Multiple sequence alignment - TraesCS1B01G140600

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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 TraesCS1B01G140600 chr1B 100.000 2339 0 0 1 2339 186794834 186797172 0.000000e+00 4320
1 TraesCS1B01G140600 chr1B 94.098 610 20 4 1 597 647926638 647927244 0.000000e+00 913
2 TraesCS1B01G140600 chr1A 96.386 913 22 3 1436 2339 134943392 134944302 0.000000e+00 1493
3 TraesCS1B01G140600 chr1D 93.992 982 23 18 1363 2336 122767318 122768271 0.000000e+00 1454
4 TraesCS1B01G140600 chr7A 96.114 772 30 0 593 1364 75026317 75025546 0.000000e+00 1260
5 TraesCS1B01G140600 chr7D 95.979 771 30 1 593 1363 497006464 497007233 0.000000e+00 1251
6 TraesCS1B01G140600 chr7D 86.536 765 97 4 592 1354 472803222 472802462 0.000000e+00 837
7 TraesCS1B01G140600 chr7D 85.075 134 18 2 461 593 579745561 579745429 4.050000e-28 135
8 TraesCS1B01G140600 chr6B 95.731 773 26 2 593 1364 367351329 367350563 0.000000e+00 1238
9 TraesCS1B01G140600 chr6B 97.063 715 21 0 649 1363 638232545 638231831 0.000000e+00 1205
10 TraesCS1B01G140600 chr6B 96.796 593 17 1 1 593 658802766 658802176 0.000000e+00 989
11 TraesCS1B01G140600 chr6B 90.286 700 60 3 667 1364 157197825 157198518 0.000000e+00 909
12 TraesCS1B01G140600 chr3B 95.213 773 31 1 593 1365 410611466 410612232 0.000000e+00 1218
13 TraesCS1B01G140600 chr3A 94.819 772 35 4 596 1367 100035392 100034626 0.000000e+00 1199
14 TraesCS1B01G140600 chr3A 92.510 494 22 3 113 593 750314271 750313780 0.000000e+00 693
15 TraesCS1B01G140600 chr3A 84.211 133 19 2 461 593 692489934 692489804 6.780000e-26 128
16 TraesCS1B01G140600 chr3A 83.582 134 20 2 461 593 99251059 99250927 8.780000e-25 124
17 TraesCS1B01G140600 chr3D 85.509 766 101 8 599 1360 339844790 339844031 0.000000e+00 791
18 TraesCS1B01G140600 chr4D 84.783 138 17 4 461 597 234843097 234843231 4.050000e-28 135
19 TraesCS1B01G140600 chr2A 82.609 138 21 3 461 597 176656555 176656420 4.080000e-23 119
20 TraesCS1B01G140600 chr5B 82.946 129 20 2 461 588 689861219 689861092 5.280000e-22 115


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 TraesCS1B01G140600 chr1B 186794834 186797172 2338 False 4320 4320 100.000 1 2339 1 chr1B.!!$F1 2338
1 TraesCS1B01G140600 chr1B 647926638 647927244 606 False 913 913 94.098 1 597 1 chr1B.!!$F2 596
2 TraesCS1B01G140600 chr1A 134943392 134944302 910 False 1493 1493 96.386 1436 2339 1 chr1A.!!$F1 903
3 TraesCS1B01G140600 chr1D 122767318 122768271 953 False 1454 1454 93.992 1363 2336 1 chr1D.!!$F1 973
4 TraesCS1B01G140600 chr7A 75025546 75026317 771 True 1260 1260 96.114 593 1364 1 chr7A.!!$R1 771
5 TraesCS1B01G140600 chr7D 497006464 497007233 769 False 1251 1251 95.979 593 1363 1 chr7D.!!$F1 770
6 TraesCS1B01G140600 chr7D 472802462 472803222 760 True 837 837 86.536 592 1354 1 chr7D.!!$R1 762
7 TraesCS1B01G140600 chr6B 367350563 367351329 766 True 1238 1238 95.731 593 1364 1 chr6B.!!$R1 771
8 TraesCS1B01G140600 chr6B 638231831 638232545 714 True 1205 1205 97.063 649 1363 1 chr6B.!!$R2 714
9 TraesCS1B01G140600 chr6B 658802176 658802766 590 True 989 989 96.796 1 593 1 chr6B.!!$R3 592
10 TraesCS1B01G140600 chr6B 157197825 157198518 693 False 909 909 90.286 667 1364 1 chr6B.!!$F1 697
11 TraesCS1B01G140600 chr3B 410611466 410612232 766 False 1218 1218 95.213 593 1365 1 chr3B.!!$F1 772
12 TraesCS1B01G140600 chr3A 100034626 100035392 766 True 1199 1199 94.819 596 1367 1 chr3A.!!$R2 771
13 TraesCS1B01G140600 chr3D 339844031 339844790 759 True 791 791 85.509 599 1360 1 chr3D.!!$R1 761

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
946 962 1.000607 CGGTCCTGAGAGACGACAAAA 60.001 52.381 0.0 0.0 37.66 2.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1819 1851 2.112718 GGATAGCAGCTGCCAGGG 59.887 66.667 34.39 0.0 43.38 4.45 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
31 32 5.945784 AGCAGTGCCATCTAGAAAACAAATA 59.054 36.000 12.58 0.0 0.00 1.40
110 111 4.405358 TCCTTGAAACCAAGAAACAAGCAT 59.595 37.500 6.73 0.0 42.71 3.79
385 386 2.202756 CTGGTCGCTAGGGTTCGC 60.203 66.667 6.70 0.0 0.00 4.70
436 450 2.048597 TTCGTGGCTTCGTGCGAT 60.049 55.556 0.00 0.0 44.05 4.58
489 503 2.203538 CCTGGGCTTGCAAGTGGT 60.204 61.111 26.55 0.0 0.00 4.16
516 530 2.228925 CCCAGGCCAAACCAATTTTTG 58.771 47.619 5.01 0.0 43.14 2.44
765 779 1.211457 ACAACCCAAAATGCCTTGCAA 59.789 42.857 0.00 0.0 43.62 4.08
946 962 1.000607 CGGTCCTGAGAGACGACAAAA 60.001 52.381 0.00 0.0 37.66 2.44
958 974 6.228258 AGAGACGACAAAAGCAGGTTTATTA 58.772 36.000 0.00 0.0 0.00 0.98
1165 1182 6.772770 TCTTCGACGATTGTTTTCATTACA 57.227 33.333 0.00 0.0 0.00 2.41
1171 1188 7.169476 TCGACGATTGTTTTCATTACACTTGTA 59.831 33.333 0.00 0.0 0.00 2.41
1318 1335 7.496747 TGTAATGATCCTCATGAACGATGTAA 58.503 34.615 9.18 0.0 37.15 2.41
1374 1391 4.385358 TCAAAGAAAAGCACCTGTTTCC 57.615 40.909 0.00 0.0 34.85 3.13
1377 1394 1.676006 AGAAAAGCACCTGTTTCCGTG 59.324 47.619 0.00 0.0 34.85 4.94
1386 1403 2.203401 CCTGTTTCCGTGTTGACGTTA 58.797 47.619 0.00 0.0 44.54 3.18
1387 1404 2.608546 CCTGTTTCCGTGTTGACGTTAA 59.391 45.455 0.00 0.0 44.54 2.01
1460 1477 4.205323 ACGATTTGTCCGACTTGTTTTC 57.795 40.909 0.00 0.0 0.00 2.29
1463 1480 5.163693 ACGATTTGTCCGACTTGTTTTCTTT 60.164 36.000 0.00 0.0 0.00 2.52
1555 1581 3.971109 GAACGGGCTCCCCTTTCCG 62.971 68.421 8.00 0.0 43.51 4.30
1641 1673 1.064825 GGTTTTCCTCCTCCACCTCA 58.935 55.000 0.00 0.0 36.94 3.86
1840 1872 0.469070 CTGGCAGCTGCTATCCTCTT 59.531 55.000 35.82 0.0 41.70 2.85
2048 2080 2.664015 ACCTACCCTTAGTCTTAGCCG 58.336 52.381 0.00 0.0 0.00 5.52
2056 2088 3.946558 CCTTAGTCTTAGCCGTGTACTCT 59.053 47.826 0.00 0.0 0.00 3.24
2077 2109 2.892374 TGATGATGTGTACTCTTGCCG 58.108 47.619 0.00 0.0 0.00 5.69
2088 2120 3.188159 ACTCTTGCCGTTAGTTTGACA 57.812 42.857 0.00 0.0 0.00 3.58
2089 2121 2.870411 ACTCTTGCCGTTAGTTTGACAC 59.130 45.455 0.00 0.0 0.00 3.67
2131 2165 1.439679 CGGAGCCTGTACCTCAAAAC 58.560 55.000 0.00 0.0 0.00 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 0.041535 TCAATGCCTTGATGCCCCTT 59.958 50.000 0.00 0.00 36.46 3.95
110 111 3.345808 GCTTTGTGTCCAGCGCGA 61.346 61.111 12.10 0.00 0.00 5.87
436 450 3.785859 CCGCCTGCCTGCTTCCTA 61.786 66.667 0.00 0.00 0.00 2.94
765 779 6.173427 AGTGCTAAAACACCCATTGAAATT 57.827 33.333 0.00 0.00 41.67 1.82
946 962 5.514500 TTTCCTCCAGTAATAAACCTGCT 57.486 39.130 0.00 0.00 0.00 4.24
958 974 2.171448 CGATCTTCCCATTTCCTCCAGT 59.829 50.000 0.00 0.00 0.00 4.00
1358 1375 1.404035 ACACGGAAACAGGTGCTTTTC 59.596 47.619 0.00 0.00 37.68 2.29
1365 1382 2.685364 CGTCAACACGGAAACAGGT 58.315 52.632 0.00 0.00 42.73 4.00
1407 1424 5.492855 TCGGGGAGAAAAGATAAACTCAA 57.507 39.130 0.00 0.00 0.00 3.02
1408 1425 5.693769 ATCGGGGAGAAAAGATAAACTCA 57.306 39.130 0.00 0.00 0.00 3.41
1409 1426 8.678593 AAATATCGGGGAGAAAAGATAAACTC 57.321 34.615 0.00 0.00 0.00 3.01
1410 1427 9.475620 AAAAATATCGGGGAGAAAAGATAAACT 57.524 29.630 0.00 0.00 0.00 2.66
1423 1440 6.350906 ACAAATCGTCTAAAAATATCGGGGA 58.649 36.000 0.00 0.00 0.00 4.81
1460 1477 3.262420 CCCAAGTCGGATGTGTCTAAAG 58.738 50.000 0.00 0.00 36.56 1.85
1463 1480 1.548719 CACCCAAGTCGGATGTGTCTA 59.451 52.381 0.00 0.00 36.56 2.59
1555 1581 4.143301 GGGTGGAATGGAGGGGGC 62.143 72.222 0.00 0.00 0.00 5.80
1594 1620 3.291101 TTACGGCGTGAGGTGAGCC 62.291 63.158 24.86 0.00 46.88 4.70
1641 1673 3.000819 TCCGAGGTGATGCCGGTT 61.001 61.111 1.90 0.00 43.40 4.44
1819 1851 2.112718 GGATAGCAGCTGCCAGGG 59.887 66.667 34.39 0.00 43.38 4.45
1840 1872 2.300433 TCGGGATCGGAGTTTTCGATA 58.700 47.619 0.00 0.00 45.81 2.92
2048 2080 6.857956 AGAGTACACATCATCAAGAGTACAC 58.142 40.000 0.00 0.00 35.51 2.90
2056 2088 3.261580 CGGCAAGAGTACACATCATCAA 58.738 45.455 0.00 0.00 0.00 2.57
2131 2165 7.921214 ACACTTAATCGTATCATGTACTTCCAG 59.079 37.037 0.00 0.00 0.00 3.86
2176 2210 4.715130 TACCAGCTGACCGGGGCT 62.715 66.667 17.39 9.89 39.60 5.19


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

AutoCloner maintained by Alex Coulton.