Multiple sequence alignment - TraesCS1B01G086200

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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 TraesCS1B01G086200 chr1B 100.000 3340 0 0 1 3340 70713485 70710146 0.000000e+00 6168
1 TraesCS1B01G086200 chr1B 89.205 843 64 12 999 1841 648588060 648587245 0.000000e+00 1027
2 TraesCS1B01G086200 chr1B 84.387 269 25 8 2085 2349 648585661 648585406 7.160000e-62 248
3 TraesCS1B01G086200 chr1B 77.828 221 23 17 2441 2642 648585388 648585175 2.720000e-21 113
4 TraesCS1B01G086200 chr1D 86.427 1643 161 34 1724 3340 50197283 50195677 0.000000e+00 1742
5 TraesCS1B01G086200 chr1D 92.355 981 60 6 805 1784 50198226 50197260 0.000000e+00 1382
6 TraesCS1B01G086200 chr1D 87.070 843 66 15 999 1841 469041406 469040607 0.000000e+00 913
7 TraesCS1B01G086200 chr1D 84.701 268 30 9 2085 2351 469035674 469035417 1.190000e-64 257
8 TraesCS1B01G086200 chr1A 91.845 981 62 10 805 1779 49367330 49366362 0.000000e+00 1352
9 TraesCS1B01G086200 chr1A 81.685 1365 168 49 1758 3088 49366257 49364941 0.000000e+00 1061
10 TraesCS1B01G086200 chr1A 89.205 843 76 7 999 1841 562034825 562033998 0.000000e+00 1038
11 TraesCS1B01G086200 chr1A 84.871 271 24 8 2085 2351 562032341 562032084 1.190000e-64 257
12 TraesCS1B01G086200 chr1A 79.452 219 24 13 2441 2642 562032068 562031854 5.810000e-28 135
13 TraesCS1B01G086200 chr7B 85.007 727 85 16 1 712 186279379 186278662 0.000000e+00 717
14 TraesCS1B01G086200 chr7B 83.172 309 42 5 2051 2351 34154514 34154208 1.180000e-69 274
15 TraesCS1B01G086200 chr7A 84.711 726 93 15 1 714 412142377 412141658 0.000000e+00 710
16 TraesCS1B01G086200 chr2A 84.594 727 95 14 1 714 431583710 431584432 0.000000e+00 706
17 TraesCS1B01G086200 chr2A 90.984 122 9 2 595 714 205684332 205684211 2.670000e-36 163
18 TraesCS1B01G086200 chr4A 85.064 703 88 14 25 714 33745574 33744876 0.000000e+00 701
19 TraesCS1B01G086200 chr6D 83.401 735 96 22 1 714 304469687 304468958 0.000000e+00 658
20 TraesCS1B01G086200 chr3A 83.811 698 91 14 23 707 485409348 485410036 0.000000e+00 643
21 TraesCS1B01G086200 chr4B 85.116 645 76 17 1 628 502701129 502701770 2.810000e-180 641
22 TraesCS1B01G086200 chrUn 84.733 655 69 25 1 633 134997018 134996373 7.870000e-176 627
23 TraesCS1B01G086200 chrUn 84.275 655 72 25 1 633 152591340 152590695 7.920000e-171 610
24 TraesCS1B01G086200 chr3B 85.305 279 30 8 2080 2351 89686435 89686161 9.130000e-71 278
25 TraesCS1B01G086200 chr3B 88.298 94 10 1 622 714 93787520 93787427 9.800000e-21 111


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 TraesCS1B01G086200 chr1B 70710146 70713485 3339 True 6168.000000 6168 100.000000 1 3340 1 chr1B.!!$R1 3339
1 TraesCS1B01G086200 chr1B 648585175 648588060 2885 True 462.666667 1027 83.806667 999 2642 3 chr1B.!!$R2 1643
2 TraesCS1B01G086200 chr1D 50195677 50198226 2549 True 1562.000000 1742 89.391000 805 3340 2 chr1D.!!$R3 2535
3 TraesCS1B01G086200 chr1D 469040607 469041406 799 True 913.000000 913 87.070000 999 1841 1 chr1D.!!$R2 842
4 TraesCS1B01G086200 chr1A 49364941 49367330 2389 True 1206.500000 1352 86.765000 805 3088 2 chr1A.!!$R1 2283
5 TraesCS1B01G086200 chr1A 562031854 562034825 2971 True 476.666667 1038 84.509333 999 2642 3 chr1A.!!$R2 1643
6 TraesCS1B01G086200 chr7B 186278662 186279379 717 True 717.000000 717 85.007000 1 712 1 chr7B.!!$R2 711
7 TraesCS1B01G086200 chr7A 412141658 412142377 719 True 710.000000 710 84.711000 1 714 1 chr7A.!!$R1 713
8 TraesCS1B01G086200 chr2A 431583710 431584432 722 False 706.000000 706 84.594000 1 714 1 chr2A.!!$F1 713
9 TraesCS1B01G086200 chr4A 33744876 33745574 698 True 701.000000 701 85.064000 25 714 1 chr4A.!!$R1 689
10 TraesCS1B01G086200 chr6D 304468958 304469687 729 True 658.000000 658 83.401000 1 714 1 chr6D.!!$R1 713
11 TraesCS1B01G086200 chr3A 485409348 485410036 688 False 643.000000 643 83.811000 23 707 1 chr3A.!!$F1 684
12 TraesCS1B01G086200 chr4B 502701129 502701770 641 False 641.000000 641 85.116000 1 628 1 chr4B.!!$F1 627
13 TraesCS1B01G086200 chrUn 134996373 134997018 645 True 627.000000 627 84.733000 1 633 1 chrUn.!!$R1 632
14 TraesCS1B01G086200 chrUn 152590695 152591340 645 True 610.000000 610 84.275000 1 633 1 chrUn.!!$R2 632

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
784 817 0.248621 ACGTGAAAAAGTGCAGCTGC 60.249 50.0 31.89 31.89 42.5 5.25 F
1307 1342 0.179100 ACGGTGATCTCTGCCATTCG 60.179 55.0 3.48 0.00 0.0 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2222 4054 0.035458 CTGTCCGTTCTGCCTCCTTT 59.965 55.0 0.0 0.0 0.00 3.11 R
2357 4189 0.107831 ACAAGTTAGACGCCTTGCCA 59.892 50.0 0.0 0.0 41.36 4.92 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
82 83 7.444629 TCATTTTCTGAAAGAGAATCACCTG 57.555 36.000 2.75 0.00 43.50 4.00
122 123 6.940430 AAGAGATTCCATTCCAACCATTTT 57.060 33.333 0.00 0.00 0.00 1.82
139 140 7.839680 ACCATTTTGAACCTTGATTTCTAGT 57.160 32.000 0.00 0.00 0.00 2.57
151 153 7.017254 ACCTTGATTTCTAGTCTTCCCAAGTTA 59.983 37.037 0.00 0.00 0.00 2.24
152 154 8.049721 CCTTGATTTCTAGTCTTCCCAAGTTAT 58.950 37.037 0.00 0.00 0.00 1.89
182 184 9.739276 TCACTCAAATAATTCTTTCACCATAGT 57.261 29.630 0.00 0.00 0.00 2.12
212 217 3.031013 TGTGAGAGAGTTGAGTGTTGGA 58.969 45.455 0.00 0.00 0.00 3.53
263 268 1.806542 AGTTCATCATCAACACACCGC 59.193 47.619 0.00 0.00 0.00 5.68
270 275 4.415881 TCATCAACACACCGCCTATTAT 57.584 40.909 0.00 0.00 0.00 1.28
284 289 5.453339 CCGCCTATTATCTTTTGGAGAGTGA 60.453 44.000 0.00 0.00 37.93 3.41
327 332 1.201429 AACTTGGGAGCCTCCGACAT 61.201 55.000 4.29 0.00 37.43 3.06
353 359 5.502079 TGTGGAGTTGAACCAAGAAGTTTA 58.498 37.500 0.00 0.00 39.22 2.01
365 371 6.494059 ACCAAGAAGTTTATAAGGGCAAGAT 58.506 36.000 0.00 0.00 0.00 2.40
366 372 6.603599 ACCAAGAAGTTTATAAGGGCAAGATC 59.396 38.462 0.00 0.00 0.00 2.75
369 375 8.689972 CAAGAAGTTTATAAGGGCAAGATCATT 58.310 33.333 0.00 0.00 0.00 2.57
405 417 2.266055 CCGAGTGAGGCAAGTCCC 59.734 66.667 0.00 0.00 34.51 4.46
432 444 1.202758 GCGATGACCATGGTGGGATAA 60.203 52.381 25.52 0.48 43.37 1.75
438 450 3.332187 TGACCATGGTGGGATAAACAAGA 59.668 43.478 25.52 0.00 43.37 3.02
441 453 6.086011 ACCATGGTGGGATAAACAAGATTA 57.914 37.500 18.99 0.00 43.37 1.75
484 497 4.680537 AGCCCTCCGTGGACTCGT 62.681 66.667 0.00 0.00 38.35 4.18
527 540 1.691976 TGAAGTCTCCATCAACGTGGT 59.308 47.619 0.00 0.00 40.27 4.16
528 541 2.894765 TGAAGTCTCCATCAACGTGGTA 59.105 45.455 0.00 0.00 40.27 3.25
529 542 3.513912 TGAAGTCTCCATCAACGTGGTAT 59.486 43.478 0.00 0.00 40.27 2.73
530 543 3.802948 AGTCTCCATCAACGTGGTATC 57.197 47.619 0.00 0.00 40.27 2.24
577 601 5.059833 GTCTCCATTGTGTTTGACTTCTCT 58.940 41.667 0.00 0.00 0.00 3.10
579 603 6.367422 GTCTCCATTGTGTTTGACTTCTCTAG 59.633 42.308 0.00 0.00 0.00 2.43
593 617 5.662597 ACTTCTCTAGACCCTTCCCTTTAA 58.337 41.667 0.00 0.00 0.00 1.52
639 671 8.951787 TTTCCGCTGCTATACTCTTAAAATTA 57.048 30.769 0.00 0.00 0.00 1.40
667 699 5.468746 GTGTAGGTTGATTGCTTGACTTGTA 59.531 40.000 0.00 0.00 0.00 2.41
687 720 9.726438 ACTTGTACTAATTGCTAAAATCTGTCT 57.274 29.630 0.00 0.00 0.00 3.41
709 742 9.137459 TGTCTACAACTAAAATTGGGAAAATGA 57.863 29.630 0.00 0.00 33.63 2.57
715 748 9.586435 CAACTAAAATTGGGAAAATGATAGACC 57.414 33.333 0.00 0.00 0.00 3.85
716 749 9.547279 AACTAAAATTGGGAAAATGATAGACCT 57.453 29.630 0.00 0.00 0.00 3.85
717 750 8.971073 ACTAAAATTGGGAAAATGATAGACCTG 58.029 33.333 0.00 0.00 0.00 4.00
718 751 6.796785 AAATTGGGAAAATGATAGACCTGG 57.203 37.500 0.00 0.00 0.00 4.45
719 752 3.951563 TGGGAAAATGATAGACCTGGG 57.048 47.619 0.00 0.00 0.00 4.45
720 753 2.091885 TGGGAAAATGATAGACCTGGGC 60.092 50.000 0.00 0.00 0.00 5.36
721 754 2.222027 GGAAAATGATAGACCTGGGCG 58.778 52.381 0.00 0.00 0.00 6.13
722 755 1.604278 GAAAATGATAGACCTGGGCGC 59.396 52.381 0.00 0.00 0.00 6.53
723 756 0.532862 AAATGATAGACCTGGGCGCG 60.533 55.000 0.00 0.00 0.00 6.86
724 757 1.399744 AATGATAGACCTGGGCGCGA 61.400 55.000 12.10 0.00 0.00 5.87
725 758 1.188219 ATGATAGACCTGGGCGCGAT 61.188 55.000 12.10 0.00 0.00 4.58
726 759 1.080434 GATAGACCTGGGCGCGATC 60.080 63.158 12.10 0.06 0.00 3.69
727 760 2.804368 GATAGACCTGGGCGCGATCG 62.804 65.000 12.10 11.69 39.07 3.69
745 778 2.355126 CGATGGATCGGACGGCTG 60.355 66.667 0.00 0.00 45.93 4.85
746 779 2.815308 GATGGATCGGACGGCTGT 59.185 61.111 0.00 0.00 0.00 4.40
747 780 1.300233 GATGGATCGGACGGCTGTC 60.300 63.158 17.83 17.83 44.72 3.51
748 781 3.138930 ATGGATCGGACGGCTGTCG 62.139 63.158 19.26 14.21 46.49 4.35
750 783 4.492160 GATCGGACGGCTGTCGCA 62.492 66.667 19.26 8.55 46.49 5.10
751 784 4.498520 ATCGGACGGCTGTCGCAG 62.499 66.667 19.26 12.91 46.49 5.18
766 799 3.642755 CAGGGTGTGCTCGTGAAC 58.357 61.111 0.00 0.00 0.00 3.18
767 800 2.029073 AGGGTGTGCTCGTGAACG 59.971 61.111 0.00 0.00 41.45 3.95
768 801 2.279918 GGGTGTGCTCGTGAACGT 60.280 61.111 2.37 0.00 40.80 3.99
769 802 2.594962 GGGTGTGCTCGTGAACGTG 61.595 63.158 2.37 1.52 40.80 4.49
770 803 1.590525 GGTGTGCTCGTGAACGTGA 60.591 57.895 8.93 0.00 40.80 4.35
771 804 1.149361 GGTGTGCTCGTGAACGTGAA 61.149 55.000 8.93 0.00 40.80 3.18
772 805 0.648441 GTGTGCTCGTGAACGTGAAA 59.352 50.000 8.93 0.00 40.80 2.69
773 806 1.061421 GTGTGCTCGTGAACGTGAAAA 59.939 47.619 8.93 0.00 40.80 2.29
774 807 1.732809 TGTGCTCGTGAACGTGAAAAA 59.267 42.857 8.93 0.00 40.80 1.94
775 808 2.222931 TGTGCTCGTGAACGTGAAAAAG 60.223 45.455 8.93 0.00 40.80 2.27
776 809 2.004017 TGCTCGTGAACGTGAAAAAGT 58.996 42.857 8.93 0.00 40.80 2.66
777 810 2.222931 TGCTCGTGAACGTGAAAAAGTG 60.223 45.455 8.93 0.00 40.80 3.16
778 811 2.363220 CTCGTGAACGTGAAAAAGTGC 58.637 47.619 2.37 0.00 40.80 4.40
779 812 1.732809 TCGTGAACGTGAAAAAGTGCA 59.267 42.857 2.37 0.00 40.80 4.57
780 813 2.101125 CGTGAACGTGAAAAAGTGCAG 58.899 47.619 0.00 0.00 34.11 4.41
781 814 1.846175 GTGAACGTGAAAAAGTGCAGC 59.154 47.619 0.00 0.00 0.00 5.25
782 815 1.742831 TGAACGTGAAAAAGTGCAGCT 59.257 42.857 0.00 0.00 0.00 4.24
783 816 2.111756 GAACGTGAAAAAGTGCAGCTG 58.888 47.619 10.11 10.11 0.00 4.24
784 817 0.248621 ACGTGAAAAAGTGCAGCTGC 60.249 50.000 31.89 31.89 42.50 5.25
794 827 4.291047 GCAGCTGCACTTGCTAGA 57.709 55.556 33.36 0.00 42.66 2.43
795 828 2.548178 GCAGCTGCACTTGCTAGAA 58.452 52.632 33.36 0.00 42.66 2.10
796 829 1.093159 GCAGCTGCACTTGCTAGAAT 58.907 50.000 33.36 0.00 42.66 2.40
797 830 1.471684 GCAGCTGCACTTGCTAGAATT 59.528 47.619 33.36 0.00 42.66 2.17
798 831 2.094854 GCAGCTGCACTTGCTAGAATTT 60.095 45.455 33.36 0.00 42.66 1.82
799 832 3.499048 CAGCTGCACTTGCTAGAATTTG 58.501 45.455 0.00 0.00 42.66 2.32
800 833 2.490903 AGCTGCACTTGCTAGAATTTGG 59.509 45.455 1.04 0.00 42.66 3.28
801 834 2.416431 GCTGCACTTGCTAGAATTTGGG 60.416 50.000 1.04 0.00 42.66 4.12
802 835 2.821969 CTGCACTTGCTAGAATTTGGGT 59.178 45.455 1.04 0.00 42.66 4.51
803 836 3.230134 TGCACTTGCTAGAATTTGGGTT 58.770 40.909 1.04 0.00 42.66 4.11
861 894 5.221661 ACAATCCCCTCCTGATTACGTAATC 60.222 44.000 32.16 32.16 41.81 1.75
864 897 2.029290 CCCTCCTGATTACGTAATCCCG 60.029 54.545 34.19 26.52 40.98 5.14
949 982 3.532155 CTCGCCTTCTCCCTCCGG 61.532 72.222 0.00 0.00 0.00 5.14
1047 1081 2.517402 CTCCCGCCGCTCTACTCT 60.517 66.667 0.00 0.00 0.00 3.24
1307 1342 0.179100 ACGGTGATCTCTGCCATTCG 60.179 55.000 3.48 0.00 0.00 3.34
1331 1366 6.562270 CGGCGTTTATTAGCAGTCTAAAGATG 60.562 42.308 0.00 0.00 38.21 2.90
1364 1399 5.092105 TGCACAATTCGTTTTGGATTATCG 58.908 37.500 5.37 0.00 0.00 2.92
1373 1408 6.491394 TCGTTTTGGATTATCGCCATTTTAG 58.509 36.000 0.00 0.00 34.90 1.85
1574 1611 0.899019 GGAGGAAGGAGAAGAAGCGT 59.101 55.000 0.00 0.00 0.00 5.07
1648 1685 5.583854 TGCAATGCTTGTTTTAATTGTGTGT 59.416 32.000 6.82 0.00 33.50 3.72
1649 1686 6.093219 TGCAATGCTTGTTTTAATTGTGTGTT 59.907 30.769 6.82 0.00 33.50 3.32
1650 1687 6.411492 GCAATGCTTGTTTTAATTGTGTGTTG 59.589 34.615 0.00 0.00 33.50 3.33
1651 1688 6.601741 ATGCTTGTTTTAATTGTGTGTTGG 57.398 33.333 0.00 0.00 0.00 3.77
1652 1689 4.331168 TGCTTGTTTTAATTGTGTGTTGGC 59.669 37.500 0.00 0.00 0.00 4.52
1653 1690 4.260579 GCTTGTTTTAATTGTGTGTTGGCC 60.261 41.667 0.00 0.00 0.00 5.36
1654 1691 4.744795 TGTTTTAATTGTGTGTTGGCCT 57.255 36.364 3.32 0.00 0.00 5.19
1655 1692 4.437239 TGTTTTAATTGTGTGTTGGCCTG 58.563 39.130 3.32 0.00 0.00 4.85
1656 1693 4.081420 TGTTTTAATTGTGTGTTGGCCTGT 60.081 37.500 3.32 0.00 0.00 4.00
1676 1713 4.411927 TGTTGGGTGTATGCAAGGTTATT 58.588 39.130 0.00 0.00 0.00 1.40
1711 1758 5.070685 GTGTCTTGGGAGTGGAAAAAGTAT 58.929 41.667 0.00 0.00 0.00 2.12
1742 1789 7.169982 CCGATGAAATTCTGAGAACATAGGTAC 59.830 40.741 12.28 0.00 0.00 3.34
1753 1800 7.970102 TGAGAACATAGGTACTTTTAACAGGT 58.030 34.615 0.00 0.00 41.75 4.00
1764 1937 6.254281 ACTTTTAACAGGTGGATGAAATCG 57.746 37.500 0.00 0.00 46.86 3.34
1772 1945 2.348666 GGTGGATGAAATCGTGAGAACG 59.651 50.000 0.00 0.00 46.86 3.95
1773 1946 2.993899 GTGGATGAAATCGTGAGAACGT 59.006 45.455 0.00 0.00 46.86 3.99
1775 1948 4.265556 GTGGATGAAATCGTGAGAACGTAG 59.734 45.833 0.00 0.00 46.86 3.51
1810 1983 8.041829 TCATGCTATCGAGTAGTCCTAAATAC 57.958 38.462 0.00 0.00 32.72 1.89
1817 1990 7.414222 TCGAGTAGTCCTAAATACCATGTTT 57.586 36.000 0.00 0.00 0.00 2.83
1819 1992 7.039882 CGAGTAGTCCTAAATACCATGTTTGT 58.960 38.462 0.00 0.00 0.00 2.83
1846 3610 7.659186 ACGGAACTAGCTAATCATAGTTTAGG 58.341 38.462 0.00 0.00 41.20 2.69
1852 3642 5.774630 AGCTAATCATAGTTTAGGCGAGTC 58.225 41.667 0.00 0.00 0.00 3.36
1853 3643 5.536916 AGCTAATCATAGTTTAGGCGAGTCT 59.463 40.000 0.00 0.00 0.00 3.24
1868 3666 4.709640 GCGAGTCTGCCTTTTAAAAGTAC 58.290 43.478 23.04 16.20 34.20 2.73
1869 3667 4.378149 GCGAGTCTGCCTTTTAAAAGTACC 60.378 45.833 23.04 13.15 34.20 3.34
1873 3671 4.512571 GTCTGCCTTTTAAAAGTACCGTGA 59.487 41.667 23.04 11.33 34.20 4.35
1880 3678 8.124823 GCCTTTTAAAAGTACCGTGATAATACC 58.875 37.037 23.04 0.00 34.20 2.73
1901 3699 9.886132 AATACCAACACCTACATTTCTAGTAAG 57.114 33.333 0.00 0.00 0.00 2.34
1902 3700 7.312415 ACCAACACCTACATTTCTAGTAAGT 57.688 36.000 0.00 0.00 0.00 2.24
1906 3704 6.932947 ACACCTACATTTCTAGTAAGTCACC 58.067 40.000 0.00 0.00 0.00 4.02
1907 3705 6.495872 ACACCTACATTTCTAGTAAGTCACCA 59.504 38.462 0.00 0.00 0.00 4.17
1925 3723 7.056635 AGTCACCATTCTATATGTTTCCTTGG 58.943 38.462 0.00 0.00 0.00 3.61
1930 3729 8.531146 ACCATTCTATATGTTTCCTTGGTTTTG 58.469 33.333 0.00 0.00 31.10 2.44
1931 3730 7.492344 CCATTCTATATGTTTCCTTGGTTTTGC 59.508 37.037 0.00 0.00 0.00 3.68
1932 3731 7.775053 TTCTATATGTTTCCTTGGTTTTGCT 57.225 32.000 0.00 0.00 0.00 3.91
1933 3732 7.775053 TCTATATGTTTCCTTGGTTTTGCTT 57.225 32.000 0.00 0.00 0.00 3.91
1934 3733 8.189119 TCTATATGTTTCCTTGGTTTTGCTTT 57.811 30.769 0.00 0.00 0.00 3.51
1935 3734 9.303116 TCTATATGTTTCCTTGGTTTTGCTTTA 57.697 29.630 0.00 0.00 0.00 1.85
1936 3735 9.921637 CTATATGTTTCCTTGGTTTTGCTTTAA 57.078 29.630 0.00 0.00 0.00 1.52
1940 3739 7.612677 TGTTTCCTTGGTTTTGCTTTAACTTA 58.387 30.769 0.00 0.00 0.00 2.24
1944 3743 6.704050 TCCTTGGTTTTGCTTTAACTTATTGC 59.296 34.615 0.00 0.00 0.00 3.56
1951 3750 6.984740 TTGCTTTAACTTATTGCGTTCTTG 57.015 33.333 0.00 0.00 0.00 3.02
1956 3755 7.326063 GCTTTAACTTATTGCGTTCTTGTCATT 59.674 33.333 0.00 0.00 0.00 2.57
1958 3757 5.940192 ACTTATTGCGTTCTTGTCATTGA 57.060 34.783 0.00 0.00 0.00 2.57
1968 3767 5.210715 GTTCTTGTCATTGACTTGAAGCTG 58.789 41.667 17.26 0.57 33.15 4.24
1970 3769 4.883585 TCTTGTCATTGACTTGAAGCTGTT 59.116 37.500 17.26 0.00 33.15 3.16
1976 3775 6.853362 GTCATTGACTTGAAGCTGTTAGTTTC 59.147 38.462 9.59 0.00 36.20 2.78
1982 3781 5.648092 ACTTGAAGCTGTTAGTTTCAACTGT 59.352 36.000 14.20 10.32 45.91 3.55
1983 3782 6.151144 ACTTGAAGCTGTTAGTTTCAACTGTT 59.849 34.615 14.20 0.00 45.91 3.16
1992 3791 8.193250 TGTTAGTTTCAACTGTTTCAGTACTC 57.807 34.615 2.26 0.00 44.62 2.59
1993 3792 7.820386 TGTTAGTTTCAACTGTTTCAGTACTCA 59.180 33.333 2.26 0.00 44.62 3.41
1994 3793 8.662141 GTTAGTTTCAACTGTTTCAGTACTCAA 58.338 33.333 2.26 0.00 44.62 3.02
1999 3798 8.589335 TTCAACTGTTTCAGTACTCAATACTC 57.411 34.615 2.80 0.00 44.62 2.59
2003 3805 7.371936 ACTGTTTCAGTACTCAATACTCTCAC 58.628 38.462 0.00 0.00 43.46 3.51
2007 3809 4.099120 CAGTACTCAATACTCTCACGCAC 58.901 47.826 0.00 0.00 42.62 5.34
2017 3819 1.546476 CTCTCACGCACCTTACCTTCT 59.454 52.381 0.00 0.00 0.00 2.85
2019 3821 3.159472 TCTCACGCACCTTACCTTCTTA 58.841 45.455 0.00 0.00 0.00 2.10
2023 3825 4.062991 CACGCACCTTACCTTCTTACTTT 58.937 43.478 0.00 0.00 0.00 2.66
2027 3850 7.546667 CACGCACCTTACCTTCTTACTTTATAA 59.453 37.037 0.00 0.00 0.00 0.98
2029 3852 8.938906 CGCACCTTACCTTCTTACTTTATAAAA 58.061 33.333 0.00 0.00 0.00 1.52
2078 3905 8.428186 AGTTCTATGTGAAACTTTTGTTACGA 57.572 30.769 0.00 0.00 42.67 3.43
2106 3933 4.993584 CACTTATGCTCTGTCCATATGTCC 59.006 45.833 1.24 0.00 33.73 4.02
2111 3938 4.201657 TGCTCTGTCCATATGTCCAATTG 58.798 43.478 1.24 0.00 0.00 2.32
2114 3945 5.048921 GCTCTGTCCATATGTCCAATTGATG 60.049 44.000 7.12 2.00 0.00 3.07
2132 3963 3.198635 TGATGACCCAGACCTGAATTCTC 59.801 47.826 7.05 0.00 0.00 2.87
2140 3971 7.512992 ACCCAGACCTGAATTCTCTATTTATG 58.487 38.462 7.05 0.00 0.00 1.90
2222 4054 6.148315 CACAATATTCTGTTGCTGTGAAGAGA 59.852 38.462 0.00 0.00 37.03 3.10
2243 4075 1.216710 GGAGGCAGAACGGACAGAG 59.783 63.158 0.00 0.00 0.00 3.35
2298 4130 0.178990 GGTGGAAAGGTTGGCAGAGT 60.179 55.000 0.00 0.00 0.00 3.24
2300 4132 1.338020 GTGGAAAGGTTGGCAGAGTTG 59.662 52.381 0.00 0.00 0.00 3.16
2318 4150 5.083533 AGTTGAAACAGATAGAGGCAGAG 57.916 43.478 0.00 0.00 0.00 3.35
2330 4162 2.166270 GGCAGAGAAGAAAGCCACG 58.834 57.895 0.00 0.00 46.26 4.94
2374 4206 2.200373 AATGGCAAGGCGTCTAACTT 57.800 45.000 0.00 0.00 0.00 2.66
2397 4229 2.720758 CTGCTGCTCCGTTTCGTCG 61.721 63.158 0.00 0.00 0.00 5.12
2404 4236 1.392510 GCTCCGTTTCGTCGCTATTTT 59.607 47.619 0.00 0.00 0.00 1.82
2405 4237 2.159747 GCTCCGTTTCGTCGCTATTTTT 60.160 45.455 0.00 0.00 0.00 1.94
2426 4258 7.839680 TTTTTCTTTCCTTTTCAGATAGCCT 57.160 32.000 0.00 0.00 0.00 4.58
2427 4259 6.824305 TTTCTTTCCTTTTCAGATAGCCTG 57.176 37.500 0.00 0.00 44.27 4.85
2461 4315 4.805192 GTGCAACAATTGTCAACAATGTCT 59.195 37.500 12.39 0.00 45.06 3.41
2473 4327 3.864789 ACAATGTCTCAACCCTTCTGT 57.135 42.857 0.00 0.00 0.00 3.41
2497 4355 1.351350 GAACTCTGGCTGTACCCCTTT 59.649 52.381 0.00 0.00 37.83 3.11
2500 4358 0.178873 TCTGGCTGTACCCCTTTCCT 60.179 55.000 0.00 0.00 37.83 3.36
2547 4412 7.148869 GCTGATTTTGTTTTAATACGGTGTTCC 60.149 37.037 0.00 0.00 0.00 3.62
2586 4454 8.833493 CATTGTAATGAAACATCTGCTCTATGA 58.167 33.333 0.00 0.00 38.70 2.15
2589 4457 5.943706 ATGAAACATCTGCTCTATGATGC 57.056 39.130 0.00 0.00 42.57 3.91
2592 4460 5.238650 TGAAACATCTGCTCTATGATGCATG 59.761 40.000 2.46 0.00 42.57 4.06
2612 4480 7.416817 TGCATGTAGAATAAACCAAATGATCG 58.583 34.615 0.00 0.00 0.00 3.69
2646 4514 6.209192 TGCTGGTAATCAGAAATGACAAATGT 59.791 34.615 0.00 0.00 46.18 2.71
2668 4536 3.181488 TGTGCAACCTTCTGTCACATTTG 60.181 43.478 0.00 0.00 34.36 2.32
2685 4553 0.745128 TTGTGGCACCGAAGTTCGTT 60.745 50.000 22.87 7.05 38.40 3.85
2686 4554 0.745128 TGTGGCACCGAAGTTCGTTT 60.745 50.000 22.87 7.61 38.40 3.60
2690 4558 0.658897 GCACCGAAGTTCGTTTGGAA 59.341 50.000 22.87 0.00 42.02 3.53
2693 4561 1.796459 ACCGAAGTTCGTTTGGAATCG 59.204 47.619 22.87 7.56 42.02 3.34
2709 4577 6.795144 TGGAATCGGTATTGGAACTACTAA 57.205 37.500 0.00 0.00 0.00 2.24
2712 4580 7.147620 TGGAATCGGTATTGGAACTACTAATGT 60.148 37.037 0.00 0.00 32.21 2.71
2718 4586 7.960738 CGGTATTGGAACTACTAATGTTTGTTG 59.039 37.037 0.00 0.00 32.21 3.33
2735 4603 6.073058 TGTTTGTTGTTGATCTACTGCTCATC 60.073 38.462 8.74 0.00 0.00 2.92
2742 4610 6.381133 TGTTGATCTACTGCTCATCTTCCTTA 59.619 38.462 8.74 0.00 0.00 2.69
2758 4626 2.647299 TCCTTACCTCCCTTTGCATTCA 59.353 45.455 0.00 0.00 0.00 2.57
2888 4765 0.842635 CCATAGCTTCCAGCCTTCCT 59.157 55.000 0.00 0.00 43.77 3.36
2889 4766 2.050144 CCATAGCTTCCAGCCTTCCTA 58.950 52.381 0.00 0.00 43.77 2.94
2897 4774 0.548031 CCAGCCTTCCTATGCTTCCA 59.452 55.000 0.00 0.00 35.12 3.53
2903 4780 3.448660 GCCTTCCTATGCTTCCATGTTTT 59.551 43.478 0.00 0.00 32.85 2.43
2939 4822 1.639635 CCTGCTATTCCAGGTGGCCT 61.640 60.000 3.32 0.00 45.87 5.19
2971 4855 1.077429 GGGCACTCTGACCCCATTC 60.077 63.158 0.00 0.00 40.64 2.67
3015 4899 1.207390 TGCGCTTTCAAACATGCAAC 58.793 45.000 9.73 0.00 0.00 4.17
3234 5125 5.935789 CGGGTTGAGATTAAGAGTTTGGTTA 59.064 40.000 0.00 0.00 0.00 2.85
3235 5126 6.092259 CGGGTTGAGATTAAGAGTTTGGTTAG 59.908 42.308 0.00 0.00 0.00 2.34
3236 5127 6.940867 GGGTTGAGATTAAGAGTTTGGTTAGT 59.059 38.462 0.00 0.00 0.00 2.24
3237 5128 7.094762 GGGTTGAGATTAAGAGTTTGGTTAGTG 60.095 40.741 0.00 0.00 0.00 2.74
3238 5129 7.298854 GTTGAGATTAAGAGTTTGGTTAGTGC 58.701 38.462 0.00 0.00 0.00 4.40
3250 5141 1.562783 GTTAGTGCTGAGTCTCCCCT 58.437 55.000 0.00 0.00 0.00 4.79
3312 5207 2.297701 GTTGCAAGGAGGTGAGTTCAA 58.702 47.619 0.00 0.00 0.00 2.69
3313 5208 2.260844 TGCAAGGAGGTGAGTTCAAG 57.739 50.000 0.00 0.00 0.00 3.02
3314 5209 1.768275 TGCAAGGAGGTGAGTTCAAGA 59.232 47.619 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 3.118482 TGGCTCTCTCCATGAATGAAGAC 60.118 47.826 0.00 0.00 0.00 3.01
69 70 3.008813 ACACATGAGCAGGTGATTCTCTT 59.991 43.478 20.38 0.00 45.01 2.85
98 99 6.940430 AAATGGTTGGAATGGAATCTCTTT 57.060 33.333 0.00 0.00 0.00 2.52
103 104 5.643348 GGTTCAAAATGGTTGGAATGGAATC 59.357 40.000 0.00 0.00 29.25 2.52
122 123 5.309543 TGGGAAGACTAGAAATCAAGGTTCA 59.690 40.000 0.00 0.00 0.00 3.18
139 140 7.889873 TTGAGTGAAAAATAACTTGGGAAGA 57.110 32.000 0.00 0.00 0.00 2.87
169 171 6.427853 CACACAGATTTGACTATGGTGAAAGA 59.572 38.462 0.00 0.00 32.63 2.52
170 172 6.427853 TCACACAGATTTGACTATGGTGAAAG 59.572 38.462 0.00 0.00 32.63 2.62
173 175 5.245977 TCTCACACAGATTTGACTATGGTGA 59.754 40.000 0.00 0.00 0.00 4.02
182 184 5.069648 ACTCAACTCTCTCACACAGATTTGA 59.930 40.000 0.00 0.00 37.27 2.69
212 217 7.279758 GCTCTTGTGCTTTAAATGATAGTCTCT 59.720 37.037 0.00 0.00 0.00 3.10
263 268 8.428063 AGACATCACTCTCCAAAAGATAATAGG 58.572 37.037 0.00 0.00 32.19 2.57
294 299 5.321927 CTCCCAAGTTACACCTAACCAATT 58.678 41.667 0.00 0.00 33.82 2.32
308 313 1.201429 ATGTCGGAGGCTCCCAAGTT 61.201 55.000 27.36 6.41 31.13 2.66
327 332 3.358111 TCTTGGTTCAACTCCACAACA 57.642 42.857 0.00 0.00 34.45 3.33
353 359 6.260936 CACGAAGTAAATGATCTTGCCCTTAT 59.739 38.462 0.00 0.00 41.61 1.73
365 371 6.570692 GGGTAGATCTTCACGAAGTAAATGA 58.429 40.000 0.00 0.00 41.61 2.57
366 372 5.459107 CGGGTAGATCTTCACGAAGTAAATG 59.541 44.000 18.15 0.00 41.61 2.32
369 375 4.264253 TCGGGTAGATCTTCACGAAGTAA 58.736 43.478 22.45 1.39 41.61 2.24
438 450 3.368116 CGAAGGGTCCACGAAGAAGTAAT 60.368 47.826 0.00 0.00 0.00 1.89
441 453 0.317479 CGAAGGGTCCACGAAGAAGT 59.683 55.000 0.00 0.00 0.00 3.01
484 497 1.675714 CCACGAAGGATAACAGCTGCA 60.676 52.381 15.27 1.58 41.22 4.41
527 540 4.331968 AGATTTTTGGCGTGGTTCTGATA 58.668 39.130 0.00 0.00 0.00 2.15
528 541 3.157087 AGATTTTTGGCGTGGTTCTGAT 58.843 40.909 0.00 0.00 0.00 2.90
529 542 2.582052 AGATTTTTGGCGTGGTTCTGA 58.418 42.857 0.00 0.00 0.00 3.27
530 543 3.308530 GAAGATTTTTGGCGTGGTTCTG 58.691 45.455 0.00 0.00 0.00 3.02
577 601 5.550403 ACATGAAGTTAAAGGGAAGGGTCTA 59.450 40.000 0.00 0.00 0.00 2.59
579 603 4.459337 CACATGAAGTTAAAGGGAAGGGTC 59.541 45.833 0.00 0.00 0.00 4.46
593 617 8.073768 CGGAAAGTAAAACATTACACATGAAGT 58.926 33.333 0.00 0.00 0.00 3.01
639 671 4.216257 GTCAAGCAATCAACCTACACATGT 59.784 41.667 0.00 0.00 0.00 3.21
667 699 9.726438 AGTTGTAGACAGATTTTAGCAATTAGT 57.274 29.630 0.00 0.00 0.00 2.24
709 742 2.920645 CGATCGCGCCCAGGTCTAT 61.921 63.158 0.26 0.00 0.00 1.98
729 762 1.300233 GACAGCCGTCCGATCCATC 60.300 63.158 0.00 0.00 36.02 3.51
730 763 2.815308 GACAGCCGTCCGATCCAT 59.185 61.111 0.00 0.00 36.02 3.41
731 764 3.822192 CGACAGCCGTCCGATCCA 61.822 66.667 0.00 0.00 39.11 3.41
733 766 4.492160 TGCGACAGCCGTCCGATC 62.492 66.667 0.00 0.00 44.33 3.69
734 767 4.498520 CTGCGACAGCCGTCCGAT 62.499 66.667 0.00 0.00 44.33 4.18
749 782 2.310233 CGTTCACGAGCACACCCTG 61.310 63.158 0.00 0.00 43.02 4.45
750 783 2.029073 CGTTCACGAGCACACCCT 59.971 61.111 0.00 0.00 43.02 4.34
751 784 2.279918 ACGTTCACGAGCACACCC 60.280 61.111 6.30 0.00 43.02 4.61
752 785 1.149361 TTCACGTTCACGAGCACACC 61.149 55.000 6.30 0.00 43.02 4.16
753 786 0.648441 TTTCACGTTCACGAGCACAC 59.352 50.000 6.30 0.00 43.02 3.82
754 787 1.360820 TTTTCACGTTCACGAGCACA 58.639 45.000 6.30 0.00 43.02 4.57
755 788 2.222953 ACTTTTTCACGTTCACGAGCAC 60.223 45.455 6.30 0.00 43.02 4.40
756 789 2.004017 ACTTTTTCACGTTCACGAGCA 58.996 42.857 6.30 0.00 43.02 4.26
757 790 2.363220 CACTTTTTCACGTTCACGAGC 58.637 47.619 6.30 0.00 43.02 5.03
758 791 2.222931 TGCACTTTTTCACGTTCACGAG 60.223 45.455 6.30 0.00 43.02 4.18
759 792 1.732809 TGCACTTTTTCACGTTCACGA 59.267 42.857 6.30 0.00 43.02 4.35
760 793 2.101125 CTGCACTTTTTCACGTTCACG 58.899 47.619 0.00 0.00 46.33 4.35
761 794 1.846175 GCTGCACTTTTTCACGTTCAC 59.154 47.619 0.00 0.00 0.00 3.18
762 795 1.742831 AGCTGCACTTTTTCACGTTCA 59.257 42.857 1.02 0.00 0.00 3.18
763 796 2.111756 CAGCTGCACTTTTTCACGTTC 58.888 47.619 0.00 0.00 0.00 3.95
764 797 1.798813 GCAGCTGCACTTTTTCACGTT 60.799 47.619 33.36 0.00 41.59 3.99
765 798 0.248621 GCAGCTGCACTTTTTCACGT 60.249 50.000 33.36 0.00 41.59 4.49
766 799 2.498892 GCAGCTGCACTTTTTCACG 58.501 52.632 33.36 0.00 41.59 4.35
777 810 1.093159 ATTCTAGCAAGTGCAGCTGC 58.907 50.000 31.89 31.89 43.33 5.25
778 811 3.499048 CAAATTCTAGCAAGTGCAGCTG 58.501 45.455 10.11 10.11 43.33 4.24
779 812 2.490903 CCAAATTCTAGCAAGTGCAGCT 59.509 45.455 6.00 4.22 45.16 4.24
780 813 2.416431 CCCAAATTCTAGCAAGTGCAGC 60.416 50.000 6.00 0.00 45.16 5.25
781 814 2.821969 ACCCAAATTCTAGCAAGTGCAG 59.178 45.455 6.00 1.63 45.16 4.41
782 815 2.875296 ACCCAAATTCTAGCAAGTGCA 58.125 42.857 6.00 0.00 45.16 4.57
783 816 3.942130 AACCCAAATTCTAGCAAGTGC 57.058 42.857 0.00 0.00 42.49 4.40
784 817 6.349363 GGTCTAAACCCAAATTCTAGCAAGTG 60.349 42.308 0.00 0.00 39.93 3.16
785 818 5.710567 GGTCTAAACCCAAATTCTAGCAAGT 59.289 40.000 0.00 0.00 39.93 3.16
786 819 6.196079 GGTCTAAACCCAAATTCTAGCAAG 57.804 41.667 0.00 0.00 39.93 4.01
800 833 3.739209 CGTAATCGAAGGGGGTCTAAACC 60.739 52.174 0.00 0.00 41.32 3.27
801 834 3.118992 ACGTAATCGAAGGGGGTCTAAAC 60.119 47.826 0.00 0.00 40.62 2.01
802 835 3.099141 ACGTAATCGAAGGGGGTCTAAA 58.901 45.455 0.00 0.00 40.62 1.85
803 836 2.689983 GACGTAATCGAAGGGGGTCTAA 59.310 50.000 0.00 0.00 40.62 2.10
814 847 9.462174 TTGTCTAAAAGTAAAAGACGTAATCGA 57.538 29.630 0.00 0.00 42.05 3.59
930 963 4.214327 GGAGGGAGAAGGCGAGCG 62.214 72.222 0.00 0.00 0.00 5.03
949 982 1.227176 CGTCGGGCTAGGGTTTAGC 60.227 63.158 0.00 0.00 39.70 3.09
950 983 1.227176 GCGTCGGGCTAGGGTTTAG 60.227 63.158 0.00 0.00 39.11 1.85
951 984 2.724273 GGCGTCGGGCTAGGGTTTA 61.724 63.158 0.00 0.00 42.94 2.01
980 1013 4.081642 CCATCGTGGAGAAGGTTCTAGAAA 60.082 45.833 6.78 0.00 40.96 2.52
1104 1138 2.444895 GGATCCAGGAGCCGGAGT 60.445 66.667 8.35 0.00 35.56 3.85
1307 1342 6.292919 CCATCTTTAGACTGCTAATAAACGCC 60.293 42.308 0.00 0.00 36.54 5.68
1314 1349 4.572389 CGTTGCCATCTTTAGACTGCTAAT 59.428 41.667 0.00 0.00 36.54 1.73
1319 1354 4.269603 CAGATCGTTGCCATCTTTAGACTG 59.730 45.833 0.00 0.00 0.00 3.51
1331 1366 1.791555 CGAATTGTGCAGATCGTTGCC 60.792 52.381 4.64 0.00 43.43 4.52
1364 1399 1.602191 CGACGCACAACTAAAATGGC 58.398 50.000 0.00 0.00 0.00 4.40
1373 1408 3.640000 ACAGCAGCGACGCACAAC 61.640 61.111 23.70 7.94 0.00 3.32
1547 1584 1.081092 CTCCTTCCTCCCCTGGACA 59.919 63.158 0.00 0.00 35.58 4.02
1550 1587 0.043334 TCTTCTCCTTCCTCCCCTGG 59.957 60.000 0.00 0.00 0.00 4.45
1574 1611 0.250234 AGTCCTTGCGCTGCTTGATA 59.750 50.000 9.73 0.00 0.00 2.15
1648 1685 0.897863 GCATACACCCAACAGGCCAA 60.898 55.000 5.01 0.00 40.58 4.52
1649 1686 1.304052 GCATACACCCAACAGGCCA 60.304 57.895 5.01 0.00 40.58 5.36
1650 1687 0.897863 TTGCATACACCCAACAGGCC 60.898 55.000 0.00 0.00 40.58 5.19
1651 1688 0.527565 CTTGCATACACCCAACAGGC 59.472 55.000 0.00 0.00 40.58 4.85
1652 1689 1.176527 CCTTGCATACACCCAACAGG 58.823 55.000 0.00 0.00 43.78 4.00
1653 1690 1.909700 ACCTTGCATACACCCAACAG 58.090 50.000 0.00 0.00 0.00 3.16
1654 1691 2.373335 AACCTTGCATACACCCAACA 57.627 45.000 0.00 0.00 0.00 3.33
1655 1692 6.518208 TTAATAACCTTGCATACACCCAAC 57.482 37.500 0.00 0.00 0.00 3.77
1656 1693 7.540474 TTTTAATAACCTTGCATACACCCAA 57.460 32.000 0.00 0.00 0.00 4.12
1676 1713 7.331026 CACTCCCAAGACACAGATAGATTTTA 58.669 38.462 0.00 0.00 0.00 1.52
1695 1732 3.017442 GCCTGATACTTTTTCCACTCCC 58.983 50.000 0.00 0.00 0.00 4.30
1711 1758 2.501316 TCTCAGAATTTCATCGGCCTGA 59.499 45.455 0.00 0.00 0.00 3.86
1742 1789 6.072728 TCACGATTTCATCCACCTGTTAAAAG 60.073 38.462 0.00 0.00 0.00 2.27
1793 1966 7.093640 ACAAACATGGTATTTAGGACTACTCGA 60.094 37.037 0.00 0.00 0.00 4.04
1802 1975 6.988622 TCCGTTACAAACATGGTATTTAGG 57.011 37.500 0.00 0.00 0.00 2.69
1810 1983 4.000988 AGCTAGTTCCGTTACAAACATGG 58.999 43.478 0.00 0.00 0.00 3.66
1817 1990 7.578310 ACTATGATTAGCTAGTTCCGTTACA 57.422 36.000 0.00 0.00 0.00 2.41
1846 3610 3.898517 ACTTTTAAAAGGCAGACTCGC 57.101 42.857 27.23 0.00 40.31 5.03
1852 3642 5.622770 ATCACGGTACTTTTAAAAGGCAG 57.377 39.130 27.23 21.32 40.31 4.85
1853 3643 7.690952 ATTATCACGGTACTTTTAAAAGGCA 57.309 32.000 27.23 14.65 40.31 4.75
1868 3666 5.013568 TGTAGGTGTTGGTATTATCACGG 57.986 43.478 0.00 0.00 0.00 4.94
1869 3667 7.494625 AGAAATGTAGGTGTTGGTATTATCACG 59.505 37.037 0.00 0.00 0.00 4.35
1880 3678 7.331193 GGTGACTTACTAGAAATGTAGGTGTTG 59.669 40.741 0.00 0.00 31.79 3.33
1897 3695 9.614792 AAGGAAACATATAGAATGGTGACTTAC 57.385 33.333 0.00 0.00 0.00 2.34
1901 3699 6.828785 ACCAAGGAAACATATAGAATGGTGAC 59.171 38.462 0.00 0.00 37.27 3.67
1902 3700 6.969043 ACCAAGGAAACATATAGAATGGTGA 58.031 36.000 0.00 0.00 37.27 4.02
1906 3704 8.253113 AGCAAAACCAAGGAAACATATAGAATG 58.747 33.333 0.00 0.00 0.00 2.67
1907 3705 8.366359 AGCAAAACCAAGGAAACATATAGAAT 57.634 30.769 0.00 0.00 0.00 2.40
1912 3710 8.428852 AGTTAAAGCAAAACCAAGGAAACATAT 58.571 29.630 0.00 0.00 0.00 1.78
1916 3714 6.978343 AAGTTAAAGCAAAACCAAGGAAAC 57.022 33.333 0.00 0.00 0.00 2.78
1917 3715 9.103861 CAATAAGTTAAAGCAAAACCAAGGAAA 57.896 29.630 0.00 0.00 0.00 3.13
1920 3718 6.346518 CGCAATAAGTTAAAGCAAAACCAAGG 60.347 38.462 9.66 0.00 0.00 3.61
1925 3723 7.389603 AGAACGCAATAAGTTAAAGCAAAAC 57.610 32.000 9.66 0.00 31.14 2.43
1930 3729 6.140110 TGACAAGAACGCAATAAGTTAAAGC 58.860 36.000 0.00 0.00 31.14 3.51
1931 3730 8.629986 CAATGACAAGAACGCAATAAGTTAAAG 58.370 33.333 0.00 0.00 31.14 1.85
1932 3731 8.346300 TCAATGACAAGAACGCAATAAGTTAAA 58.654 29.630 0.00 0.00 31.14 1.52
1933 3732 7.801315 GTCAATGACAAGAACGCAATAAGTTAA 59.199 33.333 8.74 0.00 32.09 2.01
1934 3733 7.172532 AGTCAATGACAAGAACGCAATAAGTTA 59.827 33.333 16.38 0.00 34.60 2.24
1935 3734 6.017109 AGTCAATGACAAGAACGCAATAAGTT 60.017 34.615 16.38 0.00 34.60 2.66
1936 3735 5.470098 AGTCAATGACAAGAACGCAATAAGT 59.530 36.000 16.38 0.00 34.60 2.24
1940 3739 4.275689 TCAAGTCAATGACAAGAACGCAAT 59.724 37.500 16.38 0.00 34.60 3.56
1944 3743 4.024556 AGCTTCAAGTCAATGACAAGAACG 60.025 41.667 16.38 12.24 34.60 3.95
1951 3750 5.931441 ACTAACAGCTTCAAGTCAATGAC 57.069 39.130 5.02 5.02 0.00 3.06
1956 3755 5.880332 AGTTGAAACTAACAGCTTCAAGTCA 59.120 36.000 5.27 0.00 38.76 3.41
1958 3757 5.648092 ACAGTTGAAACTAACAGCTTCAAGT 59.352 36.000 5.27 5.96 41.83 3.16
1968 3767 8.193250 TGAGTACTGAAACAGTTGAAACTAAC 57.807 34.615 0.00 0.37 42.59 2.34
1970 3769 8.958119 ATTGAGTACTGAAACAGTTGAAACTA 57.042 30.769 0.00 0.00 42.59 2.24
1976 3775 7.867909 TGAGAGTATTGAGTACTGAAACAGTTG 59.132 37.037 0.00 0.00 42.59 3.16
1982 3781 5.048294 TGCGTGAGAGTATTGAGTACTGAAA 60.048 40.000 0.00 0.00 43.66 2.69
1983 3782 4.457949 TGCGTGAGAGTATTGAGTACTGAA 59.542 41.667 0.00 0.00 43.66 3.02
1992 3791 3.119101 AGGTAAGGTGCGTGAGAGTATTG 60.119 47.826 0.00 0.00 0.00 1.90
1993 3792 3.097614 AGGTAAGGTGCGTGAGAGTATT 58.902 45.455 0.00 0.00 0.00 1.89
1994 3793 2.736347 AGGTAAGGTGCGTGAGAGTAT 58.264 47.619 0.00 0.00 0.00 2.12
1999 3798 2.457366 AAGAAGGTAAGGTGCGTGAG 57.543 50.000 0.00 0.00 0.00 3.51
2003 3805 8.483307 TTTATAAAGTAAGAAGGTAAGGTGCG 57.517 34.615 0.00 0.00 0.00 5.34
2029 3852 9.131791 ACTACATTATGAAAAGACAGGTTTGTT 57.868 29.630 0.00 0.00 37.76 2.83
2031 3854 9.612620 GAACTACATTATGAAAAGACAGGTTTG 57.387 33.333 0.00 0.00 0.00 2.93
2061 3888 6.964934 AGTGAACATCGTAACAAAAGTTTCAC 59.035 34.615 0.00 0.00 0.00 3.18
2062 3889 7.079182 AGTGAACATCGTAACAAAAGTTTCA 57.921 32.000 0.00 0.00 0.00 2.69
2063 3890 7.964545 AAGTGAACATCGTAACAAAAGTTTC 57.035 32.000 0.00 0.00 0.00 2.78
2076 3903 3.553511 GGACAGAGCATAAGTGAACATCG 59.446 47.826 0.00 0.00 0.00 3.84
2078 3905 4.558226 TGGACAGAGCATAAGTGAACAT 57.442 40.909 0.00 0.00 0.00 2.71
2106 3933 3.354948 TCAGGTCTGGGTCATCAATTG 57.645 47.619 0.00 0.00 0.00 2.32
2111 3938 3.454082 AGAGAATTCAGGTCTGGGTCATC 59.546 47.826 8.44 0.00 0.00 2.92
2114 3945 5.622346 AATAGAGAATTCAGGTCTGGGTC 57.378 43.478 8.44 0.00 0.00 4.46
2146 3978 7.761249 GCCAAAGCAAGATAAATGAATGTAAGT 59.239 33.333 0.00 0.00 39.53 2.24
2180 4012 0.312102 GTGCTTTGCGCTTCCTCTTT 59.688 50.000 9.73 0.00 40.11 2.52
2201 4033 6.373774 CCTTTCTCTTCACAGCAACAGAATAT 59.626 38.462 0.00 0.00 0.00 1.28
2222 4054 0.035458 CTGTCCGTTCTGCCTCCTTT 59.965 55.000 0.00 0.00 0.00 3.11
2243 4075 1.372087 CCACGGCAGCCATCTTTCTC 61.372 60.000 13.30 0.00 0.00 2.87
2298 4130 5.481824 TCTTCTCTGCCTCTATCTGTTTCAA 59.518 40.000 0.00 0.00 0.00 2.69
2300 4132 5.590530 TCTTCTCTGCCTCTATCTGTTTC 57.409 43.478 0.00 0.00 0.00 2.78
2356 4188 1.271379 ACAAGTTAGACGCCTTGCCAT 60.271 47.619 0.00 0.00 41.36 4.40
2357 4189 0.107831 ACAAGTTAGACGCCTTGCCA 59.892 50.000 0.00 0.00 41.36 4.92
2374 4206 0.944386 GAAACGGAGCAGCAGAAACA 59.056 50.000 0.00 0.00 0.00 2.83
2404 4236 6.824305 CAGGCTATCTGAAAAGGAAAGAAA 57.176 37.500 0.00 0.00 46.18 2.52
2417 4249 5.178996 GCACAGAACATATTCAGGCTATCTG 59.821 44.000 0.00 0.00 44.68 2.90
2418 4250 5.163269 TGCACAGAACATATTCAGGCTATCT 60.163 40.000 0.00 0.00 37.29 1.98
2419 4251 5.059161 TGCACAGAACATATTCAGGCTATC 58.941 41.667 0.00 0.00 37.29 2.08
2420 4252 5.039920 TGCACAGAACATATTCAGGCTAT 57.960 39.130 0.00 0.00 37.29 2.97
2421 4253 4.486125 TGCACAGAACATATTCAGGCTA 57.514 40.909 0.00 0.00 37.29 3.93
2422 4254 3.354948 TGCACAGAACATATTCAGGCT 57.645 42.857 0.00 0.00 37.29 4.58
2423 4255 3.191162 TGTTGCACAGAACATATTCAGGC 59.809 43.478 0.00 0.00 37.29 4.85
2424 4256 5.375417 TTGTTGCACAGAACATATTCAGG 57.625 39.130 0.00 0.00 35.77 3.86
2425 4257 6.864685 ACAATTGTTGCACAGAACATATTCAG 59.135 34.615 4.92 0.00 35.77 3.02
2426 4258 6.747125 ACAATTGTTGCACAGAACATATTCA 58.253 32.000 4.92 0.00 35.77 2.57
2427 4259 6.862608 TGACAATTGTTGCACAGAACATATTC 59.137 34.615 13.36 0.00 35.77 1.75
2428 4260 6.747125 TGACAATTGTTGCACAGAACATATT 58.253 32.000 13.36 0.00 35.77 1.28
2429 4261 6.330004 TGACAATTGTTGCACAGAACATAT 57.670 33.333 13.36 0.00 35.77 1.78
2430 4262 5.764487 TGACAATTGTTGCACAGAACATA 57.236 34.783 13.36 0.00 35.77 2.29
2431 4263 4.652421 TGACAATTGTTGCACAGAACAT 57.348 36.364 13.36 0.00 35.77 2.71
2432 4264 4.172505 GTTGACAATTGTTGCACAGAACA 58.827 39.130 13.36 0.00 33.96 3.18
2433 4265 4.172505 TGTTGACAATTGTTGCACAGAAC 58.827 39.130 13.36 7.84 0.00 3.01
2446 4300 4.473444 AGGGTTGAGACATTGTTGACAAT 58.527 39.130 3.60 3.60 46.62 2.71
2459 4313 1.801242 TCCACACAGAAGGGTTGAGA 58.199 50.000 0.00 0.00 0.00 3.27
2461 4315 1.843851 AGTTCCACACAGAAGGGTTGA 59.156 47.619 0.00 0.00 0.00 3.18
2473 4327 0.685097 GGTACAGCCAGAGTTCCACA 59.315 55.000 0.00 0.00 37.17 4.17
2497 4355 2.673775 TTGGGATTGCTGTTGAAGGA 57.326 45.000 0.00 0.00 0.00 3.36
2535 4400 4.830600 AGACAAATTTGGGAACACCGTATT 59.169 37.500 21.74 0.00 44.64 1.89
2539 4404 3.067461 TGAAGACAAATTTGGGAACACCG 59.933 43.478 21.74 0.00 44.64 4.94
2541 4406 6.048509 ACAATGAAGACAAATTTGGGAACAC 58.951 36.000 21.74 8.73 42.67 3.32
2573 4441 5.721232 TCTACATGCATCATAGAGCAGATG 58.279 41.667 11.57 0.00 44.94 2.90
2577 4445 7.388776 GGTTTATTCTACATGCATCATAGAGCA 59.611 37.037 14.12 4.96 45.92 4.26
2579 4447 8.837788 TGGTTTATTCTACATGCATCATAGAG 57.162 34.615 14.12 0.00 0.00 2.43
2586 4454 8.077991 CGATCATTTGGTTTATTCTACATGCAT 58.922 33.333 0.00 0.00 0.00 3.96
2592 4460 9.916397 CAACTACGATCATTTGGTTTATTCTAC 57.084 33.333 0.00 0.00 0.00 2.59
2612 4480 4.566004 TCTGATTACCAGCACACAACTAC 58.434 43.478 0.00 0.00 42.62 2.73
2646 4514 2.346766 ATGTGACAGAAGGTTGCACA 57.653 45.000 0.00 0.00 38.49 4.57
2668 4536 0.316689 CAAACGAACTTCGGTGCCAC 60.317 55.000 15.42 0.00 39.92 5.01
2674 4542 1.127951 CCGATTCCAAACGAACTTCGG 59.872 52.381 15.42 0.00 45.59 4.30
2675 4543 1.796459 ACCGATTCCAAACGAACTTCG 59.204 47.619 9.68 9.68 46.93 3.79
2685 4553 5.687166 AGTAGTTCCAATACCGATTCCAA 57.313 39.130 0.00 0.00 0.00 3.53
2686 4554 6.795144 TTAGTAGTTCCAATACCGATTCCA 57.205 37.500 0.00 0.00 0.00 3.53
2690 4558 8.044908 ACAAACATTAGTAGTTCCAATACCGAT 58.955 33.333 0.00 0.00 0.00 4.18
2693 4561 8.789762 ACAACAAACATTAGTAGTTCCAATACC 58.210 33.333 0.00 0.00 0.00 2.73
2709 4577 5.764686 TGAGCAGTAGATCAACAACAAACAT 59.235 36.000 0.00 0.00 37.20 2.71
2712 4580 6.233434 AGATGAGCAGTAGATCAACAACAAA 58.767 36.000 0.00 0.00 44.32 2.83
2718 4586 5.275067 AGGAAGATGAGCAGTAGATCAAC 57.725 43.478 0.00 0.00 44.32 3.18
2735 4603 2.879103 TGCAAAGGGAGGTAAGGAAG 57.121 50.000 0.00 0.00 0.00 3.46
2742 4610 1.632589 GGTTGAATGCAAAGGGAGGT 58.367 50.000 0.00 0.00 35.42 3.85
2758 4626 1.630878 GACATCAGAACTGAGGGGGTT 59.369 52.381 18.19 0.22 44.76 4.11
2903 4780 2.553028 GCAGGGATGGAGACTGACAAAA 60.553 50.000 0.00 0.00 34.21 2.44
2998 4882 2.347846 GCAAGTTGCATGTTTGAAAGCG 60.348 45.455 22.90 0.00 44.26 4.68
3015 4899 0.935898 GATCGCTCATCCACTGCAAG 59.064 55.000 0.00 0.00 42.29 4.01
3028 4912 0.957395 CTGCAACAACAGGGATCGCT 60.957 55.000 6.44 6.44 33.85 4.93
3029 4913 1.503542 CTGCAACAACAGGGATCGC 59.496 57.895 0.54 0.54 33.85 4.58
3142 5033 1.277557 AGAACAGGTCATCTGAGTGCC 59.722 52.381 0.00 0.00 46.18 5.01
3143 5034 2.758736 AGAACAGGTCATCTGAGTGC 57.241 50.000 0.00 0.00 46.18 4.40
3234 5125 1.611851 CCAGGGGAGACTCAGCACT 60.612 63.158 4.53 0.00 0.00 4.40
3235 5126 2.664081 CCCAGGGGAGACTCAGCAC 61.664 68.421 4.53 0.00 37.50 4.40
3236 5127 2.284921 CCCAGGGGAGACTCAGCA 60.285 66.667 4.53 0.00 37.50 4.41
3237 5128 3.791586 GCCCAGGGGAGACTCAGC 61.792 72.222 7.91 0.00 37.50 4.26
3238 5129 2.040278 AGCCCAGGGGAGACTCAG 59.960 66.667 7.91 0.00 37.50 3.35
3250 5141 1.500474 ATGATTCCGAGAAGAGCCCA 58.500 50.000 0.00 0.00 0.00 5.36
3312 5207 4.040217 ACAAGCAAAGAGACAGTCTGATCT 59.960 41.667 8.15 6.68 34.84 2.75
3313 5208 4.152045 CACAAGCAAAGAGACAGTCTGATC 59.848 45.833 8.15 4.36 34.84 2.92
3314 5209 4.063689 CACAAGCAAAGAGACAGTCTGAT 58.936 43.478 8.15 0.00 34.84 2.90


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

AutoCloner maintained by Alex Coulton.