Multiple sequence alignment - TraesCS6D01G360000

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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 TraesCS6D01G360000 chr6D 100.000 5821 0 0 569 6389 451913526 451907706 0.000000e+00 10750.0
1 TraesCS6D01G360000 chr6D 100.000 496 0 0 6715 7210 451907380 451906885 0.000000e+00 917.0
2 TraesCS6D01G360000 chr6D 79.406 471 73 20 2345 2812 451911148 451910699 1.950000e-80 311.0
3 TraesCS6D01G360000 chr6D 79.406 471 73 20 2947 3396 451911750 451911283 1.950000e-80 311.0
4 TraesCS6D01G360000 chr6D 100.000 168 0 0 1 168 451914094 451913927 1.950000e-80 311.0
5 TraesCS6D01G360000 chr6B 95.018 4055 161 30 2340 6389 686419851 686415833 0.000000e+00 6331.0
6 TraesCS6D01G360000 chr6B 87.122 1289 70 34 1328 2600 686421844 686420636 0.000000e+00 1373.0
7 TraesCS6D01G360000 chr6B 89.267 764 29 23 569 1303 686422660 686421921 0.000000e+00 907.0
8 TraesCS6D01G360000 chr6B 91.111 495 21 7 1030 1519 562774251 562773775 0.000000e+00 649.0
9 TraesCS6D01G360000 chr6B 84.472 483 18 12 6715 7162 686415798 686415338 2.400000e-114 424.0
10 TraesCS6D01G360000 chr6B 80.258 466 73 18 2947 3396 686419846 686419384 4.170000e-87 333.0
11 TraesCS6D01G360000 chr6B 79.193 471 73 20 2345 2812 686419250 686418802 3.270000e-78 303.0
12 TraesCS6D01G360000 chr6B 82.271 361 53 8 2593 2950 686420228 686419876 1.180000e-77 302.0
13 TraesCS6D01G360000 chr6B 86.567 134 5 6 4 130 686422863 686422736 1.260000e-27 135.0
14 TraesCS6D01G360000 chr6B 85.714 119 12 4 2961 3074 686420855 686420737 3.530000e-23 121.0
15 TraesCS6D01G360000 chr6B 97.297 37 1 0 4362 4398 663782831 663782867 6.040000e-06 63.9
16 TraesCS6D01G360000 chr6A 95.632 2404 90 12 3994 6389 597833576 597831180 0.000000e+00 3843.0
17 TraesCS6D01G360000 chr6A 88.889 1026 98 10 2947 3962 597834598 597833579 0.000000e+00 1249.0
18 TraesCS6D01G360000 chr6A 89.367 837 28 14 1317 2142 597836361 597835575 0.000000e+00 996.0
19 TraesCS6D01G360000 chr6A 91.161 758 17 16 569 1309 597837158 597836434 0.000000e+00 983.0
20 TraesCS6D01G360000 chr6A 87.831 756 68 17 2203 2950 597835367 597834628 0.000000e+00 865.0
21 TraesCS6D01G360000 chr6A 87.234 423 27 11 6754 7162 597830716 597830307 2.370000e-124 457.0
22 TraesCS6D01G360000 chr6A 78.174 449 78 14 2967 3396 597835203 597834756 1.190000e-67 268.0
23 TraesCS6D01G360000 chr6A 82.759 174 7 7 2 168 597837342 597837185 4.540000e-27 134.0
24 TraesCS6D01G360000 chr6A 93.478 46 0 1 7165 7210 597830317 597830275 1.680000e-06 65.8
25 TraesCS6D01G360000 chr3B 93.320 494 16 6 1031 1519 122393178 122392697 0.000000e+00 713.0
26 TraesCS6D01G360000 chr3B 90.060 503 22 10 1031 1519 467719111 467719599 1.710000e-175 627.0
27 TraesCS6D01G360000 chr3B 84.265 483 62 10 3917 4398 14238453 14237984 6.590000e-125 459.0
28 TraesCS6D01G360000 chr3B 91.371 197 16 1 3531 3727 14238671 14238476 1.190000e-67 268.0
29 TraesCS6D01G360000 chr7B 91.383 499 25 8 1029 1519 91101100 91100612 0.000000e+00 667.0
30 TraesCS6D01G360000 chr3A 83.851 483 63 10 3917 4398 434426440 434426908 5.130000e-121 446.0
31 TraesCS6D01G360000 chr7A 83.505 485 64 13 3917 4398 691619986 691620457 8.590000e-119 438.0
32 TraesCS6D01G360000 chr7A 89.697 165 16 1 3563 3727 691619800 691619963 7.330000e-50 209.0
33 TraesCS6D01G360000 chr1A 83.437 483 65 10 3917 4398 465097160 465096692 1.110000e-117 435.0
34 TraesCS6D01G360000 chr1A 90.741 162 14 1 3566 3727 465097343 465097183 1.580000e-51 215.0
35 TraesCS6D01G360000 chr4B 83.230 483 66 11 3917 4398 62875119 62874651 5.170000e-116 429.0
36 TraesCS6D01G360000 chr4B 91.057 123 11 0 3605 3727 62875264 62875142 4.470000e-37 167.0
37 TraesCS6D01G360000 chr4D 80.087 231 43 3 5916 6144 497129188 497128959 1.240000e-37 169.0


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 TraesCS6D01G360000 chr6D 451906885 451914094 7209 True 2520.000000 10750 91.762400 1 7210 5 chr6D.!!$R1 7209
1 TraesCS6D01G360000 chr6B 686415338 686422863 7525 True 1136.555556 6331 85.542444 4 7162 9 chr6B.!!$R2 7158
2 TraesCS6D01G360000 chr6A 597830275 597837342 7067 True 984.533333 3843 88.280556 2 7210 9 chr6A.!!$R1 7208
3 TraesCS6D01G360000 chr3B 14237984 14238671 687 True 363.500000 459 87.818000 3531 4398 2 chr3B.!!$R2 867
4 TraesCS6D01G360000 chr7A 691619800 691620457 657 False 323.500000 438 86.601000 3563 4398 2 chr7A.!!$F1 835
5 TraesCS6D01G360000 chr1A 465096692 465097343 651 True 325.000000 435 87.089000 3566 4398 2 chr1A.!!$R1 832
6 TraesCS6D01G360000 chr4B 62874651 62875264 613 True 298.000000 429 87.143500 3605 4398 2 chr4B.!!$R1 793

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
724 771 1.293498 CAACACTCACCCCTCCTCG 59.707 63.158 0.00 0.00 0.00 4.63 F
1443 1590 0.109179 GCTTCCAATGATGCACGCAA 60.109 50.000 0.00 0.00 40.43 4.85 F
1495 1642 0.167908 ACAAACACACACACGCACAG 59.832 50.000 0.00 0.00 0.00 3.66 F
2087 2270 0.321210 TGGAATCAATGACGTGGCGT 60.321 50.000 0.00 0.00 45.10 5.68 F
3497 4882 0.612732 CATGAGCCCACCACCATGTT 60.613 55.000 0.00 0.00 33.62 2.71 F
3810 5195 0.905809 TTAGCTGGACCACGGGCTTA 60.906 55.000 11.60 0.78 36.40 3.09 F
4655 6056 0.532862 ACTTGTGTGAGGCAACCGAG 60.533 55.000 0.00 0.00 37.17 4.63 F
4808 6209 1.065928 CGTACCCGGAGATGACAGC 59.934 63.158 0.73 0.00 0.00 4.40 F
5636 7037 1.336440 CAAGGTTGTGGCGATGAAACA 59.664 47.619 0.00 0.00 0.00 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1885 2066 0.186630 TCCCAGGCATCCATTCCATG 59.813 55.000 0.00 0.00 0.00 3.66 R
3380 4763 0.838122 AGTGGGGGTCTGAGAACAGG 60.838 60.000 0.00 0.00 43.60 4.00 R
3480 4865 1.228521 CAACATGGTGGTGGGCTCA 60.229 57.895 1.63 0.00 29.70 4.26 R
3803 5188 0.887933 ATGTTGCAAGGTTAAGCCCG 59.112 50.000 0.00 0.00 38.26 6.13 R
4655 6056 0.257039 AACATCCCTGCTGATGGTCC 59.743 55.000 13.48 0.00 45.16 4.46 R
5603 7004 0.179001 AACCTTGGGGAACGTTCAGG 60.179 55.000 28.24 25.71 36.25 3.86 R
5621 7022 0.310543 GTGCTGTTTCATCGCCACAA 59.689 50.000 0.00 0.00 0.00 3.33 R
5708 7109 1.333636 CCGGCCTGGAGATCTTCACT 61.334 60.000 0.00 0.00 42.00 3.41 R
7166 8712 0.175073 CTACTACCCACCAACGCCTC 59.825 60.000 0.00 0.00 0.00 4.70 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
22 23 2.815211 CACGGCCACCATCGACAG 60.815 66.667 2.24 0.00 0.00 3.51
65 71 2.575525 CGCTCGCTCACTCACTCG 60.576 66.667 0.00 0.00 0.00 4.18
104 110 4.053983 CCTTCTTTCCAGCTTTTCTTTGC 58.946 43.478 0.00 0.00 0.00 3.68
710 755 3.874383 TCTTTGTCCCAGATTCCAACA 57.126 42.857 0.00 0.00 0.00 3.33
724 771 1.293498 CAACACTCACCCCTCCTCG 59.707 63.158 0.00 0.00 0.00 4.63
755 802 2.257409 TTAGTGCCTGCCTGCTAGCC 62.257 60.000 13.29 0.00 0.00 3.93
759 806 4.906792 CCTGCCTGCTAGCCGCTC 62.907 72.222 20.72 7.37 40.11 5.03
760 807 3.847602 CTGCCTGCTAGCCGCTCT 61.848 66.667 20.72 0.00 40.11 4.09
761 808 4.152964 TGCCTGCTAGCCGCTCTG 62.153 66.667 20.72 1.41 40.11 3.35
777 824 2.666190 TGCGCACCTCTGCTTCAC 60.666 61.111 5.66 0.00 41.77 3.18
911 966 4.537688 ACCTACCTACCAGTACAGTCACTA 59.462 45.833 0.00 0.00 0.00 2.74
923 978 4.181309 ACAGTCACTAAGTAGCAAGCTC 57.819 45.455 0.00 0.00 0.00 4.09
924 979 3.829601 ACAGTCACTAAGTAGCAAGCTCT 59.170 43.478 0.00 0.00 0.00 4.09
925 980 4.082463 ACAGTCACTAAGTAGCAAGCTCTC 60.082 45.833 0.00 0.00 0.00 3.20
926 981 4.157656 CAGTCACTAAGTAGCAAGCTCTCT 59.842 45.833 0.00 0.00 0.00 3.10
927 982 4.398044 AGTCACTAAGTAGCAAGCTCTCTC 59.602 45.833 0.00 0.00 0.00 3.20
928 983 4.156922 GTCACTAAGTAGCAAGCTCTCTCA 59.843 45.833 0.00 0.00 0.00 3.27
929 984 4.397730 TCACTAAGTAGCAAGCTCTCTCAG 59.602 45.833 0.00 0.00 0.00 3.35
1150 1214 4.150454 CGGCCTCCTCCTCCTCCT 62.150 72.222 0.00 0.00 0.00 3.69
1309 1385 2.277072 CACCACCACCACCACCAA 59.723 61.111 0.00 0.00 0.00 3.67
1310 1386 1.380515 CACCACCACCACCACCAAA 60.381 57.895 0.00 0.00 0.00 3.28
1311 1387 1.380650 ACCACCACCACCACCAAAC 60.381 57.895 0.00 0.00 0.00 2.93
1312 1388 1.076339 CCACCACCACCACCAAACT 60.076 57.895 0.00 0.00 0.00 2.66
1315 1391 0.920438 ACCACCACCACCAAACTACA 59.080 50.000 0.00 0.00 0.00 2.74
1348 1494 6.091305 TGTGTTGATTTATCTCTGCTTTCTCG 59.909 38.462 0.00 0.00 0.00 4.04
1401 1548 4.790765 ACTTAAAAGCTTGGATTCAGGC 57.209 40.909 0.00 0.00 45.04 4.85
1438 1585 2.516906 TCTTGTGCTTCCAATGATGCA 58.483 42.857 0.00 0.00 46.05 3.96
1441 1588 1.507630 TGCTTCCAATGATGCACGC 59.492 52.632 0.00 0.00 44.13 5.34
1442 1589 1.242665 TGCTTCCAATGATGCACGCA 61.243 50.000 0.00 0.00 44.13 5.24
1443 1590 0.109179 GCTTCCAATGATGCACGCAA 60.109 50.000 0.00 0.00 40.43 4.85
1444 1591 1.621107 CTTCCAATGATGCACGCAAC 58.379 50.000 0.00 0.00 0.00 4.17
1445 1592 1.200716 CTTCCAATGATGCACGCAACT 59.799 47.619 0.00 0.00 0.00 3.16
1446 1593 2.106477 TCCAATGATGCACGCAACTA 57.894 45.000 0.00 0.00 0.00 2.24
1447 1594 2.642427 TCCAATGATGCACGCAACTAT 58.358 42.857 0.00 0.00 0.00 2.12
1448 1595 2.613595 TCCAATGATGCACGCAACTATC 59.386 45.455 0.00 0.00 0.00 2.08
1453 1600 0.734889 ATGCACGCAACTATCCAAGC 59.265 50.000 0.00 0.00 0.00 4.01
1455 1602 0.521291 GCACGCAACTATCCAAGCAA 59.479 50.000 0.00 0.00 0.00 3.91
1465 1612 4.003648 ACTATCCAAGCAACTTTCTTCCG 58.996 43.478 0.00 0.00 0.00 4.30
1478 1625 4.698304 ACTTTCTTCCGTTCTTTCAACACA 59.302 37.500 0.00 0.00 0.00 3.72
1479 1626 5.182380 ACTTTCTTCCGTTCTTTCAACACAA 59.818 36.000 0.00 0.00 0.00 3.33
1495 1642 0.167908 ACAAACACACACACGCACAG 59.832 50.000 0.00 0.00 0.00 3.66
1538 1688 1.279558 GGTGGAAAAGGAGGAGGAGAC 59.720 57.143 0.00 0.00 0.00 3.36
1579 1729 3.726557 TGGGGAATATCATCATGGAGC 57.273 47.619 0.00 0.00 0.00 4.70
1601 1751 3.751698 CGGGGGAGTTTGTCTTTCTTTAG 59.248 47.826 0.00 0.00 0.00 1.85
1689 1848 5.103601 CCTTTTCCTCCTAGTCCTAGTCCTA 60.104 48.000 0.96 0.00 0.00 2.94
1690 1849 5.649970 TTTCCTCCTAGTCCTAGTCCTAG 57.350 47.826 6.12 6.12 0.00 3.02
1728 1887 2.092538 CCAGCCATCCTCATTCACTTCT 60.093 50.000 0.00 0.00 0.00 2.85
1751 1910 4.695455 TCTTCTTTTCGTGGAGGCATAAAG 59.305 41.667 0.00 0.00 0.00 1.85
1752 1911 3.343617 TCTTTTCGTGGAGGCATAAAGG 58.656 45.455 0.00 0.00 0.00 3.11
1753 1912 2.122783 TTTCGTGGAGGCATAAAGGG 57.877 50.000 0.00 0.00 0.00 3.95
1754 1913 0.988832 TTCGTGGAGGCATAAAGGGT 59.011 50.000 0.00 0.00 0.00 4.34
2024 2207 5.627040 GCAGTATCCCTAGTTAAGTTGCAGT 60.627 44.000 0.00 0.00 0.00 4.40
2025 2208 6.406624 GCAGTATCCCTAGTTAAGTTGCAGTA 60.407 42.308 0.00 0.00 0.00 2.74
2026 2209 7.687103 GCAGTATCCCTAGTTAAGTTGCAGTAT 60.687 40.741 0.00 0.00 0.00 2.12
2027 2210 7.868415 CAGTATCCCTAGTTAAGTTGCAGTATC 59.132 40.741 0.00 0.00 0.00 2.24
2028 2211 5.609533 TCCCTAGTTAAGTTGCAGTATCC 57.390 43.478 0.00 0.00 0.00 2.59
2029 2212 4.407945 TCCCTAGTTAAGTTGCAGTATCCC 59.592 45.833 0.00 0.00 0.00 3.85
2030 2213 4.409247 CCCTAGTTAAGTTGCAGTATCCCT 59.591 45.833 0.00 0.00 0.00 4.20
2031 2214 5.601313 CCCTAGTTAAGTTGCAGTATCCCTA 59.399 44.000 0.00 0.00 0.00 3.53
2032 2215 6.239345 CCCTAGTTAAGTTGCAGTATCCCTAG 60.239 46.154 0.00 0.00 0.00 3.02
2033 2216 6.324254 CCTAGTTAAGTTGCAGTATCCCTAGT 59.676 42.308 0.00 0.00 0.00 2.57
2034 2217 6.622427 AGTTAAGTTGCAGTATCCCTAGTT 57.378 37.500 0.00 0.00 0.00 2.24
2035 2218 7.729124 AGTTAAGTTGCAGTATCCCTAGTTA 57.271 36.000 0.00 0.00 0.00 2.24
2036 2219 8.142485 AGTTAAGTTGCAGTATCCCTAGTTAA 57.858 34.615 0.00 0.00 0.00 2.01
2037 2220 8.258708 AGTTAAGTTGCAGTATCCCTAGTTAAG 58.741 37.037 0.00 0.00 0.00 1.85
2038 2221 6.622427 AAGTTGCAGTATCCCTAGTTAAGT 57.378 37.500 0.00 0.00 0.00 2.24
2039 2222 6.622427 AGTTGCAGTATCCCTAGTTAAGTT 57.378 37.500 0.00 0.00 0.00 2.66
2040 2223 6.407202 AGTTGCAGTATCCCTAGTTAAGTTG 58.593 40.000 0.00 0.00 0.00 3.16
2041 2224 4.766375 TGCAGTATCCCTAGTTAAGTTGC 58.234 43.478 0.00 0.00 0.00 4.17
2042 2225 4.224147 TGCAGTATCCCTAGTTAAGTTGCA 59.776 41.667 0.00 0.00 35.70 4.08
2043 2226 5.183228 GCAGTATCCCTAGTTAAGTTGCAA 58.817 41.667 0.00 0.00 0.00 4.08
2087 2270 0.321210 TGGAATCAATGACGTGGCGT 60.321 50.000 0.00 0.00 45.10 5.68
2123 2306 1.075305 GGGGGCGGTTTAGGTTTGA 59.925 57.895 0.00 0.00 0.00 2.69
2180 2363 4.826274 TCTTCTTCCTGGTCTTACATGG 57.174 45.455 0.00 0.00 0.00 3.66
2182 2365 3.981071 TCTTCCTGGTCTTACATGGTG 57.019 47.619 0.00 0.00 0.00 4.17
2195 2378 5.763204 TCTTACATGGTGAGGTGTTTTCTTC 59.237 40.000 0.00 0.00 0.00 2.87
2196 2379 3.222603 ACATGGTGAGGTGTTTTCTTCC 58.777 45.455 0.00 0.00 0.00 3.46
2205 2532 4.461198 AGGTGTTTTCTTCCGTCAGAAAT 58.539 39.130 7.00 0.00 41.42 2.17
2206 2533 4.275936 AGGTGTTTTCTTCCGTCAGAAATG 59.724 41.667 7.00 0.00 41.42 2.32
2207 2534 4.537015 GTGTTTTCTTCCGTCAGAAATGG 58.463 43.478 7.00 0.00 41.42 3.16
2276 2607 1.756538 CACCACCCCCTTGCATTATTC 59.243 52.381 0.00 0.00 0.00 1.75
2290 2621 8.872845 CCTTGCATTATTCCAACAAAGATAAAC 58.127 33.333 0.00 0.00 0.00 2.01
2305 2636 2.426431 TAAACCAGAACAGGAGGGGA 57.574 50.000 0.00 0.00 0.00 4.81
2306 2637 1.760405 AAACCAGAACAGGAGGGGAT 58.240 50.000 0.00 0.00 0.00 3.85
2307 2638 2.661176 AACCAGAACAGGAGGGGATA 57.339 50.000 0.00 0.00 0.00 2.59
2310 2641 1.072965 CCAGAACAGGAGGGGATATGC 59.927 57.143 0.00 0.00 0.00 3.14
2331 2662 3.560896 GCATTCTCATCTCTCTTTGGAGC 59.439 47.826 0.00 0.00 39.31 4.70
2440 2772 5.580691 CACCTACATCACTCGAAAATGCTAA 59.419 40.000 0.00 0.00 0.00 3.09
2554 3928 4.222124 ACTCAAAGTCTGAAAGTGTGGT 57.778 40.909 0.00 0.00 32.17 4.16
2597 3971 8.635765 TTTTTATCTGACAAAAGCCTGATAGT 57.364 30.769 0.00 0.00 0.00 2.12
2600 3974 4.973168 TCTGACAAAAGCCTGATAGTGTT 58.027 39.130 0.00 0.00 0.00 3.32
2621 3995 5.632764 TGTTGCATTTGACAATGGTATTTCG 59.367 36.000 0.00 0.00 40.36 3.46
2633 4007 3.395639 TGGTATTTCGAGTGTGGTCAAC 58.604 45.455 0.00 0.00 0.00 3.18
2634 4008 2.410730 GGTATTTCGAGTGTGGTCAACG 59.589 50.000 0.00 0.00 0.00 4.10
2830 4205 4.013050 CCCCTTCTTGAATTCTCTCAACC 58.987 47.826 7.05 0.00 32.00 3.77
2880 4255 3.019564 GGGATTGTTAAGATGCAGTGCT 58.980 45.455 17.60 1.28 0.00 4.40
2889 4264 6.127054 TGTTAAGATGCAGTGCTCCTAGTTAT 60.127 38.462 17.60 0.00 0.00 1.89
2906 4281 8.432013 TCCTAGTTATGTTACTGCATCATTGAT 58.568 33.333 0.00 0.00 0.00 2.57
2924 4299 2.563620 TGATGTGTAACGGTCCTAAGCA 59.436 45.455 0.00 0.00 42.39 3.91
2945 4320 1.369692 CACAGGGACACGGTTAGCA 59.630 57.895 0.00 0.00 0.00 3.49
2957 4332 3.689161 CACGGTTAGCATTTGATCTTCCA 59.311 43.478 0.00 0.00 0.00 3.53
2969 4344 7.013083 GCATTTGATCTTCCAGTCTTACATGAT 59.987 37.037 0.00 0.00 0.00 2.45
3078 4453 6.889722 TGTAAATTAGCTTGACTATGGGCTTT 59.110 34.615 0.00 0.00 36.40 3.51
3160 4536 1.802715 CGGCGCCTGAGCATTTTTG 60.803 57.895 26.68 0.00 39.83 2.44
3213 4596 2.232399 GGCAAAGGTTTTTCGAGGGTA 58.768 47.619 0.00 0.00 0.00 3.69
3218 4601 4.426736 AAGGTTTTTCGAGGGTAGTTGA 57.573 40.909 0.00 0.00 0.00 3.18
3272 4655 7.123098 AGCAATCCATGACTTATTCATCACAAA 59.877 33.333 0.00 0.00 43.68 2.83
3393 4776 2.550180 GCTTTGTTCCTGTTCTCAGACC 59.450 50.000 0.00 0.00 43.76 3.85
3426 4809 4.202503 TGGGCATTATTCTCAGATCCCTTC 60.203 45.833 0.00 0.00 33.77 3.46
3432 4817 7.067981 GCATTATTCTCAGATCCCTTCTTGTTT 59.932 37.037 0.00 0.00 29.93 2.83
3473 4858 3.853355 AACAAGAGAGGGCATATGGAG 57.147 47.619 4.56 0.00 0.00 3.86
3495 4880 1.755395 CCATGAGCCCACCACCATG 60.755 63.158 0.00 0.00 36.92 3.66
3497 4882 0.612732 CATGAGCCCACCACCATGTT 60.613 55.000 0.00 0.00 33.62 2.71
3550 4935 8.004801 TGGAACAGGAATAGTACTCTGATGATA 58.995 37.037 14.41 0.00 0.00 2.15
3630 5015 2.027625 GTGGTGCGAAGAAGACCCG 61.028 63.158 0.00 0.00 0.00 5.28
3674 5059 6.213677 GTTTTGAAATGTAACTGGAAGGTCC 58.786 40.000 0.00 0.00 39.30 4.46
3727 5112 6.653320 GTGAGGTGTATTGGTTAGTCATCAAA 59.347 38.462 0.00 0.00 0.00 2.69
3731 5116 7.942341 AGGTGTATTGGTTAGTCATCAAAGAAA 59.058 33.333 0.00 0.00 0.00 2.52
3803 5188 4.097892 CCCATTGTAAATTAGCTGGACCAC 59.902 45.833 0.00 0.00 0.00 4.16
3810 5195 0.905809 TTAGCTGGACCACGGGCTTA 60.906 55.000 11.60 0.78 36.40 3.09
3818 5203 1.602323 CCACGGGCTTAACCTTGCA 60.602 57.895 0.00 0.00 39.10 4.08
3840 5225 5.123820 GCAACATGACTATACCTTGAGCAAA 59.876 40.000 0.00 0.00 0.00 3.68
3851 5236 5.596836 ACCTTGAGCAAATTTGTTCTTCA 57.403 34.783 28.14 18.94 38.92 3.02
3881 5266 1.449601 CTGAAAGTGCGGCCGGTAT 60.450 57.895 29.38 0.00 0.00 2.73
3886 5271 3.436055 GTGCGGCCGGTATGCAAA 61.436 61.111 29.38 0.00 40.83 3.68
3908 5293 9.986833 GCAAAGTTTTGTTTGTTTATTCTGATT 57.013 25.926 6.48 0.00 39.27 2.57
3934 5319 2.945008 CCTGAAACTGTCAAACTGCAGA 59.055 45.455 23.35 0.00 35.22 4.26
3940 5325 5.581126 AACTGTCAAACTGCAGAATTTGA 57.419 34.783 23.35 22.53 41.38 2.69
3969 5355 7.042335 AGGTTTATAGAGAAAGGTCGACAATG 58.958 38.462 18.91 0.00 0.00 2.82
3977 5365 7.952671 AGAGAAAGGTCGACAATGCTAATATA 58.047 34.615 18.91 0.00 0.00 0.86
3978 5366 8.085296 AGAGAAAGGTCGACAATGCTAATATAG 58.915 37.037 18.91 0.00 0.00 1.31
3979 5367 7.727181 AGAAAGGTCGACAATGCTAATATAGT 58.273 34.615 18.91 0.00 0.00 2.12
4069 5458 7.771927 AATGATGAGGACAATTGAAGAAAGT 57.228 32.000 13.59 0.00 0.00 2.66
4082 5471 5.772825 TGAAGAAAGTGAAAAGTCATGGG 57.227 39.130 0.00 0.00 35.80 4.00
4222 5615 3.634448 TGAAAAACGCTTTCCCAGATTCA 59.366 39.130 7.82 0.00 0.00 2.57
4223 5616 4.280677 TGAAAAACGCTTTCCCAGATTCAT 59.719 37.500 7.82 0.00 0.00 2.57
4586 5987 2.677836 TCGCCTTCATCATGTAACTTGC 59.322 45.455 0.00 0.00 0.00 4.01
4646 6047 2.222027 GAACCCTTGGACTTGTGTGAG 58.778 52.381 0.00 0.00 0.00 3.51
4655 6056 0.532862 ACTTGTGTGAGGCAACCGAG 60.533 55.000 0.00 0.00 37.17 4.63
4796 6197 1.429463 CTCAGAGTTTGCACGTACCC 58.571 55.000 0.00 0.00 0.00 3.69
4808 6209 1.065928 CGTACCCGGAGATGACAGC 59.934 63.158 0.73 0.00 0.00 4.40
5378 6779 3.834231 CTGGTGGGACCTTTTCATTCATT 59.166 43.478 0.00 0.00 39.58 2.57
5393 6794 4.467438 TCATTCATTGAGACAGAGGCTACA 59.533 41.667 0.00 0.00 0.00 2.74
5519 6920 2.450867 TCAGATCAGGCAGCTACTCT 57.549 50.000 0.00 0.00 0.00 3.24
5570 6971 3.308117 GGTCCATTGATGTTGGTGACCTA 60.308 47.826 2.11 0.00 35.64 3.08
5603 7004 6.427441 AGAGGAAAGGGATTTTCTTATGACC 58.573 40.000 0.36 0.00 43.81 4.02
5621 7022 1.454539 CCTGAACGTTCCCCAAGGT 59.545 57.895 24.78 0.00 31.80 3.50
5630 7031 2.035626 CCCCAAGGTTGTGGCGAT 59.964 61.111 0.00 0.00 37.34 4.58
5636 7037 1.336440 CAAGGTTGTGGCGATGAAACA 59.664 47.619 0.00 0.00 0.00 2.83
5708 7109 0.178995 TCAACATGGCTGAGGTGCAA 60.179 50.000 0.00 0.00 34.04 4.08
5786 7187 1.578206 GGCAGAAGAACCGCCTTCAC 61.578 60.000 11.26 4.89 43.68 3.18
5891 7292 2.106166 GAGAATGATCATGGGGTCAGCT 59.894 50.000 9.46 0.00 0.00 4.24
5894 7295 1.288188 TGATCATGGGGTCAGCTTCA 58.712 50.000 0.00 0.00 0.00 3.02
5987 7388 2.408241 GCAGAGGTACGAGGCGTCT 61.408 63.158 4.69 0.00 41.54 4.18
6089 7490 2.620234 CCTGATCCAGGCCTACCAA 58.380 57.895 3.98 0.00 45.13 3.67
6214 7615 2.523138 ACCCTCAGCCTAGGTAGGTAAT 59.477 50.000 19.56 7.55 45.42 1.89
6360 7762 0.334676 GTGATGGGATTGGGTTGGGA 59.665 55.000 0.00 0.00 0.00 4.37
6384 7786 6.544650 AGTGGTACAAATGGTGTGGTATAAA 58.455 36.000 0.00 0.00 44.16 1.40
6733 8135 0.845102 GGGGTGGGGGTATATGGAGG 60.845 65.000 0.00 0.00 0.00 4.30
6773 8274 4.715297 AGGTAATTCTGTACTGTAGTGGGG 59.285 45.833 0.00 0.00 0.00 4.96
6815 8317 3.372675 GGTATAAGTGTGCTGGGGGAAAT 60.373 47.826 0.00 0.00 0.00 2.17
6819 8321 0.831711 GTGTGCTGGGGGAAATTGGT 60.832 55.000 0.00 0.00 0.00 3.67
6820 8322 0.780637 TGTGCTGGGGGAAATTGGTA 59.219 50.000 0.00 0.00 0.00 3.25
6822 8324 1.824852 GTGCTGGGGGAAATTGGTAAG 59.175 52.381 0.00 0.00 0.00 2.34
6824 8326 1.273041 GCTGGGGGAAATTGGTAAGGT 60.273 52.381 0.00 0.00 0.00 3.50
6825 8327 2.024751 GCTGGGGGAAATTGGTAAGGTA 60.025 50.000 0.00 0.00 0.00 3.08
6906 8420 6.070767 ACTCCAGTATTGTTGTATGTACTGCT 60.071 38.462 5.99 0.00 41.52 4.24
6907 8421 7.123697 ACTCCAGTATTGTTGTATGTACTGCTA 59.876 37.037 5.99 0.00 41.52 3.49
6908 8422 7.489160 TCCAGTATTGTTGTATGTACTGCTAG 58.511 38.462 5.99 0.00 41.52 3.42
6909 8423 6.201044 CCAGTATTGTTGTATGTACTGCTAGC 59.799 42.308 8.10 8.10 41.52 3.42
6950 8471 5.708230 GGTGGTTGGTGATGTACATAAAGAA 59.292 40.000 8.71 0.00 0.00 2.52
6996 8532 2.811431 CCAACTCTTTGGTGAACGCATA 59.189 45.455 0.00 0.00 46.63 3.14
7025 8561 1.614903 CCTGATCTTTGTTGCAAGGCA 59.385 47.619 0.00 0.00 36.47 4.75
7079 8615 4.400567 GGTTAATTTGCAGGCTCTGAATCT 59.599 41.667 6.40 0.00 32.44 2.40
7080 8616 5.105595 GGTTAATTTGCAGGCTCTGAATCTT 60.106 40.000 6.40 0.00 32.44 2.40
7081 8617 6.095440 GGTTAATTTGCAGGCTCTGAATCTTA 59.905 38.462 6.40 0.00 32.44 2.10
7082 8618 5.573337 AATTTGCAGGCTCTGAATCTTAC 57.427 39.130 6.40 0.00 32.44 2.34
7083 8619 3.988976 TTGCAGGCTCTGAATCTTACT 57.011 42.857 6.40 0.00 32.44 2.24
7084 8620 3.533606 TGCAGGCTCTGAATCTTACTC 57.466 47.619 6.40 0.00 32.44 2.59
7085 8621 3.102972 TGCAGGCTCTGAATCTTACTCT 58.897 45.455 6.40 0.00 32.44 3.24
7086 8622 3.131933 TGCAGGCTCTGAATCTTACTCTC 59.868 47.826 6.40 0.00 32.44 3.20
7087 8623 3.384467 GCAGGCTCTGAATCTTACTCTCT 59.616 47.826 6.40 0.00 32.44 3.10
7088 8624 4.737352 GCAGGCTCTGAATCTTACTCTCTG 60.737 50.000 6.40 0.00 32.44 3.35
7089 8625 4.402155 CAGGCTCTGAATCTTACTCTCTGT 59.598 45.833 0.00 0.00 32.44 3.41
7090 8626 4.402155 AGGCTCTGAATCTTACTCTCTGTG 59.598 45.833 0.00 0.00 0.00 3.66
7091 8627 4.159506 GGCTCTGAATCTTACTCTCTGTGT 59.840 45.833 0.00 0.00 0.00 3.72
7092 8628 5.337169 GGCTCTGAATCTTACTCTCTGTGTT 60.337 44.000 0.00 0.00 0.00 3.32
7093 8629 5.576384 GCTCTGAATCTTACTCTCTGTGTTG 59.424 44.000 0.00 0.00 0.00 3.33
7123 8669 7.459394 TTTACTGTACTTCAGAACTTTGTCG 57.541 36.000 1.79 0.00 46.27 4.35
7131 8677 4.609691 TCAGAACTTTGTCGGTTTGTTC 57.390 40.909 0.00 0.00 37.76 3.18
7132 8678 4.004314 TCAGAACTTTGTCGGTTTGTTCA 58.996 39.130 0.00 0.00 39.33 3.18
7159 8705 0.178767 CTGATGGATGTTGGAGGCGA 59.821 55.000 0.00 0.00 0.00 5.54
7162 8708 0.548031 ATGGATGTTGGAGGCGATGT 59.452 50.000 0.00 0.00 0.00 3.06
7163 8709 0.107703 TGGATGTTGGAGGCGATGTC 60.108 55.000 0.00 0.00 0.00 3.06
7164 8710 0.179000 GGATGTTGGAGGCGATGTCT 59.821 55.000 0.00 0.00 0.00 3.41
7166 8712 0.107508 ATGTTGGAGGCGATGTCTGG 60.108 55.000 0.00 0.00 0.00 3.86
7167 8713 1.191489 TGTTGGAGGCGATGTCTGGA 61.191 55.000 0.00 0.00 0.00 3.86
7168 8714 0.460987 GTTGGAGGCGATGTCTGGAG 60.461 60.000 0.00 0.00 0.00 3.86
7169 8715 1.617018 TTGGAGGCGATGTCTGGAGG 61.617 60.000 0.00 0.00 0.00 4.30
7170 8716 2.107953 GAGGCGATGTCTGGAGGC 59.892 66.667 0.00 0.00 0.00 4.70
7171 8717 3.781770 GAGGCGATGTCTGGAGGCG 62.782 68.421 0.00 0.00 0.00 5.52
7172 8718 4.148825 GGCGATGTCTGGAGGCGT 62.149 66.667 0.00 0.00 0.00 5.68
7173 8719 2.125512 GCGATGTCTGGAGGCGTT 60.126 61.111 0.00 0.00 0.00 4.84
7174 8720 2.456119 GCGATGTCTGGAGGCGTTG 61.456 63.158 0.00 0.00 0.00 4.10
7175 8721 1.811266 CGATGTCTGGAGGCGTTGG 60.811 63.158 0.00 0.00 0.00 3.77
7176 8722 1.296715 GATGTCTGGAGGCGTTGGT 59.703 57.895 0.00 0.00 0.00 3.67
7177 8723 1.003355 ATGTCTGGAGGCGTTGGTG 60.003 57.895 0.00 0.00 0.00 4.17
7178 8724 2.358737 GTCTGGAGGCGTTGGTGG 60.359 66.667 0.00 0.00 0.00 4.61
7179 8725 3.636231 TCTGGAGGCGTTGGTGGG 61.636 66.667 0.00 0.00 0.00 4.61
7180 8726 3.953775 CTGGAGGCGTTGGTGGGT 61.954 66.667 0.00 0.00 0.00 4.51
7181 8727 2.527123 TGGAGGCGTTGGTGGGTA 60.527 61.111 0.00 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.518572 CGATGGTGGCCGTGAGTAC 60.519 63.158 0.00 0.00 0.00 2.73
1 2 1.679641 TCGATGGTGGCCGTGAGTA 60.680 57.895 0.00 0.00 0.00 2.59
2 3 2.994995 TCGATGGTGGCCGTGAGT 60.995 61.111 0.00 0.00 0.00 3.41
3 4 2.509336 GTCGATGGTGGCCGTGAG 60.509 66.667 0.00 0.00 0.00 3.51
4 5 3.295304 CTGTCGATGGTGGCCGTGA 62.295 63.158 0.00 0.00 0.00 4.35
5 6 2.815211 CTGTCGATGGTGGCCGTG 60.815 66.667 0.00 0.00 0.00 4.94
6 7 4.760047 GCTGTCGATGGTGGCCGT 62.760 66.667 0.00 0.00 0.00 5.68
7 8 3.958147 AAGCTGTCGATGGTGGCCG 62.958 63.158 0.00 0.00 0.00 6.13
8 9 2.045926 AAGCTGTCGATGGTGGCC 60.046 61.111 0.00 0.00 0.00 5.36
9 10 1.375908 TCAAGCTGTCGATGGTGGC 60.376 57.895 0.00 0.00 0.00 5.01
22 23 1.739562 CGAGGTGCTCAGGTCAAGC 60.740 63.158 0.00 0.00 40.26 4.01
65 71 1.118356 AGGAGATGATGGCGAGGACC 61.118 60.000 0.00 0.00 0.00 4.46
104 110 3.478274 GGAGGGAGGAGGCAGCTG 61.478 72.222 10.11 10.11 0.00 4.24
710 755 1.075896 GGATCGAGGAGGGGTGAGT 60.076 63.158 0.00 0.00 0.00 3.41
724 771 6.094603 CAGGCAGGCACTAATATAAATGGATC 59.905 42.308 0.00 0.00 36.02 3.36
764 811 1.205893 GGTAGAGGTGAAGCAGAGGTG 59.794 57.143 0.00 0.00 0.00 4.00
765 812 1.562783 GGTAGAGGTGAAGCAGAGGT 58.437 55.000 0.00 0.00 0.00 3.85
766 813 0.827368 GGGTAGAGGTGAAGCAGAGG 59.173 60.000 0.00 0.00 0.00 3.69
777 824 1.457604 CATGGCCATGGGGTAGAGG 59.542 63.158 34.31 8.65 35.24 3.69
911 966 2.671130 GCTGAGAGAGCTTGCTACTT 57.329 50.000 0.00 0.00 45.21 2.24
923 978 4.819082 GCTGAGCTGAGCTGAGAG 57.181 61.111 24.94 12.16 42.26 3.20
934 989 3.662378 AAGCCGAGCTGAGCTGAGC 62.662 63.158 18.32 18.32 39.88 4.26
935 990 1.810441 CAAGCCGAGCTGAGCTGAG 60.810 63.158 13.71 5.51 39.88 3.35
936 991 2.263852 CAAGCCGAGCTGAGCTGA 59.736 61.111 13.71 0.00 39.88 4.26
995 1059 1.301558 CATCTGCTCTCCATCCGCC 60.302 63.158 0.00 0.00 0.00 6.13
1142 1206 2.128507 GTGGCGTAGGAGGAGGAGG 61.129 68.421 0.00 0.00 0.00 4.30
1143 1207 2.128507 GGTGGCGTAGGAGGAGGAG 61.129 68.421 0.00 0.00 0.00 3.69
1144 1208 2.043248 GGTGGCGTAGGAGGAGGA 60.043 66.667 0.00 0.00 0.00 3.71
1145 1209 2.363795 TGGTGGCGTAGGAGGAGG 60.364 66.667 0.00 0.00 0.00 4.30
1146 1210 3.082579 GCTGGTGGCGTAGGAGGAG 62.083 68.421 0.00 0.00 0.00 3.69
1147 1211 3.075005 GCTGGTGGCGTAGGAGGA 61.075 66.667 0.00 0.00 0.00 3.71
1309 1385 9.905713 ATAAATCAACACACTGGATATGTAGTT 57.094 29.630 0.00 0.00 0.00 2.24
1310 1386 9.547753 GATAAATCAACACACTGGATATGTAGT 57.452 33.333 0.00 0.00 0.00 2.73
1311 1387 9.770097 AGATAAATCAACACACTGGATATGTAG 57.230 33.333 0.00 0.00 0.00 2.74
1312 1388 9.764363 GAGATAAATCAACACACTGGATATGTA 57.236 33.333 0.00 0.00 0.00 2.29
1315 1391 7.443575 GCAGAGATAAATCAACACACTGGATAT 59.556 37.037 0.00 0.00 0.00 1.63
1348 1494 7.280356 TGTGAGGGATTAGAGCTTAATTAACC 58.720 38.462 0.00 0.02 0.00 2.85
1378 1524 6.096001 CAGCCTGAATCCAAGCTTTTAAGTAT 59.904 38.462 0.00 0.00 37.96 2.12
1387 1534 1.630369 TGTACAGCCTGAATCCAAGCT 59.370 47.619 0.00 0.00 40.52 3.74
1401 1548 2.794910 CAAGAACGTCACAGGTGTACAG 59.205 50.000 0.00 0.00 0.00 2.74
1438 1585 2.185004 AGTTGCTTGGATAGTTGCGT 57.815 45.000 0.00 0.00 0.00 5.24
1441 1588 5.617751 CGGAAGAAAGTTGCTTGGATAGTTG 60.618 44.000 0.00 0.00 0.00 3.16
1442 1589 4.455877 CGGAAGAAAGTTGCTTGGATAGTT 59.544 41.667 0.00 0.00 0.00 2.24
1443 1590 4.003648 CGGAAGAAAGTTGCTTGGATAGT 58.996 43.478 0.00 0.00 0.00 2.12
1444 1591 4.003648 ACGGAAGAAAGTTGCTTGGATAG 58.996 43.478 0.00 0.00 0.00 2.08
1445 1592 4.015872 ACGGAAGAAAGTTGCTTGGATA 57.984 40.909 0.00 0.00 0.00 2.59
1446 1593 2.863809 ACGGAAGAAAGTTGCTTGGAT 58.136 42.857 0.00 0.00 0.00 3.41
1447 1594 2.341846 ACGGAAGAAAGTTGCTTGGA 57.658 45.000 0.00 0.00 0.00 3.53
1448 1595 2.618709 AGAACGGAAGAAAGTTGCTTGG 59.381 45.455 0.00 0.00 0.00 3.61
1453 1600 5.511729 GTGTTGAAAGAACGGAAGAAAGTTG 59.488 40.000 0.00 0.00 0.00 3.16
1455 1602 4.698304 TGTGTTGAAAGAACGGAAGAAAGT 59.302 37.500 0.00 0.00 0.00 2.66
1465 1612 4.979197 TGTGTGTGTTTGTGTTGAAAGAAC 59.021 37.500 0.00 0.00 0.00 3.01
1478 1625 0.726827 CTCTGTGCGTGTGTGTGTTT 59.273 50.000 0.00 0.00 0.00 2.83
1479 1626 0.391130 ACTCTGTGCGTGTGTGTGTT 60.391 50.000 0.00 0.00 0.00 3.32
1495 1642 1.543429 CCTGTGTTCTTCACCCCACTC 60.543 57.143 0.00 0.00 45.61 3.51
1579 1729 2.271944 AAGAAAGACAAACTCCCCCG 57.728 50.000 0.00 0.00 0.00 5.73
1601 1751 3.403558 GGAGGAGGACCCCAGCAC 61.404 72.222 2.29 0.00 36.73 4.40
1689 1848 2.378547 CTGGCTATCTAGGAGGAGGACT 59.621 54.545 0.00 0.00 0.00 3.85
1690 1849 2.802719 CTGGCTATCTAGGAGGAGGAC 58.197 57.143 0.00 0.00 0.00 3.85
1728 1887 2.859165 ATGCCTCCACGAAAAGAAGA 57.141 45.000 0.00 0.00 0.00 2.87
1751 1910 1.557269 ATGTCACTGCCTCCTCACCC 61.557 60.000 0.00 0.00 0.00 4.61
1752 1911 1.134670 GTATGTCACTGCCTCCTCACC 60.135 57.143 0.00 0.00 0.00 4.02
1753 1912 1.550524 TGTATGTCACTGCCTCCTCAC 59.449 52.381 0.00 0.00 0.00 3.51
1754 1913 1.937191 TGTATGTCACTGCCTCCTCA 58.063 50.000 0.00 0.00 0.00 3.86
1885 2066 0.186630 TCCCAGGCATCCATTCCATG 59.813 55.000 0.00 0.00 0.00 3.66
1886 2067 0.481567 CTCCCAGGCATCCATTCCAT 59.518 55.000 0.00 0.00 0.00 3.41
1887 2068 1.925120 CTCCCAGGCATCCATTCCA 59.075 57.895 0.00 0.00 0.00 3.53
1888 2069 1.530183 GCTCCCAGGCATCCATTCC 60.530 63.158 0.00 0.00 0.00 3.01
1889 2070 1.530183 GGCTCCCAGGCATCCATTC 60.530 63.158 0.00 0.00 40.97 2.67
1890 2071 2.605299 GGCTCCCAGGCATCCATT 59.395 61.111 0.00 0.00 40.97 3.16
1891 2072 3.505773 GGGCTCCCAGGCATCCAT 61.506 66.667 0.00 0.00 43.44 3.41
1955 2136 2.821546 TCATCTGGCGGAAACTAATCG 58.178 47.619 0.00 0.00 0.00 3.34
2024 2207 7.516209 AGGGATATTGCAACTTAACTAGGGATA 59.484 37.037 0.00 0.00 0.00 2.59
2025 2208 6.332901 AGGGATATTGCAACTTAACTAGGGAT 59.667 38.462 0.00 0.00 0.00 3.85
2026 2209 5.670361 AGGGATATTGCAACTTAACTAGGGA 59.330 40.000 0.00 0.00 0.00 4.20
2027 2210 5.941788 AGGGATATTGCAACTTAACTAGGG 58.058 41.667 0.00 0.00 0.00 3.53
2028 2211 7.736893 ACTAGGGATATTGCAACTTAACTAGG 58.263 38.462 22.53 11.85 0.00 3.02
2031 2214 9.561069 CATAACTAGGGATATTGCAACTTAACT 57.439 33.333 0.00 0.30 0.00 2.24
2032 2215 8.290325 GCATAACTAGGGATATTGCAACTTAAC 58.710 37.037 0.00 0.00 0.00 2.01
2033 2216 8.217799 AGCATAACTAGGGATATTGCAACTTAA 58.782 33.333 0.00 0.00 0.00 1.85
2034 2217 7.745717 AGCATAACTAGGGATATTGCAACTTA 58.254 34.615 0.00 0.00 0.00 2.24
2035 2218 6.605119 AGCATAACTAGGGATATTGCAACTT 58.395 36.000 0.00 0.00 0.00 2.66
2036 2219 6.192970 AGCATAACTAGGGATATTGCAACT 57.807 37.500 0.00 0.00 0.00 3.16
2037 2220 7.978982 CATAGCATAACTAGGGATATTGCAAC 58.021 38.462 0.00 0.00 33.29 4.17
2123 2306 2.104622 CCCCCACAAGCATTTGAAAACT 59.895 45.455 0.00 0.00 37.73 2.66
2180 2363 2.544267 CTGACGGAAGAAAACACCTCAC 59.456 50.000 0.00 0.00 0.00 3.51
2182 2365 3.107642 TCTGACGGAAGAAAACACCTC 57.892 47.619 0.00 0.00 0.00 3.85
2195 2378 7.706159 TGATTTGAATAATCCATTTCTGACGG 58.294 34.615 0.00 0.00 0.00 4.79
2196 2379 9.229784 CTTGATTTGAATAATCCATTTCTGACG 57.770 33.333 0.00 0.00 0.00 4.35
2205 2532 5.898397 TGGATGCCTTGATTTGAATAATCCA 59.102 36.000 0.00 0.00 38.90 3.41
2206 2533 6.183360 TGTGGATGCCTTGATTTGAATAATCC 60.183 38.462 0.00 0.00 33.23 3.01
2207 2534 6.808829 TGTGGATGCCTTGATTTGAATAATC 58.191 36.000 0.00 0.00 0.00 1.75
2256 2587 1.756538 GAATAATGCAAGGGGGTGGTG 59.243 52.381 0.00 0.00 0.00 4.17
2276 2607 5.534654 TCCTGTTCTGGTTTATCTTTGTTGG 59.465 40.000 0.00 0.00 0.00 3.77
2290 2621 1.072965 GCATATCCCCTCCTGTTCTGG 59.927 57.143 0.00 0.00 0.00 3.86
2305 2636 7.075851 TCCAAAGAGAGATGAGAATGCATAT 57.924 36.000 0.00 0.00 0.00 1.78
2306 2637 6.490241 TCCAAAGAGAGATGAGAATGCATA 57.510 37.500 0.00 0.00 0.00 3.14
2307 2638 5.369409 TCCAAAGAGAGATGAGAATGCAT 57.631 39.130 0.00 0.00 0.00 3.96
2310 2641 4.571580 GTGCTCCAAAGAGAGATGAGAATG 59.428 45.833 0.00 0.00 43.39 2.67
2331 2662 1.558756 AGATCAAAGAGCCTCTGGGTG 59.441 52.381 0.00 0.00 31.55 4.61
2440 2772 9.533831 AATTTACAATTGGAAGTGGTAATCTCT 57.466 29.630 10.83 0.00 0.00 3.10
2554 3928 9.515226 AGATAAAAAGAACACCTTACTAATGCA 57.485 29.630 0.00 0.00 34.00 3.96
2597 3971 5.632764 CGAAATACCATTGTCAAATGCAACA 59.367 36.000 0.00 0.00 41.66 3.33
2600 3974 5.182950 ACTCGAAATACCATTGTCAAATGCA 59.817 36.000 0.00 0.00 41.66 3.96
2621 3995 5.408356 ACATTAGTATCGTTGACCACACTC 58.592 41.667 0.00 0.00 0.00 3.51
2633 4007 9.394477 TGACGATGAAGAAATACATTAGTATCG 57.606 33.333 0.00 0.00 40.00 2.92
2676 4051 7.988737 TGCATAGATAGTTTTGTTCCAATGAG 58.011 34.615 0.00 0.00 0.00 2.90
2880 4255 7.791029 TCAATGATGCAGTAACATAACTAGGA 58.209 34.615 0.00 0.00 0.00 2.94
2906 4281 2.029649 GTCTGCTTAGGACCGTTACACA 60.030 50.000 0.00 0.00 0.00 3.72
2924 4299 0.966920 CTAACCGTGTCCCTGTGTCT 59.033 55.000 0.00 0.00 0.00 3.41
2945 4320 8.270030 TCATCATGTAAGACTGGAAGATCAAAT 58.730 33.333 0.00 0.00 37.43 2.32
2969 4344 5.070446 CCTGGCTGACTAATAATACACCTCA 59.930 44.000 0.00 0.00 0.00 3.86
3078 4453 1.471287 AGTTAGTCATGTAGCGACGCA 59.529 47.619 23.70 5.17 38.46 5.24
3160 4536 4.704057 AGAATCAGGCTTCCATCAGAAAAC 59.296 41.667 0.00 0.00 32.88 2.43
3213 4596 6.887626 AAAAATACGGTGGTATTGTCAACT 57.112 33.333 0.67 0.00 46.12 3.16
3380 4763 0.838122 AGTGGGGGTCTGAGAACAGG 60.838 60.000 0.00 0.00 43.60 4.00
3409 4792 8.940397 AAAAACAAGAAGGGATCTGAGAATAA 57.060 30.769 0.00 0.00 38.79 1.40
3439 4824 8.478066 GCCCTCTCTTGTTTTATGGAAAAATAT 58.522 33.333 0.00 0.00 36.32 1.28
3442 4827 5.600484 TGCCCTCTCTTGTTTTATGGAAAAA 59.400 36.000 0.00 0.00 36.32 1.94
3449 4834 6.126361 ACTCCATATGCCCTCTCTTGTTTTAT 60.126 38.462 0.00 0.00 0.00 1.40
3452 4837 3.525199 ACTCCATATGCCCTCTCTTGTTT 59.475 43.478 0.00 0.00 0.00 2.83
3453 4838 3.118531 ACTCCATATGCCCTCTCTTGTT 58.881 45.455 0.00 0.00 0.00 2.83
3457 4842 2.334023 GGAACTCCATATGCCCTCTCT 58.666 52.381 0.00 0.00 35.64 3.10
3473 4858 1.678970 GTGGTGGGCTCATGGGAAC 60.679 63.158 0.00 0.00 0.00 3.62
3480 4865 1.228521 CAACATGGTGGTGGGCTCA 60.229 57.895 1.63 0.00 29.70 4.26
3529 4914 6.721668 TGGGTATCATCAGAGTACTATTCCTG 59.278 42.308 0.00 0.00 0.00 3.86
3591 4976 4.155099 CACCGCACACCACTGATTTTATAA 59.845 41.667 0.00 0.00 0.00 0.98
3630 5015 2.436911 ACCCAATACTAATCGTGTCCCC 59.563 50.000 0.00 0.00 0.00 4.81
3674 5059 3.988976 TGACCAGAAGATCAAAGGGAG 57.011 47.619 0.00 0.00 0.00 4.30
3746 5131 9.862149 TCTAACATTATGTGAGTGATCTAGGTA 57.138 33.333 9.36 0.00 30.64 3.08
3803 5188 0.887933 ATGTTGCAAGGTTAAGCCCG 59.112 50.000 0.00 0.00 38.26 6.13
3810 5195 5.179452 AGGTATAGTCATGTTGCAAGGTT 57.821 39.130 0.00 0.00 0.00 3.50
3818 5203 7.944729 AATTTGCTCAAGGTATAGTCATGTT 57.055 32.000 0.00 0.00 0.00 2.71
3840 5225 6.049263 GACTTTCAGTCGTGAAGAACAAAT 57.951 37.500 0.00 0.00 43.66 2.32
3881 5266 8.539770 TCAGAATAAACAAACAAAACTTTGCA 57.460 26.923 2.07 0.00 41.79 4.08
3908 5293 3.378112 CAGTTTGACAGTTTCAGGCTTCA 59.622 43.478 0.00 0.00 34.94 3.02
3940 5325 6.872547 GTCGACCTTTCTCTATAAACCTTTGT 59.127 38.462 3.51 0.00 0.00 2.83
3977 5365 6.311735 TGGGTTGCTTAATTCCTAAAGAACT 58.688 36.000 0.00 0.00 37.29 3.01
3978 5366 6.584185 TGGGTTGCTTAATTCCTAAAGAAC 57.416 37.500 0.00 0.00 37.29 3.01
3979 5367 6.951198 TCATGGGTTGCTTAATTCCTAAAGAA 59.049 34.615 0.00 0.00 39.32 2.52
4064 5453 4.051237 GTTGCCCATGACTTTTCACTTTC 58.949 43.478 0.00 0.00 33.38 2.62
4067 5456 2.949447 AGTTGCCCATGACTTTTCACT 58.051 42.857 0.00 0.00 33.38 3.41
4069 5458 3.295093 TGAAGTTGCCCATGACTTTTCA 58.705 40.909 0.00 0.00 36.31 2.69
4082 5471 8.654230 TGTATAGATCAAGAAGATGAAGTTGC 57.346 34.615 0.00 0.00 37.00 4.17
4499 5900 1.363145 CGCCATTTTGCTGCCCATTG 61.363 55.000 0.00 0.00 0.00 2.82
4586 5987 0.947244 GGTCAGTGTCAGGCAACAAG 59.053 55.000 0.00 0.00 41.41 3.16
4646 6047 1.450312 CTGATGGTCCTCGGTTGCC 60.450 63.158 0.00 0.00 0.00 4.52
4655 6056 0.257039 AACATCCCTGCTGATGGTCC 59.743 55.000 13.48 0.00 45.16 4.46
4796 6197 2.202987 GGGCTGCTGTCATCTCCG 60.203 66.667 0.00 0.00 0.00 4.63
5378 6779 2.820178 TGGATTGTAGCCTCTGTCTCA 58.180 47.619 0.00 0.00 0.00 3.27
5393 6794 4.811969 TTGAGCAAATGCATCTTGGATT 57.188 36.364 17.53 0.00 40.20 3.01
5570 6971 5.659849 AATCCCTTTCCTCTTCAGCATAT 57.340 39.130 0.00 0.00 0.00 1.78
5603 7004 0.179001 AACCTTGGGGAACGTTCAGG 60.179 55.000 28.24 25.71 36.25 3.86
5621 7022 0.310543 GTGCTGTTTCATCGCCACAA 59.689 50.000 0.00 0.00 0.00 3.33
5630 7031 4.142403 CCAACTTTGAGAAGTGCTGTTTCA 60.142 41.667 0.00 0.00 45.18 2.69
5636 7037 3.129287 CACAACCAACTTTGAGAAGTGCT 59.871 43.478 0.00 0.00 45.18 4.40
5708 7109 1.333636 CCGGCCTGGAGATCTTCACT 61.334 60.000 0.00 0.00 42.00 3.41
5780 7181 2.031516 CACCTCTGCTGCGTGAAGG 61.032 63.158 7.58 7.58 0.00 3.46
5786 7187 3.200593 GCCATCACCTCTGCTGCG 61.201 66.667 0.00 0.00 0.00 5.18
5831 7232 4.240103 ACAGCGTGTGCCAGCTCA 62.240 61.111 0.00 0.00 42.52 4.26
5993 7394 4.814294 CCCGACAGCACGTAGGCC 62.814 72.222 0.00 0.00 38.99 5.19
6360 7762 4.650972 ATACCACACCATTTGTACCACT 57.349 40.909 0.00 0.00 35.67 4.00
6720 8122 4.500452 ACTTAACTCCCTCCATATACCCC 58.500 47.826 0.00 0.00 0.00 4.95
6733 8135 8.319881 AGAATTACCTCACCTTAACTTAACTCC 58.680 37.037 0.00 0.00 0.00 3.85
6785 8287 1.475213 GCACACTTATACCAGCCCCTC 60.475 57.143 0.00 0.00 0.00 4.30
6906 8420 2.497675 CCACACAAAGGAGAGCTAGCTA 59.502 50.000 19.38 0.00 0.00 3.32
6907 8421 1.277557 CCACACAAAGGAGAGCTAGCT 59.722 52.381 19.45 19.45 0.00 3.32
6908 8422 1.002544 ACCACACAAAGGAGAGCTAGC 59.997 52.381 6.62 6.62 0.00 3.42
6909 8423 2.613977 CCACCACACAAAGGAGAGCTAG 60.614 54.545 0.00 0.00 0.00 3.42
6950 8471 8.686334 GGATTCAGTTCACAAATGTATACCATT 58.314 33.333 0.00 0.00 45.81 3.16
6996 8532 4.337555 GCAACAAAGATCAGGTATGCATCT 59.662 41.667 0.19 0.00 33.00 2.90
7025 8561 4.677182 ACACAGGGGCAGATTAGATTTTT 58.323 39.130 0.00 0.00 0.00 1.94
7027 8563 3.525199 AGACACAGGGGCAGATTAGATTT 59.475 43.478 0.00 0.00 0.00 2.17
7028 8564 3.118112 CAGACACAGGGGCAGATTAGATT 60.118 47.826 0.00 0.00 0.00 2.40
7029 8565 2.437281 CAGACACAGGGGCAGATTAGAT 59.563 50.000 0.00 0.00 0.00 1.98
7031 8567 1.833630 TCAGACACAGGGGCAGATTAG 59.166 52.381 0.00 0.00 0.00 1.73
7032 8568 1.951209 TCAGACACAGGGGCAGATTA 58.049 50.000 0.00 0.00 0.00 1.75
7080 8616 9.826574 ACAGTAAAAATAACAACACAGAGAGTA 57.173 29.630 0.00 0.00 0.00 2.59
7081 8617 8.732746 ACAGTAAAAATAACAACACAGAGAGT 57.267 30.769 0.00 0.00 0.00 3.24
7083 8619 9.826574 AGTACAGTAAAAATAACAACACAGAGA 57.173 29.630 0.00 0.00 0.00 3.10
7123 8669 2.229792 TCAGCACAGGATGAACAAACC 58.770 47.619 0.00 0.00 39.69 3.27
7132 8678 2.651455 CAACATCCATCAGCACAGGAT 58.349 47.619 0.00 0.00 42.71 3.24
7159 8705 1.003355 CACCAACGCCTCCAGACAT 60.003 57.895 0.00 0.00 0.00 3.06
7162 8708 3.636231 CCCACCAACGCCTCCAGA 61.636 66.667 0.00 0.00 0.00 3.86
7163 8709 2.521958 CTACCCACCAACGCCTCCAG 62.522 65.000 0.00 0.00 0.00 3.86
7164 8710 2.527123 TACCCACCAACGCCTCCA 60.527 61.111 0.00 0.00 0.00 3.86
7166 8712 0.175073 CTACTACCCACCAACGCCTC 59.825 60.000 0.00 0.00 0.00 4.70
7167 8713 1.262640 CCTACTACCCACCAACGCCT 61.263 60.000 0.00 0.00 0.00 5.52
7168 8714 1.219935 CCTACTACCCACCAACGCC 59.780 63.158 0.00 0.00 0.00 5.68
7169 8715 0.390735 CACCTACTACCCACCAACGC 60.391 60.000 0.00 0.00 0.00 4.84
7170 8716 0.248289 CCACCTACTACCCACCAACG 59.752 60.000 0.00 0.00 0.00 4.10
7171 8717 1.648116 TCCACCTACTACCCACCAAC 58.352 55.000 0.00 0.00 0.00 3.77
7172 8718 2.193127 CATCCACCTACTACCCACCAA 58.807 52.381 0.00 0.00 0.00 3.67
7173 8719 1.874129 CATCCACCTACTACCCACCA 58.126 55.000 0.00 0.00 0.00 4.17
7174 8720 0.468648 GCATCCACCTACTACCCACC 59.531 60.000 0.00 0.00 0.00 4.61
7175 8721 1.497161 AGCATCCACCTACTACCCAC 58.503 55.000 0.00 0.00 0.00 4.61
7176 8722 2.246588 AGTAGCATCCACCTACTACCCA 59.753 50.000 0.00 0.00 42.63 4.51
7177 8723 2.628657 CAGTAGCATCCACCTACTACCC 59.371 54.545 1.22 0.00 42.58 3.69
7178 8724 3.563223 TCAGTAGCATCCACCTACTACC 58.437 50.000 1.22 0.00 42.58 3.18
7179 8725 5.793030 AATCAGTAGCATCCACCTACTAC 57.207 43.478 1.22 0.00 42.58 2.73
7180 8726 5.009710 CGAAATCAGTAGCATCCACCTACTA 59.990 44.000 1.22 0.00 42.58 1.82
7181 8727 4.202161 CGAAATCAGTAGCATCCACCTACT 60.202 45.833 0.00 0.00 44.65 2.57


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

AutoCloner maintained by Alex Coulton.