Multiple sequence alignment - TraesCS6A01G326500

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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 TraesCS6A01G326500 chr6A 100.000 4205 0 0 1 4205 560035458 560031254 0.000000e+00 7766.0
1 TraesCS6A01G326500 chr6B 94.584 4228 173 28 1 4205 625782018 625777824 0.000000e+00 6488.0
2 TraesCS6A01G326500 chr6D 94.888 3912 135 22 1 3893 415030367 415026502 0.000000e+00 6056.0
3 TraesCS6A01G326500 chr3A 90.826 109 9 1 3721 3829 713682687 713682794 1.220000e-30 145.0
4 TraesCS6A01G326500 chr3A 87.500 72 7 2 2630 2700 172964411 172964341 9.690000e-12 82.4
5 TraesCS6A01G326500 chr3D 85.484 124 12 5 3710 3829 578145284 578145405 1.590000e-24 124.0
6 TraesCS6A01G326500 chr3D 89.041 73 6 2 2630 2701 154180335 154180264 5.790000e-14 89.8
7 TraesCS6A01G326500 chr2B 86.538 104 12 2 3722 3824 27921903 27921801 3.440000e-21 113.0
8 TraesCS6A01G326500 chr7D 85.294 102 15 0 2600 2701 55252731 55252832 5.750000e-19 106.0
9 TraesCS6A01G326500 chr7D 85.294 102 15 0 2600 2701 55269813 55269914 5.750000e-19 106.0
10 TraesCS6A01G326500 chr7A 84.314 102 16 0 2600 2701 59204447 59204548 2.680000e-17 100.0
11 TraesCS6A01G326500 chr7A 78.125 128 23 4 3713 3838 255895390 255895266 4.510000e-10 76.8
12 TraesCS6A01G326500 chr3B 82.692 104 14 4 2600 2701 226789214 226789315 5.790000e-14 89.8
13 TraesCS6A01G326500 chr4A 90.625 64 6 0 3767 3830 34052262 34052199 7.490000e-13 86.1


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 TraesCS6A01G326500 chr6A 560031254 560035458 4204 True 7766 7766 100.000 1 4205 1 chr6A.!!$R1 4204
1 TraesCS6A01G326500 chr6B 625777824 625782018 4194 True 6488 6488 94.584 1 4205 1 chr6B.!!$R1 4204
2 TraesCS6A01G326500 chr6D 415026502 415030367 3865 True 6056 6056 94.888 1 3893 1 chr6D.!!$R1 3892

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
388 394 1.394266 AATGGCCGGCCTGCATTTAG 61.394 55.000 43.34 0.00 36.94 1.85 F
1277 1284 0.041488 GCTGCTGCTGATAACGATGC 60.041 55.000 10.92 0.00 36.03 3.91 F
1303 1310 1.006805 GGCATCGACGATGAGGAGG 60.007 63.158 35.61 13.28 42.09 4.30 F
1572 1579 1.320344 ACAAGATGCTCCGGCGAGTA 61.320 55.000 9.30 3.83 42.25 2.59 F
2814 2844 0.858369 CCTACCTCAGCCCCTACCTA 59.142 60.000 0.00 0.00 0.00 3.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1332 1339 1.091771 CCGCCTCTACCATGTGCTTG 61.092 60.000 0.00 0.0 0.00 4.01 R
2586 2616 0.524862 GCACCTGCACCATCTCAAAG 59.475 55.000 0.00 0.0 41.59 2.77 R
2814 2844 1.268283 GGGAGCTAGAGTTGGGCTGT 61.268 60.000 0.00 0.0 36.37 4.40 R
2856 2886 1.681780 CCCATGTTGCCGGACATTAGT 60.682 52.381 5.05 0.0 38.15 2.24 R
4183 4224 0.733729 ACACGCGCCACACTTTTAAA 59.266 45.000 5.73 0.0 0.00 1.52 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
111 115 4.298626 AGGGAGTATATGCTTGGACAAGA 58.701 43.478 15.76 2.05 40.79 3.02
129 133 6.183360 GGACAAGACATTAATTACTTGAGCCC 60.183 42.308 25.29 20.11 41.16 5.19
180 184 6.096673 TGCCTTCTTATTTGAAAAGTTCCC 57.903 37.500 0.00 0.00 0.00 3.97
311 317 3.054576 TGAACCACCAGGGGTACTAAAA 58.945 45.455 0.00 0.00 41.32 1.52
313 319 4.263594 TGAACCACCAGGGGTACTAAAATC 60.264 45.833 0.00 0.00 41.32 2.17
388 394 1.394266 AATGGCCGGCCTGCATTTAG 61.394 55.000 43.34 0.00 36.94 1.85
389 395 3.904479 GGCCGGCCTGCATTTAGC 61.904 66.667 38.76 7.31 45.96 3.09
782 789 3.933332 GTGTACATGTTCCTAGAGCCAAC 59.067 47.826 2.30 0.00 0.00 3.77
1140 1147 2.012673 CAAATCAAGGAAGGAGAGGCG 58.987 52.381 0.00 0.00 0.00 5.52
1233 1240 3.864789 ACTCAACAAGGAGGTGTGATT 57.135 42.857 0.00 0.00 39.27 2.57
1275 1282 1.579698 CTGCTGCTGCTGATAACGAT 58.420 50.000 17.00 0.00 40.01 3.73
1277 1284 0.041488 GCTGCTGCTGATAACGATGC 60.041 55.000 10.92 0.00 36.03 3.91
1303 1310 1.006805 GGCATCGACGATGAGGAGG 60.007 63.158 35.61 13.28 42.09 4.30
1332 1339 2.035442 GGGAACTGGCGCAGAAGAC 61.035 63.158 10.83 3.91 35.18 3.01
1451 1458 2.692557 TGTGGTGCAACAAGTAGCAAAT 59.307 40.909 5.70 0.00 41.93 2.32
1452 1459 3.131933 TGTGGTGCAACAAGTAGCAAATT 59.868 39.130 5.70 0.00 41.93 1.82
1572 1579 1.320344 ACAAGATGCTCCGGCGAGTA 61.320 55.000 9.30 3.83 42.25 2.59
1876 1897 5.141182 ACCATCTGGATTCTAGATACGTGT 58.859 41.667 11.70 0.00 38.94 4.49
2339 2366 2.380941 TCATTCTCGATCCCCACGTTA 58.619 47.619 0.00 0.00 0.00 3.18
2347 2374 2.618053 GATCCCCACGTTACACTCTTG 58.382 52.381 0.00 0.00 0.00 3.02
2358 2385 5.532406 ACGTTACACTCTTGTTGGAGTACTA 59.468 40.000 0.00 0.00 43.75 1.82
2547 2577 2.041891 ACCAGCACTCTAGTCTACCTGT 59.958 50.000 0.00 0.00 0.00 4.00
2586 2616 1.331756 CCGTGCATGGATCTTAACTGC 59.668 52.381 21.08 0.00 0.00 4.40
2814 2844 0.858369 CCTACCTCAGCCCCTACCTA 59.142 60.000 0.00 0.00 0.00 3.08
2819 2849 1.382695 TCAGCCCCTACCTACAGCC 60.383 63.158 0.00 0.00 0.00 4.85
2856 2886 4.147449 CACTCATCCGCCTCGCCA 62.147 66.667 0.00 0.00 0.00 5.69
2921 2951 0.107017 ATGTTCGGGCATTCCTCTGG 60.107 55.000 0.00 0.00 0.00 3.86
3156 3186 4.529731 GGGAAGGATGGGCAGGCC 62.530 72.222 5.91 5.91 0.00 5.19
3217 3250 2.863809 GTGGTTGAATCACTTCCACCT 58.136 47.619 15.64 0.00 44.05 4.00
3302 3335 5.574891 TTAGAGTTGTTGTGTGCAAACAT 57.425 34.783 11.33 0.00 36.22 2.71
3470 3503 6.765036 TCAACCAATCAAAGCTTGCAAAATAA 59.235 30.769 0.00 0.00 0.00 1.40
3494 3527 2.578940 CCAAGGTGGGTAATCTGGGTTA 59.421 50.000 0.00 0.00 32.67 2.85
3496 3529 3.216230 AGGTGGGTAATCTGGGTTACT 57.784 47.619 4.13 0.00 35.43 2.24
3497 3530 4.357313 AGGTGGGTAATCTGGGTTACTA 57.643 45.455 4.13 0.00 35.43 1.82
3498 3531 4.904373 AGGTGGGTAATCTGGGTTACTAT 58.096 43.478 4.13 0.00 35.43 2.12
3499 3532 6.046917 AGGTGGGTAATCTGGGTTACTATA 57.953 41.667 4.13 0.00 35.43 1.31
3528 3561 7.571080 TTTGTAACGTAAATCCAAGTCCTTT 57.429 32.000 0.00 0.00 0.00 3.11
3590 3623 7.116233 CCATGAAAATAAAAGGTGCAACACTAC 59.884 37.037 3.64 0.00 39.98 2.73
3674 3707 8.625651 CGGGTACTCTCTCCATATCATAAATAG 58.374 40.741 0.00 0.00 0.00 1.73
3681 3714 9.039165 TCTCTCCATATCATAAATAGCATGTCA 57.961 33.333 0.00 0.00 0.00 3.58
3705 3738 3.806949 TGGACCTGTCTTAAGCCAAAT 57.193 42.857 0.00 0.00 0.00 2.32
3708 3741 5.636123 TGGACCTGTCTTAAGCCAAATTTA 58.364 37.500 0.00 0.00 0.00 1.40
3740 3773 4.688879 TGCTACAAATCGAACGTCTGATTT 59.311 37.500 17.46 17.46 43.60 2.17
3770 3805 5.106752 GCATGGCAAATTGAACGGTTTTTAT 60.107 36.000 0.00 0.00 0.00 1.40
3786 3821 9.699703 ACGGTTTTTATAGCAAATTATGTTGTT 57.300 25.926 0.00 0.00 0.00 2.83
3787 3822 9.950858 CGGTTTTTATAGCAAATTATGTTGTTG 57.049 29.630 0.00 0.00 0.00 3.33
3793 3828 2.923020 GCAAATTATGTTGTTGCGAGGG 59.077 45.455 0.00 0.00 38.39 4.30
3819 3854 4.621274 GCAATTTCCTTTAGCAAGCATGGA 60.621 41.667 0.00 0.00 0.00 3.41
3867 3902 4.591929 AGCATTTGCCATGCCTAAAAATT 58.408 34.783 13.06 0.00 45.59 1.82
3924 3959 6.538945 ACCTTTGACCACTAACAATGTTTT 57.461 33.333 3.17 0.00 0.00 2.43
4009 4044 7.429636 AAAATTGCGTTGTGTACACTATAGT 57.570 32.000 25.60 0.00 0.00 2.12
4010 4045 8.537049 AAAATTGCGTTGTGTACACTATAGTA 57.463 30.769 25.60 13.39 0.00 1.82
4011 4046 7.515957 AATTGCGTTGTGTACACTATAGTAC 57.484 36.000 25.60 12.73 43.58 2.73
4035 4070 7.847096 ACAAGTTTTTGGTCAAAGGTAAATCT 58.153 30.769 0.00 0.00 38.66 2.40
4037 4072 8.817100 CAAGTTTTTGGTCAAAGGTAAATCTTC 58.183 33.333 0.00 0.00 0.00 2.87
4041 4076 7.889873 TTTGGTCAAAGGTAAATCTTCTCAA 57.110 32.000 0.00 0.00 0.00 3.02
4070 4105 9.812347 TCCAAAGCTAATATTTGTGATATGGAT 57.188 29.630 0.00 0.00 36.18 3.41
4084 4123 5.182570 GTGATATGGATGAACATCATGTGGG 59.817 44.000 15.22 0.00 37.20 4.61
4140 4181 4.264804 TGCTCAAATCCCCTAATCCCTTTT 60.265 41.667 0.00 0.00 0.00 2.27
4141 4182 4.716784 GCTCAAATCCCCTAATCCCTTTTT 59.283 41.667 0.00 0.00 0.00 1.94
4147 4188 3.926671 TCCCCTAATCCCTTTTTGAAGGA 59.073 43.478 6.76 0.00 42.62 3.36
4148 4189 4.548250 TCCCCTAATCCCTTTTTGAAGGAT 59.452 41.667 6.76 0.00 42.62 3.24
4197 4238 4.237349 AGAATGGTTTAAAAGTGTGGCG 57.763 40.909 0.00 0.00 0.00 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 47 8.708742 GGCTTATTTGGTTTGTAAGTCAAATTC 58.291 33.333 0.00 0.00 45.88 2.17
47 49 7.962441 AGGCTTATTTGGTTTGTAAGTCAAAT 58.038 30.769 0.00 0.00 45.88 2.32
50 52 6.737346 GCAAGGCTTATTTGGTTTGTAAGTCA 60.737 38.462 0.00 0.00 33.61 3.41
111 115 2.949644 GGCGGGCTCAAGTAATTAATGT 59.050 45.455 0.00 0.00 0.00 2.71
129 133 2.116736 TTTGAGTTGCTTGAGCGGCG 62.117 55.000 0.51 0.51 45.83 6.46
208 212 9.740239 AAGAGCAAATATAACAACATGCAATAG 57.260 29.630 0.00 0.00 36.30 1.73
337 343 9.665719 TCGTACGGGTATACATATTGAGTTATA 57.334 33.333 16.52 0.00 0.00 0.98
1140 1147 0.032540 CAACAACCTCTTTGGCTGGC 59.967 55.000 0.00 0.00 39.84 4.85
1233 1240 1.339438 GCAGATTGCTTGTCCTCCTCA 60.339 52.381 0.00 0.00 40.96 3.86
1321 1328 1.580845 ATGTGCTTGTCTTCTGCGCC 61.581 55.000 4.18 0.00 36.51 6.53
1332 1339 1.091771 CCGCCTCTACCATGTGCTTG 61.092 60.000 0.00 0.00 0.00 4.01
2012 2039 3.103911 GTGTCGTCGCTTCCCACG 61.104 66.667 0.00 0.00 37.36 4.94
2339 2366 6.229936 TGTTTAGTACTCCAACAAGAGTGT 57.770 37.500 15.10 0.00 46.54 3.55
2347 2374 9.874215 GAATTGTAACTTGTTTAGTACTCCAAC 57.126 33.333 0.00 4.74 35.54 3.77
2358 2385 5.402270 GCAAGCATCGAATTGTAACTTGTTT 59.598 36.000 9.31 0.00 36.34 2.83
2539 2569 2.007608 CGTGACGATCAGACAGGTAGA 58.992 52.381 0.00 0.00 0.00 2.59
2547 2577 1.198408 GGTACACACGTGACGATCAGA 59.802 52.381 25.01 0.00 0.00 3.27
2586 2616 0.524862 GCACCTGCACCATCTCAAAG 59.475 55.000 0.00 0.00 41.59 2.77
2682 2712 1.376683 GGTTGACGCCATGGCTGTA 60.377 57.895 33.07 16.49 39.32 2.74
2718 2748 1.974875 CAGCATGAAGGTGGCAGCA 60.975 57.895 20.04 0.00 41.98 4.41
2814 2844 1.268283 GGGAGCTAGAGTTGGGCTGT 61.268 60.000 0.00 0.00 36.37 4.40
2819 2849 2.771943 TGGTATTGGGAGCTAGAGTTGG 59.228 50.000 0.00 0.00 0.00 3.77
2856 2886 1.681780 CCCATGTTGCCGGACATTAGT 60.682 52.381 5.05 0.00 38.15 2.24
2937 2967 2.092882 GTACTTGAGGTGCGTCGCC 61.093 63.158 15.88 5.94 0.00 5.54
3036 3066 2.028484 GTTGGCCTGACGTCGTCA 59.972 61.111 25.51 25.51 40.50 4.35
3117 3147 3.071459 GACGTTGCTGATCGCGGTG 62.071 63.158 6.13 0.00 43.27 4.94
3138 3168 3.424105 GCCTGCCCATCCTTCCCT 61.424 66.667 0.00 0.00 0.00 4.20
3156 3186 2.673523 CCCTCCTTGCTCCTGGTG 59.326 66.667 0.00 0.00 0.00 4.17
3197 3227 2.814336 GAGGTGGAAGTGATTCAACCAC 59.186 50.000 20.83 20.83 45.55 4.16
3217 3250 6.039829 GTGTCACTCACATATCCTACTCATGA 59.960 42.308 0.00 0.00 45.51 3.07
3302 3335 3.039011 GTGTTCCCCTCCTAGCTTGATA 58.961 50.000 0.00 0.00 0.00 2.15
3470 3503 2.783510 CCCAGATTACCCACCTTGGTAT 59.216 50.000 0.00 0.00 40.49 2.73
3528 3561 7.765695 AGAAAATTCTAAGCCATTTCTCACA 57.234 32.000 0.00 0.00 35.96 3.58
3567 3600 6.322712 AGGTAGTGTTGCACCTTTTATTTTCA 59.677 34.615 0.00 0.00 42.68 2.69
3568 3601 6.640907 CAGGTAGTGTTGCACCTTTTATTTTC 59.359 38.462 0.00 0.00 42.68 2.29
3577 3610 0.766674 TCCCAGGTAGTGTTGCACCT 60.767 55.000 0.00 0.00 46.29 4.00
3590 3623 7.210718 ACTATTTTTCGTAAACTTTCCCAGG 57.789 36.000 0.00 0.00 0.00 4.45
3681 3714 4.112634 TGGCTTAAGACAGGTCCAAAAT 57.887 40.909 7.01 0.00 0.00 1.82
3705 3738 9.134734 GTTCGATTTGTAGCAAAATCCAATAAA 57.865 29.630 11.61 0.00 41.52 1.40
3708 3741 5.799936 CGTTCGATTTGTAGCAAAATCCAAT 59.200 36.000 11.61 0.00 41.52 3.16
3740 3773 4.450419 CCGTTCAATTTGCCATGCTAAAAA 59.550 37.500 0.00 0.00 0.00 1.94
3757 3792 9.915629 AACATAATTTGCTATAAAAACCGTTCA 57.084 25.926 0.00 0.00 0.00 3.18
3770 3805 4.142491 CCCTCGCAACAACATAATTTGCTA 60.142 41.667 4.22 0.00 42.86 3.49
3786 3821 1.976474 GGAAATTGCCACCCTCGCA 60.976 57.895 0.00 0.00 0.00 5.10
3787 3822 1.250840 AAGGAAATTGCCACCCTCGC 61.251 55.000 4.92 0.00 0.00 5.03
3793 3828 2.995939 GCTTGCTAAAGGAAATTGCCAC 59.004 45.455 4.92 0.00 33.68 5.01
3819 3854 5.990120 AAGCTGAACATAGCAAGGATTTT 57.010 34.783 0.00 0.00 46.07 1.82
3867 3902 4.497300 GAATGCTAAAAATCTGCTGCCAA 58.503 39.130 0.00 0.00 0.00 4.52
3872 3907 6.350629 AGTTTGGAATGCTAAAAATCTGCT 57.649 33.333 0.00 0.00 0.00 4.24
3990 4025 5.625921 TGTACTATAGTGTACACAACGCA 57.374 39.130 27.06 13.09 45.16 5.24
3998 4033 9.480053 TGACCAAAAACTTGTACTATAGTGTAC 57.520 33.333 15.90 7.22 42.10 2.90
4000 4035 8.967664 TTGACCAAAAACTTGTACTATAGTGT 57.032 30.769 15.90 1.65 0.00 3.55
4001 4036 9.878599 CTTTGACCAAAAACTTGTACTATAGTG 57.121 33.333 15.90 0.98 0.00 2.74
4003 4038 9.063615 ACCTTTGACCAAAAACTTGTACTATAG 57.936 33.333 0.00 0.00 0.00 1.31
4004 4039 8.983702 ACCTTTGACCAAAAACTTGTACTATA 57.016 30.769 0.00 0.00 0.00 1.31
4005 4040 7.891498 ACCTTTGACCAAAAACTTGTACTAT 57.109 32.000 0.00 0.00 0.00 2.12
4006 4041 8.804912 TTACCTTTGACCAAAAACTTGTACTA 57.195 30.769 0.00 0.00 0.00 1.82
4007 4042 7.706100 TTACCTTTGACCAAAAACTTGTACT 57.294 32.000 0.00 0.00 0.00 2.73
4008 4043 8.936070 ATTTACCTTTGACCAAAAACTTGTAC 57.064 30.769 0.00 0.00 0.00 2.90
4009 4044 8.973182 AGATTTACCTTTGACCAAAAACTTGTA 58.027 29.630 0.00 0.00 0.00 2.41
4010 4045 7.847096 AGATTTACCTTTGACCAAAAACTTGT 58.153 30.769 0.00 0.00 0.00 3.16
4011 4046 8.716646 AAGATTTACCTTTGACCAAAAACTTG 57.283 30.769 0.00 0.00 0.00 3.16
4012 4047 8.758829 AGAAGATTTACCTTTGACCAAAAACTT 58.241 29.630 0.00 0.00 0.00 2.66
4013 4048 8.306313 AGAAGATTTACCTTTGACCAAAAACT 57.694 30.769 0.00 0.00 0.00 2.66
4014 4049 8.194769 TGAGAAGATTTACCTTTGACCAAAAAC 58.805 33.333 0.00 0.00 0.00 2.43
4015 4050 8.299990 TGAGAAGATTTACCTTTGACCAAAAA 57.700 30.769 0.00 0.00 0.00 1.94
4070 4105 5.010516 CCTACAAAAACCCACATGATGTTCA 59.989 40.000 0.00 0.00 0.00 3.18
4183 4224 0.733729 ACACGCGCCACACTTTTAAA 59.266 45.000 5.73 0.00 0.00 1.52
4184 4225 1.579698 TACACGCGCCACACTTTTAA 58.420 45.000 5.73 0.00 0.00 1.52
4186 4227 2.624169 ATACACGCGCCACACTTTT 58.376 47.368 5.73 0.00 0.00 2.27


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

AutoCloner maintained by Alex Coulton.