Multiple sequence alignment - TraesCS5A01G322000

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 TraesCS5A01G322000 chr5A 100.000 2477 0 0 1 2477 534624071 534621595 0 4575
1 TraesCS5A01G322000 chr5A 89.050 1169 106 15 1 1154 107748853 107750014 0 1430
2 TraesCS5A01G322000 chr5A 79.614 1501 282 19 2 1485 81479727 81481220 0 1055
3 TraesCS5A01G322000 chr3D 89.870 1382 112 15 1 1367 11552120 11553488 0 1751
4 TraesCS5A01G322000 chr3D 87.450 996 104 10 517 1503 452411137 452410154 0 1127
5 TraesCS5A01G322000 chr2A 82.577 1521 231 22 1 1506 728563699 728565200 0 1310
6 TraesCS5A01G322000 chr5D 90.564 975 68 16 1506 2477 421213131 421212178 0 1269
7 TraesCS5A01G322000 chr4B 82.866 1354 198 20 53 1390 560005196 560003861 0 1184
8 TraesCS5A01G322000 chr5B 80.146 1511 283 14 8 1505 8879672 8878166 0 1112
9 TraesCS5A01G322000 chr5B 81.951 892 139 14 1506 2384 507569407 507568525 0 736
10 TraesCS5A01G322000 chr1D 87.022 994 111 14 1 982 55395550 55394563 0 1105
11 TraesCS5A01G322000 chr1B 85.141 996 124 19 1 982 90872596 90871611 0 998
12 TraesCS5A01G322000 chr2D 79.119 1475 278 26 30 1485 49897319 49895856 0 990
13 TraesCS5A01G322000 chr2B 79.914 1389 245 30 137 1503 625421391 625420015 0 989
14 TraesCS5A01G322000 chr1A 78.861 1457 280 23 1 1438 521871667 521870220 0 959
15 TraesCS5A01G322000 chr4D 77.279 1514 307 29 12 1506 312917233 312918728 0 856


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 TraesCS5A01G322000 chr5A 534621595 534624071 2476 True 4575 4575 100.000 1 2477 1 chr5A.!!$R1 2476
1 TraesCS5A01G322000 chr5A 107748853 107750014 1161 False 1430 1430 89.050 1 1154 1 chr5A.!!$F2 1153
2 TraesCS5A01G322000 chr5A 81479727 81481220 1493 False 1055 1055 79.614 2 1485 1 chr5A.!!$F1 1483
3 TraesCS5A01G322000 chr3D 11552120 11553488 1368 False 1751 1751 89.870 1 1367 1 chr3D.!!$F1 1366
4 TraesCS5A01G322000 chr3D 452410154 452411137 983 True 1127 1127 87.450 517 1503 1 chr3D.!!$R1 986
5 TraesCS5A01G322000 chr2A 728563699 728565200 1501 False 1310 1310 82.577 1 1506 1 chr2A.!!$F1 1505
6 TraesCS5A01G322000 chr5D 421212178 421213131 953 True 1269 1269 90.564 1506 2477 1 chr5D.!!$R1 971
7 TraesCS5A01G322000 chr4B 560003861 560005196 1335 True 1184 1184 82.866 53 1390 1 chr4B.!!$R1 1337
8 TraesCS5A01G322000 chr5B 8878166 8879672 1506 True 1112 1112 80.146 8 1505 1 chr5B.!!$R1 1497
9 TraesCS5A01G322000 chr5B 507568525 507569407 882 True 736 736 81.951 1506 2384 1 chr5B.!!$R2 878
10 TraesCS5A01G322000 chr1D 55394563 55395550 987 True 1105 1105 87.022 1 982 1 chr1D.!!$R1 981
11 TraesCS5A01G322000 chr1B 90871611 90872596 985 True 998 998 85.141 1 982 1 chr1B.!!$R1 981
12 TraesCS5A01G322000 chr2D 49895856 49897319 1463 True 990 990 79.119 30 1485 1 chr2D.!!$R1 1455
13 TraesCS5A01G322000 chr2B 625420015 625421391 1376 True 989 989 79.914 137 1503 1 chr2B.!!$R1 1366
14 TraesCS5A01G322000 chr1A 521870220 521871667 1447 True 959 959 78.861 1 1438 1 chr1A.!!$R1 1437
15 TraesCS5A01G322000 chr4D 312917233 312918728 1495 False 856 856 77.279 12 1506 1 chr4D.!!$F1 1494


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
199 206 0.179048 GATGCATGGATCCCACACGA 60.179 55.0 15.86 0.0 35.8 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1851 1920 0.755327 GACCACAACAAGGCCAAGGT 60.755 55.0 5.01 0.99 0.0 3.5 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
159 165 0.960364 TCTGGCGAGTTGGAAATGGC 60.960 55.000 0.00 0.00 0.00 4.40
163 169 1.669795 GGCGAGTTGGAAATGGCAAAG 60.670 52.381 0.00 0.00 0.00 2.77
199 206 0.179048 GATGCATGGATCCCACACGA 60.179 55.000 15.86 0.00 35.80 4.35
210 217 0.390603 CCCACACGACGCAAATAGGA 60.391 55.000 0.00 0.00 0.00 2.94
305 312 1.606350 GACGAAGACTTGGTGCGACG 61.606 60.000 7.66 0.00 0.00 5.12
528 552 6.602410 TGGTGCAAGATTTGGAAATTATCA 57.398 33.333 0.00 0.00 30.97 2.15
539 563 3.631686 TGGAAATTATCATGCCCGACAAG 59.368 43.478 0.00 0.00 0.00 3.16
544 572 2.799126 ATCATGCCCGACAAGGTAAA 57.201 45.000 0.00 0.00 38.74 2.01
545 573 2.570415 TCATGCCCGACAAGGTAAAA 57.430 45.000 0.00 0.00 38.74 1.52
619 651 6.484364 TGCCAATAGACACATGAAGATCTA 57.516 37.500 0.00 1.20 0.00 1.98
665 703 9.490379 GGACCAGAAGATACGAAATATGTATTT 57.510 33.333 0.00 0.00 38.51 1.40
747 787 3.359033 AGGCATGTGCTATTGATTGTGT 58.641 40.909 4.84 0.00 41.70 3.72
771 811 5.185635 TGGGAGAGGCAATACTTGAATTTTG 59.814 40.000 0.00 0.00 0.00 2.44
855 896 8.706322 TCACTATAACAGCTTGGTATCTATGA 57.294 34.615 0.00 0.00 31.72 2.15
858 899 9.314133 ACTATAACAGCTTGGTATCTATGATGA 57.686 33.333 0.00 0.00 31.72 2.92
997 1042 0.548682 AGGTGGATGGAGCAGACCTT 60.549 55.000 0.00 0.00 32.97 3.50
1066 1114 2.284331 TTAGAGGCACGGCTGGGA 60.284 61.111 0.00 0.00 0.00 4.37
1082 1141 3.175438 TGGGACTGTTCTCAGAGATGA 57.825 47.619 0.00 0.00 43.76 2.92
1083 1142 2.828520 TGGGACTGTTCTCAGAGATGAC 59.171 50.000 0.00 0.00 43.76 3.06
1084 1143 2.828520 GGGACTGTTCTCAGAGATGACA 59.171 50.000 0.00 2.84 43.76 3.58
1085 1144 3.259374 GGGACTGTTCTCAGAGATGACAA 59.741 47.826 0.00 0.00 43.76 3.18
1086 1145 4.081198 GGGACTGTTCTCAGAGATGACAAT 60.081 45.833 0.00 0.00 43.76 2.71
1247 1309 5.892160 ATGGAAGTCATCAACACAATGAG 57.108 39.130 0.00 0.00 33.94 2.90
1324 1390 4.589216 TTGGCTTGTGATTTTCCTCTTG 57.411 40.909 0.00 0.00 0.00 3.02
1331 1397 4.326826 TGTGATTTTCCTCTTGCTAGGTG 58.673 43.478 0.00 0.00 37.91 4.00
1360 1426 7.716612 ACATTGTAATAGGGAAGCAAATAAGC 58.283 34.615 0.00 0.00 0.00 3.09
1367 1433 1.064654 GGAAGCAAATAAGCTGGCTCG 59.935 52.381 0.00 0.00 45.89 5.03
1397 1463 4.343609 GCTAGGTTAGCGAAATTTTCTGC 58.656 43.478 14.13 14.13 42.62 4.26
1408 1474 2.270352 ATTTTCTGCGACAAGGGACA 57.730 45.000 0.00 0.00 0.00 4.02
1550 1617 9.683069 ATTGCAATAAAACTAGCTATATTGTGC 57.317 29.630 11.02 15.37 37.81 4.57
1634 1702 2.445155 GCCCCCTGGTCATTGGTT 59.555 61.111 0.00 0.00 0.00 3.67
1640 1708 1.354368 CCCTGGTCATTGGTTGTAGGT 59.646 52.381 0.00 0.00 0.00 3.08
1704 1773 1.730064 CGTGGAATAACTCGGTGTTGG 59.270 52.381 5.75 0.00 39.55 3.77
1707 1776 1.003928 GGAATAACTCGGTGTTGGGGT 59.996 52.381 5.75 0.00 39.55 4.95
1751 1820 0.529337 CGATCTTGCATGCGTCCTCT 60.529 55.000 14.09 0.00 0.00 3.69
1801 1870 2.070639 GGAGCTGTGGGTTCTCCTT 58.929 57.895 0.00 0.00 42.31 3.36
1873 1942 0.467290 TTGGCCTTGTTGTGGTCCTC 60.467 55.000 3.32 0.00 0.00 3.71
1885 1954 4.779733 GTCCTCCTCCTCGGCCCA 62.780 72.222 0.00 0.00 0.00 5.36
1969 2048 2.494059 CTCGCCTGACTTCCAAAGAAA 58.506 47.619 0.00 0.00 0.00 2.52
2009 2088 4.457496 CACGCGCCACCTCCTCAT 62.457 66.667 5.73 0.00 0.00 2.90
2011 2090 4.457496 CGCGCCACCTCCTCATGT 62.457 66.667 0.00 0.00 0.00 3.21
2036 2115 1.559831 GAACTTGCCAAGCAACACAC 58.440 50.000 3.88 0.00 43.99 3.82
2088 2167 2.300967 CCTACTTGCCCCTCAGCCA 61.301 63.158 0.00 0.00 0.00 4.75
2100 2179 2.121992 CTCAGCCAGAGCCCAACACT 62.122 60.000 0.00 0.00 41.25 3.55
2124 2203 4.129148 CCTAGGGGGTGCTTGGGC 62.129 72.222 0.00 0.00 39.26 5.36
2149 2228 3.981212 TGTGACATCTCCTATGGTGAGA 58.019 45.455 0.00 0.00 42.68 3.27
2160 2239 4.026744 CCTATGGTGAGAAAGAGGTCAGA 58.973 47.826 0.00 0.00 0.00 3.27
2197 2276 1.133598 CGTCGGTGTAGCAAGGACATA 59.866 52.381 0.00 0.00 0.00 2.29
2254 2333 1.243902 GTCCTTGGTGCCGATTTTGA 58.756 50.000 0.00 0.00 0.00 2.69
2263 2342 2.120909 CCGATTTTGAGGGCGGCAT 61.121 57.895 12.47 2.18 37.08 4.40
2264 2343 1.064621 CGATTTTGAGGGCGGCATG 59.935 57.895 12.47 0.00 0.00 4.06
2265 2344 1.375853 CGATTTTGAGGGCGGCATGA 61.376 55.000 12.47 0.00 0.00 3.07
2266 2345 0.817013 GATTTTGAGGGCGGCATGAA 59.183 50.000 12.47 0.00 0.00 2.57
2267 2346 1.410153 GATTTTGAGGGCGGCATGAAT 59.590 47.619 12.47 3.70 0.00 2.57
2268 2347 0.817013 TTTTGAGGGCGGCATGAATC 59.183 50.000 12.47 0.78 0.00 2.52
2269 2348 1.375853 TTTGAGGGCGGCATGAATCG 61.376 55.000 12.47 0.00 0.00 3.34
2270 2349 2.974698 GAGGGCGGCATGAATCGG 60.975 66.667 12.47 0.00 0.00 4.18
2271 2350 4.569180 AGGGCGGCATGAATCGGG 62.569 66.667 12.47 0.00 0.00 5.14
2333 2430 2.049248 GCGACGACGGGTTGGTAA 60.049 61.111 9.67 0.00 40.15 2.85
2366 2463 1.816863 GACCGTGAGAGTGGAGGCAA 61.817 60.000 0.00 0.00 0.00 4.52
2389 2486 0.107017 CTGTTGGAATCGGCTGGGAT 60.107 55.000 0.00 0.00 0.00 3.85
2399 2496 2.599597 GCTGGGATGGATGCAGGT 59.400 61.111 0.00 0.00 0.00 4.00
2401 2498 1.152819 CTGGGATGGATGCAGGTGG 60.153 63.158 0.00 0.00 0.00 4.61
2409 2506 1.271840 GGATGCAGGTGGGGTAGTGA 61.272 60.000 0.00 0.00 0.00 3.41
2426 2523 3.417101 AGTGATAACGTTCAAATGGGCA 58.583 40.909 2.82 0.00 0.00 5.36
2433 2530 0.667184 GTTCAAATGGGCAGCGGTTG 60.667 55.000 0.00 0.00 0.00 3.77
2465 2563 2.930682 GCTGCGTTTTTGGTTTTGGTAA 59.069 40.909 0.00 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
102 104 5.995282 CAGAGAATTTACACCCGCCATAATA 59.005 40.000 0.00 0.00 0.00 0.98
159 165 9.716531 TGCATCTCTCCAAATATCTATACTTTG 57.283 33.333 0.00 0.00 0.00 2.77
163 169 8.481314 TCCATGCATCTCTCCAAATATCTATAC 58.519 37.037 0.00 0.00 0.00 1.47
199 206 7.339466 AGGAGTGATAATTTTTCCTATTTGCGT 59.661 33.333 0.00 0.00 36.54 5.24
265 272 2.819608 CCCAACAATTCGTGACTGGATT 59.180 45.455 0.00 0.00 36.44 3.01
305 312 3.887716 AGCATCAATTGGCCATAGAGTTC 59.112 43.478 6.09 0.00 0.00 3.01
410 420 4.245660 CTCCAAGTAAGCAGATCGAACAA 58.754 43.478 0.00 0.00 0.00 2.83
544 572 5.525378 TGCAAAGTACGCCAAATGAATTTTT 59.475 32.000 0.00 0.00 0.00 1.94
545 573 5.053145 TGCAAAGTACGCCAAATGAATTTT 58.947 33.333 0.00 0.00 0.00 1.82
619 651 4.804420 TCGAGGGGCAGATGGGCT 62.804 66.667 0.00 0.00 42.84 5.19
771 811 6.112058 AGTTCTTGATCTGGCATAAGAAGTC 58.888 40.000 13.20 6.48 37.98 3.01
855 896 8.813951 TCATGAATCAGCTTACATCTATCTCAT 58.186 33.333 0.00 0.00 0.00 2.90
858 899 8.095792 CCTTCATGAATCAGCTTACATCTATCT 58.904 37.037 8.96 0.00 0.00 1.98
1066 1114 5.735285 TCATTGTCATCTCTGAGAACAGT 57.265 39.130 12.00 6.58 43.81 3.55
1086 1145 6.258287 CAGTTTCTGCCAACAATGAATTTTCA 59.742 34.615 0.00 0.00 42.14 2.69
1247 1309 1.160329 CGCCGATTGTCCTCCATTCC 61.160 60.000 0.00 0.00 0.00 3.01
1324 1390 5.527582 CCCTATTACAATGTTCACACCTAGC 59.472 44.000 0.00 0.00 0.00 3.42
1331 1397 6.509418 TTGCTTCCCTATTACAATGTTCAC 57.491 37.500 0.00 0.00 0.00 3.18
1360 1426 1.354040 CTAGCAAGTTCACGAGCCAG 58.646 55.000 0.00 0.00 0.00 4.85
1397 1463 1.873591 CCTCAAAACTGTCCCTTGTCG 59.126 52.381 0.00 0.00 0.00 4.35
1408 1474 3.160269 CATTCAAGGGCTCCTCAAAACT 58.840 45.455 0.00 0.00 30.89 2.66
1548 1615 7.046033 GTGAGTATTAGGGCTAGTTTTTAGCA 58.954 38.462 8.29 0.00 42.06 3.49
1550 1617 7.562135 TGGTGAGTATTAGGGCTAGTTTTTAG 58.438 38.462 0.00 0.00 0.00 1.85
1640 1708 0.787084 AGGAGGAGAAGGTGGAGTCA 59.213 55.000 0.00 0.00 0.00 3.41
1675 1744 4.260907 CCGAGTTATTCCACGAGTTCGATA 60.261 45.833 8.72 0.00 43.02 2.92
1704 1773 1.212751 GTGAGCAAATCGCCAACCC 59.787 57.895 0.00 0.00 44.04 4.11
1707 1776 0.874390 GAGTGTGAGCAAATCGCCAA 59.126 50.000 0.00 0.00 44.04 4.52
1751 1820 4.751060 ACAACACGTTCTTTGAGTCACTA 58.249 39.130 8.02 0.00 0.00 2.74
1801 1870 3.113514 TTGGTGGCCAAGCTCGTCA 62.114 57.895 7.24 0.00 38.75 4.35
1851 1920 0.755327 GACCACAACAAGGCCAAGGT 60.755 55.000 5.01 0.99 0.00 3.50
1969 2048 2.519771 ATGATGCCACAACACTCCAT 57.480 45.000 0.00 0.00 0.00 3.41
1973 2052 1.004628 TGCCTATGATGCCACAACACT 59.995 47.619 0.00 0.00 0.00 3.55
1974 2053 1.133025 GTGCCTATGATGCCACAACAC 59.867 52.381 0.00 0.00 0.00 3.32
2000 2079 1.480212 TTCGCCACACATGAGGAGGT 61.480 55.000 0.00 0.00 0.00 3.85
2030 2109 2.926901 TACACGGGCAAGCGTGTGTT 62.927 55.000 24.16 6.24 46.83 3.32
2036 2115 3.202001 CCCATACACGGGCAAGCG 61.202 66.667 0.00 0.00 40.07 4.68
2088 2167 2.214216 TACCGCAGTGTTGGGCTCT 61.214 57.895 8.20 0.00 36.03 4.09
2123 2202 2.205074 CATAGGAGATGTCACAACCGC 58.795 52.381 0.00 0.00 0.00 5.68
2124 2203 2.168521 ACCATAGGAGATGTCACAACCG 59.831 50.000 0.00 0.00 0.00 4.44
2149 2228 1.558756 CATGCCTCCTCTGACCTCTTT 59.441 52.381 0.00 0.00 0.00 2.52
2160 2239 4.479993 GACTGCGCCATGCCTCCT 62.480 66.667 4.18 0.00 45.60 3.69
2197 2276 3.797353 CTAGCCACGCCACCCCAT 61.797 66.667 0.00 0.00 0.00 4.00
2245 2324 2.120909 ATGCCGCCCTCAAAATCGG 61.121 57.895 0.00 0.00 44.29 4.18
2254 2333 4.569180 CCCGATTCATGCCGCCCT 62.569 66.667 0.00 0.00 0.00 5.19
2354 2451 1.115930 ACAGTCGTTGCCTCCACTCT 61.116 55.000 0.00 0.00 0.00 3.24
2366 2463 0.670546 CAGCCGATTCCAACAGTCGT 60.671 55.000 0.00 0.00 33.77 4.34
2389 2486 1.229820 ACTACCCCACCTGCATCCA 60.230 57.895 0.00 0.00 0.00 3.41
2399 2496 4.620589 TTTGAACGTTATCACTACCCCA 57.379 40.909 0.00 0.00 0.00 4.96
2401 2498 4.334481 CCCATTTGAACGTTATCACTACCC 59.666 45.833 0.00 0.00 0.00 3.69
2409 2506 1.132262 CGCTGCCCATTTGAACGTTAT 59.868 47.619 0.00 0.00 0.00 1.89
2434 2531 2.141122 AAAACGCAGCCACGGGAATG 62.141 55.000 0.00 0.00 37.37 2.67
2440 2538 0.804156 AAACCAAAAACGCAGCCACG 60.804 50.000 0.00 0.00 39.50 4.94



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

AutoCloner maintained by Alex Coulton.