Multiple sequence alignment - TraesCS7D01G285300

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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 TraesCS7D01G285300 chr7D 100.000 2369 0 0 1 2369 306910652 306913020 0 4375
1 TraesCS7D01G285300 chr7D 96.911 1651 50 1 1 1650 203518116 203519766 0 2765
2 TraesCS7D01G285300 chr7D 95.730 726 28 3 1646 2369 203519791 203520515 0 1166
3 TraesCS7D01G285300 chr7B 96.792 1652 51 2 1 1650 644470081 644471732 0 2756
4 TraesCS7D01G285300 chr7B 95.730 726 28 3 1646 2369 644471757 644472481 0 1166
5 TraesCS7D01G285300 chr4D 96.792 1652 51 2 1 1650 123302528 123304179 0 2756
6 TraesCS7D01G285300 chr4D 96.124 1651 61 2 1 1650 123719144 123720792 0 2691
7 TraesCS7D01G285300 chr4D 95.586 725 30 2 1646 2369 123720817 123721540 0 1160
8 TraesCS7D01G285300 chr7A 96.731 1652 52 2 1 1650 60120928 60119277 0 2750
9 TraesCS7D01G285300 chr7A 96.247 1652 59 3 1 1650 63429289 63430939 0 2704
10 TraesCS7D01G285300 chr7A 95.730 726 28 3 1646 2369 60303935 60304659 0 1166
11 TraesCS7D01G285300 chr7A 95.568 722 30 2 1649 2369 60353578 60352858 0 1155
12 TraesCS7D01G285300 chr6B 96.245 1651 61 1 1 1650 306993350 306991700 0 2704
13 TraesCS7D01G285300 chr6B 95.983 722 27 2 1649 2369 306991672 306990952 0 1171
14 TraesCS7D01G285300 chr3A 96.245 1651 60 2 1 1650 633113888 633115537 0 2704
15 TraesCS7D01G285300 chr3A 95.592 726 29 3 1646 2369 633115562 633116286 0 1160
16 TraesCS7D01G285300 chr1B 96.065 1652 63 2 1 1650 638698026 638696375 0 2689
17 TraesCS7D01G285300 chr1B 95.455 726 31 2 1645 2369 672483468 672484192 0 1157
18 TraesCS7D01G285300 chr4B 95.429 722 31 2 1649 2369 209073203 209072483 0 1149


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 TraesCS7D01G285300 chr7D 306910652 306913020 2368 False 4375.0 4375 100.0000 1 2369 1 chr7D.!!$F1 2368
1 TraesCS7D01G285300 chr7D 203518116 203520515 2399 False 1965.5 2765 96.3205 1 2369 2 chr7D.!!$F2 2368
2 TraesCS7D01G285300 chr7B 644470081 644472481 2400 False 1961.0 2756 96.2610 1 2369 2 chr7B.!!$F1 2368
3 TraesCS7D01G285300 chr4D 123302528 123304179 1651 False 2756.0 2756 96.7920 1 1650 1 chr4D.!!$F1 1649
4 TraesCS7D01G285300 chr4D 123719144 123721540 2396 False 1925.5 2691 95.8550 1 2369 2 chr4D.!!$F2 2368
5 TraesCS7D01G285300 chr7A 60119277 60120928 1651 True 2750.0 2750 96.7310 1 1650 1 chr7A.!!$R1 1649
6 TraesCS7D01G285300 chr7A 63429289 63430939 1650 False 2704.0 2704 96.2470 1 1650 1 chr7A.!!$F2 1649
7 TraesCS7D01G285300 chr7A 60303935 60304659 724 False 1166.0 1166 95.7300 1646 2369 1 chr7A.!!$F1 723
8 TraesCS7D01G285300 chr7A 60352858 60353578 720 True 1155.0 1155 95.5680 1649 2369 1 chr7A.!!$R2 720
9 TraesCS7D01G285300 chr6B 306990952 306993350 2398 True 1937.5 2704 96.1140 1 2369 2 chr6B.!!$R1 2368
10 TraesCS7D01G285300 chr3A 633113888 633116286 2398 False 1932.0 2704 95.9185 1 2369 2 chr3A.!!$F1 2368
11 TraesCS7D01G285300 chr1B 638696375 638698026 1651 True 2689.0 2689 96.0650 1 1650 1 chr1B.!!$R1 1649
12 TraesCS7D01G285300 chr1B 672483468 672484192 724 False 1157.0 1157 95.4550 1645 2369 1 chr1B.!!$F1 724
13 TraesCS7D01G285300 chr4B 209072483 209073203 720 True 1149.0 1149 95.4290 1649 2369 1 chr4B.!!$R1 720

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
175 176 0.326048 AGCTGCATCCCTACTCACCT 60.326 55.0 1.02 0.0 0.0 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1754 1788 0.039617 TGCATTTTGGCGCAGTGTAC 60.04 50.0 10.83 0.0 36.28 2.9 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
175 176 0.326048 AGCTGCATCCCTACTCACCT 60.326 55.000 1.02 0.00 0.00 4.00
188 189 1.276421 ACTCACCTGGTCTATGCACAC 59.724 52.381 0.00 0.00 0.00 3.82
408 409 1.064240 AGTCCCCGTTTCAGGTGTTTT 60.064 47.619 0.00 0.00 0.00 2.43
456 457 5.235850 TGTATGTGCCAGGAAGTTTCTTA 57.764 39.130 0.00 0.00 0.00 2.10
551 552 4.685924 GGTTATAAGTAACGTAGCCAGCA 58.314 43.478 0.00 0.00 40.89 4.41
555 556 7.115947 GGTTATAAGTAACGTAGCCAGCATAAG 59.884 40.741 0.00 0.00 40.89 1.73
602 603 3.640967 AGGGCTTTGTTTGTGCAATCTTA 59.359 39.130 0.00 0.00 0.00 2.10
603 604 4.284234 AGGGCTTTGTTTGTGCAATCTTAT 59.716 37.500 0.00 0.00 0.00 1.73
763 765 1.603678 GCTCCACGTACGGTTTGAAGA 60.604 52.381 21.06 4.32 0.00 2.87
777 779 1.048601 TGAAGACGAGCCTTTCCAGT 58.951 50.000 0.00 0.00 0.00 4.00
865 867 0.535335 GGGATTAGTGCGTGAGACCA 59.465 55.000 0.00 0.00 0.00 4.02
882 884 0.462937 CCACGACCCACAAACTGACA 60.463 55.000 0.00 0.00 0.00 3.58
1104 1106 1.405872 TGTACGTTGTCACACTCCCT 58.594 50.000 0.00 0.00 0.00 4.20
1116 1118 1.464198 ACTCCCTGCCCTCCAAAGT 60.464 57.895 0.00 0.00 0.00 2.66
1172 1174 1.414061 CCCAGGAGCGGATTCCTCAT 61.414 60.000 0.30 0.00 45.86 2.90
1189 1191 1.997874 ATGAGCAGGGGGACAGGAC 60.998 63.158 0.00 0.00 0.00 3.85
1230 1232 1.369692 CGACCTACAGGCAACACCA 59.630 57.895 0.00 0.00 43.14 4.17
1239 1241 2.031163 GCAACACCAGCGAGACCT 59.969 61.111 0.00 0.00 0.00 3.85
1276 1278 5.246203 CGATTGGGAGTTAGAGGATCCATAA 59.754 44.000 15.82 9.84 34.62 1.90
1394 1399 2.429610 ACTCGGCACAACCTAACGATAT 59.570 45.455 0.00 0.00 35.61 1.63
1426 1431 4.240888 CAATGATCTGTGCCTACCGATAG 58.759 47.826 0.00 0.00 31.89 2.08
1526 1531 0.471211 ACTCCTCCCGACACCTCAAA 60.471 55.000 0.00 0.00 0.00 2.69
1575 1580 2.427245 CCGTGCCTACTCAGGGAGG 61.427 68.421 0.00 0.00 44.00 4.30
1624 1629 0.179029 CCACAAAGACCAACGACCCT 60.179 55.000 0.00 0.00 0.00 4.34
1641 1646 1.339151 CCCTTCCCGAAGAGAAGTTGG 60.339 57.143 6.01 0.00 40.95 3.77
1647 1681 2.005451 CCGAAGAGAAGTTGGCTGATG 58.995 52.381 0.00 0.00 0.00 3.07
1698 1732 2.093235 CAGGGGTTGCCAACAAAAAGAA 60.093 45.455 10.18 0.00 37.58 2.52
1705 1739 5.356751 GGTTGCCAACAAAAAGAAAGGAAAT 59.643 36.000 10.18 0.00 37.58 2.17
1747 1781 1.560505 GTACCGTACCCCAAGGAAGA 58.439 55.000 0.00 0.00 36.73 2.87
1754 1788 3.573110 CGTACCCCAAGGAAGAGGTATAG 59.427 52.174 0.00 0.00 37.22 1.31
1757 1791 4.554683 ACCCCAAGGAAGAGGTATAGTAC 58.445 47.826 0.00 0.00 36.73 2.73
1880 1914 8.238631 GCCCTTCTTCTCGTATTCTATACTAAG 58.761 40.741 0.00 0.00 0.00 2.18
1946 1981 2.551504 GGAAGGGCGGTTAGAACAAAGA 60.552 50.000 0.00 0.00 0.00 2.52
1979 2014 1.360820 TTCAATGCGCGAAATCCGTA 58.639 45.000 12.10 0.00 41.15 4.02
2016 2051 1.208614 CTTCTTGCTGCAGCCGTTC 59.791 57.895 34.64 8.86 41.18 3.95
2040 2075 2.881074 TCGCTGCTTGCTACTTTCTAG 58.119 47.619 0.00 0.00 40.11 2.43
2078 2113 9.914131 AGATGAATGAATGAATAGATTGCATTG 57.086 29.630 0.00 0.00 32.80 2.82
2117 2155 8.001300 TCTATAGTCTAGATTCCATTCCCTCA 57.999 38.462 0.00 0.00 0.00 3.86
2127 2165 4.007581 TCCATTCCCTCAATCCACTCTA 57.992 45.455 0.00 0.00 0.00 2.43
2128 2166 3.969976 TCCATTCCCTCAATCCACTCTAG 59.030 47.826 0.00 0.00 0.00 2.43
2271 2309 1.210478 CCTTCCCACAGAATCATCGGT 59.790 52.381 0.00 0.00 34.06 4.69
2288 2326 4.516365 TCGGTCTTGACTTTCCTTACTC 57.484 45.455 0.61 0.00 0.00 2.59
2299 2337 0.494551 TCCTTACTCTCCCAACCCCA 59.505 55.000 0.00 0.00 0.00 4.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 55 1.404843 GGCTCCGTCCTAGAATCTGT 58.595 55.000 0.00 0.00 0.00 3.41
77 78 2.401592 CGTGAGACTCTCGCCTCG 59.598 66.667 13.40 6.29 37.68 4.63
188 189 0.674895 CAACCTCCTGGAAAGAGCGG 60.675 60.000 0.00 0.00 37.04 5.52
297 298 1.315257 AAATGCTGCACGGACCCATC 61.315 55.000 3.57 0.00 0.00 3.51
551 552 5.221661 CCCGCAACCCTATTCTAGAACTTAT 60.222 44.000 7.48 0.00 0.00 1.73
555 556 2.835027 CCCGCAACCCTATTCTAGAAC 58.165 52.381 7.48 0.00 0.00 3.01
602 603 0.250513 GAGGAGAGGGTGTTGCGAAT 59.749 55.000 0.00 0.00 0.00 3.34
603 604 1.671742 GAGGAGAGGGTGTTGCGAA 59.328 57.895 0.00 0.00 0.00 4.70
763 765 1.065418 CCCATTACTGGAAAGGCTCGT 60.065 52.381 0.00 0.00 46.37 4.18
777 779 1.460689 CGGTCCCTAGGCCCCATTA 60.461 63.158 2.05 0.00 0.00 1.90
834 836 0.393077 CTAATCCCTACAGGTGCCCG 59.607 60.000 0.00 0.00 36.75 6.13
865 867 0.250793 TGTGTCAGTTTGTGGGTCGT 59.749 50.000 0.00 0.00 0.00 4.34
869 871 0.961019 CCCATGTGTCAGTTTGTGGG 59.039 55.000 0.00 0.00 40.22 4.61
989 991 0.918310 AGGCCTCATCTCCAAAGCCT 60.918 55.000 0.00 0.00 45.72 4.58
1084 1086 1.968493 AGGGAGTGTGACAACGTACAT 59.032 47.619 0.00 0.00 0.00 2.29
1150 1152 3.483869 GAATCCGCTCCTGGGGCT 61.484 66.667 17.97 0.00 44.90 5.19
1169 1171 1.997311 CCTGTCCCCCTGCTCATGA 60.997 63.158 0.00 0.00 0.00 3.07
1172 1174 2.607750 GTCCTGTCCCCCTGCTCA 60.608 66.667 0.00 0.00 0.00 4.26
1263 1265 4.023980 CTGCGGGTATTATGGATCCTCTA 58.976 47.826 14.23 1.76 0.00 2.43
1394 1399 5.073554 AGGCACAGATCATTGGTATTGGATA 59.926 40.000 0.00 0.00 0.00 2.59
1559 1564 0.537653 GTTCCTCCCTGAGTAGGCAC 59.462 60.000 0.00 0.00 43.16 5.01
1575 1580 1.000506 TGTCAGCCGTGGTAGAAGTTC 59.999 52.381 0.00 0.00 0.00 3.01
1624 1629 1.056660 AGCCAACTTCTCTTCGGGAA 58.943 50.000 0.00 0.00 0.00 3.97
1698 1732 5.734031 AATTCACTAGGGCCTATTTCCTT 57.266 39.130 14.95 3.03 34.75 3.36
1705 1739 5.610982 ACCATATCAAATTCACTAGGGCCTA 59.389 40.000 13.73 13.73 0.00 3.93
1747 1781 1.771565 TGGCGCAGTGTACTATACCT 58.228 50.000 10.83 0.00 0.00 3.08
1754 1788 0.039617 TGCATTTTGGCGCAGTGTAC 60.040 50.000 10.83 0.00 36.28 2.90
1757 1791 0.935898 TTTTGCATTTTGGCGCAGTG 59.064 45.000 10.83 0.00 39.75 3.66
1908 1943 7.094075 CCGCCCTTCCTTTAAGTTTTAGTATTT 60.094 37.037 0.00 0.00 32.89 1.40
1915 1950 2.953453 ACCGCCCTTCCTTTAAGTTTT 58.047 42.857 0.00 0.00 32.89 2.43
1946 1981 3.057315 CGCATTGAAAGTGTCATCCCTTT 60.057 43.478 0.00 0.00 35.70 3.11
1979 2014 3.851976 AGTTTCGCACTCTAACTCGAT 57.148 42.857 0.00 0.00 0.00 3.59
2117 2155 7.872138 TCCCATCATTTAAACTAGAGTGGATT 58.128 34.615 0.00 0.00 0.00 3.01
2127 2165 3.711190 GGCCCAATCCCATCATTTAAACT 59.289 43.478 0.00 0.00 0.00 2.66
2128 2166 3.454082 TGGCCCAATCCCATCATTTAAAC 59.546 43.478 0.00 0.00 0.00 2.01
2181 2219 5.163581 CCCAATCCTTGAAGTTATGAAGCAG 60.164 44.000 0.00 0.00 0.00 4.24
2191 2229 1.918957 CCTCCTCCCAATCCTTGAAGT 59.081 52.381 0.00 0.00 0.00 3.01
2271 2309 4.489737 TGGGAGAGTAAGGAAAGTCAAGA 58.510 43.478 0.00 0.00 0.00 3.02
2288 2326 1.946984 TACAGTAGTGGGGTTGGGAG 58.053 55.000 1.92 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.