Multiple sequence alignment - TraesCS3B01G482600

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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 TraesCS3B01G482600 chr3B 100.000 3280 0 0 1 3280 729707072 729703793 0.000000e+00 6058.0
1 TraesCS3B01G482600 chr3D 90.123 1873 88 30 370 2208 550245003 550243194 0.000000e+00 2344.0
2 TraesCS3B01G482600 chr3D 94.823 367 15 3 9 373 550248336 550247972 1.320000e-158 569.0
3 TraesCS3B01G482600 chr3D 92.661 218 13 3 3021 3237 550242479 550242264 8.840000e-81 311.0
4 TraesCS3B01G482600 chr3A 92.282 1192 53 12 1051 2220 687059105 687057931 0.000000e+00 1655.0
5 TraesCS3B01G482600 chr3A 95.628 366 16 0 8 373 687061946 687061581 3.650000e-164 588.0
6 TraesCS3B01G482600 chr3A 79.621 898 84 54 2375 3237 687057570 687056737 1.330000e-153 553.0
7 TraesCS3B01G482600 chr3A 87.500 344 28 8 557 899 687059918 687059589 1.850000e-102 383.0
8 TraesCS3B01G482600 chr6D 86.943 314 31 4 1535 1848 424712580 424712883 8.710000e-91 344.0
9 TraesCS3B01G482600 chr6D 85.032 314 37 4 1535 1848 424745258 424745561 8.840000e-81 311.0
10 TraesCS3B01G482600 chr6D 90.385 104 10 0 1218 1321 424712400 424712503 1.590000e-28 137.0
11 TraesCS3B01G482600 chr6A 89.474 76 7 1 1150 1225 569589438 569589512 9.690000e-16 95.3


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 TraesCS3B01G482600 chr3B 729703793 729707072 3279 True 6058.000000 6058 100.000000 1 3280 1 chr3B.!!$R1 3279
1 TraesCS3B01G482600 chr3D 550242264 550248336 6072 True 1074.666667 2344 92.535667 9 3237 3 chr3D.!!$R1 3228
2 TraesCS3B01G482600 chr3A 687056737 687061946 5209 True 794.750000 1655 88.757750 8 3237 4 chr3A.!!$R1 3229

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
572 3976 0.035317 TAGCCAGCACACTTGACTGG 59.965 55.0 14.84 14.84 44.01 4.00 F
579 3983 0.535102 CACACTTGACTGGTGGGACC 60.535 60.0 0.00 0.00 40.20 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1677 5433 0.454620 CGTCGGACGAGAAGTTGGAG 60.455 60.0 25.29 0.0 46.05 3.86 R
2380 6445 0.955428 GGCCGTCTGTGCATCTTTGA 60.955 55.0 0.00 0.0 0.00 2.69 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
50 51 1.007387 CTTTTGTGGCCGGAGTTGC 60.007 57.895 5.05 0.00 0.00 4.17
51 52 1.733402 CTTTTGTGGCCGGAGTTGCA 61.733 55.000 5.05 0.00 0.00 4.08
120 121 2.690778 GGCTGCCGTGGTGAACATC 61.691 63.158 1.35 0.00 0.00 3.06
127 128 2.741985 TGGTGAACATCGCTGCGG 60.742 61.111 23.03 9.56 0.00 5.69
158 159 1.001597 CTCTAATCCGAGGCACGTACC 60.002 57.143 0.00 0.00 40.78 3.34
212 213 4.143137 GCATTATTGCGTTGAAAAGTTGGG 60.143 41.667 0.00 0.00 39.49 4.12
231 232 0.177604 GGCACAGGATCACCAGAGAG 59.822 60.000 0.00 0.00 38.94 3.20
340 342 1.134401 AGTAGATGTTGTGGCCATCCG 60.134 52.381 9.72 0.00 39.62 4.18
362 364 1.456331 ACGTACGTAGGGGATGGGG 60.456 63.158 21.41 0.00 0.00 4.96
389 3363 0.874390 CTCACACGAACAACCATGGG 59.126 55.000 18.09 0.85 0.00 4.00
392 3366 2.282887 ACGAACAACCATGGGGGC 60.283 61.111 18.09 3.97 42.05 5.80
393 3367 2.282816 CGAACAACCATGGGGGCA 60.283 61.111 18.09 0.00 42.05 5.36
395 3369 1.899617 GAACAACCATGGGGGCATG 59.100 57.895 18.09 9.21 42.05 4.06
415 3390 2.034687 ATGCCCTGCGCTCTGTTT 59.965 55.556 9.73 0.00 38.78 2.83
494 3478 1.352622 TGTTGGGGTTGGTCTCTGCT 61.353 55.000 0.00 0.00 0.00 4.24
516 3500 6.882140 TGCTTGAAGGATTAATTCTTACCGAA 59.118 34.615 9.07 0.47 35.78 4.30
521 3505 9.947433 TGAAGGATTAATTCTTACCGAAAGTAA 57.053 29.630 9.07 0.00 38.65 2.24
548 3952 7.921786 AACGAAACATTCATCCAAAGATAGA 57.078 32.000 0.00 0.00 0.00 1.98
549 3953 8.511604 AACGAAACATTCATCCAAAGATAGAT 57.488 30.769 0.00 0.00 0.00 1.98
550 3954 9.613428 AACGAAACATTCATCCAAAGATAGATA 57.387 29.630 0.00 0.00 0.00 1.98
551 3955 9.046296 ACGAAACATTCATCCAAAGATAGATAC 57.954 33.333 0.00 0.00 0.00 2.24
552 3956 8.217115 CGAAACATTCATCCAAAGATAGATACG 58.783 37.037 0.00 0.00 0.00 3.06
553 3957 8.964476 AAACATTCATCCAAAGATAGATACGT 57.036 30.769 0.00 0.00 0.00 3.57
555 3959 9.698309 AACATTCATCCAAAGATAGATACGTAG 57.302 33.333 0.08 0.00 0.00 3.51
572 3976 0.035317 TAGCCAGCACACTTGACTGG 59.965 55.000 14.84 14.84 44.01 4.00
577 3981 1.148273 GCACACTTGACTGGTGGGA 59.852 57.895 0.00 0.00 40.20 4.37
579 3983 0.535102 CACACTTGACTGGTGGGACC 60.535 60.000 0.00 0.00 40.20 4.46
602 4006 3.435327 CACAGTAAACGGTGCATGTGTAT 59.565 43.478 4.94 0.00 35.47 2.29
604 4008 3.435327 CAGTAAACGGTGCATGTGTATGT 59.565 43.478 0.00 0.00 36.65 2.29
606 4010 4.868171 AGTAAACGGTGCATGTGTATGTAG 59.132 41.667 0.00 0.00 36.65 2.74
608 4012 4.459390 AACGGTGCATGTGTATGTAGTA 57.541 40.909 0.00 0.00 36.65 1.82
609 4013 4.459390 ACGGTGCATGTGTATGTAGTAA 57.541 40.909 0.00 0.00 36.65 2.24
610 4014 4.430007 ACGGTGCATGTGTATGTAGTAAG 58.570 43.478 0.00 0.00 36.65 2.34
611 4015 4.081862 ACGGTGCATGTGTATGTAGTAAGT 60.082 41.667 0.00 0.00 36.65 2.24
612 4016 5.125900 ACGGTGCATGTGTATGTAGTAAGTA 59.874 40.000 0.00 0.00 36.65 2.24
613 4017 6.037726 CGGTGCATGTGTATGTAGTAAGTAA 58.962 40.000 0.00 0.00 36.65 2.24
624 4028 8.847196 TGTATGTAGTAAGTAATCTACCAGCAG 58.153 37.037 0.00 0.00 36.63 4.24
650 4054 1.771255 ACTTGTCTGAACCAAGGAGCT 59.229 47.619 11.32 0.00 42.84 4.09
651 4055 2.224402 ACTTGTCTGAACCAAGGAGCTC 60.224 50.000 4.71 4.71 42.84 4.09
699 4103 1.253116 CATTTGTGCTTGTGCGATCG 58.747 50.000 11.69 11.69 43.34 3.69
700 4104 1.136000 CATTTGTGCTTGTGCGATCGA 60.136 47.619 21.57 0.59 43.34 3.59
701 4105 1.155889 TTTGTGCTTGTGCGATCGAT 58.844 45.000 21.57 0.00 43.34 3.59
702 4106 0.721154 TTGTGCTTGTGCGATCGATC 59.279 50.000 21.57 15.68 43.34 3.69
703 4107 1.083806 TGTGCTTGTGCGATCGATCC 61.084 55.000 21.57 12.54 43.34 3.36
705 4109 2.247437 GCTTGTGCGATCGATCCCC 61.247 63.158 21.57 11.25 0.00 4.81
707 4111 0.877649 CTTGTGCGATCGATCCCCTG 60.878 60.000 21.57 6.74 0.00 4.45
709 4113 2.839632 TGCGATCGATCCCCTGCT 60.840 61.111 21.57 0.00 0.00 4.24
710 4114 2.423446 GCGATCGATCCCCTGCTT 59.577 61.111 21.57 0.00 0.00 3.91
768 4172 2.772622 CCGCCCTTCCCCACCTAT 60.773 66.667 0.00 0.00 0.00 2.57
990 4403 1.657804 TCCTTCCTCCTCCCTTTCAC 58.342 55.000 0.00 0.00 0.00 3.18
992 4405 1.662686 CTTCCTCCTCCCTTTCACCT 58.337 55.000 0.00 0.00 0.00 4.00
1023 4436 0.983905 ATATACCGGCACCACCACCA 60.984 55.000 0.00 0.00 39.03 4.17
1032 4445 4.676951 CCACCACCACCGCCCAAT 62.677 66.667 0.00 0.00 0.00 3.16
1049 4794 3.118186 CCCAATTCCACATTGCAATCCAT 60.118 43.478 9.53 0.00 0.00 3.41
1084 4830 2.279252 ACCACACACACGAGCGAC 60.279 61.111 0.00 0.00 0.00 5.19
1124 4870 1.506493 GACACAGACAGGCTTGAGTG 58.494 55.000 1.40 10.63 34.12 3.51
1191 4938 4.554036 GCGAGGAGGATGTGGGGC 62.554 72.222 0.00 0.00 0.00 5.80
1197 4944 0.988678 GGAGGATGTGGGGCTACCTT 60.989 60.000 0.00 0.00 41.11 3.50
1200 4947 1.523938 GATGTGGGGCTACCTTCGC 60.524 63.158 0.00 0.00 41.11 4.70
1327 5074 4.596585 CCCACCACCACCACCACC 62.597 72.222 0.00 0.00 0.00 4.61
1328 5075 3.814906 CCACCACCACCACCACCA 61.815 66.667 0.00 0.00 0.00 4.17
1329 5076 2.518349 CACCACCACCACCACCAC 60.518 66.667 0.00 0.00 0.00 4.16
1330 5077 4.183858 ACCACCACCACCACCACG 62.184 66.667 0.00 0.00 0.00 4.94
1331 5078 4.947147 CCACCACCACCACCACGG 62.947 72.222 0.00 0.00 42.50 4.94
1437 5184 4.479993 CTCGCCTTCCCCTGCCTG 62.480 72.222 0.00 0.00 0.00 4.85
1521 5277 2.351835 GCGGCACATGATCGAGTACTAT 60.352 50.000 0.00 0.00 0.00 2.12
1671 5427 4.368543 GACGGCGGGTTCTCGGTT 62.369 66.667 13.24 0.00 0.00 4.44
1674 5430 4.368543 GGCGGGTTCTCGGTTCGT 62.369 66.667 0.00 0.00 0.00 3.85
1677 5433 1.731969 CGGGTTCTCGGTTCGTGTC 60.732 63.158 0.00 0.00 0.00 3.67
1692 5448 1.666311 CGTGTCTCCAACTTCTCGTCC 60.666 57.143 0.00 0.00 0.00 4.79
1800 5556 3.499737 CGCCAGAACCACATCGGC 61.500 66.667 0.00 0.00 39.03 5.54
2137 5912 7.832503 TGTATGTCAGTGTAAAGATGTGATG 57.167 36.000 0.00 0.00 0.00 3.07
2163 5938 3.119029 CGAGTCCCGGATGGTTTTTAGTA 60.119 47.826 0.73 0.00 34.77 1.82
2170 5945 3.288092 GGATGGTTTTTAGTAGCTGGGG 58.712 50.000 0.00 0.00 0.00 4.96
2177 5952 0.618458 TTAGTAGCTGGGGCCAAGTG 59.382 55.000 10.29 0.00 39.73 3.16
2200 5982 7.867403 AGTGTACTTTGCATTGTAAATTCCTTG 59.133 33.333 0.22 0.00 0.00 3.61
2246 6092 7.549839 ACTTGAACATTTTATATGTGCATGCT 58.450 30.769 20.33 0.40 37.41 3.79
2262 6108 8.530804 TGTGCATGCTATCTATATATCTCACT 57.469 34.615 20.33 0.00 0.00 3.41
2264 6110 7.802720 GTGCATGCTATCTATATATCTCACTCG 59.197 40.741 20.33 0.00 0.00 4.18
2265 6111 7.500559 TGCATGCTATCTATATATCTCACTCGT 59.499 37.037 20.33 0.00 0.00 4.18
2273 6119 9.915629 ATCTATATATCTCACTCGTTTTTCACC 57.084 33.333 0.00 0.00 0.00 4.02
2274 6120 9.132923 TCTATATATCTCACTCGTTTTTCACCT 57.867 33.333 0.00 0.00 0.00 4.00
2277 6123 9.751542 ATATATCTCACTCGTTTTTCACCTAAG 57.248 33.333 0.00 0.00 0.00 2.18
2278 6124 5.524971 TCTCACTCGTTTTTCACCTAAGA 57.475 39.130 0.00 0.00 0.00 2.10
2279 6125 5.909477 TCTCACTCGTTTTTCACCTAAGAA 58.091 37.500 0.00 0.00 0.00 2.52
2280 6126 6.342906 TCTCACTCGTTTTTCACCTAAGAAA 58.657 36.000 0.00 0.00 35.82 2.52
2281 6127 6.990349 TCTCACTCGTTTTTCACCTAAGAAAT 59.010 34.615 0.00 0.00 37.35 2.17
2282 6128 8.145767 TCTCACTCGTTTTTCACCTAAGAAATA 58.854 33.333 0.00 0.00 37.35 1.40
2283 6129 8.665643 TCACTCGTTTTTCACCTAAGAAATAA 57.334 30.769 0.00 0.00 37.35 1.40
2284 6130 9.111613 TCACTCGTTTTTCACCTAAGAAATAAA 57.888 29.630 0.00 0.00 37.35 1.40
2285 6131 9.893305 CACTCGTTTTTCACCTAAGAAATAAAT 57.107 29.630 0.00 0.00 37.35 1.40
2318 6164 6.070995 ACTCGTTTGAAGTACTATTCCCATCA 60.071 38.462 0.00 0.00 0.00 3.07
2337 6183 7.185120 TCCCATCATATTCATATCCAAGTCCAT 59.815 37.037 0.00 0.00 0.00 3.41
2338 6184 7.284716 CCCATCATATTCATATCCAAGTCCATG 59.715 40.741 0.00 0.00 0.00 3.66
2340 6186 7.333779 TCATATTCATATCCAAGTCCATGGT 57.666 36.000 12.58 0.00 41.46 3.55
2342 6188 5.651612 ATTCATATCCAAGTCCATGGTGA 57.348 39.130 12.58 1.39 41.46 4.02
2344 6190 5.651612 TCATATCCAAGTCCATGGTGAAT 57.348 39.130 12.58 0.00 41.46 2.57
2345 6191 5.379187 TCATATCCAAGTCCATGGTGAATG 58.621 41.667 12.58 7.08 41.46 2.67
2346 6192 3.744940 ATCCAAGTCCATGGTGAATGT 57.255 42.857 12.58 0.00 41.46 2.71
2347 6193 4.860802 ATCCAAGTCCATGGTGAATGTA 57.139 40.909 12.58 0.00 41.46 2.29
2348 6194 4.860802 TCCAAGTCCATGGTGAATGTAT 57.139 40.909 12.58 0.00 41.46 2.29
2349 6195 5.191727 TCCAAGTCCATGGTGAATGTATT 57.808 39.130 12.58 0.00 41.46 1.89
2350 6196 5.192927 TCCAAGTCCATGGTGAATGTATTC 58.807 41.667 12.58 0.00 41.46 1.75
2351 6197 5.044919 TCCAAGTCCATGGTGAATGTATTCT 60.045 40.000 12.58 0.00 41.46 2.40
2354 6200 7.503566 CCAAGTCCATGGTGAATGTATTCTATT 59.496 37.037 12.58 0.00 37.67 1.73
2358 6204 8.131100 GTCCATGGTGAATGTATTCTATTTGTG 58.869 37.037 12.58 0.00 37.67 3.33
2360 6206 7.916977 CCATGGTGAATGTATTCTATTTGTGTG 59.083 37.037 2.57 0.00 37.67 3.82
2363 6209 9.241919 TGGTGAATGTATTCTATTTGTGTGAAT 57.758 29.630 6.21 0.00 37.67 2.57
2381 6446 9.868277 TGTGTGAATTATTTTTGGGAATACATC 57.132 29.630 0.00 0.00 0.00 3.06
2399 6464 0.955428 TCAAAGATGCACAGACGGCC 60.955 55.000 0.00 0.00 0.00 6.13
2415 6480 4.848685 CCCTACGGCACATGTACC 57.151 61.111 4.87 4.87 0.00 3.34
2427 6496 2.228822 CACATGTACCTGGAAAACCAGC 59.771 50.000 10.37 0.00 36.57 4.85
2439 6508 2.009681 AAACCAGCCCCCAGTTTTAG 57.990 50.000 0.00 0.00 29.64 1.85
2461 6530 2.507407 TATTTGAGTGGAACCAGCCC 57.493 50.000 0.00 0.00 37.80 5.19
2474 6543 1.823899 CAGCCCCCGAATTGGTAGC 60.824 63.158 0.00 0.00 35.15 3.58
2476 6545 2.904905 CCCCCGAATTGGTAGCGA 59.095 61.111 0.00 0.00 35.15 4.93
2499 6686 7.148474 GCGAGAATATGGTTTTCACTTTCAGTA 60.148 37.037 0.00 0.00 0.00 2.74
2529 6716 5.738118 TCGAAATTTCAGTAACGTTGGTT 57.262 34.783 17.99 0.00 40.20 3.67
2530 6717 6.121613 TCGAAATTTCAGTAACGTTGGTTT 57.878 33.333 17.99 1.56 37.58 3.27
2550 6766 6.316140 TGGTTTCGGTCAGAATATTTCATCAG 59.684 38.462 0.00 0.00 38.86 2.90
2646 6863 4.262164 CCAAGTGAAAATTCTGGTCCCTTG 60.262 45.833 0.00 0.00 0.00 3.61
2655 6872 0.611896 CTGGTCCCTTGGCCGAAATT 60.612 55.000 0.00 0.00 0.00 1.82
2660 6877 3.007074 GGTCCCTTGGCCGAAATTAAAAA 59.993 43.478 0.00 0.00 0.00 1.94
2699 6918 9.911788 ATTCAGTGAAAATCAGTAATATCACCT 57.088 29.630 10.14 0.00 36.04 4.00
2700 6919 9.739276 TTCAGTGAAAATCAGTAATATCACCTT 57.261 29.630 2.20 0.00 36.04 3.50
2701 6920 9.739276 TCAGTGAAAATCAGTAATATCACCTTT 57.261 29.630 0.00 0.00 36.04 3.11
2702 6921 9.994432 CAGTGAAAATCAGTAATATCACCTTTC 57.006 33.333 0.00 0.00 36.04 2.62
2703 6922 9.739276 AGTGAAAATCAGTAATATCACCTTTCA 57.261 29.630 0.00 0.00 36.04 2.69
2704 6923 9.774742 GTGAAAATCAGTAATATCACCTTTCAC 57.225 33.333 7.77 7.77 41.36 3.18
2705 6924 8.956426 TGAAAATCAGTAATATCACCTTTCACC 58.044 33.333 0.00 0.00 0.00 4.02
2706 6925 9.178758 GAAAATCAGTAATATCACCTTTCACCT 57.821 33.333 0.00 0.00 0.00 4.00
2715 6934 1.950909 CACCTTTCACCTACGCCAAAA 59.049 47.619 0.00 0.00 0.00 2.44
2720 6939 5.479027 ACCTTTCACCTACGCCAAAAATATT 59.521 36.000 0.00 0.00 0.00 1.28
2721 6940 5.804979 CCTTTCACCTACGCCAAAAATATTG 59.195 40.000 0.00 0.00 0.00 1.90
2722 6941 4.364415 TCACCTACGCCAAAAATATTGC 57.636 40.909 0.00 0.00 0.00 3.56
2723 6942 4.013728 TCACCTACGCCAAAAATATTGCT 58.986 39.130 0.00 0.00 0.00 3.91
2724 6943 4.104776 CACCTACGCCAAAAATATTGCTG 58.895 43.478 0.00 0.00 0.00 4.41
2725 6944 4.013728 ACCTACGCCAAAAATATTGCTGA 58.986 39.130 0.00 0.00 0.00 4.26
2726 6945 4.461081 ACCTACGCCAAAAATATTGCTGAA 59.539 37.500 0.00 0.00 0.00 3.02
2727 6946 5.047660 ACCTACGCCAAAAATATTGCTGAAA 60.048 36.000 0.00 0.00 0.00 2.69
2728 6947 5.288472 CCTACGCCAAAAATATTGCTGAAAC 59.712 40.000 0.00 0.00 0.00 2.78
2729 6948 3.993736 ACGCCAAAAATATTGCTGAAACC 59.006 39.130 0.00 0.00 0.00 3.27
2730 6949 3.060628 CGCCAAAAATATTGCTGAAACCG 59.939 43.478 0.00 0.00 0.00 4.44
2731 6950 4.241681 GCCAAAAATATTGCTGAAACCGA 58.758 39.130 0.00 0.00 0.00 4.69
2732 6951 4.327087 GCCAAAAATATTGCTGAAACCGAG 59.673 41.667 0.00 0.00 0.00 4.63
2745 6964 1.919240 AACCGAGATTCAAAACCCCC 58.081 50.000 0.00 0.00 0.00 5.40
2750 6969 3.306019 CCGAGATTCAAAACCCCCAAAAG 60.306 47.826 0.00 0.00 0.00 2.27
2771 6990 4.376450 GTGCAACTTCTAAACAGTCTCG 57.624 45.455 0.00 0.00 0.00 4.04
2772 6991 4.049186 GTGCAACTTCTAAACAGTCTCGA 58.951 43.478 0.00 0.00 0.00 4.04
2773 6992 4.149046 GTGCAACTTCTAAACAGTCTCGAG 59.851 45.833 5.93 5.93 0.00 4.04
2774 6993 3.675698 GCAACTTCTAAACAGTCTCGAGG 59.324 47.826 13.56 0.00 0.00 4.63
2777 6996 3.896272 ACTTCTAAACAGTCTCGAGGGTT 59.104 43.478 13.56 11.88 0.00 4.11
2778 6997 4.344390 ACTTCTAAACAGTCTCGAGGGTTT 59.656 41.667 23.88 23.88 37.28 3.27
2779 6998 4.950205 TCTAAACAGTCTCGAGGGTTTT 57.050 40.909 24.87 16.48 35.33 2.43
2780 6999 5.286267 TCTAAACAGTCTCGAGGGTTTTT 57.714 39.130 24.87 16.74 35.33 1.94
2781 7000 5.295152 TCTAAACAGTCTCGAGGGTTTTTC 58.705 41.667 24.87 6.47 35.33 2.29
2782 7001 3.553828 AACAGTCTCGAGGGTTTTTCA 57.446 42.857 13.56 0.00 0.00 2.69
2783 7002 2.835027 ACAGTCTCGAGGGTTTTTCAC 58.165 47.619 13.56 0.12 0.00 3.18
2786 7005 3.877508 CAGTCTCGAGGGTTTTTCACTTT 59.122 43.478 13.56 0.00 0.00 2.66
2787 7006 4.335594 CAGTCTCGAGGGTTTTTCACTTTT 59.664 41.667 13.56 0.00 0.00 2.27
2788 7007 4.575236 AGTCTCGAGGGTTTTTCACTTTTC 59.425 41.667 13.56 0.00 0.00 2.29
2789 7008 3.558418 TCTCGAGGGTTTTTCACTTTTCG 59.442 43.478 13.56 0.00 0.00 3.46
2790 7009 2.614983 TCGAGGGTTTTTCACTTTTCGG 59.385 45.455 0.00 0.00 0.00 4.30
2791 7010 2.614983 CGAGGGTTTTTCACTTTTCGGA 59.385 45.455 0.00 0.00 0.00 4.55
2792 7011 3.547413 CGAGGGTTTTTCACTTTTCGGAC 60.547 47.826 0.00 0.00 0.00 4.79
2793 7012 2.356695 AGGGTTTTTCACTTTTCGGACG 59.643 45.455 0.00 0.00 0.00 4.79
2796 7015 3.427909 GGTTTTTCACTTTTCGGACGGTT 60.428 43.478 0.00 0.00 0.00 4.44
2815 7034 4.346129 GGTTTGCTGAGATGCTTTAATCG 58.654 43.478 0.00 0.00 0.00 3.34
2820 7039 5.847304 TGCTGAGATGCTTTAATCGACTAT 58.153 37.500 0.00 0.00 0.00 2.12
2821 7040 6.981722 TGCTGAGATGCTTTAATCGACTATA 58.018 36.000 0.00 0.00 0.00 1.31
2822 7041 7.087007 TGCTGAGATGCTTTAATCGACTATAG 58.913 38.462 0.00 0.00 0.00 1.31
2823 7042 6.529829 GCTGAGATGCTTTAATCGACTATAGG 59.470 42.308 4.43 0.00 0.00 2.57
2824 7043 7.526142 TGAGATGCTTTAATCGACTATAGGT 57.474 36.000 4.43 0.00 0.00 3.08
2825 7044 7.371159 TGAGATGCTTTAATCGACTATAGGTG 58.629 38.462 4.43 0.00 0.00 4.00
2826 7045 6.159988 AGATGCTTTAATCGACTATAGGTGC 58.840 40.000 4.43 0.00 0.00 5.01
2827 7046 5.531122 TGCTTTAATCGACTATAGGTGCT 57.469 39.130 4.43 0.00 0.00 4.40
2828 7047 5.914033 TGCTTTAATCGACTATAGGTGCTT 58.086 37.500 4.43 0.00 0.00 3.91
2833 7052 1.136305 TCGACTATAGGTGCTTGTGCC 59.864 52.381 4.43 0.00 38.71 5.01
2836 7055 3.343617 GACTATAGGTGCTTGTGCCAAA 58.656 45.455 4.43 0.00 38.71 3.28
2841 7060 1.735360 GTGCTTGTGCCAAAGAGCA 59.265 52.632 0.00 0.00 42.36 4.26
2842 7061 0.102844 GTGCTTGTGCCAAAGAGCAA 59.897 50.000 0.00 0.00 46.19 3.91
2861 7080 5.508124 GCAATCGCTAGATACAGACAATC 57.492 43.478 0.00 0.00 35.74 2.67
2862 7081 4.984785 GCAATCGCTAGATACAGACAATCA 59.015 41.667 0.00 0.00 35.74 2.57
2863 7082 5.636965 GCAATCGCTAGATACAGACAATCAT 59.363 40.000 0.00 0.00 35.74 2.45
2864 7083 6.146837 GCAATCGCTAGATACAGACAATCATT 59.853 38.462 0.00 0.00 35.74 2.57
2893 7112 6.765512 AGAGCTGTATTTTCTTCTCCATTAGC 59.234 38.462 0.00 0.00 0.00 3.09
2900 7119 7.968014 ATTTTCTTCTCCATTAGCAGGAAAT 57.032 32.000 0.00 0.00 33.32 2.17
2901 7120 7.396540 TTTTCTTCTCCATTAGCAGGAAATC 57.603 36.000 0.00 0.00 34.08 2.17
2904 7123 4.156455 TCTCCATTAGCAGGAAATCCAC 57.844 45.455 1.67 0.00 38.89 4.02
2928 7147 1.884579 CCCTTGCATGGCTGATGATAC 59.115 52.381 13.15 0.00 33.31 2.24
2937 7156 5.563475 GCATGGCTGATGATACATGGTTAAC 60.563 44.000 0.00 0.00 40.66 2.01
2967 7186 7.599245 TCTTCTAATCTCCTCGTGAAGAAAAAC 59.401 37.037 0.00 0.00 37.53 2.43
2970 7189 6.693315 AATCTCCTCGTGAAGAAAAACAAA 57.307 33.333 0.00 0.00 0.00 2.83
2996 7216 1.928868 TCATCTGCACTGTCCTCTGA 58.071 50.000 0.00 0.00 0.00 3.27
2997 7217 1.547820 TCATCTGCACTGTCCTCTGAC 59.452 52.381 0.00 0.00 42.12 3.51
2999 7219 0.964700 TCTGCACTGTCCTCTGACTG 59.035 55.000 0.00 0.00 43.76 3.51
3000 7220 0.037512 CTGCACTGTCCTCTGACTGG 60.038 60.000 4.91 0.00 42.80 4.00
3001 7221 1.375268 GCACTGTCCTCTGACTGGC 60.375 63.158 4.91 2.37 42.80 4.85
3002 7222 1.825281 GCACTGTCCTCTGACTGGCT 61.825 60.000 4.91 0.00 42.80 4.75
3003 7223 1.550327 CACTGTCCTCTGACTGGCTA 58.450 55.000 4.91 0.00 42.80 3.93
3004 7224 1.203523 CACTGTCCTCTGACTGGCTAC 59.796 57.143 4.91 0.00 42.80 3.58
3005 7225 0.453793 CTGTCCTCTGACTGGCTACG 59.546 60.000 0.00 0.00 42.28 3.51
3006 7226 0.251209 TGTCCTCTGACTGGCTACGT 60.251 55.000 0.00 0.00 42.28 3.57
3007 7227 0.171455 GTCCTCTGACTGGCTACGTG 59.829 60.000 0.00 0.00 38.53 4.49
3008 7228 0.251209 TCCTCTGACTGGCTACGTGT 60.251 55.000 0.00 0.00 0.00 4.49
3009 7229 0.603569 CCTCTGACTGGCTACGTGTT 59.396 55.000 0.00 0.00 0.00 3.32
3010 7230 1.402984 CCTCTGACTGGCTACGTGTTC 60.403 57.143 0.00 0.00 0.00 3.18
3011 7231 1.542030 CTCTGACTGGCTACGTGTTCT 59.458 52.381 0.00 0.00 0.00 3.01
3012 7232 1.540267 TCTGACTGGCTACGTGTTCTC 59.460 52.381 0.00 0.00 0.00 2.87
3013 7233 1.269723 CTGACTGGCTACGTGTTCTCA 59.730 52.381 0.00 0.00 0.00 3.27
3014 7234 1.269723 TGACTGGCTACGTGTTCTCAG 59.730 52.381 0.00 1.56 0.00 3.35
3015 7235 1.269998 GACTGGCTACGTGTTCTCAGT 59.730 52.381 0.00 4.97 38.05 3.41
3016 7236 2.486982 GACTGGCTACGTGTTCTCAGTA 59.513 50.000 0.00 0.00 35.87 2.74
3017 7237 3.090037 ACTGGCTACGTGTTCTCAGTAT 58.910 45.455 0.00 0.00 34.24 2.12
3018 7238 3.119459 ACTGGCTACGTGTTCTCAGTATG 60.119 47.826 0.00 0.00 34.24 2.39
3019 7239 2.194271 GGCTACGTGTTCTCAGTATGC 58.806 52.381 0.00 0.00 34.76 3.14
3020 7240 2.194271 GCTACGTGTTCTCAGTATGCC 58.806 52.381 0.00 0.00 34.76 4.40
3021 7241 2.810650 CTACGTGTTCTCAGTATGCCC 58.189 52.381 0.00 0.00 34.76 5.36
3022 7242 1.267121 ACGTGTTCTCAGTATGCCCT 58.733 50.000 0.00 0.00 34.76 5.19
3023 7243 1.204941 ACGTGTTCTCAGTATGCCCTC 59.795 52.381 0.00 0.00 34.76 4.30
3024 7244 1.478510 CGTGTTCTCAGTATGCCCTCT 59.521 52.381 0.00 0.00 34.76 3.69
3025 7245 2.736719 CGTGTTCTCAGTATGCCCTCTG 60.737 54.545 0.00 0.00 34.76 3.35
3026 7246 2.234908 GTGTTCTCAGTATGCCCTCTGT 59.765 50.000 0.00 0.00 34.76 3.41
3027 7247 2.497675 TGTTCTCAGTATGCCCTCTGTC 59.502 50.000 0.00 0.00 34.76 3.51
3028 7248 2.763448 GTTCTCAGTATGCCCTCTGTCT 59.237 50.000 0.00 0.00 34.76 3.41
3120 7340 4.137872 GCAGCGGCGGGTACAGTA 62.138 66.667 9.78 0.00 0.00 2.74
3127 7347 2.897972 CGGGTACAGTACAGGGCC 59.102 66.667 12.89 0.00 0.00 5.80
3163 7383 2.548480 GAGCAGCCCCGATTTGTATAAC 59.452 50.000 0.00 0.00 0.00 1.89
3216 7436 1.574428 CAAAGCTGTGCCCACGTAC 59.426 57.895 0.00 0.00 0.00 3.67
3218 7438 0.250727 AAAGCTGTGCCCACGTACAT 60.251 50.000 0.00 0.00 33.83 2.29
3278 7498 7.374272 AGGATCATAGTATATATCGTGCATGC 58.626 38.462 11.82 11.82 0.00 4.06
3279 7499 7.232330 AGGATCATAGTATATATCGTGCATGCT 59.768 37.037 20.33 0.00 0.00 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.663602 CGAGCATGCGGTATATCTCAAC 59.336 50.000 13.01 0.00 0.00 3.18
3 4 1.886542 ACGAGCATGCGGTATATCTCA 59.113 47.619 13.01 0.00 35.12 3.27
4 5 2.254459 CACGAGCATGCGGTATATCTC 58.746 52.381 13.01 0.24 35.12 2.75
5 6 1.067565 CCACGAGCATGCGGTATATCT 60.068 52.381 13.01 0.00 35.12 1.98
6 7 1.350193 CCACGAGCATGCGGTATATC 58.650 55.000 13.01 1.85 35.12 1.63
50 51 3.656045 GGGTGGCGGTTTGACGTG 61.656 66.667 0.00 0.00 35.98 4.49
51 52 4.941309 GGGGTGGCGGTTTGACGT 62.941 66.667 0.00 0.00 35.98 4.34
127 128 0.321996 GGATTAGAGATGGGCCGGAC 59.678 60.000 5.05 0.00 0.00 4.79
158 159 1.008995 CCGGAAAAAGTGTGCGTGG 60.009 57.895 0.00 0.00 0.00 4.94
179 180 1.160137 GCAATAATGCGAGGGCTAGG 58.840 55.000 0.00 0.00 43.83 3.02
212 213 0.177604 CTCTCTGGTGATCCTGTGCC 59.822 60.000 0.00 0.00 34.80 5.01
231 232 3.189285 CAATGATCGTGGCCATTTTTCC 58.811 45.455 9.72 0.00 31.25 3.13
340 342 0.383231 CATCCCCTACGTACGTGTCC 59.617 60.000 30.25 0.00 0.00 4.02
362 364 3.246619 GTTGTTCGTGTGAGATCTCCTC 58.753 50.000 20.03 13.12 42.30 3.71
452 3427 4.093998 AGAAGAAACAACTGCATGCTATCG 59.906 41.667 20.33 7.69 0.00 2.92
453 3428 5.106396 ACAGAAGAAACAACTGCATGCTATC 60.106 40.000 20.33 6.53 35.38 2.08
454 3429 4.763793 ACAGAAGAAACAACTGCATGCTAT 59.236 37.500 20.33 3.57 35.38 2.97
465 3440 2.763448 CCAACCCCAACAGAAGAAACAA 59.237 45.455 0.00 0.00 0.00 2.83
494 3478 8.857694 ACTTTCGGTAAGAATTAATCCTTCAA 57.142 30.769 1.12 0.00 38.86 2.69
530 3934 7.815068 GCTACGTATCTATCTTTGGATGAATGT 59.185 37.037 0.00 0.00 33.71 2.71
547 3951 1.927174 CAAGTGTGCTGGCTACGTATC 59.073 52.381 0.00 0.00 0.00 2.24
548 3952 1.548719 TCAAGTGTGCTGGCTACGTAT 59.451 47.619 0.00 0.00 0.00 3.06
549 3953 0.963225 TCAAGTGTGCTGGCTACGTA 59.037 50.000 0.00 0.00 0.00 3.57
550 3954 0.600255 GTCAAGTGTGCTGGCTACGT 60.600 55.000 0.00 0.00 0.00 3.57
551 3955 0.319900 AGTCAAGTGTGCTGGCTACG 60.320 55.000 0.00 0.00 0.00 3.51
552 3956 1.151668 CAGTCAAGTGTGCTGGCTAC 58.848 55.000 0.00 0.00 0.00 3.58
553 3957 0.035317 CCAGTCAAGTGTGCTGGCTA 59.965 55.000 10.18 0.00 40.10 3.93
554 3958 1.228063 CCAGTCAAGTGTGCTGGCT 60.228 57.895 10.18 0.00 40.10 4.75
555 3959 1.526917 ACCAGTCAAGTGTGCTGGC 60.527 57.895 17.96 0.00 45.49 4.85
577 3981 0.109723 ATGCACCGTTTACTGTGGGT 59.890 50.000 6.57 0.00 32.67 4.51
579 3983 1.069296 CACATGCACCGTTTACTGTGG 60.069 52.381 5.15 0.00 32.67 4.17
582 3986 3.435327 ACATACACATGCACCGTTTACTG 59.565 43.478 0.00 0.00 35.39 2.74
602 4006 7.067129 CAGACTGCTGGTAGATTACTTACTACA 59.933 40.741 0.00 0.00 40.19 2.74
604 4008 7.344134 TCAGACTGCTGGTAGATTACTTACTA 58.656 38.462 0.00 0.00 42.53 1.82
606 4010 6.452494 TCAGACTGCTGGTAGATTACTTAC 57.548 41.667 0.00 0.00 42.53 2.34
608 4012 5.482175 AGTTCAGACTGCTGGTAGATTACTT 59.518 40.000 0.00 0.00 42.53 2.24
609 4013 5.020132 AGTTCAGACTGCTGGTAGATTACT 58.980 41.667 0.00 0.00 42.53 2.24
610 4014 5.331876 AGTTCAGACTGCTGGTAGATTAC 57.668 43.478 0.00 0.00 42.53 1.89
611 4015 5.246203 ACAAGTTCAGACTGCTGGTAGATTA 59.754 40.000 0.00 0.00 42.53 1.75
612 4016 4.040952 ACAAGTTCAGACTGCTGGTAGATT 59.959 41.667 0.00 0.00 42.53 2.40
613 4017 3.580458 ACAAGTTCAGACTGCTGGTAGAT 59.420 43.478 0.00 0.00 42.53 1.98
624 4028 3.561725 CCTTGGTTCAGACAAGTTCAGAC 59.438 47.826 0.00 0.00 42.84 3.51
650 4054 1.676529 CTTCGCTATCCTTCTGACCGA 59.323 52.381 0.00 0.00 0.00 4.69
651 4055 1.676529 TCTTCGCTATCCTTCTGACCG 59.323 52.381 0.00 0.00 0.00 4.79
707 4111 3.569902 GCAAAGCAATGCCCAAGC 58.430 55.556 0.00 0.00 40.49 4.01
751 4155 2.772622 ATAGGTGGGGAAGGGCGG 60.773 66.667 0.00 0.00 0.00 6.13
752 4156 1.345715 AAGATAGGTGGGGAAGGGCG 61.346 60.000 0.00 0.00 0.00 6.13
753 4157 0.474614 GAAGATAGGTGGGGAAGGGC 59.525 60.000 0.00 0.00 0.00 5.19
754 4158 1.141185 GGAAGATAGGTGGGGAAGGG 58.859 60.000 0.00 0.00 0.00 3.95
966 4379 0.990818 AGGGAGGAGGAAGGAATGGC 60.991 60.000 0.00 0.00 0.00 4.40
990 4403 2.621998 CGGTATATATAGGCACGGGAGG 59.378 54.545 0.00 0.00 0.00 4.30
992 4405 2.658285 CCGGTATATATAGGCACGGGA 58.342 52.381 13.33 0.00 36.45 5.14
1023 4436 1.887344 GCAATGTGGAATTGGGCGGT 61.887 55.000 0.67 0.00 0.00 5.68
1025 4438 0.037512 TTGCAATGTGGAATTGGGCG 60.038 50.000 0.00 0.00 0.00 6.13
1032 4445 1.134753 GCGATGGATTGCAATGTGGAA 59.865 47.619 18.59 0.00 37.15 3.53
1084 4830 0.894141 CTGTGTCCCTGACTCTCTGG 59.106 60.000 0.00 0.00 35.51 3.86
1124 4870 1.305549 TCGTACCACCTTCCCCTCC 60.306 63.158 0.00 0.00 0.00 4.30
1191 4938 1.872679 GAAGACGGCGCGAAGGTAG 60.873 63.158 12.10 0.00 0.00 3.18
1197 4944 1.805539 CATGAAGAAGACGGCGCGA 60.806 57.895 12.10 0.00 0.00 5.87
1200 4947 0.302890 GCATCATGAAGAAGACGGCG 59.697 55.000 4.80 4.80 0.00 6.46
1203 4950 1.001624 TGCGCATCATGAAGAAGACG 58.998 50.000 5.66 0.00 0.00 4.18
1497 5253 4.889856 TCGATCATGTGCCGCGGG 62.890 66.667 29.38 10.00 0.00 6.13
1671 5427 1.266175 GACGAGAAGTTGGAGACACGA 59.734 52.381 0.00 0.00 42.67 4.35
1674 5430 0.596577 CGGACGAGAAGTTGGAGACA 59.403 55.000 0.00 0.00 39.83 3.41
1677 5433 0.454620 CGTCGGACGAGAAGTTGGAG 60.455 60.000 25.29 0.00 46.05 3.86
1800 5556 2.683933 AGGTGGTACGGGAGCAGG 60.684 66.667 0.00 0.00 35.85 4.85
1813 5569 4.785453 GGCGGCTTCCTGGAGGTG 62.785 72.222 7.71 2.11 36.34 4.00
1898 5654 2.033801 CGTCCAAGCAATCATGGAATCC 59.966 50.000 0.00 0.00 46.78 3.01
2163 5938 1.427072 AAGTACACTTGGCCCCAGCT 61.427 55.000 0.00 0.00 39.73 4.24
2177 5952 9.855021 ATACAAGGAATTTACAATGCAAAGTAC 57.145 29.630 0.00 0.00 0.00 2.73
2255 6101 6.097915 TCTTAGGTGAAAAACGAGTGAGAT 57.902 37.500 0.00 0.00 0.00 2.75
2258 6104 8.665643 TTATTTCTTAGGTGAAAAACGAGTGA 57.334 30.769 0.00 0.00 39.08 3.41
2286 6132 9.953697 GAATAGTACTTCAAACGAGTGAGATAT 57.046 33.333 0.00 0.00 0.00 1.63
2287 6133 8.404000 GGAATAGTACTTCAAACGAGTGAGATA 58.596 37.037 0.00 0.00 0.00 1.98
2288 6134 7.259161 GGAATAGTACTTCAAACGAGTGAGAT 58.741 38.462 0.00 0.00 0.00 2.75
2289 6135 6.349944 GGGAATAGTACTTCAAACGAGTGAGA 60.350 42.308 0.00 0.00 0.00 3.27
2290 6136 5.805994 GGGAATAGTACTTCAAACGAGTGAG 59.194 44.000 0.00 0.00 0.00 3.51
2291 6137 5.244402 TGGGAATAGTACTTCAAACGAGTGA 59.756 40.000 0.00 0.00 0.00 3.41
2292 6138 5.475719 TGGGAATAGTACTTCAAACGAGTG 58.524 41.667 0.00 0.00 0.00 3.51
2293 6139 5.733620 TGGGAATAGTACTTCAAACGAGT 57.266 39.130 0.00 0.00 0.00 4.18
2294 6140 6.338146 TGATGGGAATAGTACTTCAAACGAG 58.662 40.000 0.00 0.00 0.00 4.18
2295 6141 6.288941 TGATGGGAATAGTACTTCAAACGA 57.711 37.500 0.00 0.00 0.00 3.85
2296 6142 8.833231 ATATGATGGGAATAGTACTTCAAACG 57.167 34.615 0.00 0.00 0.00 3.60
2318 6164 7.333779 TCACCATGGACTTGGATATGAATAT 57.666 36.000 21.47 0.00 39.25 1.28
2328 6174 5.195940 AGAATACATTCACCATGGACTTGG 58.804 41.667 21.47 7.33 39.23 3.61
2330 6176 8.906867 CAAATAGAATACATTCACCATGGACTT 58.093 33.333 21.47 0.00 39.23 3.01
2332 6178 8.131100 CACAAATAGAATACATTCACCATGGAC 58.869 37.037 21.47 0.00 39.23 4.02
2333 6179 7.833682 ACACAAATAGAATACATTCACCATGGA 59.166 33.333 21.47 0.00 39.23 3.41
2334 6180 7.916977 CACACAAATAGAATACATTCACCATGG 59.083 37.037 11.19 11.19 39.23 3.66
2337 6183 8.628630 TTCACACAAATAGAATACATTCACCA 57.371 30.769 4.85 0.00 39.23 4.17
2363 6209 9.598517 GCATCTTTGATGTATTCCCAAAAATAA 57.401 29.630 8.98 0.00 30.56 1.40
2365 6211 7.550196 GTGCATCTTTGATGTATTCCCAAAAAT 59.450 33.333 8.98 0.00 30.56 1.82
2366 6212 6.873076 GTGCATCTTTGATGTATTCCCAAAAA 59.127 34.615 8.98 0.00 30.56 1.94
2371 6217 4.883585 TCTGTGCATCTTTGATGTATTCCC 59.116 41.667 8.98 0.00 0.00 3.97
2372 6218 5.503031 CGTCTGTGCATCTTTGATGTATTCC 60.503 44.000 8.98 0.00 0.00 3.01
2373 6438 5.496387 CGTCTGTGCATCTTTGATGTATTC 58.504 41.667 8.98 0.00 0.00 1.75
2380 6445 0.955428 GGCCGTCTGTGCATCTTTGA 60.955 55.000 0.00 0.00 0.00 2.69
2381 6446 1.503542 GGCCGTCTGTGCATCTTTG 59.496 57.895 0.00 0.00 0.00 2.77
2427 6496 6.295067 CCACTCAAATAAACTAAAACTGGGGG 60.295 42.308 0.00 0.00 0.00 5.40
2439 6508 3.056821 GGGCTGGTTCCACTCAAATAAAC 60.057 47.826 0.00 0.00 0.00 2.01
2461 6530 2.240493 ATTCTCGCTACCAATTCGGG 57.760 50.000 0.00 0.00 40.22 5.14
2516 6703 2.203401 TGACCGAAACCAACGTTACTG 58.797 47.619 0.00 0.00 0.00 2.74
2517 6704 2.101249 TCTGACCGAAACCAACGTTACT 59.899 45.455 0.00 0.00 0.00 2.24
2519 6706 2.886862 TCTGACCGAAACCAACGTTA 57.113 45.000 0.00 0.00 0.00 3.18
2523 6710 6.249035 TGAAATATTCTGACCGAAACCAAC 57.751 37.500 0.00 0.00 34.79 3.77
2525 6712 6.176896 TGATGAAATATTCTGACCGAAACCA 58.823 36.000 0.00 0.00 34.79 3.67
2529 6716 6.878317 AGACTGATGAAATATTCTGACCGAA 58.122 36.000 0.00 0.00 35.78 4.30
2530 6717 6.471233 AGACTGATGAAATATTCTGACCGA 57.529 37.500 0.00 0.00 0.00 4.69
2623 6840 3.500343 AGGGACCAGAATTTTCACTTGG 58.500 45.455 0.00 0.00 0.00 3.61
2636 6853 0.611896 AATTTCGGCCAAGGGACCAG 60.612 55.000 2.24 0.00 0.00 4.00
2677 6896 9.739276 TGAAAGGTGATATTACTGATTTTCACT 57.261 29.630 11.85 0.00 33.52 3.41
2696 6915 2.351706 TTTTGGCGTAGGTGAAAGGT 57.648 45.000 0.00 0.00 0.00 3.50
2697 6916 3.934457 ATTTTTGGCGTAGGTGAAAGG 57.066 42.857 0.00 0.00 0.00 3.11
2699 6918 5.047660 AGCAATATTTTTGGCGTAGGTGAAA 60.048 36.000 0.00 0.00 0.00 2.69
2700 6919 4.461081 AGCAATATTTTTGGCGTAGGTGAA 59.539 37.500 0.00 0.00 0.00 3.18
2701 6920 4.013728 AGCAATATTTTTGGCGTAGGTGA 58.986 39.130 0.00 0.00 0.00 4.02
2702 6921 4.104776 CAGCAATATTTTTGGCGTAGGTG 58.895 43.478 0.00 0.00 0.00 4.00
2703 6922 4.013728 TCAGCAATATTTTTGGCGTAGGT 58.986 39.130 0.00 0.00 0.00 3.08
2704 6923 4.630894 TCAGCAATATTTTTGGCGTAGG 57.369 40.909 0.00 0.00 0.00 3.18
2705 6924 5.288472 GGTTTCAGCAATATTTTTGGCGTAG 59.712 40.000 0.00 0.00 0.00 3.51
2706 6925 5.164954 GGTTTCAGCAATATTTTTGGCGTA 58.835 37.500 0.00 0.00 0.00 4.42
2715 6934 6.757897 TTGAATCTCGGTTTCAGCAATATT 57.242 33.333 0.00 0.00 34.76 1.28
2720 6939 3.004315 GGTTTTGAATCTCGGTTTCAGCA 59.996 43.478 0.00 0.00 34.76 4.41
2721 6940 3.565516 GGTTTTGAATCTCGGTTTCAGC 58.434 45.455 0.00 0.00 34.76 4.26
2722 6941 3.057526 GGGGTTTTGAATCTCGGTTTCAG 60.058 47.826 0.00 0.00 34.76 3.02
2723 6942 2.888414 GGGGTTTTGAATCTCGGTTTCA 59.112 45.455 0.00 0.00 0.00 2.69
2724 6943 2.230508 GGGGGTTTTGAATCTCGGTTTC 59.769 50.000 0.00 0.00 0.00 2.78
2725 6944 2.244695 GGGGGTTTTGAATCTCGGTTT 58.755 47.619 0.00 0.00 0.00 3.27
2726 6945 1.146152 TGGGGGTTTTGAATCTCGGTT 59.854 47.619 0.00 0.00 0.00 4.44
2727 6946 0.774908 TGGGGGTTTTGAATCTCGGT 59.225 50.000 0.00 0.00 0.00 4.69
2728 6947 1.917872 TTGGGGGTTTTGAATCTCGG 58.082 50.000 0.00 0.00 0.00 4.63
2729 6948 3.320826 ACTTTTGGGGGTTTTGAATCTCG 59.679 43.478 0.00 0.00 0.00 4.04
2730 6949 4.631131 CACTTTTGGGGGTTTTGAATCTC 58.369 43.478 0.00 0.00 0.00 2.75
2731 6950 3.181455 GCACTTTTGGGGGTTTTGAATCT 60.181 43.478 0.00 0.00 0.00 2.40
2732 6951 3.138304 GCACTTTTGGGGGTTTTGAATC 58.862 45.455 0.00 0.00 0.00 2.52
2745 6964 6.555315 AGACTGTTTAGAAGTTGCACTTTTG 58.445 36.000 0.00 0.00 38.80 2.44
2750 6969 4.049186 TCGAGACTGTTTAGAAGTTGCAC 58.951 43.478 0.00 0.00 0.00 4.57
2763 6982 2.434702 AGTGAAAAACCCTCGAGACTGT 59.565 45.455 15.71 5.15 0.00 3.55
2764 6983 3.113260 AGTGAAAAACCCTCGAGACTG 57.887 47.619 15.71 4.44 0.00 3.51
2765 6984 3.840124 AAGTGAAAAACCCTCGAGACT 57.160 42.857 15.71 3.44 0.00 3.24
2766 6985 4.552184 CGAAAAGTGAAAAACCCTCGAGAC 60.552 45.833 15.71 0.73 30.24 3.36
2768 6987 3.303791 CCGAAAAGTGAAAAACCCTCGAG 60.304 47.826 5.13 5.13 30.24 4.04
2771 6990 3.547413 CGTCCGAAAAGTGAAAAACCCTC 60.547 47.826 0.00 0.00 0.00 4.30
2772 6991 2.356695 CGTCCGAAAAGTGAAAAACCCT 59.643 45.455 0.00 0.00 0.00 4.34
2773 6992 2.542205 CCGTCCGAAAAGTGAAAAACCC 60.542 50.000 0.00 0.00 0.00 4.11
2774 6993 2.097954 ACCGTCCGAAAAGTGAAAAACC 59.902 45.455 0.00 0.00 0.00 3.27
2777 6996 3.760537 CAAACCGTCCGAAAAGTGAAAA 58.239 40.909 0.00 0.00 0.00 2.29
2778 6997 2.478200 GCAAACCGTCCGAAAAGTGAAA 60.478 45.455 0.00 0.00 0.00 2.69
2779 6998 1.064357 GCAAACCGTCCGAAAAGTGAA 59.936 47.619 0.00 0.00 0.00 3.18
2780 6999 0.658897 GCAAACCGTCCGAAAAGTGA 59.341 50.000 0.00 0.00 0.00 3.41
2781 7000 0.661020 AGCAAACCGTCCGAAAAGTG 59.339 50.000 0.00 0.00 0.00 3.16
2782 7001 0.661020 CAGCAAACCGTCCGAAAAGT 59.339 50.000 0.00 0.00 0.00 2.66
2783 7002 0.941542 TCAGCAAACCGTCCGAAAAG 59.058 50.000 0.00 0.00 0.00 2.27
2786 7005 0.320374 ATCTCAGCAAACCGTCCGAA 59.680 50.000 0.00 0.00 0.00 4.30
2787 7006 0.389817 CATCTCAGCAAACCGTCCGA 60.390 55.000 0.00 0.00 0.00 4.55
2788 7007 1.970917 GCATCTCAGCAAACCGTCCG 61.971 60.000 0.00 0.00 0.00 4.79
2789 7008 0.674895 AGCATCTCAGCAAACCGTCC 60.675 55.000 0.00 0.00 36.85 4.79
2790 7009 1.160137 AAGCATCTCAGCAAACCGTC 58.840 50.000 0.00 0.00 36.85 4.79
2791 7010 1.609208 AAAGCATCTCAGCAAACCGT 58.391 45.000 0.00 0.00 36.85 4.83
2792 7011 3.829886 TTAAAGCATCTCAGCAAACCG 57.170 42.857 0.00 0.00 36.85 4.44
2793 7012 4.094887 TCGATTAAAGCATCTCAGCAAACC 59.905 41.667 0.00 0.00 36.85 3.27
2796 7015 4.507710 AGTCGATTAAAGCATCTCAGCAA 58.492 39.130 0.00 0.00 36.85 3.91
2815 7034 2.691409 TGGCACAAGCACCTATAGTC 57.309 50.000 0.00 0.00 44.61 2.59
2820 7039 4.721211 TGCTCTTTGGCACAAGCACCTA 62.721 50.000 12.18 0.00 43.65 3.08
2822 7041 1.737355 TGCTCTTTGGCACAAGCACC 61.737 55.000 12.18 0.00 43.65 5.01
2823 7042 1.735360 TGCTCTTTGGCACAAGCAC 59.265 52.632 12.18 4.80 43.65 4.40
2824 7043 1.000060 GATTGCTCTTTGGCACAAGCA 60.000 47.619 12.18 12.18 46.32 3.91
2826 7045 1.993842 GCGATTGCTCTTTGGCACAAG 60.994 52.381 0.00 0.00 42.27 3.16
2827 7046 0.039256 GCGATTGCTCTTTGGCACAA 60.039 50.000 0.00 0.00 42.27 3.33
2828 7047 1.580942 GCGATTGCTCTTTGGCACA 59.419 52.632 0.00 0.00 42.27 4.57
2841 7060 9.935241 AATAATGATTGTCTGTATCTAGCGATT 57.065 29.630 0.00 0.00 0.00 3.34
2893 7112 2.450476 CAAGGGGAAGTGGATTTCCTG 58.550 52.381 4.92 0.00 44.90 3.86
2900 7119 1.383799 CCATGCAAGGGGAAGTGGA 59.616 57.895 0.00 0.00 31.11 4.02
2901 7120 2.353610 GCCATGCAAGGGGAAGTGG 61.354 63.158 10.51 1.90 38.99 4.00
2904 7123 0.396695 ATCAGCCATGCAAGGGGAAG 60.397 55.000 10.51 0.00 38.99 3.46
2928 7147 9.401058 AGGAGATTAGAAGATTTGTTAACCATG 57.599 33.333 2.48 0.00 0.00 3.66
2937 7156 7.261325 TCTTCACGAGGAGATTAGAAGATTTG 58.739 38.462 0.00 0.00 37.24 2.32
2967 7186 6.318144 AGGACAGTGCAGATGAAGATATTTTG 59.682 38.462 5.87 0.00 0.00 2.44
2970 7189 5.366186 AGAGGACAGTGCAGATGAAGATATT 59.634 40.000 5.87 0.00 0.00 1.28
2996 7216 1.329256 ACTGAGAACACGTAGCCAGT 58.671 50.000 0.00 0.00 0.00 4.00
2997 7217 3.439293 CATACTGAGAACACGTAGCCAG 58.561 50.000 0.00 0.00 0.00 4.85
2999 7219 2.194271 GCATACTGAGAACACGTAGCC 58.806 52.381 0.00 0.00 0.00 3.93
3000 7220 2.194271 GGCATACTGAGAACACGTAGC 58.806 52.381 0.00 0.00 0.00 3.58
3001 7221 2.427453 AGGGCATACTGAGAACACGTAG 59.573 50.000 0.00 0.00 0.00 3.51
3002 7222 2.426024 GAGGGCATACTGAGAACACGTA 59.574 50.000 0.00 0.00 0.00 3.57
3003 7223 1.204941 GAGGGCATACTGAGAACACGT 59.795 52.381 0.00 0.00 0.00 4.49
3004 7224 1.478510 AGAGGGCATACTGAGAACACG 59.521 52.381 0.00 0.00 0.00 4.49
3005 7225 2.234908 ACAGAGGGCATACTGAGAACAC 59.765 50.000 10.72 0.00 37.54 3.32
3006 7226 2.497675 GACAGAGGGCATACTGAGAACA 59.502 50.000 10.72 0.00 37.54 3.18
3007 7227 2.763448 AGACAGAGGGCATACTGAGAAC 59.237 50.000 10.72 2.08 37.54 3.01
3008 7228 2.762887 CAGACAGAGGGCATACTGAGAA 59.237 50.000 10.72 0.00 37.54 2.87
3009 7229 2.382882 CAGACAGAGGGCATACTGAGA 58.617 52.381 10.72 0.00 37.54 3.27
3010 7230 1.411977 CCAGACAGAGGGCATACTGAG 59.588 57.143 10.72 0.00 37.54 3.35
3011 7231 1.489481 CCAGACAGAGGGCATACTGA 58.511 55.000 10.72 0.00 37.54 3.41
3019 7239 1.513158 CACGTAGCCAGACAGAGGG 59.487 63.158 0.00 0.00 0.00 4.30
3020 7240 1.153745 GCACGTAGCCAGACAGAGG 60.154 63.158 0.00 0.00 37.23 3.69
3021 7241 4.485554 GCACGTAGCCAGACAGAG 57.514 61.111 0.00 0.00 37.23 3.35
3113 7333 2.897972 CCCGGCCCTGTACTGTAC 59.102 66.667 10.98 10.98 0.00 2.90
3120 7340 3.721370 GATCATTGCCCGGCCCTGT 62.721 63.158 7.03 0.00 0.00 4.00
3127 7347 1.353103 GCTCGTTGATCATTGCCCG 59.647 57.895 0.00 0.00 0.00 6.13
3171 7391 6.442513 AAATCTTCATTAAGCTACACTGGC 57.557 37.500 0.00 0.00 32.36 4.85
3173 7393 6.749118 GCCAAAATCTTCATTAAGCTACACTG 59.251 38.462 0.00 0.00 32.36 3.66
3174 7394 6.434028 TGCCAAAATCTTCATTAAGCTACACT 59.566 34.615 0.00 0.00 32.36 3.55
3175 7395 6.620678 TGCCAAAATCTTCATTAAGCTACAC 58.379 36.000 0.00 0.00 32.36 2.90
3252 7472 8.515414 GCATGCACGATATATACTATGATCCTA 58.485 37.037 14.21 0.00 0.00 2.94
3253 7473 7.232330 AGCATGCACGATATATACTATGATCCT 59.768 37.037 21.98 0.00 0.00 3.24
3254 7474 7.374272 AGCATGCACGATATATACTATGATCC 58.626 38.462 21.98 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.