Multiple sequence alignment - TraesCS6A01G051800

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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 TraesCS6A01G051800 chr6A 100.000 2732 0 0 1 2732 26951147 26953878 0.000000e+00 5046
1 TraesCS6A01G051800 chr6A 85.440 1092 150 6 990 2078 26961588 26962673 0.000000e+00 1127
2 TraesCS6A01G051800 chr6A 84.551 1081 160 4 990 2068 27108789 27107714 0.000000e+00 1064
3 TraesCS6A01G051800 chrUn 97.143 1995 42 10 746 2732 95707282 95709269 0.000000e+00 3354
4 TraesCS6A01G051800 chrUn 85.199 1081 153 4 990 2068 95982985 95984060 0.000000e+00 1103
5 TraesCS6A01G051800 chrUn 85.272 1066 146 7 990 2051 95812297 95813355 0.000000e+00 1088
6 TraesCS6A01G051800 chrUn 85.028 1082 146 13 992 2068 95763592 95764662 0.000000e+00 1086
7 TraesCS6A01G051800 chr4B 92.992 956 57 7 1348 2298 9544176 9545126 0.000000e+00 1386
8 TraesCS6A01G051800 chr4B 95.467 353 14 1 393 745 592281064 592280714 1.840000e-156 562
9 TraesCS6A01G051800 chr4B 86.822 258 19 6 2296 2541 9545287 9545541 9.640000e-70 274
10 TraesCS6A01G051800 chr4B 84.021 194 7 7 2539 2732 9545571 9545740 6.050000e-37 165
11 TraesCS6A01G051800 chr6B 84.879 1078 153 9 994 2068 47271380 47270310 0.000000e+00 1079
12 TraesCS6A01G051800 chr6B 84.524 1092 158 8 992 2079 47143983 47142899 0.000000e+00 1070
13 TraesCS6A01G051800 chr6B 93.401 394 16 5 4 396 143713897 143714281 2.360000e-160 575
14 TraesCS6A01G051800 chr3B 96.000 350 13 1 393 742 203550560 203550212 3.950000e-158 568
15 TraesCS6A01G051800 chr3B 87.980 391 28 12 10 396 203553426 203553051 6.940000e-121 444
16 TraesCS6A01G051800 chr2B 86.981 530 29 17 2 527 32052475 32052968 6.610000e-156 560
17 TraesCS6A01G051800 chr2B 92.152 395 23 3 4 397 594974994 594975381 3.980000e-153 551
18 TraesCS6A01G051800 chr1A 86.767 529 36 14 1 527 16759329 16759825 2.380000e-155 558
19 TraesCS6A01G051800 chr5B 94.930 355 15 3 393 747 396156012 396156363 1.110000e-153 553
20 TraesCS6A01G051800 chr5B 92.132 394 23 3 4 396 396155476 396155862 1.430000e-152 549
21 TraesCS6A01G051800 chr5B 92.612 379 21 2 18 396 585523765 585524136 3.100000e-149 538
22 TraesCS6A01G051800 chr5B 94.034 352 18 3 393 744 585524789 585525137 5.180000e-147 531
23 TraesCS6A01G051800 chr7A 97.161 317 9 0 1 317 680111737 680112053 1.110000e-148 536
24 TraesCS6A01G051800 chr7A 92.000 350 26 1 393 742 621763058 621762711 8.790000e-135 490
25 TraesCS6A01G051800 chr7A 94.576 295 11 3 449 742 680114735 680115025 4.150000e-123 451
26 TraesCS6A01G051800 chr7A 90.909 77 3 2 669 745 89508351 89508423 1.730000e-17 100
27 TraesCS6A01G051800 chr1B 89.326 356 33 4 393 745 29977713 29978066 2.500000e-120 442
28 TraesCS6A01G051800 chr1B 83.728 338 49 5 393 729 604143329 604143661 5.680000e-82 315
29 TraesCS6A01G051800 chr3D 88.136 354 39 3 393 745 598251938 598252289 4.210000e-113 418


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 TraesCS6A01G051800 chr6A 26951147 26953878 2731 False 5046.000000 5046 100.0000 1 2732 1 chr6A.!!$F1 2731
1 TraesCS6A01G051800 chr6A 26961588 26962673 1085 False 1127.000000 1127 85.4400 990 2078 1 chr6A.!!$F2 1088
2 TraesCS6A01G051800 chr6A 27107714 27108789 1075 True 1064.000000 1064 84.5510 990 2068 1 chr6A.!!$R1 1078
3 TraesCS6A01G051800 chrUn 95707282 95709269 1987 False 3354.000000 3354 97.1430 746 2732 1 chrUn.!!$F1 1986
4 TraesCS6A01G051800 chrUn 95982985 95984060 1075 False 1103.000000 1103 85.1990 990 2068 1 chrUn.!!$F4 1078
5 TraesCS6A01G051800 chrUn 95812297 95813355 1058 False 1088.000000 1088 85.2720 990 2051 1 chrUn.!!$F3 1061
6 TraesCS6A01G051800 chrUn 95763592 95764662 1070 False 1086.000000 1086 85.0280 992 2068 1 chrUn.!!$F2 1076
7 TraesCS6A01G051800 chr4B 9544176 9545740 1564 False 608.333333 1386 87.9450 1348 2732 3 chr4B.!!$F1 1384
8 TraesCS6A01G051800 chr6B 47270310 47271380 1070 True 1079.000000 1079 84.8790 994 2068 1 chr6B.!!$R2 1074
9 TraesCS6A01G051800 chr6B 47142899 47143983 1084 True 1070.000000 1070 84.5240 992 2079 1 chr6B.!!$R1 1087
10 TraesCS6A01G051800 chr3B 203550212 203553426 3214 True 506.000000 568 91.9900 10 742 2 chr3B.!!$R1 732
11 TraesCS6A01G051800 chr5B 396155476 396156363 887 False 551.000000 553 93.5310 4 747 2 chr5B.!!$F1 743
12 TraesCS6A01G051800 chr5B 585523765 585525137 1372 False 534.500000 538 93.3230 18 744 2 chr5B.!!$F2 726
13 TraesCS6A01G051800 chr7A 680111737 680115025 3288 False 493.500000 536 95.8685 1 742 2 chr7A.!!$F2 741

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
679 3348 0.755327 ACGCACCAAAAGGAAGGCTT 60.755 50.0 0.0 0.0 0.0 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1783 4460 0.317269 CTGAAGCACAGCCAACAACG 60.317 55.0 0.0 0.0 39.86 4.1 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
56 58 7.561021 TTCAGTTTCAAATACACAAGCACTA 57.439 32.000 0.00 0.00 0.00 2.74
82 84 4.237976 TGTAAGGAACAACCAACTTCCA 57.762 40.909 0.00 0.00 38.81 3.53
88 90 4.100963 AGGAACAACCAACTTCCAATTTCC 59.899 41.667 0.00 0.00 38.81 3.13
130 132 3.508793 CCTGAAGTGGCACTGAATTCATT 59.491 43.478 22.83 1.74 30.13 2.57
358 369 8.642020 GTTTAGACATGAGAATGTGCAATTTTC 58.358 33.333 0.00 0.00 34.45 2.29
390 401 8.281212 AGTTTGTGATGGGAGAATGTTTATAC 57.719 34.615 0.00 0.00 0.00 1.47
458 3044 4.035558 GCATCAAGGATCGCAAAGTTATCA 59.964 41.667 0.00 0.00 0.00 2.15
679 3348 0.755327 ACGCACCAAAAGGAAGGCTT 60.755 50.000 0.00 0.00 0.00 4.35
756 3425 3.660571 CCCCTGGTGGTGGATGCA 61.661 66.667 0.00 0.00 0.00 3.96
768 3437 2.476051 GATGCAACGCAGGTCACG 59.524 61.111 0.00 0.00 43.65 4.35
1017 3692 4.555511 GCAAAAATGGCGATGATCCTAGAC 60.556 45.833 0.00 0.00 0.00 2.59
1059 3734 3.393089 AATATGCTCACGGAGATGGTC 57.607 47.619 5.24 0.00 0.00 4.02
1098 3773 2.158928 GCTGCTTGGAGTCAGAGATGAT 60.159 50.000 0.00 0.00 32.26 2.45
1487 4162 1.837439 TGGAAATACCAGCCGTGAGAT 59.163 47.619 0.00 0.00 44.64 2.75
1661 4336 1.272092 TGCCCAGAAGGTCTTCAATGG 60.272 52.381 12.54 11.34 41.84 3.16
1663 4338 1.272092 CCCAGAAGGTCTTCAATGGCA 60.272 52.381 12.54 0.00 41.84 4.92
1707 4382 6.435430 TGATAACACAATATGGTTGAGCAC 57.565 37.500 0.33 0.00 0.00 4.40
1783 4460 3.194861 GGGAAAACACTGGTGAAAAAGC 58.805 45.455 7.78 0.00 0.00 3.51
1784 4461 2.857748 GGAAAACACTGGTGAAAAAGCG 59.142 45.455 7.78 0.00 0.00 4.68
1785 4462 3.507786 GAAAACACTGGTGAAAAAGCGT 58.492 40.909 7.78 0.00 0.00 5.07
1826 4503 1.267121 TTCTCACTACTGCCCTGACC 58.733 55.000 0.00 0.00 0.00 4.02
1839 4516 1.123928 CCTGACCGGGAAGAAGCTAT 58.876 55.000 6.32 0.00 0.00 2.97
1864 4541 1.908619 TGGTGCTAGATGATGTGTGGT 59.091 47.619 0.00 0.00 0.00 4.16
2068 4745 1.667236 TAGCCAAACTCCATGCATCG 58.333 50.000 0.00 0.00 0.00 3.84
2110 4787 3.190118 GGCAAGTCCAGATTGTGAGAAAG 59.810 47.826 0.00 0.00 34.01 2.62
2151 4828 2.912956 AGATTAAGGAAGCCACCACTCA 59.087 45.455 0.00 0.00 0.00 3.41
2247 4924 1.663379 GGCCCAATAACCAACTCGGC 61.663 60.000 0.00 0.00 39.03 5.54
2252 4929 0.037590 AATAACCAACTCGGCTGGCA 59.962 50.000 1.08 0.00 39.03 4.92
2264 4941 0.248289 GGCTGGCATGCATTCTTGTT 59.752 50.000 21.36 0.00 34.04 2.83
2392 5235 5.709594 AGATAGGAAAAATGGAGGATTGGG 58.290 41.667 0.00 0.00 0.00 4.12
2393 5236 3.120468 AGGAAAAATGGAGGATTGGGG 57.880 47.619 0.00 0.00 0.00 4.96
2560 5447 3.700538 TCCTGCAAATCAAGCACCTATT 58.299 40.909 0.00 0.00 37.02 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 2.551270 CGGTCTGTTCGCTGTTGC 59.449 61.111 0.00 0.00 0.00 4.17
16 18 2.744202 ACTGAATCAATGCGGTCTGTTC 59.256 45.455 0.00 0.00 0.00 3.18
82 84 6.824553 TCAGAGATGAGATGATTCGGAAATT 58.175 36.000 0.00 0.00 0.00 1.82
88 90 4.983538 CAGGTTCAGAGATGAGATGATTCG 59.016 45.833 0.00 0.00 0.00 3.34
246 250 6.013206 TGGTGAAAATACTTACTTAGGAGCCA 60.013 38.462 0.00 0.00 0.00 4.75
358 369 6.588719 TTCTCCCATCACAAACTTAAATGG 57.411 37.500 0.00 0.00 37.27 3.16
390 401 5.649395 TCCTCATCCTTAACTTGCAAGAATG 59.351 40.000 32.50 21.18 0.00 2.67
519 3187 5.428496 AATTGTTCGACATATCATGGCAG 57.572 39.130 0.00 0.00 38.56 4.85
646 3315 8.024285 CCTTTTGGTGCGTAAAACTGATTATAA 58.976 33.333 0.00 0.00 34.07 0.98
696 3365 6.811954 ACCGTGTATTCAAAATTTGGAAACT 58.188 32.000 11.99 0.00 0.00 2.66
697 3366 6.921307 AGACCGTGTATTCAAAATTTGGAAAC 59.079 34.615 11.99 11.37 0.00 2.78
701 3370 6.442952 TCAAGACCGTGTATTCAAAATTTGG 58.557 36.000 5.83 0.00 0.00 3.28
756 3425 2.105528 AACGTCGTGACCTGCGTT 59.894 55.556 0.00 0.00 41.79 4.84
833 3508 1.078528 TCGTCACCCAGACCCAGAT 59.921 57.895 0.00 0.00 44.66 2.90
906 3581 2.046507 GACTGCTGTCAGCTGGGG 60.047 66.667 28.73 17.21 43.38 4.96
1017 3692 2.389713 GCACATAGTATGCAAAGGCG 57.610 50.000 10.16 0.00 45.35 5.52
1059 3734 0.524862 GCATGTGCACTTCCTCCTTG 59.475 55.000 19.41 4.20 41.59 3.61
1098 3773 6.161855 AGCTTAACATCCATCTTGTCGATA 57.838 37.500 0.00 0.00 0.00 2.92
1487 4162 1.133575 ACCGATCGAACTCCCCTGATA 60.134 52.381 18.66 0.00 0.00 2.15
1661 4336 2.954611 GGCCTTCACGGTTTCTGC 59.045 61.111 0.00 0.00 34.25 4.26
1663 4338 1.004918 CTCGGCCTTCACGGTTTCT 60.005 57.895 0.00 0.00 34.25 2.52
1707 4382 0.320771 CCTGTCGAAGTCCTGGTTGG 60.321 60.000 0.00 0.00 37.10 3.77
1783 4460 0.317269 CTGAAGCACAGCCAACAACG 60.317 55.000 0.00 0.00 39.86 4.10
1784 4461 3.557207 CTGAAGCACAGCCAACAAC 57.443 52.632 0.00 0.00 39.86 3.32
1839 4516 3.011818 CACATCATCTAGCACCAGCAAA 58.988 45.455 0.00 0.00 45.49 3.68
1864 4541 1.302431 CACCCCATGCTTCGTGACA 60.302 57.895 0.00 0.00 0.00 3.58
2068 4745 5.757886 TGCCAAATAAGCATAATTAGCGAC 58.242 37.500 0.00 0.00 34.69 5.19
2151 4828 3.804325 CCAATTCGACGATAGCAAGACAT 59.196 43.478 0.00 0.00 42.67 3.06
2192 4869 1.671979 GCCTGTTACGGTTTATCCCC 58.328 55.000 0.00 0.00 0.00 4.81
2247 4924 3.853831 TGTAACAAGAATGCATGCCAG 57.146 42.857 16.68 0.00 0.00 4.85
2252 4929 9.624373 ATTCTCTTCTATGTAACAAGAATGCAT 57.376 29.630 0.00 0.00 32.38 3.96
2393 5236 3.365472 AGAATTCAAATGGGCAGGGTAC 58.635 45.455 8.44 0.00 0.00 3.34


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

AutoCloner maintained by Alex Coulton.