Multiple sequence alignment - TraesCS6D01G037200

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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 TraesCS6D01G037200 chr6D 100.000 3527 0 0 1 3527 15386158 15382632 0.000000e+00 6514
1 TraesCS6D01G037200 chr6D 93.825 1927 100 9 806 2729 15419808 15417898 0.000000e+00 2881
2 TraesCS6D01G037200 chr6D 84.878 1759 251 11 799 2549 15799469 15797718 0.000000e+00 1760
3 TraesCS6D01G037200 chr6D 85.625 480 50 7 3058 3527 15417710 15417240 1.470000e-133 486
4 TraesCS6D01G037200 chr6D 81.461 356 39 14 463 802 15420192 15419848 2.090000e-67 267
5 TraesCS6D01G037200 chr6D 82.888 187 21 6 2835 3021 15417885 15417710 1.310000e-34 158
6 TraesCS6D01G037200 chr6A 92.835 3545 181 33 5 3524 15954394 15950898 0.000000e+00 5072
7 TraesCS6D01G037200 chr6A 90.657 2237 154 18 798 3031 16100366 16098182 0.000000e+00 2922
8 TraesCS6D01G037200 chr6A 85.566 1739 239 9 799 2530 16400901 16399168 0.000000e+00 1810
9 TraesCS6D01G037200 chr6A 85.081 1736 239 14 799 2523 16410227 16408501 0.000000e+00 1753
10 TraesCS6D01G037200 chr6A 86.770 514 48 9 3023 3527 16088874 16088372 3.980000e-154 555
11 TraesCS6D01G037200 chr6A 83.807 352 30 11 469 802 16100740 16100398 3.420000e-80 309
12 TraesCS6D01G037200 chr6B 93.165 2297 109 23 645 2936 27124735 27122482 0.000000e+00 3328
13 TraesCS6D01G037200 chr6B 92.700 1863 119 8 797 2657 27171441 27169594 0.000000e+00 2671
14 TraesCS6D01G037200 chr6B 89.731 1597 146 15 1071 2655 27181753 27180163 0.000000e+00 2025
15 TraesCS6D01G037200 chr6B 95.517 513 23 0 3015 3527 27122461 27121949 0.000000e+00 821
16 TraesCS6D01G037200 chr6B 89.506 648 44 11 9 644 27125470 27124835 0.000000e+00 798
17 TraesCS6D01G037200 chr6B 81.935 703 72 28 2835 3527 27169489 27168832 8.610000e-151 544
18 TraesCS6D01G037200 chr6B 82.353 357 38 9 463 802 27171820 27171472 1.600000e-73 287
19 TraesCS6D01G037200 chr1A 80.586 273 39 11 1 261 507075423 507075693 7.720000e-47 198
20 TraesCS6D01G037200 chr7D 82.805 221 31 4 74 292 17422064 17422279 1.290000e-44 191
21 TraesCS6D01G037200 chr7A 82.589 224 32 4 74 292 16725847 16726068 1.290000e-44 191
22 TraesCS6D01G037200 chr5A 80.144 277 37 12 1 261 74670739 74671013 1.290000e-44 191
23 TraesCS6D01G037200 chr5A 79.061 277 40 12 1 261 546802446 546802720 1.300000e-39 174
24 TraesCS6D01G037200 chr2D 80.913 241 39 7 10 243 186756402 186756642 2.160000e-42 183
25 TraesCS6D01G037200 chr5B 78.986 276 46 10 1 266 588793054 588793327 1.010000e-40 178
26 TraesCS6D01G037200 chr5B 78.799 283 40 15 1 266 586912992 586912713 4.680000e-39 172


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 TraesCS6D01G037200 chr6D 15382632 15386158 3526 True 6514.000000 6514 100.000000 1 3527 1 chr6D.!!$R1 3526
1 TraesCS6D01G037200 chr6D 15797718 15799469 1751 True 1760.000000 1760 84.878000 799 2549 1 chr6D.!!$R2 1750
2 TraesCS6D01G037200 chr6D 15417240 15420192 2952 True 948.000000 2881 85.949750 463 3527 4 chr6D.!!$R3 3064
3 TraesCS6D01G037200 chr6A 15950898 15954394 3496 True 5072.000000 5072 92.835000 5 3524 1 chr6A.!!$R1 3519
4 TraesCS6D01G037200 chr6A 16399168 16400901 1733 True 1810.000000 1810 85.566000 799 2530 1 chr6A.!!$R3 1731
5 TraesCS6D01G037200 chr6A 16408501 16410227 1726 True 1753.000000 1753 85.081000 799 2523 1 chr6A.!!$R4 1724
6 TraesCS6D01G037200 chr6A 16098182 16100740 2558 True 1615.500000 2922 87.232000 469 3031 2 chr6A.!!$R5 2562
7 TraesCS6D01G037200 chr6A 16088372 16088874 502 True 555.000000 555 86.770000 3023 3527 1 chr6A.!!$R2 504
8 TraesCS6D01G037200 chr6B 27180163 27181753 1590 True 2025.000000 2025 89.731000 1071 2655 1 chr6B.!!$R1 1584
9 TraesCS6D01G037200 chr6B 27121949 27125470 3521 True 1649.000000 3328 92.729333 9 3527 3 chr6B.!!$R2 3518
10 TraesCS6D01G037200 chr6B 27168832 27171820 2988 True 1167.333333 2671 85.662667 463 3527 3 chr6B.!!$R3 3064

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
927 1109 1.199615 ACCTAGCTCTTGCCTCTTCC 58.8 55.0 0.0 0.0 40.8 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2907 3117 2.434336 TGCTAGAATACGCCATTGACCT 59.566 45.455 0.0 0.0 0.0 3.85 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
38 39 8.807948 AGCTCAAATGCTCCTAGTATTAAAAA 57.192 30.769 0.00 0.00 39.34 1.94
139 153 8.377681 GCAAAGTTTCATCATGTAATCACATTG 58.622 33.333 0.00 0.00 42.98 2.82
179 193 2.163010 ACAATCAGAGCTCCAAAATGCG 59.837 45.455 10.93 0.00 0.00 4.73
205 219 5.938322 TGAAAGTAACATTTTCGGAGCATC 58.062 37.500 0.00 0.00 37.36 3.91
206 220 5.471797 TGAAAGTAACATTTTCGGAGCATCA 59.528 36.000 0.00 0.00 37.36 3.07
262 276 7.809331 TCTGATTACATCATGAAACTTTGCAAC 59.191 33.333 0.00 0.00 38.85 4.17
265 279 4.370917 ACATCATGAAACTTTGCAACCAC 58.629 39.130 0.00 0.00 0.00 4.16
313 332 8.877864 TCACCACTTTATTGAATTTACCATCT 57.122 30.769 0.00 0.00 0.00 2.90
320 339 5.818136 ATTGAATTTACCATCTGTGACCG 57.182 39.130 0.00 0.00 0.00 4.79
344 363 5.064325 GGATTAAATGCGTTCGAAAGTACCT 59.936 40.000 12.65 2.13 0.00 3.08
345 364 5.927954 TTAAATGCGTTCGAAAGTACCTT 57.072 34.783 12.65 7.95 0.00 3.50
346 365 4.823790 AAATGCGTTCGAAAGTACCTTT 57.176 36.364 12.65 4.28 36.29 3.11
347 366 4.823790 AATGCGTTCGAAAGTACCTTTT 57.176 36.364 12.65 0.00 33.49 2.27
400 421 5.262804 AGATACTCCACGTCCTACTTTTCT 58.737 41.667 0.00 0.00 0.00 2.52
460 481 5.994416 AGGTTGGTCATAGTGGGAAATAT 57.006 39.130 0.00 0.00 0.00 1.28
520 544 9.276590 TGCACATACCTAAGATATGAGAAAATG 57.723 33.333 0.00 0.00 34.65 2.32
532 556 8.689972 AGATATGAGAAAATGTCCAATGGAAAC 58.310 33.333 2.31 0.00 31.38 2.78
660 800 8.898792 GTTTTATAACCTGTTAAAGCTCAAACG 58.101 33.333 6.64 0.00 0.00 3.60
671 811 7.968956 TGTTAAAGCTCAAACGTATTTTTCACA 59.031 29.630 0.00 0.00 0.00 3.58
672 812 8.800031 GTTAAAGCTCAAACGTATTTTTCACAA 58.200 29.630 0.00 0.00 0.00 3.33
674 814 6.131544 AGCTCAAACGTATTTTTCACAAGT 57.868 33.333 0.00 0.00 0.00 3.16
700 840 5.243730 ACCATGATAACTTCAACCAAACAGG 59.756 40.000 0.00 0.00 38.03 4.00
701 841 4.846779 TGATAACTTCAACCAAACAGGC 57.153 40.909 0.00 0.00 43.14 4.85
702 842 4.211125 TGATAACTTCAACCAAACAGGCA 58.789 39.130 0.00 0.00 43.14 4.75
703 843 4.646945 TGATAACTTCAACCAAACAGGCAA 59.353 37.500 0.00 0.00 43.14 4.52
704 844 3.971245 AACTTCAACCAAACAGGCAAA 57.029 38.095 0.00 0.00 43.14 3.68
705 845 3.245518 ACTTCAACCAAACAGGCAAAC 57.754 42.857 0.00 0.00 43.14 2.93
706 846 2.564947 ACTTCAACCAAACAGGCAAACA 59.435 40.909 0.00 0.00 43.14 2.83
927 1109 1.199615 ACCTAGCTCTTGCCTCTTCC 58.800 55.000 0.00 0.00 40.80 3.46
1375 1559 1.626654 GGTGTTCTGCATGTCCGTCG 61.627 60.000 0.00 0.00 0.00 5.12
1602 1786 2.733593 GCGACTCGTTTCACCGCT 60.734 61.111 0.00 0.00 42.24 5.52
1971 2155 0.396811 ACCTTGGTGCTCGCTACTTT 59.603 50.000 0.00 0.00 0.00 2.66
2190 2374 4.722700 ATGACCGGTGCAGGTGGC 62.723 66.667 14.63 0.00 46.09 5.01
2698 2900 3.221771 GGGGCTTGTATCATGTTATGCA 58.778 45.455 0.00 0.00 0.00 3.96
2823 3026 8.810427 GCTTACCATGTGATTAATTTCATTGTG 58.190 33.333 14.66 6.20 0.00 3.33
2833 3036 7.492020 TGATTAATTTCATTGTGCCTTGCATAC 59.508 33.333 0.00 0.00 41.91 2.39
2847 3050 5.765176 CCTTGCATACATACCATGTGATTG 58.235 41.667 2.07 0.00 44.60 2.67
2904 3114 9.468532 TGTTACGAGAAAGATCAATATGAGATG 57.531 33.333 0.00 0.00 0.00 2.90
2969 3179 2.294074 ACTTCTTGCACGCCAAAGTAA 58.706 42.857 0.00 0.00 31.94 2.24
2976 3186 0.767687 CACGCCAAAGTAAAAACGCG 59.232 50.000 3.53 3.53 44.78 6.01
2978 3188 1.468895 CGCCAAAGTAAAAACGCGTT 58.531 45.000 20.79 20.79 35.15 4.84
3142 3353 2.601398 CGATGGCGGTGCTATGCAG 61.601 63.158 0.00 0.00 40.08 4.41
3211 3426 0.036952 ACCTCTCAACAGCGACATGG 60.037 55.000 0.00 0.00 0.00 3.66
3398 3614 0.386352 TCGATCGACACGTGGTTCAC 60.386 55.000 21.57 7.32 0.00 3.18
3453 3669 5.651530 GACGAAGACATGACTGGATCTAAA 58.348 41.667 0.00 0.00 0.00 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 3.684037 AGCATTTGAGCTCGAGCGTGA 62.684 52.381 30.39 18.26 42.18 4.35
5 6 1.357258 AGCATTTGAGCTCGAGCGTG 61.357 55.000 30.39 23.34 42.18 5.34
7 8 3.791539 AGCATTTGAGCTCGAGCG 58.208 55.556 30.39 16.74 42.18 5.03
87 93 9.474920 CAAGCACTCCAAACATTTCTTAAAATA 57.525 29.630 0.00 0.00 33.27 1.40
89 95 6.257630 GCAAGCACTCCAAACATTTCTTAAAA 59.742 34.615 0.00 0.00 0.00 1.52
159 173 2.163010 ACGCATTTTGGAGCTCTGATTG 59.837 45.455 14.64 6.75 0.00 2.67
160 174 2.440409 ACGCATTTTGGAGCTCTGATT 58.560 42.857 14.64 0.00 0.00 2.57
161 175 2.119801 ACGCATTTTGGAGCTCTGAT 57.880 45.000 14.64 0.00 0.00 2.90
179 193 5.974751 TGCTCCGAAAATGTTACTTTCAAAC 59.025 36.000 0.00 0.00 33.25 2.93
294 308 7.910162 CGGTCACAGATGGTAAATTCAATAAAG 59.090 37.037 0.00 0.00 0.00 1.85
313 332 2.102070 ACGCATTTAATCCGGTCACA 57.898 45.000 0.00 0.00 0.00 3.58
320 339 5.064325 AGGTACTTTCGAACGCATTTAATCC 59.936 40.000 0.00 0.00 27.25 3.01
396 417 9.291664 CGTTTCAAATGTACCAAGTAAAAGAAA 57.708 29.630 0.00 0.00 0.00 2.52
400 421 7.098074 ACCGTTTCAAATGTACCAAGTAAAA 57.902 32.000 0.00 0.00 0.00 1.52
520 544 4.024133 GCAACAATTTGGTTTCCATTGGAC 60.024 41.667 4.45 0.00 30.36 4.02
671 811 8.357402 GTTTGGTTGAAGTTATCATGGTTACTT 58.643 33.333 10.03 10.03 38.03 2.24
672 812 7.504238 TGTTTGGTTGAAGTTATCATGGTTACT 59.496 33.333 0.00 0.00 38.03 2.24
674 814 7.040062 CCTGTTTGGTTGAAGTTATCATGGTTA 60.040 37.037 0.00 0.00 38.03 2.85
686 826 3.189285 CTGTTTGCCTGTTTGGTTGAAG 58.811 45.455 0.00 0.00 38.35 3.02
700 840 2.819608 TGAACTTATCAGGGCTGTTTGC 59.180 45.455 0.00 0.00 35.68 3.68
701 841 4.613622 CGTTGAACTTATCAGGGCTGTTTG 60.614 45.833 0.00 0.00 39.77 2.93
702 842 3.502211 CGTTGAACTTATCAGGGCTGTTT 59.498 43.478 0.00 0.00 39.77 2.83
703 843 3.074412 CGTTGAACTTATCAGGGCTGTT 58.926 45.455 0.00 0.00 39.77 3.16
704 844 2.301870 TCGTTGAACTTATCAGGGCTGT 59.698 45.455 0.00 0.00 39.77 4.40
705 845 2.932614 CTCGTTGAACTTATCAGGGCTG 59.067 50.000 0.00 0.00 39.77 4.85
706 846 2.832129 TCTCGTTGAACTTATCAGGGCT 59.168 45.455 0.00 0.00 39.77 5.19
1254 1438 0.326264 AGAAGATGGCACCAGACACC 59.674 55.000 0.00 0.00 33.89 4.16
1375 1559 2.903855 TCCGGCGGGACTATCGAC 60.904 66.667 27.98 0.00 37.43 4.20
2698 2900 8.182227 CGATGCATATTCTCATATTGCTCATTT 58.818 33.333 0.00 0.00 0.00 2.32
2823 3026 3.213506 TCACATGGTATGTATGCAAGGC 58.786 45.455 0.00 0.00 42.70 4.35
2833 3036 9.454585 GTACAATGAAATCAATCACATGGTATG 57.545 33.333 0.00 0.00 33.60 2.39
2847 3050 6.759497 AGCCCTTACAAGTACAATGAAATC 57.241 37.500 5.77 0.00 0.00 2.17
2903 3113 4.955811 AGAATACGCCATTGACCTATCA 57.044 40.909 0.00 0.00 0.00 2.15
2904 3114 4.865365 GCTAGAATACGCCATTGACCTATC 59.135 45.833 0.00 0.00 0.00 2.08
2907 3117 2.434336 TGCTAGAATACGCCATTGACCT 59.566 45.455 0.00 0.00 0.00 3.85
2969 3179 1.263217 GTGGAGTCATGAACGCGTTTT 59.737 47.619 27.32 14.16 0.00 2.43
3021 3231 0.032403 TACACAAGCGCACCGTACTT 59.968 50.000 11.47 0.00 0.00 2.24
3142 3353 0.739813 ACTCCGTACGCTTTCATGCC 60.740 55.000 10.49 0.00 0.00 4.40
3191 3402 1.609061 CCATGTCGCTGTTGAGAGGTT 60.609 52.381 0.00 0.00 0.00 3.50
3211 3426 4.503741 TGGTTAGAGAAAATGCAAGTGC 57.496 40.909 0.00 0.00 42.50 4.40
3373 3589 2.576053 CGTGTCGATCGACCCGTG 60.576 66.667 37.58 23.41 43.97 4.94
3398 3614 3.612860 GCTAGTAAACGGTCATGTCTGTG 59.387 47.826 5.15 0.00 0.00 3.66
3401 3617 6.466885 AATAGCTAGTAAACGGTCATGTCT 57.533 37.500 0.00 0.00 0.00 3.41
3453 3669 2.830704 GAATCTTGGACCGACGGCGT 62.831 60.000 14.65 14.65 35.23 5.68


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

AutoCloner maintained by Alex Coulton.