Multiple sequence alignment - TraesCS2B01G135600

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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 TraesCS2B01G135600 chr2B 100.000 3373 0 0 1 3373 102124791 102128163 0 6229
1 TraesCS2B01G135600 chr2B 95.708 699 27 3 2677 3373 452910177 452910874 0 1122
2 TraesCS2B01G135600 chr2B 95.415 698 31 1 2677 3373 666052418 666053115 0 1110
3 TraesCS2B01G135600 chr2A 85.725 2732 176 90 59 2680 66320326 66317699 0 2687
4 TraesCS2B01G135600 chr2D 89.500 1381 58 36 1348 2680 68733044 68734385 0 1666
5 TraesCS2B01G135600 chr2D 86.337 688 27 15 693 1348 68732185 68732837 0 688
6 TraesCS2B01G135600 chr2D 86.287 649 50 25 73 691 68731493 68732132 0 669
7 TraesCS2B01G135600 chr7B 95.720 701 26 3 2677 3373 739379293 739379993 0 1125
8 TraesCS2B01G135600 chr7B 95.422 699 30 2 2676 3373 498599770 498599073 0 1112
9 TraesCS2B01G135600 chr6B 95.559 698 30 1 2677 3373 26217740 26218437 0 1116
10 TraesCS2B01G135600 chr6B 95.272 698 32 1 2677 3373 599981103 599981800 0 1105
11 TraesCS2B01G135600 chrUn 95.422 699 30 2 2677 3373 263185294 263185992 0 1112
12 TraesCS2B01G135600 chrUn 95.279 699 31 2 2677 3373 50438337 50437639 0 1107
13 TraesCS2B01G135600 chr3B 95.415 698 30 2 2677 3372 708392763 708392066 0 1110


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 TraesCS2B01G135600 chr2B 102124791 102128163 3372 False 6229.000000 6229 100.000000 1 3373 1 chr2B.!!$F1 3372
1 TraesCS2B01G135600 chr2B 452910177 452910874 697 False 1122.000000 1122 95.708000 2677 3373 1 chr2B.!!$F2 696
2 TraesCS2B01G135600 chr2B 666052418 666053115 697 False 1110.000000 1110 95.415000 2677 3373 1 chr2B.!!$F3 696
3 TraesCS2B01G135600 chr2A 66317699 66320326 2627 True 2687.000000 2687 85.725000 59 2680 1 chr2A.!!$R1 2621
4 TraesCS2B01G135600 chr2D 68731493 68734385 2892 False 1007.666667 1666 87.374667 73 2680 3 chr2D.!!$F1 2607
5 TraesCS2B01G135600 chr7B 739379293 739379993 700 False 1125.000000 1125 95.720000 2677 3373 1 chr7B.!!$F1 696
6 TraesCS2B01G135600 chr7B 498599073 498599770 697 True 1112.000000 1112 95.422000 2676 3373 1 chr7B.!!$R1 697
7 TraesCS2B01G135600 chr6B 26217740 26218437 697 False 1116.000000 1116 95.559000 2677 3373 1 chr6B.!!$F1 696
8 TraesCS2B01G135600 chr6B 599981103 599981800 697 False 1105.000000 1105 95.272000 2677 3373 1 chr6B.!!$F2 696
9 TraesCS2B01G135600 chrUn 263185294 263185992 698 False 1112.000000 1112 95.422000 2677 3373 1 chrUn.!!$F1 696
10 TraesCS2B01G135600 chrUn 50437639 50438337 698 True 1107.000000 1107 95.279000 2677 3373 1 chrUn.!!$R1 696
11 TraesCS2B01G135600 chr3B 708392066 708392763 697 True 1110.000000 1110 95.415000 2677 3372 1 chr3B.!!$R1 695

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
735 842 0.179000 ATCCATCCAACGAGACCTGC 59.821 55.0 0.00 0.00 0.00 4.85 F
997 1106 0.512518 AGTACGTGCGCGCGTATATA 59.487 50.0 45.62 30.91 46.81 0.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1755 2110 0.381801 GAGGTGTTGTTGTGCTGGTG 59.618 55.0 0.00 0.00 0.0 4.17 R
2987 3418 0.036388 GTCGGGTGCCAGATCTGAAA 60.036 55.0 24.62 8.71 0.0 2.69 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
17 18 3.621225 TCGGCCAGAGTGGATGAG 58.379 61.111 2.24 0.00 40.96 2.90
18 19 1.000359 TCGGCCAGAGTGGATGAGA 60.000 57.895 2.24 0.00 40.96 3.27
19 20 0.397675 TCGGCCAGAGTGGATGAGAT 60.398 55.000 2.24 0.00 40.96 2.75
20 21 0.467384 CGGCCAGAGTGGATGAGATT 59.533 55.000 2.24 0.00 40.96 2.40
21 22 1.809271 CGGCCAGAGTGGATGAGATTG 60.809 57.143 2.24 0.00 40.96 2.67
22 23 1.487976 GGCCAGAGTGGATGAGATTGA 59.512 52.381 0.00 0.00 40.96 2.57
23 24 2.092753 GGCCAGAGTGGATGAGATTGAA 60.093 50.000 0.00 0.00 40.96 2.69
24 25 3.614092 GCCAGAGTGGATGAGATTGAAA 58.386 45.455 0.00 0.00 40.96 2.69
25 26 4.205587 GCCAGAGTGGATGAGATTGAAAT 58.794 43.478 0.00 0.00 40.96 2.17
26 27 5.371526 GCCAGAGTGGATGAGATTGAAATA 58.628 41.667 0.00 0.00 40.96 1.40
27 28 5.824624 GCCAGAGTGGATGAGATTGAAATAA 59.175 40.000 0.00 0.00 40.96 1.40
28 29 6.238593 GCCAGAGTGGATGAGATTGAAATAAC 60.239 42.308 0.00 0.00 40.96 1.89
29 30 6.261826 CCAGAGTGGATGAGATTGAAATAACC 59.738 42.308 0.00 0.00 40.96 2.85
30 31 6.825213 CAGAGTGGATGAGATTGAAATAACCA 59.175 38.462 0.00 0.00 0.00 3.67
31 32 7.012138 CAGAGTGGATGAGATTGAAATAACCAG 59.988 40.741 0.00 0.00 0.00 4.00
32 33 6.725364 AGTGGATGAGATTGAAATAACCAGT 58.275 36.000 0.00 0.00 0.00 4.00
33 34 6.825721 AGTGGATGAGATTGAAATAACCAGTC 59.174 38.462 0.00 0.00 0.00 3.51
34 35 6.599244 GTGGATGAGATTGAAATAACCAGTCA 59.401 38.462 0.00 0.00 0.00 3.41
35 36 7.121168 GTGGATGAGATTGAAATAACCAGTCAA 59.879 37.037 0.00 0.00 35.83 3.18
36 37 7.121168 TGGATGAGATTGAAATAACCAGTCAAC 59.879 37.037 0.00 0.00 34.28 3.18
37 38 6.817765 TGAGATTGAAATAACCAGTCAACC 57.182 37.500 0.00 0.00 34.28 3.77
38 39 6.303054 TGAGATTGAAATAACCAGTCAACCA 58.697 36.000 0.00 0.00 34.28 3.67
39 40 6.775142 TGAGATTGAAATAACCAGTCAACCAA 59.225 34.615 0.00 0.00 34.28 3.67
40 41 6.981722 AGATTGAAATAACCAGTCAACCAAC 58.018 36.000 0.00 0.00 34.28 3.77
41 42 5.523438 TTGAAATAACCAGTCAACCAACC 57.477 39.130 0.00 0.00 0.00 3.77
42 43 3.892588 TGAAATAACCAGTCAACCAACCC 59.107 43.478 0.00 0.00 0.00 4.11
43 44 3.603965 AATAACCAGTCAACCAACCCA 57.396 42.857 0.00 0.00 0.00 4.51
44 45 3.825908 ATAACCAGTCAACCAACCCAT 57.174 42.857 0.00 0.00 0.00 4.00
45 46 1.703411 AACCAGTCAACCAACCCATG 58.297 50.000 0.00 0.00 0.00 3.66
46 47 0.555769 ACCAGTCAACCAACCCATGT 59.444 50.000 0.00 0.00 0.00 3.21
47 48 0.961019 CCAGTCAACCAACCCATGTG 59.039 55.000 0.00 0.00 0.00 3.21
48 49 1.691196 CAGTCAACCAACCCATGTGT 58.309 50.000 0.00 0.00 0.00 3.72
49 50 2.488167 CCAGTCAACCAACCCATGTGTA 60.488 50.000 0.00 0.00 0.00 2.90
50 51 3.218453 CAGTCAACCAACCCATGTGTAA 58.782 45.455 0.00 0.00 0.00 2.41
51 52 3.634448 CAGTCAACCAACCCATGTGTAAA 59.366 43.478 0.00 0.00 0.00 2.01
52 53 4.098654 CAGTCAACCAACCCATGTGTAAAA 59.901 41.667 0.00 0.00 0.00 1.52
53 54 4.098807 AGTCAACCAACCCATGTGTAAAAC 59.901 41.667 0.00 0.00 0.00 2.43
54 55 4.023980 TCAACCAACCCATGTGTAAAACA 58.976 39.130 0.00 0.00 44.79 2.83
55 56 4.651503 TCAACCAACCCATGTGTAAAACAT 59.348 37.500 0.00 0.00 44.51 2.71
56 57 4.599047 ACCAACCCATGTGTAAAACATG 57.401 40.909 10.77 10.77 44.51 3.21
57 58 4.219115 ACCAACCCATGTGTAAAACATGA 58.781 39.130 17.74 0.00 44.51 3.07
58 59 4.837860 ACCAACCCATGTGTAAAACATGAT 59.162 37.500 17.74 5.06 44.51 2.45
59 60 5.306678 ACCAACCCATGTGTAAAACATGATT 59.693 36.000 17.74 9.97 44.51 2.57
60 61 6.183361 ACCAACCCATGTGTAAAACATGATTT 60.183 34.615 17.74 2.25 44.51 2.17
61 62 6.709846 CCAACCCATGTGTAAAACATGATTTT 59.290 34.615 17.74 8.39 44.51 1.82
62 63 7.228308 CCAACCCATGTGTAAAACATGATTTTT 59.772 33.333 17.74 3.01 44.51 1.94
63 64 7.727331 ACCCATGTGTAAAACATGATTTTTG 57.273 32.000 17.74 2.57 44.51 2.44
64 65 7.504403 ACCCATGTGTAAAACATGATTTTTGA 58.496 30.769 17.74 0.00 44.51 2.69
65 66 7.440856 ACCCATGTGTAAAACATGATTTTTGAC 59.559 33.333 17.74 0.10 44.51 3.18
66 67 7.095271 CCCATGTGTAAAACATGATTTTTGACC 60.095 37.037 17.74 0.00 44.51 4.02
97 98 2.362369 CCTGGCTGAGTCGGACCAT 61.362 63.158 13.43 0.00 0.00 3.55
110 111 4.345257 AGTCGGACCATAGATGCAAAGTAT 59.655 41.667 4.14 0.00 0.00 2.12
137 138 2.736144 AGATGCATGCAACCAAACAG 57.264 45.000 26.68 0.00 0.00 3.16
226 256 6.015350 GGATATTCCTCCTCGTTTATGACAGA 60.015 42.308 0.00 0.00 32.53 3.41
284 314 2.124653 GAGAGACCTCGCGGGAGA 60.125 66.667 29.21 0.00 43.27 3.71
285 315 2.124487 AGAGACCTCGCGGGAGAG 60.124 66.667 29.21 20.58 43.27 3.20
286 316 2.124653 GAGACCTCGCGGGAGAGA 60.125 66.667 29.21 0.00 43.27 3.10
287 317 1.749638 GAGACCTCGCGGGAGAGAA 60.750 63.158 29.21 0.00 43.27 2.87
288 318 1.076632 AGACCTCGCGGGAGAGAAT 60.077 57.895 29.21 12.37 43.27 2.40
289 319 1.066587 GACCTCGCGGGAGAGAATG 59.933 63.158 29.21 14.99 43.27 2.67
290 320 2.356818 GACCTCGCGGGAGAGAATGG 62.357 65.000 29.21 15.46 43.27 3.16
291 321 2.419198 CTCGCGGGAGAGAATGGG 59.581 66.667 24.08 0.00 43.27 4.00
292 322 2.043349 TCGCGGGAGAGAATGGGA 60.043 61.111 6.13 0.00 35.14 4.37
293 323 1.457643 TCGCGGGAGAGAATGGGAT 60.458 57.895 6.13 0.00 35.14 3.85
294 324 1.048724 TCGCGGGAGAGAATGGGATT 61.049 55.000 6.13 0.00 35.14 3.01
295 325 0.179045 CGCGGGAGAGAATGGGATTT 60.179 55.000 0.00 0.00 0.00 2.17
296 326 1.598882 GCGGGAGAGAATGGGATTTC 58.401 55.000 0.00 0.00 0.00 2.17
297 327 1.141858 GCGGGAGAGAATGGGATTTCT 59.858 52.381 0.00 0.00 38.65 2.52
316 346 1.048724 TCGCGGGAGAGAATGGGATT 61.049 55.000 6.13 0.00 35.14 3.01
426 461 2.024825 GCGGGATCCTACTGTCTGTCT 61.025 57.143 12.58 0.00 0.00 3.41
428 463 2.741145 GGGATCCTACTGTCTGTCTGT 58.259 52.381 12.58 0.00 0.00 3.41
473 521 2.487532 CGGTCGTCGGCCTTATCCT 61.488 63.158 15.06 0.00 34.75 3.24
546 594 1.212935 CAGAACGGAATGGGAATCCCT 59.787 52.381 20.55 0.00 45.70 4.20
548 596 2.311841 AGAACGGAATGGGAATCCCTTT 59.688 45.455 20.55 19.27 45.70 3.11
721 828 4.325895 GGATCAATCCATCCATCCATCCAT 60.326 45.833 4.09 0.00 46.38 3.41
725 832 2.430963 TCCATCCATCCATCCATCCAA 58.569 47.619 0.00 0.00 0.00 3.53
726 833 2.108776 TCCATCCATCCATCCATCCAAC 59.891 50.000 0.00 0.00 0.00 3.77
728 835 1.506025 TCCATCCATCCATCCAACGA 58.494 50.000 0.00 0.00 0.00 3.85
729 836 1.417517 TCCATCCATCCATCCAACGAG 59.582 52.381 0.00 0.00 0.00 4.18
730 837 1.417517 CCATCCATCCATCCAACGAGA 59.582 52.381 0.00 0.00 0.00 4.04
732 839 0.830648 TCCATCCATCCAACGAGACC 59.169 55.000 0.00 0.00 0.00 3.85
733 840 0.833287 CCATCCATCCAACGAGACCT 59.167 55.000 0.00 0.00 0.00 3.85
734 841 1.473965 CCATCCATCCAACGAGACCTG 60.474 57.143 0.00 0.00 0.00 4.00
735 842 0.179000 ATCCATCCAACGAGACCTGC 59.821 55.000 0.00 0.00 0.00 4.85
737 844 1.811266 CATCCAACGAGACCTGCGG 60.811 63.158 0.00 0.00 0.00 5.69
765 872 1.690633 ATGGAGATGGAGGTGCCGT 60.691 57.895 0.00 0.00 40.66 5.68
928 1035 4.596180 CGCCCACGCATCGCAATC 62.596 66.667 0.00 0.00 34.03 2.67
929 1036 4.596180 GCCCACGCATCGCAATCG 62.596 66.667 0.00 0.00 34.03 3.34
930 1037 4.596180 CCCACGCATCGCAATCGC 62.596 66.667 0.00 0.00 35.26 4.58
931 1038 3.863543 CCACGCATCGCAATCGCA 61.864 61.111 0.00 0.00 38.40 5.10
932 1039 2.325511 CACGCATCGCAATCGCAT 59.674 55.556 0.00 0.00 38.40 4.73
933 1040 2.001880 CACGCATCGCAATCGCATG 61.002 57.895 0.00 0.00 38.40 4.06
934 1041 2.426261 CGCATCGCAATCGCATGG 60.426 61.111 0.00 0.00 38.40 3.66
935 1042 2.728383 GCATCGCAATCGCATGGC 60.728 61.111 0.00 0.00 38.40 4.40
936 1043 3.028130 CATCGCAATCGCATGGCT 58.972 55.556 0.00 0.00 38.40 4.75
937 1044 1.082300 CATCGCAATCGCATGGCTC 60.082 57.895 0.00 0.00 38.40 4.70
938 1045 1.227764 ATCGCAATCGCATGGCTCT 60.228 52.632 0.00 0.00 38.40 4.09
939 1046 1.226686 ATCGCAATCGCATGGCTCTC 61.227 55.000 0.00 0.00 38.40 3.20
940 1047 2.890109 CGCAATCGCATGGCTCTCC 61.890 63.158 0.00 0.00 38.40 3.71
941 1048 1.525535 GCAATCGCATGGCTCTCCT 60.526 57.895 0.00 0.00 38.36 3.69
942 1049 1.505477 GCAATCGCATGGCTCTCCTC 61.505 60.000 0.00 0.00 38.36 3.71
950 1057 0.760189 ATGGCTCTCCTCTCAGCTCC 60.760 60.000 0.00 0.00 35.82 4.70
954 1061 2.003658 CTCTCCTCTCAGCTCCACGC 62.004 65.000 0.00 0.00 39.57 5.34
995 1104 1.368019 GAGTACGTGCGCGCGTATA 60.368 57.895 45.62 31.94 46.81 1.47
997 1106 0.512518 AGTACGTGCGCGCGTATATA 59.487 50.000 45.62 30.91 46.81 0.86
1073 1196 4.034258 GACGGTGAGCGACCACGA 62.034 66.667 12.27 0.00 46.55 4.35
1116 1239 3.785859 CCGCTCAAGCCCAGCCTA 61.786 66.667 0.00 0.00 37.91 3.93
1286 1418 2.806818 CCCAGCAATCATCATCTCTTCG 59.193 50.000 0.00 0.00 0.00 3.79
1464 1813 2.585791 GAAGGAGAAGCAGCCCGAGG 62.586 65.000 0.00 0.00 0.00 4.63
1532 1881 2.357034 GGAGACAGCGGCGACAAA 60.357 61.111 12.98 0.00 0.00 2.83
1575 1924 1.899814 ACGACAAGGACAGCAAGGATA 59.100 47.619 0.00 0.00 0.00 2.59
1686 2041 2.044946 GCCGGTTCCTGGAAGCAT 60.045 61.111 31.17 0.00 39.64 3.79
1726 2081 1.072648 CTACGGTTGGTTCCCTTTCCA 59.927 52.381 0.00 0.00 0.00 3.53
1731 2086 2.593026 GTTGGTTCCCTTTCCATCACA 58.407 47.619 0.00 0.00 33.50 3.58
1737 2092 4.158579 GGTTCCCTTTCCATCACAAGATTC 59.841 45.833 0.00 0.00 30.20 2.52
1755 2110 6.481954 AGATTCGTTATTTTGCGATATCCC 57.518 37.500 0.00 0.00 36.97 3.85
1762 2117 0.254462 TTTGCGATATCCCACCAGCA 59.746 50.000 0.00 0.00 0.00 4.41
1765 2120 0.463654 GCGATATCCCACCAGCACAA 60.464 55.000 0.00 0.00 0.00 3.33
1766 2121 1.299541 CGATATCCCACCAGCACAAC 58.700 55.000 0.00 0.00 0.00 3.32
1793 2155 5.178067 CACCTCATCAAAAATCAAAGTTGCC 59.822 40.000 0.00 0.00 0.00 4.52
1928 2290 0.951040 GGTCAGTCGGTGCTTCTTGG 60.951 60.000 0.00 0.00 0.00 3.61
1932 2294 0.249911 AGTCGGTGCTTCTTGGTGAC 60.250 55.000 0.00 0.00 0.00 3.67
1934 2296 0.249868 TCGGTGCTTCTTGGTGACAG 60.250 55.000 0.00 0.00 44.54 3.51
1935 2297 1.230635 CGGTGCTTCTTGGTGACAGG 61.231 60.000 0.00 0.00 44.54 4.00
1962 2330 0.392060 CCCTAGTTAACCCGGCACAC 60.392 60.000 0.88 0.00 0.00 3.82
1979 2347 2.417933 CACACCATCTTGCTTAGTGCTC 59.582 50.000 0.00 0.00 43.37 4.26
1986 2366 5.293079 CCATCTTGCTTAGTGCTCTTAAGAC 59.707 44.000 0.00 0.00 43.37 3.01
2024 2404 4.037446 TGTTGCATTGGGTTTCAGAAGTAC 59.963 41.667 0.00 0.00 0.00 2.73
2193 2585 0.179129 CAATGTTGCATCGGGAAGCC 60.179 55.000 0.00 0.00 0.00 4.35
2251 2643 0.881796 GGGTTGAAGCCACACTTAGC 59.118 55.000 8.81 0.00 39.29 3.09
2269 2661 1.687494 GCAAAGCAGTCGAGTAGGCG 61.687 60.000 0.00 0.00 0.00 5.52
2279 2671 1.751927 GAGTAGGCGGTCGGAAGGA 60.752 63.158 0.00 0.00 0.00 3.36
2396 2802 3.953542 ATAACCTTGGGAGTTGGGATC 57.046 47.619 0.00 0.00 0.00 3.36
2398 2804 2.661176 ACCTTGGGAGTTGGGATCTA 57.339 50.000 0.00 0.00 0.00 1.98
2400 2806 3.474920 ACCTTGGGAGTTGGGATCTATT 58.525 45.455 0.00 0.00 0.00 1.73
2401 2807 4.641868 ACCTTGGGAGTTGGGATCTATTA 58.358 43.478 0.00 0.00 0.00 0.98
2402 2808 4.412528 ACCTTGGGAGTTGGGATCTATTAC 59.587 45.833 0.00 0.00 0.00 1.89
2404 2810 5.073691 CCTTGGGAGTTGGGATCTATTACAT 59.926 44.000 0.00 0.00 0.00 2.29
2405 2811 6.272324 CCTTGGGAGTTGGGATCTATTACATA 59.728 42.308 0.00 0.00 0.00 2.29
2406 2812 6.681729 TGGGAGTTGGGATCTATTACATAC 57.318 41.667 0.00 0.00 0.00 2.39
2407 2813 6.390504 TGGGAGTTGGGATCTATTACATACT 58.609 40.000 0.00 0.00 0.00 2.12
2408 2814 7.541074 TGGGAGTTGGGATCTATTACATACTA 58.459 38.462 0.00 0.00 0.00 1.82
2409 2815 7.453752 TGGGAGTTGGGATCTATTACATACTAC 59.546 40.741 0.00 0.00 0.00 2.73
2415 2824 9.824216 TTGGGATCTATTACATACTACTAGCTT 57.176 33.333 0.00 0.00 0.00 3.74
2498 2907 9.956640 ATTTGTTGATGTAGAGAAGAGAGAAAT 57.043 29.630 0.00 0.00 0.00 2.17
2499 2908 9.784531 TTTGTTGATGTAGAGAAGAGAGAAATT 57.215 29.630 0.00 0.00 0.00 1.82
2503 2916 6.820656 TGATGTAGAGAAGAGAGAAATTTGCC 59.179 38.462 0.00 0.00 0.00 4.52
2518 2931 2.300956 TTGCCTTTATGCCTTGTGGA 57.699 45.000 0.00 0.00 34.57 4.02
2523 2936 2.161855 CTTTATGCCTTGTGGACAGCA 58.838 47.619 0.00 0.00 40.00 4.41
2583 3012 2.677914 AGCTTTGCCAAGGGTAGTTTT 58.322 42.857 0.00 0.00 0.00 2.43
2859 3290 1.866015 AGAATGACGGATCACCTCCA 58.134 50.000 0.00 0.00 45.24 3.86
2941 3372 1.761784 ACCAAAAGTGAAGCCATTGCA 59.238 42.857 0.00 0.00 41.13 4.08
2987 3418 1.445942 CCCGGACACGCCATCTAAT 59.554 57.895 0.73 0.00 39.22 1.73
3004 3435 1.755179 AATTTCAGATCTGGCACCCG 58.245 50.000 22.42 0.00 0.00 5.28
3017 3448 1.214589 CACCCGACCACGACTAAGG 59.785 63.158 0.00 0.00 42.66 2.69
3057 3488 1.302431 CTGCCATCCACGAACCACA 60.302 57.895 0.00 0.00 0.00 4.17
3191 3622 2.636412 CGAAGCCCGAGGACACAGA 61.636 63.158 0.00 0.00 41.76 3.41
3328 3759 2.178892 TTCAGCGTCGTCATCGTCGT 62.179 55.000 8.59 0.00 46.29 4.34
3342 3773 3.411351 TCGTCGCCGAAGCAAAGC 61.411 61.111 0.00 0.00 40.86 3.51
3343 3774 3.711842 CGTCGCCGAAGCAAAGCA 61.712 61.111 0.00 0.00 39.83 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 0.467384 AATCTCATCCACTCTGGCCG 59.533 55.000 0.00 0.00 37.47 6.13
2 3 1.487976 TCAATCTCATCCACTCTGGCC 59.512 52.381 0.00 0.00 37.47 5.36
3 4 2.996249 TCAATCTCATCCACTCTGGC 57.004 50.000 0.00 0.00 37.47 4.85
4 5 6.261826 GGTTATTTCAATCTCATCCACTCTGG 59.738 42.308 0.00 0.00 39.43 3.86
5 6 6.825213 TGGTTATTTCAATCTCATCCACTCTG 59.175 38.462 0.00 0.00 0.00 3.35
7 8 6.825721 ACTGGTTATTTCAATCTCATCCACTC 59.174 38.462 0.00 0.00 0.00 3.51
8 9 6.725364 ACTGGTTATTTCAATCTCATCCACT 58.275 36.000 0.00 0.00 0.00 4.00
9 10 6.599244 TGACTGGTTATTTCAATCTCATCCAC 59.401 38.462 0.00 0.00 0.00 4.02
10 11 6.720309 TGACTGGTTATTTCAATCTCATCCA 58.280 36.000 0.00 0.00 0.00 3.41
11 12 7.415653 GGTTGACTGGTTATTTCAATCTCATCC 60.416 40.741 0.00 0.00 32.10 3.51
12 13 7.121168 TGGTTGACTGGTTATTTCAATCTCATC 59.879 37.037 0.00 0.00 32.52 2.92
13 14 6.947733 TGGTTGACTGGTTATTTCAATCTCAT 59.052 34.615 0.00 0.00 32.52 2.90
14 15 6.303054 TGGTTGACTGGTTATTTCAATCTCA 58.697 36.000 0.00 0.00 32.52 3.27
15 16 6.817765 TGGTTGACTGGTTATTTCAATCTC 57.182 37.500 0.00 0.00 32.52 2.75
16 17 6.015434 GGTTGGTTGACTGGTTATTTCAATCT 60.015 38.462 0.00 0.00 32.52 2.40
17 18 6.156519 GGTTGGTTGACTGGTTATTTCAATC 58.843 40.000 0.00 0.00 32.10 2.67
18 19 5.011635 GGGTTGGTTGACTGGTTATTTCAAT 59.988 40.000 0.00 0.00 32.10 2.57
19 20 4.342665 GGGTTGGTTGACTGGTTATTTCAA 59.657 41.667 0.00 0.00 0.00 2.69
20 21 3.892588 GGGTTGGTTGACTGGTTATTTCA 59.107 43.478 0.00 0.00 0.00 2.69
21 22 3.892588 TGGGTTGGTTGACTGGTTATTTC 59.107 43.478 0.00 0.00 0.00 2.17
22 23 3.917300 TGGGTTGGTTGACTGGTTATTT 58.083 40.909 0.00 0.00 0.00 1.40
23 24 3.603965 TGGGTTGGTTGACTGGTTATT 57.396 42.857 0.00 0.00 0.00 1.40
24 25 3.181423 ACATGGGTTGGTTGACTGGTTAT 60.181 43.478 0.00 0.00 0.00 1.89
25 26 2.175931 ACATGGGTTGGTTGACTGGTTA 59.824 45.455 0.00 0.00 0.00 2.85
26 27 1.063266 ACATGGGTTGGTTGACTGGTT 60.063 47.619 0.00 0.00 0.00 3.67
27 28 0.555769 ACATGGGTTGGTTGACTGGT 59.444 50.000 0.00 0.00 0.00 4.00
28 29 0.961019 CACATGGGTTGGTTGACTGG 59.039 55.000 0.00 0.00 0.00 4.00
29 30 1.691196 ACACATGGGTTGGTTGACTG 58.309 50.000 0.00 0.00 0.00 3.51
30 31 3.586470 TTACACATGGGTTGGTTGACT 57.414 42.857 5.59 0.00 0.00 3.41
31 32 4.142138 TGTTTTACACATGGGTTGGTTGAC 60.142 41.667 5.59 0.00 0.00 3.18
32 33 4.023980 TGTTTTACACATGGGTTGGTTGA 58.976 39.130 5.59 0.00 0.00 3.18
33 34 4.392921 TGTTTTACACATGGGTTGGTTG 57.607 40.909 5.59 0.00 0.00 3.77
44 45 6.565234 ACGGTCAAAAATCATGTTTTACACA 58.435 32.000 2.25 0.00 40.71 3.72
45 46 8.736751 ATACGGTCAAAAATCATGTTTTACAC 57.263 30.769 2.25 4.89 0.00 2.90
46 47 9.400638 GAATACGGTCAAAAATCATGTTTTACA 57.599 29.630 2.25 0.00 0.00 2.41
47 48 9.400638 TGAATACGGTCAAAAATCATGTTTTAC 57.599 29.630 2.25 0.00 0.00 2.01
48 49 9.400638 GTGAATACGGTCAAAAATCATGTTTTA 57.599 29.630 2.25 0.00 0.00 1.52
49 50 8.141268 AGTGAATACGGTCAAAAATCATGTTTT 58.859 29.630 0.00 0.00 0.00 2.43
50 51 7.657336 AGTGAATACGGTCAAAAATCATGTTT 58.343 30.769 0.00 0.00 0.00 2.83
51 52 7.040755 TGAGTGAATACGGTCAAAAATCATGTT 60.041 33.333 0.00 0.00 0.00 2.71
52 53 6.429692 TGAGTGAATACGGTCAAAAATCATGT 59.570 34.615 0.00 0.00 0.00 3.21
53 54 6.841119 TGAGTGAATACGGTCAAAAATCATG 58.159 36.000 0.00 0.00 0.00 3.07
54 55 6.403636 GCTGAGTGAATACGGTCAAAAATCAT 60.404 38.462 0.00 0.00 0.00 2.45
55 56 5.106712 GCTGAGTGAATACGGTCAAAAATCA 60.107 40.000 0.00 0.00 0.00 2.57
56 57 5.324697 GCTGAGTGAATACGGTCAAAAATC 58.675 41.667 0.00 0.00 0.00 2.17
57 58 4.156008 GGCTGAGTGAATACGGTCAAAAAT 59.844 41.667 0.00 0.00 0.00 1.82
58 59 3.500680 GGCTGAGTGAATACGGTCAAAAA 59.499 43.478 0.00 0.00 0.00 1.94
59 60 3.071479 GGCTGAGTGAATACGGTCAAAA 58.929 45.455 0.00 0.00 0.00 2.44
60 61 2.301870 AGGCTGAGTGAATACGGTCAAA 59.698 45.455 0.00 0.00 0.00 2.69
61 62 1.899814 AGGCTGAGTGAATACGGTCAA 59.100 47.619 0.00 0.00 0.00 3.18
62 63 1.204704 CAGGCTGAGTGAATACGGTCA 59.795 52.381 9.42 0.00 0.00 4.02
63 64 1.471676 CCAGGCTGAGTGAATACGGTC 60.472 57.143 17.94 0.00 0.00 4.79
64 65 0.537188 CCAGGCTGAGTGAATACGGT 59.463 55.000 17.94 0.00 0.00 4.83
65 66 0.811616 GCCAGGCTGAGTGAATACGG 60.812 60.000 17.94 0.00 0.00 4.02
66 67 0.176680 AGCCAGGCTGAGTGAATACG 59.823 55.000 15.24 0.00 37.57 3.06
93 94 7.807977 ATTTTCGATACTTTGCATCTATGGT 57.192 32.000 0.00 0.00 0.00 3.55
97 98 8.712363 GCATCTATTTTCGATACTTTGCATCTA 58.288 33.333 0.00 0.00 0.00 1.98
110 111 3.693578 TGGTTGCATGCATCTATTTTCGA 59.306 39.130 23.37 0.00 0.00 3.71
137 138 2.190578 CCGAGGATCACCAAGGCC 59.809 66.667 0.00 0.00 38.94 5.19
167 178 2.672961 TTCATAGGTTGGTCAGCTCG 57.327 50.000 0.00 0.00 34.13 5.03
226 256 1.967066 CTCACACACTCTCTTCCCTGT 59.033 52.381 0.00 0.00 0.00 4.00
284 314 0.179045 CCCGCGAGAAATCCCATTCT 60.179 55.000 8.23 0.00 42.24 2.40
285 315 0.179056 TCCCGCGAGAAATCCCATTC 60.179 55.000 8.23 0.00 0.00 2.67
286 316 0.179045 CTCCCGCGAGAAATCCCATT 60.179 55.000 8.23 0.00 38.52 3.16
287 317 1.048724 TCTCCCGCGAGAAATCCCAT 61.049 55.000 8.23 0.00 42.33 4.00
288 318 1.676678 CTCTCCCGCGAGAAATCCCA 61.677 60.000 8.23 0.00 44.62 4.37
289 319 1.068250 CTCTCCCGCGAGAAATCCC 59.932 63.158 8.23 0.00 44.62 3.85
290 320 0.460311 TTCTCTCCCGCGAGAAATCC 59.540 55.000 8.23 0.00 44.62 3.01
295 325 2.127869 CCCATTCTCTCCCGCGAGA 61.128 63.158 8.23 0.00 43.08 4.04
296 326 1.467678 ATCCCATTCTCTCCCGCGAG 61.468 60.000 8.23 0.00 37.48 5.03
297 327 1.048724 AATCCCATTCTCTCCCGCGA 61.049 55.000 8.23 0.00 0.00 5.87
310 340 2.172717 GGAAGATTCCCGAGAAATCCCA 59.827 50.000 0.00 0.00 41.62 4.37
410 445 2.356382 CGGACAGACAGACAGTAGGATC 59.644 54.545 0.00 0.00 0.00 3.36
416 451 2.131294 GACGCGGACAGACAGACAGT 62.131 60.000 12.47 0.00 0.00 3.55
473 521 0.607217 TTACTCGAGTGGGTGAGCGA 60.607 55.000 28.12 1.06 35.61 4.93
546 594 0.107831 CGGGCAGGATATTCGGGAAA 59.892 55.000 0.00 0.00 0.00 3.13
548 596 1.458777 ACGGGCAGGATATTCGGGA 60.459 57.895 0.00 0.00 0.00 5.14
716 823 0.179000 GCAGGTCTCGTTGGATGGAT 59.821 55.000 0.00 0.00 0.00 3.41
746 853 1.227764 CGGCACCTCCATCTCCATG 60.228 63.158 0.00 0.00 34.01 3.66
797 904 4.057943 AGGTAGTCCCGGAGCCGT 62.058 66.667 0.73 0.00 38.74 5.68
912 1019 4.596180 CGATTGCGATGCGTGGGC 62.596 66.667 0.00 0.00 40.82 5.36
913 1020 4.596180 GCGATTGCGATGCGTGGG 62.596 66.667 0.00 0.00 40.82 4.61
923 1030 1.505477 GAGGAGAGCCATGCGATTGC 61.505 60.000 0.00 0.00 38.04 3.56
924 1031 0.106335 AGAGGAGAGCCATGCGATTG 59.894 55.000 0.00 0.00 36.29 2.67
925 1032 0.392336 GAGAGGAGAGCCATGCGATT 59.608 55.000 0.00 0.00 36.29 3.34
926 1033 0.758310 TGAGAGGAGAGCCATGCGAT 60.758 55.000 0.00 0.00 36.29 4.58
927 1034 1.380380 TGAGAGGAGAGCCATGCGA 60.380 57.895 0.00 0.00 36.29 5.10
928 1035 1.067749 CTGAGAGGAGAGCCATGCG 59.932 63.158 0.00 0.00 36.29 4.73
929 1036 1.227615 GCTGAGAGGAGAGCCATGC 60.228 63.158 0.00 0.00 36.29 4.06
930 1037 0.390124 GAGCTGAGAGGAGAGCCATG 59.610 60.000 0.00 0.00 35.69 3.66
931 1038 0.760189 GGAGCTGAGAGGAGAGCCAT 60.760 60.000 0.00 0.00 35.69 4.40
932 1039 1.381056 GGAGCTGAGAGGAGAGCCA 60.381 63.158 0.00 0.00 35.69 4.75
933 1040 1.381056 TGGAGCTGAGAGGAGAGCC 60.381 63.158 0.00 0.00 35.69 4.70
934 1041 1.815866 GTGGAGCTGAGAGGAGAGC 59.184 63.158 0.00 0.00 35.28 4.09
935 1042 2.003658 GCGTGGAGCTGAGAGGAGAG 62.004 65.000 0.00 0.00 44.04 3.20
936 1043 2.049185 GCGTGGAGCTGAGAGGAGA 61.049 63.158 0.00 0.00 44.04 3.71
937 1044 2.493973 GCGTGGAGCTGAGAGGAG 59.506 66.667 0.00 0.00 44.04 3.69
954 1061 5.122554 TCCTTAATTAGATCGAGCTAGCGAG 59.877 44.000 10.71 7.63 44.26 5.03
956 1063 5.106475 ACTCCTTAATTAGATCGAGCTAGCG 60.106 44.000 10.71 0.00 0.00 4.26
995 1104 3.995048 CTCGATTGCTGCAGACATCATAT 59.005 43.478 20.43 5.39 0.00 1.78
997 1106 2.210961 CTCGATTGCTGCAGACATCAT 58.789 47.619 20.43 6.47 0.00 2.45
1286 1418 7.634522 CAGCAATCTGTATTTAGCTACCTTTC 58.365 38.462 0.00 0.00 35.61 2.62
1372 1721 1.522355 CATGGCAGCACCTAGTCGG 60.522 63.158 0.00 0.00 40.22 4.79
1374 1723 1.078214 TGCATGGCAGCACCTAGTC 60.078 57.895 7.40 0.00 40.11 2.59
1532 1881 3.231889 CTCAGTGTCGCTGGTGGCT 62.232 63.158 13.36 0.00 45.08 4.75
1575 1924 4.944619 TGTCTGTGTCTTTCTCAGTGAT 57.055 40.909 0.00 0.00 38.39 3.06
1680 2035 1.153823 CCAGCTGCTGCAATGCTTC 60.154 57.895 23.86 0.00 42.74 3.86
1726 2081 6.176975 TCGCAAAATAACGAATCTTGTGAT 57.823 33.333 0.00 0.00 34.93 3.06
1731 2086 6.485313 TGGGATATCGCAAAATAACGAATCTT 59.515 34.615 19.24 0.00 42.31 2.40
1737 2092 3.562141 TGGTGGGATATCGCAAAATAACG 59.438 43.478 22.62 0.00 40.56 3.18
1755 2110 0.381801 GAGGTGTTGTTGTGCTGGTG 59.618 55.000 0.00 0.00 0.00 4.17
1762 2117 6.219417 TGATTTTTGATGAGGTGTTGTTGT 57.781 33.333 0.00 0.00 0.00 3.32
1765 2120 6.877236 ACTTTGATTTTTGATGAGGTGTTGT 58.123 32.000 0.00 0.00 0.00 3.32
1766 2121 7.623770 CAACTTTGATTTTTGATGAGGTGTTG 58.376 34.615 0.00 0.00 0.00 3.33
1793 2155 6.128956 CGGCACCAATTAAATGTTGTTGTTAG 60.129 38.462 0.00 0.00 0.00 2.34
1803 2165 2.911819 ACGACGGCACCAATTAAATG 57.088 45.000 0.00 0.00 0.00 2.32
1979 2347 5.931146 ACAAATGTCAGCTCAGAGTCTTAAG 59.069 40.000 0.00 0.00 0.00 1.85
1986 2366 2.551032 TGCAACAAATGTCAGCTCAGAG 59.449 45.455 10.82 0.00 32.45 3.35
1995 2375 4.125703 TGAAACCCAATGCAACAAATGTC 58.874 39.130 0.00 0.00 0.00 3.06
2024 2404 2.310233 CCTTGACGTGTGCAGACGG 61.310 63.158 35.35 19.87 43.84 4.79
2193 2585 1.849097 GGAGCGTATACTTGGTTCGG 58.151 55.000 0.56 0.00 0.00 4.30
2223 2615 0.899717 GGCTTCAACCCTGATGGCAA 60.900 55.000 0.00 0.00 46.02 4.52
2251 2643 1.078759 CCGCCTACTCGACTGCTTTG 61.079 60.000 0.00 0.00 0.00 2.77
2297 2689 3.682885 TCCGAGTTAACGCCGCCA 61.683 61.111 14.97 4.40 0.00 5.69
2400 2806 9.636789 TGTATTTCTCCAAGCTAGTAGTATGTA 57.363 33.333 0.00 0.00 0.00 2.29
2401 2807 8.534954 TGTATTTCTCCAAGCTAGTAGTATGT 57.465 34.615 0.00 0.00 0.00 2.29
2402 2808 8.851145 TCTGTATTTCTCCAAGCTAGTAGTATG 58.149 37.037 0.00 0.00 0.00 2.39
2404 2810 8.053963 ACTCTGTATTTCTCCAAGCTAGTAGTA 58.946 37.037 0.00 0.00 0.00 1.82
2405 2811 6.893005 ACTCTGTATTTCTCCAAGCTAGTAGT 59.107 38.462 0.00 0.00 0.00 2.73
2406 2812 7.284489 AGACTCTGTATTTCTCCAAGCTAGTAG 59.716 40.741 0.00 0.00 0.00 2.57
2407 2813 7.120051 AGACTCTGTATTTCTCCAAGCTAGTA 58.880 38.462 0.00 0.00 0.00 1.82
2408 2814 5.955355 AGACTCTGTATTTCTCCAAGCTAGT 59.045 40.000 0.00 0.00 0.00 2.57
2409 2815 6.463995 AGACTCTGTATTTCTCCAAGCTAG 57.536 41.667 0.00 0.00 0.00 3.42
2440 2849 5.061311 CGTACCTTACTGTAAAATGTGACCG 59.939 44.000 1.46 1.98 0.00 4.79
2503 2916 2.095059 GTGCTGTCCACAAGGCATAAAG 60.095 50.000 0.00 0.00 44.06 1.85
2523 2936 6.098982 AGCTATATGAGTCACCTTAAGCTTGT 59.901 38.462 9.86 0.00 34.26 3.16
2539 2952 5.252547 TGTGGCAAAACTCAAGCTATATGA 58.747 37.500 0.00 0.00 0.00 2.15
2583 3012 1.405105 GTGAGCTCCACAGTGCAAAAA 59.595 47.619 12.15 0.00 45.03 1.94
2684 3113 6.215495 TGAATGAGACACGTATTACCATGA 57.785 37.500 0.00 0.00 0.00 3.07
2817 3248 2.145397 TTTTGGTGGCTGTTGTGGTA 57.855 45.000 0.00 0.00 0.00 3.25
2941 3372 1.337823 CCCGGTCTGATTCGTTCAACT 60.338 52.381 0.00 0.00 32.78 3.16
2984 3415 2.503765 TCGGGTGCCAGATCTGAAATTA 59.496 45.455 24.62 2.53 0.00 1.40
2987 3418 0.036388 GTCGGGTGCCAGATCTGAAA 60.036 55.000 24.62 8.71 0.00 2.69
3004 3435 2.508663 GGCGCCTTAGTCGTGGTC 60.509 66.667 22.15 0.00 0.00 4.02
3017 3448 3.125573 GGTTTCCTCCTTCGGCGC 61.126 66.667 0.00 0.00 0.00 6.53
3057 3488 3.836151 GGAACGTGTGCTGGGTTT 58.164 55.556 0.00 0.00 0.00 3.27
3191 3622 2.911143 GGCATCCTCGTGGTGGAT 59.089 61.111 2.99 0.21 44.44 3.41
3225 3656 4.516698 GGAAATCAGTCTGTTCAAGCAAGA 59.483 41.667 0.00 0.00 0.00 3.02
3328 3759 1.209898 CATTGCTTTGCTTCGGCGA 59.790 52.632 4.99 4.99 45.37 5.54
3342 3773 8.166422 AGTCTAGGTTTTTAGGTTGTTCATTG 57.834 34.615 0.00 0.00 0.00 2.82
3343 3774 9.281371 GTAGTCTAGGTTTTTAGGTTGTTCATT 57.719 33.333 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.