Multiple sequence alignment - TraesCS1B01G112400

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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 TraesCS1B01G112400 chr1B 100.000 2780 0 0 1 2780 130363246 130360467 0.000000e+00 5134
1 TraesCS1B01G112400 chr1B 95.054 647 32 0 1 647 634503025 634503671 0.000000e+00 1018
2 TraesCS1B01G112400 chr1A 93.609 1064 50 8 1728 2780 98021687 98020631 0.000000e+00 1572
3 TraesCS1B01G112400 chr1A 90.194 826 46 16 673 1488 98023033 98022233 0.000000e+00 1044
4 TraesCS1B01G112400 chr1D 96.000 925 32 5 1856 2780 79169455 79168536 0.000000e+00 1498
5 TraesCS1B01G112400 chr1D 92.773 844 36 9 673 1506 79170621 79169793 0.000000e+00 1197
6 TraesCS1B01G112400 chr1D 88.088 319 28 4 1564 1872 79169786 79169468 1.220000e-98 370
7 TraesCS1B01G112400 chr3B 95.428 678 30 1 1 678 611425486 611424810 0.000000e+00 1079
8 TraesCS1B01G112400 chr3B 95.549 674 30 0 1 674 790394574 790395247 0.000000e+00 1079
9 TraesCS1B01G112400 chr3B 95.133 678 33 0 1 678 691447191 691446514 0.000000e+00 1070
10 TraesCS1B01G112400 chr3B 93.935 676 38 2 1 673 753263546 753264221 0.000000e+00 1018
11 TraesCS1B01G112400 chr6B 95.280 678 31 1 1 678 608190935 608190259 0.000000e+00 1074
12 TraesCS1B01G112400 chr7B 94.248 678 39 0 1 678 35153068 35152391 0.000000e+00 1037
13 TraesCS1B01G112400 chr5D 93.491 676 39 4 1 673 435674087 435673414 0.000000e+00 1000
14 TraesCS1B01G112400 chr7D 93.088 680 45 1 1 678 152355849 152355170 0.000000e+00 994


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 TraesCS1B01G112400 chr1B 130360467 130363246 2779 True 5134.000000 5134 100.0000 1 2780 1 chr1B.!!$R1 2779
1 TraesCS1B01G112400 chr1B 634503025 634503671 646 False 1018.000000 1018 95.0540 1 647 1 chr1B.!!$F1 646
2 TraesCS1B01G112400 chr1A 98020631 98023033 2402 True 1308.000000 1572 91.9015 673 2780 2 chr1A.!!$R1 2107
3 TraesCS1B01G112400 chr1D 79168536 79170621 2085 True 1021.666667 1498 92.2870 673 2780 3 chr1D.!!$R1 2107
4 TraesCS1B01G112400 chr3B 611424810 611425486 676 True 1079.000000 1079 95.4280 1 678 1 chr3B.!!$R1 677
5 TraesCS1B01G112400 chr3B 790394574 790395247 673 False 1079.000000 1079 95.5490 1 674 1 chr3B.!!$F2 673
6 TraesCS1B01G112400 chr3B 691446514 691447191 677 True 1070.000000 1070 95.1330 1 678 1 chr3B.!!$R2 677
7 TraesCS1B01G112400 chr3B 753263546 753264221 675 False 1018.000000 1018 93.9350 1 673 1 chr3B.!!$F1 672
8 TraesCS1B01G112400 chr6B 608190259 608190935 676 True 1074.000000 1074 95.2800 1 678 1 chr6B.!!$R1 677
9 TraesCS1B01G112400 chr7B 35152391 35153068 677 True 1037.000000 1037 94.2480 1 678 1 chr7B.!!$R1 677
10 TraesCS1B01G112400 chr5D 435673414 435674087 673 True 1000.000000 1000 93.4910 1 673 1 chr5D.!!$R1 672
11 TraesCS1B01G112400 chr7D 152355170 152355849 679 True 994.000000 994 93.0880 1 678 1 chr7D.!!$R1 677

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
22 23 0.037590 ACCCCTGCAGCAAAACGATA 59.962 50.0 8.66 0.0 0.00 2.92 F
1009 1024 0.444651 TGCAAACGCCGCATTAGTAC 59.555 50.0 0.00 0.0 33.55 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1688 1721 0.039618 CTGGCTTACCACCCACCAAT 59.96 55.000 0.00 0.00 42.67 3.16 R
2685 3122 2.359900 CAGTGGCCACCTTAGATTGTC 58.64 52.381 32.29 2.46 0.00 3.18 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
22 23 0.037590 ACCCCTGCAGCAAAACGATA 59.962 50.000 8.66 0.00 0.00 2.92
77 78 0.467290 ACGGAACAATTGCCACCACT 60.467 50.000 5.05 0.00 0.00 4.00
270 271 1.064832 GGCAAAGCAGAATCTCCCTCT 60.065 52.381 0.00 0.00 0.00 3.69
514 515 3.086282 GCCCGGAGAAACTTATTCCAAA 58.914 45.455 0.73 0.00 0.00 3.28
610 613 2.125225 GTTCCCCCTCCCTCCTGT 59.875 66.667 0.00 0.00 0.00 4.00
683 686 2.030862 GGAAACCCACGTACGGCA 59.969 61.111 21.06 0.00 0.00 5.69
687 690 2.999739 AAACCCACGTACGGCACCAG 63.000 60.000 21.06 4.44 0.00 4.00
789 796 1.790755 TCATCGTGACCTGGAAAACG 58.209 50.000 0.00 7.45 37.38 3.60
813 820 1.515954 CAGGGGCCGTACAGTACAG 59.484 63.158 11.37 0.31 0.00 2.74
956 963 1.442857 CTCAGGTCAGACGTCGCAC 60.443 63.158 10.46 10.50 0.00 5.34
1009 1024 0.444651 TGCAAACGCCGCATTAGTAC 59.555 50.000 0.00 0.00 33.55 2.73
1048 1065 5.241064 GTGGTTAGCTCATAACTCCTCGATA 59.759 44.000 0.00 0.00 42.93 2.92
1056 1073 0.461961 AACTCCTCGATAGCCTGCAC 59.538 55.000 0.00 0.00 0.00 4.57
1057 1074 0.684479 ACTCCTCGATAGCCTGCACA 60.684 55.000 0.00 0.00 0.00 4.57
1058 1075 0.678395 CTCCTCGATAGCCTGCACAT 59.322 55.000 0.00 0.00 0.00 3.21
1059 1076 1.889170 CTCCTCGATAGCCTGCACATA 59.111 52.381 0.00 0.00 0.00 2.29
1060 1077 1.613925 TCCTCGATAGCCTGCACATAC 59.386 52.381 0.00 0.00 0.00 2.39
1062 1079 1.001268 CTCGATAGCCTGCACATACGT 60.001 52.381 0.00 0.00 0.00 3.57
1065 1082 2.031069 CGATAGCCTGCACATACGTACT 60.031 50.000 0.00 0.00 0.00 2.73
1066 1083 3.187842 CGATAGCCTGCACATACGTACTA 59.812 47.826 0.00 0.00 0.00 1.82
1067 1084 2.865343 AGCCTGCACATACGTACTAC 57.135 50.000 0.00 0.00 0.00 2.73
1301 1319 2.808206 CCTACATGGTCCGCCTCCC 61.808 68.421 0.00 0.00 35.27 4.30
1371 1389 1.811679 GGAGTAGAGCGGTGCTTGC 60.812 63.158 0.00 0.00 39.88 4.01
1386 1404 0.534412 CTTGCCTCTGTCCATCGACT 59.466 55.000 0.00 0.00 39.94 4.18
1500 1522 1.000145 GCGTCTCCGATCCTTTCAAC 59.000 55.000 0.00 0.00 35.63 3.18
1501 1523 1.404315 GCGTCTCCGATCCTTTCAACT 60.404 52.381 0.00 0.00 35.63 3.16
1502 1524 2.931320 GCGTCTCCGATCCTTTCAACTT 60.931 50.000 0.00 0.00 35.63 2.66
1503 1525 3.326747 CGTCTCCGATCCTTTCAACTTT 58.673 45.455 0.00 0.00 35.63 2.66
1504 1526 3.368236 CGTCTCCGATCCTTTCAACTTTC 59.632 47.826 0.00 0.00 35.63 2.62
1505 1527 4.315803 GTCTCCGATCCTTTCAACTTTCA 58.684 43.478 0.00 0.00 0.00 2.69
1506 1528 4.152580 GTCTCCGATCCTTTCAACTTTCAC 59.847 45.833 0.00 0.00 0.00 3.18
1519 1541 4.638421 TCAACTTTCACGTTCCATTTCACT 59.362 37.500 0.00 0.00 0.00 3.41
1520 1542 4.552166 ACTTTCACGTTCCATTTCACTG 57.448 40.909 0.00 0.00 0.00 3.66
1529 1551 6.797033 CACGTTCCATTTCACTGTTAATTCTC 59.203 38.462 0.00 0.00 0.00 2.87
1530 1552 6.072673 ACGTTCCATTTCACTGTTAATTCTCC 60.073 38.462 0.00 0.00 0.00 3.71
1556 1578 8.230486 CGAAAAGATTGCATTTCACTACTACTT 58.770 33.333 10.29 0.00 35.72 2.24
1558 1580 8.621532 AAAGATTGCATTTCACTACTACTTCA 57.378 30.769 0.00 0.00 0.00 3.02
1559 1581 8.798859 AAGATTGCATTTCACTACTACTTCAT 57.201 30.769 0.00 0.00 0.00 2.57
1560 1582 8.798859 AGATTGCATTTCACTACTACTTCATT 57.201 30.769 0.00 0.00 0.00 2.57
1561 1583 9.890629 AGATTGCATTTCACTACTACTTCATTA 57.109 29.630 0.00 0.00 0.00 1.90
1567 1595 9.708222 CATTTCACTACTACTTCATTAATGTGC 57.292 33.333 14.97 0.00 0.00 4.57
1591 1619 3.868757 ATACGTCAGCTGCTTAACTGA 57.131 42.857 9.47 0.00 40.54 3.41
1602 1630 3.857052 TGCTTAACTGAGATTGGTACCG 58.143 45.455 7.57 0.00 0.00 4.02
1603 1631 3.195661 GCTTAACTGAGATTGGTACCGG 58.804 50.000 7.57 0.00 0.00 5.28
1604 1632 3.118884 GCTTAACTGAGATTGGTACCGGA 60.119 47.826 9.46 0.00 0.00 5.14
1606 1634 3.611766 AACTGAGATTGGTACCGGAAG 57.388 47.619 9.46 1.61 0.00 3.46
1621 1649 3.118738 ACCGGAAGAGCAATTCTCGTAAT 60.119 43.478 9.46 0.00 46.44 1.89
1622 1650 3.246226 CCGGAAGAGCAATTCTCGTAATG 59.754 47.826 0.00 0.00 46.44 1.90
1623 1651 3.865745 CGGAAGAGCAATTCTCGTAATGT 59.134 43.478 1.56 0.00 46.44 2.71
1627 1655 6.128282 GGAAGAGCAATTCTCGTAATGTCAAA 60.128 38.462 1.56 0.00 46.44 2.69
1637 1665 6.791303 TCTCGTAATGTCAAATATTTTGGGC 58.209 36.000 0.00 0.00 0.00 5.36
1654 1687 2.954989 TGGGCGCTAATTGATGCAATTA 59.045 40.909 7.64 10.97 41.50 1.40
1657 1690 4.499696 GGGCGCTAATTGATGCAATTAACT 60.500 41.667 7.64 0.00 43.01 2.24
1679 1712 2.551459 GCATAGCTTAACATGGCTCCAG 59.449 50.000 0.00 0.00 39.65 3.86
1688 1721 3.788227 ACATGGCTCCAGTCTTACAAA 57.212 42.857 0.00 0.00 0.00 2.83
1866 2292 3.031736 TGACTGACCTAATACAGAGGGC 58.968 50.000 0.00 0.00 43.20 5.19
1888 2314 3.551082 CAGTTTCGCAGCAAACATTTCAA 59.449 39.130 17.38 0.00 38.53 2.69
1933 2359 7.670364 ACTAAAATTAAACAGAAGCAAGGCAT 58.330 30.769 0.00 0.00 0.00 4.40
1976 2402 1.776969 CCTTCCCTGGCCCTTCTTT 59.223 57.895 0.00 0.00 0.00 2.52
2063 2494 6.018994 GGTAATGTTAAGATAGGCTTGTCACG 60.019 42.308 0.00 0.00 37.42 4.35
2132 2563 7.665559 CCTAAGTTTAGGGCTATTATGCATGAA 59.334 37.037 10.16 0.11 45.29 2.57
2156 2587 7.678947 AATTTCAGTGATGGAAGTGAGTAAG 57.321 36.000 0.00 0.00 31.29 2.34
2189 2620 2.229784 GGGCTGAAAATGGTCAGAACAG 59.770 50.000 9.55 0.00 46.76 3.16
2396 2833 6.610075 ATCAATTTGGCCTATGAAAACACT 57.390 33.333 3.32 0.00 0.00 3.55
2454 2891 5.300286 GCCCAAGTTCTGCTCATGTAATATT 59.700 40.000 0.00 0.00 0.00 1.28
2457 2894 9.071276 CCCAAGTTCTGCTCATGTAATATTATT 57.929 33.333 0.00 0.00 0.00 1.40
2629 3066 5.581605 ACAACAGAAACACAATAGCACAAG 58.418 37.500 0.00 0.00 0.00 3.16
2685 3122 8.348507 GCAAGGAATGAATTACTCCTAAATCAG 58.651 37.037 3.51 0.00 38.69 2.90
2709 3146 0.250727 TCTAAGGTGGCCACTGCAAC 60.251 55.000 33.91 17.83 41.01 4.17
2755 3192 5.721000 TGGCCACTGAAATCCTAAATCAAAT 59.279 36.000 0.00 0.00 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 0.732571 CGCCTGGTTGCATATCGTTT 59.267 50.000 0.00 0.00 0.00 3.60
22 23 4.060038 GCTTGCGCCTGGTTGCAT 62.060 61.111 14.86 0.00 41.42 3.96
270 271 1.957177 CCTTCCTCTACGCTGATGCTA 59.043 52.381 0.00 0.00 36.97 3.49
281 282 4.021016 GCTGTTGTTCTTCTCCTTCCTCTA 60.021 45.833 0.00 0.00 0.00 2.43
693 696 0.745845 ATGCACGTCAAGGAGCCATC 60.746 55.000 0.00 0.00 0.00 3.51
813 820 0.109597 CGTGAAATGCAGGCAAGGTC 60.110 55.000 0.00 0.00 0.00 3.85
875 882 0.390735 AACGTGCGTAGTGGGAATCC 60.391 55.000 0.00 0.00 0.00 3.01
1033 1049 2.558795 GCAGGCTATCGAGGAGTTATGA 59.441 50.000 0.00 0.00 0.00 2.15
1037 1053 0.461961 GTGCAGGCTATCGAGGAGTT 59.538 55.000 0.00 0.00 0.00 3.01
1048 1065 1.065102 CGTAGTACGTATGTGCAGGCT 59.935 52.381 14.62 0.00 36.74 4.58
1062 1079 4.445718 CGCTTCGATCCTTAGTACGTAGTA 59.554 45.833 6.02 6.02 45.11 1.82
1065 1082 2.032549 GCGCTTCGATCCTTAGTACGTA 60.033 50.000 0.00 0.00 0.00 3.57
1066 1083 1.268437 GCGCTTCGATCCTTAGTACGT 60.268 52.381 0.00 0.00 0.00 3.57
1067 1084 1.396644 GCGCTTCGATCCTTAGTACG 58.603 55.000 0.00 0.00 0.00 3.67
1072 1089 2.654085 CGCGCGCTTCGATCCTTA 60.654 61.111 30.48 0.00 41.67 2.69
1125 1142 1.085796 TGATGGCCCCTTCCCCTTA 59.914 57.895 0.00 0.00 0.00 2.69
1371 1389 1.893062 TGCAGTCGATGGACAGAGG 59.107 57.895 10.69 0.00 45.92 3.69
1425 1444 7.150783 AGGCATGAAAAGAATCAAGAACTAC 57.849 36.000 0.00 0.00 32.06 2.73
1463 1482 4.280929 AGACGCCATCACATATGCTACTAA 59.719 41.667 1.58 0.00 0.00 2.24
1500 1522 4.552166 ACAGTGAAATGGAACGTGAAAG 57.448 40.909 0.00 0.00 0.00 2.62
1501 1523 4.974368 AACAGTGAAATGGAACGTGAAA 57.026 36.364 0.00 0.00 0.00 2.69
1502 1524 6.627395 ATTAACAGTGAAATGGAACGTGAA 57.373 33.333 0.00 0.00 0.00 3.18
1503 1525 6.485313 AGAATTAACAGTGAAATGGAACGTGA 59.515 34.615 0.00 0.00 0.00 4.35
1504 1526 6.668323 AGAATTAACAGTGAAATGGAACGTG 58.332 36.000 0.00 0.00 0.00 4.49
1505 1527 6.072673 GGAGAATTAACAGTGAAATGGAACGT 60.073 38.462 0.00 0.00 0.00 3.99
1506 1528 6.314784 GGAGAATTAACAGTGAAATGGAACG 58.685 40.000 0.00 0.00 0.00 3.95
1519 1541 6.567687 TGCAATCTTTTCGGAGAATTAACA 57.432 33.333 0.00 0.00 45.90 2.41
1520 1542 8.466086 AAATGCAATCTTTTCGGAGAATTAAC 57.534 30.769 0.00 0.00 45.90 2.01
1529 1551 5.942872 AGTAGTGAAATGCAATCTTTTCGG 58.057 37.500 0.00 0.00 38.48 4.30
1530 1552 7.743104 AGTAGTAGTGAAATGCAATCTTTTCG 58.257 34.615 0.00 0.00 38.48 3.46
1567 1595 4.500837 CAGTTAAGCAGCTGACGTATACAG 59.499 45.833 20.43 0.00 35.12 2.74
1591 1619 1.568504 TGCTCTTCCGGTACCAATCT 58.431 50.000 13.54 0.00 0.00 2.40
1602 1630 4.870426 TGACATTACGAGAATTGCTCTTCC 59.130 41.667 0.00 0.00 41.66 3.46
1603 1631 6.408858 TTGACATTACGAGAATTGCTCTTC 57.591 37.500 0.00 0.00 41.66 2.87
1604 1632 6.801539 TTTGACATTACGAGAATTGCTCTT 57.198 33.333 0.00 0.00 41.66 2.85
1606 1634 9.722056 AAATATTTGACATTACGAGAATTGCTC 57.278 29.630 0.00 0.00 40.38 4.26
1621 1649 5.590530 ATTAGCGCCCAAAATATTTGACA 57.409 34.783 2.29 0.00 0.00 3.58
1622 1650 6.039616 TCAATTAGCGCCCAAAATATTTGAC 58.960 36.000 2.29 0.00 0.00 3.18
1623 1651 6.214191 TCAATTAGCGCCCAAAATATTTGA 57.786 33.333 2.29 4.66 0.00 2.69
1627 1655 4.039004 TGCATCAATTAGCGCCCAAAATAT 59.961 37.500 2.29 0.00 0.00 1.28
1637 1665 5.550701 GCAGTTAATTGCATCAATTAGCG 57.449 39.130 17.20 12.67 45.45 4.26
1654 1687 3.624777 AGCCATGTTAAGCTATGCAGTT 58.375 40.909 0.00 0.00 37.64 3.16
1657 1690 2.092484 TGGAGCCATGTTAAGCTATGCA 60.092 45.455 0.00 0.00 40.11 3.96
1662 1695 1.912043 AGACTGGAGCCATGTTAAGCT 59.088 47.619 0.00 0.00 43.55 3.74
1679 1712 3.227614 ACCACCCACCAATTTGTAAGAC 58.772 45.455 0.00 0.00 0.00 3.01
1688 1721 0.039618 CTGGCTTACCACCCACCAAT 59.960 55.000 0.00 0.00 42.67 3.16
1800 2196 4.590647 TGGCAATGATGGGTTTGTTTCTTA 59.409 37.500 0.00 0.00 0.00 2.10
1866 2292 3.114809 TGAAATGTTTGCTGCGAAACTG 58.885 40.909 20.24 0.00 36.86 3.16
1888 2314 4.848357 AGTACTGATTTGGCAGCTAATGT 58.152 39.130 0.00 0.00 39.51 2.71
1933 2359 6.077197 CGTGCGATCAAGAGAAACAAATAAA 58.923 36.000 0.00 0.00 0.00 1.40
2063 2494 4.911514 TTTGGTGCTTAGGAGTGTTTTC 57.088 40.909 0.00 0.00 0.00 2.29
2116 2547 6.643770 CACTGAAATTTCATGCATAATAGCCC 59.356 38.462 20.76 0.00 36.46 5.19
2132 2563 6.150140 GCTTACTCACTTCCATCACTGAAATT 59.850 38.462 0.00 0.00 0.00 1.82
2189 2620 7.095229 TGCGTCAATTAATTATAGCAGATCACC 60.095 37.037 15.26 0.00 0.00 4.02
2336 2773 3.000727 GTTCCTTACTAGCACGTGCATT 58.999 45.455 39.21 25.15 45.16 3.56
2396 2833 3.414269 TGCTGAATTCTCTGATGTTGCA 58.586 40.909 7.05 0.00 0.00 4.08
2653 3090 4.843728 AGTAATTCATTCCTTGCTCGGAA 58.156 39.130 9.25 9.25 46.37 4.30
2671 3108 9.268282 ACCTTAGATTGTCTGATTTAGGAGTAA 57.732 33.333 0.00 0.00 0.00 2.24
2685 3122 2.359900 CAGTGGCCACCTTAGATTGTC 58.640 52.381 32.29 2.46 0.00 3.18
2709 3146 5.220854 CCACCTTAGATTGTTCTATTTGGCG 60.221 44.000 0.00 0.00 34.44 5.69


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

AutoCloner maintained by Alex Coulton.