Multiple sequence alignment - TraesCS5B01G561900

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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 TraesCS5B01G561900 chr5B 100.000 2498 0 0 1 2498 708181977 708179480 0.000000e+00 4614
1 TraesCS5B01G561900 chr5B 90.143 2171 128 28 1 2164 498514148 498516239 0.000000e+00 2745
2 TraesCS5B01G561900 chr5B 94.667 75 4 0 2424 2498 498521453 498521527 1.570000e-22 117
3 TraesCS5B01G561900 chr1D 93.797 1983 99 14 3 1968 829095 831070 0.000000e+00 2959
4 TraesCS5B01G561900 chr1D 88.844 2456 163 38 115 2498 335412440 335414856 0.000000e+00 2915
5 TraesCS5B01G561900 chr1D 90.637 534 34 9 1966 2498 843678 844196 0.000000e+00 695
6 TraesCS5B01G561900 chr6B 87.262 2151 190 51 1 2095 12466006 12468128 0.000000e+00 2377
7 TraesCS5B01G561900 chr5D 91.391 1754 100 28 3 1724 274114297 274116031 0.000000e+00 2355
8 TraesCS5B01G561900 chr5D 87.612 1445 135 27 1028 2457 257416325 257414910 0.000000e+00 1637
9 TraesCS5B01G561900 chr7B 84.933 2396 241 69 192 2498 53112094 53109730 0.000000e+00 2314
10 TraesCS5B01G561900 chr3B 90.760 1710 132 17 1 1701 638378303 638379995 0.000000e+00 2259
11 TraesCS5B01G561900 chr3B 92.760 1395 70 10 1133 2498 609965006 609966398 0.000000e+00 1988
12 TraesCS5B01G561900 chr3D 89.905 1783 102 32 3 1730 502047850 502046091 0.000000e+00 2224
13 TraesCS5B01G561900 chr2B 91.211 1627 85 18 874 2498 80094011 80092441 0.000000e+00 2159
14 TraesCS5B01G561900 chr2B 88.344 1510 128 26 890 2375 706691347 706689862 0.000000e+00 1770
15 TraesCS5B01G561900 chr2B 92.191 794 49 8 92 879 80103327 80102541 0.000000e+00 1110
16 TraesCS5B01G561900 chr6D 89.032 1714 118 27 3 1701 63805944 63807602 0.000000e+00 2060
17 TraesCS5B01G561900 chr1B 87.385 975 83 17 1391 2335 168421677 168422641 0.000000e+00 1083
18 TraesCS5B01G561900 chr1B 89.583 816 65 10 1 814 572992192 572991395 0.000000e+00 1018
19 TraesCS5B01G561900 chr4B 92.308 754 52 4 1 753 37138305 37139053 0.000000e+00 1066
20 TraesCS5B01G561900 chr4A 92.382 617 38 2 1883 2498 708361668 708361060 0.000000e+00 870
21 TraesCS5B01G561900 chr4D 90.610 607 42 7 1713 2315 97479339 97478744 0.000000e+00 791


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 TraesCS5B01G561900 chr5B 708179480 708181977 2497 True 4614 4614 100.000 1 2498 1 chr5B.!!$R1 2497
1 TraesCS5B01G561900 chr5B 498514148 498516239 2091 False 2745 2745 90.143 1 2164 1 chr5B.!!$F1 2163
2 TraesCS5B01G561900 chr1D 829095 831070 1975 False 2959 2959 93.797 3 1968 1 chr1D.!!$F1 1965
3 TraesCS5B01G561900 chr1D 335412440 335414856 2416 False 2915 2915 88.844 115 2498 1 chr1D.!!$F3 2383
4 TraesCS5B01G561900 chr1D 843678 844196 518 False 695 695 90.637 1966 2498 1 chr1D.!!$F2 532
5 TraesCS5B01G561900 chr6B 12466006 12468128 2122 False 2377 2377 87.262 1 2095 1 chr6B.!!$F1 2094
6 TraesCS5B01G561900 chr5D 274114297 274116031 1734 False 2355 2355 91.391 3 1724 1 chr5D.!!$F1 1721
7 TraesCS5B01G561900 chr5D 257414910 257416325 1415 True 1637 1637 87.612 1028 2457 1 chr5D.!!$R1 1429
8 TraesCS5B01G561900 chr7B 53109730 53112094 2364 True 2314 2314 84.933 192 2498 1 chr7B.!!$R1 2306
9 TraesCS5B01G561900 chr3B 638378303 638379995 1692 False 2259 2259 90.760 1 1701 1 chr3B.!!$F2 1700
10 TraesCS5B01G561900 chr3B 609965006 609966398 1392 False 1988 1988 92.760 1133 2498 1 chr3B.!!$F1 1365
11 TraesCS5B01G561900 chr3D 502046091 502047850 1759 True 2224 2224 89.905 3 1730 1 chr3D.!!$R1 1727
12 TraesCS5B01G561900 chr2B 80092441 80094011 1570 True 2159 2159 91.211 874 2498 1 chr2B.!!$R1 1624
13 TraesCS5B01G561900 chr2B 706689862 706691347 1485 True 1770 1770 88.344 890 2375 1 chr2B.!!$R3 1485
14 TraesCS5B01G561900 chr2B 80102541 80103327 786 True 1110 1110 92.191 92 879 1 chr2B.!!$R2 787
15 TraesCS5B01G561900 chr6D 63805944 63807602 1658 False 2060 2060 89.032 3 1701 1 chr6D.!!$F1 1698
16 TraesCS5B01G561900 chr1B 168421677 168422641 964 False 1083 1083 87.385 1391 2335 1 chr1B.!!$F1 944
17 TraesCS5B01G561900 chr1B 572991395 572992192 797 True 1018 1018 89.583 1 814 1 chr1B.!!$R1 813
18 TraesCS5B01G561900 chr4B 37138305 37139053 748 False 1066 1066 92.308 1 753 1 chr4B.!!$F1 752
19 TraesCS5B01G561900 chr4A 708361060 708361668 608 True 870 870 92.382 1883 2498 1 chr4A.!!$R1 615
20 TraesCS5B01G561900 chr4D 97478744 97479339 595 True 791 791 90.610 1713 2315 1 chr4D.!!$R1 602

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
227 264 0.612732 CTGCCATGCCTTCCTGGAAA 60.613 55.0 10.86 0.00 38.35 3.13 F
745 867 1.107538 GGCCTCACATGATGCAGCAT 61.108 55.0 12.63 12.63 37.41 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1081 1244 0.829182 AGCTTGGCCAACTCCCTTTG 60.829 55.000 16.05 3.07 0.0 2.77 R
2011 2299 1.974236 CCTCCTCCTTCTCTGTTGTGT 59.026 52.381 0.00 0.00 0.0 3.72 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
39 40 1.816074 GGTTGTTGATGGCCGTTAGA 58.184 50.000 0.00 0.00 0.00 2.10
118 133 3.386237 GCTCGCTCACTCCCCTGT 61.386 66.667 0.00 0.00 0.00 4.00
153 185 1.463214 TCCCACTCCCCTGCTTCAA 60.463 57.895 0.00 0.00 0.00 2.69
166 203 0.806102 GCTTCAATACGAGCTCGCCA 60.806 55.000 34.83 23.43 44.43 5.69
227 264 0.612732 CTGCCATGCCTTCCTGGAAA 60.613 55.000 10.86 0.00 38.35 3.13
381 439 6.373216 TGCTTAGTTAGTGTTGTTGTTGTCTT 59.627 34.615 0.00 0.00 0.00 3.01
500 585 7.883391 TTCACTGTTTAGGGTTAATGAACAA 57.117 32.000 0.00 0.00 37.29 2.83
577 672 2.304761 GGAGGAACCAGACACCATTGTA 59.695 50.000 0.00 0.00 35.69 2.41
590 685 2.291605 ACCATTGTAGAGCCCCTTTTCC 60.292 50.000 0.00 0.00 0.00 3.13
745 867 1.107538 GGCCTCACATGATGCAGCAT 61.108 55.000 12.63 12.63 37.41 3.79
749 871 3.444916 CCTCACATGATGCAGCATTTTC 58.555 45.455 16.22 0.00 0.00 2.29
764 886 8.689061 TGCAGCATTTTCTTACTGATATGAAAT 58.311 29.630 0.00 0.00 35.51 2.17
880 1039 7.476540 TGGAACTGAAATTAGCTAGTACTCA 57.523 36.000 0.00 0.00 0.00 3.41
935 1094 3.465871 GCAAATGGTGTGAATTGTGGTT 58.534 40.909 0.00 0.00 0.00 3.67
936 1095 3.494251 GCAAATGGTGTGAATTGTGGTTC 59.506 43.478 0.00 0.00 0.00 3.62
972 1132 1.562672 GGCCTTGGCCTCCAGTTCTA 61.563 60.000 22.47 0.00 33.81 2.10
1044 1204 5.311121 TGGAAGGGTACTTGACAAGGATAAA 59.689 40.000 19.16 0.00 36.97 1.40
1066 1226 1.434188 TGAGAAGGAGTTGGCCAAGA 58.566 50.000 21.21 0.00 0.00 3.02
1081 1244 4.943705 TGGCCAAGATTAAGAGTGAACATC 59.056 41.667 0.61 0.00 0.00 3.06
1108 1271 3.347216 GAGTTGGCCAAGCTTAAGATGA 58.653 45.455 21.21 0.00 0.00 2.92
1206 1391 2.158726 GGTGGACAAGAAGGTGTACCAA 60.159 50.000 3.56 0.00 38.89 3.67
1379 1573 4.702131 GGCTATGAAGGATGTTGAAGTTGT 59.298 41.667 0.00 0.00 0.00 3.32
1451 1645 4.019411 TGAGCTGTTGAAAGATGGGTATGA 60.019 41.667 0.00 0.00 0.00 2.15
1537 1736 4.422073 TGAAGTACATCCAAGGCCTATG 57.578 45.455 5.16 9.39 0.00 2.23
1828 2090 5.530915 CCAGTAGTCTGTGACCAAATGAAAA 59.469 40.000 0.00 0.00 39.82 2.29
1887 2156 4.166144 CACTGTCAATATAAACCCCTCCCT 59.834 45.833 0.00 0.00 0.00 4.20
1961 2249 2.247372 TGGATCCTGACATGGACCTAGA 59.753 50.000 14.23 0.00 39.17 2.43
2011 2299 2.530151 AGGTGAGGCCTCCAGCAA 60.530 61.111 29.95 8.09 46.96 3.91
2071 2365 2.361610 CCGCCCAGGACAAGCAAT 60.362 61.111 0.00 0.00 45.00 3.56
2124 2418 1.467734 GTGCTGGAGAAGTGCAATGAG 59.532 52.381 0.00 0.00 38.50 2.90
2236 2530 1.705873 TCCAGCTACTAGGGCTAAGC 58.294 55.000 11.24 4.20 38.03 3.09
2244 2538 3.363410 TAGGGCTAAGCGGGGTCGA 62.363 63.158 0.00 0.00 39.00 4.20
2407 2761 5.878332 TGTAATACTGGTGTTTGATGCTG 57.122 39.130 0.00 0.00 0.00 4.41
2417 2771 2.751259 TGTTTGATGCTGCTCTGAATCC 59.249 45.455 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 1.072489 TGGTCTAACGGCCATCAACAA 59.928 47.619 2.24 0.00 0.00 2.83
118 133 2.038007 AGCAGGGGAGAGAGCGAA 59.962 61.111 0.00 0.00 0.00 4.70
153 185 4.570663 GCGGTGGCGAGCTCGTAT 62.571 66.667 34.46 0.00 42.22 3.06
166 203 3.916392 CTCAAAGACGGCGAGCGGT 62.916 63.158 16.62 8.01 0.00 5.68
197 234 1.751927 CATGGCAGCAAGGAGGTCC 60.752 63.158 0.00 0.00 0.00 4.46
227 264 1.275291 TCGGAGCTCATTTCCTCGTTT 59.725 47.619 17.19 0.00 32.34 3.60
381 439 8.152898 CCTCACTAATCAAGATCCATATCACAA 58.847 37.037 0.00 0.00 34.28 3.33
500 585 6.418101 ACTCAATACCACAATCAACTAGCAT 58.582 36.000 0.00 0.00 0.00 3.79
577 672 2.757077 CCACGGAAAAGGGGCTCT 59.243 61.111 0.00 0.00 0.00 4.09
590 685 1.283793 CAAGCTCAAGTTGGCCACG 59.716 57.895 3.88 0.00 0.00 4.94
880 1039 9.062524 TGTAAATGTGATAAGTTAGTGCAAGTT 57.937 29.630 0.00 0.00 34.15 2.66
935 1094 1.191535 CCCATCAACCCACTCTACGA 58.808 55.000 0.00 0.00 0.00 3.43
936 1095 0.462047 GCCCATCAACCCACTCTACG 60.462 60.000 0.00 0.00 0.00 3.51
972 1132 3.498774 AGCTTGGACAAACATCTCTGT 57.501 42.857 0.00 0.00 37.12 3.41
1044 1204 2.978156 TGGCCAACTCCTTCTCAAAT 57.022 45.000 0.61 0.00 0.00 2.32
1066 1226 6.784031 ACTCCCTTTGATGTTCACTCTTAAT 58.216 36.000 0.00 0.00 0.00 1.40
1081 1244 0.829182 AGCTTGGCCAACTCCCTTTG 60.829 55.000 16.05 3.07 0.00 2.77
1108 1271 5.818857 ACTCAATGCAAAGCTTGTCATTTTT 59.181 32.000 18.39 7.71 36.20 1.94
1206 1391 4.079730 AGTTCTTCCTCCTCCACTTGTTTT 60.080 41.667 0.00 0.00 0.00 2.43
1379 1573 7.093552 CCTTCTCCTTCTTAAGAACATCTCTGA 60.094 40.741 13.99 3.69 33.37 3.27
1435 1629 4.299586 TGCTGTCATACCCATCTTTCAA 57.700 40.909 0.00 0.00 0.00 2.69
1451 1645 2.634940 TGCTCTAACTTCTCCTTGCTGT 59.365 45.455 0.00 0.00 0.00 4.40
1537 1736 5.070580 AGACAGTTAGGCCACATCCTTATAC 59.929 44.000 5.01 0.00 37.66 1.47
1769 1992 8.198109 GCCCAATACCACTGTACATATCTATAG 58.802 40.741 0.00 0.00 0.00 1.31
1828 2090 4.786454 TGGGTTTTAGTAGGCCTAAGTCAT 59.214 41.667 15.83 0.97 36.98 3.06
1887 2156 2.235761 GGCTGGGAAAGGGTGGGTA 61.236 63.158 0.00 0.00 0.00 3.69
1961 2249 3.012959 TCCCTCCTCCTCTGTTACATCTT 59.987 47.826 0.00 0.00 0.00 2.40
2011 2299 1.974236 CCTCCTCCTTCTCTGTTGTGT 59.026 52.381 0.00 0.00 0.00 3.72
2244 2538 2.159240 TCAGTCATAGCGCACGAAGAAT 60.159 45.455 11.47 0.00 0.00 2.40
2407 2761 9.664332 AAATACATAGATACATGGATTCAGAGC 57.336 33.333 0.00 0.00 38.30 4.09
2440 2794 6.741992 TCCACAACATACATTCATTCAGAC 57.258 37.500 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.