Multiple sequence alignment - TraesCS1A01G184200

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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 TraesCS1A01G184200 chr1A 100.000 3536 0 0 1 3536 334076924 334073389 0.000000e+00 6530
1 TraesCS1A01G184200 chr2D 97.715 3239 69 4 1 3235 635037258 635040495 0.000000e+00 5566
2 TraesCS1A01G184200 chr7B 97.684 3239 69 2 1 3233 743066303 743069541 0.000000e+00 5561
3 TraesCS1A01G184200 chr7B 96.382 304 8 2 3234 3536 743073145 743073446 6.820000e-137 497
4 TraesCS1A01G184200 chr3D 97.654 3239 72 3 1 3235 202611944 202615182 0.000000e+00 5557
5 TraesCS1A01G184200 chr5A 97.595 3243 70 3 1 3235 16623277 16620035 0.000000e+00 5550
6 TraesCS1A01G184200 chr7A 97.593 3240 72 3 1 3235 671960570 671957332 0.000000e+00 5546
7 TraesCS1A01G184200 chr7A 97.529 3238 74 4 1 3235 120828850 120825616 0.000000e+00 5531
8 TraesCS1A01G184200 chr7A 96.040 303 10 1 3234 3536 120918865 120918565 3.170000e-135 492
9 TraesCS1A01G184200 chr4D 97.532 3242 71 4 1 3235 123367640 123370879 0.000000e+00 5535
10 TraesCS1A01G184200 chr4D 95.395 304 11 2 3234 3536 123374638 123374939 6.870000e-132 481
11 TraesCS1A01G184200 chr4D 95.395 304 8 2 3234 3536 123585429 123585727 2.470000e-131 479
12 TraesCS1A01G184200 chr2A 97.502 3242 72 4 1 3235 735172797 735176036 0.000000e+00 5529
13 TraesCS1A01G184200 chr4A 97.467 3237 78 4 1 3235 432419669 432422903 0.000000e+00 5520
14 TraesCS1A01G184200 chr4A 97.039 304 8 1 3234 3536 552102096 552101793 8.760000e-141 510
15 TraesCS1A01G184200 chr7D 96.382 304 8 2 3234 3536 382004502 382004201 6.820000e-137 497
16 TraesCS1A01G184200 chr7D 95.380 303 10 1 3234 3536 297148473 297148771 2.470000e-131 479
17 TraesCS1A01G184200 chr6B 96.370 303 9 2 3234 3535 525685045 525685346 6.820000e-137 497
18 TraesCS1A01G184200 chr3B 95.425 306 9 3 3234 3536 201628681 201628378 1.910000e-132 483


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 TraesCS1A01G184200 chr1A 334073389 334076924 3535 True 6530 6530 100.0000 1 3536 1 chr1A.!!$R1 3535
1 TraesCS1A01G184200 chr2D 635037258 635040495 3237 False 5566 5566 97.7150 1 3235 1 chr2D.!!$F1 3234
2 TraesCS1A01G184200 chr7B 743066303 743073446 7143 False 3029 5561 97.0330 1 3536 2 chr7B.!!$F1 3535
3 TraesCS1A01G184200 chr3D 202611944 202615182 3238 False 5557 5557 97.6540 1 3235 1 chr3D.!!$F1 3234
4 TraesCS1A01G184200 chr5A 16620035 16623277 3242 True 5550 5550 97.5950 1 3235 1 chr5A.!!$R1 3234
5 TraesCS1A01G184200 chr7A 671957332 671960570 3238 True 5546 5546 97.5930 1 3235 1 chr7A.!!$R3 3234
6 TraesCS1A01G184200 chr7A 120825616 120828850 3234 True 5531 5531 97.5290 1 3235 1 chr7A.!!$R1 3234
7 TraesCS1A01G184200 chr4D 123367640 123374939 7299 False 3008 5535 96.4635 1 3536 2 chr4D.!!$F2 3535
8 TraesCS1A01G184200 chr2A 735172797 735176036 3239 False 5529 5529 97.5020 1 3235 1 chr2A.!!$F1 3234
9 TraesCS1A01G184200 chr4A 432419669 432422903 3234 False 5520 5520 97.4670 1 3235 1 chr4A.!!$F1 3234


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
91 92 0.526662 ACGCAGTACAGACAGTAGGC 59.473 55.0 0.00 0.0 41.94 3.93 F
1194 1200 0.744874 TCGATCCTTCTACGGCCAAG 59.255 55.0 2.24 0.0 0.00 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1496 1502 2.042831 CCCCTGCAGAGGAAAAGCG 61.043 63.158 17.39 0.0 42.93 4.68 R
2638 2651 0.958382 TGGCGCCGCTCACTAAATTT 60.958 50.000 23.90 0.0 0.00 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
91 92 0.526662 ACGCAGTACAGACAGTAGGC 59.473 55.000 0.00 0.0 41.94 3.93
462 464 3.403038 CTCCGTTGGTGACTTTCTGATT 58.597 45.455 0.00 0.0 0.00 2.57
502 504 1.176527 CCCAACGCCATTCATCTTGT 58.823 50.000 0.00 0.0 0.00 3.16
595 597 5.104151 TGGCACCATCATCTCATTACCTTAA 60.104 40.000 0.00 0.0 0.00 1.85
607 609 9.768215 ATCTCATTACCTTAATTTTTCCCTTCA 57.232 29.630 0.00 0.0 0.00 3.02
850 856 2.254152 AGCCTCATGACTTCCCACTA 57.746 50.000 0.00 0.0 0.00 2.74
893 899 5.104941 CCCACCTACTCACTCATCAATTACA 60.105 44.000 0.00 0.0 0.00 2.41
1031 1037 6.363577 ACATTTCTGTGAATGCTATTACGG 57.636 37.500 0.00 0.0 39.97 4.02
1052 1058 5.104193 ACGGTCTAAGTGGTCCTATTCTCTA 60.104 44.000 0.00 0.0 0.00 2.43
1081 1087 4.627058 GCTAGGAAGCATTACTCCTCTTC 58.373 47.826 0.00 0.0 28.40 2.87
1123 1129 5.524971 AAGACCGATACGATTGATTGGTA 57.475 39.130 0.00 0.0 40.59 3.25
1194 1200 0.744874 TCGATCCTTCTACGGCCAAG 59.255 55.000 2.24 0.0 0.00 3.61
1426 1432 4.622695 GCATGCTGGATCCTCTACTATTCC 60.623 50.000 14.23 0.0 0.00 3.01
1496 1502 3.735237 TCTTCTATTCGCTGGGATCAC 57.265 47.619 0.00 0.0 0.00 3.06
1633 1639 2.285834 GCATAGCATTTCTGGTCGAACG 60.286 50.000 0.00 0.0 34.31 3.95
2029 2042 8.573035 CCTTAGGATAAGTTGCTAAAACAAACA 58.427 33.333 0.00 0.0 37.74 2.83
2030 2043 9.612620 CTTAGGATAAGTTGCTAAAACAAACAG 57.387 33.333 0.00 0.0 37.74 3.16
2321 2334 1.266989 GTCAAGGCGGAAAAGACAAGG 59.733 52.381 0.00 0.0 0.00 3.61
2417 2430 1.986413 CCTGAGAAGGGAGTGGGTG 59.014 63.158 0.00 0.0 0.00 4.61
2454 2467 2.158579 ACCAACTACCACCGGTCAATTT 60.159 45.455 2.59 0.0 37.09 1.82
2511 2524 0.464452 GGGTATGGGGTTCGAGACAG 59.536 60.000 0.00 0.0 0.00 3.51
2533 2546 5.531659 CAGAGAAAGATCAAGGCAGCATATT 59.468 40.000 0.00 0.0 0.00 1.28
2563 2576 9.455144 TTTTCCTATATACTTTACTGGGATCCA 57.545 33.333 15.23 0.0 0.00 3.41
2882 2896 7.707035 CACTCCTTTCATTTATACTCTAAGCGT 59.293 37.037 0.00 0.0 0.00 5.07
2967 2981 2.848678 ACTCCTCAGTAGCCCATACA 57.151 50.000 0.00 0.0 36.79 2.29
3101 3115 3.847081 ACCTACTAGCAATAGGGGAGAC 58.153 50.000 9.17 0.0 43.19 3.36
3313 7095 2.742372 GTGCTTGCGATGGGACGT 60.742 61.111 0.00 0.0 35.59 4.34
3395 7178 5.068215 TCCATTTCTTTGTTACCCCAGAA 57.932 39.130 0.00 0.0 0.00 3.02
3436 7219 0.984995 AGAGAAAGAAAGGACGGGGG 59.015 55.000 0.00 0.0 0.00 5.40
3478 7261 0.536687 ACTTCTCGACCGTGTCTCCA 60.537 55.000 3.15 0.0 0.00 3.86
3496 7279 1.202651 CCAAGGGACAGTTGAACGAGT 60.203 52.381 0.00 0.0 0.00 4.18
3518 7301 1.001020 TCATGAATGCTGCCGGGTT 60.001 52.632 2.18 0.0 0.00 4.11
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
91 92 2.161609 GTCAGATAAACCAAACTGCCGG 59.838 50.000 0.00 0.00 0.00 6.13
426 428 3.577649 ACGGAGCCATACAATCTATCG 57.422 47.619 0.00 0.00 0.00 2.92
462 464 3.198872 GGTTTTTCAAATGAAACCCGCA 58.801 40.909 8.04 0.00 45.73 5.69
502 504 2.487762 GCATGAAAGACCGGATTTGACA 59.512 45.455 9.46 4.68 0.00 3.58
595 597 3.230976 AGCCGAAGTTGAAGGGAAAAAT 58.769 40.909 0.00 0.00 0.00 1.82
607 609 2.017049 GCATTGGTCATAGCCGAAGTT 58.983 47.619 0.00 0.00 0.00 2.66
850 856 4.715130 TAGGTGCACCCCTCGCCT 62.715 66.667 32.29 14.48 45.54 5.52
893 899 1.303309 GTGCAAGTCAGCTGAACACT 58.697 50.000 20.19 9.57 34.99 3.55
1007 1013 6.183360 ACCGTAATAGCATTCACAGAAATGTG 60.183 38.462 1.95 1.95 38.60 3.21
1028 1034 3.952967 GAGAATAGGACCACTTAGACCGT 59.047 47.826 0.00 0.00 0.00 4.83
1031 1037 6.434965 GGGATAGAGAATAGGACCACTTAGAC 59.565 46.154 0.00 0.00 0.00 2.59
1081 1087 7.912250 CGGTCTTATTGAAGAATTTGGAATGAG 59.088 37.037 0.00 0.00 43.38 2.90
1194 1200 4.037923 TGAAGGCTTTCCACAAATTGAGAC 59.962 41.667 6.06 0.00 32.09 3.36
1426 1432 2.574322 CACGCTTTCGGAAAGAACATG 58.426 47.619 29.49 17.73 41.02 3.21
1496 1502 2.042831 CCCCTGCAGAGGAAAAGCG 61.043 63.158 17.39 0.00 42.93 4.68
1549 1555 6.401394 GGGACCTTTACTACTTTACGACAAT 58.599 40.000 0.00 0.00 0.00 2.71
1633 1639 3.982576 AAAAAGATGTGTGGTTCGGTC 57.017 42.857 0.00 0.00 0.00 4.79
2029 2042 2.609920 GGGTCGATCCTCCCCTCT 59.390 66.667 7.71 0.00 37.89 3.69
2030 2043 2.913060 CGGGTCGATCCTCCCCTC 60.913 72.222 14.05 0.00 40.54 4.30
2321 2334 4.381411 GCCCTTGTCATTAGACCACTATC 58.619 47.826 0.00 0.00 44.33 2.08
2415 2428 2.743928 CGAAGCTCCAGTGGGCAC 60.744 66.667 20.50 14.01 0.00 5.01
2417 2430 2.435059 GTCGAAGCTCCAGTGGGC 60.435 66.667 9.92 11.84 0.00 5.36
2511 2524 6.709846 ACTAATATGCTGCCTTGATCTTTCTC 59.290 38.462 0.00 0.00 0.00 2.87
2638 2651 0.958382 TGGCGCCGCTCACTAAATTT 60.958 50.000 23.90 0.00 0.00 1.82
3101 3115 2.967459 TGTTGCGACATGCTAAGTTG 57.033 45.000 1.50 0.00 46.63 3.16
3129 3143 1.730064 GTTTTGCTGACGCCTCGAATA 59.270 47.619 0.00 0.00 34.43 1.75
3208 3222 2.973899 CTGCTGTCTGCGTAGGGT 59.026 61.111 0.00 0.00 46.63 4.34
3240 7022 0.600057 GGTAGTTCAACGGACGGTCT 59.400 55.000 8.23 0.00 0.00 3.85
3313 7095 6.455647 CATTACTTATGAGGGAAGTCGCATA 58.544 40.000 0.00 0.00 38.16 3.14
3478 7261 1.760613 TCACTCGTTCAACTGTCCCTT 59.239 47.619 0.00 0.00 0.00 3.95
3496 7279 0.745486 CCGGCAGCATTCATGAGTCA 60.745 55.000 0.00 0.00 0.00 3.41



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

AutoCloner maintained by Alex Coulton.