Multiple sequence alignment - TraesCS6B01G210300

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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 TraesCS6B01G210300 chr6B 100.000 2749 0 0 1 2749 277625587 277622839 0.000000e+00 5077.0
1 TraesCS6B01G210300 chr6A 96.466 2377 57 9 390 2749 206353119 206350753 0.000000e+00 3899.0
2 TraesCS6B01G210300 chr6A 95.833 408 16 1 1 408 206353537 206353131 0.000000e+00 658.0
3 TraesCS6B01G210300 chr6D 95.518 2075 51 10 689 2749 153865973 153863927 0.000000e+00 3278.0
4 TraesCS6B01G210300 chr6D 97.500 120 3 0 1 120 153866848 153866729 3.590000e-49 206.0
5 TraesCS6B01G210300 chr6D 90.323 62 6 0 1024 1085 443741329 443741268 6.310000e-12 82.4
6 TraesCS6B01G210300 chr7A 82.507 383 45 19 1213 1574 549357823 549357442 1.590000e-82 316.0
7 TraesCS6B01G210300 chr7A 86.364 110 14 1 988 1097 549358129 549358021 4.810000e-23 119.0
8 TraesCS6B01G210300 chr7A 94.231 52 3 0 1035 1086 97266971 97267022 2.270000e-11 80.5
9 TraesCS6B01G210300 chr7B 81.316 380 52 14 1213 1574 508195344 508194966 9.630000e-75 291.0
10 TraesCS6B01G210300 chr7B 88.298 94 10 1 998 1090 508195648 508195555 8.050000e-21 111.0
11 TraesCS6B01G210300 chr7D 83.721 129 16 4 988 1115 482134350 482134226 1.730000e-22 117.0
12 TraesCS6B01G210300 chr7D 94.231 52 3 0 1035 1086 93949351 93949300 2.270000e-11 80.5
13 TraesCS6B01G210300 chr7D 94.231 52 3 0 1035 1086 94005584 94005635 2.270000e-11 80.5


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 TraesCS6B01G210300 chr6B 277622839 277625587 2748 True 5077.0 5077 100.0000 1 2749 1 chr6B.!!$R1 2748
1 TraesCS6B01G210300 chr6A 206350753 206353537 2784 True 2278.5 3899 96.1495 1 2749 2 chr6A.!!$R1 2748
2 TraesCS6B01G210300 chr6D 153863927 153866848 2921 True 1742.0 3278 96.5090 1 2749 2 chr6D.!!$R2 2748
3 TraesCS6B01G210300 chr7A 549357442 549358129 687 True 217.5 316 84.4355 988 1574 2 chr7A.!!$R1 586
4 TraesCS6B01G210300 chr7B 508194966 508195648 682 True 201.0 291 84.8070 998 1574 2 chr7B.!!$R1 576

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
980 1623 0.596577 TCGTTCCCTCGTCTGTGAAG 59.403 55.0 0.0 0.0 0.0 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1804 2615 1.16342 TGCTTGCGTACCAACCAGTG 61.163 55.0 0.0 0.0 0.0 3.66 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
124 473 7.066284 GCACAAGTCTTACCATATTGACAATCT 59.934 37.037 3.36 0.00 32.41 2.40
144 493 9.950496 ACAATCTAAACAGAAGTCTTGACATAT 57.050 29.630 3.49 0.00 0.00 1.78
191 540 3.520862 CATGCGTCCCATGGCACC 61.521 66.667 6.09 0.00 46.09 5.01
217 566 2.605257 CCATGATTGGATTGGGCATCT 58.395 47.619 0.00 0.00 46.92 2.90
275 876 4.441356 GGTGAGCTCTCTTTCTGTATCTGG 60.441 50.000 16.19 0.00 0.00 3.86
292 893 1.606668 CTGGCTCGGTTTTACTTGCAA 59.393 47.619 0.00 0.00 0.00 4.08
425 1056 9.883142 AATAATAATCTCGGGATCTGATCTTTC 57.117 33.333 16.61 6.82 0.00 2.62
550 1181 4.216411 AGGTGAGCGTGTTTATTACCAT 57.784 40.909 0.00 0.00 0.00 3.55
671 1302 1.075425 CGCTCTTGTCTTCTGCCTCG 61.075 60.000 0.00 0.00 0.00 4.63
980 1623 0.596577 TCGTTCCCTCGTCTGTGAAG 59.403 55.000 0.00 0.00 0.00 3.02
994 1641 2.666317 TGTGAAGGACAGACAGACAGA 58.334 47.619 0.00 0.00 0.00 3.41
995 1642 3.031013 TGTGAAGGACAGACAGACAGAA 58.969 45.455 0.00 0.00 0.00 3.02
996 1643 3.181475 TGTGAAGGACAGACAGACAGAAC 60.181 47.826 0.00 0.00 0.00 3.01
997 1644 3.031013 TGAAGGACAGACAGACAGAACA 58.969 45.455 0.00 0.00 0.00 3.18
1023 1670 3.355626 GTGCAACCCAAGAAGAAGTTC 57.644 47.619 0.00 0.00 0.00 3.01
1102 1756 1.004361 TAAGCCCCTCCCCTCCTTC 59.996 63.158 0.00 0.00 0.00 3.46
1133 1916 3.068873 CCTCGATTCCCTCTAACTTCCTG 59.931 52.174 0.00 0.00 0.00 3.86
1140 1923 6.607004 TTCCCTCTAACTTCCTGTAAAGAG 57.393 41.667 0.00 0.00 38.05 2.85
1204 1989 2.810852 TGCATGCGTGTCTTTGTGAATA 59.189 40.909 14.09 0.00 0.00 1.75
1679 2490 1.094073 GGCTCACGCTGCAGATGATT 61.094 55.000 20.43 0.00 36.09 2.57
1771 2582 0.806868 AGCATGGACGAAACAGCATG 59.193 50.000 0.00 0.00 46.00 4.06
1804 2615 0.882474 CCGAGATCAGGATCCCGTAC 59.118 60.000 8.55 0.00 37.35 3.67
2106 2922 7.325660 ACATGATGAAGGTGATATTTGTGAC 57.674 36.000 0.00 0.00 0.00 3.67
2126 2942 3.215975 ACGAAGACCTCAGCTCTATACC 58.784 50.000 0.00 0.00 0.00 2.73
2165 2981 4.827789 ACCATGGGCTCTAGAGGTTTATA 58.172 43.478 21.23 0.00 0.00 0.98
2168 2984 6.440965 ACCATGGGCTCTAGAGGTTTATATAC 59.559 42.308 21.23 1.02 0.00 1.47
2182 2998 9.331282 GAGGTTTATATACACAGAAGAAAGCAT 57.669 33.333 1.66 0.00 0.00 3.79
2201 3017 8.538409 AAAGCATCAACCATTTTCTTGTATTC 57.462 30.769 0.00 0.00 0.00 1.75
2398 3217 3.692593 CACAATTCCATCATCTGCAGTCA 59.307 43.478 14.67 0.00 0.00 3.41
2563 3382 8.764287 CGTAGATGTATGAGTATGCATTTTTCA 58.236 33.333 3.54 7.22 39.34 2.69
2611 3430 2.977808 ACTCTCCCAGACCAAAGAAGA 58.022 47.619 0.00 0.00 0.00 2.87
2707 3526 5.105716 CCTTGAGAGTCGTATTTCTCCTCAA 60.106 44.000 0.00 0.00 39.23 3.02
2709 3528 5.895928 TGAGAGTCGTATTTCTCCTCAATG 58.104 41.667 0.00 0.00 39.23 2.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 54 3.699779 TTTTGTGCTTTGTGTGCGATA 57.300 38.095 0.00 0.00 0.00 2.92
98 99 6.494893 TTGTCAATATGGTAAGACTTGTGC 57.505 37.500 0.00 0.00 32.41 4.57
124 473 8.807118 AGACTGATATGTCAAGACTTCTGTTTA 58.193 33.333 1.53 0.00 39.27 2.01
144 493 2.878406 GGCACTTAACTGCAAAGACTGA 59.122 45.455 8.98 0.00 39.08 3.41
217 566 0.978667 TAGCTAATGGCCGTGGTCCA 60.979 55.000 0.00 4.83 43.05 4.02
275 876 3.349488 AAGTTGCAAGTAAAACCGAGC 57.651 42.857 7.33 0.00 0.00 5.03
292 893 7.833285 ATAATGTTACAAACCAGGACAAAGT 57.167 32.000 0.00 0.00 0.00 2.66
425 1056 4.205065 AGCCATGTCTTCTCTTCTTCTG 57.795 45.455 0.00 0.00 0.00 3.02
434 1065 4.353777 TCCTACAACTAGCCATGTCTTCT 58.646 43.478 0.20 0.00 0.00 2.85
550 1181 1.906574 CCACCTTCCCTGCTAGTACAA 59.093 52.381 0.00 0.00 0.00 2.41
868 1510 0.801251 CAGCCTGTACTTGCTTCTGC 59.199 55.000 6.93 0.00 35.12 4.26
869 1511 1.446907 CCAGCCTGTACTTGCTTCTG 58.553 55.000 6.93 0.58 35.12 3.02
870 1512 0.326264 CCCAGCCTGTACTTGCTTCT 59.674 55.000 6.93 0.00 35.12 2.85
871 1513 1.308783 GCCCAGCCTGTACTTGCTTC 61.309 60.000 6.93 0.00 35.12 3.86
872 1514 1.303643 GCCCAGCCTGTACTTGCTT 60.304 57.895 6.93 0.00 35.12 3.91
873 1515 2.352805 GCCCAGCCTGTACTTGCT 59.647 61.111 4.17 4.17 38.67 3.91
980 1623 4.023707 CCATTTTGTTCTGTCTGTCTGTCC 60.024 45.833 0.00 0.00 0.00 4.02
986 1629 3.023119 TGCACCATTTTGTTCTGTCTGT 58.977 40.909 0.00 0.00 0.00 3.41
991 1638 2.158986 TGGGTTGCACCATTTTGTTCTG 60.159 45.455 7.49 0.00 41.02 3.02
992 1639 2.114616 TGGGTTGCACCATTTTGTTCT 58.885 42.857 7.49 0.00 41.02 3.01
993 1640 2.611225 TGGGTTGCACCATTTTGTTC 57.389 45.000 7.49 0.00 41.02 3.18
994 1641 2.503356 TCTTGGGTTGCACCATTTTGTT 59.497 40.909 0.00 0.00 41.02 2.83
995 1642 2.114616 TCTTGGGTTGCACCATTTTGT 58.885 42.857 0.00 0.00 41.02 2.83
996 1643 2.906691 TCTTGGGTTGCACCATTTTG 57.093 45.000 0.00 0.00 41.02 2.44
997 1644 3.037549 TCTTCTTGGGTTGCACCATTTT 58.962 40.909 0.00 0.00 41.02 1.82
1102 1756 0.682292 GGGAATCGAGGGAAGCTAGG 59.318 60.000 0.00 0.00 0.00 3.02
1133 1916 3.808174 ACGAAGAAACCACTGCTCTTTAC 59.192 43.478 0.00 0.00 29.59 2.01
1140 1923 1.390463 GATCGACGAAGAAACCACTGC 59.610 52.381 0.00 0.00 0.00 4.40
1204 1989 2.177016 AGCCACACCCTCCTTTTACTTT 59.823 45.455 0.00 0.00 0.00 2.66
1804 2615 1.163420 TGCTTGCGTACCAACCAGTG 61.163 55.000 0.00 0.00 0.00 3.66
2024 2837 3.411446 TGAAGTTGAACGAAGGCATGAT 58.589 40.909 0.00 0.00 0.00 2.45
2106 2922 3.003897 GTGGTATAGAGCTGAGGTCTTCG 59.996 52.174 20.11 0.00 40.94 3.79
2126 2942 5.068198 CCCATGGTCCTTAGAAATGATTGTG 59.932 44.000 11.73 0.00 0.00 3.33
2165 2981 5.316167 TGGTTGATGCTTTCTTCTGTGTAT 58.684 37.500 0.00 0.00 0.00 2.29
2168 2984 4.778534 ATGGTTGATGCTTTCTTCTGTG 57.221 40.909 0.00 0.00 0.00 3.66
2182 2998 6.072230 TCGCATGAATACAAGAAAATGGTTGA 60.072 34.615 0.00 0.00 0.00 3.18
2201 3017 7.751793 ACAATAAATGCATACACATATCGCATG 59.248 33.333 0.00 0.00 36.50 4.06
2337 3156 2.754946 CCAAGTTGTAGGCTTCGGTA 57.245 50.000 1.45 0.00 0.00 4.02
2563 3382 9.907229 CTAGGTGGATTTCTTAGGATTTAGTTT 57.093 33.333 0.00 0.00 0.00 2.66
2611 3430 5.010282 GGTTGATCATTCACACCCTTAAGT 58.990 41.667 0.00 0.00 31.89 2.24
2707 3526 3.861113 GTGCATTGCATTTCGTCATTCAT 59.139 39.130 15.49 0.00 41.91 2.57
2709 3528 3.244156 TGTGCATTGCATTTCGTCATTC 58.756 40.909 15.49 0.00 41.91 2.67


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

AutoCloner maintained by Alex Coulton.