Multiple sequence alignment - TraesCS4B01G218600

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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 TraesCS4B01G218600 chr4B 100.000 2271 0 0 1 2271 460375180 460377450 0.000000e+00 4194.0
1 TraesCS4B01G218600 chr4B 97.349 830 21 1 1442 2271 474025010 474024182 0.000000e+00 1410.0
2 TraesCS4B01G218600 chr4B 98.058 412 8 0 1442 1853 507148939 507149350 0.000000e+00 717.0
3 TraesCS4B01G218600 chr4B 98.058 412 8 0 1442 1853 565012822 565013233 0.000000e+00 717.0
4 TraesCS4B01G218600 chr4B 98.058 412 8 0 1442 1853 627406921 627406510 0.000000e+00 717.0
5 TraesCS4B01G218600 chr4B 94.545 440 6 5 1850 2271 567457714 567457275 0.000000e+00 664.0
6 TraesCS4B01G218600 chr4B 94.318 440 7 1 1850 2271 627405812 627405373 0.000000e+00 658.0
7 TraesCS4B01G218600 chr4B 98.276 116 1 1 2156 2271 137632883 137632769 3.830000e-48 202.0
8 TraesCS4B01G218600 chr4B 98.276 116 1 1 2156 2271 456635234 456635348 3.830000e-48 202.0
9 TraesCS4B01G218600 chr3B 93.037 1149 41 14 326 1441 736677927 736676785 0.000000e+00 1642.0
10 TraesCS4B01G218600 chr3B 93.636 440 5 2 1850 2271 575219761 575219327 8.850000e-179 636.0
11 TraesCS4B01G218600 chr3B 99.405 168 1 0 1 168 303127085 303126918 2.830000e-79 305.0
12 TraesCS4B01G218600 chr3B 92.000 125 6 2 168 292 736678046 736677926 3.000000e-39 172.0
13 TraesCS4B01G218600 chr1B 91.802 1171 56 11 203 1337 550913675 550912509 0.000000e+00 1594.0
14 TraesCS4B01G218600 chr1B 99.405 168 1 0 1 168 163261513 163261346 2.830000e-79 305.0
15 TraesCS4B01G218600 chr1B 99.405 168 1 0 1 168 514418606 514418439 2.830000e-79 305.0
16 TraesCS4B01G218600 chr6B 88.471 1223 98 22 250 1441 647587990 647586780 0.000000e+00 1437.0
17 TraesCS4B01G218600 chr6B 97.831 830 18 0 1442 2271 630248074 630247245 0.000000e+00 1434.0
18 TraesCS4B01G218600 chr6B 100.000 168 0 0 1 168 556034332 556034165 6.090000e-81 311.0
19 TraesCS4B01G218600 chr6B 99.138 116 0 1 2156 2271 511332057 511331943 8.220000e-50 207.0
20 TraesCS4B01G218600 chr6B 98.291 117 1 1 2155 2271 255853784 255853899 1.060000e-48 204.0
21 TraesCS4B01G218600 chr2B 97.229 830 22 1 1442 2271 686684672 686685500 0.000000e+00 1404.0
22 TraesCS4B01G218600 chr2B 96.627 830 27 1 1442 2271 686704978 686705806 0.000000e+00 1376.0
23 TraesCS4B01G218600 chr2B 83.923 1188 156 17 258 1441 702712875 702711719 0.000000e+00 1103.0
24 TraesCS4B01G218600 chr2B 78.661 478 83 9 976 1445 631603704 631604170 1.320000e-77 300.0
25 TraesCS4B01G218600 chr6D 85.627 1308 127 23 184 1441 227818784 227820080 0.000000e+00 1317.0
26 TraesCS4B01G218600 chr6D 91.250 80 4 3 1365 1442 27028293 27028215 3.090000e-19 106.0
27 TraesCS4B01G218600 chr6D 96.552 58 2 0 1384 1441 356746875 356746932 1.860000e-16 97.1
28 TraesCS4B01G218600 chr2D 84.182 1296 166 22 167 1441 19528514 19527237 0.000000e+00 1221.0
29 TraesCS4B01G218600 chr2D 99.405 168 1 0 1 168 163864317 163864484 2.830000e-79 305.0
30 TraesCS4B01G218600 chr7D 84.761 1214 130 19 246 1437 123494382 123493202 0.000000e+00 1166.0
31 TraesCS4B01G218600 chr7D 83.856 861 115 10 431 1282 579084202 579085047 0.000000e+00 798.0
32 TraesCS4B01G218600 chr3D 84.095 1226 154 24 169 1375 7705982 7707185 0.000000e+00 1146.0
33 TraesCS4B01G218600 chr5A 83.362 1172 137 20 322 1441 626973492 626974657 0.000000e+00 1031.0
34 TraesCS4B01G218600 chr5A 81.579 152 11 4 168 305 626972679 626972827 2.380000e-20 110.0
35 TraesCS4B01G218600 chr4A 82.154 1244 146 38 265 1447 626068682 626069910 0.000000e+00 998.0
36 TraesCS4B01G218600 chrUn 87.846 831 60 21 168 965 24957130 24957952 0.000000e+00 937.0
37 TraesCS4B01G218600 chrUn 100.000 168 0 0 1 168 64263038 64263205 6.090000e-81 311.0
38 TraesCS4B01G218600 chrUn 99.405 168 1 0 1 168 73590308 73590141 2.830000e-79 305.0
39 TraesCS4B01G218600 chrUn 86.667 105 9 4 1345 1447 266535312 266535211 6.630000e-21 111.0
40 TraesCS4B01G218600 chr7B 98.301 412 7 0 1442 1853 197227554 197227143 0.000000e+00 723.0
41 TraesCS4B01G218600 chr7B 98.058 412 8 0 1442 1853 198354062 198354473 0.000000e+00 717.0
42 TraesCS4B01G218600 chr7B 94.521 438 6 5 1850 2269 504386657 504386220 0.000000e+00 660.0
43 TraesCS4B01G218600 chr7B 99.405 168 1 0 1 168 12628612 12628445 2.830000e-79 305.0
44 TraesCS4B01G218600 chr7B 99.405 168 1 0 1 168 46209669 46209836 2.830000e-79 305.0
45 TraesCS4B01G218600 chr7B 98.305 118 0 2 2154 2271 333239168 333239283 2.960000e-49 206.0
46 TraesCS4B01G218600 chr5B 94.318 440 7 1 1850 2271 118762458 118762019 0.000000e+00 658.0
47 TraesCS4B01G218600 chr1D 89.474 152 14 2 1145 1296 450148347 450148496 8.280000e-45 191.0
48 TraesCS4B01G218600 chr1D 91.139 79 4 3 1365 1441 440050860 440050783 1.110000e-18 104.0
49 TraesCS4B01G218600 chr1D 89.286 84 5 4 1365 1445 59955135 59955053 3.990000e-18 102.0
50 TraesCS4B01G218600 chr3A 78.947 209 20 11 169 376 572139940 572139755 1.100000e-23 121.0


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 TraesCS4B01G218600 chr4B 460375180 460377450 2270 False 4194.0 4194 100.0000 1 2271 1 chr4B.!!$F2 2270
1 TraesCS4B01G218600 chr4B 474024182 474025010 828 True 1410.0 1410 97.3490 1442 2271 1 chr4B.!!$R2 829
2 TraesCS4B01G218600 chr4B 627405373 627406921 1548 True 687.5 717 96.1880 1442 2271 2 chr4B.!!$R4 829
3 TraesCS4B01G218600 chr3B 736676785 736678046 1261 True 907.0 1642 92.5185 168 1441 2 chr3B.!!$R3 1273
4 TraesCS4B01G218600 chr1B 550912509 550913675 1166 True 1594.0 1594 91.8020 203 1337 1 chr1B.!!$R3 1134
5 TraesCS4B01G218600 chr6B 647586780 647587990 1210 True 1437.0 1437 88.4710 250 1441 1 chr6B.!!$R4 1191
6 TraesCS4B01G218600 chr6B 630247245 630248074 829 True 1434.0 1434 97.8310 1442 2271 1 chr6B.!!$R3 829
7 TraesCS4B01G218600 chr2B 686684672 686685500 828 False 1404.0 1404 97.2290 1442 2271 1 chr2B.!!$F2 829
8 TraesCS4B01G218600 chr2B 686704978 686705806 828 False 1376.0 1376 96.6270 1442 2271 1 chr2B.!!$F3 829
9 TraesCS4B01G218600 chr2B 702711719 702712875 1156 True 1103.0 1103 83.9230 258 1441 1 chr2B.!!$R1 1183
10 TraesCS4B01G218600 chr6D 227818784 227820080 1296 False 1317.0 1317 85.6270 184 1441 1 chr6D.!!$F1 1257
11 TraesCS4B01G218600 chr2D 19527237 19528514 1277 True 1221.0 1221 84.1820 167 1441 1 chr2D.!!$R1 1274
12 TraesCS4B01G218600 chr7D 123493202 123494382 1180 True 1166.0 1166 84.7610 246 1437 1 chr7D.!!$R1 1191
13 TraesCS4B01G218600 chr7D 579084202 579085047 845 False 798.0 798 83.8560 431 1282 1 chr7D.!!$F1 851
14 TraesCS4B01G218600 chr3D 7705982 7707185 1203 False 1146.0 1146 84.0950 169 1375 1 chr3D.!!$F1 1206
15 TraesCS4B01G218600 chr5A 626972679 626974657 1978 False 570.5 1031 82.4705 168 1441 2 chr5A.!!$F1 1273
16 TraesCS4B01G218600 chr4A 626068682 626069910 1228 False 998.0 998 82.1540 265 1447 1 chr4A.!!$F1 1182
17 TraesCS4B01G218600 chrUn 24957130 24957952 822 False 937.0 937 87.8460 168 965 1 chrUn.!!$F1 797

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
665 1453 0.527385 CACCACAAAAAGCACACGGG 60.527 55.0 0.0 0.0 0.0 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1920 3494 2.292292 GTGACAACCAAACAGGCGTAAT 59.708 45.455 0.0 0.0 43.14 1.89 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
25 26 8.537049 TCAACTAAAATCGAAGTCGGAATAAA 57.463 30.769 0.11 0.00 40.29 1.40
26 27 8.991026 TCAACTAAAATCGAAGTCGGAATAAAA 58.009 29.630 0.11 0.00 40.29 1.52
27 28 9.047871 CAACTAAAATCGAAGTCGGAATAAAAC 57.952 33.333 0.11 0.00 40.29 2.43
28 29 7.745972 ACTAAAATCGAAGTCGGAATAAAACC 58.254 34.615 0.11 0.00 40.29 3.27
43 44 8.751302 GGAATAAAACCGAGCTTTAATTTTGA 57.249 30.769 0.00 0.00 0.00 2.69
44 45 9.366216 GGAATAAAACCGAGCTTTAATTTTGAT 57.634 29.630 0.00 0.00 0.00 2.57
48 49 8.926715 AAAACCGAGCTTTAATTTTGATATCC 57.073 30.769 0.00 0.00 0.00 2.59
49 50 6.635030 ACCGAGCTTTAATTTTGATATCCC 57.365 37.500 0.00 0.00 0.00 3.85
50 51 6.365520 ACCGAGCTTTAATTTTGATATCCCT 58.634 36.000 0.00 0.00 0.00 4.20
51 52 6.263168 ACCGAGCTTTAATTTTGATATCCCTG 59.737 38.462 0.00 0.00 0.00 4.45
52 53 6.263168 CCGAGCTTTAATTTTGATATCCCTGT 59.737 38.462 0.00 0.00 0.00 4.00
53 54 7.444183 CCGAGCTTTAATTTTGATATCCCTGTA 59.556 37.037 0.00 0.00 0.00 2.74
54 55 8.836413 CGAGCTTTAATTTTGATATCCCTGTAA 58.164 33.333 0.00 0.00 0.00 2.41
56 57 8.633561 AGCTTTAATTTTGATATCCCTGTAAGC 58.366 33.333 0.00 7.03 33.78 3.09
57 58 8.413229 GCTTTAATTTTGATATCCCTGTAAGCA 58.587 33.333 0.00 0.00 33.79 3.91
60 61 7.716799 AATTTTGATATCCCTGTAAGCAACA 57.283 32.000 0.00 0.00 36.42 3.33
61 62 7.716799 ATTTTGATATCCCTGTAAGCAACAA 57.283 32.000 0.00 0.00 37.74 2.83
62 63 7.716799 TTTTGATATCCCTGTAAGCAACAAT 57.283 32.000 0.00 0.00 37.74 2.71
63 64 8.815565 TTTTGATATCCCTGTAAGCAACAATA 57.184 30.769 0.00 0.00 37.74 1.90
64 65 8.450578 TTTGATATCCCTGTAAGCAACAATAG 57.549 34.615 0.00 0.00 37.74 1.73
65 66 6.533730 TGATATCCCTGTAAGCAACAATAGG 58.466 40.000 0.00 0.00 37.74 2.57
66 67 4.862641 ATCCCTGTAAGCAACAATAGGT 57.137 40.909 0.00 0.00 37.74 3.08
67 68 5.968676 ATCCCTGTAAGCAACAATAGGTA 57.031 39.130 0.00 0.00 37.74 3.08
68 69 5.968676 TCCCTGTAAGCAACAATAGGTAT 57.031 39.130 0.00 0.00 37.74 2.73
69 70 7.626999 ATCCCTGTAAGCAACAATAGGTATA 57.373 36.000 0.00 0.00 37.74 1.47
70 71 7.440505 TCCCTGTAAGCAACAATAGGTATAA 57.559 36.000 0.00 0.00 37.74 0.98
71 72 7.506114 TCCCTGTAAGCAACAATAGGTATAAG 58.494 38.462 0.00 0.00 37.74 1.73
72 73 6.710744 CCCTGTAAGCAACAATAGGTATAAGG 59.289 42.308 0.00 0.00 37.74 2.69
73 74 6.710744 CCTGTAAGCAACAATAGGTATAAGGG 59.289 42.308 0.00 0.00 37.74 3.95
74 75 7.419750 CCTGTAAGCAACAATAGGTATAAGGGA 60.420 40.741 0.00 0.00 37.74 4.20
75 76 7.863722 TGTAAGCAACAATAGGTATAAGGGAA 58.136 34.615 0.00 0.00 34.29 3.97
76 77 8.330247 TGTAAGCAACAATAGGTATAAGGGAAA 58.670 33.333 0.00 0.00 34.29 3.13
77 78 7.640597 AAGCAACAATAGGTATAAGGGAAAC 57.359 36.000 0.00 0.00 0.00 2.78
78 79 6.727394 AGCAACAATAGGTATAAGGGAAACA 58.273 36.000 0.00 0.00 0.00 2.83
79 80 7.179269 AGCAACAATAGGTATAAGGGAAACAA 58.821 34.615 0.00 0.00 0.00 2.83
80 81 7.839200 AGCAACAATAGGTATAAGGGAAACAAT 59.161 33.333 0.00 0.00 0.00 2.71
81 82 8.474831 GCAACAATAGGTATAAGGGAAACAATT 58.525 33.333 0.00 0.00 0.00 2.32
88 89 8.388656 AGGTATAAGGGAAACAATTACTGAGA 57.611 34.615 0.00 0.00 0.00 3.27
89 90 8.832735 AGGTATAAGGGAAACAATTACTGAGAA 58.167 33.333 0.00 0.00 0.00 2.87
90 91 9.457436 GGTATAAGGGAAACAATTACTGAGAAA 57.543 33.333 0.00 0.00 0.00 2.52
96 97 8.971073 AGGGAAACAATTACTGAGAAATAATGG 58.029 33.333 0.00 0.00 0.00 3.16
97 98 8.749354 GGGAAACAATTACTGAGAAATAATGGT 58.251 33.333 0.00 0.00 0.00 3.55
105 106 9.911788 ATTACTGAGAAATAATGGTTGATGACT 57.088 29.630 0.00 0.00 0.00 3.41
106 107 9.739276 TTACTGAGAAATAATGGTTGATGACTT 57.261 29.630 0.00 0.00 0.00 3.01
107 108 8.048534 ACTGAGAAATAATGGTTGATGACTTG 57.951 34.615 0.00 0.00 0.00 3.16
108 109 7.667219 ACTGAGAAATAATGGTTGATGACTTGT 59.333 33.333 0.00 0.00 0.00 3.16
109 110 8.044060 TGAGAAATAATGGTTGATGACTTGTC 57.956 34.615 0.00 0.00 0.00 3.18
110 111 7.884877 TGAGAAATAATGGTTGATGACTTGTCT 59.115 33.333 2.35 0.00 0.00 3.41
111 112 8.641498 AGAAATAATGGTTGATGACTTGTCTT 57.359 30.769 2.35 0.00 0.00 3.01
112 113 9.739276 AGAAATAATGGTTGATGACTTGTCTTA 57.261 29.630 2.35 0.00 0.00 2.10
116 117 6.764308 ATGGTTGATGACTTGTCTTAATGG 57.236 37.500 2.35 0.00 0.00 3.16
117 118 5.009631 TGGTTGATGACTTGTCTTAATGGG 58.990 41.667 2.35 0.00 0.00 4.00
118 119 5.222027 TGGTTGATGACTTGTCTTAATGGGA 60.222 40.000 2.35 0.00 0.00 4.37
119 120 5.710099 GGTTGATGACTTGTCTTAATGGGAA 59.290 40.000 2.35 0.00 0.00 3.97
120 121 6.208599 GGTTGATGACTTGTCTTAATGGGAAA 59.791 38.462 2.35 0.00 0.00 3.13
121 122 6.817765 TGATGACTTGTCTTAATGGGAAAC 57.182 37.500 2.35 0.00 0.00 2.78
122 123 6.303054 TGATGACTTGTCTTAATGGGAAACA 58.697 36.000 2.35 0.00 0.00 2.83
123 124 6.775142 TGATGACTTGTCTTAATGGGAAACAA 59.225 34.615 2.35 0.00 0.00 2.83
124 125 7.286546 TGATGACTTGTCTTAATGGGAAACAAA 59.713 33.333 2.35 0.00 30.16 2.83
125 126 7.038154 TGACTTGTCTTAATGGGAAACAAAG 57.962 36.000 2.35 0.00 30.16 2.77
126 127 5.842907 ACTTGTCTTAATGGGAAACAAAGC 58.157 37.500 0.00 0.00 30.16 3.51
127 128 5.362430 ACTTGTCTTAATGGGAAACAAAGCA 59.638 36.000 0.00 0.00 30.16 3.91
128 129 5.452078 TGTCTTAATGGGAAACAAAGCAG 57.548 39.130 0.00 0.00 0.00 4.24
129 130 4.280677 TGTCTTAATGGGAAACAAAGCAGG 59.719 41.667 0.00 0.00 0.00 4.85
130 131 4.522789 GTCTTAATGGGAAACAAAGCAGGA 59.477 41.667 0.00 0.00 0.00 3.86
131 132 4.766891 TCTTAATGGGAAACAAAGCAGGAG 59.233 41.667 0.00 0.00 0.00 3.69
132 133 2.978156 ATGGGAAACAAAGCAGGAGA 57.022 45.000 0.00 0.00 0.00 3.71
133 134 2.276732 TGGGAAACAAAGCAGGAGAG 57.723 50.000 0.00 0.00 0.00 3.20
134 135 1.202927 TGGGAAACAAAGCAGGAGAGG 60.203 52.381 0.00 0.00 0.00 3.69
135 136 1.073923 GGGAAACAAAGCAGGAGAGGA 59.926 52.381 0.00 0.00 0.00 3.71
136 137 2.431454 GGAAACAAAGCAGGAGAGGAG 58.569 52.381 0.00 0.00 0.00 3.69
137 138 1.809547 GAAACAAAGCAGGAGAGGAGC 59.190 52.381 0.00 0.00 0.00 4.70
138 139 0.767375 AACAAAGCAGGAGAGGAGCA 59.233 50.000 0.00 0.00 0.00 4.26
139 140 0.767375 ACAAAGCAGGAGAGGAGCAA 59.233 50.000 0.00 0.00 0.00 3.91
140 141 1.353694 ACAAAGCAGGAGAGGAGCAAT 59.646 47.619 0.00 0.00 0.00 3.56
141 142 2.224967 ACAAAGCAGGAGAGGAGCAATT 60.225 45.455 0.00 0.00 0.00 2.32
142 143 2.416680 AAGCAGGAGAGGAGCAATTC 57.583 50.000 0.00 0.00 0.00 2.17
143 144 1.582389 AGCAGGAGAGGAGCAATTCT 58.418 50.000 0.00 0.00 0.00 2.40
144 145 1.485895 AGCAGGAGAGGAGCAATTCTC 59.514 52.381 3.55 3.55 41.15 2.87
155 156 3.603532 GAGCAATTCTCCATCAGTGTGA 58.396 45.455 0.00 0.00 35.77 3.58
156 157 4.197750 GAGCAATTCTCCATCAGTGTGAT 58.802 43.478 0.00 0.00 35.77 3.06
157 158 4.597004 AGCAATTCTCCATCAGTGTGATT 58.403 39.130 0.00 0.00 34.28 2.57
158 159 4.639310 AGCAATTCTCCATCAGTGTGATTC 59.361 41.667 0.00 0.00 34.28 2.52
159 160 4.397103 GCAATTCTCCATCAGTGTGATTCA 59.603 41.667 0.00 0.00 34.28 2.57
160 161 5.067413 GCAATTCTCCATCAGTGTGATTCAT 59.933 40.000 0.00 0.00 34.28 2.57
161 162 6.405508 GCAATTCTCCATCAGTGTGATTCATT 60.406 38.462 0.00 0.00 34.28 2.57
162 163 6.939132 ATTCTCCATCAGTGTGATTCATTC 57.061 37.500 0.00 0.00 34.28 2.67
163 164 5.425196 TCTCCATCAGTGTGATTCATTCA 57.575 39.130 0.00 0.00 34.28 2.57
164 165 5.997843 TCTCCATCAGTGTGATTCATTCAT 58.002 37.500 0.00 0.00 34.28 2.57
165 166 7.128234 TCTCCATCAGTGTGATTCATTCATA 57.872 36.000 0.00 0.00 34.28 2.15
313 991 1.138247 GCCTTTCAGCCTTCATGCG 59.862 57.895 0.00 0.00 36.02 4.73
315 993 1.226211 CTTTCAGCCTTCATGCGCG 60.226 57.895 0.00 0.00 36.02 6.86
323 1015 3.239275 CTTCATGCGCGCACACACA 62.239 57.895 39.05 17.58 0.00 3.72
324 1016 3.519799 TTCATGCGCGCACACACAC 62.520 57.895 39.05 1.69 0.00 3.82
346 1039 1.163420 ACACGATCGCAAGCCAAACA 61.163 50.000 16.60 0.00 37.18 2.83
414 1122 6.748333 TTGCTTCTTTCATCCTTCACATAG 57.252 37.500 0.00 0.00 0.00 2.23
415 1123 6.053632 TGCTTCTTTCATCCTTCACATAGA 57.946 37.500 0.00 0.00 0.00 1.98
416 1124 6.475504 TGCTTCTTTCATCCTTCACATAGAA 58.524 36.000 0.00 0.00 34.41 2.10
417 1125 6.942005 TGCTTCTTTCATCCTTCACATAGAAA 59.058 34.615 0.00 0.00 35.40 2.52
418 1126 7.448161 TGCTTCTTTCATCCTTCACATAGAAAA 59.552 33.333 0.00 0.00 35.40 2.29
419 1127 8.299570 GCTTCTTTCATCCTTCACATAGAAAAA 58.700 33.333 0.00 0.00 35.40 1.94
420 1128 9.837525 CTTCTTTCATCCTTCACATAGAAAAAG 57.162 33.333 0.00 0.00 35.40 2.27
490 1218 1.768870 CGTGATTTCCCTACCTCCCAT 59.231 52.381 0.00 0.00 0.00 4.00
582 1369 6.503944 TCCTAGTCTCCTTCCTAATTCAGTT 58.496 40.000 0.00 0.00 0.00 3.16
642 1430 5.755375 GCTTGATCAATAGTTCTCCGAATCA 59.245 40.000 8.96 0.00 0.00 2.57
647 1435 5.487433 TCAATAGTTCTCCGAATCAAAGCA 58.513 37.500 0.00 0.00 0.00 3.91
665 1453 0.527385 CACCACAAAAAGCACACGGG 60.527 55.000 0.00 0.00 0.00 5.28
791 1590 7.935338 ATTACTTTTTCAGAATTGTGTGCTG 57.065 32.000 2.11 0.00 0.00 4.41
813 1612 0.605319 ATGCCGCCGAGAAACAAGAA 60.605 50.000 0.00 0.00 0.00 2.52
1079 1881 4.277174 TCATTGCATCTTGTTTACGGTGTT 59.723 37.500 0.00 0.00 0.00 3.32
1093 1895 1.664659 CGGTGTTTGTGACGGTTGTAA 59.335 47.619 0.00 0.00 0.00 2.41
1132 1938 5.591099 TCAAAGCTGGAATTGTTGAAGAAC 58.409 37.500 0.00 0.00 0.00 3.01
1139 1945 7.014615 AGCTGGAATTGTTGAAGAACTATTTGT 59.985 33.333 0.00 0.00 37.56 2.83
1169 1976 4.674281 ATGACTCGAGGGAGGTTAAATC 57.326 45.455 18.41 1.29 44.93 2.17
1458 2331 4.115516 CCCTGTTCATATTGACTGAGACG 58.884 47.826 0.00 0.00 0.00 4.18
1681 2554 8.462016 GTTAATTAATTCTGAGAGTGGCATTGT 58.538 33.333 3.39 0.00 0.00 2.71
1696 2569 5.698545 GTGGCATTGTTTAATTTTACCAGCA 59.301 36.000 0.00 0.00 0.00 4.41
1756 2629 2.680841 GAGTGGGCGCAACAACAATATA 59.319 45.455 10.83 0.00 0.00 0.86
1789 2662 4.601406 ACTTATAAAGGGGGTGATGCAA 57.399 40.909 0.00 0.00 0.00 4.08
1920 3494 9.059260 GGTGACTTAAAACCAGTGACTTATAAA 57.941 33.333 0.00 0.00 36.41 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.537049 TTTATTCCGACTTCGATTTTAGTTGA 57.463 30.769 0.00 0.00 43.02 3.18
1 2 9.047871 GTTTTATTCCGACTTCGATTTTAGTTG 57.952 33.333 0.00 0.00 43.02 3.16
2 3 8.232513 GGTTTTATTCCGACTTCGATTTTAGTT 58.767 33.333 0.00 0.00 43.02 2.24
3 4 7.745972 GGTTTTATTCCGACTTCGATTTTAGT 58.254 34.615 0.00 0.00 43.02 2.24
18 19 8.751302 TCAAAATTAAAGCTCGGTTTTATTCC 57.249 30.769 6.36 0.00 0.00 3.01
23 24 7.979537 GGGATATCAAAATTAAAGCTCGGTTTT 59.020 33.333 4.83 0.00 0.00 2.43
24 25 7.342026 AGGGATATCAAAATTAAAGCTCGGTTT 59.658 33.333 4.83 0.00 0.00 3.27
25 26 6.833933 AGGGATATCAAAATTAAAGCTCGGTT 59.166 34.615 4.83 0.00 0.00 4.44
26 27 6.263168 CAGGGATATCAAAATTAAAGCTCGGT 59.737 38.462 4.83 0.00 0.00 4.69
27 28 6.263168 ACAGGGATATCAAAATTAAAGCTCGG 59.737 38.462 4.83 0.00 0.00 4.63
28 29 7.264373 ACAGGGATATCAAAATTAAAGCTCG 57.736 36.000 4.83 0.00 0.00 5.03
30 31 8.633561 GCTTACAGGGATATCAAAATTAAAGCT 58.366 33.333 4.83 0.00 32.48 3.74
31 32 8.413229 TGCTTACAGGGATATCAAAATTAAAGC 58.587 33.333 4.83 10.31 35.01 3.51
34 35 9.249053 TGTTGCTTACAGGGATATCAAAATTAA 57.751 29.630 4.83 0.00 31.68 1.40
35 36 8.815565 TGTTGCTTACAGGGATATCAAAATTA 57.184 30.769 4.83 0.00 31.68 1.40
36 37 7.716799 TGTTGCTTACAGGGATATCAAAATT 57.283 32.000 4.83 0.00 31.68 1.82
37 38 7.716799 TTGTTGCTTACAGGGATATCAAAAT 57.283 32.000 4.83 0.00 38.19 1.82
38 39 7.716799 ATTGTTGCTTACAGGGATATCAAAA 57.283 32.000 4.83 0.00 38.19 2.44
39 40 7.502226 CCTATTGTTGCTTACAGGGATATCAAA 59.498 37.037 4.83 0.00 38.19 2.69
40 41 6.998074 CCTATTGTTGCTTACAGGGATATCAA 59.002 38.462 4.83 0.00 38.19 2.57
41 42 6.101150 ACCTATTGTTGCTTACAGGGATATCA 59.899 38.462 4.83 0.00 38.19 2.15
42 43 6.534634 ACCTATTGTTGCTTACAGGGATATC 58.465 40.000 0.00 0.00 38.19 1.63
43 44 6.515512 ACCTATTGTTGCTTACAGGGATAT 57.484 37.500 11.70 0.00 38.19 1.63
44 45 5.968676 ACCTATTGTTGCTTACAGGGATA 57.031 39.130 11.70 1.53 38.19 2.59
45 46 4.862641 ACCTATTGTTGCTTACAGGGAT 57.137 40.909 11.70 0.70 38.19 3.85
46 47 5.968676 ATACCTATTGTTGCTTACAGGGA 57.031 39.130 11.70 0.00 38.19 4.20
47 48 6.710744 CCTTATACCTATTGTTGCTTACAGGG 59.289 42.308 0.00 0.00 38.19 4.45
48 49 6.710744 CCCTTATACCTATTGTTGCTTACAGG 59.289 42.308 0.00 0.00 38.19 4.00
49 50 7.506114 TCCCTTATACCTATTGTTGCTTACAG 58.494 38.462 0.00 0.00 38.19 2.74
50 51 7.440505 TCCCTTATACCTATTGTTGCTTACA 57.559 36.000 0.00 0.00 34.12 2.41
51 52 8.618677 GTTTCCCTTATACCTATTGTTGCTTAC 58.381 37.037 0.00 0.00 0.00 2.34
52 53 8.330247 TGTTTCCCTTATACCTATTGTTGCTTA 58.670 33.333 0.00 0.00 0.00 3.09
53 54 7.179269 TGTTTCCCTTATACCTATTGTTGCTT 58.821 34.615 0.00 0.00 0.00 3.91
54 55 6.727394 TGTTTCCCTTATACCTATTGTTGCT 58.273 36.000 0.00 0.00 0.00 3.91
55 56 7.399245 TTGTTTCCCTTATACCTATTGTTGC 57.601 36.000 0.00 0.00 0.00 4.17
62 63 9.496710 TCTCAGTAATTGTTTCCCTTATACCTA 57.503 33.333 0.00 0.00 0.00 3.08
63 64 8.388656 TCTCAGTAATTGTTTCCCTTATACCT 57.611 34.615 0.00 0.00 0.00 3.08
64 65 9.457436 TTTCTCAGTAATTGTTTCCCTTATACC 57.543 33.333 0.00 0.00 0.00 2.73
70 71 8.971073 CCATTATTTCTCAGTAATTGTTTCCCT 58.029 33.333 0.00 0.00 0.00 4.20
71 72 8.749354 ACCATTATTTCTCAGTAATTGTTTCCC 58.251 33.333 0.00 0.00 0.00 3.97
79 80 9.911788 AGTCATCAACCATTATTTCTCAGTAAT 57.088 29.630 0.00 0.00 0.00 1.89
80 81 9.739276 AAGTCATCAACCATTATTTCTCAGTAA 57.261 29.630 0.00 0.00 0.00 2.24
81 82 9.166173 CAAGTCATCAACCATTATTTCTCAGTA 57.834 33.333 0.00 0.00 0.00 2.74
82 83 7.667219 ACAAGTCATCAACCATTATTTCTCAGT 59.333 33.333 0.00 0.00 0.00 3.41
83 84 8.048534 ACAAGTCATCAACCATTATTTCTCAG 57.951 34.615 0.00 0.00 0.00 3.35
84 85 7.884877 AGACAAGTCATCAACCATTATTTCTCA 59.115 33.333 2.72 0.00 0.00 3.27
85 86 8.273780 AGACAAGTCATCAACCATTATTTCTC 57.726 34.615 2.72 0.00 0.00 2.87
86 87 8.641498 AAGACAAGTCATCAACCATTATTTCT 57.359 30.769 2.72 0.00 0.00 2.52
90 91 8.906867 CCATTAAGACAAGTCATCAACCATTAT 58.093 33.333 2.72 0.00 0.00 1.28
91 92 7.339212 CCCATTAAGACAAGTCATCAACCATTA 59.661 37.037 2.72 0.00 0.00 1.90
92 93 6.153340 CCCATTAAGACAAGTCATCAACCATT 59.847 38.462 2.72 0.00 0.00 3.16
93 94 5.653769 CCCATTAAGACAAGTCATCAACCAT 59.346 40.000 2.72 0.00 0.00 3.55
94 95 5.009631 CCCATTAAGACAAGTCATCAACCA 58.990 41.667 2.72 0.00 0.00 3.67
95 96 5.253330 TCCCATTAAGACAAGTCATCAACC 58.747 41.667 2.72 0.00 0.00 3.77
96 97 6.817765 TTCCCATTAAGACAAGTCATCAAC 57.182 37.500 2.72 0.00 0.00 3.18
97 98 6.775142 TGTTTCCCATTAAGACAAGTCATCAA 59.225 34.615 2.72 0.00 0.00 2.57
98 99 6.303054 TGTTTCCCATTAAGACAAGTCATCA 58.697 36.000 2.72 0.00 0.00 3.07
99 100 6.817765 TGTTTCCCATTAAGACAAGTCATC 57.182 37.500 2.72 0.00 0.00 2.92
100 101 7.595819 TTTGTTTCCCATTAAGACAAGTCAT 57.404 32.000 2.72 0.00 32.50 3.06
101 102 6.460953 GCTTTGTTTCCCATTAAGACAAGTCA 60.461 38.462 2.72 0.00 32.50 3.41
102 103 5.920840 GCTTTGTTTCCCATTAAGACAAGTC 59.079 40.000 0.00 0.00 32.50 3.01
103 104 5.362430 TGCTTTGTTTCCCATTAAGACAAGT 59.638 36.000 0.00 0.00 32.50 3.16
104 105 5.841810 TGCTTTGTTTCCCATTAAGACAAG 58.158 37.500 0.00 0.00 32.50 3.16
105 106 5.221422 CCTGCTTTGTTTCCCATTAAGACAA 60.221 40.000 0.00 0.00 0.00 3.18
106 107 4.280677 CCTGCTTTGTTTCCCATTAAGACA 59.719 41.667 0.00 0.00 0.00 3.41
107 108 4.522789 TCCTGCTTTGTTTCCCATTAAGAC 59.477 41.667 0.00 0.00 0.00 3.01
108 109 4.735369 TCCTGCTTTGTTTCCCATTAAGA 58.265 39.130 0.00 0.00 0.00 2.10
109 110 4.766891 TCTCCTGCTTTGTTTCCCATTAAG 59.233 41.667 0.00 0.00 0.00 1.85
110 111 4.735369 TCTCCTGCTTTGTTTCCCATTAA 58.265 39.130 0.00 0.00 0.00 1.40
111 112 4.335416 CTCTCCTGCTTTGTTTCCCATTA 58.665 43.478 0.00 0.00 0.00 1.90
112 113 3.160269 CTCTCCTGCTTTGTTTCCCATT 58.840 45.455 0.00 0.00 0.00 3.16
113 114 2.556114 CCTCTCCTGCTTTGTTTCCCAT 60.556 50.000 0.00 0.00 0.00 4.00
114 115 1.202927 CCTCTCCTGCTTTGTTTCCCA 60.203 52.381 0.00 0.00 0.00 4.37
115 116 1.073923 TCCTCTCCTGCTTTGTTTCCC 59.926 52.381 0.00 0.00 0.00 3.97
116 117 2.431454 CTCCTCTCCTGCTTTGTTTCC 58.569 52.381 0.00 0.00 0.00 3.13
117 118 1.809547 GCTCCTCTCCTGCTTTGTTTC 59.190 52.381 0.00 0.00 0.00 2.78
118 119 1.143684 TGCTCCTCTCCTGCTTTGTTT 59.856 47.619 0.00 0.00 0.00 2.83
119 120 0.767375 TGCTCCTCTCCTGCTTTGTT 59.233 50.000 0.00 0.00 0.00 2.83
120 121 0.767375 TTGCTCCTCTCCTGCTTTGT 59.233 50.000 0.00 0.00 0.00 2.83
121 122 2.125773 ATTGCTCCTCTCCTGCTTTG 57.874 50.000 0.00 0.00 0.00 2.77
122 123 2.308275 AGAATTGCTCCTCTCCTGCTTT 59.692 45.455 0.00 0.00 0.00 3.51
123 124 1.914798 AGAATTGCTCCTCTCCTGCTT 59.085 47.619 0.00 0.00 0.00 3.91
124 125 1.485895 GAGAATTGCTCCTCTCCTGCT 59.514 52.381 0.00 0.00 37.69 4.24
125 126 1.952193 GAGAATTGCTCCTCTCCTGC 58.048 55.000 0.00 0.00 37.69 4.85
134 135 3.603532 TCACACTGATGGAGAATTGCTC 58.396 45.455 0.00 0.00 43.17 4.26
135 136 3.708403 TCACACTGATGGAGAATTGCT 57.292 42.857 0.00 0.00 0.00 3.91
136 137 4.397103 TGAATCACACTGATGGAGAATTGC 59.603 41.667 0.00 0.00 37.15 3.56
137 138 6.694877 ATGAATCACACTGATGGAGAATTG 57.305 37.500 0.00 0.00 37.15 2.32
138 139 6.888088 TGAATGAATCACACTGATGGAGAATT 59.112 34.615 0.00 0.00 37.15 2.17
139 140 6.420638 TGAATGAATCACACTGATGGAGAAT 58.579 36.000 0.00 0.00 37.15 2.40
140 141 5.807909 TGAATGAATCACACTGATGGAGAA 58.192 37.500 0.00 0.00 37.15 2.87
141 142 5.425196 TGAATGAATCACACTGATGGAGA 57.575 39.130 0.00 0.00 37.15 3.71
142 143 7.981102 ATATGAATGAATCACACTGATGGAG 57.019 36.000 0.00 0.00 41.93 3.86
143 144 7.994334 TGAATATGAATGAATCACACTGATGGA 59.006 33.333 0.00 0.00 41.93 3.41
144 145 8.161699 TGAATATGAATGAATCACACTGATGG 57.838 34.615 0.00 0.00 41.93 3.51
145 146 8.290325 CCTGAATATGAATGAATCACACTGATG 58.710 37.037 0.00 0.00 41.93 3.07
146 147 7.447545 CCCTGAATATGAATGAATCACACTGAT 59.552 37.037 0.00 0.00 41.93 2.90
147 148 6.769341 CCCTGAATATGAATGAATCACACTGA 59.231 38.462 0.00 0.00 41.93 3.41
148 149 6.514541 GCCCTGAATATGAATGAATCACACTG 60.515 42.308 0.00 0.00 41.93 3.66
149 150 5.533903 GCCCTGAATATGAATGAATCACACT 59.466 40.000 0.00 0.00 41.93 3.55
150 151 5.278660 GGCCCTGAATATGAATGAATCACAC 60.279 44.000 0.00 0.00 41.93 3.82
151 152 4.828939 GGCCCTGAATATGAATGAATCACA 59.171 41.667 0.00 0.00 41.93 3.58
152 153 4.083110 CGGCCCTGAATATGAATGAATCAC 60.083 45.833 0.00 0.00 41.93 3.06
153 154 4.074259 CGGCCCTGAATATGAATGAATCA 58.926 43.478 0.00 0.00 43.67 2.57
154 155 3.441572 CCGGCCCTGAATATGAATGAATC 59.558 47.826 0.00 0.00 0.00 2.52
155 156 3.424703 CCGGCCCTGAATATGAATGAAT 58.575 45.455 0.00 0.00 0.00 2.57
156 157 2.862541 CCGGCCCTGAATATGAATGAA 58.137 47.619 0.00 0.00 0.00 2.57
157 158 1.545428 GCCGGCCCTGAATATGAATGA 60.545 52.381 18.11 0.00 0.00 2.57
158 159 0.883833 GCCGGCCCTGAATATGAATG 59.116 55.000 18.11 0.00 0.00 2.67
159 160 0.251341 GGCCGGCCCTGAATATGAAT 60.251 55.000 36.64 0.00 0.00 2.57
160 161 1.150536 GGCCGGCCCTGAATATGAA 59.849 57.895 36.64 0.00 0.00 2.57
161 162 2.836154 GGCCGGCCCTGAATATGA 59.164 61.111 36.64 0.00 0.00 2.15
210 212 3.419580 CTAGCATGTGGGGGCCCA 61.420 66.667 26.86 7.88 45.02 5.36
315 993 2.748546 GATCGTGTGCGTGTGTGTGC 62.749 60.000 0.00 0.00 39.49 4.57
323 1015 3.777925 GCTTGCGATCGTGTGCGT 61.778 61.111 17.81 0.00 39.49 5.24
324 1016 4.505217 GGCTTGCGATCGTGTGCG 62.505 66.667 17.81 2.56 39.92 5.34
414 1122 5.142962 CAGCAGATCGTTGTCTTCTTTTTC 58.857 41.667 0.00 0.00 0.00 2.29
415 1123 4.576463 ACAGCAGATCGTTGTCTTCTTTTT 59.424 37.500 2.28 0.00 33.03 1.94
416 1124 4.130118 ACAGCAGATCGTTGTCTTCTTTT 58.870 39.130 2.28 0.00 33.03 2.27
417 1125 3.733337 ACAGCAGATCGTTGTCTTCTTT 58.267 40.909 2.28 0.00 33.03 2.52
418 1126 3.393089 ACAGCAGATCGTTGTCTTCTT 57.607 42.857 2.28 0.00 33.03 2.52
642 1430 2.345876 GTGTGCTTTTTGTGGTGCTTT 58.654 42.857 0.00 0.00 0.00 3.51
647 1435 1.813192 CCCGTGTGCTTTTTGTGGT 59.187 52.632 0.00 0.00 0.00 4.16
665 1453 3.370366 GTCGAATCCATGATAGCATCAGC 59.630 47.826 0.00 0.00 43.53 4.26
791 1590 1.022451 TTGTTTCTCGGCGGCATACC 61.022 55.000 10.53 0.00 0.00 2.73
813 1612 8.629158 TCCTTTTATTGCTAAACGATGCATATT 58.371 29.630 0.00 0.00 39.07 1.28
1057 1856 4.159377 ACACCGTAAACAAGATGCAATG 57.841 40.909 0.00 0.00 0.00 2.82
1068 1870 1.665169 ACCGTCACAAACACCGTAAAC 59.335 47.619 0.00 0.00 0.00 2.01
1079 1881 1.876799 CAGCCATTACAACCGTCACAA 59.123 47.619 0.00 0.00 0.00 3.33
1139 1945 2.901192 TCCCTCGAGTCATTGTTAACCA 59.099 45.455 12.31 0.00 0.00 3.67
1169 1976 3.247411 TCGATGCATAATGTAGCCAAACG 59.753 43.478 0.00 0.00 0.00 3.60
1458 2331 6.919721 TGAACCAAGGCATTGTTAAGATAAC 58.080 36.000 10.60 0.00 34.39 1.89
1696 2569 9.503427 GTTTATGCTTTTCGTTAATCTAATGCT 57.497 29.630 0.00 0.00 0.00 3.79
1756 2629 6.240292 CCCCCTTTATAAGTAGATGGAAGCAT 60.240 42.308 0.00 0.00 0.00 3.79
1920 3494 2.292292 GTGACAACCAAACAGGCGTAAT 59.708 45.455 0.00 0.00 43.14 1.89


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

AutoCloner maintained by Alex Coulton.