Multiple sequence alignment - TraesCS7D01G304200

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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 TraesCS7D01G304200 chr7D 100.000 5460 0 0 1 5460 386353130 386358589 0.000000e+00 10083
1 TraesCS7D01G304200 chr7D 82.609 115 18 2 2472 2585 424268184 424268297 3.480000e-17 100
2 TraesCS7D01G304200 chr7A 96.986 5475 121 24 1 5460 434734069 434739514 0.000000e+00 9156
3 TraesCS7D01G304200 chr7B 94.080 2196 99 17 2578 4763 380509626 380511800 0.000000e+00 3306
4 TraesCS7D01G304200 chr7B 96.754 1787 48 4 1 1779 380506713 380508497 0.000000e+00 2970
5 TraesCS7D01G304200 chr7B 95.179 643 20 4 1778 2412 380508566 380509205 0.000000e+00 1005
6 TraesCS7D01G304200 chr7B 93.220 531 31 4 4931 5460 380536706 380537232 0.000000e+00 776
7 TraesCS7D01G304200 chr7B 96.053 76 3 0 2409 2484 380509552 380509627 2.070000e-24 124
8 TraesCS7D01G304200 chr7B 83.333 108 17 1 2472 2579 326671119 326671225 1.250000e-16 99
9 TraesCS7D01G304200 chr6B 86.000 100 14 0 2483 2582 530560462 530560363 2.080000e-19 108
10 TraesCS7D01G304200 chr2D 84.404 109 15 2 2477 2583 566989107 566988999 7.480000e-19 106
11 TraesCS7D01G304200 chr2B 84.545 110 13 4 2477 2583 679898355 679898247 7.480000e-19 106
12 TraesCS7D01G304200 chr2A 84.545 110 13 4 2477 2583 706753010 706752902 7.480000e-19 106
13 TraesCS7D01G304200 chr1B 83.962 106 17 0 2473 2578 67444539 67444644 9.680000e-18 102
14 TraesCS7D01G304200 chr4D 82.609 115 18 2 2472 2585 503868571 503868684 3.480000e-17 100


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 TraesCS7D01G304200 chr7D 386353130 386358589 5459 False 10083.00 10083 100.0000 1 5460 1 chr7D.!!$F1 5459
1 TraesCS7D01G304200 chr7A 434734069 434739514 5445 False 9156.00 9156 96.9860 1 5460 1 chr7A.!!$F1 5459
2 TraesCS7D01G304200 chr7B 380506713 380511800 5087 False 1851.25 3306 95.5165 1 4763 4 chr7B.!!$F3 4762
3 TraesCS7D01G304200 chr7B 380536706 380537232 526 False 776.00 776 93.2200 4931 5460 1 chr7B.!!$F2 529

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
238 242 0.820871 CTAGGCTTCCTGCTCGTTCT 59.179 55.000 0.00 0.0 42.39 3.01 F
1038 1042 1.754803 GGTCTGATCATCGGTACCACA 59.245 52.381 13.54 0.0 0.00 4.17 F
1476 1480 0.250338 GAAGCTCCTGTCGTGGGTTT 60.250 55.000 0.00 0.0 0.00 3.27 F
1532 1542 1.145119 ACCAACTCCAAGGGTTCCTTC 59.855 52.381 0.00 0.0 42.67 3.46 F
3301 3748 1.936547 GCTATACACTGGAAGCAGCAC 59.063 52.381 0.00 0.0 37.60 4.40 F
3563 4015 0.543749 GCCCAGCCTACTCATGTTCT 59.456 55.000 0.00 0.0 0.00 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1445 1449 3.181440 ACAGGAGCTTCATTTCAGAACCA 60.181 43.478 0.00 0.00 0.00 3.67 R
2880 3321 0.392193 CCCATCTCAGTGGTGCACTC 60.392 60.000 17.98 10.45 43.43 3.51 R
3430 3878 3.438781 TCCGTGAATTTTCTGTGGCATAC 59.561 43.478 0.00 0.00 0.00 2.39 R
3445 3893 5.759506 TTAAGCAAAGAATGTTCCGTGAA 57.240 34.783 0.00 0.00 0.00 3.18 R
4147 4601 0.404040 AGTCGGCAATTTCCTCCCAA 59.596 50.000 0.00 0.00 0.00 4.12 R
4834 5288 1.026182 CGCTATGCAGAAACTGGCCA 61.026 55.000 4.71 4.71 31.21 5.36 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
102 103 1.074872 GTCCGCTCCCGTAAGTTTCG 61.075 60.000 0.00 0.00 0.00 3.46
198 202 1.289530 TGGGTTTTGGTGGTTCTTCCT 59.710 47.619 0.00 0.00 37.07 3.36
238 242 0.820871 CTAGGCTTCCTGCTCGTTCT 59.179 55.000 0.00 0.00 42.39 3.01
376 380 7.172868 TCTGTGATTTGCATTGGTGATTTAT 57.827 32.000 0.00 0.00 0.00 1.40
377 381 8.291191 TCTGTGATTTGCATTGGTGATTTATA 57.709 30.769 0.00 0.00 0.00 0.98
1038 1042 1.754803 GGTCTGATCATCGGTACCACA 59.245 52.381 13.54 0.00 0.00 4.17
1356 1360 7.936496 TCTCTATCTATTCTCATGGTAGCAG 57.064 40.000 0.00 0.00 0.00 4.24
1374 1378 8.141909 TGGTAGCAGTATTCATAGTTGTATCAC 58.858 37.037 0.00 0.00 0.00 3.06
1476 1480 0.250338 GAAGCTCCTGTCGTGGGTTT 60.250 55.000 0.00 0.00 0.00 3.27
1532 1542 1.145119 ACCAACTCCAAGGGTTCCTTC 59.855 52.381 0.00 0.00 42.67 3.46
1556 1567 7.826690 TCTTTTAGCTTTTTGTCTTGTTGACT 58.173 30.769 0.00 0.00 45.54 3.41
1563 1574 4.963276 TTTGTCTTGTTGACTTGTCAGG 57.037 40.909 3.61 0.00 45.54 3.86
1566 1577 3.452990 TGTCTTGTTGACTTGTCAGGGTA 59.547 43.478 3.61 0.00 45.54 3.69
2336 2420 9.976511 CACTTATACGGTATTTATTCTCTCCAA 57.023 33.333 5.89 0.00 0.00 3.53
2403 2494 3.000041 TCGTGCTTTGTTGCTACCATAG 59.000 45.455 0.00 0.00 0.00 2.23
2519 2960 8.520351 GTCCTAATTAAATGTTGCTGGTTTAGT 58.480 33.333 0.00 0.00 0.00 2.24
2555 2996 4.803098 AAGTTGTACTAATCCAGCGACT 57.197 40.909 0.00 0.00 0.00 4.18
2570 3011 8.768501 ATCCAGCGACTATTAATATGGATAGA 57.231 34.615 19.37 4.51 42.70 1.98
2577 3018 9.191479 CGACTATTAATATGGATAGAAGGGAGT 57.809 37.037 10.86 0.00 31.75 3.85
2668 3109 3.072768 ACTCGGTAAAATAACCACCACCA 59.927 43.478 0.00 0.00 39.71 4.17
2880 3321 6.742109 ACATTCTGTGAATTCAGGTGAAAAG 58.258 36.000 8.80 11.88 37.61 2.27
2904 3345 2.225091 TGCACCACTGAGATGGGATTTT 60.225 45.455 6.14 0.00 44.81 1.82
2998 3439 8.803235 ACTCATAATTTGAATCATGATCCATGG 58.197 33.333 9.06 4.97 36.88 3.66
3007 3448 7.516452 TGAATCATGATCCATGGTGTAATACA 58.484 34.615 12.58 3.52 41.66 2.29
3138 3579 6.647067 GGGTATGCTGTACATCTCTGTAATTC 59.353 42.308 0.00 0.00 39.51 2.17
3146 3587 7.139392 TGTACATCTCTGTAATTCGTCATAGC 58.861 38.462 0.00 0.00 39.51 2.97
3247 3688 6.428159 AGTTTGCACCTCTGTATTCTTAACTG 59.572 38.462 0.00 0.00 0.00 3.16
3248 3689 4.253685 TGCACCTCTGTATTCTTAACTGC 58.746 43.478 0.00 0.00 0.00 4.40
3249 3690 3.623510 GCACCTCTGTATTCTTAACTGCC 59.376 47.826 0.00 0.00 0.00 4.85
3250 3691 3.865745 CACCTCTGTATTCTTAACTGCCG 59.134 47.826 0.00 0.00 0.00 5.69
3251 3692 3.767673 ACCTCTGTATTCTTAACTGCCGA 59.232 43.478 0.00 0.00 0.00 5.54
3252 3693 4.113354 CCTCTGTATTCTTAACTGCCGAC 58.887 47.826 0.00 0.00 0.00 4.79
3254 3695 5.339008 TCTGTATTCTTAACTGCCGACAT 57.661 39.130 0.00 0.00 0.00 3.06
3301 3748 1.936547 GCTATACACTGGAAGCAGCAC 59.063 52.381 0.00 0.00 37.60 4.40
3430 3878 6.183360 ACCAATGTAGTAGCGTACTTACTGAG 60.183 42.308 13.96 0.00 40.14 3.35
3445 3893 6.476378 ACTTACTGAGTATGCCACAGAAAAT 58.524 36.000 11.25 0.00 36.65 1.82
3539 3991 1.448013 GTTGGCTAGAGGTGCGACC 60.448 63.158 0.00 0.00 38.99 4.79
3563 4015 0.543749 GCCCAGCCTACTCATGTTCT 59.456 55.000 0.00 0.00 0.00 3.01
3729 4181 7.624360 TTGTAAAGACACATGAGTTTTCTGT 57.376 32.000 0.00 0.00 34.48 3.41
3778 4230 2.517959 CATTCCCTCTGTTGCCTTTCA 58.482 47.619 0.00 0.00 0.00 2.69
4039 4493 3.674997 TGTTGAGCTTGTAAGGATGTCC 58.325 45.455 0.00 0.00 0.00 4.02
4147 4601 1.376424 CGCTGATGGCAAGACTGGT 60.376 57.895 0.00 0.00 41.91 4.00
4500 4954 0.322546 CCCTACTGTTGTTCCTGGCC 60.323 60.000 0.00 0.00 0.00 5.36
4748 5202 5.980698 CACTAGATGATGTGCTGGTTTAG 57.019 43.478 0.00 0.00 0.00 1.85
4799 5253 7.780271 AGGAAAAGTAAAGATCTTCTGTTTGGT 59.220 33.333 8.78 0.00 0.00 3.67
4800 5254 7.862873 GGAAAAGTAAAGATCTTCTGTTTGGTG 59.137 37.037 8.78 0.00 0.00 4.17
4865 5319 6.691754 TTCTGCATAGCGAAAATGGAAATA 57.308 33.333 0.00 0.00 0.00 1.40
4867 5321 4.843147 TGCATAGCGAAAATGGAAATACG 58.157 39.130 0.00 0.00 0.00 3.06
4895 5349 9.482627 TGTTTATAATTTTGATTCGGTGCTTTT 57.517 25.926 0.00 0.00 0.00 2.27
4931 5385 4.928661 ATCAGACAAAATTCGTTCGGAG 57.071 40.909 0.00 0.00 0.00 4.63
4935 5389 4.025229 CAGACAAAATTCGTTCGGAGTTCA 60.025 41.667 0.00 0.00 0.00 3.18
5256 5711 1.079681 CCAAAAGCATGGCACGCAT 60.080 52.632 8.75 0.00 32.78 4.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 62 3.664025 CTGAATGCGGGCGGAGACA 62.664 63.158 0.00 0.00 37.00 3.41
102 103 5.858581 CCAAAGATCAAGAAACCGAATCAAC 59.141 40.000 0.00 0.00 0.00 3.18
198 202 3.388024 AGAATAGCGAGGCATAAACTGGA 59.612 43.478 0.00 0.00 0.00 3.86
376 380 4.890088 ACGCTTATCTCCACAAACACTTA 58.110 39.130 0.00 0.00 0.00 2.24
377 381 3.740115 ACGCTTATCTCCACAAACACTT 58.260 40.909 0.00 0.00 0.00 3.16
405 409 5.420409 AGAACTCGGAAAATATCACCTGAC 58.580 41.667 0.00 0.00 0.00 3.51
734 738 9.717892 CACATCAAAATATCAGATCTTTGACAG 57.282 33.333 17.15 15.34 39.78 3.51
1038 1042 0.991920 CCCCTATCACCACACCAACT 59.008 55.000 0.00 0.00 0.00 3.16
1374 1378 5.652452 AGCAAATTTTGTAGGGCCTAGTTAG 59.348 40.000 15.05 0.22 0.00 2.34
1445 1449 3.181440 ACAGGAGCTTCATTTCAGAACCA 60.181 43.478 0.00 0.00 0.00 3.67
1556 1567 6.216662 TCCTATGGAAATTTCTACCCTGACAA 59.783 38.462 17.42 0.00 0.00 3.18
1846 1928 7.891183 TCCAGGGTCATACTTAAATTAGCAAAA 59.109 33.333 0.00 0.00 0.00 2.44
2336 2420 7.859325 AAGGAGTGTTATTACAAATACGCAT 57.141 32.000 0.00 0.00 35.69 4.73
2568 3009 7.363968 GCAAGACTGTAATTACTACTCCCTTCT 60.364 40.741 16.33 4.29 0.00 2.85
2570 3011 6.212791 TGCAAGACTGTAATTACTACTCCCTT 59.787 38.462 16.33 8.25 0.00 3.95
2880 3321 0.392193 CCCATCTCAGTGGTGCACTC 60.392 60.000 17.98 10.45 43.43 3.51
2904 3345 8.750298 GCAACATCTAGAGCTATATTTACCCTA 58.250 37.037 0.00 0.00 0.00 3.53
3007 3448 8.325046 AGTTAAGCCAGATGAAGTAATCTCTTT 58.675 33.333 0.00 0.00 34.60 2.52
3146 3587 6.160684 ACAATTGTTCAACATGTCATGGATG 58.839 36.000 17.08 14.42 33.60 3.51
3247 3688 3.636282 AAGTACAAACCAAATGTCGGC 57.364 42.857 0.00 0.00 32.27 5.54
3248 3689 6.150474 AGGATAAAGTACAAACCAAATGTCGG 59.850 38.462 0.00 0.00 32.27 4.79
3249 3690 7.021196 CAGGATAAAGTACAAACCAAATGTCG 58.979 38.462 0.00 0.00 32.27 4.35
3250 3691 6.806739 GCAGGATAAAGTACAAACCAAATGTC 59.193 38.462 0.00 0.00 32.27 3.06
3251 3692 6.266558 TGCAGGATAAAGTACAAACCAAATGT 59.733 34.615 0.00 0.00 34.81 2.71
3252 3693 6.686630 TGCAGGATAAAGTACAAACCAAATG 58.313 36.000 0.00 0.00 0.00 2.32
3254 3695 6.909550 ATGCAGGATAAAGTACAAACCAAA 57.090 33.333 0.00 0.00 0.00 3.28
3301 3748 9.650371 CATATAACATCATAAACAAAGTCACCG 57.350 33.333 0.00 0.00 0.00 4.94
3430 3878 3.438781 TCCGTGAATTTTCTGTGGCATAC 59.561 43.478 0.00 0.00 0.00 2.39
3438 3886 6.346040 GCAAAGAATGTTCCGTGAATTTTCTG 60.346 38.462 11.24 6.06 31.19 3.02
3445 3893 5.759506 TTAAGCAAAGAATGTTCCGTGAA 57.240 34.783 0.00 0.00 0.00 3.18
3539 3991 2.590007 GAGTAGGCTGGGCATGCG 60.590 66.667 12.44 0.00 29.18 4.73
3714 4166 4.898829 TGGACAACAGAAAACTCATGTG 57.101 40.909 0.00 0.00 0.00 3.21
3729 4181 7.601856 CAAGCAAACCTATTATCTTTGGACAA 58.398 34.615 0.00 0.00 0.00 3.18
3778 4230 9.014297 CATGTCTAGGAATAAAACTTCCAAACT 57.986 33.333 5.70 0.00 46.02 2.66
3928 4382 6.821160 TGTACACATCACTCTTCTTTGTGAAA 59.179 34.615 8.22 0.00 44.81 2.69
4039 4493 7.509141 AAATTCTGCAACAAAAATAAAGGGG 57.491 32.000 0.00 0.00 0.00 4.79
4147 4601 0.404040 AGTCGGCAATTTCCTCCCAA 59.596 50.000 0.00 0.00 0.00 4.12
4705 5159 6.835174 AGTGCAACATATAGACCAGATGATT 58.165 36.000 0.00 0.00 41.43 2.57
4748 5202 3.366374 GCAAGGCAGTTGTATGAAAGGAC 60.366 47.826 0.54 0.00 38.55 3.85
4781 5235 7.445402 CCTTCTTCACCAAACAGAAGATCTTTA 59.555 37.037 9.87 0.00 46.72 1.85
4799 5253 5.868454 TGATCTGTGATTCAACCTTCTTCA 58.132 37.500 0.00 0.00 0.00 3.02
4800 5254 5.936956 ACTGATCTGTGATTCAACCTTCTTC 59.063 40.000 4.21 0.00 0.00 2.87
4834 5288 1.026182 CGCTATGCAGAAACTGGCCA 61.026 55.000 4.71 4.71 31.21 5.36
4865 5319 7.431084 GCACCGAATCAAAATTATAAACATCGT 59.569 33.333 0.00 0.00 0.00 3.73
4867 5321 8.856490 AGCACCGAATCAAAATTATAAACATC 57.144 30.769 0.00 0.00 0.00 3.06
4931 5385 7.891183 TCAAATAGCTCAAAGTAGTCTGAAC 57.109 36.000 0.00 0.00 0.00 3.18
4935 5389 7.982354 GTGGTATCAAATAGCTCAAAGTAGTCT 59.018 37.037 0.00 0.00 34.47 3.24
5140 5594 4.258543 TCTTTCAGTTTGTTGTTCGGTCT 58.741 39.130 0.00 0.00 0.00 3.85
5142 5596 5.277154 CGTATCTTTCAGTTTGTTGTTCGGT 60.277 40.000 0.00 0.00 0.00 4.69
5149 5603 6.094325 TGTTGTTCCGTATCTTTCAGTTTGTT 59.906 34.615 0.00 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.