Multiple sequence alignment - TraesCS2B01G604800

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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 TraesCS2B01G604800 chr2B 100.000 2779 0 0 1323 4101 786228290 786225512 0.000000e+00 5132
1 TraesCS2B01G604800 chr2B 100.000 1064 0 0 1 1064 786229612 786228549 0.000000e+00 1965
2 TraesCS2B01G604800 chr2D 88.681 2721 199 60 1447 4101 650324152 650321475 0.000000e+00 3217
3 TraesCS2B01G604800 chr2D 91.130 1071 68 17 1 1064 650325513 650324463 0.000000e+00 1426
4 TraesCS2B01G604800 chr2A 86.303 2088 189 52 2070 4098 774572889 774574938 0.000000e+00 2182
5 TraesCS2B01G604800 chr2A 91.463 1066 76 11 1 1062 774570918 774571972 0.000000e+00 1450
6 TraesCS2B01G604800 chr2A 90.625 320 21 7 1447 1763 774572300 774572613 2.280000e-112 416
7 TraesCS2B01G604800 chrUn 89.041 365 27 9 3315 3670 96707544 96707904 1.350000e-119 440
8 TraesCS2B01G604800 chr6B 89.720 321 29 4 3356 3676 47898731 47899047 1.370000e-109 407
9 TraesCS2B01G604800 chr6B 89.247 93 8 2 3069 3159 47898511 47898603 9.320000e-22 115
10 TraesCS2B01G604800 chr6A 85.366 328 42 3 3775 4101 27197546 27197868 6.570000e-88 335


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 TraesCS2B01G604800 chr2B 786225512 786229612 4100 True 3548.500000 5132 100.000000 1 4101 2 chr2B.!!$R1 4100
1 TraesCS2B01G604800 chr2D 650321475 650325513 4038 True 2321.500000 3217 89.905500 1 4101 2 chr2D.!!$R1 4100
2 TraesCS2B01G604800 chr2A 774570918 774574938 4020 False 1349.333333 2182 89.463667 1 4098 3 chr2A.!!$F1 4097
3 TraesCS2B01G604800 chr6B 47898511 47899047 536 False 261.000000 407 89.483500 3069 3676 2 chr6B.!!$F1 607

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
946 960 0.035458 AGTGCTGCCGCTTAACTCTT 59.965 50.0 0.7 0.0 36.97 2.85 F
1422 1436 0.035725 GGAACGGGGGTCTTTGTAGG 60.036 60.0 0.0 0.0 0.00 3.18 F
2197 2271 0.034337 GCTGTGGAACTTCACCCGTA 59.966 55.0 0.0 0.0 38.04 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2180 2254 0.034337 GCTACGGGTGAAGTTCCACA 59.966 55.000 0.00 0.0 38.74 4.17 R
2348 2449 1.142060 TGGATCCAAACACAGAACGGT 59.858 47.619 13.46 0.0 0.00 4.83 R
4023 4178 0.174162 GCGACCAACCTACATACGGT 59.826 55.000 0.00 0.0 35.97 4.83 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
49 50 0.967380 CATGAGGCACCCAAGGTTCC 60.967 60.000 0.00 0.00 39.28 3.62
51 52 2.852075 AGGCACCCAAGGTTCCGA 60.852 61.111 0.00 0.00 43.65 4.55
58 59 1.966451 CCAAGGTTCCGACACAGGC 60.966 63.158 0.00 0.00 0.00 4.85
60 61 0.535102 CAAGGTTCCGACACAGGCTT 60.535 55.000 0.00 0.00 0.00 4.35
66 67 1.738099 CCGACACAGGCTTCCTTCG 60.738 63.158 0.00 0.00 32.96 3.79
75 76 2.383527 GCTTCCTTCGACGCCAGTG 61.384 63.158 0.00 0.00 0.00 3.66
90 91 1.151668 CAGTGAACTTCTTCAGGCGG 58.848 55.000 0.00 0.00 37.06 6.13
218 219 4.967575 CCGTGTTGTTATTTGTGACTGTTC 59.032 41.667 0.00 0.00 0.00 3.18
262 263 4.277672 TGTCTATCGTATTAGGTGCTGGAC 59.722 45.833 0.00 0.00 0.00 4.02
341 342 8.982685 TGCTCTGATCGTTTATGAAATATCTTC 58.017 33.333 0.00 0.00 0.00 2.87
401 402 4.452455 GTGGTCATCTGTGTTTCTAACCAG 59.548 45.833 0.00 0.00 36.30 4.00
440 441 3.076621 TCTACAAGCATTTCTGTGGCTG 58.923 45.455 0.00 0.00 38.04 4.85
458 460 2.715046 CTGGTTTCTGCTGGCTGATTA 58.285 47.619 3.21 0.00 0.00 1.75
465 467 2.773661 TCTGCTGGCTGATTATCCTTGA 59.226 45.455 0.00 0.00 0.00 3.02
523 525 6.385649 TTTCCGAATATGCCTTTATTGGAC 57.614 37.500 0.00 0.00 0.00 4.02
524 526 4.394729 TCCGAATATGCCTTTATTGGACC 58.605 43.478 0.00 0.00 0.00 4.46
529 531 6.538742 CGAATATGCCTTTATTGGACCGATAT 59.461 38.462 2.03 0.00 0.00 1.63
535 537 6.183360 TGCCTTTATTGGACCGATATTGTTTC 60.183 38.462 2.03 0.00 0.00 2.78
555 557 5.488645 TTCGACTTTTGTAACTGTTTCCC 57.511 39.130 0.00 0.00 0.00 3.97
572 574 5.880332 TGTTTCCCTATGACTCTACATTTGC 59.120 40.000 0.00 0.00 0.00 3.68
575 577 3.393800 CCTATGACTCTACATTTGCCCG 58.606 50.000 0.00 0.00 0.00 6.13
579 581 2.301870 TGACTCTACATTTGCCCGAACT 59.698 45.455 0.00 0.00 0.00 3.01
608 610 5.516044 AGTAACACTGTTTTCTTCCCCTTT 58.484 37.500 0.00 0.00 0.00 3.11
625 627 5.185635 TCCCCTTTCATTTGCATTCTAACAG 59.814 40.000 0.00 0.00 0.00 3.16
644 648 8.426489 TCTAACAGTAGTTTTAAAAGCTCTCCA 58.574 33.333 0.00 0.00 39.15 3.86
663 667 6.985117 TCTCCATTCAAAGAATGTCCAAAAG 58.015 36.000 16.04 2.52 0.00 2.27
664 668 5.540911 TCCATTCAAAGAATGTCCAAAAGC 58.459 37.500 16.04 0.00 0.00 3.51
719 723 7.093945 GGCCCAAAATATTTTGTCTACTTCTCA 60.094 37.037 29.82 0.00 44.52 3.27
727 731 9.890629 ATATTTTGTCTACTTCTCATTGTAGCA 57.109 29.630 0.00 0.00 36.88 3.49
749 753 7.558435 GCATTCTCTGCCATTAATATTTTCG 57.442 36.000 0.00 0.00 45.66 3.46
751 755 8.025445 GCATTCTCTGCCATTAATATTTTCGAT 58.975 33.333 0.00 0.00 45.66 3.59
769 773 2.738846 CGATTCAGGAATAGCCCATTCG 59.261 50.000 0.00 0.00 43.53 3.34
780 785 5.991328 ATAGCCCATTCGAATATAATGCG 57.009 39.130 10.97 0.00 33.80 4.73
860 872 9.484806 AAATAATGAGGAATTCCAAGACATTCT 57.515 29.630 26.22 18.06 38.89 2.40
861 873 6.770746 AATGAGGAATTCCAAGACATTCTG 57.229 37.500 26.22 0.00 38.89 3.02
862 874 5.503634 TGAGGAATTCCAAGACATTCTGA 57.496 39.130 26.22 0.00 38.89 3.27
863 875 5.494724 TGAGGAATTCCAAGACATTCTGAG 58.505 41.667 26.22 0.00 38.89 3.35
864 876 5.249163 TGAGGAATTCCAAGACATTCTGAGA 59.751 40.000 26.22 0.00 38.89 3.27
865 877 5.495640 AGGAATTCCAAGACATTCTGAGAC 58.504 41.667 26.22 0.00 38.89 3.36
894 906 5.591472 TGAGATGCACAAATAAATCTCAGGG 59.409 40.000 8.02 0.00 46.22 4.45
946 960 0.035458 AGTGCTGCCGCTTAACTCTT 59.965 50.000 0.70 0.00 36.97 2.85
947 961 0.875059 GTGCTGCCGCTTAACTCTTT 59.125 50.000 0.70 0.00 36.97 2.52
948 962 1.135944 GTGCTGCCGCTTAACTCTTTC 60.136 52.381 0.70 0.00 36.97 2.62
949 963 1.270839 TGCTGCCGCTTAACTCTTTCT 60.271 47.619 0.70 0.00 36.97 2.52
960 974 6.176896 GCTTAACTCTTTCTTCTCCAATCCT 58.823 40.000 0.00 0.00 0.00 3.24
989 1003 5.897377 AGTGGAAACATTACAGTATTGCC 57.103 39.130 2.86 0.00 46.14 4.52
990 1004 5.321102 AGTGGAAACATTACAGTATTGCCA 58.679 37.500 2.86 0.00 46.14 4.92
992 1006 6.266558 AGTGGAAACATTACAGTATTGCCAAA 59.733 34.615 2.86 0.00 46.14 3.28
1005 1019 2.845019 GCCAAAAGCAAAGATGGGC 58.155 52.632 0.00 0.00 42.97 5.36
1008 1022 0.319727 CAAAAGCAAAGATGGGCGCA 60.320 50.000 10.83 5.70 34.54 6.09
1053 1067 0.389948 GCTCCGTCCATGACTTCGTT 60.390 55.000 0.00 0.00 0.00 3.85
1368 1382 6.907741 TCGTATGAATGATTTGCTTGTGAAA 58.092 32.000 0.00 0.00 0.00 2.69
1369 1383 6.801377 TCGTATGAATGATTTGCTTGTGAAAC 59.199 34.615 0.00 0.00 37.35 2.78
1370 1384 6.803320 CGTATGAATGATTTGCTTGTGAAACT 59.197 34.615 0.00 0.00 38.04 2.66
1371 1385 7.326789 CGTATGAATGATTTGCTTGTGAAACTT 59.673 33.333 0.00 0.00 38.04 2.66
1372 1386 8.981647 GTATGAATGATTTGCTTGTGAAACTTT 58.018 29.630 0.00 0.00 38.04 2.66
1374 1388 8.939201 TGAATGATTTGCTTGTGAAACTTTAA 57.061 26.923 0.00 0.00 38.04 1.52
1376 1390 9.636965 GAATGATTTGCTTGTGAAACTTTAAAC 57.363 29.630 0.00 0.00 38.04 2.01
1379 1393 8.993121 TGATTTGCTTGTGAAACTTTAAACAAA 58.007 25.926 0.00 0.00 38.04 2.83
1380 1394 9.818796 GATTTGCTTGTGAAACTTTAAACAAAA 57.181 25.926 0.00 0.00 38.04 2.44
1383 1397 6.128418 TGCTTGTGAAACTTTAAACAAAAGCC 60.128 34.615 20.40 9.56 46.59 4.35
1384 1398 8.432006 TGCTTGTGAAACTTTAAACAAAAGCCA 61.432 33.333 20.40 11.21 46.59 4.75
1395 1409 9.906660 CTTTAAACAAAAGCCATGTTATCTGTA 57.093 29.630 0.45 0.00 39.98 2.74
1399 1413 8.986477 AACAAAAGCCATGTTATCTGTAATTC 57.014 30.769 0.00 0.00 39.14 2.17
1400 1414 8.121305 ACAAAAGCCATGTTATCTGTAATTCA 57.879 30.769 0.00 0.00 0.00 2.57
1401 1415 8.584157 ACAAAAGCCATGTTATCTGTAATTCAA 58.416 29.630 0.00 0.00 0.00 2.69
1404 1418 7.281040 AGCCATGTTATCTGTAATTCAATGG 57.719 36.000 0.00 0.00 0.00 3.16
1405 1419 7.062322 AGCCATGTTATCTGTAATTCAATGGA 58.938 34.615 0.00 0.00 0.00 3.41
1406 1420 7.560991 AGCCATGTTATCTGTAATTCAATGGAA 59.439 33.333 0.00 0.00 37.45 3.53
1407 1421 7.649306 GCCATGTTATCTGTAATTCAATGGAAC 59.351 37.037 0.00 0.00 35.46 3.62
1408 1422 7.857389 CCATGTTATCTGTAATTCAATGGAACG 59.143 37.037 0.00 0.00 35.46 3.95
1409 1423 7.315247 TGTTATCTGTAATTCAATGGAACGG 57.685 36.000 0.00 0.00 35.46 4.44
1410 1424 6.317642 TGTTATCTGTAATTCAATGGAACGGG 59.682 38.462 0.00 0.00 35.46 5.28
1411 1425 3.616219 TCTGTAATTCAATGGAACGGGG 58.384 45.455 0.00 0.00 35.46 5.73
1412 1426 2.687935 CTGTAATTCAATGGAACGGGGG 59.312 50.000 0.00 0.00 35.46 5.40
1413 1427 2.041891 TGTAATTCAATGGAACGGGGGT 59.958 45.455 0.00 0.00 35.46 4.95
1414 1428 1.847328 AATTCAATGGAACGGGGGTC 58.153 50.000 0.00 0.00 35.46 4.46
1415 1429 0.999712 ATTCAATGGAACGGGGGTCT 59.000 50.000 0.00 0.00 35.46 3.85
1417 1431 0.774908 TCAATGGAACGGGGGTCTTT 59.225 50.000 0.00 0.00 0.00 2.52
1418 1432 0.887933 CAATGGAACGGGGGTCTTTG 59.112 55.000 0.00 0.00 0.00 2.77
1419 1433 0.481128 AATGGAACGGGGGTCTTTGT 59.519 50.000 0.00 0.00 0.00 2.83
1420 1434 1.364269 ATGGAACGGGGGTCTTTGTA 58.636 50.000 0.00 0.00 0.00 2.41
1421 1435 0.688487 TGGAACGGGGGTCTTTGTAG 59.312 55.000 0.00 0.00 0.00 2.74
1422 1436 0.035725 GGAACGGGGGTCTTTGTAGG 60.036 60.000 0.00 0.00 0.00 3.18
1424 1438 2.125269 CGGGGGTCTTTGTAGGCG 60.125 66.667 0.00 0.00 0.00 5.52
1425 1439 2.652095 CGGGGGTCTTTGTAGGCGA 61.652 63.158 0.00 0.00 0.00 5.54
1427 1441 0.675837 GGGGGTCTTTGTAGGCGAAC 60.676 60.000 0.00 0.00 0.00 3.95
1428 1442 0.035739 GGGGTCTTTGTAGGCGAACA 59.964 55.000 0.00 0.00 0.00 3.18
1429 1443 1.543871 GGGGTCTTTGTAGGCGAACAA 60.544 52.381 4.62 4.62 37.58 2.83
1430 1444 1.804748 GGGTCTTTGTAGGCGAACAAG 59.195 52.381 8.18 4.56 40.29 3.16
1431 1445 2.549349 GGGTCTTTGTAGGCGAACAAGA 60.549 50.000 8.18 6.32 40.29 3.02
1432 1446 3.135994 GGTCTTTGTAGGCGAACAAGAA 58.864 45.455 8.18 0.25 40.29 2.52
1433 1447 3.562557 GGTCTTTGTAGGCGAACAAGAAA 59.437 43.478 8.18 0.00 40.29 2.52
1434 1448 4.319549 GGTCTTTGTAGGCGAACAAGAAAG 60.320 45.833 8.18 4.73 40.29 2.62
1435 1449 4.510340 GTCTTTGTAGGCGAACAAGAAAGA 59.490 41.667 8.18 6.57 40.29 2.52
1436 1450 5.179555 GTCTTTGTAGGCGAACAAGAAAGAT 59.820 40.000 8.18 0.00 40.29 2.40
1437 1451 6.367969 GTCTTTGTAGGCGAACAAGAAAGATA 59.632 38.462 8.18 0.00 40.29 1.98
1438 1452 6.932400 TCTTTGTAGGCGAACAAGAAAGATAA 59.068 34.615 8.18 0.00 40.29 1.75
1439 1453 7.442969 TCTTTGTAGGCGAACAAGAAAGATAAA 59.557 33.333 8.18 0.00 40.29 1.40
1440 1454 7.681939 TTGTAGGCGAACAAGAAAGATAAAT 57.318 32.000 4.62 0.00 34.50 1.40
1441 1455 7.681939 TGTAGGCGAACAAGAAAGATAAATT 57.318 32.000 0.00 0.00 0.00 1.82
1442 1456 7.748847 TGTAGGCGAACAAGAAAGATAAATTC 58.251 34.615 0.00 0.00 0.00 2.17
1443 1457 6.817765 AGGCGAACAAGAAAGATAAATTCA 57.182 33.333 0.00 0.00 0.00 2.57
1444 1458 6.846350 AGGCGAACAAGAAAGATAAATTCAG 58.154 36.000 0.00 0.00 0.00 3.02
1445 1459 6.431234 AGGCGAACAAGAAAGATAAATTCAGT 59.569 34.615 0.00 0.00 0.00 3.41
1574 1588 0.999228 CGCATCTCGATGGTAGCGTC 60.999 60.000 8.81 3.96 41.67 5.19
1578 1592 3.550233 GCATCTCGATGGTAGCGTCTTTA 60.550 47.826 12.09 0.00 39.16 1.85
1598 1612 9.181805 GTCTTTAGCAGTTTTAGTTTGAAATCC 57.818 33.333 0.00 0.00 0.00 3.01
1599 1613 9.131791 TCTTTAGCAGTTTTAGTTTGAAATCCT 57.868 29.630 0.00 0.00 0.00 3.24
1600 1614 9.750125 CTTTAGCAGTTTTAGTTTGAAATCCTT 57.250 29.630 0.00 0.00 0.00 3.36
1623 1639 7.013274 CCTTCTCCTGTTTGAATCTGTGTTTAA 59.987 37.037 0.00 0.00 0.00 1.52
1626 1642 7.338196 TCTCCTGTTTGAATCTGTGTTTAACAA 59.662 33.333 0.00 0.00 38.67 2.83
1639 1655 9.337396 TCTGTGTTTAACAACTGAGTTGATATT 57.663 29.630 30.03 16.80 45.28 1.28
1733 1750 7.119846 AGGTACTTGTTTTCTATAGCTTTGCAG 59.880 37.037 0.00 0.00 27.25 4.41
1737 1754 5.883661 TGTTTTCTATAGCTTTGCAGATGC 58.116 37.500 0.00 0.00 42.50 3.91
1740 1757 4.155063 TCTATAGCTTTGCAGATGCCAA 57.845 40.909 1.72 0.00 41.18 4.52
1741 1758 4.525996 TCTATAGCTTTGCAGATGCCAAA 58.474 39.130 1.72 2.87 41.18 3.28
1763 1780 2.359214 TCCACTAATCGCAGTAGCTCTG 59.641 50.000 0.00 0.00 46.12 3.35
1783 1847 6.488683 GCTCTGACTGATTAGGTACTCTGTAT 59.511 42.308 0.00 0.00 41.75 2.29
1784 1848 7.013846 GCTCTGACTGATTAGGTACTCTGTATT 59.986 40.741 0.00 0.00 41.75 1.89
1803 1867 6.919721 TGTATTGCTCTTAACCATTGTTTCC 58.080 36.000 0.00 0.00 35.87 3.13
1808 1872 5.774690 TGCTCTTAACCATTGTTTCCTGATT 59.225 36.000 0.00 0.00 35.87 2.57
1907 1971 5.708736 TGGTTGTATATCTCATTGTGGGT 57.291 39.130 0.00 0.00 0.00 4.51
1935 1999 1.596727 GAAGCTCTTCGATGCATCACC 59.403 52.381 25.70 7.21 0.00 4.02
2000 2065 5.343307 CCATTGGCTTTGGCTTTACTATT 57.657 39.130 0.00 0.00 38.73 1.73
2009 2076 7.327975 GCTTTGGCTTTACTATTAACCCAAAT 58.672 34.615 13.05 0.00 37.75 2.32
2042 2110 6.954944 TGTTTCATAAAGACCTTATATGCGC 58.045 36.000 0.00 0.00 0.00 6.09
2044 2112 5.222079 TCATAAAGACCTTATATGCGCCA 57.778 39.130 4.18 0.00 0.00 5.69
2047 2115 7.390823 TCATAAAGACCTTATATGCGCCATTA 58.609 34.615 4.18 0.00 0.00 1.90
2055 2123 6.818644 ACCTTATATGCGCCATTACTCATAAG 59.181 38.462 4.18 8.22 0.00 1.73
2056 2124 6.818644 CCTTATATGCGCCATTACTCATAAGT 59.181 38.462 4.18 0.00 39.66 2.24
2057 2125 7.010552 CCTTATATGCGCCATTACTCATAAGTC 59.989 40.741 4.18 0.00 36.92 3.01
2058 2126 3.535280 TGCGCCATTACTCATAAGTCA 57.465 42.857 4.18 0.00 36.92 3.41
2059 2127 4.071961 TGCGCCATTACTCATAAGTCAT 57.928 40.909 4.18 0.00 36.92 3.06
2060 2128 5.208463 TGCGCCATTACTCATAAGTCATA 57.792 39.130 4.18 0.00 36.92 2.15
2061 2129 5.606505 TGCGCCATTACTCATAAGTCATAA 58.393 37.500 4.18 0.00 36.92 1.90
2062 2130 5.465390 TGCGCCATTACTCATAAGTCATAAC 59.535 40.000 4.18 0.00 36.92 1.89
2063 2131 5.107065 GCGCCATTACTCATAAGTCATAACC 60.107 44.000 0.00 0.00 36.92 2.85
2068 2136 4.423625 ACTCATAAGTCATAACCCCTGC 57.576 45.455 0.00 0.00 0.00 4.85
2078 2146 4.576463 GTCATAACCCCTGCAAACTCATAG 59.424 45.833 0.00 0.00 0.00 2.23
2096 2164 6.320418 ACTCATAGCAGATGCAATTCAATCAA 59.680 34.615 7.68 0.00 45.16 2.57
2129 2203 2.972713 TGGCACCTGAGTAGTTTCTCTT 59.027 45.455 0.00 0.00 35.68 2.85
2148 2222 6.413892 TCTCTTGGTCATAATGTGTGCATAA 58.586 36.000 0.00 0.00 34.39 1.90
2173 2247 6.868622 AGAATACACTTCACCTGCTTACTAG 58.131 40.000 0.00 0.00 0.00 2.57
2180 2254 3.165875 TCACCTGCTTACTAGACAAGCT 58.834 45.455 24.27 10.10 46.85 3.74
2190 2264 3.996480 ACTAGACAAGCTGTGGAACTTC 58.004 45.455 0.00 0.00 38.04 3.01
2191 2265 3.388024 ACTAGACAAGCTGTGGAACTTCA 59.612 43.478 0.00 0.00 38.04 3.02
2192 2266 2.565841 AGACAAGCTGTGGAACTTCAC 58.434 47.619 0.00 0.00 38.04 3.18
2195 2269 0.535102 AAGCTGTGGAACTTCACCCG 60.535 55.000 0.00 0.00 38.04 5.28
2196 2270 1.227853 GCTGTGGAACTTCACCCGT 60.228 57.895 0.00 0.00 38.04 5.28
2197 2271 0.034337 GCTGTGGAACTTCACCCGTA 59.966 55.000 0.00 0.00 38.04 4.02
2198 2272 1.939838 GCTGTGGAACTTCACCCGTAG 60.940 57.143 0.00 0.00 38.04 3.51
2206 2286 0.528684 CTTCACCCGTAGCTAGCTGC 60.529 60.000 27.68 24.53 43.29 5.25
2230 2310 1.761784 AGAGCATGGCTTCTCAGGTAG 59.238 52.381 0.00 0.00 39.88 3.18
2252 2332 8.808092 GGTAGAGGCTTATACTATGACTGAATT 58.192 37.037 0.39 0.00 0.00 2.17
2287 2368 8.879759 GTCGTATTTTCATCCTTTCATAAGACA 58.120 33.333 0.00 0.00 32.92 3.41
2338 2439 3.905784 GTTTGCTTCCCATCAAACAGAG 58.094 45.455 11.53 0.00 46.65 3.35
2348 2449 6.778821 TCCCATCAAACAGAGATTACAGAAA 58.221 36.000 0.00 0.00 0.00 2.52
2350 2451 6.127897 CCCATCAAACAGAGATTACAGAAACC 60.128 42.308 0.00 0.00 0.00 3.27
2351 2452 6.402550 CCATCAAACAGAGATTACAGAAACCG 60.403 42.308 0.00 0.00 0.00 4.44
2353 2454 6.053005 TCAAACAGAGATTACAGAAACCGTT 58.947 36.000 0.00 0.00 0.00 4.44
2383 2485 4.517285 TGGATCCACTATTCAAGTTGAGC 58.483 43.478 11.44 0.00 35.95 4.26
2402 2504 5.482908 TGAGCTAGTTTTCAGATTGGAGAC 58.517 41.667 0.00 0.00 0.00 3.36
2407 2509 4.904241 AGTTTTCAGATTGGAGACTGGAG 58.096 43.478 0.00 0.00 35.20 3.86
2444 2571 8.230112 GCTAAATAGCGGTAGAAGAGAAATAC 57.770 38.462 0.00 0.00 39.82 1.89
2448 2575 5.599999 AGCGGTAGAAGAGAAATACACAT 57.400 39.130 0.00 0.00 0.00 3.21
2475 2602 9.754382 TTTATGTTAGGCTTATACTCTTTACGG 57.246 33.333 0.00 0.00 0.00 4.02
2481 2611 6.514063 AGGCTTATACTCTTTACGGTGAATC 58.486 40.000 0.00 0.00 0.00 2.52
2534 2664 1.273048 TGCAGGCCAAATAACTTGCAG 59.727 47.619 5.01 0.00 33.27 4.41
2536 2666 2.491693 GCAGGCCAAATAACTTGCAGTA 59.508 45.455 5.01 0.00 33.27 2.74
2542 2674 6.663523 AGGCCAAATAACTTGCAGTATACTTT 59.336 34.615 5.01 0.00 33.27 2.66
2543 2675 7.178451 AGGCCAAATAACTTGCAGTATACTTTT 59.822 33.333 5.01 0.00 33.27 2.27
2584 2716 2.054687 TTGAAATGCTTTCTGCTGCG 57.945 45.000 0.00 0.00 43.37 5.18
2587 2719 2.159476 TGAAATGCTTTCTGCTGCGATC 60.159 45.455 0.00 0.00 43.37 3.69
2612 2744 1.507140 TGGAGATATTGGCGTTCCCT 58.493 50.000 0.00 0.00 0.00 4.20
2645 2777 1.338136 CCGGGCAGGAACCAGATAGT 61.338 60.000 0.00 0.00 45.00 2.12
2711 2843 5.535030 AGAGTTTCCTATTTTTCGCAAGGTT 59.465 36.000 0.00 0.00 38.47 3.50
2726 2858 3.305744 GCAAGGTTTATCCAGCGGAAAAA 60.306 43.478 1.44 0.00 39.02 1.94
2755 2887 6.038161 CCTTTCTATTTTCTGTGTGTGTGTGA 59.962 38.462 0.00 0.00 0.00 3.58
2777 2909 3.756933 AGCTTCCAAACACAAATGCAT 57.243 38.095 0.00 0.00 0.00 3.96
2861 2993 3.882888 CCCTGCTGTACAAGTTCTTGAAA 59.117 43.478 17.75 4.39 0.00 2.69
2951 3083 0.928229 GGCACGTCATGAACCGATAC 59.072 55.000 12.18 1.92 0.00 2.24
3004 3136 4.390297 GGTGATGCTCTAACTCAACAGTTC 59.610 45.833 0.00 0.00 42.27 3.01
3150 3289 3.125146 GCGTGTCATGTGTATGTGTCATT 59.875 43.478 0.00 0.00 35.73 2.57
3175 3314 5.176774 TGTTCTTTTCGCTACTGTATGTGTG 59.823 40.000 0.00 0.00 0.00 3.82
3243 3382 5.365619 ACTCTGTTTTCTACACGGTGAAAT 58.634 37.500 16.29 0.00 33.04 2.17
3250 3398 8.077386 TGTTTTCTACACGGTGAAATAATTTCC 58.923 33.333 16.29 0.00 38.90 3.13
3253 3401 3.768878 ACACGGTGAAATAATTTCCCCA 58.231 40.909 16.29 0.00 37.07 4.96
3258 3406 6.652900 CACGGTGAAATAATTTCCCCAAAATT 59.347 34.615 0.74 1.83 46.72 1.82
3307 3457 2.763448 ACACAGCCTGGAGAGTAATCTC 59.237 50.000 11.76 11.76 40.70 2.75
3442 3592 7.665690 TCCTCTAGAAGAGTTGATATCAATGC 58.334 38.462 20.65 15.01 40.72 3.56
3473 3623 2.158957 TCGTGTCAAATATCCCAGAGCC 60.159 50.000 0.00 0.00 0.00 4.70
3582 3732 3.371063 GTGAGCGAGTCGGGACCA 61.371 66.667 15.52 0.00 0.00 4.02
3628 3778 2.875296 TGGACTTTGATTTGGACCCTG 58.125 47.619 0.00 0.00 0.00 4.45
3648 3798 2.230660 GCTTGCACAAAAGTCCCTAGT 58.769 47.619 0.00 0.00 0.00 2.57
3676 3827 4.382254 CCTGCACATGCCAAACAGAATTAT 60.382 41.667 0.49 0.00 41.18 1.28
3677 3828 5.149973 TGCACATGCCAAACAGAATTATT 57.850 34.783 0.49 0.00 41.18 1.40
3701 3852 5.746990 ACTTCTATGCTGTATGATACCCC 57.253 43.478 0.00 0.00 0.00 4.95
3703 3854 6.562228 ACTTCTATGCTGTATGATACCCCTA 58.438 40.000 0.00 0.00 0.00 3.53
3709 3860 5.155161 TGCTGTATGATACCCCTATCTGTT 58.845 41.667 0.00 0.00 31.36 3.16
3710 3861 5.606749 TGCTGTATGATACCCCTATCTGTTT 59.393 40.000 0.00 0.00 31.36 2.83
3711 3862 6.785466 TGCTGTATGATACCCCTATCTGTTTA 59.215 38.462 0.00 0.00 31.36 2.01
3738 3889 9.515226 TTAGGAACAAAATAAAGTAGATGCTGT 57.485 29.630 0.00 0.00 0.00 4.40
3739 3890 8.409358 AGGAACAAAATAAAGTAGATGCTGTT 57.591 30.769 0.00 0.00 0.00 3.16
3748 3899 4.946478 AGTAGATGCTGTTAGATGGGTC 57.054 45.455 0.00 0.00 0.00 4.46
3749 3900 4.290093 AGTAGATGCTGTTAGATGGGTCA 58.710 43.478 0.00 0.00 0.00 4.02
3754 3905 2.292267 GCTGTTAGATGGGTCACATGG 58.708 52.381 0.00 0.00 40.72 3.66
3755 3906 2.923121 CTGTTAGATGGGTCACATGGG 58.077 52.381 0.00 0.00 40.72 4.00
3758 3909 1.965414 TAGATGGGTCACATGGGTGT 58.035 50.000 0.00 0.00 45.45 4.16
3773 3924 6.016360 CACATGGGTGTATCTTTTCAGTTGAA 60.016 38.462 0.00 0.00 40.24 2.69
3784 3939 6.281405 TCTTTTCAGTTGAAGTCTGGTAGAC 58.719 40.000 0.79 0.79 45.38 2.59
3855 4010 2.911636 CCTCCAATGATATGCCTCTCCT 59.088 50.000 0.00 0.00 0.00 3.69
3934 4089 4.811969 TGTAAGAGCCGGATAAACTCAA 57.188 40.909 5.05 0.00 32.71 3.02
3947 4102 8.673711 CCGGATAAACTCAAGATTTCATACAAA 58.326 33.333 0.00 0.00 0.00 2.83
3954 4109 7.458397 ACTCAAGATTTCATACAAACCCTACA 58.542 34.615 0.00 0.00 0.00 2.74
3965 4120 4.447290 ACAAACCCTACAAAACAAATGCC 58.553 39.130 0.00 0.00 0.00 4.40
3973 4128 3.677190 ACAAAACAAATGCCCATCATGG 58.323 40.909 0.00 0.00 35.13 3.66
3987 4142 4.505566 CCCATCATGGAGGGTTACATACAG 60.506 50.000 4.75 0.00 40.96 2.74
4003 4158 0.612229 ACAGGTCTCAGGTGCATCAG 59.388 55.000 0.00 0.00 0.00 2.90
4013 4168 4.401022 TCAGGTGCATCAGTTCTTTGATT 58.599 39.130 0.00 0.00 35.67 2.57
4018 4173 5.403466 GGTGCATCAGTTCTTTGATTTGTTC 59.597 40.000 0.00 0.00 35.67 3.18
4022 4177 6.071952 GCATCAGTTCTTTGATTTGTTCCCTA 60.072 38.462 0.00 0.00 35.67 3.53
4023 4178 7.523709 GCATCAGTTCTTTGATTTGTTCCCTAA 60.524 37.037 0.00 0.00 35.67 2.69
4024 4179 7.272037 TCAGTTCTTTGATTTGTTCCCTAAC 57.728 36.000 0.00 0.00 36.07 2.34
4025 4180 6.264518 TCAGTTCTTTGATTTGTTCCCTAACC 59.735 38.462 0.00 0.00 34.49 2.85
4026 4181 5.240844 AGTTCTTTGATTTGTTCCCTAACCG 59.759 40.000 0.00 0.00 34.49 4.44
4027 4182 4.721132 TCTTTGATTTGTTCCCTAACCGT 58.279 39.130 0.00 0.00 34.49 4.83
4030 4185 6.373216 TCTTTGATTTGTTCCCTAACCGTATG 59.627 38.462 0.00 0.00 34.49 2.39
4035 4190 3.711863 TGTTCCCTAACCGTATGTAGGT 58.288 45.455 0.00 0.00 45.29 3.08
4061 4216 1.138266 GCCTACCTCGTAAATGGCAGA 59.862 52.381 0.00 0.00 40.04 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 1.304381 GAACCCTCCCAATGCTGCA 60.304 57.895 4.13 4.13 0.00 4.41
15 16 1.072965 CTCATGGCATAGAACCCTCCC 59.927 57.143 0.00 0.00 0.00 4.30
42 43 0.250338 GAAGCCTGTGTCGGAACCTT 60.250 55.000 0.00 0.00 0.00 3.50
49 50 1.009389 GTCGAAGGAAGCCTGTGTCG 61.009 60.000 0.00 0.00 34.04 4.35
51 52 1.006102 CGTCGAAGGAAGCCTGTGT 60.006 57.895 0.00 0.00 32.13 3.72
58 59 0.319555 TTCACTGGCGTCGAAGGAAG 60.320 55.000 0.00 0.00 0.00 3.46
60 61 1.006571 GTTCACTGGCGTCGAAGGA 60.007 57.895 0.00 0.00 0.00 3.36
66 67 1.795286 CTGAAGAAGTTCACTGGCGTC 59.205 52.381 5.50 0.00 37.79 5.19
75 76 1.916697 GCAGCCGCCTGAAGAAGTTC 61.917 60.000 0.00 0.00 41.77 3.01
193 194 2.946329 AGTCACAAATAACAACACGGCA 59.054 40.909 0.00 0.00 0.00 5.69
218 219 0.237761 ACTCGAAGTCCTGAACGACG 59.762 55.000 0.00 0.00 37.85 5.12
262 263 3.355378 TGTCAGCACATTATTCCCTTGG 58.645 45.455 0.00 0.00 0.00 3.61
264 265 3.019564 GCTGTCAGCACATTATTCCCTT 58.980 45.455 20.16 0.00 41.89 3.95
341 342 4.451629 AGGGTACTGAACATTACACGAG 57.548 45.455 0.00 0.00 0.00 4.18
401 402 6.509418 TGTAGAAAGATGCAATTACCCAAC 57.491 37.500 0.00 0.00 0.00 3.77
440 441 2.620585 GGATAATCAGCCAGCAGAAACC 59.379 50.000 0.00 0.00 0.00 3.27
458 460 7.053316 TCACATGAACACAAAAATCAAGGAT 57.947 32.000 0.00 0.00 0.00 3.24
465 467 7.277539 ACGTCAAAATCACATGAACACAAAAAT 59.722 29.630 0.00 0.00 0.00 1.82
516 518 5.909477 AGTCGAAACAATATCGGTCCAATA 58.091 37.500 0.00 0.00 40.59 1.90
523 525 7.477422 CAGTTACAAAAGTCGAAACAATATCGG 59.523 37.037 0.00 0.00 40.59 4.18
524 526 8.007716 ACAGTTACAAAAGTCGAAACAATATCG 58.992 33.333 0.00 0.00 41.53 2.92
529 531 6.802834 GGAAACAGTTACAAAAGTCGAAACAA 59.197 34.615 0.00 0.00 0.00 2.83
535 537 6.425721 TCATAGGGAAACAGTTACAAAAGTCG 59.574 38.462 0.00 0.00 0.00 4.18
555 557 4.322080 TCGGGCAAATGTAGAGTCATAG 57.678 45.455 0.00 0.00 0.00 2.23
572 574 0.682852 TGTTACTCCACCAGTTCGGG 59.317 55.000 0.00 0.00 40.22 5.14
575 577 3.470645 ACAGTGTTACTCCACCAGTTC 57.529 47.619 0.00 0.00 36.43 3.01
579 581 4.497291 AGAAAACAGTGTTACTCCACCA 57.503 40.909 9.37 0.00 35.93 4.17
625 627 9.399403 CTTTGAATGGAGAGCTTTTAAAACTAC 57.601 33.333 0.00 0.00 0.00 2.73
637 641 4.012374 TGGACATTCTTTGAATGGAGAGC 58.988 43.478 20.04 7.56 32.14 4.09
641 645 5.070180 TGCTTTTGGACATTCTTTGAATGGA 59.930 36.000 20.04 5.45 32.14 3.41
644 648 6.585416 ACTTGCTTTTGGACATTCTTTGAAT 58.415 32.000 0.00 0.00 0.00 2.57
663 667 3.372206 CACCAGCTACTACAATGACTTGC 59.628 47.826 0.00 0.00 35.69 4.01
664 668 4.569943 ACACCAGCTACTACAATGACTTG 58.430 43.478 0.00 0.00 38.39 3.16
747 751 3.554960 CGAATGGGCTATTCCTGAATCGA 60.555 47.826 16.68 0.00 41.78 3.59
748 752 2.738846 CGAATGGGCTATTCCTGAATCG 59.261 50.000 16.68 1.56 41.78 3.34
749 753 4.008074 TCGAATGGGCTATTCCTGAATC 57.992 45.455 16.68 0.00 41.78 2.52
751 755 3.924114 TTCGAATGGGCTATTCCTGAA 57.076 42.857 16.68 12.42 41.78 3.02
769 773 7.112397 CACACAAATTGCAACGCATTATATTC 58.888 34.615 0.00 0.00 38.76 1.75
780 785 1.860326 GACAGCCACACAAATTGCAAC 59.140 47.619 0.00 0.00 0.00 4.17
850 862 5.047448 TCTCAGGAAGTCTCAGAATGTCTTG 60.047 44.000 0.00 0.00 37.40 3.02
856 868 3.773667 TGCATCTCAGGAAGTCTCAGAAT 59.226 43.478 0.00 0.00 0.00 2.40
857 869 3.056250 GTGCATCTCAGGAAGTCTCAGAA 60.056 47.826 0.00 0.00 0.00 3.02
858 870 2.495270 GTGCATCTCAGGAAGTCTCAGA 59.505 50.000 0.00 0.00 0.00 3.27
859 871 2.233186 TGTGCATCTCAGGAAGTCTCAG 59.767 50.000 0.00 0.00 0.00 3.35
860 872 2.250924 TGTGCATCTCAGGAAGTCTCA 58.749 47.619 0.00 0.00 0.00 3.27
861 873 3.325293 TTGTGCATCTCAGGAAGTCTC 57.675 47.619 0.00 0.00 0.00 3.36
862 874 3.777106 TTTGTGCATCTCAGGAAGTCT 57.223 42.857 0.00 0.00 0.00 3.24
863 875 6.500684 TTTATTTGTGCATCTCAGGAAGTC 57.499 37.500 0.00 0.00 0.00 3.01
864 876 6.888632 AGATTTATTTGTGCATCTCAGGAAGT 59.111 34.615 0.00 0.00 0.00 3.01
865 877 7.066645 TGAGATTTATTTGTGCATCTCAGGAAG 59.933 37.037 8.02 0.00 44.31 3.46
894 906 2.337532 CAAGTGGCAAGCACCTGC 59.662 61.111 0.00 0.00 41.85 4.85
946 960 6.000219 CACTTGAGAAAGGATTGGAGAAGAA 59.000 40.000 0.00 0.00 0.00 2.52
947 961 5.513788 CCACTTGAGAAAGGATTGGAGAAGA 60.514 44.000 0.00 0.00 0.00 2.87
948 962 4.699257 CCACTTGAGAAAGGATTGGAGAAG 59.301 45.833 0.00 0.00 0.00 2.85
949 963 4.350816 TCCACTTGAGAAAGGATTGGAGAA 59.649 41.667 0.00 0.00 0.00 2.87
960 974 8.918202 ATACTGTAATGTTTCCACTTGAGAAA 57.082 30.769 0.00 0.00 0.00 2.52
989 1003 0.319727 TGCGCCCATCTTTGCTTTTG 60.320 50.000 4.18 0.00 0.00 2.44
990 1004 0.037975 CTGCGCCCATCTTTGCTTTT 60.038 50.000 4.18 0.00 0.00 2.27
992 1006 2.998279 GCTGCGCCCATCTTTGCTT 61.998 57.895 4.18 0.00 0.00 3.91
999 1013 2.894387 GACTCTGCTGCGCCCATC 60.894 66.667 4.18 0.00 0.00 3.51
1005 1019 0.108472 TGGAAGATGACTCTGCTGCG 60.108 55.000 0.00 0.00 0.00 5.18
1008 1022 1.907936 AGCTTGGAAGATGACTCTGCT 59.092 47.619 0.00 0.00 0.00 4.24
1035 1049 1.336887 ACAACGAAGTCATGGACGGAG 60.337 52.381 0.00 0.00 45.00 4.63
1346 1360 8.524870 AAGTTTCACAAGCAAATCATTCATAC 57.475 30.769 0.00 0.00 0.00 2.39
1348 1362 9.545105 TTAAAGTTTCACAAGCAAATCATTCAT 57.455 25.926 0.00 0.00 0.00 2.57
1351 1365 9.160496 TGTTTAAAGTTTCACAAGCAAATCATT 57.840 25.926 0.00 0.00 0.00 2.57
1364 1378 7.913674 AACATGGCTTTTGTTTAAAGTTTCA 57.086 28.000 0.00 0.00 44.21 2.69
1368 1382 8.421002 ACAGATAACATGGCTTTTGTTTAAAGT 58.579 29.630 0.00 0.99 44.21 2.66
1369 1383 8.816640 ACAGATAACATGGCTTTTGTTTAAAG 57.183 30.769 0.00 0.00 44.99 1.85
1374 1388 8.584157 TGAATTACAGATAACATGGCTTTTGTT 58.416 29.630 0.00 6.36 40.30 2.83
1376 1390 8.984891 TTGAATTACAGATAACATGGCTTTTG 57.015 30.769 0.00 0.00 0.00 2.44
1379 1393 7.560991 TCCATTGAATTACAGATAACATGGCTT 59.439 33.333 0.00 0.00 0.00 4.35
1380 1394 7.062322 TCCATTGAATTACAGATAACATGGCT 58.938 34.615 0.00 0.00 0.00 4.75
1381 1395 7.275888 TCCATTGAATTACAGATAACATGGC 57.724 36.000 0.00 0.00 0.00 4.40
1382 1396 7.857389 CGTTCCATTGAATTACAGATAACATGG 59.143 37.037 0.00 0.00 31.98 3.66
1383 1397 7.857389 CCGTTCCATTGAATTACAGATAACATG 59.143 37.037 0.00 0.00 31.98 3.21
1384 1398 7.013274 CCCGTTCCATTGAATTACAGATAACAT 59.987 37.037 0.00 0.00 31.98 2.71
1386 1400 6.238648 CCCCGTTCCATTGAATTACAGATAAC 60.239 42.308 0.00 0.00 31.98 1.89
1389 1403 4.207165 CCCCGTTCCATTGAATTACAGAT 58.793 43.478 0.00 0.00 31.98 2.90
1390 1404 3.616219 CCCCGTTCCATTGAATTACAGA 58.384 45.455 0.00 0.00 31.98 3.41
1391 1405 2.687935 CCCCCGTTCCATTGAATTACAG 59.312 50.000 0.00 0.00 31.98 2.74
1393 1407 2.686405 GACCCCCGTTCCATTGAATTAC 59.314 50.000 0.00 0.00 31.98 1.89
1395 1409 1.357761 AGACCCCCGTTCCATTGAATT 59.642 47.619 0.00 0.00 31.98 2.17
1396 1410 0.999712 AGACCCCCGTTCCATTGAAT 59.000 50.000 0.00 0.00 31.98 2.57
1397 1411 0.774908 AAGACCCCCGTTCCATTGAA 59.225 50.000 0.00 0.00 0.00 2.69
1398 1412 0.774908 AAAGACCCCCGTTCCATTGA 59.225 50.000 0.00 0.00 0.00 2.57
1399 1413 0.887933 CAAAGACCCCCGTTCCATTG 59.112 55.000 0.00 0.00 0.00 2.82
1400 1414 0.481128 ACAAAGACCCCCGTTCCATT 59.519 50.000 0.00 0.00 0.00 3.16
1401 1415 1.280998 CTACAAAGACCCCCGTTCCAT 59.719 52.381 0.00 0.00 0.00 3.41
1404 1418 0.675837 GCCTACAAAGACCCCCGTTC 60.676 60.000 0.00 0.00 0.00 3.95
1405 1419 1.377612 GCCTACAAAGACCCCCGTT 59.622 57.895 0.00 0.00 0.00 4.44
1406 1420 2.951101 CGCCTACAAAGACCCCCGT 61.951 63.158 0.00 0.00 0.00 5.28
1407 1421 2.125269 CGCCTACAAAGACCCCCG 60.125 66.667 0.00 0.00 0.00 5.73
1408 1422 0.675837 GTTCGCCTACAAAGACCCCC 60.676 60.000 0.00 0.00 0.00 5.40
1409 1423 0.035739 TGTTCGCCTACAAAGACCCC 59.964 55.000 0.00 0.00 0.00 4.95
1410 1424 1.804748 CTTGTTCGCCTACAAAGACCC 59.195 52.381 0.66 0.00 37.55 4.46
1411 1425 2.762745 TCTTGTTCGCCTACAAAGACC 58.237 47.619 0.66 0.00 37.55 3.85
1412 1426 4.510340 TCTTTCTTGTTCGCCTACAAAGAC 59.490 41.667 0.66 0.00 37.55 3.01
1413 1427 4.699637 TCTTTCTTGTTCGCCTACAAAGA 58.300 39.130 0.66 0.00 37.55 2.52
1414 1428 5.613358 ATCTTTCTTGTTCGCCTACAAAG 57.387 39.130 0.66 0.00 37.55 2.77
1415 1429 7.499321 TTTATCTTTCTTGTTCGCCTACAAA 57.501 32.000 0.66 0.00 37.55 2.83
1417 1431 7.389330 TGAATTTATCTTTCTTGTTCGCCTACA 59.611 33.333 0.00 0.00 0.00 2.74
1418 1432 7.748847 TGAATTTATCTTTCTTGTTCGCCTAC 58.251 34.615 0.00 0.00 0.00 3.18
1419 1433 7.606456 ACTGAATTTATCTTTCTTGTTCGCCTA 59.394 33.333 0.00 0.00 0.00 3.93
1420 1434 6.431234 ACTGAATTTATCTTTCTTGTTCGCCT 59.569 34.615 0.00 0.00 0.00 5.52
1421 1435 6.612306 ACTGAATTTATCTTTCTTGTTCGCC 58.388 36.000 0.00 0.00 0.00 5.54
1422 1436 9.214953 CATACTGAATTTATCTTTCTTGTTCGC 57.785 33.333 0.00 0.00 0.00 4.70
1437 1451 9.388506 CAGTTAGAAGGATGACATACTGAATTT 57.611 33.333 0.00 0.00 35.06 1.82
1438 1452 8.762645 TCAGTTAGAAGGATGACATACTGAATT 58.237 33.333 0.00 0.00 38.15 2.17
1439 1453 8.311395 TCAGTTAGAAGGATGACATACTGAAT 57.689 34.615 0.00 0.00 38.15 2.57
1440 1454 7.718334 TCAGTTAGAAGGATGACATACTGAA 57.282 36.000 0.00 0.00 38.15 3.02
1441 1455 7.718334 TTCAGTTAGAAGGATGACATACTGA 57.282 36.000 0.00 5.94 39.02 3.41
1442 1456 7.819415 TGTTTCAGTTAGAAGGATGACATACTG 59.181 37.037 0.00 3.56 37.57 2.74
1443 1457 7.819900 GTGTTTCAGTTAGAAGGATGACATACT 59.180 37.037 0.00 0.00 37.57 2.12
1444 1458 7.819900 AGTGTTTCAGTTAGAAGGATGACATAC 59.180 37.037 0.00 0.00 37.57 2.39
1445 1459 7.907389 AGTGTTTCAGTTAGAAGGATGACATA 58.093 34.615 0.00 0.00 37.57 2.29
1449 1463 5.470368 CGAGTGTTTCAGTTAGAAGGATGA 58.530 41.667 0.00 0.00 37.57 2.92
1574 1588 9.750125 AAGGATTTCAAACTAAAACTGCTAAAG 57.250 29.630 0.00 0.00 0.00 1.85
1578 1592 7.255625 GGAGAAGGATTTCAAACTAAAACTGCT 60.256 37.037 0.00 0.00 35.70 4.24
1598 1612 6.382869 AAACACAGATTCAAACAGGAGAAG 57.617 37.500 0.00 0.00 0.00 2.85
1599 1613 7.338196 TGTTAAACACAGATTCAAACAGGAGAA 59.662 33.333 0.00 0.00 0.00 2.87
1600 1614 6.826231 TGTTAAACACAGATTCAAACAGGAGA 59.174 34.615 0.00 0.00 0.00 3.71
1623 1639 6.000219 ACTGCAAGAATATCAACTCAGTTGT 59.000 36.000 17.27 7.54 40.06 3.32
1626 1642 4.940046 CCACTGCAAGAATATCAACTCAGT 59.060 41.667 0.00 0.00 37.43 3.41
1639 1655 0.106769 TTTGCCAGACCACTGCAAGA 60.107 50.000 0.00 0.00 42.25 3.02
1733 1750 2.618241 TGCGATTAGTGGATTTGGCATC 59.382 45.455 0.00 0.00 0.00 3.91
1737 1754 3.248602 GCTACTGCGATTAGTGGATTTGG 59.751 47.826 0.00 0.00 31.51 3.28
1740 1757 3.639094 AGAGCTACTGCGATTAGTGGATT 59.361 43.478 0.00 0.00 45.42 3.01
1741 1758 3.005261 CAGAGCTACTGCGATTAGTGGAT 59.995 47.826 0.00 0.00 45.42 3.41
1763 1780 7.013846 AGAGCAATACAGAGTACCTAATCAGTC 59.986 40.741 0.00 0.00 0.00 3.51
1783 1847 5.136828 TCAGGAAACAATGGTTAAGAGCAA 58.863 37.500 0.00 0.00 35.82 3.91
1784 1848 4.724399 TCAGGAAACAATGGTTAAGAGCA 58.276 39.130 0.00 0.00 35.82 4.26
1820 1884 3.832276 TGTGTTCAGTTTCAGCACAAAC 58.168 40.909 2.99 2.99 37.16 2.93
1876 1940 9.874205 CAATGAGATATACAACCAAACCATTTT 57.126 29.630 0.00 0.00 0.00 1.82
1907 1971 3.310774 GCATCGAAGAGCTTCAAGCATTA 59.689 43.478 13.10 0.00 45.56 1.90
1935 1999 7.219484 GGAACATTCCCCATGACATATAAAG 57.781 40.000 0.00 0.00 41.62 1.85
2026 2094 5.621193 AGTAATGGCGCATATAAGGTCTTT 58.379 37.500 10.83 0.00 0.00 2.52
2038 2106 3.535280 TGACTTATGAGTAATGGCGCA 57.465 42.857 10.83 0.00 35.88 6.09
2039 2107 5.107065 GGTTATGACTTATGAGTAATGGCGC 60.107 44.000 0.00 0.00 35.88 6.53
2042 2110 6.936900 CAGGGGTTATGACTTATGAGTAATGG 59.063 42.308 0.00 0.00 35.88 3.16
2044 2112 6.101150 TGCAGGGGTTATGACTTATGAGTAAT 59.899 38.462 0.00 0.00 35.88 1.89
2047 2115 3.780294 TGCAGGGGTTATGACTTATGAGT 59.220 43.478 0.00 0.00 39.32 3.41
2055 2123 2.790433 TGAGTTTGCAGGGGTTATGAC 58.210 47.619 0.00 0.00 0.00 3.06
2056 2124 3.737559 ATGAGTTTGCAGGGGTTATGA 57.262 42.857 0.00 0.00 0.00 2.15
2057 2125 3.316308 GCTATGAGTTTGCAGGGGTTATG 59.684 47.826 0.00 0.00 0.00 1.90
2058 2126 3.053693 TGCTATGAGTTTGCAGGGGTTAT 60.054 43.478 0.00 0.00 32.55 1.89
2059 2127 2.307392 TGCTATGAGTTTGCAGGGGTTA 59.693 45.455 0.00 0.00 32.55 2.85
2060 2128 1.075374 TGCTATGAGTTTGCAGGGGTT 59.925 47.619 0.00 0.00 32.55 4.11
2061 2129 0.698238 TGCTATGAGTTTGCAGGGGT 59.302 50.000 0.00 0.00 32.55 4.95
2062 2130 3.575506 TGCTATGAGTTTGCAGGGG 57.424 52.632 0.00 0.00 32.55 4.79
2068 2136 5.886992 TGAATTGCATCTGCTATGAGTTTG 58.113 37.500 3.53 0.00 42.66 2.93
2078 2146 4.239304 TGTGTTGATTGAATTGCATCTGC 58.761 39.130 0.00 0.00 42.50 4.26
2096 2164 2.305635 TCAGGTGCCATATCTGTTGTGT 59.694 45.455 0.00 0.00 38.71 3.72
2129 2203 7.643569 ATTCTTTATGCACACATTATGACCA 57.356 32.000 0.00 0.00 37.74 4.02
2148 2222 6.115448 AGTAAGCAGGTGAAGTGTATTCTT 57.885 37.500 0.00 0.00 0.00 2.52
2173 2247 1.604278 GGTGAAGTTCCACAGCTTGTC 59.396 52.381 0.00 0.00 38.74 3.18
2180 2254 0.034337 GCTACGGGTGAAGTTCCACA 59.966 55.000 0.00 0.00 38.74 4.17
2198 2272 4.928398 TGCTCTTGAGCAGCTAGC 57.072 55.556 19.87 6.62 40.23 3.42
2206 2286 2.281517 CTGAGAAGCCATGCTCTTGAG 58.718 52.381 3.58 0.00 38.25 3.02
2272 2353 6.394345 AGGGACTTTGTCTTATGAAAGGAT 57.606 37.500 0.00 0.00 34.12 3.24
2274 2355 6.947464 TCTAGGGACTTTGTCTTATGAAAGG 58.053 40.000 0.00 0.00 41.75 3.11
2276 2357 7.974504 ACTTCTAGGGACTTTGTCTTATGAAA 58.025 34.615 0.00 0.00 41.75 2.69
2279 2360 7.386851 TCAACTTCTAGGGACTTTGTCTTATG 58.613 38.462 0.00 0.00 41.75 1.90
2287 2368 4.202472 CCAGGTTCAACTTCTAGGGACTTT 60.202 45.833 0.00 0.00 41.75 2.66
2290 2371 2.638363 ACCAGGTTCAACTTCTAGGGAC 59.362 50.000 0.00 0.00 0.00 4.46
2291 2372 2.904434 GACCAGGTTCAACTTCTAGGGA 59.096 50.000 0.00 0.00 0.00 4.20
2292 2373 2.637872 TGACCAGGTTCAACTTCTAGGG 59.362 50.000 0.00 0.00 0.00 3.53
2348 2449 1.142060 TGGATCCAAACACAGAACGGT 59.858 47.619 13.46 0.00 0.00 4.83
2350 2451 2.494059 AGTGGATCCAAACACAGAACG 58.506 47.619 18.20 0.00 39.99 3.95
2351 2452 5.705441 TGAATAGTGGATCCAAACACAGAAC 59.295 40.000 18.20 0.00 39.99 3.01
2353 2454 5.497464 TGAATAGTGGATCCAAACACAGA 57.503 39.130 18.20 0.00 39.99 3.41
2383 2485 6.042638 TCCAGTCTCCAATCTGAAAACTAG 57.957 41.667 0.00 0.00 34.02 2.57
2402 2504 1.966451 GCCCCAACGTTGACTCCAG 60.966 63.158 29.35 11.17 0.00 3.86
2407 2509 2.096980 GCTATTTAGCCCCAACGTTGAC 59.903 50.000 29.35 17.30 43.39 3.18
2413 2515 2.103601 TCTACCGCTATTTAGCCCCAAC 59.896 50.000 4.08 0.00 46.34 3.77
2414 2516 2.400573 TCTACCGCTATTTAGCCCCAA 58.599 47.619 4.08 0.00 46.34 4.12
2416 2518 2.631545 TCTTCTACCGCTATTTAGCCCC 59.368 50.000 4.08 0.00 46.34 5.80
2573 2705 1.950828 ATCCTGATCGCAGCAGAAAG 58.049 50.000 3.44 0.00 40.91 2.62
2584 2716 3.937706 CGCCAATATCTCCAATCCTGATC 59.062 47.826 0.00 0.00 0.00 2.92
2587 2719 3.131709 ACGCCAATATCTCCAATCCTG 57.868 47.619 0.00 0.00 0.00 3.86
2645 2777 4.456911 GCAAACTCCACAATCTTCTCATCA 59.543 41.667 0.00 0.00 0.00 3.07
2726 2858 6.040842 ACACACACAGAAAATAGAAAGGCATT 59.959 34.615 0.00 0.00 0.00 3.56
2729 2861 5.215160 CACACACACAGAAAATAGAAAGGC 58.785 41.667 0.00 0.00 0.00 4.35
2741 2873 3.554960 GGAAGCTATCACACACACACAGA 60.555 47.826 0.00 0.00 0.00 3.41
2742 2874 2.738846 GGAAGCTATCACACACACACAG 59.261 50.000 0.00 0.00 0.00 3.66
2743 2875 2.103941 TGGAAGCTATCACACACACACA 59.896 45.455 0.00 0.00 0.00 3.72
2744 2876 2.766313 TGGAAGCTATCACACACACAC 58.234 47.619 0.00 0.00 0.00 3.82
2755 2887 4.870123 TGCATTTGTGTTTGGAAGCTAT 57.130 36.364 0.00 0.00 0.00 2.97
2842 2974 6.054941 TCTGATTTCAAGAACTTGTACAGCA 58.945 36.000 13.15 7.47 41.16 4.41
2861 2993 2.969821 ATAGACCGCCTCTCTCTGAT 57.030 50.000 0.00 0.00 0.00 2.90
3004 3136 6.147821 GGTGGAGACGAACAATATGGAATATG 59.852 42.308 0.00 0.00 38.94 1.78
3048 3180 1.978782 GCGAAAGGCGAAAACATTCAG 59.021 47.619 0.00 0.00 44.57 3.02
3150 3289 5.756347 ACACATACAGTAGCGAAAAGAACAA 59.244 36.000 0.00 0.00 0.00 2.83
3202 3341 3.449018 AGAGTAGCATACAACAGACTGGG 59.551 47.826 7.51 1.00 46.26 4.45
3268 3416 6.757947 GGCTGTGTTTTGTTGCATCAATATAT 59.242 34.615 10.87 0.00 0.00 0.86
3307 3457 7.912250 CCATTCGGTTTTTGAGATCATTCTTAG 59.088 37.037 0.00 0.00 30.30 2.18
3442 3592 5.292101 GGATATTTGACACGAGAAGTTCCAG 59.708 44.000 0.00 0.00 0.00 3.86
3628 3778 2.230660 ACTAGGGACTTTTGTGCAAGC 58.769 47.619 0.00 0.00 42.95 4.01
3648 3798 0.178978 TTTGGCATGTGCAGGTGGTA 60.179 50.000 7.36 0.00 44.36 3.25
3676 3827 7.512746 AGGGGTATCATACAGCATAGAAGTTAA 59.487 37.037 0.00 0.00 0.00 2.01
3677 3828 7.016914 AGGGGTATCATACAGCATAGAAGTTA 58.983 38.462 0.00 0.00 0.00 2.24
3736 3887 2.026356 CACCCATGTGACCCATCTAACA 60.026 50.000 0.00 0.00 45.76 2.41
3738 3889 2.274542 ACACCCATGTGACCCATCTAA 58.725 47.619 0.00 0.00 45.76 2.10
3739 3890 1.965414 ACACCCATGTGACCCATCTA 58.035 50.000 0.00 0.00 45.76 1.98
3742 3893 2.492025 AGATACACCCATGTGACCCAT 58.508 47.619 0.00 0.00 45.76 4.00
3744 3895 3.366052 AAAGATACACCCATGTGACCC 57.634 47.619 0.00 0.00 45.76 4.46
3748 3899 7.786060 CTTCAACTGAAAAGATACACCCATGTG 60.786 40.741 0.00 0.00 39.88 3.21
3749 3900 5.630121 TCAACTGAAAAGATACACCCATGT 58.370 37.500 0.00 0.00 43.30 3.21
3754 3905 6.073003 CCAGACTTCAACTGAAAAGATACACC 60.073 42.308 0.00 0.00 37.54 4.16
3755 3906 6.483640 ACCAGACTTCAACTGAAAAGATACAC 59.516 38.462 0.00 0.00 37.54 2.90
3758 3909 8.088981 GTCTACCAGACTTCAACTGAAAAGATA 58.911 37.037 0.00 0.00 41.88 1.98
3934 4089 8.472007 TGTTTTGTAGGGTTTGTATGAAATCT 57.528 30.769 0.00 0.00 0.00 2.40
3947 4102 2.683768 TGGGCATTTGTTTTGTAGGGT 58.316 42.857 0.00 0.00 0.00 4.34
3954 4109 3.054948 CCTCCATGATGGGCATTTGTTTT 60.055 43.478 12.26 0.00 38.32 2.43
3965 4120 4.505566 CCTGTATGTAACCCTCCATGATGG 60.506 50.000 4.74 4.74 39.43 3.51
3973 4128 3.385111 CCTGAGACCTGTATGTAACCCTC 59.615 52.174 0.00 0.00 0.00 4.30
3987 4142 1.277557 AGAACTGATGCACCTGAGACC 59.722 52.381 0.00 0.00 0.00 3.85
4003 4158 5.009310 ACGGTTAGGGAACAAATCAAAGAAC 59.991 40.000 0.00 0.00 37.29 3.01
4013 4168 4.095946 ACCTACATACGGTTAGGGAACAA 58.904 43.478 8.76 0.00 37.29 2.83
4018 4173 2.767960 ACCAACCTACATACGGTTAGGG 59.232 50.000 8.76 0.00 42.63 3.53
4022 4177 1.404583 GCGACCAACCTACATACGGTT 60.405 52.381 0.00 0.00 45.26 4.44
4023 4178 0.174162 GCGACCAACCTACATACGGT 59.826 55.000 0.00 0.00 35.97 4.83
4024 4179 0.529119 GGCGACCAACCTACATACGG 60.529 60.000 0.00 0.00 0.00 4.02
4025 4180 0.458669 AGGCGACCAACCTACATACG 59.541 55.000 0.00 0.00 35.10 3.06
4061 4216 5.779241 TCATCCTCCTTCCTACAACAATT 57.221 39.130 0.00 0.00 0.00 2.32


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

AutoCloner maintained by Alex Coulton.