Multiple sequence alignment - TraesCS1B01G100600

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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 TraesCS1B01G100600 chr1B 100.000 3548 0 0 1 3548 109727468 109731015 0.000000e+00 6553
1 TraesCS1B01G100600 chr1B 83.588 262 27 6 2982 3234 217805927 217805673 7.660000e-57 231
2 TraesCS1B01G100600 chr1D 96.272 3568 95 16 1 3548 68445102 68448651 0.000000e+00 5818
3 TraesCS1B01G100600 chr1A 95.776 3575 102 19 1 3548 66891532 66895084 0.000000e+00 5720
4 TraesCS1B01G100600 chr3A 84.892 139 21 0 1268 1406 470829761 470829623 1.330000e-29 141
5 TraesCS1B01G100600 chr7B 84.553 123 15 4 1280 1400 452961950 452962070 6.220000e-23 119
6 TraesCS1B01G100600 chr7A 84.127 126 16 4 1280 1403 486237271 486237148 6.220000e-23 119
7 TraesCS1B01G100600 chr2B 86.667 105 14 0 1280 1384 152844326 152844222 2.240000e-22 117
8 TraesCS1B01G100600 chr2A 89.247 93 10 0 1280 1372 100826054 100825962 2.240000e-22 117
9 TraesCS1B01G100600 chr7D 88.421 95 7 4 1280 1372 436114205 436114297 1.040000e-20 111
10 TraesCS1B01G100600 chr2D 90.476 84 8 0 1289 1372 101872844 101872761 1.040000e-20 111


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 TraesCS1B01G100600 chr1B 109727468 109731015 3547 False 6553 6553 100.000 1 3548 1 chr1B.!!$F1 3547
1 TraesCS1B01G100600 chr1D 68445102 68448651 3549 False 5818 5818 96.272 1 3548 1 chr1D.!!$F1 3547
2 TraesCS1B01G100600 chr1A 66891532 66895084 3552 False 5720 5720 95.776 1 3548 1 chr1A.!!$F1 3547

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
864 884 0.039618 TCTGCATTTCCCACCCCTTC 59.960 55.0 0.00 0.0 0.00 3.46 F
865 885 0.040204 CTGCATTTCCCACCCCTTCT 59.960 55.0 0.00 0.0 0.00 2.85 F
920 940 0.543883 AGAGGAGGCTTCTGCTGTGA 60.544 55.0 0.00 0.0 39.36 3.58 F
1437 1458 0.764369 AGTTGCACTCTGAGGACCCA 60.764 55.0 9.85 0.0 0.00 4.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1953 1978 0.322648 CATCTCCACTGCCACACTCA 59.677 55.000 0.00 0.00 0.00 3.41 R
2021 2046 0.399454 AGTGGAGATTGTGCTGCAGT 59.601 50.000 16.64 0.00 36.89 4.40 R
2022 2047 0.803117 CAGTGGAGATTGTGCTGCAG 59.197 55.000 10.11 10.11 36.89 4.41 R
2691 2716 1.003116 GCACTGCATGATCTTTAGCCG 60.003 52.381 0.00 0.00 0.00 5.52 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
80 81 4.410555 GGAGATAGAGGACAATTCTTGGGT 59.589 45.833 0.00 0.00 34.12 4.51
112 114 0.846427 ATCTTCTTGCAGGTGGGGGA 60.846 55.000 0.00 0.00 0.00 4.81
199 201 0.767375 AGCAGCAGAAGAAAGGTGGA 59.233 50.000 0.00 0.00 34.05 4.02
348 353 0.804989 GGTGTACACTGAATGCTGCC 59.195 55.000 24.55 0.96 0.00 4.85
390 395 1.617536 ATGGGAGGAGCAGGAGCAA 60.618 57.895 0.00 0.00 45.49 3.91
469 487 6.395426 TTGTGCTCAAAGAAACAGATGAAT 57.605 33.333 0.00 0.00 0.00 2.57
512 531 3.491639 CCGCGACATTAAAATATCGGTGA 59.508 43.478 8.23 0.00 35.96 4.02
863 883 0.040204 CTCTGCATTTCCCACCCCTT 59.960 55.000 0.00 0.00 0.00 3.95
864 884 0.039618 TCTGCATTTCCCACCCCTTC 59.960 55.000 0.00 0.00 0.00 3.46
865 885 0.040204 CTGCATTTCCCACCCCTTCT 59.960 55.000 0.00 0.00 0.00 2.85
892 912 3.212685 CATGGATTCCTGAAGAAGCTCC 58.787 50.000 3.95 0.00 40.83 4.70
894 914 1.208293 GGATTCCTGAAGAAGCTCCGT 59.792 52.381 0.00 0.00 40.83 4.69
908 928 1.379977 TCCGTGCTACCAGAGGAGG 60.380 63.158 0.00 0.00 0.00 4.30
920 940 0.543883 AGAGGAGGCTTCTGCTGTGA 60.544 55.000 0.00 0.00 39.36 3.58
935 955 1.000607 CTGTGAGCAATTGCAAGCTGT 60.001 47.619 30.89 10.32 45.16 4.40
952 972 1.300697 GTGTGAGTTCCGCGAACCT 60.301 57.895 8.23 0.00 42.85 3.50
1086 1106 4.824479 TGAGAAGCTCATGAACCACATA 57.176 40.909 0.00 0.00 35.39 2.29
1171 1191 5.624344 ATTCTGCATTTCACTCTTGTCAG 57.376 39.130 0.00 0.00 0.00 3.51
1175 1195 5.466728 TCTGCATTTCACTCTTGTCAGTTAC 59.533 40.000 0.00 0.00 0.00 2.50
1176 1196 5.122519 TGCATTTCACTCTTGTCAGTTACA 58.877 37.500 0.00 0.00 35.88 2.41
1193 1213 6.264518 TCAGTTACAAACTTCCATTCTTTCCC 59.735 38.462 0.00 0.00 40.46 3.97
1234 1255 2.745968 AGGCTTCCCTCTCTTAGTCAG 58.254 52.381 0.00 0.00 36.46 3.51
1235 1256 1.760029 GGCTTCCCTCTCTTAGTCAGG 59.240 57.143 0.00 0.00 0.00 3.86
1246 1267 6.183361 CCTCTCTTAGTCAGGCCAATTATCTT 60.183 42.308 5.01 0.00 0.00 2.40
1284 1305 2.116125 GCAGGGCTCCAAAGGTGT 59.884 61.111 0.00 0.00 0.00 4.16
1392 1413 1.610522 GTTGAACTCCATGCTGTGCTT 59.389 47.619 0.00 0.00 0.00 3.91
1417 1438 5.125578 GGGAACAGGTGAATTTTAAGCCTAG 59.874 44.000 0.00 0.00 0.00 3.02
1423 1444 5.416013 AGGTGAATTTTAAGCCTAGAGTTGC 59.584 40.000 0.00 0.00 0.00 4.17
1427 1448 6.149474 TGAATTTTAAGCCTAGAGTTGCACTC 59.851 38.462 7.88 7.88 45.38 3.51
1437 1458 0.764369 AGTTGCACTCTGAGGACCCA 60.764 55.000 9.85 0.00 0.00 4.51
1641 1666 3.580319 ACCCACAAGCCCCTCACC 61.580 66.667 0.00 0.00 0.00 4.02
1730 1755 2.666190 GTCAAGCGCTGGTGCTCA 60.666 61.111 12.58 0.00 46.60 4.26
1770 1795 2.169789 CAGCGAGACAGCCCAATCG 61.170 63.158 0.00 0.00 38.01 3.34
1802 1827 1.943968 GCCGGTGTATGACAAGAAGCA 60.944 52.381 1.90 0.00 0.00 3.91
1953 1978 2.360165 GCAGCAATTAGGCTACAGCAAT 59.640 45.455 12.68 0.00 43.68 3.56
1986 2011 4.641989 AGTGGAGATGGTGCAAATATGAAC 59.358 41.667 0.00 0.00 33.94 3.18
1987 2012 4.398988 GTGGAGATGGTGCAAATATGAACA 59.601 41.667 0.00 0.00 36.75 3.18
1988 2013 5.068198 GTGGAGATGGTGCAAATATGAACAT 59.932 40.000 0.00 0.00 36.75 2.71
1989 2014 5.068067 TGGAGATGGTGCAAATATGAACATG 59.932 40.000 0.00 0.00 36.75 3.21
1990 2015 5.300034 GGAGATGGTGCAAATATGAACATGA 59.700 40.000 0.00 0.00 36.75 3.07
1991 2016 6.183360 GGAGATGGTGCAAATATGAACATGAA 60.183 38.462 0.00 0.00 36.75 2.57
2027 2052 4.778534 ACCAGAATGATTTCAACTGCAG 57.221 40.909 13.48 13.48 39.69 4.41
2034 2059 3.904571 TGATTTCAACTGCAGCACAATC 58.095 40.909 15.27 15.89 0.00 2.67
2076 2101 1.305297 ACCATCAGCCCTCTCGACA 60.305 57.895 0.00 0.00 0.00 4.35
2130 2155 2.602438 CATGGGGGCACTGGCATA 59.398 61.111 4.78 0.00 43.71 3.14
2289 2314 2.060050 TCGGAGTTGGGCAAGAAAAA 57.940 45.000 0.00 0.00 0.00 1.94
2550 2575 6.259608 CCTTGTCTTTTGAGCATATCTAGGTG 59.740 42.308 0.00 0.00 0.00 4.00
2592 2617 4.322650 GGAACAGAGAAGATCAGCAGAAGT 60.323 45.833 0.00 0.00 0.00 3.01
2594 2619 4.819769 ACAGAGAAGATCAGCAGAAGTTC 58.180 43.478 0.00 0.00 0.00 3.01
2667 2692 3.126001 ACATATGCGGGTTGATACAGG 57.874 47.619 1.58 0.00 0.00 4.00
2691 2716 0.771755 AACCCTCCACAACCTTCCTC 59.228 55.000 0.00 0.00 0.00 3.71
2694 2719 1.376037 CTCCACAACCTTCCTCGGC 60.376 63.158 0.00 0.00 0.00 5.54
2918 2945 2.223829 GCATGTGTCGGTAGCTATCACT 60.224 50.000 4.57 0.00 0.00 3.41
2927 2954 3.568430 CGGTAGCTATCACTGACCATACA 59.432 47.826 4.57 0.00 0.00 2.29
2938 2965 3.769844 ACTGACCATACAAGTAGTCCCAG 59.230 47.826 0.00 0.00 0.00 4.45
3030 3057 0.100503 GTTGCCGACAAACTGCAGTT 59.899 50.000 26.36 26.36 39.62 3.16
3069 3098 6.408434 GGCAGAAAATTGGAATATTGACCCAT 60.408 38.462 0.00 0.00 0.00 4.00
3075 3104 4.458256 TGGAATATTGACCCATGAGCAT 57.542 40.909 0.00 0.00 0.00 3.79
3164 3194 7.324178 ACTTGATCGCTTTCTACTTCAATACT 58.676 34.615 0.00 0.00 0.00 2.12
3375 3406 3.376859 TGGTTTGTCCATGATTACATCGC 59.623 43.478 0.00 0.00 41.93 4.58
3538 3569 1.557371 ACCTCCAGAAAAGCTAGCCTC 59.443 52.381 12.13 6.02 0.00 4.70
3542 3573 3.441101 TCCAGAAAAGCTAGCCTCTACA 58.559 45.455 12.13 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
80 81 6.149973 CCTGCAAGAAGATTTTATGTGTCAGA 59.850 38.462 0.00 0.00 34.07 3.27
112 114 3.568093 GCATGTGCACCTCGTTTTT 57.432 47.368 15.69 0.00 41.59 1.94
390 395 3.686691 GCATTATCAGGAAAGGGACTGCT 60.687 47.826 0.00 0.00 40.86 4.24
422 427 2.222445 CAGTGAAAGTAAAACGGGTCCG 59.778 50.000 7.97 7.97 46.03 4.79
469 487 4.693566 CGGCCTTGTTTATGAAACTCTACA 59.306 41.667 0.00 0.00 41.90 2.74
589 608 2.306847 TCTTCACTTTGGTTGCTTCCC 58.693 47.619 0.00 0.00 0.00 3.97
600 619 6.007485 ACCCTTCTTCTTCTTCTTCACTTT 57.993 37.500 0.00 0.00 0.00 2.66
822 842 8.061920 CAGAGGGGATAGTGACTTATATATGGA 58.938 40.741 0.00 0.00 0.00 3.41
841 861 1.380380 GGTGGGAAATGCAGAGGGG 60.380 63.158 0.00 0.00 0.00 4.79
863 883 2.199208 TCAGGAATCCATGGCTGAAGA 58.801 47.619 15.13 3.52 0.00 2.87
864 884 2.723322 TCAGGAATCCATGGCTGAAG 57.277 50.000 15.13 1.36 0.00 3.02
865 885 2.577563 TCTTCAGGAATCCATGGCTGAA 59.422 45.455 23.19 23.19 0.00 3.02
892 912 1.608717 AAGCCTCCTCTGGTAGCACG 61.609 60.000 0.00 0.00 0.00 5.34
894 914 0.041833 AGAAGCCTCCTCTGGTAGCA 59.958 55.000 0.00 0.00 0.00 3.49
920 940 1.000607 CTCACACAGCTTGCAATTGCT 60.001 47.619 29.37 7.34 42.66 3.91
923 943 2.035066 GGAACTCACACAGCTTGCAATT 59.965 45.455 0.00 0.00 0.00 2.32
935 955 1.006571 GAGGTTCGCGGAACTCACA 60.007 57.895 27.63 0.00 41.70 3.58
952 972 0.734942 GAAATTCGCAGACCCGACGA 60.735 55.000 0.00 0.00 36.90 4.20
1086 1106 2.662070 GCCATGGCCATGCTTGGTT 61.662 57.895 36.08 2.21 45.57 3.67
1149 1169 5.068636 ACTGACAAGAGTGAAATGCAGAAT 58.931 37.500 0.00 0.00 0.00 2.40
1165 1185 7.639113 AAGAATGGAAGTTTGTAACTGACAA 57.361 32.000 0.00 0.00 46.56 3.18
1166 1186 7.201785 GGAAAGAATGGAAGTTTGTAACTGACA 60.202 37.037 0.00 0.00 41.91 3.58
1171 1191 5.279306 GGGGGAAAGAATGGAAGTTTGTAAC 60.279 44.000 0.00 0.00 0.00 2.50
1175 1195 3.961480 GGGGGAAAGAATGGAAGTTTG 57.039 47.619 0.00 0.00 0.00 2.93
1193 1213 3.406512 TCTTAGGAGGAGAAGAAGGGG 57.593 52.381 0.00 0.00 0.00 4.79
1235 1256 5.831997 ACGAGGCAAATTAAGATAATTGGC 58.168 37.500 11.93 11.93 45.51 4.52
1246 1267 4.082517 TGCAGCAATTTACGAGGCAAATTA 60.083 37.500 0.00 0.00 34.61 1.40
1392 1413 3.576550 GGCTTAAAATTCACCTGTTCCCA 59.423 43.478 0.00 0.00 0.00 4.37
1423 1444 1.694150 TCTGTTTGGGTCCTCAGAGTG 59.306 52.381 0.00 0.00 33.77 3.51
1427 1448 3.754965 TGAATTCTGTTTGGGTCCTCAG 58.245 45.455 7.05 0.00 0.00 3.35
1428 1449 3.754965 CTGAATTCTGTTTGGGTCCTCA 58.245 45.455 7.05 0.00 0.00 3.86
1437 1458 7.040478 TGCAGTTACTAATGCTGAATTCTGTTT 60.040 33.333 13.17 9.92 42.98 2.83
1503 1528 2.619931 TGAGACCACCTTCTCATGGAA 58.380 47.619 0.00 0.00 45.79 3.53
1730 1755 0.685660 GAGGTGACCGAAGTTCCCTT 59.314 55.000 0.00 0.00 0.00 3.95
1770 1795 3.058160 ACCGGCAGCAGCATTGAC 61.058 61.111 0.00 0.00 44.61 3.18
1802 1827 1.986882 CAAGCTTGGAGTTTCAGGGT 58.013 50.000 19.14 0.00 0.00 4.34
1878 1903 2.178890 GCAGCTTGATGGGCTCTCG 61.179 63.158 0.00 0.00 38.03 4.04
1953 1978 0.322648 CATCTCCACTGCCACACTCA 59.677 55.000 0.00 0.00 0.00 3.41
1986 2011 5.063204 TGGTTAAACCAGAGTGAGTTCATG 58.937 41.667 0.00 0.00 44.79 3.07
1987 2012 5.304686 TGGTTAAACCAGAGTGAGTTCAT 57.695 39.130 0.00 0.00 44.79 2.57
1988 2013 4.764050 TGGTTAAACCAGAGTGAGTTCA 57.236 40.909 0.00 0.00 44.79 3.18
2021 2046 0.399454 AGTGGAGATTGTGCTGCAGT 59.601 50.000 16.64 0.00 36.89 4.40
2022 2047 0.803117 CAGTGGAGATTGTGCTGCAG 59.197 55.000 10.11 10.11 36.89 4.41
2027 2052 1.131883 GCATCACAGTGGAGATTGTGC 59.868 52.381 0.00 0.00 43.31 4.57
2034 2059 1.162698 CTGTTGGCATCACAGTGGAG 58.837 55.000 10.51 0.00 0.00 3.86
2076 2101 1.265454 GGAGGTTCAGTCCCATCGGT 61.265 60.000 0.00 0.00 0.00 4.69
2153 2178 2.939103 CTGCTGCTAGGATTAACACCAC 59.061 50.000 0.00 0.00 0.00 4.16
2289 2314 5.580998 TCCACTAACTGAACTCTGGTATCT 58.419 41.667 0.00 0.00 0.00 1.98
2592 2617 5.006649 CACGAAATTGTGAGACAAGTCTGAA 59.993 40.000 7.57 0.00 41.94 3.02
2594 2619 4.507756 TCACGAAATTGTGAGACAAGTCTG 59.492 41.667 7.57 0.00 43.62 3.51
2667 2692 2.586648 AGGTTGTGGAGGGTTGATTC 57.413 50.000 0.00 0.00 0.00 2.52
2691 2716 1.003116 GCACTGCATGATCTTTAGCCG 60.003 52.381 0.00 0.00 0.00 5.52
2694 2719 2.031314 CGTGGCACTGCATGATCTTTAG 59.969 50.000 16.72 0.00 0.00 1.85
2918 2945 3.767673 GTCTGGGACTACTTGTATGGTCA 59.232 47.826 0.00 0.00 31.98 4.02
2927 2954 5.368989 CAGTTGAAAAGTCTGGGACTACTT 58.631 41.667 0.41 0.00 42.59 2.24
2938 2965 2.669364 CATGGCAGCAGTTGAAAAGTC 58.331 47.619 0.00 0.00 0.00 3.01
3030 3057 9.868277 CCAATTTTCTGCCTTTACAAATATACA 57.132 29.630 0.00 0.00 0.00 2.29
3069 3098 3.256631 GGAAAGCCAGAGAAAAATGCTCA 59.743 43.478 0.00 0.00 34.85 4.26
3075 3104 3.641436 GGAAAGGGAAAGCCAGAGAAAAA 59.359 43.478 0.00 0.00 35.15 1.94
3164 3194 4.671831 TCAACCAATCCTTTTCCATGCTA 58.328 39.130 0.00 0.00 0.00 3.49
3375 3406 2.704725 AGGTACATTTTGCAACGCTG 57.295 45.000 0.00 0.00 0.00 5.18
3392 3423 3.055094 TGAGCTCCTAGCCAAGTTTAAGG 60.055 47.826 12.15 0.00 43.77 2.69
3444 3475 5.867174 GTGATAAACCAAATAAGCACCCAAC 59.133 40.000 0.00 0.00 0.00 3.77
3479 3510 1.004511 AGTGTCACCTAGCTCGTACCT 59.995 52.381 0.00 0.00 0.00 3.08
3512 3543 3.876309 AGCTTTTCTGGAGGTTGGTTA 57.124 42.857 0.00 0.00 0.00 2.85


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

AutoCloner maintained by Alex Coulton.