Multiple sequence alignment - TraesCS3A01G203000

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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 TraesCS3A01G203000 chr3A 100.000 2366 0 0 1 2366 347832935 347830570 0.000000e+00 4370
1 TraesCS3A01G203000 chr5A 95.564 2367 95 7 4 2365 176943787 176941426 0.000000e+00 3781
2 TraesCS3A01G203000 chr5A 87.590 693 71 13 4 690 131342924 131342241 0.000000e+00 789
3 TraesCS3A01G203000 chr5A 87.446 693 75 11 4 690 131335349 131334663 0.000000e+00 787
4 TraesCS3A01G203000 chr5A 90.456 241 20 3 1330 1570 198343397 198343160 4.910000e-82 315
5 TraesCS3A01G203000 chr6A 95.399 2369 98 7 1 2365 266026588 266028949 0.000000e+00 3760
6 TraesCS3A01G203000 chr6A 95.353 2367 96 10 1 2362 266018710 266021067 0.000000e+00 3749
7 TraesCS3A01G203000 chr6A 87.370 1346 134 30 4 1328 259362605 259361275 0.000000e+00 1511
8 TraesCS3A01G203000 chr6A 85.127 1264 150 31 4 1239 430709006 430707753 0.000000e+00 1258
9 TraesCS3A01G203000 chr6A 92.793 777 49 6 1294 2067 259361195 259360423 0.000000e+00 1118
10 TraesCS3A01G203000 chr6A 90.095 525 45 6 1845 2366 312689354 312689874 0.000000e+00 675
11 TraesCS3A01G203000 chr4A 94.309 2372 120 13 4 2366 197215286 197212921 0.000000e+00 3618
12 TraesCS3A01G203000 chr4A 86.860 1347 137 29 1 1328 205924351 205925676 0.000000e+00 1471
13 TraesCS3A01G203000 chr4A 86.573 1348 145 29 1 1328 205932277 205933608 0.000000e+00 1454
14 TraesCS3A01G203000 chr4A 92.458 769 41 6 1298 2064 205925761 205926514 0.000000e+00 1083
15 TraesCS3A01G203000 chr4A 91.935 744 44 5 1323 2064 205933716 205934445 0.000000e+00 1027
16 TraesCS3A01G203000 chr7A 96.552 1740 53 6 629 2366 420702004 420703738 0.000000e+00 2874
17 TraesCS3A01G203000 chr7A 98.113 636 11 1 1 636 420701349 420701983 0.000000e+00 1107
18 TraesCS3A01G203000 chr7A 84.983 586 51 10 1498 2053 324976859 324977437 5.710000e-156 560
19 TraesCS3A01G203000 chr7A 90.253 277 21 6 1295 1570 324967844 324968115 8.040000e-95 357
20 TraesCS3A01G203000 chr7A 92.683 82 5 1 1248 1328 324967678 324967759 1.490000e-22 117
21 TraesCS3A01G203000 chr2A 87.717 692 76 8 1 690 305113650 305114334 0.000000e+00 798
22 TraesCS3A01G203000 chr2A 87.608 694 75 10 1 690 305105797 305106483 0.000000e+00 795
23 TraesCS3A01G203000 chr2A 84.301 758 83 29 4 742 510966291 510965551 0.000000e+00 708
24 TraesCS3A01G203000 chr1A 91.603 524 39 5 1845 2366 385002421 385002941 0.000000e+00 719
25 TraesCS3A01G203000 chr1A 91.412 524 40 4 1845 2366 326543230 326542710 0.000000e+00 713
26 TraesCS3A01G203000 chr1A 91.396 523 40 4 1846 2366 326535656 326535137 0.000000e+00 712
27 TraesCS3A01G203000 chr5B 94.203 69 3 1 1321 1388 259615448 259615516 1.160000e-18 104


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 TraesCS3A01G203000 chr3A 347830570 347832935 2365 True 4370.0 4370 100.0000 1 2366 1 chr3A.!!$R1 2365
1 TraesCS3A01G203000 chr5A 176941426 176943787 2361 True 3781.0 3781 95.5640 4 2365 1 chr5A.!!$R3 2361
2 TraesCS3A01G203000 chr5A 131342241 131342924 683 True 789.0 789 87.5900 4 690 1 chr5A.!!$R2 686
3 TraesCS3A01G203000 chr5A 131334663 131335349 686 True 787.0 787 87.4460 4 690 1 chr5A.!!$R1 686
4 TraesCS3A01G203000 chr6A 266026588 266028949 2361 False 3760.0 3760 95.3990 1 2365 1 chr6A.!!$F2 2364
5 TraesCS3A01G203000 chr6A 266018710 266021067 2357 False 3749.0 3749 95.3530 1 2362 1 chr6A.!!$F1 2361
6 TraesCS3A01G203000 chr6A 259360423 259362605 2182 True 1314.5 1511 90.0815 4 2067 2 chr6A.!!$R2 2063
7 TraesCS3A01G203000 chr6A 430707753 430709006 1253 True 1258.0 1258 85.1270 4 1239 1 chr6A.!!$R1 1235
8 TraesCS3A01G203000 chr6A 312689354 312689874 520 False 675.0 675 90.0950 1845 2366 1 chr6A.!!$F3 521
9 TraesCS3A01G203000 chr4A 197212921 197215286 2365 True 3618.0 3618 94.3090 4 2366 1 chr4A.!!$R1 2362
10 TraesCS3A01G203000 chr4A 205924351 205926514 2163 False 1277.0 1471 89.6590 1 2064 2 chr4A.!!$F1 2063
11 TraesCS3A01G203000 chr4A 205932277 205934445 2168 False 1240.5 1454 89.2540 1 2064 2 chr4A.!!$F2 2063
12 TraesCS3A01G203000 chr7A 420701349 420703738 2389 False 1990.5 2874 97.3325 1 2366 2 chr7A.!!$F3 2365
13 TraesCS3A01G203000 chr7A 324976859 324977437 578 False 560.0 560 84.9830 1498 2053 1 chr7A.!!$F1 555
14 TraesCS3A01G203000 chr2A 305113650 305114334 684 False 798.0 798 87.7170 1 690 1 chr2A.!!$F2 689
15 TraesCS3A01G203000 chr2A 305105797 305106483 686 False 795.0 795 87.6080 1 690 1 chr2A.!!$F1 689
16 TraesCS3A01G203000 chr2A 510965551 510966291 740 True 708.0 708 84.3010 4 742 1 chr2A.!!$R1 738
17 TraesCS3A01G203000 chr1A 385002421 385002941 520 False 719.0 719 91.6030 1845 2366 1 chr1A.!!$F1 521
18 TraesCS3A01G203000 chr1A 326542710 326543230 520 True 713.0 713 91.4120 1845 2366 1 chr1A.!!$R2 521
19 TraesCS3A01G203000 chr1A 326535137 326535656 519 True 712.0 712 91.3960 1846 2366 1 chr1A.!!$R1 520

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
939 1015 2.479837 CAGTGACAGGTAAAACAGCGA 58.52 47.619 0.0 0.0 0.0 4.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2194 2644 0.250513 GGTCTCCGGAAACAGATGCT 59.749 55.0 10.72 0.0 0.0 3.79 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
73 76 2.481952 GCAAAGTGCAACAACCAAAACA 59.518 40.909 0.00 0.00 44.26 2.83
117 121 2.559998 CAACGGGTTGCATATTGACC 57.440 50.000 0.00 0.00 33.45 4.02
594 613 9.906660 CATGGTTCAAAAGTTATTAGCAGTTAA 57.093 29.630 0.00 0.00 0.00 2.01
621 640 6.691255 AATAGGGGCCGTTCTGTAAATATA 57.309 37.500 3.09 0.00 0.00 0.86
939 1015 2.479837 CAGTGACAGGTAAAACAGCGA 58.520 47.619 0.00 0.00 0.00 4.93
1098 1174 4.406763 AGGAGGAGCTCGGGCCTT 62.407 66.667 2.00 0.00 39.73 4.35
1382 1797 2.205462 ACCTGCTGGTGGGTCTCT 59.795 61.111 15.36 0.00 46.51 3.10
1449 1864 0.685660 GTTGGGGAAGAACTCGAGGT 59.314 55.000 18.41 11.06 0.00 3.85
1483 1898 0.601558 GGTGCTCTCCTGTTCGTACA 59.398 55.000 0.00 0.00 0.00 2.90
1580 1995 1.609210 TCCTGGTCGCAGGTGATGA 60.609 57.895 8.68 0.00 42.79 2.92
1665 2080 1.308216 CAAGGGGATCAGGGGAGGT 60.308 63.158 0.00 0.00 0.00 3.85
1670 2085 2.191641 GATCAGGGGAGGTGCTGC 59.808 66.667 0.00 0.00 0.00 5.25
1694 2109 2.424234 GGTGCAGACTAGGGAGAGATCT 60.424 54.545 0.00 0.00 0.00 2.75
1712 2127 0.183014 CTAGAGGTGGAGGGCTACGA 59.817 60.000 0.00 0.00 0.00 3.43
1723 2138 0.034863 GGGCTACGATTTGGGTGGAA 60.035 55.000 0.00 0.00 0.00 3.53
1799 2214 1.705997 AACAAGGAAGAGCGGGTGGT 61.706 55.000 0.00 0.00 0.00 4.16
2194 2644 0.032615 GAGAAGAGAGAGAGGGCCCA 60.033 60.000 27.56 0.00 0.00 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
73 76 7.093814 TGCATATTGAGCTCCACTTAATTTGTT 60.094 33.333 12.15 0.0 36.40 2.83
117 121 6.677781 ACTAAATAATGGATGTGGTGTTCG 57.322 37.500 0.00 0.0 0.00 3.95
666 721 2.663852 CAGTTTCGGCCCGTTCGT 60.664 61.111 1.63 0.0 0.00 3.85
922 998 1.067364 TCGTCGCTGTTTTACCTGTCA 59.933 47.619 0.00 0.0 0.00 3.58
939 1015 2.045926 GCCAAGTCCCTGCATCGT 60.046 61.111 0.00 0.0 0.00 3.73
1075 1151 2.790791 CCGAGCTCCTCCTGCGATT 61.791 63.158 8.47 0.0 35.28 3.34
1382 1797 4.697756 CCGGCAGTTTCCTCGCCA 62.698 66.667 0.00 0.0 46.60 5.69
1449 1864 1.971505 GCACCCGACTCCATGGATGA 61.972 60.000 16.63 0.0 0.00 2.92
1483 1898 2.520120 TCCCTCTCCATCTCTGTACCAT 59.480 50.000 0.00 0.0 0.00 3.55
1495 1910 1.996291 TCTCTCTCAACTCCCTCTCCA 59.004 52.381 0.00 0.0 0.00 3.86
1670 2085 1.480137 CTCTCCCTAGTCTGCACCAAG 59.520 57.143 0.00 0.0 0.00 3.61
1694 2109 0.851469 ATCGTAGCCCTCCACCTCTA 59.149 55.000 0.00 0.0 0.00 2.43
1712 2127 2.637872 TCTTCTCTCGTTCCACCCAAAT 59.362 45.455 0.00 0.0 0.00 2.32
1799 2214 4.794648 CCAATCCCGAAGCCGCCA 62.795 66.667 0.00 0.0 0.00 5.69
2111 2556 0.815734 CCTCTTCGCTTCCGGAGTTA 59.184 55.000 3.34 0.0 40.99 2.24
2194 2644 0.250513 GGTCTCCGGAAACAGATGCT 59.749 55.000 10.72 0.0 0.00 3.79


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

AutoCloner maintained by Alex Coulton.