Multiple sequence alignment - TraesCS6D01G295200

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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 TraesCS6D01G295200 chr6D 100.000 2111 0 0 1 2111 406196774 406198884 0.000000e+00 3899.0
1 TraesCS6D01G295200 chr6D 89.258 512 36 9 1059 1553 406167787 406168296 8.230000e-175 623.0
2 TraesCS6D01G295200 chr6D 100.000 275 0 0 2432 2706 406199205 406199479 2.400000e-140 508.0
3 TraesCS6D01G295200 chr6B 90.745 1718 90 28 1 1691 610084308 610085983 0.000000e+00 2228.0
4 TraesCS6D01G295200 chr6B 82.295 1011 89 39 597 1553 610064551 610065525 0.000000e+00 793.0
5 TraesCS6D01G295200 chr6B 83.077 65 7 4 123 183 717881008 717880944 3.760000e-04 56.5
6 TraesCS6D01G295200 chr6A 88.875 1555 102 46 382 1913 552712393 552713899 0.000000e+00 1847.0
7 TraesCS6D01G295200 chr6A 82.360 839 64 37 769 1553 552590577 552591385 0.000000e+00 652.0
8 TraesCS6D01G295200 chr6A 86.111 216 23 5 2447 2661 552716972 552717181 2.710000e-55 226.0
9 TraesCS6D01G295200 chr2D 79.237 236 39 8 1839 2065 74764327 74764093 3.610000e-34 156.0
10 TraesCS6D01G295200 chr2D 77.273 220 34 12 1811 2018 608554606 608554821 6.120000e-22 115.0
11 TraesCS6D01G295200 chr2D 92.000 50 1 3 2013 2061 378738717 378738670 1.740000e-07 67.6
12 TraesCS6D01G295200 chr2A 79.812 213 34 7 1840 2044 48349810 48349599 2.170000e-31 147.0
13 TraesCS6D01G295200 chr7D 76.046 263 48 15 1814 2065 474264770 474264512 3.660000e-24 122.0
14 TraesCS6D01G295200 chr4D 75.889 253 49 11 1815 2060 119404668 119404915 4.730000e-23 119.0
15 TraesCS6D01G295200 chr4D 90.476 42 4 0 2665 2706 14916682 14916641 3.760000e-04 56.5
16 TraesCS6D01G295200 chr5B 80.503 159 19 10 1898 2048 546776830 546776676 7.920000e-21 111.0
17 TraesCS6D01G295200 chr5B 76.984 126 27 2 1830 1954 552297976 552297852 1.340000e-08 71.3
18 TraesCS6D01G295200 chr5B 89.583 48 5 0 2659 2706 453988254 453988207 8.090000e-06 62.1
19 TraesCS6D01G295200 chr5B 88.889 45 5 0 2662 2706 528683016 528683060 3.760000e-04 56.5
20 TraesCS6D01G295200 chr5B 100.000 28 0 0 2679 2706 12269621 12269648 5.000000e-03 52.8
21 TraesCS6D01G295200 chr5B 100.000 28 0 0 2679 2706 324789219 324789192 5.000000e-03 52.8
22 TraesCS6D01G295200 chr5B 100.000 28 0 0 2679 2706 526527170 526527143 5.000000e-03 52.8
23 TraesCS6D01G295200 chr4B 82.114 123 21 1 1830 1951 659590525 659590647 1.330000e-18 104.0
24 TraesCS6D01G295200 chr4B 77.953 127 26 2 1829 1954 649711229 649711354 8.030000e-11 78.7
25 TraesCS6D01G295200 chrUn 89.362 47 5 0 2660 2706 62157425 62157379 2.910000e-05 60.2
26 TraesCS6D01G295200 chr4A 94.595 37 1 1 147 183 48527602 48527637 3.760000e-04 56.5
27 TraesCS6D01G295200 chr1B 87.500 48 6 0 2659 2706 530994327 530994374 3.760000e-04 56.5
28 TraesCS6D01G295200 chr1D 100.000 28 0 0 2679 2706 477491201 477491174 5.000000e-03 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 TraesCS6D01G295200 chr6D 406196774 406199479 2705 False 2203.5 3899 100.000 1 2706 2 chr6D.!!$F2 2705
1 TraesCS6D01G295200 chr6D 406167787 406168296 509 False 623.0 623 89.258 1059 1553 1 chr6D.!!$F1 494
2 TraesCS6D01G295200 chr6B 610084308 610085983 1675 False 2228.0 2228 90.745 1 1691 1 chr6B.!!$F2 1690
3 TraesCS6D01G295200 chr6B 610064551 610065525 974 False 793.0 793 82.295 597 1553 1 chr6B.!!$F1 956
4 TraesCS6D01G295200 chr6A 552712393 552717181 4788 False 1036.5 1847 87.493 382 2661 2 chr6A.!!$F2 2279
5 TraesCS6D01G295200 chr6A 552590577 552591385 808 False 652.0 652 82.360 769 1553 1 chr6A.!!$F1 784

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
935 975 0.037734 AACATCCACGAAACTCCCCC 59.962 55.0 0.0 0.0 0.0 5.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1984 4927 0.249573 ACCCCTGTAAACACGACACG 60.25 55.0 0.0 0.0 0.0 4.49 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
26 27 3.706698 TCAAGCTATGCTCATGACGTAC 58.293 45.455 0.00 0.00 38.25 3.67
28 29 4.578928 TCAAGCTATGCTCATGACGTACTA 59.421 41.667 0.00 0.00 38.25 1.82
30 31 5.303747 AGCTATGCTCATGACGTACTATC 57.696 43.478 0.00 0.00 30.62 2.08
45 46 4.982295 CGTACTATCGATGGATGCAAAAGA 59.018 41.667 16.43 0.00 34.00 2.52
51 52 5.300969 TCGATGGATGCAAAAGAAAGAAG 57.699 39.130 0.00 0.00 0.00 2.85
53 54 5.122869 TCGATGGATGCAAAAGAAAGAAGAG 59.877 40.000 0.00 0.00 0.00 2.85
60 61 3.003793 GCAAAAGAAAGAAGAGTTCGGCT 59.996 43.478 0.00 0.00 34.02 5.52
134 135 6.248433 AGACTTCAGCATCCCAAGATTTTAA 58.752 36.000 0.00 0.00 0.00 1.52
138 139 7.178983 ACTTCAGCATCCCAAGATTTTAAATGA 59.821 33.333 0.00 0.00 0.00 2.57
191 192 3.051581 AGGACATGTGATATGCTCCCTT 58.948 45.455 1.15 0.00 0.00 3.95
192 193 3.072184 AGGACATGTGATATGCTCCCTTC 59.928 47.826 1.15 0.00 0.00 3.46
194 195 1.802960 CATGTGATATGCTCCCTTCGC 59.197 52.381 0.00 0.00 0.00 4.70
195 196 0.106708 TGTGATATGCTCCCTTCGCC 59.893 55.000 0.00 0.00 0.00 5.54
197 198 1.003233 GATATGCTCCCTTCGCCCC 60.003 63.158 0.00 0.00 0.00 5.80
204 205 1.680338 CTCCCTTCGCCCCAAAATAG 58.320 55.000 0.00 0.00 0.00 1.73
205 206 0.257616 TCCCTTCGCCCCAAAATAGG 59.742 55.000 0.00 0.00 0.00 2.57
304 305 7.457024 AAAACGGCCATGTACTAGTATTTTT 57.543 32.000 5.75 0.73 0.00 1.94
341 342 6.426937 ACAACGAGTTAATGAACAACATAGCT 59.573 34.615 0.00 0.00 38.38 3.32
488 500 1.682087 GGTTCTGCAGTAACCCATCCC 60.682 57.143 25.55 7.28 40.49 3.85
489 501 1.282157 GTTCTGCAGTAACCCATCCCT 59.718 52.381 14.67 0.00 0.00 4.20
490 502 2.504175 GTTCTGCAGTAACCCATCCCTA 59.496 50.000 14.67 0.00 0.00 3.53
492 504 3.393687 TCTGCAGTAACCCATCCCTATT 58.606 45.455 14.67 0.00 0.00 1.73
493 505 3.136443 TCTGCAGTAACCCATCCCTATTG 59.864 47.826 14.67 0.00 0.00 1.90
494 506 2.230660 GCAGTAACCCATCCCTATTGC 58.769 52.381 0.00 0.00 0.00 3.56
495 507 2.158608 GCAGTAACCCATCCCTATTGCT 60.159 50.000 0.00 0.00 0.00 3.91
496 508 3.072476 GCAGTAACCCATCCCTATTGCTA 59.928 47.826 0.00 0.00 0.00 3.49
497 509 4.263506 GCAGTAACCCATCCCTATTGCTAT 60.264 45.833 0.00 0.00 0.00 2.97
498 510 5.749032 GCAGTAACCCATCCCTATTGCTATT 60.749 44.000 0.00 0.00 0.00 1.73
499 511 5.707298 CAGTAACCCATCCCTATTGCTATTG 59.293 44.000 0.00 0.00 0.00 1.90
541 553 1.064952 CCACTGACGAAACACCCAAAC 59.935 52.381 0.00 0.00 0.00 2.93
551 563 4.259610 CGAAACACCCAAACAATTTCAACG 60.260 41.667 0.00 0.00 31.11 4.10
560 573 4.647424 AACAATTTCAACGGAAAGCAGA 57.353 36.364 0.00 0.00 45.58 4.26
586 599 1.589414 ACAGGGGAGAAGAATGGAGG 58.411 55.000 0.00 0.00 0.00 4.30
620 634 2.943033 CCGTGAAACCCAAGGATATGAC 59.057 50.000 0.00 0.00 45.72 3.06
621 635 3.370527 CCGTGAAACCCAAGGATATGACT 60.371 47.826 0.00 0.00 45.72 3.41
622 636 3.871594 CGTGAAACCCAAGGATATGACTC 59.128 47.826 0.00 0.00 0.00 3.36
623 637 4.200092 GTGAAACCCAAGGATATGACTCC 58.800 47.826 0.00 0.00 35.37 3.85
650 664 2.124570 CCCCTCGTGCAATCCCAG 60.125 66.667 0.00 0.00 0.00 4.45
791 819 3.958147 CTGCCGGTGCGAGGAACAT 62.958 63.158 1.90 0.00 41.78 2.71
935 975 0.037734 AACATCCACGAAACTCCCCC 59.962 55.000 0.00 0.00 0.00 5.40
936 976 1.131303 ACATCCACGAAACTCCCCCA 61.131 55.000 0.00 0.00 0.00 4.96
940 980 3.239253 ACGAAACTCCCCCAGCGT 61.239 61.111 0.00 0.00 0.00 5.07
979 1025 4.555313 CGTACCCACGTATATATATGCCCG 60.555 50.000 11.23 7.44 43.31 6.13
1021 1071 5.019498 CACAAACAACAACGACAACTACTC 58.981 41.667 0.00 0.00 0.00 2.59
1025 1075 5.266733 ACAACAACGACAACTACTCCTAA 57.733 39.130 0.00 0.00 0.00 2.69
1026 1076 5.045872 ACAACAACGACAACTACTCCTAAC 58.954 41.667 0.00 0.00 0.00 2.34
1027 1077 4.924305 ACAACGACAACTACTCCTAACA 57.076 40.909 0.00 0.00 0.00 2.41
1028 1078 5.266733 ACAACGACAACTACTCCTAACAA 57.733 39.130 0.00 0.00 0.00 2.83
1029 1079 5.045872 ACAACGACAACTACTCCTAACAAC 58.954 41.667 0.00 0.00 0.00 3.32
1030 1080 3.893720 ACGACAACTACTCCTAACAACG 58.106 45.455 0.00 0.00 0.00 4.10
1050 1100 1.141657 GACCTGAGCATCCTATTGGCA 59.858 52.381 0.00 0.00 0.00 4.92
1052 1102 1.134007 CCTGAGCATCCTATTGGCACA 60.134 52.381 0.00 0.00 0.00 4.57
1244 1332 2.125229 TCGGACTCGGACTCGGAG 60.125 66.667 11.17 11.17 36.95 4.63
1719 1832 4.846779 TCTGTTAGGTTTGATTTGGTGC 57.153 40.909 0.00 0.00 0.00 5.01
1723 1836 2.460757 AGGTTTGATTTGGTGCATGC 57.539 45.000 11.82 11.82 0.00 4.06
1736 1849 4.314121 TGGTGCATGCCAAAGTTATTTTC 58.686 39.130 16.68 0.00 35.25 2.29
1737 1850 3.367630 GGTGCATGCCAAAGTTATTTTCG 59.632 43.478 16.68 0.00 0.00 3.46
1738 1851 4.233789 GTGCATGCCAAAGTTATTTTCGA 58.766 39.130 16.68 0.00 0.00 3.71
1739 1852 4.864247 GTGCATGCCAAAGTTATTTTCGAT 59.136 37.500 16.68 0.00 0.00 3.59
1740 1853 6.033341 GTGCATGCCAAAGTTATTTTCGATA 58.967 36.000 16.68 0.00 0.00 2.92
1780 1894 4.003648 CACAAATTCTAGACCCACCTCAC 58.996 47.826 0.00 0.00 0.00 3.51
1805 1919 4.331717 CACCGTATTCACACAAATAGACCC 59.668 45.833 0.00 0.00 0.00 4.46
1815 1929 0.392998 AAATAGACCCCAGCACGCAG 60.393 55.000 0.00 0.00 0.00 5.18
1826 1940 1.873591 CAGCACGCAGGAGTTTAAGTT 59.126 47.619 0.00 0.00 0.00 2.66
1847 1961 7.807977 AGTTATGGTGCTTGTATTATCTTGG 57.192 36.000 0.00 0.00 0.00 3.61
1885 1999 1.428370 TATGATGCGCGTTCAGTGGC 61.428 55.000 16.53 0.00 0.00 5.01
1890 2004 3.114616 CGCGTTCAGTGGCAGGAG 61.115 66.667 0.00 0.00 0.00 3.69
1896 2010 0.468226 TTCAGTGGCAGGAGACGTTT 59.532 50.000 0.00 0.00 0.00 3.60
1897 2011 0.033504 TCAGTGGCAGGAGACGTTTC 59.966 55.000 0.00 0.00 0.00 2.78
1899 2013 2.027625 GTGGCAGGAGACGTTTCCG 61.028 63.158 18.59 14.34 42.29 4.30
1913 2027 2.095768 CGTTTCCGTCGACTACAAGGTA 60.096 50.000 14.70 0.00 0.00 3.08
1914 2028 3.609175 CGTTTCCGTCGACTACAAGGTAA 60.609 47.826 14.70 4.30 0.00 2.85
1915 2029 3.559238 TTCCGTCGACTACAAGGTAAC 57.441 47.619 14.70 0.00 0.00 2.50
1916 2030 1.812571 TCCGTCGACTACAAGGTAACC 59.187 52.381 14.70 0.00 37.17 2.85
1917 2031 1.541147 CCGTCGACTACAAGGTAACCA 59.459 52.381 14.70 0.00 37.17 3.67
1929 4867 1.975680 AGGTAACCATGGTGACTTCGT 59.024 47.619 28.30 10.07 30.34 3.85
1936 4874 2.932614 CCATGGTGACTTCGTCAATCTC 59.067 50.000 2.57 0.00 44.49 2.75
1944 4882 6.128172 GGTGACTTCGTCAATCTCAAAATGAT 60.128 38.462 0.00 0.00 44.49 2.45
1948 4886 7.412853 ACTTCGTCAATCTCAAAATGATATGC 58.587 34.615 0.00 0.00 0.00 3.14
1954 4892 3.554934 TCTCAAAATGATATGCCGGCTT 58.445 40.909 29.70 24.47 0.00 4.35
1955 4893 3.953612 TCTCAAAATGATATGCCGGCTTT 59.046 39.130 29.70 15.72 0.00 3.51
1956 4894 4.402155 TCTCAAAATGATATGCCGGCTTTT 59.598 37.500 29.70 20.77 0.00 2.27
1974 4917 2.260844 TTTTGAGGTGCTCACAGAGG 57.739 50.000 2.21 0.00 40.46 3.69
1977 4920 2.238084 TGAGGTGCTCACAGAGGTAT 57.762 50.000 2.21 0.00 35.39 2.73
1984 4927 3.557595 GTGCTCACAGAGGTATTATGTGC 59.442 47.826 0.00 0.00 43.16 4.57
1990 4933 2.789339 CAGAGGTATTATGTGCGTGTCG 59.211 50.000 0.00 0.00 0.00 4.35
1997 4940 3.774282 TTATGTGCGTGTCGTGTTTAC 57.226 42.857 0.00 0.00 0.00 2.01
1999 4942 0.924777 TGTGCGTGTCGTGTTTACAG 59.075 50.000 0.00 0.00 0.00 2.74
2002 4945 1.562575 GCGTGTCGTGTTTACAGGGG 61.563 60.000 3.09 0.00 34.22 4.79
2004 4947 1.223187 GTGTCGTGTTTACAGGGGTG 58.777 55.000 3.09 0.00 33.00 4.61
2011 4954 3.396560 GTGTTTACAGGGGTGAGTGTAC 58.603 50.000 0.00 0.00 0.00 2.90
2019 4962 1.138266 GGGGTGAGTGTACGCATGTAT 59.862 52.381 9.48 0.00 35.43 2.29
2027 4970 6.251589 GTGAGTGTACGCATGTATATATGAGC 59.748 42.308 13.18 0.00 32.02 4.26
2036 4979 6.028368 GCATGTATATATGAGCGTCTACGTT 58.972 40.000 13.18 0.00 42.22 3.99
2037 4980 6.527023 GCATGTATATATGAGCGTCTACGTTT 59.473 38.462 13.18 0.00 42.22 3.60
2038 4981 7.461546 GCATGTATATATGAGCGTCTACGTTTG 60.462 40.741 13.18 0.00 42.22 2.93
2039 4982 6.962686 TGTATATATGAGCGTCTACGTTTGT 58.037 36.000 0.00 0.00 42.22 2.83
2040 4983 8.086851 TGTATATATGAGCGTCTACGTTTGTA 57.913 34.615 0.00 0.00 42.22 2.41
2041 4984 8.011673 TGTATATATGAGCGTCTACGTTTGTAC 58.988 37.037 0.00 0.00 42.22 2.90
2050 4993 4.378030 CGTCTACGTTTGTACTGTGTTCTC 59.622 45.833 0.00 0.00 34.11 2.87
2056 4999 6.311723 ACGTTTGTACTGTGTTCTCAAAAAG 58.688 36.000 0.00 0.00 31.45 2.27
2058 5001 7.018826 CGTTTGTACTGTGTTCTCAAAAAGAA 58.981 34.615 0.00 0.00 41.81 2.52
2059 5002 7.535940 CGTTTGTACTGTGTTCTCAAAAAGAAA 59.464 33.333 0.00 0.00 45.50 2.52
2061 5004 9.921637 TTTGTACTGTGTTCTCAAAAAGAAAAT 57.078 25.926 0.00 0.00 45.50 1.82
2066 5009 9.788960 ACTGTGTTCTCAAAAAGAAAATAAGTC 57.211 29.630 0.00 0.00 45.50 3.01
2071 5014 8.420189 GTTCTCAAAAAGAAAATAAGTCATGCG 58.580 33.333 0.00 0.00 45.50 4.73
2072 5015 6.582295 TCTCAAAAAGAAAATAAGTCATGCGC 59.418 34.615 0.00 0.00 0.00 6.09
2073 5016 6.446318 TCAAAAAGAAAATAAGTCATGCGCT 58.554 32.000 9.73 0.00 0.00 5.92
2074 5017 7.589395 TCAAAAAGAAAATAAGTCATGCGCTA 58.411 30.769 9.73 0.00 0.00 4.26
2075 5018 8.079203 TCAAAAAGAAAATAAGTCATGCGCTAA 58.921 29.630 9.73 0.00 0.00 3.09
2076 5019 8.368126 CAAAAAGAAAATAAGTCATGCGCTAAG 58.632 33.333 9.73 0.00 0.00 2.18
2102 5045 7.390162 GCAATCCAAATAATTGAAAAAGGTCCA 59.610 33.333 0.25 0.00 38.94 4.02
2464 5412 2.735134 GCACCGAGTACCTAAAACACAG 59.265 50.000 0.00 0.00 0.00 3.66
2497 5445 3.133901 TGAATTCTCTGGCACCGCTAATA 59.866 43.478 7.05 0.00 0.00 0.98
2515 5463 1.252215 TATGAGGCGGTCGGACACAA 61.252 55.000 10.76 0.00 0.00 3.33
2527 5475 3.206246 ACACAACCGCCGTGTTGG 61.206 61.111 18.18 11.65 45.12 3.77
2535 5483 2.818274 GCCGTGTTGGATCGACCC 60.818 66.667 0.00 0.00 42.00 4.46
2538 5486 1.507630 CGTGTTGGATCGACCCGTA 59.492 57.895 0.00 0.00 38.00 4.02
2543 5491 2.101249 TGTTGGATCGACCCGTATAACC 59.899 50.000 0.00 0.00 38.00 2.85
2544 5492 1.331214 TGGATCGACCCGTATAACCC 58.669 55.000 0.00 0.00 38.00 4.11
2549 5497 0.319405 CGACCCGTATAACCCCATCC 59.681 60.000 0.00 0.00 0.00 3.51
2550 5498 0.689055 GACCCGTATAACCCCATCCC 59.311 60.000 0.00 0.00 0.00 3.85
2568 5516 2.578940 TCCCGGACCAAATCCTAAACAT 59.421 45.455 0.73 0.00 46.69 2.71
2571 5519 4.013728 CCGGACCAAATCCTAAACATTCA 58.986 43.478 0.00 0.00 46.69 2.57
2574 5522 5.356751 CGGACCAAATCCTAAACATTCATCA 59.643 40.000 0.00 0.00 46.69 3.07
2576 5524 6.378280 GGACCAAATCCTAAACATTCATCACT 59.622 38.462 0.00 0.00 45.22 3.41
2578 5526 7.177878 ACCAAATCCTAAACATTCATCACTCT 58.822 34.615 0.00 0.00 0.00 3.24
2579 5527 7.337942 ACCAAATCCTAAACATTCATCACTCTC 59.662 37.037 0.00 0.00 0.00 3.20
2580 5528 7.555554 CCAAATCCTAAACATTCATCACTCTCT 59.444 37.037 0.00 0.00 0.00 3.10
2581 5529 8.610896 CAAATCCTAAACATTCATCACTCTCTC 58.389 37.037 0.00 0.00 0.00 3.20
2582 5530 5.895928 TCCTAAACATTCATCACTCTCTCG 58.104 41.667 0.00 0.00 0.00 4.04
2583 5531 5.419155 TCCTAAACATTCATCACTCTCTCGT 59.581 40.000 0.00 0.00 0.00 4.18
2586 5534 2.098280 ACATTCATCACTCTCTCGTCCG 59.902 50.000 0.00 0.00 0.00 4.79
2596 5544 1.068472 TCTCTCGTCCGTTCAGCTTTC 60.068 52.381 0.00 0.00 0.00 2.62
2600 5548 0.784778 CGTCCGTTCAGCTTTCACTC 59.215 55.000 0.00 0.00 0.00 3.51
2630 5579 1.202498 CGTCTATTCCTTTCCCGTCCC 60.202 57.143 0.00 0.00 0.00 4.46
2661 5610 1.226211 CGCGTCGTCCGTCATAACT 60.226 57.895 0.00 0.00 39.32 2.24
2662 5611 0.026674 CGCGTCGTCCGTCATAACTA 59.973 55.000 0.00 0.00 39.32 2.24
2663 5612 1.739618 GCGTCGTCCGTCATAACTAG 58.260 55.000 0.00 0.00 39.32 2.57
2664 5613 1.328680 GCGTCGTCCGTCATAACTAGA 59.671 52.381 0.00 0.00 39.32 2.43
2665 5614 2.848751 GCGTCGTCCGTCATAACTAGAC 60.849 54.545 0.00 0.00 39.32 2.59
2666 5615 2.286067 CGTCGTCCGTCATAACTAGACC 60.286 54.545 0.00 0.00 32.41 3.85
2667 5616 2.941720 GTCGTCCGTCATAACTAGACCT 59.058 50.000 0.00 0.00 32.41 3.85
2668 5617 2.941064 TCGTCCGTCATAACTAGACCTG 59.059 50.000 0.00 0.00 32.41 4.00
2669 5618 2.541178 CGTCCGTCATAACTAGACCTGC 60.541 54.545 0.00 0.00 32.41 4.85
2670 5619 2.688958 GTCCGTCATAACTAGACCTGCT 59.311 50.000 0.00 0.00 32.41 4.24
2671 5620 2.950309 TCCGTCATAACTAGACCTGCTC 59.050 50.000 0.00 0.00 32.41 4.26
2672 5621 2.688446 CCGTCATAACTAGACCTGCTCA 59.312 50.000 0.00 0.00 32.41 4.26
2673 5622 3.319405 CCGTCATAACTAGACCTGCTCAT 59.681 47.826 0.00 0.00 32.41 2.90
2674 5623 4.202161 CCGTCATAACTAGACCTGCTCATT 60.202 45.833 0.00 0.00 32.41 2.57
2675 5624 4.979197 CGTCATAACTAGACCTGCTCATTC 59.021 45.833 0.00 0.00 32.41 2.67
2676 5625 5.221145 CGTCATAACTAGACCTGCTCATTCT 60.221 44.000 0.00 0.00 32.41 2.40
2677 5626 6.212955 GTCATAACTAGACCTGCTCATTCTC 58.787 44.000 0.00 0.00 0.00 2.87
2678 5627 5.303078 TCATAACTAGACCTGCTCATTCTCC 59.697 44.000 0.00 0.00 0.00 3.71
2679 5628 2.028130 ACTAGACCTGCTCATTCTCCG 58.972 52.381 0.00 0.00 0.00 4.63
2680 5629 1.339610 CTAGACCTGCTCATTCTCCGG 59.660 57.143 0.00 0.00 0.00 5.14
2681 5630 1.144936 GACCTGCTCATTCTCCGGG 59.855 63.158 0.00 0.00 0.00 5.73
2682 5631 2.203126 CCTGCTCATTCTCCGGGC 60.203 66.667 0.00 0.00 0.00 6.13
2683 5632 2.203126 CTGCTCATTCTCCGGGCC 60.203 66.667 0.00 0.00 0.00 5.80
2684 5633 4.161295 TGCTCATTCTCCGGGCCG 62.161 66.667 21.46 21.46 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 3.711086 AGTACGTCATGAGCATAGCTTG 58.289 45.455 0.00 0.00 39.88 4.01
26 27 6.609237 TCTTTCTTTTGCATCCATCGATAG 57.391 37.500 0.00 0.00 0.00 2.08
28 29 5.649395 TCTTCTTTCTTTTGCATCCATCGAT 59.351 36.000 0.00 0.00 0.00 3.59
30 31 5.106396 ACTCTTCTTTCTTTTGCATCCATCG 60.106 40.000 0.00 0.00 0.00 3.84
45 46 0.325272 GGGGAGCCGAACTCTTCTTT 59.675 55.000 5.56 0.00 45.48 2.52
51 52 1.627297 ATCTTGGGGGAGCCGAACTC 61.627 60.000 0.00 0.00 45.45 3.01
53 54 0.323451 AAATCTTGGGGGAGCCGAAC 60.323 55.000 0.00 0.00 0.00 3.95
85 86 6.189859 TCTTCCTTTTGCATCCATTGATAGT 58.810 36.000 0.00 0.00 0.00 2.12
91 92 5.082425 AGTCTTCTTCCTTTTGCATCCATT 58.918 37.500 0.00 0.00 0.00 3.16
104 105 2.026822 TGGGATGCTGAAGTCTTCTTCC 60.027 50.000 13.67 12.87 46.66 3.46
105 106 7.301553 AATCTTGGGATGCTGAAGTCTTCTTC 61.302 42.308 13.67 6.03 40.01 2.87
138 139 9.088987 ACACACCCTTTCACAAGAATAATAATT 57.911 29.630 0.00 0.00 32.89 1.40
159 160 5.689383 ATCACATGTCCTTACAAACACAC 57.311 39.130 0.00 0.00 39.58 3.82
191 192 3.042682 TGAGATACCTATTTTGGGGCGA 58.957 45.455 0.00 0.00 0.00 5.54
192 193 3.485463 TGAGATACCTATTTTGGGGCG 57.515 47.619 0.00 0.00 0.00 6.13
194 195 5.388599 AGGTTGAGATACCTATTTTGGGG 57.611 43.478 0.00 0.00 46.65 4.96
222 223 7.086685 ACTCCTTCAGTCCCAAAATAAGTTA 57.913 36.000 0.00 0.00 0.00 2.24
287 288 7.865706 AGCCTTGAAAAATACTAGTACATGG 57.134 36.000 4.31 10.58 0.00 3.66
304 305 1.134220 ACTCGTTGTTCCAAGCCTTGA 60.134 47.619 5.89 0.00 0.00 3.02
341 342 2.103094 GGACTGGATGTCGATGGATTGA 59.897 50.000 0.00 0.00 46.24 2.57
493 505 6.884280 ACTAGGAATATTTGTGCCAATAGC 57.116 37.500 0.00 0.00 44.14 2.97
494 506 7.307989 CGGAACTAGGAATATTTGTGCCAATAG 60.308 40.741 0.00 0.00 0.00 1.73
495 507 6.485313 CGGAACTAGGAATATTTGTGCCAATA 59.515 38.462 0.00 0.00 0.00 1.90
496 508 5.299279 CGGAACTAGGAATATTTGTGCCAAT 59.701 40.000 0.00 0.00 0.00 3.16
497 509 4.638421 CGGAACTAGGAATATTTGTGCCAA 59.362 41.667 0.00 0.00 0.00 4.52
498 510 4.196193 CGGAACTAGGAATATTTGTGCCA 58.804 43.478 0.00 0.00 0.00 4.92
499 511 3.003378 GCGGAACTAGGAATATTTGTGCC 59.997 47.826 0.00 0.00 0.00 5.01
541 553 3.243367 TGGTCTGCTTTCCGTTGAAATTG 60.243 43.478 0.00 0.00 39.65 2.32
551 563 0.595095 CTGTTGCTGGTCTGCTTTCC 59.405 55.000 1.84 0.00 0.00 3.13
560 573 0.768221 TCTTCTCCCCTGTTGCTGGT 60.768 55.000 0.00 0.00 0.00 4.00
586 599 1.245376 TTCACGGCGGGGAATTTTCC 61.245 55.000 10.28 0.41 46.82 3.13
620 634 1.270907 CGAGGGGGATATTCAGGGAG 58.729 60.000 0.00 0.00 0.00 4.30
621 635 0.566176 ACGAGGGGGATATTCAGGGA 59.434 55.000 0.00 0.00 0.00 4.20
622 636 0.687354 CACGAGGGGGATATTCAGGG 59.313 60.000 0.00 0.00 0.00 4.45
623 637 0.035458 GCACGAGGGGGATATTCAGG 59.965 60.000 0.00 0.00 0.00 3.86
741 755 2.479560 GCACGGCTTTGTTTTCTGTTCT 60.480 45.455 0.00 0.00 0.00 3.01
957 997 4.794003 GCGGGCATATATATACGTGGGTAC 60.794 50.000 0.00 0.00 0.00 3.34
958 998 3.318839 GCGGGCATATATATACGTGGGTA 59.681 47.826 0.00 0.00 0.00 3.69
993 1043 0.247340 TCGTTGTTGTTTGTGCGTCG 60.247 50.000 0.00 0.00 0.00 5.12
1021 1071 2.271800 GATGCTCAGGTCGTTGTTAGG 58.728 52.381 0.00 0.00 0.00 2.69
1025 1075 1.557099 TAGGATGCTCAGGTCGTTGT 58.443 50.000 0.00 0.00 0.00 3.32
1026 1076 2.868583 CAATAGGATGCTCAGGTCGTTG 59.131 50.000 0.00 0.00 0.00 4.10
1027 1077 2.158900 CCAATAGGATGCTCAGGTCGTT 60.159 50.000 0.00 0.00 36.89 3.85
1028 1078 1.414181 CCAATAGGATGCTCAGGTCGT 59.586 52.381 0.00 0.00 36.89 4.34
1029 1079 1.875576 GCCAATAGGATGCTCAGGTCG 60.876 57.143 0.00 0.00 36.89 4.79
1030 1080 1.141657 TGCCAATAGGATGCTCAGGTC 59.858 52.381 0.00 0.00 36.89 3.85
1050 1100 1.887956 GCCCATCACCATCTGTGTTGT 60.888 52.381 0.00 0.00 45.61 3.32
1052 1102 0.405198 TGCCCATCACCATCTGTGTT 59.595 50.000 0.00 0.00 45.61 3.32
1053 1103 0.405198 TTGCCCATCACCATCTGTGT 59.595 50.000 0.00 0.00 45.61 3.72
1694 1806 6.682861 GCACCAAATCAAACCTAACAGAAGTT 60.683 38.462 0.00 0.00 41.74 2.66
1699 1811 4.582701 TGCACCAAATCAAACCTAACAG 57.417 40.909 0.00 0.00 0.00 3.16
1736 1849 9.983804 TTGTGTAATCGTATAGCTAGATTATCG 57.016 33.333 13.87 4.10 38.57 2.92
1780 1894 2.892373 ATTTGTGTGAATACGGTGCG 57.108 45.000 0.00 0.00 0.00 5.34
1805 1919 0.798776 CTTAAACTCCTGCGTGCTGG 59.201 55.000 11.17 11.17 36.53 4.85
1815 1929 5.959618 ACAAGCACCATAACTTAAACTCC 57.040 39.130 0.00 0.00 0.00 3.85
1826 1940 8.995027 AAATCCAAGATAATACAAGCACCATA 57.005 30.769 0.00 0.00 0.00 2.74
1864 1978 1.396648 CCACTGAACGCGCATCATAAA 59.603 47.619 14.58 0.00 0.00 1.40
1865 1979 1.006086 CCACTGAACGCGCATCATAA 58.994 50.000 14.58 0.00 0.00 1.90
1866 1980 1.428370 GCCACTGAACGCGCATCATA 61.428 55.000 14.58 0.00 0.00 2.15
1867 1981 2.753966 GCCACTGAACGCGCATCAT 61.754 57.895 14.58 4.23 0.00 2.45
1868 1982 3.422303 GCCACTGAACGCGCATCA 61.422 61.111 5.73 10.82 0.00 3.07
1877 1991 0.468226 AAACGTCTCCTGCCACTGAA 59.532 50.000 0.00 0.00 0.00 3.02
1896 2010 1.812571 GGTTACCTTGTAGTCGACGGA 59.187 52.381 10.46 0.00 0.00 4.69
1897 2011 1.541147 TGGTTACCTTGTAGTCGACGG 59.459 52.381 10.46 7.42 0.00 4.79
1899 2013 3.056322 ACCATGGTTACCTTGTAGTCGAC 60.056 47.826 13.00 7.70 0.00 4.20
1908 2022 2.370849 ACGAAGTCACCATGGTTACCTT 59.629 45.455 22.81 19.43 29.74 3.50
1929 4867 4.022935 GCCGGCATATCATTTTGAGATTGA 60.023 41.667 24.80 0.00 0.00 2.57
1954 4892 2.092429 ACCTCTGTGAGCACCTCAAAAA 60.092 45.455 0.00 0.00 42.46 1.94
1955 4893 1.490490 ACCTCTGTGAGCACCTCAAAA 59.510 47.619 0.00 0.00 42.46 2.44
1956 4894 1.131638 ACCTCTGTGAGCACCTCAAA 58.868 50.000 0.00 0.00 42.46 2.69
1958 4896 2.238084 ATACCTCTGTGAGCACCTCA 57.762 50.000 0.00 0.00 38.25 3.86
1962 4905 3.557595 GCACATAATACCTCTGTGAGCAC 59.442 47.826 6.12 0.00 42.20 4.40
1973 4916 2.264813 ACACGACACGCACATAATACC 58.735 47.619 0.00 0.00 0.00 2.73
1974 4917 3.984018 AACACGACACGCACATAATAC 57.016 42.857 0.00 0.00 0.00 1.89
1977 4920 3.121544 TGTAAACACGACACGCACATAA 58.878 40.909 0.00 0.00 0.00 1.90
1984 4927 0.249573 ACCCCTGTAAACACGACACG 60.250 55.000 0.00 0.00 0.00 4.49
1990 4933 2.632987 ACACTCACCCCTGTAAACAC 57.367 50.000 0.00 0.00 0.00 3.32
1997 4940 0.740868 CATGCGTACACTCACCCCTG 60.741 60.000 0.00 0.00 0.00 4.45
1999 4942 0.533491 TACATGCGTACACTCACCCC 59.467 55.000 0.00 0.00 0.00 4.95
2002 4945 6.251589 GCTCATATATACATGCGTACACTCAC 59.748 42.308 0.00 0.00 0.00 3.51
2004 4947 5.452623 CGCTCATATATACATGCGTACACTC 59.547 44.000 13.50 0.00 38.81 3.51
2019 4962 6.037500 ACAGTACAAACGTAGACGCTCATATA 59.962 38.462 1.14 0.00 44.43 0.86
2027 4970 4.285292 AGAACACAGTACAAACGTAGACG 58.715 43.478 0.00 0.00 46.33 4.18
2030 4973 6.578020 TTTGAGAACACAGTACAAACGTAG 57.422 37.500 0.00 0.00 0.00 3.51
2032 4975 5.866335 TTTTGAGAACACAGTACAAACGT 57.134 34.783 0.00 0.00 31.71 3.99
2040 4983 9.788960 GACTTATTTTCTTTTTGAGAACACAGT 57.211 29.630 0.00 0.00 43.90 3.55
2041 4984 9.787532 TGACTTATTTTCTTTTTGAGAACACAG 57.212 29.630 0.00 0.00 43.90 3.66
2050 4993 6.695292 AGCGCATGACTTATTTTCTTTTTG 57.305 33.333 11.47 0.00 0.00 2.44
2056 4999 4.908736 TGCTTAGCGCATGACTTATTTTC 58.091 39.130 11.47 0.00 45.47 2.29
2066 5009 8.418920 TCAATTATTTGGATTGCTTAGCGCATG 61.419 37.037 11.47 0.00 39.83 4.06
2068 5011 5.163571 TCAATTATTTGGATTGCTTAGCGCA 60.164 36.000 11.47 0.00 39.04 6.09
2071 5014 9.977762 CTTTTTCAATTATTTGGATTGCTTAGC 57.022 29.630 0.00 0.00 35.10 3.09
2074 5017 8.922931 ACCTTTTTCAATTATTTGGATTGCTT 57.077 26.923 0.00 0.00 35.10 3.91
2075 5018 7.607607 GGACCTTTTTCAATTATTTGGATTGCT 59.392 33.333 0.00 0.00 35.10 3.91
2076 5019 7.390162 TGGACCTTTTTCAATTATTTGGATTGC 59.610 33.333 0.00 0.00 35.10 3.56
2077 5020 8.845413 TGGACCTTTTTCAATTATTTGGATTG 57.155 30.769 0.00 0.00 36.15 2.67
2078 5021 9.859152 TTTGGACCTTTTTCAATTATTTGGATT 57.141 25.926 0.00 0.00 33.44 3.01
2443 5386 2.735134 CTGTGTTTTAGGTACTCGGTGC 59.265 50.000 0.00 0.00 41.75 5.01
2464 5412 7.358830 GTGCCAGAGAATTCAGATATTTAAGC 58.641 38.462 8.44 0.00 0.00 3.09
2475 5423 0.901827 TAGCGGTGCCAGAGAATTCA 59.098 50.000 8.44 0.00 0.00 2.57
2476 5424 2.024176 TTAGCGGTGCCAGAGAATTC 57.976 50.000 0.00 0.00 0.00 2.17
2481 5429 2.611473 CCTCATATTAGCGGTGCCAGAG 60.611 54.545 0.00 0.00 0.00 3.35
2497 5445 2.579657 TTGTGTCCGACCGCCTCAT 61.580 57.895 0.00 0.00 0.00 2.90
2515 5463 3.687102 TCGATCCAACACGGCGGT 61.687 61.111 13.24 3.10 33.14 5.68
2521 5469 3.118542 GTTATACGGGTCGATCCAACAC 58.881 50.000 16.61 0.00 38.11 3.32
2522 5470 2.101249 GGTTATACGGGTCGATCCAACA 59.899 50.000 16.61 0.00 38.11 3.33
2526 5474 0.605083 GGGGTTATACGGGTCGATCC 59.395 60.000 4.00 4.00 0.00 3.36
2527 5475 1.331214 TGGGGTTATACGGGTCGATC 58.669 55.000 0.00 0.00 0.00 3.69
2535 5483 0.319405 GTCCGGGATGGGGTTATACG 59.681 60.000 0.00 0.00 38.76 3.06
2538 5486 0.625091 TTGGTCCGGGATGGGGTTAT 60.625 55.000 0.00 0.00 38.76 1.89
2543 5491 1.152756 GGATTTGGTCCGGGATGGG 60.153 63.158 0.00 0.00 37.23 4.00
2544 5492 4.579127 GGATTTGGTCCGGGATGG 57.421 61.111 0.00 0.00 37.23 3.51
2568 5516 1.822506 ACGGACGAGAGAGTGATGAA 58.177 50.000 0.00 0.00 0.00 2.57
2571 5519 1.740585 CTGAACGGACGAGAGAGTGAT 59.259 52.381 0.00 0.00 0.00 3.06
2574 5522 0.606944 AGCTGAACGGACGAGAGAGT 60.607 55.000 0.00 0.00 0.00 3.24
2576 5524 0.959553 AAAGCTGAACGGACGAGAGA 59.040 50.000 0.00 0.00 0.00 3.10
2578 5526 0.671796 TGAAAGCTGAACGGACGAGA 59.328 50.000 0.00 0.00 0.00 4.04
2579 5527 0.784778 GTGAAAGCTGAACGGACGAG 59.215 55.000 0.00 0.00 0.00 4.18
2580 5528 0.387929 AGTGAAAGCTGAACGGACGA 59.612 50.000 0.00 0.00 0.00 4.20
2581 5529 0.784778 GAGTGAAAGCTGAACGGACG 59.215 55.000 0.00 0.00 0.00 4.79
2582 5530 2.062519 GAGAGTGAAAGCTGAACGGAC 58.937 52.381 0.00 0.00 0.00 4.79
2583 5531 1.000955 GGAGAGTGAAAGCTGAACGGA 59.999 52.381 0.00 0.00 0.00 4.69
2586 5534 3.584834 GAGAGGAGAGTGAAAGCTGAAC 58.415 50.000 0.00 0.00 0.00 3.18
2596 5544 2.992124 TAGACGAGGAGAGGAGAGTG 57.008 55.000 0.00 0.00 0.00 3.51
2600 5548 3.502123 AGGAATAGACGAGGAGAGGAG 57.498 52.381 0.00 0.00 0.00 3.69
2661 5610 1.403814 CCGGAGAATGAGCAGGTCTA 58.596 55.000 0.00 0.00 0.00 2.59
2662 5611 1.333636 CCCGGAGAATGAGCAGGTCT 61.334 60.000 0.73 0.00 0.00 3.85
2663 5612 1.144936 CCCGGAGAATGAGCAGGTC 59.855 63.158 0.73 0.00 0.00 3.85
2664 5613 3.036429 GCCCGGAGAATGAGCAGGT 62.036 63.158 0.73 0.00 0.00 4.00
2665 5614 2.203126 GCCCGGAGAATGAGCAGG 60.203 66.667 0.73 0.00 0.00 4.85
2666 5615 2.203126 GGCCCGGAGAATGAGCAG 60.203 66.667 0.73 0.00 0.00 4.24
2667 5616 4.161295 CGGCCCGGAGAATGAGCA 62.161 66.667 0.73 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.