Multiple sequence alignment - TraesCS6B01G197900

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 TraesCS6B01G197900 chr6B 100.000 2350 0 0 1 2350 236517743 236520092 0 4340
1 TraesCS6B01G197900 chr7A 94.543 1356 65 2 995 2350 60095004 60093658 0 2085
2 TraesCS6B01G197900 chr7A 93.658 1356 77 2 995 2350 211236935 211235589 0 2019
3 TraesCS6B01G197900 chrUn 94.469 1356 66 2 995 2350 233524074 233522728 0 2080
4 TraesCS6B01G197900 chrUn 94.469 1356 66 2 995 2350 257945311 257946657 0 2080
5 TraesCS6B01G197900 chrUn 94.469 1356 66 2 995 2350 369795369 369796715 0 2080
6 TraesCS6B01G197900 chr1D 94.395 1356 67 2 995 2350 212430068 212431414 0 2074
7 TraesCS6B01G197900 chr1D 93.675 996 62 1 1 995 265700864 265701859 0 1489
8 TraesCS6B01G197900 chr5B 94.322 1356 68 2 995 2350 713111769 713110423 0 2069
9 TraesCS6B01G197900 chr5B 93.687 998 59 4 1 995 425115002 425114006 0 1491
10 TraesCS6B01G197900 chr7B 94.248 1356 68 3 995 2350 698125739 698124394 0 2063
11 TraesCS6B01G197900 chr7B 93.882 997 60 1 2 997 500670419 500671415 0 1502
12 TraesCS6B01G197900 chr7B 93.882 997 58 3 1 995 125526760 125527755 0 1500
13 TraesCS6B01G197900 chr7B 93.781 997 59 3 1 995 411740591 411739596 0 1495
14 TraesCS6B01G197900 chr4D 94.174 1356 70 2 995 2350 123690161 123691507 0 2058
15 TraesCS6B01G197900 chr2D 94.100 1356 69 4 995 2350 637307506 637306162 0 2050
16 TraesCS6B01G197900 chr2D 93.869 995 60 1 2 995 550004524 550005518 0 1498
17 TraesCS6B01G197900 chr5A 93.658 1356 76 3 995 2350 238817711 238816366 0 2019
18 TraesCS6B01G197900 chr7D 93.068 1356 65 7 995 2350 578991965 578993291 0 1956
19 TraesCS6B01G197900 chr3D 93.882 997 58 3 1 995 540840365 540841360 0 1500
20 TraesCS6B01G197900 chr2B 93.687 998 61 2 1 997 214615576 214614580 0 1493
21 TraesCS6B01G197900 chr2B 93.675 996 62 1 1 995 78956175 78955180 0 1489


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 TraesCS6B01G197900 chr6B 236517743 236520092 2349 False 4340 4340 100.000 1 2350 1 chr6B.!!$F1 2349
1 TraesCS6B01G197900 chr7A 60093658 60095004 1346 True 2085 2085 94.543 995 2350 1 chr7A.!!$R1 1355
2 TraesCS6B01G197900 chr7A 211235589 211236935 1346 True 2019 2019 93.658 995 2350 1 chr7A.!!$R2 1355
3 TraesCS6B01G197900 chrUn 233522728 233524074 1346 True 2080 2080 94.469 995 2350 1 chrUn.!!$R1 1355
4 TraesCS6B01G197900 chrUn 257945311 257946657 1346 False 2080 2080 94.469 995 2350 1 chrUn.!!$F1 1355
5 TraesCS6B01G197900 chrUn 369795369 369796715 1346 False 2080 2080 94.469 995 2350 1 chrUn.!!$F2 1355
6 TraesCS6B01G197900 chr1D 212430068 212431414 1346 False 2074 2074 94.395 995 2350 1 chr1D.!!$F1 1355
7 TraesCS6B01G197900 chr1D 265700864 265701859 995 False 1489 1489 93.675 1 995 1 chr1D.!!$F2 994
8 TraesCS6B01G197900 chr5B 713110423 713111769 1346 True 2069 2069 94.322 995 2350 1 chr5B.!!$R2 1355
9 TraesCS6B01G197900 chr5B 425114006 425115002 996 True 1491 1491 93.687 1 995 1 chr5B.!!$R1 994
10 TraesCS6B01G197900 chr7B 698124394 698125739 1345 True 2063 2063 94.248 995 2350 1 chr7B.!!$R2 1355
11 TraesCS6B01G197900 chr7B 500670419 500671415 996 False 1502 1502 93.882 2 997 1 chr7B.!!$F2 995
12 TraesCS6B01G197900 chr7B 125526760 125527755 995 False 1500 1500 93.882 1 995 1 chr7B.!!$F1 994
13 TraesCS6B01G197900 chr7B 411739596 411740591 995 True 1495 1495 93.781 1 995 1 chr7B.!!$R1 994
14 TraesCS6B01G197900 chr4D 123690161 123691507 1346 False 2058 2058 94.174 995 2350 1 chr4D.!!$F1 1355
15 TraesCS6B01G197900 chr2D 637306162 637307506 1344 True 2050 2050 94.100 995 2350 1 chr2D.!!$R1 1355
16 TraesCS6B01G197900 chr2D 550004524 550005518 994 False 1498 1498 93.869 2 995 1 chr2D.!!$F1 993
17 TraesCS6B01G197900 chr5A 238816366 238817711 1345 True 2019 2019 93.658 995 2350 1 chr5A.!!$R1 1355
18 TraesCS6B01G197900 chr7D 578991965 578993291 1326 False 1956 1956 93.068 995 2350 1 chr7D.!!$F1 1355
19 TraesCS6B01G197900 chr3D 540840365 540841360 995 False 1500 1500 93.882 1 995 1 chr3D.!!$F1 994
20 TraesCS6B01G197900 chr2B 214614580 214615576 996 True 1493 1493 93.687 1 997 1 chr2B.!!$R2 996
21 TraesCS6B01G197900 chr2B 78955180 78956175 995 True 1489 1489 93.675 1 995 1 chr2B.!!$R1 994

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
109 110 0.591659 GACTCCAAACAACCTTCGGC 59.408 55.0 0.0 0.0 0.0 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1399 1402 0.17668 AATGAGCCTTGCGACGAGAT 59.823 50.0 0.0 0.0 0.0 2.75 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
109 110 0.591659 GACTCCAAACAACCTTCGGC 59.408 55.000 0.00 0.00 0.00 5.54
169 172 2.726691 CGTTAAGCGTGCGACCCTG 61.727 63.158 0.00 0.00 35.54 4.45
244 247 4.762289 ATAGTGGAACCTGGATTCTCAC 57.238 45.455 0.00 10.45 37.80 3.51
257 260 3.871594 GGATTCTCACATTGGTTCCTACG 59.128 47.826 0.00 0.00 0.00 3.51
363 366 6.509418 TTCGATCATCGGTATCATCATACA 57.491 37.500 7.33 0.00 40.88 2.29
404 407 3.554337 GGCAAGTCTCTTTACTCGTTCCA 60.554 47.826 0.00 0.00 0.00 3.53
423 426 7.709182 TCGTTCCATAATACTTCATACCACAAG 59.291 37.037 0.00 0.00 0.00 3.16
425 428 8.827677 GTTCCATAATACTTCATACCACAAGTC 58.172 37.037 0.00 0.00 34.60 3.01
439 442 5.240891 ACCACAAGTCACTCATTAGTCATG 58.759 41.667 0.00 0.00 31.97 3.07
565 568 1.414181 ACACCTTCAGAGACACCTGTG 59.586 52.381 0.00 0.00 35.71 3.66
695 698 4.453819 AGTCATGAAGAAAGCAGTAGCAAC 59.546 41.667 0.00 0.00 45.49 4.17
708 711 4.669197 GCAGTAGCAACGAAACTGTAATGG 60.669 45.833 0.00 0.00 42.10 3.16
714 717 5.351465 AGCAACGAAACTGTAATGGTCATAG 59.649 40.000 0.00 0.00 0.00 2.23
778 781 6.855667 TCCTAATGATGTGATCCCATTCATT 58.144 36.000 14.88 14.88 39.34 2.57
792 795 6.686630 TCCCATTCATTAAATGACAACACAC 58.313 36.000 0.00 0.00 46.54 3.82
815 818 6.814644 CACGTCTATGGTTAGGAAACATAACA 59.185 38.462 8.19 0.00 37.34 2.41
852 855 5.176407 AGCTAGTCAAGTAGAAGCATACG 57.824 43.478 0.00 0.00 33.43 3.06
911 914 8.532977 TGTACTAAGTTTCCGGTTAATACAAC 57.467 34.615 0.00 0.00 0.00 3.32
913 916 9.855021 GTACTAAGTTTCCGGTTAATACAACTA 57.145 33.333 0.00 0.00 0.00 2.24
1003 1006 7.529555 AGGGCATATTTCCTTCAAAGATATGA 58.470 34.615 11.33 0.00 34.27 2.15
1024 1027 6.126863 TGATGTTTTCTATCAGTCCCAAGT 57.873 37.500 0.00 0.00 31.35 3.16
1075 1078 1.103987 CGAGGAAGAGATGCGGGAGA 61.104 60.000 0.00 0.00 0.00 3.71
1112 1115 3.216230 AGTTGGGTTGGGGTATAGAGT 57.784 47.619 0.00 0.00 0.00 3.24
1137 1140 2.446994 ACGGTGGGGGTGACAGAA 60.447 61.111 0.00 0.00 0.00 3.02
1147 1150 1.002430 GGGTGACAGAAGATGTGCTCA 59.998 52.381 0.00 0.00 44.17 4.26
1166 1169 5.186198 GCTCATACAGTTCATAGTTGGGTT 58.814 41.667 0.00 0.00 0.00 4.11
1188 1191 5.484173 TTGATATTCTCGTGGATTGTTGC 57.516 39.130 0.00 0.00 0.00 4.17
1204 1207 3.961182 TGTTGCGAACGTCCTCTATATC 58.039 45.455 0.00 0.00 0.00 1.63
1217 1220 6.262496 CGTCCTCTATATCCGAAATATGCCTA 59.738 42.308 0.00 0.00 0.00 3.93
1218 1221 7.520776 CGTCCTCTATATCCGAAATATGCCTAG 60.521 44.444 0.00 0.00 0.00 3.02
1219 1222 7.502895 GTCCTCTATATCCGAAATATGCCTAGA 59.497 40.741 0.00 0.00 0.00 2.43
1220 1223 8.059461 TCCTCTATATCCGAAATATGCCTAGAA 58.941 37.037 0.00 0.00 0.00 2.10
1221 1224 8.356657 CCTCTATATCCGAAATATGCCTAGAAG 58.643 40.741 0.00 0.00 0.00 2.85
1222 1225 7.717568 TCTATATCCGAAATATGCCTAGAAGC 58.282 38.462 0.00 0.00 0.00 3.86
1223 1226 3.402628 TCCGAAATATGCCTAGAAGCC 57.597 47.619 0.00 0.00 0.00 4.35
1224 1227 2.972713 TCCGAAATATGCCTAGAAGCCT 59.027 45.455 0.00 0.00 0.00 4.58
1245 1248 5.047943 GCCTTTCTAGGAGCATTACGATCTA 60.048 44.000 0.00 0.00 45.05 1.98
1271 1274 4.706962 GCTCAAATGGTCCCTTATGAAGTT 59.293 41.667 0.00 0.00 0.00 2.66
1278 1281 9.547279 AAATGGTCCCTTATGAAGTTTCTATTT 57.453 29.630 0.00 0.00 0.00 1.40
1302 1305 6.110033 TGTCTTATTCTTATTGTGCGCCTTA 58.890 36.000 4.18 0.00 0.00 2.69
1321 1324 2.425143 ATGAGCACGTTTGGATCCAT 57.575 45.000 17.06 0.00 0.00 3.41
1356 1359 1.134189 GGATCTTCCCCTAACCCAACG 60.134 57.143 0.00 0.00 0.00 4.10
1368 1371 2.030562 CCAACGCGGGAACAGACT 59.969 61.111 12.47 0.00 0.00 3.24
1421 1424 1.197721 CTCGTCGCAAGGCTCATTTTT 59.802 47.619 0.00 0.00 42.28 1.94
1489 1492 0.828677 GGTACTACCCAGGTGCGAAT 59.171 55.000 0.00 0.00 30.04 3.34
1549 1552 0.716108 CAGCCTAAACGACGAGCAAG 59.284 55.000 0.00 0.00 0.00 4.01
1636 1639 2.297033 GAGGCAAGAACCATGCTTTCAA 59.703 45.455 7.74 0.00 43.34 2.69
1662 1665 1.389609 GGCGGTCCGAATCCACTCTA 61.390 60.000 17.49 0.00 0.00 2.43
1753 1756 4.949238 CCTTCATGTATGGGTGACAAATCA 59.051 41.667 0.00 0.00 0.00 2.57
1818 1821 3.310727 CATACGATGATGCTGCCCA 57.689 52.632 0.00 0.00 0.00 5.36
1841 1844 1.358152 TCATTTCGTGGAAGTCCCCT 58.642 50.000 0.00 0.00 34.29 4.79
1895 1898 2.352960 CTGCTTCTTAGGGCGATGAAAC 59.647 50.000 0.00 0.00 0.00 2.78
2012 2015 1.499438 AGCTAAATAGGAAAGGGGGCC 59.501 52.381 0.00 0.00 0.00 5.80
2031 2034 2.819608 GCCACTGATGACTGCCTTTTTA 59.180 45.455 0.00 0.00 0.00 1.52
2057 2060 4.898320 AGAAATCAAAAAGGGTGGAATGC 58.102 39.130 0.00 0.00 0.00 3.56
2203 2206 8.661352 TCTCGATGCACATATTTGAGATTTAA 57.339 30.769 0.82 0.00 0.00 1.52
2222 2225 3.790089 AAAATCTCTTTCCGACCAGGT 57.210 42.857 0.00 0.00 41.99 4.00
2307 2310 0.965866 CACTCCAGTCCAGTCGCCTA 60.966 60.000 0.00 0.00 0.00 3.93
2309 2312 0.965866 CTCCAGTCCAGTCGCCTACA 60.966 60.000 0.00 0.00 0.00 2.74
2316 2319 2.426024 GTCCAGTCGCCTACAATCAGTA 59.574 50.000 0.00 0.00 0.00 2.74
2335 2338 2.419057 GCTTGTCAGCCACCAAACT 58.581 52.632 0.00 0.00 40.61 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
169 172 2.357009 TCTACATAGTTCTCGAACCCGC 59.643 50.000 6.20 0.00 42.06 6.13
257 260 8.288208 TGACCGATAAAGATCTTCGTAGAATAC 58.712 37.037 8.78 0.00 45.90 1.89
363 366 4.839121 TGCCGGTAACAAGATTGAACTAT 58.161 39.130 1.90 0.00 0.00 2.12
404 407 8.758829 TGAGTGACTTGTGGTATGAAGTATTAT 58.241 33.333 0.00 0.00 32.47 1.28
416 419 4.955811 TGACTAATGAGTGACTTGTGGT 57.044 40.909 0.00 0.00 35.45 4.16
439 442 3.879295 TCACTATAAGCCTTGCAAGCATC 59.121 43.478 21.43 11.62 0.00 3.91
565 568 4.164843 TGGGTGATTATAAAGGTGCTCC 57.835 45.455 0.00 0.00 0.00 4.70
695 698 4.870426 AGCACTATGACCATTACAGTTTCG 59.130 41.667 0.00 0.00 0.00 3.46
708 711 4.303086 TCCGTTAGCTTAGCACTATGAC 57.697 45.455 7.07 0.00 0.00 3.06
714 717 1.134491 ACCCATCCGTTAGCTTAGCAC 60.134 52.381 7.07 0.00 0.00 4.40
778 781 5.543714 ACCATAGACGTGTGTTGTCATTTA 58.456 37.500 0.00 0.00 38.83 1.40
792 795 7.837202 TTGTTATGTTTCCTAACCATAGACG 57.163 36.000 0.00 0.00 33.15 4.18
815 818 7.819900 ACTTGACTAGCTCGTTAATCAAAGATT 59.180 33.333 0.00 0.00 0.00 2.40
1003 1006 5.014123 TCCACTTGGGACTGATAGAAAACAT 59.986 40.000 0.00 0.00 42.15 2.71
1075 1078 3.185203 TTGCTCTGGCCCTGGGTT 61.185 61.111 15.56 0.00 37.74 4.11
1112 1115 3.697747 CCCCCACCGTGCTTACGA 61.698 66.667 0.86 0.00 34.64 3.43
1137 1140 6.477053 ACTATGAACTGTATGAGCACATCT 57.523 37.500 0.00 0.00 37.87 2.90
1147 1150 9.920946 AATATCAAACCCAACTATGAACTGTAT 57.079 29.630 0.00 0.00 0.00 2.29
1166 1169 4.033932 CGCAACAATCCACGAGAATATCAA 59.966 41.667 0.00 0.00 0.00 2.57
1188 1191 4.478843 TTTCGGATATAGAGGACGTTCG 57.521 45.455 0.00 0.00 0.00 3.95
1204 1207 3.409026 AGGCTTCTAGGCATATTTCGG 57.591 47.619 3.01 0.00 44.19 4.30
1217 1220 4.442192 CGTAATGCTCCTAGAAAGGCTTCT 60.442 45.833 0.00 2.29 43.31 2.85
1218 1221 3.804873 CGTAATGCTCCTAGAAAGGCTTC 59.195 47.826 0.00 0.00 43.31 3.86
1219 1222 3.451178 TCGTAATGCTCCTAGAAAGGCTT 59.549 43.478 0.00 0.00 43.31 4.35
1220 1223 3.031736 TCGTAATGCTCCTAGAAAGGCT 58.968 45.455 0.00 0.00 43.31 4.58
1221 1224 3.454371 TCGTAATGCTCCTAGAAAGGC 57.546 47.619 0.00 0.00 43.31 4.35
1222 1225 5.461032 AGATCGTAATGCTCCTAGAAAGG 57.539 43.478 0.00 0.00 45.21 3.11
1223 1226 6.971602 TGTAGATCGTAATGCTCCTAGAAAG 58.028 40.000 0.00 0.00 0.00 2.62
1224 1227 6.515200 GCTGTAGATCGTAATGCTCCTAGAAA 60.515 42.308 0.00 0.00 0.00 2.52
1245 1248 3.266772 TCATAAGGGACCATTTGAGCTGT 59.733 43.478 0.00 0.00 0.00 4.40
1278 1281 4.513442 AGGCGCACAATAAGAATAAGACA 58.487 39.130 10.83 0.00 0.00 3.41
1302 1305 2.019249 CATGGATCCAAACGTGCTCAT 58.981 47.619 20.67 0.00 0.00 2.90
1321 1324 1.833630 AGATCCGAGTGATTGCCTTCA 59.166 47.619 0.00 0.00 32.41 3.02
1356 1359 2.266055 CCTCCAGTCTGTTCCCGC 59.734 66.667 0.00 0.00 0.00 6.13
1368 1371 1.001764 CATGCTGCAGTTCCCTCCA 60.002 57.895 16.64 2.74 0.00 3.86
1399 1402 0.176680 AATGAGCCTTGCGACGAGAT 59.823 50.000 0.00 0.00 0.00 2.75
1421 1424 1.210967 CCGCCCTATGACCCAAAACTA 59.789 52.381 0.00 0.00 0.00 2.24
1489 1492 2.497792 TACAGTCGCCTCCGGGGTTA 62.498 60.000 0.00 0.00 36.95 2.85
1507 1510 7.517614 TGGTGAGTTACATTTTTGCTCATTA 57.482 32.000 0.00 0.00 38.28 1.90
1558 1561 0.615331 GGTGATCCCTTGCTCTCACA 59.385 55.000 4.19 0.00 39.77 3.58
1636 1639 0.391263 GATTCGGACCGCCACTTCTT 60.391 55.000 9.66 0.00 0.00 2.52
1711 1714 3.708544 CTTGGCCCCGTCCCGTAA 61.709 66.667 0.00 0.00 0.00 3.18
1779 1782 0.392461 TCGACATTAGTTGCCCTGGC 60.392 55.000 0.00 0.00 42.35 4.85
1813 1816 2.242926 TCCACGAAATGAAAATGGGCA 58.757 42.857 0.00 0.00 0.00 5.36
1818 1821 3.509967 GGGGACTTCCACGAAATGAAAAT 59.490 43.478 0.00 0.00 37.91 1.82
1841 1844 0.615331 CTACAGCCCTTTCCTCTGCA 59.385 55.000 0.00 0.00 0.00 4.41
1957 1960 3.983044 ATTATGAGAATAGGTCCCGGC 57.017 47.619 0.00 0.00 0.00 6.13
1987 1990 4.281657 CCCCTTTCCTATTTAGCTTTGCT 58.718 43.478 0.00 0.00 43.41 3.91
2012 2015 5.695851 AACTAAAAAGGCAGTCATCAGTG 57.304 39.130 0.00 0.00 0.00 3.66
2031 2034 7.670364 CATTCCACCCTTTTTGATTTCTAACT 58.330 34.615 0.00 0.00 0.00 2.24
2057 2060 0.322975 AGCCAGCCATATTAGCTCCG 59.677 55.000 0.00 0.00 38.95 4.63
2194 2197 7.165485 TGGTCGGAAAGAGATTTTAAATCTCA 58.835 34.615 34.82 19.26 45.18 3.27
2203 2206 2.637872 TGACCTGGTCGGAAAGAGATTT 59.362 45.455 21.15 0.00 34.95 2.17
2325 2328 0.036875 AGGAGCTACAGTTTGGTGGC 59.963 55.000 0.00 0.00 44.60 5.01


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

AutoCloner maintained by Alex Coulton.