Multiple sequence alignment - TraesCS3D01G189700

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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 TraesCS3D01G189700 chr3D 100.000 5527 0 0 1 5527 177374069 177368543 0.000000e+00 10207.0
1 TraesCS3D01G189700 chr3D 100.000 38 0 0 5328 5365 177368704 177368667 2.760000e-08 71.3
2 TraesCS3D01G189700 chr3D 100.000 38 0 0 5366 5403 177368742 177368705 2.760000e-08 71.3
3 TraesCS3D01G189700 chr3A 96.031 5392 138 30 34 5365 217987307 217981932 0.000000e+00 8702.0
4 TraesCS3D01G189700 chr3A 98.148 162 3 0 5366 5527 217981969 217981808 3.260000e-72 283.0
5 TraesCS3D01G189700 chr3B 96.564 2532 61 7 2999 5527 256252466 256249958 0.000000e+00 4170.0
6 TraesCS3D01G189700 chr3B 96.226 1325 42 4 702 2021 256255127 256253806 0.000000e+00 2163.0
7 TraesCS3D01G189700 chr3B 91.421 711 37 8 2323 3017 256253289 256252587 0.000000e+00 953.0
8 TraesCS3D01G189700 chr3B 90.457 503 36 4 22 521 256262350 256261857 0.000000e+00 652.0
9 TraesCS3D01G189700 chr3B 86.007 586 50 8 22 575 491522970 491522385 2.850000e-167 599.0
10 TraesCS3D01G189700 chr3B 92.557 309 17 4 2020 2324 256253712 256253406 6.570000e-119 438.0
11 TraesCS3D01G189700 chr3B 96.809 188 6 0 517 704 256255430 256255243 1.160000e-81 315.0
12 TraesCS3D01G189700 chr3B 100.000 38 0 0 5328 5365 256250119 256250082 2.760000e-08 71.3
13 TraesCS3D01G189700 chr1B 86.348 586 48 9 22 575 7970032 7970617 1.320000e-170 610.0
14 TraesCS3D01G189700 chr1B 83.614 415 41 12 22 409 667813665 667814079 1.130000e-96 364.0
15 TraesCS3D01G189700 chr5B 86.177 586 49 9 22 575 672843440 672844025 6.120000e-169 604.0
16 TraesCS3D01G189700 chr5B 85.279 197 18 6 22 207 341551057 341551253 5.650000e-45 193.0
17 TraesCS3D01G189700 chr7B 85.763 583 54 11 22 575 678853655 678854237 1.710000e-164 590.0
18 TraesCS3D01G189700 chr7B 84.696 477 44 8 22 469 520113359 520112883 3.040000e-122 449.0
19 TraesCS3D01G189700 chr1D 83.885 453 43 13 22 444 479585431 479585883 6.670000e-109 405.0
20 TraesCS3D01G189700 chr6B 88.339 283 20 4 22 292 42760417 42760698 1.480000e-85 327.0
21 TraesCS3D01G189700 chr2A 82.308 130 18 5 575 701 631535139 631535012 2.110000e-19 108.0
22 TraesCS3D01G189700 chr6D 87.143 70 8 1 293 361 128082458 128082389 1.650000e-10 78.7
23 TraesCS3D01G189700 chr2B 79.646 113 19 4 293 403 416811943 416811833 1.650000e-10 78.7
24 TraesCS3D01G189700 chr4D 84.746 59 7 2 297 354 337469193 337469250 2.150000e-04 58.4


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 TraesCS3D01G189700 chr3D 177368543 177374069 5526 True 10207.000000 10207 100.000000 1 5527 1 chr3D.!!$R1 5526
1 TraesCS3D01G189700 chr3A 217981808 217987307 5499 True 4492.500000 8702 97.089500 34 5527 2 chr3A.!!$R1 5493
2 TraesCS3D01G189700 chr3B 256249958 256255430 5472 True 1351.716667 4170 95.596167 517 5527 6 chr3B.!!$R3 5010
3 TraesCS3D01G189700 chr3B 491522385 491522970 585 True 599.000000 599 86.007000 22 575 1 chr3B.!!$R2 553
4 TraesCS3D01G189700 chr1B 7970032 7970617 585 False 610.000000 610 86.348000 22 575 1 chr1B.!!$F1 553
5 TraesCS3D01G189700 chr5B 672843440 672844025 585 False 604.000000 604 86.177000 22 575 1 chr5B.!!$F2 553
6 TraesCS3D01G189700 chr7B 678853655 678854237 582 False 590.000000 590 85.763000 22 575 1 chr7B.!!$F1 553

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
354 384 0.179094 CACCATGCCCATCAATGCAC 60.179 55.000 0.00 0.00 40.88 4.57 F
658 692 0.929824 CAAACAACTGCGAGGCGTTG 60.930 55.000 17.27 17.27 43.13 4.10 F
1297 1465 1.099295 ATACACCGCCGTCGATCTCA 61.099 55.000 0.00 0.00 38.10 3.27 F
2495 2894 1.073897 GCCAGTCACAGCCCTTCTT 59.926 57.895 0.00 0.00 0.00 2.52 F
2768 3176 3.424703 TGCTTCAAGAGGGAAAAGATGG 58.575 45.455 0.00 0.00 0.00 3.51 F
4147 4700 2.708325 GGAGATACAGGCCAGGATTCTT 59.292 50.000 5.01 0.00 0.00 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1648 1816 1.127567 TCCCCATCCTTATCGCCAGG 61.128 60.000 0.00 0.0 0.00 4.45 R
2351 2738 1.277557 GTCATTCCAGCAGAGAGGTGT 59.722 52.381 0.00 0.0 44.16 4.16 R
2786 3194 6.897966 TCCAGACTTTGATAGTACAGGAGAAT 59.102 38.462 0.00 0.0 37.17 2.40 R
4148 4701 1.210538 AGCTTCCATGATGAGCCAGA 58.789 50.000 2.86 0.0 37.11 3.86 R
4150 4703 1.282738 TGAAGCTTCCATGATGAGCCA 59.717 47.619 23.42 0.0 37.11 4.75 R
5346 5902 2.431782 AGCAAGAACCAGTGCAACAAAT 59.568 40.909 0.00 0.0 43.42 2.32 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
31 32 1.782028 GCCGCGTCCAAGTCTTTGTT 61.782 55.000 4.92 0.00 32.21 2.83
73 74 1.418334 ATTCGGACTGCTAGGCATCT 58.582 50.000 0.00 0.00 38.13 2.90
110 111 5.991328 ATGTTGATATTTGCTCCAGTACG 57.009 39.130 0.00 0.00 0.00 3.67
117 118 3.746045 TTTGCTCCAGTACGAACTCTT 57.254 42.857 0.00 0.00 31.97 2.85
139 150 2.730934 TATGTGTCCTCTCGTAGCCT 57.269 50.000 0.00 0.00 0.00 4.58
153 164 5.415077 TCTCGTAGCCTAACTATTATGCTCC 59.585 44.000 2.21 0.00 38.01 4.70
199 211 2.486592 CGGACCCGCTTTCAGTAAATTT 59.513 45.455 0.00 0.00 0.00 1.82
237 250 2.149578 GCTCTGAGAACAGTTGCACAT 58.850 47.619 9.28 0.00 43.81 3.21
272 285 6.183360 GGTTTTGTGATCAACCTCCAACTTTA 60.183 38.462 7.00 0.00 39.62 1.85
286 299 7.722285 ACCTCCAACTTTACTTTGCTAACATAA 59.278 33.333 0.00 0.00 0.00 1.90
294 307 7.807687 TTACTTTGCTAACATAACGAGACTC 57.192 36.000 0.00 0.00 0.00 3.36
295 308 6.026947 ACTTTGCTAACATAACGAGACTCT 57.973 37.500 0.03 0.00 0.00 3.24
354 384 0.179094 CACCATGCCCATCAATGCAC 60.179 55.000 0.00 0.00 40.88 4.57
363 393 3.696051 GCCCATCAATGCACTCTCTTTTA 59.304 43.478 0.00 0.00 0.00 1.52
369 399 8.896744 CCATCAATGCACTCTCTTTTATTCTAA 58.103 33.333 0.00 0.00 0.00 2.10
459 489 9.606631 ATTAAAAACTGCCATAACAAAAACAGA 57.393 25.926 0.00 0.00 0.00 3.41
470 500 4.078639 ACAAAAACAGAGAGAGACTGGG 57.921 45.455 0.00 0.00 39.38 4.45
658 692 0.929824 CAAACAACTGCGAGGCGTTG 60.930 55.000 17.27 17.27 43.13 4.10
675 709 2.297701 GTTGGCTGTGAGTTTCTTCCA 58.702 47.619 0.00 0.00 0.00 3.53
841 999 1.606994 CCACAGTTTGTAGCGTGGCTA 60.607 52.381 0.00 0.00 42.24 3.93
900 1068 1.673665 CTGAGCTGTGCCTCCAACC 60.674 63.158 0.00 0.00 0.00 3.77
992 1160 3.012518 CCACCTGATTTTGAGATTCGCT 58.987 45.455 0.00 0.00 0.00 4.93
1257 1425 2.738521 CCGTCCTCAACCACAGCG 60.739 66.667 0.00 0.00 0.00 5.18
1297 1465 1.099295 ATACACCGCCGTCGATCTCA 61.099 55.000 0.00 0.00 38.10 3.27
1389 1557 3.260100 CTGGTGGGTCCCAGGCTT 61.260 66.667 12.21 0.00 46.89 4.35
1434 1602 1.650528 ACCTTCTTCTGAGGTCAGGG 58.349 55.000 7.14 2.88 43.91 4.45
1584 1752 9.651913 GAGAAGCTTAATCTTAGGGATAATCTG 57.348 37.037 0.00 0.00 33.71 2.90
1648 1816 1.349627 CACATTGCCGCATCGTCTC 59.650 57.895 0.00 0.00 0.00 3.36
1929 2098 4.183865 TGCTAACAACGAGAGATGGAATG 58.816 43.478 0.00 0.00 38.32 2.67
1935 2104 3.428746 ACGAGAGATGGAATGAAGACG 57.571 47.619 0.00 0.00 0.00 4.18
2495 2894 1.073897 GCCAGTCACAGCCCTTCTT 59.926 57.895 0.00 0.00 0.00 2.52
2768 3176 3.424703 TGCTTCAAGAGGGAAAAGATGG 58.575 45.455 0.00 0.00 0.00 3.51
2776 3184 6.012508 TCAAGAGGGAAAAGATGGAGTGTTAT 60.013 38.462 0.00 0.00 0.00 1.89
3779 4332 4.899457 TGGAGGTTCTTTTCAGTACTCAGA 59.101 41.667 0.00 0.00 0.00 3.27
3892 4445 4.558226 AGAGATCACACAGGTGCATTTA 57.442 40.909 0.00 0.00 44.87 1.40
3909 4462 7.899330 GGTGCATTTATTTGATCATTTTCAACG 59.101 33.333 0.00 0.00 35.42 4.10
4147 4700 2.708325 GGAGATACAGGCCAGGATTCTT 59.292 50.000 5.01 0.00 0.00 2.52
4148 4701 3.137360 GGAGATACAGGCCAGGATTCTTT 59.863 47.826 5.01 0.00 0.00 2.52
4149 4702 4.384940 GAGATACAGGCCAGGATTCTTTC 58.615 47.826 5.01 0.00 0.00 2.62
4150 4703 4.043596 AGATACAGGCCAGGATTCTTTCT 58.956 43.478 5.01 0.00 0.00 2.52
4302 4855 7.569297 TGTTAATTTCGTTGTGTCTGATGTAC 58.431 34.615 0.00 0.00 0.00 2.90
4508 5061 4.937620 GCTCCTAAATATGCCGATGATGAA 59.062 41.667 0.00 0.00 0.00 2.57
4754 5307 3.773860 ACAACTGTGAATTTGCACGAA 57.226 38.095 0.00 0.00 41.63 3.85
4783 5336 7.410120 ACTTTTGAAACAGTTTTCTCCAGAT 57.590 32.000 0.00 0.00 41.64 2.90
5346 5902 1.305219 GCTACATGTGGCGCCTTTCA 61.305 55.000 29.70 22.92 0.00 2.69
5487 6043 7.069578 GGAGTCTGTTACCATAACTATCCTTGA 59.930 40.741 0.81 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 0.818040 AGACTTGGACGCGGCTTTTT 60.818 50.000 13.91 0.00 0.00 1.94
8 9 0.818040 AAGACTTGGACGCGGCTTTT 60.818 50.000 13.91 0.00 0.00 2.27
9 10 0.818040 AAAGACTTGGACGCGGCTTT 60.818 50.000 13.91 0.00 0.00 3.51
10 11 1.227853 AAAGACTTGGACGCGGCTT 60.228 52.632 13.91 0.00 0.00 4.35
11 12 1.961277 CAAAGACTTGGACGCGGCT 60.961 57.895 13.91 0.00 0.00 5.52
12 13 1.782028 AACAAAGACTTGGACGCGGC 61.782 55.000 12.47 7.53 36.82 6.53
13 14 0.234884 GAACAAAGACTTGGACGCGG 59.765 55.000 12.47 0.00 36.82 6.46
14 15 1.217882 AGAACAAAGACTTGGACGCG 58.782 50.000 3.53 3.53 36.82 6.01
15 16 3.692791 AAAGAACAAAGACTTGGACGC 57.307 42.857 0.00 0.00 36.82 5.19
16 17 6.114221 TGTAAAAGAACAAAGACTTGGACG 57.886 37.500 0.00 0.00 36.82 4.79
17 18 7.085052 ACTGTAAAAGAACAAAGACTTGGAC 57.915 36.000 0.00 0.00 36.82 4.02
18 19 7.696992 AACTGTAAAAGAACAAAGACTTGGA 57.303 32.000 0.00 0.00 36.82 3.53
110 111 5.163602 ACGAGAGGACACATATGAAGAGTTC 60.164 44.000 10.38 1.48 0.00 3.01
117 118 2.885266 GGCTACGAGAGGACACATATGA 59.115 50.000 10.38 0.00 0.00 2.15
153 164 3.268023 AGGATCCTCTTTTACTTGGCG 57.732 47.619 9.02 0.00 0.00 5.69
199 211 4.523173 CAGAGCTAAGTATTACCCGATGGA 59.477 45.833 0.00 0.00 34.81 3.41
237 250 8.482128 AGGTTGATCACAAAACCAAATTCTTTA 58.518 29.630 15.12 0.00 46.91 1.85
272 285 6.026947 AGAGTCTCGTTATGTTAGCAAAGT 57.973 37.500 0.00 0.00 0.00 2.66
286 299 0.824759 GCATGGGGTTAGAGTCTCGT 59.175 55.000 0.00 0.00 0.00 4.18
294 307 1.496429 AGAATGGAGGCATGGGGTTAG 59.504 52.381 0.00 0.00 0.00 2.34
295 308 1.607225 AGAATGGAGGCATGGGGTTA 58.393 50.000 0.00 0.00 0.00 2.85
354 384 9.990360 GGGGAGATACTTTAGAATAAAAGAGAG 57.010 37.037 3.51 0.00 38.50 3.20
363 393 6.652205 TTTGGTGGGGAGATACTTTAGAAT 57.348 37.500 0.00 0.00 0.00 2.40
369 399 2.649816 AGCTTTTGGTGGGGAGATACTT 59.350 45.455 0.00 0.00 0.00 2.24
449 479 3.456277 ACCCAGTCTCTCTCTGTTTTTGT 59.544 43.478 0.00 0.00 0.00 2.83
459 489 2.614134 AGCTGTTACCCAGTCTCTCT 57.386 50.000 0.00 0.00 43.55 3.10
508 541 3.502211 TGAAGGTCTGGCGAGAAAAATTC 59.498 43.478 0.00 3.63 0.00 2.17
658 692 2.810852 CTCTTGGAAGAAACTCACAGCC 59.189 50.000 0.00 0.00 34.03 4.85
675 709 0.690762 TAGCCGGCAAAGGTTCTCTT 59.309 50.000 31.54 5.27 37.28 2.85
731 889 2.042433 TCGATTTGGGTTTTGGGAGGAT 59.958 45.455 0.00 0.00 0.00 3.24
900 1068 1.400629 CCTGCGCATTCACTCAAACAG 60.401 52.381 12.24 0.00 0.00 3.16
992 1160 2.046988 CGTCAGCCATGGTCAGCA 60.047 61.111 14.67 0.00 0.00 4.41
1297 1465 2.432628 GTACAGACTGCGGCGCTT 60.433 61.111 33.26 19.97 0.00 4.68
1387 1555 2.152699 CGTCGGCGCAGTACAGAAG 61.153 63.158 10.83 0.00 0.00 2.85
1389 1557 3.035576 CTCGTCGGCGCAGTACAGA 62.036 63.158 10.83 3.42 38.14 3.41
1584 1752 3.325135 TGAACAAGAGGGTCTTCTCCTTC 59.675 47.826 0.00 0.00 33.78 3.46
1648 1816 1.127567 TCCCCATCCTTATCGCCAGG 61.128 60.000 0.00 0.00 0.00 4.45
1929 2098 4.939271 AGGAATAAAGAGCTAGCGTCTTC 58.061 43.478 21.82 10.70 32.93 2.87
1935 2104 3.068307 TGGACGAGGAATAAAGAGCTAGC 59.932 47.826 6.62 6.62 0.00 3.42
2315 2584 6.575847 GCCTACCACATCATCACTATCATCAT 60.576 42.308 0.00 0.00 0.00 2.45
2351 2738 1.277557 GTCATTCCAGCAGAGAGGTGT 59.722 52.381 0.00 0.00 44.16 4.16
2495 2894 9.184523 CTTAAATTTTATCATACCTGGTCCACA 57.815 33.333 0.63 0.00 0.00 4.17
2786 3194 6.897966 TCCAGACTTTGATAGTACAGGAGAAT 59.102 38.462 0.00 0.00 37.17 2.40
3892 4445 9.906660 TTTTACTAGCGTTGAAAATGATCAAAT 57.093 25.926 0.00 0.00 40.76 2.32
4147 4700 1.562942 AGCTTCCATGATGAGCCAGAA 59.437 47.619 2.86 0.00 37.11 3.02
4148 4701 1.210538 AGCTTCCATGATGAGCCAGA 58.789 50.000 2.86 0.00 37.11 3.86
4149 4702 1.948145 GAAGCTTCCATGATGAGCCAG 59.052 52.381 15.97 0.00 37.11 4.85
4150 4703 1.282738 TGAAGCTTCCATGATGAGCCA 59.717 47.619 23.42 0.00 37.11 4.75
4204 4757 4.793071 TCTTCAATGCAAACACCGTAATG 58.207 39.130 0.00 0.00 0.00 1.90
4302 4855 6.428385 AAATGAAGAGCTAATCTCCAAACG 57.572 37.500 0.00 0.00 42.90 3.60
4460 5013 4.253685 CGTTTCTAGGCAGGAATTCTTCA 58.746 43.478 5.23 0.00 0.00 3.02
4508 5061 6.291648 TGTTTCTACTCTGCAAGATCAGAT 57.708 37.500 0.00 0.00 45.62 2.90
4783 5336 3.109928 TCTCATTCAGGATCCAAGCAGA 58.890 45.455 15.82 5.32 0.00 4.26
5145 5700 6.113411 CGGAAAATAACAACCTACTCAGGAT 58.887 40.000 0.00 0.00 45.91 3.24
5346 5902 2.431782 AGCAAGAACCAGTGCAACAAAT 59.568 40.909 0.00 0.00 43.42 2.32
5487 6043 5.535333 TCGAAGTTATCCTTGTTTCGACTT 58.465 37.500 3.80 0.00 43.00 3.01


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

AutoCloner maintained by Alex Coulton.