Multiple sequence alignment - TraesCS3D01G382900

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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 TraesCS3D01G382900 chr3D 100.000 2370 0 0 1 2370 498400402 498398033 0.000000e+00 4377
1 TraesCS3D01G382900 chr3D 88.469 1457 121 23 1 1431 362051959 362050524 0.000000e+00 1716
2 TraesCS3D01G382900 chr3D 98.644 885 11 1 1487 2370 13680406 13681290 0.000000e+00 1567
3 TraesCS3D01G382900 chr3D 98.641 883 10 2 1488 2370 528107954 528107074 0.000000e+00 1563
4 TraesCS3D01G382900 chr5B 86.974 1520 142 27 1 1487 88345759 88344263 0.000000e+00 1659
5 TraesCS3D01G382900 chr7D 86.451 1513 172 18 1 1487 616482410 616483915 0.000000e+00 1628
6 TraesCS3D01G382900 chr7D 98.867 883 10 0 1488 2370 636324400 636325282 0.000000e+00 1576
7 TraesCS3D01G382900 chr7D 98.422 887 14 0 1484 2370 93663034 93663920 0.000000e+00 1561
8 TraesCS3D01G382900 chr7D 85.030 1503 184 28 1 1487 104637324 104635847 0.000000e+00 1491
9 TraesCS3D01G382900 chr7D 84.934 1520 177 29 1 1487 412230120 412231620 0.000000e+00 1491
10 TraesCS3D01G382900 chr7D 84.950 1495 191 23 15 1487 594139757 594141239 0.000000e+00 1483
11 TraesCS3D01G382900 chr6D 86.530 1507 168 20 1 1487 463789073 463787582 0.000000e+00 1626
12 TraesCS3D01G382900 chr6D 98.528 883 13 0 1488 2370 258541788 258540906 0.000000e+00 1559
13 TraesCS3D01G382900 chr1D 86.499 1511 149 33 1 1485 493226579 493228060 0.000000e+00 1609
14 TraesCS3D01G382900 chr1D 86.178 1541 148 31 1 1490 415632915 415631389 0.000000e+00 1605
15 TraesCS3D01G382900 chr1D 98.754 883 10 1 1488 2370 153888297 153889178 0.000000e+00 1568
16 TraesCS3D01G382900 chr1D 98.529 884 13 0 1487 2370 438212348 438213231 0.000000e+00 1561
17 TraesCS3D01G382900 chr1A 86.141 1508 172 18 1 1487 249132305 249130814 0.000000e+00 1592
18 TraesCS3D01G382900 chr5D 98.754 883 11 0 1488 2370 142663910 142664792 0.000000e+00 1570
19 TraesCS3D01G382900 chr5D 98.422 887 14 0 1484 2370 408365188 408364302 0.000000e+00 1561
20 TraesCS3D01G382900 chr5D 84.758 1509 173 32 1 1487 432509480 432510953 0.000000e+00 1459
21 TraesCS3D01G382900 chr5D 83.916 1517 192 31 3 1487 216993768 216995264 0.000000e+00 1402
22 TraesCS3D01G382900 chr2D 85.242 1511 188 20 1 1487 77401621 77403120 0.000000e+00 1522
23 TraesCS3D01G382900 chr7B 84.771 1484 181 25 41 1487 610812637 610814112 0.000000e+00 1447
24 TraesCS3D01G382900 chr7B 83.929 1512 199 29 1 1485 654022269 654020775 0.000000e+00 1406
25 TraesCS3D01G382900 chrUn 87.684 1226 90 33 1 1181 61035722 61034513 0.000000e+00 1371
26 TraesCS3D01G382900 chrUn 83.366 1533 166 38 1 1487 35058709 35057220 0.000000e+00 1336
27 TraesCS3D01G382900 chrUn 79.882 338 44 11 5 329 67048791 67048465 2.370000e-55 226
28 TraesCS3D01G382900 chrUn 79.882 338 44 11 5 329 293305226 293305552 2.370000e-55 226
29 TraesCS3D01G382900 chrUn 79.882 338 44 11 5 329 293310623 293310949 2.370000e-55 226


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 TraesCS3D01G382900 chr3D 498398033 498400402 2369 True 4377 4377 100.000 1 2370 1 chr3D.!!$R2 2369
1 TraesCS3D01G382900 chr3D 362050524 362051959 1435 True 1716 1716 88.469 1 1431 1 chr3D.!!$R1 1430
2 TraesCS3D01G382900 chr3D 13680406 13681290 884 False 1567 1567 98.644 1487 2370 1 chr3D.!!$F1 883
3 TraesCS3D01G382900 chr3D 528107074 528107954 880 True 1563 1563 98.641 1488 2370 1 chr3D.!!$R3 882
4 TraesCS3D01G382900 chr5B 88344263 88345759 1496 True 1659 1659 86.974 1 1487 1 chr5B.!!$R1 1486
5 TraesCS3D01G382900 chr7D 616482410 616483915 1505 False 1628 1628 86.451 1 1487 1 chr7D.!!$F4 1486
6 TraesCS3D01G382900 chr7D 636324400 636325282 882 False 1576 1576 98.867 1488 2370 1 chr7D.!!$F5 882
7 TraesCS3D01G382900 chr7D 93663034 93663920 886 False 1561 1561 98.422 1484 2370 1 chr7D.!!$F1 886
8 TraesCS3D01G382900 chr7D 104635847 104637324 1477 True 1491 1491 85.030 1 1487 1 chr7D.!!$R1 1486
9 TraesCS3D01G382900 chr7D 412230120 412231620 1500 False 1491 1491 84.934 1 1487 1 chr7D.!!$F2 1486
10 TraesCS3D01G382900 chr7D 594139757 594141239 1482 False 1483 1483 84.950 15 1487 1 chr7D.!!$F3 1472
11 TraesCS3D01G382900 chr6D 463787582 463789073 1491 True 1626 1626 86.530 1 1487 1 chr6D.!!$R2 1486
12 TraesCS3D01G382900 chr6D 258540906 258541788 882 True 1559 1559 98.528 1488 2370 1 chr6D.!!$R1 882
13 TraesCS3D01G382900 chr1D 493226579 493228060 1481 False 1609 1609 86.499 1 1485 1 chr1D.!!$F3 1484
14 TraesCS3D01G382900 chr1D 415631389 415632915 1526 True 1605 1605 86.178 1 1490 1 chr1D.!!$R1 1489
15 TraesCS3D01G382900 chr1D 153888297 153889178 881 False 1568 1568 98.754 1488 2370 1 chr1D.!!$F1 882
16 TraesCS3D01G382900 chr1D 438212348 438213231 883 False 1561 1561 98.529 1487 2370 1 chr1D.!!$F2 883
17 TraesCS3D01G382900 chr1A 249130814 249132305 1491 True 1592 1592 86.141 1 1487 1 chr1A.!!$R1 1486
18 TraesCS3D01G382900 chr5D 142663910 142664792 882 False 1570 1570 98.754 1488 2370 1 chr5D.!!$F1 882
19 TraesCS3D01G382900 chr5D 408364302 408365188 886 True 1561 1561 98.422 1484 2370 1 chr5D.!!$R1 886
20 TraesCS3D01G382900 chr5D 432509480 432510953 1473 False 1459 1459 84.758 1 1487 1 chr5D.!!$F3 1486
21 TraesCS3D01G382900 chr5D 216993768 216995264 1496 False 1402 1402 83.916 3 1487 1 chr5D.!!$F2 1484
22 TraesCS3D01G382900 chr2D 77401621 77403120 1499 False 1522 1522 85.242 1 1487 1 chr2D.!!$F1 1486
23 TraesCS3D01G382900 chr7B 610812637 610814112 1475 False 1447 1447 84.771 41 1487 1 chr7B.!!$F1 1446
24 TraesCS3D01G382900 chr7B 654020775 654022269 1494 True 1406 1406 83.929 1 1485 1 chr7B.!!$R1 1484
25 TraesCS3D01G382900 chrUn 61034513 61035722 1209 True 1371 1371 87.684 1 1181 1 chrUn.!!$R2 1180
26 TraesCS3D01G382900 chrUn 35057220 35058709 1489 True 1336 1336 83.366 1 1487 1 chrUn.!!$R1 1486

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
202 267 1.228033 CAAAAACCCTCCCGTCCGT 60.228 57.895 0.0 0.0 0.0 4.69 F
985 1139 1.244019 GCCGTCCACCTTTGAGCAAT 61.244 55.000 0.0 0.0 0.0 3.56 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1272 1430 0.179084 ACGGTCGATGCGAATCCAAT 60.179 50.0 0.0 0.0 37.72 3.16 R
2068 2237 0.728843 ATTGGACTAGGGAAGGGGGA 59.271 55.0 0.0 0.0 0.00 4.81 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
81 84 2.369015 ACCCATTCCCGGCCCATA 60.369 61.111 0.00 0.00 0.00 2.74
99 102 2.766970 TATTTAAGCCGGATTTGCGC 57.233 45.000 11.69 0.00 0.00 6.09
148 167 2.687566 GCCTTCTCCTTCCCCCGA 60.688 66.667 0.00 0.00 0.00 5.14
202 267 1.228033 CAAAAACCCTCCCGTCCGT 60.228 57.895 0.00 0.00 0.00 4.69
213 280 4.525576 CGTCCGTGCGCGCTACTA 62.526 66.667 33.29 9.09 36.67 1.82
359 463 2.668550 ACGCCCAAGCCGAAGAAC 60.669 61.111 0.00 0.00 34.57 3.01
475 579 2.797278 CGGCCGCATAGAAGGAGGT 61.797 63.158 14.67 0.00 0.00 3.85
504 615 3.990806 CGTCGCGTCGGCAACAAA 61.991 61.111 17.87 0.00 39.92 2.83
670 791 1.592400 CTTCCACGTCTACCCGCAGA 61.592 60.000 0.00 0.00 0.00 4.26
682 803 3.458163 CGCAGACCTCCCGCCTTA 61.458 66.667 0.00 0.00 0.00 2.69
794 927 4.735132 CGGAGGCGCGAGGAAACA 62.735 66.667 12.10 0.00 0.00 2.83
946 1097 1.862806 GACGAGACACAAAGCCAGC 59.137 57.895 0.00 0.00 0.00 4.85
981 1135 2.030562 ACGCCGTCCACCTTTGAG 59.969 61.111 0.00 0.00 0.00 3.02
985 1139 1.244019 GCCGTCCACCTTTGAGCAAT 61.244 55.000 0.00 0.00 0.00 3.56
1164 1318 2.029844 GAAGCCGAAGCGCAAGAGT 61.030 57.895 11.47 0.00 46.67 3.24
1208 1363 1.609072 GGCCGAGAACAAGCTTCTTTT 59.391 47.619 0.00 0.00 0.00 2.27
1272 1430 2.354704 CCGAACAAGAGGCATCAACCTA 60.355 50.000 0.00 0.00 41.32 3.08
1282 1441 2.030805 GGCATCAACCTATTGGATTCGC 60.031 50.000 0.00 0.00 36.39 4.70
1283 1442 2.618241 GCATCAACCTATTGGATTCGCA 59.382 45.455 0.00 0.00 36.39 5.10
1286 1445 3.130633 TCAACCTATTGGATTCGCATCG 58.869 45.455 0.00 0.00 36.39 3.84
1369 1529 3.442273 GGGTGTCCATTTTGAAGCGATAA 59.558 43.478 0.00 0.00 0.00 1.75
1677 1846 2.048877 CCGAACGTACGGCACCTT 60.049 61.111 21.06 3.75 46.20 3.50
2068 2237 2.531942 AAGGAAGGAAGGGGGCGT 60.532 61.111 0.00 0.00 0.00 5.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 41 3.107661 CGGACGAAAACCGGACGG 61.108 66.667 9.46 9.56 45.65 4.79
81 84 3.641031 GCGCAAATCCGGCTTAAAT 57.359 47.368 0.30 0.00 0.00 1.40
99 102 3.041940 GTCTTGTGTCCACGCCGG 61.042 66.667 0.00 0.00 0.00 6.13
131 150 2.687566 TCGGGGGAAGGAGAAGGC 60.688 66.667 0.00 0.00 0.00 4.35
132 151 2.736826 GCTCGGGGGAAGGAGAAGG 61.737 68.421 0.00 0.00 31.90 3.46
427 531 1.146930 GCGATGGCTTCATCCCTCA 59.853 57.895 1.08 0.00 43.19 3.86
458 562 0.033642 GTACCTCCTTCTATGCGGCC 59.966 60.000 0.00 0.00 0.00 6.13
464 568 1.761198 GGCGTTGGTACCTCCTTCTAT 59.239 52.381 14.36 0.00 37.07 1.98
466 570 1.551019 GGGCGTTGGTACCTCCTTCT 61.551 60.000 14.36 0.00 37.07 2.85
467 571 1.078637 GGGCGTTGGTACCTCCTTC 60.079 63.158 14.36 0.13 37.07 3.46
469 573 3.387947 CGGGCGTTGGTACCTCCT 61.388 66.667 14.36 0.00 37.07 3.69
494 605 2.668212 CGCCTCCTTTGTTGCCGA 60.668 61.111 0.00 0.00 0.00 5.54
504 615 1.043116 TAGCATGTACAGCGCCTCCT 61.043 55.000 14.63 1.70 37.01 3.69
646 766 2.643232 GGTAGACGTGGAAGCCGGT 61.643 63.158 1.90 0.00 0.00 5.28
670 791 2.687566 CCTGGTAAGGCGGGAGGT 60.688 66.667 0.00 0.00 36.56 3.85
734 867 1.374252 GTGGCGTTGAGGTCGATGT 60.374 57.895 0.00 0.00 0.00 3.06
829 962 2.235016 CGTCGAACAGGTTGCGTGT 61.235 57.895 0.00 0.00 33.76 4.49
864 997 1.161843 TCTGCATGTAGTCGTCGTCA 58.838 50.000 10.80 0.00 0.00 4.35
915 1066 1.892862 CTCGTCGGGATCGTAGCCT 60.893 63.158 0.00 0.00 37.69 4.58
962 1113 3.353836 CAAAGGTGGACGGCGTGG 61.354 66.667 21.19 0.00 0.00 4.94
981 1135 0.819259 TGAAGGCCGCCTGATATTGC 60.819 55.000 14.19 0.00 32.13 3.56
985 1139 1.227943 GCATGAAGGCCGCCTGATA 60.228 57.895 14.19 2.59 32.13 2.15
1164 1318 0.906066 TGTATGCCTTGGTCCGCTTA 59.094 50.000 0.00 0.00 0.00 3.09
1208 1363 3.494924 CCAATGTCTCTCCAACACTCACA 60.495 47.826 0.00 0.00 0.00 3.58
1259 1417 3.499918 CGAATCCAATAGGTTGATGCCTC 59.500 47.826 0.00 0.00 39.94 4.70
1272 1430 0.179084 ACGGTCGATGCGAATCCAAT 60.179 50.000 0.00 0.00 37.72 3.16
1282 1441 1.135112 TCATGGAACTCACGGTCGATG 60.135 52.381 0.00 0.00 0.00 3.84
1283 1442 1.135139 CTCATGGAACTCACGGTCGAT 59.865 52.381 0.00 0.00 0.00 3.59
1286 1445 1.078759 CGCTCATGGAACTCACGGTC 61.079 60.000 0.00 0.00 0.00 4.79
1369 1529 2.815589 GCACTCTTGTTGGATCACCCTT 60.816 50.000 0.00 0.00 35.38 3.95
1677 1846 2.603892 GCTGAACGTGTGTAGAACTCGA 60.604 50.000 6.91 0.00 46.19 4.04
1910 2079 2.980548 TGCTCCTTTATATACGGGGGT 58.019 47.619 0.56 0.00 0.00 4.95
2068 2237 0.728843 ATTGGACTAGGGAAGGGGGA 59.271 55.000 0.00 0.00 0.00 4.81


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

AutoCloner maintained by Alex Coulton.