Multiple sequence alignment - TraesCS6B01G350200

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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 TraesCS6B01G350200 chr6B 100.000 3098 0 0 1 3098 615255342 615258439 0.000000e+00 5722
1 TraesCS6B01G350200 chr6B 94.486 2430 119 7 2 2426 615181429 615183848 0.000000e+00 3731
2 TraesCS6B01G350200 chr6B 86.669 2738 309 36 283 2972 615365776 615368505 0.000000e+00 2983
3 TraesCS6B01G350200 chr6B 86.773 688 54 12 2427 3095 615184235 615184904 0.000000e+00 732
4 TraesCS6B01G350200 chr6D 94.598 2999 148 12 2 2989 409523830 409526825 0.000000e+00 4628
5 TraesCS6B01G350200 chr6D 90.000 90 9 0 3008 3097 409546734 409546823 1.950000e-22 117


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 TraesCS6B01G350200 chr6B 615255342 615258439 3097 False 5722.0 5722 100.0000 1 3098 1 chr6B.!!$F1 3097
1 TraesCS6B01G350200 chr6B 615365776 615368505 2729 False 2983.0 2983 86.6690 283 2972 1 chr6B.!!$F2 2689
2 TraesCS6B01G350200 chr6B 615181429 615184904 3475 False 2231.5 3731 90.6295 2 3095 2 chr6B.!!$F3 3093
3 TraesCS6B01G350200 chr6D 409523830 409526825 2995 False 4628.0 4628 94.5980 2 2989 1 chr6D.!!$F1 2987

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
209 210 0.250513 ATCTTCCTCCAACGCTGACC 59.749 55.000 0.00 0.0 0.00 4.02 F
223 224 0.753262 CTGACCTAGGCGCTTGGTAT 59.247 55.000 9.30 0.0 39.48 2.73 F
1427 1434 1.000394 TCATTTTGCCGTCGAGACTCA 60.000 47.619 2.82 0.0 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1806 1815 0.251165 GGAAAAGTGCCTGGCTACCA 60.251 55.000 21.03 0.00 0.00 3.25 R
1986 2002 2.027561 AGCGTAGGTTACTTCATTGGCA 60.028 45.455 0.00 0.00 27.67 4.92 R
3039 3504 0.321298 CCGGACGACCAGGTCAAAAT 60.321 55.000 20.13 1.32 38.70 1.82 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
88 89 5.012148 ACTGCATTTCTGTGACCTTAGTAGT 59.988 40.000 0.00 0.00 0.00 2.73
209 210 0.250513 ATCTTCCTCCAACGCTGACC 59.749 55.000 0.00 0.00 0.00 4.02
211 212 0.895530 CTTCCTCCAACGCTGACCTA 59.104 55.000 0.00 0.00 0.00 3.08
223 224 0.753262 CTGACCTAGGCGCTTGGTAT 59.247 55.000 9.30 0.00 39.48 2.73
295 297 2.581365 TCTAGGTCTCCCTCTAACCCA 58.419 52.381 0.00 0.00 41.45 4.51
323 325 7.508636 TGACTTCTCTAGATCCAATTAGCATCT 59.491 37.037 0.00 0.00 0.00 2.90
327 329 8.433249 TCTCTAGATCCAATTAGCATCTGATT 57.567 34.615 0.00 0.00 0.00 2.57
335 337 3.998913 TTAGCATCTGATTCCACACCA 57.001 42.857 0.00 0.00 0.00 4.17
353 355 1.511850 CATGTGCGAACCAGTCAAGA 58.488 50.000 0.00 0.00 0.00 3.02
515 517 8.970859 AATTGAATGACCCAAATTTTGTTACA 57.029 26.923 8.26 5.42 0.00 2.41
625 629 3.872696 TCAATGTAGCAACATCGTGGAT 58.127 40.909 0.00 0.00 45.79 3.41
740 744 5.412594 GTGAGTTTAGTTCTCCATGATGCAA 59.587 40.000 0.00 0.00 0.00 4.08
762 766 4.530094 TTTGCTAGGTTTCGAATATGCG 57.470 40.909 0.00 0.00 0.00 4.73
933 939 6.370442 TGTGCATGTACTTAGAATGTACCAAC 59.630 38.462 15.25 0.00 39.42 3.77
1006 1012 9.944376 TTATTGAGTTAGTTCTAGCAATGTCTT 57.056 29.630 0.00 0.00 0.00 3.01
1427 1434 1.000394 TCATTTTGCCGTCGAGACTCA 60.000 47.619 2.82 0.00 0.00 3.41
1441 1448 1.285373 AGACTCACGGTGTCCCTAGAT 59.715 52.381 8.17 0.00 35.21 1.98
1496 1503 7.011763 CCCTCAAGTCATGTGTTATGATGTTAG 59.988 40.741 0.00 0.00 0.00 2.34
1503 1510 9.325198 GTCATGTGTTATGATGTTAGTAATGGA 57.675 33.333 0.00 0.00 0.00 3.41
1605 1612 7.272037 ACTTTTCCATAATCGTCAGTTGTTT 57.728 32.000 0.00 0.00 0.00 2.83
1719 1726 2.365941 GGTAGTATCTGGAGGAGGCAAC 59.634 54.545 0.00 0.00 0.00 4.17
1752 1759 2.034305 GGTCATTGGCATTGCAGAGATC 59.966 50.000 11.39 0.00 0.00 2.75
1806 1815 6.770746 ACCGCTGTCCGTATCTATAATATT 57.229 37.500 0.00 0.00 34.38 1.28
1877 1886 3.491792 GCCGAAAATTTCCCAACTGTCAA 60.492 43.478 0.00 0.00 0.00 3.18
1967 1983 2.890371 GAGGCCTCGGAAGCGTAA 59.110 61.111 19.06 0.00 0.00 3.18
1968 1984 1.227002 GAGGCCTCGGAAGCGTAAG 60.227 63.158 19.06 0.00 43.44 2.34
1969 1985 1.664321 GAGGCCTCGGAAGCGTAAGA 61.664 60.000 19.06 0.00 43.02 2.10
1970 1986 1.043673 AGGCCTCGGAAGCGTAAGAT 61.044 55.000 0.00 0.00 43.02 2.40
1988 2004 8.633408 GCGTAAGATTTATCATCAATCATTTGC 58.367 33.333 0.00 0.00 43.02 3.68
2089 2105 1.049402 GTGTAGGAGGCCACTATCCC 58.951 60.000 5.01 0.00 36.14 3.85
2276 2294 9.602568 AATTTATATGCATGCTTTTGATGTTCA 57.397 25.926 20.33 0.00 0.00 3.18
2288 2306 9.665719 TGCTTTTGATGTTCATAGTAACTCATA 57.334 29.630 0.00 0.00 0.00 2.15
2329 2347 6.070251 TGGACCATTTAGTGATGACTGTATGT 60.070 38.462 0.00 0.00 33.21 2.29
2355 2403 8.201464 TCTACACTTCACAAGATAAGTTGACAA 58.799 33.333 0.00 0.00 33.72 3.18
2506 2952 2.968574 TGGTTTCTATTTGGCAAAGGCA 59.031 40.909 18.61 5.29 43.71 4.75
2567 3014 8.514330 ACAGACAGTAACATAACCAAGAAAAA 57.486 30.769 0.00 0.00 0.00 1.94
2592 3039 5.917541 AGAGATAGTGTTTTCGCGAAAAA 57.082 34.783 39.57 27.89 41.37 1.94
2640 3088 6.946229 AGTGATGTAACGTGTACAATTCTC 57.054 37.500 12.42 7.83 0.00 2.87
2759 3215 1.871039 CTGAAACCGGTCGAAACACAT 59.129 47.619 8.04 0.00 0.00 3.21
2763 3219 1.004320 CCGGTCGAAACACATCCCA 60.004 57.895 0.00 0.00 0.00 4.37
2767 3223 1.950909 GGTCGAAACACATCCCAAACA 59.049 47.619 0.00 0.00 0.00 2.83
2774 3230 3.025322 ACACATCCCAAACAAACCTCA 57.975 42.857 0.00 0.00 0.00 3.86
2818 3274 1.415200 TGGTTTTGGGCTGGTTAACC 58.585 50.000 18.27 18.27 38.92 2.85
2826 3282 3.498334 TGGGCTGGTTAACCGTTTTTAT 58.502 40.909 19.65 0.00 39.43 1.40
2858 3314 3.587061 TGTTGACTGGGTAGATCCACATT 59.413 43.478 0.00 0.00 38.11 2.71
2882 3338 9.880157 ATTAGCAATTAATCTCAACAAAGCATT 57.120 25.926 0.00 0.00 0.00 3.56
2891 3348 6.826893 TCTCAACAAAGCATTGCTAAAAAC 57.173 33.333 12.39 0.00 38.25 2.43
2994 3452 5.194432 TCTACTAACTCACTAAGCTCCCTG 58.806 45.833 0.00 0.00 0.00 4.45
3004 3462 0.408309 AAGCTCCCTGGGGTAAAACC 59.592 55.000 14.00 0.00 37.60 3.27
3005 3463 0.774491 AGCTCCCTGGGGTAAAACCA 60.774 55.000 14.00 0.00 41.02 3.67
3031 3496 2.684881 CCACGCTATCAATTTGGCTTCT 59.315 45.455 0.00 0.00 0.00 2.85
3034 3499 3.375299 ACGCTATCAATTTGGCTTCTCAC 59.625 43.478 0.00 0.00 0.00 3.51
3036 3501 3.375299 GCTATCAATTTGGCTTCTCACGT 59.625 43.478 0.00 0.00 0.00 4.49
3039 3504 3.210227 TCAATTTGGCTTCTCACGTCAA 58.790 40.909 0.00 0.00 0.00 3.18
3056 3521 2.500229 TCAATTTTGACCTGGTCGTCC 58.500 47.619 21.15 0.00 34.95 4.79
3072 3537 4.619227 CCGGCCGTGTGAGTTGGT 62.619 66.667 26.12 0.00 0.00 3.67
3077 3542 0.032952 GCCGTGTGAGTTGGTCTGTA 59.967 55.000 0.00 0.00 0.00 2.74
3095 3560 1.165284 TACCGTGGGCCGTTTTTGTC 61.165 55.000 0.00 0.00 33.66 3.18
3096 3561 2.482333 CCGTGGGCCGTTTTTGTCA 61.482 57.895 0.00 0.00 33.66 3.58
3097 3562 1.433879 CGTGGGCCGTTTTTGTCAA 59.566 52.632 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
88 89 0.895530 CGAACCAAGGACCTAGAGCA 59.104 55.000 0.00 0.00 0.00 4.26
209 210 1.160329 GCACCATACCAAGCGCCTAG 61.160 60.000 2.29 0.00 0.00 3.02
211 212 2.438434 GCACCATACCAAGCGCCT 60.438 61.111 2.29 0.00 0.00 5.52
295 297 8.027524 TGCTAATTGGATCTAGAGAAGTCAAT 57.972 34.615 0.00 1.46 0.00 2.57
335 337 2.079158 CATCTTGACTGGTTCGCACAT 58.921 47.619 0.00 0.00 0.00 3.21
353 355 1.216990 GTGGTGGAGGGGATTCTCAT 58.783 55.000 0.00 0.00 35.58 2.90
607 611 4.991056 GTGATATCCACGATGTTGCTACAT 59.009 41.667 13.75 13.75 40.72 2.29
740 744 4.814234 TCGCATATTCGAAACCTAGCAAAT 59.186 37.500 0.00 0.00 35.31 2.32
793 797 5.179742 TGCACCAAATCATGAAAAATTGAGC 59.820 36.000 0.00 10.64 0.00 4.26
961 967 7.526041 TCAATAATAAACTGCATAGGGGACAT 58.474 34.615 0.00 0.00 0.00 3.06
1006 1012 3.563224 AGGTGCAGACTGCCAGCA 61.563 61.111 24.33 2.79 44.23 4.41
1201 1207 2.614829 ACCAATACCCGATGTACAGC 57.385 50.000 0.00 0.00 30.62 4.40
1322 1329 7.360361 CCATAGTTTGACAAAGTAAGGTTCAC 58.640 38.462 21.32 1.26 32.90 3.18
1335 1342 3.010027 TGAATGGCTCCCATAGTTTGACA 59.990 43.478 0.00 0.00 44.40 3.58
1386 1393 1.880675 GAAGGCTGCTGATGGATGATG 59.119 52.381 0.00 0.00 0.00 3.07
1427 1434 2.635915 TGAAACAATCTAGGGACACCGT 59.364 45.455 0.00 0.00 43.47 4.83
1441 1448 0.251742 CCTCCAGGGGCATGAAACAA 60.252 55.000 0.00 0.00 0.00 2.83
1496 1503 7.745620 AATCGAACCTCCATATTTCCATTAC 57.254 36.000 0.00 0.00 0.00 1.89
1503 1510 5.505780 TCACCAAATCGAACCTCCATATTT 58.494 37.500 0.00 0.00 0.00 1.40
1507 1514 3.652057 ATCACCAAATCGAACCTCCAT 57.348 42.857 0.00 0.00 0.00 3.41
1605 1612 1.125633 GACCAGCCCCGGTTATCTTA 58.874 55.000 0.00 0.00 40.22 2.10
1719 1726 3.763360 TGCCAATGACCACAATAAGAAGG 59.237 43.478 0.00 0.00 0.00 3.46
1806 1815 0.251165 GGAAAAGTGCCTGGCTACCA 60.251 55.000 21.03 0.00 0.00 3.25
1877 1886 7.094248 TGCATGCTTGATATACACAGTTTTCTT 60.094 33.333 20.33 0.00 0.00 2.52
1967 1983 9.489084 CATTGGCAAATGATTGATGATAAATCT 57.511 29.630 8.21 0.00 45.17 2.40
1968 1984 9.483916 TCATTGGCAAATGATTGATGATAAATC 57.516 29.630 12.71 0.00 45.76 2.17
1986 2002 2.027561 AGCGTAGGTTACTTCATTGGCA 60.028 45.455 0.00 0.00 27.67 4.92
1988 2004 4.124851 AGAGCGTAGGTTACTTCATTGG 57.875 45.455 0.00 0.00 39.88 3.16
2089 2105 4.918588 ACCCAACTTAATCCTTACACCTG 58.081 43.478 0.00 0.00 0.00 4.00
2295 2313 9.104713 TCATCACTAAATGGTCCATCTATGTAT 57.895 33.333 4.39 0.00 0.00 2.29
2329 2347 7.722363 TGTCAACTTATCTTGTGAAGTGTAGA 58.278 34.615 0.00 0.00 36.05 2.59
2506 2952 4.945543 AGTACGAAAAACAGTTTTCCCACT 59.054 37.500 11.77 9.72 46.69 4.00
2567 3014 7.591006 TTTTCGCGAAAACACTATCTCTTAT 57.409 32.000 35.98 0.00 35.57 1.73
2584 3031 7.744715 AGAACTTCATAGTACAAATTTTTCGCG 59.255 33.333 0.00 0.00 33.17 5.87
2680 3128 4.502259 CGGGGTTGAAATGTGGAATTTTCA 60.502 41.667 0.00 0.00 39.42 2.69
2686 3134 1.957877 GTTCGGGGTTGAAATGTGGAA 59.042 47.619 0.00 0.00 0.00 3.53
2759 3215 4.541705 TGAATCTTGAGGTTTGTTTGGGA 58.458 39.130 0.00 0.00 0.00 4.37
2763 3219 7.610865 TGAGTTTTGAATCTTGAGGTTTGTTT 58.389 30.769 0.00 0.00 0.00 2.83
2767 3223 6.406961 GGGTTGAGTTTTGAATCTTGAGGTTT 60.407 38.462 0.00 0.00 0.00 3.27
2774 3230 6.842676 AGACTAGGGTTGAGTTTTGAATCTT 58.157 36.000 0.00 0.00 0.00 2.40
2850 3306 8.523915 TGTTGAGATTAATTGCTAATGTGGAT 57.476 30.769 0.00 0.00 29.89 3.41
2858 3314 7.276218 GCAATGCTTTGTTGAGATTAATTGCTA 59.724 33.333 13.29 0.00 42.40 3.49
2882 3338 5.303078 TCACCTTTTGGCATAGTTTTTAGCA 59.697 36.000 0.00 0.00 45.59 3.49
2994 3452 4.402851 GGGTCGTGGTTTTACCCC 57.597 61.111 0.00 0.00 46.12 4.95
3004 3462 1.651987 AATTGATAGCGTGGGTCGTG 58.348 50.000 0.00 0.00 42.13 4.35
3005 3463 2.006888 CAAATTGATAGCGTGGGTCGT 58.993 47.619 0.00 0.00 42.13 4.34
3007 3465 1.065551 GCCAAATTGATAGCGTGGGTC 59.934 52.381 0.00 0.00 0.00 4.46
3008 3466 1.102978 GCCAAATTGATAGCGTGGGT 58.897 50.000 0.00 0.00 0.00 4.51
3009 3467 1.392589 AGCCAAATTGATAGCGTGGG 58.607 50.000 0.00 0.00 0.00 4.61
3010 3468 2.684881 AGAAGCCAAATTGATAGCGTGG 59.315 45.455 0.00 0.00 0.00 4.94
3011 3469 3.374988 TGAGAAGCCAAATTGATAGCGTG 59.625 43.478 0.00 0.00 0.00 5.34
3012 3470 3.375299 GTGAGAAGCCAAATTGATAGCGT 59.625 43.478 0.00 0.00 0.00 5.07
3034 3499 5.191742 GGACGACCAGGTCAAAATTGACG 62.192 52.174 20.13 5.23 45.55 4.35
3036 3501 2.500229 GGACGACCAGGTCAAAATTGA 58.500 47.619 20.13 0.00 38.70 2.57
3039 3504 0.321298 CCGGACGACCAGGTCAAAAT 60.321 55.000 20.13 1.32 38.70 1.82
3056 3521 3.041940 GACCAACTCACACGGCCG 61.042 66.667 26.86 26.86 0.00 6.13
3060 3525 1.779569 GGTACAGACCAACTCACACG 58.220 55.000 0.00 0.00 46.12 4.49
3072 3537 2.042404 AAAACGGCCCACGGTACAGA 62.042 55.000 0.00 0.00 45.59 3.41


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

AutoCloner maintained by Alex Coulton.