Multiple sequence alignment - TraesCS5B01G085300

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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 TraesCS5B01G085300 chr5B 100.000 4632 0 0 1 4632 108054038 108049407 0.000000e+00 8554.0
1 TraesCS5B01G085300 chr5B 97.433 4636 94 17 1 4632 107948135 107943521 0.000000e+00 7878.0
2 TraesCS5B01G085300 chr5B 92.308 65 3 2 1250 1314 14743426 14743488 1.770000e-14 91.6
3 TraesCS5B01G085300 chr5A 96.624 2133 71 1 1321 3452 104147508 104149640 0.000000e+00 3539.0
4 TraesCS5B01G085300 chr5A 96.980 1192 23 4 3441 4632 104149770 104150948 0.000000e+00 1989.0
5 TraesCS5B01G085300 chr5A 91.221 467 27 11 785 1243 104147058 104147518 1.420000e-174 623.0
6 TraesCS5B01G085300 chr5A 86.875 160 15 6 396 552 582977383 582977227 1.710000e-39 174.0
7 TraesCS5B01G085300 chr5A 87.582 153 13 5 406 553 89031658 89031809 6.160000e-39 172.0
8 TraesCS5B01G085300 chr5A 88.235 68 8 0 786 853 648964365 648964432 1.070000e-11 82.4
9 TraesCS5B01G085300 chr1D 85.658 1534 181 26 2079 3591 45695123 45693608 0.000000e+00 1578.0
10 TraesCS5B01G085300 chr1D 81.384 795 105 20 2327 3110 46236510 46237272 3.960000e-170 608.0
11 TraesCS5B01G085300 chr1D 90.513 390 33 4 1 388 448967905 448968292 3.200000e-141 512.0
12 TraesCS5B01G085300 chr1D 82.012 328 42 11 4306 4626 45687727 45687410 3.550000e-66 263.0
13 TraesCS5B01G085300 chr1D 83.406 229 35 3 2104 2331 46234747 46234973 4.700000e-50 209.0
14 TraesCS5B01G085300 chr4B 95.009 541 21 6 1 540 650862433 650862968 0.000000e+00 845.0
15 TraesCS5B01G085300 chr4B 96.436 505 17 1 1 504 650794116 650794620 0.000000e+00 832.0
16 TraesCS5B01G085300 chr4B 90.513 390 34 3 1 388 396636659 396636271 3.200000e-141 512.0
17 TraesCS5B01G085300 chr4B 92.537 67 3 2 1248 1314 184333986 184334050 1.370000e-15 95.3
18 TraesCS5B01G085300 chr6B 95.146 515 23 2 1 514 445887016 445887529 0.000000e+00 811.0
19 TraesCS5B01G085300 chr6B 86.792 159 17 4 396 550 79642561 79642403 1.710000e-39 174.0
20 TraesCS5B01G085300 chr2A 91.683 517 37 5 1 514 240134454 240133941 0.000000e+00 712.0
21 TraesCS5B01G085300 chr2A 81.159 138 22 4 557 691 31830510 31830374 1.760000e-19 108.0
22 TraesCS5B01G085300 chr2A 92.857 70 5 0 785 854 23484314 23484245 8.200000e-18 102.0
23 TraesCS5B01G085300 chr1A 84.274 585 63 13 2079 2656 45756539 45755977 1.130000e-150 544.0
24 TraesCS5B01G085300 chr1A 87.387 111 14 0 579 689 22887144 22887034 1.350000e-25 128.0
25 TraesCS5B01G085300 chr1A 87.037 108 14 0 581 688 12388569 12388676 6.290000e-24 122.0
26 TraesCS5B01G085300 chr3A 90.769 390 32 4 1 388 609670091 609669704 6.870000e-143 518.0
27 TraesCS5B01G085300 chr3A 91.429 70 6 0 785 854 31797136 31797205 3.810000e-16 97.1
28 TraesCS5B01G085300 chr7A 90.513 390 34 3 1 388 72699962 72699574 3.200000e-141 512.0
29 TraesCS5B01G085300 chr4A 89.349 169 14 4 356 521 580666066 580666233 4.700000e-50 209.0
30 TraesCS5B01G085300 chr5D 86.111 108 15 0 581 688 519660091 519659984 2.930000e-22 117.0
31 TraesCS5B01G085300 chr5D 96.226 53 2 0 785 837 419036203 419036151 2.300000e-13 87.9
32 TraesCS5B01G085300 chr3B 93.333 75 5 0 1247 1321 368915365 368915291 1.360000e-20 111.0
33 TraesCS5B01G085300 chr3B 92.308 65 5 0 788 852 156620429 156620365 4.930000e-15 93.5
34 TraesCS5B01G085300 chr1B 91.667 72 5 1 1250 1321 611319018 611318948 1.060000e-16 99.0
35 TraesCS5B01G085300 chr6A 92.424 66 3 2 1246 1309 39550539 39550604 4.930000e-15 93.5
36 TraesCS5B01G085300 chr6A 79.825 114 17 3 581 688 55560423 55560536 1.380000e-10 78.7
37 TraesCS5B01G085300 chr2B 91.176 68 4 2 1248 1313 613917488 613917555 1.770000e-14 91.6
38 TraesCS5B01G085300 chr2B 89.189 74 5 3 1249 1321 303839343 303839272 6.380000e-14 89.8
39 TraesCS5B01G085300 chr7B 87.179 78 9 1 1243 1320 375450429 375450505 2.300000e-13 87.9


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 TraesCS5B01G085300 chr5B 108049407 108054038 4631 True 8554.000000 8554 100.000000 1 4632 1 chr5B.!!$R2 4631
1 TraesCS5B01G085300 chr5B 107943521 107948135 4614 True 7878.000000 7878 97.433000 1 4632 1 chr5B.!!$R1 4631
2 TraesCS5B01G085300 chr5A 104147058 104150948 3890 False 2050.333333 3539 94.941667 785 4632 3 chr5A.!!$F3 3847
3 TraesCS5B01G085300 chr1D 45693608 45695123 1515 True 1578.000000 1578 85.658000 2079 3591 1 chr1D.!!$R2 1512
4 TraesCS5B01G085300 chr1D 46234747 46237272 2525 False 408.500000 608 82.395000 2104 3110 2 chr1D.!!$F2 1006
5 TraesCS5B01G085300 chr4B 650862433 650862968 535 False 845.000000 845 95.009000 1 540 1 chr4B.!!$F3 539
6 TraesCS5B01G085300 chr4B 650794116 650794620 504 False 832.000000 832 96.436000 1 504 1 chr4B.!!$F2 503
7 TraesCS5B01G085300 chr6B 445887016 445887529 513 False 811.000000 811 95.146000 1 514 1 chr6B.!!$F1 513
8 TraesCS5B01G085300 chr2A 240133941 240134454 513 True 712.000000 712 91.683000 1 514 1 chr2A.!!$R3 513
9 TraesCS5B01G085300 chr1A 45755977 45756539 562 True 544.000000 544 84.274000 2079 2656 1 chr1A.!!$R2 577

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
704 709 0.967887 CTCCTCTCAGTCCGGCAGAA 60.968 60.000 0.0 0.0 0.00 3.02 F
2209 2233 0.667993 CTCACACGGTTGCCATTGTT 59.332 50.000 0.0 0.0 0.00 2.83 F
3375 4959 3.054802 AGAGATGTGATCCGCCTCTTTTT 60.055 43.478 0.0 0.0 30.75 1.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2249 2273 0.035036 TTGGACGTGGCGATAACCAA 59.965 50.000 0.0 0.0 42.7 3.67 R
3623 5348 1.420430 TCTTCCGGTCCTCAGTGTTT 58.580 50.000 0.0 0.0 0.0 2.83 R
4604 6329 3.131400 CCTCTCTCTGGTGCCTACTAAAC 59.869 52.174 0.0 0.0 0.0 2.01 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
25 27 5.416083 CATGATGTCCTCACCGTTTTAGTA 58.584 41.667 0.00 0.00 36.48 1.82
128 131 7.154656 ACCTTTTTACCTCAAATCTTTCATGC 58.845 34.615 0.00 0.00 0.00 4.06
309 312 6.832384 ACTGTCACTCGTATATTTAGAGGGAA 59.168 38.462 7.88 1.27 44.82 3.97
433 438 4.380531 CATCGACATACAAATACCTGGCT 58.619 43.478 0.00 0.00 0.00 4.75
496 501 6.753107 AACCAAACCAAGAATACCTATTCG 57.247 37.500 0.39 0.00 45.10 3.34
505 510 9.841295 ACCAAGAATACCTATTCGCTTTAATAA 57.159 29.630 0.39 0.00 45.10 1.40
605 610 7.396540 TTTTTGCAAAAGATTAGGCCAAAAA 57.603 28.000 22.78 1.49 30.90 1.94
607 612 6.799926 TTGCAAAAGATTAGGCCAAAAATC 57.200 33.333 5.01 11.32 33.21 2.17
616 621 3.751479 AGGCCAAAAATCAGTGGTTTC 57.249 42.857 5.01 0.00 37.23 2.78
617 622 3.308401 AGGCCAAAAATCAGTGGTTTCT 58.692 40.909 5.01 0.00 37.23 2.52
618 623 3.070015 AGGCCAAAAATCAGTGGTTTCTG 59.930 43.478 5.01 0.00 37.23 3.02
619 624 3.069443 GGCCAAAAATCAGTGGTTTCTGA 59.931 43.478 3.66 0.00 46.39 3.27
620 625 4.051237 GCCAAAAATCAGTGGTTTCTGAC 58.949 43.478 3.66 0.00 45.40 3.51
699 704 1.257743 TTTCACTCCTCTCAGTCCGG 58.742 55.000 0.00 0.00 0.00 5.14
704 709 0.967887 CTCCTCTCAGTCCGGCAGAA 60.968 60.000 0.00 0.00 0.00 3.02
733 738 2.034221 AAGCGCCTCTGTTTCCCC 59.966 61.111 2.29 0.00 0.00 4.81
838 843 3.307906 AAGGCACGCCGTGACCTA 61.308 61.111 25.80 0.00 43.69 3.08
930 951 4.333913 AGAAAGCGCATATGTCTCTGAT 57.666 40.909 11.47 0.00 0.00 2.90
931 952 4.305769 AGAAAGCGCATATGTCTCTGATC 58.694 43.478 11.47 0.00 0.00 2.92
932 953 2.739885 AGCGCATATGTCTCTGATCC 57.260 50.000 11.47 0.00 0.00 3.36
933 954 1.966354 AGCGCATATGTCTCTGATCCA 59.034 47.619 11.47 0.00 0.00 3.41
935 956 2.681706 CGCATATGTCTCTGATCCACC 58.318 52.381 4.29 0.00 0.00 4.61
936 957 2.036346 CGCATATGTCTCTGATCCACCA 59.964 50.000 4.29 0.00 0.00 4.17
940 961 2.967599 TGTCTCTGATCCACCAATCG 57.032 50.000 0.00 0.00 0.00 3.34
941 962 2.179427 TGTCTCTGATCCACCAATCGT 58.821 47.619 0.00 0.00 0.00 3.73
944 965 1.482182 CTCTGATCCACCAATCGTCCA 59.518 52.381 0.00 0.00 0.00 4.02
954 975 3.188460 CACCAATCGTCCAAATCGAACTT 59.812 43.478 0.00 0.00 40.61 2.66
1162 1183 3.685835 CGAGGATGAAGACCTAGGTGAGA 60.686 52.174 22.10 0.00 37.93 3.27
1859 1880 5.123502 GTGAGTTTGATGAGCAATCTGATGT 59.876 40.000 0.00 0.00 36.82 3.06
2045 2067 7.944729 AATTTCAGTTGTGGCATACTCTTAT 57.055 32.000 0.00 0.00 0.00 1.73
2209 2233 0.667993 CTCACACGGTTGCCATTGTT 59.332 50.000 0.00 0.00 0.00 2.83
2249 2273 6.751157 TGCAGTTCATTGATCTCAAAATTGT 58.249 32.000 0.00 0.00 39.55 2.71
2833 4404 7.704047 GGGCATCATTCAAACTCTTCTTTAATC 59.296 37.037 0.00 0.00 0.00 1.75
3337 4921 6.128486 TGGCCTTAATCTGAATCTTTATGCA 58.872 36.000 3.32 0.00 0.00 3.96
3375 4959 3.054802 AGAGATGTGATCCGCCTCTTTTT 60.055 43.478 0.00 0.00 30.75 1.94
3408 4992 5.048224 CAGAATCAGGTTGCAGAATGAGTTT 60.048 40.000 3.67 0.00 39.69 2.66
3623 5348 5.466728 GCTGTGAAGAGTTTACATGACTTGA 59.533 40.000 0.00 0.00 0.00 3.02
3655 5380 2.439507 ACCGGAAGAATCTGCCATGTAT 59.560 45.455 9.46 0.00 0.00 2.29
3935 5660 6.202762 TGAAGCATAGTAATGGAAATAGTGCG 59.797 38.462 0.00 0.00 35.39 5.34
3968 5693 2.872245 CCATTTCATACAACGAGCGGAT 59.128 45.455 0.00 0.00 0.00 4.18
4084 5809 2.204136 TGGTGCCTCCCTGTCCAT 60.204 61.111 0.00 0.00 34.77 3.41
4497 6222 3.012518 AGACAGCAAATGTGGATACTGC 58.987 45.455 0.00 0.00 44.17 4.40
4540 6265 3.782523 AGAGCCCTTCATCATCTTGGTTA 59.217 43.478 0.00 0.00 0.00 2.85
4613 6338 2.711542 CCAAGCCTGGTGTTTAGTAGG 58.288 52.381 0.00 0.00 38.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 27 5.908590 AGAAAAGGAAGGATTTGATTCCCT 58.091 37.500 0.44 0.00 45.13 4.20
167 170 4.970640 AGAAAGGATATGGGTAAACCGGTA 59.029 41.667 8.00 0.00 44.64 4.02
309 312 6.340522 GCCTTTCACATTTACTAATGCCAAT 58.659 36.000 0.00 0.00 44.05 3.16
404 408 3.916359 TTTGTATGTCGATGGGCCTTA 57.084 42.857 4.53 0.00 0.00 2.69
433 438 6.338146 AGTTTATACACGCTAAGCAATCTGA 58.662 36.000 0.00 0.00 0.00 3.27
547 552 3.451526 GGCTTTGGCTCATTTGCTAATC 58.548 45.455 0.00 0.00 38.73 1.75
605 610 5.180117 CGAATTTCTGTCAGAAACCACTGAT 59.820 40.000 26.44 9.38 45.83 2.90
607 612 4.273480 ACGAATTTCTGTCAGAAACCACTG 59.727 41.667 26.44 17.39 45.83 3.66
616 621 9.840427 AAATATTGGTTTACGAATTTCTGTCAG 57.160 29.630 0.00 0.00 0.00 3.51
713 718 1.374252 GGAAACAGAGGCGCTTCGA 60.374 57.895 14.34 0.00 0.00 3.71
733 738 2.328099 GCGTGGGCTGAGGAAACAG 61.328 63.158 0.00 0.00 40.43 3.16
838 843 3.474570 GGGTGCCTCGCCAGATCT 61.475 66.667 0.00 0.00 35.42 2.75
930 951 1.276705 TCGATTTGGACGATTGGTGGA 59.723 47.619 0.00 0.00 34.85 4.02
931 952 1.732941 TCGATTTGGACGATTGGTGG 58.267 50.000 0.00 0.00 34.85 4.61
932 953 2.742053 AGTTCGATTTGGACGATTGGTG 59.258 45.455 0.00 0.00 39.45 4.17
933 954 3.053831 AGTTCGATTTGGACGATTGGT 57.946 42.857 0.00 0.00 39.45 3.67
935 956 4.404507 ACAAGTTCGATTTGGACGATTG 57.595 40.909 12.92 0.00 39.45 2.67
936 957 4.390909 GGTACAAGTTCGATTTGGACGATT 59.609 41.667 15.41 0.00 39.73 3.34
940 961 4.612939 GCAAGGTACAAGTTCGATTTGGAC 60.613 45.833 14.18 14.18 38.41 4.02
941 962 3.500680 GCAAGGTACAAGTTCGATTTGGA 59.499 43.478 12.92 3.62 0.00 3.53
944 965 5.531287 AGAAAGCAAGGTACAAGTTCGATTT 59.469 36.000 0.00 0.00 0.00 2.17
954 975 3.904339 AGAGGAAGAGAAAGCAAGGTACA 59.096 43.478 0.00 0.00 0.00 2.90
1162 1183 3.068732 CGTCATCAGGATACACATGGAGT 59.931 47.826 0.00 0.00 41.41 3.85
1370 1391 1.153449 TGCTCCGGTGAAATAGCCG 60.153 57.895 7.92 0.00 46.80 5.52
1859 1880 7.773489 TGAATATCAGGATTTTGGAACACAA 57.227 32.000 0.00 0.00 39.29 3.33
2119 2141 9.578576 AATAAAGGAAGCATGTGACATATACAT 57.421 29.630 0.00 0.00 39.23 2.29
2185 2209 1.106351 TGGCAACCGTGTGAGCAATT 61.106 50.000 0.00 0.00 0.00 2.32
2249 2273 0.035036 TTGGACGTGGCGATAACCAA 59.965 50.000 0.00 0.00 42.70 3.67
2833 4404 6.005583 TGAAAGATAAGTTTGAGCTTGCAG 57.994 37.500 0.00 0.00 0.00 4.41
3337 4921 1.964223 TCTCTGAAGCCACTCGTCTTT 59.036 47.619 0.00 0.00 0.00 2.52
3375 4959 3.253188 GCAACCTGATTCTGTAACTGCAA 59.747 43.478 0.00 0.00 0.00 4.08
3378 4962 4.318332 TCTGCAACCTGATTCTGTAACTG 58.682 43.478 0.00 0.00 0.00 3.16
3408 4992 2.801077 TCTCATCACTCCTACGACCA 57.199 50.000 0.00 0.00 0.00 4.02
3604 5329 7.852945 CAGTGTTTCAAGTCATGTAAACTCTTC 59.147 37.037 0.00 0.00 34.48 2.87
3623 5348 1.420430 TCTTCCGGTCCTCAGTGTTT 58.580 50.000 0.00 0.00 0.00 2.83
3935 5660 5.907207 TGTATGAAATGGACTCTACTGCTC 58.093 41.667 0.00 0.00 0.00 4.26
3994 5719 7.215085 AGAAGCAAAAGCAAGAAATGAAGAAT 58.785 30.769 0.00 0.00 0.00 2.40
4084 5809 5.200483 GACAATGTGGGATAAATCCTTGGA 58.800 41.667 8.85 0.00 46.35 3.53
4220 5945 5.705905 GGAAAACTGATAACTAGCTGGTGTT 59.294 40.000 2.40 5.20 0.00 3.32
4497 6222 3.475566 ACATCACTTCATACCGATGGG 57.524 47.619 0.00 0.00 39.64 4.00
4540 6265 5.701750 GCAGATATGAGATTGACAAGATGCT 59.298 40.000 0.00 0.00 0.00 3.79
4604 6329 3.131400 CCTCTCTCTGGTGCCTACTAAAC 59.869 52.174 0.00 0.00 0.00 2.01


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

AutoCloner maintained by Alex Coulton.