Multiple sequence alignment - TraesCS5A01G111200

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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 TraesCS5A01G111200 chr5A 100.000 1329 0 0 909 2237 213284745 213286073 0.000000e+00 2455.0
1 TraesCS5A01G111200 chr5A 85.270 1351 169 19 909 2234 213302345 213303690 0.000000e+00 1365.0
2 TraesCS5A01G111200 chr5A 100.000 569 0 0 1 569 213283837 213284405 0.000000e+00 1051.0
3 TraesCS5A01G111200 chr5A 82.898 421 66 6 1817 2234 173003134 173003551 7.540000e-100 374.0
4 TraesCS5A01G111200 chr5A 82.783 424 63 10 1817 2234 172995653 172996072 9.760000e-99 370.0
5 TraesCS5A01G111200 chr3A 85.587 1346 167 8 909 2230 304510777 304512119 0.000000e+00 1386.0
6 TraesCS5A01G111200 chr3A 83.727 1229 143 21 1033 2237 304540344 304541539 0.000000e+00 1109.0
7 TraesCS5A01G111200 chr3A 91.566 415 28 4 157 569 304510220 304510629 1.160000e-157 566.0
8 TraesCS5A01G111200 chr3A 77.506 409 70 20 143 539 228963961 228963563 2.240000e-55 226.0
9 TraesCS5A01G111200 chr6B 81.595 652 80 20 1071 1698 106980045 106980680 9.220000e-139 503.0
10 TraesCS5A01G111200 chr6B 91.573 178 13 2 1688 1864 106982270 106982446 6.170000e-61 244.0
11 TraesCS5A01G111200 chr6B 85.065 154 23 0 1 154 277552284 277552437 8.270000e-35 158.0
12 TraesCS5A01G111200 chr4A 84.248 419 63 3 1817 2233 463783 463366 2.670000e-109 405.0
13 TraesCS5A01G111200 chr4A 83.250 400 61 5 1833 2230 97977508 97977113 1.630000e-96 363.0
14 TraesCS5A01G111200 chr4A 81.609 87 13 3 915 999 323911243 323911328 3.990000e-08 69.4
15 TraesCS5A01G111200 chr7D 83.610 421 68 1 1817 2237 417770052 417769633 5.790000e-106 394.0
16 TraesCS5A01G111200 chr7D 85.714 147 21 0 1 147 87073598 87073744 2.970000e-34 156.0
17 TraesCS5A01G111200 chr5D 82.169 415 64 4 1817 2230 420137963 420137558 4.570000e-92 348.0
18 TraesCS5A01G111200 chr5D 81.604 424 64 12 155 569 190736450 190736868 2.750000e-89 339.0
19 TraesCS5A01G111200 chr5D 75.772 421 88 13 153 569 540528146 540527736 1.350000e-47 200.0
20 TraesCS5A01G111200 chr3B 79.474 380 66 11 153 526 199608876 199608503 2.200000e-65 259.0
21 TraesCS5A01G111200 chr3B 85.714 154 21 1 1 154 320830036 320830188 6.390000e-36 161.0
22 TraesCS5A01G111200 chrUn 78.446 399 65 19 153 539 470474887 470474498 7.980000e-60 241.0
23 TraesCS5A01G111200 chr6A 78.446 399 65 19 153 539 457069207 457068818 7.980000e-60 241.0
24 TraesCS5A01G111200 chr2D 86.574 216 25 4 1565 1776 403707807 403707592 3.710000e-58 235.0
25 TraesCS5A01G111200 chr2D 87.640 178 19 3 1602 1776 403714220 403714043 1.050000e-48 204.0
26 TraesCS5A01G111200 chr2D 86.620 142 19 0 6 147 395732400 395732259 8.270000e-35 158.0
27 TraesCS5A01G111200 chr2D 84.076 157 25 0 1 157 478380019 478379863 3.850000e-33 152.0
28 TraesCS5A01G111200 chr2D 84.314 153 24 0 1 153 442300878 442300726 1.380000e-32 150.0
29 TraesCS5A01G111200 chr1A 78.141 398 67 18 153 539 119360351 119359963 3.710000e-58 235.0
30 TraesCS5A01G111200 chr1A 78.086 397 66 18 155 539 327262819 327263206 4.800000e-57 231.0
31 TraesCS5A01G111200 chr2B 77.975 395 69 17 155 539 151638290 151638676 4.800000e-57 231.0
32 TraesCS5A01G111200 chr5B 77.953 381 71 12 152 526 377302582 377302209 2.240000e-55 226.0
33 TraesCS5A01G111200 chr1B 87.234 188 20 3 1149 1335 415394278 415394094 6.260000e-51 211.0
34 TraesCS5A01G111200 chr1B 84.416 154 24 0 1 154 217306514 217306667 3.850000e-33 152.0
35 TraesCS5A01G111200 chr2A 85.802 162 18 4 1180 1340 150419103 150418946 1.370000e-37 167.0
36 TraesCS5A01G111200 chr2A 86.111 144 20 0 6 149 308793793 308793936 2.970000e-34 156.0
37 TraesCS5A01G111200 chr7B 85.350 157 23 0 1 157 352679770 352679926 1.780000e-36 163.0
38 TraesCS5A01G111200 chr1D 84.167 120 15 3 1216 1334 76710498 76710614 1.820000e-21 113.0


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 TraesCS5A01G111200 chr5A 213283837 213286073 2236 False 1753.0 2455 100.0000 1 2237 2 chr5A.!!$F4 2236
1 TraesCS5A01G111200 chr5A 213302345 213303690 1345 False 1365.0 1365 85.2700 909 2234 1 chr5A.!!$F3 1325
2 TraesCS5A01G111200 chr3A 304540344 304541539 1195 False 1109.0 1109 83.7270 1033 2237 1 chr3A.!!$F1 1204
3 TraesCS5A01G111200 chr3A 304510220 304512119 1899 False 976.0 1386 88.5765 157 2230 2 chr3A.!!$F2 2073
4 TraesCS5A01G111200 chr6B 106980045 106982446 2401 False 373.5 503 86.5840 1071 1864 2 chr6B.!!$F2 793

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
66 67 0.099613 TCGAACGATCTCTGCTGCTC 59.900 55.0 0.0 0.0 0.0 4.26 F
68 69 0.174389 GAACGATCTCTGCTGCTCCA 59.826 55.0 0.0 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1145 1148 1.069090 GTGATGGCGAGGCGGATTA 59.931 57.895 0.0 0.0 0.0 1.75 R
1889 3532 1.077716 GGCCCTGTTGACCGCTTAT 60.078 57.895 0.0 0.0 0.0 1.73 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
20 21 1.825090 CTGAAATACAGTGCCTGCCA 58.175 50.000 2.50 0.00 41.30 4.92
21 22 1.470098 CTGAAATACAGTGCCTGCCAC 59.530 52.381 2.50 0.00 45.01 5.01
31 32 4.655647 CCTGCCACTGCTGCACCT 62.656 66.667 0.00 0.00 38.71 4.00
32 33 2.596631 CTGCCACTGCTGCACCTT 60.597 61.111 0.00 0.00 38.71 3.50
33 34 2.595463 TGCCACTGCTGCACCTTC 60.595 61.111 0.00 0.00 38.71 3.46
34 35 2.595463 GCCACTGCTGCACCTTCA 60.595 61.111 0.00 0.00 33.53 3.02
35 36 2.623915 GCCACTGCTGCACCTTCAG 61.624 63.158 0.00 0.00 37.15 3.02
41 42 4.883026 CTGCACCTTCAGCAATGC 57.117 55.556 0.00 0.00 42.17 3.56
42 43 2.264124 CTGCACCTTCAGCAATGCT 58.736 52.632 0.00 0.00 42.17 3.79
52 53 2.846371 AGCAATGCTGACCTCGAAC 58.154 52.632 7.07 0.00 37.57 3.95
53 54 1.016130 AGCAATGCTGACCTCGAACG 61.016 55.000 7.07 0.00 37.57 3.95
54 55 1.014044 GCAATGCTGACCTCGAACGA 61.014 55.000 0.00 0.00 0.00 3.85
55 56 1.645034 CAATGCTGACCTCGAACGAT 58.355 50.000 0.00 0.00 0.00 3.73
56 57 1.590238 CAATGCTGACCTCGAACGATC 59.410 52.381 0.00 0.00 0.00 3.69
57 58 1.107114 ATGCTGACCTCGAACGATCT 58.893 50.000 0.00 0.00 0.00 2.75
58 59 0.452184 TGCTGACCTCGAACGATCTC 59.548 55.000 0.00 0.00 0.00 2.75
59 60 0.736053 GCTGACCTCGAACGATCTCT 59.264 55.000 0.00 0.00 0.00 3.10
60 61 1.532921 GCTGACCTCGAACGATCTCTG 60.533 57.143 0.00 1.67 0.00 3.35
61 62 0.452184 TGACCTCGAACGATCTCTGC 59.548 55.000 0.00 0.00 0.00 4.26
62 63 0.736053 GACCTCGAACGATCTCTGCT 59.264 55.000 0.00 0.00 0.00 4.24
63 64 0.453793 ACCTCGAACGATCTCTGCTG 59.546 55.000 0.00 0.00 0.00 4.41
64 65 0.869454 CCTCGAACGATCTCTGCTGC 60.869 60.000 0.00 0.00 0.00 5.25
65 66 0.100325 CTCGAACGATCTCTGCTGCT 59.900 55.000 0.00 0.00 0.00 4.24
66 67 0.099613 TCGAACGATCTCTGCTGCTC 59.900 55.000 0.00 0.00 0.00 4.26
67 68 0.869454 CGAACGATCTCTGCTGCTCC 60.869 60.000 0.00 0.00 0.00 4.70
68 69 0.174389 GAACGATCTCTGCTGCTCCA 59.826 55.000 0.00 0.00 0.00 3.86
69 70 0.175302 AACGATCTCTGCTGCTCCAG 59.825 55.000 0.00 0.00 34.12 3.86
70 71 0.682532 ACGATCTCTGCTGCTCCAGA 60.683 55.000 0.00 6.69 39.42 3.86
71 72 0.248990 CGATCTCTGCTGCTCCAGAC 60.249 60.000 0.00 0.00 36.96 3.51
72 73 0.248990 GATCTCTGCTGCTCCAGACG 60.249 60.000 0.00 0.00 36.96 4.18
73 74 0.682532 ATCTCTGCTGCTCCAGACGA 60.683 55.000 0.00 6.03 36.96 4.20
74 75 0.682532 TCTCTGCTGCTCCAGACGAT 60.683 55.000 0.00 0.00 36.96 3.73
75 76 0.248990 CTCTGCTGCTCCAGACGATC 60.249 60.000 0.00 0.00 36.96 3.69
76 77 1.227205 CTGCTGCTCCAGACGATCC 60.227 63.158 0.00 0.00 34.77 3.36
77 78 2.107953 GCTGCTCCAGACGATCCC 59.892 66.667 0.00 0.00 32.44 3.85
78 79 2.430610 GCTGCTCCAGACGATCCCT 61.431 63.158 0.00 0.00 32.44 4.20
79 80 1.739049 CTGCTCCAGACGATCCCTC 59.261 63.158 0.00 0.00 32.44 4.30
80 81 1.743321 CTGCTCCAGACGATCCCTCC 61.743 65.000 0.00 0.00 32.44 4.30
81 82 2.503382 GCTCCAGACGATCCCTCCC 61.503 68.421 0.00 0.00 0.00 4.30
82 83 2.123854 TCCAGACGATCCCTCCCG 60.124 66.667 0.00 0.00 0.00 5.14
83 84 2.123854 CCAGACGATCCCTCCCGA 60.124 66.667 0.00 0.00 0.00 5.14
84 85 1.756950 CCAGACGATCCCTCCCGAA 60.757 63.158 0.00 0.00 0.00 4.30
85 86 1.736586 CAGACGATCCCTCCCGAAG 59.263 63.158 0.00 0.00 0.00 3.79
86 87 1.038130 CAGACGATCCCTCCCGAAGT 61.038 60.000 0.00 0.00 0.00 3.01
87 88 0.549950 AGACGATCCCTCCCGAAGTA 59.450 55.000 0.00 0.00 0.00 2.24
88 89 0.953003 GACGATCCCTCCCGAAGTAG 59.047 60.000 0.00 0.00 0.00 2.57
89 90 0.549950 ACGATCCCTCCCGAAGTAGA 59.450 55.000 0.00 0.00 0.00 2.59
90 91 1.240256 CGATCCCTCCCGAAGTAGAG 58.760 60.000 0.00 0.00 0.00 2.43
109 110 3.322191 AGGGACTCCTTGTAGATCTCC 57.678 52.381 0.00 0.00 41.56 3.71
110 111 2.862597 AGGGACTCCTTGTAGATCTCCT 59.137 50.000 0.00 0.00 41.56 3.69
111 112 2.962421 GGGACTCCTTGTAGATCTCCTG 59.038 54.545 0.00 0.00 0.00 3.86
112 113 3.373220 GGGACTCCTTGTAGATCTCCTGA 60.373 52.174 0.00 0.00 0.00 3.86
113 114 4.479158 GGACTCCTTGTAGATCTCCTGAT 58.521 47.826 0.00 0.00 35.26 2.90
114 115 4.898861 GGACTCCTTGTAGATCTCCTGATT 59.101 45.833 0.00 0.00 32.19 2.57
115 116 5.010617 GGACTCCTTGTAGATCTCCTGATTC 59.989 48.000 0.00 0.00 32.19 2.52
116 117 4.898861 ACTCCTTGTAGATCTCCTGATTCC 59.101 45.833 0.00 0.00 32.19 3.01
117 118 5.147032 CTCCTTGTAGATCTCCTGATTCCT 58.853 45.833 0.00 0.00 32.19 3.36
118 119 5.144100 TCCTTGTAGATCTCCTGATTCCTC 58.856 45.833 0.00 0.00 32.19 3.71
119 120 4.022416 CCTTGTAGATCTCCTGATTCCTCG 60.022 50.000 0.00 0.00 32.19 4.63
120 121 2.887783 TGTAGATCTCCTGATTCCTCGC 59.112 50.000 0.00 0.00 32.19 5.03
121 122 1.337118 AGATCTCCTGATTCCTCGCC 58.663 55.000 0.00 0.00 32.19 5.54
122 123 1.133199 AGATCTCCTGATTCCTCGCCT 60.133 52.381 0.00 0.00 32.19 5.52
123 124 1.691434 GATCTCCTGATTCCTCGCCTT 59.309 52.381 0.00 0.00 32.19 4.35
124 125 1.573108 TCTCCTGATTCCTCGCCTTT 58.427 50.000 0.00 0.00 0.00 3.11
125 126 1.208052 TCTCCTGATTCCTCGCCTTTG 59.792 52.381 0.00 0.00 0.00 2.77
126 127 0.392998 TCCTGATTCCTCGCCTTTGC 60.393 55.000 0.00 0.00 0.00 3.68
137 138 4.368808 CCTTTGCGTCGGCGTGTG 62.369 66.667 12.58 0.00 44.10 3.82
140 141 4.649310 TTGCGTCGGCGTGTGCTA 62.649 61.111 12.58 3.78 44.10 3.49
150 151 2.046314 GTGTGCTACGGCCATGGT 60.046 61.111 14.67 0.00 37.74 3.55
151 152 2.046411 TGTGCTACGGCCATGGTG 60.046 61.111 14.67 9.14 37.74 4.17
152 153 2.824041 GTGCTACGGCCATGGTGG 60.824 66.667 14.67 8.14 41.55 4.61
180 181 2.742530 CGCCCGGGTAATTAAGCTACAA 60.743 50.000 24.63 0.00 0.00 2.41
205 206 3.417101 ACCTTTGTTAATGATGCCACGA 58.583 40.909 0.00 0.00 0.00 4.35
211 212 0.180171 TAATGATGCCACGACCCCTG 59.820 55.000 0.00 0.00 0.00 4.45
212 213 2.556840 AATGATGCCACGACCCCTGG 62.557 60.000 0.00 0.00 0.00 4.45
231 232 6.414732 CCCTGGATTACTGTTGTTAATCTCA 58.585 40.000 0.00 0.00 32.46 3.27
241 242 6.982141 ACTGTTGTTAATCTCACGTTAGTTCA 59.018 34.615 0.00 0.00 0.00 3.18
245 246 9.493206 GTTGTTAATCTCACGTTAGTTCAAAAA 57.507 29.630 0.00 0.00 0.00 1.94
327 329 2.307768 TGTTCCGGTTGTGGCAAATAA 58.692 42.857 0.00 0.00 0.00 1.40
332 334 2.232452 CCGGTTGTGGCAAATAATCCAA 59.768 45.455 0.00 0.00 33.57 3.53
333 335 3.510719 CGGTTGTGGCAAATAATCCAAG 58.489 45.455 0.00 0.00 33.57 3.61
344 346 8.703743 TGGCAAATAATCCAAGCTAATTATTGT 58.296 29.630 16.36 8.67 37.83 2.71
357 359 7.305474 AGCTAATTATTGTTGAAGAAACCACG 58.695 34.615 0.00 0.00 38.06 4.94
403 405 8.459635 TGCACTATTATAATTAAAACAACGGCA 58.540 29.630 2.68 0.00 0.00 5.69
421 423 9.657121 ACAACGGCAAAAACAATTATTTAAATG 57.343 25.926 11.05 0.00 0.00 2.32
486 489 2.024176 AGCTAATTGTGGTAGTGGCG 57.976 50.000 0.00 0.00 0.00 5.69
972 975 2.936829 TAGGCACTCGCGCTTGATCG 62.937 60.000 5.56 0.00 41.75 3.69
983 986 0.248377 GCTTGATCGTTGCCATGCTC 60.248 55.000 0.00 0.00 32.70 4.26
988 991 2.520465 ATCGTTGCCATGCTCGTCCA 62.520 55.000 0.00 0.00 0.00 4.02
1001 1004 2.679716 GTCCAGCCCTCTGCCAAT 59.320 61.111 0.00 0.00 42.71 3.16
1031 1034 3.006728 CGCCCCAGTAGTTCCCCA 61.007 66.667 0.00 0.00 0.00 4.96
1044 1047 4.101448 CCCCACGCCCCTCTTCTG 62.101 72.222 0.00 0.00 0.00 3.02
1103 1106 2.031012 CAACCTGCAGGCACTCGA 59.969 61.111 33.06 0.00 34.60 4.04
1109 1112 2.047844 GCAGGCACTCGAGCAAGA 60.048 61.111 13.61 0.00 34.60 3.02
1114 1117 1.522580 GCACTCGAGCAAGATCCCC 60.523 63.158 13.61 0.00 0.00 4.81
1121 1124 2.240162 GAGCAAGATCCCCCGACGTT 62.240 60.000 0.00 0.00 0.00 3.99
1147 1150 2.595095 CCGCTCCCCTTGCCATAA 59.405 61.111 0.00 0.00 0.00 1.90
1265 1268 1.002857 CACCTTTCCCCCTCAATCCT 58.997 55.000 0.00 0.00 0.00 3.24
1272 1275 2.669133 CCCCTCAATCCTGTCGCCA 61.669 63.158 0.00 0.00 0.00 5.69
1274 1277 0.816825 CCCTCAATCCTGTCGCCATG 60.817 60.000 0.00 0.00 0.00 3.66
1276 1279 1.407299 CCTCAATCCTGTCGCCATGAA 60.407 52.381 0.00 0.00 0.00 2.57
1277 1280 2.358957 CTCAATCCTGTCGCCATGAAA 58.641 47.619 0.00 0.00 0.00 2.69
1410 1433 1.919956 CTGTACCTCGTCGTCCGCTT 61.920 60.000 0.00 0.00 36.19 4.68
1447 1470 2.814336 GCTTGCCTACTGCTTACTTTGT 59.186 45.455 0.00 0.00 42.00 2.83
1458 1481 2.063266 CTTACTTTGTTGCTCGCCGTA 58.937 47.619 0.00 0.00 0.00 4.02
1472 1495 4.525576 CGTACGCTACCGCTCGCA 62.526 66.667 0.52 0.00 38.22 5.10
1600 1628 2.962569 CGGGTCGTTCTGCTCTCA 59.037 61.111 0.00 0.00 0.00 3.27
1614 1642 4.320456 CTCACTGCACCCACGGCT 62.320 66.667 0.00 0.00 0.00 5.52
1668 1698 0.957395 CGAAGGCTGGCTTGTGTCAT 60.957 55.000 21.96 0.00 0.00 3.06
1690 1720 0.612744 CCAAATGGGCCCGACAATTT 59.387 50.000 19.37 14.59 0.00 1.82
1763 3394 8.934507 AATCTTTGTGCTAACTAGAGTATGTC 57.065 34.615 0.00 0.00 0.00 3.06
1764 3395 6.552629 TCTTTGTGCTAACTAGAGTATGTCG 58.447 40.000 0.00 0.00 0.00 4.35
1820 3463 9.874205 AAAACAATATGATAAAACATGGGTCTG 57.126 29.630 0.00 0.00 0.00 3.51
1877 3520 4.101898 TCAACCCAGTTAGCAAGTTGACTA 59.898 41.667 7.16 5.06 41.25 2.59
1885 3528 6.425114 CAGTTAGCAAGTTGACTATTGACTGT 59.575 38.462 7.16 0.00 0.00 3.55
1889 3532 5.822519 AGCAAGTTGACTATTGACTGTTGAA 59.177 36.000 7.16 0.00 0.00 2.69
1892 3535 8.289618 GCAAGTTGACTATTGACTGTTGAATAA 58.710 33.333 7.16 0.00 0.00 1.40
1950 3593 5.958380 TCATATCTCTGGGTACACTTCTGTT 59.042 40.000 0.00 0.00 0.00 3.16
1975 3618 9.790389 TTTACCCGTAGCATTTTGTATTTAATG 57.210 29.630 0.00 0.00 35.39 1.90
2091 3734 6.882610 TTGTACATGAAAGTTGCTCAGAAT 57.117 33.333 0.00 0.00 0.00 2.40
2099 3742 5.766670 TGAAAGTTGCTCAGAATGACAAGAT 59.233 36.000 0.00 0.00 42.56 2.40
2106 3749 6.408869 TGCTCAGAATGACAAGATGAATACA 58.591 36.000 0.00 0.00 42.56 2.29
2118 3761 6.818644 ACAAGATGAATACAAATACGCAGTCT 59.181 34.615 0.00 0.00 43.93 3.24
2119 3762 6.834959 AGATGAATACAAATACGCAGTCTG 57.165 37.500 0.00 0.00 43.93 3.51
2125 3768 6.985188 ATACAAATACGCAGTCTGTTCATT 57.015 33.333 0.93 0.00 43.93 2.57
2150 3793 0.039978 CACGTCCCTAGCATAGCGAG 60.040 60.000 0.00 0.00 37.37 5.03
2164 3808 0.961857 AGCGAGCATGCAACAATCCA 60.962 50.000 21.98 0.00 37.31 3.41
2169 3813 1.180029 GCATGCAACAATCCACCTCT 58.820 50.000 14.21 0.00 0.00 3.69
2212 3856 1.426751 AACACCGGGAGTACTTTCCA 58.573 50.000 6.32 0.00 39.09 3.53
2222 3866 5.077564 GGGAGTACTTTCCAGGATGTTTTT 58.922 41.667 0.00 0.00 39.09 1.94
2227 3871 2.319025 TTCCAGGATGTTTTTCCCCC 57.681 50.000 0.00 0.00 36.35 5.40
2229 3873 1.792651 TCCAGGATGTTTTTCCCCCTT 59.207 47.619 0.00 0.00 36.35 3.95
2231 3875 2.302733 CCAGGATGTTTTTCCCCCTTTG 59.697 50.000 0.00 0.00 36.35 2.77
2233 3877 1.003118 GGATGTTTTTCCCCCTTTGCC 59.997 52.381 0.00 0.00 0.00 4.52
2234 3878 1.696884 GATGTTTTTCCCCCTTTGCCA 59.303 47.619 0.00 0.00 0.00 4.92
2235 3879 1.127343 TGTTTTTCCCCCTTTGCCAG 58.873 50.000 0.00 0.00 0.00 4.85
2236 3880 1.128200 GTTTTTCCCCCTTTGCCAGT 58.872 50.000 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 4.655647 AGGTGCAGCAGTGGCAGG 62.656 66.667 19.63 0.00 42.85 4.85
15 16 2.596631 AAGGTGCAGCAGTGGCAG 60.597 61.111 19.63 0.00 42.85 4.85
16 17 2.595463 GAAGGTGCAGCAGTGGCA 60.595 61.111 19.63 0.00 44.61 4.92
17 18 2.595463 TGAAGGTGCAGCAGTGGC 60.595 61.111 19.63 2.77 41.61 5.01
18 19 3.664495 CTGAAGGTGCAGCAGTGG 58.336 61.111 19.63 1.65 0.00 4.00
24 25 2.264124 AGCATTGCTGAAGGTGCAG 58.736 52.632 11.09 0.00 41.71 4.41
25 26 4.506039 AGCATTGCTGAAGGTGCA 57.494 50.000 11.09 0.00 37.57 4.57
34 35 1.016130 CGTTCGAGGTCAGCATTGCT 61.016 55.000 5.03 5.03 40.77 3.91
35 36 1.014044 TCGTTCGAGGTCAGCATTGC 61.014 55.000 0.00 0.00 0.00 3.56
36 37 1.590238 GATCGTTCGAGGTCAGCATTG 59.410 52.381 0.80 0.00 0.00 2.82
37 38 1.478510 AGATCGTTCGAGGTCAGCATT 59.521 47.619 0.80 0.00 0.00 3.56
38 39 1.066303 GAGATCGTTCGAGGTCAGCAT 59.934 52.381 0.80 0.00 0.00 3.79
39 40 0.452184 GAGATCGTTCGAGGTCAGCA 59.548 55.000 0.80 0.00 0.00 4.41
40 41 0.736053 AGAGATCGTTCGAGGTCAGC 59.264 55.000 0.80 0.00 0.00 4.26
41 42 1.532921 GCAGAGATCGTTCGAGGTCAG 60.533 57.143 0.80 0.00 0.00 3.51
42 43 0.452184 GCAGAGATCGTTCGAGGTCA 59.548 55.000 0.80 0.00 0.00 4.02
43 44 0.736053 AGCAGAGATCGTTCGAGGTC 59.264 55.000 0.80 0.52 0.00 3.85
44 45 0.453793 CAGCAGAGATCGTTCGAGGT 59.546 55.000 0.80 0.00 0.00 3.85
45 46 0.869454 GCAGCAGAGATCGTTCGAGG 60.869 60.000 0.80 0.00 0.00 4.63
46 47 0.100325 AGCAGCAGAGATCGTTCGAG 59.900 55.000 0.00 0.00 0.00 4.04
47 48 0.099613 GAGCAGCAGAGATCGTTCGA 59.900 55.000 0.00 0.00 0.00 3.71
48 49 0.869454 GGAGCAGCAGAGATCGTTCG 60.869 60.000 0.00 0.00 0.00 3.95
49 50 0.174389 TGGAGCAGCAGAGATCGTTC 59.826 55.000 0.00 0.00 0.00 3.95
50 51 0.175302 CTGGAGCAGCAGAGATCGTT 59.825 55.000 0.00 0.00 0.00 3.85
51 52 0.682532 TCTGGAGCAGCAGAGATCGT 60.683 55.000 0.00 0.00 0.00 3.73
52 53 0.248990 GTCTGGAGCAGCAGAGATCG 60.249 60.000 0.00 0.00 0.00 3.69
53 54 0.248990 CGTCTGGAGCAGCAGAGATC 60.249 60.000 0.00 0.00 0.00 2.75
54 55 0.682532 TCGTCTGGAGCAGCAGAGAT 60.683 55.000 0.00 0.00 0.00 2.75
55 56 0.682532 ATCGTCTGGAGCAGCAGAGA 60.683 55.000 0.00 0.00 0.00 3.10
56 57 0.248990 GATCGTCTGGAGCAGCAGAG 60.249 60.000 0.00 0.00 0.00 3.35
57 58 1.670949 GGATCGTCTGGAGCAGCAGA 61.671 60.000 0.00 0.00 30.89 4.26
58 59 1.227205 GGATCGTCTGGAGCAGCAG 60.227 63.158 0.00 0.00 30.89 4.24
59 60 2.725312 GGGATCGTCTGGAGCAGCA 61.725 63.158 0.00 0.00 30.89 4.41
60 61 2.107953 GGGATCGTCTGGAGCAGC 59.892 66.667 0.00 0.00 30.89 5.25
61 62 1.739049 GAGGGATCGTCTGGAGCAG 59.261 63.158 0.00 0.00 30.89 4.24
62 63 1.758514 GGAGGGATCGTCTGGAGCA 60.759 63.158 0.00 0.00 30.89 4.26
63 64 2.503382 GGGAGGGATCGTCTGGAGC 61.503 68.421 0.00 0.00 0.00 4.70
64 65 2.196925 CGGGAGGGATCGTCTGGAG 61.197 68.421 0.00 0.00 0.00 3.86
65 66 2.123854 CGGGAGGGATCGTCTGGA 60.124 66.667 0.00 0.00 0.00 3.86
66 67 1.739338 CTTCGGGAGGGATCGTCTGG 61.739 65.000 0.00 0.00 0.00 3.86
67 68 1.038130 ACTTCGGGAGGGATCGTCTG 61.038 60.000 0.00 0.00 0.00 3.51
68 69 0.549950 TACTTCGGGAGGGATCGTCT 59.450 55.000 0.00 0.00 0.00 4.18
69 70 0.953003 CTACTTCGGGAGGGATCGTC 59.047 60.000 0.00 0.00 0.00 4.20
70 71 0.549950 TCTACTTCGGGAGGGATCGT 59.450 55.000 0.00 0.00 0.00 3.73
71 72 1.240256 CTCTACTTCGGGAGGGATCG 58.760 60.000 0.00 0.00 0.00 3.69
72 73 1.623163 CCTCTACTTCGGGAGGGATC 58.377 60.000 0.00 0.00 43.78 3.36
73 74 3.852558 CCTCTACTTCGGGAGGGAT 57.147 57.895 0.00 0.00 43.78 3.85
78 79 3.706601 AAGGAGTCCCTCTACTTCGGGA 61.707 54.545 5.25 0.00 43.28 5.14
79 80 0.259356 AGGAGTCCCTCTACTTCGGG 59.741 60.000 5.25 0.00 38.86 5.14
80 81 1.751924 CAAGGAGTCCCTCTACTTCGG 59.248 57.143 5.25 0.00 43.28 4.30
81 82 2.448453 ACAAGGAGTCCCTCTACTTCG 58.552 52.381 5.25 0.00 43.28 3.79
82 83 4.857679 TCTACAAGGAGTCCCTCTACTTC 58.142 47.826 5.25 0.00 43.28 3.01
84 85 4.729881 AGATCTACAAGGAGTCCCTCTACT 59.270 45.833 5.25 0.00 43.48 2.57
85 86 5.056553 AGATCTACAAGGAGTCCCTCTAC 57.943 47.826 5.25 0.00 43.48 2.59
86 87 4.105057 GGAGATCTACAAGGAGTCCCTCTA 59.895 50.000 5.25 0.00 43.48 2.43
87 88 3.117284 GGAGATCTACAAGGAGTCCCTCT 60.117 52.174 5.25 0.00 43.48 3.69
88 89 3.117284 AGGAGATCTACAAGGAGTCCCTC 60.117 52.174 7.93 2.38 43.48 4.30
89 90 8.309431 AATCAGGAGATCTACAAGGAGTCCCT 62.309 46.154 7.93 0.00 37.76 4.20
90 91 2.962421 CAGGAGATCTACAAGGAGTCCC 59.038 54.545 7.93 0.00 0.00 4.46
91 92 3.904717 TCAGGAGATCTACAAGGAGTCC 58.095 50.000 7.93 0.00 0.00 3.85
92 93 5.010617 GGAATCAGGAGATCTACAAGGAGTC 59.989 48.000 7.93 9.99 31.90 3.36
93 94 4.898861 GGAATCAGGAGATCTACAAGGAGT 59.101 45.833 7.93 0.66 31.90 3.85
94 95 5.147032 AGGAATCAGGAGATCTACAAGGAG 58.853 45.833 7.93 0.00 31.90 3.69
95 96 5.144100 GAGGAATCAGGAGATCTACAAGGA 58.856 45.833 7.93 1.96 31.90 3.36
96 97 4.022416 CGAGGAATCAGGAGATCTACAAGG 60.022 50.000 7.93 0.00 31.90 3.61
97 98 4.558496 GCGAGGAATCAGGAGATCTACAAG 60.558 50.000 7.93 0.00 31.90 3.16
98 99 3.319405 GCGAGGAATCAGGAGATCTACAA 59.681 47.826 7.93 0.00 31.90 2.41
99 100 2.887783 GCGAGGAATCAGGAGATCTACA 59.112 50.000 7.93 0.00 31.90 2.74
100 101 2.230266 GGCGAGGAATCAGGAGATCTAC 59.770 54.545 0.00 0.00 31.90 2.59
101 102 2.109128 AGGCGAGGAATCAGGAGATCTA 59.891 50.000 0.00 0.00 31.90 1.98
102 103 1.133199 AGGCGAGGAATCAGGAGATCT 60.133 52.381 0.00 0.00 31.90 2.75
103 104 1.337118 AGGCGAGGAATCAGGAGATC 58.663 55.000 0.00 0.00 31.90 2.75
104 105 1.799933 AAGGCGAGGAATCAGGAGAT 58.200 50.000 0.00 0.00 35.53 2.75
105 106 1.208052 CAAAGGCGAGGAATCAGGAGA 59.792 52.381 0.00 0.00 0.00 3.71
106 107 1.661341 CAAAGGCGAGGAATCAGGAG 58.339 55.000 0.00 0.00 0.00 3.69
107 108 0.392998 GCAAAGGCGAGGAATCAGGA 60.393 55.000 0.00 0.00 0.00 3.86
108 109 2.101700 GCAAAGGCGAGGAATCAGG 58.898 57.895 0.00 0.00 0.00 3.86
120 121 4.368808 CACACGCCGACGCAAAGG 62.369 66.667 0.00 0.00 45.53 3.11
123 124 4.649310 TAGCACACGCCGACGCAA 62.649 61.111 0.00 0.00 45.53 4.85
133 134 2.046314 ACCATGGCCGTAGCACAC 60.046 61.111 13.04 0.00 42.56 3.82
134 135 2.046411 CACCATGGCCGTAGCACA 60.046 61.111 13.04 0.00 42.56 4.57
135 136 2.824041 CCACCATGGCCGTAGCAC 60.824 66.667 13.04 0.00 42.56 4.40
144 145 3.434319 GCGTCACAGCCACCATGG 61.434 66.667 11.19 11.19 41.55 3.66
152 153 3.675619 ATTACCCGGGCGTCACAGC 62.676 63.158 24.08 0.00 0.00 4.40
153 154 0.176219 TAATTACCCGGGCGTCACAG 59.824 55.000 24.08 0.00 0.00 3.66
154 155 0.612229 TTAATTACCCGGGCGTCACA 59.388 50.000 24.08 0.00 0.00 3.58
155 156 1.292992 CTTAATTACCCGGGCGTCAC 58.707 55.000 24.08 0.00 0.00 3.67
180 181 6.151985 TCGTGGCATCATTAACAAAGGTTTAT 59.848 34.615 0.00 0.00 38.45 1.40
205 206 5.253096 AGATTAACAACAGTAATCCAGGGGT 59.747 40.000 0.00 0.00 32.28 4.95
211 212 6.963049 ACGTGAGATTAACAACAGTAATCC 57.037 37.500 0.00 0.00 32.28 3.01
212 213 9.136952 ACTAACGTGAGATTAACAACAGTAATC 57.863 33.333 7.01 0.00 0.00 1.75
231 232 9.360093 TGAATTTGAATGTTTTTGAACTAACGT 57.640 25.926 0.00 0.00 0.00 3.99
308 310 3.507786 GATTATTTGCCACAACCGGAAC 58.492 45.455 9.46 0.00 0.00 3.62
327 329 9.860898 GTTTCTTCAACAATAATTAGCTTGGAT 57.139 29.630 0.00 0.00 35.18 3.41
332 334 7.305474 CGTGGTTTCTTCAACAATAATTAGCT 58.695 34.615 0.00 0.00 37.07 3.32
333 335 6.033513 GCGTGGTTTCTTCAACAATAATTAGC 59.966 38.462 0.00 0.00 37.07 3.09
344 346 2.639065 ACAGAAGCGTGGTTTCTTCAA 58.361 42.857 5.02 0.00 40.72 2.69
357 359 6.476706 AGTGCAATTGAAAACTTTACAGAAGC 59.523 34.615 10.34 0.00 0.00 3.86
454 457 4.851558 CACAATTAGCTTCGCACCTAAAAC 59.148 41.667 0.00 0.00 0.00 2.43
455 458 4.083003 CCACAATTAGCTTCGCACCTAAAA 60.083 41.667 0.00 0.00 0.00 1.52
456 459 3.438781 CCACAATTAGCTTCGCACCTAAA 59.561 43.478 0.00 0.00 0.00 1.85
457 460 3.006940 CCACAATTAGCTTCGCACCTAA 58.993 45.455 0.00 0.00 0.00 2.69
475 478 6.204108 AGCATTAATAATTACGCCACTACCAC 59.796 38.462 0.00 0.00 0.00 4.16
911 914 3.690206 TGGGGGTCGAGGGGATCA 61.690 66.667 0.00 0.00 0.00 2.92
972 975 3.181367 CTGGACGAGCATGGCAAC 58.819 61.111 0.00 0.00 0.00 4.17
983 986 3.335356 ATTGGCAGAGGGCTGGACG 62.335 63.158 0.00 0.00 42.53 4.79
1010 1013 2.590092 GAACTACTGGGGCGGCAT 59.410 61.111 12.47 0.00 0.00 4.40
1022 1025 2.686106 GAGGGGCGTGGGGAACTA 60.686 66.667 0.00 0.00 0.00 2.24
1031 1034 4.400961 GCTGCAGAAGAGGGGCGT 62.401 66.667 20.43 0.00 0.00 5.68
1091 1094 2.176314 ATCTTGCTCGAGTGCCTGCA 62.176 55.000 15.13 1.99 0.00 4.41
1096 1099 1.522580 GGGGATCTTGCTCGAGTGC 60.523 63.158 15.13 1.33 0.00 4.40
1103 1106 2.291043 AACGTCGGGGGATCTTGCT 61.291 57.895 0.00 0.00 0.00 3.91
1129 1132 2.357593 ATTATGGCAAGGGGAGCGGG 62.358 60.000 0.00 0.00 0.00 6.13
1145 1148 1.069090 GTGATGGCGAGGCGGATTA 59.931 57.895 0.00 0.00 0.00 1.75
1147 1150 4.241555 GGTGATGGCGAGGCGGAT 62.242 66.667 0.00 0.00 0.00 4.18
1191 1194 2.852075 AAGGGGTCGGTGAAGCCA 60.852 61.111 0.00 0.00 38.60 4.75
1272 1275 2.746277 GACGTGGGCGGCTTTCAT 60.746 61.111 9.56 0.00 44.12 2.57
1388 1391 2.393768 GGACGACGAGGTACAGCGA 61.394 63.158 12.65 0.00 32.97 4.93
1596 1624 4.314440 GCCGTGGGTGCAGTGAGA 62.314 66.667 0.00 0.00 0.00 3.27
1600 1628 4.320456 CTCAGCCGTGGGTGCAGT 62.320 66.667 13.14 0.00 42.66 4.40
1745 3376 5.453648 CATCCGACATACTCTAGTTAGCAC 58.546 45.833 0.00 0.00 0.00 4.40
1802 3445 5.569355 TGTCACAGACCCATGTTTTATCAT 58.431 37.500 0.00 0.00 0.00 2.45
1820 3463 2.575532 CATGTGGGGTCCATATGTCAC 58.424 52.381 13.33 0.00 44.49 3.67
1877 3520 4.323417 TGACCGCTTATTCAACAGTCAAT 58.677 39.130 0.00 0.00 30.35 2.57
1885 3528 2.432444 CCCTGTTGACCGCTTATTCAA 58.568 47.619 0.00 0.00 0.00 2.69
1889 3532 1.077716 GGCCCTGTTGACCGCTTAT 60.078 57.895 0.00 0.00 0.00 1.73
1950 3593 8.958506 ACATTAAATACAAAATGCTACGGGTAA 58.041 29.630 0.00 0.00 36.72 2.85
2091 3734 6.593770 ACTGCGTATTTGTATTCATCTTGTCA 59.406 34.615 0.00 0.00 0.00 3.58
2099 3742 5.929415 TGAACAGACTGCGTATTTGTATTCA 59.071 36.000 1.25 0.00 0.00 2.57
2106 3749 4.154195 GGTGAATGAACAGACTGCGTATTT 59.846 41.667 1.25 0.00 0.00 1.40
2118 3761 1.588674 GGACGTGTGGTGAATGAACA 58.411 50.000 0.00 0.00 0.00 3.18
2119 3762 0.872388 GGGACGTGTGGTGAATGAAC 59.128 55.000 0.00 0.00 0.00 3.18
2125 3768 0.902984 ATGCTAGGGACGTGTGGTGA 60.903 55.000 0.00 0.00 0.00 4.02
2150 3793 1.135199 CAGAGGTGGATTGTTGCATGC 60.135 52.381 11.82 11.82 0.00 4.06
2164 3808 1.606889 GGACAGACGGACCAGAGGT 60.607 63.158 0.00 0.00 39.44 3.85
2169 3813 0.682852 ATTTTCGGACAGACGGACCA 59.317 50.000 0.00 0.00 0.00 4.02
2203 3847 4.219944 GGGGAAAAACATCCTGGAAAGTAC 59.780 45.833 0.00 0.00 39.57 2.73
2212 3856 1.977854 GCAAAGGGGGAAAAACATCCT 59.022 47.619 0.00 0.00 39.57 3.24


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

AutoCloner maintained by Alex Coulton.