Multiple sequence alignment - TraesCS3D01G429000

Loading Multiple Alignment...

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 TraesCS3D01G429000 chr3D 100.000 2743 0 0 1 2743 543527150 543529892 0 5066
1 TraesCS3D01G429000 chr3D 93.794 999 57 5 1748 2743 244279608 244280604 0 1496
2 TraesCS3D01G429000 chr3D 89.754 976 93 7 783 1756 373979269 373978299 0 1242
3 TraesCS3D01G429000 chr5D 91.270 1764 132 20 1 1756 507981111 507979362 0 2385
4 TraesCS3D01G429000 chr4D 90.062 1761 129 15 1 1756 195027703 195029422 0 2241
5 TraesCS3D01G429000 chr4D 94.753 991 48 4 1754 2743 426573038 426572051 0 1539
6 TraesCS3D01G429000 chr4D 94.046 991 56 3 1754 2743 432444913 432443925 0 1500
7 TraesCS3D01G429000 chr4D 93.939 990 59 1 1754 2743 400714753 400713765 0 1495
8 TraesCS3D01G429000 chr4D 90.676 976 86 5 783 1756 52082144 52081172 0 1293
9 TraesCS3D01G429000 chr7A 89.153 1770 168 19 1 1756 133739965 133738206 0 2183
10 TraesCS3D01G429000 chr7B 89.021 1767 165 24 1 1754 337178512 337176762 0 2161
11 TraesCS3D01G429000 chr7B 88.158 684 71 7 1 683 622480342 622479668 0 806
12 TraesCS3D01G429000 chr7B 88.576 639 64 6 2 639 222673132 222673762 0 767
13 TraesCS3D01G429000 chr2A 86.759 1586 152 30 50 1604 298491858 298493416 0 1712
14 TraesCS3D01G429000 chr1D 94.147 991 57 1 1754 2743 279250882 279249892 0 1507
15 TraesCS3D01G429000 chr1D 88.923 984 100 9 778 1756 403383956 403384935 0 1205
16 TraesCS3D01G429000 chr1D 89.189 851 74 14 1 847 165160135 165159299 0 1046
17 TraesCS3D01G429000 chr2D 94.147 991 55 2 1754 2743 479159016 479158028 0 1506
18 TraesCS3D01G429000 chr2D 93.775 996 59 2 1748 2743 561011005 561011997 0 1493
19 TraesCS3D01G429000 chr7D 93.888 998 58 3 1748 2743 131418240 131417244 0 1502
20 TraesCS3D01G429000 chr7D 93.775 996 60 2 1748 2743 449588792 449589785 0 1495
21 TraesCS3D01G429000 chr3B 90.134 973 92 4 785 1756 703418296 703417327 0 1262
22 TraesCS3D01G429000 chr3B 89.605 885 78 13 1 878 703419149 703418272 0 1112
23 TraesCS3D01G429000 chr4B 89.447 976 98 5 783 1755 324939666 324940639 0 1227
24 TraesCS3D01G429000 chr6B 86.498 711 75 15 1 708 360393579 360394271 0 761


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 TraesCS3D01G429000 chr3D 543527150 543529892 2742 False 5066 5066 100.0000 1 2743 1 chr3D.!!$F2 2742
1 TraesCS3D01G429000 chr3D 244279608 244280604 996 False 1496 1496 93.7940 1748 2743 1 chr3D.!!$F1 995
2 TraesCS3D01G429000 chr3D 373978299 373979269 970 True 1242 1242 89.7540 783 1756 1 chr3D.!!$R1 973
3 TraesCS3D01G429000 chr5D 507979362 507981111 1749 True 2385 2385 91.2700 1 1756 1 chr5D.!!$R1 1755
4 TraesCS3D01G429000 chr4D 195027703 195029422 1719 False 2241 2241 90.0620 1 1756 1 chr4D.!!$F1 1755
5 TraesCS3D01G429000 chr4D 426572051 426573038 987 True 1539 1539 94.7530 1754 2743 1 chr4D.!!$R3 989
6 TraesCS3D01G429000 chr4D 432443925 432444913 988 True 1500 1500 94.0460 1754 2743 1 chr4D.!!$R4 989
7 TraesCS3D01G429000 chr4D 400713765 400714753 988 True 1495 1495 93.9390 1754 2743 1 chr4D.!!$R2 989
8 TraesCS3D01G429000 chr4D 52081172 52082144 972 True 1293 1293 90.6760 783 1756 1 chr4D.!!$R1 973
9 TraesCS3D01G429000 chr7A 133738206 133739965 1759 True 2183 2183 89.1530 1 1756 1 chr7A.!!$R1 1755
10 TraesCS3D01G429000 chr7B 337176762 337178512 1750 True 2161 2161 89.0210 1 1754 1 chr7B.!!$R1 1753
11 TraesCS3D01G429000 chr7B 622479668 622480342 674 True 806 806 88.1580 1 683 1 chr7B.!!$R2 682
12 TraesCS3D01G429000 chr7B 222673132 222673762 630 False 767 767 88.5760 2 639 1 chr7B.!!$F1 637
13 TraesCS3D01G429000 chr2A 298491858 298493416 1558 False 1712 1712 86.7590 50 1604 1 chr2A.!!$F1 1554
14 TraesCS3D01G429000 chr1D 279249892 279250882 990 True 1507 1507 94.1470 1754 2743 1 chr1D.!!$R2 989
15 TraesCS3D01G429000 chr1D 403383956 403384935 979 False 1205 1205 88.9230 778 1756 1 chr1D.!!$F1 978
16 TraesCS3D01G429000 chr1D 165159299 165160135 836 True 1046 1046 89.1890 1 847 1 chr1D.!!$R1 846
17 TraesCS3D01G429000 chr2D 479158028 479159016 988 True 1506 1506 94.1470 1754 2743 1 chr2D.!!$R1 989
18 TraesCS3D01G429000 chr2D 561011005 561011997 992 False 1493 1493 93.7750 1748 2743 1 chr2D.!!$F1 995
19 TraesCS3D01G429000 chr7D 131417244 131418240 996 True 1502 1502 93.8880 1748 2743 1 chr7D.!!$R1 995
20 TraesCS3D01G429000 chr7D 449588792 449589785 993 False 1495 1495 93.7750 1748 2743 1 chr7D.!!$F1 995
21 TraesCS3D01G429000 chr3B 703417327 703419149 1822 True 1187 1262 89.8695 1 1756 2 chr3B.!!$R1 1755
22 TraesCS3D01G429000 chr4B 324939666 324940639 973 False 1227 1227 89.4470 783 1755 1 chr4B.!!$F1 972
23 TraesCS3D01G429000 chr6B 360393579 360394271 692 False 761 761 86.4980 1 708 1 chr6B.!!$F1 707

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
458 482 0.319405 GCTGGTTTGAAGCTGCCATT 59.681 50.0 12.04 0.0 42.93 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1943 2128 1.160137 CCCTTTCTGAGACCGCAAAG 58.84 55.0 0.0 0.0 0.0 2.77 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
48 50 6.204688 CCAAGACAACAAGACACTTAATAGCA 59.795 38.462 0.00 0.00 0.00 3.49
61 63 4.080356 ACTTAATAGCATGTGGGAGAAGCA 60.080 41.667 0.00 0.00 0.00 3.91
165 167 3.313803 TGTTTTGAAGCGTTACATGAGCA 59.686 39.130 0.00 0.00 0.00 4.26
194 197 1.345089 TCATTGCTGCAGTTTGCCAAT 59.655 42.857 16.64 12.63 44.23 3.16
356 359 9.478768 TTTAACAAGTAAGTGAATGATCGTACA 57.521 29.630 0.00 0.00 0.00 2.90
458 482 0.319405 GCTGGTTTGAAGCTGCCATT 59.681 50.000 12.04 0.00 42.93 3.16
473 497 4.559300 GCTGCCATTTGTAGTGAACACATT 60.559 41.667 7.68 0.00 38.00 2.71
551 582 3.111098 GCTGTTGCTTGTTGTGAAAGAG 58.889 45.455 0.00 0.00 36.03 2.85
572 603 4.144297 AGAGTGTAGCTGCCATTTTGAAA 58.856 39.130 0.00 0.00 0.00 2.69
573 604 4.768968 AGAGTGTAGCTGCCATTTTGAAAT 59.231 37.500 0.00 0.00 0.00 2.17
595 626 1.112315 GTGTGGTTGCCATGTGGGAA 61.112 55.000 1.51 1.51 43.49 3.97
630 661 5.153513 GCCATGTATAATGCAAACGGTATG 58.846 41.667 0.00 0.00 0.00 2.39
668 699 7.036996 TGAACTAATGTGCATTGAGAACAAA 57.963 32.000 7.60 0.00 39.54 2.83
694 725 3.207474 GCAGTTGCACTAACATGAAGG 57.793 47.619 0.00 0.00 41.88 3.46
733 764 1.812235 TGCACTGTAGTTGCCATCTG 58.188 50.000 0.00 0.00 0.00 2.90
787 820 7.509546 CCCAGGATTACACTAGACACATAAAT 58.490 38.462 0.00 0.00 0.00 1.40
810 843 9.553064 AAATTGTAGTTGCCATGTGAAATAAAA 57.447 25.926 0.00 0.00 0.00 1.52
844 877 5.212532 TGTGAAATAAACTGCATTTGCCT 57.787 34.783 0.00 0.00 41.18 4.75
845 878 4.989797 TGTGAAATAAACTGCATTTGCCTG 59.010 37.500 0.00 0.00 41.18 4.85
846 879 4.990426 GTGAAATAAACTGCATTTGCCTGT 59.010 37.500 0.00 0.00 41.18 4.00
847 880 4.989797 TGAAATAAACTGCATTTGCCTGTG 59.010 37.500 0.00 0.00 41.18 3.66
956 1133 3.190535 CGTTTGCTATGTTTTGCCCTACT 59.809 43.478 0.00 0.00 0.00 2.57
959 1136 3.352648 TGCTATGTTTTGCCCTACTTCC 58.647 45.455 0.00 0.00 0.00 3.46
963 1140 2.303175 TGTTTTGCCCTACTTCCACAC 58.697 47.619 0.00 0.00 0.00 3.82
1010 1191 6.734137 AGAATTTAACGAGCACAAAACATGA 58.266 32.000 0.00 0.00 0.00 3.07
1026 1207 6.830873 AAACATGAAGATTCCAGGAAGAAG 57.169 37.500 8.20 0.00 0.00 2.85
1035 1216 4.877378 TTCCAGGAAGAAGTAAAGCGTA 57.123 40.909 0.00 0.00 0.00 4.42
1068 1249 2.699954 CAGCTTACCAGGTTGACGAAT 58.300 47.619 0.00 0.00 0.00 3.34
1146 1327 5.511888 CCGGACAAGGGAAGAAACTACTTTA 60.512 44.000 0.00 0.00 0.00 1.85
1247 1428 7.646526 CACATACTCAAAATAATGGACATGCAG 59.353 37.037 0.00 0.00 0.00 4.41
1287 1469 1.282817 CCATTTCATACGACGGCGAA 58.717 50.000 22.49 0.00 41.64 4.70
1340 1522 5.236047 GCCACAAACATCAAATGCAGTTTTA 59.764 36.000 0.00 0.00 32.34 1.52
1365 1547 4.344104 TGTACATGATGACAGACCAGAGA 58.656 43.478 0.00 0.00 0.00 3.10
1366 1548 4.958581 TGTACATGATGACAGACCAGAGAT 59.041 41.667 0.00 0.00 0.00 2.75
1460 1642 1.419387 GATGAGATAGCAAGGGTGGCT 59.581 52.381 0.00 0.00 45.18 4.75
1541 1724 2.644798 AGAAGCATTACACAGGTTCCCT 59.355 45.455 0.00 0.00 41.74 4.20
1731 1914 4.895297 ACAAGAAAGCAAAGAAAGGGATGA 59.105 37.500 0.00 0.00 0.00 2.92
1733 1916 4.734266 AGAAAGCAAAGAAAGGGATGAGT 58.266 39.130 0.00 0.00 0.00 3.41
1821 2006 1.272781 CGCCAGAAACTAAGAGAGCG 58.727 55.000 0.00 0.00 36.06 5.03
1836 2021 2.005451 AGAGCGCAACTGTCATGATTC 58.995 47.619 11.47 0.00 0.00 2.52
1929 2114 1.268079 GCTGCTTGAACTTTGGAGGTC 59.732 52.381 0.00 0.00 40.18 3.85
1934 2119 3.008049 GCTTGAACTTTGGAGGTCCTCTA 59.992 47.826 18.58 10.10 38.94 2.43
1943 2128 4.689612 TGGAGGTCCTCTACATTTATGC 57.310 45.455 18.58 0.00 36.82 3.14
2066 2252 5.636543 TCGCTAGCTGATTATGTCATTGATG 59.363 40.000 13.93 0.00 35.97 3.07
2281 2470 5.928601 CGTCTCCAACGTATCTACTTTTC 57.071 43.478 0.00 0.00 46.42 2.29
2305 2494 2.535574 CACGCTTTTCCTCTTGTTTTGC 59.464 45.455 0.00 0.00 0.00 3.68
2408 2597 6.080406 GTGCAGAAATAAAAGTTCTCGGAAG 58.920 40.000 0.00 0.00 32.96 3.46
2423 2612 4.944930 TCTCGGAAGGAAACAAAACTTTGA 59.055 37.500 9.12 0.00 40.55 2.69
2466 2655 5.505181 AAGAGAATTACTGGAGCCAAGAA 57.495 39.130 0.00 0.00 0.00 2.52
2471 2660 1.729586 TACTGGAGCCAAGAACCACT 58.270 50.000 0.00 0.00 0.00 4.00
2630 2821 7.630242 AAATCAGGAAGAAAGAATTATCGCA 57.370 32.000 0.00 0.00 0.00 5.10
2671 2863 0.401738 CCAAGCCCTGTTCTTCCTCA 59.598 55.000 0.00 0.00 0.00 3.86
2699 2891 0.902531 GATCTGGAGTCCGTTTGGGA 59.097 55.000 4.30 0.00 44.68 4.37
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 50 4.012374 CAGTACATTTGCTTCTCCCACAT 58.988 43.478 0.00 0.00 0.00 3.21
194 197 5.963176 TCTGTTGCAAAGCTGAATATTGA 57.037 34.783 0.00 0.00 0.00 2.57
412 436 9.131791 AGACATGGCGAACCTATTTTATTTATT 57.868 29.630 0.00 0.00 36.63 1.40
413 437 8.567948 CAGACATGGCGAACCTATTTTATTTAT 58.432 33.333 0.00 0.00 36.63 1.40
414 438 7.468084 GCAGACATGGCGAACCTATTTTATTTA 60.468 37.037 0.00 0.00 36.63 1.40
415 439 6.680378 GCAGACATGGCGAACCTATTTTATTT 60.680 38.462 0.00 0.00 36.63 1.40
418 442 3.625764 GCAGACATGGCGAACCTATTTTA 59.374 43.478 0.00 0.00 36.63 1.52
425 449 2.401766 CCAGCAGACATGGCGAACC 61.402 63.158 0.00 0.00 36.08 3.62
429 453 1.210931 CAAACCAGCAGACATGGCG 59.789 57.895 0.00 0.00 41.87 5.69
458 482 7.976175 TGTTTTGCATTAATGTGTTCACTACAA 59.024 29.630 16.61 6.33 38.80 2.41
551 582 4.503741 TTTCAAAATGGCAGCTACACTC 57.496 40.909 0.00 0.00 0.00 3.51
572 603 0.680618 CACATGGCAACCACACCAAT 59.319 50.000 0.00 0.00 39.96 3.16
573 604 1.398174 CCACATGGCAACCACACCAA 61.398 55.000 0.00 0.00 39.96 3.67
595 626 9.130661 TGCATTATACATGGCAATTAAACTACT 57.869 29.630 0.00 0.00 32.54 2.57
650 681 6.128391 GCATCATTTTGTTCTCAATGCACATT 60.128 34.615 0.00 0.00 35.74 2.71
733 764 3.811722 TGAAACGATCAGCATGTCAAC 57.188 42.857 0.00 0.00 37.40 3.18
787 820 8.147058 ACATTTTATTTCACATGGCAACTACAA 58.853 29.630 0.00 0.00 37.61 2.41
810 843 7.315142 CAGTTTATTTCACATGGCAACTACAT 58.685 34.615 0.00 0.00 37.61 2.29
844 877 6.658816 ACATGGAAACTGCATACTATTTCACA 59.341 34.615 0.00 0.00 33.58 3.58
845 878 6.968904 CACATGGAAACTGCATACTATTTCAC 59.031 38.462 0.00 0.00 33.58 3.18
846 879 6.095300 CCACATGGAAACTGCATACTATTTCA 59.905 38.462 0.00 0.00 37.39 2.69
847 880 6.318648 TCCACATGGAAACTGCATACTATTTC 59.681 38.462 0.00 0.00 42.18 2.17
902 1078 3.904136 ACGATGGCAGAGAAAGTTTTG 57.096 42.857 0.00 0.00 0.00 2.44
947 1124 1.493022 ACTTGTGTGGAAGTAGGGCAA 59.507 47.619 0.00 0.00 34.29 4.52
956 1133 5.184096 TCTTTTTGTAGCAACTTGTGTGGAA 59.816 36.000 0.00 0.00 0.00 3.53
959 1136 8.801715 ATATTCTTTTTGTAGCAACTTGTGTG 57.198 30.769 0.00 0.00 0.00 3.82
1010 1191 4.938226 CGCTTTACTTCTTCCTGGAATCTT 59.062 41.667 10.03 0.00 0.00 2.40
1026 1207 3.920112 GTACATGCTGGTACGCTTTAC 57.080 47.619 0.00 0.00 34.84 2.01
1035 1216 0.249120 TAAGCTGCGTACATGCTGGT 59.751 50.000 5.24 2.51 44.72 4.00
1146 1327 3.947834 CCTTTGTTTATCGAGGCCTTCAT 59.052 43.478 6.77 4.44 0.00 2.57
1287 1469 2.932234 CGTCAGCGTCCCAAGTCCT 61.932 63.158 0.00 0.00 0.00 3.85
1340 1522 2.833943 TGGTCTGTCATCATGTACAGCT 59.166 45.455 15.97 0.00 42.31 4.24
1365 1547 1.762957 CCTCACGGAGTCCATGGTTAT 59.237 52.381 12.58 0.00 41.61 1.89
1366 1548 1.191535 CCTCACGGAGTCCATGGTTA 58.808 55.000 12.58 0.00 41.61 2.85
1395 1577 4.573900 AGTTCAGCATAGTTCTTGGTCAG 58.426 43.478 0.00 0.00 0.00 3.51
1460 1642 1.901464 GGCCTTCCCGTGCTTTTCA 60.901 57.895 0.00 0.00 0.00 2.69
1731 1914 3.259876 TCCACAGTTGCTTACGGATTACT 59.740 43.478 0.00 0.00 0.00 2.24
1733 1916 3.369052 CCTCCACAGTTGCTTACGGATTA 60.369 47.826 0.00 0.00 0.00 1.75
1821 2006 3.497297 TGCATGAATCATGACAGTTGC 57.503 42.857 25.77 11.23 43.81 4.17
1836 2021 5.239359 ACATTAGCTACACACAATGCATG 57.761 39.130 0.00 0.00 32.76 4.06
1901 2086 2.645730 AGTTCAAGCAGCGACTAGAG 57.354 50.000 0.00 0.00 0.00 2.43
1929 2114 3.627577 ACCGCAAAGCATAAATGTAGAGG 59.372 43.478 0.00 0.00 0.00 3.69
1934 2119 3.081061 TGAGACCGCAAAGCATAAATGT 58.919 40.909 0.00 0.00 0.00 2.71
1943 2128 1.160137 CCCTTTCTGAGACCGCAAAG 58.840 55.000 0.00 0.00 0.00 2.77
1998 2184 3.611986 CAGCAACACGTTGTCAAAACAAT 59.388 39.130 11.33 0.00 46.58 2.71
2281 2470 1.884235 ACAAGAGGAAAAGCGTGAGG 58.116 50.000 0.00 0.00 0.00 3.86
2305 2494 8.920509 TCATTCAAATCATGCAAATTAGAGTG 57.079 30.769 0.00 0.00 0.00 3.51
2408 2597 8.492673 AAAAATCCTCTCAAAGTTTTGTTTCC 57.507 30.769 4.67 0.00 39.18 3.13
2466 2655 2.369001 GGGCCCCTCTCTAGTGGT 59.631 66.667 12.23 0.00 0.00 4.16
2471 2660 3.779083 CCCAGGGGCCCCTCTCTA 61.779 72.222 42.42 0.00 46.28 2.43
2614 2805 5.584649 TCGTGGAATGCGATAATTCTTTCTT 59.415 36.000 0.00 0.00 36.87 2.52
2630 2821 2.893398 GGCTCCGTCTCGTGGAAT 59.107 61.111 0.00 0.00 34.44 3.01
2671 2863 1.501604 GGACTCCAGATCTACCCTCCT 59.498 57.143 0.00 0.00 0.00 3.69
2678 2870 2.108168 CCCAAACGGACTCCAGATCTA 58.892 52.381 0.00 0.00 0.00 1.98
2699 2891 1.595058 AAGATCCCCCTCTCCGGAGT 61.595 60.000 30.17 9.94 37.86 3.85


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

AutoCloner maintained by Alex Coulton.