Multiple sequence alignment - TraesCS1B01G247400

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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 TraesCS1B01G247400 chr1B 100.000 2150 0 0 1 2150 438040304 438038155 0.000000e+00 3971
1 TraesCS1B01G247400 chr1A 93.157 2119 108 20 43 2148 418916987 418919081 0.000000e+00 3075
2 TraesCS1B01G247400 chr1D 93.333 1395 64 16 215 1596 325597895 325596517 0.000000e+00 2034
3 TraesCS1B01G247400 chr1D 91.429 560 33 3 1591 2150 325595967 325595423 0.000000e+00 754
4 TraesCS1B01G247400 chr1D 91.342 231 9 4 1 226 325598682 325598458 2.680000e-79 305


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 TraesCS1B01G247400 chr1B 438038155 438040304 2149 True 3971 3971 100.000000 1 2150 1 chr1B.!!$R1 2149
1 TraesCS1B01G247400 chr1A 418916987 418919081 2094 False 3075 3075 93.157000 43 2148 1 chr1A.!!$F1 2105
2 TraesCS1B01G247400 chr1D 325595423 325598682 3259 True 1031 2034 92.034667 1 2150 3 chr1D.!!$R1 2149

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
371 964 0.036105 ATTCACACCGAGAGCATGCA 60.036 50.0 21.98 0.0 0.0 3.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1317 1922 0.249784 CAGATGGAGATGGACAGCCG 60.25 60.0 0.0 0.0 36.79 5.52 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 8.254508 TGTGGTTAATACCCAAATTAAAGCATC 58.745 33.333 0.00 0.00 44.35 3.91
84 89 2.878406 CCACCGAAAACAGTGTCAATCT 59.122 45.455 0.00 0.00 31.88 2.40
85 90 3.058914 CCACCGAAAACAGTGTCAATCTC 60.059 47.826 0.00 0.00 31.88 2.75
86 91 3.058914 CACCGAAAACAGTGTCAATCTCC 60.059 47.826 0.00 0.00 0.00 3.71
87 92 3.181454 ACCGAAAACAGTGTCAATCTCCT 60.181 43.478 0.00 0.00 0.00 3.69
88 93 4.039973 ACCGAAAACAGTGTCAATCTCCTA 59.960 41.667 0.00 0.00 0.00 2.94
89 94 5.178797 CCGAAAACAGTGTCAATCTCCTAT 58.821 41.667 0.00 0.00 0.00 2.57
113 118 4.039973 TCTCCTGATAACAAAACCGTGTCT 59.960 41.667 0.00 0.00 0.00 3.41
129 134 3.553096 CGTGTCTAGCTGAAGTTGGACTT 60.553 47.826 10.98 0.00 41.95 3.01
189 195 0.162507 CTTCACGCTCGCTTGTCTTG 59.837 55.000 0.00 0.00 0.00 3.02
319 908 2.047830 CCACCTAATCCCTACCACCTC 58.952 57.143 0.00 0.00 0.00 3.85
320 909 2.047830 CACCTAATCCCTACCACCTCC 58.952 57.143 0.00 0.00 0.00 4.30
321 910 1.945317 ACCTAATCCCTACCACCTCCT 59.055 52.381 0.00 0.00 0.00 3.69
368 961 1.276138 TCACATTCACACCGAGAGCAT 59.724 47.619 0.00 0.00 0.00 3.79
371 964 0.036105 ATTCACACCGAGAGCATGCA 60.036 50.000 21.98 0.00 0.00 3.96
394 987 1.134367 CTACGTTCTCTCCATCGCCAA 59.866 52.381 0.00 0.00 0.00 4.52
395 988 0.537188 ACGTTCTCTCCATCGCCAAT 59.463 50.000 0.00 0.00 0.00 3.16
396 989 1.066143 ACGTTCTCTCCATCGCCAATT 60.066 47.619 0.00 0.00 0.00 2.32
397 990 1.594862 CGTTCTCTCCATCGCCAATTC 59.405 52.381 0.00 0.00 0.00 2.17
398 991 1.594862 GTTCTCTCCATCGCCAATTCG 59.405 52.381 0.00 0.00 0.00 3.34
399 992 0.530650 TCTCTCCATCGCCAATTCGC 60.531 55.000 0.00 0.00 0.00 4.70
400 993 1.502163 CTCTCCATCGCCAATTCGCC 61.502 60.000 0.00 0.00 0.00 5.54
401 994 1.819208 CTCCATCGCCAATTCGCCA 60.819 57.895 0.00 0.00 0.00 5.69
443 1036 1.282157 GGGGACAAGTAGCCATCAACT 59.718 52.381 0.00 0.00 0.00 3.16
483 1076 4.100373 AGGATATCAGAATACCAGCCCTC 58.900 47.826 4.83 0.00 0.00 4.30
582 1175 2.022129 GTCAAGTGACCGCGTCCAG 61.022 63.158 4.92 0.00 39.07 3.86
589 1182 1.248101 TGACCGCGTCCAGAAGATCA 61.248 55.000 4.92 0.00 0.00 2.92
659 1252 1.980232 CCATGCTGAAAGGCAGGCA 60.980 57.895 0.00 0.00 45.75 4.75
737 1331 4.436113 TGATCAGCCTAACAATGCCATA 57.564 40.909 0.00 0.00 0.00 2.74
788 1382 4.453093 GCATAGGCTGAGCTGTCC 57.547 61.111 3.72 0.00 36.96 4.02
840 1434 3.501445 GGCATCATTGAAGACCTGATAGC 59.499 47.826 0.00 0.00 0.00 2.97
843 1437 4.944619 TCATTGAAGACCTGATAGCGAT 57.055 40.909 0.00 0.00 0.00 4.58
847 1441 1.342819 GAAGACCTGATAGCGATGCCT 59.657 52.381 0.00 0.00 0.00 4.75
868 1463 0.613292 AACAAACTGGCCACACCACA 60.613 50.000 0.00 0.00 46.36 4.17
896 1491 1.208535 TGGCCGTGGTGGTATAAGAAG 59.791 52.381 0.00 0.00 41.21 2.85
897 1492 1.296727 GCCGTGGTGGTATAAGAAGC 58.703 55.000 0.00 0.00 41.21 3.86
900 1495 3.340034 CCGTGGTGGTATAAGAAGCAAA 58.660 45.455 0.00 0.00 0.00 3.68
904 1499 5.163854 CGTGGTGGTATAAGAAGCAAAGAAG 60.164 44.000 0.00 0.00 0.00 2.85
959 1557 1.203174 TGACCACCACTGATCTCCAGA 60.203 52.381 0.00 0.00 45.78 3.86
984 1582 2.597510 GCACCGGGAAGCAACCTT 60.598 61.111 6.32 0.00 0.00 3.50
1107 1705 0.671472 TGTTCATGCTCCTCTGCACG 60.671 55.000 0.00 0.00 46.33 5.34
1254 1855 4.278419 CCTGGTTTTCTTCGGTTCAGAAAT 59.722 41.667 0.00 0.00 39.46 2.17
1255 1856 5.472137 CCTGGTTTTCTTCGGTTCAGAAATA 59.528 40.000 0.00 0.00 39.46 1.40
1257 1858 7.309194 CCTGGTTTTCTTCGGTTCAGAAATAAT 60.309 37.037 0.00 0.00 39.46 1.28
1260 1861 8.912658 GGTTTTCTTCGGTTCAGAAATAATTTC 58.087 33.333 0.00 0.00 39.46 2.17
1302 1903 3.192001 ACTCGTCGAAACTGTAAGCCATA 59.808 43.478 0.00 0.00 37.60 2.74
1311 1912 5.941948 AACTGTAAGCCATATTTATCGGC 57.058 39.130 0.00 0.00 46.62 5.54
1349 1954 4.026052 TCTCCATCTGTAGCATGAACTGA 58.974 43.478 0.00 3.78 0.00 3.41
1350 1955 4.652881 TCTCCATCTGTAGCATGAACTGAT 59.347 41.667 12.35 12.35 36.36 2.90
1351 1956 5.835280 TCTCCATCTGTAGCATGAACTGATA 59.165 40.000 15.72 6.06 34.81 2.15
1352 1957 5.847304 TCCATCTGTAGCATGAACTGATAC 58.153 41.667 15.72 0.00 45.09 2.24
1365 1970 4.347876 TGAACTGATACATACATCTGGGGG 59.652 45.833 0.00 0.00 0.00 5.40
1440 2045 5.010516 TCTCTCTTTCTCTCCTCTGTTTGTG 59.989 44.000 0.00 0.00 0.00 3.33
1461 2066 8.687824 TTGTGTTTTGTTTTCTCTTTCAGATC 57.312 30.769 0.00 0.00 0.00 2.75
1465 2070 9.927668 TGTTTTGTTTTCTCTTTCAGATCTTTT 57.072 25.926 0.00 0.00 0.00 2.27
1489 2094 9.549509 TTTTATATGATCGTAACACAAAAGCAC 57.450 29.630 0.00 0.00 0.00 4.40
1495 2100 4.185394 TCGTAACACAAAAGCACAGAAGA 58.815 39.130 0.00 0.00 0.00 2.87
1515 2120 2.512692 TTGGCTATCTGTTGGCACAT 57.487 45.000 0.00 0.00 39.30 3.21
1519 2124 2.579873 GCTATCTGTTGGCACATCCAT 58.420 47.619 0.00 0.00 46.04 3.41
1589 2194 3.305720 AGTGGTTCTGTAGTGACTCCAA 58.694 45.455 0.00 0.00 0.00 3.53
1661 2821 6.575162 AACAGGGCTACAAAATAGTTCAAG 57.425 37.500 0.00 0.00 0.00 3.02
1667 2827 8.548877 AGGGCTACAAAATAGTTCAAGATTAGA 58.451 33.333 0.00 0.00 0.00 2.10
1738 2898 5.248640 TCTGAAGAAGACCATCATTCAACC 58.751 41.667 0.00 0.00 30.10 3.77
1740 2900 2.359900 AGAAGACCATCATTCAACCGC 58.640 47.619 0.00 0.00 0.00 5.68
1792 2952 4.346734 AATTGTCAGTGCATCTTAAGCG 57.653 40.909 0.00 0.00 33.85 4.68
1796 2956 0.376152 CAGTGCATCTTAAGCGGCAG 59.624 55.000 17.63 6.96 36.86 4.85
1827 2987 2.102161 CCGGTATTGCTTTGCGGC 59.898 61.111 0.00 0.00 0.00 6.53
1842 3002 1.069204 TGCGGCTCATGGTTATCTCTC 59.931 52.381 0.00 0.00 0.00 3.20
1857 3017 7.234782 TGGTTATCTCTCTTTGTTTGTCTAGGA 59.765 37.037 0.00 0.00 0.00 2.94
1950 3110 1.548582 CCTGCAGAATGTCACCCCTTT 60.549 52.381 17.39 0.00 39.31 3.11
1957 3117 4.768968 CAGAATGTCACCCCTTTTTCTGAT 59.231 41.667 4.84 0.00 41.47 2.90
2032 3192 5.122396 AGGAATCTTGCTTGCTAGTTTAACG 59.878 40.000 4.25 0.00 0.00 3.18
2096 3256 2.667969 TGCAACGATCTCTTCATGAACG 59.332 45.455 3.38 8.88 0.00 3.95
2121 3281 6.176183 CCCATTTCACACTTCAGTTCTATCT 58.824 40.000 0.00 0.00 0.00 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 4.037923 ACGGCTATGATGCTTTAATTTGGG 59.962 41.667 0.00 0.0 0.00 4.12
53 58 4.995487 ACTGTTTTCGGTGGTTTCTATCTC 59.005 41.667 0.00 0.0 38.10 2.75
84 89 6.070424 ACGGTTTTGTTATCAGGAGAATAGGA 60.070 38.462 0.00 0.0 0.00 2.94
85 90 6.037172 CACGGTTTTGTTATCAGGAGAATAGG 59.963 42.308 0.00 0.0 0.00 2.57
86 91 6.594159 ACACGGTTTTGTTATCAGGAGAATAG 59.406 38.462 0.00 0.0 0.00 1.73
87 92 6.469410 ACACGGTTTTGTTATCAGGAGAATA 58.531 36.000 0.00 0.0 0.00 1.75
88 93 5.313712 ACACGGTTTTGTTATCAGGAGAAT 58.686 37.500 0.00 0.0 0.00 2.40
89 94 4.710324 ACACGGTTTTGTTATCAGGAGAA 58.290 39.130 0.00 0.0 0.00 2.87
129 134 1.257750 TTCCTGGCTCAGCTAAGCGA 61.258 55.000 1.88 0.0 43.45 4.93
189 195 5.094134 CCTTACAGCTTCGTCTAACACTAC 58.906 45.833 0.00 0.0 0.00 2.73
319 908 4.218852 GTCCCCGTCTCTATCTATTTGAGG 59.781 50.000 0.00 0.0 0.00 3.86
320 909 4.083217 CGTCCCCGTCTCTATCTATTTGAG 60.083 50.000 0.00 0.0 0.00 3.02
321 910 3.819337 CGTCCCCGTCTCTATCTATTTGA 59.181 47.826 0.00 0.0 0.00 2.69
368 961 1.211969 GGAGAGAACGTAGCGTGCA 59.788 57.895 2.35 0.0 39.99 4.57
371 964 0.377554 CGATGGAGAGAACGTAGCGT 59.622 55.000 0.00 0.0 43.97 5.07
394 987 2.481568 CGATAGCATTGTGATGGCGAAT 59.518 45.455 0.00 0.0 33.72 3.34
395 988 1.866601 CGATAGCATTGTGATGGCGAA 59.133 47.619 0.00 0.0 33.72 4.70
396 989 1.501169 CGATAGCATTGTGATGGCGA 58.499 50.000 0.00 0.0 33.72 5.54
397 990 0.514255 CCGATAGCATTGTGATGGCG 59.486 55.000 0.00 0.0 33.72 5.69
398 991 1.532868 GTCCGATAGCATTGTGATGGC 59.467 52.381 0.00 0.0 33.72 4.40
399 992 2.837498 TGTCCGATAGCATTGTGATGG 58.163 47.619 0.00 0.0 33.72 3.51
400 993 5.064325 CCATATGTCCGATAGCATTGTGATG 59.936 44.000 1.24 0.0 36.32 3.07
401 994 5.181009 CCATATGTCCGATAGCATTGTGAT 58.819 41.667 1.24 0.0 0.00 3.06
443 1036 4.177537 TCCTCCTGGTGAAATTCAAACA 57.822 40.909 0.00 0.0 34.23 2.83
483 1076 9.770097 ATACATGTATGAAAAGTACAGGATCAG 57.230 33.333 17.60 0.0 37.31 2.90
577 1170 0.532573 TCGCTGGTGATCTTCTGGAC 59.467 55.000 0.00 0.0 0.00 4.02
582 1175 1.202359 GGTCTCTCGCTGGTGATCTTC 60.202 57.143 0.00 0.0 0.00 2.87
659 1252 6.573094 GCAAACAGATCTGGCCTTTCTTTTAT 60.573 38.462 26.08 0.0 34.19 1.40
788 1382 1.671901 GCTCCCCTTCCGTCTCTGAG 61.672 65.000 0.00 0.0 0.00 3.35
840 1434 0.109597 GCCAGTTTGTTGAGGCATCG 60.110 55.000 0.00 0.0 46.26 3.84
847 1441 0.323816 TGGTGTGGCCAGTTTGTTGA 60.324 50.000 5.11 0.0 43.61 3.18
868 1463 3.785859 ACCACGGCCATGATCGCT 61.786 61.111 0.00 0.0 0.00 4.93
904 1499 0.806492 GCTTCCTAGCAGTGGTACGC 60.806 60.000 0.00 0.0 46.95 4.42
959 1557 2.606519 TTCCCGGTGCTGCCTACT 60.607 61.111 0.00 0.0 34.25 2.57
1230 1831 2.436542 TCTGAACCGAAGAAAACCAGGA 59.563 45.455 0.00 0.0 0.00 3.86
1261 1862 5.942236 ACGAGTCCTACAATTCAGTAGTGTA 59.058 40.000 0.00 0.0 39.84 2.90
1262 1863 4.765856 ACGAGTCCTACAATTCAGTAGTGT 59.234 41.667 0.00 0.0 39.84 3.55
1263 1864 5.312120 ACGAGTCCTACAATTCAGTAGTG 57.688 43.478 0.00 0.0 39.84 2.74
1302 1903 3.674997 ACAGCCGAATATGCCGATAAAT 58.325 40.909 0.00 0.0 0.00 1.40
1311 1912 2.037641 TGGAGATGGACAGCCGAATATG 59.962 50.000 0.00 0.0 36.79 1.78
1317 1922 0.249784 CAGATGGAGATGGACAGCCG 60.250 60.000 0.00 0.0 36.79 5.52
1465 2070 8.257830 TGTGCTTTTGTGTTACGATCATATAA 57.742 30.769 0.00 0.0 0.00 0.98
1466 2071 7.762159 TCTGTGCTTTTGTGTTACGATCATATA 59.238 33.333 0.00 0.0 0.00 0.86
1481 2086 3.655276 AGCCAATCTTCTGTGCTTTTG 57.345 42.857 0.00 0.0 0.00 2.44
1489 2094 3.314635 GCCAACAGATAGCCAATCTTCTG 59.685 47.826 0.00 0.0 42.62 3.02
1495 2100 2.512692 TGTGCCAACAGATAGCCAAT 57.487 45.000 0.00 0.0 0.00 3.16
1509 2114 2.902705 AATTGCATCATGGATGTGCC 57.097 45.000 7.92 0.0 41.60 5.01
1589 2194 2.949451 CACTAAGACGTGCATCCTCT 57.051 50.000 0.00 0.0 0.00 3.69
1631 2791 3.306472 TTTGTAGCCCTGTTTCTGGTT 57.694 42.857 0.00 0.0 0.00 3.67
1661 2821 9.660180 AAGAAGTGTAGAATCTTTGGTCTAATC 57.340 33.333 0.00 0.0 29.35 1.75
1667 2827 6.876257 CAGCTAAGAAGTGTAGAATCTTTGGT 59.124 38.462 0.00 0.0 37.21 3.67
1827 2987 7.605691 AGACAAACAAAGAGAGATAACCATGAG 59.394 37.037 0.00 0.0 0.00 2.90
1842 3002 5.416013 GGGGAAAGATCCTAGACAAACAAAG 59.584 44.000 0.00 0.0 45.77 2.77
1857 3017 2.439880 GAGATTCTTCCGGGGGAAAGAT 59.560 50.000 0.00 0.0 41.54 2.40
2032 3192 1.704070 AGCAGATCTTCATGGATCCCC 59.296 52.381 9.90 0.0 42.02 4.81
2096 3256 2.887152 AGAACTGAAGTGTGAAATGGGC 59.113 45.455 0.00 0.0 0.00 5.36
2121 3281 4.464008 AGTTTCAGTGCAGGAATTCAGAA 58.536 39.130 7.93 0.0 0.00 3.02


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

AutoCloner maintained by Alex Coulton.