Multiple sequence alignment - TraesCS4D01G085700

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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 TraesCS4D01G085700 chr4D 100.000 6464 0 0 1 6464 60875765 60882228 0.000000e+00 11937
1 TraesCS4D01G085700 chr4D 96.875 256 8 0 6209 6464 434278374 434278119 4.630000e-116 429
2 TraesCS4D01G085700 chr4D 96.484 256 9 0 6209 6464 75227639 75227894 2.150000e-114 424
3 TraesCS4D01G085700 chr4B 95.464 4343 73 38 1893 6208 91752384 91756629 0.000000e+00 6815
4 TraesCS4D01G085700 chr4B 94.229 1005 29 11 899 1897 91750861 91751842 0.000000e+00 1507
5 TraesCS4D01G085700 chr4A 91.779 4464 202 59 1560 5949 290371643 290367271 0.000000e+00 6058
6 TraesCS4D01G085700 chr4A 89.756 615 41 9 948 1548 290372590 290371984 0.000000e+00 767
7 TraesCS4D01G085700 chr3B 98.439 897 13 1 1 897 564035070 564034175 0.000000e+00 1578
8 TraesCS4D01G085700 chr3B 97.550 898 20 2 1 897 51239293 51238397 0.000000e+00 1535
9 TraesCS4D01G085700 chr3D 98.331 899 13 2 1 898 462842882 462841985 0.000000e+00 1576
10 TraesCS4D01G085700 chr3D 96.139 259 9 1 6206 6464 458183903 458184160 7.750000e-114 422
11 TraesCS4D01G085700 chr3A 97.775 899 16 3 1 898 441897872 441898767 0.000000e+00 1546
12 TraesCS4D01G085700 chr3A 97.664 899 18 2 1 897 500896464 500895567 0.000000e+00 1541
13 TraesCS4D01G085700 chr5B 97.553 899 20 2 1 898 133421169 133420272 0.000000e+00 1537
14 TraesCS4D01G085700 chr7A 97.550 898 20 2 1 897 710811959 710811063 0.000000e+00 1535
15 TraesCS4D01G085700 chr6A 97.439 898 21 2 1 897 416744966 416744070 0.000000e+00 1530
16 TraesCS4D01G085700 chr2A 97.336 901 20 3 1 898 69339719 69340618 0.000000e+00 1528
17 TraesCS4D01G085700 chr1B 96.206 659 22 1 4444 5099 364949184 364949842 0.000000e+00 1075
18 TraesCS4D01G085700 chr5D 96.875 256 8 0 6209 6464 255469886 255469631 4.630000e-116 429
19 TraesCS4D01G085700 chr5D 96.484 256 9 0 6209 6464 440155597 440155852 2.150000e-114 424
20 TraesCS4D01G085700 chr2D 96.875 256 8 0 6209 6464 124470069 124470324 4.630000e-116 429
21 TraesCS4D01G085700 chr7D 96.484 256 9 0 6209 6464 586745250 586745505 2.150000e-114 424
22 TraesCS4D01G085700 chr1D 96.094 256 10 0 6209 6464 417251243 417251498 1.000000e-112 418
23 TraesCS4D01G085700 chr1D 96.094 256 10 0 6209 6464 432697248 432697503 1.000000e-112 418


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 TraesCS4D01G085700 chr4D 60875765 60882228 6463 False 11937.0 11937 100.0000 1 6464 1 chr4D.!!$F1 6463
1 TraesCS4D01G085700 chr4B 91750861 91756629 5768 False 4161.0 6815 94.8465 899 6208 2 chr4B.!!$F1 5309
2 TraesCS4D01G085700 chr4A 290367271 290372590 5319 True 3412.5 6058 90.7675 948 5949 2 chr4A.!!$R1 5001
3 TraesCS4D01G085700 chr3B 564034175 564035070 895 True 1578.0 1578 98.4390 1 897 1 chr3B.!!$R2 896
4 TraesCS4D01G085700 chr3B 51238397 51239293 896 True 1535.0 1535 97.5500 1 897 1 chr3B.!!$R1 896
5 TraesCS4D01G085700 chr3D 462841985 462842882 897 True 1576.0 1576 98.3310 1 898 1 chr3D.!!$R1 897
6 TraesCS4D01G085700 chr3A 441897872 441898767 895 False 1546.0 1546 97.7750 1 898 1 chr3A.!!$F1 897
7 TraesCS4D01G085700 chr3A 500895567 500896464 897 True 1541.0 1541 97.6640 1 897 1 chr3A.!!$R1 896
8 TraesCS4D01G085700 chr5B 133420272 133421169 897 True 1537.0 1537 97.5530 1 898 1 chr5B.!!$R1 897
9 TraesCS4D01G085700 chr7A 710811063 710811959 896 True 1535.0 1535 97.5500 1 897 1 chr7A.!!$R1 896
10 TraesCS4D01G085700 chr6A 416744070 416744966 896 True 1530.0 1530 97.4390 1 897 1 chr6A.!!$R1 896
11 TraesCS4D01G085700 chr2A 69339719 69340618 899 False 1528.0 1528 97.3360 1 898 1 chr2A.!!$F1 897
12 TraesCS4D01G085700 chr1B 364949184 364949842 658 False 1075.0 1075 96.2060 4444 5099 1 chr1B.!!$F1 655

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
900 907 0.037160 TAAGGGTTTGAGGGTTCGGC 59.963 55.000 0.00 0.00 0.00 5.54 F
904 911 0.037160 GGTTTGAGGGTTCGGCCTTA 59.963 55.000 0.00 0.00 37.43 2.69 F
1256 1263 1.066587 GCGACGAGGAGGATGAAGG 59.933 63.158 0.00 0.00 0.00 3.46 F
1444 1462 2.289002 CAGGCAAATTACTGGAGATCGC 59.711 50.000 0.00 0.00 0.00 4.58 F
2244 3197 2.356135 CTTGTCGGGGTATTCCACTTG 58.644 52.381 0.00 0.00 34.37 3.16 F
3936 4923 0.170561 GCACCAGAGCTGCTTCATTG 59.829 55.000 2.53 0.74 0.00 2.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2764 3722 5.065602 AGGGAAACAAAACTTGAGTCGTTAC 59.934 40.000 0.00 0.0 0.00 2.50 R
2863 3823 7.547227 ACAATGGGTAACTCAAAAATGATAGC 58.453 34.615 0.00 0.0 0.00 2.97 R
3236 4220 4.945543 AGCAGCACAATCACAAAGATATCA 59.054 37.500 5.32 0.0 35.39 2.15 R
3237 4221 5.496133 AGCAGCACAATCACAAAGATATC 57.504 39.130 0.00 0.0 35.39 1.63 R
3948 4935 1.673993 CAGCATACCGGTGTTGGCA 60.674 57.895 19.93 0.0 38.36 4.92 R
5512 6513 0.245539 TGCCGTGGTACTGCTAACTC 59.754 55.000 0.00 0.0 0.00 3.01 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
680 684 8.991243 ATTGTTTTATGTCAAATGTGATGGAG 57.009 30.769 0.00 0.00 35.80 3.86
789 794 6.987403 AATCCAACCCTTAAAGCAGTTTAA 57.013 33.333 0.00 0.00 36.05 1.52
819 824 4.445879 GGGTTTGAGGGTTCTAGTCTTTGT 60.446 45.833 0.00 0.00 0.00 2.83
822 827 3.583228 TGAGGGTTCTAGTCTTTGTCCA 58.417 45.455 0.00 0.00 0.00 4.02
898 905 3.203716 GCTATAAGGGTTTGAGGGTTCG 58.796 50.000 0.00 0.00 0.00 3.95
899 906 2.801077 ATAAGGGTTTGAGGGTTCGG 57.199 50.000 0.00 0.00 0.00 4.30
900 907 0.037160 TAAGGGTTTGAGGGTTCGGC 59.963 55.000 0.00 0.00 0.00 5.54
901 908 2.675423 GGGTTTGAGGGTTCGGCC 60.675 66.667 0.00 0.00 0.00 6.13
902 909 2.434774 GGTTTGAGGGTTCGGCCT 59.565 61.111 0.00 0.00 37.43 5.19
903 910 1.228459 GGTTTGAGGGTTCGGCCTT 60.228 57.895 0.00 0.00 37.43 4.35
904 911 0.037160 GGTTTGAGGGTTCGGCCTTA 59.963 55.000 0.00 0.00 37.43 2.69
905 912 1.340697 GGTTTGAGGGTTCGGCCTTAT 60.341 52.381 0.00 0.00 37.43 1.73
906 913 2.443416 GTTTGAGGGTTCGGCCTTATT 58.557 47.619 0.00 0.00 37.43 1.40
907 914 2.122783 TTGAGGGTTCGGCCTTATTG 57.877 50.000 0.00 0.00 37.43 1.90
927 934 2.106683 GGTCGGTGAGAATTGGCCG 61.107 63.158 0.00 0.00 44.95 6.13
933 940 2.706890 GGTGAGAATTGGCCGAAGTTA 58.293 47.619 0.00 0.00 0.00 2.24
1050 1057 3.164269 CCGCCTATCCTGCACCCT 61.164 66.667 0.00 0.00 0.00 4.34
1052 1059 1.668294 CGCCTATCCTGCACCCTAG 59.332 63.158 0.00 0.00 0.00 3.02
1209 1216 3.196685 ACGAAAATGGAGAGGAGGAAGAG 59.803 47.826 0.00 0.00 0.00 2.85
1256 1263 1.066587 GCGACGAGGAGGATGAAGG 59.933 63.158 0.00 0.00 0.00 3.46
1444 1462 2.289002 CAGGCAAATTACTGGAGATCGC 59.711 50.000 0.00 0.00 0.00 4.58
1468 1489 4.636648 TGGTCTTTTCACTTTTGCTTCGTA 59.363 37.500 0.00 0.00 0.00 3.43
1486 1508 5.913137 TCGTAATTCATTCCCTTGCATTT 57.087 34.783 0.00 0.00 0.00 2.32
1487 1509 7.397892 TTCGTAATTCATTCCCTTGCATTTA 57.602 32.000 0.00 0.00 0.00 1.40
1488 1510 7.581213 TCGTAATTCATTCCCTTGCATTTAT 57.419 32.000 0.00 0.00 0.00 1.40
1489 1511 8.684386 TCGTAATTCATTCCCTTGCATTTATA 57.316 30.769 0.00 0.00 0.00 0.98
1490 1512 8.783093 TCGTAATTCATTCCCTTGCATTTATAG 58.217 33.333 0.00 0.00 0.00 1.31
1491 1513 8.783093 CGTAATTCATTCCCTTGCATTTATAGA 58.217 33.333 0.00 0.00 0.00 1.98
1492 1514 9.899226 GTAATTCATTCCCTTGCATTTATAGAC 57.101 33.333 0.00 0.00 0.00 2.59
1501 1523 9.154632 TCCCTTGCATTTATAGACTATAGTGAA 57.845 33.333 10.90 0.00 0.00 3.18
1551 1910 7.181125 TGCCCAAAATACCCTTGTTACAATTAT 59.819 33.333 0.00 0.00 0.00 1.28
1552 1911 8.697292 GCCCAAAATACCCTTGTTACAATTATA 58.303 33.333 0.00 0.00 0.00 0.98
1791 2197 7.973048 TCCTAGTCAAGTAGATGTTGGTAAT 57.027 36.000 0.00 0.00 0.00 1.89
1801 2207 7.852263 AGTAGATGTTGGTAATTAGCAAGACT 58.148 34.615 26.10 23.79 43.40 3.24
2244 3197 2.356135 CTTGTCGGGGTATTCCACTTG 58.644 52.381 0.00 0.00 34.37 3.16
2252 3205 3.560453 GGGGTATTCCACTTGCTTACACA 60.560 47.826 0.00 0.00 37.22 3.72
2260 3213 6.892658 TCCACTTGCTTACACAAACATAAT 57.107 33.333 0.00 0.00 0.00 1.28
2705 3658 9.626045 AGCAACTATTTTATCTGTTACTTTTGC 57.374 29.630 0.00 0.00 34.66 3.68
2749 3707 6.875076 ACTAGCTCGGTTTAATATGAACAGT 58.125 36.000 0.00 0.00 0.00 3.55
2838 3798 6.963796 TGAGAAGATTCTTCTTGACAAAAGC 58.036 36.000 25.71 12.74 42.34 3.51
2863 3823 6.233430 GCATAACTTGCCAGTGATAGTATG 57.767 41.667 0.00 0.00 46.15 2.39
3166 4129 9.132521 AGTTCATTTGCATTTCGAAAAGATTAG 57.867 29.630 15.66 3.22 0.00 1.73
3173 4136 6.527722 TGCATTTCGAAAAGATTAGACAATGC 59.472 34.615 15.66 14.94 40.22 3.56
3211 4174 6.877611 AGGTTATATTTTGGACAATAGCGG 57.122 37.500 0.00 0.00 0.00 5.52
3224 4208 4.770795 ACAATAGCGGCTAATGAGAACTT 58.229 39.130 27.07 7.17 0.00 2.66
3225 4209 4.572389 ACAATAGCGGCTAATGAGAACTTG 59.428 41.667 27.07 18.99 0.00 3.16
3226 4210 4.672587 ATAGCGGCTAATGAGAACTTGA 57.327 40.909 14.54 0.00 0.00 3.02
3227 4211 3.550437 AGCGGCTAATGAGAACTTGAT 57.450 42.857 0.00 0.00 0.00 2.57
3228 4212 4.672587 AGCGGCTAATGAGAACTTGATA 57.327 40.909 0.00 0.00 0.00 2.15
3229 4213 4.372656 AGCGGCTAATGAGAACTTGATAC 58.627 43.478 0.00 0.00 0.00 2.24
3230 4214 4.100189 AGCGGCTAATGAGAACTTGATACT 59.900 41.667 0.00 0.00 0.00 2.12
3231 4215 5.302059 AGCGGCTAATGAGAACTTGATACTA 59.698 40.000 0.00 0.00 0.00 1.82
3232 4216 5.631512 GCGGCTAATGAGAACTTGATACTAG 59.368 44.000 0.00 0.00 0.00 2.57
3233 4217 5.631512 CGGCTAATGAGAACTTGATACTAGC 59.368 44.000 0.00 0.00 0.00 3.42
3234 4218 6.516718 GGCTAATGAGAACTTGATACTAGCA 58.483 40.000 0.00 0.00 32.70 3.49
3235 4219 6.422400 GGCTAATGAGAACTTGATACTAGCAC 59.578 42.308 0.00 0.00 32.70 4.40
3236 4220 7.206687 GCTAATGAGAACTTGATACTAGCACT 58.793 38.462 0.00 0.00 31.66 4.40
3237 4221 7.168972 GCTAATGAGAACTTGATACTAGCACTG 59.831 40.741 0.00 0.00 31.66 3.66
3238 4222 6.782082 ATGAGAACTTGATACTAGCACTGA 57.218 37.500 0.00 0.00 0.00 3.41
3239 4223 6.782082 TGAGAACTTGATACTAGCACTGAT 57.218 37.500 0.00 0.00 0.00 2.90
3240 4224 7.881775 TGAGAACTTGATACTAGCACTGATA 57.118 36.000 0.00 0.00 0.00 2.15
3241 4225 8.470657 TGAGAACTTGATACTAGCACTGATAT 57.529 34.615 0.00 0.00 0.00 1.63
3242 4226 8.572185 TGAGAACTTGATACTAGCACTGATATC 58.428 37.037 0.00 0.00 0.00 1.63
3243 4227 8.704849 AGAACTTGATACTAGCACTGATATCT 57.295 34.615 3.98 0.00 0.00 1.98
3244 4228 9.142014 AGAACTTGATACTAGCACTGATATCTT 57.858 33.333 3.98 0.00 0.00 2.40
3367 4351 8.627208 AATATCAATAACTTATGCCAGACCAG 57.373 34.615 0.00 0.00 0.00 4.00
3368 4352 5.692115 TCAATAACTTATGCCAGACCAGA 57.308 39.130 0.00 0.00 0.00 3.86
3445 4429 1.757118 TCTTTAGCTATGCAGTCGGCT 59.243 47.619 0.00 9.69 45.15 5.52
3468 4452 9.346725 GGCTGTATTTATATTTATTTGCTGCTC 57.653 33.333 0.00 0.00 0.00 4.26
3689 4676 6.583912 TCTTTTTGATATAAAGTCGAGGCG 57.416 37.500 0.00 0.00 34.86 5.52
3936 4923 0.170561 GCACCAGAGCTGCTTCATTG 59.829 55.000 2.53 0.74 0.00 2.82
3971 4958 3.067106 CCAACACCGGTATGCTGATATC 58.933 50.000 6.87 0.00 0.00 1.63
4672 5662 7.383687 TGTTACATACTTCAAAGTCCCTACAG 58.616 38.462 0.00 0.00 40.37 2.74
4734 5724 0.034896 GTGTAGTGGGTGACTGGGTG 59.965 60.000 0.00 0.00 35.96 4.61
4807 5797 7.450014 TCCTCTATGAACTTATGTTTGCCAAAA 59.550 33.333 0.00 0.00 36.39 2.44
5277 6277 1.008329 TTCGTCCACCAACGTTTGTC 58.992 50.000 1.37 0.00 43.08 3.18
5475 6476 1.464608 GCGAGTTAGCATGTGAAGCAA 59.535 47.619 0.00 0.00 37.05 3.91
5512 6513 3.385193 AAGAAAAGGAAAATGTGGCGG 57.615 42.857 0.00 0.00 0.00 6.13
5517 6518 2.871096 AGGAAAATGTGGCGGAGTTA 57.129 45.000 0.00 0.00 0.00 2.24
5524 6525 0.245539 TGTGGCGGAGTTAGCAGTAC 59.754 55.000 0.00 0.00 36.08 2.73
5583 6584 1.344942 GGCTGCGAACGTGTGACTAG 61.345 60.000 0.00 0.00 0.00 2.57
5722 6726 3.860536 GGTCTCTCAAATGCTAGAACGTC 59.139 47.826 0.00 0.00 0.00 4.34
5785 6790 7.027874 AGAGTGAATTACATTCTTTACCCCA 57.972 36.000 0.00 0.00 41.66 4.96
5786 6791 7.643123 AGAGTGAATTACATTCTTTACCCCAT 58.357 34.615 0.00 0.00 41.66 4.00
5787 6792 8.778059 AGAGTGAATTACATTCTTTACCCCATA 58.222 33.333 0.00 0.00 41.66 2.74
5788 6793 8.980481 AGTGAATTACATTCTTTACCCCATAG 57.020 34.615 0.00 0.00 39.96 2.23
5789 6794 7.998964 AGTGAATTACATTCTTTACCCCATAGG 59.001 37.037 0.00 0.00 39.96 2.57
5906 6912 8.574196 ACCTCATTTATGTTTTTCTTGTTTCG 57.426 30.769 0.00 0.00 0.00 3.46
6000 7008 0.738412 ATCAAACCGAACTACCCGCG 60.738 55.000 0.00 0.00 0.00 6.46
6043 7051 2.099141 CATGGACCTCATGTTCGTGT 57.901 50.000 0.00 0.00 46.11 4.49
6044 7052 1.733912 CATGGACCTCATGTTCGTGTG 59.266 52.381 0.00 0.00 46.11 3.82
6045 7053 0.034756 TGGACCTCATGTTCGTGTGG 59.965 55.000 10.39 10.39 38.42 4.17
6046 7054 0.673644 GGACCTCATGTTCGTGTGGG 60.674 60.000 14.76 10.03 37.13 4.61
6047 7055 1.298859 GACCTCATGTTCGTGTGGGC 61.299 60.000 14.76 9.76 37.13 5.36
6048 7056 1.003355 CCTCATGTTCGTGTGGGCT 60.003 57.895 0.00 0.00 0.00 5.19
6049 7057 1.021390 CCTCATGTTCGTGTGGGCTC 61.021 60.000 0.00 0.00 0.00 4.70
6050 7058 0.320683 CTCATGTTCGTGTGGGCTCA 60.321 55.000 0.00 0.00 0.00 4.26
6051 7059 0.320683 TCATGTTCGTGTGGGCTCAG 60.321 55.000 0.00 0.00 0.00 3.35
6052 7060 1.003355 ATGTTCGTGTGGGCTCAGG 60.003 57.895 0.00 0.00 0.00 3.86
6053 7061 1.480212 ATGTTCGTGTGGGCTCAGGA 61.480 55.000 0.00 0.00 0.00 3.86
6054 7062 1.668151 GTTCGTGTGGGCTCAGGAC 60.668 63.158 0.00 0.00 33.05 3.85
6055 7063 2.879233 TTCGTGTGGGCTCAGGACC 61.879 63.158 0.00 0.00 42.24 4.46
6056 7064 3.314331 CGTGTGGGCTCAGGACCT 61.314 66.667 0.00 0.00 42.43 3.85
6057 7065 2.665603 GTGTGGGCTCAGGACCTC 59.334 66.667 0.00 0.00 42.43 3.85
6058 7066 2.997315 TGTGGGCTCAGGACCTCG 60.997 66.667 0.00 0.00 42.43 4.63
6090 7098 2.892373 TTAGCCGCAAAGAATCAACG 57.108 45.000 0.00 0.00 0.00 4.10
6093 7101 1.812571 AGCCGCAAAGAATCAACGAAT 59.187 42.857 0.00 0.00 0.00 3.34
6105 7113 6.166279 AGAATCAACGAATGAACTTAGCAGA 58.834 36.000 0.00 0.00 42.54 4.26
6172 7189 1.356527 GCCACCATACGTTCGGACAC 61.357 60.000 9.72 0.00 0.00 3.67
6214 7231 4.819082 GCATGCATGCGGACAAAT 57.181 50.000 33.99 0.00 44.67 2.32
6215 7232 3.053662 GCATGCATGCGGACAAATT 57.946 47.368 33.99 0.00 44.67 1.82
6216 7233 1.361793 GCATGCATGCGGACAAATTT 58.638 45.000 33.99 0.00 44.67 1.82
6217 7234 1.061421 GCATGCATGCGGACAAATTTG 59.939 47.619 33.99 16.67 44.67 2.32
6218 7235 2.608268 CATGCATGCGGACAAATTTGA 58.392 42.857 24.64 1.90 0.00 2.69
6219 7236 2.063156 TGCATGCGGACAAATTTGAC 57.937 45.000 24.64 17.82 0.00 3.18
6220 7237 1.336702 TGCATGCGGACAAATTTGACC 60.337 47.619 24.64 24.46 39.19 4.02
6221 7238 1.067635 GCATGCGGACAAATTTGACCT 60.068 47.619 28.71 13.93 40.18 3.85
6222 7239 2.163412 GCATGCGGACAAATTTGACCTA 59.837 45.455 28.71 20.65 40.18 3.08
6223 7240 3.181487 GCATGCGGACAAATTTGACCTAT 60.181 43.478 28.71 21.62 40.18 2.57
6224 7241 4.036262 GCATGCGGACAAATTTGACCTATA 59.964 41.667 28.71 18.46 40.18 1.31
6225 7242 5.751680 CATGCGGACAAATTTGACCTATAG 58.248 41.667 28.71 18.19 40.18 1.31
6226 7243 5.092554 TGCGGACAAATTTGACCTATAGA 57.907 39.130 28.71 11.47 40.18 1.98
6227 7244 4.873827 TGCGGACAAATTTGACCTATAGAC 59.126 41.667 28.71 15.63 40.18 2.59
6228 7245 4.025979 GCGGACAAATTTGACCTATAGACG 60.026 45.833 28.71 18.20 40.18 4.18
6229 7246 5.345702 CGGACAAATTTGACCTATAGACGA 58.654 41.667 28.71 0.00 40.18 4.20
6230 7247 5.808540 CGGACAAATTTGACCTATAGACGAA 59.191 40.000 28.71 2.06 40.18 3.85
6231 7248 6.311935 CGGACAAATTTGACCTATAGACGAAA 59.688 38.462 28.71 0.00 40.18 3.46
6232 7249 7.011109 CGGACAAATTTGACCTATAGACGAAAT 59.989 37.037 28.71 2.89 40.18 2.17
6233 7250 8.674607 GGACAAATTTGACCTATAGACGAAATT 58.325 33.333 26.10 5.70 39.42 1.82
6241 7258 9.878667 TTGACCTATAGACGAAATTAAATCACA 57.121 29.630 0.00 0.00 0.00 3.58
6242 7259 9.529325 TGACCTATAGACGAAATTAAATCACAG 57.471 33.333 0.00 0.00 0.00 3.66
6243 7260 9.745880 GACCTATAGACGAAATTAAATCACAGA 57.254 33.333 0.00 0.00 0.00 3.41
6250 7267 9.003658 AGACGAAATTAAATCACAGAATGAACT 57.996 29.630 0.00 0.00 41.93 3.01
6275 7292 0.800012 TGAAACTATTTCACGCGGCC 59.200 50.000 12.47 0.00 44.21 6.13
6276 7293 0.247537 GAAACTATTTCACGCGGCCG 60.248 55.000 24.05 24.05 39.45 6.13
6277 7294 0.671163 AAACTATTTCACGCGGCCGA 60.671 50.000 33.48 6.95 38.29 5.54
6278 7295 1.356527 AACTATTTCACGCGGCCGAC 61.357 55.000 33.48 19.66 38.29 4.79
6279 7296 2.509786 TATTTCACGCGGCCGACC 60.510 61.111 33.48 11.71 38.29 4.79
6280 7297 2.901051 CTATTTCACGCGGCCGACCT 62.901 60.000 33.48 6.57 38.29 3.85
6281 7298 2.510064 TATTTCACGCGGCCGACCTT 62.510 55.000 33.48 5.76 38.29 3.50
6282 7299 3.964641 TATTTCACGCGGCCGACCTTT 62.965 52.381 33.48 9.05 38.29 3.11
6283 7300 4.612412 TCACGCGGCCGACCTTTT 62.612 61.111 33.48 1.42 38.29 2.27
6284 7301 3.656045 CACGCGGCCGACCTTTTT 61.656 61.111 33.48 0.00 38.29 1.94
6285 7302 3.656045 ACGCGGCCGACCTTTTTG 61.656 61.111 33.48 9.36 38.29 2.44
6286 7303 3.656045 CGCGGCCGACCTTTTTGT 61.656 61.111 33.48 0.00 36.29 2.83
6287 7304 2.050442 GCGGCCGACCTTTTTGTG 60.050 61.111 33.48 0.00 0.00 3.33
6288 7305 2.841160 GCGGCCGACCTTTTTGTGT 61.841 57.895 33.48 0.00 0.00 3.72
6289 7306 1.008995 CGGCCGACCTTTTTGTGTG 60.009 57.895 24.07 0.00 0.00 3.82
6290 7307 1.440938 CGGCCGACCTTTTTGTGTGA 61.441 55.000 24.07 0.00 0.00 3.58
6291 7308 0.030235 GGCCGACCTTTTTGTGTGAC 59.970 55.000 0.00 0.00 0.00 3.67
6292 7309 0.316689 GCCGACCTTTTTGTGTGACG 60.317 55.000 0.00 0.00 0.00 4.35
6293 7310 0.316689 CCGACCTTTTTGTGTGACGC 60.317 55.000 0.00 0.00 0.00 5.19
6294 7311 0.316689 CGACCTTTTTGTGTGACGCC 60.317 55.000 0.00 0.00 0.00 5.68
6295 7312 0.030235 GACCTTTTTGTGTGACGCCC 59.970 55.000 0.00 0.00 0.00 6.13
6296 7313 1.008995 CCTTTTTGTGTGACGCCCG 60.009 57.895 0.00 0.00 0.00 6.13
6297 7314 1.440938 CCTTTTTGTGTGACGCCCGA 61.441 55.000 0.00 0.00 0.00 5.14
6298 7315 0.316689 CTTTTTGTGTGACGCCCGAC 60.317 55.000 0.00 0.00 0.00 4.79
6317 7334 2.048597 CGAAGGCGCCACACTACA 60.049 61.111 31.54 0.00 0.00 2.74
6318 7335 2.380410 CGAAGGCGCCACACTACAC 61.380 63.158 31.54 8.98 0.00 2.90
6319 7336 1.004918 GAAGGCGCCACACTACACT 60.005 57.895 31.54 0.00 0.00 3.55
6320 7337 1.291877 GAAGGCGCCACACTACACTG 61.292 60.000 31.54 0.00 0.00 3.66
6321 7338 2.030562 GGCGCCACACTACACTGT 59.969 61.111 24.80 0.00 0.00 3.55
6322 7339 2.317609 GGCGCCACACTACACTGTG 61.318 63.158 24.80 6.19 41.19 3.66
6323 7340 2.954753 GCGCCACACTACACTGTGC 61.955 63.158 7.90 0.00 40.33 4.57
6324 7341 1.594021 CGCCACACTACACTGTGCA 60.594 57.895 7.90 0.00 40.33 4.57
6325 7342 1.157257 CGCCACACTACACTGTGCAA 61.157 55.000 7.90 0.00 40.33 4.08
6326 7343 0.307760 GCCACACTACACTGTGCAAC 59.692 55.000 7.90 0.00 40.33 4.17
6327 7344 0.581529 CCACACTACACTGTGCAACG 59.418 55.000 7.90 0.00 42.39 4.10
6328 7345 0.042188 CACACTACACTGTGCAACGC 60.042 55.000 7.90 0.00 42.39 4.84
6329 7346 1.157870 ACACTACACTGTGCAACGCC 61.158 55.000 7.90 0.00 42.39 5.68
6330 7347 0.880278 CACTACACTGTGCAACGCCT 60.880 55.000 7.90 0.00 42.39 5.52
6331 7348 0.179056 ACTACACTGTGCAACGCCTT 60.179 50.000 7.90 0.00 42.39 4.35
6332 7349 1.069513 ACTACACTGTGCAACGCCTTA 59.930 47.619 7.90 0.00 42.39 2.69
6333 7350 1.459592 CTACACTGTGCAACGCCTTAC 59.540 52.381 7.90 0.00 42.39 2.34
6334 7351 0.462937 ACACTGTGCAACGCCTTACA 60.463 50.000 7.90 0.00 42.39 2.41
6335 7352 0.041312 CACTGTGCAACGCCTTACAC 60.041 55.000 0.00 0.00 42.39 2.90
6336 7353 0.462937 ACTGTGCAACGCCTTACACA 60.463 50.000 0.00 2.18 42.39 3.72
6337 7354 0.874390 CTGTGCAACGCCTTACACAT 59.126 50.000 2.51 0.00 41.80 3.21
6338 7355 2.073056 CTGTGCAACGCCTTACACATA 58.927 47.619 2.51 0.00 41.80 2.29
6339 7356 2.073056 TGTGCAACGCCTTACACATAG 58.927 47.619 0.00 0.00 42.39 2.23
6340 7357 1.396996 GTGCAACGCCTTACACATAGG 59.603 52.381 0.00 0.00 35.80 2.57
6347 7364 2.882927 CCTTACACATAGGCGCTACA 57.117 50.000 7.64 0.00 0.00 2.74
6348 7365 2.470821 CCTTACACATAGGCGCTACAC 58.529 52.381 7.64 0.00 0.00 2.90
6350 7367 0.382873 TACACATAGGCGCTACACGG 59.617 55.000 7.64 0.00 43.93 4.94
6374 7391 2.261361 TCGCACCCGTGTGATCAG 59.739 61.111 0.90 0.00 45.76 2.90
6375 7392 2.261361 CGCACCCGTGTGATCAGA 59.739 61.111 0.90 0.00 45.76 3.27
6376 7393 1.374125 CGCACCCGTGTGATCAGAA 60.374 57.895 0.90 0.00 45.76 3.02
6377 7394 0.948623 CGCACCCGTGTGATCAGAAA 60.949 55.000 0.90 0.00 45.76 2.52
6378 7395 1.234821 GCACCCGTGTGATCAGAAAA 58.765 50.000 0.90 0.00 45.76 2.29
6379 7396 1.812571 GCACCCGTGTGATCAGAAAAT 59.187 47.619 0.90 0.00 45.76 1.82
6380 7397 2.228822 GCACCCGTGTGATCAGAAAATT 59.771 45.455 0.90 0.00 45.76 1.82
6381 7398 3.438781 GCACCCGTGTGATCAGAAAATTA 59.561 43.478 0.90 0.00 45.76 1.40
6382 7399 4.671766 GCACCCGTGTGATCAGAAAATTAC 60.672 45.833 0.90 0.00 45.76 1.89
6383 7400 4.695455 CACCCGTGTGATCAGAAAATTACT 59.305 41.667 0.00 0.00 45.76 2.24
6384 7401 5.872617 CACCCGTGTGATCAGAAAATTACTA 59.127 40.000 0.00 0.00 45.76 1.82
6385 7402 6.370442 CACCCGTGTGATCAGAAAATTACTAA 59.630 38.462 0.00 0.00 45.76 2.24
6386 7403 6.594159 ACCCGTGTGATCAGAAAATTACTAAG 59.406 38.462 0.00 0.00 0.00 2.18
6387 7404 6.594159 CCCGTGTGATCAGAAAATTACTAAGT 59.406 38.462 0.00 0.00 0.00 2.24
6388 7405 7.201530 CCCGTGTGATCAGAAAATTACTAAGTC 60.202 40.741 0.00 0.00 0.00 3.01
6389 7406 7.330946 CCGTGTGATCAGAAAATTACTAAGTCA 59.669 37.037 0.00 0.00 0.00 3.41
6390 7407 8.376203 CGTGTGATCAGAAAATTACTAAGTCAG 58.624 37.037 0.00 0.00 0.00 3.51
6391 7408 9.209175 GTGTGATCAGAAAATTACTAAGTCAGT 57.791 33.333 0.00 0.00 41.62 3.41
6392 7409 9.208022 TGTGATCAGAAAATTACTAAGTCAGTG 57.792 33.333 0.00 0.00 38.24 3.66
6393 7410 9.209175 GTGATCAGAAAATTACTAAGTCAGTGT 57.791 33.333 0.00 0.00 38.24 3.55
6394 7411 9.208022 TGATCAGAAAATTACTAAGTCAGTGTG 57.792 33.333 0.00 0.00 38.24 3.82
6395 7412 7.421530 TCAGAAAATTACTAAGTCAGTGTGC 57.578 36.000 0.00 0.00 38.24 4.57
6396 7413 6.989759 TCAGAAAATTACTAAGTCAGTGTGCA 59.010 34.615 0.00 0.00 38.24 4.57
6397 7414 7.171508 TCAGAAAATTACTAAGTCAGTGTGCAG 59.828 37.037 0.00 0.00 38.24 4.41
6398 7415 5.613358 AAATTACTAAGTCAGTGTGCAGC 57.387 39.130 0.00 0.00 38.24 5.25
6399 7416 2.347697 TACTAAGTCAGTGTGCAGCG 57.652 50.000 0.00 0.00 38.24 5.18
6400 7417 0.946221 ACTAAGTCAGTGTGCAGCGC 60.946 55.000 0.00 0.00 35.62 5.92
6401 7418 1.630244 CTAAGTCAGTGTGCAGCGCC 61.630 60.000 2.29 0.00 0.00 6.53
6402 7419 2.099652 TAAGTCAGTGTGCAGCGCCT 62.100 55.000 2.29 0.00 0.00 5.52
6403 7420 3.720193 GTCAGTGTGCAGCGCCTG 61.720 66.667 2.29 14.85 34.12 4.85
6404 7421 3.927548 TCAGTGTGCAGCGCCTGA 61.928 61.111 18.04 18.04 32.44 3.86
6405 7422 3.420606 CAGTGTGCAGCGCCTGAG 61.421 66.667 15.59 0.00 32.44 3.35
6406 7423 3.619767 AGTGTGCAGCGCCTGAGA 61.620 61.111 2.29 0.00 32.44 3.27
6407 7424 3.117171 GTGTGCAGCGCCTGAGAG 61.117 66.667 2.29 0.00 32.44 3.20
6417 7434 3.150335 CCTGAGAGCTAGGCGCCA 61.150 66.667 31.54 14.00 40.39 5.69
6418 7435 2.105930 CTGAGAGCTAGGCGCCAC 59.894 66.667 31.54 17.93 40.39 5.01
6419 7436 2.679996 TGAGAGCTAGGCGCCACA 60.680 61.111 31.54 15.42 40.39 4.17
6420 7437 2.202810 GAGAGCTAGGCGCCACAC 60.203 66.667 31.54 17.11 40.39 3.82
6421 7438 3.724914 GAGAGCTAGGCGCCACACC 62.725 68.421 31.54 13.77 40.39 4.16
6422 7439 4.082523 GAGCTAGGCGCCACACCA 62.083 66.667 31.54 6.88 40.39 4.17
6423 7440 3.391665 GAGCTAGGCGCCACACCAT 62.392 63.158 31.54 9.39 40.39 3.55
6424 7441 2.028125 GAGCTAGGCGCCACACCATA 62.028 60.000 31.54 10.17 40.39 2.74
6425 7442 1.887707 GCTAGGCGCCACACCATAC 60.888 63.158 31.54 4.76 0.00 2.39
6426 7443 1.520192 CTAGGCGCCACACCATACA 59.480 57.895 31.54 0.33 0.00 2.29
6427 7444 0.530650 CTAGGCGCCACACCATACAG 60.531 60.000 31.54 6.91 0.00 2.74
6428 7445 1.261938 TAGGCGCCACACCATACAGT 61.262 55.000 31.54 5.27 0.00 3.55
6429 7446 2.398554 GGCGCCACACCATACAGTG 61.399 63.158 24.80 0.00 43.65 3.66
6436 7453 2.677971 CACCATACAGTGTAGCGCC 58.322 57.895 2.29 0.00 32.89 6.53
6437 7454 0.175760 CACCATACAGTGTAGCGCCT 59.824 55.000 2.29 0.00 32.89 5.52
6438 7455 1.407618 CACCATACAGTGTAGCGCCTA 59.592 52.381 2.29 0.00 32.89 3.93
6439 7456 1.681793 ACCATACAGTGTAGCGCCTAG 59.318 52.381 2.29 0.00 0.00 3.02
6453 7470 1.068250 CCTAGCTCCTAGGCGTTGC 59.932 63.158 2.96 5.87 45.64 4.17
6454 7471 1.676678 CCTAGCTCCTAGGCGTTGCA 61.677 60.000 2.96 0.00 45.64 4.08
6455 7472 0.528684 CTAGCTCCTAGGCGTTGCAC 60.529 60.000 2.96 0.00 37.29 4.57
6456 7473 0.970937 TAGCTCCTAGGCGTTGCACT 60.971 55.000 2.96 0.00 37.29 4.40
6457 7474 0.970937 AGCTCCTAGGCGTTGCACTA 60.971 55.000 2.96 0.00 37.29 2.74
6458 7475 0.528684 GCTCCTAGGCGTTGCACTAG 60.529 60.000 2.96 2.78 37.12 2.57
6459 7476 0.818296 CTCCTAGGCGTTGCACTAGT 59.182 55.000 2.96 0.00 35.93 2.57
6460 7477 0.530744 TCCTAGGCGTTGCACTAGTG 59.469 55.000 18.93 18.93 35.93 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
119 120 5.392380 CCATTTTTCTCCTTGATGGACTTCG 60.392 44.000 0.00 0.00 40.56 3.79
789 794 0.639943 AACCCTCAAACCCAACCCTT 59.360 50.000 0.00 0.00 0.00 3.95
819 824 7.044798 CACTTTTAAGGGTTGAAAAACATGGA 58.955 34.615 0.00 0.00 32.77 3.41
822 827 7.616313 TGACACTTTTAAGGGTTGAAAAACAT 58.384 30.769 0.00 0.00 44.15 2.71
898 905 1.453197 CACCGACCCCAATAAGGCC 60.453 63.158 0.00 0.00 35.39 5.19
899 906 0.463833 CTCACCGACCCCAATAAGGC 60.464 60.000 0.00 0.00 35.39 4.35
900 907 1.200519 TCTCACCGACCCCAATAAGG 58.799 55.000 0.00 0.00 37.03 2.69
901 908 3.560636 ATTCTCACCGACCCCAATAAG 57.439 47.619 0.00 0.00 0.00 1.73
902 909 3.616219 CAATTCTCACCGACCCCAATAA 58.384 45.455 0.00 0.00 0.00 1.40
903 910 2.092646 CCAATTCTCACCGACCCCAATA 60.093 50.000 0.00 0.00 0.00 1.90
904 911 1.340991 CCAATTCTCACCGACCCCAAT 60.341 52.381 0.00 0.00 0.00 3.16
905 912 0.037590 CCAATTCTCACCGACCCCAA 59.962 55.000 0.00 0.00 0.00 4.12
906 913 1.682849 CCAATTCTCACCGACCCCA 59.317 57.895 0.00 0.00 0.00 4.96
907 914 1.749258 GCCAATTCTCACCGACCCC 60.749 63.158 0.00 0.00 0.00 4.95
927 934 2.007608 GCTGGTCGTGGGAATAACTTC 58.992 52.381 0.00 0.00 0.00 3.01
933 940 1.141053 GATAAGGCTGGTCGTGGGAAT 59.859 52.381 0.00 0.00 0.00 3.01
1050 1057 0.766131 TGTTCGGGGTTTTGGAGCTA 59.234 50.000 0.00 0.00 0.00 3.32
1052 1059 0.822121 AGTGTTCGGGGTTTTGGAGC 60.822 55.000 0.00 0.00 0.00 4.70
1209 1216 0.475906 CATCATCCTCCACCCCTTCC 59.524 60.000 0.00 0.00 0.00 3.46
1256 1263 2.663196 CCTCCACGTCCAACTCCC 59.337 66.667 0.00 0.00 0.00 4.30
1377 1385 2.586635 GACCACACCGCACGACAA 60.587 61.111 0.00 0.00 0.00 3.18
1379 1387 4.936823 ACGACCACACCGCACGAC 62.937 66.667 0.00 0.00 0.00 4.34
1444 1462 4.037690 CGAAGCAAAAGTGAAAAGACCAG 58.962 43.478 0.00 0.00 0.00 4.00
1468 1489 8.773033 AGTCTATAAATGCAAGGGAATGAATT 57.227 30.769 0.00 0.00 29.39 2.17
1488 1510 9.998106 AAGCTTCAAAGTTTTCACTATAGTCTA 57.002 29.630 1.26 0.00 30.68 2.59
1489 1511 8.910351 AAGCTTCAAAGTTTTCACTATAGTCT 57.090 30.769 1.26 0.00 30.68 3.24
1490 1512 8.231161 GGAAGCTTCAAAGTTTTCACTATAGTC 58.769 37.037 27.02 0.00 30.68 2.59
1491 1513 7.095187 CGGAAGCTTCAAAGTTTTCACTATAGT 60.095 37.037 27.02 0.00 30.68 2.12
1492 1514 7.237173 CGGAAGCTTCAAAGTTTTCACTATAG 58.763 38.462 27.02 0.00 30.68 1.31
1501 1523 1.398692 TGCCGGAAGCTTCAAAGTTT 58.601 45.000 27.02 0.00 44.23 2.66
1551 1910 6.128200 CGACCACACTGTATTGTACTGTACTA 60.128 42.308 17.98 11.58 38.55 1.82
1552 1911 5.335426 CGACCACACTGTATTGTACTGTACT 60.335 44.000 17.98 2.56 38.55 2.73
1553 1912 4.855388 CGACCACACTGTATTGTACTGTAC 59.145 45.833 10.98 10.98 38.55 2.90
1554 1913 4.082625 CCGACCACACTGTATTGTACTGTA 60.083 45.833 0.00 0.00 38.55 2.74
1555 1914 3.305813 CCGACCACACTGTATTGTACTGT 60.306 47.826 0.00 0.00 40.80 3.55
1556 1915 3.250744 CCGACCACACTGTATTGTACTG 58.749 50.000 0.00 0.00 0.00 2.74
1557 1916 2.232941 CCCGACCACACTGTATTGTACT 59.767 50.000 0.00 0.00 0.00 2.73
1558 1917 2.028748 ACCCGACCACACTGTATTGTAC 60.029 50.000 0.00 0.00 0.00 2.90
1611 1971 0.168128 CACAAAATTCCTCGTCGGGC 59.832 55.000 0.00 0.00 0.00 6.13
1908 2861 7.913674 AGTGAATGAAGTAAGCTTTTAGAGG 57.086 36.000 3.20 0.00 34.61 3.69
2252 3205 8.715191 TGCAGAAACAAACTGAAATTATGTTT 57.285 26.923 2.18 2.18 44.36 2.83
2260 3213 6.529829 GTGTACATTGCAGAAACAAACTGAAA 59.470 34.615 0.00 0.00 37.32 2.69
2749 3707 7.537715 TGAGTCGTTACGAGGTAAATATTGAA 58.462 34.615 8.02 0.00 36.23 2.69
2764 3722 5.065602 AGGGAAACAAAACTTGAGTCGTTAC 59.934 40.000 0.00 0.00 0.00 2.50
2863 3823 7.547227 ACAATGGGTAACTCAAAAATGATAGC 58.453 34.615 0.00 0.00 0.00 2.97
3166 4129 6.096001 ACCTAAAAGATCATTCCAGCATTGTC 59.904 38.462 0.00 0.00 0.00 3.18
3211 4174 7.168972 CAGTGCTAGTATCAAGTTCTCATTAGC 59.831 40.741 0.00 0.00 33.46 3.09
3224 4208 8.237811 TCACAAAGATATCAGTGCTAGTATCA 57.762 34.615 14.52 0.00 32.25 2.15
3225 4209 9.703892 AATCACAAAGATATCAGTGCTAGTATC 57.296 33.333 14.52 0.00 35.39 2.24
3226 4210 9.486497 CAATCACAAAGATATCAGTGCTAGTAT 57.514 33.333 14.52 4.29 35.39 2.12
3227 4211 8.478066 ACAATCACAAAGATATCAGTGCTAGTA 58.522 33.333 14.52 0.00 35.39 1.82
3228 4212 7.279536 CACAATCACAAAGATATCAGTGCTAGT 59.720 37.037 14.52 10.62 35.39 2.57
3229 4213 7.628235 CACAATCACAAAGATATCAGTGCTAG 58.372 38.462 14.52 10.19 35.39 3.42
3230 4214 6.037500 GCACAATCACAAAGATATCAGTGCTA 59.962 38.462 14.52 3.67 42.14 3.49
3231 4215 5.163683 GCACAATCACAAAGATATCAGTGCT 60.164 40.000 14.52 6.02 42.14 4.40
3232 4216 5.032863 GCACAATCACAAAGATATCAGTGC 58.967 41.667 14.52 0.00 40.60 4.40
3233 4217 6.255950 CAGCACAATCACAAAGATATCAGTG 58.744 40.000 5.32 10.49 35.39 3.66
3234 4218 5.163683 GCAGCACAATCACAAAGATATCAGT 60.164 40.000 5.32 0.00 35.39 3.41
3235 4219 5.066117 AGCAGCACAATCACAAAGATATCAG 59.934 40.000 5.32 0.00 35.39 2.90
3236 4220 4.945543 AGCAGCACAATCACAAAGATATCA 59.054 37.500 5.32 0.00 35.39 2.15
3237 4221 5.496133 AGCAGCACAATCACAAAGATATC 57.504 39.130 0.00 0.00 35.39 1.63
3238 4222 8.681486 TTATAGCAGCACAATCACAAAGATAT 57.319 30.769 0.00 0.00 35.39 1.63
3239 4223 8.681486 ATTATAGCAGCACAATCACAAAGATA 57.319 30.769 0.00 0.00 35.39 1.98
3240 4224 7.578310 ATTATAGCAGCACAATCACAAAGAT 57.422 32.000 0.00 0.00 39.09 2.40
3241 4225 8.504812 TTATTATAGCAGCACAATCACAAAGA 57.495 30.769 0.00 0.00 0.00 2.52
3242 4226 9.571810 TTTTATTATAGCAGCACAATCACAAAG 57.428 29.630 0.00 0.00 0.00 2.77
3243 4227 9.571810 CTTTTATTATAGCAGCACAATCACAAA 57.428 29.630 0.00 0.00 0.00 2.83
3244 4228 8.955388 TCTTTTATTATAGCAGCACAATCACAA 58.045 29.630 0.00 0.00 0.00 3.33
3364 4348 5.709164 AGAGTTGGAAGACAATTGATTCTGG 59.291 40.000 13.59 0.00 41.95 3.86
3365 4349 6.609533 CAGAGTTGGAAGACAATTGATTCTG 58.390 40.000 13.59 5.88 41.95 3.02
3366 4350 6.814506 CAGAGTTGGAAGACAATTGATTCT 57.185 37.500 13.59 2.25 41.95 2.40
3445 4429 8.020819 GCCGAGCAGCAAATAAATATAAATACA 58.979 33.333 0.00 0.00 0.00 2.29
3468 4452 3.323403 AGGAATAGAGGAAAGATGAGCCG 59.677 47.826 0.00 0.00 0.00 5.52
3588 4573 6.418057 AGGCCAAACATTATCTGAACAAAA 57.582 33.333 5.01 0.00 0.00 2.44
3689 4676 4.715297 TCCAATCCTTCTAGTCCCTGTAAC 59.285 45.833 0.00 0.00 0.00 2.50
3948 4935 1.673993 CAGCATACCGGTGTTGGCA 60.674 57.895 19.93 0.00 38.36 4.92
3971 4958 3.763097 TGTATTTCTGCGGCATTTGAG 57.237 42.857 1.75 0.00 0.00 3.02
4357 5344 4.461081 ACACGAAGCTTCTCTCTTACATCT 59.539 41.667 23.50 0.00 0.00 2.90
4734 5724 6.803154 AGCAAGAAAGTTACAGTAACCATC 57.197 37.500 18.27 16.00 39.47 3.51
4807 5797 4.082571 GCATGTCCAGTAAGCACAGAAAAT 60.083 41.667 0.00 0.00 0.00 1.82
5475 6476 5.412526 TTTCTTTTCGAACGTAGCAACAT 57.587 34.783 0.00 0.00 0.00 2.71
5512 6513 0.245539 TGCCGTGGTACTGCTAACTC 59.754 55.000 0.00 0.00 0.00 3.01
5517 6518 2.584608 GGATGCCGTGGTACTGCT 59.415 61.111 0.00 0.00 0.00 4.24
5524 6525 1.000896 AGGAAAAGGGATGCCGTGG 60.001 57.895 0.00 0.00 0.00 4.94
5583 6584 0.803380 GAACCTCATTGGCGCATTGC 60.803 55.000 10.83 0.00 45.38 3.56
5722 6726 5.694910 AGTGCAGCAAAAGATCAAATTTCAG 59.305 36.000 0.00 0.00 0.00 3.02
5783 6788 5.355910 ACAAACGTAAAACTATGGCCTATGG 59.644 40.000 3.32 0.26 0.00 2.74
5784 6789 6.092944 TCACAAACGTAAAACTATGGCCTATG 59.907 38.462 3.32 0.00 0.00 2.23
5785 6790 6.093082 GTCACAAACGTAAAACTATGGCCTAT 59.907 38.462 3.32 0.00 0.00 2.57
5786 6791 5.409214 GTCACAAACGTAAAACTATGGCCTA 59.591 40.000 3.32 0.00 0.00 3.93
5787 6792 4.214758 GTCACAAACGTAAAACTATGGCCT 59.785 41.667 3.32 0.00 0.00 5.19
5788 6793 4.023878 TGTCACAAACGTAAAACTATGGCC 60.024 41.667 0.00 0.00 0.00 5.36
5789 6794 5.098218 TGTCACAAACGTAAAACTATGGC 57.902 39.130 0.00 0.00 0.00 4.40
5840 6845 8.821894 GTTTGCTTAAATTGTGTAAAATGTGGA 58.178 29.630 0.00 0.00 0.00 4.02
5841 6846 8.825745 AGTTTGCTTAAATTGTGTAAAATGTGG 58.174 29.630 0.00 0.00 0.00 4.17
6003 7011 4.821589 GAGGAGGGGTTCGCGCAG 62.822 72.222 8.75 0.00 0.00 5.18
6037 7045 2.741092 GTCCTGAGCCCACACGAA 59.259 61.111 0.00 0.00 0.00 3.85
6038 7046 3.311110 GGTCCTGAGCCCACACGA 61.311 66.667 0.00 0.00 0.00 4.35
6039 7047 3.302347 GAGGTCCTGAGCCCACACG 62.302 68.421 0.00 0.00 0.00 4.49
6040 7048 2.665603 GAGGTCCTGAGCCCACAC 59.334 66.667 0.00 0.00 0.00 3.82
6041 7049 2.997315 CGAGGTCCTGAGCCCACA 60.997 66.667 0.00 0.00 0.00 4.17
6042 7050 2.680352 TCGAGGTCCTGAGCCCAC 60.680 66.667 0.00 0.00 0.00 4.61
6043 7051 2.680352 GTCGAGGTCCTGAGCCCA 60.680 66.667 0.00 0.00 0.00 5.36
6044 7052 3.462678 GGTCGAGGTCCTGAGCCC 61.463 72.222 0.00 0.00 0.00 5.19
6045 7053 3.827898 CGGTCGAGGTCCTGAGCC 61.828 72.222 0.00 0.00 0.00 4.70
6046 7054 4.500116 GCGGTCGAGGTCCTGAGC 62.500 72.222 0.00 3.33 0.00 4.26
6047 7055 3.827898 GGCGGTCGAGGTCCTGAG 61.828 72.222 0.00 0.00 0.00 3.35
6057 7065 0.788391 GGCTAATTAATCGGCGGTCG 59.212 55.000 7.21 0.00 40.90 4.79
6058 7066 0.788391 CGGCTAATTAATCGGCGGTC 59.212 55.000 19.40 0.00 42.10 4.79
6090 7098 2.349886 CACCGCTCTGCTAAGTTCATTC 59.650 50.000 0.00 0.00 0.00 2.67
6093 7101 0.679505 ACACCGCTCTGCTAAGTTCA 59.320 50.000 0.00 0.00 0.00 3.18
6105 7113 0.810031 GTGATCGCCATTACACCGCT 60.810 55.000 0.00 0.00 0.00 5.52
6159 7167 0.109132 GGAACCGTGTCCGAACGTAT 60.109 55.000 0.00 0.00 42.01 3.06
6161 7169 2.028043 GGAACCGTGTCCGAACGT 59.972 61.111 4.90 0.00 42.01 3.99
6172 7189 1.648467 GCTTGGCTAGCTTGGAACCG 61.648 60.000 15.72 0.00 46.77 4.44
6215 7232 9.878667 TGTGATTTAATTTCGTCTATAGGTCAA 57.121 29.630 0.00 0.00 0.00 3.18
6216 7233 9.529325 CTGTGATTTAATTTCGTCTATAGGTCA 57.471 33.333 0.00 0.00 0.00 4.02
6217 7234 9.745880 TCTGTGATTTAATTTCGTCTATAGGTC 57.254 33.333 0.00 0.00 0.00 3.85
6224 7241 9.003658 AGTTCATTCTGTGATTTAATTTCGTCT 57.996 29.630 0.00 0.00 36.54 4.18
6232 7249 9.430623 TCACGAATAGTTCATTCTGTGATTTAA 57.569 29.630 14.64 0.00 43.76 1.52
6233 7250 8.996024 TCACGAATAGTTCATTCTGTGATTTA 57.004 30.769 14.64 1.88 43.76 1.40
6234 7251 7.905604 TCACGAATAGTTCATTCTGTGATTT 57.094 32.000 14.64 0.00 43.76 2.17
6235 7252 7.905604 TTCACGAATAGTTCATTCTGTGATT 57.094 32.000 17.15 0.00 45.52 2.57
6236 7253 7.604164 AGTTTCACGAATAGTTCATTCTGTGAT 59.396 33.333 17.15 7.47 45.52 3.06
6237 7254 6.929049 AGTTTCACGAATAGTTCATTCTGTGA 59.071 34.615 14.64 14.64 45.11 3.58
6238 7255 7.121974 AGTTTCACGAATAGTTCATTCTGTG 57.878 36.000 0.00 11.93 42.74 3.66
6239 7256 9.436957 AATAGTTTCACGAATAGTTCATTCTGT 57.563 29.630 0.00 0.00 40.89 3.41
6256 7273 0.800012 GGCCGCGTGAAATAGTTTCA 59.200 50.000 4.92 1.24 46.68 2.69
6257 7274 0.247537 CGGCCGCGTGAAATAGTTTC 60.248 55.000 14.67 0.00 40.08 2.78
6258 7275 0.671163 TCGGCCGCGTGAAATAGTTT 60.671 50.000 23.51 0.00 0.00 2.66
6259 7276 1.079681 TCGGCCGCGTGAAATAGTT 60.080 52.632 23.51 0.00 0.00 2.24
6260 7277 1.808390 GTCGGCCGCGTGAAATAGT 60.808 57.895 23.51 0.00 0.00 2.12
6261 7278 2.522638 GGTCGGCCGCGTGAAATAG 61.523 63.158 23.51 0.00 0.00 1.73
6262 7279 2.509786 GGTCGGCCGCGTGAAATA 60.510 61.111 23.51 0.00 0.00 1.40
6263 7280 3.894547 AAGGTCGGCCGCGTGAAAT 62.895 57.895 23.51 0.00 40.50 2.17
6264 7281 4.612412 AAGGTCGGCCGCGTGAAA 62.612 61.111 23.51 0.00 40.50 2.69
6265 7282 4.612412 AAAGGTCGGCCGCGTGAA 62.612 61.111 23.51 0.00 40.50 3.18
6266 7283 4.612412 AAAAGGTCGGCCGCGTGA 62.612 61.111 23.51 0.00 40.50 4.35
6267 7284 3.656045 AAAAAGGTCGGCCGCGTG 61.656 61.111 23.51 0.00 40.50 5.34
6268 7285 3.656045 CAAAAAGGTCGGCCGCGT 61.656 61.111 23.51 14.69 40.50 6.01
6269 7286 3.656045 ACAAAAAGGTCGGCCGCG 61.656 61.111 23.51 0.00 40.50 6.46
6270 7287 2.050442 CACAAAAAGGTCGGCCGC 60.050 61.111 23.51 16.04 40.50 6.53
6271 7288 1.008995 CACACAAAAAGGTCGGCCG 60.009 57.895 22.12 22.12 40.50 6.13
6272 7289 0.030235 GTCACACAAAAAGGTCGGCC 59.970 55.000 0.00 0.00 0.00 6.13
6273 7290 0.316689 CGTCACACAAAAAGGTCGGC 60.317 55.000 0.00 0.00 0.00 5.54
6274 7291 0.316689 GCGTCACACAAAAAGGTCGG 60.317 55.000 0.00 0.00 0.00 4.79
6275 7292 0.316689 GGCGTCACACAAAAAGGTCG 60.317 55.000 0.00 0.00 0.00 4.79
6276 7293 0.030235 GGGCGTCACACAAAAAGGTC 59.970 55.000 0.00 0.00 0.00 3.85
6277 7294 1.720694 CGGGCGTCACACAAAAAGGT 61.721 55.000 0.00 0.00 0.00 3.50
6278 7295 1.008995 CGGGCGTCACACAAAAAGG 60.009 57.895 0.00 0.00 0.00 3.11
6279 7296 0.316689 GTCGGGCGTCACACAAAAAG 60.317 55.000 0.00 0.00 0.00 2.27
6280 7297 1.722677 GTCGGGCGTCACACAAAAA 59.277 52.632 0.00 0.00 0.00 1.94
6281 7298 2.526993 CGTCGGGCGTCACACAAAA 61.527 57.895 0.00 0.00 35.54 2.44
6282 7299 2.962786 CGTCGGGCGTCACACAAA 60.963 61.111 0.00 0.00 35.54 2.83
6300 7317 2.048597 TGTAGTGTGGCGCCTTCG 60.049 61.111 29.70 0.00 39.07 3.79
6301 7318 1.004918 AGTGTAGTGTGGCGCCTTC 60.005 57.895 29.70 20.58 0.00 3.46
6302 7319 1.301716 CAGTGTAGTGTGGCGCCTT 60.302 57.895 29.70 13.03 0.00 4.35
6303 7320 2.343758 CAGTGTAGTGTGGCGCCT 59.656 61.111 29.70 9.99 0.00 5.52
6304 7321 2.030562 ACAGTGTAGTGTGGCGCC 59.969 61.111 22.73 22.73 0.00 6.53
6305 7322 2.954753 GCACAGTGTAGTGTGGCGC 61.955 63.158 18.52 0.00 46.73 6.53
6306 7323 1.157257 TTGCACAGTGTAGTGTGGCG 61.157 55.000 18.52 0.00 46.73 5.69
6307 7324 0.307760 GTTGCACAGTGTAGTGTGGC 59.692 55.000 18.52 12.34 46.73 5.01
6308 7325 0.581529 CGTTGCACAGTGTAGTGTGG 59.418 55.000 18.52 1.81 46.73 4.17
6310 7327 1.157870 GGCGTTGCACAGTGTAGTGT 61.158 55.000 1.61 0.00 41.52 3.55
6311 7328 0.880278 AGGCGTTGCACAGTGTAGTG 60.880 55.000 1.61 0.00 42.37 2.74
6312 7329 0.179056 AAGGCGTTGCACAGTGTAGT 60.179 50.000 1.61 0.00 0.00 2.73
6313 7330 1.459592 GTAAGGCGTTGCACAGTGTAG 59.540 52.381 1.61 0.00 0.00 2.74
6314 7331 1.202545 TGTAAGGCGTTGCACAGTGTA 60.203 47.619 5.79 0.00 0.00 2.90
6315 7332 0.462937 TGTAAGGCGTTGCACAGTGT 60.463 50.000 5.79 0.00 0.00 3.55
6316 7333 0.041312 GTGTAAGGCGTTGCACAGTG 60.041 55.000 27.99 0.00 45.71 3.66
6317 7334 2.317230 GTGTAAGGCGTTGCACAGT 58.683 52.632 27.99 0.00 45.71 3.55
6320 7337 1.396996 CCTATGTGTAAGGCGTTGCAC 59.603 52.381 26.80 26.80 46.37 4.57
6321 7338 1.732941 CCTATGTGTAAGGCGTTGCA 58.267 50.000 5.79 5.79 0.00 4.08
6328 7345 2.470821 GTGTAGCGCCTATGTGTAAGG 58.529 52.381 2.29 0.00 37.17 2.69
6329 7346 2.117137 CGTGTAGCGCCTATGTGTAAG 58.883 52.381 2.29 0.00 0.00 2.34
6330 7347 1.202325 CCGTGTAGCGCCTATGTGTAA 60.202 52.381 2.29 0.00 39.71 2.41
6331 7348 0.382873 CCGTGTAGCGCCTATGTGTA 59.617 55.000 2.29 0.00 39.71 2.90
6332 7349 1.141019 CCGTGTAGCGCCTATGTGT 59.859 57.895 2.29 0.00 39.71 3.72
6333 7350 2.237751 GCCGTGTAGCGCCTATGTG 61.238 63.158 2.29 0.00 39.71 3.21
6334 7351 2.106332 GCCGTGTAGCGCCTATGT 59.894 61.111 2.29 0.00 39.71 2.29
6335 7352 2.661866 GGCCGTGTAGCGCCTATG 60.662 66.667 2.29 0.00 39.71 2.23
6336 7353 3.151710 TGGCCGTGTAGCGCCTAT 61.152 61.111 2.29 0.00 39.71 2.57
6337 7354 3.833645 CTGGCCGTGTAGCGCCTA 61.834 66.667 2.29 0.00 39.71 3.93
6355 7372 3.179265 GATCACACGGGTGCGACG 61.179 66.667 14.50 0.00 44.87 5.12
6356 7373 2.048597 TGATCACACGGGTGCGAC 60.049 61.111 14.50 7.33 44.87 5.19
6357 7374 1.811645 TTCTGATCACACGGGTGCGA 61.812 55.000 14.50 3.83 44.87 5.10
6358 7375 0.948623 TTTCTGATCACACGGGTGCG 60.949 55.000 14.50 1.20 44.87 5.34
6359 7376 1.234821 TTTTCTGATCACACGGGTGC 58.765 50.000 14.50 0.00 44.87 5.01
6360 7377 4.695455 AGTAATTTTCTGATCACACGGGTG 59.305 41.667 12.84 12.84 46.66 4.61
6361 7378 4.906618 AGTAATTTTCTGATCACACGGGT 58.093 39.130 0.00 0.00 0.00 5.28
6362 7379 6.594159 ACTTAGTAATTTTCTGATCACACGGG 59.406 38.462 0.00 0.00 0.00 5.28
6363 7380 7.330946 TGACTTAGTAATTTTCTGATCACACGG 59.669 37.037 0.00 0.00 0.00 4.94
6364 7381 8.239681 TGACTTAGTAATTTTCTGATCACACG 57.760 34.615 0.00 0.00 0.00 4.49
6365 7382 9.209175 ACTGACTTAGTAATTTTCTGATCACAC 57.791 33.333 0.00 0.00 38.04 3.82
6366 7383 9.208022 CACTGACTTAGTAATTTTCTGATCACA 57.792 33.333 0.00 0.00 37.60 3.58
6367 7384 9.209175 ACACTGACTTAGTAATTTTCTGATCAC 57.791 33.333 0.00 0.00 37.60 3.06
6368 7385 9.208022 CACACTGACTTAGTAATTTTCTGATCA 57.792 33.333 0.00 0.00 37.60 2.92
6369 7386 8.171840 GCACACTGACTTAGTAATTTTCTGATC 58.828 37.037 0.00 0.00 37.60 2.92
6370 7387 7.661437 TGCACACTGACTTAGTAATTTTCTGAT 59.339 33.333 0.00 0.00 37.60 2.90
6371 7388 6.989759 TGCACACTGACTTAGTAATTTTCTGA 59.010 34.615 0.00 0.00 37.60 3.27
6372 7389 7.189693 TGCACACTGACTTAGTAATTTTCTG 57.810 36.000 0.00 0.00 37.60 3.02
6373 7390 6.073003 GCTGCACACTGACTTAGTAATTTTCT 60.073 38.462 0.00 0.00 37.60 2.52
6374 7391 6.080406 GCTGCACACTGACTTAGTAATTTTC 58.920 40.000 0.00 0.00 37.60 2.29
6375 7392 5.334105 CGCTGCACACTGACTTAGTAATTTT 60.334 40.000 0.00 0.00 37.60 1.82
6376 7393 4.152402 CGCTGCACACTGACTTAGTAATTT 59.848 41.667 0.00 0.00 37.60 1.82
6377 7394 3.679980 CGCTGCACACTGACTTAGTAATT 59.320 43.478 0.00 0.00 37.60 1.40
6378 7395 3.254060 CGCTGCACACTGACTTAGTAAT 58.746 45.455 0.00 0.00 37.60 1.89
6379 7396 2.672714 CGCTGCACACTGACTTAGTAA 58.327 47.619 0.00 0.00 37.60 2.24
6380 7397 1.668919 GCGCTGCACACTGACTTAGTA 60.669 52.381 0.00 0.00 37.60 1.82
6381 7398 0.946221 GCGCTGCACACTGACTTAGT 60.946 55.000 0.00 0.00 41.36 2.24
6382 7399 1.630244 GGCGCTGCACACTGACTTAG 61.630 60.000 7.64 0.00 0.00 2.18
6383 7400 1.667830 GGCGCTGCACACTGACTTA 60.668 57.895 7.64 0.00 0.00 2.24
6384 7401 2.974698 GGCGCTGCACACTGACTT 60.975 61.111 7.64 0.00 0.00 3.01
6385 7402 3.933722 AGGCGCTGCACACTGACT 61.934 61.111 7.64 0.00 0.00 3.41
6386 7403 3.720193 CAGGCGCTGCACACTGAC 61.720 66.667 7.64 0.00 32.86 3.51
6387 7404 3.871248 CTCAGGCGCTGCACACTGA 62.871 63.158 7.64 9.54 37.61 3.41
6388 7405 3.420606 CTCAGGCGCTGCACACTG 61.421 66.667 7.64 4.89 0.00 3.66
6389 7406 3.586461 CTCTCAGGCGCTGCACACT 62.586 63.158 7.64 0.00 0.00 3.55
6390 7407 3.117171 CTCTCAGGCGCTGCACAC 61.117 66.667 7.64 0.00 0.00 3.82
6392 7409 3.362399 TAGCTCTCAGGCGCTGCAC 62.362 63.158 7.64 0.00 37.05 4.57
6393 7410 3.070576 TAGCTCTCAGGCGCTGCA 61.071 61.111 7.64 0.00 37.05 4.41
6394 7411 2.279385 CTAGCTCTCAGGCGCTGC 60.279 66.667 7.64 2.66 37.05 5.25
6395 7412 2.416678 CCTAGCTCTCAGGCGCTG 59.583 66.667 7.64 3.67 37.05 5.18
6408 7425 0.530650 CTGTATGGTGTGGCGCCTAG 60.531 60.000 29.70 7.79 34.70 3.02
6409 7426 1.261938 ACTGTATGGTGTGGCGCCTA 61.262 55.000 29.70 14.39 34.70 3.93
6410 7427 2.268920 CTGTATGGTGTGGCGCCT 59.731 61.111 29.70 8.67 34.70 5.52
6411 7428 2.046314 ACTGTATGGTGTGGCGCC 60.046 61.111 22.73 22.73 34.12 6.53
6412 7429 1.671054 ACACTGTATGGTGTGGCGC 60.671 57.895 0.00 0.00 46.93 6.53
6413 7430 4.693532 ACACTGTATGGTGTGGCG 57.306 55.556 0.00 0.00 46.93 5.69
6418 7435 0.175760 AGGCGCTACACTGTATGGTG 59.824 55.000 7.64 0.00 42.34 4.17
6419 7436 1.681793 CTAGGCGCTACACTGTATGGT 59.318 52.381 7.64 0.00 0.00 3.55
6420 7437 1.603172 GCTAGGCGCTACACTGTATGG 60.603 57.143 7.64 0.00 35.14 2.74
6421 7438 1.772182 GCTAGGCGCTACACTGTATG 58.228 55.000 7.64 0.00 35.14 2.39
6436 7453 0.528684 GTGCAACGCCTAGGAGCTAG 60.529 60.000 14.75 3.92 34.16 3.42
6437 7454 0.970937 AGTGCAACGCCTAGGAGCTA 60.971 55.000 14.75 0.00 45.86 3.32
6438 7455 0.970937 TAGTGCAACGCCTAGGAGCT 60.971 55.000 14.75 3.79 45.86 4.09
6439 7456 0.528684 CTAGTGCAACGCCTAGGAGC 60.529 60.000 14.75 10.85 45.86 4.70
6440 7457 0.818296 ACTAGTGCAACGCCTAGGAG 59.182 55.000 14.75 12.99 45.86 3.69
6441 7458 0.530744 CACTAGTGCAACGCCTAGGA 59.469 55.000 14.75 0.00 45.86 2.94
6442 7459 3.050703 CACTAGTGCAACGCCTAGG 57.949 57.895 10.54 3.67 45.86 3.02


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

AutoCloner maintained by Alex Coulton.