Multiple sequence alignment - TraesCS2B01G325400

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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 TraesCS2B01G325400 chr2B 100.000 2211 0 0 1 2211 464996298 464998508 0.000000e+00 4084
1 TraesCS2B01G325400 chr2B 94.656 2227 88 11 1 2211 474913327 474911116 0.000000e+00 3424
2 TraesCS2B01G325400 chr3B 95.867 2226 74 6 1 2211 101916063 101913841 0.000000e+00 3585
3 TraesCS2B01G325400 chr3B 95.326 2225 87 6 1 2211 201531911 201529690 0.000000e+00 3517
4 TraesCS2B01G325400 chr3B 92.282 609 34 2 1574 2169 392551793 392551185 0.000000e+00 852
5 TraesCS2B01G325400 chrUn 95.416 2225 79 7 1 2211 216513722 216515937 0.000000e+00 3522
6 TraesCS2B01G325400 chrUn 95.416 2225 79 7 1 2211 286269661 286267446 0.000000e+00 3522
7 TraesCS2B01G325400 chr5D 95.330 2227 81 6 1 2211 503223103 503220884 0.000000e+00 3515
8 TraesCS2B01G325400 chr5D 92.686 1627 72 14 613 2211 432426897 432425290 0.000000e+00 2302
9 TraesCS2B01G325400 chr3A 95.099 2224 88 6 1 2211 672905129 672907344 0.000000e+00 3483
10 TraesCS2B01G325400 chr3A 95.864 1789 65 9 1 1787 66012738 66014519 0.000000e+00 2885
11 TraesCS2B01G325400 chr1A 95.741 2113 73 6 113 2211 554517023 554514914 0.000000e+00 3387
12 TraesCS2B01G325400 chr4D 94.290 2224 104 7 1 2211 19933452 19931239 0.000000e+00 3382
13 TraesCS2B01G325400 chr4D 92.594 2228 144 8 1 2211 207365383 207367606 0.000000e+00 3181
14 TraesCS2B01G325400 chr6D 95.703 2071 68 7 1 2057 168262553 168260490 0.000000e+00 3312
15 TraesCS2B01G325400 chr5A 96.281 1909 66 5 1 1907 510135609 510137514 0.000000e+00 3127
16 TraesCS2B01G325400 chr5A 92.568 444 21 1 1780 2211 164645963 164646406 5.180000e-176 627
17 TraesCS2B01G325400 chr1D 94.833 1800 72 6 426 2211 51922212 51924004 0.000000e+00 2789
18 TraesCS2B01G325400 chr6A 93.786 515 20 1 1709 2211 567833816 567833302 0.000000e+00 763


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 TraesCS2B01G325400 chr2B 464996298 464998508 2210 False 4084 4084 100.000 1 2211 1 chr2B.!!$F1 2210
1 TraesCS2B01G325400 chr2B 474911116 474913327 2211 True 3424 3424 94.656 1 2211 1 chr2B.!!$R1 2210
2 TraesCS2B01G325400 chr3B 101913841 101916063 2222 True 3585 3585 95.867 1 2211 1 chr3B.!!$R1 2210
3 TraesCS2B01G325400 chr3B 201529690 201531911 2221 True 3517 3517 95.326 1 2211 1 chr3B.!!$R2 2210
4 TraesCS2B01G325400 chr3B 392551185 392551793 608 True 852 852 92.282 1574 2169 1 chr3B.!!$R3 595
5 TraesCS2B01G325400 chrUn 216513722 216515937 2215 False 3522 3522 95.416 1 2211 1 chrUn.!!$F1 2210
6 TraesCS2B01G325400 chrUn 286267446 286269661 2215 True 3522 3522 95.416 1 2211 1 chrUn.!!$R1 2210
7 TraesCS2B01G325400 chr5D 503220884 503223103 2219 True 3515 3515 95.330 1 2211 1 chr5D.!!$R2 2210
8 TraesCS2B01G325400 chr5D 432425290 432426897 1607 True 2302 2302 92.686 613 2211 1 chr5D.!!$R1 1598
9 TraesCS2B01G325400 chr3A 672905129 672907344 2215 False 3483 3483 95.099 1 2211 1 chr3A.!!$F2 2210
10 TraesCS2B01G325400 chr3A 66012738 66014519 1781 False 2885 2885 95.864 1 1787 1 chr3A.!!$F1 1786
11 TraesCS2B01G325400 chr1A 554514914 554517023 2109 True 3387 3387 95.741 113 2211 1 chr1A.!!$R1 2098
12 TraesCS2B01G325400 chr4D 19931239 19933452 2213 True 3382 3382 94.290 1 2211 1 chr4D.!!$R1 2210
13 TraesCS2B01G325400 chr4D 207365383 207367606 2223 False 3181 3181 92.594 1 2211 1 chr4D.!!$F1 2210
14 TraesCS2B01G325400 chr6D 168260490 168262553 2063 True 3312 3312 95.703 1 2057 1 chr6D.!!$R1 2056
15 TraesCS2B01G325400 chr5A 510135609 510137514 1905 False 3127 3127 96.281 1 1907 1 chr5A.!!$F2 1906
16 TraesCS2B01G325400 chr1D 51922212 51924004 1792 False 2789 2789 94.833 426 2211 1 chr1D.!!$F1 1785
17 TraesCS2B01G325400 chr6A 567833302 567833816 514 True 763 763 93.786 1709 2211 1 chr6A.!!$R1 502

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
41 42 2.368875 ACGAATGTCACCTTCTTCTGGT 59.631 45.455 0.0 0.0 38.53 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1754 1765 0.609151 CATGATTTGGGCTGGCACAA 59.391 50.0 6.13 6.13 38.7 3.33 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
27 28 9.410556 CCTTTTTATTTCTCATCAAACGAATGT 57.589 29.630 0.00 0.00 0.00 2.71
30 31 8.948853 TTTATTTCTCATCAAACGAATGTCAC 57.051 30.769 0.00 0.00 0.00 3.67
41 42 2.368875 ACGAATGTCACCTTCTTCTGGT 59.631 45.455 0.00 0.00 38.53 4.00
82 83 9.653516 TTAGCATGATTTTTGGGAATATCCTTA 57.346 29.630 0.00 0.00 36.57 2.69
115 116 7.644490 TCAAACAAGTATGAAACGTATGCTTT 58.356 30.769 0.00 0.00 29.71 3.51
134 135 3.313012 TTCATATTCGTCCATAGGGCG 57.687 47.619 3.22 3.22 35.78 6.13
259 260 9.284594 GAACTTTCGCTTGCATTGTATTATTTA 57.715 29.630 0.00 0.00 0.00 1.40
353 354 8.670490 TCTCTCTTTAGCCCTATGTCTCTTATA 58.330 37.037 0.00 0.00 0.00 0.98
354 355 9.474313 CTCTCTTTAGCCCTATGTCTCTTATAT 57.526 37.037 0.00 0.00 0.00 0.86
553 555 7.057894 ACCCCTTATGTGCGAAATTATAGAAA 58.942 34.615 0.00 0.00 0.00 2.52
574 576 8.127150 AGAAAATCCCCTTTAAGATCAAACAG 57.873 34.615 0.00 0.00 0.00 3.16
590 592 4.083324 TCAAACAGTTCCATCGAATTGAGC 60.083 41.667 2.67 0.00 37.80 4.26
648 650 7.725397 CAGGAATATCAATGAACCCCATTCTTA 59.275 37.037 0.00 0.00 43.27 2.10
707 709 8.268605 GGTCTATTTCTTAGTTCAAGATCCCTT 58.731 37.037 0.00 0.00 42.88 3.95
933 935 6.812998 TCCCTACGTCCTTACATTCTATTTG 58.187 40.000 0.00 0.00 0.00 2.32
1030 1032 5.496556 TCTTTGGGCTTCTATTGAATCGAA 58.503 37.500 0.00 0.00 0.00 3.71
1107 1109 7.453752 ACATATAAGGTGTCCTACGGATAATGT 59.546 37.037 0.00 0.00 32.73 2.71
1108 1110 6.742559 ATAAGGTGTCCTACGGATAATGTT 57.257 37.500 0.00 0.00 32.73 2.71
1136 1138 5.578336 CGAAGCTATTTGATGTCTGACTCAA 59.422 40.000 9.51 12.57 0.00 3.02
1178 1180 4.282449 TCGAAATACTTCAAGACTCCACCA 59.718 41.667 0.00 0.00 0.00 4.17
1279 1281 2.604046 AATGGTAGACATGCGAGACC 57.396 50.000 0.00 0.00 40.44 3.85
1409 1411 0.601057 GGCGCTCTCCTCTATCTTCC 59.399 60.000 7.64 0.00 0.00 3.46
1420 1422 4.076394 CCTCTATCTTCCGAGGTCCTTAG 58.924 52.174 0.00 0.00 41.49 2.18
1450 1452 6.756221 TCCCTGAGAAAAGTAGACAGTAAAC 58.244 40.000 0.00 0.00 0.00 2.01
1520 1524 6.041751 TCCTCGAAGGAGATAATAAAGAACCC 59.958 42.308 0.11 0.00 40.06 4.11
1523 1527 7.626390 TCGAAGGAGATAATAAAGAACCCAAA 58.374 34.615 0.00 0.00 0.00 3.28
1524 1528 7.769044 TCGAAGGAGATAATAAAGAACCCAAAG 59.231 37.037 0.00 0.00 0.00 2.77
1525 1529 7.467403 CGAAGGAGATAATAAAGAACCCAAAGC 60.467 40.741 0.00 0.00 0.00 3.51
1527 1531 6.830838 AGGAGATAATAAAGAACCCAAAGCAG 59.169 38.462 0.00 0.00 0.00 4.24
1528 1532 6.828785 GGAGATAATAAAGAACCCAAAGCAGA 59.171 38.462 0.00 0.00 0.00 4.26
1529 1533 7.503902 GGAGATAATAAAGAACCCAAAGCAGAT 59.496 37.037 0.00 0.00 0.00 2.90
1530 1534 8.230472 AGATAATAAAGAACCCAAAGCAGATG 57.770 34.615 0.00 0.00 0.00 2.90
1533 1537 2.957402 AGAACCCAAAGCAGATGTGA 57.043 45.000 0.00 0.00 0.00 3.58
1681 1687 2.224161 CCCCTTTTTGTTTGCGAATCCA 60.224 45.455 0.00 0.00 0.00 3.41
1696 1702 5.883115 TGCGAATCCATGTTTGTATCCTTTA 59.117 36.000 0.00 0.00 0.00 1.85
1743 1749 9.309516 CGATCAAATCAAGGAAATCAATCAAAT 57.690 29.630 0.00 0.00 0.00 2.32
1754 1765 9.388672 AGGAAATCAATCAAATGATCCCAATAT 57.611 29.630 0.00 0.00 39.08 1.28
1881 1892 1.896465 ACAGAAACCGAGGAAGAGGAG 59.104 52.381 0.00 0.00 0.00 3.69
1929 1940 6.049149 AGTCTCGTCTTTTGTCATTCTTTGA 58.951 36.000 0.00 0.00 0.00 2.69
1932 1943 6.705825 TCTCGTCTTTTGTCATTCTTTGATCA 59.294 34.615 0.00 0.00 36.54 2.92
1952 1963 7.252708 TGATCATTTTTCACTCAATGATTCCG 58.747 34.615 8.41 0.00 45.89 4.30
2057 2101 3.091633 AGGGATTGGATTGGTGACTTG 57.908 47.619 0.00 0.00 0.00 3.16
2079 2123 1.270550 CCATTCAGTGACTTTGGCACC 59.729 52.381 0.00 0.00 36.95 5.01
2084 2128 1.525077 GTGACTTTGGCACCGGACA 60.525 57.895 9.46 0.24 0.00 4.02
2176 2220 6.402981 TTTCTTCTCCTTTTAGGGCCTATT 57.597 37.500 15.37 0.00 35.59 1.73
2178 2222 5.036916 TCTTCTCCTTTTAGGGCCTATTCA 58.963 41.667 15.37 0.00 35.59 2.57
2194 2238 7.001073 GGCCTATTCAAAAGAGAATCCAGTAT 58.999 38.462 0.00 0.00 38.97 2.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 4.406003 GCTAGGATTACCAGAAGAAGGTGA 59.594 45.833 0.00 0.00 40.26 4.02
30 31 6.926630 ATAGCTAGGATTACCAGAAGAAGG 57.073 41.667 0.00 0.00 38.94 3.46
82 83 9.485206 ACGTTTCATACTTGTTTGAGTAATAGT 57.515 29.630 0.00 0.00 35.86 2.12
115 116 2.521126 TCGCCCTATGGACGAATATGA 58.479 47.619 0.00 0.00 37.28 2.15
219 220 4.876107 GCGAAAGTTCCTAGATTCATGGAA 59.124 41.667 6.37 6.37 37.51 3.53
240 241 7.736017 CGTAGACTAAATAATACAATGCAAGCG 59.264 37.037 0.00 0.00 0.00 4.68
438 439 5.394333 GCTCGTAAGGAGTCCTATTGAAACT 60.394 44.000 13.43 0.00 45.03 2.66
553 555 6.437477 GGAACTGTTTGATCTTAAAGGGGATT 59.563 38.462 0.00 0.00 0.00 3.01
574 576 3.624861 AGTCATGCTCAATTCGATGGAAC 59.375 43.478 0.00 0.00 34.37 3.62
590 592 6.221659 AGATGCTATCACACATACAGTCATG 58.778 40.000 0.00 0.00 0.00 3.07
621 623 5.668135 ATGGGGTTCATTGATATTCCTGA 57.332 39.130 0.00 0.00 30.55 3.86
648 650 3.118531 AGAGGGTATCCTGAGCAATTGT 58.881 45.455 0.00 0.00 45.05 2.71
726 728 4.897076 TGGGCGGAACAGATCTACTAATTA 59.103 41.667 0.00 0.00 0.00 1.40
933 935 7.387643 GTCTGATTACACCTATTCCTAATCCC 58.612 42.308 0.00 0.00 0.00 3.85
1107 1109 7.981789 AGTCAGACATCAAATAGCTTCGATTAA 59.018 33.333 2.66 0.00 0.00 1.40
1108 1110 7.492524 AGTCAGACATCAAATAGCTTCGATTA 58.507 34.615 2.66 0.00 0.00 1.75
1136 1138 2.614520 CGATCGATCGGTCATATAGGCT 59.385 50.000 34.54 0.00 45.93 4.58
1165 1167 5.698741 ATATGACAATGGTGGAGTCTTGA 57.301 39.130 0.00 0.00 33.56 3.02
1213 1215 8.539770 AGTGAATCGTATTCCATGAATATGAC 57.460 34.615 16.80 9.10 46.48 3.06
1279 1281 2.159599 GCTCTTCAGCACGAGATTTTGG 60.160 50.000 0.00 0.00 46.06 3.28
1409 1411 0.676736 GGAGATGGCTAAGGACCTCG 59.323 60.000 0.00 0.00 0.00 4.63
1420 1422 2.797177 ACTTTTCTCAGGGAGATGGC 57.203 50.000 0.00 0.00 38.56 4.40
1482 1484 4.287585 TCCTTCGAGGAATTTTTAGGACCA 59.712 41.667 0.00 0.00 42.51 4.02
1484 1486 5.731591 TCTCCTTCGAGGAATTTTTAGGAC 58.268 41.667 0.00 0.00 45.28 3.85
1520 1524 5.178996 GCAGTAGGATATCACATCTGCTTTG 59.821 44.000 22.23 6.81 42.00 2.77
1523 1527 3.899980 TGCAGTAGGATATCACATCTGCT 59.100 43.478 25.94 13.58 44.42 4.24
1524 1528 4.263018 TGCAGTAGGATATCACATCTGC 57.737 45.455 22.49 22.49 44.39 4.26
1525 1529 5.236282 CCTTGCAGTAGGATATCACATCTG 58.764 45.833 4.83 8.22 37.50 2.90
1527 1531 4.040952 ACCCTTGCAGTAGGATATCACATC 59.959 45.833 5.98 0.00 37.50 3.06
1528 1532 3.976654 ACCCTTGCAGTAGGATATCACAT 59.023 43.478 5.98 0.00 37.50 3.21
1529 1533 3.134623 CACCCTTGCAGTAGGATATCACA 59.865 47.826 5.98 0.00 37.50 3.58
1530 1534 3.495100 CCACCCTTGCAGTAGGATATCAC 60.495 52.174 5.98 0.00 37.50 3.06
1533 1537 2.706190 GACCACCCTTGCAGTAGGATAT 59.294 50.000 5.98 0.00 37.50 1.63
1640 1646 4.758165 GGGGAATTCGTAGTCACTTTTTCA 59.242 41.667 0.00 0.00 0.00 2.69
1681 1687 4.457603 TGTGCGCTTAAAGGATACAAACAT 59.542 37.500 9.73 0.00 41.41 2.71
1696 1702 2.356135 CTACTTAATGGGTGTGCGCTT 58.644 47.619 9.73 0.00 0.00 4.68
1743 1749 2.309613 GCTGGCACAATATTGGGATCA 58.690 47.619 22.03 16.02 38.70 2.92
1754 1765 0.609151 CATGATTTGGGCTGGCACAA 59.391 50.000 6.13 6.13 38.70 3.33
1820 1831 3.379688 GCTTTTCATGGTTCTCATCTCCC 59.620 47.826 0.00 0.00 32.92 4.30
1821 1832 4.012374 TGCTTTTCATGGTTCTCATCTCC 58.988 43.478 0.00 0.00 32.92 3.71
1881 1892 4.857509 ACTAGTCTTCACTCTTGTGGTC 57.142 45.455 0.00 0.00 43.94 4.02
1932 1943 5.411361 TCGACGGAATCATTGAGTGAAAAAT 59.589 36.000 0.00 0.00 40.97 1.82
2027 2070 5.310331 ACCAATCCAATCCCTTTGACAAATT 59.690 36.000 0.05 0.00 37.53 1.82
2057 2101 0.244721 GCCAAAGTCACTGAATGGGC 59.755 55.000 6.66 6.66 0.00 5.36
2079 2123 0.955905 ACCCGTTTTTGGAATGTCCG 59.044 50.000 0.00 0.00 40.17 4.79
2084 2128 4.080975 TCCGATAGTACCCGTTTTTGGAAT 60.081 41.667 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.