Multiple sequence alignment - TraesCS6B01G259100

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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 TraesCS6B01G259100 chr6B 100.000 5159 0 0 1 5159 467461908 467456750 0.000000e+00 9527
1 TraesCS6B01G259100 chr6A 97.757 4413 95 3 558 4967 414864700 414869111 0.000000e+00 7598
2 TraesCS6B01G259100 chr6A 96.591 176 6 0 4984 5159 414869397 414869572 5.050000e-75 292
3 TraesCS6B01G259100 chr6D 97.690 3940 77 8 536 4466 302061118 302057184 0.000000e+00 6759
4 TraesCS6B01G259100 chr6D 97.854 699 13 1 4463 5159 302057025 302056327 0.000000e+00 1206
5 TraesCS6B01G259100 chr2B 98.893 542 4 1 1 540 256955171 256954630 0.000000e+00 966
6 TraesCS6B01G259100 chr2B 98.706 541 5 1 1 539 325907130 325906590 0.000000e+00 959
7 TraesCS6B01G259100 chr5B 98.887 539 3 2 1 536 682530616 682530078 0.000000e+00 959
8 TraesCS6B01G259100 chr5B 98.521 541 6 1 1 539 54499507 54498967 0.000000e+00 953
9 TraesCS6B01G259100 chr2A 98.887 539 3 2 1 536 238721561 238721023 0.000000e+00 959
10 TraesCS6B01G259100 chr1A 98.701 539 4 2 1 536 11150899 11150361 0.000000e+00 953
11 TraesCS6B01G259100 chr1A 98.701 539 4 2 1 536 366259896 366260434 0.000000e+00 953
12 TraesCS6B01G259100 chr1A 98.343 543 7 1 1 541 132125307 132124765 0.000000e+00 952
13 TraesCS6B01G259100 chr5A 97.645 552 10 2 1 549 44125501 44126052 0.000000e+00 944


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 TraesCS6B01G259100 chr6B 467456750 467461908 5158 True 9527.0 9527 100.000 1 5159 1 chr6B.!!$R1 5158
1 TraesCS6B01G259100 chr6A 414864700 414869572 4872 False 3945.0 7598 97.174 558 5159 2 chr6A.!!$F1 4601
2 TraesCS6B01G259100 chr6D 302056327 302061118 4791 True 3982.5 6759 97.772 536 5159 2 chr6D.!!$R1 4623
3 TraesCS6B01G259100 chr2B 256954630 256955171 541 True 966.0 966 98.893 1 540 1 chr2B.!!$R1 539
4 TraesCS6B01G259100 chr2B 325906590 325907130 540 True 959.0 959 98.706 1 539 1 chr2B.!!$R2 538
5 TraesCS6B01G259100 chr5B 682530078 682530616 538 True 959.0 959 98.887 1 536 1 chr5B.!!$R2 535
6 TraesCS6B01G259100 chr5B 54498967 54499507 540 True 953.0 953 98.521 1 539 1 chr5B.!!$R1 538
7 TraesCS6B01G259100 chr2A 238721023 238721561 538 True 959.0 959 98.887 1 536 1 chr2A.!!$R1 535
8 TraesCS6B01G259100 chr1A 11150361 11150899 538 True 953.0 953 98.701 1 536 1 chr1A.!!$R1 535
9 TraesCS6B01G259100 chr1A 366259896 366260434 538 False 953.0 953 98.701 1 536 1 chr1A.!!$F1 535
10 TraesCS6B01G259100 chr1A 132124765 132125307 542 True 952.0 952 98.343 1 541 1 chr1A.!!$R2 540
11 TraesCS6B01G259100 chr5A 44125501 44126052 551 False 944.0 944 97.645 1 549 1 chr5A.!!$F1 548

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
878 889 0.263172 TCACCTCTCTCCCTCATCCC 59.737 60.000 0.00 0.00 0.0 3.85 F
1203 1214 0.318699 CGCTCTCAAACACGACCTCA 60.319 55.000 0.00 0.00 0.0 3.86 F
1933 1944 0.683973 CTCTGCACAGTCCAACCTCT 59.316 55.000 0.00 0.00 0.0 3.69 F
2730 2741 1.741525 CATATTGCCGGGCTTTGGG 59.258 57.895 21.46 3.37 0.0 4.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1796 1807 1.417890 CAAACCTCGGGCTCATCCTAT 59.582 52.381 0.00 0.00 34.39 2.57 R
2256 2267 1.616159 GGCTTGTTAGGCTTGGACAA 58.384 50.000 0.00 1.30 43.31 3.18 R
3399 3410 0.608035 TCTGGCCAAAATCACCCGAC 60.608 55.000 7.01 0.00 0.00 4.79 R
4223 4234 1.499056 CTAGCACAAACGCTGGCAG 59.501 57.895 10.94 10.94 43.68 4.85 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
128 131 4.731853 TGGGGAGGGATGTCGGCA 62.732 66.667 0.00 0.00 0.00 5.69
287 291 2.881266 GCGTGCGAGCAAACAGTGA 61.881 57.895 0.00 0.00 37.05 3.41
446 450 5.499004 TGTGTTTCTAATTAGAGCACCCT 57.501 39.130 29.25 0.00 38.29 4.34
549 553 7.188157 CGTTATACTAGTCAGTCTGGTTCTTC 58.812 42.308 0.00 0.00 38.73 2.87
553 557 4.583489 ACTAGTCAGTCTGGTTCTTCGAAA 59.417 41.667 0.00 0.00 34.16 3.46
664 675 1.645710 AGGAAGAAGGAAAGCGAGGA 58.354 50.000 0.00 0.00 0.00 3.71
665 676 2.192263 AGGAAGAAGGAAAGCGAGGAT 58.808 47.619 0.00 0.00 0.00 3.24
878 889 0.263172 TCACCTCTCTCCCTCATCCC 59.737 60.000 0.00 0.00 0.00 3.85
881 892 0.539438 CCTCTCTCCCTCATCCCTCG 60.539 65.000 0.00 0.00 0.00 4.63
954 965 5.679638 GCTCCTGAACACAACAAACAAGAAT 60.680 40.000 0.00 0.00 0.00 2.40
955 966 6.279513 TCCTGAACACAACAAACAAGAATT 57.720 33.333 0.00 0.00 0.00 2.17
972 983 6.210185 ACAAGAATTTCTCTTCCCCATTCAAG 59.790 38.462 0.00 0.00 42.84 3.02
987 998 3.555527 TTCAAGAGCATCAGCATAGCT 57.444 42.857 0.00 0.00 45.49 3.32
995 1006 2.548904 GCATCAGCATAGCTCTTCTTGG 59.451 50.000 0.00 0.00 36.40 3.61
1053 1064 0.529378 GGCCAAGCTGTTTCATCCTG 59.471 55.000 0.00 0.00 0.00 3.86
1080 1091 0.319900 TGTCCGTGCAGCTTCTCTTC 60.320 55.000 0.00 0.00 0.00 2.87
1149 1160 0.896940 ATGGTGCACTGGAAGGCTTG 60.897 55.000 17.98 0.00 39.30 4.01
1203 1214 0.318699 CGCTCTCAAACACGACCTCA 60.319 55.000 0.00 0.00 0.00 3.86
1233 1244 4.682334 TGCTGTGCATGGGTGGGG 62.682 66.667 0.00 0.00 31.71 4.96
1377 1388 3.402681 CTCCGTGGTGCCATCCCT 61.403 66.667 0.00 0.00 0.00 4.20
1387 1398 4.181010 CCATCCCTGCACCCCTCG 62.181 72.222 0.00 0.00 0.00 4.63
1399 1410 1.144936 CCCCTCGTTCAGCTCCATC 59.855 63.158 0.00 0.00 0.00 3.51
1419 1430 3.561213 CTGCAGCGGCTCGATGTG 61.561 66.667 10.92 4.77 45.34 3.21
1458 1469 2.114411 ACATTCCCGGCCAACGTT 59.886 55.556 2.24 0.00 42.24 3.99
1500 1511 6.013379 AGGTCTTCAACATATCCTTCAACTCA 60.013 38.462 0.00 0.00 0.00 3.41
1626 1637 1.401905 TCTCGAGTGATCCGTGTGATG 59.598 52.381 13.13 0.00 32.41 3.07
1864 1875 7.233348 AGCTGGACATTTCTTTTAATTCCTTCA 59.767 33.333 0.00 0.00 0.00 3.02
1933 1944 0.683973 CTCTGCACAGTCCAACCTCT 59.316 55.000 0.00 0.00 0.00 3.69
1968 1979 2.751259 GCCTGCTTCATTGTCTCAATCA 59.249 45.455 0.00 0.00 0.00 2.57
2256 2267 4.101585 TCGGCATTATCTGTCCTTCAAGAT 59.898 41.667 0.00 0.00 0.00 2.40
2730 2741 1.741525 CATATTGCCGGGCTTTGGG 59.258 57.895 21.46 3.37 0.00 4.12
2751 2762 3.451178 GGAGCCTCAAGAACCTGTATGTA 59.549 47.826 0.00 0.00 0.00 2.29
3399 3410 4.409570 CAAAGATCGCCATCAAAAGACTG 58.590 43.478 0.00 0.00 0.00 3.51
4223 4234 3.214328 CCCATGAACTAGTGTTATGGCC 58.786 50.000 20.10 0.00 36.77 5.36
4284 4295 6.295039 AGTTTAATAACAGTGACCAACACG 57.705 37.500 0.00 0.00 41.66 4.49
4300 4311 4.090930 CCAACACGGAAATACTTGTACTCG 59.909 45.833 0.00 0.00 36.56 4.18
4320 4331 5.604650 ACTCGATTTCTCCCCTCTTGAATAT 59.395 40.000 0.00 0.00 0.00 1.28
4363 4377 9.626045 CTGTACGATAGACTGATTATTGCATAA 57.374 33.333 0.00 0.00 41.38 1.90
4476 4652 3.804325 CGTTCCATAGTAGAAGGCACATG 59.196 47.826 0.00 0.00 0.00 3.21
4698 4874 5.885912 ACGTGCCTTATATTTTGGAACAGAT 59.114 36.000 0.00 0.00 42.39 2.90
4702 4878 6.547141 TGCCTTATATTTTGGAACAGATGAGG 59.453 38.462 0.00 0.00 42.39 3.86
4710 4886 5.560722 TTGGAACAGATGAGGAACAGTAA 57.439 39.130 0.00 0.00 42.39 2.24
4715 4891 3.584848 ACAGATGAGGAACAGTAAAGCCT 59.415 43.478 0.00 0.00 0.00 4.58
5038 5483 8.682710 TGCCTAAAATGAAAGGAACATACATAC 58.317 33.333 0.00 0.00 34.58 2.39
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
128 131 0.104487 CATGATGACCTCGAGCAGCT 59.896 55.000 6.99 0.00 0.00 4.24
287 291 6.069381 AGTGCCTATCCCTTTTAGAATCAACT 60.069 38.462 0.00 0.00 0.00 3.16
446 450 6.971240 TCATCCCCTCATATTGGGTGATTATA 59.029 38.462 9.13 0.00 43.09 0.98
553 557 9.081204 TGCATACAAAATGGATATTGCTAGATT 57.919 29.630 0.00 0.00 0.00 2.40
664 675 1.353022 TGGCCTAACCGTCCTTTTCAT 59.647 47.619 3.32 0.00 43.94 2.57
665 676 0.766131 TGGCCTAACCGTCCTTTTCA 59.234 50.000 3.32 0.00 43.94 2.69
878 889 2.898840 AATGATGGCGGCAGCGAG 60.899 61.111 22.65 0.00 46.35 5.03
881 892 1.517694 CAACAATGATGGCGGCAGC 60.518 57.895 21.51 21.51 44.18 5.25
954 965 3.074390 TGCTCTTGAATGGGGAAGAGAAA 59.926 43.478 11.95 0.00 45.51 2.52
955 966 2.644299 TGCTCTTGAATGGGGAAGAGAA 59.356 45.455 11.95 0.00 45.51 2.87
987 998 1.640149 TGCCCCATTGATCCAAGAAGA 59.360 47.619 0.00 0.00 0.00 2.87
992 1003 1.854939 AGAGATGCCCCATTGATCCAA 59.145 47.619 0.00 0.00 0.00 3.53
995 1006 3.219176 TCAAGAGATGCCCCATTGATC 57.781 47.619 0.00 0.00 0.00 2.92
1053 1064 2.896801 CTGCACGGACAAGCACCAC 61.897 63.158 0.00 0.00 36.62 4.16
1080 1091 0.752376 GGGAGTAGACCGGAGACAGG 60.752 65.000 9.46 0.00 0.00 4.00
1149 1160 2.219325 CTCCGGTGACACCTCTCAGC 62.219 65.000 22.14 0.00 35.66 4.26
1203 1214 0.820891 CACAGCAGTTGGCCACTTCT 60.821 55.000 3.88 3.01 46.50 2.85
1233 1244 3.490759 CTGGCGTCGCATGTGACC 61.491 66.667 28.80 21.60 35.40 4.02
1249 1260 3.790437 CCTGATGACCCAGCCGCT 61.790 66.667 0.00 0.00 32.97 5.52
1255 1266 2.300967 GGTCCAGCCTGATGACCCA 61.301 63.158 8.50 0.00 42.21 4.51
1377 1388 3.240134 GAGCTGAACGAGGGGTGCA 62.240 63.158 0.00 0.00 31.66 4.57
1416 1427 4.855105 AGCTCGTTGTTGCTCACA 57.145 50.000 0.00 0.00 33.90 3.58
1458 1469 1.218047 CTCAATCACCGGGAGCGAA 59.782 57.895 6.32 0.00 0.00 4.70
1500 1511 2.124151 GGATGGGTGCCGCTGAAT 60.124 61.111 0.00 0.00 0.00 2.57
1739 1750 7.543172 TCTTCAGAAATTGCAACTTGAATATGC 59.457 33.333 0.00 0.00 40.45 3.14
1796 1807 1.417890 CAAACCTCGGGCTCATCCTAT 59.582 52.381 0.00 0.00 34.39 2.57
1968 1979 6.349611 GCAAGTACAACATCTTCAATGATGGT 60.350 38.462 8.96 0.00 44.34 3.55
2256 2267 1.616159 GGCTTGTTAGGCTTGGACAA 58.384 50.000 0.00 1.30 43.31 3.18
2576 2587 3.008813 AGTCTCTGTGGATTGCTGTGATT 59.991 43.478 0.00 0.00 0.00 2.57
2577 2588 2.570752 AGTCTCTGTGGATTGCTGTGAT 59.429 45.455 0.00 0.00 0.00 3.06
2730 2741 3.618690 ACATACAGGTTCTTGAGGCTC 57.381 47.619 7.79 7.79 0.00 4.70
2751 2762 2.363306 TGTTGTTGCTGAGGTCCAAT 57.637 45.000 0.00 0.00 0.00 3.16
3399 3410 0.608035 TCTGGCCAAAATCACCCGAC 60.608 55.000 7.01 0.00 0.00 4.79
4223 4234 1.499056 CTAGCACAAACGCTGGCAG 59.501 57.895 10.94 10.94 43.68 4.85
4284 4295 6.479331 GGGAGAAATCGAGTACAAGTATTTCC 59.521 42.308 14.31 5.38 37.29 3.13
4363 4377 5.163120 ACTCCCATGAAGCACATCATATTCT 60.163 40.000 0.00 0.00 37.96 2.40
4450 4464 3.065786 TGCCTTCTACTATGGAACGTACG 59.934 47.826 15.01 15.01 0.00 3.67
4451 4465 4.142315 TGTGCCTTCTACTATGGAACGTAC 60.142 45.833 0.00 0.00 34.20 3.67
4476 4652 6.748132 TGGAATCTTGACTTTCCACAAATTC 58.252 36.000 0.37 0.00 44.92 2.17
4698 4874 4.164843 ACAAAGGCTTTACTGTTCCTCA 57.835 40.909 12.95 0.00 0.00 3.86
4702 4878 4.671766 CGGCATACAAAGGCTTTACTGTTC 60.672 45.833 12.95 6.60 31.60 3.18
4710 4886 3.206150 CTCATACGGCATACAAAGGCTT 58.794 45.455 0.00 0.00 31.60 4.35
4715 4891 7.269316 TCTCATTTACTCATACGGCATACAAA 58.731 34.615 0.00 0.00 0.00 2.83
4799 4975 9.679661 TTAAAACATCTTCCATAGCTTCATACA 57.320 29.630 0.00 0.00 0.00 2.29
5013 5458 8.682710 TGTATGTATGTTCCTTTCATTTTAGGC 58.317 33.333 0.00 0.00 0.00 3.93
5038 5483 1.749063 TCCGTACACAGCTCTACCATG 59.251 52.381 0.00 0.00 0.00 3.66


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

AutoCloner maintained by Alex Coulton.