Multiple sequence alignment - TraesCS7A01G392200

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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 TraesCS7A01G392200 chr7A 100.000 1395 0 0 975 2369 568579791 568581185 0.000000e+00 2577.0
1 TraesCS7A01G392200 chr7A 90.239 1086 66 15 975 2021 569112557 569111473 0.000000e+00 1382.0
2 TraesCS7A01G392200 chr7A 100.000 693 0 0 1 693 568578817 568579509 0.000000e+00 1280.0
3 TraesCS7A01G392200 chr7A 95.903 781 26 4 1593 2369 568130432 568131210 0.000000e+00 1260.0
4 TraesCS7A01G392200 chr7A 94.208 518 23 3 975 1485 568129808 568130325 0.000000e+00 784.0
5 TraesCS7A01G392200 chr7A 85.918 490 46 15 13 483 569113420 569112935 3.520000e-138 501.0
6 TraesCS7A01G392200 chr7A 89.323 384 33 7 975 1350 568695744 568695361 2.130000e-130 475.0
7 TraesCS7A01G392200 chr7A 88.169 355 35 6 2016 2369 569076099 569075751 1.310000e-112 416.0
8 TraesCS7A01G392200 chr7A 79.357 373 31 24 300 667 568129407 568129738 1.100000e-53 220.0
9 TraesCS7A01G392200 chr7A 91.667 60 4 1 425 483 568696133 568696074 5.430000e-12 82.4
10 TraesCS7A01G392200 chr7D 89.985 649 52 8 978 1620 501777905 501777264 0.000000e+00 826.0
11 TraesCS7A01G392200 chr7D 93.810 517 29 2 975 1488 501599923 501600439 0.000000e+00 774.0
12 TraesCS7A01G392200 chr7D 92.511 454 29 3 1911 2361 501776276 501775825 0.000000e+00 645.0
13 TraesCS7A01G392200 chr7D 90.765 379 27 6 977 1349 501610057 501609681 1.260000e-137 499.0
14 TraesCS7A01G392200 chr7D 90.769 325 18 8 1484 1802 501600475 501600793 7.830000e-115 424.0
15 TraesCS7A01G392200 chr7D 85.570 298 30 6 18 302 501597799 501598096 1.380000e-77 300.0
16 TraesCS7A01G392200 chr7D 84.762 315 16 5 1620 1913 501776740 501776437 1.070000e-73 287.0
17 TraesCS7A01G392200 chr7D 84.228 298 34 7 18 302 501787192 501786895 6.450000e-71 278.0
18 TraesCS7A01G392200 chr7D 93.143 175 11 1 305 479 501786844 501786671 3.020000e-64 255.0
19 TraesCS7A01G392200 chr7D 90.286 175 6 7 497 667 501599706 501599873 3.960000e-53 219.0
20 TraesCS7A01G392200 chr7D 87.179 117 12 3 1905 2019 501601051 501601166 1.910000e-26 130.0
21 TraesCS7A01G392200 chr7D 94.521 73 4 0 305 377 501598147 501598219 1.920000e-21 113.0
22 TraesCS7A01G392200 chr7B 91.000 500 35 4 997 1488 531180120 531180617 0.000000e+00 665.0
23 TraesCS7A01G392200 chr7B 87.473 455 39 13 978 1417 530869884 530870335 2.100000e-140 508.0
24 TraesCS7A01G392200 chr7B 86.739 460 40 13 975 1417 531222394 531221939 2.120000e-135 492.0
25 TraesCS7A01G392200 chr7B 84.906 265 24 7 13 263 531231156 531230894 1.090000e-63 254.0
26 TraesCS7A01G392200 chr7B 79.178 365 49 21 314 658 531179698 531180055 6.590000e-56 228.0
27 TraesCS7A01G392200 chr7B 95.082 122 6 0 1484 1605 531180653 531180774 2.400000e-45 193.0
28 TraesCS7A01G392200 chr7B 82.427 239 22 15 84 302 530869004 530869242 8.640000e-45 191.0
29 TraesCS7A01G392200 chr7B 91.489 47 2 2 439 483 530869492 530869538 1.970000e-06 63.9


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 TraesCS7A01G392200 chr7A 568578817 568581185 2368 False 1928.500000 2577 100.000000 1 2369 2 chr7A.!!$F2 2368
1 TraesCS7A01G392200 chr7A 569111473 569113420 1947 True 941.500000 1382 88.078500 13 2021 2 chr7A.!!$R3 2008
2 TraesCS7A01G392200 chr7A 568129407 568131210 1803 False 754.666667 1260 89.822667 300 2369 3 chr7A.!!$F1 2069
3 TraesCS7A01G392200 chr7A 568695361 568696133 772 True 278.700000 475 90.495000 425 1350 2 chr7A.!!$R2 925
4 TraesCS7A01G392200 chr7D 501775825 501777905 2080 True 586.000000 826 89.086000 978 2361 3 chr7D.!!$R2 1383
5 TraesCS7A01G392200 chr7D 501597799 501601166 3367 False 326.666667 774 90.355833 18 2019 6 chr7D.!!$F1 2001
6 TraesCS7A01G392200 chr7D 501786671 501787192 521 True 266.500000 278 88.685500 18 479 2 chr7D.!!$R3 461
7 TraesCS7A01G392200 chr7B 531179698 531180774 1076 False 362.000000 665 88.420000 314 1605 3 chr7B.!!$F2 1291
8 TraesCS7A01G392200 chr7B 530869004 530870335 1331 False 254.300000 508 87.129667 84 1417 3 chr7B.!!$F1 1333

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
126 138 0.523072 GTTGGTGATCATGCGCTGTT 59.477 50.0 9.73 0.0 0.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1401 3056 0.676736 TGAACAAAATTGGTCCCGCC 59.323 50.0 8.62 0.0 44.2 6.13 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
55 56 4.728102 TCAACAGTACGCGCCGGG 62.728 66.667 5.73 0.00 0.00 5.73
82 83 3.121030 GCAACTGCTCCGTCGCAT 61.121 61.111 0.00 0.00 39.52 4.73
126 138 0.523072 GTTGGTGATCATGCGCTGTT 59.477 50.000 9.73 0.00 0.00 3.16
158 170 0.882927 TCGGTTTGTTCAAGCCTCCG 60.883 55.000 14.46 12.56 38.16 4.63
285 324 3.953612 TGATTTGCACATGGATAGGTTCC 59.046 43.478 0.00 0.00 45.69 3.62
292 331 4.796606 CACATGGATAGGTTCCCTGAATT 58.203 43.478 0.00 0.00 44.77 2.17
404 1744 7.810658 AGTCACAGAAATTAATTGCAGTACAG 58.189 34.615 8.91 0.00 0.00 2.74
411 1751 8.028938 AGAAATTAATTGCAGTACAGCGAATTT 58.971 29.630 18.34 17.69 37.31 1.82
412 1752 9.284594 GAAATTAATTGCAGTACAGCGAATTTA 57.715 29.630 18.34 13.26 37.31 1.40
568 2140 2.043450 CCGCTCTCTCTCACCCCT 60.043 66.667 0.00 0.00 0.00 4.79
596 2174 1.435577 CGCGCCACCTATAAATACCC 58.564 55.000 0.00 0.00 0.00 3.69
598 2176 1.942586 GCGCCACCTATAAATACCCCG 60.943 57.143 0.00 0.00 0.00 5.73
599 2177 1.817357 GCCACCTATAAATACCCCGC 58.183 55.000 0.00 0.00 0.00 6.13
601 2179 1.982958 CCACCTATAAATACCCCGCCT 59.017 52.381 0.00 0.00 0.00 5.52
603 2181 2.027469 CACCTATAAATACCCCGCCTCC 60.027 54.545 0.00 0.00 0.00 4.30
605 2183 2.547990 CTATAAATACCCCGCCTCCCT 58.452 52.381 0.00 0.00 0.00 4.20
658 2257 1.801178 CACAGAAGAAGCGAGAAACCC 59.199 52.381 0.00 0.00 0.00 4.11
659 2258 1.416401 ACAGAAGAAGCGAGAAACCCA 59.584 47.619 0.00 0.00 0.00 4.51
660 2259 2.072298 CAGAAGAAGCGAGAAACCCAG 58.928 52.381 0.00 0.00 0.00 4.45
682 2312 1.212688 TCTGCCCAGAGAGAGAGAGAG 59.787 57.143 0.00 0.00 32.82 3.20
688 2318 3.070734 CCCAGAGAGAGAGAGAGAGAGAG 59.929 56.522 0.00 0.00 0.00 3.20
691 2321 4.039004 CAGAGAGAGAGAGAGAGAGAGAGG 59.961 54.167 0.00 0.00 0.00 3.69
995 2625 1.804151 ACATCCGTTTGATTCACCGTG 59.196 47.619 0.00 0.00 0.00 4.94
1260 2899 2.681778 CTCGACAGGGAGCCCAGT 60.682 66.667 8.53 5.73 38.58 4.00
1271 2910 2.733593 GCCCAGTGTCGTCGTCAC 60.734 66.667 13.70 13.70 36.22 3.67
1479 3186 8.503458 TTTGTCACCAGTAGTAGTATCTAGTC 57.497 38.462 0.00 0.00 0.00 2.59
1480 3187 6.279123 TGTCACCAGTAGTAGTATCTAGTCG 58.721 44.000 0.00 0.00 0.00 4.18
1481 3188 6.097412 TGTCACCAGTAGTAGTATCTAGTCGA 59.903 42.308 0.00 0.00 0.00 4.20
1482 3189 6.642131 GTCACCAGTAGTAGTATCTAGTCGAG 59.358 46.154 0.00 0.00 0.00 4.04
1538 3290 0.179078 TTGCTTGGTTTTGCCTGCTG 60.179 50.000 0.00 0.00 37.93 4.41
1657 3935 5.708697 TCTCTCGTAGTGGTAAATCTCAACA 59.291 40.000 0.00 0.00 0.00 3.33
2263 4894 8.883731 CGTATCATATTTTCAGAGGTGTTCTTT 58.116 33.333 0.00 0.00 32.41 2.52
2326 4957 1.541233 GGTTGGCGAGGATATGTGAGG 60.541 57.143 0.00 0.00 0.00 3.86
2335 4966 2.174210 AGGATATGTGAGGCATGCTTGT 59.826 45.455 18.92 2.16 38.47 3.16
2361 4992 2.273179 TTCGGGGTCTCGGACACAG 61.273 63.158 8.29 4.73 37.77 3.66
2362 4993 4.436998 CGGGGTCTCGGACACAGC 62.437 72.222 8.29 0.00 37.77 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.015109 GCAGGCACATCAGATCAGTG 58.985 55.000 0.00 0.00 36.39 3.66
1 2 0.616891 TGCAGGCACATCAGATCAGT 59.383 50.000 0.00 0.00 0.00 3.41
2 3 1.604278 CATGCAGGCACATCAGATCAG 59.396 52.381 0.00 0.00 0.00 2.90
3 4 1.675552 CATGCAGGCACATCAGATCA 58.324 50.000 0.00 0.00 0.00 2.92
4 5 0.952280 CCATGCAGGCACATCAGATC 59.048 55.000 0.00 0.00 0.00 2.75
5 6 0.467474 CCCATGCAGGCACATCAGAT 60.467 55.000 0.00 0.00 35.39 2.90
6 7 1.077285 CCCATGCAGGCACATCAGA 60.077 57.895 0.00 0.00 35.39 3.27
7 8 3.521605 CCCATGCAGGCACATCAG 58.478 61.111 0.00 0.00 35.39 2.90
82 83 3.914605 CTGCGCCGTCAGCTGTACA 62.915 63.158 14.67 0.00 40.39 2.90
150 162 1.482593 CCTAGACACATTCGGAGGCTT 59.517 52.381 0.00 0.00 0.00 4.35
158 170 3.686726 CCTTGTTGCTCCTAGACACATTC 59.313 47.826 0.00 0.00 0.00 2.67
256 295 3.637432 TCCATGTGCAAATCAAACGAAC 58.363 40.909 0.00 0.00 0.00 3.95
258 297 4.096231 CCTATCCATGTGCAAATCAAACGA 59.904 41.667 0.00 0.00 0.00 3.85
285 324 1.341383 CCCAGGTGGAGGAAATTCAGG 60.341 57.143 0.00 0.00 37.39 3.86
292 331 2.852075 AACGCCCAGGTGGAGGAA 60.852 61.111 1.72 0.00 38.44 3.36
404 1744 8.690840 CGGATTCTTTGGATAAAATAAATTCGC 58.309 33.333 0.00 0.00 30.96 4.70
428 1768 3.669251 TTGCCTTTGGATAAAAACCGG 57.331 42.857 0.00 0.00 0.00 5.28
995 2625 0.034476 TCTGATCGGCCTCATGATGC 59.966 55.000 13.99 13.99 0.00 3.91
1259 2898 2.380410 GGCATGGTGACGACGACAC 61.380 63.158 19.83 19.83 37.51 3.67
1260 2899 2.048597 GGCATGGTGACGACGACA 60.049 61.111 0.00 0.00 0.00 4.35
1397 3050 0.897863 CAAAATTGGTCCCGCCTCCA 60.898 55.000 0.00 0.00 38.35 3.86
1401 3056 0.676736 TGAACAAAATTGGTCCCGCC 59.323 50.000 8.62 0.00 44.20 6.13
1461 3118 6.209192 TCTCCTCGACTAGATACTACTACTGG 59.791 46.154 0.00 0.00 0.00 4.00
1462 3119 7.218228 TCTCCTCGACTAGATACTACTACTG 57.782 44.000 0.00 0.00 0.00 2.74
1479 3186 1.133216 TCGCTTTCACAGATCTCCTCG 59.867 52.381 0.00 0.00 0.00 4.63
1480 3187 2.949451 TCGCTTTCACAGATCTCCTC 57.051 50.000 0.00 0.00 0.00 3.71
1481 3188 3.196469 TCATTCGCTTTCACAGATCTCCT 59.804 43.478 0.00 0.00 0.00 3.69
1482 3189 3.525537 TCATTCGCTTTCACAGATCTCC 58.474 45.455 0.00 0.00 0.00 3.71
1538 3290 2.412089 CGAGTGGAAAATCGAACTGGAC 59.588 50.000 0.00 0.00 41.40 4.02
1657 3935 4.154195 GTGGTTAATGCTTCGTGACTCATT 59.846 41.667 0.00 0.00 34.08 2.57
1667 3945 5.132897 TGATGGTTTGTGGTTAATGCTTC 57.867 39.130 0.00 0.00 0.00 3.86
1758 4045 3.718036 CGTCATTTCGCACAAACTCGTAG 60.718 47.826 0.00 0.00 0.00 3.51
2127 4758 2.229792 TGATTGTTTGACTGGAGTGCC 58.770 47.619 0.00 0.00 0.00 5.01
2233 4864 6.126883 ACACCTCTGAAAATATGATACGGGAA 60.127 38.462 0.00 0.00 0.00 3.97


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

AutoCloner maintained by Alex Coulton.