Multiple sequence alignment - TraesCS7A01G256400

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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 TraesCS7A01G256400 chr7A 100.000 3380 0 0 1 3380 244671597 244674976 0.000000e+00 6242
1 TraesCS7A01G256400 chr7A 80.682 352 55 10 573 916 243852577 243852231 9.300000e-66 261
2 TraesCS7A01G256400 chr7B 97.209 2401 61 3 986 3380 203282907 203285307 0.000000e+00 4058
3 TraesCS7A01G256400 chr7B 91.524 991 77 4 1 985 203281868 203282857 0.000000e+00 1358
4 TraesCS7A01G256400 chr7B 82.353 476 63 8 2355 2815 203284754 203285223 8.790000e-106 394
5 TraesCS7A01G256400 chr7B 80.117 342 45 15 573 902 202505995 202505665 2.030000e-57 233
6 TraesCS7A01G256400 chr7D 96.552 2407 69 5 986 3380 232499002 232501406 0.000000e+00 3973
7 TraesCS7A01G256400 chr7D 89.990 989 64 5 1 985 232497996 232498953 0.000000e+00 1245
8 TraesCS7A01G256400 chr7D 81.386 505 63 14 2355 2834 232500844 232501342 1.900000e-102 383
9 TraesCS7A01G256400 chr7D 79.501 361 56 11 568 916 230993131 230992777 1.210000e-59 241


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 TraesCS7A01G256400 chr7A 244671597 244674976 3379 False 6242.000000 6242 100.000000 1 3380 1 chr7A.!!$F1 3379
1 TraesCS7A01G256400 chr7B 203281868 203285307 3439 False 1936.666667 4058 90.362000 1 3380 3 chr7B.!!$F1 3379
2 TraesCS7A01G256400 chr7D 232497996 232501406 3410 False 1867.000000 3973 89.309333 1 3380 3 chr7D.!!$F1 3379

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
731 738 0.177141 CGAGGCTAAAATCACCCGGA 59.823 55.000 0.73 0.0 0.0 5.14 F
1449 1505 1.679898 CCTCTCTCCGGCAACCTTT 59.320 57.895 0.00 0.0 0.0 3.11 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2211 2267 0.324943 CATCCAAGAACCGACCACCT 59.675 55.0 0.0 0.0 0.00 4.0 R
3196 3268 0.179018 GTGAAAGCACCTGGTCCACT 60.179 55.0 0.0 0.0 39.14 4.0 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
77 81 5.176039 GGTAAAACTAAAACACAAATGCCCG 59.824 40.000 0.00 0.00 0.00 6.13
89 93 1.200519 AATGCCCGGCTAAGTGTCTA 58.799 50.000 11.61 0.00 0.00 2.59
96 100 4.321082 GCCCGGCTAAGTGTCTACTATAAG 60.321 50.000 0.71 0.00 35.69 1.73
111 115 5.582689 ACTATAAGCTTTCAACCCAATGC 57.417 39.130 3.20 0.00 0.00 3.56
178 182 5.691508 AAACATTAGTCGTTCGGTTATCG 57.308 39.130 0.00 0.00 40.90 2.92
229 233 5.395214 GGTTTCCACCTTCAGAAAACACAAT 60.395 40.000 0.00 0.00 39.10 2.71
257 261 8.833231 ATTTCTACAGCAACATACGCTAATAT 57.167 30.769 0.00 0.00 37.72 1.28
259 263 6.084277 TCTACAGCAACATACGCTAATATCG 58.916 40.000 0.00 0.00 37.72 2.92
262 266 5.628193 ACAGCAACATACGCTAATATCGTAC 59.372 40.000 0.00 0.00 43.88 3.67
269 273 7.864686 ACATACGCTAATATCGTACAACACTA 58.135 34.615 0.00 0.00 43.88 2.74
289 293 2.148916 TCGTGCTGAATCAACGACTT 57.851 45.000 6.12 0.00 0.00 3.01
297 301 4.766007 CTGAATCAACGACTTCAACACTG 58.234 43.478 0.00 0.00 31.40 3.66
324 329 5.414789 TTCACAGTAACATAGCCTAAGCA 57.585 39.130 0.00 0.00 43.56 3.91
361 366 3.624900 GCATACAGCGACTACGTATCAA 58.375 45.455 0.00 0.00 41.98 2.57
398 405 1.996798 AAACGTCAGAGACCTCCAGA 58.003 50.000 0.00 0.00 0.00 3.86
403 410 3.634448 ACGTCAGAGACCTCCAGATTATG 59.366 47.826 0.00 0.00 0.00 1.90
408 415 4.755629 CAGAGACCTCCAGATTATGCAATG 59.244 45.833 0.00 0.00 0.00 2.82
409 416 4.070716 GAGACCTCCAGATTATGCAATGG 58.929 47.826 0.00 0.00 0.00 3.16
468 475 1.597742 AGTTGAAACGACAGCATGCT 58.402 45.000 16.30 16.30 42.53 3.79
494 501 3.426903 CGGGATCTAGAACCGGGTA 57.573 57.895 24.06 0.00 43.69 3.69
534 541 4.624015 CAATCAAAACATGAGGCACTTGT 58.376 39.130 0.00 0.00 41.55 3.16
537 544 6.594788 ATCAAAACATGAGGCACTTGTAAT 57.405 33.333 0.00 0.00 41.55 1.89
545 552 6.099701 ACATGAGGCACTTGTAATATCCACTA 59.900 38.462 0.00 0.00 41.55 2.74
552 559 7.815068 GGCACTTGTAATATCCACTACATAGAG 59.185 40.741 0.00 0.00 0.00 2.43
559 566 7.546250 AATATCCACTACATAGAGGTCTTGG 57.454 40.000 2.79 0.00 35.80 3.61
569 576 1.722851 AGAGGTCTTGGGGAAGAGGTA 59.277 52.381 0.00 0.00 0.00 3.08
642 649 3.436243 ACCCTCTTCTTCACGATCTTCT 58.564 45.455 0.00 0.00 0.00 2.85
689 696 0.400213 ATCTGTCGGGCAAAACCAGA 59.600 50.000 0.00 0.00 40.73 3.86
696 703 0.969149 GGGCAAAACCAGAAGAAGGG 59.031 55.000 0.00 0.00 42.05 3.95
710 717 2.257207 AGAAGGGGTTCGAATCAGACA 58.743 47.619 11.19 0.00 0.00 3.41
717 724 1.390463 GTTCGAATCAGACAACGAGGC 59.610 52.381 0.00 0.00 36.22 4.70
731 738 0.177141 CGAGGCTAAAATCACCCGGA 59.823 55.000 0.73 0.00 0.00 5.14
786 793 2.609183 CTACCTTCGGGAGCGAACGG 62.609 65.000 0.00 0.00 38.77 4.44
968 975 1.896220 TAACTTGCCCAGTTGCAGAG 58.104 50.000 8.34 0.00 45.98 3.35
1449 1505 1.679898 CCTCTCTCCGGCAACCTTT 59.320 57.895 0.00 0.00 0.00 3.11
1458 1514 2.050442 GCAACCTTTTCGGCGGTG 60.050 61.111 7.21 0.00 35.61 4.94
2041 2097 2.543848 GCATTCCGATTGTTCTATGCGA 59.456 45.455 0.00 0.00 0.00 5.10
2211 2267 3.693578 TGCTTGTCAAAATGTGTGTGAGA 59.306 39.130 0.00 0.00 0.00 3.27
2301 2357 3.363280 CGCCAACCTTTAACGTTGTAGTC 60.363 47.826 11.99 0.00 39.16 2.59
2400 2456 0.673985 TGGATCCGGAAGTAGATGCG 59.326 55.000 9.01 0.00 33.89 4.73
2444 2500 9.691362 GAATTGCTTGGTAAAGTTTCTGAATTA 57.309 29.630 0.00 0.00 35.69 1.40
2446 2502 7.817418 TGCTTGGTAAAGTTTCTGAATTACT 57.183 32.000 10.51 1.75 35.69 2.24
2451 2507 9.856162 TTGGTAAAGTTTCTGAATTACTAGGTT 57.144 29.630 10.51 0.17 0.00 3.50
2472 2528 4.357918 TGGGCTCCTATCTTCTAATTGC 57.642 45.455 0.00 0.00 0.00 3.56
2519 2575 0.179048 TGCTGTTGGACTGTGACTGG 60.179 55.000 0.00 0.00 0.00 4.00
2595 2653 5.312079 GCCATCAGATAGCCTCAACTAATT 58.688 41.667 0.00 0.00 0.00 1.40
2660 2718 4.021368 GTGGAGTAGGCACTAAGTTCAGAA 60.021 45.833 0.00 0.00 45.48 3.02
2819 2880 7.435192 GCCATGCTACCTTGTATGATTTAAAAC 59.565 37.037 0.00 0.00 32.93 2.43
2860 2921 6.813649 TCACTAGAAGGAAACTGAATGAATCG 59.186 38.462 0.00 0.00 42.68 3.34
2948 3009 6.825610 AGGATTCCTGTCTTCTGATTGTATC 58.174 40.000 3.86 0.00 29.57 2.24
3007 3068 4.641541 TGGATATGCTGGTCAAGTGATTTG 59.358 41.667 0.00 0.00 38.17 2.32
3031 3092 4.733077 TGTTTTGGGTAGGAAGGATCAA 57.267 40.909 0.00 0.00 0.00 2.57
3139 3210 7.078228 GCAGTAAGTTGAGTGGAATTTAAGTG 58.922 38.462 0.00 0.00 0.00 3.16
3196 3268 0.538516 CCCCATCGGTGTTTGACCAA 60.539 55.000 0.00 0.00 46.55 3.67
3280 3352 6.899089 TGTAGAATAAAGATTGGAGCCATGA 58.101 36.000 0.00 0.00 0.00 3.07
3298 3370 5.050091 GCCATGATACCTTGTACGATTTGAG 60.050 44.000 0.00 0.00 0.00 3.02
3332 3404 6.401537 AGAGATAGGGCTGACTACTGATAT 57.598 41.667 0.00 0.00 0.00 1.63
3336 3408 4.679373 AGGGCTGACTACTGATATTGTG 57.321 45.455 0.00 0.00 0.00 3.33
3370 3443 3.874392 AGGCAAATCACTTACCATTGC 57.126 42.857 0.00 0.00 44.18 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 65 1.333177 AGCCGGGCATTTGTGTTTTA 58.667 45.000 23.09 0.00 0.00 1.52
77 81 7.490000 TGAAAGCTTATAGTAGACACTTAGCC 58.510 38.462 0.00 0.00 35.08 3.93
89 93 5.264395 AGCATTGGGTTGAAAGCTTATAGT 58.736 37.500 0.00 0.00 0.00 2.12
96 100 2.997986 CAATGAGCATTGGGTTGAAAGC 59.002 45.455 13.94 0.00 43.25 3.51
111 115 7.431376 GCACTTGTACATCAAATCATCAATGAG 59.569 37.037 0.00 0.00 34.69 2.90
171 175 5.457140 TGAACAAGCACAAATTCGATAACC 58.543 37.500 0.00 0.00 0.00 2.85
178 182 9.807649 ATTTAGGATATGAACAAGCACAAATTC 57.192 29.630 0.00 0.00 0.00 2.17
180 184 8.199449 CCATTTAGGATATGAACAAGCACAAAT 58.801 33.333 0.00 0.00 41.22 2.32
229 233 6.978343 AGCGTATGTTGCTGTAGAAATTTA 57.022 33.333 0.00 0.00 42.14 1.40
269 273 2.370281 AGTCGTTGATTCAGCACGAT 57.630 45.000 14.63 4.31 35.28 3.73
289 293 2.653726 ACTGTGAAATGGCAGTGTTGA 58.346 42.857 0.00 0.00 43.45 3.18
297 301 3.947834 AGGCTATGTTACTGTGAAATGGC 59.052 43.478 2.93 2.93 0.00 4.40
324 329 5.105756 GCTGTATGCCAAATTTACCACTTCT 60.106 40.000 0.00 0.00 35.15 2.85
384 391 3.646534 TGCATAATCTGGAGGTCTCTGA 58.353 45.455 0.00 0.00 0.00 3.27
387 394 4.070716 CCATTGCATAATCTGGAGGTCTC 58.929 47.826 0.00 0.00 0.00 3.36
398 405 6.772605 TGCTGTAGTATCTCCATTGCATAAT 58.227 36.000 0.00 0.00 0.00 1.28
403 410 3.397482 CCTGCTGTAGTATCTCCATTGC 58.603 50.000 0.00 0.00 0.00 3.56
408 415 1.414158 TGGCCTGCTGTAGTATCTCC 58.586 55.000 3.32 0.00 0.00 3.71
409 416 2.630098 TCATGGCCTGCTGTAGTATCTC 59.370 50.000 3.32 0.00 0.00 2.75
458 465 2.223340 CCCGATTGTTAAGCATGCTGTC 60.223 50.000 23.48 14.79 0.00 3.51
468 475 4.202182 CCGGTTCTAGATCCCGATTGTTAA 60.202 45.833 25.14 0.00 44.41 2.01
519 526 5.590259 GTGGATATTACAAGTGCCTCATGTT 59.410 40.000 0.00 0.00 0.00 2.71
534 541 7.674348 CCCAAGACCTCTATGTAGTGGATATTA 59.326 40.741 13.49 0.00 38.84 0.98
537 544 5.394738 CCCAAGACCTCTATGTAGTGGATA 58.605 45.833 13.49 0.00 38.84 2.59
545 552 3.379452 CTCTTCCCCAAGACCTCTATGT 58.621 50.000 0.00 0.00 34.71 2.29
552 559 2.249309 TCTACCTCTTCCCCAAGACC 57.751 55.000 0.00 0.00 34.71 3.85
569 576 3.181450 GCTACATTGGCCTCAAGGTATCT 60.181 47.826 3.32 0.00 45.27 1.98
642 649 2.357034 GGTGCCGCTTCTGACGAA 60.357 61.111 0.00 0.00 0.00 3.85
689 696 2.637872 TGTCTGATTCGAACCCCTTCTT 59.362 45.455 0.00 0.00 0.00 2.52
696 703 1.993370 CCTCGTTGTCTGATTCGAACC 59.007 52.381 0.00 0.00 32.12 3.62
710 717 1.677820 CCGGGTGATTTTAGCCTCGTT 60.678 52.381 0.00 0.00 36.08 3.85
717 724 4.379082 CCTCGTTTTTCCGGGTGATTTTAG 60.379 45.833 0.00 0.00 0.00 1.85
731 738 0.602905 CGAGCTCCCACCTCGTTTTT 60.603 55.000 8.47 0.00 45.17 1.94
786 793 1.551883 TCTTCGTGTTAGGGTTAGGGC 59.448 52.381 0.00 0.00 0.00 5.19
968 975 0.175989 CTCTAGAAACGGAGGCCCAC 59.824 60.000 0.00 0.00 0.00 4.61
1068 1124 4.849329 GCGTAGTCGGGGAGCGTG 62.849 72.222 0.00 0.00 37.56 5.34
1449 1505 2.488355 GACGAGATCACCGCCGAA 59.512 61.111 7.33 0.00 0.00 4.30
1866 1922 2.357034 TGGGCGAGCGAGTTGAAC 60.357 61.111 0.00 0.00 0.00 3.18
2041 2097 0.469917 CGGTGGCCATCCTCAATAGT 59.530 55.000 9.72 0.00 0.00 2.12
2169 2225 2.022764 TCACATACACAGGCCGATTG 57.977 50.000 0.00 0.00 0.00 2.67
2211 2267 0.324943 CATCCAAGAACCGACCACCT 59.675 55.000 0.00 0.00 0.00 4.00
2301 2357 4.923942 AGATGCCGCAGCCCATCG 62.924 66.667 4.68 0.00 41.98 3.84
2400 2456 4.840005 GCAGCGCCCCACTAGACC 62.840 72.222 2.29 0.00 0.00 3.85
2444 2500 3.051727 AGAAGATAGGAGCCCAACCTAGT 60.052 47.826 0.00 0.00 42.26 2.57
2446 2502 3.708236 AGAAGATAGGAGCCCAACCTA 57.292 47.619 0.00 0.00 42.99 3.08
2451 2507 3.716353 TGCAATTAGAAGATAGGAGCCCA 59.284 43.478 0.00 0.00 0.00 5.36
2519 2575 6.813152 ACAAATAAATCACTTGCCAAGCATAC 59.187 34.615 3.88 0.00 38.76 2.39
2660 2718 5.590530 TGCAACCACAAAACTTACATTCT 57.409 34.783 0.00 0.00 0.00 2.40
2751 2809 1.162698 CATGGAGCACAGAGTTGGTG 58.837 55.000 0.00 0.00 39.25 4.17
2819 2880 7.490725 CCTTCTAGTGACATCTCAACAATACAG 59.509 40.741 0.00 0.00 0.00 2.74
2860 2921 3.068873 CCACTAGACAGCATCTACTTCCC 59.931 52.174 0.00 0.00 39.04 3.97
2948 3009 6.035843 GCATAACATTGGTTTATGTCACAGG 58.964 40.000 8.14 0.00 37.76 4.00
3007 3068 4.830600 TGATCCTTCCTACCCAAAACAAAC 59.169 41.667 0.00 0.00 0.00 2.93
3031 3092 7.925622 TGAGGCTATCCAATGATCTTATTCAT 58.074 34.615 0.00 0.00 37.96 2.57
3139 3210 8.243426 TCAAAATCTAATCTATGCAACCACAAC 58.757 33.333 0.00 0.00 0.00 3.32
3196 3268 0.179018 GTGAAAGCACCTGGTCCACT 60.179 55.000 0.00 0.00 39.14 4.00
3280 3352 4.982916 GCGATCTCAAATCGTACAAGGTAT 59.017 41.667 8.96 0.00 42.90 2.73
3298 3370 2.668834 GCCCTATCTCTACAACGCGATC 60.669 54.545 15.93 0.00 0.00 3.69
3332 3404 2.023673 CCTTGAGGTTTCAGCACACAA 58.976 47.619 0.00 0.00 34.15 3.33
3336 3408 1.032014 TTGCCTTGAGGTTTCAGCAC 58.968 50.000 0.00 0.00 35.13 4.40


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

AutoCloner maintained by Alex Coulton.