Multiple sequence alignment - TraesCS6B01G207100

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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 TraesCS6B01G207100 chr6B 100.000 5574 0 0 1 5574 261526560 261532133 0.000000e+00 10294
1 TraesCS6B01G207100 chr6B 90.461 608 51 6 4970 5574 576441137 576440534 0.000000e+00 795
2 TraesCS6B01G207100 chr6D 95.777 2652 76 21 2216 4846 148766277 148768913 0.000000e+00 4244
3 TraesCS6B01G207100 chr6D 91.446 1286 41 28 632 1905 148764798 148766026 0.000000e+00 1701
4 TraesCS6B01G207100 chr6D 94.318 264 12 1 1940 2200 148766028 148766291 8.700000e-108 401
5 TraesCS6B01G207100 chr6A 95.929 2407 66 14 2216 4609 198366669 198364282 0.000000e+00 3873
6 TraesCS6B01G207100 chr6A 93.032 775 23 9 703 1458 198368006 198367244 0.000000e+00 1103
7 TraesCS6B01G207100 chr6A 94.062 320 15 2 1586 1905 198367235 198366920 3.020000e-132 483
8 TraesCS6B01G207100 chr6A 94.697 264 11 1 1940 2200 198366918 198366655 1.870000e-109 407
9 TraesCS6B01G207100 chr6A 86.319 307 13 9 4526 4824 198364286 198364001 1.950000e-79 307
10 TraesCS6B01G207100 chr6A 89.583 144 2 3 1341 1474 9429244 9429104 2.670000e-38 171
11 TraesCS6B01G207100 chr4B 98.203 612 10 1 1 611 627179701 627179090 0.000000e+00 1068
12 TraesCS6B01G207100 chr4B 97.561 615 13 2 1 614 627181069 627180456 0.000000e+00 1051
13 TraesCS6B01G207100 chr3A 98.039 612 10 2 1 611 468614060 468614670 0.000000e+00 1062
14 TraesCS6B01G207100 chr3B 97.709 611 12 2 1 611 764538469 764539077 0.000000e+00 1050
15 TraesCS6B01G207100 chr3B 94.281 612 11 3 1 611 694163248 694162660 0.000000e+00 915
16 TraesCS6B01G207100 chr3B 98.677 378 4 1 1 377 777835659 777836036 0.000000e+00 669
17 TraesCS6B01G207100 chr3B 80.861 209 25 11 346 543 797133405 797133609 3.480000e-32 150
18 TraesCS6B01G207100 chr3B 98.462 65 0 1 552 616 777836437 777836500 4.560000e-21 113
19 TraesCS6B01G207100 chr5B 97.377 610 15 1 1 610 273858415 273859023 0.000000e+00 1037
20 TraesCS6B01G207100 chr5B 97.674 215 5 0 397 611 6859666 6859452 2.450000e-98 370
21 TraesCS6B01G207100 chr7B 96.078 612 14 3 1 610 706852263 706851660 0.000000e+00 989
22 TraesCS6B01G207100 chr7B 85.253 217 15 10 1001 1201 468854435 468854220 2.040000e-49 207
23 TraesCS6B01G207100 chr4D 89.718 603 53 6 4976 5574 108830270 108830867 0.000000e+00 761
24 TraesCS6B01G207100 chr3D 95.751 353 14 1 1 352 325975459 325975107 8.100000e-158 568
25 TraesCS6B01G207100 chr3D 81.731 208 22 9 346 543 594155249 594155450 5.780000e-35 159
26 TraesCS6B01G207100 chr7A 81.240 629 89 21 2558 3167 545949185 545949803 1.090000e-131 481
27 TraesCS6B01G207100 chr7A 80.000 305 50 10 3515 3817 545950112 545950407 1.220000e-51 215
28 TraesCS6B01G207100 chr7A 84.332 217 17 10 1001 1201 545947896 545948111 4.410000e-46 196
29 TraesCS6B01G207100 chr7D 84.793 217 16 10 1001 1201 451051619 451051404 9.470000e-48 202


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 TraesCS6B01G207100 chr6B 261526560 261532133 5573 False 10294.000000 10294 100.000000 1 5574 1 chr6B.!!$F1 5573
1 TraesCS6B01G207100 chr6B 576440534 576441137 603 True 795.000000 795 90.461000 4970 5574 1 chr6B.!!$R1 604
2 TraesCS6B01G207100 chr6D 148764798 148768913 4115 False 2115.333333 4244 93.847000 632 4846 3 chr6D.!!$F1 4214
3 TraesCS6B01G207100 chr6A 198364001 198368006 4005 True 1234.600000 3873 92.807800 703 4824 5 chr6A.!!$R2 4121
4 TraesCS6B01G207100 chr4B 627179090 627181069 1979 True 1059.500000 1068 97.882000 1 614 2 chr4B.!!$R1 613
5 TraesCS6B01G207100 chr3A 468614060 468614670 610 False 1062.000000 1062 98.039000 1 611 1 chr3A.!!$F1 610
6 TraesCS6B01G207100 chr3B 764538469 764539077 608 False 1050.000000 1050 97.709000 1 611 1 chr3B.!!$F1 610
7 TraesCS6B01G207100 chr3B 694162660 694163248 588 True 915.000000 915 94.281000 1 611 1 chr3B.!!$R1 610
8 TraesCS6B01G207100 chr3B 777835659 777836500 841 False 391.000000 669 98.569500 1 616 2 chr3B.!!$F3 615
9 TraesCS6B01G207100 chr5B 273858415 273859023 608 False 1037.000000 1037 97.377000 1 610 1 chr5B.!!$F1 609
10 TraesCS6B01G207100 chr7B 706851660 706852263 603 True 989.000000 989 96.078000 1 610 1 chr7B.!!$R2 609
11 TraesCS6B01G207100 chr4D 108830270 108830867 597 False 761.000000 761 89.718000 4976 5574 1 chr4D.!!$F1 598
12 TraesCS6B01G207100 chr7A 545947896 545950407 2511 False 297.333333 481 81.857333 1001 3817 3 chr7A.!!$F1 2816

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
472 1844 0.035458 CTTCCATGATAGCCGGGGAC 59.965 60.0 2.18 0.00 0.00 4.46 F
1303 2934 0.822164 GAACCCTAGCTTGCTCCGTA 59.178 55.0 0.00 0.00 0.00 4.02 F
2157 3801 0.475632 AGGTGGTGAAGGTCATGGGA 60.476 55.0 0.00 0.00 0.00 4.37 F
2423 4295 2.093235 GGCTGTTAGTCTGCTGGAGATT 60.093 50.0 1.19 0.15 40.19 2.40 F
4004 5947 0.323957 TGCTGAGAAGCATGCTCACT 59.676 50.0 22.93 22.22 45.93 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2010 3651 1.465354 GCTCATGCAAAGAAGCGTCAG 60.465 52.381 1.61 0.0 39.41 3.51 R
2362 4234 1.478510 AGCCTATCACTGTTCCTCACG 59.521 52.381 0.00 0.0 0.00 4.35 R
3509 5450 0.178995 TTGCCATCAGAACCTGCACA 60.179 50.000 0.00 0.0 0.00 4.57 R
4134 6077 0.179045 CCAACTATTCAGGCCCTCGG 60.179 60.000 0.00 0.0 0.00 4.63 R
5196 7229 0.111446 TTGTGGGGGCGAAGAATGAA 59.889 50.000 0.00 0.0 0.00 2.57 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
153 155 1.966493 GAAGCTTTTCGCCGCATCGA 61.966 55.000 0.00 0.00 40.39 3.59
244 246 3.965539 GAGCTCGTGTGCCATGGCT 62.966 63.158 35.53 14.60 42.51 4.75
348 1718 2.441410 ACGAGATGCAGTTGAGAGAGA 58.559 47.619 0.00 0.00 0.00 3.10
472 1844 0.035458 CTTCCATGATAGCCGGGGAC 59.965 60.000 2.18 0.00 0.00 4.46
611 2209 1.001181 CCGTCTCCAAACGTTTCCCTA 59.999 52.381 11.37 0.00 41.01 3.53
612 2210 2.354403 CCGTCTCCAAACGTTTCCCTAT 60.354 50.000 11.37 0.00 41.01 2.57
613 2211 3.119029 CCGTCTCCAAACGTTTCCCTATA 60.119 47.826 11.37 0.00 41.01 1.31
614 2212 4.110482 CGTCTCCAAACGTTTCCCTATAG 58.890 47.826 11.37 2.92 37.86 1.31
615 2213 4.142315 CGTCTCCAAACGTTTCCCTATAGA 60.142 45.833 11.37 5.17 37.86 1.98
616 2214 5.451520 CGTCTCCAAACGTTTCCCTATAGAT 60.452 44.000 11.37 0.00 37.86 1.98
617 2215 6.238842 CGTCTCCAAACGTTTCCCTATAGATA 60.239 42.308 11.37 0.00 37.86 1.98
618 2216 7.523380 CGTCTCCAAACGTTTCCCTATAGATAT 60.523 40.741 11.37 0.00 37.86 1.63
619 2217 8.800332 GTCTCCAAACGTTTCCCTATAGATATA 58.200 37.037 11.37 0.00 0.00 0.86
620 2218 9.021807 TCTCCAAACGTTTCCCTATAGATATAG 57.978 37.037 11.37 0.62 36.32 1.31
621 2219 8.945195 TCCAAACGTTTCCCTATAGATATAGA 57.055 34.615 11.37 0.00 38.30 1.98
622 2220 9.543231 TCCAAACGTTTCCCTATAGATATAGAT 57.457 33.333 11.37 0.00 38.30 1.98
689 2287 8.779354 AGTTTCATAGTTTCAGGACTTATCAC 57.221 34.615 0.00 0.00 0.00 3.06
690 2288 7.545965 AGTTTCATAGTTTCAGGACTTATCACG 59.454 37.037 0.00 0.00 0.00 4.35
691 2289 6.525578 TCATAGTTTCAGGACTTATCACGT 57.474 37.500 0.00 0.00 0.00 4.49
692 2290 7.634671 TCATAGTTTCAGGACTTATCACGTA 57.365 36.000 0.00 0.00 0.00 3.57
693 2291 8.234136 TCATAGTTTCAGGACTTATCACGTAT 57.766 34.615 0.00 0.00 0.00 3.06
694 2292 8.692710 TCATAGTTTCAGGACTTATCACGTATT 58.307 33.333 0.00 0.00 0.00 1.89
695 2293 9.314321 CATAGTTTCAGGACTTATCACGTATTT 57.686 33.333 0.00 0.00 0.00 1.40
696 2294 7.596749 AGTTTCAGGACTTATCACGTATTTG 57.403 36.000 0.00 0.00 0.00 2.32
697 2295 7.383687 AGTTTCAGGACTTATCACGTATTTGA 58.616 34.615 0.00 0.00 0.00 2.69
698 2296 7.331193 AGTTTCAGGACTTATCACGTATTTGAC 59.669 37.037 0.00 0.00 0.00 3.18
699 2297 6.525578 TCAGGACTTATCACGTATTTGACT 57.474 37.500 0.00 0.00 0.00 3.41
700 2298 6.561614 TCAGGACTTATCACGTATTTGACTC 58.438 40.000 0.00 0.00 0.00 3.36
701 2299 6.152154 TCAGGACTTATCACGTATTTGACTCA 59.848 38.462 0.00 0.00 0.00 3.41
763 2361 2.637383 GGACTCGGCTCCGTTGTCT 61.637 63.158 23.72 2.95 40.51 3.41
770 2372 1.001597 CGGCTCCGTTGTCTATAGTCC 60.002 57.143 0.00 0.00 34.35 3.85
779 2381 4.857588 CGTTGTCTATAGTCCACACACTTC 59.142 45.833 0.00 0.00 0.00 3.01
828 2430 6.877322 CAGGAACCGACTATAAAGAAAGGAAA 59.123 38.462 0.00 0.00 0.00 3.13
862 2464 2.520458 CACCAGACCCAGCCCAAA 59.480 61.111 0.00 0.00 0.00 3.28
863 2465 1.604593 CACCAGACCCAGCCCAAAG 60.605 63.158 0.00 0.00 0.00 2.77
864 2466 2.084930 ACCAGACCCAGCCCAAAGT 61.085 57.895 0.00 0.00 0.00 2.66
986 2592 3.118775 AGCAGAAGAAACCAAACCAAACC 60.119 43.478 0.00 0.00 0.00 3.27
987 2593 3.792401 CAGAAGAAACCAAACCAAACCC 58.208 45.455 0.00 0.00 0.00 4.11
988 2594 2.769663 AGAAGAAACCAAACCAAACCCC 59.230 45.455 0.00 0.00 0.00 4.95
989 2595 2.255770 AGAAACCAAACCAAACCCCA 57.744 45.000 0.00 0.00 0.00 4.96
990 2596 2.115427 AGAAACCAAACCAAACCCCAG 58.885 47.619 0.00 0.00 0.00 4.45
1250 2871 1.550130 CCCCAAACCCTAGCGACAGA 61.550 60.000 0.00 0.00 0.00 3.41
1271 2901 5.007626 CAGAGACTTTTTCGTGAACCATTGA 59.992 40.000 0.00 0.00 0.00 2.57
1303 2934 0.822164 GAACCCTAGCTTGCTCCGTA 59.178 55.000 0.00 0.00 0.00 4.02
1386 3017 4.933330 TGTGCCGATATGTAGAACTTCTC 58.067 43.478 0.00 0.00 0.00 2.87
1494 3135 3.243168 GCGAATTGCTCATATTCTTGGCA 60.243 43.478 0.00 0.00 41.73 4.92
1518 3159 2.433838 CTCTGGGCTGACTGCGTG 60.434 66.667 0.00 0.00 44.05 5.34
1548 3189 2.433436 AGTGGTTTCCCGTATTTCTGC 58.567 47.619 0.00 0.00 0.00 4.26
1558 3199 6.801539 TCCCGTATTTCTGCAATGATATTC 57.198 37.500 0.00 0.00 0.00 1.75
1559 3200 5.408299 TCCCGTATTTCTGCAATGATATTCG 59.592 40.000 0.00 0.00 0.00 3.34
1563 3204 7.132213 CGTATTTCTGCAATGATATTCGGTTT 58.868 34.615 0.00 0.00 0.00 3.27
1565 3206 4.291540 TCTGCAATGATATTCGGTTTGC 57.708 40.909 0.00 0.00 42.23 3.68
1567 3208 4.652421 TGCAATGATATTCGGTTTGCAT 57.348 36.364 4.66 0.00 45.42 3.96
1571 3212 5.051508 GCAATGATATTCGGTTTGCATGAAC 60.052 40.000 0.00 0.00 41.67 3.18
1572 3213 4.630894 TGATATTCGGTTTGCATGAACC 57.369 40.909 9.86 9.86 44.51 3.62
1580 3221 3.993920 GGTTTGCATGAACCACAAAGAT 58.006 40.909 14.26 0.00 46.66 2.40
1650 3291 8.153550 TCTTCAATAGCTAGATTCTCCCAATTC 58.846 37.037 0.00 0.00 0.00 2.17
1855 3496 7.288852 ACTCTCAAGCATACATACTCTTGGTAT 59.711 37.037 0.00 0.00 41.38 2.73
1860 3501 8.501580 CAAGCATACATACTCTTGGTATCAATG 58.498 37.037 0.00 0.00 38.92 2.82
1905 3546 3.225104 ACAACTGGACTGTGCAATTGAT 58.775 40.909 26.04 10.58 0.00 2.57
1906 3547 3.638160 ACAACTGGACTGTGCAATTGATT 59.362 39.130 26.04 5.75 0.00 2.57
1907 3548 4.826733 ACAACTGGACTGTGCAATTGATTA 59.173 37.500 26.04 0.00 0.00 1.75
1908 3549 5.301551 ACAACTGGACTGTGCAATTGATTAA 59.698 36.000 26.04 0.00 0.00 1.40
1909 3550 6.183360 ACAACTGGACTGTGCAATTGATTAAA 60.183 34.615 26.04 0.00 0.00 1.52
1910 3551 5.772521 ACTGGACTGTGCAATTGATTAAAC 58.227 37.500 10.34 0.00 0.00 2.01
1911 3552 5.536161 ACTGGACTGTGCAATTGATTAAACT 59.464 36.000 10.34 0.00 0.00 2.66
1912 3553 6.714810 ACTGGACTGTGCAATTGATTAAACTA 59.285 34.615 10.34 0.00 0.00 2.24
1913 3554 7.394359 ACTGGACTGTGCAATTGATTAAACTAT 59.606 33.333 10.34 0.00 0.00 2.12
1914 3555 7.761409 TGGACTGTGCAATTGATTAAACTATC 58.239 34.615 10.34 1.71 0.00 2.08
1915 3556 7.611467 TGGACTGTGCAATTGATTAAACTATCT 59.389 33.333 10.34 0.00 0.00 1.98
1916 3557 8.462016 GGACTGTGCAATTGATTAAACTATCTT 58.538 33.333 10.34 0.00 0.00 2.40
1917 3558 9.846248 GACTGTGCAATTGATTAAACTATCTTT 57.154 29.630 10.34 0.00 0.00 2.52
1918 3559 9.846248 ACTGTGCAATTGATTAAACTATCTTTC 57.154 29.630 10.34 0.00 0.00 2.62
1920 3561 9.844790 TGTGCAATTGATTAAACTATCTTTCTG 57.155 29.630 10.34 0.00 0.00 3.02
1921 3562 9.846248 GTGCAATTGATTAAACTATCTTTCTGT 57.154 29.630 10.34 0.00 0.00 3.41
1927 3568 9.793259 TTGATTAAACTATCTTTCTGTTGTCCT 57.207 29.630 0.00 0.00 0.00 3.85
2010 3651 5.046231 ACTCTTCCTATCTTGGTTCAAGGAC 60.046 44.000 7.67 0.00 41.33 3.85
2013 3654 4.425772 TCCTATCTTGGTTCAAGGACTGA 58.574 43.478 7.67 0.00 41.33 3.41
2039 3683 5.220989 GCTTCTTTGCATGAGCTATTCATCA 60.221 40.000 0.00 0.00 44.76 3.07
2062 3706 3.009473 AGTGCTTCCTCTAAATTGGCTCA 59.991 43.478 0.00 0.00 0.00 4.26
2115 3759 3.131400 GGGAAGAGCTACAGTTACTCCAG 59.869 52.174 0.00 0.00 0.00 3.86
2157 3801 0.475632 AGGTGGTGAAGGTCATGGGA 60.476 55.000 0.00 0.00 0.00 4.37
2172 3816 5.012046 GGTCATGGGAAAATCAAAGGTTCTT 59.988 40.000 0.00 0.00 0.00 2.52
2203 3971 8.890718 AGGTAAATTATTTCTTCCTTTACTCGC 58.109 33.333 0.00 0.00 34.36 5.03
2207 3975 9.974980 AAATTATTTCTTCCTTTACTCGCAAAA 57.025 25.926 0.00 0.00 0.00 2.44
2208 3976 9.974980 AATTATTTCTTCCTTTACTCGCAAAAA 57.025 25.926 0.00 0.00 0.00 1.94
2240 4008 6.817765 TTTCTTCCTTTACACATTGCCTAG 57.182 37.500 0.00 0.00 0.00 3.02
2277 4045 8.786826 TTTATCTGTATGACAAAGGTACAAGG 57.213 34.615 0.00 0.00 0.00 3.61
2362 4234 5.238432 TGAACTCAAACATCACACATACACC 59.762 40.000 0.00 0.00 0.00 4.16
2423 4295 2.093235 GGCTGTTAGTCTGCTGGAGATT 60.093 50.000 1.19 0.15 40.19 2.40
2424 4296 3.604582 GCTGTTAGTCTGCTGGAGATTT 58.395 45.455 1.19 0.00 37.88 2.17
2502 4376 4.459089 GGTCTGGCCGTCTGCTCC 62.459 72.222 0.00 0.00 40.92 4.70
2525 4399 6.309494 TCCGAGTTATAATATTTTCGCCATCG 59.691 38.462 0.00 0.00 0.00 3.84
2788 4662 5.882557 GCAAATCAAGGAGATCAAAGAGGTA 59.117 40.000 0.00 0.00 35.39 3.08
2821 4695 3.516615 TCGATGCGTTGTCATTGTATCA 58.483 40.909 0.00 0.00 0.00 2.15
2828 4702 5.049129 TGCGTTGTCATTGTATCATGTTTGA 60.049 36.000 0.00 0.00 36.00 2.69
2935 4812 8.260114 CCAGCCAAAGGTTTGATTATTTAGAAT 58.740 33.333 3.95 0.00 40.55 2.40
3004 4887 2.689983 CACTCTTCTTTTGCAGGGTGTT 59.310 45.455 0.00 0.00 38.96 3.32
3509 5450 3.200605 TCATGATGCCCTGTATGTGTTCT 59.799 43.478 0.00 0.00 0.00 3.01
3757 5700 1.003580 AGGATGAACTTGATGCGTGGT 59.996 47.619 0.00 0.00 0.00 4.16
3897 5840 4.469657 TCAATTTGGGTCTGTTTAGTGCT 58.530 39.130 0.00 0.00 0.00 4.40
3898 5841 4.278170 TCAATTTGGGTCTGTTTAGTGCTG 59.722 41.667 0.00 0.00 0.00 4.41
3913 5856 7.608376 TGTTTAGTGCTGTTGCTTATATAACCA 59.392 33.333 0.00 0.00 40.48 3.67
4004 5947 0.323957 TGCTGAGAAGCATGCTCACT 59.676 50.000 22.93 22.22 45.93 3.41
4060 6003 3.887716 CCTGTTCATGAATGATCCCTTCC 59.112 47.826 12.12 0.00 36.56 3.46
4065 6008 2.174685 TGAATGATCCCTTCCGAGGA 57.825 50.000 0.00 0.00 46.74 3.71
4095 6038 5.534654 CCTAGTTCTTCTATGTAGCTCTGCT 59.465 44.000 0.00 0.00 43.41 4.24
4299 6243 6.973474 CAGAAGTAGTATGGTAAGACTTTCCG 59.027 42.308 6.40 0.00 30.66 4.30
4301 6245 3.160777 AGTATGGTAAGACTTTCCGCG 57.839 47.619 0.00 0.00 0.00 6.46
4468 6423 1.425428 CGGAATGTTTGCTCTCCGC 59.575 57.895 0.00 0.00 43.83 5.54
4640 6667 3.067106 ACGTTGCTGGACTTGTATTCTG 58.933 45.455 0.00 0.00 0.00 3.02
4707 6734 7.564128 CATGTGGTAGCATAATTAACTACGTG 58.436 38.462 16.70 12.77 37.70 4.49
4756 6784 2.828128 GCTACGCAATCTGCCTGCC 61.828 63.158 0.00 0.00 41.12 4.85
4763 6791 1.602311 CAATCTGCCTGCCTATGGTC 58.398 55.000 0.00 0.00 0.00 4.02
4791 6821 2.751259 TCTTACCACGTAGCAGTACCTG 59.249 50.000 0.00 0.00 34.12 4.00
4804 6834 2.626088 GTACCTGCGTACGAGTTTCT 57.374 50.000 21.65 0.00 35.81 2.52
4864 6894 7.519347 TTTACTCCCTCCATATTAGGTTTGT 57.481 36.000 1.16 0.46 31.70 2.83
4865 6895 5.632034 ACTCCCTCCATATTAGGTTTGTC 57.368 43.478 1.16 0.00 31.70 3.18
4866 6896 5.289510 ACTCCCTCCATATTAGGTTTGTCT 58.710 41.667 1.16 0.00 31.70 3.41
4867 6897 5.731678 ACTCCCTCCATATTAGGTTTGTCTT 59.268 40.000 1.16 0.00 31.70 3.01
4868 6898 6.001449 TCCCTCCATATTAGGTTTGTCTTG 57.999 41.667 1.16 0.00 31.70 3.02
4869 6899 5.729229 TCCCTCCATATTAGGTTTGTCTTGA 59.271 40.000 1.16 0.00 31.70 3.02
4870 6900 6.058183 CCCTCCATATTAGGTTTGTCTTGAG 58.942 44.000 1.16 0.00 31.70 3.02
4871 6901 6.353082 CCCTCCATATTAGGTTTGTCTTGAGT 60.353 42.308 1.16 0.00 31.70 3.41
4872 6902 6.763610 CCTCCATATTAGGTTTGTCTTGAGTC 59.236 42.308 0.00 0.00 0.00 3.36
4873 6903 7.252612 TCCATATTAGGTTTGTCTTGAGTCA 57.747 36.000 0.00 0.00 0.00 3.41
4874 6904 7.685481 TCCATATTAGGTTTGTCTTGAGTCAA 58.315 34.615 5.25 5.25 0.00 3.18
4875 6905 8.160765 TCCATATTAGGTTTGTCTTGAGTCAAA 58.839 33.333 7.06 0.38 32.37 2.69
4876 6906 8.237267 CCATATTAGGTTTGTCTTGAGTCAAAC 58.763 37.037 18.93 18.93 46.05 2.93
4884 6914 8.736751 GTTTGTCTTGAGTCAAACACTAAAAA 57.263 30.769 20.91 8.29 46.05 1.94
4885 6915 8.850452 GTTTGTCTTGAGTCAAACACTAAAAAG 58.150 33.333 20.91 0.00 46.05 2.27
4886 6916 7.681939 TGTCTTGAGTCAAACACTAAAAAGT 57.318 32.000 7.06 0.00 34.41 2.66
4887 6917 8.106247 TGTCTTGAGTCAAACACTAAAAAGTT 57.894 30.769 7.06 0.00 34.41 2.66
4888 6918 8.573035 TGTCTTGAGTCAAACACTAAAAAGTTT 58.427 29.630 7.06 0.00 38.40 2.66
4932 6962 8.497554 ACATTCACAATAAACATCAACATTTGC 58.502 29.630 0.00 0.00 0.00 3.68
4933 6963 8.496751 CATTCACAATAAACATCAACATTTGCA 58.503 29.630 0.00 0.00 0.00 4.08
4934 6964 8.429493 TTCACAATAAACATCAACATTTGCAA 57.571 26.923 0.00 0.00 0.00 4.08
4935 6965 8.429493 TCACAATAAACATCAACATTTGCAAA 57.571 26.923 15.44 15.44 0.00 3.68
4936 6966 8.549548 TCACAATAAACATCAACATTTGCAAAG 58.450 29.630 18.19 11.80 0.00 2.77
4937 6967 8.336806 CACAATAAACATCAACATTTGCAAAGT 58.663 29.630 18.19 12.41 0.00 2.66
4938 6968 8.891720 ACAATAAACATCAACATTTGCAAAGTT 58.108 25.926 18.19 17.10 0.00 2.66
4939 6969 9.719279 CAATAAACATCAACATTTGCAAAGTTT 57.281 25.926 18.19 19.50 0.00 2.66
4940 6970 9.719279 AATAAACATCAACATTTGCAAAGTTTG 57.281 25.926 23.12 22.32 0.00 2.93
4941 6971 5.738118 ACATCAACATTTGCAAAGTTTGG 57.262 34.783 24.61 16.61 0.00 3.28
4942 6972 5.426504 ACATCAACATTTGCAAAGTTTGGA 58.573 33.333 24.61 11.84 0.00 3.53
4943 6973 5.294060 ACATCAACATTTGCAAAGTTTGGAC 59.706 36.000 24.61 2.24 0.00 4.02
4944 6974 5.083533 TCAACATTTGCAAAGTTTGGACT 57.916 34.783 24.61 1.94 37.87 3.85
4946 6976 5.580297 TCAACATTTGCAAAGTTTGGACTTC 59.420 36.000 24.61 0.82 45.18 3.01
4947 6977 5.083533 ACATTTGCAAAGTTTGGACTTCA 57.916 34.783 18.19 3.47 45.18 3.02
4948 6978 5.111293 ACATTTGCAAAGTTTGGACTTCAG 58.889 37.500 18.19 5.45 45.18 3.02
4949 6979 5.105392 ACATTTGCAAAGTTTGGACTTCAGA 60.105 36.000 18.19 2.33 45.18 3.27
4950 6980 4.370364 TTGCAAAGTTTGGACTTCAGAC 57.630 40.909 17.11 0.00 45.18 3.51
4951 6981 3.351740 TGCAAAGTTTGGACTTCAGACA 58.648 40.909 17.11 0.69 45.18 3.41
4952 6982 3.761218 TGCAAAGTTTGGACTTCAGACAA 59.239 39.130 17.11 0.00 45.18 3.18
4953 6983 4.219507 TGCAAAGTTTGGACTTCAGACAAA 59.780 37.500 17.11 0.00 45.18 2.83
4954 6984 5.105392 TGCAAAGTTTGGACTTCAGACAAAT 60.105 36.000 17.11 0.00 45.18 2.32
4955 6985 5.460091 GCAAAGTTTGGACTTCAGACAAATC 59.540 40.000 17.11 0.00 45.18 2.17
4956 6986 6.681368 GCAAAGTTTGGACTTCAGACAAATCT 60.681 38.462 17.11 0.00 45.18 2.40
4957 6987 7.260603 CAAAGTTTGGACTTCAGACAAATCTT 58.739 34.615 7.78 0.00 45.18 2.40
4958 6988 7.410120 AAGTTTGGACTTCAGACAAATCTTT 57.590 32.000 0.00 0.00 42.35 2.52
4959 6989 7.410120 AGTTTGGACTTCAGACAAATCTTTT 57.590 32.000 0.00 0.00 36.60 2.27
4960 6990 8.519799 AGTTTGGACTTCAGACAAATCTTTTA 57.480 30.769 0.00 0.00 36.60 1.52
4961 6991 8.624776 AGTTTGGACTTCAGACAAATCTTTTAG 58.375 33.333 0.00 0.00 36.60 1.85
4962 6992 7.510549 TTGGACTTCAGACAAATCTTTTAGG 57.489 36.000 0.00 0.00 30.42 2.69
4963 6993 6.003950 TGGACTTCAGACAAATCTTTTAGGG 58.996 40.000 0.00 0.00 30.42 3.53
4964 6994 6.183361 TGGACTTCAGACAAATCTTTTAGGGA 60.183 38.462 0.00 0.00 30.42 4.20
4965 6995 6.715264 GGACTTCAGACAAATCTTTTAGGGAA 59.285 38.462 0.00 0.00 30.42 3.97
4966 6996 7.230712 GGACTTCAGACAAATCTTTTAGGGAAA 59.769 37.037 0.00 0.00 30.42 3.13
4967 6997 8.712228 ACTTCAGACAAATCTTTTAGGGAAAT 57.288 30.769 0.00 0.00 30.42 2.17
4968 6998 8.579863 ACTTCAGACAAATCTTTTAGGGAAATG 58.420 33.333 0.00 0.00 30.42 2.32
4988 7018 2.945398 TTTGAAAACAGCGCACCGGC 62.945 55.000 11.47 0.00 0.00 6.13
5024 7054 2.321060 CGCTTGCTTCATACCGCG 59.679 61.111 0.00 0.00 34.50 6.46
5025 7055 2.023320 GCTTGCTTCATACCGCGC 59.977 61.111 0.00 0.00 0.00 6.86
5101 7134 1.351017 TCTCCTCATCCAAACACACCC 59.649 52.381 0.00 0.00 0.00 4.61
5116 7149 2.347490 CCCGTGGACAACTCCTGG 59.653 66.667 0.00 0.00 37.48 4.45
5131 7164 1.687612 CTGGCCACACCTTCCTGAT 59.312 57.895 0.00 0.00 40.22 2.90
5163 7196 1.687612 CCATGGACACCTGCCTTCT 59.312 57.895 5.56 0.00 0.00 2.85
5168 7201 1.739562 GACACCTGCCTTCTGCTCG 60.740 63.158 0.00 0.00 42.00 5.03
5206 7239 1.421410 CGTCGCCCCTTCATTCTTCG 61.421 60.000 0.00 0.00 0.00 3.79
5212 7245 1.302949 CCTTCATTCTTCGCCCCCA 59.697 57.895 0.00 0.00 0.00 4.96
5228 7261 1.270252 CCCCACAAGTCCAACAATTGC 60.270 52.381 5.05 0.00 0.00 3.56
5244 7277 1.418097 TTGCTTCTCCACTGCCCTCA 61.418 55.000 0.00 0.00 0.00 3.86
5362 7396 1.003003 GCTTTCTCTCCTTCCTGCTGT 59.997 52.381 0.00 0.00 0.00 4.40
5372 7406 2.420687 CCTTCCTGCTGTAATCCTCCAC 60.421 54.545 0.00 0.00 0.00 4.02
5374 7408 0.824109 CCTGCTGTAATCCTCCACGA 59.176 55.000 0.00 0.00 0.00 4.35
5398 7432 1.133823 ACACAAGATTGAGCCCACACA 60.134 47.619 0.00 0.00 0.00 3.72
5447 7481 2.711185 GAACCGGTGTTTGCTGCGAC 62.711 60.000 8.52 0.00 33.97 5.19
5451 7485 2.186826 GGTGTTTGCTGCGACCTGT 61.187 57.895 0.00 0.00 0.00 4.00
5485 7519 1.210413 CGACCGGTGAGTGTCTCAG 59.790 63.158 14.63 0.00 41.46 3.35
5486 7520 1.587054 GACCGGTGAGTGTCTCAGG 59.413 63.158 14.63 2.25 41.46 3.86
5488 7522 0.111832 ACCGGTGAGTGTCTCAGGTA 59.888 55.000 6.12 0.00 41.46 3.08
5494 7528 0.601558 GAGTGTCTCAGGTACGGCAA 59.398 55.000 0.00 0.00 0.00 4.52
5547 7581 4.574421 GCTACCAGCAATGTTTTTGGTTTT 59.426 37.500 0.00 0.00 40.94 2.43
5553 7587 3.119352 GCAATGTTTTTGGTTTTGCCCAA 60.119 39.130 0.00 0.00 42.69 4.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
153 155 2.684881 CGGCATTCTGGAAAGCTACAAT 59.315 45.455 9.77 0.00 35.57 2.71
244 246 4.025858 GAGCTCACAGGCAGGGCA 62.026 66.667 9.40 0.00 34.17 5.36
348 1718 1.076632 CCCGAGCTAGTGTCCTCCT 60.077 63.158 0.00 0.00 0.00 3.69
472 1844 5.652452 CCTTTCCTAGTACTTTTTCCCCATG 59.348 44.000 0.00 0.00 0.00 3.66
626 2224 9.292195 GCCAATCTACCTATAGACCTATCTATC 57.708 40.741 0.00 0.00 43.51 2.08
628 2226 8.053963 GTGCCAATCTACCTATAGACCTATCTA 58.946 40.741 0.00 0.00 40.32 1.98
629 2227 6.893005 GTGCCAATCTACCTATAGACCTATCT 59.107 42.308 0.00 0.00 40.32 1.98
630 2228 6.663953 TGTGCCAATCTACCTATAGACCTATC 59.336 42.308 0.00 0.00 40.32 2.08
642 2240 2.489938 TGAAGGTGTGCCAATCTACC 57.510 50.000 0.00 0.00 37.19 3.18
643 2241 5.186198 ACTATTGAAGGTGTGCCAATCTAC 58.814 41.667 0.00 0.00 37.19 2.59
644 2242 5.435686 ACTATTGAAGGTGTGCCAATCTA 57.564 39.130 0.00 0.00 37.19 1.98
645 2243 4.307032 ACTATTGAAGGTGTGCCAATCT 57.693 40.909 0.00 0.00 37.19 2.40
646 2244 5.048083 TGAAACTATTGAAGGTGTGCCAATC 60.048 40.000 0.00 0.00 37.19 2.67
651 2249 6.743575 ACTATGAAACTATTGAAGGTGTGC 57.256 37.500 0.00 0.00 0.00 4.57
688 2286 9.620660 GGTAAAATCAAAATGAGTCAAATACGT 57.379 29.630 0.00 0.00 0.00 3.57
689 2287 8.785101 CGGTAAAATCAAAATGAGTCAAATACG 58.215 33.333 0.00 0.00 0.00 3.06
690 2288 8.583765 GCGGTAAAATCAAAATGAGTCAAATAC 58.416 33.333 0.00 0.00 0.00 1.89
691 2289 7.483375 CGCGGTAAAATCAAAATGAGTCAAATA 59.517 33.333 0.00 0.00 0.00 1.40
692 2290 6.307800 CGCGGTAAAATCAAAATGAGTCAAAT 59.692 34.615 0.00 0.00 0.00 2.32
693 2291 5.627367 CGCGGTAAAATCAAAATGAGTCAAA 59.373 36.000 0.00 0.00 0.00 2.69
694 2292 5.150683 CGCGGTAAAATCAAAATGAGTCAA 58.849 37.500 0.00 0.00 0.00 3.18
695 2293 4.214545 ACGCGGTAAAATCAAAATGAGTCA 59.785 37.500 12.47 0.00 0.00 3.41
696 2294 4.553429 CACGCGGTAAAATCAAAATGAGTC 59.447 41.667 12.47 0.00 0.00 3.36
697 2295 4.023536 ACACGCGGTAAAATCAAAATGAGT 60.024 37.500 12.47 0.00 0.00 3.41
698 2296 4.472286 ACACGCGGTAAAATCAAAATGAG 58.528 39.130 12.47 0.00 0.00 2.90
699 2297 4.491234 ACACGCGGTAAAATCAAAATGA 57.509 36.364 12.47 0.00 0.00 2.57
700 2298 5.282778 CAGTACACGCGGTAAAATCAAAATG 59.717 40.000 12.47 0.00 32.72 2.32
701 2299 5.179742 TCAGTACACGCGGTAAAATCAAAAT 59.820 36.000 12.47 0.00 32.72 1.82
763 2361 3.192001 GTCGGTGAAGTGTGTGGACTATA 59.808 47.826 0.00 0.00 0.00 1.31
770 2372 0.939577 CCGAGTCGGTGAAGTGTGTG 60.940 60.000 23.83 0.00 42.73 3.82
828 2430 4.899239 GCCGCTGGCTCGCTATGT 62.899 66.667 11.61 0.00 46.69 2.29
854 2456 1.118838 TTGTTTGGGACTTTGGGCTG 58.881 50.000 0.00 0.00 0.00 4.85
855 2457 1.119684 GTTGTTTGGGACTTTGGGCT 58.880 50.000 0.00 0.00 0.00 5.19
856 2458 0.105964 GGTTGTTTGGGACTTTGGGC 59.894 55.000 0.00 0.00 0.00 5.36
859 2461 2.100749 GAGTGGGTTGTTTGGGACTTTG 59.899 50.000 0.00 0.00 0.00 2.77
860 2462 2.384828 GAGTGGGTTGTTTGGGACTTT 58.615 47.619 0.00 0.00 0.00 2.66
862 2464 0.185175 GGAGTGGGTTGTTTGGGACT 59.815 55.000 0.00 0.00 0.00 3.85
863 2465 1.170290 CGGAGTGGGTTGTTTGGGAC 61.170 60.000 0.00 0.00 0.00 4.46
864 2466 1.149627 CGGAGTGGGTTGTTTGGGA 59.850 57.895 0.00 0.00 0.00 4.37
904 2510 2.035442 GCGGCGGAAGAAGAAAGCT 61.035 57.895 9.78 0.00 0.00 3.74
986 2592 4.517934 CCATGGAGCTGGGCTGGG 62.518 72.222 5.56 0.00 39.88 4.45
1250 2871 5.828299 TTCAATGGTTCACGAAAAAGTCT 57.172 34.783 0.00 0.00 0.00 3.24
1271 2901 1.226888 GGGTTCGACTAGCGCGATT 60.227 57.895 12.10 0.00 40.61 3.34
1548 3189 5.459762 GGTTCATGCAAACCGAATATCATTG 59.540 40.000 4.58 0.00 39.40 2.82
1563 3204 2.607526 CGCAATCTTTGTGGTTCATGCA 60.608 45.455 0.00 0.00 37.51 3.96
1565 3206 3.495193 CTCGCAATCTTTGTGGTTCATG 58.505 45.455 1.39 0.00 41.37 3.07
1566 3207 2.489329 CCTCGCAATCTTTGTGGTTCAT 59.511 45.455 1.39 0.00 41.37 2.57
1567 3208 1.879380 CCTCGCAATCTTTGTGGTTCA 59.121 47.619 1.39 0.00 41.37 3.18
1571 3212 1.879380 TGTTCCTCGCAATCTTTGTGG 59.121 47.619 1.39 0.00 41.37 4.17
1572 3213 2.807967 TCTGTTCCTCGCAATCTTTGTG 59.192 45.455 0.00 0.00 42.36 3.33
1575 3216 3.251004 GTGTTCTGTTCCTCGCAATCTTT 59.749 43.478 0.00 0.00 0.00 2.52
1577 3218 2.037772 AGTGTTCTGTTCCTCGCAATCT 59.962 45.455 0.00 0.00 0.00 2.40
1578 3219 2.158449 CAGTGTTCTGTTCCTCGCAATC 59.842 50.000 0.00 0.00 36.97 2.67
1580 3221 1.581934 CAGTGTTCTGTTCCTCGCAA 58.418 50.000 0.00 0.00 36.97 4.85
1679 3320 5.428184 AAAACACAAATTTCTCACCCCAA 57.572 34.783 0.00 0.00 0.00 4.12
1714 3355 5.249622 TGGATTGTTGGTACCAAGAGTATGA 59.750 40.000 27.77 11.42 36.52 2.15
1823 3464 8.531982 AGAGTATGTATGCTTGAGAGTAACAAA 58.468 33.333 0.00 0.00 0.00 2.83
1855 3496 7.954835 AGAAAAGTCATGTTTTGGATCATTGA 58.045 30.769 0.00 0.00 29.58 2.57
1860 3501 7.706179 TGTTCAAGAAAAGTCATGTTTTGGATC 59.294 33.333 0.00 0.00 29.58 3.36
1930 3571 9.114952 TGCTATACATCGTCATGGAAATAAAAA 57.885 29.630 0.00 0.00 33.82 1.94
1931 3572 8.669946 TGCTATACATCGTCATGGAAATAAAA 57.330 30.769 0.00 0.00 33.82 1.52
1932 3573 7.095229 GCTGCTATACATCGTCATGGAAATAAA 60.095 37.037 0.00 0.00 33.82 1.40
1933 3574 6.368791 GCTGCTATACATCGTCATGGAAATAA 59.631 38.462 0.00 0.00 33.82 1.40
1934 3575 5.869344 GCTGCTATACATCGTCATGGAAATA 59.131 40.000 0.00 0.00 33.82 1.40
1935 3576 4.692625 GCTGCTATACATCGTCATGGAAAT 59.307 41.667 0.00 0.00 33.82 2.17
1936 3577 4.058124 GCTGCTATACATCGTCATGGAAA 58.942 43.478 0.00 0.00 33.82 3.13
1937 3578 3.069443 TGCTGCTATACATCGTCATGGAA 59.931 43.478 0.00 0.00 33.82 3.53
1938 3579 2.627699 TGCTGCTATACATCGTCATGGA 59.372 45.455 0.00 0.00 33.82 3.41
2010 3651 1.465354 GCTCATGCAAAGAAGCGTCAG 60.465 52.381 1.61 0.00 39.41 3.51
2013 3654 2.099141 TAGCTCATGCAAAGAAGCGT 57.901 45.000 0.00 0.00 42.74 5.07
2039 3683 4.013050 GAGCCAATTTAGAGGAAGCACTT 58.987 43.478 0.00 0.00 0.00 3.16
2075 3719 4.142609 TCCCTAAGCATTCTAACTGCAG 57.857 45.455 13.48 13.48 42.15 4.41
2212 3980 9.474313 AGGCAATGTGTAAAGGAAGAAATATTA 57.526 29.630 0.00 0.00 0.00 0.98
2215 3983 8.107095 ACTAGGCAATGTGTAAAGGAAGAAATA 58.893 33.333 0.00 0.00 0.00 1.40
2216 3984 6.948309 ACTAGGCAATGTGTAAAGGAAGAAAT 59.052 34.615 0.00 0.00 0.00 2.17
2217 3985 6.303839 ACTAGGCAATGTGTAAAGGAAGAAA 58.696 36.000 0.00 0.00 0.00 2.52
2218 3986 5.876357 ACTAGGCAATGTGTAAAGGAAGAA 58.124 37.500 0.00 0.00 0.00 2.52
2220 3988 6.407202 AGTACTAGGCAATGTGTAAAGGAAG 58.593 40.000 0.00 0.00 0.00 3.46
2222 3990 7.670605 ATAGTACTAGGCAATGTGTAAAGGA 57.329 36.000 8.85 0.00 0.00 3.36
2223 3991 7.769044 ACAATAGTACTAGGCAATGTGTAAAGG 59.231 37.037 8.85 0.00 0.00 3.11
2224 3992 8.718102 ACAATAGTACTAGGCAATGTGTAAAG 57.282 34.615 8.85 0.00 0.00 1.85
2277 4045 5.261209 AGAGCACTGATGAGATCTTACAC 57.739 43.478 0.00 0.00 0.00 2.90
2342 4110 3.745975 ACGGTGTATGTGTGATGTTTGAG 59.254 43.478 0.00 0.00 0.00 3.02
2362 4234 1.478510 AGCCTATCACTGTTCCTCACG 59.521 52.381 0.00 0.00 0.00 4.35
2371 4243 2.706339 AAGGAAGCAGCCTATCACTG 57.294 50.000 0.00 0.00 37.26 3.66
2470 4344 3.636764 GCCAGACCAATAAACCCAATAGG 59.363 47.826 0.00 0.00 43.78 2.57
2473 4347 2.466846 GGCCAGACCAATAAACCCAAT 58.533 47.619 0.00 0.00 38.86 3.16
2502 4376 7.273188 TCGATGGCGAAAATATTATAACTCG 57.727 36.000 0.00 0.00 44.78 4.18
2525 4399 5.652744 TCTGAAAAGTTAGCGACAACTTC 57.347 39.130 13.23 5.27 45.68 3.01
2530 4404 7.172532 ACAATTACATCTGAAAAGTTAGCGACA 59.827 33.333 0.00 0.00 0.00 4.35
2531 4405 7.519002 ACAATTACATCTGAAAAGTTAGCGAC 58.481 34.615 0.00 0.00 0.00 5.19
2533 4407 8.015087 TGAACAATTACATCTGAAAAGTTAGCG 58.985 33.333 0.00 0.00 0.00 4.26
2534 4408 9.334693 CTGAACAATTACATCTGAAAAGTTAGC 57.665 33.333 0.00 0.00 0.00 3.09
2535 4409 9.831737 CCTGAACAATTACATCTGAAAAGTTAG 57.168 33.333 0.00 0.00 0.00 2.34
2538 4412 7.651808 CACCTGAACAATTACATCTGAAAAGT 58.348 34.615 0.00 0.00 0.00 2.66
2539 4413 6.583806 GCACCTGAACAATTACATCTGAAAAG 59.416 38.462 0.00 0.00 0.00 2.27
2788 4662 5.938322 ACAACGCATCGAAATTCTAAACAT 58.062 33.333 0.00 0.00 0.00 2.71
2821 4695 4.206477 TCATGAGTCGGATGTCAAACAT 57.794 40.909 0.00 0.00 42.43 2.71
2828 4702 2.179427 TGGAGTTCATGAGTCGGATGT 58.821 47.619 0.00 0.00 0.00 3.06
2976 4859 6.775629 ACCCTGCAAAAGAAGAGTGTAAAATA 59.224 34.615 0.00 0.00 0.00 1.40
2984 4867 2.736670 ACACCCTGCAAAAGAAGAGT 57.263 45.000 0.00 0.00 0.00 3.24
3509 5450 0.178995 TTGCCATCAGAACCTGCACA 60.179 50.000 0.00 0.00 0.00 4.57
3637 5580 6.677913 TCATGCAGAATCATCAAGCATTATG 58.322 36.000 0.00 0.00 42.96 1.90
3757 5700 5.885352 TCCCGCAATCTTTTTCAGATCAATA 59.115 36.000 0.00 0.00 41.93 1.90
4004 5947 4.835615 GGATCAGCAGGAGGAGACTATAAA 59.164 45.833 0.00 0.00 44.43 1.40
4065 6008 5.067544 GCTACATAGAAGAACTAGGAACGGT 59.932 44.000 0.00 0.00 36.52 4.83
4134 6077 0.179045 CCAACTATTCAGGCCCTCGG 60.179 60.000 0.00 0.00 0.00 4.63
4235 6179 1.593196 TGCTAACCAGATAATGCGGC 58.407 50.000 0.00 0.00 0.00 6.53
4299 6243 1.002468 TGTTTTCAAGCAGAAGAGCGC 60.002 47.619 0.00 0.00 37.57 5.92
4301 6245 3.978718 AGTGTTTTCAAGCAGAAGAGC 57.021 42.857 0.00 0.00 37.57 4.09
4468 6423 0.242825 TTACGTGCACCCTTCTCTCG 59.757 55.000 12.15 0.00 0.00 4.04
4640 6667 6.148150 TGTTAACCATGGAACGACATAAGTTC 59.852 38.462 21.47 0.89 45.16 3.01
4707 6734 6.866179 ACGAGTTCGAGTATCAAACATTAC 57.134 37.500 8.72 0.00 43.02 1.89
4720 6748 4.202558 CGTAGCTAATTCAACGAGTTCGAG 59.797 45.833 8.72 0.81 43.02 4.04
4791 6821 1.731969 ACGGCAGAAACTCGTACGC 60.732 57.895 11.24 0.00 35.23 4.42
4802 6832 2.591429 CAACACAGCCACGGCAGA 60.591 61.111 11.35 0.00 44.88 4.26
4804 6834 3.208383 CACAACACAGCCACGGCA 61.208 61.111 11.35 0.00 44.88 5.69
4846 6876 6.001449 TCAAGACAAACCTAATATGGAGGG 57.999 41.667 8.45 0.00 38.52 4.30
4847 6877 6.653989 ACTCAAGACAAACCTAATATGGAGG 58.346 40.000 2.91 2.91 40.22 4.30
4848 6878 7.331026 TGACTCAAGACAAACCTAATATGGAG 58.669 38.462 0.00 0.00 0.00 3.86
4849 6879 7.252612 TGACTCAAGACAAACCTAATATGGA 57.747 36.000 0.00 0.00 0.00 3.41
4850 6880 7.921786 TTGACTCAAGACAAACCTAATATGG 57.078 36.000 0.00 0.00 0.00 2.74
4860 6890 8.573035 ACTTTTTAGTGTTTGACTCAAGACAAA 58.427 29.630 4.00 4.00 37.36 2.83
4861 6891 8.106247 ACTTTTTAGTGTTTGACTCAAGACAA 57.894 30.769 7.79 0.00 35.96 3.18
4862 6892 7.681939 ACTTTTTAGTGTTTGACTCAAGACA 57.318 32.000 6.03 4.95 35.96 3.41
4863 6893 8.965986 AAACTTTTTAGTGTTTGACTCAAGAC 57.034 30.769 0.00 0.00 35.40 3.01
4906 6936 8.497554 GCAAATGTTGATGTTTATTGTGAATGT 58.502 29.630 0.00 0.00 0.00 2.71
4907 6937 8.496751 TGCAAATGTTGATGTTTATTGTGAATG 58.503 29.630 0.00 0.00 0.00 2.67
4908 6938 8.604640 TGCAAATGTTGATGTTTATTGTGAAT 57.395 26.923 0.00 0.00 0.00 2.57
4909 6939 8.429493 TTGCAAATGTTGATGTTTATTGTGAA 57.571 26.923 0.00 0.00 0.00 3.18
4910 6940 8.429493 TTTGCAAATGTTGATGTTTATTGTGA 57.571 26.923 8.05 0.00 0.00 3.58
4911 6941 8.336806 ACTTTGCAAATGTTGATGTTTATTGTG 58.663 29.630 13.23 0.00 28.79 3.33
4912 6942 8.436046 ACTTTGCAAATGTTGATGTTTATTGT 57.564 26.923 13.23 0.00 28.79 2.71
4913 6943 9.719279 AAACTTTGCAAATGTTGATGTTTATTG 57.281 25.926 20.34 5.45 42.49 1.90
4914 6944 9.719279 CAAACTTTGCAAATGTTGATGTTTATT 57.281 25.926 21.74 6.49 42.49 1.40
4915 6945 8.344098 CCAAACTTTGCAAATGTTGATGTTTAT 58.656 29.630 25.38 9.39 42.49 1.40
4916 6946 7.550551 TCCAAACTTTGCAAATGTTGATGTTTA 59.449 29.630 25.38 10.82 42.49 2.01
4917 6947 6.373774 TCCAAACTTTGCAAATGTTGATGTTT 59.626 30.769 25.38 20.10 42.49 2.83
4918 6948 5.879223 TCCAAACTTTGCAAATGTTGATGTT 59.121 32.000 25.38 16.54 42.49 2.71
4919 6949 5.294060 GTCCAAACTTTGCAAATGTTGATGT 59.706 36.000 25.38 12.45 42.49 3.06
4920 6950 5.524646 AGTCCAAACTTTGCAAATGTTGATG 59.475 36.000 25.38 19.05 42.49 3.07
4921 6951 5.673514 AGTCCAAACTTTGCAAATGTTGAT 58.326 33.333 25.38 14.18 42.49 2.57
4922 6952 5.083533 AGTCCAAACTTTGCAAATGTTGA 57.916 34.783 25.38 16.82 42.49 3.18
4923 6953 5.350914 TGAAGTCCAAACTTTGCAAATGTTG 59.649 36.000 20.34 20.32 45.80 3.33
4924 6954 5.486526 TGAAGTCCAAACTTTGCAAATGTT 58.513 33.333 13.23 15.23 45.80 2.71
4925 6955 5.083533 TGAAGTCCAAACTTTGCAAATGT 57.916 34.783 13.23 10.11 45.80 2.71
4926 6956 5.232838 GTCTGAAGTCCAAACTTTGCAAATG 59.767 40.000 13.23 8.30 45.80 2.32
4927 6957 5.105392 TGTCTGAAGTCCAAACTTTGCAAAT 60.105 36.000 13.23 0.00 45.80 2.32
4928 6958 4.219507 TGTCTGAAGTCCAAACTTTGCAAA 59.780 37.500 12.14 12.14 45.80 3.68
4929 6959 3.761218 TGTCTGAAGTCCAAACTTTGCAA 59.239 39.130 0.00 0.00 45.80 4.08
4930 6960 3.351740 TGTCTGAAGTCCAAACTTTGCA 58.648 40.909 0.00 0.00 45.80 4.08
4931 6961 4.370364 TTGTCTGAAGTCCAAACTTTGC 57.630 40.909 0.00 0.00 45.80 3.68
4932 6962 6.799512 AGATTTGTCTGAAGTCCAAACTTTG 58.200 36.000 0.00 0.00 45.80 2.77
4933 6963 7.410120 AAGATTTGTCTGAAGTCCAAACTTT 57.590 32.000 0.00 0.00 45.80 2.66
4935 6965 7.410120 AAAAGATTTGTCTGAAGTCCAAACT 57.590 32.000 0.00 0.00 37.32 2.66
4936 6966 7.862873 CCTAAAAGATTTGTCTGAAGTCCAAAC 59.137 37.037 0.00 0.00 31.50 2.93
4937 6967 7.014230 CCCTAAAAGATTTGTCTGAAGTCCAAA 59.986 37.037 0.00 0.00 33.09 3.28
4938 6968 6.490040 CCCTAAAAGATTTGTCTGAAGTCCAA 59.510 38.462 0.00 0.00 0.00 3.53
4939 6969 6.003950 CCCTAAAAGATTTGTCTGAAGTCCA 58.996 40.000 0.00 0.00 0.00 4.02
4940 6970 6.238648 TCCCTAAAAGATTTGTCTGAAGTCC 58.761 40.000 0.00 0.00 0.00 3.85
4941 6971 7.745620 TTCCCTAAAAGATTTGTCTGAAGTC 57.254 36.000 0.00 0.00 0.00 3.01
4942 6972 8.579863 CATTTCCCTAAAAGATTTGTCTGAAGT 58.420 33.333 0.00 0.00 0.00 3.01
4943 6973 8.579863 ACATTTCCCTAAAAGATTTGTCTGAAG 58.420 33.333 0.00 0.00 0.00 3.02
4944 6974 8.477419 ACATTTCCCTAAAAGATTTGTCTGAA 57.523 30.769 0.00 0.00 0.00 3.02
4945 6975 8.477419 AACATTTCCCTAAAAGATTTGTCTGA 57.523 30.769 0.00 0.00 0.00 3.27
4946 6976 8.981647 CAAACATTTCCCTAAAAGATTTGTCTG 58.018 33.333 0.00 0.00 34.25 3.51
4947 6977 8.923270 TCAAACATTTCCCTAAAAGATTTGTCT 58.077 29.630 0.00 0.00 37.15 3.41
4948 6978 9.541143 TTCAAACATTTCCCTAAAAGATTTGTC 57.459 29.630 0.00 0.00 37.15 3.18
4949 6979 9.898152 TTTCAAACATTTCCCTAAAAGATTTGT 57.102 25.926 0.00 0.00 37.15 2.83
4952 6982 9.898152 TGTTTTCAAACATTTCCCTAAAAGATT 57.102 25.926 0.79 0.00 43.45 2.40
4953 6983 9.546428 CTGTTTTCAAACATTTCCCTAAAAGAT 57.454 29.630 5.59 0.00 46.71 2.40
4954 6984 7.494298 GCTGTTTTCAAACATTTCCCTAAAAGA 59.506 33.333 5.59 0.00 46.71 2.52
4955 6985 7.516627 CGCTGTTTTCAAACATTTCCCTAAAAG 60.517 37.037 5.59 0.00 46.71 2.27
4956 6986 6.256757 CGCTGTTTTCAAACATTTCCCTAAAA 59.743 34.615 5.59 0.00 46.71 1.52
4957 6987 5.751028 CGCTGTTTTCAAACATTTCCCTAAA 59.249 36.000 5.59 0.00 46.71 1.85
4958 6988 5.285651 CGCTGTTTTCAAACATTTCCCTAA 58.714 37.500 5.59 0.00 46.71 2.69
4959 6989 4.794655 GCGCTGTTTTCAAACATTTCCCTA 60.795 41.667 0.00 0.00 46.71 3.53
4960 6990 3.716601 CGCTGTTTTCAAACATTTCCCT 58.283 40.909 5.59 0.00 46.71 4.20
4961 6991 2.220824 GCGCTGTTTTCAAACATTTCCC 59.779 45.455 0.00 0.00 46.71 3.97
4962 6992 2.863137 TGCGCTGTTTTCAAACATTTCC 59.137 40.909 9.73 0.00 46.71 3.13
4963 6993 3.302415 GGTGCGCTGTTTTCAAACATTTC 60.302 43.478 9.73 0.00 46.71 2.17
4964 6994 2.607180 GGTGCGCTGTTTTCAAACATTT 59.393 40.909 9.73 0.00 46.71 2.32
4965 6995 2.200899 GGTGCGCTGTTTTCAAACATT 58.799 42.857 9.73 0.00 46.71 2.71
4966 6996 1.851658 GGTGCGCTGTTTTCAAACAT 58.148 45.000 9.73 0.00 46.71 2.71
4967 6997 0.524392 CGGTGCGCTGTTTTCAAACA 60.524 50.000 9.73 5.05 45.88 2.83
4968 6998 1.206115 CCGGTGCGCTGTTTTCAAAC 61.206 55.000 9.73 0.00 39.33 2.93
5011 7041 2.883730 GTCGCGCGGTATGAAGCA 60.884 61.111 31.69 3.44 0.00 3.91
5101 7134 2.358737 GGCCAGGAGTTGTCCACG 60.359 66.667 0.00 0.00 46.80 4.94
5104 7137 1.600916 GTGTGGCCAGGAGTTGTCC 60.601 63.158 5.11 0.00 44.33 4.02
5142 7175 2.439156 GGCAGGTGTCCATGGCTC 60.439 66.667 6.96 3.18 38.83 4.70
5196 7229 0.111446 TTGTGGGGGCGAAGAATGAA 59.889 50.000 0.00 0.00 0.00 2.57
5206 7239 0.831711 ATTGTTGGACTTGTGGGGGC 60.832 55.000 0.00 0.00 0.00 5.80
5212 7245 3.319122 GGAGAAGCAATTGTTGGACTTGT 59.681 43.478 7.40 0.00 0.00 3.16
5228 7261 1.078567 GCTGAGGGCAGTGGAGAAG 60.079 63.158 0.00 0.00 44.17 2.85
5244 7277 1.594331 GGACGAAGAAGTGGTTTGCT 58.406 50.000 0.00 0.00 0.00 3.91
5253 7286 4.150897 TGGAATTATGGGGACGAAGAAG 57.849 45.455 0.00 0.00 0.00 2.85
5362 7396 1.972075 TGTGTGGTTCGTGGAGGATTA 59.028 47.619 0.00 0.00 0.00 1.75
5372 7406 1.197721 GGCTCAATCTTGTGTGGTTCG 59.802 52.381 0.00 0.00 0.00 3.95
5374 7408 1.133513 TGGGCTCAATCTTGTGTGGTT 60.134 47.619 0.00 0.00 0.00 3.67
5447 7481 2.030562 GTCACCCACCGTCACAGG 59.969 66.667 0.00 0.00 37.30 4.00
5480 7514 0.541063 TCTGGTTGCCGTACCTGAGA 60.541 55.000 0.00 0.00 40.09 3.27
5485 7519 1.078426 AGCATCTGGTTGCCGTACC 60.078 57.895 0.70 0.00 43.83 3.34
5486 7520 1.369091 CCAGCATCTGGTTGCCGTAC 61.369 60.000 4.74 0.00 45.82 3.67
5488 7522 2.360350 CCAGCATCTGGTTGCCGT 60.360 61.111 4.74 0.00 45.82 5.68
5512 7546 1.130561 GCTGGTAGCAAAAACTAGGCG 59.869 52.381 0.00 0.00 41.89 5.52
5547 7581 6.205658 GGTAGCAAAAATGTAAAATTTGGGCA 59.794 34.615 0.00 0.00 35.21 5.36


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

AutoCloner maintained by Alex Coulton.