Multiple sequence alignment - TraesCS6A01G361100

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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 TraesCS6A01G361100 chr6A 100.000 3305 0 0 1 3305 591797429 591800733 0.000000e+00 6104
1 TraesCS6A01G361100 chr6D 94.470 2604 80 25 755 3305 444454169 444456761 0.000000e+00 3952
2 TraesCS6A01G361100 chr6D 88.757 338 26 3 7 333 444452072 444452408 1.430000e-108 403
3 TraesCS6A01G361100 chr6D 82.535 355 27 6 6 340 444453826 444454165 2.510000e-71 279
4 TraesCS6A01G361100 chr6B 93.651 2457 100 28 892 3305 668904513 668906956 0.000000e+00 3622
5 TraesCS6A01G361100 chr6B 89.109 1616 131 26 1084 2683 580278923 580280509 0.000000e+00 1967
6 TraesCS6A01G361100 chr6B 86.577 149 12 5 198 343 668903054 668903197 1.230000e-34 158
7 TraesCS6A01G361100 chr7B 97.537 406 9 1 345 749 528020894 528021299 0.000000e+00 693
8 TraesCS6A01G361100 chr7B 94.511 419 21 2 345 761 11881103 11880685 0.000000e+00 645
9 TraesCS6A01G361100 chr5B 97.311 409 10 1 345 752 491231113 491230705 0.000000e+00 693
10 TraesCS6A01G361100 chr4B 97.537 406 9 1 345 749 476363532 476363937 0.000000e+00 693
11 TraesCS6A01G361100 chr4B 96.059 406 11 2 345 749 660566839 660566438 0.000000e+00 656
12 TraesCS6A01G361100 chr1A 96.386 415 13 2 346 758 8311259 8310845 0.000000e+00 682
13 TraesCS6A01G361100 chrUn 94.245 417 21 3 345 758 9333242 9332826 4.650000e-178 634
14 TraesCS6A01G361100 chrUn 94.245 417 21 3 345 758 9337124 9336708 4.650000e-178 634
15 TraesCS6A01G361100 chrUn 94.048 420 22 3 342 758 9479363 9479782 4.650000e-178 634


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 TraesCS6A01G361100 chr6A 591797429 591800733 3304 False 6104.000000 6104 100.000000 1 3305 1 chr6A.!!$F1 3304
1 TraesCS6A01G361100 chr6D 444452072 444456761 4689 False 1544.666667 3952 88.587333 6 3305 3 chr6D.!!$F1 3299
2 TraesCS6A01G361100 chr6B 580278923 580280509 1586 False 1967.000000 1967 89.109000 1084 2683 1 chr6B.!!$F1 1599
3 TraesCS6A01G361100 chr6B 668903054 668906956 3902 False 1890.000000 3622 90.114000 198 3305 2 chr6B.!!$F2 3107
4 TraesCS6A01G361100 chrUn 9332826 9337124 4298 True 634.000000 634 94.245000 345 758 2 chrUn.!!$R1 413

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
749 2525 0.324943 GAGCAGTCCTAAACAGGCCA 59.675 55.000 5.01 0.0 32.58 5.36 F
882 3928 2.110352 CCGCCACCAACGAATACCC 61.110 63.158 0.00 0.0 0.00 3.69 F
1698 4769 0.612453 AGGAGACCAGGGACTTCGAC 60.612 60.000 0.00 0.0 34.60 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1698 4769 0.877649 CGATGAAGAGGATGTGCCCG 60.878 60.000 0.0 0.0 37.37 6.13 R
1821 4902 1.002366 CTTTCGCCTTGACATCGGAG 58.998 55.000 0.0 0.0 0.00 4.63 R
3236 8228 2.125512 CGGACGGAGAAAGCTGGG 60.126 66.667 0.0 0.0 0.00 4.45 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
26 27 1.679680 CATTTGCCTCGCCATCTTCAT 59.320 47.619 0.00 0.00 0.00 2.57
35 36 2.173356 TCGCCATCTTCATTCTTCCCAT 59.827 45.455 0.00 0.00 0.00 4.00
43 44 5.694995 TCTTCATTCTTCCCATATTCCACC 58.305 41.667 0.00 0.00 0.00 4.61
47 48 1.507141 CTTCCCATATTCCACCGCGC 61.507 60.000 0.00 0.00 0.00 6.86
58 59 2.281208 ACCGCGCCTTGCAGTTAA 60.281 55.556 0.00 0.00 46.97 2.01
62 63 0.523335 CGCGCCTTGCAGTTAAATCC 60.523 55.000 0.00 0.00 46.97 3.01
74 75 1.588861 GTTAAATCCTCGCTCTGTCGC 59.411 52.381 0.00 0.00 0.00 5.19
81 82 0.371645 CTCGCTCTGTCGCCAATTTC 59.628 55.000 0.00 0.00 0.00 2.17
83 84 0.729116 CGCTCTGTCGCCAATTTCAT 59.271 50.000 0.00 0.00 0.00 2.57
88 89 4.795278 GCTCTGTCGCCAATTTCATAAAAG 59.205 41.667 0.00 0.00 0.00 2.27
89 90 5.309323 TCTGTCGCCAATTTCATAAAAGG 57.691 39.130 0.00 0.00 0.00 3.11
136 137 1.538047 TTGCTGCAACCTCTTGGATC 58.462 50.000 11.69 0.00 37.04 3.36
140 141 3.054139 TGCTGCAACCTCTTGGATCTATT 60.054 43.478 0.00 0.00 37.04 1.73
150 151 6.127026 ACCTCTTGGATCTATTGTACCAACTC 60.127 42.308 0.00 0.00 37.46 3.01
180 181 3.746492 AGATCGTCCTTTGTTTTTCGAGG 59.254 43.478 0.00 0.00 0.00 4.63
188 189 4.335594 CCTTTGTTTTTCGAGGTTGAGACT 59.664 41.667 0.00 0.00 0.00 3.24
190 191 4.402056 TGTTTTTCGAGGTTGAGACTCT 57.598 40.909 3.68 0.00 32.83 3.24
268 280 3.560068 CACATATTCCGGTTACAAGGAGC 59.440 47.826 0.00 0.00 37.88 4.70
276 288 4.897076 TCCGGTTACAAGGAGCATATTAGA 59.103 41.667 0.00 0.00 31.95 2.10
277 289 5.010719 TCCGGTTACAAGGAGCATATTAGAG 59.989 44.000 0.00 0.00 31.95 2.43
341 2116 9.598517 CAGATTCAGCTATTCTTTCTTCTTACT 57.401 33.333 0.00 0.00 0.00 2.24
360 2135 2.225547 ACTAGGAGCCTGTTTGGGACTA 60.226 50.000 0.00 0.00 36.00 2.59
361 2136 0.984995 AGGAGCCTGTTTGGGACTAC 59.015 55.000 0.00 0.00 36.00 2.73
372 2147 2.327325 TGGGACTACTCTGCTCCTTT 57.673 50.000 0.00 0.00 0.00 3.11
388 2163 3.270877 TCCTTTAAATTCAGCTCCGCTC 58.729 45.455 0.00 0.00 36.40 5.03
426 2201 1.416401 ACGGGGTAGCTCCACAATATG 59.584 52.381 0.00 0.00 40.26 1.78
434 2209 1.224069 CTCCACAATATGCCGCTCCG 61.224 60.000 0.00 0.00 0.00 4.63
464 2239 6.919775 AACTAGAATCTGGTGTACAACTCT 57.080 37.500 13.07 8.94 0.00 3.24
465 2240 6.518208 ACTAGAATCTGGTGTACAACTCTC 57.482 41.667 13.07 3.49 0.00 3.20
548 2324 2.346284 TTACCCACCACTGCCACCAC 62.346 60.000 0.00 0.00 0.00 4.16
657 2433 4.365514 TGACAGCCAAACATTCTCCTTA 57.634 40.909 0.00 0.00 0.00 2.69
722 2498 3.404899 AGTGGAGCGAAACCGATTTTTA 58.595 40.909 0.00 0.00 0.00 1.52
749 2525 0.324943 GAGCAGTCCTAAACAGGCCA 59.675 55.000 5.01 0.00 32.58 5.36
752 2528 2.171448 AGCAGTCCTAAACAGGCCATAG 59.829 50.000 5.01 1.49 32.58 2.23
753 2529 2.170607 GCAGTCCTAAACAGGCCATAGA 59.829 50.000 5.01 0.00 0.00 1.98
778 2554 5.984695 AACTAAGCTGGGGAAGAATTTTC 57.015 39.130 0.00 0.00 0.00 2.29
882 3928 2.110352 CCGCCACCAACGAATACCC 61.110 63.158 0.00 0.00 0.00 3.69
1599 4670 3.537874 GGCGAGCCGGACCAGTAT 61.538 66.667 5.05 0.00 0.00 2.12
1675 4746 3.860930 AACACCGTGTGGGATGGGC 62.861 63.158 4.57 0.00 40.75 5.36
1698 4769 0.612453 AGGAGACCAGGGACTTCGAC 60.612 60.000 0.00 0.00 34.60 4.20
1821 4902 4.794439 GCCGTCAATTTGGCGCCC 62.794 66.667 26.77 6.44 45.27 6.13
1956 5037 2.224079 GCAGTTCTGCGACTTTGATGAA 59.776 45.455 9.04 0.00 0.00 2.57
1986 5067 2.552315 GGATATAACCATGTGGGCAACG 59.448 50.000 3.77 0.00 42.05 4.10
2061 5143 1.807377 GCTGCACATTTTGGCAAGTGT 60.807 47.619 16.42 14.61 39.93 3.55
2262 5344 2.694760 CCGGGAGCTTTGCTTGAGC 61.695 63.158 0.00 0.00 39.88 4.26
2268 5350 2.139210 GCTTTGCTTGAGCTTTGCG 58.861 52.632 4.44 0.00 42.66 4.85
2292 5374 6.183360 CGTACATGTACCATGTTAAAGACACC 60.183 42.308 26.37 0.03 35.41 4.16
2551 5638 7.410800 TTGTTTCAAGATCATTTGCAACATC 57.589 32.000 11.64 1.12 41.44 3.06
2605 5692 8.589335 TGTTTAACTGAAGTACTGCTTTCTAG 57.411 34.615 1.64 0.00 37.59 2.43
2649 5737 7.068348 GGATGCTTAATGCCTATTGATGATCAT 59.932 37.037 8.25 8.25 42.00 2.45
2683 5771 3.887621 TGCCTTACCATGTCTAGTGAC 57.112 47.619 0.00 0.00 43.20 3.67
2722 5810 6.033341 GTGACATCTGTATCTCTTGTCTGTC 58.967 44.000 0.00 0.00 38.00 3.51
2731 5819 7.418408 TGTATCTCTTGTCTGTCGTATGATTC 58.582 38.462 0.00 0.00 0.00 2.52
2814 5917 8.225603 TCTTCTTCAGTTTTGTATGCTTCTTT 57.774 30.769 0.00 0.00 0.00 2.52
2821 5924 6.583806 CAGTTTTGTATGCTTCTTTCATGGTC 59.416 38.462 0.00 0.00 0.00 4.02
2837 5940 9.565213 CTTTCATGGTCTTTCTATTTTTAGCTG 57.435 33.333 0.00 0.00 0.00 4.24
2880 5983 6.376299 TCATCTACTCTTGATTTTGCATGCTT 59.624 34.615 20.33 0.66 0.00 3.91
2882 5985 4.595762 ACTCTTGATTTTGCATGCTTGT 57.404 36.364 20.33 2.01 0.00 3.16
2925 6028 3.252215 TGGTGAAATTTTAGACAGGCACG 59.748 43.478 0.00 0.00 0.00 5.34
3132 6269 4.578105 GCTAAGAAAGGATTCATGGAGTGG 59.422 45.833 0.00 0.00 38.06 4.00
3236 8228 3.118956 TGACCACAAATCACAACCAAACC 60.119 43.478 0.00 0.00 0.00 3.27
3254 8246 2.657237 CCAGCTTTCTCCGTCCGT 59.343 61.111 0.00 0.00 0.00 4.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 2.948840 GATGGCGAGGCAAATGCAGC 62.949 60.000 7.80 9.11 44.36 5.25
3 4 1.065273 GATGGCGAGGCAAATGCAG 59.935 57.895 7.80 0.00 44.36 4.41
6 7 1.097232 TGAAGATGGCGAGGCAAATG 58.903 50.000 2.86 0.00 0.00 2.32
7 8 2.062971 ATGAAGATGGCGAGGCAAAT 57.937 45.000 2.86 0.00 0.00 2.32
8 9 1.745087 GAATGAAGATGGCGAGGCAAA 59.255 47.619 2.86 0.00 0.00 3.68
9 10 1.065199 AGAATGAAGATGGCGAGGCAA 60.065 47.619 2.86 0.00 0.00 4.52
10 11 0.543277 AGAATGAAGATGGCGAGGCA 59.457 50.000 0.88 0.88 0.00 4.75
11 12 1.601430 GAAGAATGAAGATGGCGAGGC 59.399 52.381 0.00 0.00 0.00 4.70
12 13 2.216898 GGAAGAATGAAGATGGCGAGG 58.783 52.381 0.00 0.00 0.00 4.63
26 27 1.474320 CGCGGTGGAATATGGGAAGAA 60.474 52.381 0.00 0.00 0.00 2.52
35 36 2.822255 GCAAGGCGCGGTGGAATA 60.822 61.111 8.83 0.00 0.00 1.75
43 44 0.523335 GGATTTAACTGCAAGGCGCG 60.523 55.000 0.00 0.00 46.97 6.86
47 48 2.352960 GAGCGAGGATTTAACTGCAAGG 59.647 50.000 0.00 0.00 39.30 3.61
58 59 1.888436 TTGGCGACAGAGCGAGGATT 61.888 55.000 0.00 0.00 44.54 3.01
62 63 0.371645 GAAATTGGCGACAGAGCGAG 59.628 55.000 0.00 0.00 44.54 5.03
81 82 8.271312 TCGGAATTTACACCTAACCTTTTATG 57.729 34.615 0.00 0.00 0.00 1.90
83 84 8.732531 CAATCGGAATTTACACCTAACCTTTTA 58.267 33.333 0.00 0.00 0.00 1.52
88 89 4.638865 AGCAATCGGAATTTACACCTAACC 59.361 41.667 0.00 0.00 0.00 2.85
89 90 5.813080 AGCAATCGGAATTTACACCTAAC 57.187 39.130 0.00 0.00 0.00 2.34
140 141 1.890489 TCTTAGCGCAGAGTTGGTACA 59.110 47.619 11.47 0.00 0.00 2.90
150 151 1.590238 CAAAGGACGATCTTAGCGCAG 59.410 52.381 11.47 0.00 0.00 5.18
239 251 8.289618 CCTTGTAACCGGAATATGTGATTATTG 58.710 37.037 9.46 0.00 0.00 1.90
257 269 9.774742 CAAAAACTCTAATATGCTCCTTGTAAC 57.225 33.333 0.00 0.00 0.00 2.50
268 280 8.686334 AGCCACCATTACAAAAACTCTAATATG 58.314 33.333 0.00 0.00 0.00 1.78
276 288 8.085909 GTGTAATTAGCCACCATTACAAAAACT 58.914 33.333 6.36 0.00 43.93 2.66
277 289 8.234887 GTGTAATTAGCCACCATTACAAAAAC 57.765 34.615 6.36 0.00 43.93 2.43
341 2116 2.185387 GTAGTCCCAAACAGGCTCCTA 58.815 52.381 0.00 0.00 35.39 2.94
342 2117 0.984995 GTAGTCCCAAACAGGCTCCT 59.015 55.000 0.00 0.00 35.39 3.69
343 2118 0.984995 AGTAGTCCCAAACAGGCTCC 59.015 55.000 0.00 0.00 35.39 4.70
360 2135 4.916183 AGCTGAATTTAAAGGAGCAGAGT 58.084 39.130 14.78 1.30 31.80 3.24
361 2136 4.335037 GGAGCTGAATTTAAAGGAGCAGAG 59.665 45.833 14.78 0.00 31.80 3.35
388 2163 2.192624 CGTTTGGCTTGTGTTTTCTGG 58.807 47.619 0.00 0.00 0.00 3.86
416 2191 1.227527 CGGAGCGGCATATTGTGGA 60.228 57.895 1.45 0.00 0.00 4.02
548 2324 4.161754 AGAAACGAAGGGGTATCCACTTAG 59.838 45.833 3.10 6.34 38.24 2.18
591 2367 7.870509 TGAGATATTTGGTGGAAAGAATCTG 57.129 36.000 0.00 0.00 33.45 2.90
638 2414 6.485171 ACTATTAAGGAGAATGTTTGGCTGT 58.515 36.000 0.00 0.00 0.00 4.40
673 2449 8.635765 ATTTACTTTGGAGCAGTTTCATCTAA 57.364 30.769 0.00 0.00 0.00 2.10
677 2453 8.860088 ACTAAATTTACTTTGGAGCAGTTTCAT 58.140 29.630 0.00 0.00 0.00 2.57
722 2498 1.195115 TTAGGACTGCTCCGCTTCAT 58.805 50.000 0.00 0.00 42.22 2.57
739 2515 7.715249 CAGCTTAGTTTATCTATGGCCTGTTTA 59.285 37.037 3.32 0.00 32.39 2.01
745 2521 4.327680 CCCAGCTTAGTTTATCTATGGCC 58.672 47.826 0.00 0.00 32.39 5.36
749 2525 7.691993 TTCTTCCCCAGCTTAGTTTATCTAT 57.308 36.000 0.00 0.00 0.00 1.98
752 2528 7.646548 AAATTCTTCCCCAGCTTAGTTTATC 57.353 36.000 0.00 0.00 0.00 1.75
753 2529 7.124298 GGAAAATTCTTCCCCAGCTTAGTTTAT 59.876 37.037 7.71 0.00 32.48 1.40
882 3928 4.320456 AGGCGCAGGTGTGGACTG 62.320 66.667 10.83 0.00 38.95 3.51
1698 4769 0.877649 CGATGAAGAGGATGTGCCCG 60.878 60.000 0.00 0.00 37.37 6.13
1755 4826 1.859427 AATCCACAAGCAGCTGCACG 61.859 55.000 38.24 29.44 45.16 5.34
1821 4902 1.002366 CTTTCGCCTTGACATCGGAG 58.998 55.000 0.00 0.00 0.00 4.63
1956 5037 6.953520 CCCACATGGTTATATCCCAATTGTAT 59.046 38.462 4.43 0.37 35.14 2.29
1986 5067 1.392510 GCTTCAAACGACGGATACACC 59.607 52.381 0.00 0.00 0.00 4.16
2292 5374 6.467677 CCTATAACCCCATCATACAGACAAG 58.532 44.000 0.00 0.00 0.00 3.16
2300 5382 3.007506 CGTGTGCCTATAACCCCATCATA 59.992 47.826 0.00 0.00 0.00 2.15
2430 5512 6.093771 GTCTCCGAATAGAGAACTGTTCTACA 59.906 42.308 22.08 13.37 44.32 2.74
2437 5519 4.505922 GCAATGTCTCCGAATAGAGAACTG 59.494 45.833 0.00 0.00 44.32 3.16
2605 5692 4.500375 GCATCCCTGAATGTTAAAGATGCC 60.500 45.833 10.22 0.00 45.84 4.40
2638 5726 6.363065 ACAGTAAGAGGCAATGATCATCAAT 58.637 36.000 9.06 0.00 0.00 2.57
2649 5737 2.656947 AAGGCAACAGTAAGAGGCAA 57.343 45.000 0.00 0.00 41.41 4.52
2693 5781 7.282224 AGACAAGAGATACAGATGTCACTAGAC 59.718 40.741 0.00 0.00 42.12 2.59
2694 5782 7.281999 CAGACAAGAGATACAGATGTCACTAGA 59.718 40.741 0.00 0.00 42.12 2.43
2695 5783 7.066887 ACAGACAAGAGATACAGATGTCACTAG 59.933 40.741 6.94 0.00 42.12 2.57
2696 5784 6.887002 ACAGACAAGAGATACAGATGTCACTA 59.113 38.462 6.94 0.00 42.12 2.74
2697 5785 5.714333 ACAGACAAGAGATACAGATGTCACT 59.286 40.000 6.94 0.00 42.12 3.41
2706 5794 6.944234 ATCATACGACAGACAAGAGATACA 57.056 37.500 0.00 0.00 0.00 2.29
2802 5905 6.240894 AGAAAGACCATGAAAGAAGCATACA 58.759 36.000 0.00 0.00 0.00 2.29
2814 5917 6.886459 AGCAGCTAAAAATAGAAAGACCATGA 59.114 34.615 0.00 0.00 0.00 3.07
2837 5940 9.810545 AGTAGATGAGTTCTAAGAAATACAAGC 57.189 33.333 0.00 0.00 38.67 4.01
2869 5972 8.972458 TCCTATAATACTACAAGCATGCAAAA 57.028 30.769 21.98 0.92 0.00 2.44
2872 5975 9.002600 CAAATCCTATAATACTACAAGCATGCA 57.997 33.333 21.98 0.00 0.00 3.96
2873 5976 9.003658 ACAAATCCTATAATACTACAAGCATGC 57.996 33.333 10.51 10.51 0.00 4.06
2880 5983 9.375974 ACCAGCTACAAATCCTATAATACTACA 57.624 33.333 0.00 0.00 0.00 2.74
2882 5985 9.596308 TCACCAGCTACAAATCCTATAATACTA 57.404 33.333 0.00 0.00 0.00 1.82
3021 6128 3.897239 TGATATGGCCACAACTTAAGGG 58.103 45.455 8.16 1.03 0.00 3.95
3236 8228 2.125512 CGGACGGAGAAAGCTGGG 60.126 66.667 0.00 0.00 0.00 4.45
3254 8246 8.350722 GGTCAGATGAGTCAAATATACTACGAA 58.649 37.037 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.