Multiple sequence alignment - TraesCS2D01G195900

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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 TraesCS2D01G195900 chr2D 100.000 4376 0 0 1 4376 142476611 142472236 0.000000e+00 8082.0
1 TraesCS2D01G195900 chr2D 91.436 1121 81 9 2414 3527 142433098 142431986 0.000000e+00 1524.0
2 TraesCS2D01G195900 chr2D 89.043 940 81 16 714 1643 142435858 142434931 0.000000e+00 1146.0
3 TraesCS2D01G195900 chr2D 83.394 277 31 7 2061 2324 142433381 142433107 4.370000e-60 243.0
4 TraesCS2D01G195900 chr2D 87.143 70 9 0 196 265 589508433 589508502 3.630000e-11 80.5
5 TraesCS2D01G195900 chr2D 100.000 29 0 0 1412 1440 26537573 26537545 2.000000e-03 54.7
6 TraesCS2D01G195900 chr2B 95.637 2796 88 16 1593 4376 200472597 200469824 0.000000e+00 4457.0
7 TraesCS2D01G195900 chr2B 95.943 1060 28 4 566 1622 200473646 200472599 0.000000e+00 1705.0
8 TraesCS2D01G195900 chr2B 91.454 1135 79 12 2432 3554 200384484 200385612 0.000000e+00 1543.0
9 TraesCS2D01G195900 chr2B 88.179 939 83 21 714 1637 200382694 200383619 0.000000e+00 1094.0
10 TraesCS2D01G195900 chr2B 91.916 569 39 3 1 567 200474291 200473728 0.000000e+00 789.0
11 TraesCS2D01G195900 chr2B 82.734 278 32 6 2060 2324 200384184 200384458 2.630000e-57 233.0
12 TraesCS2D01G195900 chr2A 92.704 2001 115 17 2387 4376 158554763 158556743 0.000000e+00 2857.0
13 TraesCS2D01G195900 chr2A 91.208 1888 105 31 1 1839 158552411 158554286 0.000000e+00 2510.0
14 TraesCS2D01G195900 chr2A 93.668 995 58 2 2472 3462 158591707 158592700 0.000000e+00 1483.0
15 TraesCS2D01G195900 chr2A 89.079 934 79 16 714 1637 158589563 158590483 0.000000e+00 1138.0
16 TraesCS2D01G195900 chr2A 94.538 476 21 3 1879 2351 158554292 158554765 0.000000e+00 730.0
17 TraesCS2D01G195900 chr2A 89.286 112 12 0 2061 2172 158591375 158591486 1.640000e-29 141.0
18 TraesCS2D01G195900 chr5D 85.500 200 20 5 4 197 432026929 432026733 2.670000e-47 200.0
19 TraesCS2D01G195900 chr5D 84.848 198 23 4 1 193 91343923 91344118 4.470000e-45 193.0
20 TraesCS2D01G195900 chr1D 85.427 199 22 5 4 197 202550900 202550704 2.670000e-47 200.0
21 TraesCS2D01G195900 chr1D 92.308 65 5 0 196 260 97911563 97911627 4.660000e-15 93.5
22 TraesCS2D01G195900 chr4D 85.714 196 19 5 7 197 81965252 81965061 9.600000e-47 198.0
23 TraesCS2D01G195900 chr5B 84.158 202 25 3 1 197 707157525 707157326 5.780000e-44 189.0
24 TraesCS2D01G195900 chr5A 81.102 254 32 6 4 243 649269771 649269520 5.780000e-44 189.0
25 TraesCS2D01G195900 chr7D 84.158 202 23 5 1 197 160427895 160428092 2.080000e-43 187.0
26 TraesCS2D01G195900 chr7D 80.769 182 24 5 1 173 117544506 117544685 9.880000e-27 132.0
27 TraesCS2D01G195900 chr4A 79.636 275 30 7 17 269 738847094 738847364 1.620000e-39 174.0
28 TraesCS2D01G195900 chr3B 93.151 73 5 0 196 268 177895715 177895643 1.660000e-19 108.0
29 TraesCS2D01G195900 chr3B 89.552 67 7 0 196 262 822818474 822818408 7.800000e-13 86.1
30 TraesCS2D01G195900 chr3B 94.872 39 0 2 507 543 405224168 405224130 4.730000e-05 60.2
31 TraesCS2D01G195900 chrUn 88.732 71 6 2 199 268 127002986 127002917 7.800000e-13 86.1
32 TraesCS2D01G195900 chrUn 100.000 29 0 0 1412 1440 17152116 17152088 2.000000e-03 54.7
33 TraesCS2D01G195900 chrUn 100.000 29 0 0 1412 1440 292609814 292609842 2.000000e-03 54.7
34 TraesCS2D01G195900 chr4B 82.979 94 12 4 267 358 657302360 657302269 1.010000e-11 82.4


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 TraesCS2D01G195900 chr2D 142472236 142476611 4375 True 8082.000000 8082 100.000000 1 4376 1 chr2D.!!$R2 4375
1 TraesCS2D01G195900 chr2D 142431986 142435858 3872 True 971.000000 1524 87.957667 714 3527 3 chr2D.!!$R3 2813
2 TraesCS2D01G195900 chr2B 200469824 200474291 4467 True 2317.000000 4457 94.498667 1 4376 3 chr2B.!!$R1 4375
3 TraesCS2D01G195900 chr2B 200382694 200385612 2918 False 956.666667 1543 87.455667 714 3554 3 chr2B.!!$F1 2840
4 TraesCS2D01G195900 chr2A 158552411 158556743 4332 False 2032.333333 2857 92.816667 1 4376 3 chr2A.!!$F1 4375
5 TraesCS2D01G195900 chr2A 158589563 158592700 3137 False 920.666667 1483 90.677667 714 3462 3 chr2A.!!$F2 2748

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
74 75 0.625849 ATTGAACGGGGGAGCTTGAT 59.374 50.0 0.00 0.00 0.00 2.57 F
1235 1376 0.035458 GCAGCACTACCTGTCCAACT 59.965 55.0 0.00 0.00 35.28 3.16 F
1854 2031 0.538584 TACTCGCCACTCGGAGTAGA 59.461 55.0 10.87 9.69 39.05 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1840 2017 0.107116 TCCTCTCTACTCCGAGTGGC 60.107 60.000 11.52 0.0 41.93 5.01 R
2354 4142 0.107897 GGTGTGTGTGTCTGTGTGGA 60.108 55.000 0.00 0.0 0.00 4.02 R
3758 5587 2.514824 GGGAAGCGAGTGCCCATC 60.515 66.667 0.00 0.0 44.31 3.51 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
69 70 1.545841 AAAGAATTGAACGGGGGAGC 58.454 50.000 0.00 0.00 0.00 4.70
74 75 0.625849 ATTGAACGGGGGAGCTTGAT 59.374 50.000 0.00 0.00 0.00 2.57
81 82 1.338020 CGGGGGAGCTTGATAAATTGC 59.662 52.381 0.00 0.00 0.00 3.56
83 84 3.747388 CGGGGGAGCTTGATAAATTGCTA 60.747 47.826 0.00 0.00 35.76 3.49
91 92 4.733523 GCTTGATAAATTGCTAACCCGGTG 60.734 45.833 0.00 0.00 0.00 4.94
98 99 2.570415 TGCTAACCCGGTGAAAATCA 57.430 45.000 0.00 0.00 0.00 2.57
99 100 2.865079 TGCTAACCCGGTGAAAATCAA 58.135 42.857 0.00 0.00 0.00 2.57
121 122 6.953520 TCAAATGACCCAATTCTGAATACCTT 59.046 34.615 2.85 0.00 0.00 3.50
211 214 8.109634 AGAGCTTTAAGACCCAATTCTAATTGA 58.890 33.333 15.37 0.00 46.72 2.57
243 246 9.691362 TTAATTGAATGTGAGCTCTTTAAAACC 57.309 29.630 16.19 0.00 0.00 3.27
245 248 6.707440 TGAATGTGAGCTCTTTAAAACCAA 57.293 33.333 16.19 0.00 0.00 3.67
317 320 4.223700 CCTAGTGGATATTGCATGAGGCTA 59.776 45.833 0.00 0.00 38.49 3.93
340 343 9.581289 GCTACATGATACTACCTATGATATCCT 57.419 37.037 0.00 0.00 0.00 3.24
447 475 5.065218 TGTTTTGCTGAGTTGAAAGAGAGAC 59.935 40.000 0.00 0.00 0.00 3.36
448 476 3.018598 TGCTGAGTTGAAAGAGAGACG 57.981 47.619 0.00 0.00 0.00 4.18
449 477 2.623416 TGCTGAGTTGAAAGAGAGACGA 59.377 45.455 0.00 0.00 0.00 4.20
450 478 3.241701 GCTGAGTTGAAAGAGAGACGAG 58.758 50.000 0.00 0.00 0.00 4.18
451 479 3.057876 GCTGAGTTGAAAGAGAGACGAGA 60.058 47.826 0.00 0.00 0.00 4.04
527 559 7.439655 GCTCTAAGAAGTTTTGAGAGTGAAAGA 59.560 37.037 9.09 0.00 36.76 2.52
609 727 7.547019 ACATTGCCTATAGATGATATGACAACG 59.453 37.037 0.00 0.00 0.00 4.10
663 782 6.927294 ACCATGCTTTTATAGAGTGCTTAC 57.073 37.500 0.00 0.00 0.00 2.34
721 842 4.501400 GCCAACAATTGCTCCTAAACAAGT 60.501 41.667 5.05 0.00 0.00 3.16
925 1049 2.115266 CACAGAACCCCCACACCC 59.885 66.667 0.00 0.00 0.00 4.61
952 1076 9.712305 CCTCTGTATTCTTTCTCTCTTTAAACA 57.288 33.333 0.00 0.00 0.00 2.83
1036 1177 6.349280 GCAATACCAACTCAAGCTGATTACAA 60.349 38.462 0.00 0.00 0.00 2.41
1235 1376 0.035458 GCAGCACTACCTGTCCAACT 59.965 55.000 0.00 0.00 35.28 3.16
1450 1591 2.604686 TTCGTGGAGGCTGAGGCT 60.605 61.111 8.79 8.79 42.48 4.58
1585 1726 4.673298 CAGGTACGCCACGCCACA 62.673 66.667 0.00 0.00 37.19 4.17
1587 1728 4.973055 GGTACGCCACGCCACACA 62.973 66.667 0.00 0.00 34.09 3.72
1597 1739 4.666532 GCCACACACGTTGCTCGC 62.667 66.667 0.00 0.00 44.19 5.03
1781 1958 4.060205 GCAAGTAACTTGGAAACGGACTA 58.940 43.478 0.00 0.00 41.31 2.59
1839 2016 6.712179 AGTATTGGTTGGCTAGTAGTACTC 57.288 41.667 5.96 0.00 0.00 2.59
1840 2017 4.650754 ATTGGTTGGCTAGTAGTACTCG 57.349 45.455 5.96 1.26 0.00 4.18
1841 2018 1.747355 TGGTTGGCTAGTAGTACTCGC 59.253 52.381 16.47 16.47 36.32 5.03
1854 2031 0.538584 TACTCGCCACTCGGAGTAGA 59.461 55.000 10.87 9.69 39.05 2.59
1910 3635 7.412137 ACAAATTTGAGTTCAATAGCTTTGC 57.588 32.000 24.64 0.00 35.55 3.68
1957 3683 4.081476 GGCAGCCAGAAATATGTTTTCCTT 60.081 41.667 6.55 0.00 0.00 3.36
1959 3685 4.866486 CAGCCAGAAATATGTTTTCCTTGC 59.134 41.667 0.00 0.00 0.00 4.01
1981 3710 7.048629 TGCAGAAATACAATGGTTTCTTCAA 57.951 32.000 11.43 1.50 41.40 2.69
2290 4078 6.469595 CGTCGAACAACCAAATTAGTCAAAAA 59.530 34.615 0.00 0.00 0.00 1.94
2354 4142 2.787601 TCGAACTGCGTAGTTTGTCT 57.212 45.000 26.61 4.11 46.79 3.41
2373 4161 0.107897 TCCACACAGACACACACACC 60.108 55.000 0.00 0.00 0.00 4.16
2374 4162 1.095228 CCACACAGACACACACACCC 61.095 60.000 0.00 0.00 0.00 4.61
2375 4163 0.392327 CACACAGACACACACACCCA 60.392 55.000 0.00 0.00 0.00 4.51
2377 4165 0.392327 CACAGACACACACACCCACA 60.392 55.000 0.00 0.00 0.00 4.17
2378 4166 0.392461 ACAGACACACACACCCACAC 60.392 55.000 0.00 0.00 0.00 3.82
2379 4167 0.392327 CAGACACACACACCCACACA 60.392 55.000 0.00 0.00 0.00 3.72
2380 4168 0.326595 AGACACACACACCCACACAA 59.673 50.000 0.00 0.00 0.00 3.33
3051 4857 4.819761 GATCTGCTGTCGGCGCCA 62.820 66.667 28.98 11.20 45.43 5.69
3243 5049 3.771160 GAGCCGACCATGTCCGGT 61.771 66.667 19.74 9.98 46.84 5.28
3458 5275 8.794335 TGCATGTGTTTGTTAGTATGGTTATA 57.206 30.769 0.00 0.00 0.00 0.98
3459 5276 8.888716 TGCATGTGTTTGTTAGTATGGTTATAG 58.111 33.333 0.00 0.00 0.00 1.31
3460 5277 8.889717 GCATGTGTTTGTTAGTATGGTTATAGT 58.110 33.333 0.00 0.00 0.00 2.12
3640 5466 4.303282 ACCAATATTTTGTTTCCACGTGC 58.697 39.130 10.91 0.00 0.00 5.34
3774 5603 2.514824 GGATGGGCACTCGCTTCC 60.515 66.667 0.00 0.00 40.49 3.46
3810 5639 1.002624 GGCAACCCGGTCTTCATGA 60.003 57.895 0.00 0.00 0.00 3.07
3853 5682 5.452777 TGAGATAATCGATTGTGAGTAGCG 58.547 41.667 20.87 0.00 30.83 4.26
3856 5685 0.249489 ATCGATTGTGAGTAGCGGGC 60.249 55.000 0.00 0.00 0.00 6.13
4251 6082 7.665561 TCTTGATTTATGACATTTCACGTCA 57.334 32.000 0.00 0.00 46.77 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
69 70 4.638421 TCACCGGGTTAGCAATTTATCAAG 59.362 41.667 6.32 0.00 0.00 3.02
74 75 5.477291 TGATTTTCACCGGGTTAGCAATTTA 59.523 36.000 6.32 0.00 0.00 1.40
81 82 5.399013 GTCATTTGATTTTCACCGGGTTAG 58.601 41.667 6.32 0.00 0.00 2.34
83 84 3.006430 GGTCATTTGATTTTCACCGGGTT 59.994 43.478 6.32 0.00 0.00 4.11
91 92 8.782339 ATTCAGAATTGGGTCATTTGATTTTC 57.218 30.769 0.00 0.00 0.00 2.29
98 99 8.893563 TTAAGGTATTCAGAATTGGGTCATTT 57.106 30.769 0.00 0.00 0.00 2.32
99 100 9.492730 AATTAAGGTATTCAGAATTGGGTCATT 57.507 29.630 0.00 0.00 0.00 2.57
211 214 6.479884 AGAGCTCACATTCAATTAAGGTCTT 58.520 36.000 17.77 0.00 38.13 3.01
317 320 9.415008 GTGAGGATATCATAGGTAGTATCATGT 57.585 37.037 4.83 0.00 40.92 3.21
340 343 7.013083 GGTTGTCTATAAGATCTTCGGTAGTGA 59.987 40.741 12.24 0.00 0.00 3.41
447 475 5.108517 CCATTTCTCTTCTCTTTCCTCTCG 58.891 45.833 0.00 0.00 0.00 4.04
448 476 5.427378 CCCATTTCTCTTCTCTTTCCTCTC 58.573 45.833 0.00 0.00 0.00 3.20
449 477 4.324176 GCCCATTTCTCTTCTCTTTCCTCT 60.324 45.833 0.00 0.00 0.00 3.69
450 478 3.944650 GCCCATTTCTCTTCTCTTTCCTC 59.055 47.826 0.00 0.00 0.00 3.71
451 479 3.591079 AGCCCATTTCTCTTCTCTTTCCT 59.409 43.478 0.00 0.00 0.00 3.36
564 596 8.230486 GGCAATGTAATAGTCAACATGTATAGC 58.770 37.037 0.00 0.00 36.47 2.97
609 727 0.876342 GCCAGCCGTGACTATAGCAC 60.876 60.000 13.93 13.93 0.00 4.40
663 782 6.903419 TCATGTTATGTAGAGCTATCACTCG 58.097 40.000 0.00 0.00 41.77 4.18
721 842 3.071023 AGAATCAGGACAAGGAAACACGA 59.929 43.478 0.00 0.00 0.00 4.35
856 977 7.506971 GTGTTTATATAGTGGAGGGTAGCTTT 58.493 38.462 0.00 0.00 0.00 3.51
925 1049 9.157104 GTTTAAAGAGAGAAAGAATACAGAGGG 57.843 37.037 0.00 0.00 0.00 4.30
952 1076 3.319405 ACGACAGAGAGAGATTTGTGTGT 59.681 43.478 0.00 0.00 0.00 3.72
1036 1177 9.263538 TGTTAGACACGAAAGTTTACATACATT 57.736 29.630 0.00 0.00 46.40 2.71
1235 1376 1.375396 CCGCGATGTTCTGGTCCAA 60.375 57.895 8.23 0.00 0.00 3.53
1603 1745 0.523072 ACGCAGTTAAAGCATGCCTG 59.477 50.000 15.66 14.90 37.78 4.85
1839 2016 1.440938 CCTCTCTACTCCGAGTGGCG 61.441 65.000 11.52 3.36 37.72 5.69
1840 2017 0.107116 TCCTCTCTACTCCGAGTGGC 60.107 60.000 11.52 0.00 41.93 5.01
1841 2018 1.487142 TCTCCTCTCTACTCCGAGTGG 59.513 57.143 11.52 8.48 42.97 4.00
1842 2019 2.940410 GTTCTCCTCTCTACTCCGAGTG 59.060 54.545 11.52 1.87 32.83 3.51
1843 2020 2.419021 CGTTCTCCTCTCTACTCCGAGT 60.419 54.545 6.25 6.25 32.83 4.18
1844 2021 2.206750 CGTTCTCCTCTCTACTCCGAG 58.793 57.143 0.00 0.00 0.00 4.63
1845 2022 1.134461 CCGTTCTCCTCTCTACTCCGA 60.134 57.143 0.00 0.00 0.00 4.55
1854 2031 1.670791 GAGTCGATCCGTTCTCCTCT 58.329 55.000 0.00 0.00 0.00 3.69
1909 3634 1.673920 TGAACTCACTTTTCAACCCGC 59.326 47.619 0.00 0.00 29.89 6.13
1910 3635 4.290155 CATTGAACTCACTTTTCAACCCG 58.710 43.478 0.00 0.00 43.84 5.28
1957 3683 6.647334 TGAAGAAACCATTGTATTTCTGCA 57.353 33.333 13.57 13.57 44.68 4.41
1959 3685 9.918630 AGAATTGAAGAAACCATTGTATTTCTG 57.081 29.630 11.74 0.00 42.89 3.02
1981 3710 7.701539 TTGGATTTAGCAATGTGTGTAGAAT 57.298 32.000 0.00 0.00 0.00 2.40
1988 3717 9.723601 AAAACATATTTGGATTTAGCAATGTGT 57.276 25.926 0.00 0.00 33.77 3.72
2077 3812 1.282382 TAGGTAGAAGTGGTTGGGCC 58.718 55.000 0.00 0.00 37.90 5.80
2264 4052 3.059461 TGACTAATTTGGTTGTTCGACGC 60.059 43.478 0.00 0.00 0.00 5.19
2290 4078 5.119931 TCATTAAATTTGCAGCAGACGTT 57.880 34.783 0.00 0.00 0.00 3.99
2354 4142 0.107897 GGTGTGTGTGTCTGTGTGGA 60.108 55.000 0.00 0.00 0.00 4.02
2393 4197 8.899776 CAAAGTAGTAGTAGTACGAACTTTGTG 58.100 37.037 32.74 23.18 46.82 3.33
2451 4257 2.292061 ACTATTGTACTGACTCCCGGGT 60.292 50.000 22.86 0.14 0.00 5.28
3758 5587 2.514824 GGGAAGCGAGTGCCCATC 60.515 66.667 0.00 0.00 44.31 3.51
3774 5603 3.121030 CTTTGCGCACCTCTCCGG 61.121 66.667 11.12 0.00 39.35 5.14
3800 5629 9.512588 AATATTTGATCCTACATCATGAAGACC 57.487 33.333 4.68 0.00 0.00 3.85
3853 5682 4.642885 TGTTATAGTGCCTTGTTTATGCCC 59.357 41.667 0.00 0.00 0.00 5.36
3856 5685 6.238103 CGTCCTGTTATAGTGCCTTGTTTATG 60.238 42.308 0.00 0.00 0.00 1.90
4152 5983 1.269726 CGGTTGCAATTTGCCTTCACT 60.270 47.619 18.27 0.00 44.23 3.41
4155 5986 2.147436 TTCGGTTGCAATTTGCCTTC 57.853 45.000 18.27 8.58 44.23 3.46
4179 6010 3.891366 ACATGTTCCTTGTAGCTTGCTTT 59.109 39.130 0.00 0.00 0.00 3.51
4220 6051 8.139350 TGAAATGTCATAAATCAAGATCATGCC 58.861 33.333 0.00 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.