Multiple sequence alignment - TraesCS2B01G517800

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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 TraesCS2B01G517800 chr2B 100.000 3575 0 0 1 3575 712642677 712639103 0.000000e+00 6602
1 TraesCS2B01G517800 chr2B 82.364 1531 242 17 1070 2584 712770520 712769002 0.000000e+00 1306
2 TraesCS2B01G517800 chr2B 76.119 1541 309 44 1074 2578 712776053 712774536 0.000000e+00 752
3 TraesCS2B01G517800 chr2B 74.090 1675 350 51 1073 2722 712830360 712828745 2.360000e-171 612
4 TraesCS2B01G517800 chr2B 75.567 1146 222 43 1099 2208 712008521 712007398 2.460000e-141 512
5 TraesCS2B01G517800 chr2B 78.331 743 128 19 1 722 712771510 712770780 1.960000e-122 449
6 TraesCS2B01G517800 chr2B 78.824 425 81 9 283 704 712360634 712360216 9.780000e-71 278
7 TraesCS2B01G517800 chr2B 73.814 569 72 32 2764 3285 712763349 712762811 1.720000e-33 154
8 TraesCS2B01G517800 chr2B 85.417 144 21 0 3421 3564 712614121 712613978 2.220000e-32 150
9 TraesCS2B01G517800 chr2B 75.850 294 36 17 2761 3024 712762478 712762190 2.260000e-22 117
10 TraesCS2B01G517800 chr2D 90.153 1899 147 20 894 2763 589071695 589069808 0.000000e+00 2435
11 TraesCS2B01G517800 chr2D 94.444 720 39 1 1 719 589072507 589071788 0.000000e+00 1107
12 TraesCS2B01G517800 chr2D 86.456 982 100 13 1789 2763 588934840 588933885 0.000000e+00 1046
13 TraesCS2B01G517800 chr2D 75.365 1644 328 54 1075 2674 589189296 589187686 0.000000e+00 721
14 TraesCS2B01G517800 chr2D 80.401 699 111 11 1094 1790 588968004 588967330 3.180000e-140 508
15 TraesCS2B01G517800 chr2D 77.920 779 124 24 1 755 589190295 589189541 3.280000e-120 442
16 TraesCS2B01G517800 chr2D 79.613 569 91 17 1070 1625 589184477 589183921 5.600000e-103 385
17 TraesCS2B01G517800 chr2D 72.671 1138 232 65 1099 2207 588735706 588734619 4.480000e-79 305
18 TraesCS2B01G517800 chr2D 79.108 426 78 11 283 704 588736414 588735996 2.100000e-72 283
19 TraesCS2B01G517800 chr2D 78.824 425 82 5 283 706 573951946 573952363 2.720000e-71 279
20 TraesCS2B01G517800 chr2D 79.152 283 34 8 3318 3575 588933431 588933149 4.750000e-39 172
21 TraesCS2B01G517800 chr2D 83.163 196 11 10 3160 3340 588933645 588933457 3.690000e-35 159
22 TraesCS2B01G517800 chr2D 91.429 105 8 1 2764 2868 589182963 589182860 3.720000e-30 143
23 TraesCS2B01G517800 chr2D 86.364 110 12 3 2761 2868 589069936 589069828 2.260000e-22 117
24 TraesCS2B01G517800 chr2D 86.111 108 13 1 2761 2868 589182123 589182018 8.110000e-22 115
25 TraesCS2B01G517800 chr2A 84.361 1362 166 21 1079 2417 723535048 723533711 0.000000e+00 1291
26 TraesCS2B01G517800 chr2A 75.500 1551 319 47 1070 2584 723579167 723577642 0.000000e+00 702
27 TraesCS2B01G517800 chr2A 81.948 698 85 17 2045 2738 723572773 723572113 1.450000e-153 553
28 TraesCS2B01G517800 chr2A 79.045 754 113 22 1 730 723580178 723579446 3.230000e-130 475
29 TraesCS2B01G517800 chr2A 73.875 1156 234 47 1099 2208 723160196 723159063 2.000000e-107 399
30 TraesCS2B01G517800 chr2A 79.121 637 82 22 2976 3573 723571967 723571343 3.350000e-105 392
31 TraesCS2B01G517800 chr2A 80.879 455 41 17 3160 3574 723532849 723532401 2.070000e-82 316
32 TraesCS2B01G517800 chr2A 72.816 1133 219 57 1099 2208 723511840 723510774 1.610000e-78 303
33 TraesCS2B01G517800 chr2A 78.118 425 84 9 283 704 723512451 723512033 9.840000e-66 261
34 TraesCS2B01G517800 chr2A 78.089 429 78 13 283 706 712538851 712539268 1.270000e-64 257
35 TraesCS2B01G517800 chr2A 80.588 340 40 8 2424 2763 723533409 723533096 4.610000e-59 239
36 TraesCS2B01G517800 chr2A 89.691 97 8 2 2767 2863 723572207 723572113 4.850000e-24 122


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 TraesCS2B01G517800 chr2B 712639103 712642677 3574 True 6602.000000 6602 100.000000 1 3575 1 chr2B.!!$R4 3574
1 TraesCS2B01G517800 chr2B 712769002 712776053 7051 True 835.666667 1306 78.938000 1 2584 3 chr2B.!!$R7 2583
2 TraesCS2B01G517800 chr2B 712828745 712830360 1615 True 612.000000 612 74.090000 1073 2722 1 chr2B.!!$R5 1649
3 TraesCS2B01G517800 chr2B 712007398 712008521 1123 True 512.000000 512 75.567000 1099 2208 1 chr2B.!!$R1 1109
4 TraesCS2B01G517800 chr2D 589069808 589072507 2699 True 1219.666667 2435 90.320333 1 2868 3 chr2D.!!$R4 2867
5 TraesCS2B01G517800 chr2D 588967330 588968004 674 True 508.000000 508 80.401000 1094 1790 1 chr2D.!!$R1 696
6 TraesCS2B01G517800 chr2D 588933149 588934840 1691 True 459.000000 1046 82.923667 1789 3575 3 chr2D.!!$R3 1786
7 TraesCS2B01G517800 chr2D 589182018 589190295 8277 True 361.200000 721 82.087600 1 2868 5 chr2D.!!$R5 2867
8 TraesCS2B01G517800 chr2D 588734619 588736414 1795 True 294.000000 305 75.889500 283 2207 2 chr2D.!!$R2 1924
9 TraesCS2B01G517800 chr2A 723532401 723535048 2647 True 615.333333 1291 81.942667 1079 3574 3 chr2A.!!$R3 2495
10 TraesCS2B01G517800 chr2A 723577642 723580178 2536 True 588.500000 702 77.272500 1 2584 2 chr2A.!!$R5 2583
11 TraesCS2B01G517800 chr2A 723159063 723160196 1133 True 399.000000 399 73.875000 1099 2208 1 chr2A.!!$R1 1109
12 TraesCS2B01G517800 chr2A 723571343 723572773 1430 True 355.666667 553 83.586667 2045 3573 3 chr2A.!!$R4 1528
13 TraesCS2B01G517800 chr2A 723510774 723512451 1677 True 282.000000 303 75.467000 283 2208 2 chr2A.!!$R2 1925

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
783 5369 0.107831 TTACAGGTTGCAGCTTCGGT 59.892 50.0 0.00 0.0 0.00 4.69 F
784 5370 0.107831 TACAGGTTGCAGCTTCGGTT 59.892 50.0 0.00 0.0 0.00 4.44 F
876 5472 0.179234 TATCAAGGATTTCCGGCGCA 59.821 50.0 10.83 0.0 42.08 6.09 F
1784 6585 0.319383 CTCAGTGAAGAGCGCACACT 60.319 55.0 11.47 16.1 44.15 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1784 6585 0.327924 ATCATGGTGAACCTCCGCAA 59.672 50.0 0.37 0.0 36.82 4.85 R
2254 11851 0.591659 CACCGTCGTCTTCAGTCTCA 59.408 55.0 0.00 0.0 0.00 3.27 R
2491 12389 0.833287 TCCAGGATCTTAGCAGCCAC 59.167 55.0 0.00 0.0 0.00 5.01 R
3388 13421 0.169672 CTTTCAGTCTTGCCATGCGG 59.830 55.0 0.00 0.0 0.00 5.69 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 4575 2.281484 GTTGGCCTCCAGCGTCAA 60.281 61.111 3.32 0.00 45.17 3.18
41 4585 0.882042 CCAGCGTCAAGTCAGCAAGT 60.882 55.000 0.00 0.00 0.00 3.16
130 4677 1.646189 GTCTCGAGAAATGGCAGGTC 58.354 55.000 18.55 0.00 0.00 3.85
172 4719 2.133281 TTGCAATAGCTGAGGCACAT 57.867 45.000 7.41 0.00 42.74 3.21
176 4723 1.863454 CAATAGCTGAGGCACATCGTC 59.137 52.381 0.00 0.00 41.70 4.20
224 4771 2.043953 GGAAGGACATGCCCCCAC 60.044 66.667 0.00 0.00 37.37 4.61
263 4810 0.856641 CTTTTTCTTCGTCGTCGCCA 59.143 50.000 0.00 0.00 36.96 5.69
266 4813 2.350899 TTTCTTCGTCGTCGCCATTA 57.649 45.000 0.00 0.00 36.96 1.90
274 4821 1.017177 TCGTCGCCATTAACACTGCC 61.017 55.000 0.00 0.00 0.00 4.85
515 5083 1.685421 GCAGCTCCTCCTCTCCTGT 60.685 63.158 0.00 0.00 0.00 4.00
543 5111 0.108756 GAAGTAGGTGTCCCAGTCGC 60.109 60.000 0.00 0.00 0.00 5.19
676 5244 4.767255 GAGGACGTGGCCCAGCAG 62.767 72.222 0.00 0.00 0.00 4.24
729 5315 2.022902 CCGACGAGGATGACGACG 59.977 66.667 0.00 0.00 45.00 5.12
740 5326 4.135493 GACGACGGCTTCTTGCGC 62.135 66.667 0.00 0.00 44.05 6.09
759 5345 0.810031 CGAAGGTGAAGCCATACCGG 60.810 60.000 0.00 0.00 41.85 5.28
763 5349 2.112815 GTGAAGCCATACCGGTGCC 61.113 63.158 19.93 2.16 36.97 5.01
766 5352 0.179468 GAAGCCATACCGGTGCCTTA 59.821 55.000 19.93 0.00 36.97 2.69
769 5355 0.814010 GCCATACCGGTGCCTTACAG 60.814 60.000 19.93 0.00 36.97 2.74
774 5360 2.332654 CCGGTGCCTTACAGGTTGC 61.333 63.158 0.00 0.00 39.49 4.17
777 5363 1.581447 GTGCCTTACAGGTTGCAGC 59.419 57.895 0.00 0.00 37.80 5.25
780 5366 0.523519 GCCTTACAGGTTGCAGCTTC 59.476 55.000 0.00 0.00 37.80 3.86
783 5369 0.107831 TTACAGGTTGCAGCTTCGGT 59.892 50.000 0.00 0.00 0.00 4.69
784 5370 0.107831 TACAGGTTGCAGCTTCGGTT 59.892 50.000 0.00 0.00 0.00 4.44
785 5371 1.166531 ACAGGTTGCAGCTTCGGTTC 61.167 55.000 0.00 0.00 0.00 3.62
787 5373 0.465460 AGGTTGCAGCTTCGGTTCAA 60.465 50.000 0.00 0.00 0.00 2.69
795 5381 0.889186 GCTTCGGTTCAAGCCTTCCA 60.889 55.000 0.00 0.00 42.68 3.53
796 5382 1.160137 CTTCGGTTCAAGCCTTCCAG 58.840 55.000 0.00 0.00 0.00 3.86
797 5383 0.250727 TTCGGTTCAAGCCTTCCAGG 60.251 55.000 0.00 0.00 38.80 4.45
798 5384 1.125093 TCGGTTCAAGCCTTCCAGGA 61.125 55.000 0.00 0.00 37.67 3.86
799 5385 0.674895 CGGTTCAAGCCTTCCAGGAG 60.675 60.000 0.00 0.00 37.67 3.69
800 5386 0.693049 GGTTCAAGCCTTCCAGGAGA 59.307 55.000 0.00 0.00 37.67 3.71
801 5387 1.073923 GGTTCAAGCCTTCCAGGAGAA 59.926 52.381 0.00 0.00 37.67 2.87
807 5393 2.124942 CTTCCAGGAGAAGCCGGC 60.125 66.667 21.89 21.89 45.38 6.13
808 5394 2.607750 TTCCAGGAGAAGCCGGCT 60.608 61.111 27.08 27.08 43.43 5.52
809 5395 1.305802 TTCCAGGAGAAGCCGGCTA 60.306 57.895 33.07 8.62 43.43 3.93
810 5396 0.691078 TTCCAGGAGAAGCCGGCTAT 60.691 55.000 33.07 22.49 43.43 2.97
811 5397 0.691078 TCCAGGAGAAGCCGGCTATT 60.691 55.000 33.07 21.51 43.43 1.73
812 5398 0.250081 CCAGGAGAAGCCGGCTATTC 60.250 60.000 33.07 27.89 43.43 1.75
813 5399 0.598680 CAGGAGAAGCCGGCTATTCG 60.599 60.000 33.07 14.11 43.43 3.34
814 5400 0.755698 AGGAGAAGCCGGCTATTCGA 60.756 55.000 33.07 0.00 43.43 3.71
815 5401 0.318762 GGAGAAGCCGGCTATTCGAT 59.681 55.000 33.07 13.77 0.00 3.59
816 5402 1.670380 GGAGAAGCCGGCTATTCGATC 60.670 57.143 33.07 22.50 0.00 3.69
817 5403 1.000163 GAGAAGCCGGCTATTCGATCA 60.000 52.381 33.07 0.00 0.00 2.92
818 5404 1.412710 AGAAGCCGGCTATTCGATCAA 59.587 47.619 33.07 0.00 0.00 2.57
819 5405 2.158957 AGAAGCCGGCTATTCGATCAAA 60.159 45.455 33.07 0.00 0.00 2.69
820 5406 1.583054 AGCCGGCTATTCGATCAAAC 58.417 50.000 31.86 0.00 0.00 2.93
821 5407 0.232303 GCCGGCTATTCGATCAAACG 59.768 55.000 22.15 0.00 0.00 3.60
822 5408 1.847818 CCGGCTATTCGATCAAACGA 58.152 50.000 0.00 0.00 40.55 3.85
823 5409 1.787155 CCGGCTATTCGATCAAACGAG 59.213 52.381 0.00 0.00 43.04 4.18
824 5410 2.543031 CCGGCTATTCGATCAAACGAGA 60.543 50.000 0.00 0.00 43.04 4.04
825 5411 2.468040 CGGCTATTCGATCAAACGAGAC 59.532 50.000 0.00 0.00 43.04 3.36
843 5429 1.950909 GACAGGAGATCGATCCGAAGT 59.049 52.381 21.66 15.07 44.65 3.01
844 5430 3.139850 GACAGGAGATCGATCCGAAGTA 58.860 50.000 21.66 0.00 44.65 2.24
846 5432 2.095466 CAGGAGATCGATCCGAAGTAGC 60.095 54.545 21.66 1.90 44.65 3.58
847 5433 1.880675 GGAGATCGATCCGAAGTAGCA 59.119 52.381 21.66 0.00 39.99 3.49
848 5434 2.350964 GGAGATCGATCCGAAGTAGCAC 60.351 54.545 21.66 0.00 39.99 4.40
849 5435 2.550606 GAGATCGATCCGAAGTAGCACT 59.449 50.000 21.66 0.00 39.99 4.40
872 5468 7.065085 CACTAGCAATATATCAAGGATTTCCGG 59.935 40.741 0.00 0.00 42.08 5.14
873 5469 4.702131 AGCAATATATCAAGGATTTCCGGC 59.298 41.667 0.00 0.00 42.08 6.13
874 5470 4.437390 GCAATATATCAAGGATTTCCGGCG 60.437 45.833 0.00 0.00 42.08 6.46
875 5471 1.523758 ATATCAAGGATTTCCGGCGC 58.476 50.000 0.00 0.00 42.08 6.53
876 5472 0.179234 TATCAAGGATTTCCGGCGCA 59.821 50.000 10.83 0.00 42.08 6.09
877 5473 0.679640 ATCAAGGATTTCCGGCGCAA 60.680 50.000 10.83 0.00 42.08 4.85
879 5475 2.686816 AAGGATTTCCGGCGCAACG 61.687 57.895 10.83 3.98 42.08 4.10
881 5477 2.399611 GATTTCCGGCGCAACGAG 59.600 61.111 10.83 0.00 35.47 4.18
882 5478 2.047655 ATTTCCGGCGCAACGAGA 60.048 55.556 10.83 1.40 35.47 4.04
885 5481 3.626680 TTCCGGCGCAACGAGAGAG 62.627 63.158 10.83 0.00 35.47 3.20
887 5483 2.876645 CGGCGCAACGAGAGAGTC 60.877 66.667 10.83 0.00 35.47 3.36
912 5508 1.078708 CCGTTTCATAGGCGGTGGT 60.079 57.895 0.00 0.00 40.53 4.16
913 5509 1.366111 CCGTTTCATAGGCGGTGGTG 61.366 60.000 0.00 0.00 40.53 4.17
917 5513 1.195442 TTCATAGGCGGTGGTGGTGA 61.195 55.000 0.00 0.00 0.00 4.02
920 5516 1.614241 ATAGGCGGTGGTGGTGAGTC 61.614 60.000 0.00 0.00 0.00 3.36
921 5517 3.936203 GGCGGTGGTGGTGAGTCA 61.936 66.667 0.00 0.00 0.00 3.41
922 5518 2.665185 GCGGTGGTGGTGAGTCAC 60.665 66.667 15.24 15.24 36.95 3.67
941 5572 1.012486 CCAGCGTGTTCCTAACGGAC 61.012 60.000 0.00 0.00 39.60 4.79
945 5576 1.670674 GCGTGTTCCTAACGGACATCA 60.671 52.381 0.00 0.00 39.60 3.07
971 5602 0.385751 AGTCGGTGGATATCTGTGCG 59.614 55.000 2.05 0.00 0.00 5.34
972 5603 0.384309 GTCGGTGGATATCTGTGCGA 59.616 55.000 2.05 0.00 0.00 5.10
973 5604 0.668535 TCGGTGGATATCTGTGCGAG 59.331 55.000 2.05 0.00 0.00 5.03
974 5605 0.941463 CGGTGGATATCTGTGCGAGC 60.941 60.000 2.05 0.00 0.00 5.03
975 5606 0.941463 GGTGGATATCTGTGCGAGCG 60.941 60.000 2.05 0.00 0.00 5.03
976 5607 1.300156 TGGATATCTGTGCGAGCGC 60.300 57.895 8.08 8.08 42.35 5.92
977 5608 2.024319 GGATATCTGTGCGAGCGCC 61.024 63.158 12.70 4.53 41.09 6.53
978 5609 2.355126 ATATCTGTGCGAGCGCCG 60.355 61.111 12.70 9.10 41.09 6.46
1013 5644 1.867373 CAAATACCAAAGGCGCGCG 60.867 57.895 28.44 28.44 0.00 6.86
1260 6004 2.282462 CCCCAAGAAAGGCACGCT 60.282 61.111 0.00 0.00 0.00 5.07
1387 6161 2.988684 GCCATGTTCCCGCCACAA 60.989 61.111 0.00 0.00 0.00 3.33
1565 6352 1.033746 CATCAAGACGCAGCCCCATT 61.034 55.000 0.00 0.00 0.00 3.16
1622 6409 1.901948 AACTGGACGCTCGACCTGA 60.902 57.895 19.73 0.00 34.35 3.86
1768 6569 0.729690 CGAGCGTCACTGAGATCTCA 59.270 55.000 23.75 23.75 38.06 3.27
1780 6581 1.133982 GAGATCTCAGTGAAGAGCGCA 59.866 52.381 18.11 0.00 36.79 6.09
1784 6585 0.319383 CTCAGTGAAGAGCGCACACT 60.319 55.000 11.47 16.10 44.15 3.55
1852 6653 3.043713 CACAGCTCGCGCCTGAAA 61.044 61.111 26.11 0.00 36.60 2.69
1933 6740 1.605457 GGAATCATGGCGCTGACGATA 60.605 52.381 7.64 0.00 43.93 2.92
2035 11614 1.406887 GCGCATCTCCACCTTTCCTTA 60.407 52.381 0.30 0.00 0.00 2.69
2306 11906 1.588824 CCGTAGTAGCCGTGTGACCA 61.589 60.000 0.00 0.00 0.00 4.02
2352 11955 2.886382 GCTTGGGCCATAAGCTGAA 58.114 52.632 27.43 0.00 45.34 3.02
2491 12389 0.673644 AACGAAAGGACCAGATGGCG 60.674 55.000 0.00 0.00 39.32 5.69
2540 12439 2.542411 CGCCATACCAGAGTAACCGTAC 60.542 54.545 0.00 0.00 30.59 3.67
2640 12540 8.439971 TCTTTTGGTAGCACAAGGATATGATAT 58.560 33.333 18.09 0.00 0.00 1.63
2750 12681 4.970860 ATAGGAGCTGATAAGCACACAT 57.029 40.909 4.45 0.00 37.25 3.21
2763 12694 5.963176 AAGCACACATCAATACAACATGA 57.037 34.783 0.00 0.00 0.00 3.07
2765 12696 7.628769 AAGCACACATCAATACAACATGATA 57.371 32.000 0.00 0.00 34.61 2.15
2766 12697 7.255491 AGCACACATCAATACAACATGATAG 57.745 36.000 0.00 0.00 34.61 2.08
2767 12698 6.261603 AGCACACATCAATACAACATGATAGG 59.738 38.462 0.00 0.00 34.61 2.57
2768 12699 6.038603 GCACACATCAATACAACATGATAGGT 59.961 38.462 0.00 0.00 34.61 3.08
2769 12700 7.226523 GCACACATCAATACAACATGATAGGTA 59.773 37.037 0.00 0.00 34.61 3.08
2770 12701 9.276590 CACACATCAATACAACATGATAGGTAT 57.723 33.333 0.00 0.00 34.61 2.73
2771 12702 9.494271 ACACATCAATACAACATGATAGGTATC 57.506 33.333 0.00 0.00 34.61 2.24
2772 12703 9.492973 CACATCAATACAACATGATAGGTATCA 57.507 33.333 0.00 2.19 45.78 2.15
2789 12720 7.992754 AGGTATCATGCTTGAATATTTCTCC 57.007 36.000 6.36 1.76 34.96 3.71
2790 12721 7.753630 AGGTATCATGCTTGAATATTTCTCCT 58.246 34.615 6.36 3.72 34.96 3.69
2791 12722 7.664731 AGGTATCATGCTTGAATATTTCTCCTG 59.335 37.037 6.36 0.00 34.96 3.86
2792 12723 7.446625 GGTATCATGCTTGAATATTTCTCCTGT 59.553 37.037 6.36 0.00 34.96 4.00
2793 12724 7.893124 ATCATGCTTGAATATTTCTCCTGTT 57.107 32.000 6.36 0.00 34.96 3.16
2794 12725 8.985315 ATCATGCTTGAATATTTCTCCTGTTA 57.015 30.769 6.36 0.00 34.96 2.41
2795 12726 8.806429 TCATGCTTGAATATTTCTCCTGTTAA 57.194 30.769 0.00 0.00 0.00 2.01
2796 12727 8.677300 TCATGCTTGAATATTTCTCCTGTTAAC 58.323 33.333 0.00 0.00 0.00 2.01
2797 12728 8.680903 CATGCTTGAATATTTCTCCTGTTAACT 58.319 33.333 7.22 0.00 0.00 2.24
2798 12729 8.268850 TGCTTGAATATTTCTCCTGTTAACTC 57.731 34.615 7.22 0.00 0.00 3.01
2799 12730 8.103305 TGCTTGAATATTTCTCCTGTTAACTCT 58.897 33.333 7.22 0.00 0.00 3.24
2800 12731 9.601217 GCTTGAATATTTCTCCTGTTAACTCTA 57.399 33.333 7.22 0.00 0.00 2.43
2809 12740 9.901172 TTTCTCCTGTTAACTCTACTTTCTTTT 57.099 29.630 7.22 0.00 0.00 2.27
2810 12741 9.901172 TTCTCCTGTTAACTCTACTTTCTTTTT 57.099 29.630 7.22 0.00 0.00 1.94
2851 12782 7.807977 CAACTAATTGGCACTATAGTTGGAT 57.192 36.000 24.58 4.85 45.74 3.41
2852 12783 7.642669 CAACTAATTGGCACTATAGTTGGATG 58.357 38.462 24.58 10.86 45.74 3.51
2853 12784 6.900194 ACTAATTGGCACTATAGTTGGATGT 58.100 36.000 1.56 0.00 0.00 3.06
2854 12785 8.029782 ACTAATTGGCACTATAGTTGGATGTA 57.970 34.615 1.56 0.00 0.00 2.29
2855 12786 7.931948 ACTAATTGGCACTATAGTTGGATGTAC 59.068 37.037 1.56 0.00 0.00 2.90
2856 12787 5.685520 TTGGCACTATAGTTGGATGTACA 57.314 39.130 1.56 0.00 0.00 2.90
2857 12788 5.276461 TGGCACTATAGTTGGATGTACAG 57.724 43.478 1.56 0.00 0.00 2.74
2858 12789 4.100963 TGGCACTATAGTTGGATGTACAGG 59.899 45.833 1.56 0.00 0.00 4.00
2859 12790 4.344102 GGCACTATAGTTGGATGTACAGGA 59.656 45.833 1.56 0.00 0.00 3.86
2860 12791 5.012148 GGCACTATAGTTGGATGTACAGGAT 59.988 44.000 1.56 0.00 0.00 3.24
2861 12792 6.159988 GCACTATAGTTGGATGTACAGGATC 58.840 44.000 1.56 0.00 0.00 3.36
2862 12793 6.015010 GCACTATAGTTGGATGTACAGGATCT 60.015 42.308 1.56 0.00 0.00 2.75
2863 12794 7.374272 CACTATAGTTGGATGTACAGGATCTG 58.626 42.308 1.56 0.00 37.52 2.90
2864 12795 7.231519 CACTATAGTTGGATGTACAGGATCTGA 59.768 40.741 1.56 0.00 35.18 3.27
2872 12803 5.540337 GGATGTACAGGATCTGATAACTCCA 59.460 44.000 0.33 0.00 35.18 3.86
2877 12808 6.909550 ACAGGATCTGATAACTCCATAGTC 57.090 41.667 1.59 0.00 33.06 2.59
2888 12819 1.069823 CTCCATAGTCGCAGAAGGCAT 59.930 52.381 0.00 0.00 45.17 4.40
2899 12830 5.294552 GTCGCAGAAGGCATAAAATTCTAGT 59.705 40.000 0.00 0.00 45.17 2.57
2935 12866 7.152645 CCAAATAACACGGTATAGCTGATAGT 58.847 38.462 0.00 0.00 0.00 2.12
2980 12915 4.592778 ACATTTTATTTCCCAGGCAACAGT 59.407 37.500 0.00 0.00 41.41 3.55
2981 12916 5.777732 ACATTTTATTTCCCAGGCAACAGTA 59.222 36.000 0.00 0.00 41.41 2.74
2982 12917 5.975693 TTTTATTTCCCAGGCAACAGTAG 57.024 39.130 0.00 0.00 41.41 2.57
2983 12918 4.650972 TTATTTCCCAGGCAACAGTAGT 57.349 40.909 0.00 0.00 41.41 2.73
2986 12921 4.440826 TTTCCCAGGCAACAGTAGTTTA 57.559 40.909 0.00 0.00 35.28 2.01
3003 12938 8.882736 CAGTAGTTTATACATGAGTTGCAATGA 58.117 33.333 0.59 0.00 0.00 2.57
3015 12950 9.577110 CATGAGTTGCAATGATAGTAACAAAAT 57.423 29.630 0.59 0.00 34.58 1.82
3045 12980 5.442391 TGGTATTATTAAGCTGGGTTGGAC 58.558 41.667 0.00 0.00 0.00 4.02
3061 12996 5.121298 GGGTTGGACGAACAAACTACTTATC 59.879 44.000 10.65 0.00 38.13 1.75
3076 13011 3.668447 ACTTATCAGGCAGACAACACAG 58.332 45.455 0.00 0.00 0.00 3.66
3077 13012 2.099141 TATCAGGCAGACAACACAGC 57.901 50.000 0.00 0.00 0.00 4.40
3078 13013 0.952497 ATCAGGCAGACAACACAGCG 60.952 55.000 0.00 0.00 0.00 5.18
3083 13018 1.630244 GCAGACAACACAGCGCCTAG 61.630 60.000 2.29 0.00 0.00 3.02
3086 13021 0.737715 GACAACACAGCGCCTAGAGG 60.738 60.000 2.29 0.00 38.53 3.69
3091 13026 0.529337 CACAGCGCCTAGAGGTCATG 60.529 60.000 2.29 0.00 37.57 3.07
3127 13098 3.621268 CACAAAGAACAGAACAACCTCGA 59.379 43.478 0.00 0.00 0.00 4.04
3128 13099 4.273480 CACAAAGAACAGAACAACCTCGAT 59.727 41.667 0.00 0.00 0.00 3.59
3129 13100 5.465390 CACAAAGAACAGAACAACCTCGATA 59.535 40.000 0.00 0.00 0.00 2.92
3130 13101 6.147821 CACAAAGAACAGAACAACCTCGATAT 59.852 38.462 0.00 0.00 0.00 1.63
3131 13102 6.369065 ACAAAGAACAGAACAACCTCGATATC 59.631 38.462 0.00 0.00 0.00 1.63
3132 13103 5.661056 AGAACAGAACAACCTCGATATCA 57.339 39.130 3.12 0.00 0.00 2.15
3133 13104 6.037786 AGAACAGAACAACCTCGATATCAA 57.962 37.500 3.12 0.00 0.00 2.57
3134 13105 6.464222 AGAACAGAACAACCTCGATATCAAA 58.536 36.000 3.12 0.00 0.00 2.69
3135 13106 6.934645 AGAACAGAACAACCTCGATATCAAAA 59.065 34.615 3.12 0.00 0.00 2.44
3136 13107 7.444183 AGAACAGAACAACCTCGATATCAAAAA 59.556 33.333 3.12 0.00 0.00 1.94
3137 13108 7.133891 ACAGAACAACCTCGATATCAAAAAG 57.866 36.000 3.12 0.00 0.00 2.27
3138 13109 6.934645 ACAGAACAACCTCGATATCAAAAAGA 59.065 34.615 3.12 0.00 0.00 2.52
3139 13110 7.444183 ACAGAACAACCTCGATATCAAAAAGAA 59.556 33.333 3.12 0.00 0.00 2.52
3140 13111 8.289618 CAGAACAACCTCGATATCAAAAAGAAA 58.710 33.333 3.12 0.00 0.00 2.52
3141 13112 8.846211 AGAACAACCTCGATATCAAAAAGAAAA 58.154 29.630 3.12 0.00 0.00 2.29
3142 13113 9.458374 GAACAACCTCGATATCAAAAAGAAAAA 57.542 29.630 3.12 0.00 0.00 1.94
3143 13114 9.463443 AACAACCTCGATATCAAAAAGAAAAAG 57.537 29.630 3.12 0.00 0.00 2.27
3144 13115 8.846211 ACAACCTCGATATCAAAAAGAAAAAGA 58.154 29.630 3.12 0.00 0.00 2.52
3145 13116 9.677567 CAACCTCGATATCAAAAAGAAAAAGAA 57.322 29.630 3.12 0.00 0.00 2.52
3205 13184 3.685139 ATGGAGATACAATACCGGCAG 57.315 47.619 0.00 0.00 0.00 4.85
3206 13185 2.673258 TGGAGATACAATACCGGCAGA 58.327 47.619 0.00 0.00 0.00 4.26
3258 13243 2.093075 AGGCATGTGAACAGGATCTGAG 60.093 50.000 0.00 0.00 35.18 3.35
3282 13267 6.547141 AGGAATACAGCATGCAAAATTAGCTA 59.453 34.615 21.98 0.00 42.53 3.32
3288 13274 7.546358 ACAGCATGCAAAATTAGCTAACATAA 58.454 30.769 21.98 0.00 42.53 1.90
3289 13275 7.703621 ACAGCATGCAAAATTAGCTAACATAAG 59.296 33.333 21.98 0.00 42.53 1.73
3388 13421 5.234466 AGGAGGGCATGAATACTCAATAC 57.766 43.478 0.00 0.00 34.49 1.89
3390 13423 3.997021 GAGGGCATGAATACTCAATACCG 59.003 47.826 0.00 0.00 34.49 4.02
3395 13428 4.378770 GCATGAATACTCAATACCGCATGG 60.379 45.833 0.00 0.00 36.76 3.66
3407 13444 0.169672 CCGCATGGCAAGACTGAAAG 59.830 55.000 0.00 0.00 42.29 2.62
3409 13446 1.129998 CGCATGGCAAGACTGAAAGAG 59.870 52.381 0.00 0.00 37.43 2.85
3411 13448 2.787994 CATGGCAAGACTGAAAGAGGT 58.212 47.619 0.00 0.00 37.43 3.85
3430 13490 1.398390 GTTTTGAGGCATAGGTCAGCG 59.602 52.381 0.00 0.00 0.00 5.18
3443 13506 2.625790 AGGTCAGCGGAATCAGATAGAC 59.374 50.000 0.00 0.00 0.00 2.59
3478 13541 9.307121 CAGAAAGATAGATAAGTACCACAAGTG 57.693 37.037 0.00 0.00 0.00 3.16
3479 13542 9.256228 AGAAAGATAGATAAGTACCACAAGTGA 57.744 33.333 0.94 0.00 0.00 3.41
3485 13548 0.035458 AGTACCACAAGTGAGCAGCC 59.965 55.000 0.94 0.00 0.00 4.85
3523 13586 9.956720 GTCATATTTGCAGAGTTTAATGCTATT 57.043 29.630 0.87 0.00 42.98 1.73
3553 13616 8.429641 AGTTAGACCTTGAAGTAAAGATGAACA 58.570 33.333 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 7 1.966451 GGAGGCCAACAACCGTCTG 60.966 63.158 5.01 0.00 0.00 3.51
31 4575 4.021925 GCCCCCGACTTGCTGACT 62.022 66.667 0.00 0.00 0.00 3.41
41 4585 4.804420 ATCTGGAGCTGCCCCCGA 62.804 66.667 1.53 0.00 34.97 5.14
176 4723 3.417275 CTCCTGTAGAGCCGTGCGG 62.417 68.421 6.22 6.22 35.31 5.69
247 4794 2.350899 TAATGGCGACGACGAAGAAA 57.649 45.000 12.29 0.00 42.66 2.52
263 4810 2.867472 GCACGCGGCAGTGTTAAT 59.133 55.556 12.47 0.00 43.61 1.40
375 4922 2.360191 CCATGGGTGGGACAAGGG 59.640 66.667 2.85 0.00 44.16 3.95
515 5083 2.089980 GACACCTACTTCTACGAGGCA 58.910 52.381 0.00 0.00 33.28 4.75
710 5278 2.110967 GTCGTCATCCTCGTCGGGA 61.111 63.158 0.00 0.00 39.95 5.14
719 5290 1.696832 GCAAGAAGCCGTCGTCATCC 61.697 60.000 0.00 0.00 37.23 3.51
720 5291 1.710339 GCAAGAAGCCGTCGTCATC 59.290 57.895 0.00 0.00 37.23 2.92
721 5292 2.094659 CGCAAGAAGCCGTCGTCAT 61.095 57.895 0.00 0.00 41.38 3.06
722 5293 2.733218 CGCAAGAAGCCGTCGTCA 60.733 61.111 0.00 0.00 41.38 4.35
729 5315 3.050275 ACCTTCGCGCAAGAAGCC 61.050 61.111 16.77 0.00 44.56 4.35
740 5326 0.810031 CCGGTATGGCTTCACCTTCG 60.810 60.000 0.00 0.00 40.22 3.79
763 5349 0.798776 CCGAAGCTGCAACCTGTAAG 59.201 55.000 1.02 0.00 0.00 2.34
766 5352 1.152963 AACCGAAGCTGCAACCTGT 60.153 52.632 1.02 0.00 0.00 4.00
769 5355 0.040067 CTTGAACCGAAGCTGCAACC 60.040 55.000 1.02 0.00 0.00 3.77
770 5356 0.661483 GCTTGAACCGAAGCTGCAAC 60.661 55.000 1.02 0.00 44.26 4.17
771 5357 1.654220 GCTTGAACCGAAGCTGCAA 59.346 52.632 1.02 0.00 44.26 4.08
774 5360 0.519077 GAAGGCTTGAACCGAAGCTG 59.481 55.000 3.46 0.00 46.43 4.24
777 5363 1.160137 CTGGAAGGCTTGAACCGAAG 58.840 55.000 3.46 0.00 33.69 3.79
791 5377 0.691078 ATAGCCGGCTTCTCCTGGAA 60.691 55.000 37.74 14.15 32.51 3.53
793 5379 0.250081 GAATAGCCGGCTTCTCCTGG 60.250 60.000 37.74 0.00 0.00 4.45
795 5381 0.755698 TCGAATAGCCGGCTTCTCCT 60.756 55.000 37.74 14.81 0.00 3.69
796 5382 0.318762 ATCGAATAGCCGGCTTCTCC 59.681 55.000 37.74 19.78 0.00 3.71
797 5383 1.000163 TGATCGAATAGCCGGCTTCTC 60.000 52.381 37.74 28.03 0.00 2.87
798 5384 1.040646 TGATCGAATAGCCGGCTTCT 58.959 50.000 37.74 22.59 0.00 2.85
799 5385 1.865865 TTGATCGAATAGCCGGCTTC 58.134 50.000 37.74 26.01 0.00 3.86
800 5386 1.940613 GTTTGATCGAATAGCCGGCTT 59.059 47.619 37.74 19.37 0.00 4.35
801 5387 1.583054 GTTTGATCGAATAGCCGGCT 58.417 50.000 34.85 34.85 0.00 5.52
802 5388 0.232303 CGTTTGATCGAATAGCCGGC 59.768 55.000 21.89 21.89 0.00 6.13
803 5389 1.787155 CTCGTTTGATCGAATAGCCGG 59.213 52.381 0.00 0.00 39.34 6.13
804 5390 2.468040 GTCTCGTTTGATCGAATAGCCG 59.532 50.000 0.00 0.00 39.34 5.52
805 5391 3.444916 TGTCTCGTTTGATCGAATAGCC 58.555 45.455 0.00 0.00 39.34 3.93
806 5392 3.487574 CCTGTCTCGTTTGATCGAATAGC 59.512 47.826 0.00 0.00 39.34 2.97
807 5393 4.921547 TCCTGTCTCGTTTGATCGAATAG 58.078 43.478 0.00 0.59 39.34 1.73
808 5394 4.638865 TCTCCTGTCTCGTTTGATCGAATA 59.361 41.667 0.00 0.00 39.34 1.75
809 5395 3.444034 TCTCCTGTCTCGTTTGATCGAAT 59.556 43.478 0.00 0.00 39.34 3.34
810 5396 2.817844 TCTCCTGTCTCGTTTGATCGAA 59.182 45.455 0.00 0.00 39.34 3.71
811 5397 2.433436 TCTCCTGTCTCGTTTGATCGA 58.567 47.619 0.00 0.00 38.19 3.59
812 5398 2.921634 TCTCCTGTCTCGTTTGATCG 57.078 50.000 0.00 0.00 0.00 3.69
813 5399 3.065510 TCGATCTCCTGTCTCGTTTGATC 59.934 47.826 0.00 0.00 34.19 2.92
814 5400 3.017442 TCGATCTCCTGTCTCGTTTGAT 58.983 45.455 0.00 0.00 34.19 2.57
815 5401 2.433436 TCGATCTCCTGTCTCGTTTGA 58.567 47.619 0.00 0.00 34.19 2.69
816 5402 2.921634 TCGATCTCCTGTCTCGTTTG 57.078 50.000 0.00 0.00 34.19 2.93
817 5403 2.359531 GGATCGATCTCCTGTCTCGTTT 59.640 50.000 23.96 0.00 34.19 3.60
818 5404 1.950909 GGATCGATCTCCTGTCTCGTT 59.049 52.381 23.96 0.00 34.19 3.85
819 5405 1.600023 GGATCGATCTCCTGTCTCGT 58.400 55.000 23.96 0.00 34.19 4.18
820 5406 0.515127 CGGATCGATCTCCTGTCTCG 59.485 60.000 23.96 12.80 32.77 4.04
821 5407 1.885560 TCGGATCGATCTCCTGTCTC 58.114 55.000 23.96 4.81 32.77 3.36
822 5408 2.226330 CTTCGGATCGATCTCCTGTCT 58.774 52.381 23.96 0.00 35.23 3.41
823 5409 1.950909 ACTTCGGATCGATCTCCTGTC 59.049 52.381 23.96 6.22 35.23 3.51
824 5410 2.060050 ACTTCGGATCGATCTCCTGT 57.940 50.000 23.96 14.95 35.23 4.00
825 5411 2.095466 GCTACTTCGGATCGATCTCCTG 60.095 54.545 23.96 14.38 35.23 3.86
843 5429 9.658799 GAAATCCTTGATATATTGCTAGTGCTA 57.341 33.333 0.00 0.00 40.48 3.49
844 5430 7.609532 GGAAATCCTTGATATATTGCTAGTGCT 59.390 37.037 0.00 0.00 40.48 4.40
846 5432 7.065085 CCGGAAATCCTTGATATATTGCTAGTG 59.935 40.741 0.00 0.00 0.00 2.74
847 5433 7.106239 CCGGAAATCCTTGATATATTGCTAGT 58.894 38.462 0.00 0.00 0.00 2.57
848 5434 6.037610 GCCGGAAATCCTTGATATATTGCTAG 59.962 42.308 5.05 0.00 0.00 3.42
849 5435 5.880332 GCCGGAAATCCTTGATATATTGCTA 59.120 40.000 5.05 0.00 0.00 3.49
872 5468 4.065238 GAGACTCTCTCGTTGCGC 57.935 61.111 0.00 0.00 33.35 6.09
895 5491 1.366111 CCACCACCGCCTATGAAACG 61.366 60.000 0.00 0.00 0.00 3.60
920 5516 1.289109 CCGTTAGGAACACGCTGGTG 61.289 60.000 0.00 0.00 44.80 4.17
921 5517 1.005394 CCGTTAGGAACACGCTGGT 60.005 57.895 0.00 0.00 41.02 4.00
922 5518 1.290955 TCCGTTAGGAACACGCTGG 59.709 57.895 0.00 0.00 45.12 4.85
923 5519 4.979204 TCCGTTAGGAACACGCTG 57.021 55.556 0.00 0.00 45.12 5.18
941 5572 2.766313 TCCACCGACTCTGTTTTGATG 58.234 47.619 0.00 0.00 0.00 3.07
945 5576 4.223032 ACAGATATCCACCGACTCTGTTTT 59.777 41.667 0.00 0.00 39.56 2.43
971 5602 0.097150 GGAAATTTGAGTCGGCGCTC 59.903 55.000 19.62 19.62 36.12 5.03
972 5603 0.321653 AGGAAATTTGAGTCGGCGCT 60.322 50.000 7.64 2.04 0.00 5.92
973 5604 0.097150 GAGGAAATTTGAGTCGGCGC 59.903 55.000 0.00 0.00 0.00 6.53
974 5605 0.370273 CGAGGAAATTTGAGTCGGCG 59.630 55.000 0.00 0.00 0.00 6.46
975 5606 1.393883 GACGAGGAAATTTGAGTCGGC 59.606 52.381 14.52 9.79 34.94 5.54
976 5607 2.683968 TGACGAGGAAATTTGAGTCGG 58.316 47.619 14.52 2.09 34.94 4.79
977 5608 4.725556 TTTGACGAGGAAATTTGAGTCG 57.274 40.909 0.00 3.70 36.71 4.18
978 5609 6.148811 TGGTATTTGACGAGGAAATTTGAGTC 59.851 38.462 0.00 0.49 0.00 3.36
1033 5664 0.713883 CGATGCGTACGTGCTTCTTT 59.286 50.000 17.90 0.00 37.01 2.52
1377 6149 4.329545 GCAGGTCTTGTGGCGGGA 62.330 66.667 0.00 0.00 0.00 5.14
1387 6161 2.279069 CCACTGGTCGAGCAGGTCT 61.279 63.158 38.90 21.96 0.00 3.85
1565 6352 2.664851 CGTGCTGCACCCGAAGAA 60.665 61.111 25.61 0.00 0.00 2.52
1759 6560 1.133982 GCGCTCTTCACTGAGATCTCA 59.866 52.381 23.75 23.75 36.23 3.27
1768 6569 1.502163 GCAAGTGTGCGCTCTTCACT 61.502 55.000 9.73 14.66 41.93 3.41
1780 6581 1.227853 GGTGAACCTCCGCAAGTGT 60.228 57.895 0.00 0.00 0.00 3.55
1784 6585 0.327924 ATCATGGTGAACCTCCGCAA 59.672 50.000 0.37 0.00 36.82 4.85
1850 6651 2.226437 CGCCTTTGTAGTGCAGTGATTT 59.774 45.455 3.69 0.00 0.00 2.17
1852 6653 1.442769 CGCCTTTGTAGTGCAGTGAT 58.557 50.000 3.69 0.00 0.00 3.06
1933 6740 4.163427 TGGAGAGGTCTTCACAGATTTCT 58.837 43.478 0.00 0.00 30.96 2.52
2254 11851 0.591659 CACCGTCGTCTTCAGTCTCA 59.408 55.000 0.00 0.00 0.00 3.27
2306 11906 4.575885 ACGTACATCTGCCACAAACTATT 58.424 39.130 0.00 0.00 0.00 1.73
2383 11986 4.814234 TGTGCAAGTATTCTTTCGAGTTGT 59.186 37.500 0.00 0.00 0.00 3.32
2491 12389 0.833287 TCCAGGATCTTAGCAGCCAC 59.167 55.000 0.00 0.00 0.00 5.01
2540 12439 6.607735 ACTTTTGTTGCCTTCAATTCAATG 57.392 33.333 0.00 0.00 34.29 2.82
2608 12508 7.775053 TCCTTGTGCTACCAAAAGAAATAAT 57.225 32.000 0.00 0.00 38.36 1.28
2714 12617 6.890268 TCAGCTCCTATACTTTCAACTACAGA 59.110 38.462 0.00 0.00 0.00 3.41
2763 12694 9.678260 GGAGAAATATTCAAGCATGATACCTAT 57.322 33.333 0.00 0.00 34.96 2.57
2765 12696 7.664731 CAGGAGAAATATTCAAGCATGATACCT 59.335 37.037 0.00 0.00 34.96 3.08
2766 12697 7.446625 ACAGGAGAAATATTCAAGCATGATACC 59.553 37.037 0.00 0.00 34.96 2.73
2767 12698 8.388484 ACAGGAGAAATATTCAAGCATGATAC 57.612 34.615 0.00 0.00 34.96 2.24
2768 12699 8.985315 AACAGGAGAAATATTCAAGCATGATA 57.015 30.769 0.00 0.00 34.96 2.15
2769 12700 7.893124 AACAGGAGAAATATTCAAGCATGAT 57.107 32.000 0.00 0.00 34.96 2.45
2770 12701 8.677300 GTTAACAGGAGAAATATTCAAGCATGA 58.323 33.333 0.00 0.00 0.00 3.07
2771 12702 8.680903 AGTTAACAGGAGAAATATTCAAGCATG 58.319 33.333 8.61 0.00 0.00 4.06
2772 12703 8.814038 AGTTAACAGGAGAAATATTCAAGCAT 57.186 30.769 8.61 0.00 0.00 3.79
2773 12704 8.103305 AGAGTTAACAGGAGAAATATTCAAGCA 58.897 33.333 8.61 0.00 0.00 3.91
2774 12705 8.499403 AGAGTTAACAGGAGAAATATTCAAGC 57.501 34.615 8.61 0.00 0.00 4.01
2783 12714 9.901172 AAAAGAAAGTAGAGTTAACAGGAGAAA 57.099 29.630 8.61 0.00 0.00 2.52
2784 12715 9.901172 AAAAAGAAAGTAGAGTTAACAGGAGAA 57.099 29.630 8.61 0.00 0.00 2.87
2807 12738 6.557568 AGTTGGGTTCCCATGATACTAAAAA 58.442 36.000 11.65 0.00 35.84 1.94
2808 12739 6.147437 AGTTGGGTTCCCATGATACTAAAA 57.853 37.500 11.65 0.00 35.84 1.52
2809 12740 5.789574 AGTTGGGTTCCCATGATACTAAA 57.210 39.130 11.65 0.00 35.84 1.85
2810 12741 6.894735 TTAGTTGGGTTCCCATGATACTAA 57.105 37.500 20.21 20.21 35.28 2.24
2811 12742 7.287061 CAATTAGTTGGGTTCCCATGATACTA 58.713 38.462 11.65 12.57 35.84 1.82
2812 12743 5.994416 ATTAGTTGGGTTCCCATGATACT 57.006 39.130 11.65 13.50 35.84 2.12
2813 12744 6.391227 CAATTAGTTGGGTTCCCATGATAC 57.609 41.667 11.65 6.84 35.84 2.24
2827 12758 7.283127 ACATCCAACTATAGTGCCAATTAGTTG 59.717 37.037 6.06 14.57 42.13 3.16
2828 12759 7.346471 ACATCCAACTATAGTGCCAATTAGTT 58.654 34.615 6.06 0.00 0.00 2.24
2829 12760 6.900194 ACATCCAACTATAGTGCCAATTAGT 58.100 36.000 6.06 0.00 0.00 2.24
2830 12761 7.931407 TGTACATCCAACTATAGTGCCAATTAG 59.069 37.037 6.06 0.00 0.00 1.73
2831 12762 7.797062 TGTACATCCAACTATAGTGCCAATTA 58.203 34.615 6.06 0.00 0.00 1.40
2832 12763 6.658849 TGTACATCCAACTATAGTGCCAATT 58.341 36.000 6.06 0.00 0.00 2.32
2833 12764 6.247229 TGTACATCCAACTATAGTGCCAAT 57.753 37.500 6.06 0.00 0.00 3.16
2834 12765 5.396324 CCTGTACATCCAACTATAGTGCCAA 60.396 44.000 6.06 0.00 0.00 4.52
2835 12766 4.100963 CCTGTACATCCAACTATAGTGCCA 59.899 45.833 6.06 0.00 0.00 4.92
2836 12767 4.344102 TCCTGTACATCCAACTATAGTGCC 59.656 45.833 6.06 0.00 0.00 5.01
2837 12768 5.531122 TCCTGTACATCCAACTATAGTGC 57.469 43.478 6.06 0.00 0.00 4.40
2838 12769 7.231519 TCAGATCCTGTACATCCAACTATAGTG 59.768 40.741 6.06 0.94 32.61 2.74
2839 12770 7.298374 TCAGATCCTGTACATCCAACTATAGT 58.702 38.462 0.00 0.00 32.61 2.12
2840 12771 7.767250 TCAGATCCTGTACATCCAACTATAG 57.233 40.000 0.00 0.00 32.61 1.31
2841 12772 9.822727 TTATCAGATCCTGTACATCCAACTATA 57.177 33.333 0.00 0.00 32.61 1.31
2842 12773 8.589338 GTTATCAGATCCTGTACATCCAACTAT 58.411 37.037 0.00 0.00 32.61 2.12
2843 12774 7.785028 AGTTATCAGATCCTGTACATCCAACTA 59.215 37.037 0.00 0.00 32.61 2.24
2844 12775 6.613271 AGTTATCAGATCCTGTACATCCAACT 59.387 38.462 0.00 0.00 32.61 3.16
2845 12776 6.821388 AGTTATCAGATCCTGTACATCCAAC 58.179 40.000 0.00 0.00 32.61 3.77
2846 12777 6.042093 GGAGTTATCAGATCCTGTACATCCAA 59.958 42.308 0.00 0.00 32.61 3.53
2847 12778 5.540337 GGAGTTATCAGATCCTGTACATCCA 59.460 44.000 0.00 0.00 32.61 3.41
2848 12779 5.540337 TGGAGTTATCAGATCCTGTACATCC 59.460 44.000 0.00 0.00 34.04 3.51
2849 12780 6.656632 TGGAGTTATCAGATCCTGTACATC 57.343 41.667 0.00 0.00 34.04 3.06
2850 12781 7.952930 ACTATGGAGTTATCAGATCCTGTACAT 59.047 37.037 0.00 0.00 34.04 2.29
2851 12782 7.298374 ACTATGGAGTTATCAGATCCTGTACA 58.702 38.462 0.00 0.00 34.04 2.90
2852 12783 7.361371 CGACTATGGAGTTATCAGATCCTGTAC 60.361 44.444 0.00 0.00 35.45 2.90
2853 12784 6.655425 CGACTATGGAGTTATCAGATCCTGTA 59.345 42.308 0.00 0.00 35.45 2.74
2854 12785 5.475220 CGACTATGGAGTTATCAGATCCTGT 59.525 44.000 0.00 0.00 35.45 4.00
2855 12786 5.621104 GCGACTATGGAGTTATCAGATCCTG 60.621 48.000 0.00 0.00 35.45 3.86
2856 12787 4.461081 GCGACTATGGAGTTATCAGATCCT 59.539 45.833 0.00 0.00 35.45 3.24
2857 12788 4.218635 TGCGACTATGGAGTTATCAGATCC 59.781 45.833 0.00 0.00 35.45 3.36
2858 12789 5.182190 TCTGCGACTATGGAGTTATCAGATC 59.818 44.000 0.00 0.00 35.45 2.75
2859 12790 5.073428 TCTGCGACTATGGAGTTATCAGAT 58.927 41.667 0.00 0.00 35.45 2.90
2860 12791 4.461198 TCTGCGACTATGGAGTTATCAGA 58.539 43.478 0.00 0.00 35.45 3.27
2861 12792 4.837896 TCTGCGACTATGGAGTTATCAG 57.162 45.455 0.00 0.00 35.45 2.90
2862 12793 4.038042 CCTTCTGCGACTATGGAGTTATCA 59.962 45.833 0.00 0.00 35.45 2.15
2863 12794 4.551388 CCTTCTGCGACTATGGAGTTATC 58.449 47.826 0.00 0.00 35.45 1.75
2864 12795 3.243907 GCCTTCTGCGACTATGGAGTTAT 60.244 47.826 0.00 0.00 35.45 1.89
2872 12803 6.058183 AGAATTTTATGCCTTCTGCGACTAT 58.942 36.000 0.00 0.00 45.60 2.12
2877 12808 5.741388 ACTAGAATTTTATGCCTTCTGCG 57.259 39.130 0.00 0.00 45.60 5.18
2922 12853 6.925718 TGTCAGATGCAAACTATCAGCTATAC 59.074 38.462 0.00 0.00 0.00 1.47
2925 12856 5.343307 TGTCAGATGCAAACTATCAGCTA 57.657 39.130 0.00 0.00 0.00 3.32
2935 12866 4.391830 GTCGATAACCTTGTCAGATGCAAA 59.608 41.667 0.00 0.00 0.00 3.68
2981 12916 9.618890 ACTATCATTGCAACTCATGTATAAACT 57.381 29.630 0.00 0.00 0.00 2.66
2986 12921 8.962884 TGTTACTATCATTGCAACTCATGTAT 57.037 30.769 0.00 0.00 0.00 2.29
3015 12950 8.041143 ACCCAGCTTAATAATACCATAGACAA 57.959 34.615 0.00 0.00 0.00 3.18
3024 12959 5.362263 TCGTCCAACCCAGCTTAATAATAC 58.638 41.667 0.00 0.00 0.00 1.89
3038 12973 5.697633 TGATAAGTAGTTTGTTCGTCCAACC 59.302 40.000 0.00 0.00 33.51 3.77
3045 12980 5.062308 GTCTGCCTGATAAGTAGTTTGTTCG 59.938 44.000 0.00 0.00 0.00 3.95
3061 12996 2.941333 CGCTGTGTTGTCTGCCTG 59.059 61.111 0.00 0.00 0.00 4.85
3076 13011 0.747255 TCTTCATGACCTCTAGGCGC 59.253 55.000 0.00 0.00 39.32 6.53
3077 13012 2.428890 ACTTCTTCATGACCTCTAGGCG 59.571 50.000 0.00 0.00 39.32 5.52
3078 13013 4.438148 GAACTTCTTCATGACCTCTAGGC 58.562 47.826 0.00 0.00 39.32 3.93
3083 13018 5.582665 GTGTATGGAACTTCTTCATGACCTC 59.417 44.000 0.00 0.00 0.00 3.85
3086 13021 6.801539 TTGTGTATGGAACTTCTTCATGAC 57.198 37.500 0.00 0.00 0.00 3.06
3091 13026 7.226720 TCTGTTCTTTGTGTATGGAACTTCTTC 59.773 37.037 0.00 0.00 38.86 2.87
3147 13118 5.127031 TCAAGCAGCTTAACCTCAAGTTTTT 59.873 36.000 7.52 0.00 40.05 1.94
3148 13119 4.644685 TCAAGCAGCTTAACCTCAAGTTTT 59.355 37.500 7.52 0.00 40.05 2.43
3149 13120 4.207165 TCAAGCAGCTTAACCTCAAGTTT 58.793 39.130 7.52 0.00 40.05 2.66
3150 13121 3.820557 TCAAGCAGCTTAACCTCAAGTT 58.179 40.909 7.52 0.00 42.83 2.66
3151 13122 3.492102 TCAAGCAGCTTAACCTCAAGT 57.508 42.857 7.52 0.00 0.00 3.16
3152 13123 4.836125 TTTCAAGCAGCTTAACCTCAAG 57.164 40.909 7.52 0.00 0.00 3.02
3153 13124 4.644685 ACTTTTCAAGCAGCTTAACCTCAA 59.355 37.500 7.52 0.00 0.00 3.02
3154 13125 4.207165 ACTTTTCAAGCAGCTTAACCTCA 58.793 39.130 7.52 0.00 0.00 3.86
3155 13126 4.837896 ACTTTTCAAGCAGCTTAACCTC 57.162 40.909 7.52 0.00 0.00 3.85
3158 13129 4.740205 GTGGAACTTTTCAAGCAGCTTAAC 59.260 41.667 7.52 0.00 0.00 2.01
3187 13158 3.511934 AGATCTGCCGGTATTGTATCTCC 59.488 47.826 1.90 0.00 0.00 3.71
3205 13184 7.711846 TGAGTAGCTTGAGTTTCTCATAGATC 58.288 38.462 0.00 0.00 40.39 2.75
3206 13185 7.652524 TGAGTAGCTTGAGTTTCTCATAGAT 57.347 36.000 0.00 3.56 40.39 1.98
3258 13243 5.594926 AGCTAATTTTGCATGCTGTATTCC 58.405 37.500 20.33 9.53 32.32 3.01
3302 13334 7.227355 TGGGGGATTTGTTTATCCTTATGTA 57.773 36.000 0.00 0.00 43.08 2.29
3304 13336 5.011023 GCTGGGGGATTTGTTTATCCTTATG 59.989 44.000 0.00 0.00 43.08 1.90
3305 13337 5.147767 GCTGGGGGATTTGTTTATCCTTAT 58.852 41.667 0.00 0.00 43.08 1.73
3306 13338 4.017037 TGCTGGGGGATTTGTTTATCCTTA 60.017 41.667 0.00 0.00 43.08 2.69
3307 13339 3.245948 TGCTGGGGGATTTGTTTATCCTT 60.246 43.478 0.00 0.00 43.08 3.36
3309 13341 2.745968 TGCTGGGGGATTTGTTTATCC 58.254 47.619 0.00 0.00 42.84 2.59
3310 13342 4.696455 CATTGCTGGGGGATTTGTTTATC 58.304 43.478 0.00 0.00 0.00 1.75
3312 13344 2.235898 GCATTGCTGGGGGATTTGTTTA 59.764 45.455 0.16 0.00 0.00 2.01
3313 13345 1.003464 GCATTGCTGGGGGATTTGTTT 59.997 47.619 0.16 0.00 0.00 2.83
3315 13347 0.544833 TGCATTGCTGGGGGATTTGT 60.545 50.000 10.49 0.00 0.00 2.83
3316 13348 0.177141 CTGCATTGCTGGGGGATTTG 59.823 55.000 10.49 0.00 0.00 2.32
3388 13421 0.169672 CTTTCAGTCTTGCCATGCGG 59.830 55.000 0.00 0.00 0.00 5.69
3390 13423 1.471684 CCTCTTTCAGTCTTGCCATGC 59.528 52.381 0.00 0.00 0.00 4.06
3395 13428 4.261363 CCTCAAAACCTCTTTCAGTCTTGC 60.261 45.833 0.00 0.00 0.00 4.01
3407 13444 3.274288 CTGACCTATGCCTCAAAACCTC 58.726 50.000 0.00 0.00 0.00 3.85
3409 13446 1.745653 GCTGACCTATGCCTCAAAACC 59.254 52.381 0.00 0.00 0.00 3.27
3411 13448 1.678728 CCGCTGACCTATGCCTCAAAA 60.679 52.381 0.00 0.00 0.00 2.44
3457 13520 6.607600 TGCTCACTTGTGGTACTTATCTATCT 59.392 38.462 0.64 0.00 0.00 1.98
3478 13541 3.660621 AGCTTCAAACGGCTGCTC 58.339 55.556 0.00 0.00 37.41 4.26
3485 13548 3.853671 GCAAATATGACCAGCTTCAAACG 59.146 43.478 0.00 0.00 0.00 3.60
3523 13586 9.273016 CATCTTTACTTCAAGGTCTAACTTTCA 57.727 33.333 0.00 0.00 0.00 2.69
3526 13589 9.274206 GTTCATCTTTACTTCAAGGTCTAACTT 57.726 33.333 0.00 0.00 0.00 2.66
3553 13616 4.751767 TCTTTTTGTTTGCAGGGTCATT 57.248 36.364 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.