Multiple sequence alignment - TraesCS6D01G308300

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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 TraesCS6D01G308300 chr6D 100.000 4264 0 0 1 4264 419269742 419265479 0.000000e+00 7875.0
1 TraesCS6D01G308300 chr6D 82.173 1436 208 25 1052 2474 375689405 375688005 0.000000e+00 1190.0
2 TraesCS6D01G308300 chr6B 94.251 4314 164 40 1 4264 632183335 632179056 0.000000e+00 6516.0
3 TraesCS6D01G308300 chr6B 81.567 1481 219 28 1052 2513 562489893 562488448 0.000000e+00 1173.0
4 TraesCS6D01G308300 chr6A 94.878 3573 123 25 726 4264 562688879 562685333 0.000000e+00 5529.0
5 TraesCS6D01G308300 chr6A 82.103 1436 209 25 1052 2474 517559763 517558363 0.000000e+00 1184.0
6 TraesCS6D01G308300 chr6A 84.660 691 47 29 2 669 562689536 562688882 6.010000e-178 634.0
7 TraesCS6D01G308300 chr2D 96.667 90 3 0 1510 1599 481595159 481595070 2.660000e-32 150.0
8 TraesCS6D01G308300 chr2D 100.000 28 0 0 2676 2703 275498 275525 8.000000e-03 52.8
9 TraesCS6D01G308300 chr2B 100.000 28 0 0 2676 2703 11077841 11077868 8.000000e-03 52.8
10 TraesCS6D01G308300 chr2A 100.000 28 0 0 2676 2703 260326 260299 8.000000e-03 52.8


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 TraesCS6D01G308300 chr6D 419265479 419269742 4263 True 7875.0 7875 100.000 1 4264 1 chr6D.!!$R2 4263
1 TraesCS6D01G308300 chr6D 375688005 375689405 1400 True 1190.0 1190 82.173 1052 2474 1 chr6D.!!$R1 1422
2 TraesCS6D01G308300 chr6B 632179056 632183335 4279 True 6516.0 6516 94.251 1 4264 1 chr6B.!!$R2 4263
3 TraesCS6D01G308300 chr6B 562488448 562489893 1445 True 1173.0 1173 81.567 1052 2513 1 chr6B.!!$R1 1461
4 TraesCS6D01G308300 chr6A 562685333 562689536 4203 True 3081.5 5529 89.769 2 4264 2 chr6A.!!$R2 4262
5 TraesCS6D01G308300 chr6A 517558363 517559763 1400 True 1184.0 1184 82.103 1052 2474 1 chr6A.!!$R1 1422

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
987 1037 0.107945 CTAGCTCAACCAGACCAGCC 60.108 60.0 0.00 0.0 31.81 4.85 F
1173 1241 0.108424 CGCTGGAGCTGCTCTACTTT 60.108 55.0 27.09 0.0 39.32 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2980 3075 0.597637 GCCTGACGACACCGATATGG 60.598 60.000 0.0 0.0 46.41 2.74 R
3349 3444 5.528043 TTTGCCAATTTAGCTCTTGTTCA 57.472 34.783 0.0 0.0 0.00 3.18 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
28 29 1.909700 TTCAGGGAACATTGACTGCC 58.090 50.000 0.00 0.00 0.00 4.85
82 83 3.373565 GGAAAGCCCGCCAACAGG 61.374 66.667 0.00 0.00 0.00 4.00
85 86 1.744320 GAAAGCCCGCCAACAGGTTT 61.744 55.000 0.00 0.00 34.16 3.27
88 89 2.520741 CCCGCCAACAGGTTTGGT 60.521 61.111 4.99 0.00 41.53 3.67
146 149 6.054860 TCTTAGCTCAGCTTCTTGGTTTAT 57.945 37.500 3.31 0.00 40.44 1.40
150 153 3.376546 GCTCAGCTTCTTGGTTTATCCTG 59.623 47.826 0.00 0.00 37.07 3.86
398 412 4.609113 CGTGCCGCTCTTTTGTGATATATG 60.609 45.833 0.00 0.00 0.00 1.78
414 428 7.335171 TGTGATATATGCCTATGAACATGCTTC 59.665 37.037 0.00 0.00 0.00 3.86
435 449 5.417754 TCTCTTCATCTGCAGAACATTCT 57.582 39.130 22.50 0.00 38.25 2.40
547 570 9.860898 GAATGCTCTTTTGTCCAGTTAATTAAT 57.139 29.630 0.31 0.00 0.00 1.40
558 581 9.602568 TGTCCAGTTAATTAATTAATACGCAGA 57.397 29.630 20.60 11.00 35.02 4.26
576 599 0.657840 GATCCGCAGAAAATGGGTCG 59.342 55.000 0.00 0.00 40.17 4.79
651 680 4.785669 GTGGCTACGAAATGAGAAGATG 57.214 45.455 0.00 0.00 0.00 2.90
669 698 1.702182 TGCATTTGCCCAGTTCTTCA 58.298 45.000 0.00 0.00 41.18 3.02
670 699 1.340889 TGCATTTGCCCAGTTCTTCAC 59.659 47.619 0.00 0.00 41.18 3.18
677 711 3.360867 TGCCCAGTTCTTCACTTTTTCA 58.639 40.909 0.00 0.00 30.92 2.69
697 731 2.507339 AAAGTTTGTCAACATGCCGG 57.493 45.000 0.00 0.00 35.05 6.13
698 732 1.398692 AAGTTTGTCAACATGCCGGT 58.601 45.000 1.90 0.00 35.05 5.28
699 733 0.951558 AGTTTGTCAACATGCCGGTC 59.048 50.000 1.90 0.00 35.05 4.79
701 735 0.950836 TTTGTCAACATGCCGGTCTG 59.049 50.000 1.90 3.26 0.00 3.51
705 753 1.336755 GTCAACATGCCGGTCTGTTTT 59.663 47.619 17.69 0.16 33.45 2.43
781 829 2.281761 CAGTCAGGGTGGTGGTGC 60.282 66.667 0.00 0.00 0.00 5.01
904 953 4.844420 GGCATCTTCTCCGACCAG 57.156 61.111 0.00 0.00 0.00 4.00
945 994 7.761704 GCATATACTACTACTGCATGCATTAGT 59.238 37.037 37.30 37.30 42.43 2.24
956 1006 0.179137 TGCATTAGTCTGACCGCTCG 60.179 55.000 3.76 0.00 0.00 5.03
962 1012 3.450507 TCTGACCGCTCGGACAAA 58.549 55.556 15.95 0.00 39.22 2.83
963 1013 1.289066 TCTGACCGCTCGGACAAAG 59.711 57.895 15.95 4.67 39.22 2.77
964 1014 2.357034 TGACCGCTCGGACAAAGC 60.357 61.111 15.95 0.00 37.04 3.51
965 1015 2.048127 GACCGCTCGGACAAAGCT 60.048 61.111 15.95 0.00 37.62 3.74
983 1033 1.202475 GCTAGCTAGCTCAACCAGACC 60.202 57.143 33.71 4.79 45.62 3.85
984 1034 2.103373 CTAGCTAGCTCAACCAGACCA 58.897 52.381 23.26 0.00 0.00 4.02
985 1035 0.901124 AGCTAGCTCAACCAGACCAG 59.099 55.000 12.68 0.00 0.00 4.00
986 1036 0.742635 GCTAGCTCAACCAGACCAGC 60.743 60.000 7.70 0.00 0.00 4.85
987 1037 0.107945 CTAGCTCAACCAGACCAGCC 60.108 60.000 0.00 0.00 31.81 4.85
989 1039 1.968540 GCTCAACCAGACCAGCCAC 60.969 63.158 0.00 0.00 0.00 5.01
990 1040 1.451504 CTCAACCAGACCAGCCACA 59.548 57.895 0.00 0.00 0.00 4.17
1173 1241 0.108424 CGCTGGAGCTGCTCTACTTT 60.108 55.000 27.09 0.00 39.32 2.66
1867 1935 0.316204 GGTCTCCAACTTCGACGGAA 59.684 55.000 0.00 0.00 0.00 4.30
1906 1974 4.582869 GAGCTCATATGCCATATTGGTGA 58.417 43.478 9.40 0.00 40.46 4.02
2077 2145 1.676967 GAGCAGAACAGGGCCTTGG 60.677 63.158 20.34 1.90 0.00 3.61
2291 2365 1.251355 CTGATGAACGACGTCGACAG 58.749 55.000 41.52 30.83 43.02 3.51
2487 2573 0.899717 AAATGGCGGGTGATGTGCTT 60.900 50.000 0.00 0.00 0.00 3.91
2589 2675 1.509923 GCCAAATCTGTCTGCAGGC 59.490 57.895 12.53 12.53 42.78 4.85
2710 2796 4.286032 AGAAGATTGTGCAGGTTGGTACTA 59.714 41.667 0.00 0.00 0.00 1.82
2711 2797 3.939066 AGATTGTGCAGGTTGGTACTAC 58.061 45.455 0.00 0.00 0.00 2.73
2726 2817 4.883585 TGGTACTACTCACTTGGTATACCG 59.116 45.833 17.13 6.35 39.43 4.02
2733 2824 6.295719 ACTCACTTGGTATACCGAAAGAAT 57.704 37.500 22.55 8.32 39.43 2.40
2754 2845 1.452145 TTTTGCAGCTCCCGGTTGTC 61.452 55.000 0.00 0.00 0.00 3.18
2921 3016 0.972471 TGAGGATCCTGCTCGCAGAA 60.972 55.000 22.02 0.00 46.30 3.02
3160 3255 2.499098 CGTGACCGTCGACGACAG 60.499 66.667 37.65 23.51 43.02 3.51
3218 3313 0.613260 TGATCCAGAAACCCCTCACG 59.387 55.000 0.00 0.00 0.00 4.35
3224 3319 1.070786 GAAACCCCTCACGCTGACA 59.929 57.895 0.00 0.00 0.00 3.58
3349 3444 2.475155 TCCACAAGCCTCTGAGATGAT 58.525 47.619 6.17 0.00 0.00 2.45
3350 3445 2.169978 TCCACAAGCCTCTGAGATGATG 59.830 50.000 6.17 2.58 0.00 3.07
3351 3446 2.169978 CCACAAGCCTCTGAGATGATGA 59.830 50.000 6.17 0.00 0.00 2.92
3359 3454 4.121317 CCTCTGAGATGATGAACAAGAGC 58.879 47.826 6.17 0.00 31.88 4.09
3425 3520 4.575645 TCATATCAATGATGACTTTGCGCA 59.424 37.500 5.66 5.66 38.69 6.09
3483 3581 3.977536 GCAATGTAATGCGCAAGAAAAC 58.022 40.909 17.11 9.07 43.02 2.43
3486 3584 3.822594 TGTAATGCGCAAGAAAACGAT 57.177 38.095 17.11 0.00 43.02 3.73
3492 3590 1.734163 CGCAAGAAAACGATAGGGGT 58.266 50.000 0.00 0.00 40.40 4.95
3494 3592 2.433436 GCAAGAAAACGATAGGGGTGT 58.567 47.619 0.00 0.00 43.77 4.16
3559 3657 2.871022 GTCACCAAGATAGCAGCATCAG 59.129 50.000 0.00 0.00 0.00 2.90
3670 3778 4.106197 GTCTTGTATTGTCCTCTGTAGCG 58.894 47.826 0.00 0.00 0.00 4.26
3750 3858 1.093159 CCTCACTGAAGATGCTTGCC 58.907 55.000 0.00 0.00 0.00 4.52
3753 3861 2.156917 TCACTGAAGATGCTTGCCAAG 58.843 47.619 0.00 0.00 0.00 3.61
3783 3891 2.271024 CTTGCGATCAGTGTCGTGCG 62.271 60.000 13.90 0.00 43.27 5.34
3967 4078 1.066430 TCGTGGAACTGGGTATTCAGC 60.066 52.381 0.00 0.00 38.26 4.26
3971 4082 2.107378 TGGAACTGGGTATTCAGCAACA 59.893 45.455 0.00 0.00 38.26 3.33
4044 4156 5.879223 AGATGCTGGATTCTTACAGTTGAAG 59.121 40.000 0.00 0.00 37.07 3.02
4060 4172 2.436417 TGAAGAATGCAGGCCTAACAC 58.564 47.619 3.98 0.00 0.00 3.32
4062 4174 0.698238 AGAATGCAGGCCTAACACCA 59.302 50.000 3.98 0.00 0.00 4.17
4247 4360 1.560860 GCCGGCGCTGATCATTACTC 61.561 60.000 20.25 0.00 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 4.517285 GCAGTCAATGTTCCCTGAATAGA 58.483 43.478 0.00 0.00 0.00 1.98
28 29 3.763360 AGTCTCTGAACCAGTCTCTGATG 59.237 47.826 0.00 0.00 32.44 3.07
82 83 0.317854 GCTTGTTGCCGAGACCAAAC 60.318 55.000 0.00 0.00 35.15 2.93
150 153 6.777526 ATAATATCTCTTCTGCGTTTCAGC 57.222 37.500 0.00 0.00 42.56 4.26
209 212 1.621992 TATTCCTGGTTGCGGCAAAA 58.378 45.000 18.23 8.12 0.00 2.44
398 412 4.194640 TGAAGAGAAGCATGTTCATAGGC 58.805 43.478 9.64 0.00 28.38 3.93
414 428 5.472320 CAGAATGTTCTGCAGATGAAGAG 57.528 43.478 19.04 1.71 46.97 2.85
435 449 2.203401 GTTGTTACACACAGGTACGCA 58.797 47.619 0.00 0.00 36.48 5.24
457 471 8.660373 CGCTCCACTAGATTATTCATTTATTCC 58.340 37.037 0.00 0.00 0.00 3.01
475 489 4.162320 TCAGAAATCCTTATTCGCTCCACT 59.838 41.667 0.00 0.00 32.04 4.00
547 570 3.446310 TTCTGCGGATCTGCGTATTAA 57.554 42.857 21.30 8.14 37.81 1.40
548 571 3.446310 TTTCTGCGGATCTGCGTATTA 57.554 42.857 21.30 2.65 37.81 0.98
549 572 2.309528 TTTCTGCGGATCTGCGTATT 57.690 45.000 21.30 0.00 37.81 1.89
550 573 2.309528 TTTTCTGCGGATCTGCGTAT 57.690 45.000 21.30 0.00 37.81 3.06
558 581 0.251916 TCGACCCATTTTCTGCGGAT 59.748 50.000 0.00 0.00 0.00 4.18
576 599 4.443978 TCCCAGGAAGATGATCCATTTC 57.556 45.455 0.00 0.00 42.27 2.17
615 638 3.699894 CACGCACTCTCCCAGCCT 61.700 66.667 0.00 0.00 0.00 4.58
651 680 1.615392 AGTGAAGAACTGGGCAAATGC 59.385 47.619 0.00 0.00 37.88 3.56
677 711 2.167487 ACCGGCATGTTGACAAACTTTT 59.833 40.909 0.00 0.00 37.19 2.27
688 722 2.293399 GAGAAAAACAGACCGGCATGTT 59.707 45.455 16.87 16.87 41.28 2.71
689 723 1.880027 GAGAAAAACAGACCGGCATGT 59.120 47.619 0.00 3.22 0.00 3.21
691 725 2.224523 TGAGAGAAAAACAGACCGGCAT 60.225 45.455 0.00 0.00 0.00 4.40
697 731 4.450757 GCTTCCTCTGAGAGAAAAACAGAC 59.549 45.833 11.82 0.00 36.04 3.51
698 732 4.503991 GGCTTCCTCTGAGAGAAAAACAGA 60.504 45.833 11.82 0.00 38.16 3.41
699 733 3.750652 GGCTTCCTCTGAGAGAAAAACAG 59.249 47.826 11.82 0.00 0.00 3.16
701 735 3.744660 TGGCTTCCTCTGAGAGAAAAAC 58.255 45.455 11.82 0.60 0.00 2.43
705 753 1.209019 GCATGGCTTCCTCTGAGAGAA 59.791 52.381 11.82 7.25 0.00 2.87
945 994 1.289066 CTTTGTCCGAGCGGTCAGA 59.711 57.895 15.89 5.85 35.03 3.27
964 1014 2.100584 CTGGTCTGGTTGAGCTAGCTAG 59.899 54.545 19.38 16.84 43.13 3.42
965 1015 2.103373 CTGGTCTGGTTGAGCTAGCTA 58.897 52.381 19.38 0.00 43.13 3.32
975 1025 1.152756 GGTTGTGGCTGGTCTGGTT 60.153 57.895 0.00 0.00 0.00 3.67
981 1031 2.594592 GCTTCGGTTGTGGCTGGT 60.595 61.111 0.00 0.00 0.00 4.00
983 1033 0.387622 CATTGCTTCGGTTGTGGCTG 60.388 55.000 0.00 0.00 0.00 4.85
984 1034 1.526575 CCATTGCTTCGGTTGTGGCT 61.527 55.000 0.00 0.00 0.00 4.75
985 1035 1.080569 CCATTGCTTCGGTTGTGGC 60.081 57.895 0.00 0.00 0.00 5.01
986 1036 1.080569 GCCATTGCTTCGGTTGTGG 60.081 57.895 0.00 0.00 33.53 4.17
987 1037 1.442520 CGCCATTGCTTCGGTTGTG 60.443 57.895 0.00 0.00 34.43 3.33
989 1039 2.504681 GCGCCATTGCTTCGGTTG 60.505 61.111 0.00 0.00 34.43 3.77
990 1040 4.101790 CGCGCCATTGCTTCGGTT 62.102 61.111 0.00 0.00 34.43 4.44
1442 1510 3.148279 GGATGAGGCCGAGGTCGT 61.148 66.667 0.00 0.00 37.74 4.34
1678 1746 4.862092 CTGCGAGCCGAGCACGAT 62.862 66.667 16.81 0.00 44.57 3.73
1726 1794 0.800683 TCGCTTGCCATTACGTCGAG 60.801 55.000 0.00 0.00 0.00 4.04
1867 1935 2.030562 CGCCACCGGTGTCTTTCT 59.969 61.111 31.80 0.00 0.00 2.52
2077 2145 4.030452 GTCCTGCTTGGCGTGCAC 62.030 66.667 6.82 6.82 36.37 4.57
2291 2365 0.942884 GTTCACCGTCAACGTCTCCC 60.943 60.000 1.48 0.00 37.74 4.30
2589 2675 6.183360 CCTGAAACTCAACACATATGCTACAG 60.183 42.308 1.58 0.00 0.00 2.74
2665 2751 1.669779 GCACATGTTGATCTGAGAGCC 59.330 52.381 0.00 0.00 0.00 4.70
2710 2796 5.733620 TTCTTTCGGTATACCAAGTGAGT 57.266 39.130 21.76 0.00 35.14 3.41
2711 2797 8.888579 AATATTCTTTCGGTATACCAAGTGAG 57.111 34.615 21.76 11.07 35.14 3.51
2726 2817 4.354587 CGGGAGCTGCAAAATATTCTTTC 58.645 43.478 7.79 0.00 0.00 2.62
2733 2824 1.173043 CAACCGGGAGCTGCAAAATA 58.827 50.000 6.32 0.00 0.00 1.40
2754 2845 3.628942 TGAAGAAATGAGGCGATGGATTG 59.371 43.478 0.00 0.00 0.00 2.67
2980 3075 0.597637 GCCTGACGACACCGATATGG 60.598 60.000 0.00 0.00 46.41 2.74
3349 3444 5.528043 TTTGCCAATTTAGCTCTTGTTCA 57.472 34.783 0.00 0.00 0.00 3.18
3350 3445 6.257630 TGTTTTTGCCAATTTAGCTCTTGTTC 59.742 34.615 0.00 0.00 0.00 3.18
3351 3446 6.112058 TGTTTTTGCCAATTTAGCTCTTGTT 58.888 32.000 0.00 0.00 0.00 2.83
3410 3505 4.505191 GCAAATTATGCGCAAAGTCATCAT 59.495 37.500 17.11 0.00 46.87 2.45
3411 3506 3.858812 GCAAATTATGCGCAAAGTCATCA 59.141 39.130 17.11 0.00 46.87 3.07
3412 3507 4.427438 GCAAATTATGCGCAAAGTCATC 57.573 40.909 17.11 0.00 46.87 2.92
3425 3520 5.581479 TCTGAAATGCATTTGCGCAAATTAT 59.419 32.000 38.50 31.10 46.87 1.28
3483 3581 2.159000 GGTTTAGTCCACACCCCTATCG 60.159 54.545 0.00 0.00 0.00 2.92
3486 3584 1.660242 GGGTTTAGTCCACACCCCTA 58.340 55.000 0.00 0.00 44.16 3.53
3513 3611 3.096495 TGTATGCTGCCCCTCCCC 61.096 66.667 0.00 0.00 0.00 4.81
3559 3657 3.512516 GGACTCATGCGCTTGGGC 61.513 66.667 22.03 14.60 0.00 5.36
3668 3776 4.788521 GCCAATAAGTAGCAATACAACCGC 60.789 45.833 0.00 0.00 0.00 5.68
3670 3778 7.745620 ATAGCCAATAAGTAGCAATACAACC 57.254 36.000 0.00 0.00 0.00 3.77
3753 3861 1.696832 GATCGCAAGTTCCGGTGAGC 61.697 60.000 0.00 0.00 39.48 4.26
3759 3867 0.716108 GACACTGATCGCAAGTTCCG 59.284 55.000 0.00 0.00 35.19 4.30
3761 3869 1.125021 CACGACACTGATCGCAAGTTC 59.875 52.381 0.00 0.00 46.22 3.01
3783 3891 0.100503 ACTTGTTGCCGTGCTGTTTC 59.899 50.000 0.00 0.00 0.00 2.78
3793 3902 1.142474 GCAGATTGCAACTTGTTGCC 58.858 50.000 28.37 16.95 46.82 4.52
3971 4082 5.689961 GGTGAAAATAATTTGCTCAACGTGT 59.310 36.000 0.00 0.00 0.00 4.49
3978 4089 5.537188 TGGTGTGGTGAAAATAATTTGCTC 58.463 37.500 0.00 0.00 0.00 4.26
4044 4156 0.811281 GTGGTGTTAGGCCTGCATTC 59.189 55.000 17.99 11.15 0.00 2.67
4060 4172 0.031043 TGTAACGTCTGTGTCCGTGG 59.969 55.000 0.00 0.00 37.38 4.94
4062 4174 2.582728 TTTGTAACGTCTGTGTCCGT 57.417 45.000 0.00 0.00 39.32 4.69


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

AutoCloner maintained by Alex Coulton.