Multiple sequence alignment - TraesCS7A01G157700

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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 TraesCS7A01G157700 chr7A 100.000 5102 0 0 1 5102 110855670 110850569 0.000000e+00 9422.0
1 TraesCS7A01G157700 chr7A 83.156 469 63 10 3893 4353 110762160 110761700 1.020000e-111 414.0
2 TraesCS7A01G157700 chr7A 84.466 103 13 2 4142 4243 110768188 110768088 1.170000e-16 99.0
3 TraesCS7A01G157700 chr7D 97.185 3837 90 12 587 4416 106077377 106073552 0.000000e+00 6471.0
4 TraesCS7A01G157700 chr7D 96.825 693 18 2 4410 5102 106073349 106072661 0.000000e+00 1155.0
5 TraesCS7A01G157700 chr7D 93.074 592 36 5 1 589 106078001 106077412 0.000000e+00 861.0
6 TraesCS7A01G157700 chr7D 80.917 545 76 19 3884 4416 106000416 105999888 6.150000e-109 405.0
7 TraesCS7A01G157700 chr7B 95.049 3191 122 20 587 3773 64729865 64726707 0.000000e+00 4985.0
8 TraesCS7A01G157700 chr7B 95.153 619 25 3 3800 4416 64726712 64726097 0.000000e+00 972.0
9 TraesCS7A01G157700 chr7B 90.416 553 40 7 1 550 64731773 64731231 0.000000e+00 715.0
10 TraesCS7A01G157700 chr7B 90.417 240 22 1 4776 5015 64699886 64699648 1.070000e-81 315.0
11 TraesCS7A01G157700 chr7B 91.781 73 6 0 4410 4482 64725852 64725780 9.040000e-18 102.0
12 TraesCS7A01G157700 chrUn 93.182 44 3 0 2786 2829 277316285 277316328 1.190000e-06 65.8
13 TraesCS7A01G157700 chr2D 93.182 44 3 0 2786 2829 282927575 282927532 1.190000e-06 65.8
14 TraesCS7A01G157700 chr2D 93.182 44 3 0 2786 2829 282927675 282927632 1.190000e-06 65.8
15 TraesCS7A01G157700 chr2B 93.182 44 3 0 2786 2829 314776829 314776786 1.190000e-06 65.8
16 TraesCS7A01G157700 chr2A 93.182 44 3 0 2786 2829 341928076 341928119 1.190000e-06 65.8
17 TraesCS7A01G157700 chr2A 93.182 44 3 0 2786 2829 341928176 341928219 1.190000e-06 65.8
18 TraesCS7A01G157700 chr5B 85.714 56 4 3 2759 2814 691181164 691181215 7.140000e-04 56.5


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 TraesCS7A01G157700 chr7A 110850569 110855670 5101 True 9422.0 9422 100.000000 1 5102 1 chr7A.!!$R3 5101
1 TraesCS7A01G157700 chr7D 106072661 106078001 5340 True 2829.0 6471 95.694667 1 5102 3 chr7D.!!$R2 5101
2 TraesCS7A01G157700 chr7D 105999888 106000416 528 True 405.0 405 80.917000 3884 4416 1 chr7D.!!$R1 532
3 TraesCS7A01G157700 chr7B 64725780 64731773 5993 True 1693.5 4985 93.099750 1 4482 4 chr7B.!!$R2 4481

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
287 290 0.250467 TGTGAGCAACTGGAGGAAGC 60.250 55.000 0.00 0.0 0.00 3.86 F
1053 2388 0.678048 GGCCTGACAATTCCGCTTCT 60.678 55.000 0.00 0.0 0.00 2.85 F
1117 2452 3.054802 AGAAGAAGGAAGTATGCCACCTG 60.055 47.826 0.00 0.0 34.43 4.00 F
2011 3346 1.131638 AGTGAGTGAAGCACAAGGGA 58.868 50.000 0.00 0.0 38.70 4.20 F
3869 5210 1.228124 CGAACTTTCCACAGGGCCA 60.228 57.895 6.18 0.0 0.00 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1327 2662 0.681733 GTGCAGTGAAGAGTCCCTGA 59.318 55.000 0.00 0.0 0.00 3.86 R
1946 3281 2.221169 GGAGCGGAATATTGCACATCA 58.779 47.619 7.78 0.0 0.00 3.07 R
2221 3557 2.371784 TGGCTTAGCACTGGCACTA 58.628 52.632 6.53 0.0 44.61 2.74 R
3880 5221 1.112113 GCGGTTGGAGGTGATAGAGA 58.888 55.000 0.00 0.0 0.00 3.10 R
5000 6606 0.972983 TGGAGGAGAAGAGGAAGCCG 60.973 60.000 0.00 0.0 0.00 5.52 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
150 152 8.859517 ATTTTGAAATTGTTTTTCATTGCCAG 57.140 26.923 1.96 0.00 38.12 4.85
152 154 6.998968 TGAAATTGTTTTTCATTGCCAGTT 57.001 29.167 0.00 0.00 33.90 3.16
153 155 7.014092 TGAAATTGTTTTTCATTGCCAGTTC 57.986 32.000 0.00 0.00 33.90 3.01
155 157 6.998968 AATTGTTTTTCATTGCCAGTTCAA 57.001 29.167 0.00 0.00 0.00 2.69
262 264 3.265479 AGATAAAGGAGAAGGCAGTGCTT 59.735 43.478 16.11 3.91 0.00 3.91
263 265 1.613836 AAAGGAGAAGGCAGTGCTTG 58.386 50.000 16.11 0.00 0.00 4.01
287 290 0.250467 TGTGAGCAACTGGAGGAAGC 60.250 55.000 0.00 0.00 0.00 3.86
364 367 5.296780 AGCTGGTTGTATTGTGTATGCATAC 59.703 40.000 26.72 26.72 0.00 2.39
446 449 4.591929 TCATGGCTGAATGTCTGAATCAA 58.408 39.130 0.00 0.00 0.00 2.57
450 453 6.688637 TGGCTGAATGTCTGAATCAATTAG 57.311 37.500 0.00 0.00 0.00 1.73
468 471 6.090898 TCAATTAGCGCTCTTTCTAACAGAAC 59.909 38.462 16.34 0.00 33.26 3.01
475 478 5.049405 CGCTCTTTCTAACAGAACCAATTGT 60.049 40.000 4.43 0.00 33.26 2.71
506 509 7.847096 TGACTGTAGAATAAAGCAGGAATGTA 58.153 34.615 0.00 0.00 33.62 2.29
570 1865 4.613437 AGGTGAATTTGGGATGCAGTTAT 58.387 39.130 0.00 0.00 0.00 1.89
904 2239 7.713942 CAGACTGTCTTCATGGATGAATGATAA 59.286 37.037 7.77 0.00 44.92 1.75
1040 2375 3.074390 TCTTTCTTTCCTTCATGGCCTGA 59.926 43.478 3.32 2.06 35.26 3.86
1053 2388 0.678048 GGCCTGACAATTCCGCTTCT 60.678 55.000 0.00 0.00 0.00 2.85
1117 2452 3.054802 AGAAGAAGGAAGTATGCCACCTG 60.055 47.826 0.00 0.00 34.43 4.00
1252 2587 4.039603 TCTGGTGAGATTCTGTCAGAGA 57.960 45.455 2.12 0.00 0.00 3.10
1327 2662 7.631377 GCAGTCTGCAAAGTAATTTAATCCCAT 60.631 37.037 20.16 0.00 44.26 4.00
1697 3032 9.760077 ATAACTGTAACATATTGGTACTACTGC 57.240 33.333 4.51 0.00 41.02 4.40
1718 3053 6.820656 ACTGCTACCTATTTCTCATTCACTTG 59.179 38.462 0.00 0.00 0.00 3.16
1768 3103 4.843220 AGCAAAGAATTTCTCAGTGGTG 57.157 40.909 0.00 0.00 35.03 4.17
1800 3135 3.450115 GGTACGGCCGAGCAGTCT 61.450 66.667 35.90 10.28 38.09 3.24
1875 3210 3.756434 TCTGCCACTAAACAGCAATAACC 59.244 43.478 0.00 0.00 33.80 2.85
1897 3232 6.454795 ACCGCAAGTTATTGTTCATTCAATT 58.545 32.000 0.00 0.00 38.68 2.32
1946 3281 5.219633 GTTCGTATTGCAGGAACAAAATGT 58.780 37.500 13.64 0.00 46.56 2.71
2011 3346 1.131638 AGTGAGTGAAGCACAAGGGA 58.868 50.000 0.00 0.00 38.70 4.20
2221 3557 5.945144 AGGCAAATTCAGCTAATGGAAAT 57.055 34.783 0.00 0.00 0.00 2.17
2302 3638 1.873698 TTGCTGAACGGGTGAGTTAC 58.126 50.000 0.00 0.00 34.00 2.50
2479 3815 4.993705 TCTCCAAGACCTTGTACCAAAT 57.006 40.909 8.72 0.00 38.85 2.32
2587 3924 7.797062 TGCAGTACATTTATATTAGTCCACCA 58.203 34.615 0.00 0.00 0.00 4.17
2764 4101 7.271511 TGAAAAGTGCAAATAACATTTGTCCT 58.728 30.769 11.97 6.48 0.00 3.85
2946 4285 3.184581 CACACTTCGGCAAACTAGAGTTC 59.815 47.826 0.00 0.00 37.25 3.01
2990 4329 3.496160 CCACTGTTTGGTTAGTGCCTAGT 60.496 47.826 0.00 0.00 42.21 2.57
3113 4453 2.736192 CGGATTTGGGCACAACAAAATC 59.264 45.455 0.00 1.00 40.74 2.17
3166 4506 7.081349 TGGTTTAGAACATTGCGAAGTTAATG 58.919 34.615 0.00 0.00 39.08 1.90
3285 4625 5.509163 GCAGGCAGATAAATCATCAATGCTT 60.509 40.000 0.00 0.00 35.91 3.91
3508 4848 4.177026 CAGAATCTCAAACTGAGGTACGG 58.823 47.826 3.92 0.00 44.39 4.02
3825 5166 4.460382 CCTTGCTTTTTCTCTAGAATGCCA 59.540 41.667 0.00 0.00 33.54 4.92
3836 5177 5.126222 TCTCTAGAATGCCAGTGTACTCAAG 59.874 44.000 0.00 0.00 0.00 3.02
3869 5210 1.228124 CGAACTTTCCACAGGGCCA 60.228 57.895 6.18 0.00 0.00 5.36
3880 5221 2.313317 CACAGGGCCATAGCAATTCAT 58.687 47.619 6.18 0.00 42.56 2.57
3889 5230 5.353678 GGCCATAGCAATTCATCTCTATCAC 59.646 44.000 0.00 0.00 42.56 3.06
4136 5477 4.804420 TGCTCCTCCCATCGGCCT 62.804 66.667 0.00 0.00 0.00 5.19
4138 5479 2.444706 CTCCTCCCATCGGCCTGA 60.445 66.667 0.00 0.00 0.00 3.86
4528 6134 5.455056 AAGGAATATGTGTAGTAGCCTCG 57.545 43.478 0.00 0.00 0.00 4.63
4567 6173 7.870954 CCCCAAAACTTTTAAGTCCATAAACTC 59.129 37.037 0.00 0.00 38.57 3.01
4617 6223 4.393680 TGCATACGTAAACCTCATTTCCAC 59.606 41.667 0.00 0.00 0.00 4.02
4630 6236 6.986231 ACCTCATTTCCACTTCATTTCAAAAC 59.014 34.615 0.00 0.00 0.00 2.43
4688 6294 8.810427 CATACATTCCAACTACATTTGAAATGC 58.190 33.333 17.19 0.00 0.00 3.56
4905 6511 3.062639 CGTGACGAGCTTGCTCAAAATAT 59.937 43.478 20.59 0.89 0.00 1.28
4925 6531 1.832883 TGTTTTGCCATATGCCGTCT 58.167 45.000 0.00 0.00 40.16 4.18
4943 6549 4.451557 CGTCTAATTGTGAAAACGTCCAC 58.548 43.478 8.25 8.25 0.00 4.02
4969 6575 2.907892 TGAGATCCTCAACCTCACCTT 58.092 47.619 0.00 0.00 37.57 3.50
4972 6578 3.517500 GAGATCCTCAACCTCACCTTCTT 59.482 47.826 0.00 0.00 0.00 2.52
4988 6594 2.564471 CTTGAGGGCAAGCTTCCTG 58.436 57.895 11.29 0.00 44.41 3.86
4994 6600 1.682257 GGCAAGCTTCCTGTCCTCT 59.318 57.895 0.00 0.00 0.00 3.69
5000 6606 1.219393 CTTCCTGTCCTCTTCCGCC 59.781 63.158 0.00 0.00 0.00 6.13
5002 6608 4.148825 CCTGTCCTCTTCCGCCGG 62.149 72.222 0.00 0.00 0.00 6.13
5012 6618 3.310860 TTCCGCCGGCTTCCTCTTC 62.311 63.158 26.68 0.00 0.00 2.87
5013 6619 3.775654 CCGCCGGCTTCCTCTTCT 61.776 66.667 26.68 0.00 0.00 2.85
5014 6620 2.202810 CGCCGGCTTCCTCTTCTC 60.203 66.667 26.68 0.00 0.00 2.87
5076 6682 4.473444 TGCCTTCACCATTTCTCTCTTTT 58.527 39.130 0.00 0.00 0.00 2.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
238 240 3.625313 GCACTGCCTTCTCCTTTATCTTC 59.375 47.826 0.00 0.00 0.00 2.87
252 254 1.454479 ACAAGCACAAGCACTGCCT 60.454 52.632 0.00 0.00 45.49 4.75
254 256 0.317603 CTCACAAGCACAAGCACTGC 60.318 55.000 0.00 0.00 45.49 4.40
287 290 4.404507 GTATGCCATAAGCCAACATACG 57.595 45.455 0.00 0.00 42.71 3.06
364 367 8.833231 TTTAGATATCGGGAGCAAGAAATAAG 57.167 34.615 0.00 0.00 0.00 1.73
446 449 4.870991 GGTTCTGTTAGAAAGAGCGCTAAT 59.129 41.667 11.50 0.00 35.75 1.73
450 453 2.413837 TGGTTCTGTTAGAAAGAGCGC 58.586 47.619 0.00 0.00 35.75 5.92
475 478 7.882791 TCCTGCTTTATTCTACAGTCAATTCAA 59.117 33.333 0.00 0.00 0.00 2.69
506 509 3.213206 TCACACTTTCAGGTGAGCATT 57.787 42.857 1.52 0.00 39.00 3.56
904 2239 1.696336 AGTGACAGCAACTGGTGATCT 59.304 47.619 15.40 7.44 45.66 2.75
1040 2375 6.203723 GCTATAATTCTCAGAAGCGGAATTGT 59.796 38.462 9.49 6.36 39.20 2.71
1053 2388 8.579850 AACCATCAACAAAGCTATAATTCTCA 57.420 30.769 0.00 0.00 0.00 3.27
1117 2452 3.742433 TCTAGCTCTGAAATAGCCTGC 57.258 47.619 0.00 0.00 41.02 4.85
1252 2587 2.159179 AGGCTGTTGGAAGGTTTGTT 57.841 45.000 0.00 0.00 0.00 2.83
1327 2662 0.681733 GTGCAGTGAAGAGTCCCTGA 59.318 55.000 0.00 0.00 0.00 3.86
1341 2676 1.334869 GTTCCAGGTGTTGAAGTGCAG 59.665 52.381 0.00 0.00 0.00 4.41
1677 3012 7.949434 AGGTAGCAGTAGTACCAATATGTTAC 58.051 38.462 0.00 1.44 42.28 2.50
1718 3053 9.046296 CCTGTATTACCACAAGAATGAATAGTC 57.954 37.037 0.00 0.00 0.00 2.59
1768 3103 2.614057 CCGTACCAAAAGATGAGATGCC 59.386 50.000 0.00 0.00 0.00 4.40
1800 3135 3.644265 TCAAACCACTACCAGCTAGTTGA 59.356 43.478 8.34 0.00 32.90 3.18
1875 3210 7.326789 ACAGAATTGAATGAACAATAACTTGCG 59.673 33.333 0.00 0.00 39.19 4.85
1946 3281 2.221169 GGAGCGGAATATTGCACATCA 58.779 47.619 7.78 0.00 0.00 3.07
2221 3557 2.371784 TGGCTTAGCACTGGCACTA 58.628 52.632 6.53 0.00 44.61 2.74
2302 3638 7.979444 TCTAGAGTGAATTTACCAAACAAGG 57.021 36.000 0.00 0.00 0.00 3.61
2615 3952 6.927936 ACCATATGTCATTCTCTTCTGATTCG 59.072 38.462 1.24 0.00 0.00 3.34
2616 3953 9.770097 TTACCATATGTCATTCTCTTCTGATTC 57.230 33.333 1.24 0.00 0.00 2.52
2764 4101 6.327365 GGCTACCCCTAACTGGTAACTATTTA 59.673 42.308 0.00 0.00 37.88 1.40
2821 4158 7.110155 CCCCTAACTGATAACTACAACAACAT 58.890 38.462 0.00 0.00 0.00 2.71
2946 4285 3.181539 GCGAGAAAAGCTCTAACTTGTCG 60.182 47.826 0.00 0.00 38.68 4.35
3036 4375 3.444642 CGTACGACACGTCAAGCC 58.555 61.111 10.44 0.00 45.82 4.35
3098 4438 2.886862 CACAGATTTTGTTGTGCCCA 57.113 45.000 0.00 0.00 38.16 5.36
3113 4453 4.100963 TGGATAACAGTATAGGTGGCACAG 59.899 45.833 20.82 2.34 41.80 3.66
3508 4848 8.736751 TCACTTTGTACAAACAGAAAAGTTTC 57.263 30.769 17.01 0.00 39.55 2.78
3526 4866 5.239306 TCACAACAAGGAGCTATTCACTTTG 59.761 40.000 0.00 0.00 0.00 2.77
3765 5106 9.725019 AATGAAGTGTTTATTCATCAGTACTGA 57.275 29.630 27.07 27.07 44.57 3.41
3825 5166 6.542370 ACAGTGCAATAAAACTTGAGTACACT 59.458 34.615 0.00 0.00 35.16 3.55
3836 5177 5.398416 GGAAAGTTCGACAGTGCAATAAAAC 59.602 40.000 0.00 0.00 0.00 2.43
3869 5210 6.499699 TGGAGGTGATAGAGATGAATTGCTAT 59.500 38.462 0.00 0.00 0.00 2.97
3880 5221 1.112113 GCGGTTGGAGGTGATAGAGA 58.888 55.000 0.00 0.00 0.00 3.10
3889 5230 1.237285 CCTTGTGAAGCGGTTGGAGG 61.237 60.000 3.70 2.56 0.00 4.30
4084 5425 2.885266 GTTTTCACCTTTCAGGAGGGAC 59.115 50.000 0.00 0.00 41.31 4.46
4136 5477 2.045561 TTTCGGCAGTTGTTTCCTCA 57.954 45.000 0.00 0.00 0.00 3.86
4138 5479 2.034558 CACATTTCGGCAGTTGTTTCCT 59.965 45.455 0.00 0.00 0.00 3.36
4340 5692 0.840617 TGCCAGACACTTGTACCCAA 59.159 50.000 0.00 0.00 0.00 4.12
4362 5714 2.919602 AGATCCATGTACAACCCAAGGT 59.080 45.455 0.00 0.00 37.65 3.50
4363 5715 3.652057 AGATCCATGTACAACCCAAGG 57.348 47.619 0.00 0.00 0.00 3.61
4364 5716 5.928976 TCATAGATCCATGTACAACCCAAG 58.071 41.667 0.00 0.00 0.00 3.61
4534 6140 5.633117 ACTTAAAAGTTTTGGGGGTCGATA 58.367 37.500 11.18 0.00 35.21 2.92
4535 6141 4.476297 ACTTAAAAGTTTTGGGGGTCGAT 58.524 39.130 11.18 0.00 35.21 3.59
4925 6531 3.059461 GCTCGTGGACGTTTTCACAATTA 60.059 43.478 14.70 1.25 40.80 1.40
4972 6578 1.376466 GACAGGAAGCTTGCCCTCA 59.624 57.895 15.04 0.00 0.00 3.86
4988 6594 4.083862 AAGCCGGCGGAAGAGGAC 62.084 66.667 33.44 10.10 33.12 3.85
4994 6600 3.310860 GAAGAGGAAGCCGGCGGAA 62.311 63.158 33.44 0.00 0.00 4.30
5000 6606 0.972983 TGGAGGAGAAGAGGAAGCCG 60.973 60.000 0.00 0.00 0.00 5.52
5002 6608 1.065782 GGTTGGAGGAGAAGAGGAAGC 60.066 57.143 0.00 0.00 0.00 3.86
5076 6682 3.775316 GGAGGAATTAGGAGAAGACACCA 59.225 47.826 0.00 0.00 0.00 4.17


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

AutoCloner maintained by Alex Coulton.