Multiple sequence alignment - TraesCS7D01G244000

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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 TraesCS7D01G244000 chr7D 100.000 4269 0 0 1 4269 211631463 211635731 0.000000e+00 7884.0
1 TraesCS7D01G244000 chr7B 94.792 4320 136 30 1 4267 189906268 189901985 0.000000e+00 6649.0
2 TraesCS7D01G244000 chr7A 94.303 3581 132 29 1 3538 223521192 223524743 0.000000e+00 5417.0
3 TraesCS7D01G244000 chr7A 89.426 766 30 21 3531 4267 223524939 223525682 0.000000e+00 918.0
4 TraesCS7D01G244000 chr1A 93.298 373 14 5 1618 1988 508205541 508205178 1.350000e-149 540.0
5 TraesCS7D01G244000 chr1A 94.100 339 17 2 2536 2871 508202803 508202465 2.940000e-141 512.0
6 TraesCS7D01G244000 chr1A 94.161 137 7 1 2187 2323 508203963 508203828 1.560000e-49 207.0
7 TraesCS7D01G244000 chr2A 94.985 339 14 2 2536 2871 651804636 651804298 2.920000e-146 529.0
8 TraesCS7D01G244000 chr2A 92.330 352 20 3 1637 1988 651807439 651807095 1.070000e-135 494.0
9 TraesCS7D01G244000 chr2A 94.161 137 7 1 2187 2323 651805877 651805742 1.560000e-49 207.0
10 TraesCS7D01G244000 chr2A 92.857 42 2 1 3462 3503 651804301 651804261 4.610000e-05 60.2
11 TraesCS7D01G244000 chr6A 92.722 371 14 6 1618 1988 558036735 558037092 1.360000e-144 523.0
12 TraesCS7D01G244000 chr6A 94.100 339 17 2 2536 2871 558039477 558039815 2.940000e-141 512.0
13 TraesCS7D01G244000 chr6A 95.420 131 5 1 2187 2317 558038315 558038444 1.560000e-49 207.0
14 TraesCS7D01G244000 chr6A 92.857 42 2 1 3462 3503 558039812 558039852 4.610000e-05 60.2


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 TraesCS7D01G244000 chr7D 211631463 211635731 4268 False 7884.000000 7884 100.00000 1 4269 1 chr7D.!!$F1 4268
1 TraesCS7D01G244000 chr7B 189901985 189906268 4283 True 6649.000000 6649 94.79200 1 4267 1 chr7B.!!$R1 4266
2 TraesCS7D01G244000 chr7A 223521192 223525682 4490 False 3167.500000 5417 91.86450 1 4267 2 chr7A.!!$F1 4266
3 TraesCS7D01G244000 chr1A 508202465 508205541 3076 True 419.666667 540 93.85300 1618 2871 3 chr1A.!!$R1 1253
4 TraesCS7D01G244000 chr2A 651804261 651807439 3178 True 322.550000 529 93.58325 1637 3503 4 chr2A.!!$R1 1866
5 TraesCS7D01G244000 chr6A 558036735 558039852 3117 False 325.550000 523 93.77475 1618 3503 4 chr6A.!!$F1 1885

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
605 610 1.261238 ACAGCCTCAGGAGTAGCCAC 61.261 60.000 0.00 0.0 40.02 5.01 F
1004 1059 1.613630 GCTGTCCTCTTCTCCCCCA 60.614 63.158 0.00 0.0 0.00 4.96 F
1822 1884 3.444805 GAGTGCGCCGGAGAGAGT 61.445 66.667 10.31 0.0 0.00 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1528 1588 0.173708 AATCGAGGCGAGACAAGGAC 59.826 55.000 0.0 0.0 39.91 3.85 R
1825 1887 1.821332 CTGCGGGATTCTTGGCTCC 60.821 63.158 0.0 0.0 0.00 4.70 R
3752 5983 0.306533 TCGCTTCAACAAGAAACCGC 59.693 50.000 0.0 0.0 35.40 5.68 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
224 225 1.812571 GTGTTCATTTGATGGCCGACT 59.187 47.619 0.00 0.00 0.00 4.18
232 233 2.309528 TGATGGCCGACTTGTATGTC 57.690 50.000 0.00 0.00 0.00 3.06
244 245 7.575909 GCCGACTTGTATGTCATACTATGATCT 60.576 40.741 20.91 0.66 42.04 2.75
323 324 9.269453 GTTGTATATATCCTTTGTAAGTCACCC 57.731 37.037 0.00 0.00 0.00 4.61
373 374 1.481363 TCATATTCCACGGGCGTGTAA 59.519 47.619 0.00 0.00 44.02 2.41
439 442 6.927933 GATTTGAAAATCGAAAACATCCGT 57.072 33.333 0.00 0.00 35.88 4.69
444 447 8.804688 TTGAAAATCGAAAACATCCGTAATTT 57.195 26.923 0.00 0.00 0.00 1.82
498 502 7.871973 CACCATCAACCAGTAATCAAATTCAAA 59.128 33.333 0.00 0.00 0.00 2.69
577 582 2.203126 GCTCGAATCCAGCAGGGG 60.203 66.667 0.00 0.00 36.82 4.79
578 583 3.036429 GCTCGAATCCAGCAGGGGT 62.036 63.158 0.00 0.00 36.82 4.95
584 589 4.980592 TCCAGCAGGGGTCCAGCA 62.981 66.667 4.25 0.00 38.55 4.41
605 610 1.261238 ACAGCCTCAGGAGTAGCCAC 61.261 60.000 0.00 0.00 40.02 5.01
631 668 3.861840 TCCAGCAGAACAGCATTAGTAC 58.138 45.455 0.00 0.00 36.85 2.73
634 671 4.806247 CCAGCAGAACAGCATTAGTACTAC 59.194 45.833 0.91 0.00 36.85 2.73
635 672 4.806247 CAGCAGAACAGCATTAGTACTACC 59.194 45.833 0.91 0.00 36.85 3.18
716 754 4.083003 ACATGCCAACACGGTTAATTACTG 60.083 41.667 0.00 0.00 39.17 2.74
718 756 4.639334 TGCCAACACGGTTAATTACTGTA 58.361 39.130 0.00 0.00 44.64 2.74
771 809 1.750193 GATCGAATCCACCAGCCAAA 58.250 50.000 0.00 0.00 0.00 3.28
873 928 3.036091 CCCCGAATAACCTAGAACCTCA 58.964 50.000 0.00 0.00 0.00 3.86
963 1018 2.271173 CCGGCCTAAACCCAGTCC 59.729 66.667 0.00 0.00 0.00 3.85
964 1019 2.271173 CGGCCTAAACCCAGTCCC 59.729 66.667 0.00 0.00 0.00 4.46
1004 1059 1.613630 GCTGTCCTCTTCTCCCCCA 60.614 63.158 0.00 0.00 0.00 4.96
1528 1588 4.918201 GGGATTGGGAGGCTCGCG 62.918 72.222 24.17 0.00 31.21 5.87
1822 1884 3.444805 GAGTGCGCCGGAGAGAGT 61.445 66.667 10.31 0.00 0.00 3.24
1825 1887 3.443925 TGCGCCGGAGAGAGTGAG 61.444 66.667 10.31 0.00 0.00 3.51
2143 2719 0.035439 GTTTCGGGATGGAGCTGGAA 60.035 55.000 0.00 0.00 0.00 3.53
2465 3911 1.731700 CCGCCGGAATCTCGTCTTA 59.268 57.895 5.05 0.00 0.00 2.10
2470 3916 4.235360 CGCCGGAATCTCGTCTTATTAAT 58.765 43.478 5.05 0.00 0.00 1.40
2479 3925 9.464714 GAATCTCGTCTTATTAATTGCTAGACA 57.535 33.333 14.57 0.00 36.00 3.41
2505 3951 5.950023 AGGTTGCATTTGATCCAGAGATAT 58.050 37.500 0.00 0.00 30.90 1.63
2507 3953 7.520798 AGGTTGCATTTGATCCAGAGATATTA 58.479 34.615 0.00 0.00 30.90 0.98
2509 3955 7.094463 GGTTGCATTTGATCCAGAGATATTAGG 60.094 40.741 0.00 0.00 30.90 2.69
3168 5157 0.036952 GTCCGGCGATCCATCATCAT 60.037 55.000 9.30 0.00 0.00 2.45
3193 5182 2.406616 CGGGAAACGGAAGCCATGG 61.407 63.158 7.63 7.63 39.42 3.66
3206 5195 1.224315 CCATGGCCCGTCATTCTCA 59.776 57.895 0.00 0.00 0.00 3.27
3232 5221 2.432146 CCATCAGCAGCAGTAGTTCCTA 59.568 50.000 0.00 0.00 0.00 2.94
3238 5227 4.937620 CAGCAGCAGTAGTTCCTAAAATCA 59.062 41.667 0.00 0.00 0.00 2.57
3407 5402 2.684374 TGATCTGGACAATTTGCATCCG 59.316 45.455 0.00 0.00 35.06 4.18
3471 5473 3.442273 ACTTTTTGCGGTGAAAACTGAGA 59.558 39.130 0.00 0.00 0.00 3.27
3561 5766 0.468029 CACCTTTGGGCCAGTTGACT 60.468 55.000 6.23 0.00 35.63 3.41
3628 5833 4.037446 TGTCAGCACATTGTCTTTTTACCC 59.963 41.667 0.00 0.00 0.00 3.69
3640 5845 3.887335 TTTACCCGTGTCCTGCCGC 62.887 63.158 0.00 0.00 0.00 6.53
3662 5881 2.076628 GTGCATGCACAGCGAAACG 61.077 57.895 39.12 0.00 45.53 3.60
3681 5900 3.594568 CCACACGCAATGGCAGAT 58.405 55.556 0.00 0.00 41.24 2.90
3682 5901 1.138036 CCACACGCAATGGCAGATG 59.862 57.895 0.00 0.00 41.24 2.90
3683 5902 1.138036 CACACGCAATGGCAGATGG 59.862 57.895 0.00 0.00 41.24 3.51
3684 5903 2.048023 ACACGCAATGGCAGATGGG 61.048 57.895 15.54 15.54 41.24 4.00
3685 5904 3.142838 ACGCAATGGCAGATGGGC 61.143 61.111 16.62 4.73 41.24 5.36
3714 5940 4.692475 GGGCAACACGCGGGTAGT 62.692 66.667 17.66 0.00 43.84 2.73
3715 5941 2.262292 GGCAACACGCGGGTAGTA 59.738 61.111 17.66 0.00 43.84 1.82
3716 5942 1.808390 GGCAACACGCGGGTAGTAG 60.808 63.158 17.66 6.62 43.84 2.57
3717 5943 1.808390 GCAACACGCGGGTAGTAGG 60.808 63.158 17.66 3.27 0.00 3.18
3718 5944 1.588082 CAACACGCGGGTAGTAGGT 59.412 57.895 17.66 0.00 0.00 3.08
3719 5945 0.037975 CAACACGCGGGTAGTAGGTT 60.038 55.000 17.66 1.84 0.00 3.50
3720 5946 0.037975 AACACGCGGGTAGTAGGTTG 60.038 55.000 17.66 0.00 0.00 3.77
3777 6008 4.499019 GGTTTCTTGTTGAAGCGAAATGGA 60.499 41.667 0.00 0.00 36.86 3.41
3800 6036 2.028112 TCGCTTTAATGACAGCCTGAGT 60.028 45.455 0.00 0.00 31.82 3.41
3858 6095 0.174162 GTGCAAGATTGGTCATGGGC 59.826 55.000 0.00 0.00 0.00 5.36
3860 6097 1.315257 GCAAGATTGGTCATGGGCGT 61.315 55.000 0.00 0.00 0.00 5.68
4062 6302 7.548097 AGAGAAGTTTTTCTTTTCCTTTCACC 58.452 34.615 0.00 0.00 43.63 4.02
4180 6420 4.333926 GCTCCTGATGACCTTGACATTTAC 59.666 45.833 0.00 0.00 0.00 2.01
4200 6440 0.321653 AATCCTGCAGACCAACCGAC 60.322 55.000 17.39 0.00 0.00 4.79
4267 6507 2.823829 GCGCTATTTGGCCCGTGAG 61.824 63.158 0.00 0.00 0.00 3.51
4268 6508 2.823829 CGCTATTTGGCCCGTGAGC 61.824 63.158 0.00 3.24 0.00 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 9.877178 TTAAAAGCAAAGTTTACTGAATTCCAA 57.123 25.926 2.27 0.00 0.00 3.53
55 56 6.128007 GGCCGAACATAAATATTGTCCATAGG 60.128 42.308 0.00 0.00 0.00 2.57
216 217 2.764010 AGTATGACATACAAGTCGGCCA 59.236 45.455 24.08 0.00 41.41 5.36
323 324 7.043192 GCAAATCAAACGATCTTTATTCCATGG 60.043 37.037 4.97 4.97 0.00 3.66
444 447 6.071221 TGCTTACAGTCTCGTAGGGATTAAAA 60.071 38.462 0.00 0.00 0.00 1.52
453 457 3.426426 GGTGTCTGCTTACAGTCTCGTAG 60.426 52.174 0.00 0.00 44.77 3.51
458 462 2.899900 TGATGGTGTCTGCTTACAGTCT 59.100 45.455 0.00 0.00 44.77 3.24
498 502 1.692749 ACTGTGTGTGGGGTCCTGT 60.693 57.895 0.00 0.00 0.00 4.00
543 547 3.186409 TCGAGCCTCTTCGTTTGAATTTG 59.814 43.478 0.00 0.00 41.22 2.32
577 582 1.670406 CTGAGGCTGTGTGCTGGAC 60.670 63.158 0.00 0.00 42.39 4.02
578 583 2.745698 CTGAGGCTGTGTGCTGGA 59.254 61.111 0.00 0.00 42.39 3.86
584 589 1.261238 GGCTACTCCTGAGGCTGTGT 61.261 60.000 0.00 0.00 36.58 3.72
605 610 0.034476 TGCTGTTCTGCTGGAGTGAG 59.966 55.000 0.00 0.00 0.00 3.51
631 668 7.597743 GGGTTAACGTTGATATCATACTGGTAG 59.402 40.741 11.99 0.00 0.00 3.18
634 671 6.423905 CAGGGTTAACGTTGATATCATACTGG 59.576 42.308 11.99 0.00 0.00 4.00
635 672 6.423905 CCAGGGTTAACGTTGATATCATACTG 59.576 42.308 11.99 6.73 0.00 2.74
873 928 0.812412 CCGGTCTGGTGTTTCGTGTT 60.812 55.000 0.00 0.00 0.00 3.32
1528 1588 0.173708 AATCGAGGCGAGACAAGGAC 59.826 55.000 0.00 0.00 39.91 3.85
1729 1789 2.203182 TTGACGAGGGACCCCACT 59.797 61.111 7.00 0.00 38.92 4.00
1738 1798 4.410400 GGGCCCTGGTTGACGAGG 62.410 72.222 17.04 5.31 40.98 4.63
1822 1884 1.907739 CGGGATTCTTGGCTCCTCA 59.092 57.895 0.00 0.00 0.00 3.86
1825 1887 1.821332 CTGCGGGATTCTTGGCTCC 60.821 63.158 0.00 0.00 0.00 4.70
1999 2061 2.675423 TCCTCGTCCCTGGTCGTG 60.675 66.667 2.94 0.97 0.00 4.35
2161 2737 2.601067 TTCCCCACGACGTAGGCA 60.601 61.111 6.97 0.00 0.00 4.75
2453 3899 9.464714 TGTCTAGCAATTAATAAGACGAGATTC 57.535 33.333 12.06 0.00 39.52 2.52
2465 3911 5.945784 TGCAACCTCTTGTCTAGCAATTAAT 59.054 36.000 0.00 0.00 36.36 1.40
2470 3916 2.928801 TGCAACCTCTTGTCTAGCAA 57.071 45.000 0.00 0.71 35.50 3.91
2479 3925 4.015084 CTCTGGATCAAATGCAACCTCTT 58.985 43.478 0.00 0.00 0.00 2.85
2505 3951 6.620877 TTCCAAGAAGCTATTCAGTCCTAA 57.379 37.500 0.00 0.00 37.94 2.69
2507 3953 5.190528 TGATTCCAAGAAGCTATTCAGTCCT 59.809 40.000 0.00 0.00 37.94 3.85
2509 3955 5.526846 CCTGATTCCAAGAAGCTATTCAGTC 59.473 44.000 0.00 0.00 37.94 3.51
3193 5182 0.876342 GGTCGATGAGAATGACGGGC 60.876 60.000 0.00 0.00 33.45 6.13
3206 5195 1.068281 CTACTGCTGCTGATGGTCGAT 59.932 52.381 13.69 0.00 0.00 3.59
3421 5417 3.582148 TGCTGCTGCATTCCGAAG 58.418 55.556 14.93 0.00 45.31 3.79
3561 5766 3.433274 GTGTCATTGTCGCATCTTTCAGA 59.567 43.478 0.00 0.00 0.00 3.27
3678 5897 1.220206 CAGTCTTCTGCGCCCATCT 59.780 57.895 4.18 0.00 34.79 2.90
3679 5898 1.817099 CCAGTCTTCTGCGCCCATC 60.817 63.158 4.18 0.00 40.09 3.51
3680 5899 2.270205 CCAGTCTTCTGCGCCCAT 59.730 61.111 4.18 0.00 40.09 4.00
3681 5900 4.020617 CCCAGTCTTCTGCGCCCA 62.021 66.667 4.18 0.00 40.09 5.36
3682 5901 4.785453 CCCCAGTCTTCTGCGCCC 62.785 72.222 4.18 0.00 40.09 6.13
3684 5903 4.704833 TGCCCCAGTCTTCTGCGC 62.705 66.667 0.00 0.00 40.09 6.09
3685 5904 2.032528 TTGCCCCAGTCTTCTGCG 59.967 61.111 0.00 0.00 40.09 5.18
3690 5909 2.594592 GCGTGTTGCCCCAGTCTT 60.595 61.111 0.00 0.00 37.76 3.01
3714 5940 1.765074 GGGCCACTGAACCAACCTA 59.235 57.895 4.39 0.00 0.00 3.08
3715 5941 2.520968 GGGCCACTGAACCAACCT 59.479 61.111 4.39 0.00 0.00 3.50
3716 5942 2.983592 CGGGCCACTGAACCAACC 60.984 66.667 4.39 0.00 0.00 3.77
3717 5943 2.203294 ACGGGCCACTGAACCAAC 60.203 61.111 4.39 0.00 0.00 3.77
3718 5944 2.203280 CACGGGCCACTGAACCAA 60.203 61.111 4.39 0.00 0.00 3.67
3719 5945 3.469863 GACACGGGCCACTGAACCA 62.470 63.158 4.39 0.00 0.00 3.67
3720 5946 1.823169 TAGACACGGGCCACTGAACC 61.823 60.000 4.39 0.00 0.00 3.62
3752 5983 0.306533 TCGCTTCAACAAGAAACCGC 59.693 50.000 0.00 0.00 35.40 5.68
3777 6008 3.609853 TCAGGCTGTCATTAAAGCGAAT 58.390 40.909 15.27 0.00 40.46 3.34
3781 6012 4.457257 AGAAACTCAGGCTGTCATTAAAGC 59.543 41.667 15.27 0.00 38.76 3.51
3858 6095 2.351060 GCATGATGGCACCAATGATACG 60.351 50.000 0.00 0.00 0.00 3.06
3860 6097 2.946785 TGCATGATGGCACCAATGATA 58.053 42.857 0.00 0.00 39.25 2.15
4043 6281 4.565166 CCACGGTGAAAGGAAAAGAAAAAC 59.435 41.667 10.28 0.00 0.00 2.43
4062 6302 2.693762 CCTTCCATGTGCTGCCACG 61.694 63.158 0.00 0.00 45.04 4.94
4180 6420 0.321564 TCGGTTGGTCTGCAGGATTG 60.322 55.000 15.13 0.00 0.00 2.67
4200 6440 5.065914 AGTGGTGAATTATTGGATCATCCG 58.934 41.667 0.00 0.00 40.17 4.18


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

AutoCloner maintained by Alex Coulton.