Multiple sequence alignment - TraesCS1D01G149200

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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 TraesCS1D01G149200 chr1D 100.000 6155 0 0 1 6155 205474847 205481001 0 11367
1 TraesCS1D01G149200 chr1A 96.516 6171 186 14 1 6151 262008572 262014733 0 10178
2 TraesCS1D01G149200 chr1B 95.812 5325 199 10 42 5345 301248814 301254135 0 8576
3 TraesCS1D01G149200 chr1B 91.905 840 42 9 5337 6155 301255721 301256555 0 1151


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 TraesCS1D01G149200 chr1D 205474847 205481001 6154 False 11367.0 11367 100.0000 1 6155 1 chr1D.!!$F1 6154
1 TraesCS1D01G149200 chr1A 262008572 262014733 6161 False 10178.0 10178 96.5160 1 6151 1 chr1A.!!$F1 6150
2 TraesCS1D01G149200 chr1B 301248814 301256555 7741 False 4863.5 8576 93.8585 42 6155 2 chr1B.!!$F1 6113

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
38 40 1.264749 ACAGCGTGGCCCTCATCTTA 61.265 55.0 0.0 0.0 0.00 2.10 F
1633 1656 0.453390 GCAATGCTTCCTGTACTGCC 59.547 55.0 0.0 0.0 0.00 4.85 F
2283 2306 0.248843 GGCTCAGAGACCTTGACCTG 59.751 60.0 0.0 0.0 0.00 4.00 F
3294 3317 0.518636 GCACGATCAAGCTGCTCAAA 59.481 50.0 1.0 0.0 0.00 2.69 F
3722 3745 0.807496 GTGCTGTTTCCTGCTCATCC 59.193 55.0 0.0 0.0 36.57 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1652 1675 3.374402 CCTGCCTCTCGACGGTGT 61.374 66.667 0.0 0.0 0.00 4.16 R
2701 2724 1.135603 CAAGTTGCACCCGATGATGTG 60.136 52.381 0.0 0.0 35.58 3.21 R
3701 3724 1.467734 GATGAGCAGGAAACAGCACAG 59.532 52.381 0.0 0.0 45.47 3.66 R
4339 4362 0.681733 GGTGCCACTTCTCTGTCTGA 59.318 55.000 0.0 0.0 0.00 3.27 R
5392 7015 0.384309 CGCGAGGGCACAAGATAGTA 59.616 55.000 0.0 0.0 39.92 1.82 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
38 40 1.264749 ACAGCGTGGCCCTCATCTTA 61.265 55.000 0.00 0.00 0.00 2.10
211 214 4.918583 ACAAACACAAACGAACGAAACAAT 59.081 33.333 0.14 0.00 0.00 2.71
783 794 2.125350 GTCCTGAGGAAGCAGCGG 60.125 66.667 0.96 0.00 34.56 5.52
888 902 1.445410 CGTCGGCACAAGGATCGAA 60.445 57.895 0.00 0.00 33.33 3.71
1005 1019 3.842923 AGGCTCGCGAGGATGGTG 61.843 66.667 35.10 11.60 0.00 4.17
1408 1431 3.691744 GACGACGAGAGCCAGCTGG 62.692 68.421 29.34 29.34 38.53 4.85
1633 1656 0.453390 GCAATGCTTCCTGTACTGCC 59.547 55.000 0.00 0.00 0.00 4.85
1640 1663 2.125512 CCTGTACTGCCCGCTGTC 60.126 66.667 2.22 0.00 0.00 3.51
1667 1690 2.697761 GCTACACCGTCGAGAGGCA 61.698 63.158 6.76 0.00 33.27 4.75
1989 2012 4.804597 TCCTGAATTCGGAGAGGATAAGA 58.195 43.478 16.17 0.00 38.43 2.10
2151 2174 2.261671 CTCAACCTGTCCCGGACG 59.738 66.667 13.02 7.62 34.95 4.79
2164 2187 3.925090 GGACGGGGATACAGGCGG 61.925 72.222 0.00 0.00 39.74 6.13
2199 2222 1.518903 GCAACCTGTGGAGCCTGAAC 61.519 60.000 0.00 0.00 0.00 3.18
2283 2306 0.248843 GGCTCAGAGACCTTGACCTG 59.751 60.000 0.00 0.00 0.00 4.00
2300 2323 3.255379 GGCTGGAACGACGATCGC 61.255 66.667 16.60 7.26 45.12 4.58
2452 2475 1.005630 GTGCACAAGCTCGAGAGGT 60.006 57.895 18.75 7.45 42.74 3.85
2546 2569 1.008881 GCGACGACACTGTGAGTCA 60.009 57.895 26.70 0.00 35.77 3.41
2577 2600 1.363744 CAACGGCTGTCAGGAAGATC 58.636 55.000 0.00 0.00 0.00 2.75
2701 2724 1.032114 CCCAAATCTTCGCCACCTCC 61.032 60.000 0.00 0.00 0.00 4.30
3294 3317 0.518636 GCACGATCAAGCTGCTCAAA 59.481 50.000 1.00 0.00 0.00 2.69
3298 3321 2.079158 CGATCAAGCTGCTCAAAAGGA 58.921 47.619 1.00 0.00 0.00 3.36
3348 3371 5.241403 TGATCAAGGACATTGTACAGGTT 57.759 39.130 1.02 0.00 40.05 3.50
3408 3431 4.657814 TTCCAAGAGCCCTTACATCTTT 57.342 40.909 0.00 0.00 30.99 2.52
3436 3459 4.240096 CAATGTGAATGCTCAAGGAAACC 58.760 43.478 0.00 0.00 31.88 3.27
3473 3496 1.482182 TGATAGTGCTGATGAGGCGTT 59.518 47.619 0.00 0.00 0.00 4.84
3573 3596 4.908736 TCGACTCAAAAGCAGTGAAAAAG 58.091 39.130 0.00 0.00 0.00 2.27
3594 3617 2.832201 GCTCCCATGGCTGAAGGC 60.832 66.667 6.09 0.00 41.50 4.35
3642 3665 1.335810 AGAAATAGCCGACGTCGCATA 59.664 47.619 31.73 24.24 38.18 3.14
3669 3692 3.009473 AGCTGGCAGAAGTTATTCCTGAA 59.991 43.478 20.86 0.00 35.94 3.02
3679 3702 5.843019 AGTTATTCCTGAAGAGGGTGAAA 57.157 39.130 0.00 0.00 40.25 2.69
3701 3724 2.873472 CTGAGGAAGATGCAGATTCAGC 59.127 50.000 13.81 0.00 0.00 4.26
3722 3745 0.807496 GTGCTGTTTCCTGCTCATCC 59.193 55.000 0.00 0.00 36.57 3.51
3724 3747 1.202915 TGCTGTTTCCTGCTCATCCAA 60.203 47.619 0.00 0.00 36.57 3.53
3730 3753 4.761739 TGTTTCCTGCTCATCCAACTAAAG 59.238 41.667 0.00 0.00 0.00 1.85
3737 3760 3.448660 GCTCATCCAACTAAAGCCCATTT 59.551 43.478 0.00 0.00 34.72 2.32
3747 3770 3.366052 AAAGCCCATTTACGAGTGGAT 57.634 42.857 0.00 0.00 37.72 3.41
3817 3840 2.604614 GGCTTGCTGTCAAAAGTTACCG 60.605 50.000 0.00 0.00 0.00 4.02
4021 4044 1.605232 TCAGTGTACGTCAAAGCGAGA 59.395 47.619 0.00 0.00 35.59 4.04
4171 4194 5.695851 AACTGAAAATAGTTCACCTGCTG 57.304 39.130 0.00 0.00 36.16 4.41
4339 4362 5.484715 CAAGAACAATGCCAGAAATTCCAT 58.515 37.500 0.00 0.00 0.00 3.41
4506 4529 0.896923 TGCCAGCCAATCCAAATCAC 59.103 50.000 0.00 0.00 0.00 3.06
4657 4680 2.393768 GGCATAGGCGCATCCATCG 61.394 63.158 10.83 0.00 42.47 3.84
4681 4704 0.171007 AATTCCTCGCATGGCAAACG 59.829 50.000 6.21 6.21 0.00 3.60
4721 4744 1.523154 TACAAAAGCAAGGCTGGGCG 61.523 55.000 5.86 0.00 39.62 6.13
5092 5118 1.469335 GGTGGTCGTCCTCCTTGTCA 61.469 60.000 11.86 0.00 42.33 3.58
5103 5129 0.615331 TCCTTGTCATCTCTGTGGCC 59.385 55.000 0.00 0.00 0.00 5.36
5110 5136 0.323178 CATCTCTGTGGCCCAGCTTT 60.323 55.000 14.49 1.58 41.25 3.51
5177 5203 1.202348 GGCCAACATGTTAACTCCAGC 59.798 52.381 11.53 5.77 0.00 4.85
5214 5241 4.724074 TTCCTGCCAAGAAATGCTAATG 57.276 40.909 0.00 0.00 0.00 1.90
5293 5320 4.643387 ACTCCGTTGGGGCTGCAC 62.643 66.667 0.50 0.00 34.94 4.57
5310 5337 1.395608 GCACCACGCTAATTCGCTTAA 59.604 47.619 0.08 0.00 37.77 1.85
5311 5338 2.031683 GCACCACGCTAATTCGCTTAAT 59.968 45.455 0.08 0.00 37.77 1.40
5312 5339 3.246699 GCACCACGCTAATTCGCTTAATA 59.753 43.478 0.08 0.00 37.77 0.98
5317 5344 5.339611 CCACGCTAATTCGCTTAATAATTGC 59.660 40.000 0.08 0.00 0.00 3.56
5350 6973 4.085302 GCTGCTGCGTCTGTAGAG 57.915 61.111 0.00 0.00 0.00 2.43
5359 6982 5.748630 TGCTGCGTCTGTAGAGTAAAATATG 59.251 40.000 0.00 0.00 0.00 1.78
5381 7004 5.076182 TGAACACATTCCTGCCAAGAAATA 58.924 37.500 0.00 0.00 33.49 1.40
5392 7015 8.548880 TCCTGCCAAGAAATACTAATAGTAGT 57.451 34.615 8.10 8.10 43.27 2.73
5393 7016 9.650714 TCCTGCCAAGAAATACTAATAGTAGTA 57.349 33.333 12.13 12.13 44.93 1.82
5408 7031 7.527568 AATAGTAGTACTATCTTGTGCCCTC 57.472 40.000 20.61 0.00 40.32 4.30
5443 7066 8.838365 GCATCAGATTGATCTCTTAAGATTTGT 58.162 33.333 5.44 0.00 42.46 2.83
5555 7178 2.500229 CCTTTGGCAAGAAGACGGTAA 58.500 47.619 0.00 0.00 30.57 2.85
5556 7179 3.081804 CCTTTGGCAAGAAGACGGTAAT 58.918 45.455 0.00 0.00 30.57 1.89
5653 7276 2.519771 TTTGGGCGGACTCTAGTCTA 57.480 50.000 9.84 0.00 44.20 2.59
5666 7289 6.462067 GGACTCTAGTCTAGTCTAGTCCAGTC 60.462 50.000 26.78 22.83 44.20 3.51
5667 7290 5.364735 ACTCTAGTCTAGTCTAGTCCAGTCC 59.635 48.000 19.35 0.00 38.66 3.85
5668 7291 5.278873 TCTAGTCTAGTCTAGTCCAGTCCA 58.721 45.833 19.35 0.39 38.66 4.02
5669 7292 4.497291 AGTCTAGTCTAGTCCAGTCCAG 57.503 50.000 6.77 0.00 0.00 3.86
5670 7293 3.847780 AGTCTAGTCTAGTCCAGTCCAGT 59.152 47.826 6.77 0.00 0.00 4.00
5680 7303 0.247736 CCAGTCCAGTACAGCACTCC 59.752 60.000 0.00 0.00 34.26 3.85
5745 7373 1.615124 TTGGGGAGGCGGAATGAGA 60.615 57.895 0.00 0.00 0.00 3.27
6052 7697 3.512724 CCAATCAATCTGCCCTTGTTCTT 59.487 43.478 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 0.179045 GATGAGGGCCACGCTGTATT 60.179 55.000 6.18 0.00 0.00 1.89
211 214 1.001764 TCTACCCTCGCCGAGACAA 60.002 57.895 17.19 0.00 0.00 3.18
766 777 2.125350 CCGCTGCTTCCTCAGGAC 60.125 66.667 0.00 0.00 34.74 3.85
989 1003 2.782222 TACACCATCCTCGCGAGCC 61.782 63.158 30.49 0.00 0.00 4.70
1005 1019 3.507009 ACCCTCGCGCTCTCGTAC 61.507 66.667 5.56 0.00 38.14 3.67
1652 1675 3.374402 CCTGCCTCTCGACGGTGT 61.374 66.667 0.00 0.00 0.00 4.16
1654 1677 3.374402 CACCTGCCTCTCGACGGT 61.374 66.667 0.00 0.00 0.00 4.83
2151 2174 2.325393 CTGGAACCGCCTGTATCCCC 62.325 65.000 0.00 0.00 37.63 4.81
2164 2187 0.036388 TTGCCGATGGACTCTGGAAC 60.036 55.000 0.00 0.00 0.00 3.62
2199 2222 0.324285 ACTCCCTCAGCAGCAAGAAG 59.676 55.000 0.00 0.00 0.00 2.85
2263 2286 0.116143 AGGTCAAGGTCTCTGAGCCT 59.884 55.000 12.87 12.87 36.51 4.58
2283 2306 3.255379 GCGATCGTCGTTCCAGCC 61.255 66.667 17.81 0.00 42.81 4.85
2307 2330 3.682292 CTGGCCTACCCTGAACGCC 62.682 68.421 3.32 0.00 40.16 5.68
2452 2475 4.753662 CTCAGACCGACCGGGGGA 62.754 72.222 19.52 6.16 41.60 4.81
2546 2569 4.988598 CCGTTGGTGTCTGCGGCT 62.989 66.667 0.00 0.00 37.69 5.52
2701 2724 1.135603 CAAGTTGCACCCGATGATGTG 60.136 52.381 0.00 0.00 35.58 3.21
3294 3317 3.419858 CCATCCACCAGGCTCCTT 58.580 61.111 0.00 0.00 33.74 3.36
3348 3371 3.359523 CCAGTCGTCGACCCGTGA 61.360 66.667 21.40 0.00 32.18 4.35
3436 3459 4.694509 ACTATCAGAAGCAGCAGTTTCAAG 59.305 41.667 8.34 0.99 37.43 3.02
3594 3617 3.684908 TGTGTTCCTATGGGTCACATTG 58.315 45.455 18.55 0.00 40.35 2.82
3642 3665 4.884164 GGAATAACTTCTGCCAGCTTATGT 59.116 41.667 0.00 0.00 0.00 2.29
3669 3692 2.977808 TCTTCCTCAGTTTCACCCTCT 58.022 47.619 0.00 0.00 0.00 3.69
3679 3702 3.682155 GCTGAATCTGCATCTTCCTCAGT 60.682 47.826 7.25 0.00 33.08 3.41
3701 3724 1.467734 GATGAGCAGGAAACAGCACAG 59.532 52.381 0.00 0.00 45.47 3.66
3722 3745 4.142687 CCACTCGTAAATGGGCTTTAGTTG 60.143 45.833 0.00 0.00 29.97 3.16
3724 3747 3.262405 TCCACTCGTAAATGGGCTTTAGT 59.738 43.478 0.00 0.00 36.56 2.24
3730 3753 3.942748 TGTTTATCCACTCGTAAATGGGC 59.057 43.478 0.00 0.00 36.56 5.36
3737 3760 2.159338 GGACGCTGTTTATCCACTCGTA 60.159 50.000 0.00 0.00 32.35 3.43
3747 3770 5.117584 TCTTTAACAACAGGACGCTGTTTA 58.882 37.500 5.78 0.00 44.18 2.01
3817 3840 2.550830 TCAGGACCAGTTTCTTGAGC 57.449 50.000 0.00 0.00 28.94 4.26
4021 4044 6.664816 TCCTCTCCTTTATTCAATGTGCATTT 59.335 34.615 0.00 0.00 0.00 2.32
4116 4139 5.013183 ACCAAATACTTTAGAGTCACTGCCT 59.987 40.000 0.00 0.00 37.33 4.75
4171 4194 2.202987 CCTGGAGCGAGCCATGAC 60.203 66.667 0.00 0.00 37.30 3.06
4317 4340 5.246656 TGATGGAATTTCTGGCATTGTTCTT 59.753 36.000 0.00 0.00 0.00 2.52
4319 4342 5.075858 TGATGGAATTTCTGGCATTGTTC 57.924 39.130 0.00 0.00 0.00 3.18
4339 4362 0.681733 GGTGCCACTTCTCTGTCTGA 59.318 55.000 0.00 0.00 0.00 3.27
4506 4529 3.615614 GCTGCATGCTTTAGATTCTTCG 58.384 45.455 20.33 0.00 38.95 3.79
4601 4624 1.517242 ACTGGCTTCTTGCTTCTTCG 58.483 50.000 0.00 0.00 42.39 3.79
4657 4680 1.745087 TGCCATGCGAGGAATTTTCTC 59.255 47.619 0.00 0.00 0.00 2.87
4857 4880 3.624410 CGATGGAGAAATGAGCATTGTCA 59.376 43.478 0.00 0.00 0.00 3.58
5103 5129 3.760151 TCCAGATGATGAACAAAAGCTGG 59.240 43.478 14.15 14.15 38.13 4.85
5177 5203 3.120060 GCAGGAATGTTACAAGTGCAGAG 60.120 47.826 0.00 0.00 0.00 3.35
5214 5241 3.669536 AGACACTAGAAAGGAGCAAAGC 58.330 45.455 0.00 0.00 0.00 3.51
5293 5320 5.339611 GCAATTATTAAGCGAATTAGCGTGG 59.660 40.000 9.09 0.00 43.00 4.94
5317 5344 1.009675 AGCGTTGCGTGCTTTCAAG 60.010 52.632 0.00 0.00 40.48 3.02
5350 6973 6.862209 TGGCAGGAATGTGTTCATATTTTAC 58.138 36.000 0.00 0.00 36.01 2.01
5359 6982 4.525912 ATTTCTTGGCAGGAATGTGTTC 57.474 40.909 13.13 0.00 25.39 3.18
5381 7004 8.226112 AGGGCACAAGATAGTACTACTATTAGT 58.774 37.037 4.31 1.30 41.21 2.24
5391 7014 1.854227 GCGAGGGCACAAGATAGTAC 58.146 55.000 0.00 0.00 39.62 2.73
5392 7015 0.384309 CGCGAGGGCACAAGATAGTA 59.616 55.000 0.00 0.00 39.92 1.82
5393 7016 1.141881 CGCGAGGGCACAAGATAGT 59.858 57.895 0.00 0.00 39.92 2.12
5408 7031 1.135717 TCAATCTGATGCAAAACCGCG 60.136 47.619 0.00 0.00 33.35 6.46
5519 7142 2.737252 CAAAGGCCTGTTCTTACGAGTC 59.263 50.000 5.69 0.00 0.00 3.36
5653 7276 3.874584 GCTGTACTGGACTGGACTAGACT 60.875 52.174 0.00 0.00 0.00 3.24
5666 7289 2.729194 AGAGTAGGAGTGCTGTACTGG 58.271 52.381 2.28 0.00 40.53 4.00
5667 7290 3.310227 CGTAGAGTAGGAGTGCTGTACTG 59.690 52.174 2.28 0.00 40.53 2.74
5668 7291 3.197333 TCGTAGAGTAGGAGTGCTGTACT 59.803 47.826 0.00 0.00 44.02 2.73
5669 7292 3.529533 TCGTAGAGTAGGAGTGCTGTAC 58.470 50.000 0.00 0.00 33.40 2.90
5670 7293 3.900966 TCGTAGAGTAGGAGTGCTGTA 57.099 47.619 0.00 0.00 0.00 2.74
5745 7373 5.176592 GGGTACGTCTTCTTATTCTGCTTT 58.823 41.667 0.00 0.00 0.00 3.51
5805 7433 1.429463 GCTTGACGAGGAACGATTGT 58.571 50.000 0.00 0.00 45.77 2.71
5926 7563 2.203153 CCGGCGGGTAGGGATTTG 60.203 66.667 20.56 0.00 0.00 2.32
6030 7673 3.094572 AGAACAAGGGCAGATTGATTGG 58.905 45.455 3.73 0.00 0.00 3.16
6036 7679 1.428912 TGGGAAGAACAAGGGCAGATT 59.571 47.619 0.00 0.00 0.00 2.40


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

AutoCloner maintained by Alex Coulton.