Multiple sequence alignment - TraesCS6A01G109900

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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 TraesCS6A01G109900 chr6A 100.000 2219 0 0 1 2219 79195943 79198161 0 4098
1 TraesCS6A01G109900 chr4D 94.674 2253 83 13 1 2219 123350115 123352364 0 3461
2 TraesCS6A01G109900 chr4D 93.792 2255 101 12 1 2219 134979417 134981668 0 3352
3 TraesCS6A01G109900 chr4D 93.372 2248 110 15 1 2217 240994781 240992542 0 3290
4 TraesCS6A01G109900 chr4D 93.914 1643 65 11 610 2219 123561662 123563302 0 2447
5 TraesCS6A01G109900 chr5D 94.358 2251 89 17 1 2219 301054394 301056638 0 3419
6 TraesCS6A01G109900 chr5D 93.282 2188 114 19 1 2178 80018444 80016280 0 3195
7 TraesCS6A01G109900 chr6D 93.911 2250 89 14 1 2219 370022511 370024743 0 3352
8 TraesCS6A01G109900 chr1D 93.467 2250 95 19 1 2218 269426755 269424526 0 3293
9 TraesCS6A01G109900 chr1D 93.142 1254 50 12 1 1221 185743768 185742518 0 1807
10 TraesCS6A01G109900 chr1D 94.368 1012 45 10 219 1221 185797629 185796621 0 1543
11 TraesCS6A01G109900 chr7D 97.397 1191 28 3 1030 2219 382029143 382027955 0 2025
12 TraesCS6A01G109900 chr7B 93.774 1317 45 12 1 1284 716784601 716785913 0 1943
13 TraesCS6A01G109900 chr7B 93.636 1320 47 12 1 1287 742948744 742947429 0 1938
14 TraesCS6A01G109900 chr7A 93.698 1317 46 12 1 1284 60084930 60086242 0 1938
15 TraesCS6A01G109900 chr7A 93.561 1320 48 12 1 1287 60168773 60167458 0 1932
16 TraesCS6A01G109900 chr5A 93.470 1317 49 12 1 1284 16544548 16545860 0 1921
17 TraesCS6A01G109900 chr5A 93.470 1317 49 12 1 1284 420185696 420187008 0 1921
18 TraesCS6A01G109900 chrUn 93.588 655 32 8 575 1221 422736166 422735514 0 968


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 TraesCS6A01G109900 chr6A 79195943 79198161 2218 False 4098 4098 100.000 1 2219 1 chr6A.!!$F1 2218
1 TraesCS6A01G109900 chr4D 123350115 123352364 2249 False 3461 3461 94.674 1 2219 1 chr4D.!!$F1 2218
2 TraesCS6A01G109900 chr4D 134979417 134981668 2251 False 3352 3352 93.792 1 2219 1 chr4D.!!$F3 2218
3 TraesCS6A01G109900 chr4D 240992542 240994781 2239 True 3290 3290 93.372 1 2217 1 chr4D.!!$R1 2216
4 TraesCS6A01G109900 chr4D 123561662 123563302 1640 False 2447 2447 93.914 610 2219 1 chr4D.!!$F2 1609
5 TraesCS6A01G109900 chr5D 301054394 301056638 2244 False 3419 3419 94.358 1 2219 1 chr5D.!!$F1 2218
6 TraesCS6A01G109900 chr5D 80016280 80018444 2164 True 3195 3195 93.282 1 2178 1 chr5D.!!$R1 2177
7 TraesCS6A01G109900 chr6D 370022511 370024743 2232 False 3352 3352 93.911 1 2219 1 chr6D.!!$F1 2218
8 TraesCS6A01G109900 chr1D 269424526 269426755 2229 True 3293 3293 93.467 1 2218 1 chr1D.!!$R3 2217
9 TraesCS6A01G109900 chr1D 185742518 185743768 1250 True 1807 1807 93.142 1 1221 1 chr1D.!!$R1 1220
10 TraesCS6A01G109900 chr1D 185796621 185797629 1008 True 1543 1543 94.368 219 1221 1 chr1D.!!$R2 1002
11 TraesCS6A01G109900 chr7D 382027955 382029143 1188 True 2025 2025 97.397 1030 2219 1 chr7D.!!$R1 1189
12 TraesCS6A01G109900 chr7B 716784601 716785913 1312 False 1943 1943 93.774 1 1284 1 chr7B.!!$F1 1283
13 TraesCS6A01G109900 chr7B 742947429 742948744 1315 True 1938 1938 93.636 1 1287 1 chr7B.!!$R1 1286
14 TraesCS6A01G109900 chr7A 60084930 60086242 1312 False 1938 1938 93.698 1 1284 1 chr7A.!!$F1 1283
15 TraesCS6A01G109900 chr7A 60167458 60168773 1315 True 1932 1932 93.561 1 1287 1 chr7A.!!$R1 1286
16 TraesCS6A01G109900 chr5A 16544548 16545860 1312 False 1921 1921 93.470 1 1284 1 chr5A.!!$F1 1283
17 TraesCS6A01G109900 chr5A 420185696 420187008 1312 False 1921 1921 93.470 1 1284 1 chr5A.!!$F2 1283
18 TraesCS6A01G109900 chrUn 422735514 422736166 652 True 968 968 93.588 575 1221 1 chrUn.!!$R1 646

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
144 145 1.076332 GCTTATCCGTCAGTTGCGTT 58.924 50.0 0.0 0.0 0.0 4.84 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1996 2043 0.392461 TTGGAGCATACCCAGAACGC 60.392 55.0 0.0 0.0 34.77 4.84 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
108 109 6.090088 CAGAGATCTTTTATCGCGGAATTAGG 59.910 42.308 6.13 0.00 0.00 2.69
139 140 3.350219 ACATTGGCTTATCCGTCAGTT 57.650 42.857 0.00 0.00 37.80 3.16
144 145 1.076332 GCTTATCCGTCAGTTGCGTT 58.924 50.000 0.00 0.00 0.00 4.84
224 225 1.286501 GCACAATATCGCGAAGTGGA 58.713 50.000 25.09 8.05 39.32 4.02
291 292 4.878397 GCATTACTCAATAGAGGTGCAAGT 59.122 41.667 11.93 0.00 46.44 3.16
296 297 6.552445 ACTCAATAGAGGTGCAAGTCTTAT 57.448 37.500 4.48 0.00 46.44 1.73
422 423 9.393512 AGACAGAATTTCTCAATATGAAGAAGG 57.606 33.333 0.00 0.00 0.00 3.46
467 468 7.663905 TCCTGAATTACAAAAATCCTTCTTCGA 59.336 33.333 0.00 0.00 0.00 3.71
506 507 6.059484 ACTAACGAAAGAAAGATGGAACCAA 58.941 36.000 0.00 0.00 0.00 3.67
507 508 4.830826 ACGAAAGAAAGATGGAACCAAC 57.169 40.909 0.00 0.00 0.00 3.77
541 542 6.378710 AAAGAAAGCACTTTGTCTTACCTC 57.621 37.500 0.00 0.00 38.45 3.85
630 632 4.584743 CCCCAATAGGCTATTTTGGACTTC 59.415 45.833 22.72 0.00 42.02 3.01
865 867 6.813152 ACAAGCCTTGCAAATTGTGATAATAC 59.187 34.615 18.38 0.00 34.71 1.89
899 901 4.103469 AGTGGTCCGCATAACCCAATATTA 59.897 41.667 4.97 0.00 35.84 0.98
903 905 5.411669 GGTCCGCATAACCCAATATTAGAAG 59.588 44.000 0.00 0.00 0.00 2.85
904 906 5.411669 GTCCGCATAACCCAATATTAGAAGG 59.588 44.000 0.00 0.00 0.00 3.46
905 907 5.308497 TCCGCATAACCCAATATTAGAAGGA 59.692 40.000 0.00 0.00 0.00 3.36
934 944 4.780815 CAGGCCCAGTACTTTGAATCATA 58.219 43.478 0.00 0.00 0.00 2.15
938 948 5.163550 GGCCCAGTACTTTGAATCATAAACC 60.164 44.000 0.00 0.00 0.00 3.27
939 949 5.163550 GCCCAGTACTTTGAATCATAAACCC 60.164 44.000 0.00 0.00 0.00 4.11
940 950 5.949354 CCCAGTACTTTGAATCATAAACCCA 59.051 40.000 0.00 0.00 0.00 4.51
947 957 8.206126 ACTTTGAATCATAAACCCAAAATCCT 57.794 30.769 0.00 0.00 0.00 3.24
948 958 8.096414 ACTTTGAATCATAAACCCAAAATCCTG 58.904 33.333 0.00 0.00 0.00 3.86
953 963 7.754091 ATCATAAACCCAAAATCCTGGAAAT 57.246 32.000 0.00 0.00 38.96 2.17
956 966 9.105844 TCATAAACCCAAAATCCTGGAAATAAA 57.894 29.630 0.00 0.00 38.96 1.40
957 967 9.161629 CATAAACCCAAAATCCTGGAAATAAAC 57.838 33.333 0.00 0.00 38.96 2.01
959 969 6.358974 ACCCAAAATCCTGGAAATAAACAG 57.641 37.500 0.00 0.00 38.96 3.16
960 970 5.843969 ACCCAAAATCCTGGAAATAAACAGT 59.156 36.000 0.00 0.00 38.96 3.55
961 971 6.165577 CCCAAAATCCTGGAAATAAACAGTG 58.834 40.000 0.00 0.00 38.96 3.66
963 973 7.441017 CCAAAATCCTGGAAATAAACAGTGAA 58.559 34.615 0.00 0.00 38.96 3.18
964 974 7.384932 CCAAAATCCTGGAAATAAACAGTGAAC 59.615 37.037 0.00 0.00 38.96 3.18
965 975 5.880054 ATCCTGGAAATAAACAGTGAACG 57.120 39.130 0.00 0.00 32.90 3.95
971 981 6.853720 TGGAAATAAACAGTGAACGAAAACA 58.146 32.000 0.00 0.00 0.00 2.83
975 985 9.180678 GAAATAAACAGTGAACGAAAACATGAT 57.819 29.630 0.00 0.00 0.00 2.45
976 986 8.728088 AATAAACAGTGAACGAAAACATGATC 57.272 30.769 0.00 0.00 0.00 2.92
984 997 7.759433 AGTGAACGAAAACATGATCAAAAAGTT 59.241 29.630 0.00 0.00 0.00 2.66
985 998 7.840797 GTGAACGAAAACATGATCAAAAAGTTG 59.159 33.333 0.00 0.00 35.95 3.16
994 1007 7.134815 ACATGATCAAAAAGTTGTTTCTCGAG 58.865 34.615 5.93 5.93 36.07 4.04
1198 1235 5.123027 GCCTTTCTGATCTCATTCGTTTTCT 59.877 40.000 0.00 0.00 0.00 2.52
1284 1321 6.654793 AAAGTCAATATCTCGTTCTCTTGC 57.345 37.500 0.00 0.00 0.00 4.01
1386 1425 0.856982 TTTTGAAAGGGCAGAGGGGA 59.143 50.000 0.00 0.00 0.00 4.81
1389 1428 1.084018 TGAAAGGGCAGAGGGGAAAT 58.916 50.000 0.00 0.00 0.00 2.17
1518 1565 8.147642 AGTTATCATTGTGATAGCTGCTTTAC 57.852 34.615 7.79 5.60 45.21 2.01
1699 1746 0.889186 GGGCTTGAAACTCCTTCGCA 60.889 55.000 0.00 0.00 36.78 5.10
1702 1749 2.029918 GGCTTGAAACTCCTTCGCATTT 60.030 45.455 0.00 0.00 36.78 2.32
1709 1756 2.338577 CTCCTTCGCATTTGGAGGAT 57.661 50.000 0.00 0.00 42.55 3.24
1712 1759 1.672881 CCTTCGCATTTGGAGGATGAC 59.327 52.381 0.00 0.00 0.00 3.06
1775 1822 6.687081 AATGACTTTGACCTTAACGAACAA 57.313 33.333 0.00 0.00 0.00 2.83
1780 1827 1.202557 TGACCTTAACGAACAACCGCT 60.203 47.619 0.00 0.00 0.00 5.52
1815 1862 4.254709 AGCAGGAACAGCCGTGCA 62.255 61.111 10.50 0.00 43.90 4.57
1835 1882 0.898326 TAGAGCAACAGCCTCGTCCA 60.898 55.000 0.00 0.00 0.00 4.02
1996 2043 2.460918 CGACAGTAATGCTAAGGACGG 58.539 52.381 0.00 0.00 0.00 4.79
2026 2073 6.619464 TGGGTATGCTCCAATTAAATACCAT 58.381 36.000 11.21 0.00 42.99 3.55
2085 2134 0.322546 GCCTTTTCCCGATGGTGTCT 60.323 55.000 0.00 0.00 0.00 3.41
2103 2152 2.945668 GTCTTTTCGGATCCTGGGAATG 59.054 50.000 10.75 0.00 0.00 2.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
88 89 3.751698 GGCCTAATTCCGCGATAAAAGAT 59.248 43.478 8.23 0.00 0.00 2.40
224 225 1.586154 CCCAAATTGAGCGAAGGCGT 61.586 55.000 0.00 0.00 46.35 5.68
291 292 5.007682 GGTTGTTTGGGCACTTCTATAAGA 58.992 41.667 0.00 0.00 36.50 2.10
296 297 2.303175 GTGGTTGTTTGGGCACTTCTA 58.697 47.619 0.00 0.00 0.00 2.10
865 867 3.191669 TGCGGACCACTAATTTGATACG 58.808 45.455 0.00 0.00 0.00 3.06
899 901 2.297129 GGCCTGCACCTCTCCTTCT 61.297 63.158 0.00 0.00 0.00 2.85
903 905 4.106925 CTGGGCCTGCACCTCTCC 62.107 72.222 4.53 0.00 0.00 3.71
904 906 1.990060 TACTGGGCCTGCACCTCTC 60.990 63.158 10.71 0.00 0.00 3.20
905 907 2.122729 TACTGGGCCTGCACCTCT 59.877 61.111 10.71 0.00 0.00 3.69
934 944 7.142995 TGTTTATTTCCAGGATTTTGGGTTT 57.857 32.000 0.00 0.00 38.81 3.27
938 948 6.991938 TCACTGTTTATTTCCAGGATTTTGG 58.008 36.000 0.00 0.00 39.70 3.28
939 949 7.114811 CGTTCACTGTTTATTTCCAGGATTTTG 59.885 37.037 0.00 0.00 32.90 2.44
940 950 7.013846 TCGTTCACTGTTTATTTCCAGGATTTT 59.986 33.333 0.00 0.00 32.90 1.82
947 957 6.853720 TGTTTTCGTTCACTGTTTATTTCCA 58.146 32.000 0.00 0.00 0.00 3.53
948 958 7.646130 TCATGTTTTCGTTCACTGTTTATTTCC 59.354 33.333 0.00 0.00 0.00 3.13
953 963 7.252965 TGATCATGTTTTCGTTCACTGTTTA 57.747 32.000 0.00 0.00 0.00 2.01
956 966 5.749596 TTGATCATGTTTTCGTTCACTGT 57.250 34.783 0.00 0.00 0.00 3.55
957 967 7.220683 ACTTTTTGATCATGTTTTCGTTCACTG 59.779 33.333 0.00 0.00 0.00 3.66
959 969 7.449934 ACTTTTTGATCATGTTTTCGTTCAC 57.550 32.000 0.00 0.00 0.00 3.18
960 970 7.543868 ACAACTTTTTGATCATGTTTTCGTTCA 59.456 29.630 0.00 0.00 36.48 3.18
961 971 7.894847 ACAACTTTTTGATCATGTTTTCGTTC 58.105 30.769 0.00 0.00 36.48 3.95
963 973 7.826260 AACAACTTTTTGATCATGTTTTCGT 57.174 28.000 0.00 0.00 36.48 3.85
964 974 8.594687 AGAAACAACTTTTTGATCATGTTTTCG 58.405 29.630 18.83 1.69 40.08 3.46
965 975 9.906111 GAGAAACAACTTTTTGATCATGTTTTC 57.094 29.630 18.83 14.88 40.08 2.29
971 981 7.264373 ACTCGAGAAACAACTTTTTGATCAT 57.736 32.000 21.68 0.00 36.48 2.45
975 985 4.865925 TCGACTCGAGAAACAACTTTTTGA 59.134 37.500 21.68 0.00 36.48 2.69
976 986 5.138800 TCGACTCGAGAAACAACTTTTTG 57.861 39.130 21.68 0.00 38.83 2.44
994 1007 3.512033 AGCACCTTCTAACATCTCGAC 57.488 47.619 0.00 0.00 0.00 4.20
1198 1235 6.762661 TGATCTCATGACTTTTTATGCGATCA 59.237 34.615 12.99 12.99 45.66 2.92
1284 1321 5.756195 TCAATAAAAAGGCCATCATCGAG 57.244 39.130 5.01 0.00 0.00 4.04
1518 1565 4.457603 CACGATCAAGGAGGGATCTACTAG 59.542 50.000 0.00 0.00 39.17 2.57
1709 1756 2.528818 CCCTGCCTTGGAGGTGTCA 61.529 63.158 0.86 0.00 39.62 3.58
1712 1759 3.260100 ACCCCTGCCTTGGAGGTG 61.260 66.667 0.86 0.00 39.62 4.00
1815 1862 0.461961 GGACGAGGCTGTTGCTCTAT 59.538 55.000 0.00 0.00 39.59 1.98
1860 1907 2.689983 GGTGGAATGGATTTGCTTCGAT 59.310 45.455 0.00 0.00 0.00 3.59
1861 1908 2.091541 GGTGGAATGGATTTGCTTCGA 58.908 47.619 0.00 0.00 0.00 3.71
1933 1980 5.180304 GGAGCTGGATATTTTTCTCGGATTC 59.820 44.000 0.00 0.00 0.00 2.52
1996 2043 0.392461 TTGGAGCATACCCAGAACGC 60.392 55.000 0.00 0.00 34.77 4.84
2085 2134 2.722094 CACATTCCCAGGATCCGAAAA 58.278 47.619 5.98 0.14 0.00 2.29
2103 2152 1.069204 TCGATCTTGATAGCCTGGCAC 59.931 52.381 22.65 12.12 0.00 5.01


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

AutoCloner maintained by Alex Coulton.