Multiple sequence alignment - TraesCS3D01G191700

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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 TraesCS3D01G191700 chr3D 100.000 9041 0 0 1 9041 181572548 181563508 0.000000e+00 16696.0
1 TraesCS3D01G191700 chr3D 88.889 108 9 2 1795 1901 266427090 266427195 7.370000e-26 130.0
2 TraesCS3D01G191700 chr3D 100.000 40 0 0 8332 8371 571593492 571593453 3.500000e-09 75.0
3 TraesCS3D01G191700 chr3B 94.765 7488 242 72 806 8167 259858832 259851369 0.000000e+00 11518.0
4 TraesCS3D01G191700 chr3B 96.944 720 21 1 3 722 259859870 259859152 0.000000e+00 1206.0
5 TraesCS3D01G191700 chr3B 94.444 144 8 0 6131 6274 766145334 766145191 1.180000e-53 222.0
6 TraesCS3D01G191700 chr3A 95.343 4939 150 39 3 4865 227407325 227412259 0.000000e+00 7773.0
7 TraesCS3D01G191700 chr3A 95.768 3403 97 21 4863 8221 227412385 227415784 0.000000e+00 5443.0
8 TraesCS3D01G191700 chr3A 83.683 668 64 18 8379 9041 227415784 227416411 1.010000e-163 588.0
9 TraesCS3D01G191700 chr5D 96.217 423 13 1 172 594 35981667 35981248 0.000000e+00 689.0
10 TraesCS3D01G191700 chr5D 94.444 144 8 0 6131 6274 69904768 69904625 1.180000e-53 222.0
11 TraesCS3D01G191700 chr5D 100.000 41 0 0 8331 8371 503288168 503288128 9.730000e-10 76.8
12 TraesCS3D01G191700 chr5D 100.000 40 0 0 8332 8371 512408683 512408722 3.500000e-09 75.0
13 TraesCS3D01G191700 chr5D 100.000 40 0 0 8332 8371 512415619 512415658 3.500000e-09 75.0
14 TraesCS3D01G191700 chr7A 74.850 668 106 34 8407 9041 518764694 518765332 7.010000e-61 246.0
15 TraesCS3D01G191700 chr4A 77.859 411 74 15 8637 9041 135676445 135676844 1.170000e-58 239.0
16 TraesCS3D01G191700 chr4A 94.444 144 8 0 6131 6274 64574173 64574030 1.180000e-53 222.0
17 TraesCS3D01G191700 chr5B 95.035 141 7 0 6131 6271 474459402 474459542 1.180000e-53 222.0
18 TraesCS3D01G191700 chr5B 87.413 143 17 1 8900 9041 278852744 278852602 7.260000e-36 163.0
19 TraesCS3D01G191700 chr5B 89.157 83 6 2 1819 1900 535463348 535463268 5.780000e-17 100.0
20 TraesCS3D01G191700 chr5B 87.356 87 9 1 1809 1895 535459047 535458963 2.080000e-16 99.0
21 TraesCS3D01G191700 chr5B 84.259 108 7 5 8234 8332 674272254 674272360 7.470000e-16 97.1
22 TraesCS3D01G191700 chr4D 94.444 144 8 0 6131 6274 23322868 23322725 1.180000e-53 222.0
23 TraesCS3D01G191700 chr1B 95.035 141 7 0 6131 6271 642706395 642706535 1.180000e-53 222.0
24 TraesCS3D01G191700 chr1B 85.185 108 14 2 8935 9041 662489454 662489560 9.600000e-20 110.0
25 TraesCS3D01G191700 chr1A 95.035 141 7 0 6131 6271 244176883 244177023 1.180000e-53 222.0
26 TraesCS3D01G191700 chr6D 80.795 151 23 4 1754 1900 4547147 4547295 7.420000e-21 113.0
27 TraesCS3D01G191700 chr6D 100.000 40 0 0 8332 8371 45510705 45510744 3.500000e-09 75.0
28 TraesCS3D01G191700 chr2A 76.126 222 48 4 8407 8625 771551602 771551821 2.670000e-20 111.0
29 TraesCS3D01G191700 chr5A 96.000 50 2 0 1851 1900 556238936 556238887 2.090000e-11 82.4
30 TraesCS3D01G191700 chr5A 100.000 40 0 0 8332 8371 607199237 607199276 3.500000e-09 75.0
31 TraesCS3D01G191700 chr7D 100.000 40 0 0 8332 8371 77242108 77242069 3.500000e-09 75.0
32 TraesCS3D01G191700 chr7D 100.000 40 0 0 8332 8371 231534775 231534814 3.500000e-09 75.0
33 TraesCS3D01G191700 chr1D 100.000 40 0 0 8332 8371 51877209 51877248 3.500000e-09 75.0


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 TraesCS3D01G191700 chr3D 181563508 181572548 9040 True 16696.000000 16696 100.0000 1 9041 1 chr3D.!!$R1 9040
1 TraesCS3D01G191700 chr3B 259851369 259859870 8501 True 6362.000000 11518 95.8545 3 8167 2 chr3B.!!$R2 8164
2 TraesCS3D01G191700 chr3A 227407325 227416411 9086 False 4601.333333 7773 91.5980 3 9041 3 chr3A.!!$F1 9038
3 TraesCS3D01G191700 chr7A 518764694 518765332 638 False 246.000000 246 74.8500 8407 9041 1 chr7A.!!$F1 634

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
74 77 0.034896 CACGTTGCACTTACCCTCCT 59.965 55.000 0.00 0.0 0.00 3.69 F
352 355 1.078567 GACTTCAGAGGCAGCAGGG 60.079 63.158 0.00 0.0 0.00 4.45 F
1327 1570 1.996798 GGATACTGATCCCGTCCTGA 58.003 55.000 0.00 0.0 45.48 3.86 F
2477 2728 0.727398 CCATCTCGGCGTTTTCTTCC 59.273 55.000 6.85 0.0 0.00 3.46 F
3193 3512 1.339824 GGGGTCGAGTAGAGTCACAGA 60.340 57.143 0.00 0.0 0.00 3.41 F
3437 3758 2.887152 GCATGGTAGAATAAAGGGCTGG 59.113 50.000 0.00 0.0 0.00 4.85 F
4315 4637 3.708563 TCAAAGCTAACAAGGCAACAC 57.291 42.857 0.00 0.0 41.41 3.32 F
6146 6624 0.615331 GGAGCCTTGTGACCATGAGA 59.385 55.000 0.00 0.0 0.00 3.27 F
6412 6901 0.465824 AGTCCCACGTATCTCCTCGG 60.466 60.000 0.00 0.0 0.00 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1113 1356 0.036294 CCACTTCTCCCTTCGGGTTC 60.036 60.000 0.00 0.0 44.74 3.62 R
1613 1856 3.319405 AGACAGTAAGCTCGGTGATATGG 59.681 47.826 0.00 0.0 0.00 2.74 R
3134 3409 2.897271 ATAATGTGGGTCCAGCACAA 57.103 45.000 5.21 0.0 32.25 3.33 R
3889 4211 2.262637 ACGGGAAGTTGGAGGAATACA 58.737 47.619 0.00 0.0 0.00 2.29 R
4288 4610 2.424956 CCTTGTTAGCTTTGATCCAGCC 59.575 50.000 9.79 0.0 38.09 4.85 R
5036 5511 5.883685 ACATCATATCATGACCTGAGTGT 57.116 39.130 12.94 13.0 43.01 3.55 R
6186 6672 1.200519 TGTACGCAGCCTTTCCCTAT 58.799 50.000 0.00 0.0 0.00 2.57 R
7875 8387 0.035534 CATTCATCCCCACACGACCA 60.036 55.000 0.00 0.0 0.00 4.02 R
8308 8840 0.025001 CTGTTCGGCAAATCGCTACG 59.975 55.000 0.00 0.0 41.91 3.51 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
27 28 8.842358 TGGAAAGAACAGAACGAGTAATTTAT 57.158 30.769 0.00 0.00 0.00 1.40
32 33 9.924650 AAGAACAGAACGAGTAATTTATACAGT 57.075 29.630 0.00 0.00 0.00 3.55
74 77 0.034896 CACGTTGCACTTACCCTCCT 59.965 55.000 0.00 0.00 0.00 3.69
161 164 3.199508 ACCTTCTCAGGGTGATCAATCAG 59.800 47.826 0.00 0.00 46.01 2.90
352 355 1.078567 GACTTCAGAGGCAGCAGGG 60.079 63.158 0.00 0.00 0.00 4.45
394 400 3.802685 CAGGCGTACTAGCTTTATTCCAC 59.197 47.826 0.00 0.00 37.29 4.02
406 412 7.352079 AGCTTTATTCCACCCAATTGAATAG 57.648 36.000 7.12 0.00 33.76 1.73
444 450 7.595819 TCCACAAAACTTGTCCAATAGAAAT 57.404 32.000 0.00 0.00 43.23 2.17
550 556 2.665165 AGTGCTGAAAAATGTGTGGGA 58.335 42.857 0.00 0.00 0.00 4.37
580 586 3.278574 GGTGCAACAACCATCTGCTATA 58.721 45.455 0.00 0.00 39.98 1.31
640 646 4.448060 GGTGAGAAAGTTACAGACGGAAAG 59.552 45.833 0.00 0.00 0.00 2.62
732 738 4.036852 CAGTTGATAGCTCACACCGAGATA 59.963 45.833 0.00 0.00 46.25 1.98
746 752 5.163478 ACACCGAGATACCAACAGTAATACC 60.163 44.000 0.00 0.00 33.70 2.73
747 753 5.068723 CACCGAGATACCAACAGTAATACCT 59.931 44.000 0.00 0.00 33.70 3.08
784 790 9.520515 TCTCCCCTGAAATATTTATTTATCTGC 57.479 33.333 0.00 0.00 36.13 4.26
1063 1306 7.518731 TTTTTGTGTTTTGTAGCATGTCTTC 57.481 32.000 0.00 0.00 0.00 2.87
1113 1356 3.643595 ATGGTGCACCCCACATCCG 62.644 63.158 32.62 0.00 46.50 4.18
1121 1364 2.666207 CCCACATCCGAACCCGAA 59.334 61.111 0.00 0.00 38.22 4.30
1158 1401 8.541133 AGTTTAAGCAGAAGACAGATAAGTTC 57.459 34.615 0.00 0.00 0.00 3.01
1327 1570 1.996798 GGATACTGATCCCGTCCTGA 58.003 55.000 0.00 0.00 45.48 3.86
1613 1856 7.541916 AGGGTTATAATCTTCTACAGTAGCC 57.458 40.000 2.26 0.00 0.00 3.93
1622 1865 4.833380 TCTTCTACAGTAGCCCATATCACC 59.167 45.833 2.26 0.00 0.00 4.02
1741 1987 3.753294 AGGTGATACTTTATGCCCGAG 57.247 47.619 0.00 0.00 0.00 4.63
1745 1991 4.051922 GTGATACTTTATGCCCGAGACAG 58.948 47.826 0.00 0.00 0.00 3.51
1770 2017 5.705609 AAGTATTCGCCATGAAACTTTGT 57.294 34.783 0.00 0.00 40.71 2.83
1780 2027 6.603095 GCCATGAAACTTTGTAGACAAGTAG 58.397 40.000 0.00 0.00 37.15 2.57
1783 2030 8.709646 CCATGAAACTTTGTAGACAAGTAGTAC 58.290 37.037 0.00 0.00 37.15 2.73
1791 2038 9.517609 CTTTGTAGACAAGTAGTACATATCCAC 57.482 37.037 2.52 0.00 37.15 4.02
1794 2041 9.856162 TGTAGACAAGTAGTACATATCCACATA 57.144 33.333 2.52 0.00 0.00 2.29
1910 2157 4.508662 AGCAATTTCCGTTTTTCCAACAA 58.491 34.783 0.00 0.00 0.00 2.83
1920 2167 8.950208 TCCGTTTTTCCAACAAAAATAAATCT 57.050 26.923 0.00 0.00 32.55 2.40
1975 2222 8.279800 TGTCATTCGAAACAAAACTAGTATGTG 58.720 33.333 13.30 6.85 0.00 3.21
2114 2362 6.889722 ACACTAGTTGCATACCCAATGTTATT 59.110 34.615 0.00 0.00 37.93 1.40
2258 2508 6.996180 TCTCCTTCTAAAAAGACTTCAGGA 57.004 37.500 0.00 0.00 0.00 3.86
2403 2653 9.140052 CTTCTGCATGAATTCAGTTGCAAACAG 62.140 40.741 27.81 21.09 40.16 3.16
2477 2728 0.727398 CCATCTCGGCGTTTTCTTCC 59.273 55.000 6.85 0.00 0.00 3.46
3193 3512 1.339824 GGGGTCGAGTAGAGTCACAGA 60.340 57.143 0.00 0.00 0.00 3.41
3214 3533 6.384305 ACAGATATAAAGGCCTACTGTCAAGT 59.616 38.462 5.16 0.00 40.67 3.16
3437 3758 2.887152 GCATGGTAGAATAAAGGGCTGG 59.113 50.000 0.00 0.00 0.00 4.85
3522 3844 6.918022 CAGAAGGTTTGGTTAACTGAATGAAC 59.082 38.462 5.42 2.53 36.93 3.18
3889 4211 8.206126 ACAAAAGGGTTCAAGGAATATCAAAT 57.794 30.769 0.00 0.00 0.00 2.32
4055 4377 9.346005 TCAAGATTTGATATACTGTTGATGCAT 57.654 29.630 0.00 0.00 34.08 3.96
4315 4637 3.708563 TCAAAGCTAACAAGGCAACAC 57.291 42.857 0.00 0.00 41.41 3.32
4372 4694 6.530019 ACTCGCTTTTTATGATTTGGGAAT 57.470 33.333 0.00 0.00 0.00 3.01
4450 4772 5.278463 GCAACAAGTATCATCCACACAGTTT 60.278 40.000 0.00 0.00 0.00 2.66
4469 4791 9.620660 CACAGTTTAACAGAAACTAACAACTTT 57.379 29.630 2.55 0.00 38.32 2.66
4548 4895 4.552883 TCATGTCTATGACCCTAGGGAA 57.447 45.455 35.38 21.64 38.37 3.97
5036 5511 4.079787 ACTCTTCTTTAAGCCCATATGCCA 60.080 41.667 0.00 0.00 32.36 4.92
5448 5924 9.129209 GTCAACAAAATAGCATAAGAAGGAAAC 57.871 33.333 0.00 0.00 0.00 2.78
5642 6118 4.636249 CAGAAGAGAAGCAACACTACCTT 58.364 43.478 0.00 0.00 0.00 3.50
5879 6355 6.016777 GCTATAATGGCAGCTTGTATCTTGTT 60.017 38.462 0.00 0.00 34.86 2.83
6146 6624 0.615331 GGAGCCTTGTGACCATGAGA 59.385 55.000 0.00 0.00 0.00 3.27
6186 6672 6.121776 TGGAAACAGCCTCTTACAGAAATA 57.878 37.500 0.00 0.00 35.01 1.40
6217 6703 2.223618 GCTGCGTACAAAAGACCCAAAA 60.224 45.455 0.00 0.00 0.00 2.44
6241 6727 4.735599 GACCCTTCCCCGGACCCT 62.736 72.222 0.73 0.00 0.00 4.34
6370 6858 2.867429 CACCTTTATGAGCAAAAGCCG 58.133 47.619 0.00 0.00 33.48 5.52
6399 6888 0.846427 ATCTCCTGCCCAAAGTCCCA 60.846 55.000 0.00 0.00 0.00 4.37
6411 6900 1.390565 AAGTCCCACGTATCTCCTCG 58.609 55.000 0.00 0.00 0.00 4.63
6412 6901 0.465824 AGTCCCACGTATCTCCTCGG 60.466 60.000 0.00 0.00 0.00 4.63
6435 6924 1.609208 AAGAAAAGACGCTGCATGGT 58.391 45.000 0.00 0.00 0.00 3.55
6442 6931 1.208052 AGACGCTGCATGGTAATGACT 59.792 47.619 0.00 0.00 35.67 3.41
6472 6961 9.691362 GAGCAATAGTTTTTCTGTTTTCCATAA 57.309 29.630 0.00 0.00 0.00 1.90
6531 7020 4.513692 TGTATACGAAGCATGCATTAACCC 59.486 41.667 21.98 1.68 0.00 4.11
6532 7021 1.832883 ACGAAGCATGCATTAACCCA 58.167 45.000 21.98 0.00 0.00 4.51
6549 7040 5.855740 AACCCATAGAGTACAGAAGTAGC 57.144 43.478 0.00 0.00 0.00 3.58
6592 7083 6.188407 AGTATAGCTAGAGAACTGGAACACA 58.812 40.000 0.00 0.00 0.00 3.72
6614 7105 3.644823 TGCACACAAAATTCAGCATCAG 58.355 40.909 0.00 0.00 0.00 2.90
6623 7114 6.872020 ACAAAATTCAGCATCAGAAGAAATGG 59.128 34.615 0.00 0.00 0.00 3.16
6625 7116 6.845758 AATTCAGCATCAGAAGAAATGGAA 57.154 33.333 0.00 0.00 0.00 3.53
6722 7213 4.796110 ACTTGGTAGATATGGCCAATGT 57.204 40.909 10.96 6.16 40.91 2.71
6910 7405 6.770286 AAAGGAGGAGGCTAATGATTATCA 57.230 37.500 0.00 0.00 0.00 2.15
7034 7532 3.052745 GTTTTGTCCTTAAGCTGCTTGC 58.947 45.455 24.35 9.76 43.29 4.01
7052 7550 7.042791 GCTGCTTGCTTTGTCTTGTAAAAATAA 60.043 33.333 0.00 0.00 38.95 1.40
7459 7957 4.681978 GCTTCGACGGCACCCAGT 62.682 66.667 4.88 0.00 0.00 4.00
7718 8216 2.741985 TGCGGCGGTGTCATTCTG 60.742 61.111 9.78 0.00 0.00 3.02
7733 8231 1.048601 TTCTGGTCCTCTTCGCTTGT 58.951 50.000 0.00 0.00 0.00 3.16
7736 8234 2.832129 TCTGGTCCTCTTCGCTTGTTAT 59.168 45.455 0.00 0.00 0.00 1.89
7737 8235 4.021229 TCTGGTCCTCTTCGCTTGTTATA 58.979 43.478 0.00 0.00 0.00 0.98
7738 8236 4.649674 TCTGGTCCTCTTCGCTTGTTATAT 59.350 41.667 0.00 0.00 0.00 0.86
7739 8237 5.128827 TCTGGTCCTCTTCGCTTGTTATATT 59.871 40.000 0.00 0.00 0.00 1.28
7741 8239 5.584649 TGGTCCTCTTCGCTTGTTATATTTG 59.415 40.000 0.00 0.00 0.00 2.32
7759 8271 2.030958 GTTGGTAACGGGGTCGCTG 61.031 63.158 0.00 0.00 40.63 5.18
7875 8387 0.541296 AGCAACAAGGCAAGGCTCAT 60.541 50.000 0.00 0.00 35.83 2.90
7885 8397 1.003355 AAGGCTCATGGTCGTGTGG 60.003 57.895 0.00 0.00 0.00 4.17
7887 8399 2.436646 GCTCATGGTCGTGTGGGG 60.437 66.667 0.00 0.00 0.00 4.96
8198 8730 6.942976 AGCTAGCTATGTACACCTTGTTAAA 58.057 36.000 17.69 0.00 0.00 1.52
8231 8763 3.989104 CCTATGTAGGGGCTGTTCG 57.011 57.895 0.00 0.00 39.86 3.95
8232 8764 0.393077 CCTATGTAGGGGCTGTTCGG 59.607 60.000 0.00 0.00 39.86 4.30
8233 8765 1.410004 CTATGTAGGGGCTGTTCGGA 58.590 55.000 0.00 0.00 0.00 4.55
8234 8766 1.068741 CTATGTAGGGGCTGTTCGGAC 59.931 57.143 0.00 0.00 0.00 4.79
8235 8767 0.617820 ATGTAGGGGCTGTTCGGACT 60.618 55.000 0.00 0.00 0.00 3.85
8236 8768 1.255667 TGTAGGGGCTGTTCGGACTC 61.256 60.000 0.00 0.00 0.00 3.36
8237 8769 0.971447 GTAGGGGCTGTTCGGACTCT 60.971 60.000 0.00 0.00 0.00 3.24
8238 8770 0.683504 TAGGGGCTGTTCGGACTCTC 60.684 60.000 0.00 0.00 0.00 3.20
8239 8771 1.985116 GGGGCTGTTCGGACTCTCT 60.985 63.158 0.00 0.00 0.00 3.10
8240 8772 1.513622 GGGCTGTTCGGACTCTCTC 59.486 63.158 0.00 0.00 0.00 3.20
8241 8773 1.251527 GGGCTGTTCGGACTCTCTCA 61.252 60.000 0.00 0.00 0.00 3.27
8242 8774 0.603569 GGCTGTTCGGACTCTCTCAA 59.396 55.000 0.00 0.00 0.00 3.02
8243 8775 1.670380 GGCTGTTCGGACTCTCTCAAC 60.670 57.143 0.00 0.00 0.00 3.18
8244 8776 1.271102 GCTGTTCGGACTCTCTCAACT 59.729 52.381 0.00 0.00 0.00 3.16
8245 8777 2.669950 GCTGTTCGGACTCTCTCAACTC 60.670 54.545 0.00 0.00 0.00 3.01
8246 8778 1.887198 TGTTCGGACTCTCTCAACTCC 59.113 52.381 0.00 0.00 0.00 3.85
8247 8779 1.887198 GTTCGGACTCTCTCAACTCCA 59.113 52.381 0.00 0.00 0.00 3.86
8248 8780 1.535833 TCGGACTCTCTCAACTCCAC 58.464 55.000 0.00 0.00 0.00 4.02
8249 8781 0.169230 CGGACTCTCTCAACTCCACG 59.831 60.000 0.00 0.00 0.00 4.94
8250 8782 0.109039 GGACTCTCTCAACTCCACGC 60.109 60.000 0.00 0.00 0.00 5.34
8251 8783 0.885196 GACTCTCTCAACTCCACGCT 59.115 55.000 0.00 0.00 0.00 5.07
8252 8784 0.600557 ACTCTCTCAACTCCACGCTG 59.399 55.000 0.00 0.00 0.00 5.18
8253 8785 0.108898 CTCTCTCAACTCCACGCTGG 60.109 60.000 0.00 0.00 39.43 4.85
8254 8786 0.539669 TCTCTCAACTCCACGCTGGA 60.540 55.000 6.57 6.57 45.98 3.86
8277 8809 4.657436 CGGAGCAGGATCTAGTTTTAGT 57.343 45.455 0.00 0.00 0.00 2.24
8278 8810 5.012328 CGGAGCAGGATCTAGTTTTAGTT 57.988 43.478 0.00 0.00 0.00 2.24
8279 8811 5.420409 CGGAGCAGGATCTAGTTTTAGTTT 58.580 41.667 0.00 0.00 0.00 2.66
8280 8812 5.292101 CGGAGCAGGATCTAGTTTTAGTTTG 59.708 44.000 0.00 0.00 0.00 2.93
8281 8813 6.174049 GGAGCAGGATCTAGTTTTAGTTTGT 58.826 40.000 0.00 0.00 0.00 2.83
8282 8814 6.092807 GGAGCAGGATCTAGTTTTAGTTTGTG 59.907 42.308 0.00 0.00 0.00 3.33
8283 8815 5.940470 AGCAGGATCTAGTTTTAGTTTGTGG 59.060 40.000 0.00 0.00 0.00 4.17
8284 8816 5.938125 GCAGGATCTAGTTTTAGTTTGTGGA 59.062 40.000 0.00 0.00 0.00 4.02
8285 8817 6.092807 GCAGGATCTAGTTTTAGTTTGTGGAG 59.907 42.308 0.00 0.00 0.00 3.86
8286 8818 7.162082 CAGGATCTAGTTTTAGTTTGTGGAGT 58.838 38.462 0.00 0.00 0.00 3.85
8287 8819 7.118390 CAGGATCTAGTTTTAGTTTGTGGAGTG 59.882 40.741 0.00 0.00 0.00 3.51
8288 8820 6.371825 GGATCTAGTTTTAGTTTGTGGAGTGG 59.628 42.308 0.00 0.00 0.00 4.00
8289 8821 5.061179 TCTAGTTTTAGTTTGTGGAGTGGC 58.939 41.667 0.00 0.00 0.00 5.01
8290 8822 3.898482 AGTTTTAGTTTGTGGAGTGGCT 58.102 40.909 0.00 0.00 0.00 4.75
8291 8823 3.632145 AGTTTTAGTTTGTGGAGTGGCTG 59.368 43.478 0.00 0.00 0.00 4.85
8292 8824 3.569194 TTTAGTTTGTGGAGTGGCTGA 57.431 42.857 0.00 0.00 0.00 4.26
8293 8825 3.569194 TTAGTTTGTGGAGTGGCTGAA 57.431 42.857 0.00 0.00 0.00 3.02
8294 8826 2.435372 AGTTTGTGGAGTGGCTGAAA 57.565 45.000 0.00 0.00 0.00 2.69
8295 8827 2.301346 AGTTTGTGGAGTGGCTGAAAG 58.699 47.619 0.00 0.00 0.00 2.62
8296 8828 1.338020 GTTTGTGGAGTGGCTGAAAGG 59.662 52.381 0.00 0.00 0.00 3.11
8297 8829 0.178992 TTGTGGAGTGGCTGAAAGGG 60.179 55.000 0.00 0.00 0.00 3.95
8298 8830 1.973812 GTGGAGTGGCTGAAAGGGC 60.974 63.158 0.00 0.00 0.00 5.19
8299 8831 2.747855 GGAGTGGCTGAAAGGGCG 60.748 66.667 0.00 0.00 34.31 6.13
8300 8832 3.435186 GAGTGGCTGAAAGGGCGC 61.435 66.667 0.00 0.00 41.60 6.53
8301 8833 3.958860 AGTGGCTGAAAGGGCGCT 61.959 61.111 7.64 0.00 45.50 5.92
8302 8834 3.435186 GTGGCTGAAAGGGCGCTC 61.435 66.667 7.64 1.48 38.86 5.03
8303 8835 4.722700 TGGCTGAAAGGGCGCTCC 62.723 66.667 2.00 4.98 34.31 4.70
8329 8861 2.485122 GCGATTTGCCGAACAGGG 59.515 61.111 0.00 0.00 41.48 4.45
8337 8869 4.743018 CCGAACAGGGCCTGAATT 57.257 55.556 38.99 24.01 35.18 2.17
8338 8870 2.961424 CCGAACAGGGCCTGAATTT 58.039 52.632 38.99 23.24 35.18 1.82
8339 8871 1.256812 CCGAACAGGGCCTGAATTTT 58.743 50.000 38.99 22.86 35.18 1.82
8340 8872 1.618343 CCGAACAGGGCCTGAATTTTT 59.382 47.619 38.99 22.47 35.18 1.94
8341 8873 2.823154 CCGAACAGGGCCTGAATTTTTA 59.177 45.455 38.99 0.00 35.18 1.52
8342 8874 3.366985 CCGAACAGGGCCTGAATTTTTAC 60.367 47.826 38.99 17.54 35.18 2.01
8343 8875 3.506067 CGAACAGGGCCTGAATTTTTACT 59.494 43.478 38.99 11.31 35.18 2.24
8344 8876 4.379499 CGAACAGGGCCTGAATTTTTACTC 60.379 45.833 38.99 17.44 35.18 2.59
8345 8877 3.431415 ACAGGGCCTGAATTTTTACTCC 58.569 45.455 38.99 0.00 35.18 3.85
8346 8878 3.076032 ACAGGGCCTGAATTTTTACTCCT 59.924 43.478 38.99 9.69 35.18 3.69
8347 8879 3.696548 CAGGGCCTGAATTTTTACTCCTC 59.303 47.826 29.96 0.00 32.44 3.71
8348 8880 2.683362 GGGCCTGAATTTTTACTCCTCG 59.317 50.000 0.84 0.00 0.00 4.63
8349 8881 2.097629 GGCCTGAATTTTTACTCCTCGC 59.902 50.000 0.00 0.00 0.00 5.03
8350 8882 2.223044 GCCTGAATTTTTACTCCTCGCG 60.223 50.000 0.00 0.00 0.00 5.87
8351 8883 3.000727 CCTGAATTTTTACTCCTCGCGT 58.999 45.455 5.77 0.00 0.00 6.01
8352 8884 3.062234 CCTGAATTTTTACTCCTCGCGTC 59.938 47.826 5.77 0.00 0.00 5.19
8353 8885 2.997986 TGAATTTTTACTCCTCGCGTCC 59.002 45.455 5.77 0.00 0.00 4.79
8354 8886 2.754946 ATTTTTACTCCTCGCGTCCA 57.245 45.000 5.77 0.00 0.00 4.02
8355 8887 2.074547 TTTTTACTCCTCGCGTCCAG 57.925 50.000 5.77 2.47 0.00 3.86
8356 8888 0.245539 TTTTACTCCTCGCGTCCAGG 59.754 55.000 5.77 5.90 0.00 4.45
8357 8889 0.609957 TTTACTCCTCGCGTCCAGGA 60.610 55.000 13.75 13.75 37.75 3.86
8358 8890 0.395311 TTACTCCTCGCGTCCAGGAT 60.395 55.000 14.70 8.45 39.44 3.24
8359 8891 0.395311 TACTCCTCGCGTCCAGGATT 60.395 55.000 14.70 11.97 39.44 3.01
8360 8892 1.066587 CTCCTCGCGTCCAGGATTC 59.933 63.158 14.70 0.00 39.44 2.52
8361 8893 2.107141 CCTCGCGTCCAGGATTCC 59.893 66.667 5.77 0.00 31.91 3.01
8362 8894 2.278857 CTCGCGTCCAGGATTCCG 60.279 66.667 5.77 0.00 0.00 4.30
8363 8895 3.064987 CTCGCGTCCAGGATTCCGT 62.065 63.158 5.77 0.00 0.00 4.69
8364 8896 2.582498 CGCGTCCAGGATTCCGTC 60.582 66.667 0.00 0.00 0.00 4.79
8373 8905 2.599216 GGATTCCGTCCTGGGTACA 58.401 57.895 0.00 0.00 44.16 2.90
8374 8906 0.906775 GGATTCCGTCCTGGGTACAA 59.093 55.000 0.00 0.00 44.16 2.41
8375 8907 1.279846 GGATTCCGTCCTGGGTACAAA 59.720 52.381 0.00 0.00 44.16 2.83
8376 8908 2.290450 GGATTCCGTCCTGGGTACAAAA 60.290 50.000 0.00 0.00 44.16 2.44
8377 8909 2.259266 TTCCGTCCTGGGTACAAAAC 57.741 50.000 0.00 0.00 38.76 2.43
8378 8910 1.129917 TCCGTCCTGGGTACAAAACA 58.870 50.000 0.00 0.00 38.76 2.83
8379 8911 1.202675 TCCGTCCTGGGTACAAAACAC 60.203 52.381 0.00 0.00 38.76 3.32
8380 8912 1.475392 CCGTCCTGGGTACAAAACACA 60.475 52.381 0.00 0.00 39.96 3.72
8381 8913 1.600485 CGTCCTGGGTACAAAACACAC 59.400 52.381 0.00 0.00 36.25 3.82
8386 8918 4.164604 TCCTGGGTACAAAACACACTAGTT 59.835 41.667 0.00 0.00 36.25 2.24
8388 8920 5.220970 CCTGGGTACAAAACACACTAGTTTG 60.221 44.000 7.49 7.49 40.60 2.93
8403 8935 7.920738 ACACTAGTTTGTGATCAAGTTTTCTC 58.079 34.615 0.00 0.00 40.12 2.87
8404 8936 7.552687 ACACTAGTTTGTGATCAAGTTTTCTCA 59.447 33.333 0.00 0.00 40.12 3.27
8475 9007 2.367567 TGATTTACGGGATGGAGGCTAC 59.632 50.000 0.00 0.00 0.00 3.58
8498 9030 1.299648 CCGGCCAGAACAGATCCAA 59.700 57.895 2.24 0.00 0.00 3.53
8504 9036 5.104941 CCGGCCAGAACAGATCCAATATATA 60.105 44.000 2.24 0.00 0.00 0.86
8505 9037 6.408548 CCGGCCAGAACAGATCCAATATATAT 60.409 42.308 2.24 0.00 0.00 0.86
8511 9043 9.948964 CAGAACAGATCCAATATATATGTCCAA 57.051 33.333 0.00 0.00 28.96 3.53
8527 9063 5.428184 TGTCCAAATTTGTTTTTGAGGGT 57.572 34.783 16.73 0.00 38.58 4.34
8532 9068 5.885352 CCAAATTTGTTTTTGAGGGTTCCTT 59.115 36.000 16.73 0.00 38.58 3.36
8575 9112 8.613060 TTTCATATCTACATGATTTGAGCTCC 57.387 34.615 12.15 0.00 41.64 4.70
8618 9155 1.719529 TAGAAACGGTTGGTGGGAGA 58.280 50.000 0.00 0.00 0.00 3.71
8627 9164 2.143925 GTTGGTGGGAGAGAAGTTTCG 58.856 52.381 0.00 0.00 0.00 3.46
8655 9192 0.742281 CATGGTCTTCCCTGAGCACG 60.742 60.000 0.00 0.00 45.40 5.34
8698 9235 3.324108 GCCACCACCGGACCCTAA 61.324 66.667 9.46 0.00 0.00 2.69
8704 9241 2.122056 ACCGGACCCTAACTGCCT 59.878 61.111 9.46 0.00 0.00 4.75
8705 9242 1.988406 ACCGGACCCTAACTGCCTC 60.988 63.158 9.46 0.00 0.00 4.70
8706 9243 2.732619 CCGGACCCTAACTGCCTCC 61.733 68.421 0.00 0.00 0.00 4.30
8707 9244 2.732619 CGGACCCTAACTGCCTCCC 61.733 68.421 0.00 0.00 0.00 4.30
8708 9245 2.376165 GGACCCTAACTGCCTCCCC 61.376 68.421 0.00 0.00 0.00 4.81
8709 9246 2.687566 ACCCTAACTGCCTCCCCG 60.688 66.667 0.00 0.00 0.00 5.73
8710 9247 4.176752 CCCTAACTGCCTCCCCGC 62.177 72.222 0.00 0.00 0.00 6.13
8711 9248 4.530857 CCTAACTGCCTCCCCGCG 62.531 72.222 0.00 0.00 0.00 6.46
8712 9249 3.458163 CTAACTGCCTCCCCGCGA 61.458 66.667 8.23 0.00 0.00 5.87
8713 9250 3.432051 CTAACTGCCTCCCCGCGAG 62.432 68.421 8.23 0.00 38.46 5.03
8758 9305 3.849951 CGCGAGGTGTAGCCCCAT 61.850 66.667 0.00 0.00 38.26 4.00
8824 9399 4.405671 TGCTGCTGCCTGCTCCTC 62.406 66.667 13.47 0.00 43.37 3.71
8895 9470 3.273048 GCATAGCGTGTTGGCCAA 58.727 55.556 16.05 16.05 0.00 4.52
8933 9510 2.821366 AAGCGCGAAGGGATGCAG 60.821 61.111 12.10 0.00 46.37 4.41
8965 9542 5.652994 TGGACCCAATTGTAATTTAGCAC 57.347 39.130 4.43 0.00 0.00 4.40
8970 9547 4.201832 CCCAATTGTAATTTAGCACGCGTA 60.202 41.667 13.44 0.00 0.00 4.42
8993 9572 2.338577 TGGGGGTTTGTGCAATTTTG 57.661 45.000 0.00 0.00 0.00 2.44
8994 9573 1.561542 TGGGGGTTTGTGCAATTTTGT 59.438 42.857 0.00 0.00 0.00 2.83
8996 9575 1.864082 GGGGTTTGTGCAATTTTGTCG 59.136 47.619 0.00 0.00 0.00 4.35
9022 9601 6.715264 GGACCATGAAATATTCTTACGGGATT 59.285 38.462 0.00 0.00 0.00 3.01
9030 9609 8.575649 AAATATTCTTACGGGATTTGTTCTGT 57.424 30.769 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.745620 AATTACTCGTTCTGTTCTTTCCATT 57.254 32.000 0.00 0.00 0.00 3.16
1 2 7.745620 AAATTACTCGTTCTGTTCTTTCCAT 57.254 32.000 0.00 0.00 0.00 3.41
74 77 5.012239 TCGGCTAAACTTCTTAGGTCTGTA 58.988 41.667 0.00 0.00 0.00 2.74
161 164 2.683211 ATGGAATATTGGGGCCTGAC 57.317 50.000 0.84 0.00 0.00 3.51
304 307 4.141846 TGCTTAGGAGTTCAGATGTCCATC 60.142 45.833 0.00 0.00 38.09 3.51
352 355 1.464997 GTGCTGAAATCGTCCTTGTCC 59.535 52.381 0.00 0.00 0.00 4.02
394 400 7.408756 TCTGATGTTTTCCTATTCAATTGGG 57.591 36.000 5.42 0.00 0.00 4.12
406 412 6.515832 AGTTTTGTGGAATCTGATGTTTTCC 58.484 36.000 1.63 1.63 39.50 3.13
444 450 2.408565 AGGGCGAGGGAATCTTGAATA 58.591 47.619 0.00 0.00 0.00 1.75
550 556 0.751643 GTTGTTGCACCCTCACACCT 60.752 55.000 0.00 0.00 0.00 4.00
640 646 6.348458 GGTTTGCTTTCCTTTTCAATAATGCC 60.348 38.462 0.00 0.00 0.00 4.40
732 738 3.113043 GGGAGGAGGTATTACTGTTGGT 58.887 50.000 0.00 0.00 0.00 3.67
784 790 3.313526 GGAAGCACATAAGGTATGCAGTG 59.686 47.826 0.00 0.00 41.97 3.66
1063 1306 3.589988 ACAAAGCAGACTCCATAACGAG 58.410 45.455 0.00 0.00 35.88 4.18
1113 1356 0.036294 CCACTTCTCCCTTCGGGTTC 60.036 60.000 0.00 0.00 44.74 3.62
1121 1364 2.979678 TGCTTAAACTCCACTTCTCCCT 59.020 45.455 0.00 0.00 0.00 4.20
1130 1373 4.955811 TCTGTCTTCTGCTTAAACTCCA 57.044 40.909 0.00 0.00 0.00 3.86
1613 1856 3.319405 AGACAGTAAGCTCGGTGATATGG 59.681 47.826 0.00 0.00 0.00 2.74
1741 1987 5.545658 TTCATGGCGAATACTTTTCTGTC 57.454 39.130 0.00 0.00 0.00 3.51
1745 1991 6.640907 ACAAAGTTTCATGGCGAATACTTTTC 59.359 34.615 0.00 0.00 39.82 2.29
1885 2132 6.284459 TGTTGGAAAAACGGAAATTGCTAAT 58.716 32.000 0.00 0.00 0.00 1.73
1920 2167 7.737869 TCTGTACAAGTAATGGAAGTAAACCA 58.262 34.615 0.00 0.00 41.83 3.67
1968 2215 6.042322 TGGTTGTACTAAAGTCACCACATACT 59.958 38.462 0.00 0.00 31.59 2.12
1975 2222 5.608449 AGTTCTGGTTGTACTAAAGTCACC 58.392 41.667 0.00 0.00 0.00 4.02
2114 2362 8.593945 AATTAATTTCCTTCATTGCTCCAGTA 57.406 30.769 0.00 0.00 0.00 2.74
2236 2484 6.525629 TGTCCTGAAGTCTTTTTAGAAGGAG 58.474 40.000 0.00 0.00 33.38 3.69
2403 2653 7.659652 ACTGAAAAGCTAACAGTGACTAATC 57.340 36.000 15.98 0.00 42.18 1.75
2411 2661 4.638865 ACCGAAAACTGAAAAGCTAACAGT 59.361 37.500 12.48 12.48 45.02 3.55
2477 2728 6.271488 TCTTTTCTTGAATGGGCAGTATTG 57.729 37.500 0.00 0.00 0.00 1.90
2935 3189 5.069914 GGTGGGTTTCTTTTCTGTGGTTTAT 59.930 40.000 0.00 0.00 0.00 1.40
3072 3346 7.455058 TGTGTGTAAATACCACTTACTGGAAT 58.545 34.615 11.08 0.00 43.95 3.01
3134 3409 2.897271 ATAATGTGGGTCCAGCACAA 57.103 45.000 5.21 0.00 32.25 3.33
3236 3555 7.936950 ATTTTAAAGTTCAAAGCAGAGAAGC 57.063 32.000 0.00 0.00 0.00 3.86
3889 4211 2.262637 ACGGGAAGTTGGAGGAATACA 58.737 47.619 0.00 0.00 0.00 2.29
3905 4227 4.741321 TGGGTAGAAACTATGTTACGGG 57.259 45.455 0.00 0.00 0.00 5.28
4055 4377 5.476599 GCATTATCCCATGTTAGCATTGGTA 59.523 40.000 9.15 0.00 38.60 3.25
4288 4610 2.424956 CCTTGTTAGCTTTGATCCAGCC 59.575 50.000 9.79 0.00 38.09 4.85
4380 4702 6.070251 ACCATCATAGTTATCAGGAACACACA 60.070 38.462 0.00 0.00 0.00 3.72
4791 5138 6.790319 AGGAGTTTCCACCTGTATATTTTGT 58.210 36.000 0.00 0.00 39.61 2.83
4823 5170 9.130661 TCACAAAAGAATAAAGATGTCCAAAGA 57.869 29.630 0.00 0.00 0.00 2.52
5036 5511 5.883685 ACATCATATCATGACCTGAGTGT 57.116 39.130 12.94 13.00 43.01 3.55
5448 5924 3.149196 ACCACTCATACTTGTTTGGCAG 58.851 45.455 0.00 0.00 32.33 4.85
5642 6118 5.203528 TCACTCTCATGACTATGACCATGA 58.796 41.667 0.00 0.00 44.66 3.07
6146 6624 4.387026 TTCCAAGACTTGAACCCATGAT 57.613 40.909 16.99 0.00 0.00 2.45
6157 6643 3.584733 AAGAGGCTGTTTCCAAGACTT 57.415 42.857 0.00 0.00 0.00 3.01
6186 6672 1.200519 TGTACGCAGCCTTTCCCTAT 58.799 50.000 0.00 0.00 0.00 2.57
6217 6703 2.691252 GGGGAAGGGTCCGACCAT 60.691 66.667 19.43 9.67 46.04 3.55
6399 6888 4.796038 TTCTTTTTCCGAGGAGATACGT 57.204 40.909 0.00 0.00 0.00 3.57
6411 6900 3.078594 TGCAGCGTCTTTTCTTTTTCC 57.921 42.857 0.00 0.00 0.00 3.13
6412 6901 3.426525 CCATGCAGCGTCTTTTCTTTTTC 59.573 43.478 0.00 0.00 0.00 2.29
6442 6931 9.691362 GGAAAACAGAAAAACTATTGCTCATTA 57.309 29.630 0.00 0.00 0.00 1.90
6592 7083 4.021807 TCTGATGCTGAATTTTGTGTGCAT 60.022 37.500 0.00 0.00 42.74 3.96
6614 7105 8.355913 AGAAAGAGTGATTTGTTCCATTTCTTC 58.644 33.333 0.00 0.00 32.19 2.87
6623 7114 9.171877 AGGATATGAAGAAAGAGTGATTTGTTC 57.828 33.333 3.02 3.02 40.81 3.18
6625 7116 9.525826 AAAGGATATGAAGAAAGAGTGATTTGT 57.474 29.630 0.00 0.00 0.00 2.83
6835 7328 5.104941 TGGTTGGTTCTCGATTATCATGACT 60.105 40.000 0.00 0.00 0.00 3.41
7052 7550 9.221933 CCACCTAAAAAGGTTTAAAACAACTTT 57.778 29.630 5.94 4.53 40.85 2.66
7072 7570 3.348119 TGAATTTACGCAATGCCACCTA 58.652 40.909 0.00 0.00 0.00 3.08
7459 7957 1.080366 CGGACCCGATGACGAACAA 60.080 57.895 1.54 0.00 42.83 2.83
7718 8216 5.585047 ACAAATATAACAAGCGAAGAGGACC 59.415 40.000 0.00 0.00 0.00 4.46
7733 8231 4.874966 CGACCCCGTTACCAACAAATATAA 59.125 41.667 0.00 0.00 0.00 0.98
7736 8234 2.697654 CGACCCCGTTACCAACAAATA 58.302 47.619 0.00 0.00 0.00 1.40
7737 8235 1.525941 CGACCCCGTTACCAACAAAT 58.474 50.000 0.00 0.00 0.00 2.32
7738 8236 1.165284 GCGACCCCGTTACCAACAAA 61.165 55.000 0.00 0.00 38.24 2.83
7739 8237 1.597578 GCGACCCCGTTACCAACAA 60.598 57.895 0.00 0.00 38.24 2.83
7741 8239 2.030958 CAGCGACCCCGTTACCAAC 61.031 63.158 0.00 0.00 38.24 3.77
7759 8271 0.229753 CGAATTGCGTAGGCGTCATC 59.770 55.000 2.53 0.00 44.10 2.92
7817 8329 2.342648 GAAGACCACCGCGTCCTT 59.657 61.111 4.92 0.15 32.91 3.36
7875 8387 0.035534 CATTCATCCCCACACGACCA 60.036 55.000 0.00 0.00 0.00 4.02
7885 8397 1.884235 CTCCGGTAAGCATTCATCCC 58.116 55.000 0.00 0.00 0.00 3.85
7887 8399 2.246719 AGCTCCGGTAAGCATTCATC 57.753 50.000 16.73 0.00 45.00 2.92
8047 8578 4.778143 CTTCCTTCCCACCGGCGG 62.778 72.222 27.06 27.06 0.00 6.13
8209 8741 1.718280 ACAGCCCCTACATAGGTAGC 58.282 55.000 9.07 6.65 44.64 3.58
8221 8753 1.950973 GAGAGAGTCCGAACAGCCCC 61.951 65.000 0.00 0.00 0.00 5.80
8222 8754 1.251527 TGAGAGAGTCCGAACAGCCC 61.252 60.000 0.00 0.00 0.00 5.19
8224 8756 1.271102 AGTTGAGAGAGTCCGAACAGC 59.729 52.381 0.00 0.00 0.00 4.40
8225 8757 2.094957 GGAGTTGAGAGAGTCCGAACAG 60.095 54.545 0.00 0.00 29.93 3.16
8226 8758 1.887198 GGAGTTGAGAGAGTCCGAACA 59.113 52.381 0.00 0.00 29.93 3.18
8227 8759 1.887198 TGGAGTTGAGAGAGTCCGAAC 59.113 52.381 0.00 0.00 41.24 3.95
8228 8760 1.887198 GTGGAGTTGAGAGAGTCCGAA 59.113 52.381 0.00 0.00 41.24 4.30
8229 8761 1.535833 GTGGAGTTGAGAGAGTCCGA 58.464 55.000 0.00 0.00 41.24 4.55
8230 8762 0.169230 CGTGGAGTTGAGAGAGTCCG 59.831 60.000 0.00 0.00 41.24 4.79
8231 8763 0.109039 GCGTGGAGTTGAGAGAGTCC 60.109 60.000 0.00 0.00 39.22 3.85
8232 8764 0.885196 AGCGTGGAGTTGAGAGAGTC 59.115 55.000 0.00 0.00 0.00 3.36
8233 8765 0.600557 CAGCGTGGAGTTGAGAGAGT 59.399 55.000 0.00 0.00 32.33 3.24
8234 8766 0.108898 CCAGCGTGGAGTTGAGAGAG 60.109 60.000 0.00 0.00 40.96 3.20
8235 8767 0.539669 TCCAGCGTGGAGTTGAGAGA 60.540 55.000 3.02 0.00 42.67 3.10
8236 8768 1.967535 TCCAGCGTGGAGTTGAGAG 59.032 57.895 3.02 0.00 42.67 3.20
8237 8769 4.191243 TCCAGCGTGGAGTTGAGA 57.809 55.556 3.02 0.00 42.67 3.27
8249 8781 3.805891 GATCCTGCTCCGCTCCAGC 62.806 68.421 0.00 0.00 37.40 4.85
8250 8782 0.825425 TAGATCCTGCTCCGCTCCAG 60.825 60.000 0.00 0.00 0.00 3.86
8251 8783 0.825425 CTAGATCCTGCTCCGCTCCA 60.825 60.000 0.00 0.00 0.00 3.86
8252 8784 0.825840 ACTAGATCCTGCTCCGCTCC 60.826 60.000 0.00 0.00 0.00 4.70
8253 8785 1.036707 AACTAGATCCTGCTCCGCTC 58.963 55.000 0.00 0.00 0.00 5.03
8254 8786 1.490574 AAACTAGATCCTGCTCCGCT 58.509 50.000 0.00 0.00 0.00 5.52
8255 8787 2.317530 AAAACTAGATCCTGCTCCGC 57.682 50.000 0.00 0.00 0.00 5.54
8256 8788 4.657436 ACTAAAACTAGATCCTGCTCCG 57.343 45.455 0.00 0.00 0.00 4.63
8257 8789 6.092807 CACAAACTAAAACTAGATCCTGCTCC 59.907 42.308 0.00 0.00 0.00 4.70
8258 8790 6.092807 CCACAAACTAAAACTAGATCCTGCTC 59.907 42.308 0.00 0.00 0.00 4.26
8259 8791 5.940470 CCACAAACTAAAACTAGATCCTGCT 59.060 40.000 0.00 0.00 0.00 4.24
8260 8792 5.938125 TCCACAAACTAAAACTAGATCCTGC 59.062 40.000 0.00 0.00 0.00 4.85
8261 8793 7.118390 CACTCCACAAACTAAAACTAGATCCTG 59.882 40.741 0.00 0.00 0.00 3.86
8262 8794 7.162082 CACTCCACAAACTAAAACTAGATCCT 58.838 38.462 0.00 0.00 0.00 3.24
8263 8795 6.371825 CCACTCCACAAACTAAAACTAGATCC 59.628 42.308 0.00 0.00 0.00 3.36
8264 8796 6.128254 GCCACTCCACAAACTAAAACTAGATC 60.128 42.308 0.00 0.00 0.00 2.75
8265 8797 5.705905 GCCACTCCACAAACTAAAACTAGAT 59.294 40.000 0.00 0.00 0.00 1.98
8266 8798 5.061179 GCCACTCCACAAACTAAAACTAGA 58.939 41.667 0.00 0.00 0.00 2.43
8267 8799 5.049405 CAGCCACTCCACAAACTAAAACTAG 60.049 44.000 0.00 0.00 0.00 2.57
8268 8800 4.819630 CAGCCACTCCACAAACTAAAACTA 59.180 41.667 0.00 0.00 0.00 2.24
8269 8801 3.632145 CAGCCACTCCACAAACTAAAACT 59.368 43.478 0.00 0.00 0.00 2.66
8270 8802 3.630312 TCAGCCACTCCACAAACTAAAAC 59.370 43.478 0.00 0.00 0.00 2.43
8271 8803 3.892284 TCAGCCACTCCACAAACTAAAA 58.108 40.909 0.00 0.00 0.00 1.52
8272 8804 3.569194 TCAGCCACTCCACAAACTAAA 57.431 42.857 0.00 0.00 0.00 1.85
8273 8805 3.569194 TTCAGCCACTCCACAAACTAA 57.431 42.857 0.00 0.00 0.00 2.24
8274 8806 3.476552 CTTTCAGCCACTCCACAAACTA 58.523 45.455 0.00 0.00 0.00 2.24
8275 8807 2.301346 CTTTCAGCCACTCCACAAACT 58.699 47.619 0.00 0.00 0.00 2.66
8276 8808 1.338020 CCTTTCAGCCACTCCACAAAC 59.662 52.381 0.00 0.00 0.00 2.93
8277 8809 1.691196 CCTTTCAGCCACTCCACAAA 58.309 50.000 0.00 0.00 0.00 2.83
8278 8810 0.178992 CCCTTTCAGCCACTCCACAA 60.179 55.000 0.00 0.00 0.00 3.33
8279 8811 1.455849 CCCTTTCAGCCACTCCACA 59.544 57.895 0.00 0.00 0.00 4.17
8280 8812 1.973812 GCCCTTTCAGCCACTCCAC 60.974 63.158 0.00 0.00 0.00 4.02
8281 8813 2.436109 GCCCTTTCAGCCACTCCA 59.564 61.111 0.00 0.00 0.00 3.86
8282 8814 2.747855 CGCCCTTTCAGCCACTCC 60.748 66.667 0.00 0.00 0.00 3.85
8283 8815 3.435186 GCGCCCTTTCAGCCACTC 61.435 66.667 0.00 0.00 0.00 3.51
8284 8816 3.909086 GAGCGCCCTTTCAGCCACT 62.909 63.158 2.29 0.00 0.00 4.00
8285 8817 3.435186 GAGCGCCCTTTCAGCCAC 61.435 66.667 2.29 0.00 0.00 5.01
8286 8818 4.722700 GGAGCGCCCTTTCAGCCA 62.723 66.667 2.29 0.00 0.00 4.75
8304 8836 1.012234 CGGCAAATCGCTACGAAGC 60.012 57.895 0.00 0.00 45.86 3.86
8305 8837 0.996462 TTCGGCAAATCGCTACGAAG 59.004 50.000 0.00 0.00 38.72 3.79
8306 8838 0.717224 GTTCGGCAAATCGCTACGAA 59.283 50.000 0.00 0.00 40.49 3.85
8307 8839 0.388778 TGTTCGGCAAATCGCTACGA 60.389 50.000 0.00 0.00 41.91 3.43
8308 8840 0.025001 CTGTTCGGCAAATCGCTACG 59.975 55.000 0.00 0.00 41.91 3.51
8309 8841 0.373716 CCTGTTCGGCAAATCGCTAC 59.626 55.000 0.00 0.00 41.91 3.58
8310 8842 0.742990 CCCTGTTCGGCAAATCGCTA 60.743 55.000 0.00 0.00 41.91 4.26
8311 8843 2.040544 CCCTGTTCGGCAAATCGCT 61.041 57.895 0.00 0.00 41.91 4.93
8312 8844 2.485122 CCCTGTTCGGCAAATCGC 59.515 61.111 0.00 0.00 41.28 4.58
8320 8852 1.256812 AAAATTCAGGCCCTGTTCGG 58.743 50.000 11.27 0.00 32.61 4.30
8321 8853 3.506067 AGTAAAAATTCAGGCCCTGTTCG 59.494 43.478 11.27 0.00 32.61 3.95
8322 8854 4.082190 GGAGTAAAAATTCAGGCCCTGTTC 60.082 45.833 11.27 0.00 32.61 3.18
8323 8855 3.832490 GGAGTAAAAATTCAGGCCCTGTT 59.168 43.478 11.27 0.00 32.61 3.16
8324 8856 3.076032 AGGAGTAAAAATTCAGGCCCTGT 59.924 43.478 11.27 0.00 32.61 4.00
8325 8857 3.696548 GAGGAGTAAAAATTCAGGCCCTG 59.303 47.826 3.69 3.69 0.00 4.45
8326 8858 3.622455 CGAGGAGTAAAAATTCAGGCCCT 60.622 47.826 0.00 0.00 0.00 5.19
8327 8859 2.683362 CGAGGAGTAAAAATTCAGGCCC 59.317 50.000 0.00 0.00 0.00 5.80
8328 8860 2.097629 GCGAGGAGTAAAAATTCAGGCC 59.902 50.000 0.00 0.00 0.00 5.19
8329 8861 2.223044 CGCGAGGAGTAAAAATTCAGGC 60.223 50.000 0.00 0.00 0.00 4.85
8330 8862 3.000727 ACGCGAGGAGTAAAAATTCAGG 58.999 45.455 15.93 0.00 0.00 3.86
8331 8863 3.062234 GGACGCGAGGAGTAAAAATTCAG 59.938 47.826 15.93 0.00 0.00 3.02
8332 8864 2.997986 GGACGCGAGGAGTAAAAATTCA 59.002 45.455 15.93 0.00 0.00 2.57
8333 8865 2.997986 TGGACGCGAGGAGTAAAAATTC 59.002 45.455 15.93 0.00 0.00 2.17
8334 8866 3.000727 CTGGACGCGAGGAGTAAAAATT 58.999 45.455 15.93 0.00 0.00 1.82
8335 8867 2.618053 CTGGACGCGAGGAGTAAAAAT 58.382 47.619 15.93 0.00 0.00 1.82
8336 8868 1.337447 CCTGGACGCGAGGAGTAAAAA 60.337 52.381 15.93 0.00 30.68 1.94
8337 8869 0.245539 CCTGGACGCGAGGAGTAAAA 59.754 55.000 15.93 0.00 30.68 1.52
8338 8870 0.609957 TCCTGGACGCGAGGAGTAAA 60.610 55.000 15.93 0.00 33.54 2.01
8339 8871 0.395311 ATCCTGGACGCGAGGAGTAA 60.395 55.000 15.93 0.00 41.41 2.24
8340 8872 0.395311 AATCCTGGACGCGAGGAGTA 60.395 55.000 15.93 0.00 41.41 2.59
8341 8873 1.668101 GAATCCTGGACGCGAGGAGT 61.668 60.000 15.93 14.88 41.41 3.85
8342 8874 1.066587 GAATCCTGGACGCGAGGAG 59.933 63.158 15.93 4.41 41.41 3.69
8343 8875 2.423898 GGAATCCTGGACGCGAGGA 61.424 63.158 15.93 16.23 42.25 3.71
8344 8876 2.107141 GGAATCCTGGACGCGAGG 59.893 66.667 15.93 10.08 0.00 4.63
8345 8877 2.278857 CGGAATCCTGGACGCGAG 60.279 66.667 15.93 0.00 0.00 5.03
8346 8878 3.060020 GACGGAATCCTGGACGCGA 62.060 63.158 15.93 0.00 0.00 5.87
8347 8879 2.582498 GACGGAATCCTGGACGCG 60.582 66.667 3.53 3.53 0.00 6.01
8348 8880 2.202892 GGACGGAATCCTGGACGC 60.203 66.667 0.00 0.00 45.22 5.19
8356 8888 2.745821 GTTTTGTACCCAGGACGGAATC 59.254 50.000 0.00 0.00 36.56 2.52
8357 8889 2.106857 TGTTTTGTACCCAGGACGGAAT 59.893 45.455 0.00 0.00 36.56 3.01
8358 8890 1.489649 TGTTTTGTACCCAGGACGGAA 59.510 47.619 0.00 0.00 36.56 4.30
8359 8891 1.129917 TGTTTTGTACCCAGGACGGA 58.870 50.000 0.00 0.00 36.56 4.69
8360 8892 1.232119 GTGTTTTGTACCCAGGACGG 58.768 55.000 0.00 0.00 0.00 4.79
8361 8893 1.600485 GTGTGTTTTGTACCCAGGACG 59.400 52.381 0.00 0.00 0.00 4.79
8362 8894 2.927028 AGTGTGTTTTGTACCCAGGAC 58.073 47.619 0.00 0.00 0.00 3.85
8363 8895 3.712733 ACTAGTGTGTTTTGTACCCAGGA 59.287 43.478 0.00 0.00 0.00 3.86
8364 8896 4.081322 ACTAGTGTGTTTTGTACCCAGG 57.919 45.455 0.00 0.00 0.00 4.45
8365 8897 5.355910 ACAAACTAGTGTGTTTTGTACCCAG 59.644 40.000 13.22 0.00 37.98 4.45
8366 8898 5.124138 CACAAACTAGTGTGTTTTGTACCCA 59.876 40.000 16.38 0.00 43.26 4.51
8367 8899 5.575019 CACAAACTAGTGTGTTTTGTACCC 58.425 41.667 16.38 0.00 43.26 3.69
8378 8910 7.552687 TGAGAAAACTTGATCACAAACTAGTGT 59.447 33.333 0.00 0.00 40.37 3.55
8379 8911 7.919690 TGAGAAAACTTGATCACAAACTAGTG 58.080 34.615 0.00 0.00 40.85 2.74
8380 8912 8.562892 CATGAGAAAACTTGATCACAAACTAGT 58.437 33.333 0.00 0.00 35.49 2.57
8381 8913 7.536622 GCATGAGAAAACTTGATCACAAACTAG 59.463 37.037 0.00 0.00 35.49 2.57
8386 8918 5.771153 TGCATGAGAAAACTTGATCACAA 57.229 34.783 0.00 0.00 34.65 3.33
8388 8920 6.093771 AGAGATGCATGAGAAAACTTGATCAC 59.906 38.462 2.46 0.00 0.00 3.06
8403 8935 1.549620 AGGATCCGCTAGAGATGCATG 59.450 52.381 2.46 0.00 34.77 4.06
8404 8936 1.549620 CAGGATCCGCTAGAGATGCAT 59.450 52.381 5.98 0.00 34.77 3.96
8475 9007 0.962356 ATCTGTTCTGGCCGGCAAAG 60.962 55.000 30.85 24.48 0.00 2.77
8483 9015 7.497249 GGACATATATATTGGATCTGTTCTGGC 59.503 40.741 0.00 0.00 0.00 4.85
8504 9036 6.000246 ACCCTCAAAAACAAATTTGGACAT 58.000 33.333 21.74 3.36 40.04 3.06
8505 9037 5.428184 ACCCTCAAAAACAAATTTGGACA 57.572 34.783 21.74 0.00 40.04 4.02
8511 9043 6.306643 TGAAGGAACCCTCAAAAACAAATT 57.693 33.333 0.00 0.00 30.89 1.82
8527 9063 1.529713 GGGCCGTGGTTTGAAGGAA 60.530 57.895 0.00 0.00 0.00 3.36
8532 9068 2.903404 AAAAAGGGCCGTGGTTTGA 58.097 47.368 0.00 0.00 0.00 2.69
8563 9100 4.215399 CCGTGTAAAAAGGAGCTCAAATCA 59.785 41.667 17.19 2.32 0.00 2.57
8575 9112 3.701532 TTTGCAGGTCCGTGTAAAAAG 57.298 42.857 1.63 0.00 30.23 2.27
8750 9297 0.966920 GCTAAGCGTAGATGGGGCTA 59.033 55.000 11.12 0.00 35.64 3.93
8933 9510 0.181350 ATTGGGTCCATCTTCCTCGC 59.819 55.000 0.00 0.00 0.00 5.03
8965 9542 0.599060 ACAAACCCCCAAAATACGCG 59.401 50.000 3.53 3.53 0.00 6.01
8970 9547 3.591695 AATTGCACAAACCCCCAAAAT 57.408 38.095 0.00 0.00 0.00 1.82
8993 9572 5.176958 CGTAAGAATATTTCATGGTCCCGAC 59.823 44.000 0.00 0.00 43.02 4.79
8994 9573 5.294356 CGTAAGAATATTTCATGGTCCCGA 58.706 41.667 0.00 0.00 43.02 5.14
8996 9575 4.760204 CCCGTAAGAATATTTCATGGTCCC 59.240 45.833 0.00 0.00 43.02 4.46


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

AutoCloner maintained by Alex Coulton.