Multiple sequence alignment - TraesCS7B01G416100

Loading Multiple Alignment...

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 TraesCS7B01G416100 chr7B 100.000 4763 0 0 1 4763 683510871 683515633 0.000000e+00 8796.0
1 TraesCS7B01G416100 chr7D 96.765 4791 117 11 4 4763 602899449 602904232 0.000000e+00 7954.0
2 TraesCS7B01G416100 chr7A 96.328 4793 136 11 4 4763 694543686 694548471 0.000000e+00 7840.0
3 TraesCS7B01G416100 chr6D 84.898 245 28 6 4523 4763 232768557 232768318 6.160000e-59 239.0
4 TraesCS7B01G416100 chr3A 93.617 47 3 0 8 54 217723299 217723345 2.380000e-08 71.3


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 TraesCS7B01G416100 chr7B 683510871 683515633 4762 False 8796 8796 100.000 1 4763 1 chr7B.!!$F1 4762
1 TraesCS7B01G416100 chr7D 602899449 602904232 4783 False 7954 7954 96.765 4 4763 1 chr7D.!!$F1 4759
2 TraesCS7B01G416100 chr7A 694543686 694548471 4785 False 7840 7840 96.328 4 4763 1 chr7A.!!$F1 4759

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
793 800 0.376152 GATGTCTTGGATGCTGCACG 59.624 55.0 3.57 0.0 0.00 5.34 F
1317 1326 1.026182 TAACTGCATTGGAGCGGCTG 61.026 55.0 7.50 0.0 44.76 4.85 F
2775 2784 0.519077 CTTTTCGGCCAGCTTCTGTC 59.481 55.0 2.24 0.0 0.00 3.51 F
3023 3032 0.321671 GCTGCTACCACCTCACTTGA 59.678 55.0 0.00 0.0 0.00 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2289 2298 0.454620 CAACGAGACGCGCTACTTCT 60.455 55.000 5.73 0.0 46.04 2.85 R
2877 2886 1.261619 GCTGTTGAAAGTGACTCACCG 59.738 52.381 5.51 0.0 34.49 4.94 R
3717 3726 1.344763 CCTGAGTCAGGTTCTTTCCGT 59.655 52.381 28.38 0.0 45.82 4.69 R
4366 4384 4.627284 TTAGTTGATTCTTTCCCCGACA 57.373 40.909 0.00 0.0 0.00 4.35 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
115 116 5.024785 GGGAGTAGTTCCTTCTTCCTAGTT 58.975 45.833 0.00 0.00 45.98 2.24
196 197 3.808189 TCCTCCTCATTCTCCTTTCCTT 58.192 45.455 0.00 0.00 0.00 3.36
202 203 5.896678 TCCTCATTCTCCTTTCCTTAGAGAG 59.103 44.000 0.00 0.00 37.90 3.20
224 225 7.908453 AGAGGCATATGTTCTTTACCTATACC 58.092 38.462 4.29 0.00 0.00 2.73
264 265 1.718396 TGAACAGCAGCTGATTCTCG 58.282 50.000 29.70 0.81 35.18 4.04
312 319 2.584835 ACTGCTGCTGTTTGGGAATA 57.415 45.000 6.33 0.00 0.00 1.75
315 322 2.421424 CTGCTGCTGTTTGGGAATAGAC 59.579 50.000 0.00 0.00 0.00 2.59
643 650 6.455647 TGGAGTGAAACAATAGTAGTGTCTG 58.544 40.000 3.33 0.00 41.43 3.51
789 796 4.134379 ACTACTGATGTCTTGGATGCTG 57.866 45.455 0.00 0.00 0.00 4.41
790 797 1.747709 ACTGATGTCTTGGATGCTGC 58.252 50.000 0.00 0.00 0.00 5.25
791 798 1.003928 ACTGATGTCTTGGATGCTGCA 59.996 47.619 4.13 4.13 0.00 4.41
792 799 1.400846 CTGATGTCTTGGATGCTGCAC 59.599 52.381 3.57 0.00 0.00 4.57
793 800 0.376152 GATGTCTTGGATGCTGCACG 59.624 55.000 3.57 0.00 0.00 5.34
899 906 2.565834 GCTACTTCTGTTGACCACCCTA 59.434 50.000 0.00 0.00 0.00 3.53
906 913 5.160607 TCTGTTGACCACCCTACTTTATG 57.839 43.478 0.00 0.00 0.00 1.90
917 926 5.531287 CACCCTACTTTATGTATTTCAGGGC 59.469 44.000 3.23 0.00 41.23 5.19
995 1004 1.339610 CAGGGAGATAAGAGCAGGACG 59.660 57.143 0.00 0.00 0.00 4.79
1004 1013 3.044059 GAGCAGGACGCACAATGCC 62.044 63.158 0.00 0.00 46.13 4.40
1117 1126 6.590068 AGAGATGCTGCTGATTTTAGTACAT 58.410 36.000 0.00 0.00 0.00 2.29
1122 1131 5.582269 TGCTGCTGATTTTAGTACATCTGAC 59.418 40.000 0.00 0.00 0.00 3.51
1317 1326 1.026182 TAACTGCATTGGAGCGGCTG 61.026 55.000 7.50 0.00 44.76 4.85
1524 1533 2.761465 GCCCCCAGAAGCTAGCCAT 61.761 63.158 12.13 0.00 0.00 4.40
1529 1538 2.019984 CCCAGAAGCTAGCCATGAAAC 58.980 52.381 12.13 0.00 0.00 2.78
1536 1545 2.488153 AGCTAGCCATGAAACGGAAAAC 59.512 45.455 12.13 0.00 0.00 2.43
1538 1547 3.670627 GCTAGCCATGAAACGGAAAACAG 60.671 47.826 2.29 0.00 0.00 3.16
1608 1617 5.670792 ACCATGATACGTTAACTTCCTCA 57.329 39.130 3.71 2.34 0.00 3.86
1610 1619 5.050490 CCATGATACGTTAACTTCCTCAGG 58.950 45.833 3.71 3.67 0.00 3.86
1695 1704 1.342275 CCAGCATCCCCAAATTCCTCA 60.342 52.381 0.00 0.00 0.00 3.86
1882 1891 6.767902 CACTGGGCATGTTACTCAAGTAATAT 59.232 38.462 5.93 6.18 41.12 1.28
2042 2051 5.235186 AGTCGTGCTCTGATAATAATGCAAC 59.765 40.000 0.00 0.00 32.10 4.17
2124 2133 3.700109 GGCAAAGAAGAAGGGCCC 58.300 61.111 16.46 16.46 38.70 5.80
2239 2248 5.277974 GCAGAGACAAAGTTGAATGCAGTAA 60.278 40.000 0.00 0.00 32.79 2.24
2257 2266 5.396884 GCAGTAAAGGGAGATAAGTCACCAT 60.397 44.000 0.00 0.00 36.89 3.55
2289 2298 7.449704 ACAGAGTATGATGATACTGATGCACTA 59.550 37.037 9.75 0.00 44.14 2.74
2349 2358 5.367060 GGAAGTAATTGACTACAGGGGAGAT 59.633 44.000 0.00 0.00 37.44 2.75
2408 2417 4.411540 AGATAGTCCTCATGTGGAAGCAAT 59.588 41.667 17.83 9.08 37.93 3.56
2445 2454 4.142093 CCCCCTGTTCATGAATCAAATGAC 60.142 45.833 12.12 0.00 33.84 3.06
2539 2548 4.687948 CAGATGACAGCGGTCCTATTAATG 59.312 45.833 14.62 0.64 43.65 1.90
2775 2784 0.519077 CTTTTCGGCCAGCTTCTGTC 59.481 55.000 2.24 0.00 0.00 3.51
2877 2886 9.937175 GTAGATGAAAGTGAAAATACTATTGCC 57.063 33.333 0.00 0.00 0.00 4.52
2961 2970 1.757118 GGAGCTGATGGTGCTAGTACA 59.243 52.381 13.26 0.00 41.30 2.90
3020 3029 0.610687 GAAGCTGCTACCACCTCACT 59.389 55.000 0.90 0.00 0.00 3.41
3023 3032 0.321671 GCTGCTACCACCTCACTTGA 59.678 55.000 0.00 0.00 0.00 3.02
3046 3055 5.282055 TGTACCATCATTCTGGAGTCATC 57.718 43.478 0.00 0.00 39.73 2.92
3255 3264 3.706594 AGAGAGTCACACTTGGACAGAAA 59.293 43.478 0.00 0.00 37.74 2.52
3381 3390 3.619038 GTGTTTTCGGCTATCCTTCTCAG 59.381 47.826 0.00 0.00 0.00 3.35
3598 3607 1.565067 TGCTCTCTCATCTGAAGGCA 58.435 50.000 0.00 0.00 0.00 4.75
3645 3654 0.883833 CTGTGCCATTCCAAGGTCAC 59.116 55.000 0.00 0.00 35.29 3.67
3657 3666 2.135933 CAAGGTCACACCGTCTTTCTC 58.864 52.381 0.00 0.00 44.90 2.87
3714 3723 3.104512 CTCTGGTACTGGGTTGGTATCA 58.895 50.000 0.00 0.00 0.00 2.15
3717 3726 4.351407 TCTGGTACTGGGTTGGTATCAAAA 59.649 41.667 0.00 0.00 34.28 2.44
4366 4384 0.468771 AAGGAGCCAGCTGCAACTTT 60.469 50.000 13.86 1.12 44.83 2.66
4730 4783 0.527385 CAACCAGCCAACCGTGTTTG 60.527 55.000 0.00 0.00 0.00 2.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.768957 TCATATCAGTCCGTATGTACTACTAC 57.231 38.462 0.00 0.00 31.75 2.73
1 2 8.591940 ACTCATATCAGTCCGTATGTACTACTA 58.408 37.037 0.00 0.00 31.75 1.82
2 3 7.388224 CACTCATATCAGTCCGTATGTACTACT 59.612 40.741 0.00 0.00 31.75 2.57
58 59 9.228949 ACTATCAGAAGACGTTCTAACTTTCTA 57.771 33.333 0.00 0.00 41.40 2.10
115 116 2.227865 GGGAAATTCAAACAGCACGCTA 59.772 45.455 0.00 0.00 0.00 4.26
196 197 8.958060 ATAGGTAAAGAACATATGCCTCTCTA 57.042 34.615 1.58 3.90 33.90 2.43
224 225 7.118971 TGTTCAAAGGAAGTTGGTTGATTTTTG 59.881 33.333 0.00 0.00 32.62 2.44
344 351 3.119101 ACGAGCTATTCCTTGTGTGGTAG 60.119 47.826 0.00 0.00 0.00 3.18
466 473 3.119990 TCAAGGCGCTTAAAATACTGCAC 60.120 43.478 7.64 0.00 0.00 4.57
643 650 4.558538 CCATGCATGGTAAGAACTAAGC 57.441 45.455 33.68 0.00 43.05 3.09
706 713 7.122055 TGATCACCTAATCAATGGTTTACAACC 59.878 37.037 0.00 0.00 41.04 3.77
772 779 1.400846 GTGCAGCATCCAAGACATCAG 59.599 52.381 0.00 0.00 0.00 2.90
789 796 8.537223 TCAATCTCTACGAATATTTAAACGTGC 58.463 33.333 10.74 0.00 39.28 5.34
869 876 3.056107 TCAACAGAAGTAGCGCAGGTATT 60.056 43.478 11.47 0.00 44.46 1.89
899 906 8.058847 TCCTAATTGCCCTGAAATACATAAAGT 58.941 33.333 0.00 0.00 0.00 2.66
906 913 6.038714 CAGAGTTCCTAATTGCCCTGAAATAC 59.961 42.308 0.00 0.00 0.00 1.89
917 926 7.108847 AGATTCACCTTCAGAGTTCCTAATTG 58.891 38.462 0.00 0.00 0.00 2.32
969 978 3.374764 TGCTCTTATCTCCCTGCAGTAA 58.625 45.455 13.81 3.29 0.00 2.24
995 1004 2.097825 AGAAATCCTCAGGCATTGTGC 58.902 47.619 0.00 0.00 44.08 4.57
1004 1013 6.929625 TCAGTCAGAGTAAAGAAATCCTCAG 58.070 40.000 0.00 0.00 0.00 3.35
1117 1126 4.040339 TGAACACTGCCTTATGAAGTCAGA 59.960 41.667 4.40 0.00 0.00 3.27
1122 1131 4.614535 GCTGTTGAACACTGCCTTATGAAG 60.615 45.833 0.00 0.00 43.00 3.02
1317 1326 7.148340 GGAGCTTTATGTATATCATCAACTGGC 60.148 40.741 0.00 0.00 37.91 4.85
1453 1462 6.266168 TGCATCTATTTGTCGGTCATTTTT 57.734 33.333 0.00 0.00 0.00 1.94
1524 1533 4.391216 TCGTGTTTACTGTTTTCCGTTTCA 59.609 37.500 0.00 0.00 0.00 2.69
1529 1538 2.347846 CCGTCGTGTTTACTGTTTTCCG 60.348 50.000 0.00 0.00 0.00 4.30
1536 1545 1.493772 TTGCTCCGTCGTGTTTACTG 58.506 50.000 0.00 0.00 0.00 2.74
1538 1547 2.477375 TCATTTGCTCCGTCGTGTTTAC 59.523 45.455 0.00 0.00 0.00 2.01
1608 1617 1.707427 AGATCCTGCAAAGGAACACCT 59.293 47.619 0.00 0.00 41.90 4.00
1610 1619 2.485814 GACAGATCCTGCAAAGGAACAC 59.514 50.000 0.00 0.00 41.90 3.32
1695 1704 3.624777 CACTAAAACCTCATGCCCATCT 58.375 45.455 0.00 0.00 0.00 2.90
1701 1710 2.095059 CACCTGCACTAAAACCTCATGC 60.095 50.000 0.00 0.00 36.81 4.06
1882 1891 2.236146 ACTTGGCATCTATGGTCGAACA 59.764 45.455 5.17 5.17 0.00 3.18
2042 2051 3.005050 TGCAAGATGGTTCAAAGCTTCAG 59.995 43.478 0.00 0.00 34.26 3.02
2124 2133 5.850614 TCATCTGTACCTGATGATGATGTG 58.149 41.667 18.71 0.75 41.50 3.21
2239 2248 4.039730 CGATGATGGTGACTTATCTCCCTT 59.960 45.833 3.04 0.00 37.65 3.95
2257 2266 6.936900 TCAGTATCATCATACTCTGTCGATGA 59.063 38.462 12.14 12.14 43.02 2.92
2289 2298 0.454620 CAACGAGACGCGCTACTTCT 60.455 55.000 5.73 0.00 46.04 2.85
2408 2417 2.203337 GGGGTTCAGTGTGCTGCA 60.203 61.111 0.00 0.00 42.29 4.41
2539 2548 3.139077 CACCCTGTGTGTTCTTTCTACC 58.861 50.000 0.00 0.00 40.26 3.18
2679 2688 3.937706 CTGGAAATACAAGTGAGCCTCTG 59.062 47.826 0.00 0.00 0.00 3.35
2775 2784 1.994507 CTCTGTCAGGAGTACGCGGG 61.995 65.000 12.47 0.00 0.00 6.13
2877 2886 1.261619 GCTGTTGAAAGTGACTCACCG 59.738 52.381 5.51 0.00 34.49 4.94
2961 2970 3.876309 TTAAGGTCAAGTTCAAGCCCT 57.124 42.857 0.00 0.00 0.00 5.19
3046 3055 2.756207 TCCATCTGCCATGACATTGTTG 59.244 45.455 0.00 0.00 0.00 3.33
3078 3087 3.623906 TGCCTTGAAGATGAAGAGGAG 57.376 47.619 0.00 0.00 0.00 3.69
3255 3264 4.269523 TTTGGGCTGCGGTGCTCT 62.270 61.111 0.00 0.00 33.90 4.09
3312 3321 4.980805 TGCGTTGACCTCACGGGC 62.981 66.667 0.00 0.00 39.55 6.13
3381 3390 1.214589 CAAAGACATGGCAGCAGGC 59.785 57.895 0.00 0.00 43.74 4.85
3475 3484 3.712907 GCCAACACCTAGGCCCGA 61.713 66.667 9.30 0.00 45.18 5.14
3495 3504 2.941720 GCTGGTGAAAGATGGATGAGAC 59.058 50.000 0.00 0.00 0.00 3.36
3598 3607 2.032681 GCCAGCTTCCCTTCGTGT 59.967 61.111 0.00 0.00 0.00 4.49
3645 3654 1.649171 CGTTCATCGAGAAAGACGGTG 59.351 52.381 0.00 0.00 42.24 4.94
3657 3666 6.140895 GTGATGTACTTCTCATACGTTCATCG 59.859 42.308 9.87 0.00 46.00 3.84
3714 3723 3.877508 CTGAGTCAGGTTCTTTCCGTTTT 59.122 43.478 12.67 0.00 0.00 2.43
3717 3726 1.344763 CCTGAGTCAGGTTCTTTCCGT 59.655 52.381 28.38 0.00 45.82 4.69
4366 4384 4.627284 TTAGTTGATTCTTTCCCCGACA 57.373 40.909 0.00 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.