Multiple sequence alignment - TraesCS1B01G193900

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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 TraesCS1B01G193900 chr1B 100.000 2192 0 0 1 2192 348908187 348910378 0 4048
1 TraesCS1B01G193900 chr1B 97.497 799 19 1 1 798 619195358 619194560 0 1363
2 TraesCS1B01G193900 chr4D 94.989 1397 63 5 799 2192 123448186 123446794 0 2185
3 TraesCS1B01G193900 chr4D 97.872 799 16 1 1 798 123449013 123448215 0 1380
4 TraesCS1B01G193900 chr3B 94.986 1396 61 5 799 2192 92295935 92294547 0 2182
5 TraesCS1B01G193900 chr3B 97.372 799 17 3 1 798 92296759 92295964 0 1356
6 TraesCS1B01G193900 chr2B 94.914 1396 60 5 799 2192 234540360 234538974 0 2174
7 TraesCS1B01G193900 chr2B 94.771 1396 62 5 799 2192 234501661 234500275 0 2163
8 TraesCS1B01G193900 chr2B 97.747 799 17 1 1 798 234541187 234540389 0 1375
9 TraesCS1B01G193900 chr3A 94.842 1396 61 5 799 2192 495103960 495102574 0 2169
10 TraesCS1B01G193900 chr3A 97.497 799 19 1 1 798 495104787 495103989 0 1363
11 TraesCS1B01G193900 chr1A 94.903 1393 59 6 799 2189 278521994 278523376 0 2169
12 TraesCS1B01G193900 chr1A 97.747 799 17 1 1 798 278521167 278521965 0 1375
13 TraesCS1B01G193900 chr6D 94.763 1394 66 6 799 2189 458940554 458939165 0 2163
14 TraesCS1B01G193900 chrUn 94.756 1392 63 4 799 2189 217908468 217909850 0 2158
15 TraesCS1B01G193900 chrUn 97.247 799 21 1 1 798 217907641 217908439 0 1352
16 TraesCS1B01G193900 chr7D 94.699 1396 62 6 799 2192 307145824 307144439 0 2158
17 TraesCS1B01G193900 chr3D 97.497 799 19 1 1 798 501838407 501837609 0 1363
18 TraesCS1B01G193900 chr6A 97.372 799 17 2 1 798 597253020 597252225 0 1356


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 TraesCS1B01G193900 chr1B 348908187 348910378 2191 False 4048.0 4048 100.0000 1 2192 1 chr1B.!!$F1 2191
1 TraesCS1B01G193900 chr1B 619194560 619195358 798 True 1363.0 1363 97.4970 1 798 1 chr1B.!!$R1 797
2 TraesCS1B01G193900 chr4D 123446794 123449013 2219 True 1782.5 2185 96.4305 1 2192 2 chr4D.!!$R1 2191
3 TraesCS1B01G193900 chr3B 92294547 92296759 2212 True 1769.0 2182 96.1790 1 2192 2 chr3B.!!$R1 2191
4 TraesCS1B01G193900 chr2B 234500275 234501661 1386 True 2163.0 2163 94.7710 799 2192 1 chr2B.!!$R1 1393
5 TraesCS1B01G193900 chr2B 234538974 234541187 2213 True 1774.5 2174 96.3305 1 2192 2 chr2B.!!$R2 2191
6 TraesCS1B01G193900 chr3A 495102574 495104787 2213 True 1766.0 2169 96.1695 1 2192 2 chr3A.!!$R1 2191
7 TraesCS1B01G193900 chr1A 278521167 278523376 2209 False 1772.0 2169 96.3250 1 2189 2 chr1A.!!$F1 2188
8 TraesCS1B01G193900 chr6D 458939165 458940554 1389 True 2163.0 2163 94.7630 799 2189 1 chr6D.!!$R1 1390
9 TraesCS1B01G193900 chrUn 217907641 217909850 2209 False 1755.0 2158 96.0015 1 2189 2 chrUn.!!$F1 2188
10 TraesCS1B01G193900 chr7D 307144439 307145824 1385 True 2158.0 2158 94.6990 799 2192 1 chr7D.!!$R1 1393
11 TraesCS1B01G193900 chr3D 501837609 501838407 798 True 1363.0 1363 97.4970 1 798 1 chr3D.!!$R1 797
12 TraesCS1B01G193900 chr6A 597252225 597253020 795 True 1356.0 1356 97.3720 1 798 1 chr6A.!!$R1 797

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
223 224 0.250858 TGGTGGAGTGGCACAAGATG 60.251 55.0 21.41 0.0 44.16 2.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1730 1769 0.107508 CTCCATGCCCAACGAGATGT 60.108 55.0 0.0 0.0 0.0 3.06 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
184 185 4.088351 TCCCGGGAGCCAGGATGA 62.088 66.667 22.63 0.00 39.69 2.92
186 187 2.190578 CCGGGAGCCAGGATGAAC 59.809 66.667 0.00 0.00 39.69 3.18
223 224 0.250858 TGGTGGAGTGGCACAAGATG 60.251 55.000 21.41 0.00 44.16 2.90
313 314 0.687354 AGAGATGTCAACCGGCAACT 59.313 50.000 0.00 0.00 0.00 3.16
443 444 6.523035 TTGATAGCAATATGGGGGAAGTTA 57.477 37.500 0.00 0.00 0.00 2.24
543 544 3.140141 CGACGTACCCGGGGCTAA 61.140 66.667 27.92 3.89 38.78 3.09
695 697 2.915659 TCTGGGCACGTCCGAACT 60.916 61.111 0.00 0.00 34.94 3.01
820 850 0.534203 TCAAAAAGCGAAGGCCGAGT 60.534 50.000 0.00 0.00 41.76 4.18
828 858 0.813184 CGAAGGCCGAGTTGTAGGTA 59.187 55.000 0.00 0.00 41.76 3.08
831 861 1.636148 AGGCCGAGTTGTAGGTAACA 58.364 50.000 0.00 0.00 41.41 2.41
884 914 0.537188 TCTCCTGGATCAAAGCGGAC 59.463 55.000 0.00 0.00 0.00 4.79
902 932 0.889186 ACCAGCTCGCCAAATTCGTT 60.889 50.000 0.00 0.00 0.00 3.85
906 936 1.812571 AGCTCGCCAAATTCGTTGATT 59.187 42.857 0.00 0.00 39.87 2.57
993 1023 1.778803 CCCCTTTCCCCCTATCCCC 60.779 68.421 0.00 0.00 0.00 4.81
994 1024 1.778803 CCCTTTCCCCCTATCCCCC 60.779 68.421 0.00 0.00 0.00 5.40
1072 1102 1.218316 GACTCCGAAAGCATCCCGT 59.782 57.895 0.00 0.00 0.00 5.28
1099 1129 5.453903 CCTCTGAGAAAGAAACTCCTCAACA 60.454 44.000 6.17 0.00 35.52 3.33
1126 1156 7.768240 TCACAAGATAAAGAAGTATGACGCTA 58.232 34.615 0.00 0.00 0.00 4.26
1150 1180 6.208988 TGTGTCTGACTCTATTGGTCATAC 57.791 41.667 9.51 0.00 41.90 2.39
1223 1253 3.960755 TCATAAGGAAAGATGCCTCTCGA 59.039 43.478 0.00 0.00 33.76 4.04
1281 1311 5.585820 ACTCCCACGTACAATTTGTTTTT 57.414 34.783 7.45 0.00 0.00 1.94
1405 1444 2.639065 GGTATGCTGGGATTCGTGAAA 58.361 47.619 0.00 0.00 0.00 2.69
1475 1514 1.881324 GGTACCAGAGGAGATCGCTAC 59.119 57.143 7.15 0.00 0.00 3.58
1491 1530 4.053983 TCGCTACGATCGTTACTGTATCT 58.946 43.478 27.88 0.00 0.00 1.98
1507 1546 5.532779 ACTGTATCTGTATCGAAGAGATGCA 59.467 40.000 17.16 17.16 44.66 3.96
1625 1664 6.591001 TCGAATGAAACTATCCATGGAATCA 58.409 36.000 20.67 17.30 0.00 2.57
1632 1671 0.178984 ATCCATGGAATCATGCGCCA 60.179 50.000 20.67 3.94 47.00 5.69
1653 1692 2.182014 TGTGAAACGTAGATCATCGCG 58.818 47.619 0.00 0.00 42.39 5.87
1730 1769 2.424842 AAAGCATCCCGAGGTTGGCA 62.425 55.000 0.00 0.00 0.00 4.92
1798 1837 0.241213 GGAGCAGTTTCTTTTCCCGC 59.759 55.000 0.00 0.00 0.00 6.13
1960 1999 1.812686 AAGCTGACACGCCGGAGTTA 61.813 55.000 8.62 0.00 0.00 2.24
2053 2093 2.501723 AGGATTCCAATGTACTGCGTCT 59.498 45.455 5.29 0.00 0.00 4.18
2074 2114 0.391661 GGATCAGAACGAGCTTGCCA 60.392 55.000 0.00 0.00 0.00 4.92
2075 2115 1.442769 GATCAGAACGAGCTTGCCAA 58.557 50.000 0.00 0.00 0.00 4.52
2086 2126 1.525995 CTTGCCAACGGACCACTGT 60.526 57.895 0.00 0.00 37.19 3.55
2097 2137 0.736325 GACCACTGTCGTCCCATTCG 60.736 60.000 0.00 0.00 0.00 3.34
2113 2153 0.966179 TTCGTTAGTGAGCTGGAGCA 59.034 50.000 0.00 0.00 45.16 4.26
2130 2170 1.561076 AGCACTGCCATCTTATCCACA 59.439 47.619 0.00 0.00 0.00 4.17
2189 2229 2.740506 AAGAAAAGGACCGGGAAACA 57.259 45.000 6.32 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
64 65 6.092670 GCATGAGTAGTTGAAGCAAGTGAATA 59.907 38.462 0.00 0.00 0.00 1.75
184 185 3.009723 CAGGTCATATGAAACTGGCGTT 58.990 45.455 22.18 0.00 31.57 4.84
186 187 1.942657 CCAGGTCATATGAAACTGGCG 59.057 52.381 29.99 16.72 41.43 5.69
230 231 6.312426 GGAATCAATATCTCGACATAAGCCAG 59.688 42.308 0.00 0.00 0.00 4.85
313 314 8.058667 TCCACTAATCGTTGTTTCTAGATACA 57.941 34.615 11.47 11.47 0.00 2.29
443 444 0.467290 AACCGTTGTTGCCTGATGGT 60.467 50.000 0.00 0.00 34.22 3.55
695 697 2.350895 CCCCGGTGAACTCATGCA 59.649 61.111 0.00 0.00 0.00 3.96
828 858 1.608590 CTTTTCGGTGCAGGTCATGTT 59.391 47.619 0.00 0.00 0.00 2.71
831 861 0.110486 ACCTTTTCGGTGCAGGTCAT 59.890 50.000 0.00 0.00 46.80 3.06
884 914 0.454957 CAACGAATTTGGCGAGCTGG 60.455 55.000 0.00 0.00 0.00 4.85
902 932 2.515991 GGGCGCCCGATTCAATCA 60.516 61.111 33.60 0.00 0.00 2.57
974 1004 1.324105 GGGATAGGGGGAAAGGGGA 59.676 63.158 0.00 0.00 0.00 4.81
993 1023 2.158608 CCTGCTCCTAAACATAAGGGGG 60.159 54.545 0.00 0.00 34.91 5.40
994 1024 2.777692 TCCTGCTCCTAAACATAAGGGG 59.222 50.000 0.00 0.00 37.69 4.79
1012 1042 0.250513 GTCGTTCTTGGGCAGATCCT 59.749 55.000 0.00 0.00 34.39 3.24
1061 1091 0.541863 CAGAGGGTACGGGATGCTTT 59.458 55.000 0.00 0.00 0.00 3.51
1066 1096 2.024273 TCTTTCTCAGAGGGTACGGGAT 60.024 50.000 0.00 0.00 0.00 3.85
1072 1102 4.753186 AGGAGTTTCTTTCTCAGAGGGTA 58.247 43.478 0.00 0.00 34.04 3.69
1099 1129 7.766278 AGCGTCATACTTCTTTATCTTGTGATT 59.234 33.333 0.00 0.00 34.32 2.57
1126 1156 5.946942 ATGACCAATAGAGTCAGACACAT 57.053 39.130 2.66 0.00 46.76 3.21
1150 1180 2.256461 GCCGCAACAGCAAGGAAG 59.744 61.111 0.00 0.00 0.00 3.46
1223 1253 3.803021 GCTCGAATCATTCTCAGATGCCT 60.803 47.826 0.00 0.00 0.00 4.75
1296 1334 2.363172 GGACCCTGTCAGGCTCCTC 61.363 68.421 21.86 9.81 32.73 3.71
1316 1354 3.636231 CCCGGGCCAAGTCAGTGA 61.636 66.667 8.08 0.00 0.00 3.41
1475 1514 6.149504 TCGATACAGATACAGTAACGATCG 57.850 41.667 14.88 14.88 40.30 3.69
1491 1530 5.120674 CACTTTGTTGCATCTCTTCGATACA 59.879 40.000 0.00 0.00 0.00 2.29
1507 1546 4.792704 GCACAATGATCCGAACACTTTGTT 60.793 41.667 0.00 0.00 44.37 2.83
1625 1664 0.726827 CTACGTTTCACATGGCGCAT 59.273 50.000 10.83 0.00 0.00 4.73
1632 1671 2.789339 CGCGATGATCTACGTTTCACAT 59.211 45.455 0.00 0.00 0.00 3.21
1730 1769 0.107508 CTCCATGCCCAACGAGATGT 60.108 55.000 0.00 0.00 0.00 3.06
1818 1857 0.391597 TGAAGAACCGGAAGCGAAGT 59.608 50.000 9.46 0.00 0.00 3.01
1960 1999 1.376466 CCCTGTTGTGCCAGTAGCT 59.624 57.895 0.00 0.00 44.23 3.32
2053 2093 1.137086 GGCAAGCTCGTTCTGATCCTA 59.863 52.381 0.00 0.00 0.00 2.94
2074 2114 2.732658 GGACGACAGTGGTCCGTT 59.267 61.111 18.08 0.00 44.04 4.44
2086 2126 1.135199 GCTCACTAACGAATGGGACGA 60.135 52.381 0.00 0.00 34.70 4.20
2097 2137 1.719600 CAGTGCTCCAGCTCACTAAC 58.280 55.000 5.55 0.00 41.19 2.34
2113 2153 4.574674 TTTCTGTGGATAAGATGGCAGT 57.425 40.909 0.00 0.00 0.00 4.40
2130 2170 1.654105 CGATAGCTTGACGCGTTTTCT 59.346 47.619 15.53 11.15 45.59 2.52


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

AutoCloner maintained by Alex Coulton.