Multiple sequence alignment - TraesCS6A01G110900

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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 TraesCS6A01G110900 chr6A 100.000 6246 0 0 1 6246 80058486 80052241 0.000000e+00 11535
1 TraesCS6A01G110900 chr6A 96.524 5150 151 16 953 6088 582863693 582858558 0.000000e+00 8493
2 TraesCS6A01G110900 chr6A 96.485 4837 133 16 950 5771 557899233 557904047 0.000000e+00 7956
3 TraesCS6A01G110900 chr6A 98.101 316 6 0 5770 6085 557905918 557906233 9.150000e-153 551
4 TraesCS6A01G110900 chr6A 97.605 167 3 1 6081 6246 557908339 557908505 1.020000e-72 285
5 TraesCS6A01G110900 chr7A 96.575 6278 158 24 1 6246 620444439 620438187 0.000000e+00 10349
6 TraesCS6A01G110900 chr7A 95.861 6282 172 29 1 6246 548012772 548019001 0.000000e+00 10080
7 TraesCS6A01G110900 chr7A 96.761 5311 138 16 950 6246 708405552 708400262 0.000000e+00 8824
8 TraesCS6A01G110900 chr7A 94.957 932 47 0 3 934 184072546 184073477 0.000000e+00 1461
9 TraesCS6A01G110900 chr7A 95.312 320 13 2 5770 6088 267448261 267447943 2.010000e-139 507
10 TraesCS6A01G110900 chr7A 98.193 166 3 0 6081 6246 267447202 267447037 2.200000e-74 291
11 TraesCS6A01G110900 chr1A 96.461 6104 157 27 1 6088 57988872 57982812 0.000000e+00 10021
12 TraesCS6A01G110900 chr1A 98.204 167 2 1 6081 6246 28821920 28821754 2.200000e-74 291
13 TraesCS6A01G110900 chr1A 97.590 166 4 0 6081 6246 57982019 57981854 1.020000e-72 285
14 TraesCS6A01G110900 chr3A 96.871 5146 130 14 950 6085 724442837 724447961 0.000000e+00 8582
15 TraesCS6A01G110900 chr3A 96.757 5149 150 11 950 6088 15651082 15645941 0.000000e+00 8567
16 TraesCS6A01G110900 chr3A 96.296 945 34 1 1 945 31887607 31888550 0.000000e+00 1550
17 TraesCS6A01G110900 chr3A 97.590 166 4 0 6081 6246 745159946 745160111 1.020000e-72 285
18 TraesCS6A01G110900 chr4A 96.325 5089 139 18 696 5771 31823989 31818936 0.000000e+00 8318
19 TraesCS6A01G110900 chr4A 97.152 316 9 0 5770 6085 573630164 573630479 9.220000e-148 534
20 TraesCS6A01G110900 chr4A 94.318 88 4 1 950 1036 594984647 594984560 3.930000e-27 134
21 TraesCS6A01G110900 chr1D 96.684 935 28 3 1 934 259729972 259730904 0.000000e+00 1552
22 TraesCS6A01G110900 chr1D 95.824 934 37 1 1 934 8588657 8589588 0.000000e+00 1507
23 TraesCS6A01G110900 chrUn 95.838 937 39 0 1 937 70481048 70480112 0.000000e+00 1515
24 TraesCS6A01G110900 chr6D 95.624 937 36 1 1 937 43980096 43979165 0.000000e+00 1498
25 TraesCS6A01G110900 chr7D 95.596 931 40 1 7 937 503891156 503890227 0.000000e+00 1491
26 TraesCS6A01G110900 chr3B 94.000 950 51 2 1 945 171005647 171004699 0.000000e+00 1434
27 TraesCS6A01G110900 chr2A 97.236 796 21 1 4977 5771 770754028 770753233 0.000000e+00 1347
28 TraesCS6A01G110900 chr5D 97.605 167 3 1 6081 6246 23792540 23792374 1.020000e-72 285


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 TraesCS6A01G110900 chr6A 80052241 80058486 6245 True 11535.000000 11535 100.0000 1 6246 1 chr6A.!!$R1 6245
1 TraesCS6A01G110900 chr6A 582858558 582863693 5135 True 8493.000000 8493 96.5240 953 6088 1 chr6A.!!$R2 5135
2 TraesCS6A01G110900 chr6A 557899233 557908505 9272 False 2930.666667 7956 97.3970 950 6246 3 chr6A.!!$F1 5296
3 TraesCS6A01G110900 chr7A 620438187 620444439 6252 True 10349.000000 10349 96.5750 1 6246 1 chr7A.!!$R1 6245
4 TraesCS6A01G110900 chr7A 548012772 548019001 6229 False 10080.000000 10080 95.8610 1 6246 1 chr7A.!!$F2 6245
5 TraesCS6A01G110900 chr7A 708400262 708405552 5290 True 8824.000000 8824 96.7610 950 6246 1 chr7A.!!$R2 5296
6 TraesCS6A01G110900 chr7A 184072546 184073477 931 False 1461.000000 1461 94.9570 3 934 1 chr7A.!!$F1 931
7 TraesCS6A01G110900 chr7A 267447037 267448261 1224 True 399.000000 507 96.7525 5770 6246 2 chr7A.!!$R3 476
8 TraesCS6A01G110900 chr1A 57981854 57988872 7018 True 5153.000000 10021 97.0255 1 6246 2 chr1A.!!$R2 6245
9 TraesCS6A01G110900 chr3A 724442837 724447961 5124 False 8582.000000 8582 96.8710 950 6085 1 chr3A.!!$F2 5135
10 TraesCS6A01G110900 chr3A 15645941 15651082 5141 True 8567.000000 8567 96.7570 950 6088 1 chr3A.!!$R1 5138
11 TraesCS6A01G110900 chr3A 31887607 31888550 943 False 1550.000000 1550 96.2960 1 945 1 chr3A.!!$F1 944
12 TraesCS6A01G110900 chr4A 31818936 31823989 5053 True 8318.000000 8318 96.3250 696 5771 1 chr4A.!!$R1 5075
13 TraesCS6A01G110900 chr1D 259729972 259730904 932 False 1552.000000 1552 96.6840 1 934 1 chr1D.!!$F2 933
14 TraesCS6A01G110900 chr1D 8588657 8589588 931 False 1507.000000 1507 95.8240 1 934 1 chr1D.!!$F1 933
15 TraesCS6A01G110900 chrUn 70480112 70481048 936 True 1515.000000 1515 95.8380 1 937 1 chrUn.!!$R1 936
16 TraesCS6A01G110900 chr6D 43979165 43980096 931 True 1498.000000 1498 95.6240 1 937 1 chr6D.!!$R1 936
17 TraesCS6A01G110900 chr7D 503890227 503891156 929 True 1491.000000 1491 95.5960 7 937 1 chr7D.!!$R1 930
18 TraesCS6A01G110900 chr3B 171004699 171005647 948 True 1434.000000 1434 94.0000 1 945 1 chr3B.!!$R1 944
19 TraesCS6A01G110900 chr2A 770753233 770754028 795 True 1347.000000 1347 97.2360 4977 5771 1 chr2A.!!$R1 794


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
952 1000 0.174617 CTCCCTTCTCGCTGTTCCTC 59.825 60.000 0.00 0.00 0.00 3.71 F
956 1004 0.539051 CTTCTCGCTGTTCCTCCCAT 59.461 55.000 0.00 0.00 0.00 4.00 F
2612 2718 1.655099 CGGCATGAAATTTTCCTTGCG 59.345 47.619 19.48 14.17 38.16 4.85 F
2968 3075 2.287977 AAAGCCACCTAGGTTTGGTC 57.712 50.000 13.15 8.06 40.29 4.02 F
3016 3123 3.258872 TGACCTTGGAATTGAATTGCCTG 59.741 43.478 6.96 0.17 0.00 4.85 F
4077 4193 0.321564 CGCTGTTGGGATCAAGTGGA 60.322 55.000 0.00 0.00 32.92 4.02 F
4408 4524 0.834612 TTGATGGGTGGGGTATCGAC 59.165 55.000 0.00 0.00 0.00 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2634 2740 1.042003 TGAGGAGCCAGAGCAGCTAG 61.042 60.000 0.00 0.0 41.75 3.42 R
2775 2881 1.373497 GGACTGACCAGAGCACACG 60.373 63.158 3.76 0.0 38.79 4.49 R
3465 3573 2.164624 CCTCTTCTTCGTTCTCATCGGT 59.835 50.000 0.00 0.0 0.00 4.69 R
3828 3940 4.337555 GGCATTTCTGAGTAAGCATGTCAT 59.662 41.667 0.00 0.0 0.00 3.06 R
4498 4614 5.399858 TGACTAGACAAAATAGCTCGTGAC 58.600 41.667 0.00 0.0 0.00 3.67 R
5216 5341 0.880718 GCAGTAAGGGCATCCGTAGC 60.881 60.000 0.00 0.0 38.33 3.58 R
6108 10221 0.748450 AGTCCAAAGTTCGTGTCCGA 59.252 50.000 0.00 0.0 42.41 4.55 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
22 23 3.592898 TGACAATGTACAGATGACGCT 57.407 42.857 16.02 0.00 0.00 5.07
194 195 1.891919 GGCACGCCAAAGAGACACA 60.892 57.895 2.36 0.00 35.81 3.72
249 250 4.690748 GTCATTCACTAGTGCTAGCAAACA 59.309 41.667 21.29 6.49 36.66 2.83
363 364 2.040813 GGTGCATGATATGGGTCCAGAT 59.959 50.000 0.00 0.00 0.00 2.90
883 931 0.912486 CGAGGGTTTTCTCCTCCCAT 59.088 55.000 4.74 0.00 46.01 4.00
945 993 4.140599 CGCTGCTCCCTTCTCGCT 62.141 66.667 0.00 0.00 0.00 4.93
946 994 2.511145 GCTGCTCCCTTCTCGCTG 60.511 66.667 0.00 0.00 0.00 5.18
947 995 2.977178 CTGCTCCCTTCTCGCTGT 59.023 61.111 0.00 0.00 0.00 4.40
948 996 1.294780 CTGCTCCCTTCTCGCTGTT 59.705 57.895 0.00 0.00 0.00 3.16
949 997 0.739112 CTGCTCCCTTCTCGCTGTTC 60.739 60.000 0.00 0.00 0.00 3.18
950 998 1.448717 GCTCCCTTCTCGCTGTTCC 60.449 63.158 0.00 0.00 0.00 3.62
951 999 1.893919 GCTCCCTTCTCGCTGTTCCT 61.894 60.000 0.00 0.00 0.00 3.36
952 1000 0.174617 CTCCCTTCTCGCTGTTCCTC 59.825 60.000 0.00 0.00 0.00 3.71
953 1001 1.219393 CCCTTCTCGCTGTTCCTCC 59.781 63.158 0.00 0.00 0.00 4.30
954 1002 1.219393 CCTTCTCGCTGTTCCTCCC 59.781 63.158 0.00 0.00 0.00 4.30
955 1003 1.544825 CCTTCTCGCTGTTCCTCCCA 61.545 60.000 0.00 0.00 0.00 4.37
956 1004 0.539051 CTTCTCGCTGTTCCTCCCAT 59.461 55.000 0.00 0.00 0.00 4.00
1036 1113 2.043248 GAGGGAGGGCCGACACTA 60.043 66.667 8.39 0.00 33.83 2.74
1040 1117 2.363925 GAGGGCCGACACTAGGGT 60.364 66.667 0.00 0.00 0.00 4.34
1042 1119 2.682494 GGGCCGACACTAGGGTCA 60.682 66.667 24.48 0.00 37.66 4.02
1222 1311 1.756950 CTGCCATGCCATCTGCCTT 60.757 57.895 0.00 0.00 40.16 4.35
1273 1362 2.161808 GGTGACGACGATGAAGAAGAGA 59.838 50.000 0.00 0.00 0.00 3.10
1285 1374 7.083858 CGATGAAGAAGAGATCAGTCCTATTC 58.916 42.308 0.00 0.00 33.42 1.75
1320 1409 2.106684 AGGTTTCCTTGTTCAGTCCCTC 59.893 50.000 0.00 0.00 0.00 4.30
1326 1415 4.624913 TCCTTGTTCAGTCCCTCATCTAT 58.375 43.478 0.00 0.00 0.00 1.98
1483 1574 8.528044 TTGTTTTTAAGATCTACCAACCACTT 57.472 30.769 0.00 0.00 0.00 3.16
1858 1950 3.027412 ACAACACCATGCCTTGTTTACA 58.973 40.909 3.54 0.00 33.59 2.41
2284 2388 2.548057 GGCGATGTCAACAAAGAAGACA 59.452 45.455 0.00 0.00 45.26 3.41
2464 2568 8.937634 TTTATTTAAGATCTACGAACCACTCC 57.062 34.615 0.00 0.00 0.00 3.85
2465 2569 4.996788 TTAAGATCTACGAACCACTCCC 57.003 45.455 0.00 0.00 0.00 4.30
2604 2710 3.192633 GGTACTTGACCGGCATGAAATTT 59.807 43.478 0.00 0.00 38.87 1.82
2612 2718 1.655099 CGGCATGAAATTTTCCTTGCG 59.345 47.619 19.48 14.17 38.16 4.85
2634 2740 2.498056 CCATTTATGTGGGCCCCGC 61.498 63.158 22.27 13.36 35.55 6.13
2968 3075 2.287977 AAAGCCACCTAGGTTTGGTC 57.712 50.000 13.15 8.06 40.29 4.02
3016 3123 3.258872 TGACCTTGGAATTGAATTGCCTG 59.741 43.478 6.96 0.17 0.00 4.85
3807 3919 4.986054 TTTCCCTTAGAAGTTACAGCCA 57.014 40.909 0.00 0.00 35.40 4.75
3828 3940 4.380761 CCACTCAAAAATGCCATCGATTCA 60.381 41.667 0.00 0.00 0.00 2.57
3885 3997 3.481112 AAAATGCCATCGTTCCGTTAC 57.519 42.857 0.00 0.00 0.00 2.50
4034 4150 3.056749 ACTTGTGAGGAGTAAGTAAGCGG 60.057 47.826 0.00 0.00 33.22 5.52
4077 4193 0.321564 CGCTGTTGGGATCAAGTGGA 60.322 55.000 0.00 0.00 32.92 4.02
4408 4524 0.834612 TTGATGGGTGGGGTATCGAC 59.165 55.000 0.00 0.00 0.00 4.20
4513 4629 5.352284 AGATACAGGTCACGAGCTATTTTG 58.648 41.667 0.00 0.00 37.39 2.44
4532 4648 5.801350 TTTGTCTAGTCATGCATGTAAGC 57.199 39.130 25.43 14.16 0.00 3.09
4906 5026 6.160576 TCGACATGTATGATTGATCCTTCA 57.839 37.500 0.00 0.00 0.00 3.02
4907 5027 6.762333 TCGACATGTATGATTGATCCTTCAT 58.238 36.000 0.00 11.07 36.57 2.57
5317 5442 2.019249 GCAGCATCAAGAATGGCTACA 58.981 47.619 0.00 0.00 35.77 2.74
5353 5478 2.354305 CCGCGTATGCCGAGTACC 60.354 66.667 4.92 0.00 39.56 3.34
5414 5539 1.207390 GCAGCTAGAACTGATGCTCG 58.793 55.000 0.00 0.00 42.68 5.03
5723 5848 9.144747 GATGTGTTATGGTATACATGATGAGTC 57.855 37.037 5.01 0.00 40.82 3.36
5777 7775 4.580167 TGACTCAAAAGGAAATGTCTGGTG 59.420 41.667 0.00 0.00 0.00 4.17
6108 10221 0.855400 AATCCCCAACCCATCCACCT 60.855 55.000 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 1.016627 GATGGCTAATGAGTGCGCAA 58.983 50.000 14.00 0.00 0.00 4.85
194 195 1.468520 GTGTGCAATATGTGAAGCCGT 59.531 47.619 0.00 0.00 0.00 5.68
249 250 2.745482 GCAGAGATGCTCATGTGGACAT 60.745 50.000 0.00 0.00 36.96 3.06
363 364 1.233950 ACGCGATGCCATGTGTTTCA 61.234 50.000 15.93 0.00 0.00 2.69
531 532 1.985473 AGGCTTGTTTCATCTGCACA 58.015 45.000 0.00 0.00 0.00 4.57
572 573 6.207417 CCCTCATTACACAGAACAAAGTCATT 59.793 38.462 0.00 0.00 0.00 2.57
883 931 4.007644 CAGGCGAGTGGTGAGGCA 62.008 66.667 0.00 0.00 0.00 4.75
929 977 2.511145 CAGCGAGAAGGGAGCAGC 60.511 66.667 0.00 0.00 0.00 5.25
941 989 2.367202 GGGATGGGAGGAACAGCGA 61.367 63.158 0.00 0.00 0.00 4.93
942 990 2.190578 GGGATGGGAGGAACAGCG 59.809 66.667 0.00 0.00 0.00 5.18
943 991 2.190578 CGGGATGGGAGGAACAGC 59.809 66.667 0.00 0.00 0.00 4.40
944 992 2.190578 GCGGGATGGGAGGAACAG 59.809 66.667 0.00 0.00 0.00 3.16
945 993 3.407967 GGCGGGATGGGAGGAACA 61.408 66.667 0.00 0.00 0.00 3.18
946 994 4.547367 CGGCGGGATGGGAGGAAC 62.547 72.222 0.00 0.00 0.00 3.62
1033 1110 1.602237 CCATGGCGTTGACCCTAGT 59.398 57.895 0.00 0.00 0.00 2.57
1035 1112 2.270850 GCCATGGCGTTGACCCTA 59.729 61.111 23.48 0.00 0.00 3.53
1483 1574 1.735973 CACGAGAGCCATGGATCGA 59.264 57.895 29.66 0.00 38.50 3.59
1694 1786 5.186409 AGCAATTGGTGTAGAGCAAATTGAT 59.814 36.000 20.48 15.49 42.66 2.57
1927 2020 9.109393 ACGTAATAGCTAAAATGTTCATGTGAT 57.891 29.630 0.00 0.00 0.00 3.06
1973 2073 3.008375 TGCCTCTGCTTCTGTTACTCAAT 59.992 43.478 0.00 0.00 38.71 2.57
2465 2569 2.014335 TGCACGAGAACCATGAGATG 57.986 50.000 0.00 0.00 0.00 2.90
2604 2710 3.376859 CACATAAATGGCTACGCAAGGAA 59.623 43.478 0.00 0.00 46.39 3.36
2612 2718 1.328279 GGGCCCACATAAATGGCTAC 58.672 55.000 19.95 0.00 44.71 3.58
2634 2740 1.042003 TGAGGAGCCAGAGCAGCTAG 61.042 60.000 0.00 0.00 41.75 3.42
2775 2881 1.373497 GGACTGACCAGAGCACACG 60.373 63.158 3.76 0.00 38.79 4.49
2968 3075 6.475727 AGCTACGTATTTGTATTAGCACAGTG 59.524 38.462 0.00 0.00 38.10 3.66
3016 3123 7.968405 AGAAAATATTTTCACAATCACCTACGC 59.032 33.333 32.22 9.44 46.81 4.42
3122 3230 6.041423 TGACAGTACTGACATGAATGACAT 57.959 37.500 29.30 1.42 40.17 3.06
3465 3573 2.164624 CCTCTTCTTCGTTCTCATCGGT 59.835 50.000 0.00 0.00 0.00 4.69
3807 3919 5.125900 TCATGAATCGATGGCATTTTTGAGT 59.874 36.000 0.00 0.00 0.00 3.41
3828 3940 4.337555 GGCATTTCTGAGTAAGCATGTCAT 59.662 41.667 0.00 0.00 0.00 3.06
3885 3997 7.168637 GTCTAATGGCATTATTGAGCAAACATG 59.831 37.037 19.55 4.49 0.00 3.21
4077 4193 5.818678 TCTCACTACAATAAAGTGTGGGT 57.181 39.130 3.40 0.00 43.88 4.51
4244 4360 7.107542 GTCCCACAATTAAGTATCACCACTAA 58.892 38.462 0.00 0.00 0.00 2.24
4498 4614 5.399858 TGACTAGACAAAATAGCTCGTGAC 58.600 41.667 0.00 0.00 0.00 3.67
4513 4629 8.085296 ACTTATAGCTTACATGCATGACTAGAC 58.915 37.037 32.75 18.53 34.99 2.59
5216 5341 0.880718 GCAGTAAGGGCATCCGTAGC 60.881 60.000 0.00 0.00 38.33 3.58
5317 5442 1.166531 GCGTGCTTCACCCTGAAAGT 61.167 55.000 0.00 0.00 35.73 2.66
5353 5478 2.015587 GCCTCAAAGAAGCCTCATCAG 58.984 52.381 0.00 0.00 0.00 2.90
5683 5808 7.882791 ACCATAACACATCAGAATCTGTTAACA 59.117 33.333 10.36 8.28 32.32 2.41
5723 5848 5.530915 TCCTTCTTGAAAACCACATGTACAG 59.469 40.000 0.00 0.00 0.00 2.74
5777 7775 4.462834 CCCCCAAAATAGAGAAAAGGACAC 59.537 45.833 0.00 0.00 0.00 3.67
5927 7929 7.025520 ACCATAGCCAGATTATTAGCAGAAT 57.974 36.000 0.00 0.00 0.00 2.40
5942 7944 2.757868 GCACAATAACCAACCATAGCCA 59.242 45.455 0.00 0.00 0.00 4.75
6108 10221 0.748450 AGTCCAAAGTTCGTGTCCGA 59.252 50.000 0.00 0.00 42.41 4.55



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

AutoCloner maintained by Alex Coulton.