Multiple sequence alignment - TraesCS2D01G583300

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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 TraesCS2D01G583300 chr2D 100.000 2627 0 0 1 2627 643661679 643659053 0.000000e+00 4852
1 TraesCS2D01G583300 chr2D 80.684 1346 247 8 953 2286 643685653 643686997 0.000000e+00 1033
2 TraesCS2D01G583300 chr2D 78.044 1585 313 22 903 2463 643719523 643721096 0.000000e+00 966
3 TraesCS2D01G583300 chr2D 74.656 1164 257 29 1087 2219 643744217 643745373 5.090000e-132 481
4 TraesCS2D01G583300 chr2B 95.118 1741 76 7 883 2615 793438986 793440725 0.000000e+00 2736
5 TraesCS2D01G583300 chr2B 78.792 1589 304 20 903 2468 793408463 793406885 0.000000e+00 1037
6 TraesCS2D01G583300 chr2B 85.354 833 105 13 1 823 793437341 793438166 0.000000e+00 846
7 TraesCS2D01G583300 chr2B 74.399 1164 260 29 1087 2219 793376614 793375458 5.120000e-127 464
8 TraesCS2D01G583300 chr2B 76.300 654 122 26 100 730 55609127 55609770 4.220000e-83 318
9 TraesCS2D01G583300 chr2B 76.642 274 61 3 1915 2187 798994258 798993987 5.860000e-32 148
10 TraesCS2D01G583300 chr2A 93.702 1683 90 6 944 2613 768467580 768465901 0.000000e+00 2507
11 TraesCS2D01G583300 chr2A 79.130 1495 289 14 928 2403 768545125 768546615 0.000000e+00 1011
12 TraesCS2D01G583300 chr2A 85.619 751 91 10 1 742 768468818 768468076 0.000000e+00 773
13 TraesCS2D01G583300 chr7D 77.121 660 115 21 106 745 44254139 44254782 1.500000e-92 350
14 TraesCS2D01G583300 chr7D 76.515 660 120 22 106 745 44060208 44060852 7.010000e-86 327
15 TraesCS2D01G583300 chr7D 76.304 671 119 27 106 753 44098807 44099460 3.260000e-84 322
16 TraesCS2D01G583300 chr7D 76.183 613 126 13 134 730 162154932 162154324 3.280000e-79 305
17 TraesCS2D01G583300 chr1A 76.710 614 113 22 134 731 471711036 471710437 5.460000e-82 315
18 TraesCS2D01G583300 chr5D 76.471 595 115 19 157 731 504091941 504091352 1.530000e-77 300


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 TraesCS2D01G583300 chr2D 643659053 643661679 2626 True 4852 4852 100.0000 1 2627 1 chr2D.!!$R1 2626
1 TraesCS2D01G583300 chr2D 643685653 643686997 1344 False 1033 1033 80.6840 953 2286 1 chr2D.!!$F1 1333
2 TraesCS2D01G583300 chr2D 643719523 643721096 1573 False 966 966 78.0440 903 2463 1 chr2D.!!$F2 1560
3 TraesCS2D01G583300 chr2D 643744217 643745373 1156 False 481 481 74.6560 1087 2219 1 chr2D.!!$F3 1132
4 TraesCS2D01G583300 chr2B 793437341 793440725 3384 False 1791 2736 90.2360 1 2615 2 chr2B.!!$F2 2614
5 TraesCS2D01G583300 chr2B 793406885 793408463 1578 True 1037 1037 78.7920 903 2468 1 chr2B.!!$R2 1565
6 TraesCS2D01G583300 chr2B 793375458 793376614 1156 True 464 464 74.3990 1087 2219 1 chr2B.!!$R1 1132
7 TraesCS2D01G583300 chr2B 55609127 55609770 643 False 318 318 76.3000 100 730 1 chr2B.!!$F1 630
8 TraesCS2D01G583300 chr2A 768465901 768468818 2917 True 1640 2507 89.6605 1 2613 2 chr2A.!!$R1 2612
9 TraesCS2D01G583300 chr2A 768545125 768546615 1490 False 1011 1011 79.1300 928 2403 1 chr2A.!!$F1 1475
10 TraesCS2D01G583300 chr7D 44254139 44254782 643 False 350 350 77.1210 106 745 1 chr7D.!!$F3 639
11 TraesCS2D01G583300 chr7D 44060208 44060852 644 False 327 327 76.5150 106 745 1 chr7D.!!$F1 639
12 TraesCS2D01G583300 chr7D 44098807 44099460 653 False 322 322 76.3040 106 753 1 chr7D.!!$F2 647
13 TraesCS2D01G583300 chr7D 162154324 162154932 608 True 305 305 76.1830 134 730 1 chr7D.!!$R1 596
14 TraesCS2D01G583300 chr1A 471710437 471711036 599 True 315 315 76.7100 134 731 1 chr1A.!!$R1 597
15 TraesCS2D01G583300 chr5D 504091352 504091941 589 True 300 300 76.4710 157 731 1 chr5D.!!$R1 574

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
339 356 0.106419 TTTTATCCCCGTCCCCATGC 60.106 55.0 0.0 0.0 0.0 4.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2052 2878 0.552848 AAGCCACCGATTCCCATCAT 59.447 50.0 0.0 0.0 0.0 2.45 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
103 105 7.939039 CCTAATTAATCATGCTCAACCCTCTTA 59.061 37.037 0.00 0.00 0.00 2.10
241 248 2.677542 GGAAGGACCCCACTCTTTTT 57.322 50.000 0.00 0.00 0.00 1.94
271 285 1.804748 GGTTCATCGACTTGGTTGGAC 59.195 52.381 0.00 0.00 0.00 4.02
272 286 2.489971 GTTCATCGACTTGGTTGGACA 58.510 47.619 0.00 0.00 0.00 4.02
277 291 0.238289 CGACTTGGTTGGACATGTGC 59.762 55.000 10.90 10.90 0.00 4.57
321 338 6.153340 CAGTTGGAATAATGTCTCCCATGTTT 59.847 38.462 0.00 0.00 32.82 2.83
322 339 6.725834 AGTTGGAATAATGTCTCCCATGTTTT 59.274 34.615 0.00 0.00 32.82 2.43
339 356 0.106419 TTTTATCCCCGTCCCCATGC 60.106 55.000 0.00 0.00 0.00 4.06
416 435 4.636206 GGATTTGATCGGTGCTAGTCTTTT 59.364 41.667 0.00 0.00 0.00 2.27
445 464 7.554118 GGATCTGTTTGGATCAAGTCTTCATTA 59.446 37.037 0.00 0.00 42.63 1.90
446 465 9.118300 GATCTGTTTGGATCAAGTCTTCATTAT 57.882 33.333 0.00 0.00 41.07 1.28
500 522 5.069251 CCCATCTACGACTTTCTTCATAGGT 59.931 44.000 0.00 0.00 0.00 3.08
534 556 4.160439 CCTCTTGTGCACTAGTCCTATGAA 59.840 45.833 24.36 5.26 0.00 2.57
552 575 1.727335 GAAGCCTTAGCACAACGACTC 59.273 52.381 0.00 0.00 43.56 3.36
561 588 1.269309 GCACAACGACTCTCTGACTGT 60.269 52.381 0.00 0.00 0.00 3.55
687 714 9.408069 GACCTAGTTGTGATATTTATTACCTCG 57.592 37.037 0.00 0.00 0.00 4.63
689 721 7.817962 CCTAGTTGTGATATTTATTACCTCGGG 59.182 40.741 0.00 0.00 0.00 5.14
704 736 0.398696 TCGGGTTTGTACTGCCATGT 59.601 50.000 0.00 0.00 0.00 3.21
748 782 5.871465 ATTTCCGGCGCAAAAATAAAAAT 57.129 30.435 10.83 0.56 0.00 1.82
756 790 8.543774 CCGGCGCAAAAATAAAAATAAATCATA 58.456 29.630 10.83 0.00 0.00 2.15
775 809 0.243907 ACTCGATCAAGTGTGACCCG 59.756 55.000 0.00 0.00 36.31 5.28
781 815 1.374758 CAAGTGTGACCCGGAGAGC 60.375 63.158 0.73 0.00 0.00 4.09
789 823 0.250338 GACCCGGAGAGCAAACAGTT 60.250 55.000 0.73 0.00 0.00 3.16
801 835 5.046910 AGCAAACAGTTAAATGATGGTCG 57.953 39.130 10.35 0.00 0.00 4.79
807 841 7.447374 AACAGTTAAATGATGGTCGATTTCA 57.553 32.000 10.35 0.00 0.00 2.69
813 847 8.586273 GTTAAATGATGGTCGATTTCAATGTTG 58.414 33.333 0.00 0.00 0.00 3.33
814 848 6.513806 AATGATGGTCGATTTCAATGTTGA 57.486 33.333 0.00 0.00 34.92 3.18
864 1123 5.687166 TTCCTTCGTCCCACAATATAAGT 57.313 39.130 0.00 0.00 0.00 2.24
873 1132 6.472163 CGTCCCACAATATAAGTCATTTTTGC 59.528 38.462 0.00 0.00 0.00 3.68
877 1136 7.818930 CCCACAATATAAGTCATTTTTGCAAGT 59.181 33.333 0.00 0.00 0.00 3.16
918 1718 5.080969 ACGTCTTAGCTTTTAGTATGGCA 57.919 39.130 0.00 0.00 0.00 4.92
920 1720 4.508124 CGTCTTAGCTTTTAGTATGGCAGG 59.492 45.833 0.00 0.00 0.00 4.85
996 1797 6.682746 ACACTCACAAGTCTAACTACTCATG 58.317 40.000 0.00 0.00 31.71 3.07
1135 1936 6.710499 TCTATGTCTCCCTCTATCTCATCA 57.290 41.667 0.00 0.00 0.00 3.07
1293 2094 0.313987 TCGCTGTCATCGTTGTCAGT 59.686 50.000 17.86 0.00 40.02 3.41
1310 2111 4.162320 TGTCAGTTACATCCAGGAGAATCC 59.838 45.833 0.00 0.00 45.36 3.01
1539 2361 2.685017 AGCATGGAGGAGGCACGA 60.685 61.111 0.00 0.00 32.16 4.35
1624 2446 7.533426 GCAGATCATGACACTCTTTAACAAAT 58.467 34.615 0.00 0.00 0.00 2.32
1790 2616 1.791103 CGGGGTTGACGTTGTTGCAT 61.791 55.000 0.00 0.00 0.00 3.96
1923 2749 2.288213 GCGATCATACCGATGAGTTGGA 60.288 50.000 0.00 0.00 45.29 3.53
2038 2864 0.745845 CTTCGCAGCCTTGGCATAGT 60.746 55.000 14.54 0.00 0.00 2.12
2112 2938 2.639347 TCACTCATTGACCACATCACCT 59.361 45.455 0.00 0.00 36.92 4.00
2117 2943 0.250858 TTGACCACATCACCTGCAGG 60.251 55.000 31.60 31.60 36.92 4.85
2195 3021 2.974489 CTGGTTGCTCGCTGGCTTG 61.974 63.158 0.00 0.00 0.00 4.01
2302 3135 2.606108 CACTAGCACTTGTACGCATCA 58.394 47.619 0.00 0.00 0.00 3.07
2586 3427 5.295950 TGGCTACCATTTTTGTGTGAAATG 58.704 37.500 3.28 3.28 41.75 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
68 69 7.230712 TGAGCATGATTAATTAGGTCGACTAGA 59.769 37.037 16.46 1.54 32.16 2.43
70 72 7.284919 TGAGCATGATTAATTAGGTCGACTA 57.715 36.000 16.46 3.09 0.00 2.59
103 105 2.952310 GGTCTTTTCTTGTGCAGGAGTT 59.048 45.455 0.00 0.00 0.00 3.01
241 248 5.468746 CCAAGTCGATGAACCTAACAAGAAA 59.531 40.000 0.00 0.00 0.00 2.52
272 286 4.408821 ATCACCACCGCCGCACAT 62.409 61.111 0.00 0.00 0.00 3.21
321 338 0.991355 AGCATGGGGACGGGGATAAA 60.991 55.000 0.00 0.00 0.00 1.40
322 339 1.385347 AGCATGGGGACGGGGATAA 60.385 57.895 0.00 0.00 0.00 1.75
354 371 4.760047 CCTTCACACGCCCTCCGG 62.760 72.222 0.00 0.00 42.52 5.14
416 435 4.042062 AGACTTGATCCAAACAGATCCACA 59.958 41.667 0.00 0.00 41.73 4.17
445 464 8.840833 AACTTGTAAACACCAAAACAAAGAAT 57.159 26.923 0.00 0.00 31.90 2.40
446 465 8.552034 CAAACTTGTAAACACCAAAACAAAGAA 58.448 29.630 0.00 0.00 31.90 2.52
500 522 1.883638 GCACAAGAGGAGCAACCATCA 60.884 52.381 2.96 0.00 42.04 3.07
534 556 0.969894 AGAGTCGTTGTGCTAAGGCT 59.030 50.000 0.00 0.00 39.59 4.58
552 575 7.155328 ACAAACCTTATTGTAGACAGTCAGAG 58.845 38.462 2.66 0.00 41.56 3.35
561 588 5.248477 AGAGCTGGACAAACCTTATTGTAGA 59.752 40.000 0.00 0.00 43.31 2.59
672 699 8.985805 CAGTACAAACCCGAGGTAATAAATATC 58.014 37.037 0.00 0.00 33.12 1.63
675 702 5.587443 GCAGTACAAACCCGAGGTAATAAAT 59.413 40.000 0.00 0.00 33.12 1.40
687 714 2.625790 TCAAACATGGCAGTACAAACCC 59.374 45.455 0.00 0.00 0.00 4.11
689 721 4.677584 TGTTCAAACATGGCAGTACAAAC 58.322 39.130 0.00 0.00 33.17 2.93
726 758 5.871465 ATTTTTATTTTTGCGCCGGAAAT 57.129 30.435 5.05 11.12 0.00 2.17
731 763 9.352163 GTATGATTTATTTTTATTTTTGCGCCG 57.648 29.630 4.18 0.00 0.00 6.46
748 782 6.978659 GGTCACACTTGATCGAGTATGATTTA 59.021 38.462 23.67 2.29 35.71 1.40
756 790 0.243907 CGGGTCACACTTGATCGAGT 59.756 55.000 10.02 10.02 33.05 4.18
762 796 1.816863 GCTCTCCGGGTCACACTTGA 61.817 60.000 0.00 0.00 0.00 3.02
767 801 1.070786 GTTTGCTCTCCGGGTCACA 59.929 57.895 0.00 0.00 0.00 3.58
769 803 1.371183 CTGTTTGCTCTCCGGGTCA 59.629 57.895 0.00 0.00 0.00 4.02
775 809 5.183904 ACCATCATTTAACTGTTTGCTCTCC 59.816 40.000 0.00 0.00 0.00 3.71
781 815 7.807433 TGAAATCGACCATCATTTAACTGTTTG 59.193 33.333 0.00 0.00 0.00 2.93
789 823 8.049655 TCAACATTGAAATCGACCATCATTTA 57.950 30.769 0.00 0.00 33.55 1.40
828 1087 8.980596 TGGGACGAAGGAAATAGTAAGTATTAA 58.019 33.333 0.00 0.00 30.55 1.40
841 1100 6.057321 ACTTATATTGTGGGACGAAGGAAA 57.943 37.500 0.00 0.00 0.00 3.13
843 1102 4.712829 TGACTTATATTGTGGGACGAAGGA 59.287 41.667 0.00 0.00 0.00 3.36
847 1106 7.627513 GCAAAAATGACTTATATTGTGGGACGA 60.628 37.037 0.00 0.00 0.00 4.20
881 1140 7.769220 AGCTAAGACGTACTTAAAGCTATCAA 58.231 34.615 16.59 0.00 44.07 2.57
899 1699 5.693769 ACCTGCCATACTAAAAGCTAAGA 57.306 39.130 0.00 0.00 0.00 2.10
996 1797 0.179020 TGCCATAGCCCTGCATGTAC 60.179 55.000 0.00 0.00 38.69 2.90
1310 2111 1.002315 CAAAGCCAATTCCCCAACCAG 59.998 52.381 0.00 0.00 0.00 4.00
1539 2361 1.359848 GCAGTAGTTGTAGCACGCAT 58.640 50.000 0.00 0.00 0.00 4.73
1698 2523 1.952635 GCACAAACAGCAAGCCAGC 60.953 57.895 0.00 0.00 0.00 4.85
1790 2616 1.105167 CCATGCCCGTACCTACTCGA 61.105 60.000 0.00 0.00 0.00 4.04
1907 2733 3.133691 CCATGTCCAACTCATCGGTATG 58.866 50.000 0.00 0.00 0.00 2.39
1923 2749 3.181434 ACATACTGTGGAACCAACCATGT 60.181 43.478 0.00 1.27 42.17 3.21
2052 2878 0.552848 AAGCCACCGATTCCCATCAT 59.447 50.000 0.00 0.00 0.00 2.45
2425 3261 3.798337 GTGCCACTCAACACAAAAAGATG 59.202 43.478 0.00 0.00 36.77 2.90
2428 3264 3.508744 AGTGCCACTCAACACAAAAAG 57.491 42.857 0.00 0.00 39.30 2.27
2586 3427 3.502191 TTGCTCGATTGGGCATAAAAC 57.498 42.857 8.74 0.00 38.30 2.43


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

AutoCloner maintained by Alex Coulton.