Multiple sequence alignment - TraesCS6B01G382600

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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 TraesCS6B01G382600 chr6B 100.000 3843 0 0 1 3843 657654352 657650510 0.000000e+00 7097
1 TraesCS6B01G382600 chr6D 97.573 2472 45 8 1382 3843 434484692 434482226 0.000000e+00 4218
2 TraesCS6B01G382600 chr6D 92.043 1106 51 10 134 1220 434486054 434484967 0.000000e+00 1520
3 TraesCS6B01G382600 chr6A 89.650 2541 128 59 1352 3843 581841404 581838950 0.000000e+00 3110
4 TraesCS6B01G382600 chr6A 88.338 1149 101 16 93 1220 581842769 581841633 0.000000e+00 1349
5 TraesCS6B01G382600 chr6A 97.260 73 1 1 5 77 581844249 581844178 5.210000e-24 122
6 TraesCS6B01G382600 chr4A 75.452 941 166 39 1917 2825 595936406 595937313 7.740000e-107 398


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 TraesCS6B01G382600 chr6B 657650510 657654352 3842 True 7097 7097 100.000000 1 3843 1 chr6B.!!$R1 3842
1 TraesCS6B01G382600 chr6D 434482226 434486054 3828 True 2869 4218 94.808000 134 3843 2 chr6D.!!$R1 3709
2 TraesCS6B01G382600 chr6A 581838950 581844249 5299 True 1527 3110 91.749333 5 3843 3 chr6A.!!$R1 3838
3 TraesCS6B01G382600 chr4A 595936406 595937313 907 False 398 398 75.452000 1917 2825 1 chr4A.!!$F1 908

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
516 1915 0.100682 TGCGATGTTCCGAGCTAGAC 59.899 55.0 0.00 0.00 0.00 2.59 F
518 1917 0.656259 CGATGTTCCGAGCTAGACGA 59.344 55.0 10.50 0.00 0.00 4.20 F
666 2065 0.659123 GCGTTTGTTTTCCGCACGAT 60.659 50.0 0.00 0.00 46.26 3.73 F
769 2175 0.839946 TTTCAGATCTGGGCCTAGGC 59.160 55.0 26.55 26.55 41.06 3.93 F
825 2233 1.451067 ACTAGAGTGACCGTTCTCCG 58.549 55.0 0.00 0.00 0.00 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2324 3877 0.185175 TGCCATAGCTCGGACTCCTA 59.815 55.000 6.28 0.0 40.80 2.94 R
2507 4074 2.355756 AGGCGCACATAAGCAACAATAG 59.644 45.455 10.83 0.0 34.54 1.73 R
2516 4083 3.684788 ACAAAGTAGAAGGCGCACATAAG 59.315 43.478 10.83 0.0 0.00 1.73 R
2783 4357 5.477291 CCAGTATGAGAATAGGACACGGTAT 59.523 44.000 0.00 0.0 39.69 2.73 R
2873 4447 7.598278 CAGAGCTAAAGAGTAACTTCTCTCAA 58.402 38.462 0.00 0.0 43.03 3.02 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
85 86 6.528014 TTTTTAAAGCATGCTGTGTTCATG 57.472 33.333 23.48 0.00 43.02 3.07
90 91 1.977188 CATGCTGTGTTCATGCTGTG 58.023 50.000 0.00 0.00 35.48 3.66
91 92 1.268625 CATGCTGTGTTCATGCTGTGT 59.731 47.619 0.00 0.00 35.48 3.72
96 1490 2.536803 CTGTGTTCATGCTGTGTTTTGC 59.463 45.455 0.00 0.00 0.00 3.68
104 1498 1.134226 GCTGTGTTTTGCAGTGATGC 58.866 50.000 0.00 0.00 36.42 3.91
110 1504 2.224018 TGTTTTGCAGTGATGCTTTCCC 60.224 45.455 0.00 0.00 35.49 3.97
112 1506 1.999648 TTGCAGTGATGCTTTCCCTT 58.000 45.000 0.00 0.00 35.49 3.95
113 1507 1.538047 TGCAGTGATGCTTTCCCTTC 58.462 50.000 0.00 0.00 35.49 3.46
115 1509 1.888512 GCAGTGATGCTTTCCCTTCAA 59.111 47.619 0.00 0.00 0.00 2.69
116 1510 2.094854 GCAGTGATGCTTTCCCTTCAAG 60.095 50.000 0.00 0.00 0.00 3.02
123 1517 1.740025 GCTTTCCCTTCAAGATGGTCG 59.260 52.381 0.00 0.00 0.00 4.79
141 1535 4.119862 GGTCGTATGATGCATTGTACAGT 58.880 43.478 17.34 0.00 0.00 3.55
352 1751 3.449227 CAGACTCGCCCCGTGCTA 61.449 66.667 0.00 0.00 38.05 3.49
354 1753 4.849329 GACTCGCCCCGTGCTACG 62.849 72.222 2.27 2.27 42.11 3.51
497 1896 3.518419 TTGTTACGGCCGCCTCGTT 62.518 57.895 28.58 7.06 41.38 3.85
516 1915 0.100682 TGCGATGTTCCGAGCTAGAC 59.899 55.000 0.00 0.00 0.00 2.59
518 1917 0.656259 CGATGTTCCGAGCTAGACGA 59.344 55.000 10.50 0.00 0.00 4.20
666 2065 0.659123 GCGTTTGTTTTCCGCACGAT 60.659 50.000 0.00 0.00 46.26 3.73
687 2086 6.485984 ACGATGTTAGGTAGTATCTCGATGTT 59.514 38.462 0.00 0.00 0.00 2.71
701 2100 2.745281 TCGATGTTGAAAATTCGGGGAC 59.255 45.455 0.00 0.00 35.76 4.46
769 2175 0.839946 TTTCAGATCTGGGCCTAGGC 59.160 55.000 26.55 26.55 41.06 3.93
777 2183 3.054779 TCTGGGCCTAGGCTATTGTTA 57.945 47.619 32.18 9.79 41.60 2.41
781 2187 2.438392 GGGCCTAGGCTATTGTTACTGT 59.562 50.000 32.18 0.00 41.60 3.55
789 2196 8.038944 CCTAGGCTATTGTTACTGTTTTGTCTA 58.961 37.037 0.00 0.00 0.00 2.59
813 2220 7.272144 AGATTTGAATTGGGGTAACTAGAGT 57.728 36.000 0.00 0.00 0.00 3.24
817 2225 4.224370 TGAATTGGGGTAACTAGAGTGACC 59.776 45.833 7.61 7.61 46.84 4.02
824 2232 3.128415 GGTAACTAGAGTGACCGTTCTCC 59.872 52.174 0.16 0.00 39.63 3.71
825 2233 1.451067 ACTAGAGTGACCGTTCTCCG 58.549 55.000 0.00 0.00 0.00 4.63
836 2244 4.218200 TGACCGTTCTCCGTAAATAGTTCA 59.782 41.667 0.00 0.00 33.66 3.18
888 2298 5.411361 TGTAACATGCAGTTGGTGATCTAAC 59.589 40.000 10.59 0.00 41.50 2.34
899 2309 9.684448 CAGTTGGTGATCTAACAGTGTATATAG 57.316 37.037 0.00 0.00 37.47 1.31
1104 2520 1.455786 CGAAGGTCAGTACAGTTTGCG 59.544 52.381 0.00 0.00 0.00 4.85
1163 2579 5.106869 TGCGTGAATTCACTTATTGTGTACC 60.107 40.000 30.45 5.56 46.27 3.34
1195 2612 3.143728 TCATGCATGCCAGTGCTTATAG 58.856 45.455 22.25 0.00 45.27 1.31
1198 2615 2.149578 GCATGCCAGTGCTTATAGAGG 58.850 52.381 6.36 0.00 41.82 3.69
1216 2693 5.463051 AGAGGGATGTTGGATCTTTGAAT 57.537 39.130 0.00 0.00 0.00 2.57
1230 2707 9.642327 TGGATCTTTGAATCAATTATGTTGTTG 57.358 29.630 0.00 0.00 0.00 3.33
1286 2785 5.914635 TCATGTTTGAATCGACTCTTTTTGC 59.085 36.000 0.00 0.00 0.00 3.68
1289 2788 6.272318 TGTTTGAATCGACTCTTTTTGCAAT 58.728 32.000 0.00 0.00 0.00 3.56
1291 2790 6.752335 TTGAATCGACTCTTTTTGCAATTG 57.248 33.333 0.00 0.00 0.00 2.32
1292 2791 6.070897 TGAATCGACTCTTTTTGCAATTGA 57.929 33.333 10.34 0.00 0.00 2.57
1323 2822 7.952671 TCAAATATGTCCTACTATCCAGTGAC 58.047 38.462 0.00 0.00 36.14 3.67
1341 2840 6.350528 CCAGTGACATGCTTTCTACTTCTAGA 60.351 42.308 0.00 0.00 0.00 2.43
1372 2916 8.830915 TTGTCTTAAGAACTCCTATCTCTGAT 57.169 34.615 6.78 0.00 0.00 2.90
1438 2982 6.207417 AGACATGCTGCTTATTTAAGTGTGTT 59.793 34.615 0.00 0.00 35.75 3.32
1451 2995 6.576662 TTAAGTGTGTTTGAACCTTGAACA 57.423 33.333 0.00 0.00 0.00 3.18
1460 3004 7.158021 TGTTTGAACCTTGAACACATTTTTCT 58.842 30.769 0.00 0.00 0.00 2.52
1463 3007 9.712305 TTTGAACCTTGAACACATTTTTCTTTA 57.288 25.926 0.00 0.00 0.00 1.85
1549 3094 7.173218 TGAGATGATCAGTTGTTCCTTTGTAAC 59.827 37.037 0.09 0.00 32.77 2.50
1555 3100 6.880484 TCAGTTGTTCCTTTGTAACTACTCA 58.120 36.000 0.00 0.00 39.70 3.41
1585 3130 7.336931 GGCTTGGTGTAGATTAAGATTTTCTCA 59.663 37.037 0.00 0.00 0.00 3.27
1825 3370 5.472148 TGGCAAATGTCTGATTAGCAAAAG 58.528 37.500 0.00 0.00 0.00 2.27
2005 3550 8.994429 TTCTGAGTTCTTAGATCATGAACTTC 57.006 34.615 20.82 16.09 46.31 3.01
2324 3877 1.751927 CCGCAGTCCTAGGTACCGT 60.752 63.158 9.08 0.00 0.00 4.83
2866 4440 0.745845 GAAGCCTGTGTCCGATGCAT 60.746 55.000 0.00 0.00 0.00 3.96
2873 4447 2.485426 CTGTGTCCGATGCATTGTTCTT 59.515 45.455 13.01 0.00 0.00 2.52
3537 5123 7.746475 CGAGAGTCAATCCATTTAAACAGTTTC 59.254 37.037 0.48 0.00 0.00 2.78
3568 5166 3.808466 TCAGCAGTCATATTCTTCGCT 57.192 42.857 0.00 0.00 0.00 4.93
3674 5307 3.508402 TCCTCGACAACTACACTGCATAA 59.492 43.478 0.00 0.00 0.00 1.90
3711 5344 2.017458 CTGCGTGCACTGCATAGTCG 62.017 60.000 27.77 16.64 41.91 4.18
3713 5346 2.802667 CGTGCACTGCATAGTCGCC 61.803 63.158 16.19 0.00 41.91 5.54
3749 5382 2.201436 CTGCACTGCGTAGTCTCCGT 62.201 60.000 2.06 0.00 34.07 4.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.502962 TGATTTCATTCAAATTTCCCGGC 58.497 39.130 0.00 0.00 34.60 6.13
1 2 6.650390 AGTTTGATTTCATTCAAATTTCCCGG 59.350 34.615 0.00 0.00 44.80 5.73
2 3 7.656707 AGTTTGATTTCATTCAAATTTCCCG 57.343 32.000 3.25 0.00 44.80 5.14
77 78 2.536803 CTGCAAAACACAGCATGAACAC 59.463 45.455 0.00 0.00 39.69 3.32
79 80 2.536803 CACTGCAAAACACAGCATGAAC 59.463 45.455 0.00 0.00 39.69 3.18
82 83 2.495409 TCACTGCAAAACACAGCATG 57.505 45.000 0.00 0.00 40.42 4.06
83 84 3.021269 CATCACTGCAAAACACAGCAT 57.979 42.857 0.00 0.00 40.42 3.79
84 85 2.495409 CATCACTGCAAAACACAGCA 57.505 45.000 0.00 0.00 38.79 4.41
90 91 7.688325 TGAAGGGAAAGCATCACTGCAAAAC 62.688 44.000 0.10 0.00 44.68 2.43
91 92 5.714796 TGAAGGGAAAGCATCACTGCAAAA 61.715 41.667 0.10 0.00 44.68 2.44
96 1490 3.415212 TCTTGAAGGGAAAGCATCACTG 58.585 45.455 0.00 0.00 42.52 3.66
104 1498 3.059352 ACGACCATCTTGAAGGGAAAG 57.941 47.619 0.00 0.00 31.53 2.62
110 1504 4.122046 TGCATCATACGACCATCTTGAAG 58.878 43.478 0.00 0.00 0.00 3.02
112 1506 3.817709 TGCATCATACGACCATCTTGA 57.182 42.857 0.00 0.00 0.00 3.02
113 1507 4.274214 ACAATGCATCATACGACCATCTTG 59.726 41.667 0.00 0.00 0.00 3.02
115 1509 4.077300 ACAATGCATCATACGACCATCT 57.923 40.909 0.00 0.00 0.00 2.90
116 1510 4.749598 TGTACAATGCATCATACGACCATC 59.250 41.667 0.00 0.00 0.00 3.51
123 1517 5.220854 GGTTGGACTGTACAATGCATCATAC 60.221 44.000 8.98 6.51 0.00 2.39
141 1535 3.135895 GCTAGTAGGCTTATTGGGTTGGA 59.864 47.826 0.00 0.00 0.00 3.53
239 1633 3.315949 GCCGGTGGTGGTACAGGA 61.316 66.667 1.90 0.00 41.80 3.86
241 1635 4.404098 GGGCCGGTGGTGGTACAG 62.404 72.222 1.90 0.00 41.80 2.74
281 1675 4.394712 AAGCGAGGCTTCCGGGTG 62.395 66.667 0.00 0.00 46.77 4.61
497 1896 0.100682 GTCTAGCTCGGAACATCGCA 59.899 55.000 0.00 0.00 0.00 5.10
666 2065 7.634671 TTCAACATCGAGATACTACCTAACA 57.365 36.000 0.00 0.00 0.00 2.41
687 2086 4.376225 ACTAAAGGTCCCCGAATTTTCA 57.624 40.909 0.00 0.00 0.00 2.69
702 2101 9.573133 CCAATTCAATTACAGCCTTAACTAAAG 57.427 33.333 0.00 0.00 34.73 1.85
719 2118 3.588842 TCTGGAGAGTCCACCAATTCAAT 59.411 43.478 7.83 0.00 42.67 2.57
777 2183 7.255942 CCCCAATTCAAATCTAGACAAAACAGT 60.256 37.037 0.00 0.00 0.00 3.55
781 2187 8.581578 GTTACCCCAATTCAAATCTAGACAAAA 58.418 33.333 0.00 0.00 0.00 2.44
789 2196 7.037586 TCACTCTAGTTACCCCAATTCAAATCT 60.038 37.037 0.00 0.00 0.00 2.40
819 2227 6.555463 ATTCCCTGAACTATTTACGGAGAA 57.445 37.500 0.00 0.00 0.00 2.87
824 2232 6.436843 AGCAAATTCCCTGAACTATTTACG 57.563 37.500 0.00 0.00 0.00 3.18
825 2233 8.732746 TCTAGCAAATTCCCTGAACTATTTAC 57.267 34.615 0.00 0.00 0.00 2.01
854 2262 4.573201 AACTGCATGTTACACAACGTAAGT 59.427 37.500 0.00 0.00 46.24 2.24
888 2298 4.278669 AGGCCGACAAGACTATATACACTG 59.721 45.833 0.00 0.00 0.00 3.66
899 2309 1.860078 CACGAAAGGCCGACAAGAC 59.140 57.895 0.00 0.00 0.00 3.01
1065 2475 1.555477 GCAAAACTCCAAACACACGG 58.445 50.000 0.00 0.00 0.00 4.94
1159 2575 3.138304 TGCATGATTATCCTTGCGGTAC 58.862 45.455 0.00 0.00 39.27 3.34
1163 2579 2.592194 GCATGCATGATTATCCTTGCG 58.408 47.619 30.64 0.00 39.27 4.85
1195 2612 5.195940 TGATTCAAAGATCCAACATCCCTC 58.804 41.667 0.00 0.00 0.00 4.30
1198 2615 9.472361 CATAATTGATTCAAAGATCCAACATCC 57.528 33.333 2.68 0.00 0.00 3.51
1255 2732 8.048534 AGAGTCGATTCAAACATGAATGAAAT 57.951 30.769 17.42 9.43 38.88 2.17
1303 2802 5.243954 GCATGTCACTGGATAGTAGGACATA 59.756 44.000 10.93 0.00 43.29 2.29
1310 2809 5.939764 AGAAAGCATGTCACTGGATAGTA 57.060 39.130 0.00 0.00 34.74 1.82
1323 2822 4.808364 GCACCTCTAGAAGTAGAAAGCATG 59.192 45.833 0.00 0.00 34.73 4.06
1341 2840 3.648545 AGGAGTTCTTAAGACAAGCACCT 59.351 43.478 4.18 6.67 0.00 4.00
1438 2982 9.712305 TTAAAGAAAAATGTGTTCAAGGTTCAA 57.288 25.926 0.00 0.00 0.00 2.69
1460 3004 9.179909 TGAAGTTCTGAACCACACTATTTTAAA 57.820 29.630 16.48 0.00 0.00 1.52
1463 3007 7.823745 ATGAAGTTCTGAACCACACTATTTT 57.176 32.000 16.48 1.62 0.00 1.82
1467 3011 7.482169 AGATATGAAGTTCTGAACCACACTA 57.518 36.000 16.48 10.95 0.00 2.74
1468 3012 6.365970 AGATATGAAGTTCTGAACCACACT 57.634 37.500 16.48 8.14 0.00 3.55
1471 3016 8.099364 TCAAAAGATATGAAGTTCTGAACCAC 57.901 34.615 16.48 11.32 0.00 4.16
1549 3094 4.832248 TCTACACCAAGCCATTTGAGTAG 58.168 43.478 10.50 10.50 41.47 2.57
1555 3100 7.961326 AATCTTAATCTACACCAAGCCATTT 57.039 32.000 0.00 0.00 0.00 2.32
1585 3130 4.999950 GTCAGTCCAACATGTCAAGAGATT 59.000 41.667 0.00 0.00 0.00 2.40
2005 3550 2.693797 AGTGTGCATCTGAAAAAGCG 57.306 45.000 0.00 0.00 0.00 4.68
2324 3877 0.185175 TGCCATAGCTCGGACTCCTA 59.815 55.000 6.28 0.00 40.80 2.94
2507 4074 2.355756 AGGCGCACATAAGCAACAATAG 59.644 45.455 10.83 0.00 34.54 1.73
2516 4083 3.684788 ACAAAGTAGAAGGCGCACATAAG 59.315 43.478 10.83 0.00 0.00 1.73
2783 4357 5.477291 CCAGTATGAGAATAGGACACGGTAT 59.523 44.000 0.00 0.00 39.69 2.73
2873 4447 7.598278 CAGAGCTAAAGAGTAACTTCTCTCAA 58.402 38.462 0.00 0.00 43.03 3.02
2971 4545 8.801715 TTTTAATGACAGAATCAGAAGCAAAC 57.198 30.769 0.00 0.00 41.91 2.93
3537 5123 1.416813 GACTGCTGATGAAGTCCGCG 61.417 60.000 0.00 0.00 41.91 6.46
3554 5152 7.436673 ACTTATTCAGACAGCGAAGAATATGAC 59.563 37.037 0.00 0.00 34.16 3.06
3568 5166 2.568956 AGCAGGCAGACTTATTCAGACA 59.431 45.455 0.00 0.00 0.00 3.41
3674 5307 2.159170 GCAGCAAGTAGAAGACGGAGAT 60.159 50.000 0.00 0.00 0.00 2.75
3711 5344 3.123620 CAGCAGGCAGAAGACGGC 61.124 66.667 0.00 0.00 45.11 5.68
3749 5382 3.181440 GGAGATGGCAAGACATTCCCATA 60.181 47.826 0.00 0.00 38.15 2.74


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

AutoCloner maintained by Alex Coulton.