Multiple sequence alignment - TraesCS6B01G133100

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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 TraesCS6B01G133100 chr6B 100.000 5990 0 0 1 5990 130073423 130079412 0.000000e+00 11062.0
1 TraesCS6B01G133100 chr6B 92.169 166 12 1 1799 1963 232734816 232734981 3.610000e-57 233.0
2 TraesCS6B01G133100 chr6B 92.121 165 12 1 1799 1962 127605809 127605973 1.300000e-56 231.0
3 TraesCS6B01G133100 chr6D 96.046 5514 137 47 32 5510 57997884 58003351 0.000000e+00 8900.0
4 TraesCS6B01G133100 chr6D 82.422 256 39 3 3122 3374 58001019 58001271 1.010000e-52 219.0
5 TraesCS6B01G133100 chr6D 90.476 147 13 1 1065 1211 57999109 57999254 6.130000e-45 193.0
6 TraesCS6B01G133100 chr6A 95.198 3769 126 20 1961 5685 73299937 73303694 0.000000e+00 5906.0
7 TraesCS6B01G133100 chr6A 92.320 1224 60 21 65 1266 73298276 73299487 0.000000e+00 1709.0
8 TraesCS6B01G133100 chr6A 93.995 433 25 1 1372 1804 73299508 73299939 0.000000e+00 654.0
9 TraesCS6B01G133100 chr6A 90.303 165 13 2 5821 5985 73303835 73303996 4.700000e-51 213.0
10 TraesCS6B01G133100 chr6A 87.692 130 9 6 4610 4735 144266549 144266675 1.740000e-30 145.0
11 TraesCS6B01G133100 chr2A 93.333 165 10 1 1799 1962 249754623 249754459 6.000000e-60 243.0
12 TraesCS6B01G133100 chr5D 92.638 163 11 1 1802 1963 150835568 150835730 3.610000e-57 233.0
13 TraesCS6B01G133100 chr3B 92.638 163 11 1 1802 1963 552226568 552226406 3.610000e-57 233.0
14 TraesCS6B01G133100 chr5B 92.121 165 11 2 1800 1963 577082745 577082582 1.300000e-56 231.0
15 TraesCS6B01G133100 chrUn 92.073 164 11 2 1799 1960 80232836 80232673 4.670000e-56 230.0
16 TraesCS6B01G133100 chr2B 90.341 176 15 2 1795 1969 477809635 477809461 4.670000e-56 230.0
17 TraesCS6B01G133100 chr2B 96.970 33 0 1 5567 5599 209748689 209748658 3.000000e-03 54.7
18 TraesCS6B01G133100 chr7D 89.764 127 10 3 4611 4736 242788000 242788124 6.210000e-35 159.0
19 TraesCS6B01G133100 chr4D 89.764 127 7 4 4615 4737 109274967 109275091 2.230000e-34 158.0
20 TraesCS6B01G133100 chr4D 94.595 37 0 2 5563 5598 350523726 350523691 8.390000e-04 56.5
21 TraesCS6B01G133100 chr4A 87.970 133 10 4 4615 4743 467246607 467246477 1.040000e-32 152.0
22 TraesCS6B01G133100 chr4A 86.923 130 11 5 4611 4737 113861579 113861453 2.250000e-29 141.0
23 TraesCS6B01G133100 chr1D 91.228 114 7 2 4619 4729 120536355 120536242 1.040000e-32 152.0
24 TraesCS6B01G133100 chr1D 100.000 28 0 0 5567 5594 485753111 485753138 1.100000e-02 52.8
25 TraesCS6B01G133100 chr2D 88.462 130 8 6 4618 4743 607675741 607675867 3.740000e-32 150.0
26 TraesCS6B01G133100 chr2D 91.111 45 4 0 5567 5611 485849200 485849244 1.800000e-05 62.1
27 TraesCS6B01G133100 chr2D 90.909 44 4 0 5567 5610 626422241 626422284 6.480000e-05 60.2
28 TraesCS6B01G133100 chr5A 92.000 50 3 1 5566 5614 478795717 478795766 1.080000e-07 69.4
29 TraesCS6B01G133100 chr3A 94.737 38 1 1 5562 5599 672807034 672807070 2.330000e-04 58.4
30 TraesCS6B01G133100 chr4B 96.875 32 0 1 5567 5598 480535929 480535899 1.100000e-02 52.8


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 TraesCS6B01G133100 chr6B 130073423 130079412 5989 False 11062.0 11062 100.000 1 5990 1 chr6B.!!$F2 5989
1 TraesCS6B01G133100 chr6D 57997884 58003351 5467 False 8900.0 8900 96.046 32 5510 1 chr6D.!!$F1 5478
2 TraesCS6B01G133100 chr6D 57999109 58001271 2162 False 206.0 219 86.449 1065 3374 2 chr6D.!!$F2 2309
3 TraesCS6B01G133100 chr6A 73298276 73303996 5720 False 2120.5 5906 92.954 65 5985 4 chr6A.!!$F2 5920

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
22 23 0.028770 CGAAGCAAACGGAAAGCACA 59.971 50.000 0.00 0.0 0.00 4.57 F
932 987 0.321210 ATTCATGGCGTCGTGTTGGA 60.321 50.000 9.42 0.0 0.00 3.53 F
1637 1694 0.529555 GCTGGTCGCTCATCTTCCTC 60.530 60.000 0.00 0.0 35.14 3.71 F
3221 3285 2.046507 CAGAGGCCACAGCAGTCC 60.047 66.667 5.01 0.0 42.56 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1355 1412 1.494721 TGGCTCAAGAAAGGTTCAGGT 59.505 47.619 0.0 0.0 0.00 4.00 R
2567 2631 2.093021 TGGAATGTCAGCATCATCCGAA 60.093 45.455 0.0 0.0 35.67 4.30 R
3345 3436 0.318120 TGACTCTGCGATGACTGCAA 59.682 50.000 0.0 0.0 42.70 4.08 R
5160 5266 0.668535 AAGAACTTTTCACCTGCCGC 59.331 50.000 0.0 0.0 0.00 6.53 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
21 22 2.783440 CGAAGCAAACGGAAAGCAC 58.217 52.632 0.00 0.00 0.00 4.40
22 23 0.028770 CGAAGCAAACGGAAAGCACA 59.971 50.000 0.00 0.00 0.00 4.57
23 24 1.334960 CGAAGCAAACGGAAAGCACAT 60.335 47.619 0.00 0.00 0.00 3.21
24 25 2.053627 GAAGCAAACGGAAAGCACATG 58.946 47.619 0.00 0.00 0.00 3.21
25 26 1.032014 AGCAAACGGAAAGCACATGT 58.968 45.000 0.00 0.00 0.00 3.21
26 27 1.408702 AGCAAACGGAAAGCACATGTT 59.591 42.857 0.00 0.00 0.00 2.71
27 28 1.522258 GCAAACGGAAAGCACATGTTG 59.478 47.619 0.00 0.00 0.00 3.33
28 29 2.126467 CAAACGGAAAGCACATGTTGG 58.874 47.619 0.00 0.00 0.00 3.77
29 30 1.398692 AACGGAAAGCACATGTTGGT 58.601 45.000 0.00 0.00 37.63 3.67
36 37 1.256812 AGCACATGTTGGTTAAGGGC 58.743 50.000 0.00 0.00 28.85 5.19
48 49 3.222603 GGTTAAGGGCATAATCACCTGG 58.777 50.000 0.00 0.00 34.17 4.45
87 88 3.118956 TGGCGGCAAAAGAAGAAAGAAAA 60.119 39.130 10.22 0.00 0.00 2.29
108 109 0.395586 TGGGCCTGCAACACCATATC 60.396 55.000 4.53 0.00 0.00 1.63
185 222 1.002544 GACCCACAGACTCTTTCCAGG 59.997 57.143 0.00 0.00 0.00 4.45
221 265 4.096003 CCCCGGGCAAGACGTCAT 62.096 66.667 17.73 1.86 0.00 3.06
275 320 4.033587 CACGCACACGCCTATTTATAAACT 59.966 41.667 0.00 0.00 45.53 2.66
711 766 1.401018 CGTCCCAGATTTGCGTTTTCC 60.401 52.381 0.00 0.00 0.00 3.13
712 767 1.886542 GTCCCAGATTTGCGTTTTCCT 59.113 47.619 0.00 0.00 0.00 3.36
732 787 1.900545 GCCTGCGGAAACCCTAGACT 61.901 60.000 0.00 0.00 0.00 3.24
892 947 6.314784 GCTCGATGCTTTCTTTAGCTAAAAA 58.685 36.000 19.10 10.99 41.76 1.94
897 952 7.803189 CGATGCTTTCTTTAGCTAAAAACTTCA 59.197 33.333 19.10 14.10 41.76 3.02
912 967 9.573133 CTAAAAACTTCAACACTCTGTGAAAAT 57.427 29.630 4.61 0.00 36.96 1.82
916 971 9.736023 AAACTTCAACACTCTGTGAAAATATTC 57.264 29.630 4.61 0.00 36.96 1.75
917 972 8.450578 ACTTCAACACTCTGTGAAAATATTCA 57.549 30.769 4.61 0.00 43.18 2.57
918 973 9.071276 ACTTCAACACTCTGTGAAAATATTCAT 57.929 29.630 4.61 0.00 46.67 2.57
919 974 9.338291 CTTCAACACTCTGTGAAAATATTCATG 57.662 33.333 4.61 0.00 46.67 3.07
921 976 6.199937 ACACTCTGTGAAAATATTCATGGC 57.800 37.500 4.61 0.00 46.67 4.40
922 977 5.163723 ACACTCTGTGAAAATATTCATGGCG 60.164 40.000 4.61 0.00 46.67 5.69
923 978 4.943705 ACTCTGTGAAAATATTCATGGCGT 59.056 37.500 0.00 0.00 46.67 5.68
924 979 5.065218 ACTCTGTGAAAATATTCATGGCGTC 59.935 40.000 0.00 0.00 46.67 5.19
925 980 4.033932 TCTGTGAAAATATTCATGGCGTCG 59.966 41.667 0.00 0.00 46.67 5.12
926 981 3.687212 TGTGAAAATATTCATGGCGTCGT 59.313 39.130 0.00 0.00 46.67 4.34
927 982 4.028383 GTGAAAATATTCATGGCGTCGTG 58.972 43.478 1.86 1.86 46.67 4.35
930 985 3.673746 AATATTCATGGCGTCGTGTTG 57.326 42.857 9.42 0.00 0.00 3.33
932 987 0.321210 ATTCATGGCGTCGTGTTGGA 60.321 50.000 9.42 0.00 0.00 3.53
951 1007 3.009363 TGGAAACTCATGAGGATTGCTGA 59.991 43.478 26.08 8.81 0.00 4.26
1121 1177 8.659527 TGGAATCATAGTTTGCTGGATATTCTA 58.340 33.333 0.00 0.00 0.00 2.10
1157 1213 9.791820 TGAACATGTATGCTTAATTCATTTGAG 57.208 29.630 0.00 0.00 0.00 3.02
1162 1218 9.888878 ATGTATGCTTAATTCATTTGAGAATCG 57.111 29.630 0.00 0.00 37.24 3.34
1171 1227 7.778470 ATTCATTTGAGAATCGAGGAACTAC 57.222 36.000 0.00 0.00 38.61 2.73
1204 1260 3.192212 TCTGTGATAGACTGACAGTGCAG 59.808 47.826 14.14 10.72 38.60 4.41
1215 1271 2.703536 TGACAGTGCAGTTCTTTCCCTA 59.296 45.455 0.00 0.00 0.00 3.53
1292 1349 2.543012 CGTAGAAGCAGCTGGAATCATG 59.457 50.000 17.12 0.00 0.00 3.07
1351 1408 9.320295 TGTAGGGTTAATTCATTTGAAAAGGAT 57.680 29.630 0.00 0.00 37.61 3.24
1353 1410 7.623630 AGGGTTAATTCATTTGAAAAGGATGG 58.376 34.615 0.00 0.00 37.61 3.51
1354 1411 7.237471 AGGGTTAATTCATTTGAAAAGGATGGT 59.763 33.333 0.00 0.00 37.61 3.55
1355 1412 8.536175 GGGTTAATTCATTTGAAAAGGATGGTA 58.464 33.333 0.00 0.00 37.61 3.25
1356 1413 9.366216 GGTTAATTCATTTGAAAAGGATGGTAC 57.634 33.333 0.00 0.00 37.61 3.34
1357 1414 9.366216 GTTAATTCATTTGAAAAGGATGGTACC 57.634 33.333 4.43 4.43 37.61 3.34
1359 1416 6.588719 TTCATTTGAAAAGGATGGTACCTG 57.411 37.500 14.36 0.00 40.49 4.00
1360 1417 5.886609 TCATTTGAAAAGGATGGTACCTGA 58.113 37.500 14.36 0.27 40.49 3.86
1361 1418 6.310941 TCATTTGAAAAGGATGGTACCTGAA 58.689 36.000 14.36 0.00 40.49 3.02
1362 1419 6.208599 TCATTTGAAAAGGATGGTACCTGAAC 59.791 38.462 14.36 0.87 40.49 3.18
1363 1420 4.028993 TGAAAAGGATGGTACCTGAACC 57.971 45.455 14.36 10.76 40.49 3.62
1364 1421 3.655777 TGAAAAGGATGGTACCTGAACCT 59.344 43.478 14.36 12.77 40.49 3.50
1365 1422 4.105697 TGAAAAGGATGGTACCTGAACCTT 59.894 41.667 14.36 17.40 40.49 3.50
1366 1423 4.741928 AAAGGATGGTACCTGAACCTTT 57.258 40.909 24.80 24.80 41.09 3.11
1367 1424 4.302559 AAGGATGGTACCTGAACCTTTC 57.697 45.455 14.36 0.00 40.49 2.62
1368 1425 3.532102 AGGATGGTACCTGAACCTTTCT 58.468 45.455 14.36 0.00 40.44 2.52
1369 1426 3.916989 AGGATGGTACCTGAACCTTTCTT 59.083 43.478 14.36 0.00 40.44 2.52
1370 1427 4.010349 GGATGGTACCTGAACCTTTCTTG 58.990 47.826 14.36 0.00 40.44 3.02
1390 1447 5.538053 TCTTGAGCCATTTCATTTGTGGTAA 59.462 36.000 0.00 0.00 35.44 2.85
1412 1469 5.179045 AGACTGACAGTGCATTTCTTTTG 57.821 39.130 14.14 0.00 0.00 2.44
1637 1694 0.529555 GCTGGTCGCTCATCTTCCTC 60.530 60.000 0.00 0.00 35.14 3.71
1688 1745 8.562892 CAAGTAAGTGTCTCTGAATTTCAATGT 58.437 33.333 0.01 0.00 0.00 2.71
1811 1868 3.768878 ACCTTCTCATATACTCCCTCCG 58.231 50.000 0.00 0.00 0.00 4.63
2085 2143 6.325919 TGGAATATTGTTGTCCACTCAAAC 57.674 37.500 0.00 0.00 36.51 2.93
2311 2375 9.636789 TCTCATTCTGATTATTGTTGATCCATT 57.363 29.630 0.00 0.00 0.00 3.16
2435 2499 8.949421 AGATTGTTAATGAGGTACAAGGGATAT 58.051 33.333 0.00 0.00 35.48 1.63
2567 2631 9.930693 GATAATCGGGACTATTCATTTCTACTT 57.069 33.333 0.00 0.00 0.00 2.24
2639 2703 2.239400 CCTTCCTTGACCCAAAAGTCC 58.761 52.381 0.00 0.00 35.83 3.85
2669 2733 7.132863 AGTTTGAACTTCTATTGCGAAACTTC 58.867 34.615 0.00 0.00 35.21 3.01
2978 3042 3.625649 AGCCAAAAGTTTCCAAGCAAA 57.374 38.095 0.00 0.00 0.00 3.68
3140 3204 4.383861 CAGAGGCCGCAGCAGTCA 62.384 66.667 9.88 0.00 42.56 3.41
3193 3257 2.433446 CCAGAGGCCACAGCAGTT 59.567 61.111 5.01 0.00 42.56 3.16
3221 3285 2.046507 CAGAGGCCACAGCAGTCC 60.047 66.667 5.01 0.00 42.56 3.85
3345 3436 2.267006 CACAGCGTGAGAGGCCAT 59.733 61.111 5.01 0.00 35.23 4.40
3473 3567 1.954528 CCAAAGACAGCTGCCACAG 59.045 57.895 15.27 1.00 34.12 3.66
3667 3761 6.560253 AAAGTAGTACTGGTGAAGCAATTG 57.440 37.500 5.39 0.00 0.00 2.32
3782 3876 4.717233 TTCTTCATTGTGTTTGTGTGCT 57.283 36.364 0.00 0.00 0.00 4.40
3888 3982 4.437239 ACGACATTGAAGATGAGGATGAC 58.563 43.478 0.00 0.00 0.00 3.06
4013 4110 8.645814 TCCGTCTGTGTATAGATTTGGTATAT 57.354 34.615 0.00 0.00 0.00 0.86
4014 4111 9.743581 TCCGTCTGTGTATAGATTTGGTATATA 57.256 33.333 0.00 0.00 0.00 0.86
4035 4132 1.002468 CAAGCTGGGTTTGTGTCTTCG 60.002 52.381 0.00 0.00 0.00 3.79
4096 4193 4.785301 ACTTAACATGGATCATGGACTGG 58.215 43.478 11.85 2.22 45.16 4.00
4520 4617 3.498397 GGTGTCTTGTCCACATTACACTG 59.502 47.826 17.75 0.00 39.64 3.66
4560 4657 7.975616 TGGCAAAAAGAAATCAGCATATTAGTC 59.024 33.333 0.00 0.00 0.00 2.59
4605 4704 6.847421 TGGTTACTTTTAGTCTACTCTCCC 57.153 41.667 0.00 0.00 0.00 4.30
5041 5144 0.871722 TTCTGGATGTTGTTTCCGCG 59.128 50.000 0.00 0.00 35.94 6.46
5190 5297 5.450412 GGTGAAAAGTTCTTGCAGATGTGAA 60.450 40.000 0.00 0.00 0.00 3.18
5292 5399 3.265791 GAGATAGTGCACCAAGGTCAAG 58.734 50.000 14.63 0.00 0.00 3.02
5294 5401 1.136828 TAGTGCACCAAGGTCAAGGT 58.863 50.000 14.63 0.00 39.10 3.50
5376 5483 9.912634 TTTTCTCATGATGTAACTGATTTTTCC 57.087 29.630 0.00 0.00 0.00 3.13
5537 5645 5.105228 GCATCATCAGGATTGGAAAAGGAAA 60.105 40.000 0.00 0.00 32.57 3.13
5567 5675 2.167900 GGACTTGATTGGCCGTACTAGT 59.832 50.000 0.00 0.00 0.00 2.57
5568 5676 3.187700 GACTTGATTGGCCGTACTAGTG 58.812 50.000 5.39 0.00 0.00 2.74
5571 5679 3.241067 TGATTGGCCGTACTAGTGAAC 57.759 47.619 5.39 0.00 0.00 3.18
5577 5685 1.673923 GCCGTACTAGTGAACCAACCC 60.674 57.143 5.39 0.00 0.00 4.11
5599 5707 3.055675 CGTGGTTGGATGGTTAGTAGGAA 60.056 47.826 0.00 0.00 0.00 3.36
5601 5709 5.318630 GTGGTTGGATGGTTAGTAGGAAAA 58.681 41.667 0.00 0.00 0.00 2.29
5604 5712 6.184789 GGTTGGATGGTTAGTAGGAAAATGA 58.815 40.000 0.00 0.00 0.00 2.57
5610 5718 7.829706 GGATGGTTAGTAGGAAAATGATATCCC 59.170 40.741 0.00 0.00 36.31 3.85
5614 5722 3.910627 AGTAGGAAAATGATATCCCGGCT 59.089 43.478 0.00 0.00 36.31 5.52
5615 5723 3.425162 AGGAAAATGATATCCCGGCTC 57.575 47.619 0.00 0.00 36.31 4.70
5633 5741 6.199393 CCGGCTCTTATTTTAAGATTTTCGG 58.801 40.000 0.00 5.75 0.00 4.30
5634 5742 6.183360 CCGGCTCTTATTTTAAGATTTTCGGT 60.183 38.462 0.00 0.00 0.00 4.69
5649 5757 2.073307 CGGTGATGCGTCTTCACTG 58.927 57.895 18.22 16.70 42.48 3.66
5650 5758 1.354337 CGGTGATGCGTCTTCACTGG 61.354 60.000 18.47 11.40 43.63 4.00
5655 5763 0.534412 ATGCGTCTTCACTGGGAGAG 59.466 55.000 0.00 0.00 0.00 3.20
5661 5769 0.528470 CTTCACTGGGAGAGGACGTC 59.472 60.000 7.13 7.13 0.00 4.34
5685 5793 2.560981 TGTCGACTTTGAGGTGCTCATA 59.439 45.455 17.92 0.00 40.39 2.15
5686 5794 3.195610 TGTCGACTTTGAGGTGCTCATAT 59.804 43.478 17.92 0.00 40.39 1.78
5689 5797 6.264518 TGTCGACTTTGAGGTGCTCATATATA 59.735 38.462 17.92 0.00 40.39 0.86
5690 5798 7.039714 TGTCGACTTTGAGGTGCTCATATATAT 60.040 37.037 17.92 0.00 40.39 0.86
5696 5804 9.149225 CTTTGAGGTGCTCATATATATGTCTTC 57.851 37.037 19.78 14.52 40.39 2.87
5697 5805 6.856895 TGAGGTGCTCATATATATGTCTTCG 58.143 40.000 19.78 7.97 35.39 3.79
5700 5808 7.093354 AGGTGCTCATATATATGTCTTCGTTG 58.907 38.462 19.78 0.00 35.26 4.10
5701 5809 6.311445 GGTGCTCATATATATGTCTTCGTTGG 59.689 42.308 19.78 4.69 35.26 3.77
5702 5810 7.090808 GTGCTCATATATATGTCTTCGTTGGA 58.909 38.462 19.78 0.00 35.26 3.53
5703 5811 7.598869 GTGCTCATATATATGTCTTCGTTGGAA 59.401 37.037 19.78 0.00 35.26 3.53
5705 5813 8.029522 GCTCATATATATGTCTTCGTTGGAAGA 58.970 37.037 19.78 2.57 46.74 2.87
5717 5825 5.723672 TCGTTGGAAGAAGACATTCTAGT 57.276 39.130 0.00 0.00 45.25 2.57
5718 5826 5.710984 TCGTTGGAAGAAGACATTCTAGTC 58.289 41.667 0.00 0.00 45.25 2.59
5719 5827 4.559251 CGTTGGAAGAAGACATTCTAGTCG 59.441 45.833 0.00 0.00 45.25 4.18
5720 5828 5.619309 CGTTGGAAGAAGACATTCTAGTCGA 60.619 44.000 0.00 0.00 45.25 4.20
5721 5829 5.312120 TGGAAGAAGACATTCTAGTCGAC 57.688 43.478 7.70 7.70 45.25 4.20
5722 5830 5.010933 TGGAAGAAGACATTCTAGTCGACT 58.989 41.667 23.66 23.66 45.25 4.18
5723 5831 5.477291 TGGAAGAAGACATTCTAGTCGACTT 59.523 40.000 25.44 3.70 45.25 3.01
5724 5832 6.031471 GGAAGAAGACATTCTAGTCGACTTC 58.969 44.000 25.44 13.90 45.25 3.01
5725 5833 5.224562 AGAAGACATTCTAGTCGACTTCG 57.775 43.478 25.44 15.29 44.14 3.79
5726 5834 4.936411 AGAAGACATTCTAGTCGACTTCGA 59.064 41.667 25.44 17.40 44.14 3.71
5727 5835 5.064198 AGAAGACATTCTAGTCGACTTCGAG 59.936 44.000 25.44 15.41 45.63 4.04
5728 5836 5.728344 GAAGACATTCTAGTCGACTTCGAGG 60.728 48.000 25.44 16.88 43.24 4.63
5729 5837 8.051081 GAAGACATTCTAGTCGACTTCGAGGT 62.051 46.154 25.44 19.49 43.24 3.85
5730 5838 9.922136 GAAGACATTCTAGTCGACTTCGAGGTG 62.922 48.148 25.44 21.04 43.24 4.00
5734 5842 4.074647 TCGACTTCGAGGTGCTCA 57.925 55.556 4.31 0.00 44.22 4.26
5735 5843 2.568003 TCGACTTCGAGGTGCTCAT 58.432 52.632 4.31 0.00 44.22 2.90
5736 5844 1.746470 TCGACTTCGAGGTGCTCATA 58.254 50.000 4.31 0.00 44.22 2.15
5737 5845 1.671328 TCGACTTCGAGGTGCTCATAG 59.329 52.381 4.31 0.00 44.22 2.23
5738 5846 1.671328 CGACTTCGAGGTGCTCATAGA 59.329 52.381 4.31 0.00 43.02 1.98
5739 5847 2.286713 CGACTTCGAGGTGCTCATAGAG 60.287 54.545 4.31 0.00 43.02 2.43
5740 5848 2.946329 GACTTCGAGGTGCTCATAGAGA 59.054 50.000 4.31 0.00 0.00 3.10
5741 5849 3.561143 ACTTCGAGGTGCTCATAGAGAT 58.439 45.455 0.00 0.00 0.00 2.75
5742 5850 4.720046 ACTTCGAGGTGCTCATAGAGATA 58.280 43.478 0.00 0.00 0.00 1.98
5743 5851 4.759693 ACTTCGAGGTGCTCATAGAGATAG 59.240 45.833 0.00 0.00 0.00 2.08
5744 5852 3.680490 TCGAGGTGCTCATAGAGATAGG 58.320 50.000 0.00 0.00 0.00 2.57
5745 5853 2.752354 CGAGGTGCTCATAGAGATAGGG 59.248 54.545 0.00 0.00 0.00 3.53
5746 5854 3.773560 GAGGTGCTCATAGAGATAGGGT 58.226 50.000 0.00 0.00 0.00 4.34
5747 5855 3.761752 GAGGTGCTCATAGAGATAGGGTC 59.238 52.174 0.00 0.00 0.00 4.46
5748 5856 2.829120 GGTGCTCATAGAGATAGGGTCC 59.171 54.545 0.00 0.00 0.00 4.46
5749 5857 2.490115 GTGCTCATAGAGATAGGGTCCG 59.510 54.545 0.00 0.00 0.00 4.79
5750 5858 1.474879 GCTCATAGAGATAGGGTCCGC 59.525 57.143 0.00 0.00 0.00 5.54
5751 5859 1.740585 CTCATAGAGATAGGGTCCGCG 59.259 57.143 0.00 0.00 0.00 6.46
5752 5860 1.073444 TCATAGAGATAGGGTCCGCGT 59.927 52.381 4.92 0.00 0.00 6.01
5753 5861 1.200252 CATAGAGATAGGGTCCGCGTG 59.800 57.143 4.92 0.00 0.00 5.34
5754 5862 0.182061 TAGAGATAGGGTCCGCGTGT 59.818 55.000 4.92 0.00 0.00 4.49
5755 5863 1.065928 GAGATAGGGTCCGCGTGTG 59.934 63.158 4.92 0.00 0.00 3.82
5756 5864 1.664321 GAGATAGGGTCCGCGTGTGT 61.664 60.000 4.92 0.00 0.00 3.72
5757 5865 1.518572 GATAGGGTCCGCGTGTGTG 60.519 63.158 4.92 0.00 0.00 3.82
5758 5866 2.221906 GATAGGGTCCGCGTGTGTGT 62.222 60.000 4.92 0.00 0.00 3.72
5759 5867 1.823169 ATAGGGTCCGCGTGTGTGTT 61.823 55.000 4.92 0.00 0.00 3.32
5760 5868 2.030490 TAGGGTCCGCGTGTGTGTTT 62.030 55.000 4.92 0.00 0.00 2.83
5761 5869 1.594836 GGGTCCGCGTGTGTGTTTA 60.595 57.895 4.92 0.00 0.00 2.01
5762 5870 0.952010 GGGTCCGCGTGTGTGTTTAT 60.952 55.000 4.92 0.00 0.00 1.40
5763 5871 1.672441 GGGTCCGCGTGTGTGTTTATA 60.672 52.381 4.92 0.00 0.00 0.98
5764 5872 1.657094 GGTCCGCGTGTGTGTTTATAG 59.343 52.381 4.92 0.00 0.00 1.31
5765 5873 2.598589 GTCCGCGTGTGTGTTTATAGA 58.401 47.619 4.92 0.00 0.00 1.98
5766 5874 2.597305 GTCCGCGTGTGTGTTTATAGAG 59.403 50.000 4.92 0.00 0.00 2.43
5767 5875 2.488937 TCCGCGTGTGTGTTTATAGAGA 59.511 45.455 4.92 0.00 0.00 3.10
5768 5876 3.129813 TCCGCGTGTGTGTTTATAGAGAT 59.870 43.478 4.92 0.00 0.00 2.75
5769 5877 4.336153 TCCGCGTGTGTGTTTATAGAGATA 59.664 41.667 4.92 0.00 0.00 1.98
5811 5919 0.518764 CGTCTGCGTCTACGTCTGTC 60.519 60.000 4.24 0.00 42.22 3.51
5816 5924 2.145536 TGCGTCTACGTCTGTCTTGTA 58.854 47.619 4.24 0.00 42.22 2.41
5819 5927 3.784994 GCGTCTACGTCTGTCTTGTATTC 59.215 47.826 4.24 0.00 42.22 1.75
5845 6016 2.489938 AATTGACTGTACCGGCATGT 57.510 45.000 0.00 0.00 0.00 3.21
5847 6018 2.665649 TTGACTGTACCGGCATGTAG 57.334 50.000 0.00 0.00 0.00 2.74
5862 6033 5.289595 GGCATGTAGATGTGAGACGATAAA 58.710 41.667 1.37 0.00 31.50 1.40
5863 6034 5.928839 GGCATGTAGATGTGAGACGATAAAT 59.071 40.000 1.37 0.00 31.50 1.40
5973 6144 3.748668 CGAAACCTGATCCAATAGCCCAT 60.749 47.826 0.00 0.00 0.00 4.00
5985 6156 4.236935 CAATAGCCCATTGTTTCACACAC 58.763 43.478 1.35 0.00 39.42 3.82
5986 6157 1.774110 AGCCCATTGTTTCACACACA 58.226 45.000 0.00 0.00 33.98 3.72
5987 6158 1.408702 AGCCCATTGTTTCACACACAC 59.591 47.619 0.00 0.00 33.98 3.82
5988 6159 1.537990 GCCCATTGTTTCACACACACC 60.538 52.381 0.00 0.00 33.98 4.16
5989 6160 1.268999 CCCATTGTTTCACACACACCG 60.269 52.381 0.00 0.00 33.98 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.660300 GCTTTCCGTTTGCTTCGGTG 60.660 55.000 12.62 7.37 46.86 4.94
1 2 1.098712 TGCTTTCCGTTTGCTTCGGT 61.099 50.000 12.62 0.00 46.86 4.69
3 4 0.028770 TGTGCTTTCCGTTTGCTTCG 59.971 50.000 0.00 0.00 0.00 3.79
4 5 2.053627 CATGTGCTTTCCGTTTGCTTC 58.946 47.619 0.00 0.00 0.00 3.86
5 6 1.408702 ACATGTGCTTTCCGTTTGCTT 59.591 42.857 0.00 0.00 0.00 3.91
6 7 1.032014 ACATGTGCTTTCCGTTTGCT 58.968 45.000 0.00 0.00 0.00 3.91
7 8 1.522258 CAACATGTGCTTTCCGTTTGC 59.478 47.619 0.00 0.00 0.00 3.68
8 9 2.126467 CCAACATGTGCTTTCCGTTTG 58.874 47.619 0.00 0.00 0.00 2.93
9 10 1.754226 ACCAACATGTGCTTTCCGTTT 59.246 42.857 0.00 0.00 0.00 3.60
10 11 1.398692 ACCAACATGTGCTTTCCGTT 58.601 45.000 0.00 0.00 0.00 4.44
11 12 1.398692 AACCAACATGTGCTTTCCGT 58.601 45.000 0.00 0.00 0.00 4.69
12 13 3.564511 CTTAACCAACATGTGCTTTCCG 58.435 45.455 0.00 0.00 0.00 4.30
13 14 3.306019 CCCTTAACCAACATGTGCTTTCC 60.306 47.826 0.00 0.00 0.00 3.13
14 15 3.860754 GCCCTTAACCAACATGTGCTTTC 60.861 47.826 0.00 0.00 0.00 2.62
15 16 2.037121 GCCCTTAACCAACATGTGCTTT 59.963 45.455 0.00 0.00 0.00 3.51
16 17 1.618343 GCCCTTAACCAACATGTGCTT 59.382 47.619 0.00 0.00 0.00 3.91
17 18 1.256812 GCCCTTAACCAACATGTGCT 58.743 50.000 0.00 0.00 0.00 4.40
18 19 0.965439 TGCCCTTAACCAACATGTGC 59.035 50.000 0.00 0.00 0.00 4.57
19 20 5.126869 TGATTATGCCCTTAACCAACATGTG 59.873 40.000 0.00 0.00 0.00 3.21
20 21 5.127031 GTGATTATGCCCTTAACCAACATGT 59.873 40.000 0.00 0.00 0.00 3.21
21 22 5.451798 GGTGATTATGCCCTTAACCAACATG 60.452 44.000 0.00 0.00 0.00 3.21
22 23 4.649218 GGTGATTATGCCCTTAACCAACAT 59.351 41.667 0.00 0.00 0.00 2.71
23 24 4.020543 GGTGATTATGCCCTTAACCAACA 58.979 43.478 0.00 0.00 0.00 3.33
24 25 4.097892 CAGGTGATTATGCCCTTAACCAAC 59.902 45.833 0.00 0.00 0.00 3.77
25 26 4.277476 CAGGTGATTATGCCCTTAACCAA 58.723 43.478 0.00 0.00 0.00 3.67
26 27 3.372566 CCAGGTGATTATGCCCTTAACCA 60.373 47.826 0.00 0.00 0.00 3.67
27 28 3.222603 CCAGGTGATTATGCCCTTAACC 58.777 50.000 0.00 0.00 0.00 2.85
28 29 3.222603 CCCAGGTGATTATGCCCTTAAC 58.777 50.000 0.00 0.00 0.00 2.01
29 30 2.176798 CCCCAGGTGATTATGCCCTTAA 59.823 50.000 0.00 0.00 0.00 1.85
30 31 1.780309 CCCCAGGTGATTATGCCCTTA 59.220 52.381 0.00 0.00 0.00 2.69
87 88 0.040942 TATGGTGTTGCAGGCCCATT 59.959 50.000 15.55 4.13 38.58 3.16
185 222 0.036022 GCTGGCCTGGATAGATGTCC 59.964 60.000 12.06 0.00 38.81 4.02
221 265 4.556233 CGAGGTAAGAAACTGACATGACA 58.444 43.478 0.00 0.00 0.00 3.58
693 748 1.885887 CAGGAAAACGCAAATCTGGGA 59.114 47.619 0.00 0.00 38.81 4.37
732 787 1.812093 CGAATAAACGAGCGGCCCA 60.812 57.895 0.00 0.00 35.09 5.36
892 947 8.450578 TGAATATTTTCACAGAGTGTTGAAGT 57.549 30.769 0.00 0.00 36.94 3.01
897 952 6.623549 CGCCATGAATATTTTCACAGAGTGTT 60.624 38.462 0.33 0.00 44.36 3.32
912 967 1.066787 TCCAACACGACGCCATGAATA 60.067 47.619 0.00 0.00 0.00 1.75
913 968 0.321210 TCCAACACGACGCCATGAAT 60.321 50.000 0.00 0.00 0.00 2.57
914 969 0.533085 TTCCAACACGACGCCATGAA 60.533 50.000 0.00 0.00 0.00 2.57
916 971 0.385473 GTTTCCAACACGACGCCATG 60.385 55.000 0.00 0.00 0.00 3.66
917 972 0.534203 AGTTTCCAACACGACGCCAT 60.534 50.000 0.00 0.00 0.00 4.40
918 973 1.153329 AGTTTCCAACACGACGCCA 60.153 52.632 0.00 0.00 0.00 5.69
919 974 1.155424 TGAGTTTCCAACACGACGCC 61.155 55.000 0.00 0.00 0.00 5.68
921 976 2.131972 TCATGAGTTTCCAACACGACG 58.868 47.619 0.00 0.00 0.00 5.12
922 977 2.480419 CCTCATGAGTTTCCAACACGAC 59.520 50.000 21.11 0.00 0.00 4.34
923 978 2.367241 TCCTCATGAGTTTCCAACACGA 59.633 45.455 21.11 4.59 0.00 4.35
924 979 2.766313 TCCTCATGAGTTTCCAACACG 58.234 47.619 21.11 2.22 0.00 4.49
925 980 4.616835 GCAATCCTCATGAGTTTCCAACAC 60.617 45.833 21.11 0.00 0.00 3.32
926 981 3.507233 GCAATCCTCATGAGTTTCCAACA 59.493 43.478 21.11 0.00 0.00 3.33
927 982 3.760684 AGCAATCCTCATGAGTTTCCAAC 59.239 43.478 21.11 4.87 0.00 3.77
930 985 3.376546 GTCAGCAATCCTCATGAGTTTCC 59.623 47.826 21.11 5.34 0.00 3.13
932 987 4.298103 AGTCAGCAATCCTCATGAGTTT 57.702 40.909 21.11 11.51 0.00 2.66
951 1007 1.002430 TCGCAGCTCCTGAATCAAAGT 59.998 47.619 0.00 0.00 32.44 2.66
981 1037 3.545124 TTGCGCCAGTGATCCCGTT 62.545 57.895 4.18 0.00 0.00 4.44
1157 1213 2.961526 TGGCTGTAGTTCCTCGATTC 57.038 50.000 0.00 0.00 0.00 2.52
1160 1216 2.565391 TGAAATGGCTGTAGTTCCTCGA 59.435 45.455 0.00 0.00 0.00 4.04
1162 1218 4.574013 CAGATGAAATGGCTGTAGTTCCTC 59.426 45.833 0.00 0.00 0.00 3.71
1171 1227 5.236695 CAGTCTATCACAGATGAAATGGCTG 59.763 44.000 0.00 0.00 38.69 4.85
1247 1304 5.048224 GGATGATAGATGCAGAAACAATGGG 60.048 44.000 0.00 0.00 0.00 4.00
1292 1349 6.292919 GGTCATAACAGAATATCGAGCAAACC 60.293 42.308 0.00 0.00 0.00 3.27
1351 1408 3.496160 GCTCAAGAAAGGTTCAGGTACCA 60.496 47.826 15.94 0.00 40.82 3.25
1353 1410 3.075148 GGCTCAAGAAAGGTTCAGGTAC 58.925 50.000 0.00 0.00 0.00 3.34
1354 1411 2.708861 TGGCTCAAGAAAGGTTCAGGTA 59.291 45.455 0.00 0.00 0.00 3.08
1355 1412 1.494721 TGGCTCAAGAAAGGTTCAGGT 59.505 47.619 0.00 0.00 0.00 4.00
1356 1413 2.276732 TGGCTCAAGAAAGGTTCAGG 57.723 50.000 0.00 0.00 0.00 3.86
1357 1414 4.279169 TGAAATGGCTCAAGAAAGGTTCAG 59.721 41.667 0.00 0.00 0.00 3.02
1359 1416 4.853924 TGAAATGGCTCAAGAAAGGTTC 57.146 40.909 0.00 0.00 0.00 3.62
1360 1417 5.813513 AATGAAATGGCTCAAGAAAGGTT 57.186 34.783 0.00 0.00 0.00 3.50
1361 1418 5.070847 ACAAATGAAATGGCTCAAGAAAGGT 59.929 36.000 0.00 0.00 0.00 3.50
1362 1419 5.407387 CACAAATGAAATGGCTCAAGAAAGG 59.593 40.000 0.00 0.00 0.00 3.11
1363 1420 5.407387 CCACAAATGAAATGGCTCAAGAAAG 59.593 40.000 0.00 0.00 0.00 2.62
1364 1421 5.163322 ACCACAAATGAAATGGCTCAAGAAA 60.163 36.000 0.00 0.00 36.96 2.52
1365 1422 4.344679 ACCACAAATGAAATGGCTCAAGAA 59.655 37.500 0.00 0.00 36.96 2.52
1366 1423 3.896888 ACCACAAATGAAATGGCTCAAGA 59.103 39.130 0.00 0.00 36.96 3.02
1367 1424 4.261578 ACCACAAATGAAATGGCTCAAG 57.738 40.909 0.00 0.00 36.96 3.02
1368 1425 5.538053 TCTTACCACAAATGAAATGGCTCAA 59.462 36.000 0.00 0.00 36.96 3.02
1369 1426 5.048083 GTCTTACCACAAATGAAATGGCTCA 60.048 40.000 0.00 0.00 36.96 4.26
1370 1427 5.183904 AGTCTTACCACAAATGAAATGGCTC 59.816 40.000 0.00 0.00 36.96 4.70
1390 1447 4.498682 GCAAAAGAAATGCACTGTCAGTCT 60.499 41.667 1.37 0.00 43.29 3.24
1412 1469 5.758296 TGATAACCCTTTTACGATGATGAGC 59.242 40.000 0.00 0.00 0.00 4.26
1637 1694 1.541233 GGGGTGGTCTTCTATCATGCG 60.541 57.143 0.00 0.00 0.00 4.73
1688 1745 2.703536 TGGACAAAGTGTAGAAGAGGCA 59.296 45.455 0.00 0.00 0.00 4.75
1913 1970 7.772757 AGCCCTTTTAGAGATTTCAATACAGAG 59.227 37.037 0.00 0.00 0.00 3.35
1948 2005 5.202004 TGATAGAAGGTACTCCCTCTGTTC 58.798 45.833 0.00 0.00 45.47 3.18
1953 2011 4.456662 TCCTGATAGAAGGTACTCCCTC 57.543 50.000 0.00 0.00 45.47 4.30
2011 2069 6.349300 AGTATGATAACTTCGCAGTTCCAAT 58.651 36.000 3.03 0.00 42.66 3.16
2085 2143 5.230942 AGACCAGTAAGACGAAATGTTGAG 58.769 41.667 0.00 0.00 0.00 3.02
2149 2213 4.261614 CCAAAGAAGGAGCCAAAACTACAC 60.262 45.833 0.00 0.00 0.00 2.90
2567 2631 2.093021 TGGAATGTCAGCATCATCCGAA 60.093 45.455 0.00 0.00 35.67 4.30
2639 2703 4.666655 CGCAATAGAAGTTCAAACTCACCG 60.667 45.833 5.50 0.00 38.57 4.94
2669 2733 5.175856 CACTCTCCACTAAACAAGAAAGACG 59.824 44.000 0.00 0.00 0.00 4.18
2720 2784 4.308265 CAGAATGCATCATCTCACGATCT 58.692 43.478 0.00 0.00 0.00 2.75
2815 2879 2.970324 GGCGTCTTTGTGCGGACA 60.970 61.111 5.33 5.33 33.19 4.02
2820 2884 2.458006 CTTTCCGGGCGTCTTTGTGC 62.458 60.000 0.00 0.00 0.00 4.57
2885 2949 2.957402 TCCTTCCATTGTCAACAGCT 57.043 45.000 0.00 0.00 0.00 4.24
2978 3042 5.131809 AGAAGGCTTATTTGCTATCTGACCT 59.868 40.000 0.00 0.00 30.89 3.85
3140 3204 1.683707 TGGTCTCTGGCTCTGCGAT 60.684 57.895 0.00 0.00 0.00 4.58
3188 3252 2.666190 TGGCTCTGCGACAACTGC 60.666 61.111 0.00 0.00 0.00 4.40
3193 3257 4.074526 GCCTCTGGCTCTGCGACA 62.075 66.667 0.73 0.00 46.69 4.35
3244 3308 1.514553 CTCTGGCTCTGCGATGACA 59.485 57.895 0.00 0.00 0.00 3.58
3291 3382 1.884926 GGCTATGCGAGGACTGCAC 60.885 63.158 0.00 0.00 46.57 4.57
3345 3436 0.318120 TGACTCTGCGATGACTGCAA 59.682 50.000 0.00 0.00 42.70 4.08
3444 3538 2.301346 CTGTCTTTGGCTTTGTGAGGT 58.699 47.619 0.00 0.00 0.00 3.85
3667 3761 5.234752 ACACCAAAAGAAAAACCAACAGAC 58.765 37.500 0.00 0.00 0.00 3.51
3747 3841 4.829064 ATGAAGAAACAAACTTAGCGCA 57.171 36.364 11.47 0.00 0.00 6.09
3782 3876 2.760650 ACTTGTCGAGATGGCTACATGA 59.239 45.455 0.00 0.00 37.47 3.07
3888 3982 1.281287 CTCCTGATCATAGCCATGGGG 59.719 57.143 15.13 2.45 32.61 4.96
3932 4026 5.655974 TGATAATATGCCCAGAAAAAGCACA 59.344 36.000 0.00 0.00 39.77 4.57
4013 4110 3.211045 GAAGACACAAACCCAGCTTGTA 58.789 45.455 0.00 0.00 35.26 2.41
4014 4111 2.024414 GAAGACACAAACCCAGCTTGT 58.976 47.619 0.00 0.00 37.49 3.16
4035 4132 1.455248 AGAGTAGACACTGACGCTCC 58.545 55.000 0.00 0.00 34.21 4.70
4096 4193 2.287915 CAGGTATTGCAATCGGTGTAGC 59.712 50.000 16.86 6.96 0.00 3.58
4520 4617 6.042143 TCTTTTTGCCACAGATTTTCTTCAC 58.958 36.000 0.00 0.00 0.00 3.18
4560 4657 2.422127 ACGAAGGGAACATATTTTGCCG 59.578 45.455 6.51 0.00 41.71 5.69
4605 4704 7.255871 GGGCGGAGGGAGTATATAATTATACTG 60.256 44.444 7.34 0.00 46.80 2.74
4726 4825 3.833070 CACACTTTACTGAGTACTCCCCT 59.167 47.826 20.11 4.99 0.00 4.79
5066 5169 1.077858 TGCACAGACAGCACCACAA 60.078 52.632 0.00 0.00 37.02 3.33
5160 5266 0.668535 AAGAACTTTTCACCTGCCGC 59.331 50.000 0.00 0.00 0.00 6.53
5190 5297 1.414919 TCAACGGTCTACAAGCCACTT 59.585 47.619 0.00 0.00 0.00 3.16
5376 5483 2.980568 TGTTTATGACCAGCTAACGGG 58.019 47.619 0.00 0.00 37.14 5.28
5490 5598 5.868801 GCATTGCATAACCACACTACAAAAT 59.131 36.000 3.15 0.00 0.00 1.82
5537 5645 3.254903 GGCCAATCAAGTCCGTTACTTTT 59.745 43.478 0.00 0.00 46.61 2.27
5546 5654 2.167900 ACTAGTACGGCCAATCAAGTCC 59.832 50.000 2.24 0.00 0.00 3.85
5577 5685 2.498481 TCCTACTAACCATCCAACCACG 59.502 50.000 0.00 0.00 0.00 4.94
5599 5707 8.934023 TTAAAATAAGAGCCGGGATATCATTT 57.066 30.769 2.18 0.00 0.00 2.32
5601 5709 7.918076 TCTTAAAATAAGAGCCGGGATATCAT 58.082 34.615 2.18 0.00 0.00 2.45
5604 5712 9.588096 AAAATCTTAAAATAAGAGCCGGGATAT 57.412 29.630 2.18 0.00 0.00 1.63
5610 5718 6.687105 CACCGAAAATCTTAAAATAAGAGCCG 59.313 38.462 6.07 6.27 0.00 5.52
5614 5722 7.908082 CGCATCACCGAAAATCTTAAAATAAGA 59.092 33.333 2.57 2.57 0.00 2.10
5615 5723 7.696453 ACGCATCACCGAAAATCTTAAAATAAG 59.304 33.333 0.00 0.00 0.00 1.73
5633 5741 0.037326 TCCCAGTGAAGACGCATCAC 60.037 55.000 7.52 7.52 45.94 3.06
5634 5742 0.247460 CTCCCAGTGAAGACGCATCA 59.753 55.000 0.00 0.00 0.00 3.07
5649 5757 2.037527 ACAGGGACGTCCTCTCCC 59.962 66.667 32.52 17.64 46.12 4.30
5650 5758 2.408241 CGACAGGGACGTCCTCTCC 61.408 68.421 32.52 16.92 46.12 3.71
5655 5763 0.666577 CAAAGTCGACAGGGACGTCC 60.667 60.000 27.04 27.04 41.81 4.79
5661 5769 0.951040 GCACCTCAAAGTCGACAGGG 60.951 60.000 19.50 13.45 0.00 4.45
5664 5772 0.750249 TGAGCACCTCAAAGTCGACA 59.250 50.000 19.50 0.00 37.57 4.35
5667 5775 7.093354 ACATATATATGAGCACCTCAAAGTCG 58.907 38.462 26.05 0.00 44.04 4.18
5696 5804 4.559251 CGACTAGAATGTCTTCTTCCAACG 59.441 45.833 0.00 0.00 41.91 4.10
5697 5805 5.573669 GTCGACTAGAATGTCTTCTTCCAAC 59.426 44.000 8.70 0.00 41.91 3.77
5700 5808 5.570234 AGTCGACTAGAATGTCTTCTTCC 57.430 43.478 18.46 0.00 41.91 3.46
5701 5809 5.735427 CGAAGTCGACTAGAATGTCTTCTTC 59.265 44.000 20.39 6.74 41.00 2.87
5702 5810 5.411977 TCGAAGTCGACTAGAATGTCTTCTT 59.588 40.000 20.39 0.00 44.22 2.52
5703 5811 4.936411 TCGAAGTCGACTAGAATGTCTTCT 59.064 41.667 20.39 0.00 44.22 2.85
5705 5813 4.095185 CCTCGAAGTCGACTAGAATGTCTT 59.905 45.833 20.39 0.00 44.22 3.01
5709 5817 3.686128 CACCTCGAAGTCGACTAGAATG 58.314 50.000 20.39 16.62 44.22 2.67
5710 5818 2.097791 GCACCTCGAAGTCGACTAGAAT 59.902 50.000 20.39 2.08 44.22 2.40
5711 5819 1.467734 GCACCTCGAAGTCGACTAGAA 59.532 52.381 20.39 6.02 44.22 2.10
5712 5820 1.085091 GCACCTCGAAGTCGACTAGA 58.915 55.000 20.39 19.33 44.22 2.43
5713 5821 1.062880 GAGCACCTCGAAGTCGACTAG 59.937 57.143 20.39 16.05 44.22 2.57
5714 5822 1.085091 GAGCACCTCGAAGTCGACTA 58.915 55.000 20.39 1.84 44.22 2.59
5715 5823 0.889638 TGAGCACCTCGAAGTCGACT 60.890 55.000 13.58 13.58 44.22 4.18
5716 5824 0.171455 ATGAGCACCTCGAAGTCGAC 59.829 55.000 7.70 7.70 44.22 4.20
5718 5826 1.671328 TCTATGAGCACCTCGAAGTCG 59.329 52.381 0.00 0.00 41.45 4.18
5719 5827 2.946329 TCTCTATGAGCACCTCGAAGTC 59.054 50.000 0.00 0.00 32.35 3.01
5720 5828 3.006112 TCTCTATGAGCACCTCGAAGT 57.994 47.619 0.00 0.00 32.35 3.01
5721 5829 4.155826 CCTATCTCTATGAGCACCTCGAAG 59.844 50.000 0.00 0.00 32.35 3.79
5722 5830 4.075682 CCTATCTCTATGAGCACCTCGAA 58.924 47.826 0.00 0.00 32.35 3.71
5723 5831 3.560239 CCCTATCTCTATGAGCACCTCGA 60.560 52.174 0.00 0.00 32.35 4.04
5724 5832 2.752354 CCCTATCTCTATGAGCACCTCG 59.248 54.545 0.00 0.00 32.35 4.63
5725 5833 3.761752 GACCCTATCTCTATGAGCACCTC 59.238 52.174 0.00 0.00 0.00 3.85
5726 5834 3.501385 GGACCCTATCTCTATGAGCACCT 60.501 52.174 0.00 0.00 0.00 4.00
5727 5835 2.829120 GGACCCTATCTCTATGAGCACC 59.171 54.545 0.00 0.00 0.00 5.01
5728 5836 2.490115 CGGACCCTATCTCTATGAGCAC 59.510 54.545 0.00 0.00 0.00 4.40
5729 5837 2.796557 CGGACCCTATCTCTATGAGCA 58.203 52.381 0.00 0.00 0.00 4.26
5730 5838 1.474879 GCGGACCCTATCTCTATGAGC 59.525 57.143 0.00 0.00 0.00 4.26
5731 5839 1.740585 CGCGGACCCTATCTCTATGAG 59.259 57.143 0.00 0.00 0.00 2.90
5732 5840 1.073444 ACGCGGACCCTATCTCTATGA 59.927 52.381 12.47 0.00 0.00 2.15
5733 5841 1.200252 CACGCGGACCCTATCTCTATG 59.800 57.143 12.47 0.00 0.00 2.23
5734 5842 1.202903 ACACGCGGACCCTATCTCTAT 60.203 52.381 12.47 0.00 0.00 1.98
5735 5843 0.182061 ACACGCGGACCCTATCTCTA 59.818 55.000 12.47 0.00 0.00 2.43
5736 5844 1.076923 ACACGCGGACCCTATCTCT 60.077 57.895 12.47 0.00 0.00 3.10
5737 5845 1.065928 CACACGCGGACCCTATCTC 59.934 63.158 12.47 0.00 0.00 2.75
5738 5846 1.681327 ACACACGCGGACCCTATCT 60.681 57.895 12.47 0.00 0.00 1.98
5739 5847 1.518572 CACACACGCGGACCCTATC 60.519 63.158 12.47 0.00 0.00 2.08
5740 5848 1.823169 AACACACACGCGGACCCTAT 61.823 55.000 12.47 0.00 0.00 2.57
5741 5849 2.030490 AAACACACACGCGGACCCTA 62.030 55.000 12.47 0.00 0.00 3.53
5742 5850 2.030490 TAAACACACACGCGGACCCT 62.030 55.000 12.47 0.00 0.00 4.34
5743 5851 0.952010 ATAAACACACACGCGGACCC 60.952 55.000 12.47 0.00 0.00 4.46
5744 5852 1.657094 CTATAAACACACACGCGGACC 59.343 52.381 12.47 0.00 0.00 4.46
5745 5853 2.597305 CTCTATAAACACACACGCGGAC 59.403 50.000 12.47 0.00 0.00 4.79
5746 5854 2.488937 TCTCTATAAACACACACGCGGA 59.511 45.455 12.47 0.00 0.00 5.54
5747 5855 2.871133 TCTCTATAAACACACACGCGG 58.129 47.619 12.47 1.27 0.00 6.46
5748 5856 5.742453 ACTTATCTCTATAAACACACACGCG 59.258 40.000 3.53 3.53 0.00 6.01
5749 5857 6.530534 ACACTTATCTCTATAAACACACACGC 59.469 38.462 0.00 0.00 0.00 5.34
5750 5858 9.731819 ATACACTTATCTCTATAAACACACACG 57.268 33.333 0.00 0.00 0.00 4.49
5779 5887 6.050454 AGACGCAGACGCTCATATATATAC 57.950 41.667 0.00 0.00 45.53 1.47
5780 5888 6.074463 CGTAGACGCAGACGCTCATATATATA 60.074 42.308 0.00 0.00 45.53 0.86
5787 5895 1.062685 CGTAGACGCAGACGCTCAT 59.937 57.895 0.00 0.00 45.53 2.90
5794 5902 1.197036 CAAGACAGACGTAGACGCAGA 59.803 52.381 1.14 0.00 44.43 4.26
5833 6004 2.100749 CTCACATCTACATGCCGGTACA 59.899 50.000 1.90 0.00 32.57 2.90
5834 6005 2.361119 TCTCACATCTACATGCCGGTAC 59.639 50.000 1.90 0.00 32.57 3.34
5837 6008 1.858091 GTCTCACATCTACATGCCGG 58.142 55.000 0.00 0.00 32.57 6.13
5839 6010 2.871182 TCGTCTCACATCTACATGCC 57.129 50.000 0.00 0.00 32.57 4.40
5896 6067 3.181497 CCGGTCGATCAAAAGCAATCATT 60.181 43.478 0.00 0.00 0.00 2.57
5908 6079 2.184322 GCTTCAGCCGGTCGATCA 59.816 61.111 1.90 0.00 34.31 2.92
5937 6108 1.551145 GTTTCGATCGAGAGGTCTGC 58.449 55.000 18.54 0.00 39.71 4.26
5939 6110 1.746220 CAGGTTTCGATCGAGAGGTCT 59.254 52.381 18.54 8.79 39.71 3.85
5941 6112 1.835494 TCAGGTTTCGATCGAGAGGT 58.165 50.000 18.54 0.77 0.00 3.85
5948 6119 3.748568 GGCTATTGGATCAGGTTTCGATC 59.251 47.826 0.00 0.00 38.86 3.69


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

AutoCloner maintained by Alex Coulton.