Multiple sequence alignment - TraesCS2B01G301500

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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 TraesCS2B01G301500 chr2B 100.000 3646 0 0 1 3646 424379396 424383041 0.000000e+00 6734.0
1 TraesCS2B01G301500 chr2B 97.527 3437 58 8 226 3646 477604215 477600790 0.000000e+00 5851.0
2 TraesCS2B01G301500 chr3A 96.042 3436 114 5 231 3646 733321652 733325085 0.000000e+00 5572.0
3 TraesCS2B01G301500 chr3A 95.553 3418 105 10 249 3645 535169841 535166450 0.000000e+00 5426.0
4 TraesCS2B01G301500 chr2D 95.452 3430 126 9 231 3646 629447994 629444581 0.000000e+00 5443.0
5 TraesCS2B01G301500 chr2D 87.013 462 49 7 672 1122 118223544 118224005 9.030000e-141 510.0
6 TraesCS2B01G301500 chrUn 94.576 3429 140 11 233 3646 178180857 178184254 0.000000e+00 5260.0
7 TraesCS2B01G301500 chrUn 94.758 248 12 1 1 248 153364533 153364779 5.710000e-103 385.0
8 TraesCS2B01G301500 chrUn 94.758 248 12 1 1 248 270238885 270238639 5.710000e-103 385.0
9 TraesCS2B01G301500 chr5D 91.470 1782 127 8 930 2689 456631233 456633011 0.000000e+00 2425.0
10 TraesCS2B01G301500 chr5D 85.351 1611 166 35 1124 2695 250404888 250403309 0.000000e+00 1604.0
11 TraesCS2B01G301500 chr5D 88.821 823 84 7 2715 3532 456633692 456634511 0.000000e+00 1003.0
12 TraesCS2B01G301500 chr5D 92.359 301 21 1 634 932 456630615 456630915 9.360000e-116 427.0
13 TraesCS2B01G301500 chr7A 93.850 1561 73 6 233 1778 713723216 713724768 0.000000e+00 2329.0
14 TraesCS2B01G301500 chr7A 94.600 500 22 3 3150 3646 713730155 713730652 0.000000e+00 769.0
15 TraesCS2B01G301500 chr7A 83.820 445 59 11 2516 2954 713729703 713730140 9.420000e-111 411.0
16 TraesCS2B01G301500 chr5B 84.801 1612 173 34 1124 2695 588572490 588570911 0.000000e+00 1554.0
17 TraesCS2B01G301500 chr5B 91.724 1015 63 7 1004 1998 558449529 558450542 0.000000e+00 1389.0
18 TraesCS2B01G301500 chr5B 89.282 933 80 11 2716 3642 558554925 558555843 0.000000e+00 1151.0
19 TraesCS2B01G301500 chr5B 89.373 781 75 7 2774 3549 558546974 558547751 0.000000e+00 976.0
20 TraesCS2B01G301500 chr5B 90.656 717 47 10 962 1659 558448807 558449522 0.000000e+00 935.0
21 TraesCS2B01G301500 chr5B 87.055 703 75 5 1993 2695 558452115 558452801 0.000000e+00 780.0
22 TraesCS2B01G301500 chr7D 91.203 1114 86 7 1317 2424 90192097 90190990 0.000000e+00 1504.0
23 TraesCS2B01G301500 chr7D 90.738 691 51 7 634 1321 90239801 90239121 0.000000e+00 909.0
24 TraesCS2B01G301500 chr7D 89.060 713 67 9 2715 3424 90183427 90182723 0.000000e+00 874.0
25 TraesCS2B01G301500 chr7D 85.646 418 43 12 226 641 90240227 90239825 1.210000e-114 424.0
26 TraesCS2B01G301500 chr3D 85.394 938 94 26 1779 2695 179161823 179160908 0.000000e+00 933.0
27 TraesCS2B01G301500 chr3B 96.983 232 6 1 1 232 351510291 351510521 4.410000e-104 388.0
28 TraesCS2B01G301500 chr3B 94.758 248 12 1 1 248 343763342 343763588 5.710000e-103 385.0
29 TraesCS2B01G301500 chr1B 96.983 232 5 2 1 232 389686497 389686726 4.410000e-104 388.0
30 TraesCS2B01G301500 chr1B 96.581 234 7 1 2 235 69492582 69492350 1.590000e-103 387.0
31 TraesCS2B01G301500 chr7B 95.473 243 10 1 1 243 226947408 226947649 1.590000e-103 387.0
32 TraesCS2B01G301500 chr7B 96.186 236 7 2 1 235 514007585 514007351 5.710000e-103 385.0
33 TraesCS2B01G301500 chr6B 96.121 232 7 1 1 232 369733064 369733293 9.560000e-101 377.0
34 TraesCS2B01G301500 chr6B 91.667 60 3 2 223 282 182035321 182035378 8.390000e-12 82.4
35 TraesCS2B01G301500 chr2A 93.220 59 2 2 223 281 88319290 88319234 6.490000e-13 86.1


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 TraesCS2B01G301500 chr2B 424379396 424383041 3645 False 6734.000000 6734 100.000000 1 3646 1 chr2B.!!$F1 3645
1 TraesCS2B01G301500 chr2B 477600790 477604215 3425 True 5851.000000 5851 97.527000 226 3646 1 chr2B.!!$R1 3420
2 TraesCS2B01G301500 chr3A 733321652 733325085 3433 False 5572.000000 5572 96.042000 231 3646 1 chr3A.!!$F1 3415
3 TraesCS2B01G301500 chr3A 535166450 535169841 3391 True 5426.000000 5426 95.553000 249 3645 1 chr3A.!!$R1 3396
4 TraesCS2B01G301500 chr2D 629444581 629447994 3413 True 5443.000000 5443 95.452000 231 3646 1 chr2D.!!$R1 3415
5 TraesCS2B01G301500 chrUn 178180857 178184254 3397 False 5260.000000 5260 94.576000 233 3646 1 chrUn.!!$F2 3413
6 TraesCS2B01G301500 chr5D 250403309 250404888 1579 True 1604.000000 1604 85.351000 1124 2695 1 chr5D.!!$R1 1571
7 TraesCS2B01G301500 chr5D 456630615 456634511 3896 False 1285.000000 2425 90.883333 634 3532 3 chr5D.!!$F1 2898
8 TraesCS2B01G301500 chr7A 713723216 713724768 1552 False 2329.000000 2329 93.850000 233 1778 1 chr7A.!!$F1 1545
9 TraesCS2B01G301500 chr7A 713729703 713730652 949 False 590.000000 769 89.210000 2516 3646 2 chr7A.!!$F2 1130
10 TraesCS2B01G301500 chr5B 588570911 588572490 1579 True 1554.000000 1554 84.801000 1124 2695 1 chr5B.!!$R1 1571
11 TraesCS2B01G301500 chr5B 558554925 558555843 918 False 1151.000000 1151 89.282000 2716 3642 1 chr5B.!!$F2 926
12 TraesCS2B01G301500 chr5B 558448807 558452801 3994 False 1034.666667 1389 89.811667 962 2695 3 chr5B.!!$F3 1733
13 TraesCS2B01G301500 chr5B 558546974 558547751 777 False 976.000000 976 89.373000 2774 3549 1 chr5B.!!$F1 775
14 TraesCS2B01G301500 chr7D 90190990 90192097 1107 True 1504.000000 1504 91.203000 1317 2424 1 chr7D.!!$R2 1107
15 TraesCS2B01G301500 chr7D 90182723 90183427 704 True 874.000000 874 89.060000 2715 3424 1 chr7D.!!$R1 709
16 TraesCS2B01G301500 chr7D 90239121 90240227 1106 True 666.500000 909 88.192000 226 1321 2 chr7D.!!$R3 1095
17 TraesCS2B01G301500 chr3D 179160908 179161823 915 True 933.000000 933 85.394000 1779 2695 1 chr3D.!!$R1 916

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
201 202 0.039074 CCTCCCAACTAGCGCTATCG 60.039 60.000 19.19 10.0 39.07 2.92 F
609 630 0.243907 CTCCACAAGTCATCGTCGGT 59.756 55.000 0.00 0.0 0.00 4.69 F
685 737 1.982395 TGGAAGATCCACCGTCGCT 60.982 57.895 0.00 0.0 42.67 4.93 F
2577 5290 0.892755 CTGACCACGCTAACCAGGTA 59.107 55.000 0.00 0.0 33.77 3.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2133 4816 1.202222 CGAGCATGAAGGAATGTTGGC 60.202 52.381 0.00 0.00 0.0 4.52 R
2262 4945 1.202687 TGAAGCTGAAGACCACACCTG 60.203 52.381 0.00 0.00 0.0 4.00 R
2617 5330 4.696877 CACTAGTTCCATGAATGAACAGCA 59.303 41.667 13.57 1.28 0.0 4.41 R
3562 6950 5.044476 TGCCCTAGTTCCATCATTTTTCCTA 60.044 40.000 0.00 0.00 0.0 2.94 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 4.996113 CGTGCGTGCAAAGTTTCT 57.004 50.000 0.00 0.00 0.00 2.52
18 19 2.483793 CGTGCGTGCAAAGTTTCTG 58.516 52.632 0.00 0.00 0.00 3.02
19 20 0.248054 CGTGCGTGCAAAGTTTCTGT 60.248 50.000 0.00 0.00 0.00 3.41
20 21 1.793714 CGTGCGTGCAAAGTTTCTGTT 60.794 47.619 0.00 0.00 0.00 3.16
21 22 2.258755 GTGCGTGCAAAGTTTCTGTTT 58.741 42.857 0.00 0.00 0.00 2.83
22 23 2.666022 GTGCGTGCAAAGTTTCTGTTTT 59.334 40.909 0.00 0.00 0.00 2.43
23 24 3.122780 GTGCGTGCAAAGTTTCTGTTTTT 59.877 39.130 0.00 0.00 0.00 1.94
24 25 3.366422 TGCGTGCAAAGTTTCTGTTTTTC 59.634 39.130 0.00 0.00 0.00 2.29
25 26 3.366422 GCGTGCAAAGTTTCTGTTTTTCA 59.634 39.130 0.00 0.00 0.00 2.69
26 27 4.490799 GCGTGCAAAGTTTCTGTTTTTCAG 60.491 41.667 0.00 0.00 44.85 3.02
27 28 4.490799 CGTGCAAAGTTTCTGTTTTTCAGC 60.491 41.667 0.00 0.00 43.32 4.26
28 29 4.388469 GTGCAAAGTTTCTGTTTTTCAGCA 59.612 37.500 0.00 0.00 43.32 4.41
29 30 4.626604 TGCAAAGTTTCTGTTTTTCAGCAG 59.373 37.500 0.00 0.00 43.32 4.24
30 31 4.864247 GCAAAGTTTCTGTTTTTCAGCAGA 59.136 37.500 0.00 0.00 43.32 4.26
31 32 5.348451 GCAAAGTTTCTGTTTTTCAGCAGAA 59.652 36.000 3.24 3.24 46.23 3.02
32 33 6.036408 GCAAAGTTTCTGTTTTTCAGCAGAAT 59.964 34.615 7.65 0.00 46.82 2.40
33 34 7.615790 CAAAGTTTCTGTTTTTCAGCAGAATC 58.384 34.615 7.65 7.33 46.82 2.52
34 35 6.455360 AGTTTCTGTTTTTCAGCAGAATCA 57.545 33.333 14.02 0.00 46.82 2.57
35 36 6.866480 AGTTTCTGTTTTTCAGCAGAATCAA 58.134 32.000 14.02 0.00 46.82 2.57
36 37 7.322664 AGTTTCTGTTTTTCAGCAGAATCAAA 58.677 30.769 14.02 0.00 46.82 2.69
37 38 7.983484 AGTTTCTGTTTTTCAGCAGAATCAAAT 59.017 29.630 14.02 0.00 46.82 2.32
38 39 7.935338 TTCTGTTTTTCAGCAGAATCAAATC 57.065 32.000 3.24 0.00 44.01 2.17
39 40 7.041635 TCTGTTTTTCAGCAGAATCAAATCA 57.958 32.000 0.00 0.00 43.32 2.57
40 41 7.490840 TCTGTTTTTCAGCAGAATCAAATCAA 58.509 30.769 0.00 0.00 43.32 2.57
41 42 7.436080 TCTGTTTTTCAGCAGAATCAAATCAAC 59.564 33.333 0.00 0.00 43.32 3.18
42 43 7.267128 TGTTTTTCAGCAGAATCAAATCAACT 58.733 30.769 0.00 0.00 32.89 3.16
43 44 8.412456 TGTTTTTCAGCAGAATCAAATCAACTA 58.588 29.630 0.00 0.00 32.89 2.24
44 45 9.415544 GTTTTTCAGCAGAATCAAATCAACTAT 57.584 29.630 0.00 0.00 32.89 2.12
45 46 9.630098 TTTTTCAGCAGAATCAAATCAACTATC 57.370 29.630 0.00 0.00 32.89 2.08
46 47 7.926674 TTCAGCAGAATCAAATCAACTATCA 57.073 32.000 0.00 0.00 0.00 2.15
47 48 8.515695 TTCAGCAGAATCAAATCAACTATCAT 57.484 30.769 0.00 0.00 0.00 2.45
48 49 8.151141 TCAGCAGAATCAAATCAACTATCATC 57.849 34.615 0.00 0.00 0.00 2.92
49 50 7.771826 TCAGCAGAATCAAATCAACTATCATCA 59.228 33.333 0.00 0.00 0.00 3.07
50 51 8.568794 CAGCAGAATCAAATCAACTATCATCAT 58.431 33.333 0.00 0.00 0.00 2.45
51 52 9.788889 AGCAGAATCAAATCAACTATCATCATA 57.211 29.630 0.00 0.00 0.00 2.15
76 77 6.497606 AGGTTATCCTATAGGTTCTACTTGGC 59.502 42.308 18.51 1.35 43.12 4.52
77 78 6.269307 GGTTATCCTATAGGTTCTACTTGGCA 59.731 42.308 18.51 0.00 36.34 4.92
78 79 5.810080 ATCCTATAGGTTCTACTTGGCAC 57.190 43.478 18.51 0.00 36.34 5.01
79 80 4.616553 TCCTATAGGTTCTACTTGGCACA 58.383 43.478 18.51 0.00 36.34 4.57
80 81 5.027460 TCCTATAGGTTCTACTTGGCACAA 58.973 41.667 18.51 0.00 39.30 3.33
81 82 5.486063 TCCTATAGGTTCTACTTGGCACAAA 59.514 40.000 18.51 0.00 39.30 2.83
82 83 6.575649 TCCTATAGGTTCTACTTGGCACAAAC 60.576 42.308 18.51 0.00 39.30 2.93
83 84 8.892569 TCCTATAGGTTCTACTTGGCACAAACA 61.893 40.741 18.51 0.00 39.30 2.83
116 117 9.466497 AAAAGATAAAAGCACATCTATCCAGAA 57.534 29.630 0.00 0.00 33.50 3.02
117 118 8.674263 AAGATAAAAGCACATCTATCCAGAAG 57.326 34.615 0.00 0.00 33.50 2.85
118 119 7.222872 AGATAAAAGCACATCTATCCAGAAGG 58.777 38.462 0.00 0.00 33.50 3.46
119 120 4.851639 AAAGCACATCTATCCAGAAGGT 57.148 40.909 0.00 0.00 33.50 3.50
120 121 5.957771 AAAGCACATCTATCCAGAAGGTA 57.042 39.130 0.00 0.00 33.50 3.08
121 122 5.543507 AAGCACATCTATCCAGAAGGTAG 57.456 43.478 0.00 0.00 33.50 3.18
122 123 4.809193 AGCACATCTATCCAGAAGGTAGA 58.191 43.478 0.00 0.00 33.50 2.59
123 124 5.401750 AGCACATCTATCCAGAAGGTAGAT 58.598 41.667 0.00 0.00 38.06 1.98
124 125 5.245751 AGCACATCTATCCAGAAGGTAGATG 59.754 44.000 17.42 17.42 46.96 2.90
125 126 5.477510 CACATCTATCCAGAAGGTAGATGC 58.522 45.833 18.47 0.00 46.39 3.91
126 127 5.011431 CACATCTATCCAGAAGGTAGATGCA 59.989 44.000 18.47 0.00 46.39 3.96
127 128 5.604231 ACATCTATCCAGAAGGTAGATGCAA 59.396 40.000 18.47 0.00 46.39 4.08
128 129 5.798125 TCTATCCAGAAGGTAGATGCAAG 57.202 43.478 0.00 0.00 35.89 4.01
129 130 5.458595 TCTATCCAGAAGGTAGATGCAAGA 58.541 41.667 0.00 0.00 35.89 3.02
130 131 6.080682 TCTATCCAGAAGGTAGATGCAAGAT 58.919 40.000 0.00 0.00 35.89 2.40
131 132 5.643421 ATCCAGAAGGTAGATGCAAGATT 57.357 39.130 0.00 0.00 35.89 2.40
132 133 5.441718 TCCAGAAGGTAGATGCAAGATTT 57.558 39.130 0.00 0.00 35.89 2.17
133 134 6.560003 TCCAGAAGGTAGATGCAAGATTTA 57.440 37.500 0.00 0.00 35.89 1.40
134 135 7.141758 TCCAGAAGGTAGATGCAAGATTTAT 57.858 36.000 0.00 0.00 35.89 1.40
135 136 7.577303 TCCAGAAGGTAGATGCAAGATTTATT 58.423 34.615 0.00 0.00 35.89 1.40
136 137 8.713971 TCCAGAAGGTAGATGCAAGATTTATTA 58.286 33.333 0.00 0.00 35.89 0.98
137 138 8.778358 CCAGAAGGTAGATGCAAGATTTATTAC 58.222 37.037 0.00 0.00 0.00 1.89
138 139 9.553064 CAGAAGGTAGATGCAAGATTTATTACT 57.447 33.333 0.00 0.00 0.00 2.24
146 147 9.905713 AGATGCAAGATTTATTACTAAACAGGA 57.094 29.630 0.00 0.00 29.85 3.86
148 149 7.985476 TGCAAGATTTATTACTAAACAGGAGC 58.015 34.615 0.00 0.00 29.85 4.70
149 150 7.609918 TGCAAGATTTATTACTAAACAGGAGCA 59.390 33.333 0.00 0.00 29.85 4.26
150 151 8.458843 GCAAGATTTATTACTAAACAGGAGCAA 58.541 33.333 0.00 0.00 29.85 3.91
159 160 9.660180 ATTACTAAACAGGAGCAAAAACAAAAA 57.340 25.926 0.00 0.00 0.00 1.94
160 161 7.595311 ACTAAACAGGAGCAAAAACAAAAAG 57.405 32.000 0.00 0.00 0.00 2.27
161 162 4.944962 AACAGGAGCAAAAACAAAAAGC 57.055 36.364 0.00 0.00 0.00 3.51
162 163 3.936564 ACAGGAGCAAAAACAAAAAGCA 58.063 36.364 0.00 0.00 0.00 3.91
163 164 4.516323 ACAGGAGCAAAAACAAAAAGCAT 58.484 34.783 0.00 0.00 0.00 3.79
164 165 5.669477 ACAGGAGCAAAAACAAAAAGCATA 58.331 33.333 0.00 0.00 0.00 3.14
165 166 6.112058 ACAGGAGCAAAAACAAAAAGCATAA 58.888 32.000 0.00 0.00 0.00 1.90
166 167 6.597280 ACAGGAGCAAAAACAAAAAGCATAAA 59.403 30.769 0.00 0.00 0.00 1.40
167 168 7.282901 ACAGGAGCAAAAACAAAAAGCATAAAT 59.717 29.630 0.00 0.00 0.00 1.40
168 169 8.772705 CAGGAGCAAAAACAAAAAGCATAAATA 58.227 29.630 0.00 0.00 0.00 1.40
169 170 9.336171 AGGAGCAAAAACAAAAAGCATAAATAA 57.664 25.926 0.00 0.00 0.00 1.40
170 171 9.943163 GGAGCAAAAACAAAAAGCATAAATAAA 57.057 25.926 0.00 0.00 0.00 1.40
196 197 2.046314 TTGCCTCCCAACTAGCGC 60.046 61.111 0.00 0.00 0.00 5.92
197 198 2.592993 TTGCCTCCCAACTAGCGCT 61.593 57.895 17.26 17.26 0.00 5.92
198 199 1.261938 TTGCCTCCCAACTAGCGCTA 61.262 55.000 17.75 17.75 0.00 4.26
199 200 1.048724 TGCCTCCCAACTAGCGCTAT 61.049 55.000 19.19 0.04 0.00 2.97
200 201 0.319986 GCCTCCCAACTAGCGCTATC 60.320 60.000 19.19 0.00 0.00 2.08
201 202 0.039074 CCTCCCAACTAGCGCTATCG 60.039 60.000 19.19 10.00 39.07 2.92
202 203 0.669077 CTCCCAACTAGCGCTATCGT 59.331 55.000 19.19 10.73 38.14 3.73
203 204 1.067212 CTCCCAACTAGCGCTATCGTT 59.933 52.381 19.19 16.39 38.14 3.85
204 205 1.479323 TCCCAACTAGCGCTATCGTTT 59.521 47.619 19.19 6.26 38.14 3.60
205 206 2.689471 TCCCAACTAGCGCTATCGTTTA 59.311 45.455 19.19 4.99 38.14 2.01
206 207 3.130869 TCCCAACTAGCGCTATCGTTTAA 59.869 43.478 19.19 4.68 38.14 1.52
207 208 3.244579 CCCAACTAGCGCTATCGTTTAAC 59.755 47.826 19.19 0.00 38.14 2.01
208 209 3.061403 CCAACTAGCGCTATCGTTTAACG 60.061 47.826 19.19 11.60 44.19 3.18
210 211 4.866301 GCGCTATCGTTTAACGCC 57.134 55.556 13.06 0.51 43.58 5.68
211 212 1.274770 GCGCTATCGTTTAACGCCC 59.725 57.895 13.06 0.17 43.58 6.13
212 213 1.929376 CGCTATCGTTTAACGCCCC 59.071 57.895 13.06 0.51 42.21 5.80
213 214 0.529119 CGCTATCGTTTAACGCCCCT 60.529 55.000 13.06 0.31 42.21 4.79
214 215 1.269206 CGCTATCGTTTAACGCCCCTA 60.269 52.381 13.06 0.00 42.21 3.53
215 216 2.401351 GCTATCGTTTAACGCCCCTAG 58.599 52.381 13.06 11.03 42.21 3.02
216 217 2.401351 CTATCGTTTAACGCCCCTAGC 58.599 52.381 13.06 0.00 42.21 3.42
217 218 0.828677 ATCGTTTAACGCCCCTAGCT 59.171 50.000 13.06 0.00 42.21 3.32
218 219 1.473258 TCGTTTAACGCCCCTAGCTA 58.527 50.000 13.06 0.00 42.21 3.32
219 220 1.406539 TCGTTTAACGCCCCTAGCTAG 59.593 52.381 14.20 14.20 42.21 3.42
220 221 1.537562 CGTTTAACGCCCCTAGCTAGG 60.538 57.143 30.05 30.05 40.39 3.02
221 222 0.466963 TTTAACGCCCCTAGCTAGGC 59.533 55.000 31.33 21.92 46.17 3.93
429 448 2.539081 GCACCCAACTCCTCCCCTT 61.539 63.158 0.00 0.00 0.00 3.95
433 452 0.252927 CCCAACTCCTCCCCTTCTCT 60.253 60.000 0.00 0.00 0.00 3.10
574 595 2.122768 CTGCTCTCTATCCCCAACCTT 58.877 52.381 0.00 0.00 0.00 3.50
609 630 0.243907 CTCCACAAGTCATCGTCGGT 59.756 55.000 0.00 0.00 0.00 4.69
685 737 1.982395 TGGAAGATCCACCGTCGCT 60.982 57.895 0.00 0.00 42.67 4.93
781 833 5.524646 GCAATCATCCTCTTTTCTCTCTCAG 59.475 44.000 0.00 0.00 0.00 3.35
1476 2569 8.340618 AGCTTGATAAATTATATCGTGCCAAT 57.659 30.769 13.82 0.00 0.00 3.16
2577 5290 0.892755 CTGACCACGCTAACCAGGTA 59.107 55.000 0.00 0.00 33.77 3.08
2617 5330 5.126061 GTGCTAAGATTGACCAATCCATGTT 59.874 40.000 16.56 8.86 46.28 2.71
3562 6950 0.816018 TGAACCGGCGTGAAACATGT 60.816 50.000 6.01 0.00 35.74 3.21
3565 6953 0.672401 ACCGGCGTGAAACATGTAGG 60.672 55.000 6.01 0.00 35.74 3.18
3586 6974 4.023291 GGAAAAATGATGGAACTAGGGCA 58.977 43.478 0.00 0.00 0.00 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.248054 ACAGAAACTTTGCACGCACG 60.248 50.000 0.00 0.00 0.00 5.34
1 2 1.908065 AACAGAAACTTTGCACGCAC 58.092 45.000 0.00 0.00 0.00 5.34
2 3 2.645730 AAACAGAAACTTTGCACGCA 57.354 40.000 0.00 0.00 0.00 5.24
3 4 3.366422 TGAAAAACAGAAACTTTGCACGC 59.634 39.130 0.00 0.00 0.00 5.34
5 6 8.941796 TTCTGCTGAAAAACAGAAACTTTGCAC 61.942 37.037 3.21 0.00 46.89 4.57
6 7 7.013787 TTCTGCTGAAAAACAGAAACTTTGCA 61.014 34.615 3.21 0.00 46.89 4.08
7 8 5.348451 TTCTGCTGAAAAACAGAAACTTTGC 59.652 36.000 3.21 0.00 46.89 3.68
8 9 6.949578 TTCTGCTGAAAAACAGAAACTTTG 57.050 33.333 3.21 0.00 46.89 2.77
17 18 7.267128 AGTTGATTTGATTCTGCTGAAAAACA 58.733 30.769 10.27 8.28 35.63 2.83
18 19 7.704789 AGTTGATTTGATTCTGCTGAAAAAC 57.295 32.000 10.27 5.98 35.63 2.43
19 20 9.630098 GATAGTTGATTTGATTCTGCTGAAAAA 57.370 29.630 10.27 7.74 35.63 1.94
20 21 8.795513 TGATAGTTGATTTGATTCTGCTGAAAA 58.204 29.630 10.27 0.98 35.63 2.29
21 22 8.339344 TGATAGTTGATTTGATTCTGCTGAAA 57.661 30.769 10.27 0.00 35.63 2.69
22 23 7.926674 TGATAGTTGATTTGATTCTGCTGAA 57.073 32.000 8.59 8.59 36.54 3.02
23 24 7.771826 TGATGATAGTTGATTTGATTCTGCTGA 59.228 33.333 0.00 0.00 0.00 4.26
24 25 7.927048 TGATGATAGTTGATTTGATTCTGCTG 58.073 34.615 0.00 0.00 0.00 4.41
25 26 8.693120 ATGATGATAGTTGATTTGATTCTGCT 57.307 30.769 0.00 0.00 0.00 4.24
52 53 6.269307 TGCCAAGTAGAACCTATAGGATAACC 59.731 42.308 26.01 9.67 38.94 2.85
53 54 7.153315 GTGCCAAGTAGAACCTATAGGATAAC 58.847 42.308 26.01 14.48 38.94 1.89
54 55 6.842280 TGTGCCAAGTAGAACCTATAGGATAA 59.158 38.462 26.01 2.65 38.94 1.75
55 56 6.378745 TGTGCCAAGTAGAACCTATAGGATA 58.621 40.000 26.01 11.68 38.94 2.59
56 57 5.216622 TGTGCCAAGTAGAACCTATAGGAT 58.783 41.667 26.01 14.17 38.94 3.24
57 58 4.616553 TGTGCCAAGTAGAACCTATAGGA 58.383 43.478 26.01 0.00 38.94 2.94
58 59 5.353394 TTGTGCCAAGTAGAACCTATAGG 57.647 43.478 17.73 17.73 42.17 2.57
59 60 6.092259 GTGTTTGTGCCAAGTAGAACCTATAG 59.908 42.308 0.00 0.00 0.00 1.31
60 61 5.935789 GTGTTTGTGCCAAGTAGAACCTATA 59.064 40.000 0.00 0.00 0.00 1.31
61 62 4.760204 GTGTTTGTGCCAAGTAGAACCTAT 59.240 41.667 0.00 0.00 0.00 2.57
62 63 4.131596 GTGTTTGTGCCAAGTAGAACCTA 58.868 43.478 0.00 0.00 0.00 3.08
63 64 2.949644 GTGTTTGTGCCAAGTAGAACCT 59.050 45.455 0.00 0.00 0.00 3.50
64 65 2.949644 AGTGTTTGTGCCAAGTAGAACC 59.050 45.455 0.00 0.00 0.00 3.62
65 66 5.744666 TTAGTGTTTGTGCCAAGTAGAAC 57.255 39.130 0.00 0.00 0.00 3.01
66 67 6.952773 AATTAGTGTTTGTGCCAAGTAGAA 57.047 33.333 0.00 0.00 0.00 2.10
67 68 8.453238 TTTAATTAGTGTTTGTGCCAAGTAGA 57.547 30.769 0.00 0.00 0.00 2.59
68 69 9.180678 CTTTTAATTAGTGTTTGTGCCAAGTAG 57.819 33.333 0.00 0.00 0.00 2.57
69 70 8.904834 TCTTTTAATTAGTGTTTGTGCCAAGTA 58.095 29.630 0.00 0.00 0.00 2.24
70 71 7.777095 TCTTTTAATTAGTGTTTGTGCCAAGT 58.223 30.769 0.00 0.00 0.00 3.16
71 72 8.816640 ATCTTTTAATTAGTGTTTGTGCCAAG 57.183 30.769 0.00 0.00 0.00 3.61
90 91 9.466497 TTCTGGATAGATGTGCTTTTATCTTTT 57.534 29.630 0.00 0.00 35.42 2.27
91 92 9.118300 CTTCTGGATAGATGTGCTTTTATCTTT 57.882 33.333 0.00 0.00 35.42 2.52
92 93 7.718753 CCTTCTGGATAGATGTGCTTTTATCTT 59.281 37.037 0.00 0.00 33.82 2.40
93 94 7.147408 ACCTTCTGGATAGATGTGCTTTTATCT 60.147 37.037 0.00 0.00 36.08 1.98
94 95 6.995091 ACCTTCTGGATAGATGTGCTTTTATC 59.005 38.462 0.00 0.00 37.04 1.75
95 96 6.904626 ACCTTCTGGATAGATGTGCTTTTAT 58.095 36.000 0.00 0.00 37.04 1.40
96 97 6.313519 ACCTTCTGGATAGATGTGCTTTTA 57.686 37.500 0.00 0.00 37.04 1.52
97 98 5.184892 ACCTTCTGGATAGATGTGCTTTT 57.815 39.130 0.00 0.00 37.04 2.27
98 99 4.851639 ACCTTCTGGATAGATGTGCTTT 57.148 40.909 0.00 0.00 37.04 3.51
99 100 5.211973 TCTACCTTCTGGATAGATGTGCTT 58.788 41.667 0.00 0.00 37.04 3.91
100 101 4.809193 TCTACCTTCTGGATAGATGTGCT 58.191 43.478 0.00 0.00 37.04 4.40
101 102 5.477510 CATCTACCTTCTGGATAGATGTGC 58.522 45.833 16.98 0.00 42.09 4.57
102 103 5.011431 TGCATCTACCTTCTGGATAGATGTG 59.989 44.000 21.30 10.41 44.71 3.21
103 104 5.150715 TGCATCTACCTTCTGGATAGATGT 58.849 41.667 21.30 4.37 44.71 3.06
104 105 5.735285 TGCATCTACCTTCTGGATAGATG 57.265 43.478 18.91 18.91 45.09 2.90
105 106 6.080682 TCTTGCATCTACCTTCTGGATAGAT 58.919 40.000 0.00 0.00 37.26 1.98
106 107 5.458595 TCTTGCATCTACCTTCTGGATAGA 58.541 41.667 0.00 0.00 37.04 1.98
107 108 5.798125 TCTTGCATCTACCTTCTGGATAG 57.202 43.478 0.00 0.00 37.04 2.08
108 109 6.753913 AATCTTGCATCTACCTTCTGGATA 57.246 37.500 0.00 0.00 37.04 2.59
109 110 5.643421 AATCTTGCATCTACCTTCTGGAT 57.357 39.130 0.00 0.00 37.04 3.41
110 111 5.441718 AAATCTTGCATCTACCTTCTGGA 57.558 39.130 0.00 0.00 37.04 3.86
111 112 7.814264 AATAAATCTTGCATCTACCTTCTGG 57.186 36.000 0.00 0.00 39.83 3.86
112 113 9.553064 AGTAATAAATCTTGCATCTACCTTCTG 57.447 33.333 0.00 0.00 0.00 3.02
120 121 9.905713 TCCTGTTTAGTAATAAATCTTGCATCT 57.094 29.630 0.00 0.00 0.00 2.90
122 123 8.624776 GCTCCTGTTTAGTAATAAATCTTGCAT 58.375 33.333 0.00 0.00 0.00 3.96
123 124 7.609918 TGCTCCTGTTTAGTAATAAATCTTGCA 59.390 33.333 0.00 4.49 0.00 4.08
124 125 7.985476 TGCTCCTGTTTAGTAATAAATCTTGC 58.015 34.615 0.00 2.25 0.00 4.01
133 134 9.660180 TTTTTGTTTTTGCTCCTGTTTAGTAAT 57.340 25.926 0.00 0.00 0.00 1.89
134 135 9.145865 CTTTTTGTTTTTGCTCCTGTTTAGTAA 57.854 29.630 0.00 0.00 0.00 2.24
135 136 7.276878 GCTTTTTGTTTTTGCTCCTGTTTAGTA 59.723 33.333 0.00 0.00 0.00 1.82
136 137 6.092122 GCTTTTTGTTTTTGCTCCTGTTTAGT 59.908 34.615 0.00 0.00 0.00 2.24
137 138 6.091986 TGCTTTTTGTTTTTGCTCCTGTTTAG 59.908 34.615 0.00 0.00 0.00 1.85
138 139 5.934625 TGCTTTTTGTTTTTGCTCCTGTTTA 59.065 32.000 0.00 0.00 0.00 2.01
139 140 4.759183 TGCTTTTTGTTTTTGCTCCTGTTT 59.241 33.333 0.00 0.00 0.00 2.83
140 141 4.322567 TGCTTTTTGTTTTTGCTCCTGTT 58.677 34.783 0.00 0.00 0.00 3.16
141 142 3.936564 TGCTTTTTGTTTTTGCTCCTGT 58.063 36.364 0.00 0.00 0.00 4.00
142 143 6.601741 TTATGCTTTTTGTTTTTGCTCCTG 57.398 33.333 0.00 0.00 0.00 3.86
143 144 7.806409 ATTTATGCTTTTTGTTTTTGCTCCT 57.194 28.000 0.00 0.00 0.00 3.69
144 145 9.943163 TTTATTTATGCTTTTTGTTTTTGCTCC 57.057 25.926 0.00 0.00 0.00 4.70
178 179 2.399356 GCGCTAGTTGGGAGGCAAC 61.399 63.158 0.00 0.00 0.00 4.17
179 180 1.261938 TAGCGCTAGTTGGGAGGCAA 61.262 55.000 14.45 0.00 0.00 4.52
180 181 1.048724 ATAGCGCTAGTTGGGAGGCA 61.049 55.000 23.37 0.00 0.00 4.75
181 182 0.319986 GATAGCGCTAGTTGGGAGGC 60.320 60.000 23.37 0.01 0.00 4.70
182 183 0.039074 CGATAGCGCTAGTTGGGAGG 60.039 60.000 23.37 1.81 0.00 4.30
183 184 0.669077 ACGATAGCGCTAGTTGGGAG 59.331 55.000 23.37 10.41 42.48 4.30
184 185 1.108776 AACGATAGCGCTAGTTGGGA 58.891 50.000 23.37 0.00 42.48 4.37
185 186 1.935933 AAACGATAGCGCTAGTTGGG 58.064 50.000 23.37 11.60 42.48 4.12
186 187 3.061403 CGTTAAACGATAGCGCTAGTTGG 60.061 47.826 23.37 10.71 46.05 3.77
187 188 3.598670 GCGTTAAACGATAGCGCTAGTTG 60.599 47.826 23.37 16.26 46.05 3.16
188 189 2.533129 GCGTTAAACGATAGCGCTAGTT 59.467 45.455 23.37 18.41 46.05 2.24
189 190 2.114825 GCGTTAAACGATAGCGCTAGT 58.885 47.619 23.37 13.27 46.05 2.57
190 191 1.450905 GGCGTTAAACGATAGCGCTAG 59.549 52.381 23.37 12.58 46.05 3.42
191 192 1.480205 GGCGTTAAACGATAGCGCTA 58.520 50.000 21.30 21.30 46.05 4.26
192 193 1.149964 GGGCGTTAAACGATAGCGCT 61.150 55.000 17.26 17.26 46.05 5.92
193 194 1.274770 GGGCGTTAAACGATAGCGC 59.725 57.895 19.47 19.47 46.05 5.92
194 195 0.529119 AGGGGCGTTAAACGATAGCG 60.529 55.000 0.00 0.00 46.05 4.26
195 196 2.401351 CTAGGGGCGTTAAACGATAGC 58.599 52.381 0.00 0.00 46.05 2.97
196 197 2.035576 AGCTAGGGGCGTTAAACGATAG 59.964 50.000 0.00 0.00 46.05 2.08
197 198 2.034124 AGCTAGGGGCGTTAAACGATA 58.966 47.619 0.00 0.00 46.05 2.92
198 199 0.828677 AGCTAGGGGCGTTAAACGAT 59.171 50.000 0.00 0.00 46.05 3.73
199 200 1.406539 CTAGCTAGGGGCGTTAAACGA 59.593 52.381 13.32 0.00 46.05 3.85
209 210 4.164843 TGTTTTTATGCCTAGCTAGGGG 57.835 45.455 35.44 17.24 43.82 4.79
210 211 4.035208 CGTTGTTTTTATGCCTAGCTAGGG 59.965 45.833 35.44 20.24 43.82 3.53
211 212 4.873827 TCGTTGTTTTTATGCCTAGCTAGG 59.126 41.667 32.12 32.12 46.42 3.02
212 213 6.417191 TTCGTTGTTTTTATGCCTAGCTAG 57.583 37.500 14.20 14.20 0.00 3.42
213 214 6.804770 TTTCGTTGTTTTTATGCCTAGCTA 57.195 33.333 0.00 0.00 0.00 3.32
214 215 5.699097 TTTCGTTGTTTTTATGCCTAGCT 57.301 34.783 0.00 0.00 0.00 3.32
215 216 7.700656 ACATATTTCGTTGTTTTTATGCCTAGC 59.299 33.333 0.00 0.00 0.00 3.42
223 224 9.692749 TGCCAAATACATATTTCGTTGTTTTTA 57.307 25.926 0.00 0.00 33.88 1.52
224 225 8.594881 TGCCAAATACATATTTCGTTGTTTTT 57.405 26.923 0.00 0.00 33.88 1.94
229 230 5.518487 GGGTTGCCAAATACATATTTCGTTG 59.482 40.000 0.00 0.00 33.88 4.10
574 595 0.395862 GGAGTCGAGGAGATGGTGGA 60.396 60.000 0.00 0.00 0.00 4.02
685 737 1.749063 CACCTGTCGATGTAGTAGGCA 59.251 52.381 0.00 0.00 31.69 4.75
1476 2569 4.619973 TCAAAGCGGTTCGAGTTAAACTA 58.380 39.130 0.00 0.00 0.00 2.24
2133 4816 1.202222 CGAGCATGAAGGAATGTTGGC 60.202 52.381 0.00 0.00 0.00 4.52
2262 4945 1.202687 TGAAGCTGAAGACCACACCTG 60.203 52.381 0.00 0.00 0.00 4.00
2617 5330 4.696877 CACTAGTTCCATGAATGAACAGCA 59.303 41.667 13.57 1.28 0.00 4.41
2894 6264 4.938226 TGGTGTTTGTATGCATGTTATCGA 59.062 37.500 10.16 0.00 0.00 3.59
3022 6394 9.535170 TCTTGGTCAAATTTACCATGGTATTTA 57.465 29.630 25.12 13.83 46.16 1.40
3441 6827 9.268268 CAACTATGTTGGTCGTATATTACCATT 57.732 33.333 9.30 0.00 44.98 3.16
3562 6950 5.044476 TGCCCTAGTTCCATCATTTTTCCTA 60.044 40.000 0.00 0.00 0.00 2.94
3565 6953 5.859205 ATGCCCTAGTTCCATCATTTTTC 57.141 39.130 0.00 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.