Multiple sequence alignment - TraesCS2B01G051200

Loading Multiple Alignment...

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 TraesCS2B01G051200 chr2B 100.000 2324 0 0 1 2324 25070378 25072701 0.000000e+00 4292
1 TraesCS2B01G051200 chr2A 94.139 2235 104 9 44 2259 15961063 15963289 0.000000e+00 3376
2 TraesCS2B01G051200 chr2D 93.962 2236 107 9 42 2258 13771480 13773706 0.000000e+00 3356
3 TraesCS2B01G051200 chr2D 95.522 67 3 0 2258 2324 13773730 13773796 8.780000e-20 108


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 TraesCS2B01G051200 chr2B 25070378 25072701 2323 False 4292 4292 100.000 1 2324 1 chr2B.!!$F1 2323
1 TraesCS2B01G051200 chr2A 15961063 15963289 2226 False 3376 3376 94.139 44 2259 1 chr2A.!!$F1 2215
2 TraesCS2B01G051200 chr2D 13771480 13773796 2316 False 1732 3356 94.742 42 2324 2 chr2D.!!$F1 2282

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
235 241 0.326264 ACCCTGTCTGATGAGCAACC 59.674 55.0 0.0 0.0 0.0 3.77 F
1152 1169 0.468226 AGGTCCTTGTCGTTGAAGCA 59.532 50.0 0.0 0.0 0.0 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1265 1282 0.449388 GACGACAACGACCTCGGTAT 59.551 55.0 0.00 0.0 44.95 2.73 R
2111 2128 1.307355 TTACCGGAGTCGTGATCGCA 61.307 55.0 9.46 0.0 36.96 5.10 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
39 40 8.956533 AAATAAAATCAAAATATTGGGGTCGG 57.043 30.769 0.00 0.00 37.15 4.79
40 41 7.669089 ATAAAATCAAAATATTGGGGTCGGT 57.331 32.000 0.00 0.00 37.15 4.69
64 65 0.813210 GATCGGCCAGAAAGAGCAGG 60.813 60.000 2.24 0.00 0.00 4.85
89 90 6.202570 GGCAAAAGTAACAAGCATGAATTCAA 59.797 34.615 13.09 0.00 0.00 2.69
165 166 2.251600 CAGCCACACTGCCTTTCTC 58.748 57.895 0.00 0.00 40.19 2.87
166 167 1.073897 AGCCACACTGCCTTTCTCC 59.926 57.895 0.00 0.00 0.00 3.71
199 205 0.451135 CTTTCGGCGAAAGTTGAGCG 60.451 55.000 40.00 22.78 42.61 5.03
235 241 0.326264 ACCCTGTCTGATGAGCAACC 59.674 55.000 0.00 0.00 0.00 3.77
267 273 7.901029 TGATTACACACTGAGAGAGATTCTTT 58.099 34.615 0.00 0.00 35.87 2.52
268 274 9.025041 TGATTACACACTGAGAGAGATTCTTTA 57.975 33.333 0.00 0.00 35.87 1.85
304 310 2.354305 GGACCGCGCGTCGAATAT 60.354 61.111 29.95 4.37 42.99 1.28
305 311 1.081906 GGACCGCGCGTCGAATATA 60.082 57.895 29.95 0.00 42.99 0.86
368 374 3.751518 AGGGTTATCGAAGTGTGCTTTT 58.248 40.909 0.00 0.00 34.61 2.27
398 404 6.457934 GCCGATGTTGATCCATGATGAATATC 60.458 42.308 0.00 3.96 33.31 1.63
505 522 3.679502 CCGGTCAAATTTTGGCTGAAATC 59.320 43.478 21.32 0.56 44.32 2.17
511 528 2.810439 TTTTGGCTGAAATCCAACCG 57.190 45.000 0.00 0.00 42.75 4.44
522 539 3.575965 AATCCAACCGCATTTTGAGTC 57.424 42.857 0.00 0.00 0.00 3.36
557 574 2.406616 CGAATCCAGGGTTTGCCGG 61.407 63.158 0.00 0.00 34.97 6.13
640 657 2.798499 CGATGAACAGTCCACCGGTATC 60.798 54.545 6.87 1.98 0.00 2.24
703 720 3.211045 CTTTCGGAGACCAAGGAAACAA 58.789 45.455 0.00 0.00 34.32 2.83
736 753 0.955905 AAAACGGCGGCAAGTAACAT 59.044 45.000 13.24 0.00 0.00 2.71
864 881 4.553323 CAACAAATTTCCTTGCTCCTCTG 58.447 43.478 0.00 0.00 0.00 3.35
997 1014 3.840102 GCCGGAGCAATCCATAACGGA 62.840 57.143 5.05 0.00 43.96 4.69
1018 1035 1.486310 CTATGGGTTCCTGTGCTAGCA 59.514 52.381 14.93 14.93 0.00 3.49
1077 1094 4.796495 GACATGCCGGTCACCCCC 62.796 72.222 1.90 0.00 37.73 5.40
1086 1103 2.520968 GTCACCCCCAAGGCTGTT 59.479 61.111 0.00 0.00 40.58 3.16
1098 1115 3.595758 GCTGTTGCTGCACCCGTT 61.596 61.111 0.00 0.00 36.03 4.44
1102 1119 1.106351 TGTTGCTGCACCCGTTGAAT 61.106 50.000 0.00 0.00 0.00 2.57
1152 1169 0.468226 AGGTCCTTGTCGTTGAAGCA 59.532 50.000 0.00 0.00 0.00 3.91
1164 1181 1.812571 GTTGAAGCACCATTGGTCGAT 59.187 47.619 5.04 0.00 31.02 3.59
1171 1188 1.069765 CCATTGGTCGATCCCTCGG 59.930 63.158 0.00 0.00 45.10 4.63
1188 1205 1.152881 GGCATCCAAAGCCGAGGAT 60.153 57.895 0.00 0.00 45.30 3.24
1191 1208 1.918253 ATCCAAAGCCGAGGATGCT 59.082 52.632 1.00 0.00 42.86 3.79
1220 1237 2.771943 TGAATGAAGAGCTTATCCCCGT 59.228 45.455 0.00 0.00 0.00 5.28
1222 1239 1.860641 TGAAGAGCTTATCCCCGTGA 58.139 50.000 0.00 0.00 0.00 4.35
1265 1282 0.411452 ACTGAGGAGGCTGAAGAGGA 59.589 55.000 0.00 0.00 0.00 3.71
1406 1423 2.076863 AGACCTTGCTGCGTTAACATC 58.923 47.619 6.39 0.00 0.00 3.06
1438 1455 1.405933 GGGATGGCCAAAATGCAACTC 60.406 52.381 10.96 0.00 35.15 3.01
1494 1511 6.114089 ACTTCAATGTCATGATTCTCAGAGG 58.886 40.000 0.00 0.00 0.00 3.69
1604 1621 7.552687 GGATACACAAATTAACAGGTGATCAGA 59.447 37.037 0.00 0.00 35.33 3.27
1605 1622 6.808008 ACACAAATTAACAGGTGATCAGAG 57.192 37.500 0.00 0.00 35.33 3.35
1621 1638 6.920758 GTGATCAGAGGATACATGTTACAGTC 59.079 42.308 2.30 0.18 41.41 3.51
1626 1643 6.016192 CAGAGGATACATGTTACAGTCGGTAT 60.016 42.308 2.30 0.00 41.41 2.73
1907 1924 1.499056 GAGGCACATGCTGTTGACG 59.501 57.895 3.48 0.00 41.70 4.35
1994 2011 1.414527 GCTGCTCGCCGAAGTAGTTC 61.415 60.000 0.00 0.00 32.21 3.01
2018 2035 3.379445 CGCGAGTACCCCCACAGT 61.379 66.667 0.00 0.00 0.00 3.55
2027 2044 3.391382 CCCCACAGTCCGTCCTCC 61.391 72.222 0.00 0.00 0.00 4.30
2237 2254 2.030540 CAGAAACACCTGCATCCAACAG 60.031 50.000 0.00 0.00 34.82 3.16
2241 2258 1.074405 ACACCTGCATCCAACAGACAT 59.926 47.619 0.00 0.00 37.32 3.06
2271 2312 4.598406 TGTCAATCATGAATTTCGACCG 57.402 40.909 0.00 0.00 37.30 4.79
2301 2342 8.249638 TGATTTATGTAGCAAAAATAGCAGCAA 58.750 29.630 0.00 0.00 0.00 3.91
2305 2346 3.308438 AGCAAAAATAGCAGCAAGGTG 57.692 42.857 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 9.389755 CCGACCCCAATATTTTGATTTTATTTT 57.610 29.630 0.00 0.00 34.60 1.82
14 15 8.544622 ACCGACCCCAATATTTTGATTTTATTT 58.455 29.630 0.00 0.00 34.60 1.40
15 16 8.084985 ACCGACCCCAATATTTTGATTTTATT 57.915 30.769 0.00 0.00 34.60 1.40
16 17 7.669089 ACCGACCCCAATATTTTGATTTTAT 57.331 32.000 0.00 0.00 34.60 1.40
17 18 8.591114 TTACCGACCCCAATATTTTGATTTTA 57.409 30.769 0.00 0.00 34.60 1.52
18 19 7.483580 TTACCGACCCCAATATTTTGATTTT 57.516 32.000 0.00 0.00 34.60 1.82
19 20 6.406512 GCTTACCGACCCCAATATTTTGATTT 60.407 38.462 0.00 0.00 34.60 2.17
20 21 5.068591 GCTTACCGACCCCAATATTTTGATT 59.931 40.000 0.00 0.00 34.60 2.57
21 22 4.583073 GCTTACCGACCCCAATATTTTGAT 59.417 41.667 0.00 0.00 34.60 2.57
22 23 3.949113 GCTTACCGACCCCAATATTTTGA 59.051 43.478 0.00 0.00 34.60 2.69
23 24 3.242936 CGCTTACCGACCCCAATATTTTG 60.243 47.826 0.00 0.00 40.02 2.44
24 25 2.946990 CGCTTACCGACCCCAATATTTT 59.053 45.455 0.00 0.00 40.02 1.82
25 26 2.171027 TCGCTTACCGACCCCAATATTT 59.829 45.455 0.00 0.00 41.89 1.40
26 27 1.764134 TCGCTTACCGACCCCAATATT 59.236 47.619 0.00 0.00 41.89 1.28
27 28 1.416243 TCGCTTACCGACCCCAATAT 58.584 50.000 0.00 0.00 41.89 1.28
28 29 2.899122 TCGCTTACCGACCCCAATA 58.101 52.632 0.00 0.00 41.89 1.90
29 30 3.716381 TCGCTTACCGACCCCAAT 58.284 55.556 0.00 0.00 41.89 3.16
37 38 2.622903 TTCTGGCCGATCGCTTACCG 62.623 60.000 10.32 5.19 37.74 4.02
38 39 0.461339 TTTCTGGCCGATCGCTTACC 60.461 55.000 10.32 8.59 37.74 2.85
39 40 0.931005 CTTTCTGGCCGATCGCTTAC 59.069 55.000 10.32 0.00 37.74 2.34
40 41 0.821517 TCTTTCTGGCCGATCGCTTA 59.178 50.000 10.32 0.00 37.74 3.09
64 65 5.695816 TGAATTCATGCTTGTTACTTTTGCC 59.304 36.000 3.38 0.00 0.00 4.52
102 103 4.896829 TGGGCCGGCGTTTGGAAA 62.897 61.111 22.54 0.00 0.00 3.13
103 104 4.669809 ATGGGCCGGCGTTTGGAA 62.670 61.111 22.54 0.10 0.00 3.53
106 107 3.124798 GATGATGGGCCGGCGTTTG 62.125 63.158 22.54 0.00 0.00 2.93
107 108 2.828549 GATGATGGGCCGGCGTTT 60.829 61.111 22.54 6.88 0.00 3.60
108 109 4.108299 TGATGATGGGCCGGCGTT 62.108 61.111 22.54 7.31 0.00 4.84
109 110 4.856801 GTGATGATGGGCCGGCGT 62.857 66.667 22.54 9.11 0.00 5.68
110 111 4.552365 AGTGATGATGGGCCGGCG 62.552 66.667 22.54 0.00 0.00 6.46
111 112 2.124151 AAGTGATGATGGGCCGGC 60.124 61.111 21.18 21.18 0.00 6.13
112 113 1.526917 GGAAGTGATGATGGGCCGG 60.527 63.158 0.00 0.00 0.00 6.13
113 114 0.533755 GAGGAAGTGATGATGGGCCG 60.534 60.000 0.00 0.00 0.00 6.13
114 115 0.842635 AGAGGAAGTGATGATGGGCC 59.157 55.000 0.00 0.00 0.00 5.80
199 205 2.832733 AGGGTAAACTAGTCTGCAGACC 59.167 50.000 37.09 22.74 45.85 3.85
235 241 2.412870 TCAGTGTGTAATCAACAGCCG 58.587 47.619 0.00 0.00 39.29 5.52
368 374 2.488204 TGGATCAACATCGGCTTTCA 57.512 45.000 0.00 0.00 0.00 2.69
398 404 1.067669 TCGCCATCGATCTCTTCAAGG 59.932 52.381 0.00 0.00 40.21 3.61
461 478 1.158007 AGGTGAACCCTGGTGGAAAT 58.842 50.000 0.00 0.00 44.08 2.17
483 500 2.810439 TTCAGCCAAAATTTGACCGG 57.190 45.000 7.37 0.00 0.00 5.28
505 522 1.608590 AGTGACTCAAAATGCGGTTGG 59.391 47.619 0.00 0.00 0.00 3.77
511 528 2.667724 GCTCAGCAGTGACTCAAAATGC 60.668 50.000 0.00 4.64 37.15 3.56
619 636 0.528924 TACCGGTGGACTGTTCATCG 59.471 55.000 19.93 14.76 38.35 3.84
703 720 1.434287 GTTTTGTTGGTTCCCGCGT 59.566 52.632 4.92 0.00 0.00 6.01
864 881 2.439880 AGGAGGAAGGGCTATTTGTAGC 59.560 50.000 0.00 0.00 42.12 3.58
905 922 1.376812 GAACGCGGGGAAGAATGGT 60.377 57.895 12.47 0.00 0.00 3.55
997 1014 1.486726 GCTAGCACAGGAACCCATAGT 59.513 52.381 10.63 0.00 0.00 2.12
1077 1094 2.337532 GGTGCAGCAACAGCCTTG 59.662 61.111 11.86 0.00 31.85 3.61
1086 1103 1.971167 GGATTCAACGGGTGCAGCA 60.971 57.895 19.06 0.00 0.00 4.41
1152 1169 1.686325 CCGAGGGATCGACCAATGGT 61.686 60.000 3.74 3.74 41.20 3.55
1164 1181 2.272146 GCTTTGGATGCCGAGGGA 59.728 61.111 0.00 0.00 0.00 4.20
1171 1188 4.567318 ATCCTCGGCTTTGGATGC 57.433 55.556 4.58 0.00 41.13 3.91
1174 1191 3.403624 AGCATCCTCGGCTTTGGA 58.596 55.556 0.00 0.00 38.81 3.53
1188 1205 2.555325 CTCTTCATTCACCTTGCAAGCA 59.445 45.455 21.43 3.89 0.00 3.91
1191 1208 2.867624 AGCTCTTCATTCACCTTGCAA 58.132 42.857 0.00 0.00 0.00 4.08
1265 1282 0.449388 GACGACAACGACCTCGGTAT 59.551 55.000 0.00 0.00 44.95 2.73
1406 1423 0.468771 GCCATCCCCAGATTTCCCAG 60.469 60.000 0.00 0.00 0.00 4.45
1438 1455 1.152777 TGGACTGCCAAACCAGGTG 60.153 57.895 0.00 0.00 42.49 4.00
1494 1511 5.243426 TCTTACTGCCAACTTTGTGTTTC 57.757 39.130 0.00 0.00 36.63 2.78
1604 1621 5.010719 CCATACCGACTGTAACATGTATCCT 59.989 44.000 0.00 0.00 31.94 3.24
1605 1622 5.221382 ACCATACCGACTGTAACATGTATCC 60.221 44.000 0.00 0.00 31.94 2.59
1621 1638 7.288317 TGTTTACGTGTAATTAACCATACCG 57.712 36.000 0.00 0.00 0.00 4.02
1626 1643 4.377226 GCGCTGTTTACGTGTAATTAACCA 60.377 41.667 0.00 0.00 0.00 3.67
1907 1924 4.814294 ATGTTCGTCGGGGCGCTC 62.814 66.667 7.64 1.18 0.00 5.03
1918 1935 3.499737 GGCAGCGGTGGATGTTCG 61.500 66.667 17.54 0.00 0.00 3.95
2018 2035 4.715130 CCCACCCTGGAGGACGGA 62.715 72.222 0.69 0.00 40.96 4.69
2027 2044 4.704833 CCGACAGTGCCCACCCTG 62.705 72.222 0.00 0.00 34.82 4.45
2036 2053 2.738521 CTGGGCGAACCGACAGTG 60.739 66.667 0.00 0.00 44.64 3.66
2063 2080 1.860676 TCGTGACCAGGAACGAAAAG 58.139 50.000 16.60 0.00 45.14 2.27
2111 2128 1.307355 TTACCGGAGTCGTGATCGCA 61.307 55.000 9.46 0.00 36.96 5.10
2237 2254 4.241590 TGATTGACAAAAGTGGCATGTC 57.758 40.909 11.14 11.14 44.33 3.06
2241 2258 4.933505 TTCATGATTGACAAAAGTGGCA 57.066 36.364 0.00 0.00 42.77 4.92
2271 2312 8.131100 TGCTATTTTTGCTACATAAATCAGCTC 58.869 33.333 16.04 3.04 36.26 4.09


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

AutoCloner maintained by Alex Coulton.