Multiple sequence alignment - TraesCS3D01G183100

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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 TraesCS3D01G183100 chr3D 100.000 7793 0 0 1 7793 167772502 167764710 0 14392
1 TraesCS3D01G183100 chr3A 96.211 7839 198 35 1 7793 201499058 201506843 0 12739
2 TraesCS3D01G183100 chr3B 96.582 5149 129 16 2677 7793 242874314 242869181 0 8490
3 TraesCS3D01G183100 chr3B 97.573 2266 52 1 1 2266 242878622 242876360 0 3877
4 TraesCS3D01G183100 chr3B 97.196 428 12 0 2263 2690 242876276 242875849 0 725


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 TraesCS3D01G183100 chr3D 167764710 167772502 7792 True 14392 14392 100.000 1 7793 1 chr3D.!!$R1 7792
1 TraesCS3D01G183100 chr3A 201499058 201506843 7785 False 12739 12739 96.211 1 7793 1 chr3A.!!$F1 7792
2 TraesCS3D01G183100 chr3B 242869181 242878622 9441 True 4364 8490 97.117 1 7793 3 chr3B.!!$R1 7792

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
107 108 0.461135 GCAGCCCCATGGTTATGTTG 59.539 55.000 11.73 5.73 32.21 3.33 F
615 616 1.080995 GCTCTTGCACACTCTAGGCG 61.081 60.000 0.00 0.00 39.41 5.52 F
914 925 1.187974 CTCATTCCAAATGGCAGGCA 58.812 50.000 0.00 0.00 34.44 4.75 F
2071 2092 1.811359 AGAGCAACAGCAGATTTCAGC 59.189 47.619 0.00 0.00 0.00 4.26 F
3095 4754 5.864418 TCCGATAGTGCAGGTTAACTAAT 57.136 39.130 5.42 0.00 32.84 1.73 F
3495 5156 2.699954 ACGAATGCTCACTAAACCCTG 58.300 47.619 0.00 0.00 0.00 4.45 F
3789 5451 3.599343 TGTGATTGATGCACTACAGACC 58.401 45.455 0.00 0.00 37.18 3.85 F
5018 6681 2.874086 TGAATGTAGCCAAGATGCATCG 59.126 45.455 20.67 8.30 0.00 3.84 F
5631 7294 2.827322 TGGAGAATGTGCTTTGGGAATG 59.173 45.455 0.00 0.00 0.00 2.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1878 1899 1.118965 TGTGTGCGGAAAGAGGGAGA 61.119 55.000 0.00 0.00 0.00 3.71 R
2071 2092 1.659601 CTCGAGCATGCTGAAAGTGAG 59.340 52.381 28.27 16.79 35.30 3.51 R
2168 2189 8.435982 CCATTCTCCTTCTATCAAGTTTAGGAT 58.564 37.037 0.00 0.00 31.82 3.24 R
3267 4927 1.041437 GATCTAAGACGGGTCCCCAG 58.959 60.000 1.00 0.00 35.37 4.45 R
4622 6285 1.177401 GCCCTCTCAAATGTTCCACC 58.823 55.000 0.00 0.00 0.00 4.61 R
4912 6575 3.076621 CTGCATTCTGACTGCCAAGTAA 58.923 45.455 16.07 0.00 38.89 2.24 R
5507 7170 1.766494 TTAGCATGCAACCATCCAGG 58.234 50.000 21.98 0.00 45.67 4.45 R
6323 7991 3.806521 CAGGAAAGTCTAATCAGCATCCG 59.193 47.826 0.00 0.00 0.00 4.18 R
7355 9035 2.103432 TGTGTGTGTACGGAAGGTCAAT 59.897 45.455 0.00 0.00 0.00 2.57 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
107 108 0.461135 GCAGCCCCATGGTTATGTTG 59.539 55.000 11.73 5.73 32.21 3.33
296 297 2.380084 TCTTTGATAGTGACACGGCC 57.620 50.000 0.00 0.00 0.00 6.13
615 616 1.080995 GCTCTTGCACACTCTAGGCG 61.081 60.000 0.00 0.00 39.41 5.52
673 674 5.692204 CCAATGTCTCGTTCATATGGTCTAC 59.308 44.000 2.13 0.00 0.00 2.59
830 841 1.503542 GGCATGCTGAAACCGTCTG 59.496 57.895 18.92 0.00 0.00 3.51
914 925 1.187974 CTCATTCCAAATGGCAGGCA 58.812 50.000 0.00 0.00 34.44 4.75
1140 1151 2.151502 TGACACCAACCAAACCACAT 57.848 45.000 0.00 0.00 0.00 3.21
1159 1170 8.331931 ACCACATAAAGTAATGGAAGAGGATA 57.668 34.615 0.00 0.00 36.04 2.59
1277 1288 6.396829 AGGCATTCCTGAAACTATTATTGC 57.603 37.500 0.00 0.00 42.34 3.56
1278 1289 6.131961 AGGCATTCCTGAAACTATTATTGCT 58.868 36.000 0.00 0.00 42.34 3.91
1279 1290 6.264067 AGGCATTCCTGAAACTATTATTGCTC 59.736 38.462 0.00 0.00 42.34 4.26
1427 1441 5.652452 ACTACTCCCAGGAATTTAATTGTGC 59.348 40.000 0.00 0.00 0.00 4.57
1481 1495 7.925993 TGGGTTTGCTTATCTGTTAATTATCG 58.074 34.615 0.00 0.00 0.00 2.92
1671 1692 5.375417 TGCTCAACACAAGGTATTTCATG 57.625 39.130 0.00 0.00 0.00 3.07
1693 1714 8.443176 TCATGAGATTTTTAATAGGAGCCATCT 58.557 33.333 0.00 0.00 0.00 2.90
1770 1791 6.708502 TGATGTATTTTCTGAAGTCGAACCAA 59.291 34.615 0.00 0.00 0.00 3.67
1843 1864 5.589050 GTCAGACAGGTAGTGGAAAAACTTT 59.411 40.000 0.00 0.00 0.00 2.66
1878 1899 4.974645 TGTACTTCATCCACCACTTTCT 57.025 40.909 0.00 0.00 0.00 2.52
2071 2092 1.811359 AGAGCAACAGCAGATTTCAGC 59.189 47.619 0.00 0.00 0.00 4.26
2168 2189 7.049754 GGGTTAAAGAATGTTCCGAGGTAATA 58.950 38.462 0.00 0.00 0.00 0.98
2294 2402 6.899393 TCAAGATATGCTGGTTTTGAACTT 57.101 33.333 0.00 0.00 0.00 2.66
3095 4754 5.864418 TCCGATAGTGCAGGTTAACTAAT 57.136 39.130 5.42 0.00 32.84 1.73
3133 4793 6.208599 TCACACCTTGTCAGTTTCTTTCTTTT 59.791 34.615 0.00 0.00 0.00 2.27
3477 5138 3.056536 TCCTGAATCAGAAGTGGAGAACG 60.057 47.826 12.53 0.00 32.44 3.95
3495 5156 2.699954 ACGAATGCTCACTAAACCCTG 58.300 47.619 0.00 0.00 0.00 4.45
3520 5181 7.337689 TGCTATGCTTGTGTAAAGAGAAATGAT 59.662 33.333 0.00 0.00 0.00 2.45
3525 5186 8.024865 TGCTTGTGTAAAGAGAAATGATTGATG 58.975 33.333 0.00 0.00 0.00 3.07
3789 5451 3.599343 TGTGATTGATGCACTACAGACC 58.401 45.455 0.00 0.00 37.18 3.85
3907 5569 5.046950 AGACAGTGATACCTTCCACTTCTTC 60.047 44.000 0.00 0.00 41.26 2.87
3939 5601 6.036191 GCAGGAATAGTAAGCTTACACAAGTC 59.964 42.308 32.48 24.41 36.12 3.01
4265 5928 6.940430 TCATCATTTCTATGAGCCTATGGA 57.060 37.500 0.00 0.00 43.70 3.41
4277 5940 5.884322 TGAGCCTATGGATCAAATATTGCT 58.116 37.500 1.76 3.75 45.57 3.91
4294 5957 9.643693 AAATATTGCTTGGTTTAGTCAATTCAG 57.356 29.630 0.00 0.00 0.00 3.02
4370 6033 6.489361 AGGCTCAATTAGATCTGCCAAATTAG 59.511 38.462 18.68 9.81 42.46 1.73
4382 6045 5.538053 TCTGCCAAATTAGTGAACATTCCAA 59.462 36.000 0.00 0.00 0.00 3.53
4426 6089 3.749226 TCATGCACACACCATGAGTAAA 58.251 40.909 0.00 0.00 42.88 2.01
4434 6097 4.707448 ACACACCATGAGTAAACCAACAAA 59.293 37.500 0.00 0.00 0.00 2.83
4435 6098 5.040635 CACACCATGAGTAAACCAACAAAC 58.959 41.667 0.00 0.00 0.00 2.93
4446 6109 8.051901 AGTAAACCAACAAACTTAGATATGGC 57.948 34.615 0.00 0.00 0.00 4.40
4622 6285 6.210078 AGAAATTAAGAAGCTCGAGGATACG 58.790 40.000 15.58 0.00 46.39 3.06
4912 6575 5.250200 TGTAAGATTTCCAGTAAATGCCGT 58.750 37.500 0.00 0.00 37.93 5.68
5018 6681 2.874086 TGAATGTAGCCAAGATGCATCG 59.126 45.455 20.67 8.30 0.00 3.84
5229 6892 3.520691 AAAGGGTTCTAACTGTTCCCC 57.479 47.619 10.50 9.49 38.97 4.81
5543 7206 3.012518 GCTAAAGCTGCCAGAATCTGAA 58.987 45.455 12.53 0.00 38.21 3.02
5553 7216 5.748402 TGCCAGAATCTGAACTCAATACAT 58.252 37.500 12.53 0.00 32.44 2.29
5554 7217 6.888105 TGCCAGAATCTGAACTCAATACATA 58.112 36.000 12.53 0.00 32.44 2.29
5631 7294 2.827322 TGGAGAATGTGCTTTGGGAATG 59.173 45.455 0.00 0.00 0.00 2.67
5664 7327 4.275936 GCGACAAAAGGGCATTATACATCT 59.724 41.667 0.00 0.00 0.00 2.90
5811 7477 5.764686 GGGCAAAAAGATCAAAATTCCAGTT 59.235 36.000 0.00 0.00 0.00 3.16
6323 7991 7.863375 ACACGAGACTTTATGATTGCTATCTAC 59.137 37.037 9.55 0.00 0.00 2.59
6329 7997 6.591834 ACTTTATGATTGCTATCTACGGATGC 59.408 38.462 9.55 0.00 33.71 3.91
6332 8000 3.573967 TGATTGCTATCTACGGATGCTGA 59.426 43.478 9.55 0.00 33.71 4.26
6383 8051 5.632347 GTGAATTCAGCAAAATCAAGTCCTG 59.368 40.000 8.80 0.00 0.00 3.86
6445 8124 4.261801 ACTAAGGAAACAACGATGGGATG 58.738 43.478 0.00 0.00 0.00 3.51
6613 8292 4.379918 GCCTAAATTTCCACTTCTGCACTC 60.380 45.833 0.00 0.00 0.00 3.51
6998 8678 8.311650 AGTGTATGAGTGAACAAACTATGAAC 57.688 34.615 0.00 0.00 0.00 3.18
7226 8906 1.908483 CAGGTAAGGGGCTCCTGTC 59.092 63.158 5.46 1.49 44.07 3.51
7240 8920 4.061596 GCTCCTGTCAGTTAATAGATGGC 58.938 47.826 0.00 0.00 0.00 4.40
7291 8971 1.108776 AGGCTCGGTTAGTTCGCATA 58.891 50.000 0.00 0.00 0.00 3.14
7323 9003 8.757982 ACAAATCTCTCATATAACAAGCCAAT 57.242 30.769 0.00 0.00 0.00 3.16
7325 9005 7.756395 AATCTCTCATATAACAAGCCAATGG 57.244 36.000 0.00 0.00 0.00 3.16
7355 9035 6.499699 ACCATCAAGGATCAGCTATCTGAATA 59.500 38.462 0.00 0.00 45.94 1.75
7477 9170 6.866480 ACATAACCAATGGATTTCATGTCAC 58.134 36.000 6.16 0.00 40.16 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
107 108 0.612453 AGGACTCGGAGGTTGGAGAC 60.612 60.000 10.23 0.00 34.40 3.36
296 297 1.500474 TCCCTCCAAGGCAGTCTATG 58.500 55.000 0.00 0.00 32.73 2.23
521 522 1.957877 GGAGTTCCCAGGTCTCTATCG 59.042 57.143 9.92 0.00 34.14 2.92
543 544 5.291971 CCCATACATTGCTTAAATCCTTGC 58.708 41.667 0.00 0.00 0.00 4.01
615 616 2.412847 GCACTTCCATACTGCGTCAAAC 60.413 50.000 0.00 0.00 0.00 2.93
624 625 4.471386 AGTTCATACCTGCACTTCCATACT 59.529 41.667 0.00 0.00 0.00 2.12
673 674 6.323203 AGAAATTTCAAGACACCACATCTG 57.677 37.500 19.99 0.00 0.00 2.90
830 841 5.403466 GTCAAAGTCAGATGCAATTCAAACC 59.597 40.000 0.00 0.00 0.00 3.27
914 925 3.213206 TCATTCTTTGCTGGTGACACT 57.787 42.857 5.39 0.00 35.60 3.55
1385 1399 7.360691 GGGAGTAGTAAATTCGACAAAAGTTCC 60.361 40.741 0.00 0.00 0.00 3.62
1481 1495 1.285078 ACTTCCTGGGGAATAAGGCAC 59.715 52.381 0.00 0.00 41.23 5.01
1671 1692 9.958234 GAAAAGATGGCTCCTATTAAAAATCTC 57.042 33.333 0.00 0.00 0.00 2.75
1770 1791 9.829507 GTAGCCATCTATAGCTGATTTTATCAT 57.170 33.333 5.14 0.00 40.28 2.45
1878 1899 1.118965 TGTGTGCGGAAAGAGGGAGA 61.119 55.000 0.00 0.00 0.00 3.71
2071 2092 1.659601 CTCGAGCATGCTGAAAGTGAG 59.340 52.381 28.27 16.79 35.30 3.51
2168 2189 8.435982 CCATTCTCCTTCTATCAAGTTTAGGAT 58.564 37.037 0.00 0.00 31.82 3.24
2287 2395 8.740123 TCTATTTGTTACAAGTGGAAGTTCAA 57.260 30.769 5.01 0.00 0.00 2.69
2294 2402 8.783093 CATTGTCTTCTATTTGTTACAAGTGGA 58.217 33.333 2.83 2.83 31.09 4.02
3095 4754 7.676004 TGACAAGGTGTGAAGATATACAGAAA 58.324 34.615 0.00 0.00 0.00 2.52
3267 4927 1.041437 GATCTAAGACGGGTCCCCAG 58.959 60.000 1.00 0.00 35.37 4.45
3374 5035 9.154847 AGGCATGCTTTCTTCAATAAAATAAAC 57.845 29.630 18.92 0.00 0.00 2.01
3477 5138 2.716217 AGCAGGGTTTAGTGAGCATTC 58.284 47.619 0.00 0.00 0.00 2.67
3495 5156 7.076842 TCATTTCTCTTTACACAAGCATAGC 57.923 36.000 0.00 0.00 0.00 2.97
3520 5181 5.465390 CGTCCTGTTCTGTTTCTAACATCAA 59.535 40.000 0.00 0.00 41.26 2.57
3525 5186 3.986277 TCCGTCCTGTTCTGTTTCTAAC 58.014 45.455 0.00 0.00 0.00 2.34
3533 5194 2.283298 CAATCCATCCGTCCTGTTCTG 58.717 52.381 0.00 0.00 0.00 3.02
3576 5238 9.926158 ATCAAACTGTTGCATAAATGAATACAA 57.074 25.926 0.00 0.00 34.50 2.41
3907 5569 5.741388 AGCTTACTATTCCTGCAAAATCG 57.259 39.130 0.00 0.00 0.00 3.34
4024 5686 5.551305 TGATACAGCATGGTAAGCTACAT 57.449 39.130 0.00 0.00 43.62 2.29
4032 5694 5.096443 TGTGAACATGATACAGCATGGTA 57.904 39.130 11.76 0.00 45.68 3.25
4277 5940 7.362056 GCATTAGCTCTGAATTGACTAAACCAA 60.362 37.037 0.00 0.00 37.91 3.67
4294 5957 4.732784 TCGAAATGTTTTGGCATTAGCTC 58.267 39.130 0.00 0.00 38.03 4.09
4352 6015 8.757982 ATGTTCACTAATTTGGCAGATCTAAT 57.242 30.769 0.00 0.00 0.00 1.73
4370 6033 9.649024 CATTGTGTTAATTTTTGGAATGTTCAC 57.351 29.630 0.00 0.00 0.00 3.18
4382 6045 9.669887 ATGAATGCATACCATTGTGTTAATTTT 57.330 25.926 0.00 0.00 44.02 1.82
4426 6089 8.644374 TTAAAGCCATATCTAAGTTTGTTGGT 57.356 30.769 0.00 0.00 0.00 3.67
4622 6285 1.177401 GCCCTCTCAAATGTTCCACC 58.823 55.000 0.00 0.00 0.00 4.61
4912 6575 3.076621 CTGCATTCTGACTGCCAAGTAA 58.923 45.455 16.07 0.00 38.89 2.24
5018 6681 3.192844 TCACCTGTTTGATCTCGTACTCC 59.807 47.826 0.00 0.00 0.00 3.85
5201 6864 4.953579 ACAGTTAGAACCCTTTTGCTTTGA 59.046 37.500 0.00 0.00 0.00 2.69
5229 6892 9.956720 ATTGAAAGTTTCTTCTTCAGTTACATG 57.043 29.630 16.33 0.00 0.00 3.21
5507 7170 1.766494 TTAGCATGCAACCATCCAGG 58.234 50.000 21.98 0.00 45.67 4.45
5631 7294 3.616821 GCCCTTTTGTCGCCAAATAAATC 59.383 43.478 0.00 0.00 40.14 2.17
5664 7327 5.775195 ACATCAACCGATCCAGATATCACTA 59.225 40.000 5.32 0.00 0.00 2.74
5714 7380 2.355010 ATGCCAAGCCATTCTCCTAC 57.645 50.000 0.00 0.00 0.00 3.18
5811 7477 8.884726 TGTTAATGCATATGAAAGCGTTAAGTA 58.115 29.630 6.97 0.00 46.70 2.24
5818 7484 8.559222 TGTTTATGTTAATGCATATGAAAGCG 57.441 30.769 6.97 0.00 32.16 4.68
6113 7781 4.463209 CAGCAGTTACATTAAACCACACG 58.537 43.478 0.00 0.00 0.00 4.49
6323 7991 3.806521 CAGGAAAGTCTAATCAGCATCCG 59.193 47.826 0.00 0.00 0.00 4.18
6383 8051 4.171234 TCCCTCCATGGAATTATCCTCTC 58.829 47.826 17.00 0.00 46.70 3.20
6613 8292 8.647796 TGTAGGGACTATATGTACATTGAAAGG 58.352 37.037 14.77 2.10 45.60 3.11
6998 8678 7.751732 TGTTTCAGGATATGTCAAATTTCTCG 58.248 34.615 0.00 0.00 0.00 4.04
7158 8838 8.814235 CATGGCTTTGAATTTTAGCTAAGAATG 58.186 33.333 6.24 0.00 35.30 2.67
7226 8906 5.063880 GGTAAGGGTGCCATCTATTAACTG 58.936 45.833 0.00 0.00 0.00 3.16
7240 8920 2.169978 GCTACAGGTAAGGGTAAGGGTG 59.830 54.545 0.00 0.00 0.00 4.61
7277 8957 4.565166 TGTTCTCATTATGCGAACTAACCG 59.435 41.667 22.95 0.00 41.29 4.44
7325 9005 3.878778 AGCTGATCCTTGATGGTGTAAC 58.121 45.455 0.00 0.00 37.07 2.50
7355 9035 2.103432 TGTGTGTGTACGGAAGGTCAAT 59.897 45.455 0.00 0.00 0.00 2.57
7477 9170 5.818136 AAATTATTGTGTGAGATCACCGG 57.182 39.130 10.34 0.00 45.88 5.28
7496 9189 9.998106 ATCCTTGCTTACATAAGATACGTAAAT 57.002 29.630 0.00 0.00 35.33 1.40


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

AutoCloner maintained by Alex Coulton.