Multiple sequence alignment - TraesCS7A01G100900

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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 TraesCS7A01G100900 chr7A 100.000 3894 0 0 1 3894 62068916 62065023 0 7191
1 TraesCS7A01G100900 chr7A 94.679 1917 43 17 1483 3396 61865623 61867483 0 2920
2 TraesCS7A01G100900 chr7A 93.810 840 36 3 662 1485 61864686 61865525 0 1249
3 TraesCS7A01G100900 chr7A 87.410 691 59 20 1 673 61834525 61835205 0 769
4 TraesCS7A01G100900 chr7A 91.781 511 30 6 3388 3894 61874875 61875377 0 701
5 TraesCS7A01G100900 chr7D 96.697 1968 45 6 1483 3438 57100422 57102381 0 3256
6 TraesCS7A01G100900 chr7D 90.690 1536 75 29 1 1485 57098811 57100329 0 1982
7 TraesCS7A01G100900 chr7D 97.390 613 12 1 3282 3894 57718989 57718381 0 1040
8 TraesCS7A01G100900 chr4A 88.793 580 36 10 314 868 673917819 673917244 0 684


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 TraesCS7A01G100900 chr7A 62065023 62068916 3893 True 7191.0 7191 100.0000 1 3894 1 chr7A.!!$R1 3893
1 TraesCS7A01G100900 chr7A 61864686 61867483 2797 False 2084.5 2920 94.2445 662 3396 2 chr7A.!!$F3 2734
2 TraesCS7A01G100900 chr7A 61834525 61835205 680 False 769.0 769 87.4100 1 673 1 chr7A.!!$F1 672
3 TraesCS7A01G100900 chr7A 61874875 61875377 502 False 701.0 701 91.7810 3388 3894 1 chr7A.!!$F2 506
4 TraesCS7A01G100900 chr7D 57098811 57102381 3570 False 2619.0 3256 93.6935 1 3438 2 chr7D.!!$F1 3437
5 TraesCS7A01G100900 chr7D 57718381 57718989 608 True 1040.0 1040 97.3900 3282 3894 1 chr7D.!!$R1 612
6 TraesCS7A01G100900 chr4A 673917244 673917819 575 True 684.0 684 88.7930 314 868 1 chr4A.!!$R1 554

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
392 434 0.034670 GATATGGCCCTGGATCCTGC 60.035 60.0 14.23 12.67 0.00 4.85 F
769 830 0.264657 AGGCCTTTGGTTCCCAGTTT 59.735 50.0 0.00 0.00 33.81 2.66 F
1114 1176 0.538584 AACATCCGCTGAGCATCTGA 59.461 50.0 4.88 0.00 35.94 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2024 2284 1.136305 TGCGGTACTAGGATGTTGCTC 59.864 52.381 0.0 0.0 0.00 4.26 R
2195 2456 8.114331 AGCAAATTTCAATCAGTGACAAGATA 57.886 30.769 0.0 0.0 35.39 1.98 R
2960 3232 5.295292 AGTTGCTCCAAAATCGATCATACAG 59.705 40.000 0.0 0.0 0.00 2.74 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
20 21 1.377725 GTCGGAGGTCAGTCCCGTA 60.378 63.158 0.00 0.00 43.40 4.02
34 35 2.178521 CGTACCGCTCGTGCTCTT 59.821 61.111 7.97 0.00 36.97 2.85
43 44 4.394712 CGTGCTCTTCCCCCGCTT 62.395 66.667 0.00 0.00 0.00 4.68
46 47 4.491409 GCTCTTCCCCCGCTTCCC 62.491 72.222 0.00 0.00 0.00 3.97
59 60 3.707189 TTCCCCCTCCCTCCCTCC 61.707 72.222 0.00 0.00 0.00 4.30
60 61 4.761304 TCCCCCTCCCTCCCTCCT 62.761 72.222 0.00 0.00 0.00 3.69
157 181 0.040603 GTTGAAGAGGTCGACGACGT 60.041 55.000 21.99 21.99 40.69 4.34
216 240 0.806102 CCGAGTGGGTAAGTGCATCG 60.806 60.000 0.00 0.00 0.00 3.84
317 352 4.666412 TGGGTCTGTTTTCCATGGATTA 57.334 40.909 17.06 3.90 0.00 1.75
345 380 5.116180 TCGGTTAGATGAATCGATGCTTTT 58.884 37.500 4.68 0.00 45.70 2.27
351 389 9.162793 GTTAGATGAATCGATGCTTTTTACATG 57.837 33.333 4.68 0.00 0.00 3.21
380 418 0.520404 CGATTGCTGCTGGATATGGC 59.480 55.000 0.00 0.00 0.00 4.40
392 434 0.034670 GATATGGCCCTGGATCCTGC 60.035 60.000 14.23 12.67 0.00 4.85
429 471 0.744057 TATCGGTGTGTGCATGCCTG 60.744 55.000 16.68 4.18 0.00 4.85
540 582 1.613925 TCTGTCGAGTCCTTGAGGTTG 59.386 52.381 0.00 0.00 36.34 3.77
722 766 2.550978 GAGCTACAACTGTGTGTGTGT 58.449 47.619 0.00 0.00 38.82 3.72
725 769 1.003108 TACAACTGTGTGTGTGTGCG 58.997 50.000 6.07 0.00 38.82 5.34
769 830 0.264657 AGGCCTTTGGTTCCCAGTTT 59.735 50.000 0.00 0.00 33.81 2.66
886 948 2.953648 TGCCTGATGTATTGCTTGATGG 59.046 45.455 0.00 0.00 0.00 3.51
1008 1070 2.045524 GCCAGAGAGAAGATGATGGGA 58.954 52.381 0.00 0.00 0.00 4.37
1083 1145 4.159506 GTCTCTGCAGGAAGAGTGAGTATT 59.840 45.833 15.13 0.00 43.57 1.89
1086 1148 4.774726 TCTGCAGGAAGAGTGAGTATTCTT 59.225 41.667 15.13 0.00 35.80 2.52
1114 1176 0.538584 AACATCCGCTGAGCATCTGA 59.461 50.000 4.88 0.00 35.94 3.27
1136 1198 2.125350 CTCCTCACTTGCCTCGGC 60.125 66.667 0.00 0.00 42.35 5.54
1160 1222 2.575532 CACTTCCTCAAGCAGACCAAA 58.424 47.619 0.00 0.00 32.09 3.28
1164 1226 2.851195 TCCTCAAGCAGACCAAAAGAC 58.149 47.619 0.00 0.00 0.00 3.01
1167 1229 2.810852 CTCAAGCAGACCAAAAGACTCC 59.189 50.000 0.00 0.00 0.00 3.85
1175 1237 3.199946 AGACCAAAAGACTCCACAGTTCA 59.800 43.478 0.00 0.00 30.63 3.18
1211 1273 2.021457 CGTTTCCACCAACCTTTCTGT 58.979 47.619 0.00 0.00 0.00 3.41
1230 1292 7.946655 TTCTGTATATGCTTAAGACATTCCG 57.053 36.000 6.67 2.16 0.00 4.30
1325 1390 4.471904 CTGACACCCAGTATAAGCTCAA 57.528 45.455 0.00 0.00 38.10 3.02
1337 1402 7.655328 CCAGTATAAGCTCAATTCTCCTAACTG 59.345 40.741 0.00 0.00 0.00 3.16
1356 1421 2.505819 CTGAACTACAGCCCCCAACTAT 59.494 50.000 0.00 0.00 39.86 2.12
1375 1440 3.806625 ATGGCTAATTTTCATTGCGCT 57.193 38.095 9.73 0.00 0.00 5.92
1382 1447 5.799936 GCTAATTTTCATTGCGCTTAGTCAA 59.200 36.000 9.73 0.00 0.00 3.18
1411 1476 2.967615 GTAATCCGCCAGCGCTCC 60.968 66.667 7.13 0.00 38.24 4.70
1541 1801 9.868277 AACTTCAAAACAATTGTAATGAAGACA 57.132 25.926 39.55 22.38 44.68 3.41
1549 1809 4.811555 TTGTAATGAAGACAGCACACAC 57.188 40.909 0.00 0.00 0.00 3.82
1554 1814 1.221414 GAAGACAGCACACACCTGAC 58.779 55.000 0.00 0.00 34.47 3.51
1630 1890 1.451567 CAGCTGCCTGTGGATGGAG 60.452 63.158 0.00 0.00 34.31 3.86
1638 1898 2.295885 CCTGTGGATGGAGATTTCTGC 58.704 52.381 0.00 0.00 34.66 4.26
1727 1987 2.095059 CAGCAAGTGTGGGAATGTTAGC 60.095 50.000 0.00 0.00 0.00 3.09
1729 1989 3.009033 AGCAAGTGTGGGAATGTTAGCTA 59.991 43.478 0.00 0.00 0.00 3.32
1746 2006 2.106511 AGCTATACATTCCGGGCAATGT 59.893 45.455 21.28 21.28 46.54 2.71
1909 2169 8.450578 TTCTGAAATCAGTTGTAGTTCATTGT 57.549 30.769 10.06 0.00 44.12 2.71
1937 2197 8.546083 AGTAGATTCTTCTTCACCATACTGAT 57.454 34.615 0.00 0.00 33.17 2.90
2195 2456 4.949238 TGCTATTTACAAGTGTGGATGCAT 59.051 37.500 0.00 0.00 0.00 3.96
2960 3232 6.147985 GGAGAAAATCTTGTCTTGGTACTGAC 59.852 42.308 0.00 0.29 34.37 3.51
3260 3535 6.399669 GCTGTAACATTGACAGTACACGTAAG 60.400 42.308 7.19 0.00 45.09 2.34
3358 3633 2.428890 ACGTCAATCCTTTTTGTTGCCA 59.571 40.909 0.00 0.00 0.00 4.92
3359 3634 3.069443 ACGTCAATCCTTTTTGTTGCCAT 59.931 39.130 0.00 0.00 0.00 4.40
3360 3635 3.429543 CGTCAATCCTTTTTGTTGCCATG 59.570 43.478 0.00 0.00 0.00 3.66
3361 3636 3.187022 GTCAATCCTTTTTGTTGCCATGC 59.813 43.478 0.00 0.00 0.00 4.06
3427 3702 9.935682 AATGTTATAACTTCGCAACTATGATTG 57.064 29.630 16.33 0.00 0.00 2.67
3503 3778 5.068987 ACTCCAAACGGTAGTAAACACTGTA 59.931 40.000 0.00 0.00 34.39 2.74
3517 3792 8.095169 AGTAAACACTGTAAACTATGGAAGGAG 58.905 37.037 0.00 0.00 0.00 3.69
3835 4114 6.991938 TGAAAAGTTAAACAGCCAGCATAAT 58.008 32.000 0.00 0.00 0.00 1.28
3852 4131 4.331443 GCATAATATGTGTTGTGTCCGTGA 59.669 41.667 1.92 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 3.707189 GGAGGGAGGGAGGGGGAA 61.707 72.222 0.00 0.00 0.00 3.97
43 44 4.761304 AGGAGGGAGGGAGGGGGA 62.761 72.222 0.00 0.00 0.00 4.81
49 50 4.507916 CGAGCGAGGAGGGAGGGA 62.508 72.222 0.00 0.00 0.00 4.20
55 56 0.318275 GATGTTAGCGAGCGAGGAGG 60.318 60.000 0.00 0.00 0.00 4.30
59 60 0.658829 CCGAGATGTTAGCGAGCGAG 60.659 60.000 0.00 0.00 0.00 5.03
60 61 1.355563 CCGAGATGTTAGCGAGCGA 59.644 57.895 0.00 0.00 0.00 4.93
200 224 0.249398 GGACGATGCACTTACCCACT 59.751 55.000 0.00 0.00 0.00 4.00
210 234 1.758514 GGGAGGAGAGGACGATGCA 60.759 63.158 0.00 0.00 0.00 3.96
214 238 2.617538 AGGGGGAGGAGAGGACGA 60.618 66.667 0.00 0.00 0.00 4.20
216 240 2.284151 GGAGGGGGAGGAGAGGAC 59.716 72.222 0.00 0.00 0.00 3.85
302 337 3.437395 CGAACCGTAATCCATGGAAAACA 59.563 43.478 20.67 0.84 36.71 2.83
317 352 2.424601 TCGATTCATCTAACCGAACCGT 59.575 45.455 0.00 0.00 0.00 4.83
345 380 4.661125 GCAATCGCTCATTCAACATGTAA 58.339 39.130 0.00 0.00 34.30 2.41
380 418 1.692042 ACAGAGGCAGGATCCAGGG 60.692 63.158 15.82 4.00 0.00 4.45
392 434 1.454201 TACAGCGAGACAGACAGAGG 58.546 55.000 0.00 0.00 0.00 3.69
429 471 0.455410 TGCAGCAGAACAACCACAAC 59.545 50.000 0.00 0.00 0.00 3.32
540 582 3.677648 CACAACAGCAGGGCAGCC 61.678 66.667 1.26 1.26 34.23 4.85
722 766 1.719725 AACGCATTGTCCACAACGCA 61.720 50.000 10.76 0.00 44.30 5.24
725 769 2.704725 ATCAACGCATTGTCCACAAC 57.295 45.000 0.00 0.00 38.86 3.32
886 948 2.355132 CAGAGCACAGATTCAGGCATTC 59.645 50.000 0.00 0.00 0.00 2.67
952 1014 3.491447 GGAGCATTCAAACAAACAGCAGT 60.491 43.478 0.00 0.00 0.00 4.40
1008 1070 2.188994 GCCATCTTCCTCGCTGCT 59.811 61.111 0.00 0.00 0.00 4.24
1083 1145 1.066143 GCGGATGTTGGAGAGGAAAGA 60.066 52.381 0.00 0.00 0.00 2.52
1086 1148 0.250234 CAGCGGATGTTGGAGAGGAA 59.750 55.000 0.00 0.00 0.00 3.36
1114 1176 1.882989 GAGGCAAGTGAGGAGCGTCT 61.883 60.000 0.00 0.00 39.36 4.18
1136 1198 0.397941 TCTGCTTGAGGAAGTGGTGG 59.602 55.000 0.00 0.00 0.00 4.61
1160 1222 5.505181 ACCAATATGAACTGTGGAGTCTT 57.495 39.130 0.00 0.00 35.04 3.01
1164 1226 4.755411 ACGTACCAATATGAACTGTGGAG 58.245 43.478 0.00 0.00 35.04 3.86
1167 1229 6.453791 CGAAAGACGTACCAATATGAACTGTG 60.454 42.308 0.00 0.00 37.22 3.66
1211 1273 9.826574 AAAAGTACGGAATGTCTTAAGCATATA 57.173 29.630 11.24 2.86 0.00 0.86
1230 1292 7.321153 TGATCTCCTAGCTTGTACAAAAGTAC 58.679 38.462 10.03 0.00 0.00 2.73
1254 1316 2.807044 CGAGATGACACTCCTGTGATG 58.193 52.381 3.03 0.00 46.55 3.07
1325 1390 4.162509 GGGCTGTAGTTCAGTTAGGAGAAT 59.837 45.833 0.00 0.00 45.23 2.40
1337 1402 2.421529 CCATAGTTGGGGGCTGTAGTTC 60.422 54.545 0.00 0.00 39.56 3.01
1356 1421 3.591196 AAGCGCAATGAAAATTAGCCA 57.409 38.095 11.47 0.00 0.00 4.75
1375 1440 8.084684 CGGATTACTCAGATCATGATTGACTAA 58.915 37.037 10.14 13.21 37.28 2.24
1382 1447 3.580022 TGGCGGATTACTCAGATCATGAT 59.420 43.478 8.25 8.25 37.28 2.45
1411 1476 4.783764 ATTAAAACTTTCAGAAGCCCGG 57.216 40.909 0.00 0.00 36.29 5.73
1559 1819 3.202818 TGATGCACCAAATGTAGGATCCT 59.797 43.478 20.48 20.48 0.00 3.24
1560 1820 3.316308 GTGATGCACCAAATGTAGGATCC 59.684 47.826 2.48 2.48 0.00 3.36
1630 1890 4.558538 AGTTCACAACACTGCAGAAATC 57.441 40.909 23.35 0.89 0.00 2.17
1638 1898 6.638063 CCAAATATCACAAGTTCACAACACTG 59.362 38.462 0.00 0.00 0.00 3.66
1727 1987 4.338118 ACAAACATTGCCCGGAATGTATAG 59.662 41.667 18.81 14.27 44.15 1.31
1729 1989 3.096092 ACAAACATTGCCCGGAATGTAT 58.904 40.909 18.81 9.00 44.15 2.29
1738 1998 2.224018 ACACACATCACAAACATTGCCC 60.224 45.455 0.00 0.00 0.00 5.36
1909 2169 8.253810 CAGTATGGTGAAGAAGAATCTACTCAA 58.746 37.037 0.00 0.00 33.77 3.02
1937 2197 9.032624 AGCCTATAACTTGACAGAGTTAGTAAA 57.967 33.333 12.57 0.00 43.25 2.01
1985 2245 8.734218 AGTACAAGTAGATGAAATACGAGAGA 57.266 34.615 0.00 0.00 0.00 3.10
2024 2284 1.136305 TGCGGTACTAGGATGTTGCTC 59.864 52.381 0.00 0.00 0.00 4.26
2026 2286 1.136305 TCTGCGGTACTAGGATGTTGC 59.864 52.381 0.00 0.00 0.00 4.17
2195 2456 8.114331 AGCAAATTTCAATCAGTGACAAGATA 57.886 30.769 0.00 0.00 35.39 1.98
2960 3232 5.295292 AGTTGCTCCAAAATCGATCATACAG 59.705 40.000 0.00 0.00 0.00 2.74
3360 3635 3.120060 ACGTTTCTTGCAGATTCTGATGC 60.120 43.478 17.87 3.68 42.86 3.91
3361 3636 4.675190 ACGTTTCTTGCAGATTCTGATG 57.325 40.909 17.87 6.30 32.44 3.07
3427 3702 2.160417 GCTACTGATGTTTCTGTGTGCC 59.840 50.000 0.00 0.00 35.81 5.01
3503 3778 3.659183 ATGCTGCTCCTTCCATAGTTT 57.341 42.857 0.00 0.00 0.00 2.66
3517 3792 2.223433 GCCTTTCACAGTGATATGCTGC 60.223 50.000 3.45 0.00 37.47 5.25
3682 3957 2.843730 TGTAAGAAGCTGCCCAAGGATA 59.156 45.455 0.00 0.00 0.00 2.59
3835 4114 2.546368 GCTTTCACGGACACAACACATA 59.454 45.455 0.00 0.00 0.00 2.29
3852 4131 7.385778 TGTTTAAGTCTTAACACACTGCTTT 57.614 32.000 4.47 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.