Multiple sequence alignment - TraesCS2A01G472200

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS2A01G472200 chr2A 100.000 2309 0 0 1 2309 713930858 713933166 0.000000e+00 4265
1 TraesCS2A01G472200 chr2B 91.916 1002 57 16 745 1740 691780264 691781247 0.000000e+00 1380
2 TraesCS2A01G472200 chr2B 87.669 592 33 13 1 560 691779614 691780197 0.000000e+00 652
3 TraesCS2A01G472200 chr2B 93.284 268 14 3 1739 2006 691787452 691787715 2.150000e-105 392
4 TraesCS2A01G472200 chr2B 91.633 251 15 3 1770 2015 691781242 691781491 2.200000e-90 342
5 TraesCS2A01G472200 chr2D 92.998 557 33 3 740 1295 575763298 575763849 0.000000e+00 808
6 TraesCS2A01G472200 chr2D 87.584 596 52 15 4 581 575762709 575763300 0.000000e+00 671
7 TraesCS2A01G472200 chr2D 93.498 323 18 2 1694 2015 575763954 575764274 5.770000e-131 477
8 TraesCS2A01G472200 chr5D 95.092 163 7 1 579 741 12270340 12270501 2.940000e-64 255
9 TraesCS2A01G472200 chr1A 93.902 164 10 0 579 742 325051900 325051737 4.930000e-62 248
10 TraesCS2A01G472200 chr6D 93.865 163 10 0 579 741 10418145 10417983 1.770000e-61 246
11 TraesCS2A01G472200 chr3D 93.865 163 10 0 579 741 137982347 137982509 1.770000e-61 246
12 TraesCS2A01G472200 chr3B 93.865 163 10 0 579 741 201028507 201028669 1.770000e-61 246
13 TraesCS2A01G472200 chr4D 93.865 163 9 1 579 741 334164552 334164391 6.370000e-61 244
14 TraesCS2A01G472200 chr5B 93.293 164 11 0 579 742 607838552 607838389 2.290000e-60 243
15 TraesCS2A01G472200 chr5B 90.960 177 12 4 575 749 554821027 554821201 3.840000e-58 235
16 TraesCS2A01G472200 chr7D 91.813 171 14 0 572 742 571261050 571260880 2.960000e-59 239


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 TraesCS2A01G472200 chr2A 713930858 713933166 2308 False 4265.000000 4265 100.000 1 2309 1 chr2A.!!$F1 2308
1 TraesCS2A01G472200 chr2B 691779614 691781491 1877 False 791.333333 1380 90.406 1 2015 3 chr2B.!!$F2 2014
2 TraesCS2A01G472200 chr2D 575762709 575764274 1565 False 652.000000 808 91.360 4 2015 3 chr2D.!!$F1 2011

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
592 668 0.249657 CATGCTACTCCCTCCGCTTC 60.25 60.0 0.0 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2260 2344 0.033781 ACGCAAGGTGCATGCAAATT 59.966 45.0 24.58 17.1 45.36 1.82 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
53 54 4.218417 ACAATCAATGGAACTTAGTGGTGC 59.782 41.667 0.00 0.00 0.00 5.01
61 62 4.083565 GGAACTTAGTGGTGCCCATTTTA 58.916 43.478 0.00 0.00 35.28 1.52
154 157 9.751542 TTTGTTATCACCGTTAACATCAAATTT 57.248 25.926 6.39 0.00 38.84 1.82
156 159 8.568794 TGTTATCACCGTTAACATCAAATTTGA 58.431 29.630 22.52 22.52 42.14 2.69
326 348 1.004745 AGCCACGGGATTTGTTCAGAT 59.995 47.619 0.00 0.00 0.00 2.90
348 370 4.130286 ACACTGAAGCTTACATCTAGCC 57.870 45.455 0.00 0.00 39.47 3.93
357 379 6.240549 AGCTTACATCTAGCCAATACTTGT 57.759 37.500 0.00 0.00 39.47 3.16
370 393 5.297776 GCCAATACTTGTCATAAGCATGTCT 59.702 40.000 0.00 0.00 33.57 3.41
381 404 9.237187 TGTCATAAGCATGTCTTGGTAAATTAA 57.763 29.630 11.24 0.00 34.16 1.40
399 422 3.818787 CATGCCGTGCCTGCTTCC 61.819 66.667 0.00 0.00 0.00 3.46
414 437 2.819608 TGCTTCCTGCTGGTGTTTATTC 59.180 45.455 9.73 0.00 43.37 1.75
415 438 2.819608 GCTTCCTGCTGGTGTTTATTCA 59.180 45.455 9.73 0.00 38.95 2.57
416 439 3.119708 GCTTCCTGCTGGTGTTTATTCAG 60.120 47.826 9.73 0.00 38.95 3.02
497 520 4.300803 TGTCAAACAAAAGATGAGCATGC 58.699 39.130 10.51 10.51 0.00 4.06
581 657 2.368548 TGACAGTTGACACCATGCTACT 59.631 45.455 0.00 0.00 0.00 2.57
582 658 2.996621 GACAGTTGACACCATGCTACTC 59.003 50.000 0.00 0.00 0.00 2.59
583 659 2.289694 ACAGTTGACACCATGCTACTCC 60.290 50.000 0.00 0.00 0.00 3.85
584 660 1.279271 AGTTGACACCATGCTACTCCC 59.721 52.381 0.00 0.00 0.00 4.30
585 661 1.279271 GTTGACACCATGCTACTCCCT 59.721 52.381 0.00 0.00 0.00 4.20
586 662 1.195115 TGACACCATGCTACTCCCTC 58.805 55.000 0.00 0.00 0.00 4.30
587 663 0.466124 GACACCATGCTACTCCCTCC 59.534 60.000 0.00 0.00 0.00 4.30
588 664 1.330655 ACACCATGCTACTCCCTCCG 61.331 60.000 0.00 0.00 0.00 4.63
589 665 2.423446 CCATGCTACTCCCTCCGC 59.577 66.667 0.00 0.00 0.00 5.54
590 666 2.136878 CCATGCTACTCCCTCCGCT 61.137 63.158 0.00 0.00 0.00 5.52
591 667 1.690219 CCATGCTACTCCCTCCGCTT 61.690 60.000 0.00 0.00 0.00 4.68
592 668 0.249657 CATGCTACTCCCTCCGCTTC 60.250 60.000 0.00 0.00 0.00 3.86
593 669 0.397816 ATGCTACTCCCTCCGCTTCT 60.398 55.000 0.00 0.00 0.00 2.85
594 670 0.257905 TGCTACTCCCTCCGCTTCTA 59.742 55.000 0.00 0.00 0.00 2.10
595 671 1.341679 TGCTACTCCCTCCGCTTCTAA 60.342 52.381 0.00 0.00 0.00 2.10
596 672 1.755380 GCTACTCCCTCCGCTTCTAAA 59.245 52.381 0.00 0.00 0.00 1.85
597 673 2.365941 GCTACTCCCTCCGCTTCTAAAT 59.634 50.000 0.00 0.00 0.00 1.40
598 674 3.573110 GCTACTCCCTCCGCTTCTAAATA 59.427 47.826 0.00 0.00 0.00 1.40
599 675 4.221041 GCTACTCCCTCCGCTTCTAAATAT 59.779 45.833 0.00 0.00 0.00 1.28
600 676 5.418209 GCTACTCCCTCCGCTTCTAAATATA 59.582 44.000 0.00 0.00 0.00 0.86
601 677 6.071503 GCTACTCCCTCCGCTTCTAAATATAA 60.072 42.308 0.00 0.00 0.00 0.98
602 678 6.347859 ACTCCCTCCGCTTCTAAATATAAG 57.652 41.667 0.00 0.00 0.00 1.73
603 679 5.839606 ACTCCCTCCGCTTCTAAATATAAGT 59.160 40.000 0.00 0.00 0.00 2.24
604 680 7.008941 ACTCCCTCCGCTTCTAAATATAAGTA 58.991 38.462 0.00 0.00 0.00 2.24
605 681 7.674772 ACTCCCTCCGCTTCTAAATATAAGTAT 59.325 37.037 0.00 0.00 0.00 2.12
606 682 8.431910 TCCCTCCGCTTCTAAATATAAGTATT 57.568 34.615 0.00 0.00 31.89 1.89
607 683 8.877195 TCCCTCCGCTTCTAAATATAAGTATTT 58.123 33.333 0.00 0.00 41.92 1.40
608 684 9.503399 CCCTCCGCTTCTAAATATAAGTATTTT 57.497 33.333 0.00 0.00 40.21 1.82
637 713 4.442401 TCCACTATGGACTACATACGGA 57.558 45.455 0.00 0.00 42.67 4.69
638 714 4.994282 TCCACTATGGACTACATACGGAT 58.006 43.478 0.00 0.00 42.67 4.18
639 715 4.765339 TCCACTATGGACTACATACGGATG 59.235 45.833 5.94 5.94 42.67 3.51
640 716 4.523173 CCACTATGGACTACATACGGATGT 59.477 45.833 19.12 19.12 44.08 3.06
641 717 5.708697 CCACTATGGACTACATACGGATGTA 59.291 44.000 19.32 19.32 41.62 2.29
642 718 6.377429 CCACTATGGACTACATACGGATGTAT 59.623 42.308 20.64 9.39 42.60 2.29
643 719 7.555195 CCACTATGGACTACATACGGATGTATA 59.445 40.741 20.64 10.04 42.60 1.47
644 720 9.121658 CACTATGGACTACATACGGATGTATAT 57.878 37.037 20.64 12.15 45.42 0.86
648 724 8.728337 TGGACTACATACGGATGTATATAGAC 57.272 38.462 20.64 10.95 45.42 2.59
649 725 8.323567 TGGACTACATACGGATGTATATAGACA 58.676 37.037 20.64 12.12 45.42 3.41
650 726 9.339850 GGACTACATACGGATGTATATAGACAT 57.660 37.037 20.64 12.70 45.42 3.06
682 758 7.440523 AGTGTAGATTCACTCATTTTGTTCC 57.559 36.000 0.00 0.00 44.07 3.62
683 759 6.147821 AGTGTAGATTCACTCATTTTGTTCCG 59.852 38.462 0.00 0.00 44.07 4.30
684 760 5.995282 TGTAGATTCACTCATTTTGTTCCGT 59.005 36.000 0.00 0.00 0.00 4.69
685 761 7.117236 GTGTAGATTCACTCATTTTGTTCCGTA 59.883 37.037 0.00 0.00 35.68 4.02
686 762 7.822334 TGTAGATTCACTCATTTTGTTCCGTAT 59.178 33.333 0.00 0.00 0.00 3.06
687 763 7.076842 AGATTCACTCATTTTGTTCCGTATG 57.923 36.000 0.00 0.00 0.00 2.39
688 764 6.655003 AGATTCACTCATTTTGTTCCGTATGT 59.345 34.615 0.00 0.00 0.00 2.29
689 765 7.822334 AGATTCACTCATTTTGTTCCGTATGTA 59.178 33.333 0.00 0.00 0.00 2.29
690 766 6.961359 TCACTCATTTTGTTCCGTATGTAG 57.039 37.500 0.00 0.00 0.00 2.74
691 767 6.460781 TCACTCATTTTGTTCCGTATGTAGT 58.539 36.000 0.00 0.00 0.00 2.73
692 768 6.588756 TCACTCATTTTGTTCCGTATGTAGTC 59.411 38.462 0.00 0.00 0.00 2.59
693 769 6.367695 CACTCATTTTGTTCCGTATGTAGTCA 59.632 38.462 0.00 0.00 0.00 3.41
694 770 7.064609 CACTCATTTTGTTCCGTATGTAGTCAT 59.935 37.037 0.00 0.00 38.00 3.06
695 771 7.606456 ACTCATTTTGTTCCGTATGTAGTCATT 59.394 33.333 0.00 0.00 35.70 2.57
696 772 8.330466 TCATTTTGTTCCGTATGTAGTCATTT 57.670 30.769 0.00 0.00 35.70 2.32
697 773 9.438228 TCATTTTGTTCCGTATGTAGTCATTTA 57.562 29.630 0.00 0.00 35.70 1.40
701 777 7.780008 TGTTCCGTATGTAGTCATTTATTGG 57.220 36.000 0.00 0.00 35.70 3.16
702 778 7.557724 TGTTCCGTATGTAGTCATTTATTGGA 58.442 34.615 0.00 0.00 35.70 3.53
703 779 8.041919 TGTTCCGTATGTAGTCATTTATTGGAA 58.958 33.333 0.00 0.00 35.70 3.53
704 780 9.052759 GTTCCGTATGTAGTCATTTATTGGAAT 57.947 33.333 0.00 0.00 35.70 3.01
705 781 8.827177 TCCGTATGTAGTCATTTATTGGAATC 57.173 34.615 0.00 0.00 35.70 2.52
706 782 8.647796 TCCGTATGTAGTCATTTATTGGAATCT 58.352 33.333 0.00 0.00 35.70 2.40
707 783 8.926710 CCGTATGTAGTCATTTATTGGAATCTC 58.073 37.037 0.00 0.00 35.70 2.75
708 784 9.698309 CGTATGTAGTCATTTATTGGAATCTCT 57.302 33.333 0.00 0.00 35.70 3.10
735 811 8.959705 AAAAGACTTATATTTAGGAACGGAGG 57.040 34.615 0.00 0.00 0.00 4.30
736 812 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
737 813 6.379579 AGACTTATATTTAGGAACGGAGGGA 58.620 40.000 0.00 0.00 0.00 4.20
738 814 6.494146 AGACTTATATTTAGGAACGGAGGGAG 59.506 42.308 0.00 0.00 0.00 4.30
739 815 6.141790 ACTTATATTTAGGAACGGAGGGAGT 58.858 40.000 0.00 0.00 0.00 3.85
740 816 7.300658 ACTTATATTTAGGAACGGAGGGAGTA 58.699 38.462 0.00 0.00 0.00 2.59
741 817 7.954620 ACTTATATTTAGGAACGGAGGGAGTAT 59.045 37.037 0.00 0.00 0.00 2.12
873 949 1.269448 CACCAAACGCAAGCCAGTAAT 59.731 47.619 0.00 0.00 45.62 1.89
874 950 2.486203 CACCAAACGCAAGCCAGTAATA 59.514 45.455 0.00 0.00 45.62 0.98
875 951 3.057876 CACCAAACGCAAGCCAGTAATAA 60.058 43.478 0.00 0.00 45.62 1.40
885 961 6.340522 GCAAGCCAGTAATAAAACATCCAAT 58.659 36.000 0.00 0.00 0.00 3.16
891 967 8.682710 GCCAGTAATAAAACATCCAATAGAACA 58.317 33.333 0.00 0.00 0.00 3.18
986 1063 0.890683 CTTCATGGGCTGGTGGTTTC 59.109 55.000 0.00 0.00 0.00 2.78
1041 1118 0.106669 GGAACCCAGGAATGGTAGGC 60.107 60.000 0.00 0.00 34.15 3.93
1065 1142 3.343617 AGTTGTTGGTATTGTGATCGGG 58.656 45.455 0.00 0.00 0.00 5.14
1077 1154 3.247162 TGTGATCGGGATGGATGGAATA 58.753 45.455 0.00 0.00 0.00 1.75
1078 1155 3.650461 TGTGATCGGGATGGATGGAATAA 59.350 43.478 0.00 0.00 0.00 1.40
1081 1158 6.051717 GTGATCGGGATGGATGGAATAATAG 58.948 44.000 0.00 0.00 0.00 1.73
1088 1165 7.184862 GGGATGGATGGAATAATAGTTGGAAT 58.815 38.462 0.00 0.00 0.00 3.01
1212 1289 1.595382 CATGGCGACCTTCGGGATC 60.595 63.158 0.00 0.00 40.84 3.36
1230 1307 3.463944 GATCGGAATGAACGGTATTGGT 58.536 45.455 0.00 0.00 0.00 3.67
1239 1316 1.173043 ACGGTATTGGTGGCATTGTG 58.827 50.000 0.00 0.00 0.00 3.33
1266 1343 0.035439 GAACTGCGGGAATGGAAGGA 60.035 55.000 0.00 0.00 0.00 3.36
1271 1348 1.005332 TGCGGGAATGGAAGGAATTGA 59.995 47.619 0.00 0.00 0.00 2.57
1281 1358 3.258872 TGGAAGGAATTGAAGGCAATGTG 59.741 43.478 0.00 0.00 43.71 3.21
1296 1373 0.893727 ATGTGGTTGGAACTTCCGGC 60.894 55.000 0.00 0.00 40.17 6.13
1299 1376 2.322830 GGTTGGAACTTCCGGCGTC 61.323 63.158 6.01 0.00 40.17 5.19
1303 1380 2.092882 GGAACTTCCGGCGTCGAAG 61.093 63.158 12.93 19.75 39.00 3.79
1348 1425 1.166531 AGCTGCCGTGTCCAAAAGAC 61.167 55.000 0.00 0.00 46.51 3.01
1435 1512 0.620556 ACCTGGAGCCATGGTAAGTG 59.379 55.000 14.67 1.50 31.50 3.16
1439 1516 1.278985 TGGAGCCATGGTAAGTGACTG 59.721 52.381 14.67 0.00 0.00 3.51
1446 1523 1.948104 TGGTAAGTGACTGTGTGTGC 58.052 50.000 0.00 0.00 0.00 4.57
1482 1561 6.095440 GGCCTTCTATGTTTATTTGCTCTGAA 59.905 38.462 0.00 0.00 0.00 3.02
1492 1571 8.886719 TGTTTATTTGCTCTGAAGATATCTGTG 58.113 33.333 5.86 0.00 0.00 3.66
1493 1572 9.102757 GTTTATTTGCTCTGAAGATATCTGTGA 57.897 33.333 5.86 4.42 0.00 3.58
1494 1573 9.671279 TTTATTTGCTCTGAAGATATCTGTGAA 57.329 29.630 5.86 0.00 0.00 3.18
1496 1575 7.783090 TTTGCTCTGAAGATATCTGTGAATC 57.217 36.000 5.86 0.00 0.00 2.52
1520 1599 4.966168 TGAGATACTGGGGCTATTTGTACA 59.034 41.667 0.00 0.00 0.00 2.90
1597 1676 1.816074 TCACCGCCCAATGTACTTTC 58.184 50.000 0.00 0.00 0.00 2.62
1617 1696 1.411977 CGAGATGCAGATCAGGGAGTT 59.588 52.381 0.00 0.00 0.00 3.01
1640 1719 1.395262 GGAAGTTCTTCGCTTAGCAGC 59.605 52.381 4.70 0.00 43.41 5.25
1664 1743 2.032634 TTGATGGACGGCGCAGTTC 61.033 57.895 15.89 14.14 0.00 3.01
1665 1744 2.434185 GATGGACGGCGCAGTTCA 60.434 61.111 24.01 24.01 33.58 3.18
1667 1746 0.529773 GATGGACGGCGCAGTTCATA 60.530 55.000 30.59 7.95 40.25 2.15
1669 1748 1.153628 GGACGGCGCAGTTCATAGT 60.154 57.895 15.89 0.00 0.00 2.12
1670 1749 1.421410 GGACGGCGCAGTTCATAGTG 61.421 60.000 15.89 0.00 0.00 2.74
1671 1750 1.421410 GACGGCGCAGTTCATAGTGG 61.421 60.000 15.89 0.00 0.00 4.00
1674 1753 0.447801 GGCGCAGTTCATAGTGGTTG 59.552 55.000 10.83 0.00 0.00 3.77
1675 1754 0.447801 GCGCAGTTCATAGTGGTTGG 59.552 55.000 0.30 0.00 0.00 3.77
1676 1755 1.086696 CGCAGTTCATAGTGGTTGGG 58.913 55.000 0.00 0.00 0.00 4.12
1677 1756 1.338674 CGCAGTTCATAGTGGTTGGGA 60.339 52.381 0.00 0.00 0.00 4.37
1678 1757 2.680805 CGCAGTTCATAGTGGTTGGGAT 60.681 50.000 0.00 0.00 0.00 3.85
1679 1758 3.356290 GCAGTTCATAGTGGTTGGGATT 58.644 45.455 0.00 0.00 0.00 3.01
1680 1759 3.763897 GCAGTTCATAGTGGTTGGGATTT 59.236 43.478 0.00 0.00 0.00 2.17
1681 1760 4.220602 GCAGTTCATAGTGGTTGGGATTTT 59.779 41.667 0.00 0.00 0.00 1.82
1682 1761 5.279456 GCAGTTCATAGTGGTTGGGATTTTT 60.279 40.000 0.00 0.00 0.00 1.94
1764 1844 5.877012 TGGGAATCTTTTTCTCTCGATGAAG 59.123 40.000 0.00 0.00 0.00 3.02
1829 1909 1.333619 CACGGTCAGGTTTCAGGTTTG 59.666 52.381 0.00 0.00 0.00 2.93
1900 1980 0.319728 TCTCTGCAGCTTGGTCACTC 59.680 55.000 9.47 0.00 0.00 3.51
1973 2057 7.479980 CATGAGACCAAAAAGACTACAAAACA 58.520 34.615 0.00 0.00 0.00 2.83
1980 2064 9.203421 ACCAAAAAGACTACAAAACAGAAAAAG 57.797 29.630 0.00 0.00 0.00 2.27
2007 2091 1.722011 ATACCGAGCAAGAAACGTGG 58.278 50.000 0.00 0.00 0.00 4.94
2015 2099 2.364324 AGCAAGAAACGTGGACTACTGA 59.636 45.455 0.00 0.00 0.00 3.41
2016 2100 3.128349 GCAAGAAACGTGGACTACTGAA 58.872 45.455 0.00 0.00 0.00 3.02
2017 2101 3.746492 GCAAGAAACGTGGACTACTGAAT 59.254 43.478 0.00 0.00 0.00 2.57
2018 2102 4.927425 GCAAGAAACGTGGACTACTGAATA 59.073 41.667 0.00 0.00 0.00 1.75
2019 2103 5.581085 GCAAGAAACGTGGACTACTGAATAT 59.419 40.000 0.00 0.00 0.00 1.28
2020 2104 6.455646 GCAAGAAACGTGGACTACTGAATATG 60.456 42.308 0.00 0.00 0.00 1.78
2021 2105 5.661458 AGAAACGTGGACTACTGAATATGG 58.339 41.667 0.00 0.00 0.00 2.74
2022 2106 4.402056 AACGTGGACTACTGAATATGGG 57.598 45.455 0.00 0.00 0.00 4.00
2023 2107 3.371965 ACGTGGACTACTGAATATGGGT 58.628 45.455 0.00 0.00 0.00 4.51
2024 2108 3.383825 ACGTGGACTACTGAATATGGGTC 59.616 47.826 0.00 0.00 0.00 4.46
2025 2109 3.383505 CGTGGACTACTGAATATGGGTCA 59.616 47.826 0.00 0.00 0.00 4.02
2026 2110 4.499865 CGTGGACTACTGAATATGGGTCAG 60.500 50.000 2.01 2.01 46.59 3.51
2027 2111 4.649674 GTGGACTACTGAATATGGGTCAGA 59.350 45.833 9.41 0.00 44.44 3.27
2028 2112 5.305644 GTGGACTACTGAATATGGGTCAGAT 59.694 44.000 9.41 0.00 44.44 2.90
2029 2113 5.305386 TGGACTACTGAATATGGGTCAGATG 59.695 44.000 9.41 4.81 44.44 2.90
2030 2114 5.220710 ACTACTGAATATGGGTCAGATGC 57.779 43.478 9.41 0.00 44.44 3.91
2031 2115 4.904251 ACTACTGAATATGGGTCAGATGCT 59.096 41.667 9.41 0.00 44.44 3.79
2032 2116 4.348863 ACTGAATATGGGTCAGATGCTC 57.651 45.455 9.41 0.00 44.44 4.26
2033 2117 3.972638 ACTGAATATGGGTCAGATGCTCT 59.027 43.478 9.41 0.00 44.44 4.09
2034 2118 4.040217 ACTGAATATGGGTCAGATGCTCTC 59.960 45.833 9.41 0.00 44.44 3.20
2035 2119 3.006217 TGAATATGGGTCAGATGCTCTCG 59.994 47.826 0.00 0.00 0.00 4.04
2036 2120 2.364972 TATGGGTCAGATGCTCTCGA 57.635 50.000 0.00 0.00 0.00 4.04
2037 2121 1.714541 ATGGGTCAGATGCTCTCGAT 58.285 50.000 0.00 0.00 0.00 3.59
2038 2122 1.489481 TGGGTCAGATGCTCTCGATT 58.511 50.000 0.00 0.00 0.00 3.34
2039 2123 2.666317 TGGGTCAGATGCTCTCGATTA 58.334 47.619 0.00 0.00 0.00 1.75
2040 2124 3.031013 TGGGTCAGATGCTCTCGATTAA 58.969 45.455 0.00 0.00 0.00 1.40
2041 2125 3.643320 TGGGTCAGATGCTCTCGATTAAT 59.357 43.478 0.00 0.00 0.00 1.40
2042 2126 4.832823 TGGGTCAGATGCTCTCGATTAATA 59.167 41.667 0.00 0.00 0.00 0.98
2043 2127 5.047731 TGGGTCAGATGCTCTCGATTAATAG 60.048 44.000 0.00 0.00 0.00 1.73
2044 2128 5.047660 GGGTCAGATGCTCTCGATTAATAGT 60.048 44.000 0.00 0.00 0.00 2.12
2045 2129 6.151312 GGGTCAGATGCTCTCGATTAATAGTA 59.849 42.308 0.00 0.00 0.00 1.82
2046 2130 7.309255 GGGTCAGATGCTCTCGATTAATAGTAA 60.309 40.741 0.00 0.00 0.00 2.24
2047 2131 8.082852 GGTCAGATGCTCTCGATTAATAGTAAA 58.917 37.037 0.00 0.00 0.00 2.01
2048 2132 9.632807 GTCAGATGCTCTCGATTAATAGTAAAT 57.367 33.333 0.00 0.00 0.00 1.40
2053 2137 8.818141 TGCTCTCGATTAATAGTAAATTCAGG 57.182 34.615 0.00 0.00 0.00 3.86
2054 2138 7.872993 TGCTCTCGATTAATAGTAAATTCAGGG 59.127 37.037 0.00 0.00 0.00 4.45
2055 2139 8.088981 GCTCTCGATTAATAGTAAATTCAGGGA 58.911 37.037 0.00 0.00 0.00 4.20
2056 2140 9.982651 CTCTCGATTAATAGTAAATTCAGGGAA 57.017 33.333 0.00 0.00 0.00 3.97
2102 2186 9.918630 AAGATTCTAAATTTTTGTGACATCCAG 57.081 29.630 0.00 0.00 0.00 3.86
2103 2187 8.526147 AGATTCTAAATTTTTGTGACATCCAGG 58.474 33.333 0.00 0.00 0.00 4.45
2104 2188 7.831691 TTCTAAATTTTTGTGACATCCAGGA 57.168 32.000 0.00 0.00 0.00 3.86
2105 2189 8.421249 TTCTAAATTTTTGTGACATCCAGGAT 57.579 30.769 0.00 0.00 0.00 3.24
2106 2190 9.527157 TTCTAAATTTTTGTGACATCCAGGATA 57.473 29.630 0.00 0.00 0.00 2.59
2107 2191 8.956426 TCTAAATTTTTGTGACATCCAGGATAC 58.044 33.333 0.00 0.00 0.00 2.24
2126 2210 7.297229 GGATACTTGAGTTTTCTAAGAGCAC 57.703 40.000 0.00 0.00 0.00 4.40
2127 2211 6.035112 GGATACTTGAGTTTTCTAAGAGCACG 59.965 42.308 0.00 0.00 0.00 5.34
2128 2212 3.495001 ACTTGAGTTTTCTAAGAGCACGC 59.505 43.478 0.00 0.00 0.00 5.34
2129 2213 3.106242 TGAGTTTTCTAAGAGCACGCA 57.894 42.857 0.00 0.00 0.00 5.24
2130 2214 3.462982 TGAGTTTTCTAAGAGCACGCAA 58.537 40.909 0.00 0.00 0.00 4.85
2131 2215 5.837782 CTTGAGTTTTCTAAGAGCACGCAAG 60.838 44.000 8.76 8.76 38.39 4.01
2132 2216 3.728845 AGTTTTCTAAGAGCACGCAAGA 58.271 40.909 0.00 0.00 43.62 3.02
2133 2217 4.319177 AGTTTTCTAAGAGCACGCAAGAT 58.681 39.130 0.00 0.00 43.62 2.40
2134 2218 4.757149 AGTTTTCTAAGAGCACGCAAGATT 59.243 37.500 0.00 0.00 43.62 2.40
2135 2219 5.239525 AGTTTTCTAAGAGCACGCAAGATTT 59.760 36.000 0.00 0.00 43.62 2.17
2136 2220 5.689383 TTTCTAAGAGCACGCAAGATTTT 57.311 34.783 0.00 0.00 43.62 1.82
2137 2221 4.668576 TCTAAGAGCACGCAAGATTTTG 57.331 40.909 0.00 0.00 43.62 2.44
2138 2222 4.065088 TCTAAGAGCACGCAAGATTTTGT 58.935 39.130 0.00 0.00 43.62 2.83
2139 2223 3.715628 AAGAGCACGCAAGATTTTGTT 57.284 38.095 0.00 0.00 43.62 2.83
2140 2224 3.715628 AGAGCACGCAAGATTTTGTTT 57.284 38.095 0.00 0.00 43.62 2.83
2141 2225 3.374745 AGAGCACGCAAGATTTTGTTTG 58.625 40.909 0.00 0.00 43.62 2.93
2142 2226 1.860326 AGCACGCAAGATTTTGTTTGC 59.140 42.857 12.97 12.97 44.67 3.68
2143 2227 1.070643 GCACGCAAGATTTTGTTTGCC 60.071 47.619 10.86 0.00 45.17 4.52
2144 2228 2.200067 CACGCAAGATTTTGTTTGCCA 58.800 42.857 3.89 0.00 45.17 4.92
2145 2229 2.606725 CACGCAAGATTTTGTTTGCCAA 59.393 40.909 3.89 0.00 45.17 4.52
2146 2230 3.063180 CACGCAAGATTTTGTTTGCCAAA 59.937 39.130 3.89 0.00 45.17 3.28
2157 2241 6.824305 TTTGTTTGCCAAAAAGGAAATTCA 57.176 29.167 0.00 0.00 40.05 2.57
2158 2242 6.434018 TTGTTTGCCAAAAAGGAAATTCAG 57.566 33.333 0.00 0.00 41.22 3.02
2159 2243 4.880696 TGTTTGCCAAAAAGGAAATTCAGG 59.119 37.500 0.00 0.00 41.22 3.86
2160 2244 3.767902 TGCCAAAAAGGAAATTCAGGG 57.232 42.857 0.00 0.00 41.22 4.45
2161 2245 3.312890 TGCCAAAAAGGAAATTCAGGGA 58.687 40.909 0.00 0.00 41.22 4.20
2162 2246 3.713764 TGCCAAAAAGGAAATTCAGGGAA 59.286 39.130 0.00 0.00 41.22 3.97
2163 2247 4.164988 TGCCAAAAAGGAAATTCAGGGAAA 59.835 37.500 0.00 0.00 41.22 3.13
2164 2248 5.129634 GCCAAAAAGGAAATTCAGGGAAAA 58.870 37.500 0.00 0.00 41.22 2.29
2165 2249 5.769662 GCCAAAAAGGAAATTCAGGGAAAAT 59.230 36.000 0.00 0.00 41.22 1.82
2166 2250 6.939730 GCCAAAAAGGAAATTCAGGGAAAATA 59.060 34.615 0.00 0.00 41.22 1.40
2167 2251 7.446931 GCCAAAAAGGAAATTCAGGGAAAATAA 59.553 33.333 0.00 0.00 41.22 1.40
2168 2252 8.783093 CCAAAAAGGAAATTCAGGGAAAATAAC 58.217 33.333 0.00 0.00 41.22 1.89
2169 2253 9.336171 CAAAAAGGAAATTCAGGGAAAATAACA 57.664 29.630 0.00 0.00 0.00 2.41
2170 2254 9.913310 AAAAAGGAAATTCAGGGAAAATAACAA 57.087 25.926 0.00 0.00 0.00 2.83
2171 2255 9.913310 AAAAGGAAATTCAGGGAAAATAACAAA 57.087 25.926 0.00 0.00 0.00 2.83
2172 2256 9.913310 AAAGGAAATTCAGGGAAAATAACAAAA 57.087 25.926 0.00 0.00 0.00 2.44
2173 2257 9.913310 AAGGAAATTCAGGGAAAATAACAAAAA 57.087 25.926 0.00 0.00 0.00 1.94
2241 2325 2.823924 TTTTCCGACGACCTCATTGA 57.176 45.000 0.00 0.00 0.00 2.57
2242 2326 2.823924 TTTCCGACGACCTCATTGAA 57.176 45.000 0.00 0.00 0.00 2.69
2243 2327 3.328382 TTTCCGACGACCTCATTGAAT 57.672 42.857 0.00 0.00 0.00 2.57
2244 2328 2.293677 TCCGACGACCTCATTGAATG 57.706 50.000 0.00 0.00 0.00 2.67
2245 2329 1.548719 TCCGACGACCTCATTGAATGT 59.451 47.619 4.93 0.00 0.00 2.71
2246 2330 1.927174 CCGACGACCTCATTGAATGTC 59.073 52.381 4.93 6.10 0.00 3.06
2250 2334 2.606108 CGACCTCATTGAATGTCGTGA 58.394 47.619 21.35 0.00 44.00 4.35
2251 2335 2.345641 CGACCTCATTGAATGTCGTGAC 59.654 50.000 21.35 0.00 44.00 3.67
2252 2336 3.325870 GACCTCATTGAATGTCGTGACA 58.674 45.455 4.99 4.99 46.44 3.58
2253 2337 3.067106 ACCTCATTGAATGTCGTGACAC 58.933 45.455 4.57 0.00 45.05 3.67
2254 2338 2.416547 CCTCATTGAATGTCGTGACACC 59.583 50.000 4.57 1.39 45.05 4.16
2255 2339 3.066380 CTCATTGAATGTCGTGACACCA 58.934 45.455 4.57 4.03 45.05 4.17
2256 2340 3.673902 TCATTGAATGTCGTGACACCAT 58.326 40.909 4.57 0.00 45.05 3.55
2257 2341 4.826556 TCATTGAATGTCGTGACACCATA 58.173 39.130 4.57 0.00 45.05 2.74
2258 2342 5.241662 TCATTGAATGTCGTGACACCATAA 58.758 37.500 4.57 0.00 45.05 1.90
2259 2343 5.351189 TCATTGAATGTCGTGACACCATAAG 59.649 40.000 4.57 0.00 45.05 1.73
2260 2344 4.529109 TGAATGTCGTGACACCATAAGA 57.471 40.909 4.57 0.00 45.05 2.10
2261 2345 4.888917 TGAATGTCGTGACACCATAAGAA 58.111 39.130 4.57 0.00 45.05 2.52
2262 2346 5.487433 TGAATGTCGTGACACCATAAGAAT 58.513 37.500 4.57 0.00 45.05 2.40
2263 2347 5.937540 TGAATGTCGTGACACCATAAGAATT 59.062 36.000 4.57 0.00 45.05 2.17
2264 2348 6.429692 TGAATGTCGTGACACCATAAGAATTT 59.570 34.615 4.57 0.00 45.05 1.82
2265 2349 5.605564 TGTCGTGACACCATAAGAATTTG 57.394 39.130 0.00 0.00 36.21 2.32
2266 2350 4.083537 TGTCGTGACACCATAAGAATTTGC 60.084 41.667 0.00 0.00 36.21 3.68
2267 2351 4.068599 TCGTGACACCATAAGAATTTGCA 58.931 39.130 0.00 0.00 0.00 4.08
2268 2352 4.699735 TCGTGACACCATAAGAATTTGCAT 59.300 37.500 0.00 0.00 0.00 3.96
2269 2353 4.794762 CGTGACACCATAAGAATTTGCATG 59.205 41.667 0.00 0.00 0.00 4.06
2270 2354 4.563976 GTGACACCATAAGAATTTGCATGC 59.436 41.667 11.82 11.82 0.00 4.06
2271 2355 4.220163 TGACACCATAAGAATTTGCATGCA 59.780 37.500 18.46 18.46 0.00 3.96
2272 2356 4.497300 ACACCATAAGAATTTGCATGCAC 58.503 39.130 22.58 9.12 0.00 4.57
2273 2357 3.866910 CACCATAAGAATTTGCATGCACC 59.133 43.478 22.58 10.06 0.00 5.01
2274 2358 3.770933 ACCATAAGAATTTGCATGCACCT 59.229 39.130 22.58 12.28 0.00 4.00
2275 2359 4.223477 ACCATAAGAATTTGCATGCACCTT 59.777 37.500 22.58 21.10 0.00 3.50
2276 2360 4.569162 CCATAAGAATTTGCATGCACCTTG 59.431 41.667 22.58 10.70 0.00 3.61
2277 2361 2.088950 AGAATTTGCATGCACCTTGC 57.911 45.000 22.58 6.73 45.29 4.01
2287 2371 1.866925 GCACCTTGCGTACTCAACC 59.133 57.895 0.00 0.00 31.71 3.77
2288 2372 0.882927 GCACCTTGCGTACTCAACCA 60.883 55.000 0.00 0.00 31.71 3.67
2289 2373 1.808411 CACCTTGCGTACTCAACCAT 58.192 50.000 0.00 0.00 0.00 3.55
2290 2374 2.151202 CACCTTGCGTACTCAACCATT 58.849 47.619 0.00 0.00 0.00 3.16
2291 2375 3.331150 CACCTTGCGTACTCAACCATTA 58.669 45.455 0.00 0.00 0.00 1.90
2292 2376 3.938963 CACCTTGCGTACTCAACCATTAT 59.061 43.478 0.00 0.00 0.00 1.28
2293 2377 3.938963 ACCTTGCGTACTCAACCATTATG 59.061 43.478 0.00 0.00 0.00 1.90
2294 2378 4.188462 CCTTGCGTACTCAACCATTATGA 58.812 43.478 0.00 0.00 0.00 2.15
2295 2379 4.034048 CCTTGCGTACTCAACCATTATGAC 59.966 45.833 0.00 0.00 0.00 3.06
2296 2380 4.465632 TGCGTACTCAACCATTATGACT 57.534 40.909 0.00 0.00 0.00 3.41
2297 2381 4.180817 TGCGTACTCAACCATTATGACTG 58.819 43.478 0.00 0.00 0.00 3.51
2298 2382 4.181578 GCGTACTCAACCATTATGACTGT 58.818 43.478 0.00 0.00 0.00 3.55
2299 2383 5.105675 TGCGTACTCAACCATTATGACTGTA 60.106 40.000 0.00 0.00 0.00 2.74
2300 2384 5.808540 GCGTACTCAACCATTATGACTGTAA 59.191 40.000 0.00 0.00 0.00 2.41
2301 2385 6.311935 GCGTACTCAACCATTATGACTGTAAA 59.688 38.462 0.00 0.00 0.00 2.01
2302 2386 7.148540 GCGTACTCAACCATTATGACTGTAAAA 60.149 37.037 0.00 0.00 0.00 1.52
2303 2387 8.714179 CGTACTCAACCATTATGACTGTAAAAA 58.286 33.333 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 62 9.816354 AGCACTAACACAGAATAACAAAATTTT 57.184 25.926 0.00 0.00 0.00 1.82
119 120 6.431198 AACGGTGATAACAAACATGGATAC 57.569 37.500 0.00 0.00 0.00 2.24
156 159 5.068636 ACTGACACATTGAAGCAAGAGATT 58.931 37.500 0.00 0.00 0.00 2.40
238 252 2.938956 ACTCCTGGACTTCCAAACAG 57.061 50.000 0.00 0.00 46.97 3.16
326 348 4.709886 TGGCTAGATGTAAGCTTCAGTGTA 59.290 41.667 0.00 0.00 39.97 2.90
348 370 7.148188 ACCAAGACATGCTTATGACAAGTATTG 60.148 37.037 0.00 0.00 43.55 1.90
357 379 9.237187 TGTTAATTTACCAAGACATGCTTATGA 57.763 29.630 0.00 0.00 34.31 2.15
370 393 3.367498 GGCACGGCATGTTAATTTACCAA 60.367 43.478 0.00 0.00 0.00 3.67
399 422 5.801947 GCATTAACTGAATAAACACCAGCAG 59.198 40.000 0.00 0.00 0.00 4.24
454 477 6.716628 TGACAGAAAGGAAAGATAGCATTTGT 59.283 34.615 0.00 0.00 0.00 2.83
455 478 7.149569 TGACAGAAAGGAAAGATAGCATTTG 57.850 36.000 0.00 0.00 0.00 2.32
544 620 7.377928 GTCAACTGTCAACAGAAAAGAATGATG 59.622 37.037 16.71 1.32 46.59 3.07
581 657 8.431910 AATACTTATATTTAGAAGCGGAGGGA 57.568 34.615 0.00 0.00 0.00 4.20
582 658 9.503399 AAAATACTTATATTTAGAAGCGGAGGG 57.497 33.333 0.00 0.00 39.61 4.30
614 690 8.401784 ACATCCGTATGTAGTCCATAGTGGAAT 61.402 40.741 4.27 4.27 45.76 3.01
615 691 7.143487 ACATCCGTATGTAGTCCATAGTGGAA 61.143 42.308 0.00 0.00 45.76 3.53
616 692 4.442401 TCCGTATGTAGTCCATAGTGGA 57.558 45.455 0.00 0.00 45.98 4.02
617 693 4.523173 ACATCCGTATGTAGTCCATAGTGG 59.477 45.833 0.00 0.00 44.66 4.00
618 694 5.707242 ACATCCGTATGTAGTCCATAGTG 57.293 43.478 0.00 0.00 44.66 2.74
659 735 6.073222 ACGGAACAAAATGAGTGAATCTACAC 60.073 38.462 0.00 0.00 40.60 2.90
660 736 5.995282 ACGGAACAAAATGAGTGAATCTACA 59.005 36.000 0.00 0.00 0.00 2.74
661 737 6.481954 ACGGAACAAAATGAGTGAATCTAC 57.518 37.500 0.00 0.00 0.00 2.59
662 738 7.822334 ACATACGGAACAAAATGAGTGAATCTA 59.178 33.333 0.00 0.00 0.00 1.98
663 739 6.655003 ACATACGGAACAAAATGAGTGAATCT 59.345 34.615 0.00 0.00 0.00 2.40
664 740 6.842163 ACATACGGAACAAAATGAGTGAATC 58.158 36.000 0.00 0.00 0.00 2.52
665 741 6.817765 ACATACGGAACAAAATGAGTGAAT 57.182 33.333 0.00 0.00 0.00 2.57
666 742 6.932400 ACTACATACGGAACAAAATGAGTGAA 59.068 34.615 0.00 0.00 0.00 3.18
667 743 6.460781 ACTACATACGGAACAAAATGAGTGA 58.539 36.000 0.00 0.00 0.00 3.41
668 744 6.367695 TGACTACATACGGAACAAAATGAGTG 59.632 38.462 0.00 0.00 0.00 3.51
669 745 6.460781 TGACTACATACGGAACAAAATGAGT 58.539 36.000 0.00 0.00 0.00 3.41
670 746 6.961359 TGACTACATACGGAACAAAATGAG 57.039 37.500 0.00 0.00 0.00 2.90
671 747 7.915293 AATGACTACATACGGAACAAAATGA 57.085 32.000 0.00 0.00 35.50 2.57
675 751 8.670135 CCAATAAATGACTACATACGGAACAAA 58.330 33.333 0.00 0.00 35.50 2.83
676 752 8.041919 TCCAATAAATGACTACATACGGAACAA 58.958 33.333 0.00 0.00 35.50 2.83
677 753 7.557724 TCCAATAAATGACTACATACGGAACA 58.442 34.615 0.00 0.00 35.50 3.18
678 754 8.428186 TTCCAATAAATGACTACATACGGAAC 57.572 34.615 0.00 0.00 35.50 3.62
679 755 9.268268 GATTCCAATAAATGACTACATACGGAA 57.732 33.333 0.00 0.00 35.50 4.30
680 756 8.647796 AGATTCCAATAAATGACTACATACGGA 58.352 33.333 0.00 0.00 35.50 4.69
681 757 8.833231 AGATTCCAATAAATGACTACATACGG 57.167 34.615 0.00 0.00 35.50 4.02
682 758 9.698309 AGAGATTCCAATAAATGACTACATACG 57.302 33.333 0.00 0.00 35.50 3.06
709 785 9.392259 CCTCCGTTCCTAAATATAAGTCTTTTT 57.608 33.333 0.00 0.00 0.00 1.94
710 786 7.991460 CCCTCCGTTCCTAAATATAAGTCTTTT 59.009 37.037 0.00 0.00 0.00 2.27
711 787 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
712 788 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
713 789 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
714 790 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
715 791 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
716 792 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
717 793 7.951806 TGATACTCCCTCCGTTCCTAAATATAA 59.048 37.037 0.00 0.00 0.00 0.98
718 794 7.472741 TGATACTCCCTCCGTTCCTAAATATA 58.527 38.462 0.00 0.00 0.00 0.86
719 795 6.320518 TGATACTCCCTCCGTTCCTAAATAT 58.679 40.000 0.00 0.00 0.00 1.28
720 796 5.708544 TGATACTCCCTCCGTTCCTAAATA 58.291 41.667 0.00 0.00 0.00 1.40
721 797 4.553678 TGATACTCCCTCCGTTCCTAAAT 58.446 43.478 0.00 0.00 0.00 1.40
722 798 3.985127 TGATACTCCCTCCGTTCCTAAA 58.015 45.455 0.00 0.00 0.00 1.85
723 799 3.675348 TGATACTCCCTCCGTTCCTAA 57.325 47.619 0.00 0.00 0.00 2.69
724 800 3.897657 ATGATACTCCCTCCGTTCCTA 57.102 47.619 0.00 0.00 0.00 2.94
725 801 2.777459 ATGATACTCCCTCCGTTCCT 57.223 50.000 0.00 0.00 0.00 3.36
726 802 2.698797 TGAATGATACTCCCTCCGTTCC 59.301 50.000 0.00 0.00 0.00 3.62
727 803 4.402056 TTGAATGATACTCCCTCCGTTC 57.598 45.455 0.00 0.00 0.00 3.95
728 804 4.837093 TTTGAATGATACTCCCTCCGTT 57.163 40.909 0.00 0.00 0.00 4.44
729 805 4.837093 TTTTGAATGATACTCCCTCCGT 57.163 40.909 0.00 0.00 0.00 4.69
885 961 9.347934 CAGTGTGTTTGTAATGTTTTTGTTCTA 57.652 29.630 0.00 0.00 0.00 2.10
918 994 4.938832 CAGGGGTTTGATTCGTACACATAA 59.061 41.667 0.00 0.00 0.00 1.90
963 1040 1.379916 CACCAGCCCATGAAGGTCA 59.620 57.895 0.00 0.00 34.66 4.02
986 1063 0.921896 ATTCATGTCCCCACCTCCAG 59.078 55.000 0.00 0.00 0.00 3.86
1041 1118 5.007626 CCCGATCACAATACCAACAACTATG 59.992 44.000 0.00 0.00 0.00 2.23
1065 1142 9.300681 TCAATTCCAACTATTATTCCATCCATC 57.699 33.333 0.00 0.00 0.00 3.51
1077 1154 4.406649 CCAATGCCCTCAATTCCAACTATT 59.593 41.667 0.00 0.00 0.00 1.73
1078 1155 3.962718 CCAATGCCCTCAATTCCAACTAT 59.037 43.478 0.00 0.00 0.00 2.12
1081 1158 1.901833 ACCAATGCCCTCAATTCCAAC 59.098 47.619 0.00 0.00 0.00 3.77
1088 1165 1.078891 ATGCCACCAATGCCCTCAA 59.921 52.632 0.00 0.00 0.00 3.02
1212 1289 1.668751 CCACCAATACCGTTCATTCCG 59.331 52.381 0.00 0.00 0.00 4.30
1230 1307 1.606668 GTTCCGAAACTCACAATGCCA 59.393 47.619 0.00 0.00 32.36 4.92
1239 1316 0.601841 TTCCCGCAGTTCCGAAACTC 60.602 55.000 0.00 0.00 43.99 3.01
1266 1343 2.971330 TCCAACCACATTGCCTTCAATT 59.029 40.909 0.00 0.00 40.74 2.32
1271 1348 2.086610 AGTTCCAACCACATTGCCTT 57.913 45.000 0.00 0.00 36.93 4.35
1281 1358 2.281276 ACGCCGGAAGTTCCAACC 60.281 61.111 21.76 7.89 35.91 3.77
1296 1373 2.507992 CCAGCTCAGCCTTCGACG 60.508 66.667 0.00 0.00 0.00 5.12
1299 1376 2.031516 CACACCAGCTCAGCCTTCG 61.032 63.158 0.00 0.00 0.00 3.79
1418 1495 1.556911 AGTCACTTACCATGGCTCCAG 59.443 52.381 13.04 5.06 0.00 3.86
1419 1496 1.278985 CAGTCACTTACCATGGCTCCA 59.721 52.381 13.04 0.00 26.46 3.86
1421 1498 2.289694 ACACAGTCACTTACCATGGCTC 60.290 50.000 13.04 0.00 26.46 4.70
1435 1512 2.720758 CTAGCGCGCACACACAGTC 61.721 63.158 35.10 0.00 0.00 3.51
1482 1561 7.396907 CCCAGTATCTCAGATTCACAGATATCT 59.603 40.741 0.00 0.00 32.91 1.98
1492 1571 5.753721 AATAGCCCCAGTATCTCAGATTC 57.246 43.478 0.00 0.00 0.00 2.52
1493 1572 5.370880 ACAAATAGCCCCAGTATCTCAGATT 59.629 40.000 0.00 0.00 0.00 2.40
1494 1573 4.910304 ACAAATAGCCCCAGTATCTCAGAT 59.090 41.667 0.00 0.00 0.00 2.90
1496 1575 4.696479 ACAAATAGCCCCAGTATCTCAG 57.304 45.455 0.00 0.00 0.00 3.35
1520 1599 6.273260 AGTGGTGGCCATAGTATATCATCTTT 59.727 38.462 9.72 0.00 35.28 2.52
1597 1676 1.039068 ACTCCCTGATCTGCATCTCG 58.961 55.000 0.00 0.00 0.00 4.04
1617 1696 2.224426 TGCTAAGCGAAGAACTTCCCAA 60.224 45.455 8.66 0.00 36.27 4.12
1640 1719 2.398554 CGCCGTCCATCAACCCAAG 61.399 63.158 0.00 0.00 0.00 3.61
1659 1738 5.982890 AAAATCCCAACCACTATGAACTG 57.017 39.130 0.00 0.00 0.00 3.16
1684 1763 9.712305 TTGGTAATCAAAAGTTCAGAACAAAAA 57.288 25.926 15.85 0.00 31.46 1.94
1685 1764 9.364989 CTTGGTAATCAAAAGTTCAGAACAAAA 57.635 29.630 15.85 0.00 34.56 2.44
1694 1773 9.394477 GTGTACAATCTTGGTAATCAAAAGTTC 57.606 33.333 0.00 0.00 34.56 3.01
1705 1784 5.474532 ACTCACTACGTGTACAATCTTGGTA 59.525 40.000 0.00 0.00 34.79 3.25
1732 1811 2.899303 AAAAGATTCCCACCCACGAT 57.101 45.000 0.00 0.00 0.00 3.73
1764 1844 1.136891 GAAATTGGTAGCCATGCCACC 59.863 52.381 0.00 0.00 41.40 4.61
1928 2012 2.224354 TGCTGCAGACTGTCTCATTTCA 60.224 45.455 20.43 0.00 0.00 2.69
1973 2057 4.833390 CTCGGTATTCCCACTCTTTTTCT 58.167 43.478 0.00 0.00 0.00 2.52
1980 2064 1.480954 TCTTGCTCGGTATTCCCACTC 59.519 52.381 0.00 0.00 0.00 3.51
2007 2091 5.011533 AGCATCTGACCCATATTCAGTAGTC 59.988 44.000 3.43 0.00 41.22 2.59
2027 2111 9.429359 CCTGAATTTACTATTAATCGAGAGCAT 57.571 33.333 0.00 0.00 0.00 3.79
2028 2112 7.872993 CCCTGAATTTACTATTAATCGAGAGCA 59.127 37.037 0.00 0.00 0.00 4.26
2029 2113 8.088981 TCCCTGAATTTACTATTAATCGAGAGC 58.911 37.037 0.00 0.00 0.00 4.09
2030 2114 9.982651 TTCCCTGAATTTACTATTAATCGAGAG 57.017 33.333 0.00 0.00 0.00 3.20
2076 2160 9.918630 CTGGATGTCACAAAAATTTAGAATCTT 57.081 29.630 0.00 0.00 0.00 2.40
2077 2161 8.526147 CCTGGATGTCACAAAAATTTAGAATCT 58.474 33.333 0.00 0.00 0.00 2.40
2078 2162 8.522830 TCCTGGATGTCACAAAAATTTAGAATC 58.477 33.333 0.00 0.00 0.00 2.52
2079 2163 8.421249 TCCTGGATGTCACAAAAATTTAGAAT 57.579 30.769 0.00 0.00 0.00 2.40
2080 2164 7.831691 TCCTGGATGTCACAAAAATTTAGAA 57.168 32.000 0.00 0.00 0.00 2.10
2081 2165 8.956426 GTATCCTGGATGTCACAAAAATTTAGA 58.044 33.333 19.42 0.00 0.00 2.10
2082 2166 8.960591 AGTATCCTGGATGTCACAAAAATTTAG 58.039 33.333 19.42 0.00 0.00 1.85
2083 2167 8.877864 AGTATCCTGGATGTCACAAAAATTTA 57.122 30.769 19.42 0.00 0.00 1.40
2084 2168 7.781324 AGTATCCTGGATGTCACAAAAATTT 57.219 32.000 19.42 0.00 0.00 1.82
2085 2169 7.451255 TCAAGTATCCTGGATGTCACAAAAATT 59.549 33.333 19.42 0.00 0.00 1.82
2086 2170 6.947733 TCAAGTATCCTGGATGTCACAAAAAT 59.052 34.615 19.42 0.00 0.00 1.82
2087 2171 6.303054 TCAAGTATCCTGGATGTCACAAAAA 58.697 36.000 19.42 0.00 0.00 1.94
2088 2172 5.875224 TCAAGTATCCTGGATGTCACAAAA 58.125 37.500 19.42 0.00 0.00 2.44
2089 2173 5.013079 ACTCAAGTATCCTGGATGTCACAAA 59.987 40.000 19.42 0.00 0.00 2.83
2090 2174 4.532126 ACTCAAGTATCCTGGATGTCACAA 59.468 41.667 19.42 0.00 0.00 3.33
2091 2175 4.096681 ACTCAAGTATCCTGGATGTCACA 58.903 43.478 19.42 0.00 0.00 3.58
2092 2176 4.744795 ACTCAAGTATCCTGGATGTCAC 57.255 45.455 19.42 9.54 0.00 3.67
2093 2177 5.762179 AAACTCAAGTATCCTGGATGTCA 57.238 39.130 19.42 0.00 0.00 3.58
2094 2178 6.410540 AGAAAACTCAAGTATCCTGGATGTC 58.589 40.000 19.42 11.71 0.00 3.06
2095 2179 6.380079 AGAAAACTCAAGTATCCTGGATGT 57.620 37.500 19.42 4.41 0.00 3.06
2096 2180 8.260818 TCTTAGAAAACTCAAGTATCCTGGATG 58.739 37.037 19.42 4.00 0.00 3.51
2097 2181 8.380742 TCTTAGAAAACTCAAGTATCCTGGAT 57.619 34.615 14.66 14.66 0.00 3.41
2098 2182 7.579723 GCTCTTAGAAAACTCAAGTATCCTGGA 60.580 40.741 0.00 0.00 0.00 3.86
2099 2183 6.536941 GCTCTTAGAAAACTCAAGTATCCTGG 59.463 42.308 0.00 0.00 0.00 4.45
2100 2184 7.064016 GTGCTCTTAGAAAACTCAAGTATCCTG 59.936 40.741 0.00 0.00 0.00 3.86
2101 2185 7.100409 GTGCTCTTAGAAAACTCAAGTATCCT 58.900 38.462 0.00 0.00 0.00 3.24
2102 2186 6.035112 CGTGCTCTTAGAAAACTCAAGTATCC 59.965 42.308 0.00 0.00 0.00 2.59
2103 2187 6.454450 GCGTGCTCTTAGAAAACTCAAGTATC 60.454 42.308 0.00 0.00 0.00 2.24
2104 2188 5.348997 GCGTGCTCTTAGAAAACTCAAGTAT 59.651 40.000 0.00 0.00 0.00 2.12
2105 2189 4.684703 GCGTGCTCTTAGAAAACTCAAGTA 59.315 41.667 0.00 0.00 0.00 2.24
2106 2190 3.495001 GCGTGCTCTTAGAAAACTCAAGT 59.505 43.478 0.00 0.00 0.00 3.16
2107 2191 3.494626 TGCGTGCTCTTAGAAAACTCAAG 59.505 43.478 0.00 0.00 0.00 3.02
2108 2192 3.462982 TGCGTGCTCTTAGAAAACTCAA 58.537 40.909 0.00 0.00 0.00 3.02
2109 2193 3.106242 TGCGTGCTCTTAGAAAACTCA 57.894 42.857 0.00 0.00 0.00 3.41
2110 2194 3.741344 TCTTGCGTGCTCTTAGAAAACTC 59.259 43.478 0.00 0.00 0.00 3.01
2111 2195 3.728845 TCTTGCGTGCTCTTAGAAAACT 58.271 40.909 0.00 0.00 0.00 2.66
2112 2196 4.670227 ATCTTGCGTGCTCTTAGAAAAC 57.330 40.909 0.00 0.00 0.00 2.43
2113 2197 5.689383 AAATCTTGCGTGCTCTTAGAAAA 57.311 34.783 0.00 0.00 0.00 2.29
2114 2198 5.008613 ACAAAATCTTGCGTGCTCTTAGAAA 59.991 36.000 0.00 0.00 35.84 2.52
2115 2199 4.515191 ACAAAATCTTGCGTGCTCTTAGAA 59.485 37.500 0.00 0.00 35.84 2.10
2116 2200 4.065088 ACAAAATCTTGCGTGCTCTTAGA 58.935 39.130 0.00 0.00 35.84 2.10
2117 2201 4.410492 ACAAAATCTTGCGTGCTCTTAG 57.590 40.909 0.00 0.00 35.84 2.18
2118 2202 4.829064 AACAAAATCTTGCGTGCTCTTA 57.171 36.364 0.00 0.00 35.84 2.10
2119 2203 3.715628 AACAAAATCTTGCGTGCTCTT 57.284 38.095 0.00 0.00 35.84 2.85
2120 2204 3.374745 CAAACAAAATCTTGCGTGCTCT 58.625 40.909 0.00 0.00 35.84 4.09
2121 2205 2.097250 GCAAACAAAATCTTGCGTGCTC 60.097 45.455 1.08 0.00 40.22 4.26
2122 2206 1.860326 GCAAACAAAATCTTGCGTGCT 59.140 42.857 1.08 0.00 40.22 4.40
2123 2207 2.283799 GCAAACAAAATCTTGCGTGC 57.716 45.000 0.00 0.00 38.66 5.34
2134 2218 6.127786 CCTGAATTTCCTTTTTGGCAAACAAA 60.128 34.615 13.10 9.62 46.82 2.83
2135 2219 5.356470 CCTGAATTTCCTTTTTGGCAAACAA 59.644 36.000 13.10 9.37 37.28 2.83
2136 2220 4.880696 CCTGAATTTCCTTTTTGGCAAACA 59.119 37.500 13.10 5.27 35.26 2.83
2137 2221 4.275689 CCCTGAATTTCCTTTTTGGCAAAC 59.724 41.667 13.10 0.00 35.26 2.93
2138 2222 4.164988 TCCCTGAATTTCCTTTTTGGCAAA 59.835 37.500 8.93 8.93 35.26 3.68
2139 2223 3.713764 TCCCTGAATTTCCTTTTTGGCAA 59.286 39.130 0.00 0.00 35.26 4.52
2140 2224 3.312890 TCCCTGAATTTCCTTTTTGGCA 58.687 40.909 0.00 0.00 35.26 4.92
2141 2225 4.350368 TTCCCTGAATTTCCTTTTTGGC 57.650 40.909 0.00 0.00 35.26 4.52
2142 2226 8.783093 GTTATTTTCCCTGAATTTCCTTTTTGG 58.217 33.333 0.00 0.00 37.10 3.28
2143 2227 9.336171 TGTTATTTTCCCTGAATTTCCTTTTTG 57.664 29.630 0.00 0.00 0.00 2.44
2144 2228 9.913310 TTGTTATTTTCCCTGAATTTCCTTTTT 57.087 25.926 0.00 0.00 0.00 1.94
2145 2229 9.913310 TTTGTTATTTTCCCTGAATTTCCTTTT 57.087 25.926 0.00 0.00 0.00 2.27
2146 2230 9.913310 TTTTGTTATTTTCCCTGAATTTCCTTT 57.087 25.926 0.00 0.00 0.00 3.11
2147 2231 9.913310 TTTTTGTTATTTTCCCTGAATTTCCTT 57.087 25.926 0.00 0.00 0.00 3.36
2221 2305 3.114668 TCAATGAGGTCGTCGGAAAAA 57.885 42.857 0.00 0.00 0.00 1.94
2222 2306 2.823924 TCAATGAGGTCGTCGGAAAA 57.176 45.000 0.00 0.00 0.00 2.29
2223 2307 2.823924 TTCAATGAGGTCGTCGGAAA 57.176 45.000 0.00 0.00 0.00 3.13
2224 2308 2.028476 ACATTCAATGAGGTCGTCGGAA 60.028 45.455 3.79 0.00 0.00 4.30
2225 2309 1.548719 ACATTCAATGAGGTCGTCGGA 59.451 47.619 3.79 0.00 0.00 4.55
2226 2310 1.927174 GACATTCAATGAGGTCGTCGG 59.073 52.381 3.79 0.00 0.00 4.79
2227 2311 1.583856 CGACATTCAATGAGGTCGTCG 59.416 52.381 22.58 16.47 45.73 5.12
2231 2315 3.123621 GTGTCACGACATTCAATGAGGTC 59.876 47.826 3.79 6.96 43.97 3.85
2232 2316 3.067106 GTGTCACGACATTCAATGAGGT 58.933 45.455 3.79 0.00 43.97 3.85
2233 2317 2.416547 GGTGTCACGACATTCAATGAGG 59.583 50.000 3.79 0.00 43.97 3.86
2234 2318 3.066380 TGGTGTCACGACATTCAATGAG 58.934 45.455 3.79 0.13 43.97 2.90
2235 2319 3.118905 TGGTGTCACGACATTCAATGA 57.881 42.857 3.79 0.00 43.97 2.57
2236 2320 5.351189 TCTTATGGTGTCACGACATTCAATG 59.649 40.000 2.72 0.00 43.97 2.82
2237 2321 5.487433 TCTTATGGTGTCACGACATTCAAT 58.513 37.500 2.72 0.00 43.97 2.57
2238 2322 4.888917 TCTTATGGTGTCACGACATTCAA 58.111 39.130 2.72 0.00 43.97 2.69
2239 2323 4.529109 TCTTATGGTGTCACGACATTCA 57.471 40.909 2.72 5.98 43.97 2.57
2240 2324 6.422776 AATTCTTATGGTGTCACGACATTC 57.577 37.500 2.72 0.42 43.97 2.67
2241 2325 6.611381 CAAATTCTTATGGTGTCACGACATT 58.389 36.000 2.72 0.00 43.97 2.71
2242 2326 5.391950 GCAAATTCTTATGGTGTCACGACAT 60.392 40.000 2.72 0.00 43.97 3.06
2243 2327 4.083537 GCAAATTCTTATGGTGTCACGACA 60.084 41.667 0.00 0.00 39.32 4.35
2244 2328 4.083537 TGCAAATTCTTATGGTGTCACGAC 60.084 41.667 0.00 0.00 0.00 4.34
2245 2329 4.068599 TGCAAATTCTTATGGTGTCACGA 58.931 39.130 0.00 0.00 0.00 4.35
2246 2330 4.418013 TGCAAATTCTTATGGTGTCACG 57.582 40.909 0.00 0.00 0.00 4.35
2247 2331 4.563976 GCATGCAAATTCTTATGGTGTCAC 59.436 41.667 14.21 0.00 0.00 3.67
2248 2332 4.220163 TGCATGCAAATTCTTATGGTGTCA 59.780 37.500 20.30 0.00 0.00 3.58
2249 2333 4.563976 GTGCATGCAAATTCTTATGGTGTC 59.436 41.667 24.58 0.00 0.00 3.67
2250 2334 4.497300 GTGCATGCAAATTCTTATGGTGT 58.503 39.130 24.58 0.00 0.00 4.16
2251 2335 3.866910 GGTGCATGCAAATTCTTATGGTG 59.133 43.478 24.58 0.00 0.00 4.17
2252 2336 3.770933 AGGTGCATGCAAATTCTTATGGT 59.229 39.130 24.58 0.00 0.00 3.55
2253 2337 4.395959 AGGTGCATGCAAATTCTTATGG 57.604 40.909 24.58 0.00 0.00 2.74
2254 2338 4.033587 GCAAGGTGCATGCAAATTCTTATG 59.966 41.667 24.58 13.65 44.26 1.90
2255 2339 4.186159 GCAAGGTGCATGCAAATTCTTAT 58.814 39.130 24.58 1.32 44.26 1.73
2256 2340 3.587923 GCAAGGTGCATGCAAATTCTTA 58.412 40.909 24.58 0.00 44.26 2.10
2257 2341 2.419667 GCAAGGTGCATGCAAATTCTT 58.580 42.857 24.58 19.22 44.26 2.52
2258 2342 1.670674 CGCAAGGTGCATGCAAATTCT 60.671 47.619 24.58 14.47 45.36 2.40
2259 2343 0.717224 CGCAAGGTGCATGCAAATTC 59.283 50.000 24.58 9.96 45.36 2.17
2260 2344 0.033781 ACGCAAGGTGCATGCAAATT 59.966 45.000 24.58 17.10 45.36 1.82
2261 2345 0.887247 TACGCAAGGTGCATGCAAAT 59.113 45.000 24.58 11.35 45.36 2.32
2262 2346 0.039617 GTACGCAAGGTGCATGCAAA 60.040 50.000 24.58 0.00 45.36 3.68
2263 2347 0.888736 AGTACGCAAGGTGCATGCAA 60.889 50.000 24.58 3.50 45.36 4.08
2264 2348 1.298157 GAGTACGCAAGGTGCATGCA 61.298 55.000 18.46 18.46 45.36 3.96
2265 2349 1.298157 TGAGTACGCAAGGTGCATGC 61.298 55.000 11.82 11.82 45.36 4.06
2266 2350 1.135972 GTTGAGTACGCAAGGTGCATG 60.136 52.381 12.62 0.00 45.36 4.06
2267 2351 1.156736 GTTGAGTACGCAAGGTGCAT 58.843 50.000 12.62 0.00 45.36 3.96
2268 2352 0.882927 GGTTGAGTACGCAAGGTGCA 60.883 55.000 12.62 0.00 45.36 4.57
2269 2353 0.882927 TGGTTGAGTACGCAAGGTGC 60.883 55.000 12.62 0.86 46.39 5.01
2270 2354 1.808411 ATGGTTGAGTACGCAAGGTG 58.192 50.000 12.62 0.00 46.39 4.00
2271 2355 2.561478 AATGGTTGAGTACGCAAGGT 57.439 45.000 12.62 0.00 46.39 3.50
2272 2356 4.034048 GTCATAATGGTTGAGTACGCAAGG 59.966 45.833 12.62 0.00 46.39 3.61
2274 2358 4.629634 CAGTCATAATGGTTGAGTACGCAA 59.370 41.667 8.05 8.05 0.00 4.85
2275 2359 4.180817 CAGTCATAATGGTTGAGTACGCA 58.819 43.478 0.00 0.00 0.00 5.24
2276 2360 4.181578 ACAGTCATAATGGTTGAGTACGC 58.818 43.478 0.00 0.00 0.00 4.42
2277 2361 7.821595 TTTACAGTCATAATGGTTGAGTACG 57.178 36.000 0.00 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.