Multiple sequence alignment - TraesCS6B01G300600

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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 TraesCS6B01G300600 chr6B 100.000 2273 0 0 1 2273 539057013 539059285 0.000000e+00 4198
1 TraesCS6B01G300600 chr6D 94.776 2029 59 9 1 2025 357566555 357568540 0.000000e+00 3116
2 TraesCS6B01G300600 chr6D 96.522 230 7 1 2045 2273 357568532 357568761 1.650000e-101 379
3 TraesCS6B01G300600 chr6A 95.897 1633 53 5 1 1631 499644286 499645906 0.000000e+00 2632
4 TraesCS6B01G300600 chr6A 97.686 389 8 1 1638 2025 499645884 499646272 0.000000e+00 667
5 TraesCS6B01G300600 chr6A 98.696 230 2 1 2045 2273 499646264 499646493 7.560000e-110 407


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 TraesCS6B01G300600 chr6B 539057013 539059285 2272 False 4198.000000 4198 100.000000 1 2273 1 chr6B.!!$F1 2272
1 TraesCS6B01G300600 chr6D 357566555 357568761 2206 False 1747.500000 3116 95.649000 1 2273 2 chr6D.!!$F1 2272
2 TraesCS6B01G300600 chr6A 499644286 499646493 2207 False 1235.333333 2632 97.426333 1 2273 3 chr6A.!!$F1 2272

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
787 791 1.154413 GGCGTGTCAACTCATTGCG 60.154 57.895 0.0 0.0 35.63 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2040 2045 0.105964 CGGACAGGTGAGGTTGTTCA 59.894 55.0 0.0 0.0 0.0 3.18 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
94 96 6.043706 ACTTGCTATATTCACTATTCAGGGCT 59.956 38.462 0.00 0.00 0.00 5.19
95 97 6.439636 TGCTATATTCACTATTCAGGGCTT 57.560 37.500 0.00 0.00 0.00 4.35
96 98 6.467677 TGCTATATTCACTATTCAGGGCTTC 58.532 40.000 0.00 0.00 0.00 3.86
97 99 6.270927 TGCTATATTCACTATTCAGGGCTTCT 59.729 38.462 0.00 0.00 0.00 2.85
98 100 6.593382 GCTATATTCACTATTCAGGGCTTCTG 59.407 42.308 1.98 1.98 44.68 3.02
99 101 4.851639 ATTCACTATTCAGGGCTTCTGT 57.148 40.909 7.32 0.00 43.76 3.41
100 102 4.640771 TTCACTATTCAGGGCTTCTGTT 57.359 40.909 7.32 1.31 43.76 3.16
101 103 4.207891 TCACTATTCAGGGCTTCTGTTC 57.792 45.455 7.32 0.00 43.76 3.18
102 104 3.055094 TCACTATTCAGGGCTTCTGTTCC 60.055 47.826 7.32 0.00 43.76 3.62
328 331 3.388350 GGTTAGTATGCACTCTAGGCCTT 59.612 47.826 12.58 0.00 36.14 4.35
486 489 2.298729 GGCCTGGTAAGTTTTTGCATCA 59.701 45.455 0.00 0.00 0.00 3.07
520 523 4.718858 TCTTCCAATACAAAACGACACG 57.281 40.909 0.00 0.00 0.00 4.49
575 578 5.011586 GGTAAGTACCAAATGCACCCTTAA 58.988 41.667 2.47 0.00 45.73 1.85
629 633 8.457238 AAAGGCAAGAATAAAGGATGTCTATC 57.543 34.615 0.00 0.00 0.00 2.08
650 654 6.710597 ATCAAGATTGTGGGATGAAATGAG 57.289 37.500 0.00 0.00 0.00 2.90
719 723 7.114095 TCCTCCCTACAAATTTAATACACACC 58.886 38.462 0.00 0.00 0.00 4.16
772 776 1.536943 GGCTCCCTCCTACATAGGCG 61.537 65.000 0.00 0.00 43.31 5.52
787 791 1.154413 GGCGTGTCAACTCATTGCG 60.154 57.895 0.00 0.00 35.63 4.85
864 868 7.345653 TCCCCCTCTATATAAATAGCACATCTG 59.654 40.741 0.00 0.00 35.90 2.90
935 939 1.558233 ACTAGTCCCCTGACCTTTCG 58.442 55.000 0.00 0.00 42.81 3.46
969 973 2.162681 CCTGCTGGGGAAACAGTAAAG 58.837 52.381 0.71 0.00 40.59 1.85
973 977 1.708551 CTGGGGAAACAGTAAAGGGGA 59.291 52.381 0.00 0.00 33.81 4.81
980 984 4.565861 GGAAACAGTAAAGGGGAAGGAGAG 60.566 50.000 0.00 0.00 0.00 3.20
983 987 4.240323 ACAGTAAAGGGGAAGGAGAGAAA 58.760 43.478 0.00 0.00 0.00 2.52
1185 1189 2.287427 GCATCACATTGAGTATGCAGGC 60.287 50.000 13.72 0.00 43.30 4.85
1221 1225 1.883084 CTACAACATCTCCGGCGCC 60.883 63.158 19.07 19.07 0.00 6.53
1310 1314 9.404348 GTACTCTCATACACACATAATCTCATG 57.596 37.037 0.00 0.00 0.00 3.07
1394 1398 2.787601 CAGTGTTTCTGCATGCTGTT 57.212 45.000 20.33 0.00 37.36 3.16
1511 1515 6.937465 AGTTTGTTCCTCCTATTCTGTTCTTC 59.063 38.462 0.00 0.00 0.00 2.87
1654 1658 3.540314 TTTTTGACTTGTGCCTTGCAT 57.460 38.095 0.00 0.00 41.91 3.96
1655 1659 4.662468 TTTTTGACTTGTGCCTTGCATA 57.338 36.364 0.00 0.00 41.91 3.14
1656 1660 4.662468 TTTTGACTTGTGCCTTGCATAA 57.338 36.364 0.00 0.00 41.91 1.90
1657 1661 3.641437 TTGACTTGTGCCTTGCATAAC 57.359 42.857 0.00 0.00 41.91 1.89
1935 1940 4.578928 GCAAGACAAGTCAACTCCCTTTTA 59.421 41.667 2.72 0.00 0.00 1.52
1940 1945 4.762251 ACAAGTCAACTCCCTTTTATCTGC 59.238 41.667 0.00 0.00 0.00 4.26
1949 1954 3.195396 TCCCTTTTATCTGCCAACAATGC 59.805 43.478 0.00 0.00 0.00 3.56
2016 2021 3.243839 TGCTGAAATTTCAAACTCCAGGC 60.244 43.478 20.82 17.24 36.64 4.85
2017 2022 3.243839 GCTGAAATTTCAAACTCCAGGCA 60.244 43.478 20.82 0.00 36.64 4.75
2018 2023 4.553323 CTGAAATTTCAAACTCCAGGCAG 58.447 43.478 20.82 2.28 36.64 4.85
2019 2024 3.243839 TGAAATTTCAAACTCCAGGCAGC 60.244 43.478 18.45 0.00 33.55 5.25
2020 2025 1.260544 ATTTCAAACTCCAGGCAGCC 58.739 50.000 1.84 1.84 0.00 4.85
2021 2026 0.185901 TTTCAAACTCCAGGCAGCCT 59.814 50.000 8.70 8.70 0.00 4.58
2022 2027 0.250901 TTCAAACTCCAGGCAGCCTC 60.251 55.000 12.53 0.00 0.00 4.70
2023 2028 1.073722 CAAACTCCAGGCAGCCTCA 59.926 57.895 12.53 0.00 0.00 3.86
2024 2029 1.073897 AAACTCCAGGCAGCCTCAC 59.926 57.895 12.53 0.00 0.00 3.51
2025 2030 1.422161 AAACTCCAGGCAGCCTCACT 61.422 55.000 12.53 0.00 0.00 3.41
2026 2031 1.422161 AACTCCAGGCAGCCTCACTT 61.422 55.000 12.53 0.00 0.00 3.16
2027 2032 1.377994 CTCCAGGCAGCCTCACTTT 59.622 57.895 12.53 0.00 0.00 2.66
2028 2033 0.251077 CTCCAGGCAGCCTCACTTTT 60.251 55.000 12.53 0.00 0.00 2.27
2029 2034 0.185901 TCCAGGCAGCCTCACTTTTT 59.814 50.000 12.53 0.00 0.00 1.94
2059 2064 0.105964 TGAACAACCTCACCTGTCCG 59.894 55.000 0.00 0.00 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 3.872771 GACGACCTTCCACTGTAACAAAA 59.127 43.478 0.00 0.00 0.00 2.44
27 28 2.557317 ACAATTTGTGTCGACGACCTT 58.443 42.857 24.33 8.02 34.38 3.50
94 96 5.441718 AGCAGAGGATATTTGGAACAGAA 57.558 39.130 0.00 0.00 42.39 3.02
95 97 5.663106 AGTAGCAGAGGATATTTGGAACAGA 59.337 40.000 0.00 0.00 42.39 3.41
96 98 5.923204 AGTAGCAGAGGATATTTGGAACAG 58.077 41.667 0.00 0.00 42.39 3.16
97 99 5.957771 AGTAGCAGAGGATATTTGGAACA 57.042 39.130 0.00 0.00 0.00 3.18
98 100 7.769044 TGTTTAGTAGCAGAGGATATTTGGAAC 59.231 37.037 0.00 0.00 0.00 3.62
99 101 7.857456 TGTTTAGTAGCAGAGGATATTTGGAA 58.143 34.615 0.00 0.00 0.00 3.53
100 102 7.432148 TGTTTAGTAGCAGAGGATATTTGGA 57.568 36.000 0.00 0.00 0.00 3.53
101 103 7.933577 TGATGTTTAGTAGCAGAGGATATTTGG 59.066 37.037 0.00 0.00 0.00 3.28
102 104 8.893219 TGATGTTTAGTAGCAGAGGATATTTG 57.107 34.615 0.00 0.00 0.00 2.32
328 331 1.002430 CAGGCAAAGCTAGTGGTCAGA 59.998 52.381 0.00 0.00 0.00 3.27
486 489 3.777106 TTGGAAGAAGCACACTGAGAT 57.223 42.857 0.00 0.00 0.00 2.75
520 523 4.754372 TCTCAAACTCACATCAACATGC 57.246 40.909 0.00 0.00 32.57 4.06
575 578 5.083533 TGTTGAAACTTGAAACCATGCTT 57.916 34.783 0.00 0.00 0.00 3.91
623 627 7.500227 TCATTTCATCCCACAATCTTGATAGAC 59.500 37.037 0.00 0.00 31.99 2.59
629 633 6.320418 TCATCTCATTTCATCCCACAATCTTG 59.680 38.462 0.00 0.00 0.00 3.02
650 654 3.769844 TGGGAGACTAGACCTTTGTCATC 59.230 47.826 0.00 0.00 44.33 2.92
689 693 9.983024 TGTATTAAATTTGTAGGGAGGAATCAA 57.017 29.630 0.00 0.00 0.00 2.57
691 695 9.403583 TGTGTATTAAATTTGTAGGGAGGAATC 57.596 33.333 0.00 0.00 0.00 2.52
719 723 2.231478 ACCGACTCACCACACTAATCTG 59.769 50.000 0.00 0.00 0.00 2.90
772 776 2.411547 GCAGTACGCAATGAGTTGACAC 60.412 50.000 0.00 0.00 41.79 3.67
787 791 4.083484 GGTGGTGATTTGTGTTAGCAGTAC 60.083 45.833 0.00 0.00 0.00 2.73
831 835 5.578157 TTTATATAGAGGGGGAAGCCAAC 57.422 43.478 0.00 0.00 0.00 3.77
832 836 6.069615 GCTATTTATATAGAGGGGGAAGCCAA 60.070 42.308 4.55 0.00 36.62 4.52
864 868 0.235926 GTGGAACAAAGAGTGAGCGC 59.764 55.000 0.00 0.00 44.16 5.92
910 914 2.590611 AGGTCAGGGGACTAGTAATGGA 59.409 50.000 0.00 0.00 43.77 3.41
935 939 2.232208 CCAGCAGGGAGAAATTTTCCAC 59.768 50.000 16.32 0.00 40.01 4.02
969 973 6.722328 TCTATTTTTCTTTCTCTCCTTCCCC 58.278 40.000 0.00 0.00 0.00 4.81
1011 1015 3.761218 TCTTGTTCTGTTTTGCTGTCCAA 59.239 39.130 0.00 0.00 0.00 3.53
1221 1225 1.207593 GTTGCCGTTGCTACTGCTG 59.792 57.895 14.76 0.00 39.67 4.41
1310 1314 3.072944 GAGCATATGAAGAGGATGCACC 58.927 50.000 6.97 0.00 46.78 5.01
1394 1398 7.575414 TGACCAAAAGCTACAAAATCAAGTA 57.425 32.000 0.00 0.00 0.00 2.24
1511 1515 2.032030 CAGACACTTAAACACAAGCCGG 60.032 50.000 0.00 0.00 0.00 6.13
1634 1638 3.540314 ATGCAAGGCACAAGTCAAAAA 57.460 38.095 0.00 0.00 43.04 1.94
1635 1639 4.099266 AGTTATGCAAGGCACAAGTCAAAA 59.901 37.500 0.00 0.00 43.04 2.44
1636 1640 3.636300 AGTTATGCAAGGCACAAGTCAAA 59.364 39.130 0.00 0.00 43.04 2.69
1637 1641 3.221771 AGTTATGCAAGGCACAAGTCAA 58.778 40.909 0.00 0.00 43.04 3.18
1638 1642 2.862541 AGTTATGCAAGGCACAAGTCA 58.137 42.857 0.00 0.00 43.04 3.41
1639 1643 3.923017 AAGTTATGCAAGGCACAAGTC 57.077 42.857 0.00 0.00 43.04 3.01
1640 1644 4.766891 ACATAAGTTATGCAAGGCACAAGT 59.233 37.500 20.52 0.00 43.04 3.16
1641 1645 5.097529 CACATAAGTTATGCAAGGCACAAG 58.902 41.667 20.52 0.00 43.04 3.16
1642 1646 4.764308 TCACATAAGTTATGCAAGGCACAA 59.236 37.500 20.52 0.00 43.04 3.33
1643 1647 4.331108 TCACATAAGTTATGCAAGGCACA 58.669 39.130 20.52 0.00 43.04 4.57
1644 1648 4.963276 TCACATAAGTTATGCAAGGCAC 57.037 40.909 20.52 0.00 43.04 5.01
1645 1649 6.828273 ACTAATCACATAAGTTATGCAAGGCA 59.172 34.615 20.52 0.00 44.86 4.75
1646 1650 7.264373 ACTAATCACATAAGTTATGCAAGGC 57.736 36.000 20.52 0.00 39.79 4.35
1647 1651 9.507280 CAAACTAATCACATAAGTTATGCAAGG 57.493 33.333 20.52 9.61 39.79 3.61
1650 1654 9.225436 TGTCAAACTAATCACATAAGTTATGCA 57.775 29.630 20.52 9.64 39.79 3.96
1935 1940 0.317799 TTTGCGCATTGTTGGCAGAT 59.682 45.000 12.75 0.00 38.04 2.90
1940 1945 2.801679 AGTTGAATTTGCGCATTGTTGG 59.198 40.909 12.75 0.00 0.00 3.77
1949 1954 7.967854 TGTATCTTCCATTTAGTTGAATTTGCG 59.032 33.333 0.00 0.00 0.00 4.85
2039 2044 1.594331 GGACAGGTGAGGTTGTTCAC 58.406 55.000 0.00 0.00 45.28 3.18
2040 2045 0.105964 CGGACAGGTGAGGTTGTTCA 59.894 55.000 0.00 0.00 0.00 3.18
2041 2046 0.106149 ACGGACAGGTGAGGTTGTTC 59.894 55.000 0.00 0.00 0.00 3.18
2042 2047 0.179056 CACGGACAGGTGAGGTTGTT 60.179 55.000 0.00 0.00 40.38 2.83
2043 2048 1.046472 TCACGGACAGGTGAGGTTGT 61.046 55.000 0.00 0.00 41.76 3.32
2059 2064 0.533531 TGCCGGCAGATCATCATCAC 60.534 55.000 29.03 0.00 0.00 3.06
2107 2112 6.276847 CACTAAACTGGATCAGATAGTGTCC 58.723 44.000 22.13 0.00 42.64 4.02


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

AutoCloner maintained by Alex Coulton.