Multiple sequence alignment - TraesCS3A01G183700

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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 TraesCS3A01G183700 chr3A 100.000 5518 0 0 1 5518 213128283 213133800 0.000000e+00 10190.0
1 TraesCS3A01G183700 chr3A 97.778 90 1 1 3610 3698 594498336 594498247 2.660000e-33 154.0
2 TraesCS3A01G183700 chr3A 97.727 88 2 0 3614 3701 213131980 213131893 9.570000e-33 152.0
3 TraesCS3A01G183700 chr3B 96.044 2932 84 14 703 3615 252929436 252932354 0.000000e+00 4743.0
4 TraesCS3A01G183700 chr3B 96.949 1049 24 4 3696 4737 252932352 252933399 0.000000e+00 1753.0
5 TraesCS3A01G183700 chr3B 90.981 754 36 6 4734 5466 252933775 252934517 0.000000e+00 987.0
6 TraesCS3A01G183700 chr3B 93.625 502 28 2 1 502 252925565 252926062 0.000000e+00 747.0
7 TraesCS3A01G183700 chr3B 86.590 261 28 4 498 755 252929334 252929590 1.170000e-71 281.0
8 TraesCS3A01G183700 chr3B 93.333 105 5 2 753 857 252929436 252929538 2.660000e-33 154.0
9 TraesCS3A01G183700 chr3B 90.090 111 11 0 1629 1739 754856156 754856266 1.600000e-30 145.0
10 TraesCS3A01G183700 chr3B 97.619 42 1 0 805 846 252929438 252929479 7.670000e-09 73.1
11 TraesCS3A01G183700 chr3D 97.159 1619 40 4 2002 3615 174415888 174417505 0.000000e+00 2730.0
12 TraesCS3A01G183700 chr3D 91.894 1357 74 14 653 2004 174414404 174415729 0.000000e+00 1864.0
13 TraesCS3A01G183700 chr3D 97.048 1050 22 8 3696 4737 174417503 174418551 0.000000e+00 1759.0
14 TraesCS3A01G183700 chr3D 92.179 358 19 5 1 349 174413859 174414216 1.070000e-136 497.0
15 TraesCS3A01G183700 chr3D 92.744 317 17 5 5204 5517 174426173 174426486 2.340000e-123 453.0
16 TraesCS3A01G183700 chr3D 88.056 360 32 9 406 763 174414213 174414563 3.070000e-112 416.0
17 TraesCS3A01G183700 chr3D 93.571 140 9 0 707 846 174414407 174414546 5.600000e-50 209.0
18 TraesCS3A01G183700 chr3D 99.091 110 1 0 5012 5121 174426052 174426161 1.210000e-46 198.0
19 TraesCS3A01G183700 chr3D 93.069 101 5 2 757 857 174414407 174414505 4.450000e-31 147.0
20 TraesCS3A01G183700 chr3D 85.039 127 6 2 4807 4920 174425918 174426044 3.490000e-22 117.0
21 TraesCS3A01G183700 chr1D 81.959 776 118 18 3777 4540 324618510 324619275 6.030000e-179 638.0
22 TraesCS3A01G183700 chr1D 95.109 184 9 0 1214 1397 324617136 324617319 1.940000e-74 291.0
23 TraesCS3A01G183700 chr1D 88.112 143 14 1 995 1134 324616902 324617044 3.420000e-37 167.0
24 TraesCS3A01G183700 chr1A 81.971 771 107 22 3783 4543 420395481 420394733 4.690000e-175 625.0
25 TraesCS3A01G183700 chr1A 94.565 184 10 0 1214 1397 420396875 420396692 9.050000e-73 285.0
26 TraesCS3A01G183700 chr1A 87.591 137 14 1 1001 1134 420397117 420396981 7.400000e-34 156.0
27 TraesCS3A01G183700 chr1A 97.778 90 1 1 3610 3698 74436523 74436434 2.660000e-33 154.0
28 TraesCS3A01G183700 chr1A 96.739 92 2 1 3610 3700 440088270 440088179 9.570000e-33 152.0
29 TraesCS3A01G183700 chr1A 89.286 112 10 2 1630 1740 115437175 115437285 7.450000e-29 139.0
30 TraesCS3A01G183700 chr7B 98.876 89 1 0 3611 3699 156955539 156955451 5.720000e-35 159.0
31 TraesCS3A01G183700 chr6D 98.889 90 0 1 3612 3700 413410127 413410038 5.720000e-35 159.0
32 TraesCS3A01G183700 chr6A 92.661 109 8 0 1629 1737 603185284 603185176 2.060000e-34 158.0
33 TraesCS3A01G183700 chr4D 91.818 110 9 0 1628 1737 83277520 83277629 2.660000e-33 154.0
34 TraesCS3A01G183700 chr2B 94.949 99 4 1 3607 3704 576567639 576567541 2.660000e-33 154.0
35 TraesCS3A01G183700 chr4A 97.727 88 2 0 3613 3700 47630557 47630470 9.570000e-33 152.0
36 TraesCS3A01G183700 chr5A 95.745 94 3 1 3606 3698 465105860 465105953 3.440000e-32 150.0
37 TraesCS3A01G183700 chrUn 90.090 111 11 0 1629 1739 40878331 40878221 1.600000e-30 145.0
38 TraesCS3A01G183700 chrUn 90.090 111 11 0 1629 1739 310312377 310312487 1.600000e-30 145.0
39 TraesCS3A01G183700 chrUn 90.090 111 11 0 1629 1739 315278002 315277892 1.600000e-30 145.0


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 TraesCS3A01G183700 chr3A 213128283 213133800 5517 False 10190.000000 10190 100.000000 1 5518 1 chr3A.!!$F1 5517
1 TraesCS3A01G183700 chr3B 252925565 252934517 8952 False 1248.300000 4743 93.591571 1 5466 7 chr3B.!!$F2 5465
2 TraesCS3A01G183700 chr3D 174413859 174418551 4692 False 1088.857143 2730 93.282286 1 4737 7 chr3D.!!$F1 4736
3 TraesCS3A01G183700 chr3D 174425918 174426486 568 False 256.000000 453 92.291333 4807 5517 3 chr3D.!!$F2 710
4 TraesCS3A01G183700 chr1D 324616902 324619275 2373 False 365.333333 638 88.393333 995 4540 3 chr1D.!!$F1 3545
5 TraesCS3A01G183700 chr1A 420394733 420397117 2384 True 355.333333 625 88.042333 1001 4543 3 chr1A.!!$R3 3542

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
677 3965 0.040425 ATGCAACGGACAAAGTTCGC 60.040 50.000 0.00 0.0 38.21 4.70 F
1095 4436 0.309302 CCGAGCAGGTCTACATCTCG 59.691 60.000 0.00 0.0 44.21 4.04 F
1428 4810 1.603172 CCGGATCGTAGATCTGTTGGC 60.603 57.143 5.18 0.0 45.12 4.52 F
2116 5724 2.551270 ACTCCTCACAGCCCTTTCATA 58.449 47.619 0.00 0.0 0.00 2.15 F
3628 7253 1.203087 TCTTGTACTCCCTCCGTTCCA 60.203 52.381 0.00 0.0 0.00 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2576 6194 0.674895 CACAAGTCAGCTGTAGGGCC 60.675 60.000 14.67 0.0 0.00 5.80 R
2923 6548 2.153401 CCCCACAACTCCTCCACCA 61.153 63.158 0.00 0.0 0.00 4.17 R
3337 6962 1.215244 CACAGCTGAGCATACATCCG 58.785 55.000 23.35 0.0 0.00 4.18 R
3672 7297 3.073356 TCCCTCCGTTCCAAATTACTTGT 59.927 43.478 0.00 0.0 32.65 3.16 R
5483 10099 0.575390 CGCGACCCGTAATTTGCTAG 59.425 55.000 0.00 0.0 0.00 3.42 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
144 145 0.323087 GGTGGGAATTAACGTGGCCT 60.323 55.000 3.32 0.00 0.00 5.19
148 149 1.475280 GGGAATTAACGTGGCCTTTCC 59.525 52.381 3.32 5.19 33.45 3.13
149 150 1.475280 GGAATTAACGTGGCCTTTCCC 59.525 52.381 3.32 0.00 0.00 3.97
183 184 2.748605 TGCCGATTGCGAAAACAAAAT 58.251 38.095 0.00 0.00 45.60 1.82
187 188 5.061560 TGCCGATTGCGAAAACAAAATTATC 59.938 36.000 0.00 0.00 45.60 1.75
262 268 3.652274 GAGCTGGTTTTATTGCTTTGCA 58.348 40.909 0.00 0.00 35.76 4.08
273 279 8.764287 GTTTTATTGCTTTGCATACAGAAAGTT 58.236 29.630 0.00 0.00 38.76 2.66
292 301 8.992835 GAAAGTTGATTTCCAGCATTAAGATT 57.007 30.769 0.00 0.00 41.32 2.40
489 500 3.904136 AGCTTGACAAAGGTTCATTCG 57.096 42.857 0.00 0.00 41.32 3.34
514 3801 7.402640 GCAACAGGAGATATTTCTTTAGAACG 58.597 38.462 0.00 0.00 33.13 3.95
516 3803 7.419711 ACAGGAGATATTTCTTTAGAACGGA 57.580 36.000 0.00 0.00 33.13 4.69
517 3804 7.848128 ACAGGAGATATTTCTTTAGAACGGAA 58.152 34.615 0.00 0.00 33.13 4.30
518 3805 8.319146 ACAGGAGATATTTCTTTAGAACGGAAA 58.681 33.333 0.00 0.00 33.13 3.13
519 3806 9.162764 CAGGAGATATTTCTTTAGAACGGAAAA 57.837 33.333 0.00 0.00 33.58 2.29
615 3903 1.426041 GCACTACGGCCCATGTAACG 61.426 60.000 0.00 0.00 0.00 3.18
651 3939 1.662044 CAGCCCACTTCAAACCAGC 59.338 57.895 0.00 0.00 0.00 4.85
652 3940 1.531602 AGCCCACTTCAAACCAGCC 60.532 57.895 0.00 0.00 0.00 4.85
653 3941 2.919494 GCCCACTTCAAACCAGCCG 61.919 63.158 0.00 0.00 0.00 5.52
654 3942 1.528309 CCCACTTCAAACCAGCCGT 60.528 57.895 0.00 0.00 0.00 5.68
655 3943 1.515521 CCCACTTCAAACCAGCCGTC 61.516 60.000 0.00 0.00 0.00 4.79
656 3944 1.515521 CCACTTCAAACCAGCCGTCC 61.516 60.000 0.00 0.00 0.00 4.79
657 3945 1.228154 ACTTCAAACCAGCCGTCCC 60.228 57.895 0.00 0.00 0.00 4.46
658 3946 1.228124 CTTCAAACCAGCCGTCCCA 60.228 57.895 0.00 0.00 0.00 4.37
659 3947 0.609131 CTTCAAACCAGCCGTCCCAT 60.609 55.000 0.00 0.00 0.00 4.00
660 3948 0.893270 TTCAAACCAGCCGTCCCATG 60.893 55.000 0.00 0.00 0.00 3.66
661 3949 2.676471 AAACCAGCCGTCCCATGC 60.676 61.111 0.00 0.00 0.00 4.06
662 3950 3.505790 AAACCAGCCGTCCCATGCA 62.506 57.895 0.00 0.00 0.00 3.96
663 3951 2.992817 AAACCAGCCGTCCCATGCAA 62.993 55.000 0.00 0.00 0.00 4.08
664 3952 3.443045 CCAGCCGTCCCATGCAAC 61.443 66.667 0.00 0.00 0.00 4.17
665 3953 3.803082 CAGCCGTCCCATGCAACG 61.803 66.667 10.20 10.20 38.58 4.10
670 3958 4.073052 GTCCCATGCAACGGACAA 57.927 55.556 23.83 2.07 46.59 3.18
671 3959 2.336341 GTCCCATGCAACGGACAAA 58.664 52.632 23.83 0.00 46.59 2.83
672 3960 0.240945 GTCCCATGCAACGGACAAAG 59.759 55.000 23.83 2.49 46.59 2.77
673 3961 0.179004 TCCCATGCAACGGACAAAGT 60.179 50.000 7.10 0.00 0.00 2.66
674 3962 0.673437 CCCATGCAACGGACAAAGTT 59.327 50.000 7.10 0.00 0.00 2.66
675 3963 1.335872 CCCATGCAACGGACAAAGTTC 60.336 52.381 7.10 0.00 0.00 3.01
676 3964 1.662876 CCATGCAACGGACAAAGTTCG 60.663 52.381 0.00 0.00 40.82 3.95
677 3965 0.040425 ATGCAACGGACAAAGTTCGC 60.040 50.000 0.00 0.00 38.21 4.70
678 3966 1.370051 GCAACGGACAAAGTTCGCC 60.370 57.895 0.00 0.00 38.21 5.54
679 3967 2.018544 CAACGGACAAAGTTCGCCA 58.981 52.632 0.00 0.00 38.21 5.69
680 3968 0.316689 CAACGGACAAAGTTCGCCAC 60.317 55.000 0.00 0.00 38.21 5.01
681 3969 1.768112 AACGGACAAAGTTCGCCACG 61.768 55.000 0.00 0.00 38.21 4.94
682 3970 2.943653 GGACAAAGTTCGCCACGG 59.056 61.111 0.00 0.00 0.00 4.94
683 3971 1.890510 GGACAAAGTTCGCCACGGT 60.891 57.895 0.00 0.00 0.00 4.83
684 3972 0.600782 GGACAAAGTTCGCCACGGTA 60.601 55.000 0.00 0.00 0.00 4.02
685 3973 0.788391 GACAAAGTTCGCCACGGTAG 59.212 55.000 0.00 0.00 0.00 3.18
686 3974 1.226030 ACAAAGTTCGCCACGGTAGC 61.226 55.000 0.00 0.00 0.00 3.58
687 3975 1.670083 AAAGTTCGCCACGGTAGCC 60.670 57.895 0.00 0.00 0.00 3.93
688 3976 3.600898 AAGTTCGCCACGGTAGCCC 62.601 63.158 0.00 0.00 0.00 5.19
689 3977 4.382320 GTTCGCCACGGTAGCCCA 62.382 66.667 0.00 0.00 0.00 5.36
690 3978 4.382320 TTCGCCACGGTAGCCCAC 62.382 66.667 0.00 0.00 0.00 4.61
692 3980 4.388499 CGCCACGGTAGCCCACTT 62.388 66.667 0.00 0.00 0.00 3.16
693 3981 2.033602 GCCACGGTAGCCCACTTT 59.966 61.111 0.00 0.00 0.00 2.66
694 3982 1.297364 GCCACGGTAGCCCACTTTA 59.703 57.895 0.00 0.00 0.00 1.85
695 3983 0.321830 GCCACGGTAGCCCACTTTAA 60.322 55.000 0.00 0.00 0.00 1.52
696 3984 1.883209 GCCACGGTAGCCCACTTTAAA 60.883 52.381 0.00 0.00 0.00 1.52
697 3985 1.808343 CCACGGTAGCCCACTTTAAAC 59.192 52.381 0.00 0.00 0.00 2.01
698 3986 1.808343 CACGGTAGCCCACTTTAAACC 59.192 52.381 0.00 0.00 0.00 3.27
699 3987 1.420891 ACGGTAGCCCACTTTAAACCA 59.579 47.619 0.00 0.00 0.00 3.67
700 3988 2.081462 CGGTAGCCCACTTTAAACCAG 58.919 52.381 0.00 0.00 0.00 4.00
701 3989 1.816835 GGTAGCCCACTTTAAACCAGC 59.183 52.381 0.00 0.00 0.00 4.85
702 3990 1.816835 GTAGCCCACTTTAAACCAGCC 59.183 52.381 0.00 0.00 0.00 4.85
703 3991 0.893727 AGCCCACTTTAAACCAGCCG 60.894 55.000 0.00 0.00 0.00 5.52
704 3992 1.873270 GCCCACTTTAAACCAGCCGG 61.873 60.000 0.00 0.00 38.77 6.13
705 3993 1.584495 CCACTTTAAACCAGCCGGC 59.416 57.895 21.89 21.89 34.57 6.13
706 3994 1.584495 CACTTTAAACCAGCCGGCC 59.416 57.895 26.15 5.07 34.57 6.13
707 3995 1.605451 ACTTTAAACCAGCCGGCCC 60.605 57.895 26.15 0.00 34.57 5.80
708 3996 1.605165 CTTTAAACCAGCCGGCCCA 60.605 57.895 26.15 0.00 34.57 5.36
709 3997 0.970427 CTTTAAACCAGCCGGCCCAT 60.970 55.000 26.15 5.23 34.57 4.00
710 3998 1.254284 TTTAAACCAGCCGGCCCATG 61.254 55.000 26.15 15.69 34.57 3.66
720 4008 3.443045 GGCCCATGCAACGGACAG 61.443 66.667 7.10 0.00 40.13 3.51
721 4009 3.443045 GCCCATGCAACGGACAGG 61.443 66.667 7.10 0.00 37.47 4.00
722 4010 2.751436 CCCATGCAACGGACAGGG 60.751 66.667 7.10 0.00 38.70 4.45
723 4011 2.034066 CCATGCAACGGACAGGGT 59.966 61.111 0.00 0.00 34.31 4.34
724 4012 1.603455 CCATGCAACGGACAGGGTT 60.603 57.895 0.00 0.00 34.31 4.11
725 4013 1.586154 CCATGCAACGGACAGGGTTC 61.586 60.000 0.00 0.00 34.31 3.62
726 4014 1.671054 ATGCAACGGACAGGGTTCG 60.671 57.895 0.00 0.00 40.82 3.95
728 4016 2.315386 GCAACGGACAGGGTTCGTC 61.315 63.158 2.83 0.00 45.26 4.20
729 4017 2.019951 CAACGGACAGGGTTCGTCG 61.020 63.158 2.83 0.00 45.26 5.12
730 4018 3.853597 AACGGACAGGGTTCGTCGC 62.854 63.158 2.83 0.00 45.26 5.19
746 4034 3.294493 GCGGCAGCCCACTTCAAA 61.294 61.111 5.63 0.00 37.42 2.69
747 4035 2.644992 CGGCAGCCCACTTCAAAC 59.355 61.111 5.63 0.00 0.00 2.93
748 4036 2.919494 CGGCAGCCCACTTCAAACC 61.919 63.158 5.63 0.00 0.00 3.27
749 4037 1.832167 GGCAGCCCACTTCAAACCA 60.832 57.895 0.00 0.00 0.00 3.67
750 4038 1.662044 GCAGCCCACTTCAAACCAG 59.338 57.895 0.00 0.00 0.00 4.00
782 4070 1.734477 CAGACAGAGTTCGCCACGG 60.734 63.158 0.00 0.00 0.00 4.94
783 4071 2.432628 GACAGAGTTCGCCACGGG 60.433 66.667 0.00 0.00 0.00 5.28
803 4091 1.832167 GCCCACTTCAAACCAGCCA 60.832 57.895 0.00 0.00 0.00 4.75
920 4256 3.056962 CAGTAGAAGACAGAAGCAGCAGA 60.057 47.826 0.00 0.00 0.00 4.26
922 4258 1.690893 AGAAGACAGAAGCAGCAGACA 59.309 47.619 0.00 0.00 0.00 3.41
923 4259 2.103771 AGAAGACAGAAGCAGCAGACAA 59.896 45.455 0.00 0.00 0.00 3.18
1095 4436 0.309302 CCGAGCAGGTCTACATCTCG 59.691 60.000 0.00 0.00 44.21 4.04
1427 4809 1.954382 TCCGGATCGTAGATCTGTTGG 59.046 52.381 0.00 9.95 45.12 3.77
1428 4810 1.603172 CCGGATCGTAGATCTGTTGGC 60.603 57.143 5.18 0.00 45.12 4.52
1443 4825 2.675423 GGCCCTGTCGTTTTCCCC 60.675 66.667 0.00 0.00 0.00 4.81
1453 4835 4.404098 TTTTCCCCTCTCCCGCGC 62.404 66.667 0.00 0.00 0.00 6.86
1477 4859 6.044682 CCAGATTTGATGCCCTTAATTTGTC 58.955 40.000 0.00 0.00 0.00 3.18
1587 4970 3.056607 GGCTTGTGTGGTTGATTTGCTAT 60.057 43.478 0.00 0.00 0.00 2.97
1631 5014 5.248477 GTGGAAGATAGGCCATATGGAGTAA 59.752 44.000 26.47 7.42 36.41 2.24
1655 5038 3.824443 CCCTCCGTTCATTTTTGTAAGGT 59.176 43.478 0.00 0.00 0.00 3.50
1924 5307 5.523883 TGGTACTTTATTTGCTTACCCCT 57.476 39.130 0.00 0.00 32.63 4.79
2116 5724 2.551270 ACTCCTCACAGCCCTTTCATA 58.449 47.619 0.00 0.00 0.00 2.15
2265 5875 5.011090 TGTACTGGCTTAGCATCTAACTG 57.989 43.478 6.53 0.00 0.00 3.16
2347 5957 5.304686 TCCACCCTTGGTTATGTATCATC 57.695 43.478 0.00 0.00 44.35 2.92
2544 6155 9.952030 TTCAGTTGAATGTGTTAGGATAATACA 57.048 29.630 2.27 2.27 0.00 2.29
3204 6829 4.406972 TGATGCTAGCTCTTAATGTGGTCT 59.593 41.667 17.23 0.00 0.00 3.85
3220 6845 2.747855 CTTTGCCGGAGCCTGGAC 60.748 66.667 5.05 0.00 38.69 4.02
3337 6962 6.442513 AAACTACCGTGTATGGAGTACTAC 57.557 41.667 0.00 0.00 34.27 2.73
3393 7018 3.054065 TGCACCCTTTGTTTCCCAATTTT 60.054 39.130 0.00 0.00 31.81 1.82
3394 7019 3.563808 GCACCCTTTGTTTCCCAATTTTC 59.436 43.478 0.00 0.00 31.81 2.29
3395 7020 4.133820 CACCCTTTGTTTCCCAATTTTCC 58.866 43.478 0.00 0.00 31.81 3.13
3617 7242 5.915758 CACATACTTCGCCTATCTTGTACTC 59.084 44.000 0.00 0.00 0.00 2.59
3618 7243 5.009811 ACATACTTCGCCTATCTTGTACTCC 59.990 44.000 0.00 0.00 0.00 3.85
3619 7244 2.694109 ACTTCGCCTATCTTGTACTCCC 59.306 50.000 0.00 0.00 0.00 4.30
3621 7246 2.584236 TCGCCTATCTTGTACTCCCTC 58.416 52.381 0.00 0.00 0.00 4.30
3622 7247 1.614413 CGCCTATCTTGTACTCCCTCC 59.386 57.143 0.00 0.00 0.00 4.30
3623 7248 1.614413 GCCTATCTTGTACTCCCTCCG 59.386 57.143 0.00 0.00 0.00 4.63
3624 7249 2.946785 CCTATCTTGTACTCCCTCCGT 58.053 52.381 0.00 0.00 0.00 4.69
3626 7251 3.318557 CCTATCTTGTACTCCCTCCGTTC 59.681 52.174 0.00 0.00 0.00 3.95
3627 7252 1.553706 TCTTGTACTCCCTCCGTTCC 58.446 55.000 0.00 0.00 0.00 3.62
3628 7253 1.203087 TCTTGTACTCCCTCCGTTCCA 60.203 52.381 0.00 0.00 0.00 3.53
3630 7255 1.719529 TGTACTCCCTCCGTTCCAAA 58.280 50.000 0.00 0.00 0.00 3.28
3631 7256 2.262637 TGTACTCCCTCCGTTCCAAAT 58.737 47.619 0.00 0.00 0.00 2.32
3632 7257 2.640826 TGTACTCCCTCCGTTCCAAATT 59.359 45.455 0.00 0.00 0.00 1.82
3633 7258 3.839490 TGTACTCCCTCCGTTCCAAATTA 59.161 43.478 0.00 0.00 0.00 1.40
3635 7260 2.910977 ACTCCCTCCGTTCCAAATTACT 59.089 45.455 0.00 0.00 0.00 2.24
3637 7262 3.681593 TCCCTCCGTTCCAAATTACTTG 58.318 45.455 0.00 0.00 34.52 3.16
3638 7263 3.073356 TCCCTCCGTTCCAAATTACTTGT 59.927 43.478 0.00 0.00 32.65 3.16
3639 7264 3.439129 CCCTCCGTTCCAAATTACTTGTC 59.561 47.826 0.00 0.00 32.65 3.18
3640 7265 3.124636 CCTCCGTTCCAAATTACTTGTCG 59.875 47.826 0.00 0.00 32.65 4.35
3643 7268 3.364565 CCGTTCCAAATTACTTGTCGTGG 60.365 47.826 0.00 0.00 32.65 4.94
3644 7269 3.249080 CGTTCCAAATTACTTGTCGTGGT 59.751 43.478 0.00 0.00 32.65 4.16
3645 7270 4.260866 CGTTCCAAATTACTTGTCGTGGTT 60.261 41.667 0.00 0.00 32.65 3.67
3646 7271 5.584442 GTTCCAAATTACTTGTCGTGGTTT 58.416 37.500 0.00 0.00 32.65 3.27
3647 7272 5.838531 TCCAAATTACTTGTCGTGGTTTT 57.161 34.783 0.00 0.00 32.65 2.43
3648 7273 6.939132 TCCAAATTACTTGTCGTGGTTTTA 57.061 33.333 0.00 0.00 32.65 1.52
3649 7274 6.961576 TCCAAATTACTTGTCGTGGTTTTAG 58.038 36.000 0.00 0.00 32.65 1.85
3651 7276 7.067251 TCCAAATTACTTGTCGTGGTTTTAGTT 59.933 33.333 0.00 0.00 32.65 2.24
3652 7277 7.377662 CCAAATTACTTGTCGTGGTTTTAGTTC 59.622 37.037 0.00 0.00 32.65 3.01
3654 7279 6.981762 TTACTTGTCGTGGTTTTAGTTCAA 57.018 33.333 0.00 0.00 0.00 2.69
3655 7280 7.556733 TTACTTGTCGTGGTTTTAGTTCAAT 57.443 32.000 0.00 0.00 0.00 2.57
3656 7281 6.445357 ACTTGTCGTGGTTTTAGTTCAATT 57.555 33.333 0.00 0.00 0.00 2.32
3657 7282 6.859017 ACTTGTCGTGGTTTTAGTTCAATTT 58.141 32.000 0.00 0.00 0.00 1.82
3658 7283 6.750039 ACTTGTCGTGGTTTTAGTTCAATTTG 59.250 34.615 0.00 0.00 0.00 2.32
3659 7284 6.438259 TGTCGTGGTTTTAGTTCAATTTGA 57.562 33.333 0.00 0.00 0.00 2.69
3660 7285 6.853720 TGTCGTGGTTTTAGTTCAATTTGAA 58.146 32.000 7.74 7.74 33.32 2.69
3674 7299 6.438259 TCAATTTGAACTAAAACCACGACA 57.562 33.333 0.00 0.00 0.00 4.35
3676 7301 6.970043 TCAATTTGAACTAAAACCACGACAAG 59.030 34.615 0.00 0.00 0.00 3.16
3677 7302 5.883503 TTTGAACTAAAACCACGACAAGT 57.116 34.783 0.00 0.00 0.00 3.16
3678 7303 6.981762 TTTGAACTAAAACCACGACAAGTA 57.018 33.333 0.00 0.00 0.00 2.24
3679 7304 6.981762 TTGAACTAAAACCACGACAAGTAA 57.018 33.333 0.00 0.00 0.00 2.24
3681 7306 7.556733 TGAACTAAAACCACGACAAGTAATT 57.443 32.000 0.00 0.00 0.00 1.40
3682 7307 7.987649 TGAACTAAAACCACGACAAGTAATTT 58.012 30.769 0.00 0.00 0.00 1.82
3683 7308 7.911205 TGAACTAAAACCACGACAAGTAATTTG 59.089 33.333 0.00 0.00 42.68 2.32
3684 7309 6.731164 ACTAAAACCACGACAAGTAATTTGG 58.269 36.000 0.00 0.00 41.25 3.28
3685 7310 5.838531 AAAACCACGACAAGTAATTTGGA 57.161 34.783 0.00 0.00 41.25 3.53
3686 7311 5.838531 AAACCACGACAAGTAATTTGGAA 57.161 34.783 0.00 0.00 41.25 3.53
3687 7312 4.823790 ACCACGACAAGTAATTTGGAAC 57.176 40.909 0.00 0.00 41.25 3.62
3689 7314 3.364565 CCACGACAAGTAATTTGGAACGG 60.365 47.826 0.00 0.00 41.25 4.44
3690 7315 3.495377 CACGACAAGTAATTTGGAACGGA 59.505 43.478 0.00 0.00 41.25 4.69
3692 7317 3.124636 CGACAAGTAATTTGGAACGGAGG 59.875 47.826 0.00 0.00 41.25 4.30
3693 7318 3.418047 ACAAGTAATTTGGAACGGAGGG 58.582 45.455 0.00 0.00 41.25 4.30
3694 7319 3.073356 ACAAGTAATTTGGAACGGAGGGA 59.927 43.478 0.00 0.00 41.25 4.20
3695 7320 3.629142 AGTAATTTGGAACGGAGGGAG 57.371 47.619 0.00 0.00 0.00 4.30
3696 7321 2.910977 AGTAATTTGGAACGGAGGGAGT 59.089 45.455 0.00 0.00 0.00 3.85
3697 7322 4.098894 AGTAATTTGGAACGGAGGGAGTA 58.901 43.478 0.00 0.00 0.00 2.59
3698 7323 4.720273 AGTAATTTGGAACGGAGGGAGTAT 59.280 41.667 0.00 0.00 0.00 2.12
3700 7325 5.703730 AATTTGGAACGGAGGGAGTATAA 57.296 39.130 0.00 0.00 0.00 0.98
3701 7326 5.703730 ATTTGGAACGGAGGGAGTATAAA 57.296 39.130 0.00 0.00 0.00 1.40
4291 8483 0.674895 GCAGGGTGAAAGTCGATGCT 60.675 55.000 0.00 0.00 0.00 3.79
4304 8496 6.654793 AAGTCGATGCTGTTTCTTAGATTC 57.345 37.500 0.00 0.00 0.00 2.52
4591 8791 1.795170 AACGCAGCAAGGCAATTCGT 61.795 50.000 0.00 0.00 0.00 3.85
4675 8875 2.094803 CGCAGCAATTTTCATGGGTGTA 60.095 45.455 0.00 0.00 0.00 2.90
4725 8925 4.495349 CCGAAGTGATCATGATTGCTGAAC 60.495 45.833 10.14 2.63 0.00 3.18
4726 8926 4.093850 CGAAGTGATCATGATTGCTGAACA 59.906 41.667 10.14 0.00 0.00 3.18
4742 9321 4.309933 CTGAACACAGCTGAATCAGTGTA 58.690 43.478 23.35 0.00 43.77 2.90
4745 9324 5.764686 TGAACACAGCTGAATCAGTGTATTT 59.235 36.000 23.35 10.51 43.77 1.40
4840 9419 2.157668 ACGAAATAGCAGTGCTTTGTCG 59.842 45.455 33.24 33.24 46.95 4.35
4960 9552 0.449388 CTGAGCCAAAACAGCGATCC 59.551 55.000 0.00 0.00 34.64 3.36
4969 9564 4.104143 CAGCGATCCCGTTGTACC 57.896 61.111 0.00 0.00 41.21 3.34
4971 9566 1.082117 CAGCGATCCCGTTGTACCAC 61.082 60.000 0.00 0.00 41.21 4.16
4982 9577 3.928375 CCGTTGTACCACTATTGTACACC 59.072 47.826 0.00 0.00 45.95 4.16
5127 9722 4.514577 TCCAGGCGCGCTAGCTTC 62.515 66.667 32.29 13.29 42.32 3.86
5198 9799 4.814294 CACTACCAGCGGGCCGTC 62.814 72.222 28.82 19.48 37.90 4.79
5427 10043 7.041107 CCTTTTTCATTTCTGTTCTTTGGACA 58.959 34.615 0.00 0.00 0.00 4.02
5470 10086 9.959749 GTCAGACTTTTAAACATGATAAACCAA 57.040 29.630 0.00 0.00 0.00 3.67
5473 10089 9.458374 AGACTTTTAAACATGATAAACCAAACG 57.542 29.630 0.00 0.00 0.00 3.60
5474 10090 9.240159 GACTTTTAAACATGATAAACCAAACGT 57.760 29.630 0.00 0.00 0.00 3.99
5475 10091 9.589111 ACTTTTAAACATGATAAACCAAACGTT 57.411 25.926 0.00 0.00 35.70 3.99
5507 10124 2.234913 AAATTACGGGTCGCGAGCCT 62.235 55.000 43.42 33.69 46.33 4.58
5508 10125 2.624437 AATTACGGGTCGCGAGCCTC 62.624 60.000 43.42 25.78 46.33 4.70
5517 10134 2.464459 CGCGAGCCTCACAATTCCC 61.464 63.158 0.00 0.00 0.00 3.97
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 2.281484 TCGGGCCACTGAACTTGC 60.281 61.111 4.39 0.00 0.00 4.01
192 193 6.620678 AGCATGTACATAATTTGTTTTCGCT 58.379 32.000 8.32 5.60 39.87 4.93
262 268 7.472334 AATGCTGGAAATCAACTTTCTGTAT 57.528 32.000 0.00 0.00 42.48 2.29
273 279 5.918426 TGCAATCTTAATGCTGGAAATCA 57.082 34.783 1.55 0.00 44.14 2.57
292 301 2.655090 TCTCAACCATGAACCTTGCA 57.345 45.000 0.00 0.00 34.49 4.08
379 389 4.716287 ACCTCCATCCCCAAATTATTGTTG 59.284 41.667 0.00 0.00 34.60 3.33
386 396 7.663501 ATAGTATTACCTCCATCCCCAAATT 57.336 36.000 0.00 0.00 0.00 1.82
458 469 4.039609 CCTTTGTCAAGCTTTGGAAATCCT 59.960 41.667 0.00 0.00 36.82 3.24
489 500 7.402640 CGTTCTAAAGAAATATCTCCTGTTGC 58.597 38.462 0.00 0.00 35.58 4.17
514 3801 8.799091 GCTTTCGCTAAAGAGAAATAATTTTCC 58.201 33.333 14.45 0.00 44.14 3.13
516 3803 8.523658 AGGCTTTCGCTAAAGAGAAATAATTTT 58.476 29.630 14.45 0.00 44.14 1.82
517 3804 7.970614 CAGGCTTTCGCTAAAGAGAAATAATTT 59.029 33.333 14.45 0.00 44.14 1.82
518 3805 7.336931 TCAGGCTTTCGCTAAAGAGAAATAATT 59.663 33.333 14.45 0.00 44.14 1.40
519 3806 6.823689 TCAGGCTTTCGCTAAAGAGAAATAAT 59.176 34.615 14.45 0.00 44.14 1.28
522 3809 4.579869 TCAGGCTTTCGCTAAAGAGAAAT 58.420 39.130 14.45 0.00 44.14 2.17
526 3813 3.238108 TCTCAGGCTTTCGCTAAAGAG 57.762 47.619 14.45 3.56 44.14 2.85
528 3815 7.653713 TCTTAATATCTCAGGCTTTCGCTAAAG 59.346 37.037 6.36 6.36 44.21 1.85
534 3821 5.923684 GGTCTCTTAATATCTCAGGCTTTCG 59.076 44.000 0.00 0.00 0.00 3.46
541 3828 6.869315 TCGTCAGGTCTCTTAATATCTCAG 57.131 41.667 0.00 0.00 0.00 3.35
611 3899 0.038892 GTGGCGAACTCTGTCCGTTA 60.039 55.000 0.00 0.00 0.00 3.18
615 3903 2.432628 CCGTGGCGAACTCTGTCC 60.433 66.667 0.00 0.00 0.00 4.02
654 3942 0.179004 ACTTTGTCCGTTGCATGGGA 60.179 50.000 5.73 4.04 0.00 4.37
655 3943 0.673437 AACTTTGTCCGTTGCATGGG 59.327 50.000 5.73 1.59 0.00 4.00
656 3944 1.662876 CGAACTTTGTCCGTTGCATGG 60.663 52.381 0.00 0.00 0.00 3.66
657 3945 1.673760 CGAACTTTGTCCGTTGCATG 58.326 50.000 0.00 0.00 0.00 4.06
658 3946 0.040425 GCGAACTTTGTCCGTTGCAT 60.040 50.000 0.00 0.00 0.00 3.96
659 3947 1.353804 GCGAACTTTGTCCGTTGCA 59.646 52.632 0.00 0.00 0.00 4.08
660 3948 1.370051 GGCGAACTTTGTCCGTTGC 60.370 57.895 0.00 0.00 0.00 4.17
661 3949 0.316689 GTGGCGAACTTTGTCCGTTG 60.317 55.000 0.00 0.00 0.00 4.10
662 3950 1.768112 CGTGGCGAACTTTGTCCGTT 61.768 55.000 0.00 0.00 0.00 4.44
663 3951 2.241880 CGTGGCGAACTTTGTCCGT 61.242 57.895 0.00 0.00 0.00 4.69
664 3952 2.549282 CGTGGCGAACTTTGTCCG 59.451 61.111 0.00 0.00 0.00 4.79
665 3953 0.600782 TACCGTGGCGAACTTTGTCC 60.601 55.000 0.00 0.00 0.00 4.02
666 3954 0.788391 CTACCGTGGCGAACTTTGTC 59.212 55.000 0.00 0.00 0.00 3.18
667 3955 1.226030 GCTACCGTGGCGAACTTTGT 61.226 55.000 0.00 0.00 0.00 2.83
668 3956 1.495951 GCTACCGTGGCGAACTTTG 59.504 57.895 0.00 0.00 0.00 2.77
669 3957 1.670083 GGCTACCGTGGCGAACTTT 60.670 57.895 0.26 0.00 0.00 2.66
670 3958 2.047560 GGCTACCGTGGCGAACTT 60.048 61.111 0.26 0.00 0.00 2.66
671 3959 4.078516 GGGCTACCGTGGCGAACT 62.079 66.667 0.26 0.00 0.00 3.01
672 3960 4.382320 TGGGCTACCGTGGCGAAC 62.382 66.667 0.26 0.00 40.75 3.95
673 3961 4.382320 GTGGGCTACCGTGGCGAA 62.382 66.667 0.26 0.00 40.75 4.70
675 3963 2.510064 TAAAGTGGGCTACCGTGGCG 62.510 60.000 0.00 0.00 40.75 5.69
676 3964 0.321830 TTAAAGTGGGCTACCGTGGC 60.322 55.000 0.00 0.00 40.75 5.01
677 3965 1.808343 GTTTAAAGTGGGCTACCGTGG 59.192 52.381 0.00 0.00 40.75 4.94
678 3966 1.808343 GGTTTAAAGTGGGCTACCGTG 59.192 52.381 0.00 0.00 40.75 4.94
679 3967 1.420891 TGGTTTAAAGTGGGCTACCGT 59.579 47.619 0.00 0.00 40.75 4.83
680 3968 2.081462 CTGGTTTAAAGTGGGCTACCG 58.919 52.381 0.00 0.00 40.75 4.02
681 3969 1.816835 GCTGGTTTAAAGTGGGCTACC 59.183 52.381 0.00 0.00 37.24 3.18
682 3970 1.816835 GGCTGGTTTAAAGTGGGCTAC 59.183 52.381 0.00 0.00 0.00 3.58
683 3971 1.612199 CGGCTGGTTTAAAGTGGGCTA 60.612 52.381 0.00 0.00 0.00 3.93
684 3972 0.893727 CGGCTGGTTTAAAGTGGGCT 60.894 55.000 0.00 0.00 0.00 5.19
685 3973 1.584495 CGGCTGGTTTAAAGTGGGC 59.416 57.895 0.00 0.00 0.00 5.36
686 3974 1.873270 GCCGGCTGGTTTAAAGTGGG 61.873 60.000 22.15 0.00 37.67 4.61
687 3975 1.584495 GCCGGCTGGTTTAAAGTGG 59.416 57.895 22.15 0.00 37.67 4.00
688 3976 1.584495 GGCCGGCTGGTTTAAAGTG 59.416 57.895 28.56 0.00 37.67 3.16
689 3977 1.605451 GGGCCGGCTGGTTTAAAGT 60.605 57.895 28.56 0.00 37.67 2.66
690 3978 0.970427 ATGGGCCGGCTGGTTTAAAG 60.970 55.000 28.56 0.00 37.67 1.85
691 3979 1.077625 ATGGGCCGGCTGGTTTAAA 59.922 52.632 28.56 3.36 37.67 1.52
692 3980 1.680651 CATGGGCCGGCTGGTTTAA 60.681 57.895 28.56 4.51 37.67 1.52
693 3981 2.044451 CATGGGCCGGCTGGTTTA 60.044 61.111 28.56 6.84 37.67 2.01
703 3991 3.443045 CTGTCCGTTGCATGGGCC 61.443 66.667 7.56 0.00 40.13 5.80
704 3992 3.443045 CCTGTCCGTTGCATGGGC 61.443 66.667 3.24 3.24 41.68 5.36
705 3993 2.751436 CCCTGTCCGTTGCATGGG 60.751 66.667 5.73 1.59 0.00 4.00
706 3994 1.586154 GAACCCTGTCCGTTGCATGG 61.586 60.000 0.00 0.00 0.00 3.66
707 3995 1.875963 GAACCCTGTCCGTTGCATG 59.124 57.895 0.00 0.00 0.00 4.06
708 3996 1.671054 CGAACCCTGTCCGTTGCAT 60.671 57.895 0.00 0.00 0.00 3.96
709 3997 2.280524 CGAACCCTGTCCGTTGCA 60.281 61.111 0.00 0.00 0.00 4.08
710 3998 2.280592 ACGAACCCTGTCCGTTGC 60.281 61.111 0.00 0.00 32.03 4.17
711 3999 2.019951 CGACGAACCCTGTCCGTTG 61.020 63.158 0.00 0.00 36.60 4.10
712 4000 2.337532 CGACGAACCCTGTCCGTT 59.662 61.111 0.00 0.00 36.60 4.44
713 4001 4.353437 GCGACGAACCCTGTCCGT 62.353 66.667 0.00 0.00 39.41 4.69
729 4017 3.294493 TTTGAAGTGGGCTGCCGC 61.294 61.111 13.40 8.19 0.00 6.53
730 4018 2.644992 GTTTGAAGTGGGCTGCCG 59.355 61.111 13.40 0.00 0.00 5.69
731 4019 1.809567 CTGGTTTGAAGTGGGCTGCC 61.810 60.000 11.05 11.05 0.00 4.85
732 4020 1.662044 CTGGTTTGAAGTGGGCTGC 59.338 57.895 0.00 0.00 0.00 5.25
733 4021 1.662044 GCTGGTTTGAAGTGGGCTG 59.338 57.895 0.00 0.00 0.00 4.85
734 4022 1.531602 GGCTGGTTTGAAGTGGGCT 60.532 57.895 0.00 0.00 0.00 5.19
735 4023 2.919494 CGGCTGGTTTGAAGTGGGC 61.919 63.158 0.00 0.00 0.00 5.36
736 4024 2.268076 CCGGCTGGTTTGAAGTGGG 61.268 63.158 2.29 0.00 0.00 4.61
737 4025 2.919494 GCCGGCTGGTTTGAAGTGG 61.919 63.158 22.15 0.00 37.67 4.00
738 4026 2.644992 GCCGGCTGGTTTGAAGTG 59.355 61.111 22.15 0.00 37.67 3.16
739 4027 2.597510 GGCCGGCTGGTTTGAAGT 60.598 61.111 28.56 0.00 37.67 3.01
740 4028 3.373565 GGGCCGGCTGGTTTGAAG 61.374 66.667 28.56 0.00 37.67 3.02
741 4029 3.521765 ATGGGCCGGCTGGTTTGAA 62.522 57.895 28.56 3.36 37.67 2.69
742 4030 3.978193 ATGGGCCGGCTGGTTTGA 61.978 61.111 28.56 2.60 37.67 2.69
743 4031 3.762247 CATGGGCCGGCTGGTTTG 61.762 66.667 28.56 13.21 37.67 2.93
763 4051 2.375766 CGTGGCGAACTCTGTCTGC 61.376 63.158 0.00 0.00 0.00 4.26
782 4070 1.527433 GCTGGTTTGAAGTGGGCTCC 61.527 60.000 0.00 0.00 0.00 4.70
783 4071 1.527433 GGCTGGTTTGAAGTGGGCTC 61.527 60.000 0.00 0.00 0.00 4.70
803 4091 0.322277 CTCTGTCTGTTGCATGGGCT 60.322 55.000 0.00 0.00 41.91 5.19
965 4303 3.138304 TGTTCGATTTGGTTCCTGAGTG 58.862 45.455 0.00 0.00 0.00 3.51
968 4306 2.882137 GGTTGTTCGATTTGGTTCCTGA 59.118 45.455 0.00 0.00 0.00 3.86
970 4308 2.235891 GGGTTGTTCGATTTGGTTCCT 58.764 47.619 0.00 0.00 0.00 3.36
1095 4436 2.683933 TTGAGGAGGGCGAGGGAC 60.684 66.667 0.00 0.00 0.00 4.46
1129 4470 1.411787 GGGAGCTAGCTTGAGGGACTA 60.412 57.143 20.42 0.00 41.55 2.59
1427 4809 1.674651 GAGGGGAAAACGACAGGGC 60.675 63.158 0.00 0.00 0.00 5.19
1428 4810 0.036294 GAGAGGGGAAAACGACAGGG 60.036 60.000 0.00 0.00 0.00 4.45
1443 4825 2.176273 CAAATCTGGCGCGGGAGAG 61.176 63.158 8.83 0.00 0.00 3.20
1453 4835 5.981174 ACAAATTAAGGGCATCAAATCTGG 58.019 37.500 0.00 0.00 0.00 3.86
1477 4859 6.238211 CCTTTTCAGCTTATCAACGAGTATGG 60.238 42.308 0.00 0.00 0.00 2.74
1587 4970 8.698973 TTCCACAAATTAACATCTGGAACTAA 57.301 30.769 0.00 0.00 33.74 2.24
1631 5014 4.705023 CCTTACAAAAATGAACGGAGGGAT 59.295 41.667 0.00 0.00 0.00 3.85
1655 5038 7.339721 TGGGTGTTGTCTTAAATGTCTAAAACA 59.660 33.333 0.00 0.00 43.51 2.83
1839 5222 1.675714 CGTGCATCAGGGCTGACTTTA 60.676 52.381 0.00 0.00 43.11 1.85
1854 5237 2.361119 GACTAGGATACCATGACGTGCA 59.639 50.000 0.00 0.00 37.17 4.57
1924 5307 5.534207 AATGGAAGTGTGAAATCAAGCAA 57.466 34.783 0.00 0.00 0.00 3.91
2116 5724 2.541466 AGAGCTGGTAAAGTGGTAGCT 58.459 47.619 0.00 0.00 46.50 3.32
2265 5875 9.639601 CCAACTCCAGGAAAATTCTTAATTTAC 57.360 33.333 0.00 0.00 40.05 2.01
2347 5957 3.999046 TGGAGATCATCATCAACGATGG 58.001 45.455 4.24 0.00 42.58 3.51
2469 6080 7.538678 CAGAAGCATAATTCAAAACTACCACAC 59.461 37.037 0.00 0.00 0.00 3.82
2576 6194 0.674895 CACAAGTCAGCTGTAGGGCC 60.675 60.000 14.67 0.00 0.00 5.80
2923 6548 2.153401 CCCCACAACTCCTCCACCA 61.153 63.158 0.00 0.00 0.00 4.17
3204 6829 2.351924 AAAGTCCAGGCTCCGGCAAA 62.352 55.000 0.00 0.00 40.87 3.68
3337 6962 1.215244 CACAGCTGAGCATACATCCG 58.785 55.000 23.35 0.00 0.00 4.18
3477 7102 6.152831 GGCCTGTCAAAGTAATTCCAAGTATT 59.847 38.462 0.00 0.00 0.00 1.89
3617 7242 3.418047 ACAAGTAATTTGGAACGGAGGG 58.582 45.455 0.00 0.00 41.25 4.30
3618 7243 3.124636 CGACAAGTAATTTGGAACGGAGG 59.875 47.826 0.00 0.00 41.25 4.30
3619 7244 3.744426 ACGACAAGTAATTTGGAACGGAG 59.256 43.478 0.00 0.00 41.25 4.63
3621 7246 3.364565 CCACGACAAGTAATTTGGAACGG 60.365 47.826 0.00 0.00 41.25 4.44
3622 7247 3.249080 ACCACGACAAGTAATTTGGAACG 59.751 43.478 0.00 0.00 41.25 3.95
3623 7248 4.823790 ACCACGACAAGTAATTTGGAAC 57.176 40.909 0.00 0.00 41.25 3.62
3624 7249 5.838531 AAACCACGACAAGTAATTTGGAA 57.161 34.783 0.00 0.00 41.25 3.53
3626 7251 6.731164 ACTAAAACCACGACAAGTAATTTGG 58.269 36.000 0.00 0.00 41.25 3.28
3627 7252 7.911205 TGAACTAAAACCACGACAAGTAATTTG 59.089 33.333 0.00 0.00 42.68 2.32
3628 7253 7.987649 TGAACTAAAACCACGACAAGTAATTT 58.012 30.769 0.00 0.00 0.00 1.82
3630 7255 7.556733 TTGAACTAAAACCACGACAAGTAAT 57.443 32.000 0.00 0.00 0.00 1.89
3631 7256 6.981762 TTGAACTAAAACCACGACAAGTAA 57.018 33.333 0.00 0.00 0.00 2.24
3632 7257 7.556733 AATTGAACTAAAACCACGACAAGTA 57.443 32.000 0.00 0.00 0.00 2.24
3633 7258 6.445357 AATTGAACTAAAACCACGACAAGT 57.555 33.333 0.00 0.00 0.00 3.16
3635 7260 6.853720 TCAAATTGAACTAAAACCACGACAA 58.146 32.000 0.00 0.00 0.00 3.18
3651 7276 6.438259 TGTCGTGGTTTTAGTTCAAATTGA 57.562 33.333 0.00 0.00 0.00 2.57
3652 7277 6.750039 ACTTGTCGTGGTTTTAGTTCAAATTG 59.250 34.615 0.00 0.00 0.00 2.32
3654 7279 6.445357 ACTTGTCGTGGTTTTAGTTCAAAT 57.555 33.333 0.00 0.00 0.00 2.32
3655 7280 5.883503 ACTTGTCGTGGTTTTAGTTCAAA 57.116 34.783 0.00 0.00 0.00 2.69
3656 7281 6.981762 TTACTTGTCGTGGTTTTAGTTCAA 57.018 33.333 0.00 0.00 0.00 2.69
3657 7282 7.556733 AATTACTTGTCGTGGTTTTAGTTCA 57.443 32.000 0.00 0.00 0.00 3.18
3658 7283 7.377662 CCAAATTACTTGTCGTGGTTTTAGTTC 59.622 37.037 0.00 0.00 32.65 3.01
3659 7284 7.067251 TCCAAATTACTTGTCGTGGTTTTAGTT 59.933 33.333 0.00 0.00 32.65 2.24
3660 7285 6.543100 TCCAAATTACTTGTCGTGGTTTTAGT 59.457 34.615 0.00 0.00 32.65 2.24
3661 7286 6.961576 TCCAAATTACTTGTCGTGGTTTTAG 58.038 36.000 0.00 0.00 32.65 1.85
3663 7288 5.838531 TCCAAATTACTTGTCGTGGTTTT 57.161 34.783 0.00 0.00 32.65 2.43
3664 7289 5.584442 GTTCCAAATTACTTGTCGTGGTTT 58.416 37.500 0.00 0.00 32.65 3.27
3665 7290 4.260866 CGTTCCAAATTACTTGTCGTGGTT 60.261 41.667 0.00 0.00 32.65 3.67
3667 7292 3.364565 CCGTTCCAAATTACTTGTCGTGG 60.365 47.826 0.00 0.00 32.65 4.94
3668 7293 3.495377 TCCGTTCCAAATTACTTGTCGTG 59.505 43.478 0.00 0.00 32.65 4.35
3669 7294 3.731089 TCCGTTCCAAATTACTTGTCGT 58.269 40.909 0.00 0.00 32.65 4.34
3670 7295 3.124636 CCTCCGTTCCAAATTACTTGTCG 59.875 47.826 0.00 0.00 32.65 4.35
3671 7296 3.439129 CCCTCCGTTCCAAATTACTTGTC 59.561 47.826 0.00 0.00 32.65 3.18
3672 7297 3.073356 TCCCTCCGTTCCAAATTACTTGT 59.927 43.478 0.00 0.00 32.65 3.16
3674 7299 3.329814 ACTCCCTCCGTTCCAAATTACTT 59.670 43.478 0.00 0.00 0.00 2.24
3676 7301 3.345508 ACTCCCTCCGTTCCAAATTAC 57.654 47.619 0.00 0.00 0.00 1.89
3677 7302 6.811634 TTATACTCCCTCCGTTCCAAATTA 57.188 37.500 0.00 0.00 0.00 1.40
3678 7303 5.703730 TTATACTCCCTCCGTTCCAAATT 57.296 39.130 0.00 0.00 0.00 1.82
3679 7304 5.703730 TTTATACTCCCTCCGTTCCAAAT 57.296 39.130 0.00 0.00 0.00 2.32
3681 7306 5.703730 AATTTATACTCCCTCCGTTCCAA 57.296 39.130 0.00 0.00 0.00 3.53
3682 7307 5.045432 ACAAATTTATACTCCCTCCGTTCCA 60.045 40.000 0.00 0.00 0.00 3.53
3683 7308 5.296035 CACAAATTTATACTCCCTCCGTTCC 59.704 44.000 0.00 0.00 0.00 3.62
3684 7309 6.110707 TCACAAATTTATACTCCCTCCGTTC 58.889 40.000 0.00 0.00 0.00 3.95
3685 7310 6.057321 TCACAAATTTATACTCCCTCCGTT 57.943 37.500 0.00 0.00 0.00 4.44
3686 7311 5.687166 TCACAAATTTATACTCCCTCCGT 57.313 39.130 0.00 0.00 0.00 4.69
3687 7312 6.995511 TTTCACAAATTTATACTCCCTCCG 57.004 37.500 0.00 0.00 0.00 4.63
3689 7314 9.232473 ACTCTTTTCACAAATTTATACTCCCTC 57.768 33.333 0.00 0.00 0.00 4.30
3690 7315 9.588096 AACTCTTTTCACAAATTTATACTCCCT 57.412 29.630 0.00 0.00 0.00 4.20
3698 7323 9.921637 AGACAACAAACTCTTTTCACAAATTTA 57.078 25.926 0.00 0.00 0.00 1.40
3700 7325 8.711457 CAAGACAACAAACTCTTTTCACAAATT 58.289 29.630 0.00 0.00 0.00 1.82
3701 7326 8.087750 TCAAGACAACAAACTCTTTTCACAAAT 58.912 29.630 0.00 0.00 0.00 2.32
4291 8483 3.244422 ACACGGCCAGAATCTAAGAAACA 60.244 43.478 2.24 0.00 0.00 2.83
4304 8496 0.659123 GCACGTAAAAACACGGCCAG 60.659 55.000 2.24 0.00 46.12 4.85
4591 8791 3.787785 TGTCGAGCAAACTGTTAGAACA 58.212 40.909 0.00 0.00 37.37 3.18
4642 8842 8.526218 TGAAAATTGCTGCGAAATTAAACATA 57.474 26.923 0.00 0.00 0.00 2.29
4675 8875 7.492344 CAGAACCAGAACTTGCAATTTTAAAGT 59.508 33.333 0.00 0.00 35.70 2.66
4725 8925 9.069078 CATTAAAAATACACTGATTCAGCTGTG 57.931 33.333 21.75 14.11 41.66 3.66
4726 8926 8.796475 ACATTAAAAATACACTGATTCAGCTGT 58.204 29.630 14.67 16.99 34.37 4.40
4769 9348 4.513406 ATTCATCCGCCTAGGGTAAAAA 57.487 40.909 11.72 0.00 41.52 1.94
4770 9349 5.836024 ATATTCATCCGCCTAGGGTAAAA 57.164 39.130 11.72 0.00 41.52 1.52
4779 9358 5.913137 TTGTTTTGAATATTCATCCGCCT 57.087 34.783 18.61 0.00 37.00 5.52
4780 9359 7.920682 ACTATTTGTTTTGAATATTCATCCGCC 59.079 33.333 18.61 6.58 37.00 6.13
4810 9389 7.566858 AGCACTGCTATTTCGTTAAAATTTG 57.433 32.000 0.21 0.00 36.99 2.32
4822 9401 2.226437 CACCGACAAAGCACTGCTATTT 59.774 45.455 3.33 0.00 38.25 1.40
4969 9564 4.127171 GGCATACCTGGTGTACAATAGTG 58.873 47.826 10.23 0.00 30.62 2.74
4982 9577 2.655723 CGCAAACGAGAGGCATACCTG 61.656 57.143 0.00 0.00 45.35 4.00
5196 9797 2.323790 CTCGATCGACGGACGGAC 59.676 66.667 15.15 0.00 42.82 4.79
5197 9798 3.570638 GCTCGATCGACGGACGGA 61.571 66.667 15.15 0.00 42.82 4.69
5198 9799 3.509296 GAGCTCGATCGACGGACGG 62.509 68.421 15.15 4.44 42.82 4.79
5199 9800 2.052941 GAGCTCGATCGACGGACG 60.053 66.667 15.15 5.25 42.82 4.79
5392 9993 0.669318 ATGAAAAAGGCGCGTCTCGA 60.669 50.000 16.36 0.00 41.67 4.04
5427 10043 7.667575 AGTCTGACATCACATTTATAGGACT 57.332 36.000 10.88 0.00 0.00 3.85
5475 10091 7.465781 GCGACCCGTAATTTGCTAGTATAAAAA 60.466 37.037 0.00 0.00 0.00 1.94
5478 10094 4.984161 GCGACCCGTAATTTGCTAGTATAA 59.016 41.667 0.00 0.00 0.00 0.98
5480 10096 3.387397 GCGACCCGTAATTTGCTAGTAT 58.613 45.455 0.00 0.00 0.00 2.12
5482 10098 1.648504 GCGACCCGTAATTTGCTAGT 58.351 50.000 0.00 0.00 0.00 2.57
5483 10099 0.575390 CGCGACCCGTAATTTGCTAG 59.425 55.000 0.00 0.00 0.00 3.42
5487 10104 1.347221 GCTCGCGACCCGTAATTTG 59.653 57.895 3.71 0.00 38.35 2.32


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

AutoCloner maintained by Alex Coulton.