Multiple sequence alignment - TraesCS3B01G161400

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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 TraesCS3B01G161400 chr3B 100.000 2709 0 0 1 2709 157922951 157920243 0 5003
1 TraesCS3B01G161400 chr3D 90.672 2798 145 53 1 2709 107072802 107070032 0 3615
2 TraesCS3B01G161400 chr3A 93.333 1935 93 21 800 2709 549619546 549621469 0 2826
3 TraesCS3B01G161400 chr3A 89.612 799 62 12 1 784 549618683 549619475 0 996


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 TraesCS3B01G161400 chr3B 157920243 157922951 2708 True 5003 5003 100.0000 1 2709 1 chr3B.!!$R1 2708
1 TraesCS3B01G161400 chr3D 107070032 107072802 2770 True 3615 3615 90.6720 1 2709 1 chr3D.!!$R1 2708
2 TraesCS3B01G161400 chr3A 549618683 549621469 2786 False 1911 2826 91.4725 1 2709 2 chr3A.!!$F1 2708

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
492 502 0.537188 TGGAGAAGAAGGATGACGCC 59.463 55.0 0.0 0.0 0.0 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1829 1984 0.294887 CTCGACGATTTGTACAGCGC 59.705 55.0 0.0 0.0 0.0 5.92 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
134 143 5.942872 AGAAATGCTGTTAACATTCGAAGG 58.057 37.500 9.13 8.51 36.74 3.46
249 258 6.073314 AGATGCCAGCATTTACCATAATCTT 58.927 36.000 6.57 0.00 36.70 2.40
304 313 1.145803 GGTAACGCGCTTCTGTTCTT 58.854 50.000 5.73 0.00 0.00 2.52
308 317 1.004277 ACGCGCTTCTGTTCTTCTCG 61.004 55.000 5.73 0.00 0.00 4.04
317 326 1.869767 CTGTTCTTCTCGCAAGCAAGT 59.130 47.619 0.00 0.00 37.18 3.16
325 334 1.197721 CTCGCAAGCAAGTACCTTTGG 59.802 52.381 0.00 0.00 37.18 3.28
326 335 0.951558 CGCAAGCAAGTACCTTTGGT 59.048 50.000 0.00 0.00 40.24 3.67
340 350 3.008594 ACCTTTGGTCCGTGATATGAACA 59.991 43.478 0.00 0.00 0.00 3.18
341 351 4.199310 CCTTTGGTCCGTGATATGAACAT 58.801 43.478 0.00 0.00 0.00 2.71
342 352 5.104693 ACCTTTGGTCCGTGATATGAACATA 60.105 40.000 0.00 0.00 0.00 2.29
347 357 4.038763 GGTCCGTGATATGAACATACCAGA 59.961 45.833 0.00 0.00 0.00 3.86
352 362 6.073602 CCGTGATATGAACATACCAGATGTTG 60.074 42.308 7.62 0.00 41.76 3.33
369 379 3.426615 TGTTGTGACACCAAACCTTTCT 58.573 40.909 2.45 0.00 0.00 2.52
410 420 2.337583 CAACGATGAAGCGGAGAAGAA 58.662 47.619 0.00 0.00 35.12 2.52
422 432 3.748868 GGAGAAGAAAATCCGTGAAGC 57.251 47.619 0.00 0.00 0.00 3.86
486 496 0.909610 TGGCCGTGGAGAAGAAGGAT 60.910 55.000 0.00 0.00 0.00 3.24
492 502 0.537188 TGGAGAAGAAGGATGACGCC 59.463 55.000 0.00 0.00 0.00 5.68
558 568 2.261052 GCAGCGAGACAGCAGACT 59.739 61.111 0.00 0.00 40.15 3.24
587 602 1.930817 GCACTGACTGTCATCGTCGTT 60.931 52.381 11.45 0.00 34.17 3.85
589 604 0.710567 CTGACTGTCATCGTCGTTGC 59.289 55.000 11.45 0.00 34.17 4.17
632 647 5.770162 ACTAGAAACTGAATTTGTCCCTTGG 59.230 40.000 0.00 0.00 0.00 3.61
633 648 4.546674 AGAAACTGAATTTGTCCCTTGGT 58.453 39.130 0.00 0.00 0.00 3.67
681 718 1.080772 GGTGTGATCGTGCTCGTCA 60.081 57.895 8.17 8.43 38.33 4.35
727 765 4.323028 CCTTGAACTCTTGAGTCATGGCTA 60.323 45.833 0.00 0.00 0.00 3.93
729 767 4.763073 TGAACTCTTGAGTCATGGCTATG 58.237 43.478 0.00 3.17 35.57 2.23
770 808 5.702209 GGCAGATCCAAATGAAAATGTGTTT 59.298 36.000 0.00 0.00 34.01 2.83
784 822 1.006043 TGTGTTTTCCTTGGGTGGTGA 59.994 47.619 0.00 0.00 0.00 4.02
815 893 3.713205 CTGCTGCGCTCTGGATCGT 62.713 63.158 9.73 0.00 0.00 3.73
873 963 1.618447 GGCCCTTCTTGTCCCCCTA 60.618 63.158 0.00 0.00 0.00 3.53
891 981 1.585668 CTACTGCTGAGTTTGCGATCG 59.414 52.381 11.69 11.69 33.21 3.69
895 985 0.642800 GCTGAGTTTGCGATCGAGAC 59.357 55.000 21.57 13.16 0.00 3.36
896 986 1.734047 GCTGAGTTTGCGATCGAGACT 60.734 52.381 21.57 17.74 0.00 3.24
897 987 2.181205 CTGAGTTTGCGATCGAGACTC 58.819 52.381 25.82 25.82 37.75 3.36
898 988 1.184349 GAGTTTGCGATCGAGACTCG 58.816 55.000 21.57 18.91 42.10 4.18
1012 1122 4.036804 GTGCAATGGCCACGCGAA 62.037 61.111 15.93 4.93 40.13 4.70
1373 1485 2.232941 CTGTAATACCGTGGACACACCT 59.767 50.000 3.12 0.00 44.86 4.00
1374 1486 2.028839 TGTAATACCGTGGACACACCTG 60.029 50.000 3.12 0.00 44.86 4.00
1383 1507 4.235762 ACACACCTGCGGCGTTCT 62.236 61.111 9.37 0.00 0.00 3.01
1401 1526 4.496341 CGTTCTGTGCTGTTCTGTTTTGAT 60.496 41.667 0.00 0.00 0.00 2.57
1402 1527 5.277297 CGTTCTGTGCTGTTCTGTTTTGATA 60.277 40.000 0.00 0.00 0.00 2.15
1699 1828 2.734079 GCTCTTCTTCGGTTCACAAGAG 59.266 50.000 0.00 0.00 42.01 2.85
1776 1931 4.201628 CCGCAAACACTTTCTCTTCTATCG 60.202 45.833 0.00 0.00 0.00 2.92
1792 1947 4.989044 TCTATCGAACGCTTACAATGTGA 58.011 39.130 0.00 0.00 0.00 3.58
1810 1965 2.628178 GTGATGATCGTCCTCCATGGTA 59.372 50.000 12.58 0.00 37.07 3.25
1829 1984 2.931536 CGTCTCTCGTCGTCCATTG 58.068 57.895 0.00 0.00 34.52 2.82
1879 2034 0.619832 TCTCCTCAGCTCTGGGCATT 60.620 55.000 0.74 0.00 44.79 3.56
1885 2040 2.825836 GCTCTGGGCATTGACGGG 60.826 66.667 0.00 0.00 41.35 5.28
2243 2398 0.109458 GTCGACCATGCACGTGTAGA 60.109 55.000 18.38 2.74 0.00 2.59
2254 2409 0.818296 ACGTGTAGAGCTCCATGGAC 59.182 55.000 11.44 8.29 0.00 4.02
2259 2414 2.238319 TAGAGCTCCATGGACGGGGT 62.238 60.000 11.44 7.17 0.00 4.95
2273 2428 0.463833 CGGGGTAATCTTGTGCTCCC 60.464 60.000 0.00 0.00 34.68 4.30
2275 2430 1.095807 GGGTAATCTTGTGCTCCCGC 61.096 60.000 0.00 0.00 0.00 6.13
2293 2448 2.286831 CCGCATCATCTGATCAAACAGC 60.287 50.000 0.00 0.00 37.75 4.40
2481 2636 2.114616 CAGGTCCCTGCTCTTCATACT 58.885 52.381 0.00 0.00 37.24 2.12
2566 2721 3.858868 GACGAGCAAGTGCCGGTCA 62.859 63.158 15.52 0.00 43.38 4.02
2665 2820 2.289257 GGTAGCTAAGGTCACCACGTTT 60.289 50.000 0.00 0.00 32.79 3.60
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
134 143 0.030638 AAGTCGGCACAACATTGCAC 59.969 50.000 0.00 0.00 44.94 4.57
317 326 4.223255 TGTTCATATCACGGACCAAAGGTA 59.777 41.667 0.00 0.00 35.25 3.08
325 334 5.196341 TCTGGTATGTTCATATCACGGAC 57.804 43.478 2.12 0.00 0.00 4.79
326 335 5.304357 ACATCTGGTATGTTCATATCACGGA 59.696 40.000 2.12 0.94 0.00 4.69
340 350 4.365514 TTGGTGTCACAACATCTGGTAT 57.634 40.909 0.00 0.00 37.41 2.73
341 351 3.847671 TTGGTGTCACAACATCTGGTA 57.152 42.857 0.00 0.00 37.41 3.25
342 352 2.687935 GTTTGGTGTCACAACATCTGGT 59.312 45.455 0.00 0.00 37.41 4.00
347 357 4.023291 AGAAAGGTTTGGTGTCACAACAT 58.977 39.130 0.00 0.00 37.81 2.71
352 362 1.602377 CGGAGAAAGGTTTGGTGTCAC 59.398 52.381 0.00 0.00 0.00 3.67
369 379 2.038813 TCCTCCATCTGCCACGGA 59.961 61.111 0.00 0.00 0.00 4.69
410 420 1.168714 GAAGGCTGCTTCACGGATTT 58.831 50.000 0.00 0.00 33.80 2.17
453 463 2.347490 GCCAGCAGGTCCTCGAAA 59.653 61.111 0.00 0.00 37.19 3.46
492 502 2.805353 CCGTGACGACGCCAGAAG 60.805 66.667 6.54 0.00 44.68 2.85
505 515 1.949847 ATCGACCTCAGCTTCCCGTG 61.950 60.000 0.00 0.00 0.00 4.94
558 568 1.313091 ACAGTCAGTGCGATCGCCTA 61.313 55.000 35.12 17.01 41.09 3.93
587 602 1.077169 TCCTGGAGTCTTAGACTGGCA 59.923 52.381 20.52 3.04 43.53 4.92
589 604 3.436243 AGTTCCTGGAGTCTTAGACTGG 58.564 50.000 20.52 14.53 43.53 4.00
632 647 4.678509 TTCAACACACACAAGTTCTCAC 57.321 40.909 0.00 0.00 0.00 3.51
633 648 4.083003 GGTTTCAACACACACAAGTTCTCA 60.083 41.667 0.00 0.00 0.00 3.27
727 765 5.131642 TCTGCCCAGTTCAGATCTTATTCAT 59.868 40.000 0.00 0.00 35.81 2.57
729 767 5.028549 TCTGCCCAGTTCAGATCTTATTC 57.971 43.478 0.00 0.00 35.81 1.75
770 808 0.923358 AACAGTCACCACCCAAGGAA 59.077 50.000 0.00 0.00 0.00 3.36
784 822 2.203308 AGCAGCAGCAGCAACAGT 60.203 55.556 12.92 0.00 45.49 3.55
873 963 0.038251 TCGATCGCAAACTCAGCAGT 60.038 50.000 11.09 0.00 0.00 4.40
891 981 1.466950 CACTCACACCTCTCGAGTCTC 59.533 57.143 13.13 0.00 37.92 3.36
895 985 1.214062 GGCACTCACACCTCTCGAG 59.786 63.158 5.93 5.93 0.00 4.04
896 986 2.626780 CGGCACTCACACCTCTCGA 61.627 63.158 0.00 0.00 0.00 4.04
897 987 2.126307 CGGCACTCACACCTCTCG 60.126 66.667 0.00 0.00 0.00 4.04
898 988 2.433318 GCGGCACTCACACCTCTC 60.433 66.667 0.00 0.00 0.00 3.20
899 989 2.116983 ATTGCGGCACTCACACCTCT 62.117 55.000 0.05 0.00 0.00 3.69
900 990 1.237285 AATTGCGGCACTCACACCTC 61.237 55.000 0.05 0.00 0.00 3.85
901 991 0.036164 TAATTGCGGCACTCACACCT 59.964 50.000 0.05 0.00 0.00 4.00
1179 1289 1.546476 GACTCCCTGTCGATGAAGTGT 59.454 52.381 0.00 0.00 35.81 3.55
1373 1485 4.908687 ACAGCACAGAACGCCGCA 62.909 61.111 0.00 0.00 0.00 5.69
1374 1486 3.579626 GAACAGCACAGAACGCCGC 62.580 63.158 0.00 0.00 0.00 6.53
1446 1575 1.367840 GTCAGGAGGTTGTCGCACT 59.632 57.895 0.00 0.00 0.00 4.40
1655 1784 2.060980 GGGTCCTGCAGATCTCGGT 61.061 63.158 17.39 0.00 0.00 4.69
1699 1828 1.803555 GAGCAAGTCTTTCAGAGTGGC 59.196 52.381 0.20 0.20 43.46 5.01
1776 1931 4.032900 ACGATCATCACATTGTAAGCGTTC 59.967 41.667 0.00 0.00 0.00 3.95
1792 1947 1.613925 CGTACCATGGAGGACGATCAT 59.386 52.381 21.47 0.00 40.83 2.45
1829 1984 0.294887 CTCGACGATTTGTACAGCGC 59.705 55.000 0.00 0.00 0.00 5.92
2065 2220 3.793144 GCGAAGGTTCTGCAGGCG 61.793 66.667 15.13 9.38 0.00 5.52
2146 2301 4.681978 GGAGCCGACCTGTGCGTT 62.682 66.667 0.00 0.00 0.00 4.84
2243 2398 0.694444 ATTACCCCGTCCATGGAGCT 60.694 55.000 16.81 0.00 0.00 4.09
2254 2409 0.463833 GGGAGCACAAGATTACCCCG 60.464 60.000 0.00 0.00 0.00 5.73
2273 2428 2.286831 GGCTGTTTGATCAGATGATGCG 60.287 50.000 0.00 0.00 37.61 4.73
2275 2430 2.289820 CCGGCTGTTTGATCAGATGATG 59.710 50.000 0.00 0.00 37.61 3.07
2481 2636 2.957489 CACGCACGGTGTTCGACA 60.957 61.111 13.72 0.00 41.89 4.35
2555 2710 1.603455 CCATGGTTGACCGGCACTT 60.603 57.895 0.00 0.00 39.43 3.16
2566 2721 0.465705 ACGCGATCAGATCCATGGTT 59.534 50.000 15.93 2.52 0.00 3.67


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

AutoCloner maintained by Alex Coulton.