Multiple sequence alignment - TraesCS7D01G284700

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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 TraesCS7D01G284700 chr7D 100.000 2316 0 0 1 2316 304919371 304917056 0 4277
1 TraesCS7D01G284700 chr7D 95.396 2324 97 6 1 2315 203556349 203554027 0 3690
2 TraesCS7D01G284700 chr7D 95.355 2325 97 6 1 2315 626698494 626696171 0 3685
3 TraesCS7D01G284700 chr5A 95.699 2325 89 7 1 2315 300072975 300075298 0 3729
4 TraesCS7D01G284700 chr5A 95.525 2324 91 8 1 2315 16602923 16600604 0 3703
5 TraesCS7D01G284700 chr7A 95.578 2329 88 7 1 2315 4959834 4962161 0 3716
6 TraesCS7D01G284700 chrUn 95.570 2325 92 6 1 2315 189392535 189394858 0 3712
7 TraesCS7D01G284700 chr2A 95.527 2325 93 6 1 2315 618279960 618277637 0 3707
8 TraesCS7D01G284700 chr6A 95.482 2324 94 7 1 2315 289128628 289130949 0 3699
9 TraesCS7D01G284700 chr7B 95.441 2325 95 7 1 2315 743086195 743088518 0 3696


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 TraesCS7D01G284700 chr7D 304917056 304919371 2315 True 4277 4277 100.000 1 2316 1 chr7D.!!$R2 2315
1 TraesCS7D01G284700 chr7D 203554027 203556349 2322 True 3690 3690 95.396 1 2315 1 chr7D.!!$R1 2314
2 TraesCS7D01G284700 chr7D 626696171 626698494 2323 True 3685 3685 95.355 1 2315 1 chr7D.!!$R3 2314
3 TraesCS7D01G284700 chr5A 300072975 300075298 2323 False 3729 3729 95.699 1 2315 1 chr5A.!!$F1 2314
4 TraesCS7D01G284700 chr5A 16600604 16602923 2319 True 3703 3703 95.525 1 2315 1 chr5A.!!$R1 2314
5 TraesCS7D01G284700 chr7A 4959834 4962161 2327 False 3716 3716 95.578 1 2315 1 chr7A.!!$F1 2314
6 TraesCS7D01G284700 chrUn 189392535 189394858 2323 False 3712 3712 95.570 1 2315 1 chrUn.!!$F1 2314
7 TraesCS7D01G284700 chr2A 618277637 618279960 2323 True 3707 3707 95.527 1 2315 1 chr2A.!!$R1 2314
8 TraesCS7D01G284700 chr6A 289128628 289130949 2321 False 3699 3699 95.482 1 2315 1 chr6A.!!$F1 2314
9 TraesCS7D01G284700 chr7B 743086195 743088518 2323 False 3696 3696 95.441 1 2315 1 chr7B.!!$F1 2314

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
926 935 0.603707 TCTCCCGTGCTTGCTTTCAG 60.604 55.0 0.0 0.0 0.0 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1985 2005 1.32868 CAGCCAGTAAGCAATGCGTAG 59.671 52.381 0.22 0.0 34.23 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
88 92 3.058639 CGGAGTTCTTTCTTTGCTTCCAG 60.059 47.826 0.00 0.00 0.00 3.86
196 200 2.823154 ACACCTTCTGCAGACTCTACTC 59.177 50.000 18.03 0.00 0.00 2.59
240 244 6.094048 AGGGTAAATATGTGCATTCATATCGC 59.906 38.462 9.55 6.78 39.26 4.58
241 245 6.258160 GGTAAATATGTGCATTCATATCGCC 58.742 40.000 9.55 8.64 39.26 5.54
242 246 6.094048 GGTAAATATGTGCATTCATATCGCCT 59.906 38.462 9.55 0.79 39.26 5.52
249 253 4.697352 GTGCATTCATATCGCCTAGGAAAT 59.303 41.667 14.75 7.27 34.11 2.17
273 277 5.215252 ACAATGACTCTTCTTCTTTCCGA 57.785 39.130 0.00 0.00 0.00 4.55
354 358 5.676837 GCATTCATTGTCACCGATCATTGAA 60.677 40.000 0.00 0.00 37.88 2.69
426 430 2.037772 CGGCTATAGACTCAAAGGGCAT 59.962 50.000 3.21 0.00 0.00 4.40
439 443 2.111878 GGCATAGACAGGCCGCAT 59.888 61.111 0.00 0.00 42.67 4.73
522 530 3.877508 GCCGATTCAACTTAGCATTACCT 59.122 43.478 0.00 0.00 0.00 3.08
545 553 3.527533 ACTCGTAACTTCAAGCACAACA 58.472 40.909 0.00 0.00 0.00 3.33
603 611 1.071699 CAAACCCAAACTCTCCTCCGA 59.928 52.381 0.00 0.00 0.00 4.55
674 682 5.105146 AGCAAGTTCCTATCGAGAACAAGAT 60.105 40.000 15.79 5.96 44.91 2.40
765 773 8.331740 TCAGTGAAATGGAATAAGGAAGAGAAT 58.668 33.333 0.00 0.00 0.00 2.40
819 827 2.746279 TGAGGTTTTCAAGCAAGGGA 57.254 45.000 0.00 0.00 31.34 4.20
830 838 5.224821 TCAAGCAAGGGATGAGATAGATG 57.775 43.478 0.00 0.00 0.00 2.90
842 850 7.256475 GGGATGAGATAGATGTACAAACCAGAT 60.256 40.741 0.00 0.00 0.00 2.90
856 864 4.978083 AACCAGATGAATTCACATCAGC 57.022 40.909 11.07 0.00 46.11 4.26
912 921 3.861840 TCGACTCACATTTTGATCTCCC 58.138 45.455 0.00 0.00 32.17 4.30
913 922 2.604914 CGACTCACATTTTGATCTCCCG 59.395 50.000 0.00 0.00 32.17 5.14
914 923 3.600388 GACTCACATTTTGATCTCCCGT 58.400 45.455 0.00 0.00 32.17 5.28
926 935 0.603707 TCTCCCGTGCTTGCTTTCAG 60.604 55.000 0.00 0.00 0.00 3.02
937 946 2.270434 TGCTTTCAGAGTCCCCCTAT 57.730 50.000 0.00 0.00 0.00 2.57
947 956 2.773918 CCCCCTATGAGCAGCCCA 60.774 66.667 0.00 0.00 0.00 5.36
976 985 2.106338 TGAAGGAGTTCATTCAGCACCA 59.894 45.455 5.22 0.00 41.05 4.17
989 998 4.749310 CACCAAGCCGAGCGAGCT 62.749 66.667 0.00 0.00 44.19 4.09
1024 1033 3.663995 TGATTGTACCGAACGAAGGAA 57.336 42.857 0.00 0.00 0.00 3.36
1027 1036 4.628333 TGATTGTACCGAACGAAGGAATTC 59.372 41.667 0.00 0.00 0.00 2.17
1291 1303 5.191426 TCTTCACTACTACCGCTTCTACAT 58.809 41.667 0.00 0.00 0.00 2.29
1346 1361 8.514136 TTTCGTTAATGGCTAAAATGTTCTTG 57.486 30.769 0.00 0.00 0.00 3.02
1355 1370 4.686091 GCTAAAATGTTCTTGGTGAAAGGC 59.314 41.667 0.00 0.00 36.30 4.35
1409 1424 8.371699 GGTCTCTAAAAGTGAATAGGAGCATAT 58.628 37.037 0.00 0.00 0.00 1.78
1441 1456 0.468226 AGCCAAACACGTCTCCTCAA 59.532 50.000 0.00 0.00 0.00 3.02
1460 1475 2.579684 ATCAAGGGTCTTCTCGCGCC 62.580 60.000 0.00 0.00 0.00 6.53
1469 1484 3.552273 GGTCTTCTCGCGCCAATAAGATA 60.552 47.826 0.00 0.00 0.00 1.98
1510 1525 1.660607 CGCTTAATGCATGTCACTCGT 59.339 47.619 0.00 0.00 43.06 4.18
1548 1563 4.321899 GCAAGTGACTCTCTCTCACAAGAT 60.322 45.833 1.67 0.00 40.56 2.40
1573 1593 6.520272 AGAGAAAGATTACCGATTCATCCAG 58.480 40.000 0.00 0.00 0.00 3.86
1590 1610 6.247676 TCATCCAGTCCAATTTGATCAGAAA 58.752 36.000 0.00 0.00 0.00 2.52
1656 1676 4.410228 ACCATTCTCAGCTAATAGAAGCCA 59.590 41.667 10.15 0.00 43.86 4.75
1683 1703 6.070309 GCTATCTATCCAGATCAGGGTTGAAT 60.070 42.308 5.70 0.00 40.81 2.57
1734 1754 8.225603 ACATAAATCCATTGCGATTAGAAACT 57.774 30.769 0.00 0.00 32.12 2.66
1746 1766 6.598457 TGCGATTAGAAACTAGTGACTCTACT 59.402 38.462 0.00 0.00 34.71 2.57
1756 1776 0.335019 TGACTCTACTGCCAGGGCTA 59.665 55.000 12.19 0.00 42.51 3.93
1867 1887 4.518249 GGACTCACTTCTCTTTTATGGGG 58.482 47.826 0.00 0.00 0.00 4.96
1872 1892 4.349636 TCACTTCTCTTTTATGGGGTGACA 59.650 41.667 0.00 0.00 0.00 3.58
1912 1932 4.873827 TCTATTTACGTGGGTGAATCAAGC 59.126 41.667 0.00 0.00 34.56 4.01
1923 1943 3.316308 GGTGAATCAAGCACAACAAGTCT 59.684 43.478 0.00 0.00 37.99 3.24
1924 1944 4.515191 GGTGAATCAAGCACAACAAGTCTA 59.485 41.667 0.00 0.00 37.99 2.59
1926 1946 4.756642 TGAATCAAGCACAACAAGTCTAGG 59.243 41.667 0.00 0.00 0.00 3.02
1927 1947 3.838244 TCAAGCACAACAAGTCTAGGT 57.162 42.857 0.00 0.00 0.00 3.08
1951 1971 2.912956 AGCTTGTGGTAGAAGATTGGGA 59.087 45.455 0.00 0.00 0.00 4.37
1953 1973 3.629398 GCTTGTGGTAGAAGATTGGGATG 59.371 47.826 0.00 0.00 0.00 3.51
1985 2005 5.872070 CAGATCCACTCAACTAGGAAAGAAC 59.128 44.000 0.00 0.00 34.62 3.01
1997 2017 3.412386 AGGAAAGAACTACGCATTGCTT 58.588 40.909 7.12 0.00 0.00 3.91
2002 2022 3.262420 AGAACTACGCATTGCTTACTGG 58.738 45.455 7.12 0.00 0.00 4.00
2077 2097 3.497884 AAGCTTCTTGCCGGTGCCT 62.498 57.895 1.90 0.00 44.23 4.75
2124 2145 0.881159 CCCACGCGTTTTCACCTACA 60.881 55.000 10.22 0.00 0.00 2.74
2127 2148 2.066262 CACGCGTTTTCACCTACAGAT 58.934 47.619 10.22 0.00 0.00 2.90
2148 2169 8.373981 ACAGATGGAGAAATCATCGAAATATCT 58.626 33.333 0.00 0.00 44.04 1.98
2156 2177 8.381636 AGAAATCATCGAAATATCTTCATCCCT 58.618 33.333 0.00 0.00 0.00 4.20
2293 2314 1.726352 AGTTAGGGGTAAGAGGGGACA 59.274 52.381 0.00 0.00 0.00 4.02
2294 2315 2.321296 AGTTAGGGGTAAGAGGGGACAT 59.679 50.000 0.00 0.00 0.00 3.06
2315 2336 4.746535 TGCCCGTATAGAAAGTCAATCA 57.253 40.909 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
88 92 5.590663 GGGTTCAAGAAGGAATCTATGTTCC 59.409 44.000 0.00 0.00 46.49 3.62
126 130 2.202570 CGAGTGAGTTACCCGCCG 60.203 66.667 0.00 0.00 0.00 6.46
135 139 2.817258 GGCTCTAGATATGCGAGTGAGT 59.183 50.000 0.00 0.00 0.00 3.41
196 200 1.881252 CGCCTCGGGAAATACCACG 60.881 63.158 0.00 0.00 41.20 4.94
240 244 6.648192 AGAAGAGTCATTGTCATTTCCTAGG 58.352 40.000 0.82 0.82 0.00 3.02
241 245 8.040132 AGAAGAAGAGTCATTGTCATTTCCTAG 58.960 37.037 0.00 0.00 0.00 3.02
242 246 7.911651 AGAAGAAGAGTCATTGTCATTTCCTA 58.088 34.615 0.00 0.00 0.00 2.94
249 253 4.991056 CGGAAAGAAGAAGAGTCATTGTCA 59.009 41.667 0.00 0.00 0.00 3.58
273 277 2.393271 GTGAGGTGCACATAGCTTCT 57.607 50.000 20.43 3.98 46.91 2.85
283 287 4.868171 GTCGTATAAGAATTGTGAGGTGCA 59.132 41.667 0.00 0.00 0.00 4.57
354 358 5.969435 CGTACGGCTTCTTTTTCTTCTTTTT 59.031 36.000 7.57 0.00 0.00 1.94
426 430 1.191535 AAGTACATGCGGCCTGTCTA 58.808 50.000 14.20 0.00 0.00 2.59
522 530 3.446310 TGTGCTTGAAGTTACGAGTCA 57.554 42.857 0.00 0.00 0.00 3.41
545 553 5.533903 CGGAGATTTTGGATTGAGATGGATT 59.466 40.000 0.00 0.00 0.00 3.01
702 710 7.280205 ACTTTTTCATGTATTCACCCGAGATAC 59.720 37.037 0.00 0.00 0.00 2.24
765 773 5.626809 GCATCTTCCCTTATCACACTACACA 60.627 44.000 0.00 0.00 0.00 3.72
819 827 8.255111 TCATCTGGTTTGTACATCTATCTCAT 57.745 34.615 0.00 0.00 0.00 2.90
830 838 7.144722 TGATGTGAATTCATCTGGTTTGTAC 57.855 36.000 12.12 0.00 43.03 2.90
842 850 2.885135 AGGGTGCTGATGTGAATTCA 57.115 45.000 3.38 3.38 0.00 2.57
856 864 1.076438 AGGGGAAGAAGGAAAGGGTG 58.924 55.000 0.00 0.00 0.00 4.61
912 921 0.514691 GGACTCTGAAAGCAAGCACG 59.485 55.000 0.00 0.00 0.00 5.34
913 922 0.877743 GGGACTCTGAAAGCAAGCAC 59.122 55.000 0.00 0.00 0.00 4.40
914 923 0.250901 GGGGACTCTGAAAGCAAGCA 60.251 55.000 0.00 0.00 0.00 3.91
926 935 1.751563 GCTGCTCATAGGGGGACTC 59.248 63.158 0.00 0.00 0.00 3.36
937 946 1.282738 TCATTGATTCTGGGCTGCTCA 59.717 47.619 0.61 0.61 0.00 4.26
1024 1033 3.279434 GTGGCTTTCGTGATAAGGGAAT 58.721 45.455 0.00 0.00 0.00 3.01
1027 1036 2.107950 TGTGGCTTTCGTGATAAGGG 57.892 50.000 0.00 0.00 0.00 3.95
1054 1063 2.093921 TGACGTGTGACTTCCTCAAACA 60.094 45.455 0.00 0.00 36.97 2.83
1110 1122 4.378961 AGGAAGAAGAGGGGATTTCTGAT 58.621 43.478 0.00 0.00 34.09 2.90
1171 1183 0.884514 TCCGCTCTGAGTCTTCTGTG 59.115 55.000 6.53 0.00 0.00 3.66
1172 1184 1.748493 GATCCGCTCTGAGTCTTCTGT 59.252 52.381 6.53 0.00 0.00 3.41
1216 1228 4.038042 TGACACGAGAATAGATCACATCCC 59.962 45.833 0.00 0.00 0.00 3.85
1390 1405 4.757149 GCCGATATGCTCCTATTCACTTTT 59.243 41.667 0.00 0.00 0.00 2.27
1409 1424 0.323269 TTTGGCTTGGATGATGCCGA 60.323 50.000 0.00 0.00 46.05 5.54
1441 1456 1.153549 GCGCGAGAAGACCCTTGAT 60.154 57.895 12.10 0.00 0.00 2.57
1477 1492 5.425941 GCATTAAGCGAAATCAGTTGTTG 57.574 39.130 0.00 0.00 0.00 3.33
1510 1525 3.636764 TCACTTGCTATATTGAGAGCGGA 59.363 43.478 0.00 0.00 43.16 5.54
1548 1563 7.287927 ACTGGATGAATCGGTAATCTTTCTCTA 59.712 37.037 0.00 0.00 0.00 2.43
1573 1593 7.596494 TGAACTCATTTCTGATCAAATTGGAC 58.404 34.615 0.00 0.00 34.97 4.02
1590 1610 6.593770 TCGCTATACAACAACAATGAACTCAT 59.406 34.615 0.00 0.00 38.41 2.90
1656 1676 5.022227 ACCCTGATCTGGATAGATAGCTT 57.978 43.478 19.59 0.00 43.63 3.74
1683 1703 1.614996 TGGCTTTTCCATTCGCTTCA 58.385 45.000 0.00 0.00 40.72 3.02
1734 1754 1.960471 GCCCTGGCAGTAGAGTCACTA 60.960 57.143 14.43 0.00 41.49 2.74
1756 1776 6.656632 TCTTTCTATCTTACATCGCCATCT 57.343 37.500 0.00 0.00 0.00 2.90
1912 1932 4.792521 AGCTCTACCTAGACTTGTTGTG 57.207 45.455 0.00 0.00 0.00 3.33
1923 1943 5.188988 TCTTCTACCACAAGCTCTACCTA 57.811 43.478 0.00 0.00 0.00 3.08
1924 1944 4.048970 TCTTCTACCACAAGCTCTACCT 57.951 45.455 0.00 0.00 0.00 3.08
1926 1946 5.112686 CCAATCTTCTACCACAAGCTCTAC 58.887 45.833 0.00 0.00 0.00 2.59
1927 1947 4.162320 CCCAATCTTCTACCACAAGCTCTA 59.838 45.833 0.00 0.00 0.00 2.43
1985 2005 1.328680 CAGCCAGTAAGCAATGCGTAG 59.671 52.381 0.22 0.00 34.23 3.51
1997 2017 2.301870 AGGATCGTTCAAACAGCCAGTA 59.698 45.455 0.00 0.00 0.00 2.74
2002 2022 5.169295 AGTAACTAGGATCGTTCAAACAGC 58.831 41.667 0.00 0.00 0.00 4.40
2077 2097 2.358898 GAGTCTGTGCTTTGCTTTTGGA 59.641 45.455 0.00 0.00 0.00 3.53
2124 2145 9.434420 GAAGATATTTCGATGATTTCTCCATCT 57.566 33.333 0.00 0.00 38.53 2.90
2127 2148 9.212641 GATGAAGATATTTCGATGATTTCTCCA 57.787 33.333 0.00 0.00 0.00 3.86
2156 2177 5.704053 GTCCTATTTTCGAGTTCCCTTTCAA 59.296 40.000 0.00 0.00 0.00 2.69
2168 2189 3.349927 TCCACTCTCGTCCTATTTTCGA 58.650 45.455 0.00 0.00 0.00 3.71
2175 2196 2.133520 ACCCTATCCACTCTCGTCCTA 58.866 52.381 0.00 0.00 0.00 2.94
2246 2267 2.113860 ATGCTGCTCTCGCCTTTTTA 57.886 45.000 0.00 0.00 34.43 1.52
2293 2314 5.290493 TGATTGACTTTCTATACGGGCAT 57.710 39.130 0.00 0.00 0.00 4.40
2294 2315 4.746535 TGATTGACTTTCTATACGGGCA 57.253 40.909 0.00 0.00 0.00 5.36


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

AutoCloner maintained by Alex Coulton.