Multiple sequence alignment - TraesCS5B01G136700

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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 TraesCS5B01G136700 chr5B 100.000 4394 0 0 1 4394 256591874 256596267 0.000000e+00 8115
1 TraesCS5B01G136700 chr5B 97.006 668 16 4 1 665 503317535 503316869 0.000000e+00 1120
2 TraesCS5B01G136700 chr5B 96.856 668 18 3 1 665 434665828 434666495 0.000000e+00 1114
3 TraesCS5B01G136700 chr5B 97.897 428 9 0 1 428 680771356 680770929 0.000000e+00 741
4 TraesCS5B01G136700 chr5B 96.635 208 6 1 459 665 680770573 680770366 1.170000e-90 344
5 TraesCS5B01G136700 chr5B 98.000 150 2 1 517 665 256586466 256586317 4.360000e-65 259
6 TraesCS5B01G136700 chr5B 97.333 150 3 1 517 665 503322906 503323055 2.030000e-63 254
7 TraesCS5B01G136700 chr5A 96.584 3718 103 14 689 4394 311542592 311546297 0.000000e+00 6141
8 TraesCS5B01G136700 chr5D 96.336 3685 99 21 722 4394 241834797 241838457 0.000000e+00 6024
9 TraesCS5B01G136700 chr6B 95.802 667 25 3 1 665 95223294 95223959 0.000000e+00 1074
10 TraesCS5B01G136700 chr6B 95.060 668 29 4 1 665 463357581 463356915 0.000000e+00 1048
11 TraesCS5B01G136700 chr6B 93.913 345 19 2 323 665 463309237 463308893 1.810000e-143 520
12 TraesCS5B01G136700 chr7B 96.471 425 14 1 1 424 15023214 15022790 0.000000e+00 701
13 TraesCS5B01G136700 chr7B 97.333 150 3 1 517 665 15028583 15028732 2.030000e-63 254
14 TraesCS5B01G136700 chr7B 72.973 481 99 27 205 664 333366901 333366431 5.930000e-29 139
15 TraesCS5B01G136700 chr2B 94.172 429 10 4 1 427 41098588 41099003 1.330000e-179 640
16 TraesCS5B01G136700 chr1A 71.667 480 107 23 205 665 405469009 405469478 6.010000e-19 106


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 TraesCS5B01G136700 chr5B 256591874 256596267 4393 False 8115.0 8115 100.000 1 4394 1 chr5B.!!$F1 4393
1 TraesCS5B01G136700 chr5B 503316869 503317535 666 True 1120.0 1120 97.006 1 665 1 chr5B.!!$R2 664
2 TraesCS5B01G136700 chr5B 434665828 434666495 667 False 1114.0 1114 96.856 1 665 1 chr5B.!!$F2 664
3 TraesCS5B01G136700 chr5B 680770366 680771356 990 True 542.5 741 97.266 1 665 2 chr5B.!!$R3 664
4 TraesCS5B01G136700 chr5A 311542592 311546297 3705 False 6141.0 6141 96.584 689 4394 1 chr5A.!!$F1 3705
5 TraesCS5B01G136700 chr5D 241834797 241838457 3660 False 6024.0 6024 96.336 722 4394 1 chr5D.!!$F1 3672
6 TraesCS5B01G136700 chr6B 95223294 95223959 665 False 1074.0 1074 95.802 1 665 1 chr6B.!!$F1 664
7 TraesCS5B01G136700 chr6B 463356915 463357581 666 True 1048.0 1048 95.060 1 665 1 chr6B.!!$R2 664

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
572 900 0.031043 TACGACCAACAGTGACCGTG 59.969 55.0 0.0 0.0 35.37 4.94 F
674 1002 0.168788 AATGACGTGAATTGGCAGCG 59.831 50.0 0.0 0.0 0.00 5.18 F
1761 2102 0.179000 CCGAGAAGGCTATTGGCAGT 59.821 55.0 3.2 0.0 44.01 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1761 2102 1.001974 CAGACACCATCGAGTTTCCCA 59.998 52.381 0.0 0.0 0.00 4.37 R
1764 2105 1.461127 GCACAGACACCATCGAGTTTC 59.539 52.381 0.0 0.0 0.00 2.78 R
3571 3913 1.153086 GCAGGTCGCCAGATTGGAT 60.153 57.895 0.0 0.0 40.96 3.41 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
155 157 0.316841 GACAATGCGGGCCAAAAAGA 59.683 50.000 4.39 0.00 0.00 2.52
229 232 3.782443 CTGTACACGGGGGAGGCC 61.782 72.222 0.00 0.00 0.00 5.19
572 900 0.031043 TACGACCAACAGTGACCGTG 59.969 55.000 0.00 0.00 35.37 4.94
616 944 2.738314 GTGACCGTAACAGCCGTATTTT 59.262 45.455 0.00 0.00 0.00 1.82
661 989 3.830801 CGTCGCAACTACAATGACG 57.169 52.632 0.00 0.00 45.06 4.35
662 990 1.057636 CGTCGCAACTACAATGACGT 58.942 50.000 5.02 0.00 45.23 4.34
663 991 1.201661 CGTCGCAACTACAATGACGTG 60.202 52.381 0.00 0.00 45.23 4.49
664 992 2.055838 GTCGCAACTACAATGACGTGA 58.944 47.619 0.00 0.00 0.00 4.35
666 994 3.122948 GTCGCAACTACAATGACGTGAAT 59.877 43.478 0.00 0.00 0.00 2.57
667 995 3.743911 TCGCAACTACAATGACGTGAATT 59.256 39.130 0.00 0.00 0.00 2.17
668 996 3.840209 CGCAACTACAATGACGTGAATTG 59.160 43.478 15.60 15.60 40.23 2.32
669 997 4.158384 GCAACTACAATGACGTGAATTGG 58.842 43.478 19.43 9.18 38.98 3.16
670 998 4.158384 CAACTACAATGACGTGAATTGGC 58.842 43.478 19.43 0.00 38.98 4.52
671 999 3.407698 ACTACAATGACGTGAATTGGCA 58.592 40.909 19.43 9.68 38.98 4.92
672 1000 2.995466 ACAATGACGTGAATTGGCAG 57.005 45.000 19.43 1.54 38.98 4.85
673 1001 1.068333 ACAATGACGTGAATTGGCAGC 60.068 47.619 19.43 0.00 38.98 5.25
674 1002 0.168788 AATGACGTGAATTGGCAGCG 59.831 50.000 0.00 0.00 0.00 5.18
675 1003 2.202349 GACGTGAATTGGCAGCGC 60.202 61.111 0.00 0.00 0.00 5.92
676 1004 3.982424 GACGTGAATTGGCAGCGCG 62.982 63.158 0.00 0.00 40.92 6.86
677 1005 3.787676 CGTGAATTGGCAGCGCGA 61.788 61.111 12.10 0.00 37.71 5.87
678 1006 2.560861 GTGAATTGGCAGCGCGAA 59.439 55.556 12.10 0.00 0.00 4.70
679 1007 1.797537 GTGAATTGGCAGCGCGAAC 60.798 57.895 12.10 0.00 0.00 3.95
680 1008 2.574212 GAATTGGCAGCGCGAACG 60.574 61.111 12.10 0.00 44.07 3.95
681 1009 3.022401 GAATTGGCAGCGCGAACGA 62.022 57.895 12.10 0.00 43.93 3.85
682 1010 2.507322 GAATTGGCAGCGCGAACGAA 62.507 55.000 12.10 1.21 43.93 3.85
683 1011 2.123988 AATTGGCAGCGCGAACGAAA 62.124 50.000 12.10 0.00 43.93 3.46
684 1012 2.123988 ATTGGCAGCGCGAACGAAAA 62.124 50.000 12.10 0.00 43.93 2.29
685 1013 2.499732 GGCAGCGCGAACGAAAAG 60.500 61.111 12.10 0.00 43.93 2.27
686 1014 2.549282 GCAGCGCGAACGAAAAGA 59.451 55.556 12.10 0.00 43.93 2.52
687 1015 1.132640 GCAGCGCGAACGAAAAGAT 59.867 52.632 12.10 0.00 43.93 2.40
699 1027 2.305927 ACGAAAAGATGGATGGGAGTGT 59.694 45.455 0.00 0.00 0.00 3.55
700 1028 3.244911 ACGAAAAGATGGATGGGAGTGTT 60.245 43.478 0.00 0.00 0.00 3.32
1177 1515 2.373169 TGATCCACTTCCTTTCTGTGCT 59.627 45.455 0.00 0.00 0.00 4.40
1180 1518 3.239449 TCCACTTCCTTTCTGTGCTCTA 58.761 45.455 0.00 0.00 0.00 2.43
1201 1539 3.995636 ACTAGAGTCCTCCTATTTGCCA 58.004 45.455 0.00 0.00 0.00 4.92
1217 1555 1.322442 GCCATGTCCTGCTATTTCCC 58.678 55.000 0.00 0.00 0.00 3.97
1344 1685 3.497115 TGGTGTCTGGCAGGCCAA 61.497 61.111 17.80 0.00 46.63 4.52
1584 1925 3.056313 GCCCAACGCTCTTCATGCC 62.056 63.158 0.00 0.00 0.00 4.40
1587 1928 0.674581 CCAACGCTCTTCATGCCTCA 60.675 55.000 0.00 0.00 0.00 3.86
1614 1955 3.058293 CGGATGTTTTTGAAGCTACTGCA 60.058 43.478 0.00 0.00 42.74 4.41
1761 2102 0.179000 CCGAGAAGGCTATTGGCAGT 59.821 55.000 3.20 0.00 44.01 4.40
1764 2105 0.257039 AGAAGGCTATTGGCAGTGGG 59.743 55.000 3.20 0.00 44.01 4.61
1794 2135 4.033894 GTCTGTGCGACAGCTGTT 57.966 55.556 22.65 4.46 45.54 3.16
1809 2150 2.740981 AGCTGTTCTGCTCAAGAATTCG 59.259 45.455 0.00 0.00 46.53 3.34
1849 2190 4.704540 GGTGGGATCATATTGTTGTGTTGA 59.295 41.667 0.00 0.00 0.00 3.18
2055 2396 0.611896 GGGTGGTCAATGTCCAAGGG 60.612 60.000 0.00 0.00 36.68 3.95
2328 2669 4.493547 GAAGATCAGAGAGACACTTGGTG 58.506 47.826 0.00 0.00 39.75 4.17
2337 2678 2.037772 GAGACACTTGGTGGACAGACAT 59.962 50.000 2.75 0.00 37.94 3.06
2661 3002 4.080807 TGGTACCAAGTTCAAAGACAGACA 60.081 41.667 13.60 0.00 0.00 3.41
2760 3101 2.992817 ATCCAGGCCCGTGCAACAAA 62.993 55.000 0.00 0.00 40.13 2.83
3161 3502 3.543680 ATATTTCTCGTGTGGTGGAGG 57.456 47.619 0.00 0.00 0.00 4.30
3571 3913 2.841215 CCTGACGGGTACTTGAAAACA 58.159 47.619 0.00 0.00 0.00 2.83
3625 3967 7.259088 ACTTGGATTTCTGACTGTATTACCT 57.741 36.000 0.00 0.00 0.00 3.08
3706 4050 0.109342 CCTCCAAGTTGGTGAGCTGT 59.891 55.000 22.69 0.00 39.03 4.40
3722 4066 0.167470 CTGTGCTTTGGCTGATGTCG 59.833 55.000 0.00 0.00 39.59 4.35
3723 4067 1.154150 GTGCTTTGGCTGATGTCGC 60.154 57.895 0.00 0.00 39.59 5.19
3737 4081 1.445582 GTCGCCGGTCGTCTTGATT 60.446 57.895 16.00 0.00 39.67 2.57
3748 4092 3.994392 GTCGTCTTGATTAGTGCCTCAAA 59.006 43.478 0.00 0.00 31.40 2.69
3761 4105 5.535333 AGTGCCTCAAATCAAATGTTGAAG 58.465 37.500 0.00 0.00 43.95 3.02
4044 4388 0.887387 TGCGTTAACCCTGACTTGGC 60.887 55.000 0.00 0.00 0.00 4.52
4092 4436 6.534436 TGTGATGTTTTGGTTTGAATTGTCTG 59.466 34.615 0.00 0.00 0.00 3.51
4133 4477 6.018832 TGGTACTGTTTTTGCTACTACGTTTC 60.019 38.462 0.00 0.00 0.00 2.78
4203 4548 1.293062 AGGATGAGGTGTGAATGCCT 58.707 50.000 0.00 0.00 37.91 4.75
4269 4614 6.009589 TCTTGATGAAAATAAGGCTGTTCCA 58.990 36.000 0.00 0.00 37.29 3.53
4314 4659 7.418840 TGTTTGTAAATTTAAGCAGCAATGG 57.581 32.000 0.00 0.00 0.00 3.16
4338 4683 0.457851 TGAAACGTTTGCCTGGTTGG 59.542 50.000 20.10 0.00 39.35 3.77
4389 4734 8.759782 AGTCCAAGTTTATACTAGCTGTACATT 58.240 33.333 0.00 0.00 33.17 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
155 157 4.798387 GCGTTTTGATGTTCAAAGACACTT 59.202 37.500 3.22 0.00 45.77 3.16
442 446 3.745723 AAAAACCTCGGGCATGTCT 57.254 47.368 0.00 0.00 0.00 3.41
572 900 5.856986 ACTATATACGATGTGACGTGAATGC 59.143 40.000 0.00 0.00 46.02 3.56
616 944 3.119388 CCCGATACGGTCACTGAACTTAA 60.119 47.826 9.28 0.00 46.80 1.85
661 989 1.797537 GTTCGCGCTGCCAATTCAC 60.798 57.895 5.56 0.00 0.00 3.18
662 990 2.560861 GTTCGCGCTGCCAATTCA 59.439 55.556 5.56 0.00 0.00 2.57
663 991 2.507322 TTCGTTCGCGCTGCCAATTC 62.507 55.000 5.56 0.00 41.05 2.17
664 992 2.123988 TTTCGTTCGCGCTGCCAATT 62.124 50.000 5.56 0.00 41.05 2.32
666 994 2.709629 CTTTTCGTTCGCGCTGCCAA 62.710 55.000 5.56 0.00 41.05 4.52
667 995 3.235292 CTTTTCGTTCGCGCTGCCA 62.235 57.895 5.56 0.00 41.05 4.92
668 996 2.240612 ATCTTTTCGTTCGCGCTGCC 62.241 55.000 5.56 0.00 41.05 4.85
669 997 1.122419 CATCTTTTCGTTCGCGCTGC 61.122 55.000 5.56 0.00 41.05 5.25
670 998 0.519175 CCATCTTTTCGTTCGCGCTG 60.519 55.000 5.56 0.00 41.05 5.18
671 999 0.669318 TCCATCTTTTCGTTCGCGCT 60.669 50.000 5.56 0.00 41.05 5.92
672 1000 0.373716 ATCCATCTTTTCGTTCGCGC 59.626 50.000 0.00 0.00 41.05 6.86
673 1001 1.267532 CCATCCATCTTTTCGTTCGCG 60.268 52.381 0.00 0.00 42.98 5.87
674 1002 1.064060 CCCATCCATCTTTTCGTTCGC 59.936 52.381 0.00 0.00 0.00 4.70
675 1003 2.609459 CTCCCATCCATCTTTTCGTTCG 59.391 50.000 0.00 0.00 0.00 3.95
676 1004 3.375299 CACTCCCATCCATCTTTTCGTTC 59.625 47.826 0.00 0.00 0.00 3.95
677 1005 3.244911 ACACTCCCATCCATCTTTTCGTT 60.245 43.478 0.00 0.00 0.00 3.85
678 1006 2.305927 ACACTCCCATCCATCTTTTCGT 59.694 45.455 0.00 0.00 0.00 3.85
679 1007 2.991250 ACACTCCCATCCATCTTTTCG 58.009 47.619 0.00 0.00 0.00 3.46
680 1008 5.728637 AAAACACTCCCATCCATCTTTTC 57.271 39.130 0.00 0.00 0.00 2.29
681 1009 5.742838 GCAAAAACACTCCCATCCATCTTTT 60.743 40.000 0.00 0.00 0.00 2.27
682 1010 4.262592 GCAAAAACACTCCCATCCATCTTT 60.263 41.667 0.00 0.00 0.00 2.52
683 1011 3.259123 GCAAAAACACTCCCATCCATCTT 59.741 43.478 0.00 0.00 0.00 2.40
684 1012 2.827921 GCAAAAACACTCCCATCCATCT 59.172 45.455 0.00 0.00 0.00 2.90
685 1013 2.562298 TGCAAAAACACTCCCATCCATC 59.438 45.455 0.00 0.00 0.00 3.51
686 1014 2.299867 GTGCAAAAACACTCCCATCCAT 59.700 45.455 0.00 0.00 37.58 3.41
687 1015 1.686052 GTGCAAAAACACTCCCATCCA 59.314 47.619 0.00 0.00 37.58 3.41
699 1027 2.357637 GTGAGGTACAGCTGTGCAAAAA 59.642 45.455 31.81 14.40 32.02 1.94
700 1028 1.946768 GTGAGGTACAGCTGTGCAAAA 59.053 47.619 31.81 16.05 32.02 2.44
813 1141 4.853468 AGAAAAAGAGGAGAGGGGATTC 57.147 45.455 0.00 0.00 0.00 2.52
953 1283 0.173935 TTGTCACTGTCACCGTCGTT 59.826 50.000 0.00 0.00 0.00 3.85
1021 1359 3.959975 GAGGCGCGCGAGATCTCT 61.960 66.667 37.18 18.85 0.00 3.10
1177 1515 5.103643 TGGCAAATAGGAGGACTCTAGTAGA 60.104 44.000 0.00 0.00 0.00 2.59
1180 1518 3.995636 TGGCAAATAGGAGGACTCTAGT 58.004 45.455 0.00 0.00 0.00 2.57
1201 1539 4.040755 AGTACTGGGAAATAGCAGGACAT 58.959 43.478 0.00 0.00 31.20 3.06
1587 1928 9.842956 GCAGTAGCTTCAAAAACATCCGATGTT 62.843 40.741 19.15 19.15 45.88 2.71
1614 1955 1.142688 AATCCTCCAGGGCAAGGTGT 61.143 55.000 0.00 0.00 34.12 4.16
1761 2102 1.001974 CAGACACCATCGAGTTTCCCA 59.998 52.381 0.00 0.00 0.00 4.37
1764 2105 1.461127 GCACAGACACCATCGAGTTTC 59.539 52.381 0.00 0.00 0.00 2.78
1794 2135 3.044235 TGCTTCGAATTCTTGAGCAGA 57.956 42.857 17.75 0.00 0.00 4.26
1809 2150 1.815003 CACCTCCCTTGTGAATGCTTC 59.185 52.381 0.00 0.00 35.74 3.86
1849 2190 6.126863 TCCAATATCAGGTCTCAACAAAGT 57.873 37.500 0.00 0.00 0.00 2.66
2055 2396 8.992835 AATCAAAATTTAGCTTGTTCAGATCC 57.007 30.769 0.00 0.00 0.00 3.36
2313 2654 1.967066 CTGTCCACCAAGTGTCTCTCT 59.033 52.381 0.00 0.00 0.00 3.10
2328 2669 3.119849 CGTTTCCATTGGAATGTCTGTCC 60.120 47.826 18.62 0.37 41.71 4.02
2337 2678 2.649531 ACAGACCGTTTCCATTGGAA 57.350 45.000 14.24 14.24 40.27 3.53
2661 3002 5.376625 TGCTTCATCAAGGTCAGTACTTTT 58.623 37.500 0.00 0.00 0.00 2.27
2847 3188 3.933955 CACCAAACAATCCGTTCCGTATA 59.066 43.478 0.00 0.00 36.59 1.47
3075 3416 2.555757 CCCTTCCTGAAGAGCAAAAGTG 59.444 50.000 8.46 0.00 40.79 3.16
3161 3502 1.744741 GAGTCAAGCTCTGGGCAGC 60.745 63.158 0.74 0.00 44.79 5.25
3187 3528 2.902486 TCTCTCTCCATTGAAGTGCACT 59.098 45.455 15.25 15.25 0.00 4.40
3571 3913 1.153086 GCAGGTCGCCAGATTGGAT 60.153 57.895 0.00 0.00 40.96 3.41
3625 3967 4.141620 GGATCTCTACTGCATTCTTGGGAA 60.142 45.833 0.00 0.00 35.78 3.97
3706 4050 3.266964 GCGACATCAGCCAAAGCA 58.733 55.556 0.00 0.00 43.56 3.91
3722 4066 1.278238 CACTAATCAAGACGACCGGC 58.722 55.000 0.00 0.00 0.00 6.13
3723 4067 1.278238 GCACTAATCAAGACGACCGG 58.722 55.000 0.00 0.00 0.00 5.28
3737 4081 6.647334 TTCAACATTTGATTTGAGGCACTA 57.353 33.333 0.00 0.00 38.20 2.74
3748 4092 8.353423 ACCACTTATAAGCTTCAACATTTGAT 57.647 30.769 12.54 0.00 39.84 2.57
3761 4105 5.221048 CCACATTTGCCTACCACTTATAAGC 60.221 44.000 12.54 0.00 0.00 3.09
4013 4357 2.717011 GGTTAACGCACAAATCAACACG 59.283 45.455 0.00 0.00 0.00 4.49
4044 4388 0.179056 ATATTTCTCCACGCACGGGG 60.179 55.000 4.57 4.57 40.85 5.73
4092 4436 5.586243 ACAGTACCATCATCATAGTGCAAAC 59.414 40.000 0.00 0.00 0.00 2.93
4133 4477 6.192360 CAGAAGTAAAAGAAAACAGACACCG 58.808 40.000 0.00 0.00 0.00 4.94
4308 4653 3.300009 CAAACGTTTCAGAGACCATTGC 58.700 45.455 11.37 0.00 0.00 3.56
4314 4659 1.264288 CCAGGCAAACGTTTCAGAGAC 59.736 52.381 11.37 1.75 0.00 3.36
4338 4683 2.015736 ACATGATCCAGTCAGCGTTC 57.984 50.000 0.00 0.00 40.92 3.95


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

AutoCloner maintained by Alex Coulton.