Multiple sequence alignment - TraesCS5A01G557900

Loading Multiple Alignment...

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 TraesCS5A01G557900 chr5A 100.000 1375 0 0 1 1375 708678951 708680325 0.000000e+00 2540.0
1 TraesCS5A01G557900 chr5A 94.209 1347 77 1 1 1346 647000795 647002141 0.000000e+00 2054.0
2 TraesCS5A01G557900 chr5A 100.000 812 0 0 1504 2315 708680454 708681265 0.000000e+00 1500.0
3 TraesCS5A01G557900 chr4A 96.729 1345 43 1 1 1345 26019051 26017708 0.000000e+00 2239.0
4 TraesCS5A01G557900 chr4A 96.296 54 2 0 1504 1557 437881524 437881577 3.170000e-14 89.8
5 TraesCS5A01G557900 chr2A 94.192 1343 77 1 1 1343 41173885 41172544 0.000000e+00 2047.0
6 TraesCS5A01G557900 chr2A 96.855 477 15 0 1839 2315 684902032 684901556 0.000000e+00 798.0
7 TraesCS5A01G557900 chr2A 93.532 201 13 0 1504 1704 684902484 684902284 1.340000e-77 300.0
8 TraesCS5A01G557900 chr4B 89.948 1343 134 1 2 1344 38781297 38782638 0.000000e+00 1731.0
9 TraesCS5A01G557900 chr4B 88.682 1343 150 2 2 1344 495080517 495081857 0.000000e+00 1637.0
10 TraesCS5A01G557900 chr4B 92.593 837 62 0 509 1345 651870283 651869447 0.000000e+00 1203.0
11 TraesCS5A01G557900 chr4B 92.262 840 61 2 509 1344 651808033 651807194 0.000000e+00 1188.0
12 TraesCS5A01G557900 chr1B 89.607 1347 134 4 2 1343 401562559 401563904 0.000000e+00 1707.0
13 TraesCS5A01G557900 chr1B 87.350 585 43 19 1560 2116 559130485 559131066 1.940000e-180 641.0
14 TraesCS5A01G557900 chr1B 87.456 574 49 12 1560 2116 593471031 593471598 6.970000e-180 640.0
15 TraesCS5A01G557900 chr1B 84.444 585 44 19 1560 2116 559144683 559145248 1.220000e-147 532.0
16 TraesCS5A01G557900 chr1B 84.274 585 45 19 1560 2116 559137759 559138324 5.670000e-146 527.0
17 TraesCS5A01G557900 chr1B 97.537 203 5 0 2113 2315 593471776 593471978 4.730000e-92 348.0
18 TraesCS5A01G557900 chr1B 96.552 203 7 0 2113 2315 559138504 559138706 1.020000e-88 337.0
19 TraesCS5A01G557900 chr1B 96.552 203 7 0 2113 2315 559145428 559145630 1.020000e-88 337.0
20 TraesCS5A01G557900 chr1B 95.567 203 9 0 2113 2315 559131246 559131448 2.220000e-85 326.0
21 TraesCS5A01G557900 chr1B 92.958 213 15 0 1758 1970 593471509 593471721 6.210000e-81 311.0
22 TraesCS5A01G557900 chr1B 90.698 215 18 1 1758 1970 559138235 559138449 3.760000e-73 285.0
23 TraesCS5A01G557900 chr1B 90.187 214 19 1 1759 1970 559145160 559145373 6.300000e-71 278.0
24 TraesCS5A01G557900 chr1B 96.296 54 2 0 1504 1557 199680293 199680240 3.170000e-14 89.8
25 TraesCS5A01G557900 chr2B 88.039 1346 156 5 2 1345 796308893 796310235 0.000000e+00 1589.0
26 TraesCS5A01G557900 chr2B 87.476 1054 130 2 15 1068 675504498 675505549 0.000000e+00 1214.0
27 TraesCS5A01G557900 chr7A 97.164 529 15 0 1787 2315 106817387 106816859 0.000000e+00 894.0
28 TraesCS5A01G557900 chr7A 95.536 224 10 0 1504 1727 106818001 106817778 2.190000e-95 359.0
29 TraesCS5A01G557900 chr7A 92.308 65 4 1 1504 1568 632041123 632041060 8.810000e-15 91.6
30 TraesCS5A01G557900 chr7A 96.226 53 2 0 1505 1557 182375100 182375152 1.140000e-13 87.9
31 TraesCS5A01G557900 chr3B 88.596 570 49 9 1556 2116 732054726 732054164 0.000000e+00 678.0
32 TraesCS5A01G557900 chr3B 96.552 203 7 0 2113 2315 732053986 732053784 1.020000e-88 337.0
33 TraesCS5A01G557900 chr3B 91.667 216 17 1 1758 1973 732054252 732054038 4.840000e-77 298.0
34 TraesCS5A01G557900 chr3B 94.737 57 3 0 1504 1560 732054833 732054777 3.170000e-14 89.8
35 TraesCS5A01G557900 chr3B 93.478 46 3 0 1678 1723 795777067 795777022 4.130000e-08 69.4
36 TraesCS5A01G557900 chr6B 87.826 115 13 1 2172 2285 462173552 462173666 1.440000e-27 134.0
37 TraesCS5A01G557900 chr6B 96.429 56 2 0 1504 1559 542942029 542942084 2.450000e-15 93.5
38 TraesCS5A01G557900 chr6B 96.000 50 2 0 1675 1724 560626961 560626912 5.300000e-12 82.4
39 TraesCS5A01G557900 chr1D 88.288 111 11 2 2174 2283 32734666 32734775 5.190000e-27 132.0
40 TraesCS5A01G557900 chrUn 94.444 54 3 0 1504 1557 24864401 24864348 1.470000e-12 84.2
41 TraesCS5A01G557900 chrUn 93.617 47 3 0 1678 1724 49383775 49383821 1.150000e-08 71.3
42 TraesCS5A01G557900 chr3D 96.000 50 2 0 2174 2223 423837259 423837308 5.300000e-12 82.4


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 TraesCS5A01G557900 chr5A 708678951 708681265 2314 False 2020.000000 2540 100.000000 1 2315 2 chr5A.!!$F2 2314
1 TraesCS5A01G557900 chr5A 647000795 647002141 1346 False 2054.000000 2054 94.209000 1 1346 1 chr5A.!!$F1 1345
2 TraesCS5A01G557900 chr4A 26017708 26019051 1343 True 2239.000000 2239 96.729000 1 1345 1 chr4A.!!$R1 1344
3 TraesCS5A01G557900 chr2A 41172544 41173885 1341 True 2047.000000 2047 94.192000 1 1343 1 chr2A.!!$R1 1342
4 TraesCS5A01G557900 chr2A 684901556 684902484 928 True 549.000000 798 95.193500 1504 2315 2 chr2A.!!$R2 811
5 TraesCS5A01G557900 chr4B 38781297 38782638 1341 False 1731.000000 1731 89.948000 2 1344 1 chr4B.!!$F1 1342
6 TraesCS5A01G557900 chr4B 495080517 495081857 1340 False 1637.000000 1637 88.682000 2 1344 1 chr4B.!!$F2 1342
7 TraesCS5A01G557900 chr4B 651869447 651870283 836 True 1203.000000 1203 92.593000 509 1345 1 chr4B.!!$R2 836
8 TraesCS5A01G557900 chr4B 651807194 651808033 839 True 1188.000000 1188 92.262000 509 1344 1 chr4B.!!$R1 835
9 TraesCS5A01G557900 chr1B 401562559 401563904 1345 False 1707.000000 1707 89.607000 2 1343 1 chr1B.!!$F1 1341
10 TraesCS5A01G557900 chr1B 559130485 559131448 963 False 483.500000 641 91.458500 1560 2315 2 chr1B.!!$F2 755
11 TraesCS5A01G557900 chr1B 593471031 593471978 947 False 433.000000 640 92.650333 1560 2315 3 chr1B.!!$F5 755
12 TraesCS5A01G557900 chr1B 559137759 559138706 947 False 383.000000 527 90.508000 1560 2315 3 chr1B.!!$F3 755
13 TraesCS5A01G557900 chr1B 559144683 559145630 947 False 382.333333 532 90.394333 1560 2315 3 chr1B.!!$F4 755
14 TraesCS5A01G557900 chr2B 796308893 796310235 1342 False 1589.000000 1589 88.039000 2 1345 1 chr2B.!!$F2 1343
15 TraesCS5A01G557900 chr2B 675504498 675505549 1051 False 1214.000000 1214 87.476000 15 1068 1 chr2B.!!$F1 1053
16 TraesCS5A01G557900 chr7A 106816859 106818001 1142 True 626.500000 894 96.350000 1504 2315 2 chr7A.!!$R2 811
17 TraesCS5A01G557900 chr3B 732053784 732054833 1049 True 350.700000 678 92.888000 1504 2315 4 chr3B.!!$R2 811

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
578 580 0.26023 TGGTTGGTTTCCTTGCTGGA 59.74 50.0 0.0 0.0 44.51 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2051 2486 0.112995 TTTCTTCCCAGCAGCACCAT 59.887 50.0 0.0 0.0 0.0 3.55 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
62 63 3.500343 ACTGGGTTTCTGATTTCCTTGG 58.500 45.455 0.00 0.00 0.00 3.61
130 132 4.586001 GGGACATGGATATTGAGCACATTT 59.414 41.667 0.00 0.00 0.00 2.32
173 175 3.236816 GCCAACGTGATGATTTTCTGTG 58.763 45.455 0.00 0.00 0.00 3.66
379 381 2.358267 GCGACAGGTACACTAGCTACAT 59.642 50.000 0.00 0.00 34.67 2.29
423 425 1.664659 CTGTCTACGACGTCTACCTGG 59.335 57.143 14.70 0.00 34.95 4.45
472 474 3.804036 TCCTTCCATGCATTAGTAACCG 58.196 45.455 0.00 0.00 0.00 4.44
578 580 0.260230 TGGTTGGTTTCCTTGCTGGA 59.740 50.000 0.00 0.00 44.51 3.86
769 776 6.851836 TGAAGATATCCTAAAGGGGAAGATGT 59.148 38.462 0.00 0.00 39.02 3.06
1077 1084 3.068691 TCCTCGGAAGCCCTGTCG 61.069 66.667 0.00 0.00 0.00 4.35
1202 1209 7.091443 AGTAGACTTCAAAATAGAGTTGTCGG 58.909 38.462 0.00 0.00 0.00 4.79
1331 1338 7.713507 TCATATGTAATGAAACTCCCTTTACCG 59.286 37.037 1.90 0.00 0.00 4.02
1359 1366 1.256812 AAAAAGATGGAACCAGGCGG 58.743 50.000 0.00 0.00 38.77 6.13
1360 1367 0.611896 AAAAGATGGAACCAGGCGGG 60.612 55.000 0.79 0.79 44.81 6.13
1361 1368 2.499303 AAAGATGGAACCAGGCGGGG 62.499 60.000 8.94 2.25 42.91 5.73
1362 1369 3.407967 GATGGAACCAGGCGGGGA 61.408 66.667 8.94 0.00 42.91 4.81
1363 1370 3.406595 GATGGAACCAGGCGGGGAG 62.407 68.421 8.94 0.00 42.91 4.30
1557 1564 3.334691 CAGCCACGTCTCCTTTTATTCA 58.665 45.455 0.00 0.00 0.00 2.57
1585 1647 1.725182 TCTCCTCTTCCTTTCCCCTCT 59.275 52.381 0.00 0.00 0.00 3.69
1586 1648 2.933825 TCTCCTCTTCCTTTCCCCTCTA 59.066 50.000 0.00 0.00 0.00 2.43
1632 1694 2.764128 CCTAGCCGCCTTCTCCCA 60.764 66.667 0.00 0.00 0.00 4.37
1637 1699 3.036429 GCCGCCTTCTCCCACAGAT 62.036 63.158 0.00 0.00 0.00 2.90
1655 1733 2.012824 ATCCTCAGCCGCCTCCTCTA 62.013 60.000 0.00 0.00 0.00 2.43
1767 1884 2.687610 CCTCCCCAGGAAGCAGCAT 61.688 63.158 0.00 0.00 43.65 3.79
1771 1888 1.601419 CCCCAGGAAGCAGCATGTTG 61.601 60.000 5.00 5.00 39.31 3.33
2070 2505 0.112995 ATGGTGCTGCTGGGAAGAAA 59.887 50.000 0.00 0.00 0.00 2.52
2072 2507 0.538287 GGTGCTGCTGGGAAGAAAGT 60.538 55.000 0.00 0.00 0.00 2.66
2271 2889 6.886459 AGTGCTCTATGTAACCATGTGATTTT 59.114 34.615 0.00 0.00 32.29 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
62 63 0.813184 CCTCCATGCACCATTGTCAC 59.187 55.000 0.00 0.00 0.00 3.67
130 132 2.352388 CGGCGAGGGTTTGATCTTTAA 58.648 47.619 0.00 0.00 0.00 1.52
173 175 1.971695 CTCCTTTCCGGGTGCCAAC 60.972 63.158 0.00 0.00 0.00 3.77
379 381 7.014326 CAGGTGTCTATAGGATTTACACAGCTA 59.986 40.741 18.24 0.00 41.69 3.32
423 425 2.896801 CTCAACACCACACAGCGGC 61.897 63.158 0.00 0.00 0.00 6.53
578 580 1.277557 GGACATCTTCAGAGCACCTGT 59.722 52.381 6.11 0.00 43.38 4.00
1077 1084 3.189287 CCAACACACCATTAGTCAAGCTC 59.811 47.826 0.00 0.00 0.00 4.09
1346 1353 3.411517 CTCCCCGCCTGGTTCCAT 61.412 66.667 0.00 0.00 0.00 3.41
1557 1564 2.047443 GGAAGAGGAGAGGACGCGT 61.047 63.158 13.85 13.85 0.00 6.01
1585 1647 2.376109 GTGACGGAGGAGGAAGTGATA 58.624 52.381 0.00 0.00 0.00 2.15
1586 1648 1.187087 GTGACGGAGGAGGAAGTGAT 58.813 55.000 0.00 0.00 0.00 3.06
1632 1694 2.364842 AGGCGGCTGAGGATCTGT 60.365 61.111 12.25 0.00 36.33 3.41
1637 1699 2.690734 TAGAGGAGGCGGCTGAGGA 61.691 63.158 19.63 0.00 0.00 3.71
1756 1843 0.250467 ACGACAACATGCTGCTTCCT 60.250 50.000 0.00 0.00 0.00 3.36
2051 2486 0.112995 TTTCTTCCCAGCAGCACCAT 59.887 50.000 0.00 0.00 0.00 3.55
2271 2889 4.154556 CGTTAGGCGGTTTTTGGAAGAATA 59.845 41.667 0.00 0.00 36.85 1.75


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

AutoCloner maintained by Alex Coulton.