Multiple sequence alignment - TraesCS3A01G145200

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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 TraesCS3A01G145200 chr3A 100.000 2417 0 0 1 2417 127864530 127866946 0.000000e+00 4464.0
1 TraesCS3A01G145200 chr3A 93.478 46 3 0 1668 1713 239238241 239238286 4.310000e-08 69.4
2 TraesCS3A01G145200 chr3A 73.367 199 39 12 1669 1858 540969034 540968841 7.220000e-06 62.1
3 TraesCS3A01G145200 chr3D 91.319 1843 96 31 614 2413 121378238 121380059 0.000000e+00 2459.0
4 TraesCS3A01G145200 chr3D 91.776 608 44 4 1 604 594522329 594522934 0.000000e+00 841.0
5 TraesCS3A01G145200 chr3B 92.336 1070 65 9 1356 2417 173035656 173036716 0.000000e+00 1506.0
6 TraesCS3A01G145200 chr3B 94.286 770 35 4 602 1368 173032176 173032939 0.000000e+00 1170.0
7 TraesCS3A01G145200 chr7A 94.380 605 30 2 1 601 102044338 102044942 0.000000e+00 926.0
8 TraesCS3A01G145200 chr7A 97.143 35 1 0 1673 1707 438146443 438146477 2.600000e-05 60.2
9 TraesCS3A01G145200 chr7D 92.345 614 38 6 1 608 552167962 552167352 0.000000e+00 865.0
10 TraesCS3A01G145200 chr7D 91.874 603 42 5 1 598 587079277 587079877 0.000000e+00 835.0
11 TraesCS3A01G145200 chr1D 90.049 613 56 3 1 608 414246381 414245769 0.000000e+00 789.0
12 TraesCS3A01G145200 chr5D 92.407 540 38 1 64 600 407997314 407996775 0.000000e+00 767.0
13 TraesCS3A01G145200 chr5D 92.683 533 34 3 1 529 29587775 29588306 0.000000e+00 763.0
14 TraesCS3A01G145200 chr5D 89.907 535 42 9 65 595 481477839 481477313 0.000000e+00 678.0
15 TraesCS3A01G145200 chr5D 89.464 541 44 6 64 600 47325042 47324511 0.000000e+00 671.0
16 TraesCS3A01G145200 chr6B 84.091 220 17 6 616 833 420847750 420847547 1.900000e-46 196.0
17 TraesCS3A01G145200 chr4A 76.526 213 39 10 1669 1873 256611848 256612057 3.290000e-19 106.0
18 TraesCS3A01G145200 chr5B 92.000 50 2 2 1668 1716 9222260 9222212 4.310000e-08 69.4
19 TraesCS3A01G145200 chr6A 91.304 46 4 0 1668 1713 273115909 273115954 2.010000e-06 63.9
20 TraesCS3A01G145200 chr1A 91.304 46 4 0 1668 1713 405379891 405379846 2.010000e-06 63.9


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 TraesCS3A01G145200 chr3A 127864530 127866946 2416 False 4464 4464 100.000 1 2417 1 chr3A.!!$F1 2416
1 TraesCS3A01G145200 chr3D 121378238 121380059 1821 False 2459 2459 91.319 614 2413 1 chr3D.!!$F1 1799
2 TraesCS3A01G145200 chr3D 594522329 594522934 605 False 841 841 91.776 1 604 1 chr3D.!!$F2 603
3 TraesCS3A01G145200 chr3B 173032176 173036716 4540 False 1338 1506 93.311 602 2417 2 chr3B.!!$F1 1815
4 TraesCS3A01G145200 chr7A 102044338 102044942 604 False 926 926 94.380 1 601 1 chr7A.!!$F1 600
5 TraesCS3A01G145200 chr7D 552167352 552167962 610 True 865 865 92.345 1 608 1 chr7D.!!$R1 607
6 TraesCS3A01G145200 chr7D 587079277 587079877 600 False 835 835 91.874 1 598 1 chr7D.!!$F1 597
7 TraesCS3A01G145200 chr1D 414245769 414246381 612 True 789 789 90.049 1 608 1 chr1D.!!$R1 607
8 TraesCS3A01G145200 chr5D 407996775 407997314 539 True 767 767 92.407 64 600 1 chr5D.!!$R2 536
9 TraesCS3A01G145200 chr5D 29587775 29588306 531 False 763 763 92.683 1 529 1 chr5D.!!$F1 528
10 TraesCS3A01G145200 chr5D 481477313 481477839 526 True 678 678 89.907 65 595 1 chr5D.!!$R3 530
11 TraesCS3A01G145200 chr5D 47324511 47325042 531 True 671 671 89.464 64 600 1 chr5D.!!$R1 536

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
315 321 0.460722 TCGTCGTGAGAAACCCAACA 59.539 50.0 0.0 0.0 45.01 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1662 4446 0.401738 CAAAGGAGCCCCAAGAGACA 59.598 55.0 0.0 0.0 33.88 3.41 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
189 194 4.138487 AGGCGGTCATACTAGGAAAAAG 57.862 45.455 0.00 0.00 0.00 2.27
271 277 4.856115 AAAAGTTTGTCAAAATGTGCCG 57.144 36.364 0.00 0.00 0.00 5.69
315 321 0.460722 TCGTCGTGAGAAACCCAACA 59.539 50.000 0.00 0.00 45.01 3.33
362 368 6.176975 TGCACGAATCAAAAGTTATACCTG 57.823 37.500 0.00 0.00 0.00 4.00
464 475 6.601332 AGTTTCCTTTTAGGATGTCAGTTGA 58.399 36.000 0.00 0.00 45.34 3.18
512 523 3.004734 GGTGGTGTGAGAAACTGATTTGG 59.995 47.826 0.00 0.00 0.00 3.28
561 573 0.949105 TTTTGGGAAGAGCGCTCGAC 60.949 55.000 30.39 25.66 34.09 4.20
623 635 2.001076 AAAACCCAGGAAAGCCAGAG 57.999 50.000 0.00 0.00 36.29 3.35
627 639 2.122768 ACCCAGGAAAGCCAGAGATAG 58.877 52.381 0.00 0.00 36.29 2.08
640 655 6.715280 AGCCAGAGATAGAAAACATCAGAAA 58.285 36.000 0.00 0.00 0.00 2.52
702 717 2.612567 CCTTAGGCAACAACGCGCA 61.613 57.895 5.73 0.00 41.41 6.09
722 737 3.111838 CACTGTCGAGTGTCTGATATGC 58.888 50.000 0.00 0.00 44.15 3.14
732 747 5.488341 AGTGTCTGATATGCCTTACGTTTT 58.512 37.500 0.00 0.00 0.00 2.43
830 848 4.057406 TCTTTTCACCCGTCTACGAAAA 57.943 40.909 3.65 2.37 43.02 2.29
831 849 3.803778 TCTTTTCACCCGTCTACGAAAAC 59.196 43.478 3.65 0.00 43.02 2.43
937 955 0.957395 CCTGCGTCAATCAAGCACCT 60.957 55.000 0.00 0.00 36.79 4.00
1045 1095 4.570663 CGATCACCTCGGCCGTCC 62.571 72.222 27.15 6.56 43.82 4.79
1107 1157 4.154347 CTGCTGGAGCGGGAGGAC 62.154 72.222 0.00 0.00 45.83 3.85
1187 1240 2.579787 CAGGATCGACGACGTGGC 60.580 66.667 4.58 0.00 40.69 5.01
1356 1409 2.266055 CGCTTCAGGGTCCTGGAC 59.734 66.667 18.65 18.65 43.75 4.02
1413 4195 3.316573 CTCGAGGAACAGGGCCCAC 62.317 68.421 27.56 12.14 0.00 4.61
1426 4208 4.666907 ACAGGGCCCACTAGTAGTACTATA 59.333 45.833 27.56 0.00 29.08 1.31
1528 4310 4.156739 GCTCCTTTGTTTATTAGCAGCACT 59.843 41.667 0.00 0.00 0.00 4.40
1538 4320 7.227711 TGTTTATTAGCAGCACTCAGTTGTAAA 59.772 33.333 0.00 0.00 0.00 2.01
1542 4324 2.618709 GCAGCACTCAGTTGTAAAGGTT 59.381 45.455 0.00 0.00 0.00 3.50
1561 4344 8.887036 AAAGGTTGACATTTAGGAAAACATTC 57.113 30.769 0.00 0.00 0.00 2.67
1613 4396 9.367160 AGAAATTTACATAAACATCTATGGGGG 57.633 33.333 0.00 0.00 34.18 5.40
1662 4446 1.609061 CGGCACCTTCATGTGAGTTCT 60.609 52.381 0.00 0.00 38.55 3.01
1663 4447 1.808945 GGCACCTTCATGTGAGTTCTG 59.191 52.381 0.00 0.00 38.55 3.02
1676 4466 0.980423 AGTTCTGTCTCTTGGGGCTC 59.020 55.000 0.00 0.00 0.00 4.70
1677 4467 0.035915 GTTCTGTCTCTTGGGGCTCC 60.036 60.000 0.00 0.00 0.00 4.70
1758 4548 8.585018 TCTATGTTTGTAGATTCACAGAGTTGA 58.415 33.333 0.00 0.00 31.70 3.18
1763 4553 6.951256 TGTAGATTCACAGAGTTGAAATCG 57.049 37.500 0.00 0.00 38.95 3.34
1776 4566 9.329913 CAGAGTTGAAATCGTTAGGTATTTTTG 57.670 33.333 0.00 0.00 0.00 2.44
1810 4600 8.263940 TCATTTGTACTAGTATGTTTTGGAGC 57.736 34.615 5.75 0.00 0.00 4.70
1823 4613 5.916318 TGTTTTGGAGCAAAAATGTCATCT 58.084 33.333 0.00 0.00 43.50 2.90
1831 4621 6.803807 GGAGCAAAAATGTCATCTACTCAAAC 59.196 38.462 0.00 0.00 0.00 2.93
1858 4648 9.334693 CTCTTGATAGAATTCCTTTGTTTTTCG 57.665 33.333 0.65 0.00 0.00 3.46
1863 4653 6.693315 AGAATTCCTTTGTTTTTCGAGTGA 57.307 33.333 0.65 0.00 0.00 3.41
1868 4658 7.737972 TTCCTTTGTTTTTCGAGTGATATCA 57.262 32.000 0.00 0.00 0.00 2.15
1919 4709 1.072116 CCAACAATTCGCATGCGTGG 61.072 55.000 36.50 30.14 40.74 4.94
1920 4710 1.072116 CAACAATTCGCATGCGTGGG 61.072 55.000 36.50 25.65 40.74 4.61
2040 4830 2.353579 ACGTTTAGTTGCGTTTCAGCTT 59.646 40.909 0.00 0.00 38.21 3.74
2109 4899 2.233305 ACTCGTCAGGTTATGGTCCT 57.767 50.000 0.00 0.00 35.45 3.85
2128 4918 8.561738 TGGTCCTATGTTATCTTGTTTTTCTC 57.438 34.615 0.00 0.00 0.00 2.87
2218 5008 8.347035 TGCATGATGTATGTTCATAGTTTGATG 58.653 33.333 0.00 0.00 39.08 3.07
2413 5204 8.652810 TCCACTAAAACAAAGTAGTAGTTCAC 57.347 34.615 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 7.170393 ACACTACTGCACACATCTAATTAGA 57.830 36.000 17.32 17.32 36.65 2.10
271 277 9.699703 GAGTACTTCAAAACTAGATCCCATATC 57.300 37.037 0.00 0.00 0.00 1.63
464 475 1.366111 CGCCCACGTGATTCCGAAAT 61.366 55.000 19.30 0.00 33.53 2.17
485 496 2.057922 AGTTTCTCACACCACCATCCT 58.942 47.619 0.00 0.00 0.00 3.24
627 639 7.278646 ACTGCTTTTCCTTTTTCTGATGTTTTC 59.721 33.333 0.00 0.00 0.00 2.29
640 655 3.007940 GGCCCATAAACTGCTTTTCCTTT 59.992 43.478 0.00 0.00 0.00 3.11
649 664 3.527427 GGCCGGCCCATAAACTGC 61.527 66.667 36.64 5.01 0.00 4.40
702 717 2.099921 GGCATATCAGACACTCGACAGT 59.900 50.000 0.00 0.00 0.00 3.55
712 727 8.138365 TGAATAAAACGTAAGGCATATCAGAC 57.862 34.615 0.00 0.00 46.39 3.51
722 737 8.702438 TCTTCGTACTTTGAATAAAACGTAAGG 58.298 33.333 0.00 0.00 46.39 2.69
769 784 3.066342 TGGACGATCACGATTCTTCCTAC 59.934 47.826 0.00 0.00 42.66 3.18
770 785 3.284617 TGGACGATCACGATTCTTCCTA 58.715 45.455 0.00 0.00 42.66 2.94
771 786 2.099921 CTGGACGATCACGATTCTTCCT 59.900 50.000 0.00 0.00 42.66 3.36
772 787 2.099263 TCTGGACGATCACGATTCTTCC 59.901 50.000 0.00 0.00 42.66 3.46
773 788 3.422417 TCTGGACGATCACGATTCTTC 57.578 47.619 0.00 0.00 42.66 2.87
860 878 2.159282 GGCTCGAGTAGAATCCGAACAA 60.159 50.000 15.13 0.00 31.59 2.83
928 946 7.001674 TCTTGGAAACTTAATTAGGTGCTTGA 58.998 34.615 0.37 0.00 0.00 3.02
937 955 6.295067 GCTTGGCCTTCTTGGAAACTTAATTA 60.295 38.462 3.32 0.00 38.35 1.40
989 1007 0.313469 CGACGACATCGCGATTGTTG 60.313 55.000 21.14 23.60 45.52 3.33
1053 1103 4.668118 TCCCGCGACGTTGGGTTC 62.668 66.667 21.69 0.00 46.13 3.62
1356 1409 4.082523 ACCGTGGTGAGGATGGCG 62.083 66.667 0.00 0.00 0.00 5.69
1528 4310 7.284074 TCCTAAATGTCAACCTTTACAACTGA 58.716 34.615 0.00 0.00 0.00 3.41
1538 4320 6.488683 TCGAATGTTTTCCTAAATGTCAACCT 59.511 34.615 0.00 0.00 0.00 3.50
1641 4425 1.237285 AACTCACATGAAGGTGCCGC 61.237 55.000 0.00 0.00 38.66 6.53
1662 4446 0.401738 CAAAGGAGCCCCAAGAGACA 59.598 55.000 0.00 0.00 33.88 3.41
1663 4447 0.693049 TCAAAGGAGCCCCAAGAGAC 59.307 55.000 0.00 0.00 33.88 3.36
1730 4520 9.950496 AACTCTGTGAATCTACAAACATAGAAT 57.050 29.630 0.00 0.00 34.86 2.40
1731 4521 9.208022 CAACTCTGTGAATCTACAAACATAGAA 57.792 33.333 0.00 0.00 34.86 2.10
1743 4533 6.591834 CCTAACGATTTCAACTCTGTGAATCT 59.408 38.462 0.00 0.00 37.36 2.40
1753 4543 7.882179 AGCAAAAATACCTAACGATTTCAACT 58.118 30.769 0.00 0.00 0.00 3.16
1758 4548 8.106247 TCTCAAGCAAAAATACCTAACGATTT 57.894 30.769 0.00 0.00 0.00 2.17
1763 4553 9.860898 AATGAATCTCAAGCAAAAATACCTAAC 57.139 29.630 0.00 0.00 0.00 2.34
1776 4566 9.319143 ACATACTAGTACAAATGAATCTCAAGC 57.681 33.333 4.31 0.00 0.00 4.01
1810 4600 8.103948 AGAGGTTTGAGTAGATGACATTTTTG 57.896 34.615 0.00 0.00 0.00 2.44
1823 4613 8.380742 AGGAATTCTATCAAGAGGTTTGAGTA 57.619 34.615 5.23 0.00 31.96 2.59
1831 4621 9.631452 GAAAAACAAAGGAATTCTATCAAGAGG 57.369 33.333 5.23 0.00 31.96 3.69
1919 4709 3.641437 TTAAACTGAAGCACATGCACC 57.359 42.857 6.64 0.00 45.16 5.01
1920 4710 4.803088 TGTTTTAAACTGAAGCACATGCAC 59.197 37.500 9.33 0.58 45.16 4.57
2040 4830 7.868906 TCAACATGAGATCTAATTTGCATCA 57.131 32.000 0.00 0.00 0.00 3.07
2104 4894 8.794335 AGAGAAAAACAAGATAACATAGGACC 57.206 34.615 0.00 0.00 0.00 4.46
2137 4927 8.821686 AACCAATTGTTTATATCTGGATCACA 57.178 30.769 4.43 0.00 31.47 3.58
2218 5008 2.147150 GAGGCGAGGAAAGATTATGGC 58.853 52.381 0.00 0.00 0.00 4.40
2384 5175 9.895138 AACTACTACTTTGTTTTAGTGGAAGAA 57.105 29.630 0.00 0.00 32.61 2.52


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

AutoCloner maintained by Alex Coulton.