Multiple sequence alignment - TraesCS3D01G481200

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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 TraesCS3D01G481200 chr3D 100.000 5344 0 0 1 5344 579424942 579419599 0.000000e+00 9869.0
1 TraesCS3D01G481200 chr3D 91.814 2822 176 15 865 3679 579396387 579393614 0.000000e+00 3880.0
2 TraesCS3D01G481200 chr3D 89.773 1721 158 13 2704 4417 579587107 579588816 0.000000e+00 2187.0
3 TraesCS3D01G481200 chr3D 91.090 1459 128 2 995 2452 579585221 579586678 0.000000e+00 1973.0
4 TraesCS3D01G481200 chr3D 89.037 748 68 10 3675 4417 579383798 579383060 0.000000e+00 915.0
5 TraesCS3D01G481200 chr3D 80.597 134 10 5 2554 2671 579586698 579586831 7.370000e-14 89.8
6 TraesCS3D01G481200 chr3B 94.959 3432 145 7 995 4417 773761161 773757749 0.000000e+00 5354.0
7 TraesCS3D01G481200 chr3B 89.211 1826 155 20 2618 4416 773900088 773901898 0.000000e+00 2242.0
8 TraesCS3D01G481200 chr3B 90.646 1315 121 2 995 2308 773898542 773899855 0.000000e+00 1746.0
9 TraesCS3D01G481200 chr3B 88.473 668 60 10 3756 4416 773743745 773743088 0.000000e+00 791.0
10 TraesCS3D01G481200 chr3B 91.209 546 42 6 1 544 773745437 773744896 0.000000e+00 737.0
11 TraesCS3D01G481200 chr3B 83.300 503 56 19 4852 5344 773878109 773878593 6.350000e-119 438.0
12 TraesCS3D01G481200 chr3B 89.434 265 25 3 5081 5344 773750172 773749910 1.110000e-86 331.0
13 TraesCS3D01G481200 chr3B 91.803 183 15 0 2292 2474 773899873 773900055 6.870000e-64 255.0
14 TraesCS3D01G481200 chr3B 89.412 170 17 1 4225 4393 773877938 773878107 4.190000e-51 213.0
15 TraesCS3D01G481200 chr3B 85.333 150 16 4 5197 5344 773513012 773513157 3.330000e-32 150.0
16 TraesCS3D01G481200 chr3B 83.969 131 15 5 4910 5035 773751420 773751291 2.610000e-23 121.0
17 TraesCS3D01G481200 chr3B 85.106 94 12 2 5252 5344 773521861 773521953 1.580000e-15 95.3
18 TraesCS3D01G481200 chr3A 89.772 3559 313 25 886 4420 714591866 714588335 0.000000e+00 4508.0
19 TraesCS3D01G481200 chr3A 89.263 1723 156 14 2704 4417 714645540 714647242 0.000000e+00 2130.0
20 TraesCS3D01G481200 chr3A 89.514 1316 135 3 995 2310 714643602 714644914 0.000000e+00 1663.0
21 TraesCS3D01G481200 chr3A 95.585 906 35 3 4416 5319 714602227 714601325 0.000000e+00 1447.0
22 TraesCS3D01G481200 chr3A 93.481 767 47 2 1858 2623 714627775 714628539 0.000000e+00 1136.0
23 TraesCS3D01G481200 chr3A 95.938 640 24 2 3783 4420 714602912 714602273 0.000000e+00 1037.0
24 TraesCS3D01G481200 chr3A 90.975 554 44 6 1 552 714593584 714593035 0.000000e+00 741.0
25 TraesCS3D01G481200 chr3A 91.199 534 39 5 1 532 714625958 714626485 0.000000e+00 719.0
26 TraesCS3D01G481200 chr3A 92.896 183 13 0 2292 2474 714644930 714645112 3.170000e-67 267.0
27 TraesCS3D01G481200 chr3A 85.714 140 14 3 5206 5344 714524133 714524267 5.580000e-30 143.0
28 TraesCS3D01G481200 chr3A 87.850 107 13 0 886 992 714643463 714643569 5.620000e-25 126.0
29 TraesCS3D01G481200 chr3A 97.561 41 1 0 1 41 714602949 714602909 2.670000e-08 71.3


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 TraesCS3D01G481200 chr3D 579419599 579424942 5343 True 9869.000000 9869 100.000000 1 5344 1 chr3D.!!$R3 5343
1 TraesCS3D01G481200 chr3D 579393614 579396387 2773 True 3880.000000 3880 91.814000 865 3679 1 chr3D.!!$R2 2814
2 TraesCS3D01G481200 chr3D 579585221 579588816 3595 False 1416.600000 2187 87.153333 995 4417 3 chr3D.!!$F1 3422
3 TraesCS3D01G481200 chr3D 579383060 579383798 738 True 915.000000 915 89.037000 3675 4417 1 chr3D.!!$R1 742
4 TraesCS3D01G481200 chr3B 773757749 773761161 3412 True 5354.000000 5354 94.959000 995 4417 1 chr3B.!!$R1 3422
5 TraesCS3D01G481200 chr3B 773898542 773901898 3356 False 1414.333333 2242 90.553333 995 4416 3 chr3B.!!$F4 3421
6 TraesCS3D01G481200 chr3B 773743088 773745437 2349 True 764.000000 791 89.841000 1 4416 2 chr3B.!!$R2 4415
7 TraesCS3D01G481200 chr3B 773877938 773878593 655 False 325.500000 438 86.356000 4225 5344 2 chr3B.!!$F3 1119
8 TraesCS3D01G481200 chr3B 773749910 773751420 1510 True 226.000000 331 86.701500 4910 5344 2 chr3B.!!$R3 434
9 TraesCS3D01G481200 chr3A 714588335 714593584 5249 True 2624.500000 4508 90.373500 1 4420 2 chr3A.!!$R1 4419
10 TraesCS3D01G481200 chr3A 714643463 714647242 3779 False 1046.500000 2130 89.880750 886 4417 4 chr3A.!!$F3 3531
11 TraesCS3D01G481200 chr3A 714625958 714628539 2581 False 927.500000 1136 92.340000 1 2623 2 chr3A.!!$F2 2622
12 TraesCS3D01G481200 chr3A 714601325 714602949 1624 True 851.766667 1447 96.361333 1 5319 3 chr3A.!!$R2 5318

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
631 672 0.032130 GGCAGTGAAGTGTCGACAGA 59.968 55.000 20.73 0.0 0.00 3.41 F
1630 2704 0.179018 GGATGGGTCAGTGCCATACC 60.179 60.000 2.57 0.0 0.00 2.73 F
3195 5010 1.067364 TGCCACTTGTTGCTGTGATTG 59.933 47.619 0.00 0.0 36.38 2.67 F
3753 5579 0.033504 GGTGGAGACGAGCAACAAGA 59.966 55.000 0.00 0.0 0.00 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1803 2877 4.858850 TGGTATTCCATCTCAACAGCATT 58.141 39.130 0.00 0.00 39.03 3.56 R
3590 5415 2.238898 GCCCTCTAGCCACTCCTTTTAA 59.761 50.000 0.00 0.00 0.00 1.52 R
4054 5882 0.323725 AAGGCATTCCGGACATTGCT 60.324 50.000 24.52 13.08 37.47 3.91 R
4958 6865 1.135315 CTGAAATTGTCGCCTGCCG 59.865 57.895 0.00 0.00 38.61 5.69 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
89 90 0.749649 AGGTCTAATGCAGAGGCTCG 59.250 55.000 9.22 5.44 41.91 5.03
131 132 4.380843 TGGGTGAAGTAATGTGTGGATT 57.619 40.909 0.00 0.00 0.00 3.01
212 213 8.807118 TGTAAATGCTTGGTTAACAAATATGGA 58.193 29.630 8.10 0.00 38.91 3.41
279 280 8.324191 TCTTGTTTCAGAGGTCAATATATCCT 57.676 34.615 0.00 0.00 0.00 3.24
296 297 2.215196 TCCTGCAACAACGGTAAGTTC 58.785 47.619 0.00 0.00 42.02 3.01
313 314 1.340889 GTTCCCAGCTGCACATGAAAA 59.659 47.619 8.66 0.00 0.00 2.29
353 354 7.716998 ACATTATCAACTGCTAATGGGACTTAG 59.283 37.037 14.53 0.00 38.03 2.18
418 419 2.886913 TGAATGCCCATGGACAGAAAA 58.113 42.857 15.22 0.00 0.00 2.29
419 420 3.443052 TGAATGCCCATGGACAGAAAAT 58.557 40.909 15.22 0.00 0.00 1.82
420 421 3.839490 TGAATGCCCATGGACAGAAAATT 59.161 39.130 15.22 0.00 0.00 1.82
430 431 5.789643 TGGACAGAAAATTGGAAGAAAGG 57.210 39.130 0.00 0.00 0.00 3.11
441 442 9.764363 AAAATTGGAAGAAAGGTACTGAAAATC 57.236 29.630 0.00 0.00 40.86 2.17
476 477 5.351465 CAGAGAAAGCTCGTTTAATGCCTTA 59.649 40.000 0.00 0.00 45.98 2.69
482 483 5.428253 AGCTCGTTTAATGCCTTATTCTCA 58.572 37.500 0.00 0.00 0.00 3.27
510 513 6.091305 GGTTTTCTTTGCCAAGATAAAGATGC 59.909 38.462 0.37 0.00 41.15 3.91
533 536 5.390461 GCATCTTATGACTTACACGTGCAAA 60.390 40.000 17.22 9.64 0.00 3.68
561 571 4.044336 GACTGAGAGAGTCCACATGATG 57.956 50.000 0.00 0.00 44.95 3.07
577 618 3.600410 ATGGCCCCTTGAAACCCCG 62.600 63.158 0.00 0.00 0.00 5.73
605 646 8.682016 GTTGAAGTCAAATGTGATTTTTCTACG 58.318 33.333 0.00 0.00 34.13 3.51
610 651 9.003658 AGTCAAATGTGATTTTTCTACGAAGAT 57.996 29.630 0.00 0.00 35.80 2.40
613 654 9.708222 CAAATGTGATTTTTCTACGAAGATAGG 57.292 33.333 0.00 0.00 0.00 2.57
615 656 6.403049 TGTGATTTTTCTACGAAGATAGGCA 58.597 36.000 0.00 0.00 0.00 4.75
618 659 6.535150 TGATTTTTCTACGAAGATAGGCAGTG 59.465 38.462 0.00 0.00 0.00 3.66
619 660 5.654603 TTTTCTACGAAGATAGGCAGTGA 57.345 39.130 0.00 0.00 0.00 3.41
621 662 4.902443 TCTACGAAGATAGGCAGTGAAG 57.098 45.455 0.00 0.00 0.00 3.02
623 664 3.238108 ACGAAGATAGGCAGTGAAGTG 57.762 47.619 0.00 0.00 0.00 3.16
625 666 3.182967 CGAAGATAGGCAGTGAAGTGTC 58.817 50.000 0.00 0.00 0.00 3.67
630 671 0.032678 AGGCAGTGAAGTGTCGACAG 59.967 55.000 20.73 6.41 0.00 3.51
631 672 0.032130 GGCAGTGAAGTGTCGACAGA 59.968 55.000 20.73 0.00 0.00 3.41
632 673 1.413382 GCAGTGAAGTGTCGACAGAG 58.587 55.000 20.73 5.05 0.00 3.35
633 674 1.932604 GCAGTGAAGTGTCGACAGAGG 60.933 57.143 20.73 5.76 0.00 3.69
635 676 1.609555 AGTGAAGTGTCGACAGAGGAC 59.390 52.381 20.73 13.43 34.99 3.85
637 678 1.609072 TGAAGTGTCGACAGAGGACAG 59.391 52.381 20.73 0.00 44.43 3.51
638 679 0.315568 AAGTGTCGACAGAGGACAGC 59.684 55.000 20.73 4.30 44.43 4.40
639 680 0.538516 AGTGTCGACAGAGGACAGCT 60.539 55.000 20.73 6.87 44.43 4.24
640 681 0.315568 GTGTCGACAGAGGACAGCTT 59.684 55.000 20.73 0.00 44.43 3.74
642 683 1.412710 TGTCGACAGAGGACAGCTTTT 59.587 47.619 15.76 0.00 39.36 2.27
643 684 2.062519 GTCGACAGAGGACAGCTTTTC 58.937 52.381 11.55 0.00 34.56 2.29
644 685 1.686587 TCGACAGAGGACAGCTTTTCA 59.313 47.619 0.00 0.00 0.00 2.69
646 687 2.478134 CGACAGAGGACAGCTTTTCAAG 59.522 50.000 0.00 0.00 0.00 3.02
648 689 4.632153 GACAGAGGACAGCTTTTCAAGTA 58.368 43.478 0.00 0.00 0.00 2.24
649 690 4.381411 ACAGAGGACAGCTTTTCAAGTAC 58.619 43.478 0.00 0.00 0.00 2.73
650 691 3.748568 CAGAGGACAGCTTTTCAAGTACC 59.251 47.826 0.00 0.00 0.00 3.34
651 692 2.737252 GAGGACAGCTTTTCAAGTACCG 59.263 50.000 0.00 0.00 0.00 4.02
652 693 1.197036 GGACAGCTTTTCAAGTACCGC 59.803 52.381 0.00 0.00 0.00 5.68
653 694 1.871039 GACAGCTTTTCAAGTACCGCA 59.129 47.619 0.00 0.00 0.00 5.69
654 695 2.484264 GACAGCTTTTCAAGTACCGCAT 59.516 45.455 0.00 0.00 0.00 4.73
655 696 2.884639 ACAGCTTTTCAAGTACCGCATT 59.115 40.909 0.00 0.00 0.00 3.56
656 697 3.236816 CAGCTTTTCAAGTACCGCATTG 58.763 45.455 0.00 0.00 0.00 2.82
657 698 2.884639 AGCTTTTCAAGTACCGCATTGT 59.115 40.909 0.00 0.00 0.00 2.71
658 699 3.317993 AGCTTTTCAAGTACCGCATTGTT 59.682 39.130 0.00 0.00 0.00 2.83
659 700 3.425193 GCTTTTCAAGTACCGCATTGTTG 59.575 43.478 0.00 0.00 0.00 3.33
660 701 3.634568 TTTCAAGTACCGCATTGTTGG 57.365 42.857 0.00 0.00 0.00 3.77
662 703 2.422597 TCAAGTACCGCATTGTTGGAG 58.577 47.619 4.38 0.00 0.00 3.86
664 705 1.808411 AGTACCGCATTGTTGGAGTG 58.192 50.000 4.38 0.00 0.00 3.51
665 706 0.802494 GTACCGCATTGTTGGAGTGG 59.198 55.000 4.38 0.00 38.83 4.00
666 707 0.398696 TACCGCATTGTTGGAGTGGT 59.601 50.000 0.00 0.00 46.87 4.16
667 708 1.172180 ACCGCATTGTTGGAGTGGTG 61.172 55.000 0.00 0.00 43.93 4.17
668 709 1.580942 CGCATTGTTGGAGTGGTGG 59.419 57.895 0.00 0.00 0.00 4.61
671 712 1.895131 GCATTGTTGGAGTGGTGGAAT 59.105 47.619 0.00 0.00 0.00 3.01
672 713 2.353011 GCATTGTTGGAGTGGTGGAATG 60.353 50.000 0.00 0.00 0.00 2.67
673 714 1.993956 TTGTTGGAGTGGTGGAATGG 58.006 50.000 0.00 0.00 0.00 3.16
674 715 1.144691 TGTTGGAGTGGTGGAATGGA 58.855 50.000 0.00 0.00 0.00 3.41
675 716 1.710244 TGTTGGAGTGGTGGAATGGAT 59.290 47.619 0.00 0.00 0.00 3.41
676 717 2.290896 TGTTGGAGTGGTGGAATGGATC 60.291 50.000 0.00 0.00 0.00 3.36
697 1111 7.455953 TGGATCCAAGTATATCACTATCAGCTT 59.544 37.037 13.46 0.00 36.04 3.74
699 1113 8.663209 ATCCAAGTATATCACTATCAGCTTCT 57.337 34.615 0.00 0.00 36.04 2.85
700 1114 8.484214 TCCAAGTATATCACTATCAGCTTCTT 57.516 34.615 0.00 0.00 36.04 2.52
703 1117 9.409312 CAAGTATATCACTATCAGCTTCTTGAG 57.591 37.037 0.00 0.00 36.04 3.02
705 1119 9.013229 AGTATATCACTATCAGCTTCTTGAGAG 57.987 37.037 0.00 0.00 41.12 3.20
708 1122 4.734398 ACTATCAGCTTCTTGAGAGTGG 57.266 45.455 2.83 0.00 45.18 4.00
709 1123 4.093011 ACTATCAGCTTCTTGAGAGTGGT 58.907 43.478 2.83 0.00 45.18 4.16
713 1127 5.489792 TCAGCTTCTTGAGAGTGGTAAAT 57.510 39.130 0.00 0.00 0.00 1.40
718 1132 5.121454 GCTTCTTGAGAGTGGTAAATGACAG 59.879 44.000 0.00 0.00 0.00 3.51
719 1133 5.152623 TCTTGAGAGTGGTAAATGACAGG 57.847 43.478 0.00 0.00 0.00 4.00
723 1137 4.020218 TGAGAGTGGTAAATGACAGGAAGG 60.020 45.833 0.00 0.00 0.00 3.46
726 1140 3.394606 AGTGGTAAATGACAGGAAGGTGT 59.605 43.478 0.00 0.00 0.00 4.16
747 1785 5.009210 GTGTTGTACCTTTCTGGCATTTACA 59.991 40.000 0.00 0.00 40.22 2.41
751 1789 5.830991 TGTACCTTTCTGGCATTTACAACTT 59.169 36.000 0.00 0.00 40.22 2.66
753 1791 5.600696 ACCTTTCTGGCATTTACAACTTTG 58.399 37.500 0.00 0.00 40.22 2.77
771 1809 7.905604 AACTTTGAAGTTGATACGATGATGA 57.094 32.000 8.24 0.00 46.80 2.92
772 1810 8.498054 AACTTTGAAGTTGATACGATGATGAT 57.502 30.769 8.24 0.00 46.80 2.45
773 1811 7.913423 ACTTTGAAGTTGATACGATGATGATG 58.087 34.615 0.00 0.00 35.21 3.07
775 1813 8.667076 TTTGAAGTTGATACGATGATGATGAT 57.333 30.769 0.00 0.00 0.00 2.45
776 1814 9.762933 TTTGAAGTTGATACGATGATGATGATA 57.237 29.630 0.00 0.00 0.00 2.15
793 1834 8.923838 ATGATGATAGTATTAGGACCCATTCT 57.076 34.615 0.00 0.00 0.00 2.40
798 1839 7.453752 TGATAGTATTAGGACCCATTCTACCAC 59.546 40.741 0.00 0.00 0.00 4.16
800 1841 5.602978 AGTATTAGGACCCATTCTACCACTG 59.397 44.000 0.00 0.00 0.00 3.66
803 1844 1.913419 GGACCCATTCTACCACTGGAA 59.087 52.381 0.71 0.00 31.38 3.53
807 1848 2.242196 CCCATTCTACCACTGGAACCAT 59.758 50.000 0.71 0.00 31.38 3.55
808 1849 3.282021 CCATTCTACCACTGGAACCATG 58.718 50.000 0.71 0.00 31.38 3.66
809 1850 2.489938 TTCTACCACTGGAACCATGC 57.510 50.000 0.71 0.00 0.00 4.06
810 1851 1.357137 TCTACCACTGGAACCATGCA 58.643 50.000 0.71 0.00 0.00 3.96
820 1861 5.389859 CTGGAACCATGCAGTATTTGAAA 57.610 39.130 0.00 0.00 39.92 2.69
822 1863 6.166984 TGGAACCATGCAGTATTTGAAAAA 57.833 33.333 0.00 0.00 0.00 1.94
823 1864 5.988561 TGGAACCATGCAGTATTTGAAAAAC 59.011 36.000 0.00 0.00 0.00 2.43
824 1865 6.183360 TGGAACCATGCAGTATTTGAAAAACT 60.183 34.615 0.00 0.00 0.00 2.66
825 1866 6.146021 GGAACCATGCAGTATTTGAAAAACTG 59.854 38.462 0.00 10.89 42.80 3.16
826 1867 6.160576 ACCATGCAGTATTTGAAAAACTGT 57.839 33.333 14.14 0.00 42.10 3.55
832 1873 5.241728 GCAGTATTTGAAAAACTGTCCCTCT 59.758 40.000 14.14 0.00 42.10 3.69
845 1886 2.705658 TGTCCCTCTGTTCACACTTCAT 59.294 45.455 0.00 0.00 0.00 2.57
847 1888 4.346709 TGTCCCTCTGTTCACACTTCATTA 59.653 41.667 0.00 0.00 0.00 1.90
848 1889 4.932200 GTCCCTCTGTTCACACTTCATTAG 59.068 45.833 0.00 0.00 0.00 1.73
851 1892 4.391216 CCTCTGTTCACACTTCATTAGCTG 59.609 45.833 0.00 0.00 0.00 4.24
852 1893 4.960938 TCTGTTCACACTTCATTAGCTGT 58.039 39.130 0.00 0.00 0.00 4.40
853 1894 4.991056 TCTGTTCACACTTCATTAGCTGTC 59.009 41.667 0.00 0.00 0.00 3.51
854 1895 4.960938 TGTTCACACTTCATTAGCTGTCT 58.039 39.130 0.00 0.00 0.00 3.41
855 1896 4.751600 TGTTCACACTTCATTAGCTGTCTG 59.248 41.667 0.00 0.00 0.00 3.51
856 1897 4.607293 TCACACTTCATTAGCTGTCTGT 57.393 40.909 0.00 0.00 0.00 3.41
857 1898 4.560128 TCACACTTCATTAGCTGTCTGTC 58.440 43.478 0.00 0.00 0.00 3.51
858 1899 4.281941 TCACACTTCATTAGCTGTCTGTCT 59.718 41.667 0.00 0.00 0.00 3.41
859 1900 4.624882 CACACTTCATTAGCTGTCTGTCTC 59.375 45.833 0.00 0.00 0.00 3.36
860 1901 4.281941 ACACTTCATTAGCTGTCTGTCTCA 59.718 41.667 0.00 0.00 0.00 3.27
861 1902 5.221521 ACACTTCATTAGCTGTCTGTCTCAA 60.222 40.000 0.00 0.00 0.00 3.02
862 1903 5.348179 CACTTCATTAGCTGTCTGTCTCAAG 59.652 44.000 0.00 0.00 0.00 3.02
863 1904 5.011533 ACTTCATTAGCTGTCTGTCTCAAGT 59.988 40.000 0.00 0.00 0.00 3.16
876 1917 7.385205 TGTCTGTCTCAAGTTCTTAACTATTGC 59.615 37.037 0.00 0.00 41.91 3.56
878 1919 6.769512 TGTCTCAAGTTCTTAACTATTGCCT 58.230 36.000 0.00 0.00 41.91 4.75
879 1920 7.224297 TGTCTCAAGTTCTTAACTATTGCCTT 58.776 34.615 0.00 0.00 41.91 4.35
880 1921 7.173218 TGTCTCAAGTTCTTAACTATTGCCTTG 59.827 37.037 0.00 0.00 41.91 3.61
881 1922 7.387948 GTCTCAAGTTCTTAACTATTGCCTTGA 59.612 37.037 0.00 0.00 41.91 3.02
882 1923 7.387948 TCTCAAGTTCTTAACTATTGCCTTGAC 59.612 37.037 0.00 0.00 41.91 3.18
883 1924 7.224297 TCAAGTTCTTAACTATTGCCTTGACT 58.776 34.615 0.00 0.00 41.91 3.41
884 1925 8.372459 TCAAGTTCTTAACTATTGCCTTGACTA 58.628 33.333 0.00 0.00 41.91 2.59
916 1958 5.536161 ACAGCAGTTCACCTATTTCAATTGT 59.464 36.000 5.13 0.00 0.00 2.71
920 1962 7.448469 AGCAGTTCACCTATTTCAATTGTAAGT 59.552 33.333 5.13 0.00 0.00 2.24
943 1985 9.498307 AAGTTTAGTTTTTGTAGTTCATTGTCG 57.502 29.630 0.00 0.00 0.00 4.35
976 2020 6.158520 TCAATCTTCTCCACCCAATCTTATCA 59.841 38.462 0.00 0.00 0.00 2.15
1012 2086 3.266510 CTGTAAGCATGCACCTTCCTA 57.733 47.619 21.98 0.00 0.00 2.94
1017 2091 2.752030 AGCATGCACCTTCCTACTCTA 58.248 47.619 21.98 0.00 0.00 2.43
1024 2098 3.510360 GCACCTTCCTACTCTACACTTGA 59.490 47.826 0.00 0.00 0.00 3.02
1034 2108 7.013750 TCCTACTCTACACTTGATCATCATCAC 59.986 40.741 0.00 0.00 38.86 3.06
1105 2179 1.604593 GTGCTTGTCCCTGGCATGT 60.605 57.895 0.00 0.00 38.27 3.21
1110 2184 0.478072 TTGTCCCTGGCATGTGTCTT 59.522 50.000 0.00 0.00 0.00 3.01
1137 2211 2.637872 TGGAAAAACTCTCACCTCGGAT 59.362 45.455 0.00 0.00 0.00 4.18
1352 2426 1.408127 CCGCCACATACTTTGGATGGA 60.408 52.381 0.00 0.00 36.02 3.41
1630 2704 0.179018 GGATGGGTCAGTGCCATACC 60.179 60.000 2.57 0.00 0.00 2.73
1683 2757 1.421268 TCCAACATGGAACTGCAGACT 59.579 47.619 23.35 6.77 45.00 3.24
1803 2877 2.298163 GGTTGACTACTCCGGAAAGACA 59.702 50.000 18.04 15.13 0.00 3.41
2091 3168 2.745281 GCCAGACAAATTTGTACGCCTA 59.255 45.455 23.33 0.00 42.43 3.93
2531 3783 7.386573 TGCTTTCAGTATTCAAACTATTCGACA 59.613 33.333 0.00 0.00 0.00 4.35
2532 3784 7.900352 GCTTTCAGTATTCAAACTATTCGACAG 59.100 37.037 0.00 0.00 0.00 3.51
2802 4597 6.780457 AGTTATACCAGCAATTTCAGCAAT 57.220 33.333 0.00 0.00 0.00 3.56
2833 4628 4.392047 TGATACTTCTATTGGCATGCCTG 58.608 43.478 35.53 22.16 36.94 4.85
3017 4816 2.465813 AGTGATGGACTTGGAGAGGAG 58.534 52.381 0.00 0.00 0.00 3.69
3041 4840 9.314321 GAGACTCATGAATTTCCGTTTATTAGA 57.686 33.333 0.00 0.00 0.00 2.10
3183 4998 6.585702 TCGACATATGAAAATTTTGCCACTTG 59.414 34.615 10.38 5.39 0.00 3.16
3195 5010 1.067364 TGCCACTTGTTGCTGTGATTG 59.933 47.619 0.00 0.00 36.38 2.67
3356 5171 9.502091 AATGAAGTAGTTGTGATTGCTAAACTA 57.498 29.630 0.00 0.00 34.76 2.24
3491 5310 6.206634 TGTTCTGACCACAAATTAATCAGTCC 59.793 38.462 0.00 0.00 38.35 3.85
3590 5415 4.265904 TGGCCGACACGATTCAATATAT 57.734 40.909 0.00 0.00 0.00 0.86
3742 5568 2.489722 GGCAAGAATCTTTGGTGGAGAC 59.510 50.000 0.00 0.00 0.00 3.36
3753 5579 0.033504 GGTGGAGACGAGCAACAAGA 59.966 55.000 0.00 0.00 0.00 3.02
3996 5824 6.567602 AAGTGGTCTAAGGATAAGCTCAAT 57.432 37.500 0.00 0.00 0.00 2.57
4181 6026 1.966354 TCTGTTTCAGAGAGCTGCTCA 59.034 47.619 29.49 7.87 46.45 4.26
4253 6098 3.770040 CCGGATGCGAGACCACCA 61.770 66.667 8.71 0.00 0.00 4.17
4263 6108 2.611971 GCGAGACCACCAATGTCAACTA 60.612 50.000 0.00 0.00 35.15 2.24
4417 6266 0.698886 TAGAGGGGCGGTAGGGTCTA 60.699 60.000 0.00 0.00 0.00 2.59
4420 6269 0.030399 AGGGGCGGTAGGGTCTAAAT 60.030 55.000 0.00 0.00 0.00 1.40
4421 6270 0.841961 GGGGCGGTAGGGTCTAAATT 59.158 55.000 0.00 0.00 0.00 1.82
4427 6327 5.936372 GGGCGGTAGGGTCTAAATTATTTAG 59.064 44.000 16.25 16.25 43.09 1.85
4445 6345 2.703798 GCTGCCACCGCAATCACAT 61.704 57.895 0.00 0.00 46.66 3.21
4548 6450 1.964223 GTGAAGTCTGGACTCTGGACA 59.036 52.381 3.60 0.00 41.58 4.02
4577 6479 4.453478 AGTTTCTATGTCGTGACGAGTACA 59.547 41.667 8.41 3.84 36.23 2.90
4590 6492 9.577110 TCGTGACGAGTACAGAATATTTATTTT 57.423 29.630 2.39 0.00 0.00 1.82
4652 6554 7.875554 CCCTTATAAGAGATACAGAAGAAAGGC 59.124 40.741 14.28 0.00 0.00 4.35
4666 6568 3.152341 AGAAAGGCTGGATGTGTTTCTG 58.848 45.455 0.00 0.00 36.38 3.02
4684 6586 0.966875 TGGATGCTGATGTTGTGGCC 60.967 55.000 0.00 0.00 0.00 5.36
4728 6630 2.093973 ACTCTTGCTGACGGTATTCTGG 60.094 50.000 0.00 0.00 0.00 3.86
4737 6639 3.958147 TGACGGTATTCTGGAGCTAATCA 59.042 43.478 0.00 0.00 0.00 2.57
4769 6671 5.363101 ACTAGTGCTGTTATCCATGACATG 58.637 41.667 8.56 8.56 0.00 3.21
4781 6683 4.650734 TCCATGACATGAAGTTGTTAGCA 58.349 39.130 17.24 0.00 0.00 3.49
4878 6780 2.292569 CTGTGGAGCATGATGCCATTAC 59.707 50.000 14.72 9.01 46.52 1.89
4958 6865 6.494835 AGCATCAAACCAAATCTTATATCCCC 59.505 38.462 0.00 0.00 0.00 4.81
4979 6886 1.937546 GCAGGCGACAATTTCAGGGG 61.938 60.000 0.00 0.00 0.00 4.79
5232 8214 0.553819 TATAATTTGGCAGGGGCGGT 59.446 50.000 0.00 0.00 42.47 5.68
5265 8247 7.520937 GCGTACCCCTTATAACACAAATTATGG 60.521 40.741 0.00 0.00 0.00 2.74
5284 8266 1.890894 CGTCCACTCTCCCACGAAT 59.109 57.895 0.00 0.00 34.06 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
89 90 4.201851 CCAATTGCAGTGTGCTATCACTAC 60.202 45.833 0.00 5.41 45.37 2.73
108 109 4.380843 TCCACACATTACTTCACCCAAT 57.619 40.909 0.00 0.00 0.00 3.16
131 132 2.028112 GCAGTACCATTCAGTGTCAGGA 60.028 50.000 4.86 0.00 0.00 3.86
212 213 3.006967 GGTATACCTGCAAGATGGACGAT 59.993 47.826 15.09 0.00 34.07 3.73
279 280 1.310904 GGGAACTTACCGTTGTTGCA 58.689 50.000 9.52 0.00 36.46 4.08
313 314 8.618677 CAGTTGATAATGTCACTGCTGATATTT 58.381 33.333 3.78 0.00 38.68 1.40
341 342 0.843984 GGCCCTGCTAAGTCCCATTA 59.156 55.000 0.00 0.00 0.00 1.90
344 345 1.431195 TTTGGCCCTGCTAAGTCCCA 61.431 55.000 0.00 0.00 29.47 4.37
369 370 5.689819 CAATAAGAAGTTGCACCTACACAC 58.310 41.667 0.00 0.00 0.00 3.82
370 371 5.940192 CAATAAGAAGTTGCACCTACACA 57.060 39.130 0.00 0.00 0.00 3.72
399 400 4.186159 CAATTTTCTGTCCATGGGCATTC 58.814 43.478 21.71 2.35 0.00 2.67
418 419 8.712228 AAGATTTTCAGTACCTTTCTTCCAAT 57.288 30.769 0.00 0.00 0.00 3.16
419 420 9.807921 ATAAGATTTTCAGTACCTTTCTTCCAA 57.192 29.630 0.00 0.00 0.00 3.53
420 421 9.807921 AATAAGATTTTCAGTACCTTTCTTCCA 57.192 29.630 0.00 0.00 0.00 3.53
441 442 6.326375 ACGAGCTTTCTCTGTACTCAATAAG 58.674 40.000 0.00 0.00 37.19 1.73
451 452 3.437049 GGCATTAAACGAGCTTTCTCTGT 59.563 43.478 0.00 0.00 37.19 3.41
476 477 3.966665 TGGCAAAGAAAACCCTTGAGAAT 59.033 39.130 0.00 0.00 0.00 2.40
482 483 6.326323 TCTTTATCTTGGCAAAGAAAACCCTT 59.674 34.615 7.83 0.00 45.44 3.95
510 513 5.778161 TTGCACGTGTAAGTCATAAGATG 57.222 39.130 15.43 0.00 0.00 2.90
526 529 2.866156 TCTCAGTCTTGACTTTTGCACG 59.134 45.455 0.00 0.00 0.00 5.34
559 569 2.449777 GGGGTTTCAAGGGGCCAT 59.550 61.111 4.39 0.00 0.00 4.40
560 570 4.293671 CGGGGTTTCAAGGGGCCA 62.294 66.667 4.39 0.00 0.00 5.36
561 571 3.938637 CTCGGGGTTTCAAGGGGCC 62.939 68.421 0.00 0.00 0.00 5.80
562 572 2.361230 CTCGGGGTTTCAAGGGGC 60.361 66.667 0.00 0.00 0.00 5.80
563 573 0.893727 CAACTCGGGGTTTCAAGGGG 60.894 60.000 0.00 0.00 35.74 4.79
564 574 0.109723 TCAACTCGGGGTTTCAAGGG 59.890 55.000 0.00 0.00 35.74 3.95
577 618 8.862550 AGAAAAATCACATTTGACTTCAACTC 57.137 30.769 0.00 0.00 35.28 3.01
605 646 3.119459 TCGACACTTCACTGCCTATCTTC 60.119 47.826 0.00 0.00 0.00 2.87
610 651 1.269723 CTGTCGACACTTCACTGCCTA 59.730 52.381 15.76 0.00 0.00 3.93
611 652 0.032678 CTGTCGACACTTCACTGCCT 59.967 55.000 15.76 0.00 0.00 4.75
612 653 0.032130 TCTGTCGACACTTCACTGCC 59.968 55.000 15.76 0.00 0.00 4.85
613 654 1.413382 CTCTGTCGACACTTCACTGC 58.587 55.000 15.76 0.00 0.00 4.40
615 656 1.609555 GTCCTCTGTCGACACTTCACT 59.390 52.381 15.76 0.00 0.00 3.41
618 659 1.667467 GCTGTCCTCTGTCGACACTTC 60.667 57.143 15.76 4.51 35.35 3.01
619 660 0.315568 GCTGTCCTCTGTCGACACTT 59.684 55.000 15.76 0.00 35.35 3.16
621 662 0.315568 AAGCTGTCCTCTGTCGACAC 59.684 55.000 15.76 5.05 35.35 3.67
623 664 2.062519 GAAAAGCTGTCCTCTGTCGAC 58.937 52.381 9.11 9.11 0.00 4.20
625 666 2.154854 TGAAAAGCTGTCCTCTGTCG 57.845 50.000 0.00 0.00 0.00 4.35
639 680 3.632604 TCCAACAATGCGGTACTTGAAAA 59.367 39.130 0.04 0.00 0.00 2.29
640 681 3.215151 TCCAACAATGCGGTACTTGAAA 58.785 40.909 0.04 0.00 0.00 2.69
642 683 2.224426 ACTCCAACAATGCGGTACTTGA 60.224 45.455 0.04 0.00 0.00 3.02
643 684 2.095768 CACTCCAACAATGCGGTACTTG 60.096 50.000 0.00 0.00 0.00 3.16
644 685 2.151202 CACTCCAACAATGCGGTACTT 58.849 47.619 0.00 0.00 0.00 2.24
646 687 0.802494 CCACTCCAACAATGCGGTAC 59.198 55.000 0.00 0.00 0.00 3.34
648 689 1.150536 ACCACTCCAACAATGCGGT 59.849 52.632 0.00 0.00 0.00 5.68
649 690 1.580942 CACCACTCCAACAATGCGG 59.419 57.895 0.00 0.00 0.00 5.69
650 691 0.888736 TCCACCACTCCAACAATGCG 60.889 55.000 0.00 0.00 0.00 4.73
651 692 1.327303 TTCCACCACTCCAACAATGC 58.673 50.000 0.00 0.00 0.00 3.56
652 693 2.231964 CCATTCCACCACTCCAACAATG 59.768 50.000 0.00 0.00 0.00 2.82
653 694 2.109834 TCCATTCCACCACTCCAACAAT 59.890 45.455 0.00 0.00 0.00 2.71
654 695 1.496857 TCCATTCCACCACTCCAACAA 59.503 47.619 0.00 0.00 0.00 2.83
655 696 1.144691 TCCATTCCACCACTCCAACA 58.855 50.000 0.00 0.00 0.00 3.33
656 697 2.369394 GATCCATTCCACCACTCCAAC 58.631 52.381 0.00 0.00 0.00 3.77
657 698 1.284785 GGATCCATTCCACCACTCCAA 59.715 52.381 6.95 0.00 44.74 3.53
658 699 0.918983 GGATCCATTCCACCACTCCA 59.081 55.000 6.95 0.00 44.74 3.86
659 700 3.808984 GGATCCATTCCACCACTCC 57.191 57.895 6.95 0.00 44.74 3.85
667 708 8.762645 TGATAGTGATATACTTGGATCCATTCC 58.237 37.037 17.06 1.85 41.83 3.01
668 709 9.814899 CTGATAGTGATATACTTGGATCCATTC 57.185 37.037 17.06 6.80 40.89 2.67
671 712 6.956435 AGCTGATAGTGATATACTTGGATCCA 59.044 38.462 11.44 11.44 40.89 3.41
672 713 7.416964 AGCTGATAGTGATATACTTGGATCC 57.583 40.000 4.20 4.20 40.89 3.36
673 714 8.748412 AGAAGCTGATAGTGATATACTTGGATC 58.252 37.037 0.00 0.00 40.89 3.36
674 715 8.663209 AGAAGCTGATAGTGATATACTTGGAT 57.337 34.615 0.00 0.00 40.89 3.41
675 716 8.363390 CAAGAAGCTGATAGTGATATACTTGGA 58.637 37.037 0.00 0.00 40.89 3.53
676 717 8.363390 TCAAGAAGCTGATAGTGATATACTTGG 58.637 37.037 0.00 0.00 40.89 3.61
679 720 8.932434 TCTCAAGAAGCTGATAGTGATATACT 57.068 34.615 0.00 0.00 43.56 2.12
680 721 8.792633 ACTCTCAAGAAGCTGATAGTGATATAC 58.207 37.037 0.00 0.00 33.03 1.47
681 722 8.791675 CACTCTCAAGAAGCTGATAGTGATATA 58.208 37.037 11.53 0.00 46.07 0.86
682 723 7.255906 CCACTCTCAAGAAGCTGATAGTGATAT 60.256 40.741 16.19 0.00 46.07 1.63
683 724 6.040278 CCACTCTCAAGAAGCTGATAGTGATA 59.960 42.308 16.19 0.00 46.07 2.15
685 726 4.159321 CCACTCTCAAGAAGCTGATAGTGA 59.841 45.833 16.19 4.03 46.07 3.41
686 727 4.081752 ACCACTCTCAAGAAGCTGATAGTG 60.082 45.833 10.50 10.50 44.29 2.74
687 728 4.093011 ACCACTCTCAAGAAGCTGATAGT 58.907 43.478 0.00 0.00 34.16 2.12
688 729 4.734398 ACCACTCTCAAGAAGCTGATAG 57.266 45.455 0.00 0.00 0.00 2.08
689 730 6.605471 TTTACCACTCTCAAGAAGCTGATA 57.395 37.500 0.00 0.00 0.00 2.15
690 731 5.489792 TTTACCACTCTCAAGAAGCTGAT 57.510 39.130 0.00 0.00 0.00 2.90
691 732 4.955811 TTTACCACTCTCAAGAAGCTGA 57.044 40.909 0.00 0.00 0.00 4.26
697 1111 4.838423 TCCTGTCATTTACCACTCTCAAGA 59.162 41.667 0.00 0.00 0.00 3.02
699 1113 5.513094 CCTTCCTGTCATTTACCACTCTCAA 60.513 44.000 0.00 0.00 0.00 3.02
700 1114 4.020218 CCTTCCTGTCATTTACCACTCTCA 60.020 45.833 0.00 0.00 0.00 3.27
703 1117 4.003648 CACCTTCCTGTCATTTACCACTC 58.996 47.826 0.00 0.00 0.00 3.51
705 1119 3.751518 ACACCTTCCTGTCATTTACCAC 58.248 45.455 0.00 0.00 0.00 4.16
707 1121 4.142038 ACAACACCTTCCTGTCATTTACC 58.858 43.478 0.00 0.00 0.00 2.85
708 1122 5.180680 GGTACAACACCTTCCTGTCATTTAC 59.819 44.000 0.00 0.00 44.79 2.01
709 1123 5.310451 GGTACAACACCTTCCTGTCATTTA 58.690 41.667 0.00 0.00 44.79 1.40
713 1127 2.922740 GGTACAACACCTTCCTGTCA 57.077 50.000 0.00 0.00 44.79 3.58
723 1137 4.584327 AAATGCCAGAAAGGTACAACAC 57.416 40.909 0.00 0.00 40.61 3.32
726 1140 5.830991 AGTTGTAAATGCCAGAAAGGTACAA 59.169 36.000 0.00 0.00 40.61 2.41
735 1773 6.463995 AACTTCAAAGTTGTAAATGCCAGA 57.536 33.333 7.32 0.00 46.80 3.86
751 1789 9.415544 CTATCATCATCATCGTATCAACTTCAA 57.584 33.333 0.00 0.00 0.00 2.69
753 1791 8.978564 ACTATCATCATCATCGTATCAACTTC 57.021 34.615 0.00 0.00 0.00 3.01
763 1801 7.068716 TGGGTCCTAATACTATCATCATCATCG 59.931 40.741 0.00 0.00 0.00 3.84
765 1803 8.866823 ATGGGTCCTAATACTATCATCATCAT 57.133 34.615 0.00 0.00 0.00 2.45
770 1808 8.697292 GGTAGAATGGGTCCTAATACTATCATC 58.303 40.741 0.00 0.00 0.00 2.92
771 1809 8.184249 TGGTAGAATGGGTCCTAATACTATCAT 58.816 37.037 0.00 0.00 0.00 2.45
772 1810 7.453752 GTGGTAGAATGGGTCCTAATACTATCA 59.546 40.741 0.00 0.00 0.00 2.15
773 1811 7.674772 AGTGGTAGAATGGGTCCTAATACTATC 59.325 40.741 0.00 0.00 0.00 2.08
775 1813 6.781014 CAGTGGTAGAATGGGTCCTAATACTA 59.219 42.308 0.00 0.00 0.00 1.82
776 1814 5.602978 CAGTGGTAGAATGGGTCCTAATACT 59.397 44.000 0.00 0.00 0.00 2.12
781 1822 2.316677 TCCAGTGGTAGAATGGGTCCTA 59.683 50.000 9.54 0.00 34.71 2.94
786 1827 1.633432 TGGTTCCAGTGGTAGAATGGG 59.367 52.381 9.54 0.00 34.71 4.00
793 1834 1.064003 ACTGCATGGTTCCAGTGGTA 58.936 50.000 9.54 0.00 40.55 3.25
798 1839 5.389859 TTTCAAATACTGCATGGTTCCAG 57.610 39.130 0.00 0.00 35.26 3.86
800 1841 6.146021 CAGTTTTTCAAATACTGCATGGTTCC 59.854 38.462 7.67 0.00 33.63 3.62
803 1844 6.160576 ACAGTTTTTCAAATACTGCATGGT 57.839 33.333 17.73 0.00 42.28 3.55
807 1848 4.892934 AGGGACAGTTTTTCAAATACTGCA 59.107 37.500 17.73 0.00 42.28 4.41
808 1849 5.241728 AGAGGGACAGTTTTTCAAATACTGC 59.758 40.000 17.73 11.63 42.28 4.40
809 1850 6.263168 ACAGAGGGACAGTTTTTCAAATACTG 59.737 38.462 16.58 16.58 43.72 2.74
810 1851 6.365520 ACAGAGGGACAGTTTTTCAAATACT 58.634 36.000 0.00 0.00 0.00 2.12
816 1857 3.945285 GTGAACAGAGGGACAGTTTTTCA 59.055 43.478 0.00 0.00 0.00 2.69
817 1858 3.945285 TGTGAACAGAGGGACAGTTTTTC 59.055 43.478 0.00 0.00 0.00 2.29
820 1861 2.505819 AGTGTGAACAGAGGGACAGTTT 59.494 45.455 0.00 0.00 0.00 2.66
822 1863 1.794714 AGTGTGAACAGAGGGACAGT 58.205 50.000 0.00 0.00 0.00 3.55
823 1864 2.103094 TGAAGTGTGAACAGAGGGACAG 59.897 50.000 0.00 0.00 0.00 3.51
824 1865 2.115427 TGAAGTGTGAACAGAGGGACA 58.885 47.619 0.00 0.00 0.00 4.02
825 1866 2.910688 TGAAGTGTGAACAGAGGGAC 57.089 50.000 0.00 0.00 0.00 4.46
826 1867 4.563580 GCTAATGAAGTGTGAACAGAGGGA 60.564 45.833 0.00 0.00 0.00 4.20
832 1873 4.751600 CAGACAGCTAATGAAGTGTGAACA 59.248 41.667 0.00 0.00 0.00 3.18
845 1886 5.537300 AAGAACTTGAGACAGACAGCTAA 57.463 39.130 0.00 0.00 0.00 3.09
847 1888 5.069781 AGTTAAGAACTTGAGACAGACAGCT 59.930 40.000 0.00 0.00 39.04 4.24
848 1889 5.293560 AGTTAAGAACTTGAGACAGACAGC 58.706 41.667 0.00 0.00 39.04 4.40
851 1892 7.148557 GGCAATAGTTAAGAACTTGAGACAGAC 60.149 40.741 0.00 0.00 42.81 3.51
852 1893 6.874134 GGCAATAGTTAAGAACTTGAGACAGA 59.126 38.462 0.00 0.00 42.81 3.41
853 1894 6.876257 AGGCAATAGTTAAGAACTTGAGACAG 59.124 38.462 0.00 0.00 42.81 3.51
854 1895 6.769512 AGGCAATAGTTAAGAACTTGAGACA 58.230 36.000 0.00 0.00 42.81 3.41
855 1896 7.387948 TCAAGGCAATAGTTAAGAACTTGAGAC 59.612 37.037 0.00 0.00 42.81 3.36
856 1897 7.387948 GTCAAGGCAATAGTTAAGAACTTGAGA 59.612 37.037 0.00 0.00 42.31 3.27
857 1898 7.389053 AGTCAAGGCAATAGTTAAGAACTTGAG 59.611 37.037 0.00 0.00 42.31 3.02
858 1899 7.224297 AGTCAAGGCAATAGTTAAGAACTTGA 58.776 34.615 0.00 0.00 42.81 3.02
859 1900 7.440523 AGTCAAGGCAATAGTTAAGAACTTG 57.559 36.000 0.00 0.00 42.81 3.16
860 1901 9.569122 TTTAGTCAAGGCAATAGTTAAGAACTT 57.431 29.630 0.00 0.00 42.81 2.66
861 1902 9.569122 TTTTAGTCAAGGCAATAGTTAAGAACT 57.431 29.630 0.00 0.00 45.40 3.01
876 1917 4.520492 ACTGCTGTTCCATTTTAGTCAAGG 59.480 41.667 0.00 0.00 0.00 3.61
878 1919 6.072112 GAACTGCTGTTCCATTTTAGTCAA 57.928 37.500 22.07 0.00 44.93 3.18
879 1920 5.689383 GAACTGCTGTTCCATTTTAGTCA 57.311 39.130 22.07 0.00 44.93 3.41
938 1980 5.643777 GGAGAAGATTGAGGAAAATCGACAA 59.356 40.000 0.00 0.00 40.75 3.18
942 1984 4.333926 GGTGGAGAAGATTGAGGAAAATCG 59.666 45.833 0.00 0.00 40.75 3.34
943 1985 4.642437 GGGTGGAGAAGATTGAGGAAAATC 59.358 45.833 0.00 0.00 36.91 2.17
976 2020 1.949799 ACAGCAGGATCAGAGAAGGT 58.050 50.000 0.00 0.00 0.00 3.50
1005 2079 6.322456 TGATGATCAAGTGTAGAGTAGGAAGG 59.678 42.308 0.00 0.00 0.00 3.46
1008 2082 7.013750 GTGATGATGATCAAGTGTAGAGTAGGA 59.986 40.741 0.00 0.00 40.39 2.94
1012 2086 5.586339 CGTGATGATGATCAAGTGTAGAGT 58.414 41.667 0.00 0.00 40.39 3.24
1017 2091 3.193263 GAGCGTGATGATGATCAAGTGT 58.807 45.455 9.52 0.00 40.39 3.55
1024 2098 3.556633 GGAATCAGGAGCGTGATGATGAT 60.557 47.826 6.45 0.00 37.24 2.45
1034 2108 1.821332 GGCCAAGGAATCAGGAGCG 60.821 63.158 0.00 0.00 0.00 5.03
1105 2179 5.365605 TGAGAGTTTTTCCAGGAGTAAGACA 59.634 40.000 0.00 0.00 0.00 3.41
1110 2184 4.232091 AGGTGAGAGTTTTTCCAGGAGTA 58.768 43.478 0.00 0.00 0.00 2.59
1137 2211 1.337447 CCTAAGGCGAACGAACCTTGA 60.337 52.381 13.42 1.98 45.84 3.02
1352 2426 1.683917 TGCCGCCAGTAATTGTGTTTT 59.316 42.857 0.00 0.00 0.00 2.43
1650 2724 4.904853 TCCATGTTGGAGTATACATAGCCA 59.095 41.667 5.50 4.35 42.67 4.75
1683 2757 5.929415 TGTCAAATACATGAGCGAACTAACA 59.071 36.000 0.00 0.00 31.43 2.41
1803 2877 4.858850 TGGTATTCCATCTCAACAGCATT 58.141 39.130 0.00 0.00 39.03 3.56
2091 3168 7.255381 GCACAGTCATCATAGCTTTTATTCCAT 60.255 37.037 0.00 0.00 0.00 3.41
2531 3783 7.285566 ACAACATCATGGAGATAGCAAATACT 58.714 34.615 0.00 0.00 34.43 2.12
2532 3784 7.227314 TGACAACATCATGGAGATAGCAAATAC 59.773 37.037 0.00 0.00 34.43 1.89
2536 3788 5.101648 TGACAACATCATGGAGATAGCAA 57.898 39.130 0.00 0.00 34.43 3.91
2802 4597 5.123820 GCCAATAGAAGTATCAGCAACACAA 59.876 40.000 0.00 0.00 0.00 3.33
2833 4628 4.380128 CCTTTAAACTTGCGGAACCATACC 60.380 45.833 0.00 0.00 0.00 2.73
2924 4723 8.843262 TCATGTTTGCCTAAGAGAAATATCATG 58.157 33.333 0.00 0.00 0.00 3.07
3041 4840 5.647658 TGTTGCATCGACTATTTCCTCAAAT 59.352 36.000 0.00 0.00 36.18 2.32
3183 4998 4.504097 GGTTCAGTTTTCAATCACAGCAAC 59.496 41.667 0.00 0.00 0.00 4.17
3356 5171 5.279758 AAGCCTTACAAGGTTTTTGTGTTGT 60.280 36.000 9.69 0.00 45.84 3.32
3491 5310 6.103330 TCAGATGTGGCATCAAATGATTTTG 58.897 36.000 11.12 0.00 42.98 2.44
3590 5415 2.238898 GCCCTCTAGCCACTCCTTTTAA 59.761 50.000 0.00 0.00 0.00 1.52
3742 5568 4.279659 GGTTAGTGTTTTCTTGTTGCTCG 58.720 43.478 0.00 0.00 0.00 5.03
3873 5701 5.638234 GGAGACATATAACCGCTGGATAAAC 59.362 44.000 1.50 0.00 0.00 2.01
3996 5824 2.553028 GGGAACTCCTTGATGTTCTGCA 60.553 50.000 0.00 0.00 41.42 4.41
4054 5882 0.323725 AAGGCATTCCGGACATTGCT 60.324 50.000 24.52 13.08 37.47 3.91
4102 5947 6.718454 CCATAGACTCCATGCCTGAATAAATT 59.282 38.462 0.00 0.00 0.00 1.82
4181 6026 5.581126 TGCAACACAAAACTTCTTCATCT 57.419 34.783 0.00 0.00 0.00 2.90
4253 6098 8.919145 TCCAAGGTTGTTAAAATAGTTGACATT 58.081 29.630 0.00 0.00 0.00 2.71
4263 6108 7.175119 GCTTCTACTCTCCAAGGTTGTTAAAAT 59.825 37.037 0.00 0.00 0.00 1.82
4417 6266 2.757868 TGCGGTGGCAGCTAAATAATTT 59.242 40.909 15.48 0.00 46.21 1.82
4420 6269 3.560534 TGCGGTGGCAGCTAAATAA 57.439 47.368 15.48 0.00 46.21 1.40
4548 6450 6.384224 TCGTCACGACATAGAAACTGTAATT 58.616 36.000 0.00 0.00 0.00 1.40
4652 6554 2.422479 CAGCATCCAGAAACACATCCAG 59.578 50.000 0.00 0.00 0.00 3.86
4666 6568 1.811860 GGCCACAACATCAGCATCC 59.188 57.895 0.00 0.00 0.00 3.51
4684 6586 3.399330 ACCGGATAAAACATATCAGGCG 58.601 45.455 9.46 1.66 41.13 5.52
4728 6630 4.756135 ACTAGTAGCCGTACTGATTAGCTC 59.244 45.833 0.00 0.00 39.96 4.09
4737 6639 2.125773 ACAGCACTAGTAGCCGTACT 57.874 50.000 11.98 0.00 42.49 2.73
4769 6671 7.755582 AACAAACTTCAATGCTAACAACTTC 57.244 32.000 0.00 0.00 0.00 3.01
4827 6729 3.917870 CGTGAGCCGGCGTATTAG 58.082 61.111 23.20 8.07 0.00 1.73
4860 6762 3.216800 GAAGTAATGGCATCATGCTCCA 58.783 45.455 10.11 0.00 44.28 3.86
4903 6805 6.595716 CCCAAAAGAACACACAACCAAAATAA 59.404 34.615 0.00 0.00 0.00 1.40
4958 6865 1.135315 CTGAAATTGTCGCCTGCCG 59.865 57.895 0.00 0.00 38.61 5.69
4979 6886 7.832769 TGGTATTAAGATTTTGTTTACCCAGC 58.167 34.615 0.00 0.00 0.00 4.85
5157 8139 7.094508 TGAAATTCAGCTGTGTTTCACTTTA 57.905 32.000 28.66 16.02 36.11 1.85
5265 8247 2.227089 ATTCGTGGGAGAGTGGACGC 62.227 60.000 0.00 0.00 0.00 5.19
5284 8266 2.639065 GCGTTGATCTACCATTTCCCA 58.361 47.619 1.57 0.00 0.00 4.37


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

AutoCloner maintained by Alex Coulton.