Multiple sequence alignment - TraesCS2A01G440200

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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 TraesCS2A01G440200 chr2A 100.000 2276 0 0 1 2276 691042698 691044973 0.000000e+00 4204
1 TraesCS2A01G440200 chr2A 97.389 881 22 1 1396 2276 375024214 375023335 0.000000e+00 1498
2 TraesCS2A01G440200 chr2A 94.819 193 9 1 1 193 393846006 393845815 1.320000e-77 300
3 TraesCS2A01G440200 chr2D 92.869 1206 82 4 191 1393 547960385 547959181 0.000000e+00 1748
4 TraesCS2A01G440200 chr2D 89.146 1124 116 5 183 1302 36746631 36747752 0.000000e+00 1395
5 TraesCS2A01G440200 chr1A 97.730 881 20 0 1396 2276 457418610 457419490 0.000000e+00 1517
6 TraesCS2A01G440200 chr1A 97.276 881 24 0 1396 2276 392034050 392033170 0.000000e+00 1495
7 TraesCS2A01G440200 chr3A 97.727 880 20 0 1394 2273 88505592 88506471 0.000000e+00 1515
8 TraesCS2A01G440200 chr3A 97.276 881 24 0 1396 2276 69921229 69920349 0.000000e+00 1495
9 TraesCS2A01G440200 chr3A 84.361 1119 171 4 189 1304 478696259 478695142 0.000000e+00 1094
10 TraesCS2A01G440200 chr3A 95.767 189 8 0 1 189 179020076 179019888 2.840000e-79 305
11 TraesCS2A01G440200 chr3A 87.097 93 10 2 1302 1393 618436770 618436679 1.110000e-18 104
12 TraesCS2A01G440200 chr6A 97.506 882 22 0 1395 2276 315460780 315459899 0.000000e+00 1507
13 TraesCS2A01G440200 chr6A 97.182 887 25 0 1390 2276 98087470 98088356 0.000000e+00 1500
14 TraesCS2A01G440200 chr6A 96.237 186 7 0 1 186 374085336 374085521 2.840000e-79 305
15 TraesCS2A01G440200 chr5A 97.389 881 23 0 1396 2276 400514684 400513804 0.000000e+00 1500
16 TraesCS2A01G440200 chr4A 97.175 885 25 0 1392 2276 467493081 467492197 0.000000e+00 1496
17 TraesCS2A01G440200 chr4A 86.095 1014 139 2 191 1203 593203509 593204521 0.000000e+00 1090
18 TraesCS2A01G440200 chr4A 96.296 189 7 0 1 189 434206200 434206012 6.100000e-81 311
19 TraesCS2A01G440200 chr4A 92.308 208 13 3 1 208 429618112 429617908 2.210000e-75 292
20 TraesCS2A01G440200 chr4A 91.905 210 13 4 1 208 485818616 485818823 7.950000e-75 291
21 TraesCS2A01G440200 chr5D 90.591 1116 101 4 189 1302 16204478 16203365 0.000000e+00 1476
22 TraesCS2A01G440200 chr3B 88.314 1121 121 9 186 1302 704440251 704441365 0.000000e+00 1336
23 TraesCS2A01G440200 chr4D 86.213 1117 148 5 189 1302 152882467 152881354 0.000000e+00 1205
24 TraesCS2A01G440200 chr1B 84.064 1117 173 5 189 1302 550645613 550646727 0.000000e+00 1072
25 TraesCS2A01G440200 chr6B 83.982 1105 175 2 189 1292 703141739 703142842 0.000000e+00 1059
26 TraesCS2A01G440200 chr4B 95.767 189 8 0 1 189 449486697 449486509 2.840000e-79 305
27 TraesCS2A01G440200 chr3D 95.767 189 8 0 1 189 596783761 596783573 2.840000e-79 305
28 TraesCS2A01G440200 chr1D 91.549 213 13 4 1 211 71547460 71547251 2.860000e-74 289


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 TraesCS2A01G440200 chr2A 691042698 691044973 2275 False 4204 4204 100.000 1 2276 1 chr2A.!!$F1 2275
1 TraesCS2A01G440200 chr2A 375023335 375024214 879 True 1498 1498 97.389 1396 2276 1 chr2A.!!$R1 880
2 TraesCS2A01G440200 chr2D 547959181 547960385 1204 True 1748 1748 92.869 191 1393 1 chr2D.!!$R1 1202
3 TraesCS2A01G440200 chr2D 36746631 36747752 1121 False 1395 1395 89.146 183 1302 1 chr2D.!!$F1 1119
4 TraesCS2A01G440200 chr1A 457418610 457419490 880 False 1517 1517 97.730 1396 2276 1 chr1A.!!$F1 880
5 TraesCS2A01G440200 chr1A 392033170 392034050 880 True 1495 1495 97.276 1396 2276 1 chr1A.!!$R1 880
6 TraesCS2A01G440200 chr3A 88505592 88506471 879 False 1515 1515 97.727 1394 2273 1 chr3A.!!$F1 879
7 TraesCS2A01G440200 chr3A 69920349 69921229 880 True 1495 1495 97.276 1396 2276 1 chr3A.!!$R1 880
8 TraesCS2A01G440200 chr3A 478695142 478696259 1117 True 1094 1094 84.361 189 1304 1 chr3A.!!$R3 1115
9 TraesCS2A01G440200 chr6A 315459899 315460780 881 True 1507 1507 97.506 1395 2276 1 chr6A.!!$R1 881
10 TraesCS2A01G440200 chr6A 98087470 98088356 886 False 1500 1500 97.182 1390 2276 1 chr6A.!!$F1 886
11 TraesCS2A01G440200 chr5A 400513804 400514684 880 True 1500 1500 97.389 1396 2276 1 chr5A.!!$R1 880
12 TraesCS2A01G440200 chr4A 467492197 467493081 884 True 1496 1496 97.175 1392 2276 1 chr4A.!!$R3 884
13 TraesCS2A01G440200 chr4A 593203509 593204521 1012 False 1090 1090 86.095 191 1203 1 chr4A.!!$F2 1012
14 TraesCS2A01G440200 chr5D 16203365 16204478 1113 True 1476 1476 90.591 189 1302 1 chr5D.!!$R1 1113
15 TraesCS2A01G440200 chr3B 704440251 704441365 1114 False 1336 1336 88.314 186 1302 1 chr3B.!!$F1 1116
16 TraesCS2A01G440200 chr4D 152881354 152882467 1113 True 1205 1205 86.213 189 1302 1 chr4D.!!$R1 1113
17 TraesCS2A01G440200 chr1B 550645613 550646727 1114 False 1072 1072 84.064 189 1302 1 chr1B.!!$F1 1113
18 TraesCS2A01G440200 chr6B 703141739 703142842 1103 False 1059 1059 83.982 189 1292 1 chr6B.!!$F1 1103

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
131 132 0.034896 TTCTGCTCCTCGTTGGGTTC 59.965 55.0 0.0 0.0 36.20 3.62 F
299 300 0.179073 CAGATTACCGGCACCTCAGG 60.179 60.0 0.0 0.0 36.01 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1225 1229 0.322816 GCCAGGAGGTTGCTGATCAA 60.323 55.0 0.00 0.0 38.14 2.57 R
1342 1349 1.025812 AGCTAGCTAACTCACGCGAT 58.974 50.0 17.69 0.0 0.00 4.58 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
24 25 7.622893 TTTACTTTTGTTACTTGTTACCCGT 57.377 32.000 0.00 0.00 0.00 5.28
25 26 7.622893 TTACTTTTGTTACTTGTTACCCGTT 57.377 32.000 0.00 0.00 0.00 4.44
26 27 8.723942 TTACTTTTGTTACTTGTTACCCGTTA 57.276 30.769 0.00 0.00 0.00 3.18
27 28 7.015226 ACTTTTGTTACTTGTTACCCGTTAC 57.985 36.000 0.00 0.00 0.00 2.50
28 29 6.597280 ACTTTTGTTACTTGTTACCCGTTACA 59.403 34.615 0.00 0.00 0.00 2.41
29 30 6.992063 TTTGTTACTTGTTACCCGTTACAA 57.008 33.333 0.13 0.13 31.07 2.41
30 31 6.992063 TTGTTACTTGTTACCCGTTACAAA 57.008 33.333 1.61 0.00 32.67 2.83
31 32 7.565323 TTGTTACTTGTTACCCGTTACAAAT 57.435 32.000 1.61 0.00 32.67 2.32
32 33 7.565323 TGTTACTTGTTACCCGTTACAAATT 57.435 32.000 1.61 0.00 32.67 1.82
33 34 8.668510 TGTTACTTGTTACCCGTTACAAATTA 57.331 30.769 1.61 0.00 32.67 1.40
34 35 9.113838 TGTTACTTGTTACCCGTTACAAATTAA 57.886 29.630 1.61 0.70 32.67 1.40
35 36 9.381027 GTTACTTGTTACCCGTTACAAATTAAC 57.619 33.333 11.32 11.32 32.67 2.01
36 37 7.806409 ACTTGTTACCCGTTACAAATTAACT 57.194 32.000 1.61 0.00 32.67 2.24
37 38 8.224389 ACTTGTTACCCGTTACAAATTAACTT 57.776 30.769 1.61 0.00 32.67 2.66
38 39 9.336171 ACTTGTTACCCGTTACAAATTAACTTA 57.664 29.630 1.61 0.00 32.67 2.24
41 42 9.499479 TGTTACCCGTTACAAATTAACTTATCA 57.501 29.630 0.00 0.00 0.00 2.15
42 43 9.759259 GTTACCCGTTACAAATTAACTTATCAC 57.241 33.333 0.00 0.00 0.00 3.06
43 44 7.982761 ACCCGTTACAAATTAACTTATCACA 57.017 32.000 0.00 0.00 0.00 3.58
44 45 8.393671 ACCCGTTACAAATTAACTTATCACAA 57.606 30.769 0.00 0.00 0.00 3.33
45 46 8.848182 ACCCGTTACAAATTAACTTATCACAAA 58.152 29.630 0.00 0.00 0.00 2.83
46 47 9.680315 CCCGTTACAAATTAACTTATCACAAAA 57.320 29.630 0.00 0.00 0.00 2.44
76 77 8.289618 TCTATTACCGATAATTTCAATGCTTGC 58.710 33.333 0.00 0.00 32.98 4.01
77 78 4.717233 ACCGATAATTTCAATGCTTGCA 57.283 36.364 0.00 0.00 0.00 4.08
78 79 5.070770 ACCGATAATTTCAATGCTTGCAA 57.929 34.783 0.00 0.00 0.00 4.08
79 80 5.477510 ACCGATAATTTCAATGCTTGCAAA 58.522 33.333 0.00 0.00 0.00 3.68
83 84 7.010738 CCGATAATTTCAATGCTTGCAAAGAAT 59.989 33.333 0.00 0.00 46.84 2.40
84 85 9.022915 CGATAATTTCAATGCTTGCAAAGAATA 57.977 29.630 0.00 5.57 42.97 1.75
86 87 6.973229 ATTTCAATGCTTGCAAAGAATACC 57.027 33.333 0.00 0.00 42.97 2.73
87 88 5.726980 TTCAATGCTTGCAAAGAATACCT 57.273 34.783 0.00 0.00 42.97 3.08
88 89 5.726980 TCAATGCTTGCAAAGAATACCTT 57.273 34.783 0.00 0.00 42.97 3.50
89 90 6.832520 TCAATGCTTGCAAAGAATACCTTA 57.167 33.333 0.00 0.00 42.97 2.69
90 91 6.620678 TCAATGCTTGCAAAGAATACCTTAC 58.379 36.000 0.00 0.00 42.97 2.34
91 92 6.434028 TCAATGCTTGCAAAGAATACCTTACT 59.566 34.615 0.00 0.00 42.97 2.24
92 93 6.529125 CAATGCTTGCAAAGAATACCTTACTG 59.471 38.462 0.00 0.00 42.97 2.74
93 94 6.434028 AATGCTTGCAAAGAATACCTTACTGA 59.566 34.615 0.00 0.00 42.97 3.41
94 95 7.039784 AATGCTTGCAAAGAATACCTTACTGAA 60.040 33.333 0.00 0.00 42.97 3.02
98 99 7.817418 TGCAAAGAATACCTTACTGAAAACT 57.183 32.000 0.00 0.00 34.00 2.66
99 100 7.648142 TGCAAAGAATACCTTACTGAAAACTG 58.352 34.615 0.00 0.00 34.00 3.16
100 101 6.582672 GCAAAGAATACCTTACTGAAAACTGC 59.417 38.462 0.00 0.00 34.00 4.40
101 102 7.522236 GCAAAGAATACCTTACTGAAAACTGCT 60.522 37.037 0.00 0.00 34.00 4.24
102 103 8.352942 CAAAGAATACCTTACTGAAAACTGCTT 58.647 33.333 0.00 0.00 34.00 3.91
103 104 9.569122 AAAGAATACCTTACTGAAAACTGCTTA 57.431 29.630 0.00 0.00 34.00 3.09
104 105 9.740710 AAGAATACCTTACTGAAAACTGCTTAT 57.259 29.630 0.00 0.00 32.24 1.73
111 112 9.788960 CCTTACTGAAAACTGCTTATAATTTCC 57.211 33.333 6.19 0.00 30.80 3.13
115 116 9.301897 ACTGAAAACTGCTTATAATTTCCTTCT 57.698 29.630 6.19 0.00 30.80 2.85
116 117 9.565213 CTGAAAACTGCTTATAATTTCCTTCTG 57.435 33.333 6.19 0.00 30.80 3.02
117 118 8.028938 TGAAAACTGCTTATAATTTCCTTCTGC 58.971 33.333 6.19 0.00 30.80 4.26
118 119 7.709149 AAACTGCTTATAATTTCCTTCTGCT 57.291 32.000 0.00 0.00 0.00 4.24
119 120 6.934048 ACTGCTTATAATTTCCTTCTGCTC 57.066 37.500 0.00 0.00 0.00 4.26
120 121 5.825151 ACTGCTTATAATTTCCTTCTGCTCC 59.175 40.000 0.00 0.00 0.00 4.70
121 122 6.006275 TGCTTATAATTTCCTTCTGCTCCT 57.994 37.500 0.00 0.00 0.00 3.69
122 123 6.058183 TGCTTATAATTTCCTTCTGCTCCTC 58.942 40.000 0.00 0.00 0.00 3.71
123 124 5.178438 GCTTATAATTTCCTTCTGCTCCTCG 59.822 44.000 0.00 0.00 0.00 4.63
124 125 4.762289 ATAATTTCCTTCTGCTCCTCGT 57.238 40.909 0.00 0.00 0.00 4.18
125 126 3.425162 AATTTCCTTCTGCTCCTCGTT 57.575 42.857 0.00 0.00 0.00 3.85
126 127 2.169832 TTTCCTTCTGCTCCTCGTTG 57.830 50.000 0.00 0.00 0.00 4.10
127 128 0.321671 TTCCTTCTGCTCCTCGTTGG 59.678 55.000 0.00 0.00 37.10 3.77
128 129 1.078848 CCTTCTGCTCCTCGTTGGG 60.079 63.158 0.00 0.00 36.20 4.12
129 130 1.674057 CTTCTGCTCCTCGTTGGGT 59.326 57.895 0.00 0.00 36.20 4.51
130 131 0.035458 CTTCTGCTCCTCGTTGGGTT 59.965 55.000 0.00 0.00 36.20 4.11
131 132 0.034896 TTCTGCTCCTCGTTGGGTTC 59.965 55.000 0.00 0.00 36.20 3.62
132 133 1.118965 TCTGCTCCTCGTTGGGTTCA 61.119 55.000 0.00 0.00 36.20 3.18
133 134 0.250295 CTGCTCCTCGTTGGGTTCAA 60.250 55.000 0.00 0.00 36.20 2.69
148 149 5.475719 TGGGTTCAACACTCTTACTTATCG 58.524 41.667 0.00 0.00 0.00 2.92
149 150 5.244402 TGGGTTCAACACTCTTACTTATCGA 59.756 40.000 0.00 0.00 0.00 3.59
150 151 6.161381 GGGTTCAACACTCTTACTTATCGAA 58.839 40.000 0.00 0.00 0.00 3.71
151 152 6.647895 GGGTTCAACACTCTTACTTATCGAAA 59.352 38.462 0.00 0.00 0.00 3.46
152 153 7.148623 GGGTTCAACACTCTTACTTATCGAAAG 60.149 40.741 0.00 0.00 0.00 2.62
153 154 7.148623 GGTTCAACACTCTTACTTATCGAAAGG 60.149 40.741 10.65 0.00 0.00 3.11
154 155 7.223260 TCAACACTCTTACTTATCGAAAGGA 57.777 36.000 10.65 1.49 0.00 3.36
155 156 7.088905 TCAACACTCTTACTTATCGAAAGGAC 58.911 38.462 10.65 0.00 0.00 3.85
156 157 6.837471 ACACTCTTACTTATCGAAAGGACT 57.163 37.500 10.65 0.00 0.00 3.85
157 158 7.934855 ACACTCTTACTTATCGAAAGGACTA 57.065 36.000 10.65 0.00 0.00 2.59
158 159 7.760437 ACACTCTTACTTATCGAAAGGACTAC 58.240 38.462 10.65 0.00 0.00 2.73
159 160 6.906143 CACTCTTACTTATCGAAAGGACTACG 59.094 42.308 10.65 0.00 0.00 3.51
160 161 6.820656 ACTCTTACTTATCGAAAGGACTACGA 59.179 38.462 10.65 0.00 40.18 3.43
161 162 7.498570 ACTCTTACTTATCGAAAGGACTACGAT 59.501 37.037 14.84 14.84 46.07 3.73
162 163 8.893219 TCTTACTTATCGAAAGGACTACGATA 57.107 34.615 13.42 13.42 44.33 2.92
163 164 8.986847 TCTTACTTATCGAAAGGACTACGATAG 58.013 37.037 15.42 13.25 45.19 2.08
164 165 8.893219 TTACTTATCGAAAGGACTACGATAGA 57.107 34.615 15.42 9.84 45.19 1.98
165 166 7.982761 ACTTATCGAAAGGACTACGATAGAT 57.017 36.000 15.42 9.33 45.19 1.98
166 167 8.031848 ACTTATCGAAAGGACTACGATAGATC 57.968 38.462 15.42 0.00 45.19 2.75
167 168 5.883503 ATCGAAAGGACTACGATAGATCC 57.116 43.478 10.82 0.00 43.32 3.36
168 169 4.070716 TCGAAAGGACTACGATAGATCCC 58.929 47.826 0.00 0.00 41.38 3.85
169 170 3.190953 CGAAAGGACTACGATAGATCCCC 59.809 52.174 0.00 0.00 41.38 4.81
170 171 4.409187 GAAAGGACTACGATAGATCCCCT 58.591 47.826 0.00 0.00 41.38 4.79
171 172 5.568392 GAAAGGACTACGATAGATCCCCTA 58.432 45.833 0.00 0.00 41.38 3.53
172 173 5.799978 AAGGACTACGATAGATCCCCTAT 57.200 43.478 0.00 0.00 40.66 2.57
173 174 6.905067 AAGGACTACGATAGATCCCCTATA 57.095 41.667 0.00 0.00 38.17 1.31
174 175 6.251255 AGGACTACGATAGATCCCCTATAC 57.749 45.833 0.00 0.00 38.17 1.47
175 176 5.971881 AGGACTACGATAGATCCCCTATACT 59.028 44.000 0.00 0.00 38.17 2.12
176 177 6.447735 AGGACTACGATAGATCCCCTATACTT 59.552 42.308 0.00 0.00 38.17 2.24
177 178 6.543100 GGACTACGATAGATCCCCTATACTTG 59.457 46.154 0.00 0.00 38.17 3.16
178 179 7.030234 ACTACGATAGATCCCCTATACTTGT 57.970 40.000 0.00 0.00 38.17 3.16
179 180 6.885376 ACTACGATAGATCCCCTATACTTGTG 59.115 42.308 0.00 0.00 38.17 3.33
180 181 5.017490 ACGATAGATCCCCTATACTTGTGG 58.983 45.833 0.00 0.00 38.17 4.17
181 182 4.402793 CGATAGATCCCCTATACTTGTGGG 59.597 50.000 0.00 0.00 38.17 4.61
182 183 3.726837 AGATCCCCTATACTTGTGGGT 57.273 47.619 0.00 0.00 39.31 4.51
183 184 3.588569 AGATCCCCTATACTTGTGGGTC 58.411 50.000 0.00 0.00 39.31 4.46
184 185 2.953093 TCCCCTATACTTGTGGGTCA 57.047 50.000 0.00 0.00 39.31 4.02
185 186 3.431411 TCCCCTATACTTGTGGGTCAT 57.569 47.619 0.00 0.00 39.31 3.06
186 187 3.743132 TCCCCTATACTTGTGGGTCATT 58.257 45.455 0.00 0.00 39.31 2.57
187 188 4.898268 TCCCCTATACTTGTGGGTCATTA 58.102 43.478 0.00 0.00 39.31 1.90
219 220 3.849911 TGAGAAGTCAGGCATTTACTCG 58.150 45.455 0.00 0.00 0.00 4.18
229 230 5.353123 TCAGGCATTTACTCGGTTAAATCAC 59.647 40.000 0.00 0.00 0.00 3.06
241 242 4.117685 GGTTAAATCACCGTATCGAGCTT 58.882 43.478 0.00 0.00 0.00 3.74
299 300 0.179073 CAGATTACCGGCACCTCAGG 60.179 60.000 0.00 0.00 36.01 3.86
313 314 2.443255 ACCTCAGGGAATCAACAACAGT 59.557 45.455 0.00 0.00 36.25 3.55
315 316 3.891366 CCTCAGGGAATCAACAACAGTTT 59.109 43.478 0.00 0.00 33.58 2.66
371 372 1.461268 TGAGGGTCTTCTGGTGGCA 60.461 57.895 0.00 0.00 0.00 4.92
455 459 5.819379 TCAGCACTTGCAAAATCTATCTAGG 59.181 40.000 0.00 0.00 45.16 3.02
472 476 1.527844 GGCATGGATGAGGACCTGC 60.528 63.158 0.00 0.00 33.87 4.85
514 518 1.503542 CATGCACGAAGGTTCTGGC 59.496 57.895 0.00 0.00 0.00 4.85
581 585 1.613925 TCAGACTTGGACGAAGGACAG 59.386 52.381 2.09 0.00 35.78 3.51
602 606 4.393062 CAGTCTATGCGATCACTGGTTTTT 59.607 41.667 0.00 0.00 33.89 1.94
631 635 4.576463 AGGAATGGTTGATCTTCATTACGC 59.424 41.667 10.55 0.00 36.96 4.42
641 645 2.236146 TCTTCATTACGCTGATGTGGGT 59.764 45.455 0.00 0.00 36.98 4.51
650 654 1.142465 GCTGATGTGGGTGATCTGGAT 59.858 52.381 0.00 0.00 0.00 3.41
707 711 4.691216 GTGGAATCCAACTTACTCTGTCAC 59.309 45.833 2.31 0.00 34.18 3.67
748 752 4.033709 CACCATCCTAGATATACCCAGGG 58.966 52.174 2.85 2.85 0.00 4.45
769 773 2.687200 AGGATGCCACGCTACCCA 60.687 61.111 0.00 0.00 0.00 4.51
778 782 0.249489 CACGCTACCCAGCTATGGTC 60.249 60.000 10.23 0.00 46.10 4.02
785 789 1.622607 CCCAGCTATGGTCGGGAACA 61.623 60.000 0.00 0.00 46.10 3.18
801 805 1.279846 GAACACCCCACGATCCCTTTA 59.720 52.381 0.00 0.00 0.00 1.85
826 830 1.079197 ATCAACACAGATGCCGCGA 60.079 52.632 8.23 0.00 0.00 5.87
850 854 3.320626 CATCTCGACGATGGTAATGCAT 58.679 45.455 13.77 0.00 44.69 3.96
865 869 3.023949 GCATGAGCGGGAGGTGTCT 62.024 63.158 0.00 0.00 43.00 3.41
922 926 1.668793 CCGGTTCCGGGTGTTACAC 60.669 63.158 21.10 6.99 44.99 2.90
1225 1229 5.456779 GGTTAGATACCACTCCTACCTTCT 58.543 45.833 0.00 0.00 46.92 2.85
1292 1297 8.157476 TGTTGAATAAAGCTCTCTAAAGTTCCT 58.843 33.333 0.00 0.00 0.00 3.36
1327 1334 6.920569 AATCGTGACTTAGAGTTTGTTTGT 57.079 33.333 0.00 0.00 0.00 2.83
1342 1349 1.201181 GTTTGTGGTCAGTTGTGTGCA 59.799 47.619 0.00 0.00 0.00 4.57
1370 1377 5.293814 CGTGAGTTAGCTAGCTACTTAGTCA 59.706 44.000 24.09 22.24 0.00 3.41
1437 1444 1.082104 CGCAACAGTTTTCGAGGGC 60.082 57.895 0.00 0.00 0.00 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 7.622893 AACGGGTAACAAGTAACAAAAGTAA 57.377 32.000 0.00 0.00 39.74 2.24
3 4 6.597280 TGTAACGGGTAACAAGTAACAAAAGT 59.403 34.615 0.00 0.00 39.74 2.66
4 5 7.014092 TGTAACGGGTAACAAGTAACAAAAG 57.986 36.000 0.00 0.00 39.74 2.27
5 6 6.992063 TGTAACGGGTAACAAGTAACAAAA 57.008 33.333 0.00 0.00 39.74 2.44
6 7 6.992063 TTGTAACGGGTAACAAGTAACAAA 57.008 33.333 0.00 0.00 39.74 2.83
7 8 6.992063 TTTGTAACGGGTAACAAGTAACAA 57.008 33.333 0.00 0.00 36.96 2.83
8 9 7.565323 AATTTGTAACGGGTAACAAGTAACA 57.435 32.000 0.00 0.00 36.96 2.41
9 10 9.381027 GTTAATTTGTAACGGGTAACAAGTAAC 57.619 33.333 0.00 0.00 36.96 2.50
10 11 9.336171 AGTTAATTTGTAACGGGTAACAAGTAA 57.664 29.630 0.00 0.00 36.96 2.24
11 12 8.900983 AGTTAATTTGTAACGGGTAACAAGTA 57.099 30.769 0.00 0.00 36.96 2.24
12 13 7.806409 AGTTAATTTGTAACGGGTAACAAGT 57.194 32.000 0.00 0.00 36.96 3.16
15 16 9.499479 TGATAAGTTAATTTGTAACGGGTAACA 57.501 29.630 0.00 0.00 39.74 2.41
16 17 9.759259 GTGATAAGTTAATTTGTAACGGGTAAC 57.241 33.333 0.00 0.00 33.00 2.50
17 18 9.499479 TGTGATAAGTTAATTTGTAACGGGTAA 57.501 29.630 0.00 0.00 33.00 2.85
18 19 9.499479 TTGTGATAAGTTAATTTGTAACGGGTA 57.501 29.630 0.00 0.00 33.00 3.69
19 20 7.982761 TGTGATAAGTTAATTTGTAACGGGT 57.017 32.000 0.00 0.00 33.00 5.28
20 21 9.680315 TTTTGTGATAAGTTAATTTGTAACGGG 57.320 29.630 0.00 0.00 33.00 5.28
62 63 7.662669 AAGGTATTCTTTGCAAGCATTGAAATT 59.337 29.630 0.00 3.20 44.63 1.82
63 64 7.163441 AAGGTATTCTTTGCAAGCATTGAAAT 58.837 30.769 0.00 6.20 44.63 2.17
64 65 6.523840 AAGGTATTCTTTGCAAGCATTGAAA 58.476 32.000 0.00 0.00 43.28 2.69
65 66 6.100404 AAGGTATTCTTTGCAAGCATTGAA 57.900 33.333 0.00 10.88 39.84 2.69
66 67 5.726980 AAGGTATTCTTTGCAAGCATTGA 57.273 34.783 0.00 0.00 39.84 2.57
67 68 6.529125 CAGTAAGGTATTCTTTGCAAGCATTG 59.471 38.462 0.00 0.00 42.07 2.82
68 69 6.434028 TCAGTAAGGTATTCTTTGCAAGCATT 59.566 34.615 0.00 0.00 36.93 3.56
69 70 5.945784 TCAGTAAGGTATTCTTTGCAAGCAT 59.054 36.000 0.00 0.00 36.93 3.79
70 71 5.312895 TCAGTAAGGTATTCTTTGCAAGCA 58.687 37.500 0.00 0.00 36.93 3.91
71 72 5.880054 TCAGTAAGGTATTCTTTGCAAGC 57.120 39.130 0.00 0.00 36.93 4.01
72 73 8.352942 AGTTTTCAGTAAGGTATTCTTTGCAAG 58.647 33.333 0.00 0.00 36.93 4.01
73 74 8.134895 CAGTTTTCAGTAAGGTATTCTTTGCAA 58.865 33.333 0.00 0.00 36.93 4.08
74 75 7.648142 CAGTTTTCAGTAAGGTATTCTTTGCA 58.352 34.615 0.00 0.00 36.93 4.08
75 76 6.582672 GCAGTTTTCAGTAAGGTATTCTTTGC 59.417 38.462 0.00 0.00 36.93 3.68
76 77 7.875971 AGCAGTTTTCAGTAAGGTATTCTTTG 58.124 34.615 0.00 0.00 36.93 2.77
77 78 8.465273 AAGCAGTTTTCAGTAAGGTATTCTTT 57.535 30.769 0.00 0.00 36.93 2.52
78 79 9.740710 ATAAGCAGTTTTCAGTAAGGTATTCTT 57.259 29.630 0.00 0.00 39.40 2.52
85 86 9.788960 GGAAATTATAAGCAGTTTTCAGTAAGG 57.211 33.333 9.54 0.00 0.00 2.69
89 90 9.301897 AGAAGGAAATTATAAGCAGTTTTCAGT 57.698 29.630 9.54 0.00 0.00 3.41
90 91 9.565213 CAGAAGGAAATTATAAGCAGTTTTCAG 57.435 33.333 9.54 0.00 0.00 3.02
91 92 8.028938 GCAGAAGGAAATTATAAGCAGTTTTCA 58.971 33.333 9.54 0.00 0.00 2.69
92 93 8.246871 AGCAGAAGGAAATTATAAGCAGTTTTC 58.753 33.333 0.00 0.00 0.00 2.29
93 94 8.127150 AGCAGAAGGAAATTATAAGCAGTTTT 57.873 30.769 0.00 0.00 0.00 2.43
94 95 7.148000 GGAGCAGAAGGAAATTATAAGCAGTTT 60.148 37.037 0.00 0.00 0.00 2.66
95 96 6.319911 GGAGCAGAAGGAAATTATAAGCAGTT 59.680 38.462 0.00 0.00 0.00 3.16
96 97 5.825151 GGAGCAGAAGGAAATTATAAGCAGT 59.175 40.000 0.00 0.00 0.00 4.40
97 98 6.060788 AGGAGCAGAAGGAAATTATAAGCAG 58.939 40.000 0.00 0.00 0.00 4.24
98 99 6.006275 AGGAGCAGAAGGAAATTATAAGCA 57.994 37.500 0.00 0.00 0.00 3.91
99 100 5.178438 CGAGGAGCAGAAGGAAATTATAAGC 59.822 44.000 0.00 0.00 0.00 3.09
100 101 6.284459 ACGAGGAGCAGAAGGAAATTATAAG 58.716 40.000 0.00 0.00 0.00 1.73
101 102 6.235231 ACGAGGAGCAGAAGGAAATTATAA 57.765 37.500 0.00 0.00 0.00 0.98
102 103 5.871396 ACGAGGAGCAGAAGGAAATTATA 57.129 39.130 0.00 0.00 0.00 0.98
103 104 4.762289 ACGAGGAGCAGAAGGAAATTAT 57.238 40.909 0.00 0.00 0.00 1.28
104 105 4.253685 CAACGAGGAGCAGAAGGAAATTA 58.746 43.478 0.00 0.00 0.00 1.40
105 106 3.077359 CAACGAGGAGCAGAAGGAAATT 58.923 45.455 0.00 0.00 0.00 1.82
106 107 2.616510 CCAACGAGGAGCAGAAGGAAAT 60.617 50.000 0.00 0.00 41.22 2.17
107 108 1.270839 CCAACGAGGAGCAGAAGGAAA 60.271 52.381 0.00 0.00 41.22 3.13
108 109 0.321671 CCAACGAGGAGCAGAAGGAA 59.678 55.000 0.00 0.00 41.22 3.36
109 110 1.544825 CCCAACGAGGAGCAGAAGGA 61.545 60.000 0.00 0.00 41.22 3.36
110 111 1.078848 CCCAACGAGGAGCAGAAGG 60.079 63.158 0.00 0.00 41.22 3.46
111 112 0.035458 AACCCAACGAGGAGCAGAAG 59.965 55.000 0.00 0.00 41.22 2.85
112 113 0.034896 GAACCCAACGAGGAGCAGAA 59.965 55.000 0.00 0.00 41.22 3.02
113 114 1.118965 TGAACCCAACGAGGAGCAGA 61.119 55.000 0.00 0.00 41.22 4.26
114 115 0.250295 TTGAACCCAACGAGGAGCAG 60.250 55.000 0.00 0.00 41.22 4.24
115 116 0.534203 GTTGAACCCAACGAGGAGCA 60.534 55.000 0.00 0.00 42.60 4.26
116 117 2.244946 GTTGAACCCAACGAGGAGC 58.755 57.895 0.00 0.00 42.60 4.70
124 125 5.929992 CGATAAGTAAGAGTGTTGAACCCAA 59.070 40.000 0.00 0.00 0.00 4.12
125 126 5.244402 TCGATAAGTAAGAGTGTTGAACCCA 59.756 40.000 0.00 0.00 0.00 4.51
126 127 5.717119 TCGATAAGTAAGAGTGTTGAACCC 58.283 41.667 0.00 0.00 0.00 4.11
127 128 7.148623 CCTTTCGATAAGTAAGAGTGTTGAACC 60.149 40.741 0.00 0.00 29.89 3.62
128 129 7.597743 TCCTTTCGATAAGTAAGAGTGTTGAAC 59.402 37.037 0.00 0.00 29.89 3.18
129 130 7.597743 GTCCTTTCGATAAGTAAGAGTGTTGAA 59.402 37.037 0.00 0.00 29.89 2.69
130 131 7.039923 AGTCCTTTCGATAAGTAAGAGTGTTGA 60.040 37.037 0.00 0.00 29.89 3.18
131 132 7.091443 AGTCCTTTCGATAAGTAAGAGTGTTG 58.909 38.462 0.00 0.00 29.89 3.33
132 133 7.229581 AGTCCTTTCGATAAGTAAGAGTGTT 57.770 36.000 0.00 0.00 29.89 3.32
133 134 6.837471 AGTCCTTTCGATAAGTAAGAGTGT 57.163 37.500 0.00 0.00 29.89 3.55
134 135 6.906143 CGTAGTCCTTTCGATAAGTAAGAGTG 59.094 42.308 0.00 0.00 29.89 3.51
135 136 6.820656 TCGTAGTCCTTTCGATAAGTAAGAGT 59.179 38.462 0.00 0.00 29.89 3.24
136 137 7.244166 TCGTAGTCCTTTCGATAAGTAAGAG 57.756 40.000 0.00 0.00 29.89 2.85
137 138 7.798596 ATCGTAGTCCTTTCGATAAGTAAGA 57.201 36.000 0.00 0.00 41.46 2.10
138 139 8.986847 TCTATCGTAGTCCTTTCGATAAGTAAG 58.013 37.037 7.65 0.00 42.90 2.34
139 140 8.893219 TCTATCGTAGTCCTTTCGATAAGTAA 57.107 34.615 7.65 0.00 42.90 2.24
140 141 9.149225 GATCTATCGTAGTCCTTTCGATAAGTA 57.851 37.037 7.65 0.00 42.90 2.24
141 142 7.119553 GGATCTATCGTAGTCCTTTCGATAAGT 59.880 40.741 7.65 1.07 42.90 2.24
142 143 7.414319 GGGATCTATCGTAGTCCTTTCGATAAG 60.414 44.444 7.65 0.00 42.90 1.73
143 144 6.373774 GGGATCTATCGTAGTCCTTTCGATAA 59.626 42.308 7.65 1.63 42.90 1.75
144 145 5.879223 GGGATCTATCGTAGTCCTTTCGATA 59.121 44.000 0.00 0.00 42.78 2.92
145 146 4.701171 GGGATCTATCGTAGTCCTTTCGAT 59.299 45.833 0.00 0.00 44.53 3.59
146 147 4.070716 GGGATCTATCGTAGTCCTTTCGA 58.929 47.826 0.00 0.00 37.96 3.71
147 148 3.190953 GGGGATCTATCGTAGTCCTTTCG 59.809 52.174 0.00 0.00 0.00 3.46
148 149 4.409187 AGGGGATCTATCGTAGTCCTTTC 58.591 47.826 0.00 0.00 0.00 2.62
149 150 4.472690 AGGGGATCTATCGTAGTCCTTT 57.527 45.455 0.00 0.00 0.00 3.11
150 151 5.799978 ATAGGGGATCTATCGTAGTCCTT 57.200 43.478 0.00 0.00 33.60 3.36
151 152 5.971881 AGTATAGGGGATCTATCGTAGTCCT 59.028 44.000 0.00 0.00 39.30 3.85
152 153 6.251255 AGTATAGGGGATCTATCGTAGTCC 57.749 45.833 0.00 0.00 39.30 3.85
153 154 7.066043 CACAAGTATAGGGGATCTATCGTAGTC 59.934 44.444 0.00 0.00 39.30 2.59
154 155 6.885376 CACAAGTATAGGGGATCTATCGTAGT 59.115 42.308 0.00 0.00 39.30 2.73
155 156 6.319152 CCACAAGTATAGGGGATCTATCGTAG 59.681 46.154 0.00 0.00 39.30 3.51
156 157 6.185511 CCACAAGTATAGGGGATCTATCGTA 58.814 44.000 0.00 0.00 39.30 3.43
157 158 5.017490 CCACAAGTATAGGGGATCTATCGT 58.983 45.833 0.00 0.00 39.30 3.73
158 159 4.402793 CCCACAAGTATAGGGGATCTATCG 59.597 50.000 0.00 0.00 43.57 2.92
159 160 5.941555 CCCACAAGTATAGGGGATCTATC 57.058 47.826 0.00 0.00 43.57 2.08
168 169 5.047847 CACGTAATGACCCACAAGTATAGG 58.952 45.833 0.00 0.00 0.00 2.57
169 170 5.047847 CCACGTAATGACCCACAAGTATAG 58.952 45.833 0.00 0.00 0.00 1.31
170 171 4.141892 CCCACGTAATGACCCACAAGTATA 60.142 45.833 0.00 0.00 0.00 1.47
171 172 3.370103 CCCACGTAATGACCCACAAGTAT 60.370 47.826 0.00 0.00 0.00 2.12
172 173 2.027929 CCCACGTAATGACCCACAAGTA 60.028 50.000 0.00 0.00 0.00 2.24
173 174 1.271163 CCCACGTAATGACCCACAAGT 60.271 52.381 0.00 0.00 0.00 3.16
174 175 1.448985 CCCACGTAATGACCCACAAG 58.551 55.000 0.00 0.00 0.00 3.16
175 176 0.606944 GCCCACGTAATGACCCACAA 60.607 55.000 0.00 0.00 0.00 3.33
176 177 1.003112 GCCCACGTAATGACCCACA 60.003 57.895 0.00 0.00 0.00 4.17
177 178 1.003112 TGCCCACGTAATGACCCAC 60.003 57.895 0.00 0.00 0.00 4.61
178 179 1.003112 GTGCCCACGTAATGACCCA 60.003 57.895 0.00 0.00 0.00 4.51
179 180 0.393808 ATGTGCCCACGTAATGACCC 60.394 55.000 0.00 0.00 0.00 4.46
180 181 0.732571 CATGTGCCCACGTAATGACC 59.267 55.000 0.00 0.00 0.00 4.02
181 182 1.665679 CTCATGTGCCCACGTAATGAC 59.334 52.381 0.00 0.00 0.00 3.06
182 183 1.552792 TCTCATGTGCCCACGTAATGA 59.447 47.619 0.00 0.00 0.00 2.57
183 184 2.022764 TCTCATGTGCCCACGTAATG 57.977 50.000 0.00 0.00 0.00 1.90
184 185 2.027192 ACTTCTCATGTGCCCACGTAAT 60.027 45.455 0.00 0.00 0.00 1.89
185 186 1.346395 ACTTCTCATGTGCCCACGTAA 59.654 47.619 0.00 0.00 0.00 3.18
186 187 0.973632 ACTTCTCATGTGCCCACGTA 59.026 50.000 0.00 0.00 0.00 3.57
187 188 0.320771 GACTTCTCATGTGCCCACGT 60.321 55.000 0.00 0.00 0.00 4.49
219 220 3.714391 AGCTCGATACGGTGATTTAACC 58.286 45.455 0.00 0.00 36.82 2.85
229 230 2.561733 TTCACTGAAGCTCGATACGG 57.438 50.000 0.00 0.00 0.00 4.02
241 242 2.226437 GGCGCTCTTTTTGATTCACTGA 59.774 45.455 7.64 0.00 0.00 3.41
299 300 5.050159 GCATTCCAAAACTGTTGTTGATTCC 60.050 40.000 13.38 0.00 36.39 3.01
313 314 3.579586 AGCTTCCAGATTGCATTCCAAAA 59.420 39.130 5.00 0.00 36.92 2.44
315 316 2.756760 GAGCTTCCAGATTGCATTCCAA 59.243 45.455 5.00 0.00 37.94 3.53
455 459 0.394762 TTGCAGGTCCTCATCCATGC 60.395 55.000 0.00 0.00 33.27 4.06
514 518 4.825422 TGAAATAGCAGTCTTGTCTCCTG 58.175 43.478 0.00 0.00 0.00 3.86
581 585 4.946784 AAAAACCAGTGATCGCATAGAC 57.053 40.909 9.33 0.00 0.00 2.59
631 635 2.172082 ACATCCAGATCACCCACATCAG 59.828 50.000 0.00 0.00 0.00 2.90
641 645 2.159240 CGGTTTCGAGACATCCAGATCA 60.159 50.000 8.50 0.00 39.00 2.92
650 654 1.664016 GCGTTAGTCGGTTTCGAGACA 60.664 52.381 8.50 0.00 46.91 3.41
707 711 1.676529 TGAGGTCTTCTCTAATCCGCG 59.323 52.381 0.00 0.00 42.86 6.46
748 752 1.884926 GTAGCGTGGCATCCTGCTC 60.885 63.158 9.27 0.76 44.28 4.26
769 773 1.623542 GGGTGTTCCCGACCATAGCT 61.624 60.000 0.00 0.00 44.74 3.32
785 789 2.201830 TGATTAAAGGGATCGTGGGGT 58.798 47.619 0.00 0.00 0.00 4.95
790 794 6.316390 GTGTTGATCTTGATTAAAGGGATCGT 59.684 38.462 0.00 0.00 36.54 3.73
791 795 6.316140 TGTGTTGATCTTGATTAAAGGGATCG 59.684 38.462 0.00 0.00 36.54 3.69
792 796 7.554118 TCTGTGTTGATCTTGATTAAAGGGATC 59.446 37.037 0.00 0.00 36.46 3.36
794 798 6.778821 TCTGTGTTGATCTTGATTAAAGGGA 58.221 36.000 0.00 0.00 36.46 4.20
801 805 3.376234 CGGCATCTGTGTTGATCTTGATT 59.624 43.478 0.00 0.00 0.00 2.57
843 847 0.179048 CACCTCCCGCTCATGCATTA 60.179 55.000 0.00 0.00 39.64 1.90
865 869 0.911769 AAGCCTGATGATGAACGGGA 59.088 50.000 0.00 0.00 34.76 5.14
873 877 1.684248 GCACCCTTGAAGCCTGATGAT 60.684 52.381 0.00 0.00 0.00 2.45
941 945 2.035632 CTCCTTCCTTCAGCGGTAGAT 58.964 52.381 0.00 0.00 0.00 1.98
946 950 0.610687 AGAACTCCTTCCTTCAGCGG 59.389 55.000 0.00 0.00 0.00 5.52
1171 1175 3.185594 GTCACGTTAAGCATACAAGCACA 59.814 43.478 0.00 0.00 36.85 4.57
1220 1224 2.026449 AGGAGGTTGCTGATCAAGAAGG 60.026 50.000 0.00 0.00 34.91 3.46
1225 1229 0.322816 GCCAGGAGGTTGCTGATCAA 60.323 55.000 0.00 0.00 38.14 2.57
1315 1321 4.079253 ACAACTGACCACAAACAAACTCT 58.921 39.130 0.00 0.00 0.00 3.24
1327 1334 1.506309 GCGATGCACACAACTGACCA 61.506 55.000 0.00 0.00 0.00 4.02
1342 1349 1.025812 AGCTAGCTAACTCACGCGAT 58.974 50.000 17.69 0.00 0.00 4.58
1370 1377 2.674033 ACACATGCATGCACGCCT 60.674 55.556 25.37 3.57 0.00 5.52
1464 1471 3.842925 TTGGCTCCCCTTGTGTCGC 62.843 63.158 0.00 0.00 0.00 5.19
1580 1587 6.074698 ACCTTTTGCTACCATTACCACTAT 57.925 37.500 0.00 0.00 0.00 2.12
1814 1821 4.365899 AAGCACGTATGACTATGTTCGA 57.634 40.909 0.00 0.00 0.00 3.71


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

AutoCloner maintained by Alex Coulton.