Multiple sequence alignment - TraesCS4A01G189500

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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 TraesCS4A01G189500 chr4A 100.000 2438 0 0 1 2438 468248931 468246494 0.000000e+00 4503
1 TraesCS4A01G189500 chr3D 90.814 1720 127 21 746 2438 504349657 504351372 0.000000e+00 2272
2 TraesCS4A01G189500 chr3D 89.840 561 57 0 1878 2438 35689491 35690051 0.000000e+00 721
3 TraesCS4A01G189500 chr5A 87.042 1721 185 18 744 2438 485529302 485527594 0.000000e+00 1908
4 TraesCS4A01G189500 chr6D 84.358 1317 173 20 767 2056 77866805 77868115 0.000000e+00 1260
5 TraesCS4A01G189500 chr4D 94.286 735 27 8 1 731 108014440 108015163 0.000000e+00 1110
6 TraesCS4A01G189500 chr4B 95.279 699 22 5 1 693 168705551 168704858 0.000000e+00 1098
7 TraesCS4A01G189500 chr6B 76.959 1736 315 53 761 2438 455450461 455452169 0.000000e+00 911
8 TraesCS4A01G189500 chr7A 81.977 860 133 15 746 1594 195546918 195546070 0.000000e+00 710
9 TraesCS4A01G189500 chr5D 77.148 512 90 12 1590 2078 188087776 188088283 3.090000e-69 272
10 TraesCS4A01G189500 chr7B 73.030 660 134 35 907 1545 18232340 18232976 2.470000e-45 193


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 TraesCS4A01G189500 chr4A 468246494 468248931 2437 True 4503 4503 100.000 1 2438 1 chr4A.!!$R1 2437
1 TraesCS4A01G189500 chr3D 504349657 504351372 1715 False 2272 2272 90.814 746 2438 1 chr3D.!!$F2 1692
2 TraesCS4A01G189500 chr3D 35689491 35690051 560 False 721 721 89.840 1878 2438 1 chr3D.!!$F1 560
3 TraesCS4A01G189500 chr5A 485527594 485529302 1708 True 1908 1908 87.042 744 2438 1 chr5A.!!$R1 1694
4 TraesCS4A01G189500 chr6D 77866805 77868115 1310 False 1260 1260 84.358 767 2056 1 chr6D.!!$F1 1289
5 TraesCS4A01G189500 chr4D 108014440 108015163 723 False 1110 1110 94.286 1 731 1 chr4D.!!$F1 730
6 TraesCS4A01G189500 chr4B 168704858 168705551 693 True 1098 1098 95.279 1 693 1 chr4B.!!$R1 692
7 TraesCS4A01G189500 chr6B 455450461 455452169 1708 False 911 911 76.959 761 2438 1 chr6B.!!$F1 1677
8 TraesCS4A01G189500 chr7A 195546070 195546918 848 True 710 710 81.977 746 1594 1 chr7A.!!$R1 848
9 TraesCS4A01G189500 chr5D 188087776 188088283 507 False 272 272 77.148 1590 2078 1 chr5D.!!$F1 488

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
785 796 1.267632 CGTTGGCGTTTTTGTCTCGAA 60.268 47.619 0.0 0.0 0.0 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2356 2413 0.24912 CAATAGCCCGGCCGATATCA 59.751 55.0 30.73 7.9 0.0 2.15 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
322 323 1.868519 GCAACCGTAGCTAGAATCGGG 60.869 57.143 20.70 8.37 46.06 5.14
327 328 1.269723 CGTAGCTAGAATCGGGCATCA 59.730 52.381 0.00 0.00 0.00 3.07
466 472 5.008019 GTGCTTTCAAGATTCAGTTCTGACA 59.992 40.000 1.72 0.00 0.00 3.58
484 490 5.880332 TCTGACACCAAATGCTATAGAAACC 59.120 40.000 3.21 0.00 0.00 3.27
522 533 7.606456 TCTGACACCAAATGTTAGACTAAATCC 59.394 37.037 0.00 0.00 46.15 3.01
646 657 9.856488 GGAAACTATTCTCTTAAAACCCAATTC 57.144 33.333 0.00 0.00 35.79 2.17
675 686 6.580963 TCAATTTTCCATTTGTCAACAACG 57.419 33.333 0.00 0.00 35.28 4.10
704 715 6.549449 GCATCAATTGCCCAAGTTTGGAATT 61.549 40.000 12.42 8.26 45.90 2.17
740 751 8.981724 AAAACTGACTTTTAGAGAAAAACCAC 57.018 30.769 0.00 0.00 34.16 4.16
741 752 7.939784 AACTGACTTTTAGAGAAAAACCACT 57.060 32.000 0.00 0.00 34.16 4.00
742 753 7.321745 ACTGACTTTTAGAGAAAAACCACTG 57.678 36.000 0.00 0.00 34.16 3.66
785 796 1.267632 CGTTGGCGTTTTTGTCTCGAA 60.268 47.619 0.00 0.00 0.00 3.71
908 923 1.912043 CCTCACCTGATCCTCAAACCT 59.088 52.381 0.00 0.00 0.00 3.50
927 942 2.031120 CTTCCACCAAAACCTTCTGCA 58.969 47.619 0.00 0.00 0.00 4.41
970 986 4.060205 TCGTAAAACACCTGTTTCTAGGC 58.940 43.478 3.92 0.00 46.47 3.93
1039 1057 3.376918 GGTTGCTGAAGGGCCTGC 61.377 66.667 6.92 5.31 0.00 4.85
1289 1307 2.420687 GGAAGGCGATTGAAGATGGACT 60.421 50.000 0.00 0.00 0.00 3.85
1309 1327 6.775142 TGGACTATGGATGTTTGACAAAGAAA 59.225 34.615 0.00 0.00 0.00 2.52
1363 1381 1.542492 GCCAGAGGATTATGCCCATG 58.458 55.000 0.00 0.00 0.00 3.66
1417 1435 3.203040 CCTTCCCCTTGGTATGATGAACT 59.797 47.826 0.00 0.00 0.00 3.01
1501 1524 3.609853 AGTCGCAATTGGCAGATTTCTA 58.390 40.909 7.72 0.00 45.17 2.10
1504 1527 4.094887 GTCGCAATTGGCAGATTTCTAAGA 59.905 41.667 7.72 0.00 45.17 2.10
1552 1575 3.390819 ACCGATTATGAGGGGGTTTACT 58.609 45.455 0.00 0.00 0.00 2.24
1567 1590 3.224269 GTTTACTCTAGCCGGAGAGGAT 58.776 50.000 20.89 6.78 46.22 3.24
1692 1721 2.223641 GCTACACGTGTGGGATTATCGA 60.224 50.000 30.83 5.86 34.19 3.59
1747 1776 2.751166 AGGGAGAACGATCACAGTTG 57.249 50.000 0.00 0.00 31.14 3.16
1790 1820 2.746359 GTCAGTGCAGAGGCTGGT 59.254 61.111 0.00 0.00 41.91 4.00
1876 1923 0.899019 GGAAGTGGGAGTGAGAGTCC 59.101 60.000 0.00 0.00 36.97 3.85
1947 1994 3.326946 AGGATGATGAGGTCACTAGCT 57.673 47.619 0.00 0.00 40.28 3.32
1948 1995 3.652055 AGGATGATGAGGTCACTAGCTT 58.348 45.455 0.00 0.00 40.28 3.74
1971 2018 4.889409 TGGTCAAAAATGACAAAGCTCTCT 59.111 37.500 10.75 0.00 40.38 3.10
1976 2023 0.622665 ATGACAAAGCTCTCTGGGGG 59.377 55.000 0.00 0.00 0.00 5.40
2000 2047 0.827507 GCAACCCCAAGAAGCTGGAA 60.828 55.000 0.00 0.00 38.96 3.53
2062 2112 0.538057 CAAGATGTGGTGGGCACTGT 60.538 55.000 0.00 0.00 0.00 3.55
2065 2115 4.892965 TGTGGTGGGCACTGTGGC 62.893 66.667 24.50 24.50 42.88 5.01
2101 2151 2.063979 CGGTGGCTATGGTCCCTGA 61.064 63.158 0.00 0.00 0.00 3.86
2110 2160 3.008485 GCTATGGTCCCTGAGAATAAGGG 59.992 52.174 1.82 1.82 44.06 3.95
2115 2165 3.049344 GTCCCTGAGAATAAGGGTGGAT 58.951 50.000 8.33 0.00 43.21 3.41
2123 2173 1.143813 ATAAGGGTGGATGGCTGGAG 58.856 55.000 0.00 0.00 0.00 3.86
2126 2176 2.592308 GGTGGATGGCTGGAGGTC 59.408 66.667 0.00 0.00 0.00 3.85
2150 2200 1.001633 AGCGGCGTAGGAGAAAAAGAA 59.998 47.619 9.37 0.00 0.00 2.52
2171 2221 1.136329 AGGCAGCAGGAGGGAAGAAA 61.136 55.000 0.00 0.00 0.00 2.52
2185 2235 6.455690 AGGGAAGAAATACAGAAAGAAGGT 57.544 37.500 0.00 0.00 0.00 3.50
2210 2260 2.303549 ATAGGACTGCTGTGGCGAGC 62.304 60.000 0.00 1.52 42.25 5.03
2211 2261 4.687215 GGACTGCTGTGGCGAGCA 62.687 66.667 10.26 10.26 46.87 4.26
2218 2268 2.666190 TGTGGCGAGCAAGCAGAC 60.666 61.111 5.80 2.60 39.27 3.51
2236 2287 2.044555 CGGTGACTACGGAGCTGGA 61.045 63.158 0.00 0.00 0.00 3.86
2237 2288 1.511768 GGTGACTACGGAGCTGGAC 59.488 63.158 0.00 0.00 0.00 4.02
2249 2300 2.284699 CTGGACGGGAAGAGGGGT 60.285 66.667 0.00 0.00 0.00 4.95
2270 2327 6.183361 GGGGTAGAATGGAAGATGAAGAAGAT 60.183 42.308 0.00 0.00 0.00 2.40
2294 2351 2.377531 GTTGGGAAAGAAGGGGAAGGTA 59.622 50.000 0.00 0.00 0.00 3.08
2312 2369 4.678256 AGGTAGATGAGAAGACACAGGAA 58.322 43.478 0.00 0.00 0.00 3.36
2356 2413 0.250467 GGTGTGAGTGCCACTGACAT 60.250 55.000 19.87 0.00 43.76 3.06
2372 2429 0.902984 ACATGATATCGGCCGGGCTA 60.903 55.000 27.83 16.72 0.00 3.93
2373 2430 0.465705 CATGATATCGGCCGGGCTAT 59.534 55.000 27.83 22.91 0.00 2.97
2374 2431 1.134401 CATGATATCGGCCGGGCTATT 60.134 52.381 27.83 12.66 0.00 1.73
2417 2474 5.399013 CAATGAAACTTATCGGTTGGAACC 58.601 41.667 0.00 0.00 45.76 3.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
228 229 1.675641 GCTTCACCATCTTGGCCGT 60.676 57.895 0.00 0.00 42.67 5.68
322 323 1.127213 CCAACTTGCGCAAATTGATGC 59.873 47.619 37.44 0.00 42.94 3.91
327 328 0.879839 GGCACCAACTTGCGCAAATT 60.880 50.000 25.01 18.62 44.00 1.82
466 472 6.680378 GCGATTTGGTTTCTATAGCATTTGGT 60.680 38.462 0.00 0.00 0.00 3.67
484 490 2.266554 GGTGTCAGAGAGAGCGATTTG 58.733 52.381 0.00 0.00 0.00 2.32
522 533 3.575256 AGAGATGCAGATTAGAGCTGAGG 59.425 47.826 0.00 0.00 35.39 3.86
597 608 9.603189 TTCCCAAAATTAGGGTTTTCTTGTATA 57.397 29.630 13.90 0.00 46.82 1.47
598 609 8.499288 TTCCCAAAATTAGGGTTTTCTTGTAT 57.501 30.769 13.90 0.00 46.82 2.29
599 610 7.916077 TTCCCAAAATTAGGGTTTTCTTGTA 57.084 32.000 13.90 0.00 46.82 2.41
623 634 9.025041 CCAGAATTGGGTTTTAAGAGAATAGTT 57.975 33.333 0.00 0.00 41.05 2.24
646 657 6.040209 TGACAAATGGAAAATTGATCCCAG 57.960 37.500 7.81 0.00 36.04 4.45
694 705 9.719355 AGTTTTAAAACAGAACAATTCCAAACT 57.281 25.926 28.03 3.11 41.30 2.66
715 726 8.803235 AGTGGTTTTTCTCTAAAAGTCAGTTTT 58.197 29.630 0.00 0.00 41.45 2.43
731 742 0.234884 CGGACTCGCAGTGGTTTTTC 59.765 55.000 0.00 0.00 0.00 2.29
732 743 0.463116 ACGGACTCGCAGTGGTTTTT 60.463 50.000 0.00 0.00 40.63 1.94
733 744 0.878961 GACGGACTCGCAGTGGTTTT 60.879 55.000 0.00 0.00 40.63 2.43
734 745 1.300697 GACGGACTCGCAGTGGTTT 60.301 57.895 0.00 0.00 40.63 3.27
735 746 2.338984 GACGGACTCGCAGTGGTT 59.661 61.111 0.00 0.00 40.63 3.67
736 747 3.681835 GGACGGACTCGCAGTGGT 61.682 66.667 0.00 0.00 40.63 4.16
737 748 4.436998 GGGACGGACTCGCAGTGG 62.437 72.222 0.00 0.00 40.63 4.00
781 792 0.249322 GATCGCCTCCGGAATTTCGA 60.249 55.000 7.98 12.22 34.56 3.71
782 793 1.222115 GGATCGCCTCCGGAATTTCG 61.222 60.000 5.23 6.79 33.29 3.46
785 796 2.829592 GGGATCGCCTCCGGAATT 59.170 61.111 5.23 0.00 46.01 2.17
908 923 2.151502 TGCAGAAGGTTTTGGTGGAA 57.848 45.000 0.00 0.00 0.00 3.53
927 942 2.189521 CGCGCCCTAGGGAAACAT 59.810 61.111 33.21 0.00 37.50 2.71
970 986 4.789123 CTTACCGCCCCAACCCCG 62.789 72.222 0.00 0.00 0.00 5.73
1039 1057 2.563179 TCCTCTCTTCCTCCGAAAGTTG 59.437 50.000 0.00 0.00 0.00 3.16
1203 1221 4.015084 CTCCAATCTCCTTGCAGTCAATT 58.985 43.478 0.00 0.00 33.20 2.32
1309 1327 1.692519 GTAGTCCTCCACCGCCATAAT 59.307 52.381 0.00 0.00 0.00 1.28
1392 1410 3.053693 TCATCATACCAAGGGGAAGGTTG 60.054 47.826 0.00 0.00 39.31 3.77
1417 1435 5.692115 TGTTACCAATATCCTCTGCTGAA 57.308 39.130 0.00 0.00 0.00 3.02
1501 1524 7.997223 TCAATCTGCATCCTGATCTTAATTCTT 59.003 33.333 0.00 0.00 0.00 2.52
1504 1527 9.803507 TTATCAATCTGCATCCTGATCTTAATT 57.196 29.630 7.58 0.00 31.20 1.40
1552 1575 1.479573 CCTTCATCCTCTCCGGCTAGA 60.480 57.143 0.00 0.00 0.00 2.43
1567 1590 2.622977 GCCATGTTTATCCACCCCTTCA 60.623 50.000 0.00 0.00 0.00 3.02
1692 1721 2.176798 TCACAGTCTTTTTCCCCATGGT 59.823 45.455 11.73 0.00 0.00 3.55
1767 1796 1.748122 CCTCTGCACTGACCCATGC 60.748 63.158 0.00 0.00 42.40 4.06
1790 1820 1.273495 ACCTCCAAGCTCTCTCATCCA 60.273 52.381 0.00 0.00 0.00 3.41
1876 1923 4.080695 TGGAATCACTCTTCCTCCATGAAG 60.081 45.833 0.00 0.00 44.27 3.02
1947 1994 5.360714 AGAGAGCTTTGTCATTTTTGACCAA 59.639 36.000 3.84 0.00 37.99 3.67
1948 1995 4.889409 AGAGAGCTTTGTCATTTTTGACCA 59.111 37.500 3.84 0.00 37.99 4.02
1976 2023 2.203625 TTCTTGGGGTTGCCCTGC 60.204 61.111 4.02 0.00 44.66 4.85
2062 2112 1.675310 CTCGGATTGCTTGGTGCCA 60.675 57.895 0.00 0.00 42.00 4.92
2065 2115 1.503542 GTGCTCGGATTGCTTGGTG 59.496 57.895 0.00 0.00 0.00 4.17
2101 2151 1.496429 CCAGCCATCCACCCTTATTCT 59.504 52.381 0.00 0.00 0.00 2.40
2110 2160 0.980231 AGAGACCTCCAGCCATCCAC 60.980 60.000 0.00 0.00 0.00 4.02
2115 2165 1.754621 CGCTAGAGACCTCCAGCCA 60.755 63.158 10.90 0.00 40.46 4.75
2123 2173 1.508808 CTCCTACGCCGCTAGAGACC 61.509 65.000 0.00 0.00 0.00 3.85
2126 2176 1.022735 TTTCTCCTACGCCGCTAGAG 58.977 55.000 0.00 0.00 0.00 2.43
2150 2200 1.136329 TCTTCCCTCCTGCTGCCTTT 61.136 55.000 0.00 0.00 0.00 3.11
2171 2221 5.604650 CCTATCCCTCACCTTCTTTCTGTAT 59.395 44.000 0.00 0.00 0.00 2.29
2185 2235 1.489481 CACAGCAGTCCTATCCCTCA 58.511 55.000 0.00 0.00 0.00 3.86
2210 2260 0.732880 CCGTAGTCACCGTCTGCTTG 60.733 60.000 0.00 0.00 0.00 4.01
2211 2261 0.892358 TCCGTAGTCACCGTCTGCTT 60.892 55.000 0.00 0.00 0.00 3.91
2218 2268 2.044555 TCCAGCTCCGTAGTCACCG 61.045 63.158 0.00 0.00 0.00 4.94
2236 2287 1.497161 CATTCTACCCCTCTTCCCGT 58.503 55.000 0.00 0.00 0.00 5.28
2237 2288 0.759346 CCATTCTACCCCTCTTCCCG 59.241 60.000 0.00 0.00 0.00 5.14
2270 2327 3.075432 CCTTCCCCTTCTTTCCCAACTTA 59.925 47.826 0.00 0.00 0.00 2.24
2294 2351 4.776837 ACATCTTCCTGTGTCTTCTCATCT 59.223 41.667 0.00 0.00 0.00 2.90
2312 2369 1.177401 TGTCAGACGCTAGCACATCT 58.823 50.000 16.45 11.21 0.00 2.90
2320 2377 1.045407 ACCCAGTTTGTCAGACGCTA 58.955 50.000 0.00 0.00 0.00 4.26
2356 2413 0.249120 CAATAGCCCGGCCGATATCA 59.751 55.000 30.73 7.90 0.00 2.15
2417 2474 4.452733 GTTCCCGAGTCCCTGGCG 62.453 72.222 0.00 0.00 0.00 5.69


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

AutoCloner maintained by Alex Coulton.