Multiple sequence alignment - TraesCS6D01G260700

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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 TraesCS6D01G260700 chr6D 100.000 2405 0 0 1 2405 368304974 368307378 0 4442
1 TraesCS6D01G260700 chr6A 90.902 2451 119 44 6 2405 508850865 508853262 0 3195
2 TraesCS6D01G260700 chr6B 90.649 1711 96 27 1 1667 553374197 553372507 0 2215
3 TraesCS6D01G260700 chr6B 90.560 625 26 11 1799 2405 553372135 553371526 0 797


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 TraesCS6D01G260700 chr6D 368304974 368307378 2404 False 4442 4442 100.0000 1 2405 1 chr6D.!!$F1 2404
1 TraesCS6D01G260700 chr6A 508850865 508853262 2397 False 3195 3195 90.9020 6 2405 1 chr6A.!!$F1 2399
2 TraesCS6D01G260700 chr6B 553371526 553374197 2671 True 1506 2215 90.6045 1 2405 2 chr6B.!!$R1 2404

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
988 1041 0.656785 GTATCTTGCTGCTGCTGAGC 59.343 55.0 17.0 7.86 46.44 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2035 2388 1.293179 CACCACCTCATCTGCGTCA 59.707 57.895 0.0 0.0 0.0 4.35 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
77 78 2.379459 GCTCCCCCTCTCTTTCCCC 61.379 68.421 0.00 0.00 0.00 4.81
78 79 1.694525 CTCCCCCTCTCTTTCCCCC 60.695 68.421 0.00 0.00 0.00 5.40
268 286 2.202690 TGTACTTCCGGCATCGCG 60.203 61.111 0.00 0.00 34.56 5.87
324 342 1.827789 CTAGCGCCAGGAGAGCTCT 60.828 63.158 18.28 18.28 41.88 4.09
406 424 1.145803 GGTCAGTTCCTCGTTTTCCG 58.854 55.000 0.00 0.00 38.13 4.30
416 434 4.581868 TCCTCGTTTTCCGTCCATTAATT 58.418 39.130 0.00 0.00 37.94 1.40
538 562 2.890808 ATCCGTCAGATGCGTATTGT 57.109 45.000 0.00 0.00 32.41 2.71
601 632 6.680810 TCTGAATTTGCATCTTTTCGATTGT 58.319 32.000 0.00 0.00 0.00 2.71
669 702 7.108194 AGAATCATACTTGCTCATTTCTCACA 58.892 34.615 0.00 0.00 0.00 3.58
671 704 8.969260 AATCATACTTGCTCATTTCTCACATA 57.031 30.769 0.00 0.00 0.00 2.29
686 719 2.805671 TCACATACACAAGCCAAGAACG 59.194 45.455 0.00 0.00 0.00 3.95
688 721 1.135689 CATACACAAGCCAAGAACGCC 60.136 52.381 0.00 0.00 0.00 5.68
704 737 3.848272 ACGCCATAGAACATTTTGGTG 57.152 42.857 0.00 0.00 43.69 4.17
747 781 3.196901 ACGGCATGTAGATTGGTTCAGTA 59.803 43.478 0.00 0.00 0.00 2.74
748 782 3.804325 CGGCATGTAGATTGGTTCAGTAG 59.196 47.826 0.00 0.00 0.00 2.57
749 783 4.680708 CGGCATGTAGATTGGTTCAGTAGT 60.681 45.833 0.00 0.00 0.00 2.73
750 784 4.811557 GGCATGTAGATTGGTTCAGTAGTC 59.188 45.833 0.00 0.00 0.00 2.59
751 785 5.419542 GCATGTAGATTGGTTCAGTAGTCA 58.580 41.667 0.00 0.00 0.00 3.41
752 786 5.521735 GCATGTAGATTGGTTCAGTAGTCAG 59.478 44.000 0.00 0.00 0.00 3.51
753 787 6.634805 CATGTAGATTGGTTCAGTAGTCAGT 58.365 40.000 0.00 0.00 0.00 3.41
768 802 9.424319 TCAGTAGTCAGTTTGTTGATTTCTATC 57.576 33.333 0.00 0.00 0.00 2.08
786 823 2.806945 TCAATCCAAATCCGAGGCTT 57.193 45.000 0.00 0.00 0.00 4.35
809 846 3.082548 TCACCTCTCGTTCAGGAGTAAG 58.917 50.000 4.38 0.00 35.52 2.34
819 857 8.311836 TCTCGTTCAGGAGTAAGAATTTGTAAT 58.688 33.333 0.00 0.00 35.52 1.89
833 871 8.492673 AGAATTTGTAATCGCTGTTCTTCATA 57.507 30.769 0.00 0.00 0.00 2.15
887 925 5.366768 AGCTGGATTATCTTAGCACAAGGTA 59.633 40.000 18.45 0.00 38.59 3.08
916 954 7.279313 TCTGTAAAACACTCCAGTTTCAGTAAC 59.721 37.037 0.00 0.00 40.60 2.50
941 986 2.760634 TGATAAACAGAAGCAGCCGA 57.239 45.000 0.00 0.00 0.00 5.54
946 991 2.119801 AACAGAAGCAGCCGATTCAT 57.880 45.000 0.10 0.00 40.09 2.57
951 996 2.092968 AGAAGCAGCCGATTCATTGGTA 60.093 45.455 0.10 0.00 40.09 3.25
971 1016 5.906495 TGGTAGCCCAAACCAATCTATAGTA 59.094 40.000 0.00 0.00 43.99 1.82
972 1017 6.561070 TGGTAGCCCAAACCAATCTATAGTAT 59.439 38.462 0.00 0.00 43.99 2.12
973 1018 7.104290 GGTAGCCCAAACCAATCTATAGTATC 58.896 42.308 0.00 0.00 36.96 2.24
988 1041 0.656785 GTATCTTGCTGCTGCTGAGC 59.343 55.000 17.00 7.86 46.44 4.26
995 1057 2.357881 TGCTGCTGAGCTGAACCG 60.358 61.111 15.78 0.00 46.39 4.44
997 1059 1.449246 GCTGCTGAGCTGAACCGAT 60.449 57.895 15.78 0.00 42.52 4.18
1038 1100 3.706373 GGCAGAGGAAGGACGGCA 61.706 66.667 0.00 0.00 0.00 5.69
1077 1139 1.518903 AAGACAAAGGAAGCAGCGGC 61.519 55.000 0.00 0.00 41.61 6.53
1092 1154 4.329545 GGCGAAGAGGTGGTGCCA 62.330 66.667 0.00 0.00 45.06 4.92
1332 1394 1.570857 AATCGGCCAGGACCAATGGA 61.571 55.000 6.16 0.00 40.51 3.41
1368 1430 4.069232 CGGAGGAAGAGCACGCCA 62.069 66.667 0.00 0.00 0.00 5.69
1407 1469 1.869767 GGCCTAGAATGCAAGTGATCG 59.130 52.381 0.00 0.00 0.00 3.69
1415 1477 0.603439 TGCAAGTGATCGCTGAGCAA 60.603 50.000 25.57 14.24 30.80 3.91
1443 1511 3.123050 GCCAATCCATACAATTTTCGGC 58.877 45.455 0.00 0.00 0.00 5.54
1444 1512 3.430098 GCCAATCCATACAATTTTCGGCA 60.430 43.478 0.00 0.00 35.86 5.69
1539 1607 3.190327 TGGACGCAAAATGTATGAACTGG 59.810 43.478 0.00 0.00 0.00 4.00
1564 1632 3.611766 AGAACACCTACGGAATCTTGG 57.388 47.619 0.00 0.00 0.00 3.61
1625 1696 3.381272 TGCTTGTTTGTAGCAGAGCTTTT 59.619 39.130 0.00 0.00 43.30 2.27
1635 1706 1.462670 GCAGAGCTTTTCTTGAGGACG 59.537 52.381 0.00 0.00 32.41 4.79
1692 1763 4.093743 TGTTGGTGCTACTCAGGATAAGA 58.906 43.478 0.00 0.00 0.00 2.10
1729 1800 6.398095 AGCAGTTTTATGTATTTTTGGCTCC 58.602 36.000 0.00 0.00 0.00 4.70
1744 1815 0.099082 GCTCCTACTCTGGTTCGTCG 59.901 60.000 0.00 0.00 0.00 5.12
1763 1834 4.325204 CGTCGATCTTATCCAAACGAAACA 59.675 41.667 0.00 0.00 31.75 2.83
1770 1841 5.637810 TCTTATCCAAACGAAACAGCTACTG 59.362 40.000 0.00 0.00 37.52 2.74
1988 2341 1.334384 AACCAACCAACCAACCAGCC 61.334 55.000 0.00 0.00 0.00 4.85
1989 2342 1.760086 CCAACCAACCAACCAGCCA 60.760 57.895 0.00 0.00 0.00 4.75
1990 2343 1.741525 CAACCAACCAACCAGCCAG 59.258 57.895 0.00 0.00 0.00 4.85
1991 2344 1.457455 AACCAACCAACCAGCCAGG 60.457 57.895 0.00 0.00 45.67 4.45
2008 2361 2.125106 GGCTCCCACACCACGATC 60.125 66.667 0.00 0.00 0.00 3.69
2035 2388 0.035630 GAGCACATGACAGGAGCCTT 60.036 55.000 5.90 0.00 0.00 4.35
2071 2424 1.079127 GGTGGTGTCGCTGTAGCAT 60.079 57.895 4.59 0.00 42.21 3.79
2158 2511 3.365265 CGGCAGCGGCTTTCCTTT 61.365 61.111 9.17 0.00 40.87 3.11
2159 2512 2.568612 GGCAGCGGCTTTCCTTTC 59.431 61.111 9.17 0.00 40.87 2.62
2160 2513 2.568612 GCAGCGGCTTTCCTTTCC 59.431 61.111 0.00 0.00 36.96 3.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
77 78 1.541233 GGCGAGAGAGAGAGAGAGAGG 60.541 61.905 0.00 0.00 0.00 3.69
78 79 1.541233 GGGCGAGAGAGAGAGAGAGAG 60.541 61.905 0.00 0.00 0.00 3.20
138 152 1.751927 CTGGCACTTCTGGATGGCC 60.752 63.158 0.00 0.00 44.82 5.36
206 224 1.013596 TTGCTATATGTGGCGTGTGC 58.986 50.000 0.00 0.00 41.71 4.57
268 286 3.367910 GGATCGGTGATAATCTCTGGCTC 60.368 52.174 0.00 0.00 0.00 4.70
343 361 0.964358 AAGCAGCAGCACCAATCTCC 60.964 55.000 3.17 0.00 45.49 3.71
416 434 4.206375 TCAACAGCTGAACCATTTCTCAA 58.794 39.130 23.35 0.00 32.36 3.02
538 562 1.264020 CAGACGCAAGCTACAGCAAAA 59.736 47.619 3.70 0.00 45.16 2.44
601 632 8.203681 AGTATGATTCTCATTGAGATCCATGA 57.796 34.615 25.66 12.25 38.56 3.07
669 702 1.165270 GGCGTTCTTGGCTTGTGTAT 58.835 50.000 0.00 0.00 0.00 2.29
671 704 0.823356 ATGGCGTTCTTGGCTTGTGT 60.823 50.000 0.00 0.00 35.06 3.72
686 719 5.329035 ACATCACCAAAATGTTCTATGGC 57.671 39.130 0.00 0.00 33.62 4.40
688 721 8.338259 GCTAGTACATCACCAAAATGTTCTATG 58.662 37.037 0.00 0.00 36.80 2.23
704 737 7.010738 TGCCGTTATAAAACAAGCTAGTACATC 59.989 37.037 0.00 0.00 36.16 3.06
768 802 3.193267 TGAAAAGCCTCGGATTTGGATTG 59.807 43.478 0.00 0.00 33.76 2.67
786 823 2.317040 ACTCCTGAACGAGAGGTGAAA 58.683 47.619 0.00 0.00 34.27 2.69
794 831 7.884816 TTACAAATTCTTACTCCTGAACGAG 57.115 36.000 0.00 0.00 35.88 4.18
795 832 7.274904 CGATTACAAATTCTTACTCCTGAACGA 59.725 37.037 0.00 0.00 0.00 3.85
796 833 7.391786 CGATTACAAATTCTTACTCCTGAACG 58.608 38.462 0.00 0.00 0.00 3.95
809 846 8.391106 AGTATGAAGAACAGCGATTACAAATTC 58.609 33.333 0.00 0.00 0.00 2.17
819 857 5.448768 GCAGTAGTAGTATGAAGAACAGCGA 60.449 44.000 0.00 0.00 0.00 4.93
854 892 9.712305 TGCTAAGATAATCCAGCTAAAGTTATC 57.288 33.333 10.17 10.17 35.05 1.75
887 925 6.591935 TGAAACTGGAGTGTTTTACAGAGAT 58.408 36.000 0.00 0.00 39.86 2.75
916 954 4.479619 GCTGCTTCTGTTTATCAGTTTGG 58.520 43.478 0.00 0.00 43.97 3.28
951 996 7.227156 CAAGATACTATAGATTGGTTTGGGCT 58.773 38.462 6.78 0.00 0.00 5.19
971 1016 3.906718 GCTCAGCAGCAGCAAGAT 58.093 55.556 3.17 0.00 46.06 2.40
988 1041 3.493350 CCTCTACCCATTGATCGGTTCAG 60.493 52.174 0.00 0.00 35.27 3.02
995 1057 3.244387 GCCTCTTCCTCTACCCATTGATC 60.244 52.174 0.00 0.00 0.00 2.92
997 1059 2.119495 GCCTCTTCCTCTACCCATTGA 58.881 52.381 0.00 0.00 0.00 2.57
1038 1100 3.664888 TGGCTCCTGGCAATGGCT 61.665 61.111 8.59 0.00 46.03 4.75
1077 1139 2.743928 GCTGGCACCACCTCTTCG 60.744 66.667 0.00 0.00 40.22 3.79
1086 1148 1.743252 CCTCTTTCTCGCTGGCACC 60.743 63.158 0.00 0.00 0.00 5.01
1092 1154 0.333312 TCCCTCTCCTCTTTCTCGCT 59.667 55.000 0.00 0.00 0.00 4.93
1332 1394 1.683011 CGGTTCCCAATCTGCCTGAAT 60.683 52.381 0.00 0.00 0.00 2.57
1383 1445 1.153086 CTTGCATTCTAGGCCCGCT 60.153 57.895 0.00 0.00 0.00 5.52
1386 1448 2.225467 GATCACTTGCATTCTAGGCCC 58.775 52.381 0.00 0.00 0.00 5.80
1389 1451 2.543012 CAGCGATCACTTGCATTCTAGG 59.457 50.000 0.00 0.00 33.84 3.02
1407 1469 2.106332 GGCATGGCATTGCTCAGC 59.894 61.111 15.47 9.51 42.38 4.26
1415 1477 2.385135 TGTATGGATTGGCATGGCAT 57.615 45.000 23.96 12.99 0.00 4.40
1443 1511 4.949856 ACAAATTATGAAGGCTACCTGGTG 59.050 41.667 10.23 0.56 32.13 4.17
1444 1512 5.193099 ACAAATTATGAAGGCTACCTGGT 57.807 39.130 4.05 4.05 32.13 4.00
1585 1653 5.875359 ACAAGCAGACCAAAATACTAGTAGC 59.125 40.000 8.85 3.07 0.00 3.58
1625 1696 2.241430 TCATCCCTAGTCGTCCTCAAGA 59.759 50.000 0.00 0.00 0.00 3.02
1635 1706 8.854614 AAATTGCAATACTATCATCCCTAGTC 57.145 34.615 13.39 0.00 31.96 2.59
1729 1800 5.334260 GGATAAGATCGACGAACCAGAGTAG 60.334 48.000 0.00 0.00 0.00 2.57
1744 1815 5.803020 AGCTGTTTCGTTTGGATAAGATC 57.197 39.130 0.00 0.00 0.00 2.75
1763 1834 9.314133 TGTCTGAACATATATAATCCAGTAGCT 57.686 33.333 0.00 0.00 0.00 3.32
1919 2271 3.192001 ACTGTCCAAATGCAATGCTACTG 59.808 43.478 6.82 0.42 0.00 2.74
1988 2341 4.704833 CGTGGTGTGGGAGCCCTG 62.705 72.222 7.16 0.00 36.94 4.45
1989 2342 4.954118 TCGTGGTGTGGGAGCCCT 62.954 66.667 7.16 0.00 36.94 5.19
1990 2343 3.682292 GATCGTGGTGTGGGAGCCC 62.682 68.421 0.00 0.00 0.00 5.19
1991 2344 2.125106 GATCGTGGTGTGGGAGCC 60.125 66.667 0.00 0.00 0.00 4.70
2008 2361 1.475280 CTGTCATGTGCTCCCAATTGG 59.525 52.381 18.21 18.21 0.00 3.16
2035 2388 1.293179 CACCACCTCATCTGCGTCA 59.707 57.895 0.00 0.00 0.00 4.35
2331 2691 1.669115 GCGATGATGATGTCCCCCG 60.669 63.158 0.00 0.00 0.00 5.73
2333 2693 1.669115 CGGCGATGATGATGTCCCC 60.669 63.158 0.00 0.00 0.00 4.81
2335 2695 2.320587 GGCGGCGATGATGATGTCC 61.321 63.158 12.98 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.