Multiple sequence alignment - TraesCS5D01G466200

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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 TraesCS5D01G466200 chr5D 100.000 4319 0 0 1 4319 508619173 508623491 0.000000e+00 7976.0
1 TraesCS5D01G466200 chr5B 92.356 1740 95 21 749 2461 638487201 638485473 0.000000e+00 2442.0
2 TraesCS5D01G466200 chr5B 90.241 748 40 16 3056 3777 638484843 638484103 0.000000e+00 946.0
3 TraesCS5D01G466200 chr5B 94.649 542 22 3 2460 2996 638485379 638484840 0.000000e+00 833.0
4 TraesCS5D01G466200 chr5B 82.633 547 45 15 3773 4287 638470744 638470216 5.130000e-119 438.0
5 TraesCS5D01G466200 chr5A 94.909 1434 67 4 1567 2996 635957579 635959010 0.000000e+00 2239.0
6 TraesCS5D01G466200 chr5A 83.550 845 90 26 669 1478 635956737 635957567 0.000000e+00 745.0
7 TraesCS5D01G466200 chr5A 86.646 644 72 9 29 668 635955917 635956550 0.000000e+00 701.0
8 TraesCS5D01G466200 chr5A 94.609 371 19 1 3056 3426 635959007 635959376 1.350000e-159 573.0
9 TraesCS5D01G466200 chr1A 77.120 861 144 39 2166 2998 407115701 407114866 2.370000e-122 449.0
10 TraesCS5D01G466200 chr1A 91.270 126 5 3 991 1110 407116969 407116844 2.670000e-37 167.0
11 TraesCS5D01G466200 chr1A 88.983 118 13 0 1622 1739 407116338 407116221 3.480000e-31 147.0
12 TraesCS5D01G466200 chr1A 86.957 92 8 4 2459 2549 556106517 556106429 2.750000e-17 100.0
13 TraesCS5D01G466200 chr1A 86.022 93 7 6 2459 2549 49000880 49000792 1.280000e-15 95.3
14 TraesCS5D01G466200 chr1B 76.240 867 147 42 2166 2998 442109391 442108550 5.200000e-109 405.0
15 TraesCS5D01G466200 chr1B 90.476 126 6 3 991 1110 442110680 442110555 1.240000e-35 161.0
16 TraesCS5D01G466200 chr1B 86.029 136 19 0 1622 1757 442110029 442109894 3.480000e-31 147.0
17 TraesCS5D01G466200 chr1B 82.524 103 17 1 3236 3337 442108515 442108413 5.950000e-14 89.8
18 TraesCS5D01G466200 chr1D 75.551 454 66 28 2166 2590 327992953 327992516 9.540000e-42 182.0
19 TraesCS5D01G466200 chr1D 89.600 125 8 2 991 1110 327994246 327994122 2.080000e-33 154.0
20 TraesCS5D01G466200 chr1D 80.978 184 32 3 1558 1739 327993655 327993473 4.500000e-30 143.0
21 TraesCS5D01G466200 chr1D 87.629 97 11 1 3236 3331 327992139 327992043 1.270000e-20 111.0
22 TraesCS5D01G466200 chr2B 82.353 187 21 6 1617 1792 106119316 106119131 7.480000e-33 152.0
23 TraesCS5D01G466200 chr4A 87.640 89 7 4 2459 2546 465335645 465335730 2.750000e-17 100.0
24 TraesCS5D01G466200 chr2D 90.566 53 3 2 2994 3046 204132625 204132575 7.750000e-08 69.4
25 TraesCS5D01G466200 chr3B 96.970 33 0 1 2988 3019 690416985 690416953 2.000000e-03 54.7


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 TraesCS5D01G466200 chr5D 508619173 508623491 4318 False 7976.000000 7976 100.000000 1 4319 1 chr5D.!!$F1 4318
1 TraesCS5D01G466200 chr5B 638484103 638487201 3098 True 1407.000000 2442 92.415333 749 3777 3 chr5B.!!$R2 3028
2 TraesCS5D01G466200 chr5B 638470216 638470744 528 True 438.000000 438 82.633000 3773 4287 1 chr5B.!!$R1 514
3 TraesCS5D01G466200 chr5A 635955917 635959376 3459 False 1064.500000 2239 89.928500 29 3426 4 chr5A.!!$F1 3397
4 TraesCS5D01G466200 chr1A 407114866 407116969 2103 True 254.333333 449 85.791000 991 2998 3 chr1A.!!$R3 2007
5 TraesCS5D01G466200 chr1B 442108413 442110680 2267 True 200.700000 405 83.817250 991 3337 4 chr1B.!!$R1 2346

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
386 391 0.110644 GCGGAGTCTGAAAGCAAACG 60.111 55.0 2.16 0.0 0.0 3.60 F
1178 1389 0.179089 CTCAGATCAGTGGGGCTTCG 60.179 60.0 0.00 0.0 0.0 3.79 F
2219 2704 0.252197 AAGAACCCATCCGTACTGGC 59.748 55.0 0.00 0.0 37.8 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1765 2096 0.240678 AAGCATGCACGCAAATCGAA 59.759 45.0 21.98 0.0 41.67 3.71 R
2751 3357 0.818296 GTACAGCAGTCGGTCATCCT 59.182 55.0 0.00 0.0 0.00 3.24 R
3889 4526 0.171231 TCTCAGTCGTTCATGGAGCG 59.829 55.0 0.00 0.0 37.60 5.03 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
26 27 9.558396 GAGGTCTGTTACTACATACTACATACT 57.442 37.037 0.00 0.00 33.29 2.12
30 31 9.784531 TCTGTTACTACATACTACATACTACCC 57.215 37.037 0.00 0.00 32.86 3.69
40 41 6.534475 ACTACATACTACCCGATTCAACAA 57.466 37.500 0.00 0.00 0.00 2.83
51 52 6.419791 ACCCGATTCAACAAATCCTTATACA 58.580 36.000 0.00 0.00 40.69 2.29
55 56 6.899771 CGATTCAACAAATCCTTATACACACG 59.100 38.462 0.00 0.00 40.69 4.49
87 88 8.447924 AACCAAAGAGTTAGTTTACTCCTTTC 57.552 34.615 0.00 0.00 44.50 2.62
90 91 9.121658 CCAAAGAGTTAGTTTACTCCTTTCTTT 57.878 33.333 0.00 0.00 44.50 2.52
129 133 5.138276 AGTGTAGTCTTAGTGAACCAGACA 58.862 41.667 11.18 0.00 39.63 3.41
175 180 9.502145 AAAAATATTAGCACATGTGTATCAACG 57.498 29.630 26.01 0.00 0.00 4.10
176 181 8.432110 AAATATTAGCACATGTGTATCAACGA 57.568 30.769 26.01 2.84 0.00 3.85
203 208 6.816134 TGCTAGTTTTCTGCATATGTTTGA 57.184 33.333 4.29 0.00 32.31 2.69
207 212 7.809806 GCTAGTTTTCTGCATATGTTTGAAGTT 59.190 33.333 4.29 0.69 0.00 2.66
208 213 7.935338 AGTTTTCTGCATATGTTTGAAGTTG 57.065 32.000 4.29 0.00 0.00 3.16
219 224 4.753233 TGTTTGAAGTTGTGGGAACAATG 58.247 39.130 0.00 0.00 46.06 2.82
220 225 4.464244 TGTTTGAAGTTGTGGGAACAATGA 59.536 37.500 0.00 0.00 46.06 2.57
225 230 3.897239 AGTTGTGGGAACAATGAAGTGA 58.103 40.909 0.00 0.00 46.06 3.41
292 297 3.848200 ATGTGGGGGTGGAGGGGTT 62.848 63.158 0.00 0.00 0.00 4.11
299 304 0.981801 GGGTGGAGGGGTTAGGACTC 60.982 65.000 0.00 0.00 0.00 3.36
301 306 1.290130 GGTGGAGGGGTTAGGACTCTA 59.710 57.143 0.00 0.00 0.00 2.43
307 312 4.387664 GGAGGGGTTAGGACTCTAAGATCA 60.388 50.000 0.00 0.00 36.27 2.92
308 313 4.810345 AGGGGTTAGGACTCTAAGATCAG 58.190 47.826 0.00 0.00 36.27 2.90
313 318 5.533528 GGTTAGGACTCTAAGATCAGAGGTC 59.466 48.000 13.14 9.60 45.36 3.85
314 319 4.178956 AGGACTCTAAGATCAGAGGTCC 57.821 50.000 13.14 15.73 45.36 4.46
315 320 3.117284 AGGACTCTAAGATCAGAGGTCCC 60.117 52.174 19.59 14.58 45.36 4.46
323 328 2.021068 ATCAGAGGTCCCGCATGACG 62.021 60.000 0.00 0.00 43.15 4.35
350 355 3.376218 GCACCTGCGAGATGATCTT 57.624 52.632 0.00 0.00 0.00 2.40
362 367 4.626042 GAGATGATCTTGCCGACATAACT 58.374 43.478 0.00 0.00 0.00 2.24
364 369 5.777802 AGATGATCTTGCCGACATAACTAG 58.222 41.667 0.00 0.00 0.00 2.57
365 370 5.536538 AGATGATCTTGCCGACATAACTAGA 59.463 40.000 0.00 0.00 0.00 2.43
386 391 0.110644 GCGGAGTCTGAAAGCAAACG 60.111 55.000 2.16 0.00 0.00 3.60
388 393 0.238553 GGAGTCTGAAAGCAAACGGC 59.761 55.000 0.00 0.00 45.30 5.68
416 421 1.527311 AGAAAAACTCGCGCTCTCAAC 59.473 47.619 5.56 0.00 0.00 3.18
417 422 1.527311 GAAAAACTCGCGCTCTCAACT 59.473 47.619 5.56 0.00 0.00 3.16
421 426 0.448593 ACTCGCGCTCTCAACTCTAC 59.551 55.000 5.56 0.00 0.00 2.59
452 457 3.199727 TGGTGATTGACTTGCATAGGCTA 59.800 43.478 0.00 0.00 41.91 3.93
464 469 9.442047 GACTTGCATAGGCTACTATCAATATTT 57.558 33.333 0.00 0.00 37.82 1.40
497 502 9.685276 ACAATTCAGACTATGACAATTGGATAA 57.315 29.630 10.83 0.00 37.40 1.75
561 566 8.050778 AGTCATCTGTATACATAGCTTCTAGC 57.949 38.462 5.91 0.00 42.84 3.42
588 593 5.987347 CACATTTGATGTCTTGGCTTTTCTT 59.013 36.000 0.00 0.00 42.70 2.52
595 600 3.638160 TGTCTTGGCTTTTCTTCATGCTT 59.362 39.130 0.00 0.00 0.00 3.91
596 601 4.826733 TGTCTTGGCTTTTCTTCATGCTTA 59.173 37.500 0.00 0.00 0.00 3.09
637 642 4.566004 TGTATCAACCCAGAAAACTCGAG 58.434 43.478 11.84 11.84 0.00 4.04
638 643 2.543777 TCAACCCAGAAAACTCGAGG 57.456 50.000 18.41 0.00 0.00 4.63
642 647 0.690762 CCCAGAAAACTCGAGGGGAA 59.309 55.000 18.41 0.00 37.80 3.97
688 879 7.619302 TGAATGGGTTAATTCAAAATAGGCTCT 59.381 33.333 0.00 0.00 42.22 4.09
693 884 7.922811 GGGTTAATTCAAAATAGGCTCTGAATG 59.077 37.037 12.16 0.00 38.27 2.67
726 920 3.812156 AGCCAAGTTGGTGGTTTTTAC 57.188 42.857 22.85 3.16 40.46 2.01
843 1041 5.558818 TCCTACTAATACTTCGGAGCTAGG 58.441 45.833 0.00 0.00 0.00 3.02
899 1097 3.537206 GACGCACCAGAACAGGCCT 62.537 63.158 0.00 0.00 0.00 5.19
942 1140 2.478033 GGCCGGAAGCAAATACGGG 61.478 63.158 5.05 0.00 46.04 5.28
1167 1378 1.409064 ACCTATTTCGCGCTCAGATCA 59.591 47.619 5.56 0.00 0.00 2.92
1174 1385 2.202987 CGCTCAGATCAGTGGGGC 60.203 66.667 0.00 0.00 0.00 5.80
1178 1389 0.179089 CTCAGATCAGTGGGGCTTCG 60.179 60.000 0.00 0.00 0.00 3.79
1201 1431 2.794981 CGCGTTATCCCAGTAGTGTCTG 60.795 54.545 0.00 0.00 35.45 3.51
1328 1622 0.917259 CAGTACATGAGCGAACGAGC 59.083 55.000 0.00 0.00 37.41 5.03
1365 1659 6.772716 GCATTAGAGAGGTGAATTGGGAATTA 59.227 38.462 0.00 0.00 0.00 1.40
1396 1696 3.003394 TCAATCATGGGTGTGATGTCC 57.997 47.619 0.00 0.00 38.76 4.02
1403 1703 1.351017 TGGGTGTGATGTCCTCCTTTC 59.649 52.381 0.00 0.00 0.00 2.62
1486 1806 9.231297 CTAGTTCATGATGTTTAGAAAAAGGGA 57.769 33.333 0.00 0.00 0.00 4.20
1492 1816 9.415544 CATGATGTTTAGAAAAAGGGAGAAAAG 57.584 33.333 0.00 0.00 0.00 2.27
1504 1828 3.014623 GGGAGAAAAGACGGGGTTTATG 58.985 50.000 0.00 0.00 0.00 1.90
1520 1844 5.351740 GGGTTTATGTCAGTTACTCTGCTTC 59.648 44.000 0.00 0.00 43.32 3.86
1531 1856 7.447545 TCAGTTACTCTGCTTCTGTTAGTTAGA 59.552 37.037 0.00 0.00 43.32 2.10
1667 1998 6.778542 TTGATCATATGGAAGGGGTTGATA 57.221 37.500 2.13 0.00 0.00 2.15
1745 2076 4.702131 CCTGGATTCAAAAGGGTCAGTTAG 59.298 45.833 0.00 0.00 0.00 2.34
1748 2079 4.156739 GGATTCAAAAGGGTCAGTTAGCTG 59.843 45.833 0.00 0.00 43.87 4.24
1761 2092 6.598064 GGTCAGTTAGCTGGTTACACAATATT 59.402 38.462 6.75 0.00 42.78 1.28
1765 2096 9.547753 CAGTTAGCTGGTTACACAATATTAGAT 57.452 33.333 0.00 0.00 39.01 1.98
1775 2107 9.092322 GTTACACAATATTAGATTCGATTTGCG 57.908 33.333 0.00 0.00 42.69 4.85
1824 2292 4.041567 TCTGAGGTGGATTTAAGTGCTTCA 59.958 41.667 0.00 0.00 0.00 3.02
1883 2351 8.180267 GTGATCAATCTAAATGTCAGAAGTTGG 58.820 37.037 0.00 0.00 0.00 3.77
1885 2353 7.672983 TCAATCTAAATGTCAGAAGTTGGAC 57.327 36.000 0.00 0.00 34.63 4.02
1909 2388 6.138088 CGTGCAATACATAGATGGACATTTG 58.862 40.000 0.00 0.00 35.43 2.32
2068 2548 1.879380 TGGCAAGTTGTATCAGTGCAC 59.121 47.619 9.40 9.40 36.93 4.57
2076 2556 5.114780 AGTTGTATCAGTGCACATCATCTC 58.885 41.667 21.04 3.75 0.00 2.75
2159 2644 3.181504 TGCTGTTGCTGAATGATTCATCG 60.182 43.478 8.50 0.00 39.30 3.84
2219 2704 0.252197 AAGAACCCATCCGTACTGGC 59.748 55.000 0.00 0.00 37.80 4.85
2368 2870 8.243426 TCCTGACAACAATAAATTAACATCTGC 58.757 33.333 0.00 0.00 0.00 4.26
2687 3292 9.836864 TCAACATCTAGCAATGTATAATTCACT 57.163 29.630 0.00 0.00 38.92 3.41
2751 3357 3.636300 CCTCCAGGTGACAACAATTTTGA 59.364 43.478 0.00 0.00 0.00 2.69
2780 3386 2.657757 CTGCTGTACGCACACGGTG 61.658 63.158 6.58 6.58 45.47 4.94
2931 3543 4.740695 GTGAACAGCTATCTTCCATACGTC 59.259 45.833 0.00 0.00 0.00 4.34
2964 3576 3.340928 CATTGTGATGACTGAGAAGCCA 58.659 45.455 0.00 0.00 35.16 4.75
3000 3612 9.911138 GTATGCTTAGTCTTATTAAGTACTCCC 57.089 37.037 0.00 1.05 32.09 4.30
3001 3613 8.785184 ATGCTTAGTCTTATTAAGTACTCCCT 57.215 34.615 0.00 0.00 32.09 4.20
3002 3614 8.235359 TGCTTAGTCTTATTAAGTACTCCCTC 57.765 38.462 0.00 0.12 32.09 4.30
3003 3615 7.287235 TGCTTAGTCTTATTAAGTACTCCCTCC 59.713 40.741 0.00 0.00 32.09 4.30
3005 3617 5.764432 AGTCTTATTAAGTACTCCCTCCGT 58.236 41.667 0.00 0.00 0.00 4.69
3006 3618 6.904626 AGTCTTATTAAGTACTCCCTCCGTA 58.095 40.000 0.00 0.00 0.00 4.02
3008 3620 6.016693 GTCTTATTAAGTACTCCCTCCGTACC 60.017 46.154 0.00 0.00 38.34 3.34
3009 3621 4.533001 ATTAAGTACTCCCTCCGTACCT 57.467 45.455 0.00 0.00 38.34 3.08
3010 3622 5.653255 ATTAAGTACTCCCTCCGTACCTA 57.347 43.478 0.00 0.00 38.34 3.08
3011 3623 5.450818 TTAAGTACTCCCTCCGTACCTAA 57.549 43.478 0.00 0.00 38.34 2.69
3012 3624 4.322057 AAGTACTCCCTCCGTACCTAAA 57.678 45.455 0.00 0.00 38.34 1.85
3013 3625 4.533001 AGTACTCCCTCCGTACCTAAAT 57.467 45.455 0.00 0.00 38.34 1.40
3014 3626 5.653255 AGTACTCCCTCCGTACCTAAATA 57.347 43.478 0.00 0.00 38.34 1.40
3016 3628 7.335127 AGTACTCCCTCCGTACCTAAATATA 57.665 40.000 0.00 0.00 38.34 0.86
3017 3629 7.937591 AGTACTCCCTCCGTACCTAAATATAT 58.062 38.462 0.00 0.00 38.34 0.86
3018 3630 7.833183 AGTACTCCCTCCGTACCTAAATATATG 59.167 40.741 0.00 0.00 38.34 1.78
3019 3631 6.797707 ACTCCCTCCGTACCTAAATATATGA 58.202 40.000 0.00 0.00 0.00 2.15
3020 3632 6.662663 ACTCCCTCCGTACCTAAATATATGAC 59.337 42.308 0.00 0.00 0.00 3.06
3024 3636 7.373493 CCTCCGTACCTAAATATATGACGTTT 58.627 38.462 0.00 0.00 0.00 3.60
3025 3637 7.869429 CCTCCGTACCTAAATATATGACGTTTT 59.131 37.037 0.00 0.00 0.00 2.43
3026 3638 8.578308 TCCGTACCTAAATATATGACGTTTTG 57.422 34.615 0.00 0.00 0.00 2.44
3027 3639 7.652909 TCCGTACCTAAATATATGACGTTTTGG 59.347 37.037 0.00 0.00 35.04 3.28
3028 3640 7.439056 CCGTACCTAAATATATGACGTTTTGGT 59.561 37.037 5.57 5.57 41.48 3.67
3029 3641 9.462174 CGTACCTAAATATATGACGTTTTGGTA 57.538 33.333 0.00 0.00 40.02 3.25
3106 3718 6.931281 ACGATGGTTGTTCTATTCCATATGAG 59.069 38.462 3.65 0.00 40.24 2.90
3156 3769 1.000506 TGCCGTCTGTTACTCTGGTTC 59.999 52.381 0.00 0.00 0.00 3.62
3167 3780 2.122768 ACTCTGGTTCATGGGAGATCC 58.877 52.381 0.00 0.00 0.00 3.36
3305 3918 0.184451 CTGGGCCTGCTGGTGATAAT 59.816 55.000 11.69 0.00 35.27 1.28
3345 3958 1.416243 ACCTTGTCACAGGGTCGTAA 58.584 50.000 5.58 0.00 39.73 3.18
3377 3990 1.132643 AGTAGCGCAGAAGTAACCGAG 59.867 52.381 11.47 0.00 0.00 4.63
3400 4013 2.726989 GCTGAAGATGTTGCATCGTGTG 60.727 50.000 2.57 0.00 0.00 3.82
3421 4034 6.019640 GTGTGTTGAATGGAAGTTTTCATGTG 60.020 38.462 0.00 0.00 32.27 3.21
3446 4071 0.902984 ATATGTATCTGGCCCGCCGA 60.903 55.000 0.00 2.13 39.42 5.54
3458 4083 1.571215 CCCGCCGAACAAGGTGTTAC 61.571 60.000 0.00 0.00 41.28 2.50
3486 4111 8.420222 CAACACTCATCTTCTGATAGTCCTAAT 58.580 37.037 0.00 0.00 32.10 1.73
3487 4112 8.177119 ACACTCATCTTCTGATAGTCCTAATC 57.823 38.462 0.00 0.00 32.10 1.75
3488 4113 7.232534 ACACTCATCTTCTGATAGTCCTAATCC 59.767 40.741 0.00 0.00 32.10 3.01
3489 4114 7.451255 CACTCATCTTCTGATAGTCCTAATCCT 59.549 40.741 0.00 0.00 32.10 3.24
3490 4115 8.674173 ACTCATCTTCTGATAGTCCTAATCCTA 58.326 37.037 0.00 0.00 32.10 2.94
3491 4116 9.527157 CTCATCTTCTGATAGTCCTAATCCTAA 57.473 37.037 0.00 0.00 32.10 2.69
3564 4189 9.528847 GTTGCATTTTCGGAAAATAAAATTCTC 57.471 29.630 23.96 9.25 38.97 2.87
3616 4241 0.609131 GTGGTTGGACCCTGGATGTG 60.609 60.000 0.00 0.00 37.50 3.21
3624 4249 0.842030 ACCCTGGATGTGCCTCTGAA 60.842 55.000 0.00 0.00 37.63 3.02
3665 4292 4.456911 TGCTGTTGAGATGAAATGGACTTC 59.543 41.667 0.00 0.00 0.00 3.01
3670 4297 4.592942 TGAGATGAAATGGACTTCCTTGG 58.407 43.478 0.00 0.00 36.82 3.61
3693 4320 4.768130 TTGTTGAAGAACCAACGTGAAA 57.232 36.364 0.00 0.00 46.89 2.69
3694 4321 4.768130 TGTTGAAGAACCAACGTGAAAA 57.232 36.364 0.00 0.00 46.89 2.29
3696 4323 4.102649 GTTGAAGAACCAACGTGAAAAGG 58.897 43.478 0.00 0.00 37.31 3.11
3700 4329 2.357952 AGAACCAACGTGAAAAGGCTTC 59.642 45.455 0.00 0.00 0.00 3.86
3703 4332 1.001378 CCAACGTGAAAAGGCTTCTGG 60.001 52.381 0.00 0.00 0.00 3.86
3718 4347 5.010012 AGGCTTCTGGTGTAAATTGAACAAG 59.990 40.000 0.00 0.00 0.00 3.16
3736 4365 9.724839 TTGAACAAGATTAAACTTTCTTTACCG 57.275 29.630 0.00 0.00 29.85 4.02
3737 4366 8.347035 TGAACAAGATTAAACTTTCTTTACCGG 58.653 33.333 0.00 0.00 29.85 5.28
3738 4367 7.812690 ACAAGATTAAACTTTCTTTACCGGT 57.187 32.000 13.98 13.98 29.85 5.28
3762 4399 5.294306 TGCACCGAAGATGATTTCTACAATC 59.706 40.000 0.00 0.00 33.05 2.67
3765 4402 5.525378 ACCGAAGATGATTTCTACAATCAGC 59.475 40.000 4.94 4.94 41.80 4.26
3771 4408 3.684305 TGATTTCTACAATCAGCCACACG 59.316 43.478 0.00 0.00 33.20 4.49
3783 4420 2.747460 CACACGGTGCCCATGAGG 60.747 66.667 8.30 0.00 39.47 3.86
3794 4431 2.689073 CCATGAGGGAGACACCTGT 58.311 57.895 0.00 0.00 42.10 4.00
3797 4434 2.093447 CCATGAGGGAGACACCTGTAAC 60.093 54.545 0.00 0.00 42.10 2.50
3813 4450 4.235360 CTGTAACACCTACCAAAGAGTCG 58.765 47.826 0.00 0.00 0.00 4.18
3822 4459 2.603776 AAAGAGTCGAGCCGGGGT 60.604 61.111 2.18 0.00 0.00 4.95
3871 4508 4.864334 CAGCACCTCGCCATCCCC 62.864 72.222 0.00 0.00 44.04 4.81
3889 4526 4.459089 GGCTCACCTCCACCTCGC 62.459 72.222 0.00 0.00 0.00 5.03
3896 4533 3.842923 CTCCACCTCGCGCTCCAT 61.843 66.667 5.56 0.00 0.00 3.41
3908 4545 0.171231 CGCTCCATGAACGACTGAGA 59.829 55.000 0.00 0.00 0.00 3.27
3912 4549 1.468914 TCCATGAACGACTGAGACGAG 59.531 52.381 11.75 0.00 34.70 4.18
3917 4568 2.143594 AACGACTGAGACGAGTGGGC 62.144 60.000 11.75 0.00 34.70 5.36
3965 4616 0.240945 CCACAATCTTTGGCGTCCAC 59.759 55.000 0.00 0.00 30.78 4.02
3966 4617 1.238439 CACAATCTTTGGCGTCCACT 58.762 50.000 0.00 0.00 30.78 4.00
3986 4637 1.453379 AGCTAGCTGGCATGCCTTG 60.453 57.895 35.53 27.40 36.94 3.61
3987 4638 1.751927 GCTAGCTGGCATGCCTTGT 60.752 57.895 35.53 21.79 36.94 3.16
4020 4671 1.842920 TCCTGCCTTGGCACTGAGA 60.843 57.895 10.65 2.88 0.00 3.27
4021 4672 1.203441 TCCTGCCTTGGCACTGAGAT 61.203 55.000 10.65 0.00 0.00 2.75
4022 4673 0.747283 CCTGCCTTGGCACTGAGATC 60.747 60.000 10.65 0.00 0.00 2.75
4023 4674 1.078918 TGCCTTGGCACTGAGATCG 60.079 57.895 10.65 0.00 0.00 3.69
4024 4675 1.078848 GCCTTGGCACTGAGATCGT 60.079 57.895 6.79 0.00 0.00 3.73
4025 4676 1.086634 GCCTTGGCACTGAGATCGTC 61.087 60.000 6.79 0.00 0.00 4.20
4026 4677 0.247460 CCTTGGCACTGAGATCGTCA 59.753 55.000 0.00 0.00 0.00 4.35
4034 4685 3.428180 GCACTGAGATCGTCAAAGCTCTA 60.428 47.826 0.00 0.00 33.60 2.43
4036 4687 4.095632 CACTGAGATCGTCAAAGCTCTAGA 59.904 45.833 0.00 0.00 33.60 2.43
4043 4694 2.280183 CGTCAAAGCTCTAGATTCGTGC 59.720 50.000 0.00 0.00 0.00 5.34
4050 4701 1.405821 CTCTAGATTCGTGCGAGGGTT 59.594 52.381 0.00 0.00 0.00 4.11
4053 4704 0.320374 AGATTCGTGCGAGGGTTTGA 59.680 50.000 0.00 0.00 0.00 2.69
4055 4706 0.250124 ATTCGTGCGAGGGTTTGACA 60.250 50.000 0.00 0.00 0.00 3.58
4059 4710 1.021968 GTGCGAGGGTTTGACAAAGT 58.978 50.000 0.00 0.00 0.00 2.66
4071 4722 1.064017 TGACAAAGTTGTGCTCCCCTT 60.064 47.619 0.42 0.00 42.43 3.95
4082 4733 0.962855 GCTCCCCTTCAAGGTGCTTC 60.963 60.000 1.78 0.00 40.07 3.86
4085 4736 1.237285 CCCCTTCAAGGTGCTTCGTG 61.237 60.000 1.78 0.00 31.93 4.35
4102 4753 0.475044 GTGGTGGGTCTTGGGTGTTA 59.525 55.000 0.00 0.00 0.00 2.41
4104 4755 0.608308 GGTGGGTCTTGGGTGTTAGC 60.608 60.000 0.00 0.00 0.00 3.09
4136 4802 1.376543 CTCATCTGATGTGGTGGTGC 58.623 55.000 16.66 0.00 0.00 5.01
4158 4824 2.661399 TGCTCTGCAGCTCAGACC 59.339 61.111 9.47 6.64 46.34 3.85
4160 4826 2.183811 CTCTGCAGCTCAGACCGG 59.816 66.667 9.47 0.00 46.34 5.28
4182 4848 2.642254 GCTGCAAGGCTTGATGGCA 61.642 57.895 30.45 19.18 44.55 4.92
4191 4857 1.514678 GCTTGATGGCACGTGTTGGA 61.515 55.000 18.38 0.00 0.00 3.53
4192 4858 0.518636 CTTGATGGCACGTGTTGGAG 59.481 55.000 18.38 4.58 0.00 3.86
4220 4886 1.272147 GGATCAGGTGGAGGTTGCTTT 60.272 52.381 0.00 0.00 0.00 3.51
4224 4890 0.538287 AGGTGGAGGTTGCTTTGAGC 60.538 55.000 0.00 0.00 42.82 4.26
4242 4908 1.115326 GCAGGTTTTCCCTTGTGCCT 61.115 55.000 0.00 0.00 42.73 4.75
4245 4911 1.780919 AGGTTTTCCCTTGTGCCTACT 59.219 47.619 0.00 0.00 42.73 2.57
4248 4914 3.694566 GGTTTTCCCTTGTGCCTACTATG 59.305 47.826 0.00 0.00 0.00 2.23
4249 4915 4.332828 GTTTTCCCTTGTGCCTACTATGT 58.667 43.478 0.00 0.00 0.00 2.29
4254 4920 2.679837 CCTTGTGCCTACTATGTTGCAG 59.320 50.000 0.00 0.00 33.80 4.41
4274 4941 0.529119 ACCACTTCGACGTTGTGTCC 60.529 55.000 16.77 0.00 45.23 4.02
4284 4951 1.340248 ACGTTGTGTCCTCCTAGTGTG 59.660 52.381 0.00 0.00 0.00 3.82
4286 4953 0.685097 TTGTGTCCTCCTAGTGTGGC 59.315 55.000 0.00 0.00 0.00 5.01
4288 4955 1.157513 TGTCCTCCTAGTGTGGCCA 59.842 57.895 0.00 0.00 0.00 5.36
4289 4956 0.904865 TGTCCTCCTAGTGTGGCCAG 60.905 60.000 5.11 0.00 0.00 4.85
4290 4957 0.905337 GTCCTCCTAGTGTGGCCAGT 60.905 60.000 5.11 0.00 0.00 4.00
4291 4958 0.904865 TCCTCCTAGTGTGGCCAGTG 60.905 60.000 5.11 0.00 0.00 3.66
4292 4959 1.194781 CCTCCTAGTGTGGCCAGTGT 61.195 60.000 5.11 0.00 0.00 3.55
4293 4960 0.687354 CTCCTAGTGTGGCCAGTGTT 59.313 55.000 5.11 0.00 0.00 3.32
4294 4961 0.396435 TCCTAGTGTGGCCAGTGTTG 59.604 55.000 5.11 0.00 0.00 3.33
4303 4970 2.669569 CCAGTGTTGGCTCCGTGG 60.670 66.667 0.00 0.00 37.73 4.94
4304 4971 2.425592 CAGTGTTGGCTCCGTGGA 59.574 61.111 0.00 0.00 0.00 4.02
4305 4972 1.669115 CAGTGTTGGCTCCGTGGAG 60.669 63.158 11.67 11.67 44.56 3.86
4306 4973 2.358737 GTGTTGGCTCCGTGGAGG 60.359 66.667 17.29 0.03 42.19 4.30
4316 4983 1.040646 TCCGTGGAGGATATGTGAGC 58.959 55.000 0.00 0.00 45.98 4.26
4317 4984 0.319040 CCGTGGAGGATATGTGAGCG 60.319 60.000 0.00 0.00 45.00 5.03
4318 4985 0.668535 CGTGGAGGATATGTGAGCGA 59.331 55.000 0.00 0.00 0.00 4.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.558396 AGTATGTAGTATGTAGTAACAGACCTC 57.442 37.037 0.03 0.00 46.75 3.85
4 5 9.784531 GGGTAGTATGTAGTATGTAGTAACAGA 57.215 37.037 0.00 0.00 39.49 3.41
5 6 8.715998 CGGGTAGTATGTAGTATGTAGTAACAG 58.284 40.741 0.00 0.00 39.49 3.16
7 8 8.833231 TCGGGTAGTATGTAGTATGTAGTAAC 57.167 38.462 0.00 0.00 0.00 2.50
9 10 9.658799 GAATCGGGTAGTATGTAGTATGTAGTA 57.341 37.037 0.00 0.00 0.00 1.82
10 11 8.159447 TGAATCGGGTAGTATGTAGTATGTAGT 58.841 37.037 0.00 0.00 0.00 2.73
11 12 8.557592 TGAATCGGGTAGTATGTAGTATGTAG 57.442 38.462 0.00 0.00 0.00 2.74
12 13 8.786898 GTTGAATCGGGTAGTATGTAGTATGTA 58.213 37.037 0.00 0.00 0.00 2.29
13 14 7.286087 TGTTGAATCGGGTAGTATGTAGTATGT 59.714 37.037 0.00 0.00 0.00 2.29
14 15 7.654568 TGTTGAATCGGGTAGTATGTAGTATG 58.345 38.462 0.00 0.00 0.00 2.39
15 16 7.828508 TGTTGAATCGGGTAGTATGTAGTAT 57.171 36.000 0.00 0.00 0.00 2.12
16 17 7.643569 TTGTTGAATCGGGTAGTATGTAGTA 57.356 36.000 0.00 0.00 0.00 1.82
17 18 6.534475 TTGTTGAATCGGGTAGTATGTAGT 57.466 37.500 0.00 0.00 0.00 2.73
18 19 7.170998 GGATTTGTTGAATCGGGTAGTATGTAG 59.829 40.741 0.00 0.00 44.21 2.74
19 20 6.987992 GGATTTGTTGAATCGGGTAGTATGTA 59.012 38.462 0.00 0.00 44.21 2.29
20 21 5.820947 GGATTTGTTGAATCGGGTAGTATGT 59.179 40.000 0.00 0.00 44.21 2.29
21 22 6.055588 AGGATTTGTTGAATCGGGTAGTATG 58.944 40.000 0.00 0.00 44.21 2.39
22 23 6.248569 AGGATTTGTTGAATCGGGTAGTAT 57.751 37.500 0.00 0.00 44.21 2.12
23 24 5.687166 AGGATTTGTTGAATCGGGTAGTA 57.313 39.130 0.00 0.00 44.21 1.82
24 25 4.569719 AGGATTTGTTGAATCGGGTAGT 57.430 40.909 0.00 0.00 44.21 2.73
25 26 7.713507 TGTATAAGGATTTGTTGAATCGGGTAG 59.286 37.037 0.00 0.00 44.21 3.18
26 27 7.496591 GTGTATAAGGATTTGTTGAATCGGGTA 59.503 37.037 0.00 0.00 44.21 3.69
27 28 6.317893 GTGTATAAGGATTTGTTGAATCGGGT 59.682 38.462 0.00 0.00 44.21 5.28
28 29 6.317642 TGTGTATAAGGATTTGTTGAATCGGG 59.682 38.462 0.00 0.00 44.21 5.14
29 30 7.186804 GTGTGTATAAGGATTTGTTGAATCGG 58.813 38.462 0.00 0.00 44.21 4.18
30 31 6.899771 CGTGTGTATAAGGATTTGTTGAATCG 59.100 38.462 0.00 0.00 44.21 3.34
40 41 7.934665 TGGTTATATTGCGTGTGTATAAGGATT 59.065 33.333 0.00 0.00 0.00 3.01
51 52 6.877322 ACTAACTCTTTGGTTATATTGCGTGT 59.123 34.615 0.00 0.00 32.25 4.49
104 105 6.774170 TGTCTGGTTCACTAAGACTACACTAA 59.226 38.462 11.91 0.00 40.79 2.24
135 139 9.781834 TGCTAATATTTTTACATACACTGCAAC 57.218 29.630 0.00 0.00 0.00 4.17
136 140 9.781834 GTGCTAATATTTTTACATACACTGCAA 57.218 29.630 0.00 0.00 0.00 4.08
154 159 6.569780 AGTCGTTGATACACATGTGCTAATA 58.430 36.000 25.68 10.87 0.00 0.98
175 180 6.846350 ACATATGCAGAAAACTAGCAAAGTC 58.154 36.000 1.58 0.00 42.15 3.01
176 181 6.824305 ACATATGCAGAAAACTAGCAAAGT 57.176 33.333 1.58 0.00 42.15 2.66
203 208 4.277476 TCACTTCATTGTTCCCACAACTT 58.723 39.130 0.00 0.00 45.88 2.66
207 212 3.156293 CCATCACTTCATTGTTCCCACA 58.844 45.455 0.00 0.00 0.00 4.17
208 213 2.094545 GCCATCACTTCATTGTTCCCAC 60.095 50.000 0.00 0.00 0.00 4.61
219 224 3.265791 ACTTCTTCATCGCCATCACTTC 58.734 45.455 0.00 0.00 0.00 3.01
220 225 3.265791 GACTTCTTCATCGCCATCACTT 58.734 45.455 0.00 0.00 0.00 3.16
225 230 4.040829 TCCATATGACTTCTTCATCGCCAT 59.959 41.667 3.65 0.00 41.53 4.40
245 250 1.314867 GAGGTCCCCTCTCCATCCA 59.685 63.158 2.98 0.00 46.41 3.41
254 259 3.477956 TTCGGTGGTGAGGTCCCCT 62.478 63.158 0.00 0.00 36.03 4.79
269 274 1.377202 CTCCACCCCCACATGTTCG 60.377 63.158 0.00 0.00 0.00 3.95
292 297 4.105057 GGGACCTCTGATCTTAGAGTCCTA 59.895 50.000 19.52 0.00 42.09 2.94
299 304 1.403814 TGCGGGACCTCTGATCTTAG 58.596 55.000 0.00 0.00 0.00 2.18
301 306 0.467384 CATGCGGGACCTCTGATCTT 59.533 55.000 0.00 0.00 0.00 2.40
307 312 4.148825 GCGTCATGCGGGACCTCT 62.149 66.667 10.70 0.00 41.69 3.69
336 341 0.249197 TCGGCAAGATCATCTCGCAG 60.249 55.000 0.00 0.00 0.00 5.18
337 342 0.528466 GTCGGCAAGATCATCTCGCA 60.528 55.000 0.00 0.00 0.00 5.10
338 343 0.528466 TGTCGGCAAGATCATCTCGC 60.528 55.000 0.00 0.00 0.00 5.03
339 344 2.145958 ATGTCGGCAAGATCATCTCG 57.854 50.000 0.00 0.00 0.00 4.04
347 352 3.733988 CGCTTCTAGTTATGTCGGCAAGA 60.734 47.826 0.00 0.00 0.00 3.02
350 355 1.202371 CCGCTTCTAGTTATGTCGGCA 60.202 52.381 0.00 0.00 0.00 5.69
353 358 3.312973 AGACTCCGCTTCTAGTTATGTCG 59.687 47.826 0.00 0.00 0.00 4.35
362 367 1.893137 TGCTTTCAGACTCCGCTTCTA 59.107 47.619 0.00 0.00 0.00 2.10
364 369 1.512926 TTGCTTTCAGACTCCGCTTC 58.487 50.000 0.00 0.00 0.00 3.86
365 370 1.604278 GTTTGCTTTCAGACTCCGCTT 59.396 47.619 0.00 0.00 0.00 4.68
386 391 1.660333 CGAGTTTTTCTCTTGTGCGCC 60.660 52.381 4.18 0.00 40.75 6.53
388 393 1.663494 GCGAGTTTTTCTCTTGTGCG 58.337 50.000 0.00 0.00 40.75 5.34
406 411 1.200252 TCACTGTAGAGTTGAGAGCGC 59.800 52.381 0.00 0.00 0.00 5.92
408 413 3.119173 AGCATCACTGTAGAGTTGAGAGC 60.119 47.826 0.00 1.68 0.00 4.09
409 414 4.422840 CAGCATCACTGTAGAGTTGAGAG 58.577 47.826 0.00 0.00 41.86 3.20
416 421 3.815856 ATCACCAGCATCACTGTAGAG 57.184 47.619 0.00 0.00 45.68 2.43
417 422 3.515104 TCAATCACCAGCATCACTGTAGA 59.485 43.478 0.00 0.00 45.68 2.59
421 426 2.708051 AGTCAATCACCAGCATCACTG 58.292 47.619 0.00 0.00 46.77 3.66
434 439 6.459066 TGATAGTAGCCTATGCAAGTCAATC 58.541 40.000 0.00 0.00 41.13 2.67
435 440 6.425210 TGATAGTAGCCTATGCAAGTCAAT 57.575 37.500 0.00 0.00 41.13 2.57
436 441 5.869649 TGATAGTAGCCTATGCAAGTCAA 57.130 39.130 0.00 0.00 41.13 3.18
535 540 9.168451 GCTAGAAGCTATGTATACAGATGACTA 57.832 37.037 11.91 9.20 38.45 2.59
553 558 5.353678 AGACATCAAATGTGAAGCTAGAAGC 59.646 40.000 0.00 0.00 45.03 3.86
561 566 4.778534 AGCCAAGACATCAAATGTGAAG 57.221 40.909 0.00 0.00 45.03 3.02
566 571 6.218019 TGAAGAAAAGCCAAGACATCAAATG 58.782 36.000 0.00 0.00 0.00 2.32
604 609 6.009589 TCTGGGTTGATACATGTTGTTTCAT 58.990 36.000 2.30 0.00 37.96 2.57
608 613 6.323739 AGTTTTCTGGGTTGATACATGTTGTT 59.676 34.615 2.30 0.00 0.00 2.83
611 616 5.181245 CGAGTTTTCTGGGTTGATACATGTT 59.819 40.000 2.30 0.00 0.00 2.71
618 623 2.290323 CCCTCGAGTTTTCTGGGTTGAT 60.290 50.000 12.31 0.00 33.03 2.57
688 879 3.230134 GGCTATGGTTATTGGGCATTCA 58.770 45.455 0.00 0.00 0.00 2.57
693 884 2.666317 ACTTGGCTATGGTTATTGGGC 58.334 47.619 0.00 0.00 0.00 5.36
726 920 9.542462 TTAAATTTATAACCATGACTCGAGGAG 57.458 33.333 18.41 3.08 35.52 3.69
775 969 4.267928 GTGACATGCAAACGAGATACTACC 59.732 45.833 0.00 0.00 0.00 3.18
776 970 4.862574 TGTGACATGCAAACGAGATACTAC 59.137 41.667 0.00 0.00 0.00 2.73
777 971 5.066968 TGTGACATGCAAACGAGATACTA 57.933 39.130 0.00 0.00 0.00 1.82
778 972 3.925379 TGTGACATGCAAACGAGATACT 58.075 40.909 0.00 0.00 0.00 2.12
779 973 4.864916 ATGTGACATGCAAACGAGATAC 57.135 40.909 0.00 0.00 0.00 2.24
783 977 6.932901 ATTTTTATGTGACATGCAAACGAG 57.067 33.333 8.61 0.00 0.00 4.18
830 1028 2.359967 GGTGCCCTAGCTCCGAAGT 61.360 63.158 0.00 0.00 42.42 3.01
831 1029 2.501610 GGTGCCCTAGCTCCGAAG 59.498 66.667 0.00 0.00 42.42 3.79
862 1060 2.808206 GGATTGGGATCGGACGGCT 61.808 63.158 0.00 0.00 32.84 5.52
899 1097 4.409218 GCTCGGTACACGTCGGCA 62.409 66.667 0.00 0.00 44.69 5.69
1174 1385 2.202824 TGGGATAACGCGGCGAAG 60.203 61.111 30.94 6.10 0.00 3.79
1178 1389 0.874607 CACTACTGGGATAACGCGGC 60.875 60.000 12.47 0.00 38.64 6.53
1201 1431 3.817647 CTCAGCATAGCCTTTTACCATCC 59.182 47.826 0.00 0.00 0.00 3.51
1243 1527 2.503356 ACCAGATCAAGAGCCGAAGAAT 59.497 45.455 0.00 0.00 0.00 2.40
1302 1595 4.326278 CGTTCGCTCATGTACTGTTTACAT 59.674 41.667 0.00 0.00 38.57 2.29
1377 1671 2.947652 GAGGACATCACACCCATGATTG 59.052 50.000 0.00 0.00 37.20 2.67
1396 1696 3.756117 AGCTGGTAGGTTTTGAAAGGAG 58.244 45.455 0.00 0.00 0.00 3.69
1403 1703 4.213482 GTGACAACTAGCTGGTAGGTTTTG 59.787 45.833 17.30 14.18 32.29 2.44
1472 1792 6.436261 CCGTCTTTTCTCCCTTTTTCTAAAC 58.564 40.000 0.00 0.00 0.00 2.01
1486 1806 4.202430 ACTGACATAAACCCCGTCTTTTCT 60.202 41.667 0.00 0.00 0.00 2.52
1492 1816 4.081807 AGAGTAACTGACATAAACCCCGTC 60.082 45.833 0.00 0.00 0.00 4.79
1520 1844 7.761038 AGAAAAACCCCAATCTAACTAACAG 57.239 36.000 0.00 0.00 0.00 3.16
1531 1856 6.041637 GGACTACAGAAAAGAAAAACCCCAAT 59.958 38.462 0.00 0.00 0.00 3.16
1667 1998 1.115930 ACTCACTCCCAGTCGCAACT 61.116 55.000 0.00 0.00 35.60 3.16
1745 2076 7.709269 TCGAATCTAATATTGTGTAACCAGC 57.291 36.000 0.00 0.00 34.36 4.85
1748 2079 9.382244 GCAAATCGAATCTAATATTGTGTAACC 57.618 33.333 0.00 0.00 34.36 2.85
1761 2092 2.286359 GCATGCACGCAAATCGAATCTA 60.286 45.455 14.21 0.00 41.67 1.98
1765 2096 0.240678 AAGCATGCACGCAAATCGAA 59.759 45.000 21.98 0.00 41.67 3.71
1773 2104 1.135603 TGATGAGAAAAGCATGCACGC 60.136 47.619 21.98 0.00 0.00 5.34
1775 2107 5.175126 GCATAATGATGAGAAAAGCATGCAC 59.825 40.000 21.98 8.21 36.97 4.57
1824 2292 7.066284 GTGGATATTTTCATACAAGCAGTGAGT 59.934 37.037 0.00 0.00 0.00 3.41
1883 2351 4.368315 TGTCCATCTATGTATTGCACGTC 58.632 43.478 0.00 0.00 0.00 4.34
1885 2353 5.929697 AATGTCCATCTATGTATTGCACG 57.070 39.130 0.00 0.00 0.00 5.34
2159 2644 3.503748 GGATATCACCCTGCAAAGCATAC 59.496 47.826 4.83 0.00 38.13 2.39
2368 2870 3.807622 CACGGCCCTACATACATAACAAG 59.192 47.826 0.00 0.00 0.00 3.16
2488 3086 8.982091 AGTAGAGTAAACTCAGATGTATAGCA 57.018 34.615 12.43 0.00 45.21 3.49
2751 3357 0.818296 GTACAGCAGTCGGTCATCCT 59.182 55.000 0.00 0.00 0.00 3.24
2998 3610 5.416952 ACGTCATATATTTAGGTACGGAGGG 59.583 44.000 0.00 0.00 33.44 4.30
3000 3612 8.697067 CAAAACGTCATATATTTAGGTACGGAG 58.303 37.037 0.00 0.00 33.44 4.63
3001 3613 7.652909 CCAAAACGTCATATATTTAGGTACGGA 59.347 37.037 0.00 0.00 33.44 4.69
3002 3614 7.439056 ACCAAAACGTCATATATTTAGGTACGG 59.561 37.037 0.00 0.00 33.44 4.02
3003 3615 8.356533 ACCAAAACGTCATATATTTAGGTACG 57.643 34.615 0.00 0.00 35.17 3.67
3029 3641 9.096823 TCCCTCCGTACTTAAATATATGACATT 57.903 33.333 0.00 0.00 0.00 2.71
3031 3643 7.727186 ACTCCCTCCGTACTTAAATATATGACA 59.273 37.037 0.00 0.00 0.00 3.58
3032 3644 8.120140 ACTCCCTCCGTACTTAAATATATGAC 57.880 38.462 0.00 0.00 0.00 3.06
3033 3645 9.986157 ATACTCCCTCCGTACTTAAATATATGA 57.014 33.333 0.00 0.00 0.00 2.15
3039 3651 9.240734 CAGTATATACTCCCTCCGTACTTAAAT 57.759 37.037 12.62 0.00 33.46 1.40
3040 3652 8.439971 TCAGTATATACTCCCTCCGTACTTAAA 58.560 37.037 12.62 0.00 33.46 1.52
3041 3653 7.880195 GTCAGTATATACTCCCTCCGTACTTAA 59.120 40.741 12.62 0.00 33.46 1.85
3042 3654 7.390027 GTCAGTATATACTCCCTCCGTACTTA 58.610 42.308 12.62 0.00 33.46 2.24
3043 3655 6.237154 GTCAGTATATACTCCCTCCGTACTT 58.763 44.000 12.62 0.00 33.46 2.24
3044 3656 5.280419 GGTCAGTATATACTCCCTCCGTACT 60.280 48.000 12.62 0.00 33.46 2.73
3045 3657 4.940654 GGTCAGTATATACTCCCTCCGTAC 59.059 50.000 12.62 2.19 33.46 3.67
3046 3658 4.598807 TGGTCAGTATATACTCCCTCCGTA 59.401 45.833 20.93 5.75 33.46 4.02
3047 3659 3.396946 TGGTCAGTATATACTCCCTCCGT 59.603 47.826 20.93 0.00 33.46 4.69
3048 3660 4.030314 TGGTCAGTATATACTCCCTCCG 57.970 50.000 20.93 8.70 33.46 4.63
3049 3661 4.527427 GGTTGGTCAGTATATACTCCCTCC 59.473 50.000 20.93 18.81 33.46 4.30
3050 3662 4.527427 GGGTTGGTCAGTATATACTCCCTC 59.473 50.000 20.46 15.38 33.46 4.30
3051 3663 4.078219 TGGGTTGGTCAGTATATACTCCCT 60.078 45.833 24.82 2.52 33.46 4.20
3052 3664 4.228824 TGGGTTGGTCAGTATATACTCCC 58.771 47.826 20.75 20.75 33.46 4.30
3053 3665 5.145564 TCTGGGTTGGTCAGTATATACTCC 58.854 45.833 12.62 12.21 33.46 3.85
3054 3666 5.244178 CCTCTGGGTTGGTCAGTATATACTC 59.756 48.000 12.62 2.91 33.46 2.59
3106 3718 4.706476 TCAAAATCTGATGGACACATTCCC 59.294 41.667 0.00 0.00 45.17 3.97
3111 3724 8.298854 CAGTTTTATCAAAATCTGATGGACACA 58.701 33.333 0.00 0.00 44.84 3.72
3156 3769 8.698210 TCTTATTTCAATTTTGGATCTCCCATG 58.302 33.333 0.00 0.00 46.10 3.66
3167 3780 9.613957 TGCATGCATTTTCTTATTTCAATTTTG 57.386 25.926 18.46 0.00 0.00 2.44
3225 3838 6.835819 ATATCAGCATTTCAGCTATTGCAT 57.164 33.333 1.12 1.71 44.54 3.96
3305 3918 5.477291 AGGTAGAATCTTCAGTCTTTCGACA 59.523 40.000 0.00 0.00 42.73 4.35
3325 3938 2.291209 TACGACCCTGTGACAAGGTA 57.709 50.000 5.74 0.00 35.34 3.08
3345 3958 3.056107 TCTGCGCTACTACAAGACCAAAT 60.056 43.478 9.73 0.00 0.00 2.32
3377 3990 2.005451 ACGATGCAACATCTTCAGCTC 58.995 47.619 6.06 0.00 0.00 4.09
3400 4013 6.418819 CAGACACATGAAAACTTCCATTCAAC 59.581 38.462 0.00 0.00 38.88 3.18
3421 4034 3.589988 CGGGCCAGATACATATTCAGAC 58.410 50.000 4.39 0.00 0.00 3.51
3458 4083 4.428209 ACTATCAGAAGATGAGTGTTGCG 58.572 43.478 0.00 0.00 42.53 4.85
3486 4111 7.437713 ACCAGATTGACATCATTAGTTAGGA 57.562 36.000 0.00 0.00 0.00 2.94
3487 4112 9.784531 ATAACCAGATTGACATCATTAGTTAGG 57.215 33.333 0.00 0.00 0.00 2.69
3490 4115 8.408601 GCAATAACCAGATTGACATCATTAGTT 58.591 33.333 0.40 0.00 38.83 2.24
3491 4116 7.557358 TGCAATAACCAGATTGACATCATTAGT 59.443 33.333 0.40 0.00 38.83 2.24
3500 4125 9.585099 TTTATTCAATGCAATAACCAGATTGAC 57.415 29.630 0.00 0.00 38.83 3.18
3532 4157 5.898630 TTTTCCGAAAATGCAACTAAAGC 57.101 34.783 2.01 0.00 0.00 3.51
3564 4189 5.333513 AGTTTTCGCTTCTGAGTCGTATAG 58.666 41.667 1.70 0.00 0.00 1.31
3575 4200 4.142138 ACCATCGAGATAGTTTTCGCTTCT 60.142 41.667 0.00 0.00 36.79 2.85
3616 4241 5.687285 CACAAAAATACAACACTTCAGAGGC 59.313 40.000 0.00 0.00 0.00 4.70
3624 4249 5.719173 ACAGCAACACAAAAATACAACACT 58.281 33.333 0.00 0.00 0.00 3.55
3670 4297 4.086199 TCACGTTGGTTCTTCAACAAAC 57.914 40.909 8.19 0.00 45.16 2.93
3685 4312 1.676006 CACCAGAAGCCTTTTCACGTT 59.324 47.619 0.00 0.00 0.00 3.99
3693 4320 4.892934 TGTTCAATTTACACCAGAAGCCTT 59.107 37.500 0.00 0.00 0.00 4.35
3694 4321 4.469657 TGTTCAATTTACACCAGAAGCCT 58.530 39.130 0.00 0.00 0.00 4.58
3696 4323 6.072112 TCTTGTTCAATTTACACCAGAAGC 57.928 37.500 0.00 0.00 0.00 3.86
3700 4329 9.965824 AGTTTAATCTTGTTCAATTTACACCAG 57.034 29.630 0.00 0.00 0.00 4.00
3718 4347 5.854866 GTGCACCGGTAAAGAAAGTTTAATC 59.145 40.000 6.87 0.00 0.00 1.75
3736 4365 2.359900 AGAAATCATCTTCGGTGCACC 58.640 47.619 26.78 26.78 33.39 5.01
3737 4366 3.932710 TGTAGAAATCATCTTCGGTGCAC 59.067 43.478 8.80 8.80 39.71 4.57
3738 4367 4.200838 TGTAGAAATCATCTTCGGTGCA 57.799 40.909 0.00 0.00 39.71 4.57
3748 4385 4.333649 CGTGTGGCTGATTGTAGAAATCAT 59.666 41.667 1.50 0.00 36.23 2.45
3753 4390 1.346395 ACCGTGTGGCTGATTGTAGAA 59.654 47.619 0.00 0.00 39.70 2.10
3783 4420 2.233186 GGTAGGTGTTACAGGTGTCTCC 59.767 54.545 0.00 0.00 33.73 3.71
3794 4431 3.057033 GCTCGACTCTTTGGTAGGTGTTA 60.057 47.826 0.00 0.00 0.00 2.41
3797 4434 1.404315 GGCTCGACTCTTTGGTAGGTG 60.404 57.143 0.00 0.00 0.00 4.00
3854 4491 4.864334 GGGGATGGCGAGGTGCTG 62.864 72.222 0.00 0.00 45.43 4.41
3871 4508 4.135153 CGAGGTGGAGGTGAGCCG 62.135 72.222 0.00 0.00 40.50 5.52
3889 4526 0.171231 TCTCAGTCGTTCATGGAGCG 59.829 55.000 0.00 0.00 37.60 5.03
3896 4533 0.591659 CCACTCGTCTCAGTCGTTCA 59.408 55.000 0.00 0.00 0.00 3.18
3917 4568 4.082523 ACCACGATGACCAGCCCG 62.083 66.667 0.00 0.00 0.00 6.13
3926 4577 3.842126 CTCGCGCACACCACGATG 61.842 66.667 8.75 0.00 34.94 3.84
3965 4616 1.892862 GGCATGCCAGCTAGCTGAG 60.893 63.158 40.03 30.09 46.30 3.35
3966 4617 1.918467 AAGGCATGCCAGCTAGCTGA 61.918 55.000 40.03 24.98 46.30 4.26
3986 4637 2.629763 GACACGGGCGACACAAAC 59.370 61.111 0.00 0.00 0.00 2.93
3987 4638 2.589442 GGACACGGGCGACACAAA 60.589 61.111 0.00 0.00 0.00 2.83
4010 4661 1.941209 GCTTTGACGATCTCAGTGCCA 60.941 52.381 0.00 0.00 0.00 4.92
4020 4671 4.355437 CACGAATCTAGAGCTTTGACGAT 58.645 43.478 0.00 0.00 0.00 3.73
4021 4672 3.759418 CACGAATCTAGAGCTTTGACGA 58.241 45.455 0.00 0.00 0.00 4.20
4022 4673 2.280183 GCACGAATCTAGAGCTTTGACG 59.720 50.000 0.00 0.00 0.00 4.35
4023 4674 2.280183 CGCACGAATCTAGAGCTTTGAC 59.720 50.000 0.00 0.00 0.00 3.18
4024 4675 2.163613 TCGCACGAATCTAGAGCTTTGA 59.836 45.455 0.00 0.00 0.00 2.69
4025 4676 2.530177 TCGCACGAATCTAGAGCTTTG 58.470 47.619 0.00 0.00 0.00 2.77
4026 4677 2.480416 CCTCGCACGAATCTAGAGCTTT 60.480 50.000 0.00 0.00 0.00 3.51
4034 4685 0.320374 TCAAACCCTCGCACGAATCT 59.680 50.000 0.00 0.00 0.00 2.40
4036 4687 0.250124 TGTCAAACCCTCGCACGAAT 60.250 50.000 0.00 0.00 0.00 3.34
4043 4694 2.794631 GCACAACTTTGTCAAACCCTCG 60.795 50.000 0.00 0.00 39.91 4.63
4050 4701 1.064017 AGGGGAGCACAACTTTGTCAA 60.064 47.619 0.00 0.00 39.91 3.18
4053 4704 1.064017 TGAAGGGGAGCACAACTTTGT 60.064 47.619 0.00 0.00 43.36 2.83
4055 4706 2.310538 CTTGAAGGGGAGCACAACTTT 58.689 47.619 0.00 0.00 0.00 2.66
4059 4710 0.178992 CACCTTGAAGGGGAGCACAA 60.179 55.000 16.78 0.00 43.10 3.33
4071 4722 1.227823 CCACCACGAAGCACCTTGA 60.228 57.895 0.00 0.00 0.00 3.02
4082 4733 2.281484 CACCCAAGACCCACCACG 60.281 66.667 0.00 0.00 0.00 4.94
4085 4736 0.608308 GCTAACACCCAAGACCCACC 60.608 60.000 0.00 0.00 0.00 4.61
4102 4753 0.833287 ATGAGGTTGCAGATACGGCT 59.167 50.000 0.00 0.00 0.00 5.52
4104 4755 2.101415 TCAGATGAGGTTGCAGATACGG 59.899 50.000 0.00 0.00 0.00 4.02
4160 4826 2.348888 ATCAAGCCTTGCAGCTGCC 61.349 57.895 34.64 19.67 44.11 4.85
4182 4848 1.594293 CAGAACGCCTCCAACACGT 60.594 57.895 0.00 0.00 42.81 4.49
4191 4857 1.599047 CACCTGATCCAGAACGCCT 59.401 57.895 0.00 0.00 32.44 5.52
4192 4858 1.450312 CCACCTGATCCAGAACGCC 60.450 63.158 0.00 0.00 32.44 5.68
4226 4892 2.287977 AGTAGGCACAAGGGAAAACC 57.712 50.000 0.00 0.00 40.67 3.27
4228 4894 4.650972 ACATAGTAGGCACAAGGGAAAA 57.349 40.909 0.00 0.00 0.00 2.29
4242 4908 3.508402 TCGAAGTGGTCTGCAACATAGTA 59.492 43.478 0.00 0.00 0.00 1.82
4245 4911 2.683968 GTCGAAGTGGTCTGCAACATA 58.316 47.619 0.00 0.00 0.00 2.29
4248 4914 0.874607 ACGTCGAAGTGGTCTGCAAC 60.875 55.000 2.31 0.00 0.00 4.17
4249 4915 0.179094 AACGTCGAAGTGGTCTGCAA 60.179 50.000 4.34 0.00 0.00 4.08
4254 4920 0.850856 GACACAACGTCGAAGTGGTC 59.149 55.000 8.69 11.11 37.58 4.02
4274 4941 0.687354 AACACTGGCCACACTAGGAG 59.313 55.000 0.00 0.00 0.00 3.69
4286 4953 2.669569 CCACGGAGCCAACACTGG 60.670 66.667 0.00 0.00 46.65 4.00
4288 4955 2.743718 CTCCACGGAGCCAACACT 59.256 61.111 0.00 0.00 35.31 3.55
4289 4956 2.358737 CCTCCACGGAGCCAACAC 60.359 66.667 7.64 0.00 40.69 3.32
4290 4957 2.525629 TCCTCCACGGAGCCAACA 60.526 61.111 7.64 0.00 40.69 3.33
4298 4965 0.319040 CGCTCACATATCCTCCACGG 60.319 60.000 0.00 0.00 0.00 4.94
4299 4966 0.668535 TCGCTCACATATCCTCCACG 59.331 55.000 0.00 0.00 0.00 4.94


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

AutoCloner maintained by Alex Coulton.