Multiple sequence alignment - TraesCS6D01G166500

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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 TraesCS6D01G166500 chr6D 100.000 3536 0 0 1 3536 148081251 148077716 0.000000e+00 6530.0
1 TraesCS6D01G166500 chr6A 95.205 2774 116 13 1 2765 199457113 199459878 0.000000e+00 4370.0
2 TraesCS6D01G166500 chr6B 93.745 2446 95 22 326 2748 260782702 260780292 0.000000e+00 3616.0
3 TraesCS6D01G166500 chr6B 90.476 336 26 4 1 333 260820774 260820442 4.190000e-119 438.0
4 TraesCS6D01G166500 chr6B 91.167 317 22 4 20 333 260820290 260819977 3.260000e-115 425.0
5 TraesCS6D01G166500 chr3D 95.840 649 25 2 2888 3536 18748167 18748813 0.000000e+00 1048.0
6 TraesCS6D01G166500 chr2B 89.744 780 69 7 2763 3531 77815632 77816411 0.000000e+00 987.0
7 TraesCS6D01G166500 chr2B 89.130 782 72 9 2763 3531 77859676 77860457 0.000000e+00 961.0
8 TraesCS6D01G166500 chr2B 78.534 764 118 32 1711 2454 6341214 6340477 8.940000e-126 460.0
9 TraesCS6D01G166500 chrUn 89.615 780 70 7 2763 3531 245559375 245560154 0.000000e+00 981.0
10 TraesCS6D01G166500 chrUn 89.359 780 72 7 2763 3531 272849508 272850287 0.000000e+00 970.0
11 TraesCS6D01G166500 chr7B 89.304 776 72 8 2765 3532 205767029 205766257 0.000000e+00 963.0
12 TraesCS6D01G166500 chr4B 89.351 770 77 3 2765 3531 570119785 570119018 0.000000e+00 963.0
13 TraesCS6D01G166500 chr1B 89.031 784 75 8 2757 3532 500626250 500625470 0.000000e+00 961.0
14 TraesCS6D01G166500 chr1B 88.590 780 78 7 2763 3531 589496095 589496874 0.000000e+00 937.0
15 TraesCS6D01G166500 chr2D 77.763 760 131 28 1711 2454 5080105 5080842 1.950000e-117 433.0
16 TraesCS6D01G166500 chr5B 78.125 192 34 8 2096 2283 610106893 610106706 8.020000e-22 115.0
17 TraesCS6D01G166500 chr5B 77.500 200 37 8 2096 2291 610281381 610281186 2.880000e-21 113.0
18 TraesCS6D01G166500 chr7D 82.946 129 18 4 2090 2216 19400658 19400784 2.880000e-21 113.0
19 TraesCS6D01G166500 chr5D 77.073 205 39 8 2085 2285 493913475 493913675 1.040000e-20 111.0
20 TraesCS6D01G166500 chr2A 77.401 177 30 10 2087 2258 735862403 735862574 2.910000e-16 97.1


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 TraesCS6D01G166500 chr6D 148077716 148081251 3535 True 6530.0 6530 100.0000 1 3536 1 chr6D.!!$R1 3535
1 TraesCS6D01G166500 chr6A 199457113 199459878 2765 False 4370.0 4370 95.2050 1 2765 1 chr6A.!!$F1 2764
2 TraesCS6D01G166500 chr6B 260780292 260782702 2410 True 3616.0 3616 93.7450 326 2748 1 chr6B.!!$R1 2422
3 TraesCS6D01G166500 chr6B 260819977 260820774 797 True 431.5 438 90.8215 1 333 2 chr6B.!!$R2 332
4 TraesCS6D01G166500 chr3D 18748167 18748813 646 False 1048.0 1048 95.8400 2888 3536 1 chr3D.!!$F1 648
5 TraesCS6D01G166500 chr2B 77815632 77816411 779 False 987.0 987 89.7440 2763 3531 1 chr2B.!!$F1 768
6 TraesCS6D01G166500 chr2B 77859676 77860457 781 False 961.0 961 89.1300 2763 3531 1 chr2B.!!$F2 768
7 TraesCS6D01G166500 chr2B 6340477 6341214 737 True 460.0 460 78.5340 1711 2454 1 chr2B.!!$R1 743
8 TraesCS6D01G166500 chrUn 245559375 245560154 779 False 981.0 981 89.6150 2763 3531 1 chrUn.!!$F1 768
9 TraesCS6D01G166500 chrUn 272849508 272850287 779 False 970.0 970 89.3590 2763 3531 1 chrUn.!!$F2 768
10 TraesCS6D01G166500 chr7B 205766257 205767029 772 True 963.0 963 89.3040 2765 3532 1 chr7B.!!$R1 767
11 TraesCS6D01G166500 chr4B 570119018 570119785 767 True 963.0 963 89.3510 2765 3531 1 chr4B.!!$R1 766
12 TraesCS6D01G166500 chr1B 500625470 500626250 780 True 961.0 961 89.0310 2757 3532 1 chr1B.!!$R1 775
13 TraesCS6D01G166500 chr1B 589496095 589496874 779 False 937.0 937 88.5900 2763 3531 1 chr1B.!!$F1 768
14 TraesCS6D01G166500 chr2D 5080105 5080842 737 False 433.0 433 77.7630 1711 2454 1 chr2D.!!$F1 743

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
624 1094 0.753262 AACTCACAAGAGACAGCCGT 59.247 50.0 0.0 0.0 44.98 5.68 F
1567 2039 0.179108 GATAGCCAACGCCGAAGACT 60.179 55.0 0.0 0.0 34.57 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2531 3013 0.027586 GCAATATTCACGCGGTCACC 59.972 55.0 12.47 0.00 0.0 4.02 R
2810 3315 1.001745 CTGGCGCGCTAAAACCAAAC 61.002 55.0 32.29 10.53 0.0 2.93 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
38 504 0.846693 GGGACTGGGCTCCACATAAT 59.153 55.000 0.00 0.00 30.97 1.28
95 562 8.932945 TTGAGTTCATGTATTTGACTAGCTAG 57.067 34.615 19.44 19.44 0.00 3.42
125 594 4.559862 GGTACCCTAGGATCCATCAATG 57.440 50.000 15.82 0.00 0.00 2.82
132 601 3.878237 AGGATCCATCAATGTGCATCT 57.122 42.857 15.82 0.00 0.00 2.90
133 602 4.180377 AGGATCCATCAATGTGCATCTT 57.820 40.909 15.82 0.00 0.00 2.40
154 623 6.889198 TCTTTAATCGAAGATGATTGGTCCT 58.111 36.000 0.00 0.00 45.12 3.85
160 629 3.118629 CGAAGATGATTGGTCCTTCCTCA 60.119 47.826 0.00 0.00 37.07 3.86
172 641 3.045634 TCCTTCCTCAGACCAACTCAAA 58.954 45.455 0.00 0.00 0.00 2.69
250 719 4.918810 GTTGAACAACAAGGGAGACAAT 57.081 40.909 12.01 0.00 40.84 2.71
265 734 4.102367 GGAGACAATGGCTCCTTCTATCTT 59.898 45.833 27.28 0.00 46.70 2.40
281 750 8.532819 CCTTCTATCTTAGACACTTGTAGGTTT 58.467 37.037 0.00 0.00 33.84 3.27
314 783 2.160813 GCTACACCATGTTTAACCGTGG 59.839 50.000 9.57 9.57 45.37 4.94
321 790 1.886886 TGTTTAACCGTGGAAGGAGC 58.113 50.000 0.00 0.00 34.73 4.70
335 804 3.406764 GAAGGAGCCGAATATGCAGAAT 58.593 45.455 0.00 0.00 0.00 2.40
361 830 9.783081 TGCACATCTATAATCTACAATTGACAT 57.217 29.630 13.59 0.00 0.00 3.06
451 920 3.125829 ACGCTCAATTAGATGCACAGTTG 59.874 43.478 0.00 0.00 0.00 3.16
579 1049 4.202111 GCGCCCATTCAAATTGTATAAGGT 60.202 41.667 0.00 0.00 0.00 3.50
614 1084 6.145534 TCAATAACGAGCACTAAACTCACAAG 59.854 38.462 0.00 0.00 33.58 3.16
624 1094 0.753262 AACTCACAAGAGACAGCCGT 59.247 50.000 0.00 0.00 44.98 5.68
732 1202 1.966451 CCTTCTGGTTGCGTGTCCC 60.966 63.158 0.00 0.00 0.00 4.46
739 1209 0.802494 GGTTGCGTGTCCCACATTAG 59.198 55.000 0.00 0.00 33.40 1.73
899 1370 2.683742 GCAGGCAGCACCCTTAGATAAA 60.684 50.000 0.00 0.00 44.79 1.40
917 1388 7.796958 AGATAAATTTGCACGTTCTAAAAGC 57.203 32.000 0.00 0.00 0.00 3.51
1374 1846 3.479269 CTTGCTCGGCCGTTCGAC 61.479 66.667 27.15 11.60 35.18 4.20
1485 1957 2.668212 CCGCGGCTGTTCTTCCAA 60.668 61.111 14.67 0.00 0.00 3.53
1494 1966 1.674651 GTTCTTCCAAGGGCCGTCC 60.675 63.158 0.00 0.00 0.00 4.79
1525 1997 1.367471 CTCTGTGACCTCAACGCCA 59.633 57.895 0.00 0.00 0.00 5.69
1567 2039 0.179108 GATAGCCAACGCCGAAGACT 60.179 55.000 0.00 0.00 34.57 3.24
1569 2041 4.090057 GCCAACGCCGAAGACTGC 62.090 66.667 0.00 0.00 0.00 4.40
2124 2605 4.803426 CAGCTCGCCGTCCTGTCC 62.803 72.222 0.00 0.00 0.00 4.02
2376 2857 1.818785 GTCAGAGCTCATGCAGGGC 60.819 63.158 17.77 0.58 42.74 5.19
2478 2959 1.135315 TCGTACGAAAGGCTTACGCAT 60.135 47.619 17.11 0.00 42.45 4.73
2512 2994 2.594592 GGCACGTGGAGGCAAAGT 60.595 61.111 18.88 0.00 0.00 2.66
2531 3013 1.093972 TACATGAACATTGCAGCGGG 58.906 50.000 0.00 0.00 0.00 6.13
2665 3152 1.668419 AGCGTGACAGCTCTTGTTTT 58.332 45.000 0.00 0.00 45.67 2.43
2702 3201 4.248859 ACACGATGGAGAGATGTTTCAAG 58.751 43.478 0.00 0.00 0.00 3.02
2733 3236 4.744795 AAAGAGTCAAGACGGCTGATAT 57.255 40.909 0.00 0.00 36.20 1.63
2734 3237 5.854010 AAAGAGTCAAGACGGCTGATATA 57.146 39.130 0.00 0.00 36.20 0.86
2735 3238 4.839668 AGAGTCAAGACGGCTGATATAC 57.160 45.455 0.00 0.00 36.20 1.47
2740 3243 3.379057 TCAAGACGGCTGATATACAACGA 59.621 43.478 0.00 0.00 34.57 3.85
2741 3244 4.037565 TCAAGACGGCTGATATACAACGAT 59.962 41.667 0.00 0.00 34.57 3.73
2783 3286 1.078848 GAGCATCTCCAACAGGCGT 60.079 57.895 0.00 0.00 0.00 5.68
2786 3291 1.746615 CATCTCCAACAGGCGTGGG 60.747 63.158 11.67 3.33 37.61 4.61
2787 3292 3.628646 ATCTCCAACAGGCGTGGGC 62.629 63.158 11.67 0.00 35.96 5.36
2813 3318 3.729698 GCCCGCGCGGTAAAGTTT 61.730 61.111 43.12 0.00 0.00 2.66
2827 3332 0.318360 AAGTTTGGTTTTAGCGCGCC 60.318 50.000 30.33 12.17 0.00 6.53
2828 3333 1.008309 GTTTGGTTTTAGCGCGCCA 60.008 52.632 30.33 12.88 0.00 5.69
2829 3334 1.001745 GTTTGGTTTTAGCGCGCCAG 61.002 55.000 30.33 0.00 32.09 4.85
2830 3335 2.741116 TTTGGTTTTAGCGCGCCAGC 62.741 55.000 30.33 19.03 40.74 4.85
3169 3703 4.764336 CGTTCCGGAGCGCGTACA 62.764 66.667 27.71 0.00 0.00 2.90
3418 3952 2.813908 CCAACGAGCGTGCCTACC 60.814 66.667 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 504 6.768483 TGATATGGAGAAGACACTCAAACAA 58.232 36.000 0.00 0.00 38.51 2.83
132 601 6.542370 GGAAGGACCAATCATCTTCGATTAAA 59.458 38.462 0.00 0.00 37.18 1.52
133 602 6.055588 GGAAGGACCAATCATCTTCGATTAA 58.944 40.000 0.00 0.00 37.18 1.40
154 623 4.855340 AGTTTTTGAGTTGGTCTGAGGAA 58.145 39.130 0.00 0.00 0.00 3.36
160 629 3.699538 GGGTCAAGTTTTTGAGTTGGTCT 59.300 43.478 0.00 0.00 43.66 3.85
250 719 4.873010 AGTGTCTAAGATAGAAGGAGCCA 58.127 43.478 0.00 0.00 36.40 4.75
261 730 8.608844 CTTGAAAACCTACAAGTGTCTAAGAT 57.391 34.615 0.00 0.00 38.72 2.40
281 750 3.500448 TGGTGTAGCCATTGACTTGAA 57.500 42.857 0.00 0.00 43.61 2.69
314 783 2.533266 TCTGCATATTCGGCTCCTTC 57.467 50.000 0.00 0.00 0.00 3.46
335 804 9.783081 ATGTCAATTGTAGATTATAGATGTGCA 57.217 29.630 5.13 0.00 0.00 4.57
361 830 9.008965 TCAGCTACAAGAAATTAAGTGCAAATA 57.991 29.630 0.00 0.00 0.00 1.40
367 836 6.798959 GTGCTTCAGCTACAAGAAATTAAGTG 59.201 38.462 8.48 0.00 42.66 3.16
451 920 1.005137 GACGACACGATAGGACGTCTC 60.005 57.143 16.46 4.27 46.97 3.36
579 1049 4.449743 GTGCTCGTTATTGAAAGGTACACA 59.550 41.667 0.00 0.00 0.00 3.72
614 1084 5.440234 TCTATATGAAGAACGGCTGTCTC 57.560 43.478 0.00 0.00 0.00 3.36
829 1299 1.566298 GCTTCCTCACCCTCACCCAT 61.566 60.000 0.00 0.00 0.00 4.00
830 1300 2.224159 GCTTCCTCACCCTCACCCA 61.224 63.158 0.00 0.00 0.00 4.51
831 1301 2.671682 GCTTCCTCACCCTCACCC 59.328 66.667 0.00 0.00 0.00 4.61
832 1302 2.266055 CGCTTCCTCACCCTCACC 59.734 66.667 0.00 0.00 0.00 4.02
888 1359 6.436843 AGAACGTGCAAATTTATCTAAGGG 57.563 37.500 0.00 0.00 0.00 3.95
899 1370 2.315901 GCGCTTTTAGAACGTGCAAAT 58.684 42.857 0.00 0.00 34.52 2.32
917 1388 8.287503 GGTATTATAATGGTCAAGTAAAAGGCG 58.712 37.037 8.28 0.00 0.00 5.52
1043 1515 3.771491 GCTGTGACGTCGCTGCAG 61.771 66.667 39.19 28.78 46.21 4.41
1315 1787 1.675641 GGAGCATCTGGGCGTTGTT 60.676 57.895 0.00 0.00 39.27 2.83
1494 1966 1.067985 TCACAGAGCGAGAAGAAGCAG 60.068 52.381 0.00 0.00 35.48 4.24
1981 2459 2.360475 GAGAAAAGGCCTGCCGCT 60.360 61.111 5.69 0.82 41.95 5.52
2288 2769 4.545706 GGATCATCACGGGCGCCA 62.546 66.667 30.85 7.96 0.00 5.69
2478 2959 1.276138 TGCCTGAAGCTTTCGATGAGA 59.724 47.619 0.00 0.00 44.23 3.27
2512 2994 1.093972 CCCGCTGCAATGTTCATGTA 58.906 50.000 0.00 0.00 0.00 2.29
2531 3013 0.027586 GCAATATTCACGCGGTCACC 59.972 55.000 12.47 0.00 0.00 4.02
2594 3076 3.541632 ACATGATTACGCCCGAAAATCT 58.458 40.909 0.00 5.29 32.12 2.40
2671 3158 3.692593 TCTCTCCATCGTGTATCGTTGAA 59.307 43.478 0.00 0.00 40.41 2.69
2676 3163 3.906014 ACATCTCTCCATCGTGTATCG 57.094 47.619 0.00 0.00 41.41 2.92
2702 3201 6.237969 GCCGTCTTGACTCTTTTTCTATGATC 60.238 42.308 0.00 0.00 0.00 2.92
2733 3236 6.919662 GGTTCTATCCATCGTTTATCGTTGTA 59.080 38.462 0.00 0.00 40.80 2.41
2734 3237 5.751990 GGTTCTATCCATCGTTTATCGTTGT 59.248 40.000 0.00 0.00 40.80 3.32
2735 3238 5.751509 TGGTTCTATCCATCGTTTATCGTTG 59.248 40.000 0.00 0.00 38.50 4.10
2740 3243 5.272283 ACGTGGTTCTATCCATCGTTTAT 57.728 39.130 0.00 0.00 39.84 1.40
2741 3244 4.724074 ACGTGGTTCTATCCATCGTTTA 57.276 40.909 0.00 0.00 39.84 2.01
2810 3315 1.001745 CTGGCGCGCTAAAACCAAAC 61.002 55.000 32.29 10.53 0.00 2.93
2813 3318 3.732892 GCTGGCGCGCTAAAACCA 61.733 61.111 32.29 17.98 0.00 3.67
2915 3422 2.822255 GGCGCGCCAAATCTACCA 60.822 61.111 43.55 0.00 35.81 3.25
3059 3593 3.723245 GGTAGCCCGAAGAACCCT 58.277 61.111 0.00 0.00 0.00 4.34
3403 3937 4.430765 CCGGTAGGCACGCTCGTT 62.431 66.667 0.00 0.00 0.00 3.85
3461 3995 4.760047 ATGCCTTTCGCCGACGCT 62.760 61.111 0.00 0.00 39.84 5.07


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

AutoCloner maintained by Alex Coulton.