Multiple sequence alignment - TraesCS4B01G335500

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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 TraesCS4B01G335500 chr4B 100.000 4908 0 0 1 4908 627318217 627323124 0.000000e+00 9064.0
1 TraesCS4B01G335500 chr4D 92.414 4614 209 58 1 4558 489174403 489178931 0.000000e+00 6451.0
2 TraesCS4B01G335500 chr4D 80.137 146 15 10 4761 4899 489179409 489179547 4.040000e-16 97.1
3 TraesCS4B01G335500 chr5A 89.110 4665 301 109 1 4559 670621466 670626029 0.000000e+00 5609.0
4 TraesCS4B01G335500 chr5A 90.411 73 4 1 4827 4899 670626948 670627017 5.230000e-15 93.5


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 TraesCS4B01G335500 chr4B 627318217 627323124 4907 False 9064.00 9064 100.0000 1 4908 1 chr4B.!!$F1 4907
1 TraesCS4B01G335500 chr4D 489174403 489179547 5144 False 3274.05 6451 86.2755 1 4899 2 chr4D.!!$F1 4898
2 TraesCS4B01G335500 chr5A 670621466 670627017 5551 False 2851.25 5609 89.7605 1 4899 2 chr5A.!!$F1 4898

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
324 356 0.114560 TTCTCTGTCCCCTCGGTCTT 59.885 55.0 0.0 0.00 0.0 3.01 F
447 487 0.687354 TCTGAGCTGTTCCTTCCACC 59.313 55.0 0.0 0.00 0.0 4.61 F
1983 2079 1.016653 GTGCTGTTCTCGGAAGGCTC 61.017 60.0 0.0 5.92 0.0 4.70 F
2658 2754 0.881118 GCTGCAACTCGGGATTTTCA 59.119 50.0 0.0 0.00 0.0 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2160 2256 1.135373 ACAGTGGTCTTATGCGTCTCG 60.135 52.381 0.0 0.0 0.00 4.04 R
2164 2260 1.893137 TCTCACAGTGGTCTTATGCGT 59.107 47.619 0.0 0.0 0.00 5.24 R
3892 4009 0.610174 TCCTTCAGTAGGTGCTGCTG 59.390 55.000 0.0 0.0 45.03 4.41 R
4330 4466 0.246360 TGCTCACCCAGATACACACG 59.754 55.000 0.0 0.0 0.00 4.49 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
30 31 4.577677 TGCAAACAGAGGCGGCCA 62.578 61.111 23.09 0.00 0.00 5.36
72 73 6.555315 TGCTCTCTTTCTTTTCAGTTTTCAC 58.445 36.000 0.00 0.00 0.00 3.18
73 74 5.974158 GCTCTCTTTCTTTTCAGTTTTCACC 59.026 40.000 0.00 0.00 0.00 4.02
74 75 6.451064 TCTCTTTCTTTTCAGTTTTCACCC 57.549 37.500 0.00 0.00 0.00 4.61
75 76 5.949354 TCTCTTTCTTTTCAGTTTTCACCCA 59.051 36.000 0.00 0.00 0.00 4.51
77 78 6.572519 TCTTTCTTTTCAGTTTTCACCCATG 58.427 36.000 0.00 0.00 0.00 3.66
78 79 4.935352 TCTTTTCAGTTTTCACCCATGG 57.065 40.909 4.14 4.14 0.00 3.66
108 131 1.275421 GGGAGTGAGGAAGAAGGGGG 61.275 65.000 0.00 0.00 0.00 5.40
121 149 0.771755 AAGGGGGAAGTGAACTGACC 59.228 55.000 0.00 0.00 0.00 4.02
143 171 4.180946 CGAGGTCGAGGGAGCACG 62.181 72.222 0.00 0.00 45.30 5.34
159 187 2.898840 CGCATAGCCCTGCACCTG 60.899 66.667 8.62 0.00 42.40 4.00
160 188 3.214845 GCATAGCCCTGCACCTGC 61.215 66.667 3.36 0.00 41.87 4.85
207 235 1.447317 GCAGTCCACACCACCACAAG 61.447 60.000 0.00 0.00 0.00 3.16
264 292 3.655211 CCTTGCTGGCCCTGACCT 61.655 66.667 0.00 0.00 0.00 3.85
265 293 2.045536 CTTGCTGGCCCTGACCTC 60.046 66.667 0.00 0.00 0.00 3.85
266 294 3.635268 CTTGCTGGCCCTGACCTCC 62.635 68.421 0.00 0.00 0.00 4.30
324 356 0.114560 TTCTCTGTCCCCTCGGTCTT 59.885 55.000 0.00 0.00 0.00 3.01
355 387 1.437986 GCTCACCTGGGTACTAGCG 59.562 63.158 0.00 0.00 34.76 4.26
356 388 2.017559 GCTCACCTGGGTACTAGCGG 62.018 65.000 0.00 0.00 34.76 5.52
362 397 2.158696 ACCTGGGTACTAGCGGTAGTAG 60.159 54.545 29.56 20.93 41.53 2.57
368 403 3.496507 GGTACTAGCGGTAGTAGTAGCAC 59.503 52.174 29.56 20.61 45.04 4.40
413 453 2.201732 CGAAGAGAGTCGAGAGAGAGG 58.798 57.143 0.00 0.00 43.86 3.69
414 454 2.418197 CGAAGAGAGTCGAGAGAGAGGT 60.418 54.545 0.00 0.00 43.86 3.85
420 460 3.383825 AGAGTCGAGAGAGAGGTAGAGAC 59.616 52.174 0.00 0.00 43.49 3.36
422 462 1.409790 TCGAGAGAGAGGTAGAGACCG 59.590 57.143 0.00 0.00 42.91 4.79
447 487 0.687354 TCTGAGCTGTTCCTTCCACC 59.313 55.000 0.00 0.00 0.00 4.61
493 534 5.112686 GGGCACATCAATATAGCTAGCTAC 58.887 45.833 26.41 9.57 0.00 3.58
550 592 5.913137 TCTTTTCTTTTTGTCAAGCTCCA 57.087 34.783 0.00 0.00 0.00 3.86
564 606 1.511305 CTCCATGCTTGCTTGGCTG 59.489 57.895 18.93 12.02 32.80 4.85
565 607 1.945354 CTCCATGCTTGCTTGGCTGG 61.945 60.000 18.93 10.09 32.80 4.85
566 608 2.280552 CCATGCTTGCTTGGCTGGT 61.281 57.895 13.32 0.00 0.00 4.00
567 609 1.214589 CATGCTTGCTTGGCTGGTC 59.785 57.895 1.19 0.00 0.00 4.02
588 635 4.568760 GTCGGTTGATTCTCTTTGATCCTC 59.431 45.833 0.00 0.00 0.00 3.71
700 747 2.027385 GATTCCAAGAATCCCAGCACC 58.973 52.381 6.11 0.00 0.00 5.01
733 780 3.008485 GGAGTTCTTGGACTTGGACAGAT 59.992 47.826 0.00 0.00 0.00 2.90
737 784 5.186797 AGTTCTTGGACTTGGACAGATAGAG 59.813 44.000 0.00 0.00 0.00 2.43
738 785 4.935578 TCTTGGACTTGGACAGATAGAGA 58.064 43.478 0.00 0.00 0.00 3.10
739 786 4.952957 TCTTGGACTTGGACAGATAGAGAG 59.047 45.833 0.00 0.00 0.00 3.20
743 790 2.587777 ACTTGGACAGATAGAGAGGGGA 59.412 50.000 0.00 0.00 0.00 4.81
870 917 3.565764 TTGATTGATCGATCCTTGGCT 57.434 42.857 22.31 0.98 0.00 4.75
886 933 4.218578 CTGCGATCCGGCTGCTCT 62.219 66.667 12.53 0.00 0.00 4.09
890 937 2.484928 CGATCCGGCTGCTCTGAGA 61.485 63.158 9.28 0.00 0.00 3.27
892 939 1.381056 ATCCGGCTGCTCTGAGAGT 60.381 57.895 11.64 0.00 31.39 3.24
899 946 3.063180 CGGCTGCTCTGAGAGTAATTTTG 59.937 47.826 11.64 0.00 31.39 2.44
900 947 4.256920 GGCTGCTCTGAGAGTAATTTTGA 58.743 43.478 11.64 0.00 31.39 2.69
901 948 4.880696 GGCTGCTCTGAGAGTAATTTTGAT 59.119 41.667 11.64 0.00 31.39 2.57
902 949 5.007528 GGCTGCTCTGAGAGTAATTTTGATC 59.992 44.000 11.64 0.00 31.39 2.92
903 950 5.816777 GCTGCTCTGAGAGTAATTTTGATCT 59.183 40.000 11.64 0.00 31.39 2.75
904 951 6.238157 GCTGCTCTGAGAGTAATTTTGATCTG 60.238 42.308 11.64 0.00 31.39 2.90
905 952 6.939622 TGCTCTGAGAGTAATTTTGATCTGA 58.060 36.000 11.64 0.00 31.39 3.27
906 953 6.815641 TGCTCTGAGAGTAATTTTGATCTGAC 59.184 38.462 11.64 0.00 31.39 3.51
907 954 6.257630 GCTCTGAGAGTAATTTTGATCTGACC 59.742 42.308 11.64 0.00 31.39 4.02
912 964 7.125792 AGAGTAATTTTGATCTGACCCGTAT 57.874 36.000 0.00 0.00 0.00 3.06
924 976 3.466836 TGACCCGTATTGATGATTCTGC 58.533 45.455 0.00 0.00 0.00 4.26
929 981 3.304257 CCGTATTGATGATTCTGCTTGGC 60.304 47.826 0.00 0.00 0.00 4.52
941 993 4.399395 CTTGGCTGCAGGCGAGGA 62.399 66.667 38.09 19.91 45.43 3.71
942 994 4.704833 TTGGCTGCAGGCGAGGAC 62.705 66.667 32.12 6.24 44.42 3.85
1116 1171 1.377202 CGGGCTGCTGTGGTACAAT 60.377 57.895 0.00 0.00 44.16 2.71
1158 1213 1.813859 CGACTTCTCCATGGCGGTA 59.186 57.895 6.96 0.00 35.57 4.02
1172 1227 2.034879 CGGTAGTGCAGGCCAACAG 61.035 63.158 5.01 0.00 0.00 3.16
1353 1412 5.301298 CCATCTCAAGAAAAATCCCCATCTC 59.699 44.000 0.00 0.00 0.00 2.75
1363 1422 7.562821 AGAAAAATCCCCATCTCCTAATTTCTG 59.437 37.037 0.00 0.00 33.53 3.02
1364 1423 3.864789 TCCCCATCTCCTAATTTCTGC 57.135 47.619 0.00 0.00 0.00 4.26
1365 1424 3.122480 TCCCCATCTCCTAATTTCTGCA 58.878 45.455 0.00 0.00 0.00 4.41
1366 1425 3.527253 TCCCCATCTCCTAATTTCTGCAA 59.473 43.478 0.00 0.00 0.00 4.08
1367 1426 3.633986 CCCCATCTCCTAATTTCTGCAAC 59.366 47.826 0.00 0.00 0.00 4.17
1368 1427 3.633986 CCCATCTCCTAATTTCTGCAACC 59.366 47.826 0.00 0.00 0.00 3.77
1369 1428 4.272489 CCATCTCCTAATTTCTGCAACCA 58.728 43.478 0.00 0.00 0.00 3.67
1370 1429 4.706476 CCATCTCCTAATTTCTGCAACCAA 59.294 41.667 0.00 0.00 0.00 3.67
1371 1430 5.185635 CCATCTCCTAATTTCTGCAACCAAA 59.814 40.000 0.00 0.00 0.00 3.28
1372 1431 6.295236 CCATCTCCTAATTTCTGCAACCAAAA 60.295 38.462 0.00 0.00 0.00 2.44
1373 1432 6.723298 TCTCCTAATTTCTGCAACCAAAAA 57.277 33.333 0.00 0.00 0.00 1.94
1375 1434 6.549364 TCTCCTAATTTCTGCAACCAAAAAGA 59.451 34.615 0.00 0.00 0.00 2.52
1378 1437 5.739752 AATTTCTGCAACCAAAAAGAAGC 57.260 34.783 0.00 0.00 30.77 3.86
1379 1438 3.883830 TTCTGCAACCAAAAAGAAGCA 57.116 38.095 0.00 0.00 0.00 3.91
1380 1439 3.883830 TCTGCAACCAAAAAGAAGCAA 57.116 38.095 0.00 0.00 0.00 3.91
1381 1440 3.784338 TCTGCAACCAAAAAGAAGCAAG 58.216 40.909 0.00 0.00 0.00 4.01
1382 1441 3.446873 TCTGCAACCAAAAAGAAGCAAGA 59.553 39.130 0.00 0.00 0.00 3.02
1384 1443 4.573900 TGCAACCAAAAAGAAGCAAGAAA 58.426 34.783 0.00 0.00 0.00 2.52
1385 1444 4.999950 TGCAACCAAAAAGAAGCAAGAAAA 59.000 33.333 0.00 0.00 0.00 2.29
1386 1445 5.647225 TGCAACCAAAAAGAAGCAAGAAAAT 59.353 32.000 0.00 0.00 0.00 1.82
1388 1447 6.037500 GCAACCAAAAAGAAGCAAGAAAATCT 59.962 34.615 0.00 0.00 0.00 2.40
1390 1449 6.283694 ACCAAAAAGAAGCAAGAAAATCTCC 58.716 36.000 0.00 0.00 0.00 3.71
1391 1450 6.098838 ACCAAAAAGAAGCAAGAAAATCTCCT 59.901 34.615 0.00 0.00 0.00 3.69
1392 1451 6.423001 CCAAAAAGAAGCAAGAAAATCTCCTG 59.577 38.462 0.00 0.00 0.00 3.86
1393 1452 6.966534 AAAAGAAGCAAGAAAATCTCCTGA 57.033 33.333 0.00 0.00 0.00 3.86
1394 1453 5.956068 AAGAAGCAAGAAAATCTCCTGAC 57.044 39.130 0.00 0.00 0.00 3.51
1396 1455 5.380043 AGAAGCAAGAAAATCTCCTGACAA 58.620 37.500 0.00 0.00 0.00 3.18
1397 1456 5.240403 AGAAGCAAGAAAATCTCCTGACAAC 59.760 40.000 0.00 0.00 0.00 3.32
1398 1457 4.723309 AGCAAGAAAATCTCCTGACAACT 58.277 39.130 0.00 0.00 0.00 3.16
1399 1458 5.136105 AGCAAGAAAATCTCCTGACAACTT 58.864 37.500 0.00 0.00 0.00 2.66
1400 1459 5.595952 AGCAAGAAAATCTCCTGACAACTTT 59.404 36.000 0.00 0.00 0.00 2.66
1402 1461 6.199719 GCAAGAAAATCTCCTGACAACTTTTG 59.800 38.462 0.00 0.00 0.00 2.44
1403 1462 5.836347 AGAAAATCTCCTGACAACTTTTGC 58.164 37.500 0.00 0.00 0.00 3.68
1406 1465 3.845781 TCTCCTGACAACTTTTGCTCT 57.154 42.857 0.00 0.00 0.00 4.09
1407 1466 3.470709 TCTCCTGACAACTTTTGCTCTG 58.529 45.455 0.00 0.00 0.00 3.35
1410 1469 4.776349 TCCTGACAACTTTTGCTCTGTTA 58.224 39.130 0.00 0.00 0.00 2.41
1412 1471 4.576463 CCTGACAACTTTTGCTCTGTTACT 59.424 41.667 0.00 0.00 0.00 2.24
1414 1473 6.428159 CCTGACAACTTTTGCTCTGTTACTAT 59.572 38.462 0.00 0.00 0.00 2.12
1415 1474 7.189693 TGACAACTTTTGCTCTGTTACTATG 57.810 36.000 0.00 0.00 0.00 2.23
1418 1477 7.417612 ACAACTTTTGCTCTGTTACTATGTTG 58.582 34.615 0.00 0.00 36.82 3.33
1419 1478 7.282224 ACAACTTTTGCTCTGTTACTATGTTGA 59.718 33.333 0.00 0.00 35.39 3.18
1420 1479 7.986085 ACTTTTGCTCTGTTACTATGTTGAT 57.014 32.000 0.00 0.00 0.00 2.57
1421 1480 8.034058 ACTTTTGCTCTGTTACTATGTTGATC 57.966 34.615 0.00 0.00 0.00 2.92
1422 1481 7.661437 ACTTTTGCTCTGTTACTATGTTGATCA 59.339 33.333 0.00 0.00 0.00 2.92
1426 1485 6.591448 TGCTCTGTTACTATGTTGATCAGTTG 59.409 38.462 0.00 0.00 0.00 3.16
1427 1486 6.591834 GCTCTGTTACTATGTTGATCAGTTGT 59.408 38.462 0.00 0.00 0.00 3.32
1431 1490 4.668576 ACTATGTTGATCAGTTGTTGCG 57.331 40.909 0.00 0.00 0.00 4.85
1438 1505 4.103365 TGATCAGTTGTTGCGTTTTTGT 57.897 36.364 0.00 0.00 0.00 2.83
1528 1602 5.869753 ACTCATTGCTGTAACATCAGAAC 57.130 39.130 0.00 0.00 37.61 3.01
1649 1735 1.950828 ATTCATCTCTTCCAGCTGCG 58.049 50.000 8.66 1.56 0.00 5.18
1685 1771 3.769739 TGGTGACATTGTTCTGCTACT 57.230 42.857 0.00 0.00 33.40 2.57
1687 1773 3.070878 TGGTGACATTGTTCTGCTACTCA 59.929 43.478 0.00 0.00 33.40 3.41
1688 1774 4.256920 GGTGACATTGTTCTGCTACTCAT 58.743 43.478 0.00 0.00 0.00 2.90
1747 1843 4.141801 TGTTAGCCTTGTTAGTGTCAGTGT 60.142 41.667 0.00 0.00 0.00 3.55
1890 1986 1.268079 TCTATGAAGCCTCAGATCGCG 59.732 52.381 0.00 0.00 34.23 5.87
1983 2079 1.016653 GTGCTGTTCTCGGAAGGCTC 61.017 60.000 0.00 5.92 0.00 4.70
2025 2121 2.633657 GCCATGCAGTTATCGGCG 59.366 61.111 0.00 0.00 37.57 6.46
2160 2256 2.349580 GGTAACCGAAATTCTGTACCGC 59.650 50.000 0.00 0.00 0.00 5.68
2164 2260 1.468565 CCGAAATTCTGTACCGCGAGA 60.469 52.381 8.23 0.00 0.00 4.04
2179 2275 1.550065 CGAGACGCATAAGACCACTG 58.450 55.000 0.00 0.00 0.00 3.66
2181 2277 2.263077 GAGACGCATAAGACCACTGTG 58.737 52.381 0.00 0.00 0.00 3.66
2272 2368 5.065731 GTCCATCTCATCACAATTCCACTTC 59.934 44.000 0.00 0.00 0.00 3.01
2305 2401 6.585322 CGTTCCGGAGTATGGATAATTACTTC 59.415 42.308 3.34 0.00 34.91 3.01
2576 2672 2.943690 CAGGAGGAAGTGATGCATTCTG 59.056 50.000 0.00 0.00 0.00 3.02
2577 2673 2.842496 AGGAGGAAGTGATGCATTCTGA 59.158 45.455 0.00 0.00 0.00 3.27
2583 2679 4.639310 GGAAGTGATGCATTCTGAAGTCAT 59.361 41.667 0.00 6.81 0.00 3.06
2639 2735 4.696877 TGAGCTAATCAACACCATCAGTTG 59.303 41.667 0.00 0.00 45.82 3.16
2658 2754 0.881118 GCTGCAACTCGGGATTTTCA 59.119 50.000 0.00 0.00 0.00 2.69
2813 2910 6.723052 TGAGGTGAGATGATATTCTGCAGATA 59.277 38.462 19.04 12.24 0.00 1.98
3266 3379 5.862811 GCTATTTCAAGCAAGTGTAGTCTG 58.137 41.667 0.00 0.00 42.30 3.51
3271 3384 8.621532 ATTTCAAGCAAGTGTAGTCTGAATTA 57.378 30.769 0.00 0.00 0.00 1.40
3297 3410 5.634896 CACTTTATCTGGATGCTTGTGTTC 58.365 41.667 0.00 0.00 0.00 3.18
3310 3423 4.515191 TGCTTGTGTTCTCAATCACTTACC 59.485 41.667 0.00 0.00 35.82 2.85
3377 3491 9.999009 GCTATTTTAAACTCTAGGCGTTATTTT 57.001 29.630 0.00 0.00 0.00 1.82
3464 3578 6.612306 CATTTACCACTTCTCCACTTAAAGC 58.388 40.000 0.00 0.00 0.00 3.51
3494 3608 3.942130 ATTTTAAGCTCCAAGTGGCAC 57.058 42.857 10.29 10.29 34.44 5.01
3543 3657 2.422479 CTCAAGTTGCATGTCATCCCTG 59.578 50.000 0.00 0.00 0.00 4.45
3571 3685 6.798482 TGCTGTATTATCAAAATCAAGCCTG 58.202 36.000 0.00 0.00 0.00 4.85
3637 3751 2.302587 TTCTTTTTCGCCAGGGGATT 57.697 45.000 7.12 0.00 0.00 3.01
3777 3891 3.041940 CGTGGTGTTCCTGGACGC 61.042 66.667 0.00 0.00 34.23 5.19
3986 4118 0.887836 TGCTTCCTGCTGCTGTGAAG 60.888 55.000 21.72 21.72 43.37 3.02
4071 4204 2.666862 ATTCCGTGGCGACGCAAA 60.667 55.556 23.09 12.20 44.68 3.68
4072 4205 2.961669 ATTCCGTGGCGACGCAAAC 61.962 57.895 23.09 17.50 44.68 2.93
4075 4208 2.735478 CGTGGCGACGCAAACCTA 60.735 61.111 23.09 0.00 42.37 3.08
4076 4209 2.858158 GTGGCGACGCAAACCTAC 59.142 61.111 23.09 2.35 41.67 3.18
4117 4251 6.547510 CCCCTTTGTTCTTTTATCTATCCCTG 59.452 42.308 0.00 0.00 0.00 4.45
4143 4277 4.838307 TCCAATGAGGGAGGAGGG 57.162 61.111 0.00 0.00 38.24 4.30
4146 4280 1.358830 CCAATGAGGGAGGAGGGCAT 61.359 60.000 0.00 0.00 0.00 4.40
4187 4321 1.059264 GAACATCGCCGTCTCTTTTCG 59.941 52.381 0.00 0.00 0.00 3.46
4188 4322 1.345176 CATCGCCGTCTCTTTTCGC 59.655 57.895 0.00 0.00 0.00 4.70
4189 4323 1.810030 ATCGCCGTCTCTTTTCGCC 60.810 57.895 0.00 0.00 0.00 5.54
4215 4349 2.104170 AGTCCGTCTTCTTCCATCTCC 58.896 52.381 0.00 0.00 0.00 3.71
4242 4376 2.663852 CGTCGAAAACCGGGTGCT 60.664 61.111 6.32 0.00 39.14 4.40
4247 4381 3.551887 GAAAACCGGGTGCTTGGCG 62.552 63.158 6.32 0.00 0.00 5.69
4265 4399 2.270986 GCCTTGGCTTGACCCTGTG 61.271 63.158 4.11 0.00 37.83 3.66
4330 4466 2.029838 ATCGGATGAACTTGGACTGC 57.970 50.000 0.00 0.00 0.00 4.40
4379 4515 1.876497 ATGGTTTGGTGCCGACATGC 61.876 55.000 0.00 0.00 0.00 4.06
4492 4629 4.878397 CACTCATCCAACAGAATTAGGTCC 59.122 45.833 0.00 0.00 0.00 4.46
4499 4636 5.964477 TCCAACAGAATTAGGTCCAGACTAT 59.036 40.000 0.00 0.00 0.00 2.12
4520 4657 2.715749 TAGCTTGGATCACACCCATG 57.284 50.000 0.00 0.00 33.04 3.66
4537 4674 2.037847 GGCCTGGGCATCAAAGGT 59.962 61.111 16.34 0.00 44.11 3.50
4551 4688 4.453480 TCAAAGGTCCCAATTGTCTCTT 57.547 40.909 4.43 0.33 0.00 2.85
4552 4689 4.398319 TCAAAGGTCCCAATTGTCTCTTC 58.602 43.478 4.43 0.00 0.00 2.87
4567 4924 1.213619 TCTTCCATGGGTGCCATCCA 61.214 55.000 13.02 0.00 43.15 3.41
4585 4942 1.135689 CCAACTTCGCCTGAAATTCGG 60.136 52.381 0.00 0.00 32.66 4.30
4587 4944 0.605319 ACTTCGCCTGAAATTCGGCA 60.605 50.000 21.72 10.97 46.62 5.69
4646 5049 5.954296 TGCAAAGGAAATCTTCTTCTGAG 57.046 39.130 0.00 0.00 33.94 3.35
4647 5050 5.380043 TGCAAAGGAAATCTTCTTCTGAGT 58.620 37.500 0.00 0.00 33.94 3.41
4648 5051 5.829924 TGCAAAGGAAATCTTCTTCTGAGTT 59.170 36.000 0.00 0.00 33.94 3.01
4649 5052 6.998074 TGCAAAGGAAATCTTCTTCTGAGTTA 59.002 34.615 0.00 0.00 33.94 2.24
4650 5053 7.502226 TGCAAAGGAAATCTTCTTCTGAGTTAA 59.498 33.333 0.00 0.00 33.94 2.01
4651 5054 8.352942 GCAAAGGAAATCTTCTTCTGAGTTAAA 58.647 33.333 0.00 0.00 33.94 1.52
4652 5055 9.890352 CAAAGGAAATCTTCTTCTGAGTTAAAG 57.110 33.333 0.00 0.00 33.94 1.85
4653 5056 9.853177 AAAGGAAATCTTCTTCTGAGTTAAAGA 57.147 29.630 0.00 0.00 33.94 2.52
4655 5058 8.655901 AGGAAATCTTCTTCTGAGTTAAAGAGT 58.344 33.333 0.00 0.00 33.32 3.24
4656 5059 9.930693 GGAAATCTTCTTCTGAGTTAAAGAGTA 57.069 33.333 0.00 0.00 33.32 2.59
4673 5076 6.841443 AAGAGTAAATCTTGCTGATGATCG 57.159 37.500 0.00 0.00 46.80 3.69
4674 5077 6.154203 AGAGTAAATCTTGCTGATGATCGA 57.846 37.500 0.00 0.00 32.99 3.59
4675 5078 6.757237 AGAGTAAATCTTGCTGATGATCGAT 58.243 36.000 0.00 0.00 32.99 3.59
4676 5079 6.867816 AGAGTAAATCTTGCTGATGATCGATC 59.132 38.462 18.72 18.72 32.99 3.69
4677 5080 5.931146 AGTAAATCTTGCTGATGATCGATCC 59.069 40.000 22.31 8.72 35.21 3.36
4703 5315 3.655276 AAACCTTCAGCTGCATTCAAG 57.345 42.857 9.47 6.99 0.00 3.02
4710 5322 1.139095 GCTGCATTCAAGGCTCAGC 59.861 57.895 7.71 7.71 42.46 4.26
4712 5324 1.003476 TGCATTCAAGGCTCAGCGA 60.003 52.632 0.00 0.00 0.00 4.93
4726 5338 4.419939 GCGAAAGGCTTTGGCGGG 62.420 66.667 27.08 8.72 39.81 6.13
4729 5341 2.283173 AAAGGCTTTGGCGGGAGG 60.283 61.111 12.53 0.00 39.81 4.30
4730 5342 3.886550 AAAGGCTTTGGCGGGAGGG 62.887 63.158 12.53 0.00 39.81 4.30
4738 5350 4.717313 GGCGGGAGGGCGAGTTTT 62.717 66.667 0.00 0.00 0.00 2.43
4739 5351 3.125573 GCGGGAGGGCGAGTTTTC 61.126 66.667 0.00 0.00 0.00 2.29
4749 5361 3.580658 CGAGTTTTCGCCCGAAATC 57.419 52.632 15.50 14.37 42.71 2.17
4750 5362 0.096454 CGAGTTTTCGCCCGAAATCC 59.904 55.000 15.50 9.98 42.71 3.01
4751 5363 1.161843 GAGTTTTCGCCCGAAATCCA 58.838 50.000 15.50 0.00 42.71 3.41
4755 5367 2.051334 TTTCGCCCGAAATCCATGAT 57.949 45.000 11.38 0.00 38.95 2.45
4756 5368 2.920724 TTCGCCCGAAATCCATGATA 57.079 45.000 0.00 0.00 0.00 2.15
4757 5369 3.417069 TTCGCCCGAAATCCATGATAT 57.583 42.857 0.00 0.00 0.00 1.63
4759 5371 4.545208 TCGCCCGAAATCCATGATATAA 57.455 40.909 0.00 0.00 0.00 0.98
4760 5372 4.250464 TCGCCCGAAATCCATGATATAAC 58.750 43.478 0.00 0.00 0.00 1.89
4764 5376 5.106555 GCCCGAAATCCATGATATAACACAG 60.107 44.000 0.00 0.00 0.00 3.66
4765 5377 5.997746 CCCGAAATCCATGATATAACACAGT 59.002 40.000 0.00 0.00 0.00 3.55
4767 5379 6.147821 CCGAAATCCATGATATAACACAGTCC 59.852 42.308 0.00 0.00 0.00 3.85
4768 5380 6.705825 CGAAATCCATGATATAACACAGTCCA 59.294 38.462 0.00 0.00 0.00 4.02
4769 5381 7.388776 CGAAATCCATGATATAACACAGTCCAT 59.611 37.037 0.00 0.00 0.00 3.41
4770 5382 7.991084 AATCCATGATATAACACAGTCCATG 57.009 36.000 0.00 0.00 0.00 3.66
4771 5383 5.308014 TCCATGATATAACACAGTCCATGC 58.692 41.667 0.00 0.00 31.37 4.06
4772 5384 4.456911 CCATGATATAACACAGTCCATGCC 59.543 45.833 0.00 0.00 31.37 4.40
4774 5565 3.457749 TGATATAACACAGTCCATGCCCA 59.542 43.478 0.00 0.00 0.00 5.36
4780 5571 1.203052 CACAGTCCATGCCCAACAATC 59.797 52.381 0.00 0.00 0.00 2.67
4791 5582 2.867647 GCCCAACAATCTCCAAACAAGC 60.868 50.000 0.00 0.00 0.00 4.01
4794 5585 1.317613 ACAATCTCCAAACAAGCGCA 58.682 45.000 11.47 0.00 0.00 6.09
4798 5589 0.667993 TCTCCAAACAAGCGCAAAGG 59.332 50.000 11.47 2.26 0.00 3.11
4800 5594 0.383949 TCCAAACAAGCGCAAAGGAC 59.616 50.000 11.47 0.00 0.00 3.85
4805 5599 2.112297 AAGCGCAAAGGACCCGAA 59.888 55.556 11.47 0.00 0.00 4.30
4806 5600 2.258726 AAGCGCAAAGGACCCGAAC 61.259 57.895 11.47 0.00 0.00 3.95
4807 5601 3.733960 GCGCAAAGGACCCGAACC 61.734 66.667 0.30 0.00 0.00 3.62
4808 5602 3.419759 CGCAAAGGACCCGAACCG 61.420 66.667 0.00 0.00 0.00 4.44
4809 5603 2.031465 GCAAAGGACCCGAACCGA 59.969 61.111 0.00 0.00 0.00 4.69
4810 5604 2.322830 GCAAAGGACCCGAACCGAC 61.323 63.158 0.00 0.00 0.00 4.79
4811 5605 2.025418 CAAAGGACCCGAACCGACG 61.025 63.158 0.00 0.00 0.00 5.12
4814 5608 2.426122 AAGGACCCGAACCGACGAAC 62.426 60.000 0.00 0.00 35.09 3.95
4815 5609 2.802414 GACCCGAACCGACGAACG 60.802 66.667 0.00 0.00 42.18 3.95
4816 5610 3.254014 GACCCGAACCGACGAACGA 62.254 63.158 0.00 0.00 45.77 3.85
4817 5611 2.050168 CCCGAACCGACGAACGAA 60.050 61.111 0.00 0.00 45.77 3.85
4818 5612 1.661197 CCCGAACCGACGAACGAAA 60.661 57.895 0.00 0.00 45.77 3.46
4819 5613 1.484232 CCGAACCGACGAACGAAAC 59.516 57.895 0.00 0.00 45.77 2.78
4823 5617 3.107661 CCGACGAACGAAACCGGG 61.108 66.667 6.32 0.00 45.77 5.73
4830 5627 1.004918 AACGAAACCGGGCAGAGAG 60.005 57.895 6.32 0.00 0.00 3.20
4859 5656 7.070447 AGGCTAGATACAAGTGATGATTGAAGA 59.930 37.037 0.00 0.00 0.00 2.87
4860 5657 7.712639 GGCTAGATACAAGTGATGATTGAAGAA 59.287 37.037 0.00 0.00 0.00 2.52
4861 5658 8.763356 GCTAGATACAAGTGATGATTGAAGAAG 58.237 37.037 0.00 0.00 0.00 2.85
4871 5668 6.825721 GTGATGATTGAAGAAGTACAAGGGAT 59.174 38.462 0.00 0.00 0.00 3.85
4872 5669 6.825213 TGATGATTGAAGAAGTACAAGGGATG 59.175 38.462 0.00 0.00 0.00 3.51
4887 5684 0.034059 GGATGTAGATCCCCGCTGTG 59.966 60.000 7.71 0.00 42.42 3.66
4899 5696 1.265905 CCCGCTGTGGTACTGTTTTTC 59.734 52.381 6.49 0.00 35.15 2.29
4900 5697 2.218603 CCGCTGTGGTACTGTTTTTCT 58.781 47.619 0.00 0.00 0.00 2.52
4901 5698 2.032030 CCGCTGTGGTACTGTTTTTCTG 60.032 50.000 0.00 0.00 0.00 3.02
4902 5699 2.602217 CGCTGTGGTACTGTTTTTCTGC 60.602 50.000 0.00 0.00 0.00 4.26
4903 5700 2.618709 GCTGTGGTACTGTTTTTCTGCT 59.381 45.455 0.00 0.00 0.00 4.24
4904 5701 3.066760 GCTGTGGTACTGTTTTTCTGCTT 59.933 43.478 0.00 0.00 0.00 3.91
4905 5702 4.440112 GCTGTGGTACTGTTTTTCTGCTTT 60.440 41.667 0.00 0.00 0.00 3.51
4906 5703 4.992688 TGTGGTACTGTTTTTCTGCTTTG 58.007 39.130 0.00 0.00 0.00 2.77
4907 5704 3.796717 GTGGTACTGTTTTTCTGCTTTGC 59.203 43.478 0.00 0.00 0.00 3.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 3.877508 GAGCATCTTTTTATAGCGGTGGT 59.122 43.478 0.00 0.00 0.00 4.16
72 73 2.044650 CACCTCACCTGCCATGGG 60.045 66.667 15.13 0.00 0.00 4.00
73 74 2.044650 CCACCTCACCTGCCATGG 60.045 66.667 7.63 7.63 0.00 3.66
74 75 2.044650 CCCACCTCACCTGCCATG 60.045 66.667 0.00 0.00 0.00 3.66
75 76 2.204136 TCCCACCTCACCTGCCAT 60.204 61.111 0.00 0.00 0.00 4.40
77 78 2.930562 ACTCCCACCTCACCTGCC 60.931 66.667 0.00 0.00 0.00 4.85
78 79 2.177594 CTCACTCCCACCTCACCTGC 62.178 65.000 0.00 0.00 0.00 4.85
108 131 1.009389 CGCTCGGGTCAGTTCACTTC 61.009 60.000 0.00 0.00 0.00 3.01
143 171 3.214845 GCAGGTGCAGGGCTATGC 61.215 66.667 8.07 8.07 46.68 3.14
176 204 3.432588 GACTGCTGCTGGCTGCTG 61.433 66.667 22.02 22.02 42.51 4.41
177 205 4.719106 GGACTGCTGCTGGCTGCT 62.719 66.667 21.19 6.06 42.51 4.24
207 235 1.896220 TCCTGATTGTTGTCACTGGC 58.104 50.000 0.00 0.00 0.00 4.85
287 319 4.574013 AGAGAAGCCATTAAATGAAGAGCG 59.426 41.667 0.00 0.00 0.00 5.03
295 327 3.529319 AGGGGACAGAGAAGCCATTAAAT 59.471 43.478 0.00 0.00 0.00 1.40
368 403 3.801997 CACCCAGCCCCAGCCTAG 61.802 72.222 0.00 0.00 41.25 3.02
390 430 2.432874 TCTCTCTCGACTCTCTTCGGAT 59.567 50.000 0.00 0.00 39.58 4.18
393 433 2.201732 CCTCTCTCTCGACTCTCTTCG 58.798 57.143 0.00 0.00 40.53 3.79
401 441 2.800629 CGGTCTCTACCTCTCTCTCGAC 60.801 59.091 0.00 0.00 44.35 4.20
420 460 3.602513 AACAGCTCAGAGGCAGCGG 62.603 63.158 0.00 0.00 42.14 5.52
422 462 1.744741 GGAACAGCTCAGAGGCAGC 60.745 63.158 0.00 0.00 37.12 5.25
447 487 0.108898 CTCTGGAACACTCGCTGGAG 60.109 60.000 0.00 0.00 46.13 3.86
523 564 7.957484 GGAGCTTGACAAAAAGAAAAGAAAAAC 59.043 33.333 0.00 0.00 0.00 2.43
550 592 2.338015 CGACCAGCCAAGCAAGCAT 61.338 57.895 0.00 0.00 0.00 3.79
564 606 3.623510 GGATCAAAGAGAATCAACCGACC 59.376 47.826 0.00 0.00 37.82 4.79
565 607 4.508662 AGGATCAAAGAGAATCAACCGAC 58.491 43.478 0.00 0.00 37.82 4.79
566 608 4.678044 CGAGGATCAAAGAGAATCAACCGA 60.678 45.833 0.00 0.00 32.84 4.69
567 609 3.553511 CGAGGATCAAAGAGAATCAACCG 59.446 47.826 0.00 0.00 32.84 4.44
607 654 1.841556 GGGTGGACTGGACTGGACA 60.842 63.158 0.00 0.00 0.00 4.02
608 655 1.415672 TTGGGTGGACTGGACTGGAC 61.416 60.000 0.00 0.00 0.00 4.02
609 656 0.475632 ATTGGGTGGACTGGACTGGA 60.476 55.000 0.00 0.00 0.00 3.86
610 657 0.035056 GATTGGGTGGACTGGACTGG 60.035 60.000 0.00 0.00 0.00 4.00
611 658 0.035056 GGATTGGGTGGACTGGACTG 60.035 60.000 0.00 0.00 0.00 3.51
612 659 0.178861 AGGATTGGGTGGACTGGACT 60.179 55.000 0.00 0.00 0.00 3.85
678 725 2.686915 GTGCTGGGATTCTTGGAATCTG 59.313 50.000 16.49 10.22 0.00 2.90
758 805 4.736759 TCGAGAGAAAGAAAGACGCAAGTT 60.737 41.667 0.00 0.00 46.87 2.66
870 917 4.519437 CAGAGCAGCCGGATCGCA 62.519 66.667 5.05 0.00 36.90 5.10
880 927 7.010367 GTCAGATCAAAATTACTCTCAGAGCAG 59.990 40.741 0.00 0.00 32.04 4.24
885 932 5.521735 CGGGTCAGATCAAAATTACTCTCAG 59.478 44.000 0.00 0.00 0.00 3.35
886 933 5.046591 ACGGGTCAGATCAAAATTACTCTCA 60.047 40.000 0.00 0.00 0.00 3.27
890 937 7.335627 TCAATACGGGTCAGATCAAAATTACT 58.664 34.615 0.00 0.00 0.00 2.24
892 939 7.990314 TCATCAATACGGGTCAGATCAAAATTA 59.010 33.333 0.00 0.00 0.00 1.40
899 946 5.636965 CAGAATCATCAATACGGGTCAGATC 59.363 44.000 0.00 0.00 0.00 2.75
900 947 5.545588 CAGAATCATCAATACGGGTCAGAT 58.454 41.667 0.00 0.00 0.00 2.90
901 948 4.740634 GCAGAATCATCAATACGGGTCAGA 60.741 45.833 0.00 0.00 0.00 3.27
902 949 3.496130 GCAGAATCATCAATACGGGTCAG 59.504 47.826 0.00 0.00 0.00 3.51
903 950 3.134623 AGCAGAATCATCAATACGGGTCA 59.865 43.478 0.00 0.00 0.00 4.02
904 951 3.733337 AGCAGAATCATCAATACGGGTC 58.267 45.455 0.00 0.00 0.00 4.46
905 952 3.845781 AGCAGAATCATCAATACGGGT 57.154 42.857 0.00 0.00 0.00 5.28
906 953 3.251729 CCAAGCAGAATCATCAATACGGG 59.748 47.826 0.00 0.00 0.00 5.28
907 954 3.304257 GCCAAGCAGAATCATCAATACGG 60.304 47.826 0.00 0.00 0.00 4.02
912 964 1.475280 GCAGCCAAGCAGAATCATCAA 59.525 47.619 0.00 0.00 0.00 2.57
924 976 4.399395 TCCTCGCCTGCAGCCAAG 62.399 66.667 8.66 4.34 38.78 3.61
938 990 4.371417 TACCTCCACCGCCGTCCT 62.371 66.667 0.00 0.00 0.00 3.85
939 991 4.139234 GTACCTCCACCGCCGTCC 62.139 72.222 0.00 0.00 0.00 4.79
940 992 4.487412 CGTACCTCCACCGCCGTC 62.487 72.222 0.00 0.00 0.00 4.79
943 995 3.834799 CTCCGTACCTCCACCGCC 61.835 72.222 0.00 0.00 0.00 6.13
944 996 3.834799 CCTCCGTACCTCCACCGC 61.835 72.222 0.00 0.00 0.00 5.68
945 997 3.834799 GCCTCCGTACCTCCACCG 61.835 72.222 0.00 0.00 0.00 4.94
946 998 3.468140 GGCCTCCGTACCTCCACC 61.468 72.222 0.00 0.00 0.00 4.61
953 1005 4.910585 CATGCCCGGCCTCCGTAC 62.911 72.222 7.03 0.00 46.80 3.67
1133 1188 1.982395 ATGGAGAAGTCGCCGGTGA 60.982 57.895 15.21 15.21 38.78 4.02
1353 1412 6.073602 GCTTCTTTTTGGTTGCAGAAATTAGG 60.074 38.462 0.00 0.00 0.00 2.69
1363 1422 5.544136 TTTTCTTGCTTCTTTTTGGTTGC 57.456 34.783 0.00 0.00 0.00 4.17
1364 1423 7.254556 GGAGATTTTCTTGCTTCTTTTTGGTTG 60.255 37.037 0.00 0.00 0.00 3.77
1365 1424 6.763135 GGAGATTTTCTTGCTTCTTTTTGGTT 59.237 34.615 0.00 0.00 0.00 3.67
1366 1425 6.098838 AGGAGATTTTCTTGCTTCTTTTTGGT 59.901 34.615 0.00 0.00 0.00 3.67
1367 1426 6.423001 CAGGAGATTTTCTTGCTTCTTTTTGG 59.577 38.462 0.00 0.00 0.00 3.28
1368 1427 7.168804 GTCAGGAGATTTTCTTGCTTCTTTTTG 59.831 37.037 0.00 0.00 33.17 2.44
1369 1428 7.147846 TGTCAGGAGATTTTCTTGCTTCTTTTT 60.148 33.333 0.00 0.00 33.17 1.94
1370 1429 6.322201 TGTCAGGAGATTTTCTTGCTTCTTTT 59.678 34.615 0.00 0.00 33.17 2.27
1371 1430 5.829924 TGTCAGGAGATTTTCTTGCTTCTTT 59.170 36.000 0.00 0.00 33.17 2.52
1372 1431 5.380043 TGTCAGGAGATTTTCTTGCTTCTT 58.620 37.500 0.00 0.00 33.17 2.52
1373 1432 4.978099 TGTCAGGAGATTTTCTTGCTTCT 58.022 39.130 0.00 0.00 33.17 2.85
1375 1434 5.136105 AGTTGTCAGGAGATTTTCTTGCTT 58.864 37.500 0.00 0.00 33.17 3.91
1378 1437 6.199719 GCAAAAGTTGTCAGGAGATTTTCTTG 59.800 38.462 0.00 0.00 34.37 3.02
1379 1438 6.097412 AGCAAAAGTTGTCAGGAGATTTTCTT 59.903 34.615 0.00 0.00 0.00 2.52
1380 1439 5.595952 AGCAAAAGTTGTCAGGAGATTTTCT 59.404 36.000 0.00 0.00 0.00 2.52
1381 1440 5.836347 AGCAAAAGTTGTCAGGAGATTTTC 58.164 37.500 0.00 0.00 0.00 2.29
1382 1441 5.595952 AGAGCAAAAGTTGTCAGGAGATTTT 59.404 36.000 0.00 0.00 0.00 1.82
1384 1443 4.518211 CAGAGCAAAAGTTGTCAGGAGATT 59.482 41.667 0.00 0.00 0.00 2.40
1385 1444 4.070716 CAGAGCAAAAGTTGTCAGGAGAT 58.929 43.478 0.00 0.00 0.00 2.75
1386 1445 3.118261 ACAGAGCAAAAGTTGTCAGGAGA 60.118 43.478 0.00 0.00 0.00 3.71
1388 1447 3.281727 ACAGAGCAAAAGTTGTCAGGA 57.718 42.857 0.00 0.00 0.00 3.86
1390 1449 5.741388 AGTAACAGAGCAAAAGTTGTCAG 57.259 39.130 0.00 0.00 0.00 3.51
1391 1450 6.765989 ACATAGTAACAGAGCAAAAGTTGTCA 59.234 34.615 0.00 0.00 0.00 3.58
1392 1451 7.190920 ACATAGTAACAGAGCAAAAGTTGTC 57.809 36.000 0.00 0.00 0.00 3.18
1393 1452 7.282224 TCAACATAGTAACAGAGCAAAAGTTGT 59.718 33.333 0.00 0.00 34.67 3.32
1394 1453 7.639039 TCAACATAGTAACAGAGCAAAAGTTG 58.361 34.615 0.00 0.00 34.44 3.16
1396 1455 7.661437 TGATCAACATAGTAACAGAGCAAAAGT 59.339 33.333 0.00 0.00 0.00 2.66
1397 1456 8.032952 TGATCAACATAGTAACAGAGCAAAAG 57.967 34.615 0.00 0.00 0.00 2.27
1398 1457 7.661437 ACTGATCAACATAGTAACAGAGCAAAA 59.339 33.333 0.00 0.00 0.00 2.44
1399 1458 7.161404 ACTGATCAACATAGTAACAGAGCAAA 58.839 34.615 0.00 0.00 0.00 3.68
1400 1459 6.701340 ACTGATCAACATAGTAACAGAGCAA 58.299 36.000 0.00 0.00 0.00 3.91
1402 1461 6.591834 ACAACTGATCAACATAGTAACAGAGC 59.408 38.462 0.00 0.00 0.00 4.09
1403 1462 8.438513 CAACAACTGATCAACATAGTAACAGAG 58.561 37.037 0.00 0.00 0.00 3.35
1406 1465 6.347321 CGCAACAACTGATCAACATAGTAACA 60.347 38.462 0.00 0.00 0.00 2.41
1407 1466 6.015504 CGCAACAACTGATCAACATAGTAAC 58.984 40.000 0.00 0.00 0.00 2.50
1410 1469 4.065088 ACGCAACAACTGATCAACATAGT 58.935 39.130 0.00 0.00 0.00 2.12
1412 1471 5.431420 AAACGCAACAACTGATCAACATA 57.569 34.783 0.00 0.00 0.00 2.29
1414 1473 3.773860 AAACGCAACAACTGATCAACA 57.226 38.095 0.00 0.00 0.00 3.33
1415 1474 4.326009 ACAAAAACGCAACAACTGATCAAC 59.674 37.500 0.00 0.00 0.00 3.18
1418 1477 4.101942 TCACAAAAACGCAACAACTGATC 58.898 39.130 0.00 0.00 0.00 2.92
1419 1478 4.103365 TCACAAAAACGCAACAACTGAT 57.897 36.364 0.00 0.00 0.00 2.90
1420 1479 3.497118 CTCACAAAAACGCAACAACTGA 58.503 40.909 0.00 0.00 0.00 3.41
1421 1480 2.027926 GCTCACAAAAACGCAACAACTG 59.972 45.455 0.00 0.00 0.00 3.16
1422 1481 2.258755 GCTCACAAAAACGCAACAACT 58.741 42.857 0.00 0.00 0.00 3.16
1426 1485 2.458951 TCATGCTCACAAAAACGCAAC 58.541 42.857 0.00 0.00 35.83 4.17
1427 1486 2.859526 TCATGCTCACAAAAACGCAA 57.140 40.000 0.00 0.00 35.83 4.85
1431 1490 7.872163 TTATCACAATCATGCTCACAAAAAC 57.128 32.000 0.00 0.00 0.00 2.43
1483 1553 4.536765 ACCAAAACTATCATAGCCCTTGG 58.463 43.478 14.43 14.43 37.74 3.61
1484 1554 6.357367 AGTACCAAAACTATCATAGCCCTTG 58.643 40.000 0.00 0.00 0.00 3.61
1492 1562 6.886459 ACAGCAATGAGTACCAAAACTATCAT 59.114 34.615 0.00 0.00 0.00 2.45
1499 1573 6.488344 TGATGTTACAGCAATGAGTACCAAAA 59.512 34.615 0.00 0.00 0.00 2.44
1528 1602 7.373493 ACTGAACCTGCAATATTTTCTTCTTG 58.627 34.615 0.00 0.00 0.00 3.02
1642 1725 2.001812 ACAGAAGACATACGCAGCTG 57.998 50.000 10.11 10.11 0.00 4.24
1649 1735 5.237815 TGTCACCATCAACAGAAGACATAC 58.762 41.667 0.00 0.00 30.43 2.39
1681 1767 7.141363 CCCAGAAACAGAAAACAAATGAGTAG 58.859 38.462 0.00 0.00 0.00 2.57
1684 1770 5.291971 CCCCAGAAACAGAAAACAAATGAG 58.708 41.667 0.00 0.00 0.00 2.90
1685 1771 4.100808 CCCCCAGAAACAGAAAACAAATGA 59.899 41.667 0.00 0.00 0.00 2.57
1687 1773 3.181455 GCCCCCAGAAACAGAAAACAAAT 60.181 43.478 0.00 0.00 0.00 2.32
1688 1774 2.169561 GCCCCCAGAAACAGAAAACAAA 59.830 45.455 0.00 0.00 0.00 2.83
1890 1986 3.060615 CAGCAAGAGCCCACTGCC 61.061 66.667 0.00 0.00 43.56 4.85
1968 2064 1.176619 TGACGAGCCTTCCGAGAACA 61.177 55.000 0.00 0.00 0.00 3.18
2160 2256 1.135373 ACAGTGGTCTTATGCGTCTCG 60.135 52.381 0.00 0.00 0.00 4.04
2164 2260 1.893137 TCTCACAGTGGTCTTATGCGT 59.107 47.619 0.00 0.00 0.00 5.24
2174 2270 3.265791 GCAGGTCTAAATCTCACAGTGG 58.734 50.000 0.00 0.00 0.00 4.00
2179 2275 5.799827 ATCTAGGCAGGTCTAAATCTCAC 57.200 43.478 0.00 0.00 0.00 3.51
2279 2375 6.266103 AAGTAATTATCCATACTCCGGAACGA 59.734 38.462 5.23 0.00 42.64 3.85
2534 2630 2.979676 CTTGCTGGCACGCTTCCA 60.980 61.111 9.68 0.00 0.00 3.53
2576 2672 4.693283 TGACGATAACCATGGATGACTTC 58.307 43.478 21.47 8.95 0.00 3.01
2577 2673 4.753516 TGACGATAACCATGGATGACTT 57.246 40.909 21.47 4.00 0.00 3.01
2583 2679 4.331443 CGTGAAAATGACGATAACCATGGA 59.669 41.667 21.47 0.00 39.21 3.41
2639 2735 0.881118 TGAAAATCCCGAGTTGCAGC 59.119 50.000 0.00 0.00 0.00 5.25
2690 2786 8.090788 AGAAAATTTACAGGAGCCTATAGACA 57.909 34.615 0.00 0.00 0.00 3.41
3263 3376 7.040892 GCATCCAGATAAAGTGCATAATTCAGA 60.041 37.037 0.00 0.00 35.93 3.27
3266 3379 7.211966 AGCATCCAGATAAAGTGCATAATTC 57.788 36.000 0.00 0.00 38.23 2.17
3271 3384 4.097437 CACAAGCATCCAGATAAAGTGCAT 59.903 41.667 0.00 0.00 38.23 3.96
3297 3410 6.767524 ACTCTCTACTGGTAAGTGATTGAG 57.232 41.667 0.00 0.00 37.19 3.02
3310 3423 7.064229 AGAGAAGGGGTAAATACTCTCTACTG 58.936 42.308 7.80 0.00 32.34 2.74
3377 3491 9.261180 GTGCATAACTCAGATTATACTTGCTTA 57.739 33.333 0.00 0.00 0.00 3.09
3464 3578 7.809806 CACTTGGAGCTTAAAATAGGAAAACAG 59.190 37.037 0.00 0.00 0.00 3.16
3543 3657 5.772825 TGATTTTGATAATACAGCAGCCC 57.227 39.130 0.00 0.00 0.00 5.19
3571 3685 0.666913 AATGATCGCATGCCAGAAGC 59.333 50.000 13.15 2.36 44.14 3.86
3637 3751 1.446099 CTTCACTAGCTTCCGCGCA 60.446 57.895 8.75 0.00 42.32 6.09
3640 3754 1.815840 GGCCTTCACTAGCTTCCGC 60.816 63.158 0.00 0.00 0.00 5.54
3643 3757 2.167861 CGCGGCCTTCACTAGCTTC 61.168 63.158 0.00 0.00 0.00 3.86
3676 3790 4.954089 AGTACCTCATCTCCCTCTTCTTT 58.046 43.478 0.00 0.00 0.00 2.52
3892 4009 0.610174 TCCTTCAGTAGGTGCTGCTG 59.390 55.000 0.00 0.00 45.03 4.41
3986 4118 4.792804 GGGTGGAGCCTGAGCAGC 62.793 72.222 0.00 0.00 43.56 5.25
4085 4218 1.076438 AAGAACAAAGGGGAGGAGGG 58.924 55.000 0.00 0.00 0.00 4.30
4143 4277 3.253230 GACAAATTTACAGCCACCATGC 58.747 45.455 0.00 0.00 0.00 4.06
4146 4280 1.883275 CGGACAAATTTACAGCCACCA 59.117 47.619 0.00 0.00 0.00 4.17
4188 4322 2.194271 GAAGAAGACGGACTATTGCGG 58.806 52.381 0.00 0.00 41.70 5.69
4189 4323 2.194271 GGAAGAAGACGGACTATTGCG 58.806 52.381 0.00 0.00 43.33 4.85
4247 4381 2.116125 ACAGGGTCAAGCCAAGGC 59.884 61.111 2.02 2.02 39.65 4.35
4248 4382 0.607489 CTCACAGGGTCAAGCCAAGG 60.607 60.000 0.44 0.00 39.65 3.61
4249 4383 0.607489 CCTCACAGGGTCAAGCCAAG 60.607 60.000 0.44 0.00 39.65 3.61
4250 4384 1.352622 ACCTCACAGGGTCAAGCCAA 61.353 55.000 0.44 0.00 40.58 4.52
4251 4385 1.770110 ACCTCACAGGGTCAAGCCA 60.770 57.895 0.44 0.00 40.58 4.75
4252 4386 3.161557 ACCTCACAGGGTCAAGCC 58.838 61.111 0.00 0.00 40.58 4.35
4260 4394 0.321122 GCACCTCTTGACCTCACAGG 60.321 60.000 0.00 0.00 42.49 4.00
4265 4399 1.194781 TGGAGGCACCTCTTGACCTC 61.195 60.000 16.08 5.61 42.97 3.85
4274 4409 2.818921 TGCAAATAATTGGAGGCACCT 58.181 42.857 1.84 0.00 39.86 4.00
4330 4466 0.246360 TGCTCACCCAGATACACACG 59.754 55.000 0.00 0.00 0.00 4.49
4379 4515 4.447054 GCGTTGATATCCTTCTCATGTGAG 59.553 45.833 3.61 3.61 43.36 3.51
4492 4629 6.393990 GGTGTGATCCAAGCTATATAGTCTG 58.606 44.000 11.38 8.50 0.00 3.51
4499 4636 3.072915 CCATGGGTGTGATCCAAGCTATA 59.927 47.826 2.85 0.00 37.87 1.31
4520 4657 2.037847 ACCTTTGATGCCCAGGCC 59.962 61.111 6.14 0.00 41.09 5.19
4537 4674 2.025037 CCCATGGAAGAGACAATTGGGA 60.025 50.000 15.22 0.00 44.15 4.37
4551 4688 1.000233 GTTGGATGGCACCCATGGA 60.000 57.895 15.22 0.00 45.26 3.41
4552 4689 0.615544 AAGTTGGATGGCACCCATGG 60.616 55.000 0.00 4.14 45.26 3.66
4567 4924 0.521735 GCCGAATTTCAGGCGAAGTT 59.478 50.000 13.73 1.01 44.22 2.66
4618 4975 8.833493 CAGAAGAAGATTTCCTTTGCAAAAATT 58.167 29.630 13.84 2.25 34.68 1.82
4620 4977 7.555087 TCAGAAGAAGATTTCCTTTGCAAAAA 58.445 30.769 13.84 5.27 34.68 1.94
4621 4978 7.111247 TCAGAAGAAGATTTCCTTTGCAAAA 57.889 32.000 13.84 0.00 34.68 2.44
4640 5043 8.993121 CAGCAAGATTTACTCTTTAACTCAGAA 58.007 33.333 0.00 0.00 41.60 3.02
4642 5045 8.539770 TCAGCAAGATTTACTCTTTAACTCAG 57.460 34.615 0.00 0.00 41.60 3.35
4646 5049 9.928236 GATCATCAGCAAGATTTACTCTTTAAC 57.072 33.333 0.00 0.00 41.60 2.01
4647 5050 8.820933 CGATCATCAGCAAGATTTACTCTTTAA 58.179 33.333 0.00 0.00 41.60 1.52
4648 5051 8.197439 TCGATCATCAGCAAGATTTACTCTTTA 58.803 33.333 0.00 0.00 41.60 1.85
4649 5052 7.044181 TCGATCATCAGCAAGATTTACTCTTT 58.956 34.615 0.00 0.00 41.60 2.52
4650 5053 6.577103 TCGATCATCAGCAAGATTTACTCTT 58.423 36.000 0.00 0.00 45.34 2.85
4651 5054 6.154203 TCGATCATCAGCAAGATTTACTCT 57.846 37.500 0.00 0.00 33.72 3.24
4652 5055 6.090628 GGATCGATCATCAGCAAGATTTACTC 59.909 42.308 25.93 0.00 33.72 2.59
4653 5056 5.931146 GGATCGATCATCAGCAAGATTTACT 59.069 40.000 25.93 0.00 33.72 2.24
4655 5058 5.698089 GTGGATCGATCATCAGCAAGATTTA 59.302 40.000 25.93 0.00 33.72 1.40
4656 5059 4.514441 GTGGATCGATCATCAGCAAGATTT 59.486 41.667 25.93 0.00 33.72 2.17
4657 5060 4.063689 GTGGATCGATCATCAGCAAGATT 58.936 43.478 25.93 0.00 33.72 2.40
4658 5061 3.324268 AGTGGATCGATCATCAGCAAGAT 59.676 43.478 25.93 2.83 37.48 2.40
4659 5062 2.697229 AGTGGATCGATCATCAGCAAGA 59.303 45.455 25.93 0.00 32.33 3.02
4660 5063 2.801111 CAGTGGATCGATCATCAGCAAG 59.199 50.000 25.93 7.60 32.33 4.01
4661 5064 2.431782 TCAGTGGATCGATCATCAGCAA 59.568 45.455 25.93 3.24 32.33 3.91
4662 5065 2.034124 TCAGTGGATCGATCATCAGCA 58.966 47.619 25.93 11.96 32.33 4.41
4664 5067 4.272018 GGTTTTCAGTGGATCGATCATCAG 59.728 45.833 25.93 14.51 32.33 2.90
4665 5068 4.080919 AGGTTTTCAGTGGATCGATCATCA 60.081 41.667 25.93 13.39 32.33 3.07
4666 5069 4.446371 AGGTTTTCAGTGGATCGATCATC 58.554 43.478 25.93 17.21 0.00 2.92
4667 5070 4.494091 AGGTTTTCAGTGGATCGATCAT 57.506 40.909 25.93 9.27 0.00 2.45
4668 5071 3.981071 AGGTTTTCAGTGGATCGATCA 57.019 42.857 25.93 10.23 0.00 2.92
4669 5072 4.253685 TGAAGGTTTTCAGTGGATCGATC 58.746 43.478 17.36 17.36 38.37 3.69
4670 5073 4.286297 TGAAGGTTTTCAGTGGATCGAT 57.714 40.909 0.00 0.00 38.37 3.59
4699 5311 1.672356 GCCTTTCGCTGAGCCTTGA 60.672 57.895 0.00 0.00 0.00 3.02
4710 5322 2.671619 TCCCGCCAAAGCCTTTCG 60.672 61.111 0.00 0.00 34.57 3.46
4712 5324 2.283173 CCTCCCGCCAAAGCCTTT 60.283 61.111 0.00 0.00 34.57 3.11
4722 5334 3.125573 GAAAACTCGCCCTCCCGC 61.126 66.667 0.00 0.00 0.00 6.13
4723 5335 2.813908 CGAAAACTCGCCCTCCCG 60.814 66.667 0.00 0.00 0.00 5.14
4731 5343 0.096454 GGATTTCGGGCGAAAACTCG 59.904 55.000 0.00 0.00 45.60 4.18
4732 5344 1.161843 TGGATTTCGGGCGAAAACTC 58.838 50.000 0.00 0.00 45.60 3.01
4733 5345 1.472480 CATGGATTTCGGGCGAAAACT 59.528 47.619 0.00 0.00 45.60 2.66
4735 5347 1.827681 TCATGGATTTCGGGCGAAAA 58.172 45.000 0.00 0.00 45.60 2.29
4738 5350 4.250464 GTTATATCATGGATTTCGGGCGA 58.750 43.478 0.00 0.00 0.00 5.54
4739 5351 4.000325 TGTTATATCATGGATTTCGGGCG 59.000 43.478 0.00 0.00 0.00 6.13
4740 5352 4.759693 TGTGTTATATCATGGATTTCGGGC 59.240 41.667 0.00 0.00 0.00 6.13
4741 5353 5.997746 ACTGTGTTATATCATGGATTTCGGG 59.002 40.000 0.00 0.00 0.00 5.14
4742 5354 6.147821 GGACTGTGTTATATCATGGATTTCGG 59.852 42.308 0.00 0.00 0.00 4.30
4743 5355 6.705825 TGGACTGTGTTATATCATGGATTTCG 59.294 38.462 0.00 0.00 0.00 3.46
4745 5357 7.040201 GCATGGACTGTGTTATATCATGGATTT 60.040 37.037 0.00 0.00 33.34 2.17
4746 5358 6.432162 GCATGGACTGTGTTATATCATGGATT 59.568 38.462 0.00 0.00 33.34 3.01
4747 5359 5.942236 GCATGGACTGTGTTATATCATGGAT 59.058 40.000 0.00 0.00 33.34 3.41
4749 5361 4.456911 GGCATGGACTGTGTTATATCATGG 59.543 45.833 0.00 0.00 33.34 3.66
4750 5362 4.456911 GGGCATGGACTGTGTTATATCATG 59.543 45.833 0.00 0.00 35.13 3.07
4751 5363 4.104579 TGGGCATGGACTGTGTTATATCAT 59.895 41.667 0.00 0.00 0.00 2.45
4755 5367 3.009584 TGTTGGGCATGGACTGTGTTATA 59.990 43.478 0.00 0.00 0.00 0.98
4756 5368 2.224992 TGTTGGGCATGGACTGTGTTAT 60.225 45.455 0.00 0.00 0.00 1.89
4757 5369 1.143889 TGTTGGGCATGGACTGTGTTA 59.856 47.619 0.00 0.00 0.00 2.41
4759 5371 0.106268 TTGTTGGGCATGGACTGTGT 60.106 50.000 0.00 0.00 0.00 3.72
4760 5372 1.203052 GATTGTTGGGCATGGACTGTG 59.797 52.381 0.00 0.00 0.00 3.66
4764 5376 1.106285 GGAGATTGTTGGGCATGGAC 58.894 55.000 0.00 0.00 0.00 4.02
4765 5377 0.703488 TGGAGATTGTTGGGCATGGA 59.297 50.000 0.00 0.00 0.00 3.41
4767 5379 2.299582 TGTTTGGAGATTGTTGGGCATG 59.700 45.455 0.00 0.00 0.00 4.06
4768 5380 2.607499 TGTTTGGAGATTGTTGGGCAT 58.393 42.857 0.00 0.00 0.00 4.40
4769 5381 2.079170 TGTTTGGAGATTGTTGGGCA 57.921 45.000 0.00 0.00 0.00 5.36
4770 5382 2.867647 GCTTGTTTGGAGATTGTTGGGC 60.868 50.000 0.00 0.00 0.00 5.36
4771 5383 2.607771 CGCTTGTTTGGAGATTGTTGGG 60.608 50.000 0.00 0.00 0.00 4.12
4772 5384 2.664916 CGCTTGTTTGGAGATTGTTGG 58.335 47.619 0.00 0.00 0.00 3.77
4774 5565 1.680735 TGCGCTTGTTTGGAGATTGTT 59.319 42.857 9.73 0.00 0.00 2.83
4780 5571 0.667993 TCCTTTGCGCTTGTTTGGAG 59.332 50.000 9.73 0.00 0.00 3.86
4791 5582 3.419759 CGGTTCGGGTCCTTTGCG 61.420 66.667 0.00 0.00 0.00 4.85
4794 5585 1.747325 TTCGTCGGTTCGGGTCCTTT 61.747 55.000 0.00 0.00 0.00 3.11
4798 5589 2.731587 TTCGTTCGTCGGTTCGGGTC 62.732 60.000 0.00 0.00 40.32 4.46
4800 5594 1.661197 TTTCGTTCGTCGGTTCGGG 60.661 57.895 0.00 0.00 40.32 5.14
4805 5599 2.355009 CCGGTTTCGTTCGTCGGT 60.355 61.111 0.00 0.00 40.32 4.69
4806 5600 3.107661 CCCGGTTTCGTTCGTCGG 61.108 66.667 0.00 0.00 40.32 4.79
4807 5601 3.770424 GCCCGGTTTCGTTCGTCG 61.770 66.667 0.00 0.00 41.41 5.12
4808 5602 2.662527 TGCCCGGTTTCGTTCGTC 60.663 61.111 0.00 0.00 33.95 4.20
4809 5603 2.663852 CTGCCCGGTTTCGTTCGT 60.664 61.111 0.00 0.00 33.95 3.85
4810 5604 2.356553 TCTGCCCGGTTTCGTTCG 60.357 61.111 0.00 0.00 33.95 3.95
4811 5605 1.005394 TCTCTGCCCGGTTTCGTTC 60.005 57.895 0.00 0.00 33.95 3.95
4814 5608 0.320421 TTTCTCTCTGCCCGGTTTCG 60.320 55.000 0.00 0.00 0.00 3.46
4815 5609 1.443802 CTTTCTCTCTGCCCGGTTTC 58.556 55.000 0.00 0.00 0.00 2.78
4816 5610 0.036875 CCTTTCTCTCTGCCCGGTTT 59.963 55.000 0.00 0.00 0.00 3.27
4817 5611 1.679898 CCTTTCTCTCTGCCCGGTT 59.320 57.895 0.00 0.00 0.00 4.44
4818 5612 2.960688 GCCTTTCTCTCTGCCCGGT 61.961 63.158 0.00 0.00 0.00 5.28
4819 5613 1.330655 TAGCCTTTCTCTCTGCCCGG 61.331 60.000 0.00 0.00 0.00 5.73
4823 5617 4.927978 TGTATCTAGCCTTTCTCTCTGC 57.072 45.455 0.00 0.00 0.00 4.26
4830 5627 7.712639 TCAATCATCACTTGTATCTAGCCTTTC 59.287 37.037 0.00 0.00 0.00 2.62
4871 5668 0.032912 TACCACAGCGGGGATCTACA 60.033 55.000 3.78 0.00 40.22 2.74
4872 5669 0.388294 GTACCACAGCGGGGATCTAC 59.612 60.000 3.78 0.00 40.22 2.59


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

AutoCloner maintained by Alex Coulton.