Multiple sequence alignment - TraesCS6D01G143200

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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 TraesCS6D01G143200 chr6D 100.000 2771 0 0 1 2771 114018076 114015306 0 5118
1 TraesCS6D01G143200 chr6D 97.662 727 16 1 2045 2771 16605156 16604431 0 1247
2 TraesCS6D01G143200 chr6D 94.186 516 29 1 2 516 321742365 321741850 0 785
3 TraesCS6D01G143200 chr6D 94.163 514 29 1 1 513 281618278 281618791 0 782
4 TraesCS6D01G143200 chr2D 95.599 1545 58 2 517 2051 260867187 260865643 0 2468
5 TraesCS6D01G143200 chr2D 96.064 1499 57 2 517 2014 613419783 613421280 0 2440
6 TraesCS6D01G143200 chr2D 95.431 1532 49 4 521 2051 451467953 451469464 0 2422
7 TraesCS6D01G143200 chr2D 92.522 1511 91 5 517 2025 520043085 520044575 0 2145
8 TraesCS6D01G143200 chr2D 97.524 727 17 1 2045 2771 451490093 451490818 0 1242
9 TraesCS6D01G143200 chr2D 96.699 727 23 1 2045 2771 260862719 260861994 0 1208
10 TraesCS6D01G143200 chr2D 96.424 727 23 3 2045 2771 241273361 241274084 0 1195
11 TraesCS6D01G143200 chr2D 93.407 728 41 5 2045 2771 35327478 35326757 0 1072
12 TraesCS6D01G143200 chr2D 94.391 517 28 1 1 516 159681491 159682007 0 793
13 TraesCS6D01G143200 chr5D 95.754 1413 59 1 640 2051 26959808 26958396 0 2276
14 TraesCS6D01G143200 chr5D 96.149 727 27 1 2045 2771 26955475 26954750 0 1186
15 TraesCS6D01G143200 chr5D 94.778 517 26 1 1 516 177461535 177461019 0 804
16 TraesCS6D01G143200 chr5D 93.992 516 30 1 1 515 291803124 291802609 0 780
17 TraesCS6D01G143200 chr5B 93.447 1526 96 3 514 2037 260234929 260236452 0 2261
18 TraesCS6D01G143200 chr7D 92.128 1537 95 10 521 2053 151511976 151513490 0 2145
19 TraesCS6D01G143200 chr7D 94.186 516 29 1 2 516 313656673 313657188 0 785
20 TraesCS6D01G143200 chr7D 94.004 517 29 2 1 516 311179983 311180498 0 782
21 TraesCS6D01G143200 chr6A 92.579 1388 92 6 517 1897 596355514 596356897 0 1982
22 TraesCS6D01G143200 chr6A 91.597 1428 114 5 514 1941 144491470 144492891 0 1967
23 TraesCS6D01G143200 chr6A 94.321 722 36 4 2045 2763 596360055 596360774 0 1101
24 TraesCS6D01G143200 chr6B 89.467 1538 131 11 517 2053 494076435 494077942 0 1914
25 TraesCS6D01G143200 chr2A 93.396 742 42 6 2027 2763 673361969 673362708 0 1092
26 TraesCS6D01G143200 chr3A 94.044 722 38 4 2045 2763 478917954 478918673 0 1090
27 TraesCS6D01G143200 chr3A 94.197 517 29 1 1 516 645005939 645006455 0 787
28 TraesCS6D01G143200 chr4D 94.197 517 28 2 1 516 346318334 346318849 0 787


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 TraesCS6D01G143200 chr6D 114015306 114018076 2770 True 5118.0 5118 100.0000 1 2771 1 chr6D.!!$R2 2770
1 TraesCS6D01G143200 chr6D 16604431 16605156 725 True 1247.0 1247 97.6620 2045 2771 1 chr6D.!!$R1 726
2 TraesCS6D01G143200 chr6D 321741850 321742365 515 True 785.0 785 94.1860 2 516 1 chr6D.!!$R3 514
3 TraesCS6D01G143200 chr6D 281618278 281618791 513 False 782.0 782 94.1630 1 513 1 chr6D.!!$F1 512
4 TraesCS6D01G143200 chr2D 613419783 613421280 1497 False 2440.0 2440 96.0640 517 2014 1 chr2D.!!$F6 1497
5 TraesCS6D01G143200 chr2D 451467953 451469464 1511 False 2422.0 2422 95.4310 521 2051 1 chr2D.!!$F3 1530
6 TraesCS6D01G143200 chr2D 520043085 520044575 1490 False 2145.0 2145 92.5220 517 2025 1 chr2D.!!$F5 1508
7 TraesCS6D01G143200 chr2D 260861994 260867187 5193 True 1838.0 2468 96.1490 517 2771 2 chr2D.!!$R2 2254
8 TraesCS6D01G143200 chr2D 451490093 451490818 725 False 1242.0 1242 97.5240 2045 2771 1 chr2D.!!$F4 726
9 TraesCS6D01G143200 chr2D 241273361 241274084 723 False 1195.0 1195 96.4240 2045 2771 1 chr2D.!!$F2 726
10 TraesCS6D01G143200 chr2D 35326757 35327478 721 True 1072.0 1072 93.4070 2045 2771 1 chr2D.!!$R1 726
11 TraesCS6D01G143200 chr2D 159681491 159682007 516 False 793.0 793 94.3910 1 516 1 chr2D.!!$F1 515
12 TraesCS6D01G143200 chr5D 26954750 26959808 5058 True 1731.0 2276 95.9515 640 2771 2 chr5D.!!$R3 2131
13 TraesCS6D01G143200 chr5D 177461019 177461535 516 True 804.0 804 94.7780 1 516 1 chr5D.!!$R1 515
14 TraesCS6D01G143200 chr5D 291802609 291803124 515 True 780.0 780 93.9920 1 515 1 chr5D.!!$R2 514
15 TraesCS6D01G143200 chr5B 260234929 260236452 1523 False 2261.0 2261 93.4470 514 2037 1 chr5B.!!$F1 1523
16 TraesCS6D01G143200 chr7D 151511976 151513490 1514 False 2145.0 2145 92.1280 521 2053 1 chr7D.!!$F1 1532
17 TraesCS6D01G143200 chr7D 313656673 313657188 515 False 785.0 785 94.1860 2 516 1 chr7D.!!$F3 514
18 TraesCS6D01G143200 chr7D 311179983 311180498 515 False 782.0 782 94.0040 1 516 1 chr7D.!!$F2 515
19 TraesCS6D01G143200 chr6A 144491470 144492891 1421 False 1967.0 1967 91.5970 514 1941 1 chr6A.!!$F1 1427
20 TraesCS6D01G143200 chr6A 596355514 596360774 5260 False 1541.5 1982 93.4500 517 2763 2 chr6A.!!$F2 2246
21 TraesCS6D01G143200 chr6B 494076435 494077942 1507 False 1914.0 1914 89.4670 517 2053 1 chr6B.!!$F1 1536
22 TraesCS6D01G143200 chr2A 673361969 673362708 739 False 1092.0 1092 93.3960 2027 2763 1 chr2A.!!$F1 736
23 TraesCS6D01G143200 chr3A 478917954 478918673 719 False 1090.0 1090 94.0440 2045 2763 1 chr3A.!!$F1 718
24 TraesCS6D01G143200 chr3A 645005939 645006455 516 False 787.0 787 94.1970 1 516 1 chr3A.!!$F2 515
25 TraesCS6D01G143200 chr4D 346318334 346318849 515 False 787.0 787 94.1970 1 516 1 chr4D.!!$F1 515

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
619 621 0.456628 AACAAAACCAAACCGGACGG 59.543 50.0 9.46 9.56 38.63 4.79 F
1460 1471 0.036388 TGGCTTCATGACCCTTCGTC 60.036 55.0 11.71 0.00 42.33 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1724 1736 0.035152 ATCGATCTTGCCCAGCACAA 60.035 50.0 0.0 0.0 38.71 3.33 R
2612 5822 0.410663 TCCCCGACCTGTTCCTTCTA 59.589 55.0 0.0 0.0 0.00 2.10 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
32 33 0.661552 CGTCGGAGAAGGCGATAGAA 59.338 55.000 0.00 0.00 42.53 2.10
105 106 1.539388 CATGCGGCTAGTTTTTGGACA 59.461 47.619 0.00 0.00 0.00 4.02
122 123 3.568007 TGGACATGTTTAAGGTCTGTTGC 59.432 43.478 0.00 0.00 0.00 4.17
253 254 2.027285 TCCGGATTGAGCTTGATGTCAA 60.027 45.455 0.00 0.00 37.10 3.18
260 261 6.127925 GGATTGAGCTTGATGTCAAATGTACA 60.128 38.462 0.00 0.00 36.31 2.90
388 389 3.433343 TCCAGGCATGTTTGAATCATGT 58.567 40.909 15.34 0.00 42.94 3.21
467 469 2.552315 GCCGTATGGGGTAATGAATGTG 59.448 50.000 2.41 0.00 35.78 3.21
574 576 0.544697 TTCGCTTTACCCCCTGATCC 59.455 55.000 0.00 0.00 0.00 3.36
619 621 0.456628 AACAAAACCAAACCGGACGG 59.543 50.000 9.46 9.56 38.63 4.79
623 625 1.472188 AAACCAAACCGGACGGAAAA 58.528 45.000 18.80 0.00 38.63 2.29
624 626 1.472188 AACCAAACCGGACGGAAAAA 58.528 45.000 18.80 0.00 38.63 1.94
769 780 0.618458 TCAGAAATCCCCCACTTCCG 59.382 55.000 0.00 0.00 0.00 4.30
915 926 1.234615 GCCGTAGCTTGCTGGAACAA 61.235 55.000 5.26 0.00 34.35 2.83
999 1010 0.676782 TGATCTCTCGCACTCCGTCA 60.677 55.000 0.00 0.00 38.35 4.35
1149 1160 1.003839 GGTGGTCATTGAGGTCGCA 60.004 57.895 0.00 0.00 0.00 5.10
1214 1225 0.761187 TGCTCTGAGGTGCTCTTGTT 59.239 50.000 6.83 0.00 33.63 2.83
1223 1234 3.144506 AGGTGCTCTTGTTGTCAATGAG 58.855 45.455 8.11 8.11 34.80 2.90
1251 1262 0.671251 GTTGCCGGTGTTGGATTCAA 59.329 50.000 1.90 0.00 0.00 2.69
1315 1326 3.321968 TCTGAAGTACAAGAGCAAGCTCA 59.678 43.478 22.68 0.34 44.99 4.26
1437 1448 1.090052 GCCGCGAGCTTGAGGTAATT 61.090 55.000 23.17 0.00 38.99 1.40
1460 1471 0.036388 TGGCTTCATGACCCTTCGTC 60.036 55.000 11.71 0.00 42.33 4.20
1502 1513 0.747255 GAGATACCTGAGCCGAAGCA 59.253 55.000 0.00 0.00 43.56 3.91
1685 1696 1.298993 CTGATGAGTGGCTGCCAGT 59.701 57.895 28.28 28.28 40.30 4.00
1724 1736 4.701765 ACTCGCAAGCATATCTTCAAGAT 58.298 39.130 4.98 4.98 36.52 2.40
1754 1766 0.532573 AAGATCGATGGCACTGACGT 59.467 50.000 0.54 0.00 0.00 4.34
1866 1903 6.043411 ACTGTGTCTTCAGTTCTACTTTGTC 58.957 40.000 0.00 0.00 44.92 3.18
1992 2048 5.874810 GGTACTATGCTGTCTTGTGAAATGA 59.125 40.000 0.00 0.00 0.00 2.57
2127 5332 6.721208 ACACCTATCCATGAAGAACACATTTT 59.279 34.615 0.00 0.00 0.00 1.82
2143 5348 5.473504 ACACATTTTTATCAGTGTCCAGTCC 59.526 40.000 0.00 0.00 40.94 3.85
2256 5462 1.279496 TGCTAACTGCTCCCTGACAT 58.721 50.000 0.00 0.00 43.37 3.06
2533 5740 4.811761 GCGCCGCCGTGAAATCAC 62.812 66.667 0.00 3.43 43.15 3.06
2539 5746 1.078709 CGCCGTGAAATCACACAGAT 58.921 50.000 13.51 0.00 46.75 2.90
2590 5800 2.029649 CGTCGACTTAGGGTTTGAGGAA 60.030 50.000 14.70 0.00 0.00 3.36
2612 5822 3.537874 GAGGATAGCGGCCGTGGT 61.538 66.667 28.70 14.51 0.00 4.16
2649 5862 1.523758 GAAGATTCACGGGTTGCACT 58.476 50.000 0.00 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 2.299326 AGGAGAAAAAGCACTGCCAT 57.701 45.000 0.00 0.00 0.00 4.40
105 106 2.858745 ACGGCAACAGACCTTAAACAT 58.141 42.857 0.00 0.00 0.00 2.71
122 123 2.668279 GCTTTGTCACAATTGGCTACGG 60.668 50.000 10.83 1.54 0.00 4.02
253 254 4.690748 CACATTCGACAACCTCTGTACATT 59.309 41.667 0.00 0.00 38.84 2.71
260 261 3.854666 CATCTCACATTCGACAACCTCT 58.145 45.455 0.00 0.00 0.00 3.69
388 389 3.642503 CGGGGCCACCTACCAACA 61.643 66.667 4.39 0.00 36.97 3.33
435 436 1.392589 CCATACGGCCATTCTGCTTT 58.607 50.000 2.24 0.00 0.00 3.51
467 469 2.281484 TCTGACCAAGCCGCAACC 60.281 61.111 0.00 0.00 0.00 3.77
574 576 4.640647 GGGTGTAGAAGGAGCCAAAATAAG 59.359 45.833 0.00 0.00 0.00 1.73
691 702 0.619543 TACCTGACAAGTAGGCCCCC 60.620 60.000 0.00 0.00 38.96 5.40
769 780 5.369993 AGAATAGGGTTAGGGATTTGGACTC 59.630 44.000 0.00 0.00 0.00 3.36
961 972 2.725312 GGACATGGCTCGCCTCTCA 61.725 63.158 9.65 0.00 36.94 3.27
999 1010 1.660560 GCAGCTCCAACGCATCCATT 61.661 55.000 0.00 0.00 0.00 3.16
1128 1139 0.608130 CGACCTCAATGACCACCTCA 59.392 55.000 0.00 0.00 0.00 3.86
1149 1160 3.249189 AGGTCGTGTGGTGGGCAT 61.249 61.111 0.00 0.00 0.00 4.40
1214 1225 3.503363 GCAACACTTGATCCTCATTGACA 59.497 43.478 0.00 0.00 0.00 3.58
1223 1234 0.889186 ACACCGGCAACACTTGATCC 60.889 55.000 0.00 0.00 0.00 3.36
1251 1262 0.665835 TTCTGCACCAACGCGAAAAT 59.334 45.000 15.93 0.00 33.35 1.82
1315 1326 1.004862 GTTAGGGAGGCCTTCAAAGCT 59.995 52.381 14.70 2.74 0.00 3.74
1437 1448 2.359850 GGGTCATGAAGCCACGCA 60.360 61.111 0.00 0.00 45.43 5.24
1460 1471 0.751277 TGTCACCACCTTGCCAACAG 60.751 55.000 0.00 0.00 0.00 3.16
1502 1513 0.535102 CTCGGGTGGCTTGTTTGTCT 60.535 55.000 0.00 0.00 0.00 3.41
1685 1696 0.331954 AGTCAGGTCCTCGCCTTCTA 59.668 55.000 0.00 0.00 36.58 2.10
1724 1736 0.035152 ATCGATCTTGCCCAGCACAA 60.035 50.000 0.00 0.00 38.71 3.33
1754 1766 4.016444 ACAAACTCAAACTCCTTCAGCAA 58.984 39.130 0.00 0.00 0.00 3.91
1866 1903 0.385390 GCTTCACCACAACAACCAGG 59.615 55.000 0.00 0.00 0.00 4.45
1966 2022 4.882842 TCACAAGACAGCATAGTACCAA 57.117 40.909 0.00 0.00 0.00 3.67
1992 2048 7.436080 CACAAACAAAGAAGCTCACAATTGTAT 59.564 33.333 11.53 0.00 31.33 2.29
2127 5332 4.019858 CTGAGAGGACTGGACACTGATAA 58.980 47.826 0.00 0.00 0.00 1.75
2143 5348 4.686191 AATGTTAGAGATGGGCTGAGAG 57.314 45.455 0.00 0.00 0.00 3.20
2360 5567 3.305720 TCTAGATTGGTTAGGCATCCGT 58.694 45.455 0.00 0.00 0.00 4.69
2444 5651 2.451490 TGCTCTGCTCTAGTTAGCTGT 58.549 47.619 0.00 0.00 43.19 4.40
2533 5740 3.561213 CGGCTGCTGCGATCTGTG 61.561 66.667 9.65 0.00 40.82 3.66
2590 5800 4.964241 GGCCGCTATCCTCCCCCT 62.964 72.222 0.00 0.00 0.00 4.79
2612 5822 0.410663 TCCCCGACCTGTTCCTTCTA 59.589 55.000 0.00 0.00 0.00 2.10
2660 5876 2.110213 TCGGAGTGTTGGTGGTGC 59.890 61.111 0.00 0.00 0.00 5.01


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

AutoCloner maintained by Alex Coulton.