Multiple sequence alignment - TraesCS5B01G467300

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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 TraesCS5B01G467300 chr5B 100.000 2264 0 0 1 2264 641182748 641180485 0.000000e+00 4181.0
1 TraesCS5B01G467300 chr5B 95.354 1485 65 4 1 1484 578837550 578836069 0.000000e+00 2357.0
2 TraesCS5B01G467300 chr5B 89.859 355 27 7 1494 1841 578835553 578835201 4.440000e-122 448.0
3 TraesCS5B01G467300 chr5B 89.136 359 31 3 1486 1838 16030371 16030727 7.420000e-120 440.0
4 TraesCS5B01G467300 chr5B 90.196 306 22 3 1620 1919 16030353 16030656 2.110000e-105 392.0
5 TraesCS5B01G467300 chr5B 89.865 296 23 4 1631 1919 641181272 641180977 7.640000e-100 374.0
6 TraesCS5B01G467300 chr5B 95.327 107 5 0 1886 1992 16030694 16030800 1.080000e-38 171.0
7 TraesCS5B01G467300 chr1B 95.976 1491 52 3 1 1484 623645158 623646647 0.000000e+00 2414.0
8 TraesCS5B01G467300 chr1B 91.871 775 38 7 1505 2264 623647118 623647882 0.000000e+00 1059.0
9 TraesCS5B01G467300 chr1B 90.458 262 22 1 1658 1919 623647118 623647376 2.150000e-90 342.0
10 TraesCS5B01G467300 chr7B 94.747 1485 75 3 1 1484 34282306 34280824 0.000000e+00 2307.0
11 TraesCS5B01G467300 chr7B 90.435 115 10 1 1504 1617 27328536 27328650 1.400000e-32 150.0
12 TraesCS5B01G467300 chr5D 94.500 1491 71 6 1 1484 387840681 387839195 0.000000e+00 2289.0
13 TraesCS5B01G467300 chr5D 92.481 266 16 4 2002 2264 557173671 557173407 5.900000e-101 377.0
14 TraesCS5B01G467300 chr5D 88.779 303 26 4 1965 2264 313380998 313380701 4.600000e-97 364.0
15 TraesCS5B01G467300 chr4A 93.842 1494 80 7 1 1484 737660731 737662222 0.000000e+00 2239.0
16 TraesCS5B01G467300 chr3A 93.742 1486 89 4 1 1484 44774224 44772741 0.000000e+00 2226.0
17 TraesCS5B01G467300 chr2A 93.401 1485 94 3 1 1484 372742764 372744245 0.000000e+00 2196.0
18 TraesCS5B01G467300 chr3B 92.962 1492 94 8 1 1484 112909780 112911268 0.000000e+00 2163.0
19 TraesCS5B01G467300 chr3B 94.395 339 19 0 1569 1907 16201572 16201234 2.580000e-144 521.0
20 TraesCS5B01G467300 chr3B 91.941 273 18 4 1995 2264 173092084 173092355 1.640000e-101 379.0
21 TraesCS5B01G467300 chr3B 90.909 286 19 2 1478 1762 16201511 16201232 5.900000e-101 377.0
22 TraesCS5B01G467300 chr3B 96.335 191 6 1 1910 2100 16197235 16197046 1.690000e-81 313.0
23 TraesCS5B01G467300 chr6B 93.358 1340 80 7 1 1333 425587411 425588748 0.000000e+00 1973.0
24 TraesCS5B01G467300 chr2B 94.525 895 44 5 590 1484 579908704 579909593 0.000000e+00 1376.0
25 TraesCS5B01G467300 chr2B 95.288 382 14 4 1886 2264 102804450 102804830 8.950000e-169 603.0
26 TraesCS5B01G467300 chr2B 92.033 364 28 1 1478 1840 102804122 102804485 5.580000e-141 510.0
27 TraesCS5B01G467300 chr2B 87.097 403 46 1 1505 1907 579910064 579910460 3.430000e-123 451.0
28 TraesCS5B01G467300 chr2B 96.029 277 9 2 1990 2264 579910500 579910776 1.230000e-122 449.0
29 TraesCS5B01G467300 chr2B 89.577 355 31 2 1569 1917 102804061 102804415 1.600000e-121 446.0
30 TraesCS5B01G467300 chr2B 89.695 262 27 0 1658 1919 579910064 579910325 3.600000e-88 335.0
31 TraesCS5B01G467300 chr2B 86.885 122 15 1 1799 1919 579910057 579910178 3.920000e-28 135.0
32 TraesCS5B01G467300 chr4B 93.701 381 22 2 1886 2264 598446916 598446536 9.070000e-159 569.0
33 TraesCS5B01G467300 chr1D 92.079 303 21 3 1965 2264 297549826 297549524 7.480000e-115 424.0
34 TraesCS5B01G467300 chr1D 100.000 49 0 0 1917 1965 490890979 490891027 8.610000e-15 91.6
35 TraesCS5B01G467300 chr7D 92.424 264 19 1 2002 2264 133434874 133435137 2.120000e-100 375.0
36 TraesCS5B01G467300 chr7D 100.000 49 0 0 1917 1965 16797218 16797170 8.610000e-15 91.6
37 TraesCS5B01G467300 chr7D 100.000 49 0 0 1917 1965 21072128 21072080 8.610000e-15 91.6
38 TraesCS5B01G467300 chr6A 100.000 49 0 0 1917 1965 79830040 79829992 8.610000e-15 91.6


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 TraesCS5B01G467300 chr5B 641180485 641182748 2263 True 2277.500000 4181 94.932500 1 2264 2 chr5B.!!$R2 2263
1 TraesCS5B01G467300 chr5B 578835201 578837550 2349 True 1402.500000 2357 92.606500 1 1841 2 chr5B.!!$R1 1840
2 TraesCS5B01G467300 chr1B 623645158 623647882 2724 False 1271.666667 2414 92.768333 1 2264 3 chr1B.!!$F1 2263
3 TraesCS5B01G467300 chr7B 34280824 34282306 1482 True 2307.000000 2307 94.747000 1 1484 1 chr7B.!!$R1 1483
4 TraesCS5B01G467300 chr5D 387839195 387840681 1486 True 2289.000000 2289 94.500000 1 1484 1 chr5D.!!$R2 1483
5 TraesCS5B01G467300 chr4A 737660731 737662222 1491 False 2239.000000 2239 93.842000 1 1484 1 chr4A.!!$F1 1483
6 TraesCS5B01G467300 chr3A 44772741 44774224 1483 True 2226.000000 2226 93.742000 1 1484 1 chr3A.!!$R1 1483
7 TraesCS5B01G467300 chr2A 372742764 372744245 1481 False 2196.000000 2196 93.401000 1 1484 1 chr2A.!!$F1 1483
8 TraesCS5B01G467300 chr3B 112909780 112911268 1488 False 2163.000000 2163 92.962000 1 1484 1 chr3B.!!$F1 1483
9 TraesCS5B01G467300 chr3B 16197046 16201572 4526 True 403.666667 521 93.879667 1478 2100 3 chr3B.!!$R1 622
10 TraesCS5B01G467300 chr6B 425587411 425588748 1337 False 1973.000000 1973 93.358000 1 1333 1 chr6B.!!$F1 1332
11 TraesCS5B01G467300 chr2B 579908704 579910776 2072 False 549.200000 1376 90.846200 590 2264 5 chr2B.!!$F2 1674
12 TraesCS5B01G467300 chr2B 102804061 102804830 769 False 519.666667 603 92.299333 1478 2264 3 chr2B.!!$F1 786

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
327 328 0.478072 TTGGACCAATCACAGTGGCT 59.522 50.0 1.69 0.0 40.02 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1831 2434 0.179234 TGACCAAAACGAGCCAGACA 59.821 50.0 0.0 0.0 0.0 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
40 41 6.751514 TCACGGCAACAAGTTATCATATTT 57.248 33.333 0.00 0.00 0.00 1.40
114 115 3.492337 ACGGTTTTCAATATGGTGGTGT 58.508 40.909 0.00 0.00 0.00 4.16
149 150 2.651361 CGAAGACTCGGTGGTGCT 59.349 61.111 0.00 0.00 41.57 4.40
192 193 0.874175 CATTGGCCATGCTCGCATTG 60.874 55.000 6.09 0.00 33.90 2.82
203 204 0.874175 CTCGCATTGGATAACGGCGA 60.874 55.000 16.62 6.85 44.46 5.54
327 328 0.478072 TTGGACCAATCACAGTGGCT 59.522 50.000 1.69 0.00 40.02 4.75
367 368 5.305644 TCATATTAAGCCAGACCCTCTTCTC 59.694 44.000 0.00 0.00 0.00 2.87
375 376 1.132689 AGACCCTCTTCTCAAGGTGGT 60.133 52.381 0.00 0.00 36.12 4.16
559 561 5.989477 AGAAAAGGAAAACCAAGAAAAGGG 58.011 37.500 0.00 0.00 0.00 3.95
605 607 1.211703 TGGTGCACAAGTTGGAAGAGA 59.788 47.619 20.43 0.00 0.00 3.10
641 643 1.138069 TCGAGGAAGCACAAGTGACAA 59.862 47.619 4.04 0.00 0.00 3.18
720 767 1.137282 GGGAGTACAAGTGCTAGAGGC 59.863 57.143 0.00 0.00 42.22 4.70
1062 1121 2.173356 CCAAGAGGACATGCCCAAGATA 59.827 50.000 0.00 0.00 37.37 1.98
1063 1122 3.474600 CAAGAGGACATGCCCAAGATAG 58.525 50.000 0.00 0.00 37.37 2.08
1115 1180 1.719063 AAGGATGTGCCCACACCACT 61.719 55.000 16.64 8.37 46.86 4.00
1160 1225 1.002430 GCTGAAGGTGTCCACTGATCA 59.998 52.381 0.00 0.00 0.00 2.92
1180 1245 5.034852 TCACAAGAAGTCATGGACAGAAA 57.965 39.130 0.00 0.00 34.60 2.52
1181 1246 5.436175 TCACAAGAAGTCATGGACAGAAAA 58.564 37.500 0.00 0.00 34.60 2.29
1188 1253 7.911651 AGAAGTCATGGACAGAAAATAGAAGA 58.088 34.615 0.00 0.00 34.60 2.87
1336 1401 5.479124 ACGTGATTTATATGTAGTCCCCC 57.521 43.478 0.00 0.00 0.00 5.40
1414 1479 1.893801 AGAGGACCAACGTCGAGATTT 59.106 47.619 0.00 0.00 40.17 2.17
1484 1549 1.668101 GGGAGCGTCGTGAGAAGGAT 61.668 60.000 0.00 0.00 45.01 3.24
1485 1550 0.173708 GGAGCGTCGTGAGAAGGATT 59.826 55.000 0.00 0.00 45.01 3.01
1486 1551 1.404315 GGAGCGTCGTGAGAAGGATTT 60.404 52.381 0.00 0.00 45.01 2.17
1488 1553 2.737252 GAGCGTCGTGAGAAGGATTTTT 59.263 45.455 0.00 0.00 45.01 1.94
1527 2106 4.410400 CCCAGACGCCAAGGACCC 62.410 72.222 0.00 0.00 0.00 4.46
1551 2130 0.878961 GTCTGGCTCGTTTTGGTCGT 60.879 55.000 0.00 0.00 0.00 4.34
1597 2176 2.224843 TGTGTCTGATGCAAACCCAGAT 60.225 45.455 12.42 0.00 38.92 2.90
1617 2196 2.063979 CCAGGGTCCATGGCGTCTA 61.064 63.158 10.19 0.00 0.00 2.59
1683 2262 2.915659 AGACGCCAAGGACCGTGA 60.916 61.111 9.22 0.00 37.87 4.35
1694 2273 2.910479 ACCGTGACGTCTGGCTCA 60.910 61.111 22.24 0.00 0.00 4.26
1831 2434 2.224159 AGACGCCAAGGACCATGGT 61.224 57.895 19.89 19.89 40.23 3.55
2022 6621 2.040278 GTGGATAAGATGCTATGGGCCA 59.960 50.000 9.61 9.61 40.92 5.36
2096 6695 1.112315 CCCTCACTCCCTCTCCATCG 61.112 65.000 0.00 0.00 0.00 3.84
2108 6709 3.093835 CCATCGCCCTAACCCCCA 61.094 66.667 0.00 0.00 0.00 4.96
2130 6731 5.471116 CCACAAATCTCTCACAAATCAGTCA 59.529 40.000 0.00 0.00 0.00 3.41
2131 6732 6.150641 CCACAAATCTCTCACAAATCAGTCAT 59.849 38.462 0.00 0.00 0.00 3.06
2139 6740 7.446319 TCTCTCACAAATCAGTCATGTTTCATT 59.554 33.333 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
132 133 0.179161 CTAGCACCACCGAGTCTTCG 60.179 60.000 0.00 0.00 46.29 3.79
149 150 2.092538 ACTTACTAGGCCTCTCGCACTA 60.093 50.000 9.68 0.00 40.31 2.74
192 193 2.235699 GCCTTCGTCGCCGTTATCC 61.236 63.158 0.00 0.00 35.01 2.59
203 204 2.736144 TGTATGTTTCTCGCCTTCGT 57.264 45.000 0.00 0.00 36.96 3.85
327 328 1.595311 ATGAGGGCCATGGTACTCAA 58.405 50.000 30.87 20.16 42.55 3.02
367 368 0.768622 TACCCTTGGTCACCACCTTG 59.231 55.000 0.00 0.00 44.17 3.61
375 376 2.904434 GTTCTCCTTCTACCCTTGGTCA 59.096 50.000 0.00 0.00 37.09 4.02
559 561 1.226746 CCACCTCCACGACTTGTTTC 58.773 55.000 0.00 0.00 0.00 2.78
590 592 2.738846 CCGTCATCTCTTCCAACTTGTG 59.261 50.000 0.00 0.00 0.00 3.33
593 595 2.289694 CCACCGTCATCTCTTCCAACTT 60.290 50.000 0.00 0.00 0.00 2.66
605 607 2.747686 GACCACCACCACCGTCAT 59.252 61.111 0.00 0.00 0.00 3.06
641 643 2.923837 GACCACCACCACCACCTT 59.076 61.111 0.00 0.00 0.00 3.50
720 767 3.414700 GTGCTTGCTCGACCACCG 61.415 66.667 0.00 0.00 40.25 4.94
1035 1094 1.296392 CATGTCCTCTTGGTCCGCA 59.704 57.895 0.00 0.00 34.23 5.69
1062 1121 2.128226 AACCTGGCCTCCATCCCT 59.872 61.111 3.32 0.00 30.82 4.20
1063 1122 2.276740 CAACCTGGCCTCCATCCC 59.723 66.667 3.32 0.00 30.82 3.85
1115 1180 3.005261 GCAAACATCACCACACCAACATA 59.995 43.478 0.00 0.00 0.00 2.29
1160 1225 7.453393 TCTATTTTCTGTCCATGACTTCTTGT 58.547 34.615 0.00 0.00 33.15 3.16
1180 1245 6.001460 TGGGACACACGAAAAATCTTCTATT 58.999 36.000 0.00 0.00 0.00 1.73
1181 1246 5.556915 TGGGACACACGAAAAATCTTCTAT 58.443 37.500 0.00 0.00 0.00 1.98
1188 1253 4.320935 GCATAGTTGGGACACACGAAAAAT 60.321 41.667 0.00 0.00 39.29 1.82
1414 1479 4.143333 GGCGCTGCCTCCGTAAGA 62.143 66.667 7.64 0.00 46.69 2.10
1485 1550 8.306502 GTGTGCACATTAGCAAACTGCAAAAA 62.307 38.462 24.69 0.00 46.77 1.94
1486 1551 6.917033 GTGTGCACATTAGCAAACTGCAAAA 61.917 40.000 24.69 0.00 46.77 2.44
1488 1553 4.039819 GTGTGCACATTAGCAAACTGCAA 61.040 43.478 24.69 0.00 46.77 4.08
1489 1554 2.543445 GTGTGCACATTAGCAAACTGCA 60.543 45.455 24.69 0.00 46.77 4.41
1490 1555 2.053627 GTGTGCACATTAGCAAACTGC 58.946 47.619 24.69 0.91 46.77 4.40
1497 1562 0.804989 GTCTGGGTGTGCACATTAGC 59.195 55.000 24.69 9.89 0.00 3.09
1498 1563 1.078709 CGTCTGGGTGTGCACATTAG 58.921 55.000 24.69 19.95 0.00 1.73
1499 1564 0.953471 GCGTCTGGGTGTGCACATTA 60.953 55.000 24.69 11.37 0.00 1.90
1502 1567 4.927782 GGCGTCTGGGTGTGCACA 62.928 66.667 17.42 17.42 0.00 4.57
1503 1568 4.927782 TGGCGTCTGGGTGTGCAC 62.928 66.667 10.75 10.75 0.00 4.57
1527 2106 1.961277 AAAACGAGCCAGACGCCAG 60.961 57.895 0.00 0.00 38.78 4.85
1551 2130 0.394192 CAAGTGTCTGGTCTCCTGCA 59.606 55.000 0.00 0.00 0.00 4.41
1617 2196 2.856760 TGCTCTCTGGATAGGAACCT 57.143 50.000 0.00 0.00 0.00 3.50
1653 2232 2.680913 GCGTCTGGGTGTGCACATC 61.681 63.158 24.69 23.43 0.00 3.06
1683 2262 1.202758 TGACCAAAATGAGCCAGACGT 60.203 47.619 0.00 0.00 0.00 4.34
1694 2273 3.412722 TCACCTGCGTGACCAAAAT 57.587 47.368 0.00 0.00 44.20 1.82
1798 2390 1.372838 CGTCTGGGTGTGCACAAACA 61.373 55.000 23.59 21.25 0.00 2.83
1831 2434 0.179234 TGACCAAAACGAGCCAGACA 59.821 50.000 0.00 0.00 0.00 3.41
1907 2510 5.378230 AAGAATCTTATCCAGATGCCACA 57.622 39.130 0.00 0.00 41.93 4.17
1913 6512 4.448347 GGGCCCAAAGAATCTTATCCAGAT 60.448 45.833 19.95 0.00 45.03 2.90
2022 6621 2.309755 TGGAATGAGAGGGCTTGATGTT 59.690 45.455 0.00 0.00 0.00 2.71
2096 6695 0.335019 AGATTTGTGGGGGTTAGGGC 59.665 55.000 0.00 0.00 0.00 5.19
2108 6709 6.713903 ACATGACTGATTTGTGAGAGATTTGT 59.286 34.615 0.00 0.00 0.00 2.83
2130 6731 4.158394 CCCGAAGATCCAACAATGAAACAT 59.842 41.667 0.00 0.00 0.00 2.71
2131 6732 3.505680 CCCGAAGATCCAACAATGAAACA 59.494 43.478 0.00 0.00 0.00 2.83
2139 6740 3.712016 TGAAATCCCGAAGATCCAACA 57.288 42.857 0.00 0.00 32.47 3.33


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

AutoCloner maintained by Alex Coulton.