Multiple sequence alignment - TraesCS1D01G171200

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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 TraesCS1D01G171200 chr1D 100.000 2117 0 0 1 2117 244484154 244482038 0.000000e+00 3910
1 TraesCS1D01G171200 chr1D 92.781 2161 106 29 3 2117 254497892 254500048 0.000000e+00 3081
2 TraesCS1D01G171200 chr5D 93.052 2159 100 23 3 2117 6201384 6199232 0.000000e+00 3110
3 TraesCS1D01G171200 chr5D 92.731 2091 102 31 67 2114 329162138 329164221 0.000000e+00 2974
4 TraesCS1D01G171200 chr5D 93.188 1967 87 27 194 2117 560872556 560874518 0.000000e+00 2846
5 TraesCS1D01G171200 chr1A 91.929 2156 122 30 3 2117 168450667 168448523 0.000000e+00 2970
6 TraesCS1D01G171200 chr4D 91.705 2158 130 27 3 2117 19916391 19918542 0.000000e+00 2948
7 TraesCS1D01G171200 chr7A 91.090 2155 149 24 3 2117 352194127 352191976 0.000000e+00 2876
8 TraesCS1D01G171200 chr7A 85.011 467 33 16 1249 1683 58647293 58647754 6.930000e-120 440
9 TraesCS1D01G171200 chr6B 93.699 1587 84 11 3 1575 22425839 22427423 0.000000e+00 2362
10 TraesCS1D01G171200 chr3D 95.122 1230 52 5 3 1226 21904520 21905747 0.000000e+00 1932
11 TraesCS1D01G171200 chr3D 89.560 364 26 6 1261 1613 10748315 10747953 3.200000e-123 451
12 TraesCS1D01G171200 chr3B 91.406 1152 56 25 1007 2117 201515580 201516729 0.000000e+00 1539
13 TraesCS1D01G171200 chr3B 93.112 813 44 6 812 1613 201514344 201515155 0.000000e+00 1181
14 TraesCS1D01G171200 chr3B 92.607 514 31 6 1610 2117 524777546 524777034 0.000000e+00 732
15 TraesCS1D01G171200 chrUn 93.662 994 51 6 631 1613 445812538 445811546 0.000000e+00 1476
16 TraesCS1D01G171200 chrUn 88.792 687 42 15 1035 1688 30306422 30305738 0.000000e+00 809
17 TraesCS1D01G171200 chr7B 92.412 514 29 8 1613 2117 102632092 102631580 0.000000e+00 725
18 TraesCS1D01G171200 chr2A 88.492 252 7 8 1534 1763 677892919 677893170 3.440000e-73 285
19 TraesCS1D01G171200 chr5B 86.636 217 6 9 1534 1728 185297260 185297045 3.540000e-53 219


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 TraesCS1D01G171200 chr1D 244482038 244484154 2116 True 3910 3910 100.000 1 2117 1 chr1D.!!$R1 2116
1 TraesCS1D01G171200 chr1D 254497892 254500048 2156 False 3081 3081 92.781 3 2117 1 chr1D.!!$F1 2114
2 TraesCS1D01G171200 chr5D 6199232 6201384 2152 True 3110 3110 93.052 3 2117 1 chr5D.!!$R1 2114
3 TraesCS1D01G171200 chr5D 329162138 329164221 2083 False 2974 2974 92.731 67 2114 1 chr5D.!!$F1 2047
4 TraesCS1D01G171200 chr5D 560872556 560874518 1962 False 2846 2846 93.188 194 2117 1 chr5D.!!$F2 1923
5 TraesCS1D01G171200 chr1A 168448523 168450667 2144 True 2970 2970 91.929 3 2117 1 chr1A.!!$R1 2114
6 TraesCS1D01G171200 chr4D 19916391 19918542 2151 False 2948 2948 91.705 3 2117 1 chr4D.!!$F1 2114
7 TraesCS1D01G171200 chr7A 352191976 352194127 2151 True 2876 2876 91.090 3 2117 1 chr7A.!!$R1 2114
8 TraesCS1D01G171200 chr6B 22425839 22427423 1584 False 2362 2362 93.699 3 1575 1 chr6B.!!$F1 1572
9 TraesCS1D01G171200 chr3D 21904520 21905747 1227 False 1932 1932 95.122 3 1226 1 chr3D.!!$F1 1223
10 TraesCS1D01G171200 chr3B 201514344 201516729 2385 False 1360 1539 92.259 812 2117 2 chr3B.!!$F1 1305
11 TraesCS1D01G171200 chr3B 524777034 524777546 512 True 732 732 92.607 1610 2117 1 chr3B.!!$R1 507
12 TraesCS1D01G171200 chrUn 445811546 445812538 992 True 1476 1476 93.662 631 1613 1 chrUn.!!$R2 982
13 TraesCS1D01G171200 chrUn 30305738 30306422 684 True 809 809 88.792 1035 1688 1 chrUn.!!$R1 653
14 TraesCS1D01G171200 chr7B 102631580 102632092 512 True 725 725 92.412 1613 2117 1 chr7B.!!$R1 504

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
662 670 0.75906 GCAGTCCAAGGGGTTGGTTT 60.759 55.0 4.14 0.0 42.62 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1709 2796 2.101415 TCACACGCTCATATTCCAGAGG 59.899 50.0 0.0 0.0 32.54 3.69 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
23 24 5.073428 TGTGGGCAATATTGAAACTGTACA 58.927 37.500 19.73 9.95 0.00 2.90
95 101 0.767998 TGTGGTATGGGTCAGCAACA 59.232 50.000 0.00 0.00 0.00 3.33
141 147 3.632333 ACTCGTTATCAGTGGGATCAGA 58.368 45.455 0.00 0.00 37.44 3.27
174 180 8.948631 TCAGCAAGAAATATATCGAAGAGTTT 57.051 30.769 0.00 0.00 43.63 2.66
274 280 9.575868 TTATATTGGTAATAATCCGGCAAAAGA 57.424 29.630 0.00 0.00 0.00 2.52
420 427 5.793026 TGAAACATTTCCAGTTGTTTTGC 57.207 34.783 2.00 0.00 43.95 3.68
498 505 7.120579 CCAAATATAGTGTTGAACAAGTAGGCA 59.879 37.037 0.00 0.00 0.00 4.75
505 512 5.414454 GTGTTGAACAAGTAGGCATAATGGA 59.586 40.000 0.00 0.00 0.00 3.41
595 603 4.007659 GAGCGTTCTCAATTAGGGGAAAA 58.992 43.478 0.00 0.00 39.16 2.29
662 670 0.759060 GCAGTCCAAGGGGTTGGTTT 60.759 55.000 4.14 0.00 42.62 3.27
735 743 2.472695 TGGCGCTAGAACATTGTTCT 57.527 45.000 29.38 29.38 0.00 3.01
750 758 7.275888 ACATTGTTCTGAGATGTTTTTGCTA 57.724 32.000 0.00 0.00 30.22 3.49
762 770 8.579850 AGATGTTTTTGCTAGTATTGATCCAA 57.420 30.769 0.00 0.00 0.00 3.53
794 802 4.321230 GCTCGAGTGGAATTTGGAACATTT 60.321 41.667 15.13 0.00 39.30 2.32
834 842 6.385759 TCCAACTATAAGGAAATAGGCAGTCA 59.614 38.462 0.00 0.00 34.34 3.41
915 923 4.911390 TCCCATCCTTTCTTTGACTCTTC 58.089 43.478 0.00 0.00 0.00 2.87
918 926 6.272324 TCCCATCCTTTCTTTGACTCTTCTTA 59.728 38.462 0.00 0.00 0.00 2.10
1048 1057 8.255905 TCCTTTTAGTTTCGACTTTAGGGATAG 58.744 37.037 0.00 0.00 0.00 2.08
1175 1185 9.089601 GGACTTCTAACTTAAATTAGTCTCTGC 57.910 37.037 3.79 0.00 34.36 4.26
1189 1199 1.002366 CTCTGCGTTCTTCGAATGGG 58.998 55.000 0.00 0.00 42.86 4.00
1241 1251 3.181469 CGCGGTATATAAGGCATACCCAT 60.181 47.826 0.00 0.00 43.39 4.00
1260 1270 9.749340 ATACCCATTAAAGCTTACAAGTAAACT 57.251 29.630 0.00 0.00 0.00 2.66
1357 1367 9.485206 AAAAGATCGTGTATTTACAACTACAGT 57.515 29.630 0.00 0.00 38.04 3.55
1381 1391 8.594550 AGTGGAATAGTATACAAAGTCAACACT 58.405 33.333 5.50 8.22 0.00 3.55
1449 1459 4.716794 TCTAAACCTAGGCCAAAACGAAA 58.283 39.130 9.30 0.00 0.00 3.46
1455 1465 1.408969 AGGCCAAAACGAAATGGTGT 58.591 45.000 5.01 0.00 39.00 4.16
1496 1506 5.539955 CCCTTGAATTCGGAATATGGGAAAT 59.460 40.000 14.85 0.00 34.34 2.17
1509 1519 1.077572 GGAAATTCGCCCCGGGTTA 60.078 57.895 21.85 0.15 0.00 2.85
1510 1520 0.466739 GGAAATTCGCCCCGGGTTAT 60.467 55.000 21.85 3.77 0.00 1.89
1511 1521 1.395635 GAAATTCGCCCCGGGTTATT 58.604 50.000 21.85 10.09 0.00 1.40
1513 1523 1.388837 AATTCGCCCCGGGTTATTGC 61.389 55.000 21.85 14.51 0.00 3.56
1516 1526 2.438795 GCCCCGGGTTATTGCGAA 60.439 61.111 21.85 0.00 0.00 4.70
1517 1527 2.047443 GCCCCGGGTTATTGCGAAA 61.047 57.895 21.85 0.00 0.00 3.46
1519 1529 1.107945 CCCCGGGTTATTGCGAAATT 58.892 50.000 21.85 0.00 0.00 1.82
1520 1530 2.299521 CCCCGGGTTATTGCGAAATTA 58.700 47.619 21.85 0.00 0.00 1.40
1521 1531 2.888414 CCCCGGGTTATTGCGAAATTAT 59.112 45.455 21.85 0.00 0.00 1.28
1522 1532 4.073549 CCCCGGGTTATTGCGAAATTATA 58.926 43.478 21.85 0.00 0.00 0.98
1523 1533 4.519730 CCCCGGGTTATTGCGAAATTATAA 59.480 41.667 21.85 0.00 0.00 0.98
1526 1536 6.804783 CCCGGGTTATTGCGAAATTATAATTC 59.195 38.462 14.18 4.77 0.00 2.17
1527 1537 7.308951 CCCGGGTTATTGCGAAATTATAATTCT 60.309 37.037 14.18 2.49 0.00 2.40
1529 1539 9.113876 CGGGTTATTGCGAAATTATAATTCTTC 57.886 33.333 11.08 5.64 0.00 2.87
1532 1542 9.659830 GTTATTGCGAAATTATAATTCTTCCGT 57.340 29.630 11.08 0.00 0.00 4.69
1619 2703 8.466798 CGGAATTTTAACCAATTAGGAAGTCAT 58.533 33.333 1.54 0.00 41.22 3.06
1724 2811 2.891580 TCGGTACCTCTGGAATATGAGC 59.108 50.000 10.90 0.00 0.00 4.26
1744 2831 3.498397 AGCGTGTGACTTGTTAGAATTGG 59.502 43.478 0.00 0.00 0.00 3.16
1847 2934 5.833082 TCTGGAACACGAAATAGATAGAGC 58.167 41.667 0.00 0.00 0.00 4.09
1898 2988 4.585879 TCACTATTAAGACCTTGCAACCC 58.414 43.478 0.00 0.00 0.00 4.11
1904 2994 1.966451 GACCTTGCAACCCGACTGG 60.966 63.158 0.00 0.00 41.37 4.00
1972 3067 5.256474 TCCAATTTTGTTTGCCCAAAAGAA 58.744 33.333 10.49 0.00 44.80 2.52
2008 3106 5.704217 GATTTGGTCGAGTCATTACACTC 57.296 43.478 0.00 0.00 39.68 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.073428 TGTACAGTTTCAATATTGCCCACA 58.927 37.500 10.76 5.03 0.00 4.17
1 2 5.637006 TGTACAGTTTCAATATTGCCCAC 57.363 39.130 10.76 6.93 0.00 4.61
23 24 2.695666 ACAGCAGCGATACTACTGGAAT 59.304 45.455 0.00 0.00 43.20 3.01
274 280 2.371510 GAGCCTGCTCTGAATAATCCCT 59.628 50.000 11.82 0.00 39.80 4.20
410 417 4.566488 CCCTCCTCATCTAGCAAAACAACT 60.566 45.833 0.00 0.00 0.00 3.16
420 427 6.518200 GCTCTAACAATTCCCTCCTCATCTAG 60.518 46.154 0.00 0.00 0.00 2.43
498 505 4.042187 GCCACCATAGAACTCCTCCATTAT 59.958 45.833 0.00 0.00 0.00 1.28
502 509 1.204146 GCCACCATAGAACTCCTCCA 58.796 55.000 0.00 0.00 0.00 3.86
505 512 1.207329 GTTCGCCACCATAGAACTCCT 59.793 52.381 0.88 0.00 40.57 3.69
573 581 2.981859 TCCCCTAATTGAGAACGCTC 57.018 50.000 0.00 0.00 41.67 5.03
574 582 3.713826 TTTCCCCTAATTGAGAACGCT 57.286 42.857 0.00 0.00 0.00 5.07
595 603 5.112129 AGTAGCCCGGTCTAATTCAAAAT 57.888 39.130 0.00 0.00 0.00 1.82
662 670 4.217550 GCAAAGGTAGCATGACCAAAAGTA 59.782 41.667 6.37 0.00 42.47 2.24
735 743 7.828717 TGGATCAATACTAGCAAAAACATCTCA 59.171 33.333 0.00 0.00 0.00 3.27
762 770 2.787473 TCCACTCGAGCATCCAAATT 57.213 45.000 13.61 0.00 0.00 1.82
775 783 7.784633 TTTTGAAATGTTCCAAATTCCACTC 57.215 32.000 0.00 0.00 33.00 3.51
794 802 4.453480 AGTTGGATCTCCCACTTTTTGA 57.547 40.909 0.00 0.00 46.62 2.69
817 825 6.382859 TGTGTATCTGACTGCCTATTTCCTTA 59.617 38.462 0.00 0.00 0.00 2.69
825 833 5.420725 AACAATGTGTATCTGACTGCCTA 57.579 39.130 0.00 0.00 0.00 3.93
892 900 5.252630 AGAAGAGTCAAAGAAAGGATGGGAT 59.747 40.000 0.00 0.00 0.00 3.85
994 1003 8.567948 CGTATAAACCAATGCTTCCATAGATTT 58.432 33.333 0.00 0.00 0.00 2.17
1065 1075 4.141688 GGAACCTTAGGTGATTCTCGGAAT 60.142 45.833 3.99 0.00 35.34 3.01
1157 1167 7.148787 CGAAGAACGCAGAGACTAATTTAAGTT 60.149 37.037 0.00 0.00 34.51 2.66
1175 1185 2.656560 AGAGACCCATTCGAAGAACG 57.343 50.000 3.35 0.00 45.90 3.95
1189 1199 5.106515 GCAACCCTCTCAACAATTAAGAGAC 60.107 44.000 0.31 0.00 39.09 3.36
1260 1270 6.010850 ACTTTAGTCGCCATCTCCATATCTA 58.989 40.000 0.00 0.00 0.00 1.98
1319 1329 6.910536 ACACGATCTTTTTGTAGATCCATC 57.089 37.500 7.77 0.00 45.00 3.51
1356 1366 8.773404 AGTGTTGACTTTGTATACTATTCCAC 57.227 34.615 4.17 1.85 0.00 4.02
1401 1411 1.812571 CTTCAACGGTTTGCATAGCCT 59.187 47.619 0.62 0.00 32.17 4.58
1407 1417 4.385825 AGAACTATCTTCAACGGTTTGCA 58.614 39.130 0.00 0.00 29.15 4.08
1408 1418 6.476243 TTAGAACTATCTTCAACGGTTTGC 57.524 37.500 0.00 0.00 37.10 3.68
1449 1459 6.470278 GGTTTCAGTAAACTACCTACACCAT 58.530 40.000 0.00 0.00 43.76 3.55
1455 1465 6.999705 TCAAGGGTTTCAGTAAACTACCTA 57.000 37.500 0.00 0.00 43.76 3.08
1496 1506 2.438795 GCAATAACCCGGGGCGAA 60.439 61.111 27.92 7.17 0.00 4.70
1509 1519 9.581099 AAAACGGAAGAATTATAATTTCGCAAT 57.419 25.926 11.92 3.39 0.00 3.56
1510 1520 8.973835 AAAACGGAAGAATTATAATTTCGCAA 57.026 26.923 11.92 0.00 0.00 4.85
1523 1533 8.718734 GGAATATAGCGAATAAAACGGAAGAAT 58.281 33.333 0.00 0.00 0.00 2.40
1526 1536 7.653767 AGGAATATAGCGAATAAAACGGAAG 57.346 36.000 0.00 0.00 0.00 3.46
1527 1537 9.362539 GATAGGAATATAGCGAATAAAACGGAA 57.637 33.333 0.00 0.00 0.00 4.30
1529 1539 8.928270 AGATAGGAATATAGCGAATAAAACGG 57.072 34.615 0.00 0.00 0.00 4.44
1588 2651 6.720288 TCCTAATTGGTTAAAATTCCGTCCAA 59.280 34.615 0.00 0.00 38.90 3.53
1709 2796 2.101415 TCACACGCTCATATTCCAGAGG 59.899 50.000 0.00 0.00 32.54 3.69
1724 2811 4.084013 GGACCAATTCTAACAAGTCACACG 60.084 45.833 0.00 0.00 0.00 4.49
1744 2831 9.384764 GCCCTTTCTATGTATTATCAATAGGAC 57.615 37.037 0.00 0.00 0.00 3.85
1898 2988 6.787085 AGAACTACTTGAATTTTCCAGTCG 57.213 37.500 0.74 0.00 35.19 4.18
1991 3089 4.744570 TGAATGAGTGTAATGACTCGACC 58.255 43.478 0.00 0.00 44.68 4.79
2008 3106 9.467258 AACCGCTTGATAATCATTTATTGAATG 57.533 29.630 0.00 0.00 45.31 2.67
2051 3149 5.127031 AGTCTCAAGCTAAACAAAAGGCAAA 59.873 36.000 0.00 0.00 0.00 3.68


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

AutoCloner maintained by Alex Coulton.