Multiple sequence alignment - TraesCS7B01G267000

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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 TraesCS7B01G267000 chr7B 100.000 5287 0 0 1 5287 490212175 490206889 0.000000e+00 9764
1 TraesCS7B01G267000 chr7B 100.000 2288 0 0 5556 7843 490206620 490204333 0.000000e+00 4226
2 TraesCS7B01G267000 chr7D 98.429 5221 51 18 1 5203 465481973 465476766 0.000000e+00 9158
3 TraesCS7B01G267000 chr7D 95.615 2212 52 16 5587 7783 465476283 465474102 0.000000e+00 3506
4 TraesCS7B01G267000 chr7A 94.559 3051 119 18 32 3048 534321246 534324283 0.000000e+00 4671
5 TraesCS7B01G267000 chr7A 96.733 2173 58 8 3041 5203 534324479 534326648 0.000000e+00 3607
6 TraesCS7B01G267000 chr7A 95.009 1723 39 20 5557 7237 534326888 534328605 0.000000e+00 2662
7 TraesCS7B01G267000 chr7A 91.988 337 25 2 7222 7557 534328623 534328958 9.210000e-129 472
8 TraesCS7B01G267000 chr7A 95.349 129 6 0 7715 7843 534334064 534334192 1.030000e-48 206
9 TraesCS7B01G267000 chr3D 94.350 177 9 1 4011 4186 87925985 87926161 3.610000e-68 270
10 TraesCS7B01G267000 chr5A 96.319 163 6 0 4024 4186 320214243 320214405 1.300000e-67 268
11 TraesCS7B01G267000 chr4D 96.319 163 6 0 4025 4187 34661688 34661526 1.300000e-67 268
12 TraesCS7B01G267000 chr2D 95.210 167 8 0 4024 4190 134301650 134301484 1.680000e-66 265
13 TraesCS7B01G267000 chr2B 95.732 164 7 0 4025 4188 608226886 608226723 1.680000e-66 265
14 TraesCS7B01G267000 chr5D 94.186 172 8 2 4024 4195 528616787 528616618 2.170000e-65 261
15 TraesCS7B01G267000 chr6B 92.350 183 13 1 4004 4186 226361699 226361518 7.810000e-65 259


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 TraesCS7B01G267000 chr7B 490204333 490212175 7842 True 6995 9764 100.00000 1 7843 2 chr7B.!!$R1 7842
1 TraesCS7B01G267000 chr7D 465474102 465481973 7871 True 6332 9158 97.02200 1 7783 2 chr7D.!!$R1 7782
2 TraesCS7B01G267000 chr7A 534321246 534328958 7712 False 2853 4671 94.57225 32 7557 4 chr7A.!!$F2 7525

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
762 797 1.102978 CGCCGGATTCCAGGAAAAAT 58.897 50.000 5.05 0.0 0.00 1.82 F
1293 1332 1.909986 GCCAACCTCTACTTCCTCCTT 59.090 52.381 0.00 0.0 0.00 3.36 F
1691 1730 5.045869 AGGATGAGACGTTTAAGGATTTCCA 60.046 40.000 0.00 0.0 38.89 3.53 F
3285 3539 4.931661 TCCGATTAGGTATTCTCCACAC 57.068 45.455 0.00 0.0 41.99 3.82 F
3518 3773 3.967332 AAAGCAAAGACATCCATTGGG 57.033 42.857 2.09 0.0 0.00 4.12 F
4533 4790 1.003866 GCTGAGTTTGCTCGTTTTCGT 60.004 47.619 0.00 0.0 44.48 3.85 F
5278 5648 2.722094 TCTGGGATGTTGTAATGGTGC 58.278 47.619 0.00 0.0 0.00 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2298 2337 3.072330 TCTGATTACAGGTCAAAGTGCCA 59.928 43.478 0.00 0.0 43.60 4.92 R
3285 3539 1.002033 GATTAAAGCATGAGCAGCCCG 60.002 52.381 0.00 0.0 45.49 6.13 R
3518 3773 2.659428 AGTTGCAATTCCCTATCAGGC 58.341 47.619 0.59 0.0 32.73 4.85 R
4533 4790 2.110213 GTCGGGTCACCTGCAACA 59.890 61.111 0.00 0.0 33.28 3.33 R
4696 4953 2.758423 TCTCCTCGCAATGCACTAGTTA 59.242 45.455 5.91 0.0 0.00 2.24 R
5555 5925 1.001406 ACAGTCACAGGCTCTTAGCAC 59.999 52.381 0.78 0.0 44.75 4.40 R
7186 7599 0.546122 CAGGGGCAATGCTACTACCA 59.454 55.000 4.82 0.0 0.00 3.25 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
29 30 3.865745 ACCACTCGCGATCTTCTTAATTG 59.134 43.478 10.36 0.00 0.00 2.32
30 31 4.112634 CCACTCGCGATCTTCTTAATTGA 58.887 43.478 10.36 0.00 0.00 2.57
62 65 4.141287 ACGGAGAAACACCAATCAATCAA 58.859 39.130 0.00 0.00 0.00 2.57
570 604 1.491505 GGCGAATGCTCCTAACGCTC 61.492 60.000 0.00 0.00 46.71 5.03
627 661 4.088823 TCCGCTTTCTAGTACGAGTTTC 57.911 45.455 2.75 0.00 0.00 2.78
688 722 1.647346 TCGTTTCGTGTTGCTGTTCT 58.353 45.000 0.00 0.00 0.00 3.01
690 724 2.029970 TCGTTTCGTGTTGCTGTTCTTC 59.970 45.455 0.00 0.00 0.00 2.87
762 797 1.102978 CGCCGGATTCCAGGAAAAAT 58.897 50.000 5.05 0.00 0.00 1.82
769 804 5.049828 CGGATTCCAGGAAAAATAATTGGC 58.950 41.667 5.81 0.00 0.00 4.52
850 887 2.105806 GATCACGGCCTGATCCCTCC 62.106 65.000 23.93 8.58 46.99 4.30
948 987 1.919600 GAGACTCCAATGCTGCCCCT 61.920 60.000 0.00 0.00 0.00 4.79
1293 1332 1.909986 GCCAACCTCTACTTCCTCCTT 59.090 52.381 0.00 0.00 0.00 3.36
1691 1730 5.045869 AGGATGAGACGTTTAAGGATTTCCA 60.046 40.000 0.00 0.00 38.89 3.53
2864 2906 8.939201 TTTCTATCTTCAGCTGAGAGTATTTG 57.061 34.615 17.43 4.38 0.00 2.32
3091 3343 7.772757 TGCTTATGTTATTACATCACCATGTGA 59.227 33.333 0.00 0.00 46.90 3.58
3285 3539 4.931661 TCCGATTAGGTATTCTCCACAC 57.068 45.455 0.00 0.00 41.99 3.82
3518 3773 3.967332 AAAGCAAAGACATCCATTGGG 57.033 42.857 2.09 0.00 0.00 4.12
3774 4029 4.389374 GTCTCAAAATCTGGGTTCTGACA 58.611 43.478 0.00 0.00 0.00 3.58
4200 4457 8.168725 ACGGAAGGAGTACTATAGATGGATTTA 58.831 37.037 6.78 0.00 0.00 1.40
4533 4790 1.003866 GCTGAGTTTGCTCGTTTTCGT 60.004 47.619 0.00 0.00 44.48 3.85
4576 4833 4.030216 TCAAAGAAGGCCTTGGAAAAACT 58.970 39.130 26.25 8.96 31.99 2.66
4924 5181 7.962918 ACATTCTGTTGAACTATATTGTTTCGC 59.037 33.333 4.03 0.00 34.71 4.70
5239 5607 4.718940 AAATAAACATGCTCGGAAAGGG 57.281 40.909 0.00 0.00 0.00 3.95
5278 5648 2.722094 TCTGGGATGTTGTAATGGTGC 58.278 47.619 0.00 0.00 0.00 5.01
5937 6342 5.753921 GTGTTCCCTTTCCGTTGATATAGAG 59.246 44.000 0.00 0.00 0.00 2.43
6149 6558 4.999950 GCACCATAGGACTTAATCTGGATG 59.000 45.833 0.00 0.00 0.00 3.51
6851 7260 2.511659 ACTGTAGCGTAGAACACCTCA 58.488 47.619 0.00 0.00 0.00 3.86
7046 7456 1.711375 TGTAATTGGTGGCCTTACCCA 59.289 47.619 9.69 4.98 40.09 4.51
7087 7498 3.311596 CCAGCCGTGTAAAAAGTATAGCC 59.688 47.826 0.00 0.00 0.00 3.93
7167 7580 7.806690 TGCAATTTTGACTATACTTGTGACTC 58.193 34.615 0.00 0.00 0.00 3.36
7177 7590 8.582657 ACTATACTTGTGACTCTGTTATCTGT 57.417 34.615 0.00 0.00 0.00 3.41
7185 7598 6.071391 TGTGACTCTGTTATCTGTAATGCTGA 60.071 38.462 0.00 0.00 0.00 4.26
7186 7599 6.983307 GTGACTCTGTTATCTGTAATGCTGAT 59.017 38.462 0.00 0.00 38.89 2.90
7187 7600 6.982724 TGACTCTGTTATCTGTAATGCTGATG 59.017 38.462 1.38 0.00 37.10 3.07
7335 7785 1.154225 GTGCGGAAAATCACTGCGG 60.154 57.895 0.00 0.00 41.87 5.69
7353 7803 3.244033 CGGGCAGCATAATTTGGAAAA 57.756 42.857 0.00 0.00 0.00 2.29
7381 7831 5.396548 CCAGTCTTCTCTCATCCACATTGAT 60.397 44.000 0.00 0.00 0.00 2.57
7408 7858 0.179081 TGCAGTTTGCTTGCATTGCA 60.179 45.000 18.77 18.77 45.31 4.08
7425 7875 6.480651 TGCATTGCAAATGATCCATTTACATC 59.519 34.615 9.33 1.09 41.40 3.06
7540 7992 4.279145 TCATCCTAAGAGCGGAAGTAGTT 58.721 43.478 0.00 0.00 33.55 2.24
7556 8008 1.749258 GTTCGGTTGGGAGGATGGC 60.749 63.158 0.00 0.00 0.00 4.40
7561 8013 1.439543 GGTTGGGAGGATGGCTAGAT 58.560 55.000 0.00 0.00 0.00 1.98
7607 8060 6.543430 AGACCATATGATCTAGATCTTGGC 57.457 41.667 29.90 24.95 36.96 4.52
7615 8068 2.845659 TCTAGATCTTGGCCCCTTTCA 58.154 47.619 0.00 0.00 0.00 2.69
7635 8088 8.036575 CCTTTCAATTTGCAGGATTCAGAATAA 58.963 33.333 8.18 0.00 0.00 1.40
7636 8089 8.761575 TTTCAATTTGCAGGATTCAGAATAAC 57.238 30.769 0.00 0.00 0.00 1.89
7637 8090 7.465353 TCAATTTGCAGGATTCAGAATAACA 57.535 32.000 0.00 0.00 0.00 2.41
7685 8142 6.996180 ATTAGCCCACTTATAGCTGAGTTA 57.004 37.500 0.00 0.00 37.45 2.24
7745 8203 5.644188 TGAATCTTTCCAGGAGGTTTGATT 58.356 37.500 0.00 0.00 33.91 2.57
7751 8209 3.115390 TCCAGGAGGTTTGATTAGAGGG 58.885 50.000 0.00 0.00 35.89 4.30
7755 8213 5.516591 CCAGGAGGTTTGATTAGAGGGAAAA 60.517 44.000 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 0.179145 TTTCTCCGTTCCGATCGCTC 60.179 55.000 10.32 0.95 0.00 5.03
30 31 0.458025 GTTTCTCCGTTCCGATCGCT 60.458 55.000 10.32 0.00 0.00 4.93
62 65 2.364002 ACTGCGCCTTTATTGTTTTGGT 59.636 40.909 4.18 0.00 0.00 3.67
661 695 1.129326 AACACGAAACGAAGAGAGCG 58.871 50.000 0.00 0.00 0.00 5.03
662 696 1.397315 GCAACACGAAACGAAGAGAGC 60.397 52.381 0.00 0.00 0.00 4.09
688 722 1.285280 ATTCATCCACCGTCAGGGAA 58.715 50.000 0.00 0.00 43.47 3.97
690 724 1.668419 GAATTCATCCACCGTCAGGG 58.332 55.000 0.00 0.00 43.47 4.45
762 797 0.736053 GAAATCCGTGCCGCCAATTA 59.264 50.000 0.00 0.00 0.00 1.40
769 804 2.125673 ACGAGGAAATCCGTGCCG 60.126 61.111 0.00 0.28 42.08 5.69
1293 1332 2.123854 AGCGAGAGGATGGCGGTA 60.124 61.111 0.00 0.00 37.77 4.02
1691 1730 3.515901 GTCTTCACACCTTATCACTCCCT 59.484 47.826 0.00 0.00 0.00 4.20
1821 1860 3.898123 TGACTACTCCATAGATGAAGGCC 59.102 47.826 0.00 0.00 34.65 5.19
2298 2337 3.072330 TCTGATTACAGGTCAAAGTGCCA 59.928 43.478 0.00 0.00 43.60 4.92
2864 2906 6.545504 TGAATAAATAGCGATCAGAAAGCC 57.454 37.500 0.00 0.00 0.00 4.35
3084 3336 4.937015 TGTAACACAGATGACATCACATGG 59.063 41.667 17.57 4.93 33.60 3.66
3285 3539 1.002033 GATTAAAGCATGAGCAGCCCG 60.002 52.381 0.00 0.00 45.49 6.13
3518 3773 2.659428 AGTTGCAATTCCCTATCAGGC 58.341 47.619 0.59 0.00 32.73 4.85
3774 4029 2.092968 TGCAGTTTCCATCTTATCGCCT 60.093 45.455 0.00 0.00 0.00 5.52
4200 4457 5.071519 AGCAAAGATGACTGCCATATAGACT 59.928 40.000 0.00 0.00 39.47 3.24
4533 4790 2.110213 GTCGGGTCACCTGCAACA 59.890 61.111 0.00 0.00 33.28 3.33
4576 4833 4.382685 GCACCATCACCTACTGCTAAAGTA 60.383 45.833 0.00 0.00 40.56 2.24
4696 4953 2.758423 TCTCCTCGCAATGCACTAGTTA 59.242 45.455 5.91 0.00 0.00 2.24
5219 5587 3.963129 TCCCTTTCCGAGCATGTTTATT 58.037 40.909 0.00 0.00 0.00 1.40
5254 5622 4.396166 CACCATTACAACATCCCAGAAGTC 59.604 45.833 0.00 0.00 0.00 3.01
5555 5925 1.001406 ACAGTCACAGGCTCTTAGCAC 59.999 52.381 0.78 0.00 44.75 4.40
5834 6219 7.975616 GTGTAACCGAAACATGGATAGTACTTA 59.024 37.037 0.00 0.00 0.00 2.24
5835 6220 6.815142 GTGTAACCGAAACATGGATAGTACTT 59.185 38.462 0.00 0.00 0.00 2.24
5836 6221 6.154021 AGTGTAACCGAAACATGGATAGTACT 59.846 38.462 0.00 0.00 37.80 2.73
6149 6558 2.418368 TGCCATATCAGTTGGTGGAC 57.582 50.000 0.00 0.00 36.57 4.02
6851 7260 3.537580 GACGAGACTACCAGATGACTCT 58.462 50.000 0.00 0.00 0.00 3.24
7002 7412 6.723298 ACCCAACATTTCTTACACAAATGA 57.277 33.333 11.20 0.00 41.81 2.57
7046 7456 4.636249 CTGGCTTCAGAACTTCTACTTGT 58.364 43.478 0.00 0.00 40.86 3.16
7087 7498 3.492102 TGTCTCTTCCAACTGAAAGGG 57.508 47.619 0.00 0.00 39.30 3.95
7157 7570 6.591834 GCATTACAGATAACAGAGTCACAAGT 59.408 38.462 0.00 0.00 0.00 3.16
7167 7580 7.212976 ACTACCATCAGCATTACAGATAACAG 58.787 38.462 0.00 0.00 0.00 3.16
7185 7598 1.143684 CAGGGGCAATGCTACTACCAT 59.856 52.381 4.82 0.00 0.00 3.55
7186 7599 0.546122 CAGGGGCAATGCTACTACCA 59.454 55.000 4.82 0.00 0.00 3.25
7187 7600 0.819666 GCAGGGGCAATGCTACTACC 60.820 60.000 4.82 0.00 40.59 3.18
7267 7717 5.639082 TGTATGAATGCTCACTAACACTGTG 59.361 40.000 6.19 6.19 33.30 3.66
7353 7803 2.909006 TGGATGAGAGAAGACTGGCTTT 59.091 45.455 0.00 0.00 36.83 3.51
7357 7807 4.081254 TCAATGTGGATGAGAGAAGACTGG 60.081 45.833 0.00 0.00 0.00 4.00
7370 7820 4.054780 GCATCAGCAAATCAATGTGGAT 57.945 40.909 0.00 0.00 41.58 3.41
7445 7895 7.888424 TGTAGCCGCTAAATATGTTATCACTA 58.112 34.615 0.46 0.00 0.00 2.74
7540 7992 1.002403 TAGCCATCCTCCCAACCGA 59.998 57.895 0.00 0.00 0.00 4.69
7556 8008 4.973051 CAGGATGAGACGTTTTCGATCTAG 59.027 45.833 0.00 0.00 42.73 2.43
7607 8060 3.261390 TGAATCCTGCAAATTGAAAGGGG 59.739 43.478 13.07 0.00 0.00 4.79
7635 8088 5.951747 TGCAGGCCTAAGATTTTTCTATTGT 59.048 36.000 3.98 0.00 0.00 2.71
7636 8089 6.455360 TGCAGGCCTAAGATTTTTCTATTG 57.545 37.500 3.98 0.00 0.00 1.90
7637 8090 7.666063 ATTGCAGGCCTAAGATTTTTCTATT 57.334 32.000 3.98 0.00 0.00 1.73
7647 8104 4.021102 GGCTAATATTGCAGGCCTAAGA 57.979 45.455 3.98 0.00 39.68 2.10
7685 8142 8.578151 TGTTTTCAACCAAACAAAGTTAGTACT 58.422 29.630 0.00 0.00 42.42 2.73


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

AutoCloner maintained by Alex Coulton.