Multiple sequence alignment - TraesCS6A01G068900

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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 TraesCS6A01G068900 chr6A 100.000 2516 0 0 1 2516 37409032 37406517 0.000000e+00 4647
1 TraesCS6A01G068900 chr6A 85.734 708 76 18 1009 1710 611536160 611536848 0.000000e+00 725
2 TraesCS6A01G068900 chr6A 83.662 710 90 20 1015 1708 611541077 611541776 0.000000e+00 645
3 TraesCS6A01G068900 chr6A 87.028 424 46 5 1057 1477 611544279 611544696 1.050000e-128 470
4 TraesCS6A01G068900 chr6D 89.957 2549 159 47 3 2516 32695829 32693343 0.000000e+00 3199
5 TraesCS6A01G068900 chr6B 88.820 2406 148 53 3 2375 68924320 68922003 0.000000e+00 2841
6 TraesCS6A01G068900 chr6B 84.648 710 80 17 1009 1709 709120388 709121077 0.000000e+00 680
7 TraesCS6A01G068900 chr6B 87.069 116 12 1 1396 1511 709099539 709099651 7.310000e-26 128
8 TraesCS6A01G068900 chr4D 79.691 517 85 18 1007 1513 1203018 1202512 3.080000e-94 355
9 TraesCS6A01G068900 chr4B 79.457 516 88 16 1007 1513 808739 809245 1.430000e-92 350
10 TraesCS6A01G068900 chr4A 79.110 517 88 17 1007 1513 603637560 603638066 3.100000e-89 339


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 TraesCS6A01G068900 chr6A 37406517 37409032 2515 True 4647.0 4647 100.000 1 2516 1 chr6A.!!$R1 2515
1 TraesCS6A01G068900 chr6A 611536160 611536848 688 False 725.0 725 85.734 1009 1710 1 chr6A.!!$F1 701
2 TraesCS6A01G068900 chr6A 611541077 611544696 3619 False 557.5 645 85.345 1015 1708 2 chr6A.!!$F2 693
3 TraesCS6A01G068900 chr6D 32693343 32695829 2486 True 3199.0 3199 89.957 3 2516 1 chr6D.!!$R1 2513
4 TraesCS6A01G068900 chr6B 68922003 68924320 2317 True 2841.0 2841 88.820 3 2375 1 chr6B.!!$R1 2372
5 TraesCS6A01G068900 chr6B 709120388 709121077 689 False 680.0 680 84.648 1009 1709 1 chr6B.!!$F2 700
6 TraesCS6A01G068900 chr4D 1202512 1203018 506 True 355.0 355 79.691 1007 1513 1 chr4D.!!$R1 506
7 TraesCS6A01G068900 chr4B 808739 809245 506 False 350.0 350 79.457 1007 1513 1 chr4B.!!$F1 506
8 TraesCS6A01G068900 chr4A 603637560 603638066 506 False 339.0 339 79.110 1007 1513 1 chr4A.!!$F1 506

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
614 627 0.034477 CACCCACCCCTTATGACACC 60.034 60.0 0.0 0.0 0.0 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1844 1891 1.069227 CACTAGAAAAAGCACACGGGC 60.069 52.381 0.0 0.0 0.0 6.13 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
125 133 5.660417 AGAGAGAAATAGGCATCTCAGTTCA 59.340 40.000 5.67 0.00 43.62 3.18
360 372 1.460699 GGCATATCCCTTCCCCACC 59.539 63.158 0.00 0.00 0.00 4.61
361 373 1.360393 GGCATATCCCTTCCCCACCA 61.360 60.000 0.00 0.00 0.00 4.17
362 374 0.178990 GCATATCCCTTCCCCACCAC 60.179 60.000 0.00 0.00 0.00 4.16
363 375 0.108585 CATATCCCTTCCCCACCACG 59.891 60.000 0.00 0.00 0.00 4.94
364 376 1.060163 ATATCCCTTCCCCACCACGG 61.060 60.000 0.00 0.00 0.00 4.94
397 409 4.394712 CGTCCCCACCACAGCCTC 62.395 72.222 0.00 0.00 0.00 4.70
416 428 2.189521 CCTGCACCCGGTCCATAC 59.810 66.667 0.00 0.00 0.00 2.39
425 437 1.400530 CCGGTCCATACACTCTCCCC 61.401 65.000 0.00 0.00 0.00 4.81
427 439 1.123928 GGTCCATACACTCTCCCCAG 58.876 60.000 0.00 0.00 0.00 4.45
488 500 2.174349 GCAGTCCAAAAGCGCGAG 59.826 61.111 12.10 0.00 0.00 5.03
499 511 2.588034 GCGCGAGTATCCCAACCC 60.588 66.667 12.10 0.00 0.00 4.11
577 590 6.070251 ACCCCCACAAAGATCCAATAAAAATC 60.070 38.462 0.00 0.00 0.00 2.17
614 627 0.034477 CACCCACCCCTTATGACACC 60.034 60.000 0.00 0.00 0.00 4.16
616 629 1.613061 CCACCCCTTATGACACCCC 59.387 63.158 0.00 0.00 0.00 4.95
628 641 4.694987 CACCCCGGGCCCACATTT 62.695 66.667 24.92 0.00 0.00 2.32
649 662 2.281276 GTCCCCACACCAACGGAC 60.281 66.667 0.00 0.00 38.18 4.79
711 724 0.249073 ATGTCATACAGCCTCGCGTC 60.249 55.000 5.77 0.00 0.00 5.19
855 868 4.853142 ATCGGACGGCTGGGGCTA 62.853 66.667 0.00 0.00 38.73 3.93
886 899 0.605589 GGCCTCGCCGCCTATTTAAT 60.606 55.000 0.00 0.00 46.10 1.40
888 901 1.068474 CCTCGCCGCCTATTTAATCG 58.932 55.000 0.00 0.00 0.00 3.34
890 903 0.249531 TCGCCGCCTATTTAATCGCA 60.250 50.000 0.00 0.00 0.00 5.10
944 968 2.654863 AGCCAAAGGTAATCCAATCCG 58.345 47.619 0.00 0.00 35.89 4.18
1685 1732 4.802051 TTGGGCCGCTGGATCTGC 62.802 66.667 0.00 0.00 0.00 4.26
1765 1812 4.556233 TGAACTCCGCTATGAATTATCCG 58.444 43.478 0.00 0.00 0.00 4.18
1783 1830 1.801771 CCGTAATTTGTGCTCGTTGGA 59.198 47.619 0.00 0.00 0.00 3.53
1788 1835 3.837213 ATTTGTGCTCGTTGGATTCAG 57.163 42.857 0.00 0.00 0.00 3.02
1791 1838 2.683968 TGTGCTCGTTGGATTCAGTAC 58.316 47.619 0.00 0.00 0.00 2.73
1803 1850 1.493772 TTCAGTACCTGTTTGTCGCG 58.506 50.000 0.00 0.00 32.61 5.87
1807 1854 1.068127 AGTACCTGTTTGTCGCGTTCT 59.932 47.619 5.77 0.00 0.00 3.01
1809 1856 1.375551 ACCTGTTTGTCGCGTTCTTT 58.624 45.000 5.77 0.00 0.00 2.52
1861 1908 1.519408 GAGCCCGTGTGCTTTTTCTA 58.481 50.000 0.00 0.00 42.95 2.10
1870 1918 5.408604 CCGTGTGCTTTTTCTAGTGTTATCT 59.591 40.000 0.00 0.00 0.00 1.98
1887 1935 1.904144 TCTACTCGATTTTCGTGCCG 58.096 50.000 0.00 0.00 41.35 5.69
1965 2017 3.882888 ACTTCTTCGGCACAAAATCTGAA 59.117 39.130 0.00 0.00 0.00 3.02
1966 2018 3.896648 TCTTCGGCACAAAATCTGAAC 57.103 42.857 0.00 0.00 0.00 3.18
1979 2046 9.462174 CACAAAATCTGAACTGTAAATTAGCAA 57.538 29.630 0.00 0.00 0.00 3.91
2051 2129 1.134640 TCATGTTCCCCCGTACATTCG 60.135 52.381 0.00 0.00 32.88 3.34
2064 2142 2.601481 ACATTCGCTTCGCTTTTCAG 57.399 45.000 0.00 0.00 0.00 3.02
2075 2153 1.069636 CGCTTTTCAGAACTGACCTGC 60.070 52.381 3.88 7.73 39.66 4.85
2079 2157 1.597742 TTCAGAACTGACCTGCTTGC 58.402 50.000 3.88 0.00 39.66 4.01
2092 2170 1.667724 CTGCTTGCTTAATCCTGACCG 59.332 52.381 0.00 0.00 0.00 4.79
2093 2171 1.017387 GCTTGCTTAATCCTGACCGG 58.983 55.000 0.00 0.00 0.00 5.28
2095 2173 2.711542 CTTGCTTAATCCTGACCGGTT 58.288 47.619 9.42 0.00 0.00 4.44
2121 2199 4.566360 GTGTTGCTTGTTTTGCACTGTAAT 59.434 37.500 0.00 0.00 40.40 1.89
2122 2200 5.063312 GTGTTGCTTGTTTTGCACTGTAATT 59.937 36.000 0.00 0.00 40.40 1.40
2125 2205 6.104439 TGCTTGTTTTGCACTGTAATTTTG 57.896 33.333 0.00 0.00 35.31 2.44
2129 2209 5.862811 TGTTTTGCACTGTAATTTTGTTGC 58.137 33.333 0.00 0.00 0.00 4.17
2144 2224 8.538409 AATTTTGTTGCTGGATCTTGATTTAC 57.462 30.769 0.00 0.00 0.00 2.01
2150 2230 5.185454 TGCTGGATCTTGATTTACGTGATT 58.815 37.500 0.00 0.00 0.00 2.57
2152 2232 6.479990 TGCTGGATCTTGATTTACGTGATTAG 59.520 38.462 0.00 0.00 0.00 1.73
2153 2233 6.480320 GCTGGATCTTGATTTACGTGATTAGT 59.520 38.462 0.00 0.00 0.00 2.24
2213 2293 4.641989 ACCTTGTTGATGCATGGATCTAAC 59.358 41.667 25.23 23.94 37.20 2.34
2214 2294 4.641541 CCTTGTTGATGCATGGATCTAACA 59.358 41.667 25.98 25.98 36.21 2.41
2216 2296 3.628942 TGTTGATGCATGGATCTAACAGC 59.371 43.478 25.98 13.78 0.00 4.40
2226 2306 3.118261 TGGATCTAACAGCATTGGGAGTC 60.118 47.826 0.00 0.00 0.00 3.36
2375 2455 1.078848 CCTCTCTTTCCAGGCGGTG 60.079 63.158 0.00 0.00 0.00 4.94
2389 2469 1.102978 GCGGTGCCCAACTATGAAAT 58.897 50.000 0.00 0.00 0.00 2.17
2390 2470 1.476488 GCGGTGCCCAACTATGAAATT 59.524 47.619 0.00 0.00 0.00 1.82
2391 2471 2.685897 GCGGTGCCCAACTATGAAATTA 59.314 45.455 0.00 0.00 0.00 1.40
2393 2473 4.202111 GCGGTGCCCAACTATGAAATTATT 60.202 41.667 0.00 0.00 0.00 1.40
2394 2474 5.519722 CGGTGCCCAACTATGAAATTATTC 58.480 41.667 0.00 0.00 36.04 1.75
2395 2475 5.507315 CGGTGCCCAACTATGAAATTATTCC 60.507 44.000 0.00 0.00 34.49 3.01
2396 2476 5.362430 GGTGCCCAACTATGAAATTATTCCA 59.638 40.000 0.00 0.00 34.49 3.53
2398 2478 7.418942 GGTGCCCAACTATGAAATTATTCCAAT 60.419 37.037 0.00 0.00 34.49 3.16
2399 2479 7.986889 GTGCCCAACTATGAAATTATTCCAATT 59.013 33.333 0.00 0.00 34.49 2.32
2400 2480 8.203485 TGCCCAACTATGAAATTATTCCAATTC 58.797 33.333 0.00 0.00 34.49 2.17
2401 2481 7.382218 GCCCAACTATGAAATTATTCCAATTCG 59.618 37.037 0.00 0.00 34.49 3.34
2405 2485 8.856490 ACTATGAAATTATTCCAATTCGTTGC 57.144 30.769 0.00 0.00 34.49 4.17
2406 2486 8.465999 ACTATGAAATTATTCCAATTCGTTGCA 58.534 29.630 0.00 0.00 34.49 4.08
2407 2487 9.467258 CTATGAAATTATTCCAATTCGTTGCAT 57.533 29.630 0.00 0.00 34.49 3.96
2408 2488 8.721019 ATGAAATTATTCCAATTCGTTGCATT 57.279 26.923 0.00 0.00 34.49 3.56
2409 2489 8.545229 TGAAATTATTCCAATTCGTTGCATTT 57.455 26.923 0.00 0.00 34.49 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.515028 TTGAATCCTTGAGATCATGGCT 57.485 40.909 9.36 0.00 40.03 4.75
1 2 5.587388 TTTTGAATCCTTGAGATCATGGC 57.413 39.130 9.36 0.00 40.03 4.40
65 66 9.470399 GGGAGGTAAAAATAAAAACTATCTGGA 57.530 33.333 0.00 0.00 0.00 3.86
80 86 7.351166 TCTCTTCTTTTTCTGGGAGGTAAAAA 58.649 34.615 0.00 0.00 32.72 1.94
81 87 6.906848 TCTCTTCTTTTTCTGGGAGGTAAAA 58.093 36.000 0.00 0.00 0.00 1.52
83 89 5.844516 TCTCTCTTCTTTTTCTGGGAGGTAA 59.155 40.000 0.00 0.00 0.00 2.85
84 90 5.403512 TCTCTCTTCTTTTTCTGGGAGGTA 58.596 41.667 0.00 0.00 0.00 3.08
85 91 4.235372 TCTCTCTTCTTTTTCTGGGAGGT 58.765 43.478 0.00 0.00 0.00 3.85
86 92 4.899352 TCTCTCTTCTTTTTCTGGGAGG 57.101 45.455 0.00 0.00 0.00 4.30
87 93 7.552330 CCTATTTCTCTCTTCTTTTTCTGGGAG 59.448 40.741 0.00 0.00 0.00 4.30
88 94 7.398024 CCTATTTCTCTCTTCTTTTTCTGGGA 58.602 38.462 0.00 0.00 0.00 4.37
89 95 6.094742 GCCTATTTCTCTCTTCTTTTTCTGGG 59.905 42.308 0.00 0.00 0.00 4.45
93 99 8.504812 AGATGCCTATTTCTCTCTTCTTTTTC 57.495 34.615 0.00 0.00 0.00 2.29
125 133 3.393941 CCTTCTCAATCTAGGGCCTGATT 59.606 47.826 18.53 18.99 33.69 2.57
195 203 3.471244 CTCATCGGGACCGTCGAGC 62.471 68.421 10.90 0.00 40.09 5.03
488 500 2.172082 GACTAGGGTTGGGTTGGGATAC 59.828 54.545 0.00 0.00 0.00 2.24
499 511 1.196104 TTGGGTCGGGACTAGGGTTG 61.196 60.000 0.00 0.00 0.00 3.77
616 629 4.733542 ACCGGAAATGTGGGCCCG 62.734 66.667 19.37 1.39 41.47 6.13
632 645 2.281276 GTCCGTTGGTGTGGGGAC 60.281 66.667 0.00 0.00 41.84 4.46
683 696 0.466189 CTGTATGACATGTGGGGCCC 60.466 60.000 18.17 18.17 0.00 5.80
711 724 2.047274 AGCACGTGACCCATTCCG 60.047 61.111 22.23 0.00 0.00 4.30
901 914 1.375098 GGCTCTGTGATCTGGCAAGC 61.375 60.000 0.00 0.00 0.00 4.01
944 968 2.425143 TGAGATGGGGATTTCTGTGC 57.575 50.000 0.00 0.00 0.00 4.57
1242 1266 2.491022 GCCGTAGATGGACTCGCCT 61.491 63.158 0.00 0.00 37.63 5.52
1765 1812 5.041951 TGAATCCAACGAGCACAAATTAC 57.958 39.130 0.00 0.00 0.00 1.89
1788 1835 1.494824 AGAACGCGACAAACAGGTAC 58.505 50.000 15.93 0.00 0.00 3.34
1791 1838 1.597663 AGAAAGAACGCGACAAACAGG 59.402 47.619 15.93 0.00 0.00 4.00
1803 1850 3.003793 GGAGCACCAGACAAAGAAAGAAC 59.996 47.826 0.00 0.00 35.97 3.01
1807 1854 2.172505 TCAGGAGCACCAGACAAAGAAA 59.827 45.455 2.07 0.00 38.94 2.52
1809 1856 1.423584 TCAGGAGCACCAGACAAAGA 58.576 50.000 2.07 0.00 38.94 2.52
1844 1891 1.069227 CACTAGAAAAAGCACACGGGC 60.069 52.381 0.00 0.00 0.00 6.13
1861 1908 5.515626 GCACGAAAATCGAGTAGATAACACT 59.484 40.000 6.78 0.00 43.74 3.55
1919 1971 3.976942 CAGAAACTTTGTCGAGCATTTGG 59.023 43.478 0.00 0.00 0.00 3.28
1947 1999 3.003689 ACAGTTCAGATTTTGTGCCGAAG 59.996 43.478 0.00 0.00 0.00 3.79
1952 2004 7.594758 TGCTAATTTACAGTTCAGATTTTGTGC 59.405 33.333 0.00 0.00 0.00 4.57
1965 2017 7.733402 TTCTTTACCGTTGCTAATTTACAGT 57.267 32.000 0.00 0.00 0.00 3.55
1966 2018 9.453325 TTTTTCTTTACCGTTGCTAATTTACAG 57.547 29.630 0.00 0.00 0.00 2.74
1993 2060 1.141657 TCTCAACAAAGTGCAGAGCCT 59.858 47.619 0.00 0.00 0.00 4.58
2001 2068 4.279169 ACCATGTTCCATCTCAACAAAGTG 59.721 41.667 0.00 0.00 37.30 3.16
2051 2129 6.596505 CAGGTCAGTTCTGAAAAGCGAAGC 62.597 50.000 3.99 0.00 44.37 3.86
2064 2142 3.127721 GGATTAAGCAAGCAGGTCAGTTC 59.872 47.826 0.00 0.00 0.00 3.01
2075 2153 2.403252 ACCGGTCAGGATTAAGCAAG 57.597 50.000 0.00 0.00 45.00 4.01
2092 2170 2.159585 GCAAAACAAGCAACACCAAACC 60.160 45.455 0.00 0.00 0.00 3.27
2093 2171 2.481952 TGCAAAACAAGCAACACCAAAC 59.518 40.909 0.00 0.00 39.39 2.93
2095 2173 2.072298 GTGCAAAACAAGCAACACCAA 58.928 42.857 0.00 0.00 44.64 3.67
2121 2199 6.148948 CGTAAATCAAGATCCAGCAACAAAA 58.851 36.000 0.00 0.00 0.00 2.44
2122 2200 5.240623 ACGTAAATCAAGATCCAGCAACAAA 59.759 36.000 0.00 0.00 0.00 2.83
2125 2205 4.391830 TCACGTAAATCAAGATCCAGCAAC 59.608 41.667 0.00 0.00 0.00 4.17
2129 2209 9.529325 TTACTAATCACGTAAATCAAGATCCAG 57.471 33.333 0.00 0.00 0.00 3.86
2167 2247 9.802039 AGGTAATTGTGTTCTCCAAATTTAGTA 57.198 29.630 0.00 0.00 0.00 1.82
2168 2248 8.706322 AGGTAATTGTGTTCTCCAAATTTAGT 57.294 30.769 0.00 0.00 0.00 2.24
2169 2249 9.410556 CAAGGTAATTGTGTTCTCCAAATTTAG 57.589 33.333 0.00 0.00 33.95 1.85
2185 2265 5.327616 TCCATGCATCAACAAGGTAATTG 57.672 39.130 0.00 0.00 45.01 2.32
2186 2266 5.895534 AGATCCATGCATCAACAAGGTAATT 59.104 36.000 0.00 0.00 30.41 1.40
2213 2293 2.802415 CGAGATCTGACTCCCAATGCTG 60.802 54.545 0.00 0.00 33.83 4.41
2214 2294 1.411977 CGAGATCTGACTCCCAATGCT 59.588 52.381 0.00 0.00 33.83 3.79
2216 2296 1.863267 GCGAGATCTGACTCCCAATG 58.137 55.000 0.00 0.00 33.83 2.82
2375 2455 7.382218 CGAATTGGAATAATTTCATAGTTGGGC 59.618 37.037 0.00 0.00 33.23 5.36
2379 2459 9.301153 GCAACGAATTGGAATAATTTCATAGTT 57.699 29.630 0.00 0.00 36.23 2.24
2382 2462 9.814899 AATGCAACGAATTGGAATAATTTCATA 57.185 25.926 0.00 0.00 39.86 2.15
2440 2520 9.880157 AAAGTTGCTAAATCTAAATGATGCATT 57.120 25.926 0.00 0.00 33.52 3.56


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

AutoCloner maintained by Alex Coulton.