Multiple sequence alignment - TraesCS6B01G408900

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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 TraesCS6B01G408900 chr6B 100.000 2826 0 0 2296 5121 682718371 682715546 0.000000e+00 5219.0
1 TraesCS6B01G408900 chr6B 94.522 2866 75 21 2296 5089 682682066 682679211 0.000000e+00 4348.0
2 TraesCS6B01G408900 chr6B 100.000 1958 0 0 1 1958 682720666 682718709 0.000000e+00 3616.0
3 TraesCS6B01G408900 chr6B 97.607 1964 40 3 1 1958 682684103 682682141 0.000000e+00 3360.0
4 TraesCS6B01G408900 chr6B 92.061 1902 132 12 2303 4196 682671244 682669354 0.000000e+00 2658.0
5 TraesCS6B01G408900 chr6B 88.600 1807 169 25 23 1810 682709718 682707930 0.000000e+00 2161.0
6 TraesCS6B01G408900 chr6B 90.019 1072 96 7 891 1956 682672569 682671503 0.000000e+00 1376.0
7 TraesCS6B01G408900 chr6B 87.836 707 67 9 23 724 682673594 682672902 0.000000e+00 811.0
8 TraesCS6B01G408900 chr6D 96.703 2123 45 7 2296 4396 450201158 450199039 0.000000e+00 3509.0
9 TraesCS6B01G408900 chr6D 91.571 1922 134 19 2300 4209 450198568 450196663 0.000000e+00 2627.0
10 TraesCS6B01G408900 chr6D 97.686 1210 23 4 750 1958 450202425 450201220 0.000000e+00 2074.0
11 TraesCS6B01G408900 chr6D 95.245 736 22 2 1 734 450203412 450202688 0.000000e+00 1153.0
12 TraesCS6B01G408900 chr6D 89.299 271 24 2 4207 4473 450196621 450196352 8.220000e-88 335.0
13 TraesCS6B01G408900 chr6D 89.787 235 18 5 1723 1956 450199036 450198807 3.880000e-76 296.0
14 TraesCS6B01G408900 chr6D 100.000 34 0 0 2418 2451 413352012 413352045 4.280000e-06 63.9
15 TraesCS6B01G408900 chr6A 97.203 1859 51 1 2296 4154 595693945 595692088 0.000000e+00 3144.0
16 TraesCS6B01G408900 chr6A 91.820 1907 138 12 2300 4197 595672891 595670994 0.000000e+00 2641.0
17 TraesCS6B01G408900 chr6A 90.449 1225 89 19 746 1956 595674174 595672964 0.000000e+00 1589.0
18 TraesCS6B01G408900 chr6A 87.696 959 80 19 4197 5121 595691989 595691035 0.000000e+00 1083.0
19 TraesCS6B01G408900 chr6A 88.098 731 61 11 8 727 595675259 595674544 0.000000e+00 845.0
20 TraesCS6B01G408900 chr6A 79.416 685 80 24 4316 4981 595670673 595670031 1.320000e-115 427.0
21 TraesCS6B01G408900 chr6A 97.531 81 2 0 1856 1936 595694406 595694326 6.910000e-29 139.0
22 TraesCS6B01G408900 chr6A 96.552 58 2 0 4140 4197 595692068 595692011 4.220000e-16 97.1
23 TraesCS6B01G408900 chr6A 100.000 34 0 0 2418 2451 558887866 558887899 4.280000e-06 63.9
24 TraesCS6B01G408900 chr5A 89.362 94 2 5 2585 2675 472754001 472754089 1.510000e-20 111.0


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 TraesCS6B01G408900 chr6B 682715546 682720666 5120 True 4417.500000 5219 100.000000 1 5121 2 chr6B.!!$R4 5120
1 TraesCS6B01G408900 chr6B 682679211 682684103 4892 True 3854.000000 4348 96.064500 1 5089 2 chr6B.!!$R3 5088
2 TraesCS6B01G408900 chr6B 682707930 682709718 1788 True 2161.000000 2161 88.600000 23 1810 1 chr6B.!!$R1 1787
3 TraesCS6B01G408900 chr6B 682669354 682673594 4240 True 1615.000000 2658 89.972000 23 4196 3 chr6B.!!$R2 4173
4 TraesCS6B01G408900 chr6D 450196352 450203412 7060 True 1665.666667 3509 93.381833 1 4473 6 chr6D.!!$R1 4472
5 TraesCS6B01G408900 chr6A 595670031 595675259 5228 True 1375.500000 2641 87.445750 8 4981 4 chr6A.!!$R1 4973
6 TraesCS6B01G408900 chr6A 595691035 595694406 3371 True 1115.775000 3144 94.745500 1856 5121 4 chr6A.!!$R2 3265

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
817 1184 2.532715 ATGGACCACACCTGCCCT 60.533 61.111 0.00 0.0 0.0 5.19 F
1092 1465 2.633967 TGCCAACTCTGCAAAATCCATT 59.366 40.909 0.00 0.0 35.4 3.16 F
2537 2940 1.977056 AGCTATACGTCGGACATGGA 58.023 50.000 9.10 0.0 0.0 3.41 F
3435 3847 3.052036 CAACAAAACGAAAGGCCTGATG 58.948 45.455 5.69 0.4 0.0 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1788 2168 6.367374 TGGATGTATTGTACTCCAAAGACA 57.633 37.500 0.0 0.0 37.37 3.41 R
2957 3368 6.280643 GTTTTAGTTCCATCCTTTTGCTGTT 58.719 36.000 0.0 0.0 0.00 3.16 R
4010 4422 1.541147 CCGGAATGTGATTGCTTGTGT 59.459 47.619 0.0 0.0 0.00 3.72 R
5098 8424 0.880278 GCAACACACTCTTGGAGCGA 60.880 55.000 0.0 0.0 32.04 4.93 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
199 201 6.746104 TTGTTTCAACAATATTGCAACTCG 57.254 33.333 15.48 0.00 43.45 4.18
433 444 9.396022 CTGAACCCATAACTTACATGTAGAATT 57.604 33.333 5.56 4.86 0.00 2.17
442 453 2.710377 ACATGTAGAATTGCCGCTGAA 58.290 42.857 0.00 0.00 0.00 3.02
477 488 8.112016 TCCGAAAAATGGTGTTATAATTGTGA 57.888 30.769 0.00 0.00 0.00 3.58
665 681 9.632807 TGCTTGGTTTGTATATATTTGAAACAC 57.367 29.630 12.40 6.18 0.00 3.32
714 730 8.519526 GGTTATTGAACAATCTACATTTGGTGA 58.480 33.333 3.23 0.00 37.29 4.02
817 1184 2.532715 ATGGACCACACCTGCCCT 60.533 61.111 0.00 0.00 0.00 5.19
995 1368 6.765512 GCAAATAGAGCTCTAGGTTTGAGAAT 59.234 38.462 33.92 15.21 33.50 2.40
1092 1465 2.633967 TGCCAACTCTGCAAAATCCATT 59.366 40.909 0.00 0.00 35.40 3.16
1132 1505 9.760077 ACTATTATGGTAAGGTTTTCTACATCG 57.240 33.333 0.00 0.00 0.00 3.84
1134 1507 3.255725 TGGTAAGGTTTTCTACATCGCG 58.744 45.455 0.00 0.00 0.00 5.87
1229 1603 8.177013 TCATGTTTTGAGATGTCATTACATTCG 58.823 33.333 14.09 7.65 46.49 3.34
1508 1887 6.449635 TTGTTTTAAAGCAGTGATGTCAGT 57.550 33.333 4.87 0.00 0.00 3.41
1923 2304 3.897239 TCTCTTTTTCTTCACCAAGGCA 58.103 40.909 0.00 0.00 0.00 4.75
2537 2940 1.977056 AGCTATACGTCGGACATGGA 58.023 50.000 9.10 0.00 0.00 3.41
2731 3141 9.158233 GTTTATGAACGCCCAATTAGCTATATA 57.842 33.333 0.00 0.00 0.00 0.86
2957 3368 5.636123 AGAAGAAGTTGGAGAGTCTGTAGA 58.364 41.667 0.00 0.00 0.00 2.59
3033 3444 5.221126 CCTGGAGAGCAAGTTTTTATATGCC 60.221 44.000 0.00 0.00 39.59 4.40
3435 3847 3.052036 CAACAAAACGAAAGGCCTGATG 58.948 45.455 5.69 0.40 0.00 3.07
3547 3959 4.926832 TCAAGAAACATCGAAAGCGTATGA 59.073 37.500 0.00 0.00 38.98 2.15
3937 4349 6.845908 ACATATAACAGGAGAAGATGGCATT 58.154 36.000 0.00 0.00 0.00 3.56
3972 4384 5.998454 AATGGCTCAAATTCATCTAGTCG 57.002 39.130 0.00 0.00 0.00 4.18
4010 4422 6.654582 TGCTCAAACATACAATTCAAGAGCTA 59.345 34.615 0.00 0.00 44.49 3.32
4121 7118 5.698545 CCAGATTCCGAGGATTCTGATTAAC 59.301 44.000 30.50 1.73 46.83 2.01
4122 7119 6.283694 CAGATTCCGAGGATTCTGATTAACA 58.716 40.000 27.31 0.00 46.83 2.41
4465 7716 1.606601 ACCCGTAGAGTCAGCTGCA 60.607 57.895 9.47 0.00 0.00 4.41
4552 7829 1.322538 GGCCACCAGCAATGGTAAGG 61.323 60.000 0.00 0.00 46.50 2.69
4594 7877 2.100631 GCTCACGATGTTGTCCGGG 61.101 63.158 0.00 0.00 0.00 5.73
4928 8251 7.007117 CGAACACTTTTTGAAACTTCCAAAAC 58.993 34.615 0.00 0.00 41.48 2.43
4982 8308 8.885494 AATTTCAATGATTTCTTTCCGAACAA 57.115 26.923 0.00 0.00 0.00 2.83
5051 8377 2.537633 ACCTACCTGAACCATACCGA 57.462 50.000 0.00 0.00 0.00 4.69
5090 8416 3.119955 CCTAAAACTAGGAAACTTGGCGC 60.120 47.826 0.00 0.00 43.67 6.53
5098 8424 0.039527 GAAACTTGGCGCGAATTGGT 60.040 50.000 12.10 0.00 0.00 3.67
5099 8425 0.039527 AAACTTGGCGCGAATTGGTC 60.040 50.000 12.10 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
192 194 3.585862 TCACATTCTCCTAACGAGTTGC 58.414 45.455 0.00 0.0 39.84 4.17
403 414 6.900194 ACATGTAAGTTATGGGTTCAGCTAT 58.100 36.000 0.00 0.0 0.00 2.97
411 422 6.546034 GGCAATTCTACATGTAAGTTATGGGT 59.454 38.462 7.06 0.0 0.00 4.51
416 427 5.293324 CAGCGGCAATTCTACATGTAAGTTA 59.707 40.000 7.06 0.0 0.00 2.24
442 453 1.747355 CATTTTTCGGAGGAGCTGCAT 59.253 47.619 8.35 0.0 0.00 3.96
817 1184 5.473162 TGCAAAAGAGCTAATAGCACAAAGA 59.527 36.000 15.28 0.0 45.56 2.52
995 1368 1.304282 GCTCTTTCTGCCATGGGGA 59.696 57.895 15.13 0.0 35.59 4.81
1132 1505 4.495422 TGAAGATAGTTCCTCTTTCACGC 58.505 43.478 0.00 0.0 33.18 5.34
1229 1603 7.174946 TGGAAAACAAGATCAACTTCACTATCC 59.825 37.037 0.00 0.0 36.61 2.59
1487 1865 7.421530 TCTACTGACATCACTGCTTTAAAAC 57.578 36.000 0.00 0.0 0.00 2.43
1508 1887 9.936759 TCTTCATTGTGTACATTGTTGTATCTA 57.063 29.630 0.00 0.0 40.35 1.98
1788 2168 6.367374 TGGATGTATTGTACTCCAAAGACA 57.633 37.500 0.00 0.0 37.37 3.41
2537 2940 7.951530 AGATTTGCTTTGATTTTCGATTTGT 57.048 28.000 0.00 0.0 0.00 2.83
2640 3045 8.918202 ACATATACCTTACACCCAACATATTG 57.082 34.615 0.00 0.0 35.40 1.90
2957 3368 6.280643 GTTTTAGTTCCATCCTTTTGCTGTT 58.719 36.000 0.00 0.0 0.00 3.16
3130 3541 7.761409 TGCATCTGAAATGAATTAACAGGTAC 58.239 34.615 0.00 0.0 0.00 3.34
3547 3959 3.922171 TGCCATGTTTTGTTCCCTTTT 57.078 38.095 0.00 0.0 0.00 2.27
3972 4384 3.243168 TGTTTGAGCAGCAACTTGATCAC 60.243 43.478 0.00 0.0 42.57 3.06
4010 4422 1.541147 CCGGAATGTGATTGCTTGTGT 59.459 47.619 0.00 0.0 0.00 3.72
4165 7196 7.575414 TCACCATAGAGTCTAGTGAGATTTC 57.425 40.000 14.98 0.0 32.75 2.17
4465 7716 3.148279 GGGAGATCGAGGTGGCGT 61.148 66.667 0.00 0.0 0.00 5.68
4928 8251 1.269309 TGTTCGCCGTTCCAAAAATGG 60.269 47.619 0.00 0.0 0.00 3.16
4936 8260 2.733517 TCAAAAATTGTTCGCCGTTCC 58.266 42.857 0.00 0.0 0.00 3.62
4982 8308 7.703058 ACCGGTTTTCTTCTGATTCAATAAT 57.297 32.000 0.00 0.0 0.00 1.28
4991 8317 5.163632 GGTTGTTTTACCGGTTTTCTTCTGA 60.164 40.000 15.04 0.0 0.00 3.27
5076 8402 1.466950 CAATTCGCGCCAAGTTTCCTA 59.533 47.619 0.00 0.0 0.00 2.94
5098 8424 0.880278 GCAACACACTCTTGGAGCGA 60.880 55.000 0.00 0.0 32.04 4.93
5099 8425 1.159713 TGCAACACACTCTTGGAGCG 61.160 55.000 0.00 0.0 32.04 5.03
5100 8426 1.068748 CATGCAACACACTCTTGGAGC 60.069 52.381 0.00 0.0 32.04 4.70
5101 8427 2.983402 CATGCAACACACTCTTGGAG 57.017 50.000 0.00 0.0 35.52 3.86


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

AutoCloner maintained by Alex Coulton.