Multiple sequence alignment - TraesCS1A01G158100

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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 TraesCS1A01G158100 chr1A 100.000 2252 0 0 1 2252 281369410 281367159 0 4159
1 TraesCS1A01G158100 chr6B 94.820 1332 63 6 1 1330 24940661 24939334 0 2073
2 TraesCS1A01G158100 chr3B 94.224 1333 77 0 1 1333 750919800 750921132 0 2036
3 TraesCS1A01G158100 chr3B 93.604 1329 83 2 1 1329 485696230 485694904 0 1982
4 TraesCS1A01G158100 chr5B 94.149 1333 76 2 1 1332 38468087 38469418 0 2028
5 TraesCS1A01G158100 chr3A 94.157 1335 67 11 1 1332 58873094 58871768 0 2023
6 TraesCS1A01G158100 chr2A 94.007 1335 69 9 1 1333 709825388 709826713 0 2012
7 TraesCS1A01G158100 chr2A 94.462 1264 69 1 1 1264 23927719 23926457 0 1945
8 TraesCS1A01G158100 chr7A 93.713 1336 80 4 1 1334 26584729 26583396 0 1999
9 TraesCS1A01G158100 chr1D 93.013 1331 90 2 1 1331 468700191 468701518 0 1940
10 TraesCS1A01G158100 chr2D 93.370 920 44 8 1334 2252 406975274 406974371 0 1345


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 TraesCS1A01G158100 chr1A 281367159 281369410 2251 True 4159 4159 100.000 1 2252 1 chr1A.!!$R1 2251
1 TraesCS1A01G158100 chr6B 24939334 24940661 1327 True 2073 2073 94.820 1 1330 1 chr6B.!!$R1 1329
2 TraesCS1A01G158100 chr3B 750919800 750921132 1332 False 2036 2036 94.224 1 1333 1 chr3B.!!$F1 1332
3 TraesCS1A01G158100 chr3B 485694904 485696230 1326 True 1982 1982 93.604 1 1329 1 chr3B.!!$R1 1328
4 TraesCS1A01G158100 chr5B 38468087 38469418 1331 False 2028 2028 94.149 1 1332 1 chr5B.!!$F1 1331
5 TraesCS1A01G158100 chr3A 58871768 58873094 1326 True 2023 2023 94.157 1 1332 1 chr3A.!!$R1 1331
6 TraesCS1A01G158100 chr2A 709825388 709826713 1325 False 2012 2012 94.007 1 1333 1 chr2A.!!$F1 1332
7 TraesCS1A01G158100 chr2A 23926457 23927719 1262 True 1945 1945 94.462 1 1264 1 chr2A.!!$R1 1263
8 TraesCS1A01G158100 chr7A 26583396 26584729 1333 True 1999 1999 93.713 1 1334 1 chr7A.!!$R1 1333
9 TraesCS1A01G158100 chr1D 468700191 468701518 1327 False 1940 1940 93.013 1 1331 1 chr1D.!!$F1 1330
10 TraesCS1A01G158100 chr2D 406974371 406975274 903 True 1345 1345 93.370 1334 2252 1 chr2D.!!$R1 918

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
183 184 1.511613 TAGGCTCTCCTTTGATGGGG 58.488 55.0 0.0 0.0 40.66 4.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2054 2058 0.388659 CCTCGCTTCTCTCCTGGATG 59.611 60.0 0.0 0.0 0.0 3.51 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
42 43 2.517875 GCATCAGCCGGGCATTCT 60.518 61.111 23.09 0.00 33.58 2.40
183 184 1.511613 TAGGCTCTCCTTTGATGGGG 58.488 55.000 0.00 0.00 40.66 4.96
190 191 2.986019 TCTCCTTTGATGGGGAGTTCAA 59.014 45.455 8.56 0.00 46.56 2.69
230 231 2.289945 GCAAAGTGACAGTCATCTCCCT 60.290 50.000 6.51 0.00 0.00 4.20
240 241 5.211973 ACAGTCATCTCCCTAGCATAGAAA 58.788 41.667 0.00 0.00 42.77 2.52
269 270 3.002583 TGTCTCAGGGCGCCATCA 61.003 61.111 30.85 13.03 0.00 3.07
377 379 4.098044 CCGGATATACTCCATGTATCGCTT 59.902 45.833 0.00 0.00 45.24 4.68
1251 1255 0.246910 TGCGGGCGTCATACAGTTAA 59.753 50.000 0.00 0.00 0.00 2.01
1298 1302 4.612264 AAAGAGCCATTTTGTGCTGAAT 57.388 36.364 0.00 0.00 38.11 2.57
1302 1306 4.992951 AGAGCCATTTTGTGCTGAATTTTC 59.007 37.500 0.00 0.00 38.11 2.29
1304 1308 3.120580 GCCATTTTGTGCTGAATTTTCGG 60.121 43.478 0.00 0.00 36.64 4.30
1338 1342 0.382158 TGTGATTTTTCACGCGGCAA 59.618 45.000 12.47 0.00 43.12 4.52
1349 1353 1.798725 CGCGGCAAAAGACATGCAG 60.799 57.895 0.00 0.00 45.60 4.41
1350 1354 1.286880 GCGGCAAAAGACATGCAGT 59.713 52.632 0.00 0.00 45.60 4.40
1451 1455 3.002965 GCTTTTACGTAGGTGTGCAAAGT 59.997 43.478 12.68 0.00 31.26 2.66
1460 1464 2.618709 AGGTGTGCAAAGTTAGCTTCAC 59.381 45.455 0.00 4.74 37.08 3.18
1480 1484 7.331934 GCTTCACGGAATAATATAGCTTGATCA 59.668 37.037 0.00 0.00 0.00 2.92
1509 1513 6.854496 TGTTCAGTTAAATGTAAACTCGCT 57.146 33.333 2.43 0.00 34.99 4.93
1510 1514 7.949903 TGTTCAGTTAAATGTAAACTCGCTA 57.050 32.000 2.43 0.00 34.99 4.26
1520 1524 4.487948 TGTAAACTCGCTATACGTGCTTT 58.512 39.130 0.00 0.00 44.19 3.51
1541 1545 0.466124 GCTTGGGTCGGCTCTAGATT 59.534 55.000 1.45 0.00 0.00 2.40
1546 1550 1.964223 GGGTCGGCTCTAGATTGATCA 59.036 52.381 0.00 0.00 0.00 2.92
1562 1566 8.529424 AGATTGATCAGATTAATTCTTGCCAA 57.471 30.769 2.09 0.00 29.93 4.52
1608 1612 9.031360 TCAAGCTTTACTACTATTTAGCGATTG 57.969 33.333 0.00 0.00 34.01 2.67
1641 1645 3.881688 CTGATGTGATTGATCCAACTCCC 59.118 47.826 0.00 0.00 0.00 4.30
1668 1672 1.144057 GGTGCTCCATCCACTACGG 59.856 63.158 0.00 0.00 33.78 4.02
1700 1704 5.555017 ACCATGATTAGCAATACCTAGCTG 58.445 41.667 0.00 0.00 41.97 4.24
1701 1705 4.940046 CCATGATTAGCAATACCTAGCTGG 59.060 45.833 0.00 0.00 41.97 4.85
1702 1706 5.280164 CCATGATTAGCAATACCTAGCTGGA 60.280 44.000 0.00 0.00 41.97 3.86
1703 1707 5.474578 TGATTAGCAATACCTAGCTGGAG 57.525 43.478 0.00 0.00 41.97 3.86
1704 1708 4.901849 TGATTAGCAATACCTAGCTGGAGT 59.098 41.667 0.00 0.00 41.97 3.85
1796 1800 4.631813 CAGGGACTTTAAGACATAGTGCAC 59.368 45.833 9.40 9.40 34.60 4.57
1798 1802 4.631813 GGGACTTTAAGACATAGTGCACTG 59.368 45.833 29.57 16.83 32.60 3.66
1800 1804 4.003648 ACTTTAAGACATAGTGCACTGCC 58.996 43.478 29.57 14.41 0.00 4.85
1804 1808 0.379669 GACATAGTGCACTGCCATGC 59.620 55.000 29.57 15.75 46.32 4.06
1927 1931 4.142790 AGATTGATGAGGCTAAAGCATGG 58.857 43.478 4.07 0.00 44.36 3.66
1981 1985 5.124457 GCCTATGCAGATTTTTGAGAGTCAA 59.876 40.000 0.00 0.00 37.47 3.18
1982 1986 6.677431 GCCTATGCAGATTTTTGAGAGTCAAG 60.677 42.308 0.00 0.00 36.09 3.02
1983 1987 5.640189 ATGCAGATTTTTGAGAGTCAAGG 57.360 39.130 0.00 0.00 37.70 3.61
1984 1988 4.717877 TGCAGATTTTTGAGAGTCAAGGA 58.282 39.130 0.00 0.00 37.70 3.36
1985 1989 5.319453 TGCAGATTTTTGAGAGTCAAGGAT 58.681 37.500 0.00 0.00 37.70 3.24
1986 1990 5.182570 TGCAGATTTTTGAGAGTCAAGGATG 59.817 40.000 0.00 0.00 37.70 3.51
1987 1991 5.413833 GCAGATTTTTGAGAGTCAAGGATGA 59.586 40.000 0.00 0.00 37.70 2.92
1995 1999 4.779489 TGAGAGTCAAGGATGAAGATTGGA 59.221 41.667 0.00 0.00 37.30 3.53
1999 2003 3.944015 GTCAAGGATGAAGATTGGACTGG 59.056 47.826 0.00 0.00 37.30 4.00
2003 2007 2.239654 GGATGAAGATTGGACTGGTGGA 59.760 50.000 0.00 0.00 0.00 4.02
2028 2032 0.886563 GCCTCTGTGCTTTGCTGAAT 59.113 50.000 0.00 0.00 0.00 2.57
2054 2058 1.135527 CATCCATCCACCAACATGCAC 59.864 52.381 0.00 0.00 0.00 4.57
2090 2094 2.939103 CGAGGCTTCAGATTTGGTAAGG 59.061 50.000 0.00 0.00 0.00 2.69
2098 2102 6.823689 GCTTCAGATTTGGTAAGGTGATAAGA 59.176 38.462 0.00 0.00 0.00 2.10
2148 2152 1.870064 TGGAGGATGAGCATGTCAGA 58.130 50.000 0.00 0.00 39.07 3.27
2172 2177 5.657474 TCAGTTCGATTTGTATAGGTGACC 58.343 41.667 0.00 0.00 0.00 4.02
2179 2184 7.557724 TCGATTTGTATAGGTGACCACAATAA 58.442 34.615 3.63 0.00 31.45 1.40
2196 2201 6.267817 CACAATAATAATGGCCAGACAACAG 58.732 40.000 13.05 0.00 0.00 3.16
2206 2211 2.787994 CCAGACAACAGAATGCTTCCT 58.212 47.619 0.00 0.00 42.53 3.36
2222 2227 0.178992 TCCTTGCAAACCAGACCCAG 60.179 55.000 0.00 0.00 0.00 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 2.942804 TGGATTGCTGAACACTTTGGA 58.057 42.857 0.00 0.00 0.00 3.53
85 86 1.911702 GAGCCAGGGGTACAAGGGAC 61.912 65.000 0.00 0.00 0.00 4.46
183 184 6.822676 AGGATGTTTCTCTGATCATTGAACTC 59.177 38.462 0.00 1.89 0.00 3.01
187 188 4.880120 GCAGGATGTTTCTCTGATCATTGA 59.120 41.667 0.00 0.00 39.31 2.57
190 191 4.498894 TGCAGGATGTTTCTCTGATCAT 57.501 40.909 0.00 0.00 39.31 2.45
230 231 9.890629 AGACACATACTTTTCATTTCTATGCTA 57.109 29.630 0.00 0.00 0.00 3.49
240 241 4.265073 GCCCTGAGACACATACTTTTCAT 58.735 43.478 0.00 0.00 0.00 2.57
325 327 2.637947 GCTTCTCCCTTTGATCTCACC 58.362 52.381 0.00 0.00 0.00 4.02
377 379 6.595326 GGTTCATGACAAGATGAAGTATGACA 59.405 38.462 0.00 0.00 41.85 3.58
416 418 3.837355 AGGGTTTTTGATCAGCTTCACT 58.163 40.909 0.00 0.00 0.00 3.41
596 598 6.061022 TGGTGTATGGAAGAAGAATTAGCA 57.939 37.500 0.00 0.00 0.00 3.49
597 599 8.854614 ATATGGTGTATGGAAGAAGAATTAGC 57.145 34.615 0.00 0.00 0.00 3.09
937 939 2.159043 TGTGGATCTGAGCCGAAGATTC 60.159 50.000 7.54 0.00 34.50 2.52
1125 1127 4.776322 CATGACGCCTCGGCCCAA 62.776 66.667 0.00 0.00 37.98 4.12
1191 1194 2.264005 ACATAACGCCTTGGTCAACA 57.736 45.000 0.00 0.00 0.00 3.33
1304 1308 0.463620 TCACAAAACTGGCCCTTTGC 59.536 50.000 17.49 0.00 36.24 3.68
1338 1342 3.853307 GCTTTGCGTAACTGCATGTCTTT 60.853 43.478 5.74 0.00 45.78 2.52
1349 1353 3.424962 CCAAGAAGCTAGCTTTGCGTAAC 60.425 47.826 29.84 15.60 36.26 2.50
1350 1354 2.742053 CCAAGAAGCTAGCTTTGCGTAA 59.258 45.455 29.84 0.00 36.26 3.18
1451 1455 8.364894 TCAAGCTATATTATTCCGTGAAGCTAA 58.635 33.333 0.00 0.00 38.06 3.09
1485 1489 7.435068 AGCGAGTTTACATTTAACTGAACAT 57.565 32.000 0.00 0.00 36.04 2.71
1496 1500 4.679662 AGCACGTATAGCGAGTTTACATT 58.320 39.130 0.00 0.00 44.77 2.71
1509 1513 2.745281 GACCCAAGCAAAAGCACGTATA 59.255 45.455 0.00 0.00 0.00 1.47
1510 1514 1.539827 GACCCAAGCAAAAGCACGTAT 59.460 47.619 0.00 0.00 0.00 3.06
1520 1524 0.902984 TCTAGAGCCGACCCAAGCAA 60.903 55.000 0.00 0.00 0.00 3.91
1529 1533 6.901081 TTAATCTGATCAATCTAGAGCCGA 57.099 37.500 0.00 0.00 0.00 5.54
1530 1534 8.034215 AGAATTAATCTGATCAATCTAGAGCCG 58.966 37.037 0.00 0.00 36.88 5.52
1541 1545 8.125978 AGTTTTGGCAAGAATTAATCTGATCA 57.874 30.769 0.00 0.00 38.79 2.92
1546 1550 7.015584 ACCTGAAGTTTTGGCAAGAATTAATCT 59.984 33.333 3.33 0.00 41.32 2.40
1578 1582 8.321716 CGCTAAATAGTAGTAAAGCTTGAAGTG 58.678 37.037 0.00 0.00 0.00 3.16
1585 1589 6.424207 GGCAATCGCTAAATAGTAGTAAAGCT 59.576 38.462 7.80 0.00 38.60 3.74
1608 1612 4.274214 TCAATCACATCAGATTCAATCGGC 59.726 41.667 0.00 0.00 36.13 5.54
1651 1655 1.144057 CCCGTAGTGGATGGAGCAC 59.856 63.158 0.00 0.00 42.00 4.40
1661 1665 3.455469 GTCCCCGGTCCCGTAGTG 61.455 72.222 0.00 0.00 37.81 2.74
1668 1672 0.396811 CTAATCATGGTCCCCGGTCC 59.603 60.000 0.00 0.05 0.00 4.46
1700 1704 6.330278 GGCCACAAATTTTATTCAGTACTCC 58.670 40.000 0.00 0.00 0.00 3.85
1701 1705 6.152831 AGGGCCACAAATTTTATTCAGTACTC 59.847 38.462 6.18 0.00 0.00 2.59
1702 1706 6.016555 AGGGCCACAAATTTTATTCAGTACT 58.983 36.000 6.18 0.00 0.00 2.73
1703 1707 6.071616 TGAGGGCCACAAATTTTATTCAGTAC 60.072 38.462 6.18 0.00 0.00 2.73
1704 1708 6.013379 TGAGGGCCACAAATTTTATTCAGTA 58.987 36.000 6.18 0.00 0.00 2.74
1773 1777 4.631813 GTGCACTATGTCTTAAAGTCCCTG 59.368 45.833 10.32 0.00 0.00 4.45
1796 1800 2.298163 GGGATAAAGGATTGCATGGCAG 59.702 50.000 0.00 0.00 40.61 4.85
1798 1802 2.560105 GAGGGATAAAGGATTGCATGGC 59.440 50.000 0.00 0.00 0.00 4.40
1800 1804 2.227388 GCGAGGGATAAAGGATTGCATG 59.773 50.000 0.00 0.00 0.00 4.06
1804 1808 3.243201 GCAAAGCGAGGGATAAAGGATTG 60.243 47.826 0.00 0.00 0.00 2.67
1927 1931 8.786898 ACTCCATTATGCATTACAATATGACAC 58.213 33.333 3.54 0.00 0.00 3.67
1974 1978 4.782156 AGTCCAATCTTCATCCTTGACTCT 59.218 41.667 0.00 0.00 0.00 3.24
1981 1985 2.240667 CCACCAGTCCAATCTTCATCCT 59.759 50.000 0.00 0.00 0.00 3.24
1982 1986 2.239654 TCCACCAGTCCAATCTTCATCC 59.760 50.000 0.00 0.00 0.00 3.51
1983 1987 3.054802 AGTCCACCAGTCCAATCTTCATC 60.055 47.826 0.00 0.00 0.00 2.92
1984 1988 2.915604 AGTCCACCAGTCCAATCTTCAT 59.084 45.455 0.00 0.00 0.00 2.57
1985 1989 2.338809 AGTCCACCAGTCCAATCTTCA 58.661 47.619 0.00 0.00 0.00 3.02
1986 1990 3.008485 AGAAGTCCACCAGTCCAATCTTC 59.992 47.826 0.00 0.00 0.00 2.87
1987 1991 2.982488 AGAAGTCCACCAGTCCAATCTT 59.018 45.455 0.00 0.00 0.00 2.40
1995 1999 0.472734 AGAGGCAGAAGTCCACCAGT 60.473 55.000 0.00 0.00 0.00 4.00
1999 2003 0.952984 GCACAGAGGCAGAAGTCCAC 60.953 60.000 0.00 0.00 0.00 4.02
2003 2007 1.602311 CAAAGCACAGAGGCAGAAGT 58.398 50.000 0.00 0.00 35.83 3.01
2028 2032 2.025510 TGTTGGTGGATGGATGTATGCA 60.026 45.455 0.00 0.00 0.00 3.96
2054 2058 0.388659 CCTCGCTTCTCTCCTGGATG 59.611 60.000 0.00 0.00 0.00 3.51
2090 2094 5.907207 TGTCATTAGCTCCACTCTTATCAC 58.093 41.667 0.00 0.00 0.00 3.06
2098 2102 4.697352 GTGATTGTTGTCATTAGCTCCACT 59.303 41.667 0.00 0.00 0.00 4.00
2131 2135 3.069872 ACTGATCTGACATGCTCATCCTC 59.930 47.826 6.60 0.00 0.00 3.71
2132 2136 3.039743 ACTGATCTGACATGCTCATCCT 58.960 45.455 6.60 0.00 0.00 3.24
2133 2137 3.472283 ACTGATCTGACATGCTCATCC 57.528 47.619 6.60 0.00 0.00 3.51
2134 2138 3.490155 CGAACTGATCTGACATGCTCATC 59.510 47.826 6.60 0.00 0.00 2.92
2135 2139 3.131755 TCGAACTGATCTGACATGCTCAT 59.868 43.478 6.60 0.00 0.00 2.90
2136 2140 2.493278 TCGAACTGATCTGACATGCTCA 59.507 45.455 6.60 0.00 0.00 4.26
2148 2152 6.127168 TGGTCACCTATACAAATCGAACTGAT 60.127 38.462 0.00 0.00 39.67 2.90
2172 2177 6.095300 TCTGTTGTCTGGCCATTATTATTGTG 59.905 38.462 5.51 0.00 0.00 3.33
2179 2184 3.382546 GCATTCTGTTGTCTGGCCATTAT 59.617 43.478 5.51 0.00 0.00 1.28
2196 2201 2.297033 TCTGGTTTGCAAGGAAGCATTC 59.703 45.455 0.00 0.00 45.19 2.67
2206 2211 2.738587 TAACTGGGTCTGGTTTGCAA 57.261 45.000 0.00 0.00 0.00 4.08


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

AutoCloner maintained by Alex Coulton.