619 0.00 0.00 33.14 3.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
615 622 5.613142 GCGATCGGTTACTTTTTCGAAAAGA 60.613 40.000 21.53 14.44 35.25 2.52
629 636 3.947196 TGGACTAGTTAAGCGATCGGTTA 59.053 43.478 30.08 30.08 37.08 2.85
630 637 2.756760 TGGACTAGTTAAGCGATCGGTT 59.243 45.455 32.14 32.14 39.33 4.44
631 638 2.372264 TGGACTAGTTAAGCGATCGGT 58.628 47.619 15.21 15.21 0.00 4.69
632 639 3.114065 GTTGGACTAGTTAAGCGATCGG 58.886 50.000 18.30 0.00 0.00 4.18
633 640 3.791887 CAGTTGGACTAGTTAAGCGATCG 59.208 47.826 11.69 11.69 0.00 3.69
634 641 4.113354 CCAGTTGGACTAGTTAAGCGATC 58.887 47.826 0.00 0.00 37.39 3.69
635 642 3.514309 ACCAGTTGGACTAGTTAAGCGAT 59.486 43.478 4.92 0.00 38.94 4.58
636 643 2.895404 ACCAGTTGGACTAGTTAAGCGA 59.105 45.455 4.92 0.00 38.94 4.93
637 644 3.314541 ACCAGTTGGACTAGTTAAGCG 57.685 47.619 4.92 0.00 38.94 4.68
638 645 4.182339 GCTACCAGTTGGACTAGTTAAGC 58.818 47.826 4.92 0.00 38.94 3.09
639 646 4.421948 CGCTACCAGTTGGACTAGTTAAG 58.578 47.826 4.92 0.00 38.94 1.85
640 647 3.194116 CCGCTACCAGTTGGACTAGTTAA 59.806 47.826 4.92 0.00 38.94 2.01
641 648 2.756760 CCGCTACCAGTTGGACTAGTTA 59.243 50.000 4.92 0.00 38.94 2.24
642 649 1.549170 CCGCTACCAGTTGGACTAGTT 59.451 52.381 4.92 0.00 38.94 2.24
643 650 1.183549 CCGCTACCAGTTGGACTAGT 58.816 55.000 4.92 0.00 38.94 2.57
644 651 1.134560 GACCGCTACCAGTTGGACTAG 59.865 57.143 4.92 0.00 38.94 2.57
645 652 1.180029 GACCGCTACCAGTTGGACTA 58.820 55.000 4.92 0.00 38.94 2.59
646 653 0.542232 AGACCGCTACCAGTTGGACT 60.542 55.000 4.92 0.00 38.94 3.85
647 654 0.389948 CAGACCGCTACCAGTTGGAC 60.390 60.000 4.92 0.00 38.94 4.02
648 655 1.541310 CCAGACCGCTACCAGTTGGA 61.541 60.000 4.92 0.00 38.94 3.53
649 656 1.079127 CCAGACCGCTACCAGTTGG 60.079 63.158 0.00 0.00 42.17 3.77
650 657 0.320374 TTCCAGACCGCTACCAGTTG 59.680 55.000 0.00 0.00 0.00 3.16
651 658 0.320697 GTTCCAGACCGCTACCAGTT 59.679 55.000 0.00 0.00 0.00 3.16
652 659 0.542232 AGTTCCAGACCGCTACCAGT 60.542 55.000 0.00 0.00 0.00 4.00
653 660 0.608640 AAGTTCCAGACCGCTACCAG 59.391 55.000 0.00 0.00 0.00 4.00
654 661 0.320374 CAAGTTCCAGACCGCTACCA 59.680 55.000 0.00 0.00 0.00 3.25
655 662 0.391263 CCAAGTTCCAGACCGCTACC 60.391 60.000 0.00 0.00 0.00 3.18
656 663 0.391263 CCCAAGTTCCAGACCGCTAC 60.391 60.000 0.00 0.00 0.00 3.58
657 664 0.543410 TCCCAAGTTCCAGACCGCTA 60.543 55.000 0.00 0.00 0.00 4.26
658 665 1.201429 ATCCCAAGTTCCAGACCGCT 61.201 55.000 0.00 0.00 0.00 5.52
659 666 0.322546 AATCCCAAGTTCCAGACCGC 60.323 55.000 0.00 0.00 0.00 5.68
660 667 1.279271 AGAATCCCAAGTTCCAGACCG 59.721 52.381 0.00 0.00 0.00 4.79
661 668 2.619074 CCAGAATCCCAAGTTCCAGACC 60.619 54.545 0.00 0.00 0.00 3.85
662 669 2.305927 TCCAGAATCCCAAGTTCCAGAC 59.694 50.000 0.00 0.00 0.00 3.51
663 670 2.631384 TCCAGAATCCCAAGTTCCAGA 58.369 47.619 0.00 0.00 0.00 3.86
664 671 3.659183 ATCCAGAATCCCAAGTTCCAG 57.341 47.619 0.00 0.00 0.00 3.86
665 672 3.459598 CCTATCCAGAATCCCAAGTTCCA 59.540 47.826 0.00 0.00 0.00 3.53
666 673 3.748989 GCCTATCCAGAATCCCAAGTTCC 60.749 52.174 0.00 0.00 0.00 3.62
667 674 3.481453 GCCTATCCAGAATCCCAAGTTC 58.519 50.000 0.00 0.00 0.00 3.01
668 675 2.158755 CGCCTATCCAGAATCCCAAGTT 60.159 50.000 0.00 0.00 0.00 2.66
669 676 1.417890 CGCCTATCCAGAATCCCAAGT 59.582 52.381 0.00 0.00 0.00 3.16
670 677 1.879796 GCGCCTATCCAGAATCCCAAG 60.880 57.143 0.00 0.00 0.00 3.61
671 678 0.108585 GCGCCTATCCAGAATCCCAA 59.891 55.000 0.00 0.00 0.00 4.12
672 679 1.754745 GCGCCTATCCAGAATCCCA 59.245 57.895 0.00 0.00 0.00 4.37
673 680 1.003233 GGCGCCTATCCAGAATCCC 60.003 63.158 22.15 0.00 0.00 3.85
674 681 1.754745 TGGCGCCTATCCAGAATCC 59.245 57.895 29.70 0.00 0.00 3.01
695 702 1.095600 GGGACGGGCAGAGATTTTTC 58.904 55.000 0.00 0.00 0.00 2.29
701 708 1.077805 TTACTGGGACGGGCAGAGA 59.922 57.895 0.00 0.00 40.47 3.10
705 712 1.373435 CAAGTTACTGGGACGGGCA 59.627 57.895 0.00 0.00 40.47 5.36
780 787 2.581354 CGCCTAGCAAGAGCAGGT 59.419 61.111 0.00 0.00 45.49 4.00
804 811 4.100373 AGTGTCTAGAGGAGAGCCATTTT 58.900 43.478 0.00 0.00 33.72 1.82
805 812 3.718723 AGTGTCTAGAGGAGAGCCATTT 58.281 45.455 0.00 0.00 33.72 2.32
807 814 3.030291 CAAGTGTCTAGAGGAGAGCCAT 58.970 50.000 0.00 0.00 33.72 4.40
808 815 2.041755 TCAAGTGTCTAGAGGAGAGCCA 59.958 50.000 0.00 0.00 33.72 4.75
865 872 1.651987 AATGGCGAGTAACCGTGATG 58.348 50.000 0.00 0.00 0.00 3.07
871 878 2.005971 AGTCGAAATGGCGAGTAACC 57.994 50.000 0.00 0.00 41.73 2.85
886 896 1.717645 GTGCTGGTTTACACGTAGTCG 59.282 52.381 0.00 0.00 41.61 4.18
1007 1027 2.555547 GGTTCTGTTGCTTGCCGCT 61.556 57.895 0.00 0.00 40.11 5.52
1239 1271 1.640069 CACGAATGCGCAGATCAGG 59.360 57.895 18.32 7.69 42.48 3.86
1503 1538 2.497928 GCGTACGTTGAGAGCGAGC 61.498 63.158 17.90 0.00 0.00 5.03
1551 1594 2.032071 GCGTGGGTGCCTAGTTGT 59.968 61.111 0.00 0.00 0.00 3.32
1552 1595 2.031919 TGCGTGGGTGCCTAGTTG 59.968 61.111 0.00 0.00 0.00 3.16
1571 1614 2.054140 TTTCTTCAACGTGTGGGCGC 62.054 55.000 0.00 0.00 34.88 6.53
1573 1616 2.159296 AGTTTTTCTTCAACGTGTGGGC 60.159 45.455 0.00 0.00 0.00 5.36
1574 1617 3.775661 AGTTTTTCTTCAACGTGTGGG 57.224 42.857 0.00 0.00 0.00 4.61
1576 1619 7.161418 CGTTAGTTAGTTTTTCTTCAACGTGTG 59.839 37.037 0.00 0.00 33.51 3.82
1583 1626 4.270566 TGCGCGTTAGTTAGTTTTTCTTCA 59.729 37.500 8.43 0.00 0.00 3.02
1594 1637 1.858458 GATCTGCATGCGCGTTAGTTA 59.142 47.619 14.09 0.00 42.97 2.24
1899 2007 0.251877 TCGACCACATACCCACCAGA 60.252 55.000 0.00 0.00 0.00 3.86
1908 2016 2.762327 GGGAAAGTAGGTCGACCACATA 59.238 50.000 35.00 17.12 38.89 2.29
2094 2205 0.535102 AGCACGTACCAAGCAAGCTT 60.535 50.000 0.59 0.59 36.60 3.74
2136 3102 0.667993 CACGGAGCAACATGGTTTGT 59.332 50.000 0.00 0.00 41.53 2.83
2151 3117 0.245539 AACGTATGGTCCTCACACGG 59.754 55.000 2.06 0.00 36.95 4.94
2154 3120 2.631062 ACAAGAACGTATGGTCCTCACA 59.369 45.455 0.00 0.00 0.00 3.58
2155 3121 3.251571 GACAAGAACGTATGGTCCTCAC 58.748 50.000 0.00 0.00 0.00 3.51
2165 3131 3.131577 AGTTGACCACTGACAAGAACGTA 59.868 43.478 0.00 0.00 32.83 3.57
2166 3132 2.093658 AGTTGACCACTGACAAGAACGT 60.094 45.455 0.00 0.00 32.83 3.99
2167 3133 2.540101 GAGTTGACCACTGACAAGAACG 59.460 50.000 0.00 0.00 35.01 3.95
2168 3134 3.798202 AGAGTTGACCACTGACAAGAAC 58.202 45.455 0.00 0.00 35.01 3.01
2169 3135 4.487714 AAGAGTTGACCACTGACAAGAA 57.512 40.909 0.00 0.00 35.01 2.52
2170 3136 4.191544 CAAAGAGTTGACCACTGACAAGA 58.808 43.478 0.00 0.00 35.01 3.02
2171 3137 3.313526 CCAAAGAGTTGACCACTGACAAG 59.686 47.826 0.00 0.00 35.01 3.16
2238 3447 3.262420 GCGGATAAGAAAGCAGAACAGA 58.738 45.455 0.00 0.00 0.00 3.41
2302 3523 1.761198 AGAACGTAGAAGCATACCCCC 59.239 52.381 0.00 0.00 0.00 5.40
2311 3532 0.526662 ACTGGCCGAGAACGTAGAAG 59.473 55.000 8.91 0.00 37.88 2.85
2324 3556 1.271163 TGGCTACAACTTGTACTGGCC 60.271 52.381 17.83 17.83 40.23 5.36
2382 3638 2.105766 AGGCCCTGCAAGAATTCATTC 58.894 47.619 8.44 0.00 34.07 2.67
2724 4047 4.767255 CCGCTCGCCTTGAAGCCT 62.767 66.667 0.00 0.00 0.00 4.58
3003 4326 2.267642 GTGATGTAGCCGGTGCCA 59.732 61.111 1.90 0.00 38.69 4.92
3202 4526 3.204382 ACAAGACAAAGAGAAAAGGGGGA 59.796 43.478 0.00 0.00 0.00 4.81
3207 4531 4.096984 ACCTGCACAAGACAAAGAGAAAAG 59.903 41.667 0.00 0.00 0.00 2.27
3265 4589 7.961827 CAGAGCACTTGAATTTTAATCTGAGTC 59.038 37.037 0.00 0.00 34.89 3.36
3271 4595 8.976986 ATGTTCAGAGCACTTGAATTTTAATC 57.023 30.769 0.00 0.00 0.00 1.75
3272 4596 9.768662 AAATGTTCAGAGCACTTGAATTTTAAT 57.231 25.926 0.00 0.00 0.00 1.40
3273 4597 9.248291 GAAATGTTCAGAGCACTTGAATTTTAA 57.752 29.630 0.00 0.00 0.00 1.52
3274 4598 8.412456 TGAAATGTTCAGAGCACTTGAATTTTA 58.588 29.630 0.00 0.00 34.08 1.52
3431 4758 5.970501 TGAGACAGAGGGAGTACTGTATA 57.029 43.478 0.00 0.00 45.54 1.47
3469 4832 7.431084 CCGTCCCAAAATAAAATAAATGTCTCG 59.569 37.037 0.00 0.00 0.00 4.04
3509 4874 7.011950 GCAATGGTGTTTGCTATACATAGTGTA 59.988 37.037 2.08 0.00 46.66 2.90
3558 4923 0.681733 GAGTTCCAGTGCACAGGAGA 59.318 55.000 27.37 17.19 32.93 3.71
3605 4975 1.378762 CGTGGGTGGGATTGGAACT 59.621 57.895 0.00 0.00 0.00 3.01
3619 4989 5.524284 TCCATACAAAATGTTGAAACGTGG 58.476 37.500 1.62 3.39 38.20 4.94
3649 5019 1.080354 ACATTCCCGACCCTCTCCA 59.920 57.895 0.00 0.00 0.00 3.86
3740 5112 3.440173 ACAACAGCAGAAAATCATACCGG 59.560 43.478 0.00 0.00 0.00 5.28
3756 5128 5.731686 GCACAAGAAGAAGGAAGAACAACAG 60.732 44.000 0.00 0.00 0.00 3.16
3809 5182 3.324108 GGCCGGACTAACCACCCA 61.324 66.667 5.05 0.00 38.90 4.51
3836 5209 1.406180 GAAGAGAACTAGGACCCGCTC 59.594 57.143 0.00 0.00 0.00 5.03
3840 5213 1.832366 GGTGGAAGAGAACTAGGACCC 59.168 57.143 0.00 0.00 0.00 4.46
3867 5241 8.774183 TGGTTTTCAATACCACTATATGTACCT 58.226 33.333 0.00 0.00 40.65 3.08
3894 5268 2.044555 CACCAGTCCTCGCCGTCTA 61.045 63.158 0.00 0.00 0.00 2.59
3904 5279 1.181098 AAACATGCCTGCACCAGTCC 61.181 55.000 0.00 0.00 0.00 3.85
3906 5281 0.467844 TCAAACATGCCTGCACCAGT 60.468 50.000 0.00 0.00 0.00 4.00
3949 5324 2.018542 TTTATTCTCTTCGGCACCGG 57.981 50.000 9.58 0.00 40.25 5.28
3965 5340 1.779221 CCATGCTGCTTCCCCATTTA 58.221 50.000 0.00 0.00 0.00 1.40
3968 5343 2.443390 GCCATGCTGCTTCCCCAT 60.443 61.111 0.00 0.00 0.00 4.00
3974 5349 2.133281 TAATCACTGCCATGCTGCTT 57.867 45.000 0.00 0.00 0.00 3.91
4016 5391 2.574450 TCTGCATTCAGACACAAGCAA 58.426 42.857 0.00 0.00 43.95 3.91
4048 5423 1.831652 AACCTTGCGAGGAGACCCTG 61.832 60.000 27.65 0.00 46.74 4.45
4081 5457 1.991965 CGAAGACTTCTGAAGCTCTGC 59.008 52.381 17.00 14.92 0.00 4.26
4119 5495 2.028484 TGTCTCGTGGGCGTTGTC 59.972 61.111 0.00 0.00 39.49 3.18
4168 5718 1.594310 GAGGATATGGGGAGAGCGC 59.406 63.158 0.00 0.00 0.00 5.92
4210 5760 0.038166 GGTGGAGAAGGCATTGGTCA 59.962 55.000 0.00 0.00 0.00 4.02
4212 5762 1.002134 CGGTGGAGAAGGCATTGGT 60.002 57.895 0.00 0.00 0.00 3.67
4291 5841 6.069440 AGAGACATGATTTGGGAGATTGGTAA 60.069 38.462 0.00 0.00 0.00 2.85
4292 5842 5.429762 AGAGACATGATTTGGGAGATTGGTA 59.570 40.000 0.00 0.00 0.00 3.25
4297 5847 6.069789 TCAGAAAGAGACATGATTTGGGAGAT 60.070 38.462 0.00 0.00 0.00 2.75
4308 5858 4.302455 ACTTCACGTCAGAAAGAGACATG 58.698 43.478 0.00 0.00 35.77 3.21
4312 5862 3.314357 TCGAACTTCACGTCAGAAAGAGA 59.686 43.478 0.00 0.00 0.00 3.10
4314 5864 3.703286 TCGAACTTCACGTCAGAAAGA 57.297 42.857 0.00 0.00 0.00 2.52
4324 5874 2.287009 CCAAGCCTTGTTCGAACTTCAC 60.287 50.000 27.32 15.05 0.00 3.18
4326 5876 1.335051 GCCAAGCCTTGTTCGAACTTC 60.335 52.381 27.32 13.93 0.00 3.01
4341 5891 2.169832 TCAAGTCCTCGAAAGCCAAG 57.830 50.000 0.00 0.00 0.00 3.61
4345 5895 3.589988 TCAAGATCAAGTCCTCGAAAGC 58.410 45.455 0.00 0.00 0.00 3.51
4350 5900 4.815269 ACTTCTTCAAGATCAAGTCCTCG 58.185 43.478 0.00 0.00 33.34 4.63
4364 5914 6.038271 GTCTACAAGAAAGCCAAACTTCTTCA 59.962 38.462 0.00 0.00 37.75 3.02
4378 5928 6.340962 TCCTTCGATGAAGTCTACAAGAAA 57.659 37.500 5.88 0.00 37.92 2.52
4382 5932 4.770531 TCCTTCCTTCGATGAAGTCTACAA 59.229 41.667 18.50 1.59 37.92 2.41
4383 5933 4.341487 TCCTTCCTTCGATGAAGTCTACA 58.659 43.478 18.50 0.00 37.92 2.74
4387 5937 5.017294 AGATTCCTTCCTTCGATGAAGTC 57.983 43.478 18.50 12.24 37.92 3.01
4407 5957 6.106673 CGCCACTAGAAAGAATTCCTTTAGA 58.893 40.000 0.65 0.00 44.63 2.10
4413 5963 3.261981 TCCGCCACTAGAAAGAATTCC 57.738 47.619 0.65 0.00 36.12 3.01
4421 5971 4.647611 TCTTGAAAAATCCGCCACTAGAA 58.352 39.130 0.00 0.00 0.00 2.10
4425 5975 3.420893 TGATCTTGAAAAATCCGCCACT 58.579 40.909 0.00 0.00 0.00 4.00
4437 5987 6.431852 TGTTGAGCATGATCTTTGATCTTGAA 59.568 34.615 20.35 8.68 30.97 2.69
4450 6000 4.586884 ACTGAGTCAATGTTGAGCATGAT 58.413 39.130 0.00 0.00 37.98 2.45
4451 6001 4.011966 ACTGAGTCAATGTTGAGCATGA 57.988 40.909 0.00 0.00 37.98 3.07
4452 6002 4.331992 CCTACTGAGTCAATGTTGAGCATG 59.668 45.833 0.00 0.00 37.98 4.06
4453 6003 4.511527 CCTACTGAGTCAATGTTGAGCAT 58.488 43.478 0.00 0.00 37.98 3.79
4454 6004 3.306989 CCCTACTGAGTCAATGTTGAGCA 60.307 47.826 0.00 0.00 37.98 4.26
4465 6015 3.954904 TGTAGAATGAGCCCTACTGAGTC 59.045 47.826 0.00 0.00 36.94 3.36
4489 6039 4.134623 GTGTCCACCAAAGCACGA 57.865 55.556 0.00 0.00 0.00 4.35
4493 6043 2.594592 AGGCGTGTCCACCAAAGC 60.595 61.111 0.00 0.00 37.29 3.51
4497 6047 2.994995 ATCGAGGCGTGTCCACCA 60.995 61.111 0.00 0.00 37.29 4.17
4498 6048 2.509336 CATCGAGGCGTGTCCACC 60.509 66.667 0.00 0.00 37.29 4.61
4499 6049 1.352156 GAACATCGAGGCGTGTCCAC 61.352 60.000 0.00 0.00 37.29 4.02
4500 6050 1.080093 GAACATCGAGGCGTGTCCA 60.080 57.895 0.00 0.00 37.29 4.02
4501 6051 0.669318 TTGAACATCGAGGCGTGTCC 60.669 55.000 0.00 0.00 0.00 4.02
4502 6052 0.716108 CTTGAACATCGAGGCGTGTC 59.284 55.000 0.00 0.00 0.00 3.67
4503 6053 0.670546 CCTTGAACATCGAGGCGTGT 60.671 55.000 0.00 0.00 40.92 4.49
4504 6054 2.081526 CCTTGAACATCGAGGCGTG 58.918 57.895 0.00 0.00 40.92 5.34
4505 6055 4.598257 CCTTGAACATCGAGGCGT 57.402 55.556 0.00 0.00 40.92 5.68
4509 6059 5.207768 CAACAAGAAACCTTGAACATCGAG 58.792 41.667 11.60 0.00 42.71 4.04
4510 6060 4.638421 ACAACAAGAAACCTTGAACATCGA 59.362 37.500 11.60 0.00 42.71 3.59
4511 6061 4.920376 ACAACAAGAAACCTTGAACATCG 58.080 39.130 11.60 0.00 42.71 3.84
4512 6062 5.890334 TGACAACAAGAAACCTTGAACATC 58.110 37.500 11.60 4.96 42.71 3.06
4513 6063 5.913137 TGACAACAAGAAACCTTGAACAT 57.087 34.783 11.60 0.00 42.71 2.71
4514 6064 5.713792 TTGACAACAAGAAACCTTGAACA 57.286 34.783 11.60 4.11 42.71 3.18
4515 6065 7.595311 ATTTTGACAACAAGAAACCTTGAAC 57.405 32.000 11.60 2.03 42.71 3.18
4516 6066 7.118971 CCAATTTTGACAACAAGAAACCTTGAA 59.881 33.333 11.60 0.00 42.71 2.69
4517 6067 6.593382 CCAATTTTGACAACAAGAAACCTTGA 59.407 34.615 11.60 0.00 42.71 3.02
4518 6068 6.371271 ACCAATTTTGACAACAAGAAACCTTG 59.629 34.615 3.85 3.85 44.92 3.61
4519 6069 6.472016 ACCAATTTTGACAACAAGAAACCTT 58.528 32.000 0.00 0.00 37.32 3.50
4520 6070 6.048732 ACCAATTTTGACAACAAGAAACCT 57.951 33.333 0.00 0.00 37.32 3.50
4521 6071 6.106003 AGACCAATTTTGACAACAAGAAACC 58.894 36.000 0.00 0.00 37.32 3.27
4522 6072 7.595311 AAGACCAATTTTGACAACAAGAAAC 57.405 32.000 0.00 0.00 37.32 2.78
4523 6073 7.875041 TGAAAGACCAATTTTGACAACAAGAAA 59.125 29.630 0.00 0.00 37.32 2.52
4524 6074 7.382110 TGAAAGACCAATTTTGACAACAAGAA 58.618 30.769 0.00 0.00 37.32 2.52
4525 6075 6.929625 TGAAAGACCAATTTTGACAACAAGA 58.070 32.000 0.00 0.00 37.32 3.02
4526 6076 7.331687 ACTTGAAAGACCAATTTTGACAACAAG 59.668 33.333 0.00 0.00 37.32 3.16
4527 6077 7.158021 ACTTGAAAGACCAATTTTGACAACAA 58.842 30.769 0.00 0.00 0.00 2.83
4528 6078 6.696411 ACTTGAAAGACCAATTTTGACAACA 58.304 32.000 0.00 0.00 0.00 3.33
4529 6079 7.545615 AGAACTTGAAAGACCAATTTTGACAAC 59.454 33.333 0.00 0.00 0.00 3.32
4530 6080 7.610865 AGAACTTGAAAGACCAATTTTGACAA 58.389 30.769 0.00 0.00 0.00 3.18
4531 6081 7.169158 AGAACTTGAAAGACCAATTTTGACA 57.831 32.000 0.00 0.00 0.00 3.58
4532 6082 9.237846 CTTAGAACTTGAAAGACCAATTTTGAC 57.762 33.333 0.00 0.00 0.00 3.18
4533 6083 8.966868 ACTTAGAACTTGAAAGACCAATTTTGA 58.033 29.630 0.00 0.00 0.00 2.69
4534 6084 9.586435 AACTTAGAACTTGAAAGACCAATTTTG 57.414 29.630 0.00 0.00 0.00 2.44
4535 6085 9.586435 CAACTTAGAACTTGAAAGACCAATTTT 57.414 29.630 0.00 0.00 0.00 1.82
4536 6086 7.706607 GCAACTTAGAACTTGAAAGACCAATTT 59.293 33.333 0.00 0.00 0.00 1.82
4537 6087 7.147915 TGCAACTTAGAACTTGAAAGACCAATT 60.148 33.333 0.00 0.00 0.00 2.32
4538 6088 6.321181 TGCAACTTAGAACTTGAAAGACCAAT 59.679 34.615 0.00 0.00 0.00 3.16
4539 6089 5.650266 TGCAACTTAGAACTTGAAAGACCAA 59.350 36.000 0.00 0.00 0.00 3.67
4540 6090 5.189928 TGCAACTTAGAACTTGAAAGACCA 58.810 37.500 0.00 0.00 0.00 4.02
4541 6091 5.751243 TGCAACTTAGAACTTGAAAGACC 57.249 39.130 0.00 0.00 0.00 3.85
4542 6092 6.959361 TGATGCAACTTAGAACTTGAAAGAC 58.041 36.000 0.00 0.00 0.00 3.01
4543 6093 7.566760 TTGATGCAACTTAGAACTTGAAAGA 57.433 32.000 0.00 0.00 0.00 2.52
4544 6094 7.380602 CCTTTGATGCAACTTAGAACTTGAAAG 59.619 37.037 0.00 0.00 0.00 2.62
4545 6095 7.068103 TCCTTTGATGCAACTTAGAACTTGAAA 59.932 33.333 0.00 0.00 0.00 2.69
4546 6096 6.545666 TCCTTTGATGCAACTTAGAACTTGAA 59.454 34.615 0.00 0.00 0.00 2.69
4547 6097 6.061441 TCCTTTGATGCAACTTAGAACTTGA 58.939 36.000 0.00 0.00 0.00 3.02
4548 6098 6.317789 TCCTTTGATGCAACTTAGAACTTG 57.682 37.500 0.00 0.00 0.00 3.16
4549 6099 6.917533 CATCCTTTGATGCAACTTAGAACTT 58.082 36.000 0.00 0.00 41.81 2.66
4550 6100 6.506500 CATCCTTTGATGCAACTTAGAACT 57.493 37.500 0.00 0.00 41.81 3.01
4560 6110 7.959899 GGCCATACCTACATCCTTTGATGCA 62.960 48.000 0.00 0.00 43.14 3.96
4561 6111 5.581867 GGCCATACCTACATCCTTTGATGC 61.582 50.000 0.00 0.00 43.14 3.91
4562 6112 4.074970 GGCCATACCTACATCCTTTGATG 58.925 47.826 0.00 1.16 44.08 3.07
4563 6113 3.721575 TGGCCATACCTACATCCTTTGAT 59.278 43.478 0.00 0.00 40.22 2.57
4564 6114 3.119319 TGGCCATACCTACATCCTTTGA 58.881 45.455 0.00 0.00 40.22 2.69
4565 6115 3.576078 TGGCCATACCTACATCCTTTG 57.424 47.619 0.00 0.00 40.22 2.77
4566 6116 4.814224 AATGGCCATACCTACATCCTTT 57.186 40.909 21.15 0.00 40.22 3.11
4567 6117 4.814224 AAATGGCCATACCTACATCCTT 57.186 40.909 21.15 1.95 40.22 3.36
4568 6118 4.167892 TCAAAATGGCCATACCTACATCCT 59.832 41.667 21.15 0.00 40.22 3.24
4569 6119 4.469657 TCAAAATGGCCATACCTACATCC 58.530 43.478 21.15 0.00 40.22 3.51
4570 6120 5.010012 CCTTCAAAATGGCCATACCTACATC 59.990 44.000 21.15 0.00 40.22 3.06
4571 6121 4.895297 CCTTCAAAATGGCCATACCTACAT 59.105 41.667 21.15 0.00 40.22 2.29
4572 6122 4.277476 CCTTCAAAATGGCCATACCTACA 58.723 43.478 21.15 0.76 40.22 2.74
4573 6123 3.636764 CCCTTCAAAATGGCCATACCTAC 59.363 47.826 21.15 0.00 40.22 3.18
4574 6124 3.529734 TCCCTTCAAAATGGCCATACCTA 59.470 43.478 21.15 2.34 40.22 3.08
4575 6125 2.314549 TCCCTTCAAAATGGCCATACCT 59.685 45.455 21.15 0.00 40.22 3.08
4576 6126 2.695147 CTCCCTTCAAAATGGCCATACC 59.305 50.000 21.15 0.00 39.84 2.73
4577 6127 2.695147 CCTCCCTTCAAAATGGCCATAC 59.305 50.000 21.15 0.00 0.00 2.39
4578 6128 2.314549 ACCTCCCTTCAAAATGGCCATA 59.685 45.455 21.15 0.00 0.00 2.74
4579 6129 1.079323 ACCTCCCTTCAAAATGGCCAT 59.921 47.619 14.09 14.09 0.00 4.40
4580 6130 0.486879 ACCTCCCTTCAAAATGGCCA 59.513 50.000 8.56 8.56 0.00 5.36
4581 6131 2.525105 TACCTCCCTTCAAAATGGCC 57.475 50.000 0.00 0.00 0.00 5.36


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

AutoCloner maintained by Alex Coulton.