Multiple sequence alignment - TraesCS5B01G281100

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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 TraesCS5B01G281100 chr5B 100.000 2561 0 0 1 2561 466620541 466623101 0.000000e+00 4730.0
1 TraesCS5B01G281100 chr5B 82.195 483 55 10 343 799 466635647 466636124 1.110000e-103 387.0
2 TraesCS5B01G281100 chr5B 97.297 37 0 1 816 852 282012795 282012760 7.650000e-06 62.1
3 TraesCS5B01G281100 chr5D 92.272 2601 121 30 1 2561 387995215 387997775 0.000000e+00 3616.0
4 TraesCS5B01G281100 chr5D 83.586 725 116 3 864 1588 388038346 388039067 0.000000e+00 676.0
5 TraesCS5B01G281100 chr5D 81.664 769 90 21 78 799 388037546 388038310 2.190000e-165 592.0
6 TraesCS5B01G281100 chr5D 96.825 63 2 0 1691 1753 388039206 388039268 3.480000e-19 106.0
7 TraesCS5B01G281100 chr5A 91.916 2573 137 27 2 2557 491165350 491167868 0.000000e+00 3533.0
8 TraesCS5B01G281100 chr5A 80.365 657 74 29 129 735 491176543 491177194 5.030000e-122 448.0
9 TraesCS5B01G281100 chr5A 96.825 63 2 0 1691 1753 491178455 491178517 3.480000e-19 106.0
10 TraesCS5B01G281100 chr2A 74.803 254 42 16 2310 2549 101898049 101897804 7.540000e-16 95.3
11 TraesCS5B01G281100 chr6B 83.838 99 12 4 2385 2482 589048042 589047947 9.760000e-15 91.6
12 TraesCS5B01G281100 chr7D 97.297 37 0 1 816 852 246023451 246023416 7.650000e-06 62.1
13 TraesCS5B01G281100 chr7B 97.297 37 0 1 816 852 619084864 619084829 7.650000e-06 62.1
14 TraesCS5B01G281100 chr3D 97.297 37 0 1 816 852 321025357 321025392 7.650000e-06 62.1
15 TraesCS5B01G281100 chr3A 97.297 37 0 1 816 852 19499490 19499455 7.650000e-06 62.1
16 TraesCS5B01G281100 chr2D 97.297 37 0 1 816 852 138806881 138806916 7.650000e-06 62.1
17 TraesCS5B01G281100 chr2D 94.872 39 2 0 2089 2127 638031959 638031997 7.650000e-06 62.1
18 TraesCS5B01G281100 chr1B 97.297 37 0 1 816 852 658923617 658923582 7.650000e-06 62.1


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 TraesCS5B01G281100 chr5B 466620541 466623101 2560 False 4730 4730 100.000000 1 2561 1 chr5B.!!$F1 2560
1 TraesCS5B01G281100 chr5D 387995215 387997775 2560 False 3616 3616 92.272000 1 2561 1 chr5D.!!$F1 2560
2 TraesCS5B01G281100 chr5D 388037546 388039268 1722 False 458 676 87.358333 78 1753 3 chr5D.!!$F2 1675
3 TraesCS5B01G281100 chr5A 491165350 491167868 2518 False 3533 3533 91.916000 2 2557 1 chr5A.!!$F1 2555
4 TraesCS5B01G281100 chr5A 491176543 491178517 1974 False 277 448 88.595000 129 1753 2 chr5A.!!$F2 1624

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
33 34 0.806102 CCACCGCCATCTAACTCACG 60.806 60.0 0.0 0.0 0.0 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1928 2330 0.386352 TTCGCAGACGGTTACAGACG 60.386 55.0 0.0 0.0 40.63 4.18 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
33 34 0.806102 CCACCGCCATCTAACTCACG 60.806 60.000 0.00 0.00 0.00 4.35
53 54 1.531602 ACTGGGGCTGTTTTGGAGC 60.532 57.895 0.00 0.00 35.57 4.70
54 55 2.597217 TGGGGCTGTTTTGGAGCG 60.597 61.111 0.00 0.00 37.32 5.03
55 56 2.282180 GGGGCTGTTTTGGAGCGA 60.282 61.111 0.00 0.00 37.32 4.93
56 57 1.901464 GGGGCTGTTTTGGAGCGAA 60.901 57.895 0.00 0.00 37.32 4.70
57 58 1.250840 GGGGCTGTTTTGGAGCGAAT 61.251 55.000 0.00 0.00 37.32 3.34
58 59 1.459450 GGGCTGTTTTGGAGCGAATA 58.541 50.000 0.00 0.00 37.32 1.75
59 60 1.816224 GGGCTGTTTTGGAGCGAATAA 59.184 47.619 0.00 0.00 37.32 1.40
60 61 2.159379 GGGCTGTTTTGGAGCGAATAAG 60.159 50.000 0.00 0.00 37.32 1.73
61 62 2.159379 GGCTGTTTTGGAGCGAATAAGG 60.159 50.000 0.00 0.00 37.32 2.69
62 63 2.732282 GCTGTTTTGGAGCGAATAAGGC 60.732 50.000 0.00 0.00 0.00 4.35
63 64 2.749621 CTGTTTTGGAGCGAATAAGGCT 59.250 45.455 0.00 0.00 45.00 4.58
64 65 3.938963 CTGTTTTGGAGCGAATAAGGCTA 59.061 43.478 0.00 0.00 41.72 3.93
65 66 4.523083 TGTTTTGGAGCGAATAAGGCTAT 58.477 39.130 0.00 0.00 41.72 2.97
66 67 4.335315 TGTTTTGGAGCGAATAAGGCTATG 59.665 41.667 0.00 0.00 41.72 2.23
67 68 3.838244 TTGGAGCGAATAAGGCTATGT 57.162 42.857 0.00 0.00 41.72 2.29
68 69 3.386768 TGGAGCGAATAAGGCTATGTC 57.613 47.619 0.00 0.00 41.72 3.06
249 252 9.274206 GGGCTAAGTAGACTTATTCCTTATTTG 57.726 37.037 15.02 0.14 37.75 2.32
526 576 6.925610 AAATGCTTCAATGCGATTAGTCTA 57.074 33.333 0.00 0.00 35.36 2.59
561 611 6.032094 GCAGCGTAACAGTATACTACTTTGA 58.968 40.000 4.74 0.00 36.76 2.69
577 627 4.668289 ACTTTGAATTTTATAAGCCGGCG 58.332 39.130 23.20 0.00 0.00 6.46
825 1186 4.873746 TTCCCTCTGTCTACTTGTCTTG 57.126 45.455 0.00 0.00 0.00 3.02
996 1360 5.731678 ACTAATTCTGTAGGGTTCCCTCATT 59.268 40.000 14.24 8.50 37.64 2.57
1278 1642 2.364632 CAGGGCGGTTTCAATATGTCA 58.635 47.619 0.00 0.00 0.00 3.58
1279 1643 2.355756 CAGGGCGGTTTCAATATGTCAG 59.644 50.000 0.00 0.00 0.00 3.51
1542 1906 0.396435 TGACTTGGTCGACATTGCCT 59.604 50.000 18.91 0.00 34.95 4.75
1582 1946 0.470766 ATTTGCCCGGCCGATACTTA 59.529 50.000 30.73 7.56 0.00 2.24
1638 2038 9.310716 GGAGGTGTAATCAAACTATTGTAGTAC 57.689 37.037 0.00 0.00 38.26 2.73
1639 2039 9.310716 GAGGTGTAATCAAACTATTGTAGTACC 57.689 37.037 0.00 0.00 38.26 3.34
1640 2040 8.818860 AGGTGTAATCAAACTATTGTAGTACCA 58.181 33.333 0.00 0.00 38.26 3.25
1642 2042 9.095065 GTGTAATCAAACTATTGTAGTACCAGG 57.905 37.037 0.00 0.00 38.26 4.45
1643 2043 8.262227 TGTAATCAAACTATTGTAGTACCAGGG 58.738 37.037 0.00 0.00 38.26 4.45
1644 2044 6.886178 ATCAAACTATTGTAGTACCAGGGT 57.114 37.500 0.00 0.00 38.26 4.34
1646 2046 7.081857 TCAAACTATTGTAGTACCAGGGTTT 57.918 36.000 0.00 2.50 38.26 3.27
1647 2047 8.204903 TCAAACTATTGTAGTACCAGGGTTTA 57.795 34.615 0.00 0.00 38.26 2.01
1648 2048 8.316214 TCAAACTATTGTAGTACCAGGGTTTAG 58.684 37.037 0.00 1.90 38.26 1.85
1649 2049 6.803366 ACTATTGTAGTACCAGGGTTTAGG 57.197 41.667 0.00 0.00 37.23 2.69
1651 2051 6.732390 ACTATTGTAGTACCAGGGTTTAGGTT 59.268 38.462 0.00 0.00 39.31 3.50
1653 2053 4.491675 TGTAGTACCAGGGTTTAGGTTGA 58.508 43.478 0.00 0.00 39.31 3.18
1654 2054 4.906664 TGTAGTACCAGGGTTTAGGTTGAA 59.093 41.667 0.00 0.00 39.31 2.69
1655 2055 5.369110 TGTAGTACCAGGGTTTAGGTTGAAA 59.631 40.000 0.00 0.00 39.31 2.69
1771 2173 0.758310 TGGTGGATTGCAAGTTGCCA 60.758 50.000 24.59 14.94 44.23 4.92
1779 2181 5.221601 TGGATTGCAAGTTGCCAATTTCTAA 60.222 36.000 24.59 10.13 44.23 2.10
1846 2248 7.309377 CCGTCATTATTTTGGCATAGATGGATT 60.309 37.037 0.00 0.00 33.78 3.01
1851 2253 3.317455 TTGGCATAGATGGATTGGCTT 57.683 42.857 0.00 0.00 36.91 4.35
1897 2299 1.078918 CGCATGAAGCCAGGTCAGA 60.079 57.895 0.00 0.00 41.38 3.27
1920 2322 0.680921 CAGGGATGCAAACGGATGGT 60.681 55.000 0.00 0.00 0.00 3.55
1928 2330 1.599419 GCAAACGGATGGTGTTCACAC 60.599 52.381 1.10 1.10 45.72 3.82
2044 2446 2.174639 ACAAGGGGTCAACAATCTGACA 59.825 45.455 6.12 0.00 46.31 3.58
2073 2475 2.583441 CGGGCTCAGGAAGGTGACA 61.583 63.158 0.00 0.00 0.00 3.58
2143 2545 0.623324 AGGGCTACAGTAATGGGCCA 60.623 55.000 23.51 9.61 46.98 5.36
2166 2568 0.099436 CATTTTAGCGCAGGTGCTCC 59.901 55.000 11.47 0.00 45.87 4.70
2191 2593 1.651240 CGCATAGCTGCCTGCACTTT 61.651 55.000 20.35 0.00 46.07 2.66
2201 2603 1.308998 CCTGCACTTTGTTCCGACTT 58.691 50.000 0.00 0.00 0.00 3.01
2211 2613 2.589720 TGTTCCGACTTGTAGGAGACA 58.410 47.619 3.08 7.80 37.88 3.41
2233 2635 5.071788 ACATTGTAGAGTTCACTCCCTTTGA 59.928 40.000 3.20 0.00 43.88 2.69
2337 2750 6.992715 TCTGGTTTCTTTGTTTTCTCTAGAGG 59.007 38.462 19.67 1.12 0.00 3.69
2469 2886 7.534085 CATTTTTAGAGCAAATGTGATGCAT 57.466 32.000 0.00 0.00 46.22 3.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 1.002366 CAGTGCGTGAGTTAGATGGC 58.998 55.000 0.00 0.00 0.00 4.40
33 34 1.809567 CTCCAAAACAGCCCCAGTGC 61.810 60.000 0.00 0.00 0.00 4.40
53 54 4.058817 GGAACCAGACATAGCCTTATTCG 58.941 47.826 0.00 0.00 0.00 3.34
54 55 5.036117 TGGAACCAGACATAGCCTTATTC 57.964 43.478 0.00 0.00 0.00 1.75
55 56 5.456763 GGATGGAACCAGACATAGCCTTATT 60.457 44.000 0.00 0.00 0.00 1.40
56 57 4.042187 GGATGGAACCAGACATAGCCTTAT 59.958 45.833 0.00 0.00 0.00 1.73
57 58 3.391296 GGATGGAACCAGACATAGCCTTA 59.609 47.826 0.00 0.00 0.00 2.69
58 59 2.173569 GGATGGAACCAGACATAGCCTT 59.826 50.000 0.00 0.00 0.00 4.35
59 60 1.771255 GGATGGAACCAGACATAGCCT 59.229 52.381 0.00 0.00 0.00 4.58
60 61 1.490490 TGGATGGAACCAGACATAGCC 59.510 52.381 0.00 0.00 34.77 3.93
61 62 3.144506 CATGGATGGAACCAGACATAGC 58.855 50.000 10.95 0.00 43.49 2.97
62 63 3.144506 GCATGGATGGAACCAGACATAG 58.855 50.000 10.95 8.18 43.49 2.23
63 64 2.509131 TGCATGGATGGAACCAGACATA 59.491 45.455 10.95 0.00 43.49 2.29
64 65 1.285667 TGCATGGATGGAACCAGACAT 59.714 47.619 0.00 3.83 43.49 3.06
65 66 0.697658 TGCATGGATGGAACCAGACA 59.302 50.000 0.00 1.59 43.49 3.41
66 67 1.679680 CATGCATGGATGGAACCAGAC 59.320 52.381 19.40 0.00 43.49 3.51
67 68 1.285667 ACATGCATGGATGGAACCAGA 59.714 47.619 29.41 0.00 43.49 3.86
68 69 1.771565 ACATGCATGGATGGAACCAG 58.228 50.000 29.41 4.66 43.49 4.00
249 252 8.428186 ACAATGTGGAATGAATAATGAAATGC 57.572 30.769 0.00 0.00 0.00 3.56
254 257 6.265196 GCCCTACAATGTGGAATGAATAATGA 59.735 38.462 0.00 0.00 0.00 2.57
526 576 5.661458 ACTGTTACGCTGCTATTTACAGAT 58.339 37.500 17.64 5.86 37.32 2.90
648 698 9.956797 CACATTTCATTCGATTTTATTTGGAAC 57.043 29.630 0.00 0.00 0.00 3.62
1234 1598 4.582656 CACTTCCGAGATGAGAACCTCTAT 59.417 45.833 0.00 0.00 0.00 1.98
1278 1642 5.578157 ACCCACTGGTAAAACATCTAACT 57.422 39.130 0.00 0.00 45.45 2.24
1582 1946 4.038282 TGTTACAACTCCACGACTACACAT 59.962 41.667 0.00 0.00 0.00 3.21
1638 2038 1.893137 GGCTTTCAACCTAAACCCTGG 59.107 52.381 0.00 0.00 0.00 4.45
1639 2039 2.876581 AGGCTTTCAACCTAAACCCTG 58.123 47.619 0.00 0.00 35.10 4.45
1640 2040 3.612795 AAGGCTTTCAACCTAAACCCT 57.387 42.857 0.00 0.00 36.14 4.34
1642 2042 3.181470 TGCAAAGGCTTTCAACCTAAACC 60.181 43.478 10.08 0.00 41.91 3.27
1643 2043 4.053469 TGCAAAGGCTTTCAACCTAAAC 57.947 40.909 10.08 0.00 41.91 2.01
1644 2044 4.953940 ATGCAAAGGCTTTCAACCTAAA 57.046 36.364 10.08 0.00 41.91 1.85
1646 2046 5.321102 TCTAATGCAAAGGCTTTCAACCTA 58.679 37.500 10.08 4.88 41.91 3.08
1647 2047 4.151883 TCTAATGCAAAGGCTTTCAACCT 58.848 39.130 10.08 4.09 41.91 3.50
1648 2048 4.519540 TCTAATGCAAAGGCTTTCAACC 57.480 40.909 10.08 0.00 41.91 3.77
1649 2049 6.393171 AGAATCTAATGCAAAGGCTTTCAAC 58.607 36.000 10.08 3.42 41.91 3.18
1651 2051 6.435277 AGAAGAATCTAATGCAAAGGCTTTCA 59.565 34.615 10.08 11.49 38.27 2.69
1653 2053 6.847421 AGAAGAATCTAATGCAAAGGCTTT 57.153 33.333 6.68 6.68 40.18 3.51
1654 2054 7.230309 GGATAGAAGAATCTAATGCAAAGGCTT 59.770 37.037 0.00 0.00 41.38 4.35
1655 2055 6.714356 GGATAGAAGAATCTAATGCAAAGGCT 59.286 38.462 0.00 0.00 41.38 4.58
1846 2248 1.846007 AACCAACTGTTGTCAAGCCA 58.154 45.000 18.38 0.00 35.31 4.75
1851 2253 5.432645 TCATCACTAAACCAACTGTTGTCA 58.567 37.500 18.38 1.03 37.23 3.58
1920 2322 1.134753 ACGGTTACAGACGTGTGAACA 59.865 47.619 20.80 0.92 42.39 3.18
1928 2330 0.386352 TTCGCAGACGGTTACAGACG 60.386 55.000 0.00 0.00 40.63 4.18
1932 2334 3.853831 TTCTATTCGCAGACGGTTACA 57.146 42.857 0.00 0.00 40.63 2.41
1994 2396 5.328691 CGATAGTCCGCAAAGCAAAAATTA 58.671 37.500 0.00 0.00 0.00 1.40
2021 2423 3.751698 GTCAGATTGTTGACCCCTTGTAC 59.248 47.826 0.00 0.00 41.24 2.90
2044 2446 4.496336 GAGCCCGCTGGAGCCAAT 62.496 66.667 0.00 0.00 37.91 3.16
2059 2461 1.079543 CGCCTGTCACCTTCCTGAG 60.080 63.158 0.00 0.00 0.00 3.35
2063 2465 1.374758 CTGTCGCCTGTCACCTTCC 60.375 63.158 0.00 0.00 0.00 3.46
2065 2467 1.069765 CACTGTCGCCTGTCACCTT 59.930 57.895 0.00 0.00 0.00 3.50
2073 2475 1.726853 GACATAAAGCACTGTCGCCT 58.273 50.000 0.00 0.00 33.14 5.52
2129 2531 0.325272 TGCGTTGGCCCATTACTGTA 59.675 50.000 0.00 0.00 38.85 2.74
2137 2539 1.589113 GCTAAAATGCGTTGGCCCA 59.411 52.632 0.00 0.00 38.85 5.36
2183 2585 1.670811 ACAAGTCGGAACAAAGTGCAG 59.329 47.619 0.00 0.00 0.00 4.41
2184 2586 1.745232 ACAAGTCGGAACAAAGTGCA 58.255 45.000 0.00 0.00 0.00 4.57
2185 2587 2.223377 CCTACAAGTCGGAACAAAGTGC 59.777 50.000 0.00 0.00 0.00 4.40
2186 2588 3.724374 TCCTACAAGTCGGAACAAAGTG 58.276 45.455 0.00 0.00 0.00 3.16
2191 2593 2.589720 TGTCTCCTACAAGTCGGAACA 58.410 47.619 0.00 1.31 34.29 3.18
2201 2603 6.010850 AGTGAACTCTACAATGTCTCCTACA 58.989 40.000 0.00 0.00 43.86 2.74
2211 2613 5.825593 TCAAAGGGAGTGAACTCTACAAT 57.174 39.130 10.17 0.00 42.48 2.71
2303 2707 7.881775 AAACAAAGAAACCAGAGTAAGATGT 57.118 32.000 0.00 0.00 0.00 3.06
2337 2750 7.598189 AGTATAGCGAAGAAAGAAAGGAAAC 57.402 36.000 0.00 0.00 0.00 2.78


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

AutoCloner maintained by Alex Coulton.