Multiple sequence alignment - TraesCS3A01G092800

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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 TraesCS3A01G092800 chr3A 100.000 4840 0 0 1 4840 58840097 58835258 0.000000e+00 8938.0
1 TraesCS3A01G092800 chr3A 85.618 591 39 19 4087 4677 58840181 58840725 3.250000e-161 579.0
2 TraesCS3A01G092800 chr3A 96.319 163 6 0 4678 4840 58843593 58843755 7.980000e-68 268.0
3 TraesCS3A01G092800 chr3D 93.456 1849 84 15 778 2600 47088368 47090205 0.000000e+00 2710.0
4 TraesCS3A01G092800 chr3D 93.942 1337 63 10 2701 4023 47090538 47091870 0.000000e+00 2004.0
5 TraesCS3A01G092800 chr3D 79.730 740 65 42 4124 4832 47086926 47086241 1.590000e-124 457.0
6 TraesCS3A01G092800 chr3D 92.653 245 13 3 23 267 47087070 47087309 9.970000e-92 348.0
7 TraesCS3A01G092800 chr3D 80.312 513 32 35 4158 4658 47092093 47092548 1.680000e-84 324.0
8 TraesCS3A01G092800 chr3D 97.143 105 3 0 4692 4796 47092550 47092654 1.380000e-40 178.0
9 TraesCS3A01G092800 chr3D 96.000 50 2 0 649 698 47088293 47088342 1.120000e-11 82.4
10 TraesCS3A01G092800 chr3B 96.399 1472 51 1 771 2242 73627504 73628973 0.000000e+00 2423.0
11 TraesCS3A01G092800 chr3B 92.514 1643 90 20 2413 4026 73629218 73630856 0.000000e+00 2322.0
12 TraesCS3A01G092800 chr3B 81.733 750 55 46 4120 4840 73627271 73626575 7.080000e-153 551.0
13 TraesCS3A01G092800 chr3B 78.972 214 25 13 499 708 73627303 73627500 1.410000e-25 128.0
14 TraesCS3A01G092800 chr1D 78.095 420 70 16 2715 3129 487546363 487546765 3.740000e-61 246.0
15 TraesCS3A01G092800 chr1A 77.619 420 72 16 2715 3129 585618114 585618516 8.100000e-58 235.0
16 TraesCS3A01G092800 chr1B 77.665 197 27 5 3337 3533 621997640 621997461 2.380000e-18 104.0


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 TraesCS3A01G092800 chr3A 58835258 58840097 4839 True 8938.000000 8938 100.0000 1 4840 1 chr3A.!!$R1 4839
1 TraesCS3A01G092800 chr3A 58840181 58843755 3574 False 423.500000 579 90.9685 4087 4840 2 chr3A.!!$F1 753
2 TraesCS3A01G092800 chr3D 47087070 47092654 5584 False 941.066667 2710 92.2510 23 4796 6 chr3D.!!$F1 4773
3 TraesCS3A01G092800 chr3D 47086241 47086926 685 True 457.000000 457 79.7300 4124 4832 1 chr3D.!!$R1 708
4 TraesCS3A01G092800 chr3B 73627303 73630856 3553 False 1624.333333 2423 89.2950 499 4026 3 chr3B.!!$F1 3527
5 TraesCS3A01G092800 chr3B 73626575 73627271 696 True 551.000000 551 81.7330 4120 4840 1 chr3B.!!$R1 720

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
398 975 0.176910 TCGATTCCTTACATGCGCCA 59.823 50.000 4.18 0.0 0.00 5.69 F
894 1544 0.179129 CCAATTGGCTGCCGATCAAC 60.179 55.000 21.44 0.0 0.00 3.18 F
957 1607 0.954452 CGAAAGCAGAGCAAAACCCT 59.046 50.000 0.00 0.0 0.00 4.34 F
958 1608 1.068954 CGAAAGCAGAGCAAAACCCTC 60.069 52.381 0.00 0.0 0.00 4.30 F
2858 3844 0.179205 GCAACGACTTCATGCTGCTC 60.179 55.000 0.00 0.0 37.12 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1395 2045 1.076923 GAGGAGGAGCACGTAGGGA 60.077 63.158 0.00 0.0 0.00 4.20 R
2421 3150 0.171007 GTCATGGACCATTTGTGGCG 59.829 55.000 3.52 0.0 0.00 5.69 R
2438 3167 1.916000 CGTTCCAAATCGTCTACCGTC 59.084 52.381 0.00 0.0 37.94 4.79 R
2936 3922 2.044252 CAGCCCTGCAGCCAGAAT 60.044 61.111 8.66 0.0 41.77 2.40 R
4411 5546 0.036732 AGTCCGACTGGTACGTGGTA 59.963 55.000 0.00 0.0 36.30 3.25 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
17 18 2.885861 CTGAGGAGTAGCGGCGTT 59.114 61.111 9.37 4.68 0.00 4.84
18 19 1.226717 CTGAGGAGTAGCGGCGTTC 60.227 63.158 9.37 1.44 0.00 3.95
19 20 1.658686 CTGAGGAGTAGCGGCGTTCT 61.659 60.000 9.37 4.45 0.00 3.01
20 21 1.226717 GAGGAGTAGCGGCGTTCTG 60.227 63.158 9.37 0.00 0.00 3.02
21 22 2.886124 GGAGTAGCGGCGTTCTGC 60.886 66.667 9.37 6.32 44.91 4.26
47 48 2.114670 CCACGGCCGATTGCATTCT 61.115 57.895 35.90 1.64 43.89 2.40
62 63 0.489567 ATTCTAGAGCCGGGGAGGAT 59.510 55.000 2.18 0.00 44.48 3.24
79 80 3.025322 GGATCTGTCCTCTTCTGGAGA 57.975 52.381 0.00 0.00 44.45 3.71
132 133 0.963225 GCAGCCCGGTTTCCTAAAAA 59.037 50.000 0.00 0.00 0.00 1.94
209 210 1.433837 AAAGTGGACGTGTCAACCGC 61.434 55.000 3.91 0.00 34.02 5.68
210 211 2.581208 AAGTGGACGTGTCAACCGCA 62.581 55.000 3.91 0.00 34.02 5.69
266 267 3.736483 GGCCATGCCGTGTATCAG 58.264 61.111 0.00 0.00 39.62 2.90
267 268 1.146041 GGCCATGCCGTGTATCAGA 59.854 57.895 0.00 0.00 39.62 3.27
268 269 0.463654 GGCCATGCCGTGTATCAGAA 60.464 55.000 0.00 0.00 39.62 3.02
269 270 1.378531 GCCATGCCGTGTATCAGAAA 58.621 50.000 0.00 0.00 0.00 2.52
270 271 1.742831 GCCATGCCGTGTATCAGAAAA 59.257 47.619 0.00 0.00 0.00 2.29
271 272 2.223340 GCCATGCCGTGTATCAGAAAAG 60.223 50.000 0.00 0.00 0.00 2.27
276 455 5.957842 TGCCGTGTATCAGAAAAGAAAAT 57.042 34.783 0.00 0.00 0.00 1.82
320 499 9.834628 ATTTACACATACAGAAAACGTTATTGG 57.165 29.630 0.00 0.00 0.00 3.16
321 500 8.604640 TTACACATACAGAAAACGTTATTGGA 57.395 30.769 0.00 0.00 0.00 3.53
322 501 7.129109 ACACATACAGAAAACGTTATTGGAG 57.871 36.000 0.00 0.00 0.00 3.86
356 933 6.072649 AGCATGGAATGGAAATACATCATCA 58.927 36.000 0.00 0.00 46.86 3.07
371 948 5.572211 ACATCATCAATCAACGGAAAATCG 58.428 37.500 0.00 0.00 0.00 3.34
372 949 4.014847 TCATCAATCAACGGAAAATCGC 57.985 40.909 0.00 0.00 0.00 4.58
373 950 3.438434 TCATCAATCAACGGAAAATCGCA 59.562 39.130 0.00 0.00 0.00 5.10
374 951 3.196007 TCAATCAACGGAAAATCGCAC 57.804 42.857 0.00 0.00 0.00 5.34
377 954 1.154301 CAACGGAAAATCGCACGGG 60.154 57.895 0.00 0.00 0.00 5.28
380 957 1.133869 CGGAAAATCGCACGGGTTC 59.866 57.895 0.00 0.00 0.00 3.62
387 964 1.956629 ATCGCACGGGTTCGATTCCT 61.957 55.000 0.59 0.00 42.03 3.36
389 966 0.458889 CGCACGGGTTCGATTCCTTA 60.459 55.000 7.03 0.00 40.11 2.69
393 970 2.607635 CACGGGTTCGATTCCTTACATG 59.392 50.000 7.03 0.00 40.11 3.21
396 973 1.003866 GGTTCGATTCCTTACATGCGC 60.004 52.381 0.00 0.00 0.00 6.09
398 975 0.176910 TCGATTCCTTACATGCGCCA 59.823 50.000 4.18 0.00 0.00 5.69
408 1030 0.949397 ACATGCGCCATCAGCTATTG 59.051 50.000 4.18 0.00 40.39 1.90
411 1033 1.516161 TGCGCCATCAGCTATTGATC 58.484 50.000 4.18 0.00 44.76 2.92
414 1036 0.801251 GCCATCAGCTATTGATCGCC 59.199 55.000 0.00 0.00 44.76 5.54
421 1043 1.620819 AGCTATTGATCGCCCGAGATT 59.379 47.619 0.00 0.00 0.00 2.40
423 1045 2.924290 GCTATTGATCGCCCGAGATTAC 59.076 50.000 0.00 0.00 0.00 1.89
425 1047 2.218953 TTGATCGCCCGAGATTACAC 57.781 50.000 0.00 0.00 0.00 2.90
459 1081 0.318614 CAACGCAAAATTGGCCTCGT 60.319 50.000 3.32 0.00 0.00 4.18
460 1082 0.318614 AACGCAAAATTGGCCTCGTG 60.319 50.000 3.32 0.00 0.00 4.35
476 1098 1.134521 TCGTGGCAAGGAAAGCGATAT 60.135 47.619 0.00 0.00 0.00 1.63
477 1099 2.101750 TCGTGGCAAGGAAAGCGATATA 59.898 45.455 0.00 0.00 0.00 0.86
478 1100 2.476619 CGTGGCAAGGAAAGCGATATAG 59.523 50.000 0.00 0.00 0.00 1.31
479 1101 2.224314 GTGGCAAGGAAAGCGATATAGC 59.776 50.000 0.00 0.00 37.41 2.97
480 1102 2.158827 TGGCAAGGAAAGCGATATAGCA 60.159 45.455 10.60 0.00 40.15 3.49
481 1103 2.481952 GGCAAGGAAAGCGATATAGCAG 59.518 50.000 10.60 0.00 40.15 4.24
482 1104 3.393800 GCAAGGAAAGCGATATAGCAGA 58.606 45.455 10.60 0.00 40.15 4.26
483 1105 3.431572 GCAAGGAAAGCGATATAGCAGAG 59.568 47.826 10.60 0.00 40.15 3.35
484 1106 4.797604 GCAAGGAAAGCGATATAGCAGAGA 60.798 45.833 10.60 0.00 40.15 3.10
485 1107 4.782019 AGGAAAGCGATATAGCAGAGAG 57.218 45.455 10.60 0.00 40.15 3.20
486 1108 3.509575 AGGAAAGCGATATAGCAGAGAGG 59.490 47.826 10.60 0.00 40.15 3.69
487 1109 3.508012 GGAAAGCGATATAGCAGAGAGGA 59.492 47.826 10.60 0.00 40.15 3.71
488 1110 4.380444 GGAAAGCGATATAGCAGAGAGGAG 60.380 50.000 10.60 0.00 40.15 3.69
489 1111 2.722094 AGCGATATAGCAGAGAGGAGG 58.278 52.381 10.60 0.00 40.15 4.30
490 1112 2.307392 AGCGATATAGCAGAGAGGAGGA 59.693 50.000 10.60 0.00 40.15 3.71
491 1113 3.085533 GCGATATAGCAGAGAGGAGGAA 58.914 50.000 2.59 0.00 37.05 3.36
503 1125 4.006319 GAGAGGAGGAAACAAATGTGGAG 58.994 47.826 0.00 0.00 0.00 3.86
545 1167 3.692367 CGATCGCCGCGTGATTCC 61.692 66.667 13.39 0.00 32.57 3.01
556 1181 2.391879 GCGTGATTCCACTACGGATAC 58.608 52.381 0.00 0.00 45.80 2.24
562 1187 6.380190 GTGATTCCACTACGGATACTACATC 58.620 44.000 0.00 0.00 45.80 3.06
566 1191 5.627135 TCCACTACGGATACTACATCATCA 58.373 41.667 0.00 0.00 39.64 3.07
567 1192 6.066032 TCCACTACGGATACTACATCATCAA 58.934 40.000 0.00 0.00 39.64 2.57
568 1193 6.719829 TCCACTACGGATACTACATCATCAAT 59.280 38.462 0.00 0.00 39.64 2.57
571 1196 8.947115 CACTACGGATACTACATCATCAATCTA 58.053 37.037 0.00 0.00 0.00 1.98
572 1197 9.688091 ACTACGGATACTACATCATCAATCTAT 57.312 33.333 0.00 0.00 0.00 1.98
637 1262 2.375014 TCCAAAGGGAAGAAACACCC 57.625 50.000 0.00 0.00 41.32 4.61
645 1270 3.239449 GGGAAGAAACACCCAAAGGAAT 58.761 45.455 0.00 0.00 44.96 3.01
688 1338 4.608445 CGAAGCTTCGCGATTTTATTAGGG 60.608 45.833 33.46 4.29 44.26 3.53
698 1348 3.553828 TTTTATTAGGGCGGTGAGAGG 57.446 47.619 0.00 0.00 0.00 3.69
700 1350 1.410004 TATTAGGGCGGTGAGAGGTG 58.590 55.000 0.00 0.00 0.00 4.00
703 1353 4.329545 GGGCGGTGAGAGGTGCAA 62.330 66.667 0.00 0.00 0.00 4.08
704 1354 2.743928 GGCGGTGAGAGGTGCAAG 60.744 66.667 0.00 0.00 0.00 4.01
707 1357 1.166531 GCGGTGAGAGGTGCAAGTTT 61.167 55.000 0.00 0.00 0.00 2.66
708 1358 1.308998 CGGTGAGAGGTGCAAGTTTT 58.691 50.000 0.00 0.00 0.00 2.43
729 1379 5.828299 TTTTTGTCCACGAGAACAAGAAT 57.172 34.783 0.00 0.00 0.00 2.40
730 1380 4.811555 TTTGTCCACGAGAACAAGAATG 57.188 40.909 0.00 0.00 0.00 2.67
731 1381 2.143122 TGTCCACGAGAACAAGAATGC 58.857 47.619 0.00 0.00 0.00 3.56
732 1382 1.126846 GTCCACGAGAACAAGAATGCG 59.873 52.381 0.00 0.00 0.00 4.73
733 1383 1.000394 TCCACGAGAACAAGAATGCGA 60.000 47.619 0.00 0.00 0.00 5.10
734 1384 1.798223 CCACGAGAACAAGAATGCGAA 59.202 47.619 0.00 0.00 0.00 4.70
735 1385 2.411547 CCACGAGAACAAGAATGCGAAC 60.412 50.000 0.00 0.00 0.00 3.95
736 1386 1.798813 ACGAGAACAAGAATGCGAACC 59.201 47.619 0.00 0.00 0.00 3.62
737 1387 1.128692 CGAGAACAAGAATGCGAACCC 59.871 52.381 0.00 0.00 0.00 4.11
738 1388 1.128692 GAGAACAAGAATGCGAACCCG 59.871 52.381 0.00 0.00 39.16 5.28
775 1425 4.104776 GAGAGAGAGAGAACAAGAATGCG 58.895 47.826 0.00 0.00 0.00 4.73
807 1457 1.941325 AAATTTCGCACCGCCAAAAA 58.059 40.000 0.00 0.00 0.00 1.94
848 1498 1.228552 GAGCTTTCCTTGTGGGCCA 60.229 57.895 0.00 0.00 34.39 5.36
849 1499 1.228675 AGCTTTCCTTGTGGGCCAG 60.229 57.895 6.40 0.00 34.39 4.85
852 1502 1.228124 TTTCCTTGTGGGCCAGACG 60.228 57.895 6.40 2.38 34.39 4.18
894 1544 0.179129 CCAATTGGCTGCCGATCAAC 60.179 55.000 21.44 0.00 0.00 3.18
921 1571 2.169832 AGCACACAACACGAGCTTAT 57.830 45.000 0.00 0.00 29.98 1.73
957 1607 0.954452 CGAAAGCAGAGCAAAACCCT 59.046 50.000 0.00 0.00 0.00 4.34
958 1608 1.068954 CGAAAGCAGAGCAAAACCCTC 60.069 52.381 0.00 0.00 0.00 4.30
1068 1718 2.811317 GTCGACGGCCTCAAGCAG 60.811 66.667 0.00 0.00 46.50 4.24
1188 1838 4.681978 GTGTCCGCTGCCGAGGTT 62.682 66.667 0.00 0.00 36.29 3.50
1227 1877 4.771356 TTCCTCGGCTTCGACGCG 62.771 66.667 3.53 3.53 38.07 6.01
1272 1922 3.207669 CCCATCGGCAAGCTGCTC 61.208 66.667 1.00 0.00 44.28 4.26
1320 1970 1.597027 CAAGGTGTGGTGGACGACC 60.597 63.158 0.00 0.00 46.37 4.79
1509 2159 1.216710 CTCCTCTGTCGTGAAGGGC 59.783 63.158 0.00 0.00 0.00 5.19
1610 2260 3.322466 CCACCTCGGCACCTTCCT 61.322 66.667 0.00 0.00 0.00 3.36
1794 2444 1.805945 GTCCATCTGCCACGACGAC 60.806 63.158 0.00 0.00 0.00 4.34
1911 2561 2.125106 GACTACAAGGGCGGCCTG 60.125 66.667 33.52 25.77 0.00 4.85
2235 2885 6.073765 ACGTCATACATGTGAGTCTTTTTCAC 60.074 38.462 9.11 0.00 44.03 3.18
2421 3150 7.412063 ACAAAAACGTGTAGAAAATGTACTCC 58.588 34.615 0.00 0.00 0.00 3.85
2567 3300 9.722056 GATAAGTATTTGACATTTGACACCATC 57.278 33.333 0.00 0.00 0.00 3.51
2581 3314 4.876679 TGACACCATCTTGAAACGTGTAAA 59.123 37.500 0.00 0.00 37.77 2.01
2604 3337 4.026356 AGAACAGCCAAGAAACTGCTAT 57.974 40.909 0.00 0.00 37.42 2.97
2605 3338 5.165961 AGAACAGCCAAGAAACTGCTATA 57.834 39.130 0.00 0.00 37.42 1.31
2610 3524 5.412904 ACAGCCAAGAAACTGCTATAACTTC 59.587 40.000 0.00 0.00 37.42 3.01
2645 3559 6.055231 TGTCACCGACAGAAACAAATAAAG 57.945 37.500 0.00 0.00 37.67 1.85
2689 3675 2.770134 TTTTTCTGACGGTGCGTGT 58.230 47.368 0.00 0.00 41.37 4.49
2690 3676 0.375454 TTTTTCTGACGGTGCGTGTG 59.625 50.000 0.00 0.00 41.37 3.82
2691 3677 2.042520 TTTTCTGACGGTGCGTGTGC 62.043 55.000 0.00 0.00 41.37 4.57
2724 3710 2.113433 GTGCAGCTGCTGGAGATGG 61.113 63.158 36.61 4.15 38.63 3.51
2783 3769 3.718210 CTACTTCCGCGGGCTCACC 62.718 68.421 27.83 0.00 0.00 4.02
2858 3844 0.179205 GCAACGACTTCATGCTGCTC 60.179 55.000 0.00 0.00 37.12 4.26
2992 3978 1.139853 CTACAACTCCCTCTGGATGGC 59.860 57.143 0.00 0.00 40.80 4.40
3170 4156 1.480219 GCACCATACTACGCTGCGAC 61.480 60.000 30.47 0.83 0.00 5.19
3255 4241 3.604582 CTCAAGATCTGGAACCTCAACC 58.395 50.000 0.40 0.00 0.00 3.77
3457 4443 0.099082 GTCTACTTCGTCGAGGCCAG 59.901 60.000 5.01 0.00 0.00 4.85
3634 4620 2.978824 GGTGCAGGCCTTCGAGTA 59.021 61.111 0.00 0.00 0.00 2.59
3646 4632 0.671472 TTCGAGTACAGCGAGGTCGA 60.671 55.000 2.94 4.35 43.02 4.20
3825 4811 2.432628 CCAAGCCGTCTCGTGTCC 60.433 66.667 0.00 0.00 0.00 4.02
3827 4813 2.022129 CAAGCCGTCTCGTGTCCAC 61.022 63.158 0.00 0.00 0.00 4.02
3840 4826 5.828328 TCTCGTGTCCACTATGTCTATTGAT 59.172 40.000 0.00 0.00 0.00 2.57
3841 4827 6.321435 TCTCGTGTCCACTATGTCTATTGATT 59.679 38.462 0.00 0.00 0.00 2.57
3842 4828 6.273071 TCGTGTCCACTATGTCTATTGATTG 58.727 40.000 0.00 0.00 0.00 2.67
3843 4829 6.096282 TCGTGTCCACTATGTCTATTGATTGA 59.904 38.462 0.00 0.00 0.00 2.57
3844 4830 6.199154 CGTGTCCACTATGTCTATTGATTGAC 59.801 42.308 0.00 0.00 33.98 3.18
3845 4831 6.199154 GTGTCCACTATGTCTATTGATTGACG 59.801 42.308 2.14 0.00 35.72 4.35
3846 4832 6.127451 TGTCCACTATGTCTATTGATTGACGT 60.127 38.462 0.00 0.00 35.72 4.34
3847 4833 6.418226 GTCCACTATGTCTATTGATTGACGTC 59.582 42.308 9.11 9.11 35.72 4.34
3848 4834 6.321435 TCCACTATGTCTATTGATTGACGTCT 59.679 38.462 17.92 0.00 35.72 4.18
3850 4836 6.358294 CACTATGTCTATTGATTGACGTCTCG 59.642 42.308 17.92 0.00 35.72 4.04
3851 4837 4.028852 TGTCTATTGATTGACGTCTCGG 57.971 45.455 17.92 0.00 35.72 4.63
3886 4886 8.157183 CGTTTCGCGTCCAAATAATTTTATTTT 58.843 29.630 5.77 0.00 37.25 1.82
3890 4890 7.432838 TCGCGTCCAAATAATTTTATTTTAGGC 59.567 33.333 5.77 11.39 40.37 3.93
4025 5025 9.569167 TTTGTTACGAGTGAGTATCTATTTCTG 57.431 33.333 0.00 0.00 34.92 3.02
4026 5026 7.704271 TGTTACGAGTGAGTATCTATTTCTGG 58.296 38.462 0.00 0.00 34.92 3.86
4028 5028 6.777213 ACGAGTGAGTATCTATTTCTGGTT 57.223 37.500 0.00 0.00 34.92 3.67
4029 5029 7.171630 ACGAGTGAGTATCTATTTCTGGTTT 57.828 36.000 0.00 0.00 34.92 3.27
4030 5030 7.612677 ACGAGTGAGTATCTATTTCTGGTTTT 58.387 34.615 0.00 0.00 34.92 2.43
4031 5031 8.095169 ACGAGTGAGTATCTATTTCTGGTTTTT 58.905 33.333 0.00 0.00 34.92 1.94
4035 5035 8.515414 GTGAGTATCTATTTCTGGTTTTTGCTT 58.485 33.333 0.00 0.00 34.92 3.91
4036 5036 9.733556 TGAGTATCTATTTCTGGTTTTTGCTTA 57.266 29.630 0.00 0.00 34.92 3.09
4055 5055 6.540323 GCTTATTCAGCGTTGTGTTTAATC 57.460 37.500 0.00 0.00 39.29 1.75
4056 5056 6.314784 GCTTATTCAGCGTTGTGTTTAATCT 58.685 36.000 0.00 0.00 39.29 2.40
4057 5057 6.249260 GCTTATTCAGCGTTGTGTTTAATCTG 59.751 38.462 0.00 0.00 39.29 2.90
4058 5058 4.481930 TTCAGCGTTGTGTTTAATCTGG 57.518 40.909 0.00 0.00 0.00 3.86
4059 5059 2.225491 TCAGCGTTGTGTTTAATCTGGC 59.775 45.455 0.00 0.00 0.00 4.85
4060 5060 1.539827 AGCGTTGTGTTTAATCTGGCC 59.460 47.619 0.00 0.00 0.00 5.36
4061 5061 1.402325 GCGTTGTGTTTAATCTGGCCC 60.402 52.381 0.00 0.00 0.00 5.80
4062 5062 2.159382 CGTTGTGTTTAATCTGGCCCT 58.841 47.619 0.00 0.00 0.00 5.19
4063 5063 2.161609 CGTTGTGTTTAATCTGGCCCTC 59.838 50.000 0.00 0.00 0.00 4.30
4064 5064 3.153919 GTTGTGTTTAATCTGGCCCTCA 58.846 45.455 0.00 0.00 0.00 3.86
4065 5065 3.517296 TGTGTTTAATCTGGCCCTCAA 57.483 42.857 0.00 0.00 0.00 3.02
4067 5067 3.572255 TGTGTTTAATCTGGCCCTCAAAC 59.428 43.478 0.00 4.51 0.00 2.93
4068 5068 2.817258 TGTTTAATCTGGCCCTCAAACG 59.183 45.455 0.00 0.00 0.00 3.60
4069 5069 2.817844 GTTTAATCTGGCCCTCAAACGT 59.182 45.455 0.00 0.00 0.00 3.99
4070 5070 2.396590 TAATCTGGCCCTCAAACGTC 57.603 50.000 0.00 0.00 0.00 4.34
4072 5072 2.521958 ATCTGGCCCTCAAACGTCCG 62.522 60.000 0.00 0.00 0.00 4.79
4073 5073 3.530910 CTGGCCCTCAAACGTCCGT 62.531 63.158 0.00 0.00 0.00 4.69
4074 5074 2.281276 GGCCCTCAAACGTCCGTT 60.281 61.111 0.00 0.00 40.45 4.44
4075 5075 2.613506 GGCCCTCAAACGTCCGTTG 61.614 63.158 5.76 1.36 38.47 4.10
4076 5076 1.595929 GCCCTCAAACGTCCGTTGA 60.596 57.895 5.76 1.50 38.47 3.18
4077 5077 1.838568 GCCCTCAAACGTCCGTTGAC 61.839 60.000 5.76 0.00 38.47 3.18
4078 5078 0.249741 CCCTCAAACGTCCGTTGACT 60.250 55.000 5.76 0.00 39.47 3.41
4080 5080 0.776451 CTCAAACGTCCGTTGACTCG 59.224 55.000 5.76 0.00 39.47 4.18
4082 5082 1.952635 AAACGTCCGTTGACTCGCC 60.953 57.895 5.76 0.00 39.47 5.54
4224 5319 5.681105 CGTTTCAGCCAAATCCGTTATATTG 59.319 40.000 0.00 0.00 0.00 1.90
4226 5321 6.371809 TTCAGCCAAATCCGTTATATTGAC 57.628 37.500 0.00 0.00 0.00 3.18
4227 5322 5.432645 TCAGCCAAATCCGTTATATTGACA 58.567 37.500 0.00 0.00 0.00 3.58
4228 5323 6.061441 TCAGCCAAATCCGTTATATTGACAT 58.939 36.000 0.00 0.00 0.00 3.06
4229 5324 6.545666 TCAGCCAAATCCGTTATATTGACATT 59.454 34.615 0.00 0.00 0.00 2.71
4230 5325 7.068103 TCAGCCAAATCCGTTATATTGACATTT 59.932 33.333 0.00 0.00 0.00 2.32
4231 5326 8.349245 CAGCCAAATCCGTTATATTGACATTTA 58.651 33.333 0.00 0.00 0.00 1.40
4232 5327 8.567948 AGCCAAATCCGTTATATTGACATTTAG 58.432 33.333 0.00 0.00 0.00 1.85
4359 5467 2.129555 AACTGCCATGCTCCCGTTCT 62.130 55.000 0.00 0.00 0.00 3.01
4393 5528 3.031660 GACCTCGTCGACAATGACC 57.968 57.895 17.16 0.00 35.40 4.02
4394 5529 0.797249 GACCTCGTCGACAATGACCG 60.797 60.000 17.16 0.00 35.40 4.79
4395 5530 1.516386 CCTCGTCGACAATGACCGG 60.516 63.158 17.16 0.00 35.40 5.28
4396 5531 1.211969 CTCGTCGACAATGACCGGT 59.788 57.895 17.16 6.92 35.40 5.28
4397 5532 0.448990 CTCGTCGACAATGACCGGTA 59.551 55.000 17.16 0.00 35.40 4.02
4398 5533 0.168788 TCGTCGACAATGACCGGTAC 59.831 55.000 17.16 1.38 35.40 3.34
4399 5534 0.169672 CGTCGACAATGACCGGTACT 59.830 55.000 17.16 0.00 35.40 2.73
4400 5535 1.401931 CGTCGACAATGACCGGTACTT 60.402 52.381 17.16 0.02 35.40 2.24
4401 5536 1.990563 GTCGACAATGACCGGTACTTG 59.009 52.381 21.23 21.23 32.61 3.16
4402 5537 0.719465 CGACAATGACCGGTACTTGC 59.281 55.000 22.26 15.80 0.00 4.01
4403 5538 1.671850 CGACAATGACCGGTACTTGCT 60.672 52.381 22.26 13.03 0.00 3.91
4404 5539 1.732259 GACAATGACCGGTACTTGCTG 59.268 52.381 22.26 11.27 0.00 4.41
4405 5540 1.071699 ACAATGACCGGTACTTGCTGT 59.928 47.619 22.26 11.81 0.00 4.40
4406 5541 2.300723 ACAATGACCGGTACTTGCTGTA 59.699 45.455 22.26 0.00 0.00 2.74
4407 5542 2.930040 CAATGACCGGTACTTGCTGTAG 59.070 50.000 7.34 0.00 0.00 2.74
4408 5543 0.245539 TGACCGGTACTTGCTGTAGC 59.754 55.000 7.34 0.00 43.87 3.58
4409 5544 0.531200 GACCGGTACTTGCTGTAGCT 59.469 55.000 7.34 0.00 44.80 3.32
4410 5545 0.246635 ACCGGTACTTGCTGTAGCTG 59.753 55.000 4.49 11.38 44.80 4.24
4411 5546 0.246635 CCGGTACTTGCTGTAGCTGT 59.753 55.000 5.38 6.84 44.80 4.40
4412 5547 1.475280 CCGGTACTTGCTGTAGCTGTA 59.525 52.381 5.38 5.95 44.80 2.74
4413 5548 2.527100 CGGTACTTGCTGTAGCTGTAC 58.473 52.381 21.06 21.06 44.80 2.90
4415 5550 3.587797 GTACTTGCTGTAGCTGTACCA 57.412 47.619 19.74 0.00 41.21 3.25
4429 5564 0.169009 GTACCACGTACCAGTCGGAC 59.831 60.000 0.00 0.00 33.38 4.79
4473 5639 5.576774 GTGTGCCCAGCTGATTAATTTAAAC 59.423 40.000 17.39 0.00 0.00 2.01
4540 5735 3.482783 GAGCCTCGACGCTTGTGC 61.483 66.667 10.32 0.00 39.87 4.57
4543 5738 2.571757 CCTCGACGCTTGTGCCTA 59.428 61.111 0.00 0.00 35.36 3.93
4545 5740 2.126071 TCGACGCTTGTGCCTAGC 60.126 61.111 0.00 0.00 35.36 3.42
4546 5741 2.125912 CGACGCTTGTGCCTAGCT 60.126 61.111 0.00 0.00 36.49 3.32
4547 5742 1.738099 CGACGCTTGTGCCTAGCTT 60.738 57.895 0.00 0.00 36.49 3.74
4548 5743 1.790387 GACGCTTGTGCCTAGCTTG 59.210 57.895 0.00 0.00 36.49 4.01
4549 5744 0.951040 GACGCTTGTGCCTAGCTTGT 60.951 55.000 0.00 0.19 36.49 3.16
4550 5745 1.230635 ACGCTTGTGCCTAGCTTGTG 61.231 55.000 0.00 0.00 36.49 3.33
4551 5746 1.878775 GCTTGTGCCTAGCTTGTGG 59.121 57.895 0.00 0.00 35.74 4.17
4552 5747 0.606401 GCTTGTGCCTAGCTTGTGGA 60.606 55.000 0.00 0.00 35.74 4.02
4553 5748 1.952367 GCTTGTGCCTAGCTTGTGGAT 60.952 52.381 0.00 0.00 35.74 3.41
4554 5749 2.440409 CTTGTGCCTAGCTTGTGGATT 58.560 47.619 0.00 0.00 0.00 3.01
4555 5750 2.113860 TGTGCCTAGCTTGTGGATTC 57.886 50.000 0.00 0.00 0.00 2.52
4556 5751 1.630369 TGTGCCTAGCTTGTGGATTCT 59.370 47.619 0.00 0.00 0.00 2.40
4557 5752 2.012673 GTGCCTAGCTTGTGGATTCTG 58.987 52.381 0.00 0.00 0.00 3.02
4558 5753 1.065199 TGCCTAGCTTGTGGATTCTGG 60.065 52.381 0.00 0.00 0.00 3.86
4559 5754 1.673168 CCTAGCTTGTGGATTCTGGC 58.327 55.000 0.00 0.00 0.00 4.85
4560 5755 1.293924 CTAGCTTGTGGATTCTGGCG 58.706 55.000 0.00 0.00 0.00 5.69
4561 5756 0.744414 TAGCTTGTGGATTCTGGCGC 60.744 55.000 0.00 0.00 0.00 6.53
4690 8794 0.812014 TCTTTCTTGTTGACGCGCCA 60.812 50.000 5.73 0.00 0.00 5.69
4780 8884 3.190118 GCTCTTCCAGGTGTTCATTTCAG 59.810 47.826 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.226717 GAACGCCGCTACTCCTCAG 60.227 63.158 0.00 0.00 0.00 3.35
3 4 2.885861 CAGAACGCCGCTACTCCT 59.114 61.111 0.00 0.00 0.00 3.69
4 5 2.886124 GCAGAACGCCGCTACTCC 60.886 66.667 0.00 0.00 32.94 3.85
37 38 1.517242 CCCGGCTCTAGAATGCAATC 58.483 55.000 0.00 0.00 0.00 2.67
38 39 0.109342 CCCCGGCTCTAGAATGCAAT 59.891 55.000 0.00 0.00 0.00 3.56
39 40 0.980754 TCCCCGGCTCTAGAATGCAA 60.981 55.000 0.00 0.00 0.00 4.08
47 48 1.153989 CAGATCCTCCCCGGCTCTA 59.846 63.158 0.00 0.00 36.12 2.43
132 133 2.032290 GGCAACTAAAAAGCGTCGTCTT 60.032 45.455 0.00 0.00 0.00 3.01
147 148 2.629656 GCATGTCTTGGCGGCAACT 61.630 57.895 21.79 2.91 0.00 3.16
151 152 4.465512 CGTGCATGTCTTGGCGGC 62.466 66.667 0.00 0.00 0.00 6.53
188 189 0.661020 GGTTGACACGTCCACTTTGG 59.339 55.000 1.93 0.00 39.43 3.28
216 217 0.179094 TACTCCAATAACCAGCCGCG 60.179 55.000 0.00 0.00 0.00 6.46
251 252 3.270027 TCTTTTCTGATACACGGCATGG 58.730 45.455 0.00 0.00 0.00 3.66
253 254 5.957842 TTTTCTTTTCTGATACACGGCAT 57.042 34.783 0.00 0.00 0.00 4.40
298 477 6.708949 ACTCCAATAACGTTTTCTGTATGTGT 59.291 34.615 5.91 0.00 0.00 3.72
299 478 7.129109 ACTCCAATAACGTTTTCTGTATGTG 57.871 36.000 5.91 0.00 0.00 3.21
305 484 6.408428 GCGTATACTCCAATAACGTTTTCTG 58.592 40.000 5.91 1.36 0.00 3.02
306 485 5.521372 GGCGTATACTCCAATAACGTTTTCT 59.479 40.000 5.91 0.00 0.00 2.52
307 486 5.291614 TGGCGTATACTCCAATAACGTTTTC 59.708 40.000 12.21 0.00 0.00 2.29
308 487 5.177326 TGGCGTATACTCCAATAACGTTTT 58.823 37.500 12.21 0.00 0.00 2.43
309 488 4.757594 TGGCGTATACTCCAATAACGTTT 58.242 39.130 12.21 0.00 0.00 3.60
311 490 4.365723 CTTGGCGTATACTCCAATAACGT 58.634 43.478 23.95 0.00 39.67 3.99
312 491 3.183775 GCTTGGCGTATACTCCAATAACG 59.816 47.826 23.95 14.99 39.67 3.18
313 492 4.124238 TGCTTGGCGTATACTCCAATAAC 58.876 43.478 23.95 17.35 39.67 1.89
314 493 4.409718 TGCTTGGCGTATACTCCAATAA 57.590 40.909 23.95 14.26 39.67 1.40
315 494 4.314961 CATGCTTGGCGTATACTCCAATA 58.685 43.478 23.95 17.27 39.67 1.90
316 495 3.141398 CATGCTTGGCGTATACTCCAAT 58.859 45.455 23.95 9.98 39.67 3.16
317 496 2.560504 CATGCTTGGCGTATACTCCAA 58.439 47.619 22.69 22.69 38.30 3.53
318 497 1.202639 CCATGCTTGGCGTATACTCCA 60.203 52.381 10.59 10.59 35.85 3.86
319 498 1.070134 TCCATGCTTGGCGTATACTCC 59.930 52.381 13.75 4.86 43.29 3.85
320 499 2.526304 TCCATGCTTGGCGTATACTC 57.474 50.000 13.75 0.00 43.29 2.59
321 500 3.141398 CATTCCATGCTTGGCGTATACT 58.859 45.455 13.75 0.00 43.29 2.12
322 501 2.226437 CCATTCCATGCTTGGCGTATAC 59.774 50.000 13.75 0.00 43.29 1.47
339 518 7.285172 TCCGTTGATTGATGATGTATTTCCATT 59.715 33.333 0.00 0.00 0.00 3.16
341 520 6.118852 TCCGTTGATTGATGATGTATTTCCA 58.881 36.000 0.00 0.00 0.00 3.53
356 933 1.135803 CCGTGCGATTTTCCGTTGATT 60.136 47.619 0.00 0.00 0.00 2.57
371 948 1.004595 GTAAGGAATCGAACCCGTGC 58.995 55.000 8.14 2.36 37.05 5.34
372 949 2.373540 TGTAAGGAATCGAACCCGTG 57.626 50.000 8.14 0.00 37.05 4.94
373 950 2.901249 CATGTAAGGAATCGAACCCGT 58.099 47.619 8.14 4.62 37.05 5.28
374 951 1.597663 GCATGTAAGGAATCGAACCCG 59.402 52.381 8.14 0.00 37.07 5.28
377 954 1.003866 GGCGCATGTAAGGAATCGAAC 60.004 52.381 10.83 0.00 0.00 3.95
380 957 1.195448 GATGGCGCATGTAAGGAATCG 59.805 52.381 10.83 0.00 0.00 3.34
387 964 5.043835 ATCAATAGCTGATGGCGCATGTAA 61.044 41.667 10.83 0.00 43.49 2.41
389 966 2.812983 ATCAATAGCTGATGGCGCATGT 60.813 45.455 10.83 0.00 43.49 3.21
393 970 0.441533 CGATCAATAGCTGATGGCGC 59.558 55.000 0.00 0.00 45.23 6.53
396 973 1.446907 GGGCGATCAATAGCTGATGG 58.553 55.000 0.00 0.00 45.23 3.51
408 1030 0.309922 TCGTGTAATCTCGGGCGATC 59.690 55.000 0.00 0.00 0.00 3.69
411 1033 1.548973 GCATCGTGTAATCTCGGGCG 61.549 60.000 0.00 0.00 0.00 6.13
414 1036 3.251817 ACGCATCGTGTAATCTCGG 57.748 52.632 0.00 0.00 39.18 4.63
425 1047 0.300491 CGTTGGGTATTCACGCATCG 59.700 55.000 9.76 9.76 46.98 3.84
438 1060 0.670239 GAGGCCAATTTTGCGTTGGG 60.670 55.000 5.01 0.00 44.96 4.12
459 1081 2.158827 TGCTATATCGCTTTCCTTGCCA 60.159 45.455 0.52 0.00 0.00 4.92
460 1082 2.481952 CTGCTATATCGCTTTCCTTGCC 59.518 50.000 0.52 0.00 0.00 4.52
462 1084 4.876125 TCTCTGCTATATCGCTTTCCTTG 58.124 43.478 0.52 0.00 0.00 3.61
476 1098 4.287067 ACATTTGTTTCCTCCTCTCTGCTA 59.713 41.667 0.00 0.00 0.00 3.49
477 1099 3.073650 ACATTTGTTTCCTCCTCTCTGCT 59.926 43.478 0.00 0.00 0.00 4.24
478 1100 3.190118 CACATTTGTTTCCTCCTCTCTGC 59.810 47.826 0.00 0.00 0.00 4.26
479 1101 3.755378 CCACATTTGTTTCCTCCTCTCTG 59.245 47.826 0.00 0.00 0.00 3.35
480 1102 3.652869 TCCACATTTGTTTCCTCCTCTCT 59.347 43.478 0.00 0.00 0.00 3.10
481 1103 4.006319 CTCCACATTTGTTTCCTCCTCTC 58.994 47.826 0.00 0.00 0.00 3.20
482 1104 3.652869 TCTCCACATTTGTTTCCTCCTCT 59.347 43.478 0.00 0.00 0.00 3.69
483 1105 4.006319 CTCTCCACATTTGTTTCCTCCTC 58.994 47.826 0.00 0.00 0.00 3.71
484 1106 3.245052 CCTCTCCACATTTGTTTCCTCCT 60.245 47.826 0.00 0.00 0.00 3.69
485 1107 3.084786 CCTCTCCACATTTGTTTCCTCC 58.915 50.000 0.00 0.00 0.00 4.30
486 1108 4.021102 TCCTCTCCACATTTGTTTCCTC 57.979 45.455 0.00 0.00 0.00 3.71
487 1109 4.664688 ATCCTCTCCACATTTGTTTCCT 57.335 40.909 0.00 0.00 0.00 3.36
488 1110 7.410120 AATTATCCTCTCCACATTTGTTTCC 57.590 36.000 0.00 0.00 0.00 3.13
489 1111 8.131731 GCTAATTATCCTCTCCACATTTGTTTC 58.868 37.037 0.00 0.00 0.00 2.78
490 1112 7.615365 TGCTAATTATCCTCTCCACATTTGTTT 59.385 33.333 0.00 0.00 0.00 2.83
491 1113 7.067494 GTGCTAATTATCCTCTCCACATTTGTT 59.933 37.037 0.00 0.00 0.00 2.83
503 1125 5.294552 AGTTTTCTGCGTGCTAATTATCCTC 59.705 40.000 0.00 0.00 0.00 3.71
545 1167 7.821652 AGATTGATGATGTAGTATCCGTAGTG 58.178 38.462 0.00 0.00 0.00 2.74
608 1233 6.358974 TTCTTCCCTTTGGATTTGGAAATC 57.641 37.500 3.85 3.85 41.40 2.17
626 1251 3.895041 TCCATTCCTTTGGGTGTTTCTTC 59.105 43.478 0.00 0.00 37.37 2.87
629 1254 3.055891 CCATCCATTCCTTTGGGTGTTTC 60.056 47.826 3.26 0.00 44.95 2.78
637 1262 6.453092 GCTAATTCATCCATCCATTCCTTTG 58.547 40.000 0.00 0.00 0.00 2.77
645 1270 2.221169 GCACGCTAATTCATCCATCCA 58.779 47.619 0.00 0.00 0.00 3.41
688 1338 1.166531 AAACTTGCACCTCTCACCGC 61.167 55.000 0.00 0.00 0.00 5.68
707 1357 5.577835 CATTCTTGTTCTCGTGGACAAAAA 58.422 37.500 12.15 6.35 0.00 1.94
708 1358 4.497340 GCATTCTTGTTCTCGTGGACAAAA 60.497 41.667 12.15 9.71 0.00 2.44
712 1362 1.126846 CGCATTCTTGTTCTCGTGGAC 59.873 52.381 0.00 0.00 0.00 4.02
714 1364 1.428448 TCGCATTCTTGTTCTCGTGG 58.572 50.000 0.00 0.00 0.00 4.94
715 1365 2.411547 GGTTCGCATTCTTGTTCTCGTG 60.412 50.000 0.00 0.00 0.00 4.35
717 1367 1.128692 GGGTTCGCATTCTTGTTCTCG 59.871 52.381 0.00 0.00 0.00 4.04
718 1368 1.128692 CGGGTTCGCATTCTTGTTCTC 59.871 52.381 0.00 0.00 0.00 2.87
719 1369 1.156736 CGGGTTCGCATTCTTGTTCT 58.843 50.000 0.00 0.00 0.00 3.01
720 1370 3.676091 CGGGTTCGCATTCTTGTTC 57.324 52.632 0.00 0.00 0.00 3.18
748 1398 7.173047 GCATTCTTGTTCTCTCTCTCTCTTTTT 59.827 37.037 0.00 0.00 0.00 1.94
749 1399 6.650390 GCATTCTTGTTCTCTCTCTCTCTTTT 59.350 38.462 0.00 0.00 0.00 2.27
750 1400 6.165577 GCATTCTTGTTCTCTCTCTCTCTTT 58.834 40.000 0.00 0.00 0.00 2.52
751 1401 5.622007 CGCATTCTTGTTCTCTCTCTCTCTT 60.622 44.000 0.00 0.00 0.00 2.85
752 1402 4.142403 CGCATTCTTGTTCTCTCTCTCTCT 60.142 45.833 0.00 0.00 0.00 3.10
753 1403 4.104776 CGCATTCTTGTTCTCTCTCTCTC 58.895 47.826 0.00 0.00 0.00 3.20
754 1404 3.761218 TCGCATTCTTGTTCTCTCTCTCT 59.239 43.478 0.00 0.00 0.00 3.10
755 1405 4.103365 TCGCATTCTTGTTCTCTCTCTC 57.897 45.455 0.00 0.00 0.00 3.20
756 1406 4.527509 TTCGCATTCTTGTTCTCTCTCT 57.472 40.909 0.00 0.00 0.00 3.10
757 1407 5.406780 TCTTTTCGCATTCTTGTTCTCTCTC 59.593 40.000 0.00 0.00 0.00 3.20
758 1408 5.300752 TCTTTTCGCATTCTTGTTCTCTCT 58.699 37.500 0.00 0.00 0.00 3.10
759 1409 5.597813 TCTTTTCGCATTCTTGTTCTCTC 57.402 39.130 0.00 0.00 0.00 3.20
760 1410 6.377327 TTTCTTTTCGCATTCTTGTTCTCT 57.623 33.333 0.00 0.00 0.00 3.10
761 1411 6.142958 CCTTTTCTTTTCGCATTCTTGTTCTC 59.857 38.462 0.00 0.00 0.00 2.87
762 1412 5.979517 CCTTTTCTTTTCGCATTCTTGTTCT 59.020 36.000 0.00 0.00 0.00 3.01
763 1413 5.977129 TCCTTTTCTTTTCGCATTCTTGTTC 59.023 36.000 0.00 0.00 0.00 3.18
764 1414 5.901552 TCCTTTTCTTTTCGCATTCTTGTT 58.098 33.333 0.00 0.00 0.00 2.83
765 1415 5.514274 TCCTTTTCTTTTCGCATTCTTGT 57.486 34.783 0.00 0.00 0.00 3.16
766 1416 6.826893 TTTCCTTTTCTTTTCGCATTCTTG 57.173 33.333 0.00 0.00 0.00 3.02
767 1417 8.437360 AATTTTCCTTTTCTTTTCGCATTCTT 57.563 26.923 0.00 0.00 0.00 2.52
768 1418 8.437360 AAATTTTCCTTTTCTTTTCGCATTCT 57.563 26.923 0.00 0.00 0.00 2.40
769 1419 7.527183 CGAAATTTTCCTTTTCTTTTCGCATTC 59.473 33.333 3.61 0.00 38.98 2.67
775 1425 6.418956 GGTGCGAAATTTTCCTTTTCTTTTC 58.581 36.000 3.61 0.00 32.18 2.29
807 1457 2.755103 GCTCCTCCGAATGGAAATGTTT 59.245 45.455 0.00 0.00 45.87 2.83
823 1473 1.063183 ACAAGGAAAGCTCTGCTCCT 58.937 50.000 0.00 0.00 38.25 3.69
848 1498 4.104102 TGGATTTATAGGGGATTTGCGTCT 59.896 41.667 0.00 0.00 0.00 4.18
849 1499 4.394729 TGGATTTATAGGGGATTTGCGTC 58.605 43.478 0.00 0.00 0.00 5.19
852 1502 3.191371 CGCTGGATTTATAGGGGATTTGC 59.809 47.826 0.00 0.00 0.00 3.68
894 1544 0.592247 GTGTTGTGTGCTTTGGCGAG 60.592 55.000 0.00 0.00 42.25 5.03
921 1571 2.394930 TCGTATGCTTGGCTTTGCTA 57.605 45.000 0.00 0.00 0.00 3.49
957 1607 3.551496 CTTGCGGTGGAGGCTTGGA 62.551 63.158 0.00 0.00 0.00 3.53
958 1608 3.058160 CTTGCGGTGGAGGCTTGG 61.058 66.667 0.00 0.00 0.00 3.61
1053 1703 2.811317 GACTGCTTGAGGCCGTCG 60.811 66.667 0.00 0.00 43.15 5.12
1257 1907 2.510012 TCGAGCAGCTTGCCGATG 60.510 61.111 4.52 0.00 46.52 3.84
1270 1920 1.406219 CTCATGAACCGCGTGTCGAG 61.406 60.000 4.92 1.39 41.67 4.04
1272 1922 3.071459 GCTCATGAACCGCGTGTCG 62.071 63.158 4.92 0.00 35.00 4.35
1395 2045 1.076923 GAGGAGGAGCACGTAGGGA 60.077 63.158 0.00 0.00 0.00 4.20
1610 2260 1.881903 CGTCTTCTCCTCCAGCAGCA 61.882 60.000 0.00 0.00 0.00 4.41
1962 2612 1.959226 GTGCCACACGTACACCTGG 60.959 63.158 0.00 0.00 0.00 4.45
2250 2900 9.393249 CGACAAAATTTGCAACTTAAGATAGAA 57.607 29.630 10.09 0.00 0.00 2.10
2251 2901 8.020819 CCGACAAAATTTGCAACTTAAGATAGA 58.979 33.333 10.09 0.00 0.00 1.98
2252 2902 7.201350 GCCGACAAAATTTGCAACTTAAGATAG 60.201 37.037 10.09 0.00 0.00 2.08
2253 2903 6.584563 GCCGACAAAATTTGCAACTTAAGATA 59.415 34.615 10.09 0.00 0.00 1.98
2369 3060 2.819115 CTCGAGAACCTCATCACATGG 58.181 52.381 6.58 0.00 0.00 3.66
2421 3150 0.171007 GTCATGGACCATTTGTGGCG 59.829 55.000 3.52 0.00 0.00 5.69
2437 3166 2.669113 CGTTCCAAATCGTCTACCGTCA 60.669 50.000 0.00 0.00 37.94 4.35
2438 3167 1.916000 CGTTCCAAATCGTCTACCGTC 59.084 52.381 0.00 0.00 37.94 4.79
2453 3182 2.633488 AGCAGAAAAGGATAGCGTTCC 58.367 47.619 0.04 0.04 35.90 3.62
2515 3248 2.657237 CGTCCAGGTCAGGTCACC 59.343 66.667 0.00 0.00 36.58 4.02
2543 3276 8.862325 AGATGGTGTCAAATGTCAAATACTTA 57.138 30.769 0.00 0.00 0.00 2.24
2567 3300 6.077838 GGCTGTTCTATTTACACGTTTCAAG 58.922 40.000 0.00 0.00 0.00 3.02
2581 3314 4.026356 AGCAGTTTCTTGGCTGTTCTAT 57.974 40.909 0.00 0.00 36.34 1.98
2645 3559 5.698545 AGTCAGCACAGTCAAGTTTATCTTC 59.301 40.000 0.00 0.00 33.63 2.87
2674 3660 2.964925 GCACACGCACCGTCAGAA 60.965 61.111 0.00 0.00 38.32 3.02
2685 3671 4.918060 CACACGCACACGCACACG 62.918 66.667 0.00 0.00 45.53 4.49
2691 3677 4.918060 CACACGCACACGCACACG 62.918 66.667 0.00 0.00 45.53 4.49
2694 3680 4.943591 CTGCACACGCACACGCAC 62.944 66.667 0.00 0.00 45.36 5.34
2697 3683 4.654904 CAGCTGCACACGCACACG 62.655 66.667 0.00 0.00 45.36 4.49
2698 3684 4.969604 GCAGCTGCACACGCACAC 62.970 66.667 33.36 0.00 45.36 3.82
2724 3710 2.506438 GCCGTACTCCTCGCACAC 60.506 66.667 0.00 0.00 0.00 3.82
2936 3922 2.044252 CAGCCCTGCAGCCAGAAT 60.044 61.111 8.66 0.00 41.77 2.40
2992 3978 2.124570 CCGGGTGGATGAAGCTGG 60.125 66.667 0.00 0.00 37.73 4.85
3080 4066 0.179134 AGTCGCTGACGTAGATTGGC 60.179 55.000 0.00 0.00 41.18 4.52
3083 4069 0.377554 CGGAGTCGCTGACGTAGATT 59.622 55.000 0.00 0.00 41.18 2.40
3084 4070 0.743701 ACGGAGTCGCTGACGTAGAT 60.744 55.000 0.00 0.00 29.74 1.98
3146 4132 1.140161 GCGTAGTATGGTGCCGTCA 59.860 57.895 0.00 0.00 0.00 4.35
3158 4144 3.299977 TGGTGGTCGCAGCGTAGT 61.300 61.111 15.93 0.00 0.00 2.73
3278 4264 3.058160 CCGCCCTGGCAGTTGAAG 61.058 66.667 14.43 0.00 42.06 3.02
3560 4546 2.165301 CGCGAACCGGATGTCCTTC 61.165 63.158 9.46 0.00 0.00 3.46
3634 4620 2.050351 CGTTGTCGACCTCGCTGT 60.050 61.111 14.12 0.00 39.71 4.40
3646 4632 4.657824 CGGTCACCTCGCCGTTGT 62.658 66.667 0.00 0.00 42.73 3.32
3814 4800 1.738350 AGACATAGTGGACACGAGACG 59.262 52.381 0.00 0.00 36.20 4.18
3825 4811 6.358294 CGAGACGTCAATCAATAGACATAGTG 59.642 42.308 19.50 0.00 34.48 2.74
3827 4813 5.853810 CCGAGACGTCAATCAATAGACATAG 59.146 44.000 19.50 0.00 34.48 2.23
3840 4826 1.214589 GCTAAGCCCGAGACGTCAA 59.785 57.895 19.50 0.00 0.00 3.18
3841 4827 1.974875 TGCTAAGCCCGAGACGTCA 60.975 57.895 19.50 0.00 0.00 4.35
3842 4828 1.516603 GTGCTAAGCCCGAGACGTC 60.517 63.158 7.70 7.70 0.00 4.34
3843 4829 2.572284 GTGCTAAGCCCGAGACGT 59.428 61.111 0.00 0.00 0.00 4.34
3844 4830 2.579787 CGTGCTAAGCCCGAGACG 60.580 66.667 0.00 0.00 0.00 4.18
3845 4831 0.669625 AAACGTGCTAAGCCCGAGAC 60.670 55.000 0.00 0.00 0.00 3.36
3846 4832 0.389426 GAAACGTGCTAAGCCCGAGA 60.389 55.000 0.00 0.00 0.00 4.04
3847 4833 1.683790 CGAAACGTGCTAAGCCCGAG 61.684 60.000 0.00 0.00 0.00 4.63
3848 4834 1.735198 CGAAACGTGCTAAGCCCGA 60.735 57.895 0.00 0.00 0.00 5.14
3850 4836 2.479198 GCGAAACGTGCTAAGCCC 59.521 61.111 0.00 0.00 0.00 5.19
3851 4837 2.095843 CGCGAAACGTGCTAAGCC 59.904 61.111 0.00 0.00 36.87 4.35
3865 4865 7.552187 GCCTAAAATAAAATTATTTGGACGCG 58.448 34.615 3.53 3.53 41.20 6.01
3886 4886 1.066430 ACAAATTCGAAGCTCCGCCTA 60.066 47.619 3.35 0.00 0.00 3.93
3890 4890 2.222819 GCTGTACAAATTCGAAGCTCCG 60.223 50.000 3.35 0.00 0.00 4.63
3991 4991 4.809426 ACTCACTCGTAACAAAAACCAGAG 59.191 41.667 0.00 0.00 0.00 3.35
4035 5035 5.391523 GCCAGATTAAACACAACGCTGAATA 60.392 40.000 0.00 0.00 0.00 1.75
4036 5036 4.615912 GCCAGATTAAACACAACGCTGAAT 60.616 41.667 0.00 0.00 0.00 2.57
4038 5038 2.225491 GCCAGATTAAACACAACGCTGA 59.775 45.455 0.00 0.00 0.00 4.26
4041 5041 1.402325 GGGCCAGATTAAACACAACGC 60.402 52.381 4.39 0.00 0.00 4.84
4042 5042 2.159382 AGGGCCAGATTAAACACAACG 58.841 47.619 6.18 0.00 0.00 4.10
4043 5043 3.153919 TGAGGGCCAGATTAAACACAAC 58.846 45.455 6.18 0.00 0.00 3.32
4044 5044 3.517296 TGAGGGCCAGATTAAACACAA 57.483 42.857 6.18 0.00 0.00 3.33
4045 5045 3.517296 TTGAGGGCCAGATTAAACACA 57.483 42.857 6.18 0.00 0.00 3.72
4047 5047 2.817258 CGTTTGAGGGCCAGATTAAACA 59.183 45.455 6.18 0.00 0.00 2.83
4048 5048 2.817844 ACGTTTGAGGGCCAGATTAAAC 59.182 45.455 6.18 8.48 0.00 2.01
4049 5049 3.078837 GACGTTTGAGGGCCAGATTAAA 58.921 45.455 6.18 0.00 0.00 1.52
4050 5050 2.617021 GGACGTTTGAGGGCCAGATTAA 60.617 50.000 6.18 0.00 0.00 1.40
4051 5051 1.065709 GGACGTTTGAGGGCCAGATTA 60.066 52.381 6.18 0.00 0.00 1.75
4052 5052 0.322546 GGACGTTTGAGGGCCAGATT 60.323 55.000 6.18 0.00 0.00 2.40
4053 5053 1.299976 GGACGTTTGAGGGCCAGAT 59.700 57.895 6.18 0.00 0.00 2.90
4054 5054 2.747686 GGACGTTTGAGGGCCAGA 59.252 61.111 6.18 0.00 0.00 3.86
4055 5055 2.742372 CGGACGTTTGAGGGCCAG 60.742 66.667 6.18 0.00 0.00 4.85
4056 5056 3.109592 AACGGACGTTTGAGGGCCA 62.110 57.895 6.18 0.00 34.22 5.36
4057 5057 2.281276 AACGGACGTTTGAGGGCC 60.281 61.111 3.99 0.00 34.22 5.80
4058 5058 1.595929 TCAACGGACGTTTGAGGGC 60.596 57.895 7.44 0.00 36.00 5.19
4059 5059 2.231820 GTCAACGGACGTTTGAGGG 58.768 57.895 7.44 0.00 36.00 4.30
4224 5319 0.638746 CGTCGTCACGGCTAAATGTC 59.361 55.000 0.00 0.00 42.73 3.06
4226 5321 3.024423 TCGTCGTCACGGCTAAATG 57.976 52.632 0.00 0.00 46.70 2.32
4314 5422 2.161486 GCTTCGCTACTCACCGCTG 61.161 63.158 0.00 0.00 0.00 5.18
4316 5424 3.248171 CGCTTCGCTACTCACCGC 61.248 66.667 0.00 0.00 0.00 5.68
4329 5437 1.806542 CATGGCAGTTAACTCACGCTT 59.193 47.619 4.77 0.00 0.00 4.68
4359 5467 0.308376 GGTCGGCGCAAAAGTTAACA 59.692 50.000 10.83 0.00 0.00 2.41
4389 5524 0.245539 GCTACAGCAAGTACCGGTCA 59.754 55.000 12.40 0.00 41.59 4.02
4390 5525 0.531200 AGCTACAGCAAGTACCGGTC 59.469 55.000 12.40 2.55 45.16 4.79
4391 5526 0.246635 CAGCTACAGCAAGTACCGGT 59.753 55.000 13.98 13.98 45.16 5.28
4392 5527 0.246635 ACAGCTACAGCAAGTACCGG 59.753 55.000 0.00 0.00 45.16 5.28
4393 5528 2.527100 GTACAGCTACAGCAAGTACCG 58.473 52.381 18.57 0.00 43.06 4.02
4395 5530 3.251571 GTGGTACAGCTACAGCAAGTAC 58.748 50.000 20.03 20.03 45.52 2.73
4396 5531 2.094906 CGTGGTACAGCTACAGCAAGTA 60.095 50.000 3.70 3.50 41.80 2.24
4397 5532 1.336887 CGTGGTACAGCTACAGCAAGT 60.337 52.381 3.70 4.45 41.80 3.16
4398 5533 1.336887 ACGTGGTACAGCTACAGCAAG 60.337 52.381 3.70 9.31 41.80 4.01
4399 5534 0.677288 ACGTGGTACAGCTACAGCAA 59.323 50.000 3.70 0.00 41.80 3.91
4400 5535 1.200716 GTACGTGGTACAGCTACAGCA 59.799 52.381 0.00 0.00 41.80 4.41
4401 5536 1.468736 GGTACGTGGTACAGCTACAGC 60.469 57.143 0.00 0.00 41.80 4.40
4402 5537 1.814394 TGGTACGTGGTACAGCTACAG 59.186 52.381 0.00 0.00 41.80 2.74
4403 5538 1.814394 CTGGTACGTGGTACAGCTACA 59.186 52.381 0.00 0.00 41.80 2.74
4404 5539 1.815003 ACTGGTACGTGGTACAGCTAC 59.185 52.381 0.00 0.00 41.80 3.58
4405 5540 2.086869 GACTGGTACGTGGTACAGCTA 58.913 52.381 0.00 0.00 41.80 3.32
4406 5541 0.886563 GACTGGTACGTGGTACAGCT 59.113 55.000 0.00 0.00 41.80 4.24
4407 5542 0.455633 CGACTGGTACGTGGTACAGC 60.456 60.000 0.00 0.00 41.80 4.40
4408 5543 0.169672 CCGACTGGTACGTGGTACAG 59.830 60.000 0.00 3.66 41.80 2.74
4409 5544 0.250684 TCCGACTGGTACGTGGTACA 60.251 55.000 0.00 0.00 40.41 2.90
4410 5545 0.169009 GTCCGACTGGTACGTGGTAC 59.831 60.000 0.00 0.00 38.19 3.34
4411 5546 0.036732 AGTCCGACTGGTACGTGGTA 59.963 55.000 0.00 0.00 36.30 3.25
4412 5547 1.228367 AGTCCGACTGGTACGTGGT 60.228 57.895 0.00 0.00 36.30 4.16
4413 5548 1.505353 GAGTCCGACTGGTACGTGG 59.495 63.158 5.57 0.00 36.30 4.94
4414 5549 1.134075 CGAGTCCGACTGGTACGTG 59.866 63.158 5.57 0.00 38.22 4.49
4415 5550 2.037136 CCGAGTCCGACTGGTACGT 61.037 63.158 5.57 0.00 38.22 3.57
4429 5564 1.336440 CATGGTCTCAGCTACTCCGAG 59.664 57.143 0.00 0.00 0.00 4.63
4473 5639 1.875813 GCAGCTCGATCACGACTGG 60.876 63.158 16.65 0.90 43.81 4.00
4540 5735 1.673168 GCCAGAATCCACAAGCTAGG 58.327 55.000 0.00 0.00 0.00 3.02
4541 5736 1.293924 CGCCAGAATCCACAAGCTAG 58.706 55.000 0.00 0.00 0.00 3.42
4543 5738 2.042831 GCGCCAGAATCCACAAGCT 61.043 57.895 0.00 0.00 0.00 3.74
4545 5740 1.741401 TCGCGCCAGAATCCACAAG 60.741 57.895 0.00 0.00 0.00 3.16
4546 5741 2.032634 GTCGCGCCAGAATCCACAA 61.033 57.895 0.00 0.00 0.00 3.33
4547 5742 2.434185 GTCGCGCCAGAATCCACA 60.434 61.111 0.00 0.00 0.00 4.17
4548 5743 2.434185 TGTCGCGCCAGAATCCAC 60.434 61.111 0.00 0.00 0.00 4.02
4549 5744 2.434185 GTGTCGCGCCAGAATCCA 60.434 61.111 0.00 0.00 0.00 3.41
4550 5745 3.554692 CGTGTCGCGCCAGAATCC 61.555 66.667 0.00 0.00 0.00 3.01
4607 5841 2.202623 AATCCTGCGACGACGAGC 60.203 61.111 12.29 7.52 42.66 5.03
4610 5844 1.991430 CTTGAATCCTGCGACGACG 59.009 57.895 2.12 2.12 42.93 5.12
4705 8809 4.280494 CTCCATACGCCCCGGACG 62.280 72.222 0.73 9.55 0.00 4.79


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

AutoCloner maintained by Alex Coulton.