Multiple sequence alignment - TraesCS2D01G204100

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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 TraesCS2D01G204100 chr2D 100.000 4524 0 0 984 5507 155834037 155829514 0.000000e+00 8355.0
1 TraesCS2D01G204100 chr2D 100.000 612 0 0 1 612 155835020 155834409 0.000000e+00 1131.0
2 TraesCS2D01G204100 chr2A 95.138 2530 89 18 2840 5350 165923104 165920590 0.000000e+00 3960.0
3 TraesCS2D01G204100 chr2A 97.632 1858 40 1 984 2841 165925022 165923169 0.000000e+00 3184.0
4 TraesCS2D01G204100 chr2A 90.453 618 38 12 1 612 165925614 165925012 0.000000e+00 795.0
5 TraesCS2D01G204100 chr2A 100.000 38 0 0 3136 3173 165922845 165922808 2.750000e-08 71.3
6 TraesCS2D01G204100 chr2B 97.896 1854 39 0 988 2841 213807185 213805332 0.000000e+00 3208.0
7 TraesCS2D01G204100 chr2B 96.555 1190 29 8 3701 4886 213804643 213803462 0.000000e+00 1960.0
8 TraesCS2D01G204100 chr2B 85.973 663 52 21 4871 5507 213803312 213802665 0.000000e+00 671.0
9 TraesCS2D01G204100 chr2B 89.432 511 29 11 20 506 213808151 213807642 6.060000e-174 621.0
10 TraesCS2D01G204100 chr2B 95.052 384 13 1 3136 3513 213805010 213804627 2.840000e-167 599.0
11 TraesCS2D01G204100 chr2B 97.000 300 7 2 2840 3137 213805270 213804971 2.290000e-138 503.0
12 TraesCS2D01G204100 chr2B 86.719 384 26 11 24 383 213808602 213808220 2.390000e-108 403.0
13 TraesCS2D01G204100 chr2B 98.343 181 2 1 3525 3704 331010389 331010209 3.200000e-82 316.0
14 TraesCS2D01G204100 chr7B 99.444 180 1 0 3522 3701 536117766 536117587 1.480000e-85 327.0
15 TraesCS2D01G204100 chr5A 98.883 179 2 0 3525 3703 664552852 664553030 2.480000e-83 320.0
16 TraesCS2D01G204100 chr4A 98.883 179 2 0 3525 3703 114586289 114586467 2.480000e-83 320.0
17 TraesCS2D01G204100 chr4A 98.876 178 2 0 3525 3702 420020549 420020372 8.900000e-83 318.0
18 TraesCS2D01G204100 chr1A 99.429 175 1 0 3525 3699 515551305 515551479 8.900000e-83 318.0
19 TraesCS2D01G204100 chr5B 98.876 178 1 1 3525 3702 654755912 654755736 3.200000e-82 316.0
20 TraesCS2D01G204100 chr5B 81.188 101 13 5 122 219 506780006 506780103 5.920000e-10 76.8
21 TraesCS2D01G204100 chr4B 98.870 177 2 0 3525 3701 588430827 588431003 3.200000e-82 316.0
22 TraesCS2D01G204100 chr6B 84.211 76 9 3 122 196 708665738 708665811 2.750000e-08 71.3


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 TraesCS2D01G204100 chr2D 155829514 155835020 5506 True 4743.000000 8355 100.00000 1 5507 2 chr2D.!!$R1 5506
1 TraesCS2D01G204100 chr2A 165920590 165925614 5024 True 2002.575000 3960 95.80575 1 5350 4 chr2A.!!$R1 5349
2 TraesCS2D01G204100 chr2B 213802665 213808602 5937 True 1137.857143 3208 92.66100 20 5507 7 chr2B.!!$R2 5487

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
269 705 0.389296 TACGAGCATGTTGTGACGGG 60.389 55.000 0.00 0.0 34.93 5.28 F
1953 2412 0.322456 TGAAGGCAGTGGGGATTTCG 60.322 55.000 0.00 0.0 0.00 3.46 F
3557 4096 1.068954 GTAAAGCTGCTGCCTTGTGAC 60.069 52.381 12.44 0.0 40.80 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2019 2478 1.290203 ACTTTGCCGTGATATCTGCG 58.710 50.0 3.98 8.54 0.0 5.18 R
3568 4107 1.235724 GTTTCCAGGACTTGAACCCG 58.764 55.0 0.00 0.00 0.0 5.28 R
4923 5631 1.919240 TCTTAGAAGGACCTGACGCA 58.081 50.0 0.00 0.00 0.0 5.24 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
41 475 3.939837 CTGGTCGTCGGTGCATGCT 62.940 63.158 20.33 0.00 0.00 3.79
59 493 1.632422 CTGCGGATTGTTTGGCATTC 58.368 50.000 0.00 0.00 34.49 2.67
180 614 2.452813 CCGAATGGCAACCTCGACG 61.453 63.158 15.80 0.00 41.90 5.12
182 616 1.289109 CGAATGGCAACCTCGACGTT 61.289 55.000 10.42 0.00 41.90 3.99
207 643 4.337060 TCCTCGACGGTGTGTGCG 62.337 66.667 0.00 0.00 0.00 5.34
220 656 0.802494 GTGTGCGTTCTTATGTGGGG 59.198 55.000 0.00 0.00 0.00 4.96
269 705 0.389296 TACGAGCATGTTGTGACGGG 60.389 55.000 0.00 0.00 34.93 5.28
343 794 7.179694 TCTCCCGACTTTAAAGAAAGAAGGATA 59.820 37.037 21.92 8.30 44.23 2.59
459 918 5.270794 TGCTCTATCCATCTATCATCAGCT 58.729 41.667 0.00 0.00 0.00 4.24
604 1063 0.903454 CCCTACACCGACACTTCCCT 60.903 60.000 0.00 0.00 0.00 4.20
605 1064 1.617804 CCCTACACCGACACTTCCCTA 60.618 57.143 0.00 0.00 0.00 3.53
606 1065 2.385803 CCTACACCGACACTTCCCTAT 58.614 52.381 0.00 0.00 0.00 2.57
607 1066 2.361438 CCTACACCGACACTTCCCTATC 59.639 54.545 0.00 0.00 0.00 2.08
608 1067 1.192428 ACACCGACACTTCCCTATCC 58.808 55.000 0.00 0.00 0.00 2.59
609 1068 1.273098 ACACCGACACTTCCCTATCCT 60.273 52.381 0.00 0.00 0.00 3.24
610 1069 1.409427 CACCGACACTTCCCTATCCTC 59.591 57.143 0.00 0.00 0.00 3.71
611 1070 1.041437 CCGACACTTCCCTATCCTCC 58.959 60.000 0.00 0.00 0.00 4.30
1545 2004 1.227556 GGTCGGCAATGCTACGGAT 60.228 57.895 4.82 0.00 0.00 4.18
1578 2037 2.764128 GATCTGCCAGGTCCCGGA 60.764 66.667 0.73 0.00 0.00 5.14
1872 2331 2.966050 AGGAAGAAAGTGAGCATCGAC 58.034 47.619 0.00 0.00 38.61 4.20
1887 2346 8.721478 GTGAGCATCGACCAATTTATATGTTAT 58.279 33.333 0.00 0.00 38.61 1.89
1953 2412 0.322456 TGAAGGCAGTGGGGATTTCG 60.322 55.000 0.00 0.00 0.00 3.46
2019 2478 6.372659 TGAAAGTGCCAAAGAAGAGATATGTC 59.627 38.462 0.00 0.00 0.00 3.06
2232 2691 6.018016 GTGGAAACTACATTGCTTTGCATTTT 60.018 34.615 0.00 0.00 38.76 1.82
2379 2838 3.640967 ACAGGGCTGCATTTTGTTTCTAA 59.359 39.130 0.50 0.00 0.00 2.10
2631 3090 6.874134 ACTACTACACAGCTGACCAAATTTAG 59.126 38.462 23.35 11.72 0.00 1.85
2936 3461 9.770097 CCTGATACATCAATAATACACTTCTGT 57.230 33.333 0.00 0.00 36.18 3.41
3113 3640 4.912214 TGAGCAATGCATTATGAGTTTCG 58.088 39.130 12.53 0.00 0.00 3.46
3173 3700 4.692625 CCTTGTCAACAGTTCCTGATAGTG 59.307 45.833 0.00 0.00 35.18 2.74
3556 4095 1.238439 GTAAAGCTGCTGCCTTGTGA 58.762 50.000 12.44 0.00 40.80 3.58
3557 4096 1.068954 GTAAAGCTGCTGCCTTGTGAC 60.069 52.381 12.44 0.00 40.80 3.67
3763 4302 2.417719 AGAGCTTGGATTGACACGAAC 58.582 47.619 0.00 0.00 0.00 3.95
4140 4680 1.202087 TGCAGTCGTTGGTTGTTTTCG 60.202 47.619 0.00 0.00 0.00 3.46
4187 4727 1.980765 AGACCAGAGCATGAAGGTTCA 59.019 47.619 0.00 0.00 42.14 3.18
4263 4803 8.552296 AGGTATATATCAATTCCCATCCACTTC 58.448 37.037 0.00 0.00 0.00 3.01
4359 4899 2.820059 TGCTCGACAAGACAATCTGT 57.180 45.000 0.00 0.00 0.00 3.41
4548 5090 5.238214 AGAGATTCATAGCGGCATTCTTTTC 59.762 40.000 1.45 0.00 0.00 2.29
4770 5312 6.009908 TGCCCATTCTCTGTACTACTACTA 57.990 41.667 0.00 0.00 0.00 1.82
4771 5313 5.826737 TGCCCATTCTCTGTACTACTACTAC 59.173 44.000 0.00 0.00 0.00 2.73
4772 5314 5.826737 GCCCATTCTCTGTACTACTACTACA 59.173 44.000 0.00 0.00 0.00 2.74
4773 5315 6.490721 GCCCATTCTCTGTACTACTACTACAT 59.509 42.308 0.00 0.00 0.00 2.29
4774 5316 7.522399 GCCCATTCTCTGTACTACTACTACATG 60.522 44.444 0.00 0.00 0.00 3.21
4775 5317 7.040340 CCCATTCTCTGTACTACTACTACATGG 60.040 44.444 0.00 0.00 0.00 3.66
4776 5318 7.720074 CCATTCTCTGTACTACTACTACATGGA 59.280 40.741 0.00 0.00 27.38 3.41
4976 5696 3.852578 ACAATCTTACAGGAGGAATGGGT 59.147 43.478 0.00 0.00 0.00 4.51
5053 5773 2.389715 CTCTAGAAGGTTCCGGTCCAT 58.610 52.381 17.60 8.21 0.00 3.41
5223 5945 5.556915 TCACAGATTAAAAACGGTGATCCT 58.443 37.500 2.70 0.00 36.62 3.24
5232 5954 8.950208 TTAAAAACGGTGATCCTTTTTCATTT 57.050 26.923 2.83 0.00 41.95 2.32
5372 6109 9.932207 TTCATGATTTTAAAACAATGCTCTCAT 57.068 25.926 15.25 10.13 33.53 2.90
5373 6110 9.932207 TCATGATTTTAAAACAATGCTCTCATT 57.068 25.926 15.25 0.00 43.31 2.57
5432 6169 5.464030 AGCATCTCTTGTTTTTCTGCAAT 57.536 34.783 0.00 0.00 0.00 3.56
5434 6171 6.385033 AGCATCTCTTGTTTTTCTGCAATAC 58.615 36.000 0.00 0.00 0.00 1.89
5435 6172 6.016024 AGCATCTCTTGTTTTTCTGCAATACA 60.016 34.615 0.00 0.00 0.00 2.29
5437 6174 7.169645 GCATCTCTTGTTTTTCTGCAATACAAA 59.830 33.333 0.00 0.00 36.31 2.83
5438 6175 9.033481 CATCTCTTGTTTTTCTGCAATACAAAA 57.967 29.630 0.00 0.00 36.31 2.44
5479 6218 6.866248 AGTAAAACACAAAGGAAAACACACAG 59.134 34.615 0.00 0.00 0.00 3.66
5489 6228 4.569180 ACACACAGCGCTTGCCCT 62.569 61.111 7.50 0.00 40.41 5.19
5493 6232 0.251916 ACACAGCGCTTGCCCTAATA 59.748 50.000 7.50 0.00 40.41 0.98
5494 6233 1.134098 ACACAGCGCTTGCCCTAATAT 60.134 47.619 7.50 0.00 40.41 1.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 4.002506 ATGCACCGACGACCAGCA 62.003 61.111 0.00 0.91 39.79 4.41
23 24 3.490759 GCATGCACCGACGACCAG 61.491 66.667 14.21 0.00 0.00 4.00
41 475 0.109365 CGAATGCCAAACAATCCGCA 60.109 50.000 0.00 0.00 35.35 5.69
59 493 3.989698 ATCGAGACTTGCACCGGCG 62.990 63.158 0.00 0.00 45.35 6.46
69 503 0.723414 CGCAAACATGCATCGAGACT 59.277 50.000 0.00 0.00 34.41 3.24
80 514 0.171007 GTAGCATGCACCGCAAACAT 59.829 50.000 21.98 0.00 43.62 2.71
180 614 0.456995 CCGTCGAGGAGAAGAGCAAC 60.457 60.000 6.70 0.00 45.00 4.17
182 616 1.303398 ACCGTCGAGGAGAAGAGCA 60.303 57.895 6.70 0.00 45.00 4.26
207 643 5.182570 GTGACCTAAAACCCCACATAAGAAC 59.817 44.000 0.00 0.00 0.00 3.01
220 656 3.945921 GGGCATCTTAGGTGACCTAAAAC 59.054 47.826 23.16 13.02 44.32 2.43
269 705 5.294552 AGAGTTGCCTGATAATTAGCGAAAC 59.705 40.000 0.00 0.00 0.00 2.78
303 751 3.738282 GTCGGGAGATCTCAAATTCATCG 59.262 47.826 23.85 12.83 43.27 3.84
459 918 0.604578 ACCTTCGCGTACTAGGCAAA 59.395 50.000 5.77 0.00 32.08 3.68
588 1047 2.024655 AGGATAGGGAAGTGTCGGTGTA 60.025 50.000 0.00 0.00 0.00 2.90
984 1443 3.314331 ATGGCGGCGGAGGATAGG 61.314 66.667 9.78 0.00 0.00 2.57
1545 2004 3.630769 GCAGATCAAGATCCAAAGCATCA 59.369 43.478 6.45 0.00 38.58 3.07
1578 2037 2.305095 CAGTTCCCTCCTCCTGCAT 58.695 57.895 0.00 0.00 0.00 3.96
1872 2331 6.077197 CGACGCCACATAACATATAAATTGG 58.923 40.000 0.00 0.00 0.00 3.16
1953 2412 1.978454 CAGCCTCAATCTTCCCCATC 58.022 55.000 0.00 0.00 0.00 3.51
2019 2478 1.290203 ACTTTGCCGTGATATCTGCG 58.710 50.000 3.98 8.54 0.00 5.18
2232 2691 3.250744 CTTAAGAAAGCCATGTCGACGA 58.749 45.455 11.62 0.00 0.00 4.20
2379 2838 6.607019 AGATAAGCCAACTACTACTAGAGCT 58.393 40.000 0.00 0.00 0.00 4.09
2631 3090 1.002087 CCCCATCAAGACCGCCTATAC 59.998 57.143 0.00 0.00 0.00 1.47
2692 3151 7.957002 TGAAGCTTACTCTATCATAAGGAAGG 58.043 38.462 0.00 0.00 34.55 3.46
2936 3461 6.116711 TGGTGGTAAGTATTGAGCACTTAA 57.883 37.500 5.05 0.00 42.38 1.85
3067 3593 6.627087 TCTCTGTAGGATTTCTTTGGACAT 57.373 37.500 0.00 0.00 0.00 3.06
3199 3726 1.414550 TCACGGAACTCACATGGTCAA 59.585 47.619 0.00 0.00 0.00 3.18
3342 3869 8.899771 CATCATGCTTCTTTGGCATATATATCA 58.100 33.333 0.82 0.00 46.94 2.15
3568 4107 1.235724 GTTTCCAGGACTTGAACCCG 58.764 55.000 0.00 0.00 0.00 5.28
3930 4469 6.366877 CCACACAGGAAAAGATAATTGCAAAG 59.633 38.462 1.71 0.00 41.22 2.77
3976 4516 2.324860 TCACATTACTGCACGAAGACG 58.675 47.619 0.00 0.00 45.75 4.18
3982 4522 4.686091 TCTCTTTCTTCACATTACTGCACG 59.314 41.667 0.00 0.00 0.00 5.34
4140 4680 0.824759 AGAGGTACTTGCCGGTCATC 59.175 55.000 1.90 0.00 41.55 2.92
4187 4727 3.094572 CAACAAGGCATCCCATTTCTCT 58.905 45.455 0.00 0.00 0.00 3.10
4263 4803 5.468746 TCAATACGAGAACCAAGACAAAAGG 59.531 40.000 0.00 0.00 0.00 3.11
4359 4899 3.684103 ATGAAAACGTTCGACAAAGCA 57.316 38.095 0.00 0.00 36.46 3.91
4548 5090 2.469465 ATCACCAGCACGTCAAGGGG 62.469 60.000 0.00 0.00 0.00 4.79
4590 5132 8.875803 CAACTCTTTTACACTTAGTTGTACACA 58.124 33.333 0.00 0.00 41.21 3.72
4652 5194 2.911332 ATAACGAACGCCGCCCGAAT 62.911 55.000 5.76 0.00 43.32 3.34
4654 5196 3.646023 AATAACGAACGCCGCCCGA 62.646 57.895 5.76 0.00 43.32 5.14
4738 5280 4.922206 ACAGAGAATGGGCATTTCACTTA 58.078 39.130 2.16 0.00 0.00 2.24
4774 5316 9.140286 GCAGAAGGTAAACTAAAATTCAATTCC 57.860 33.333 0.00 0.00 0.00 3.01
4775 5317 9.691362 TGCAGAAGGTAAACTAAAATTCAATTC 57.309 29.630 0.00 0.00 0.00 2.17
4776 5318 9.476202 GTGCAGAAGGTAAACTAAAATTCAATT 57.524 29.630 0.00 0.00 0.00 2.32
4923 5631 1.919240 TCTTAGAAGGACCTGACGCA 58.081 50.000 0.00 0.00 0.00 5.24
4976 5696 5.428131 AGCTTATTGGAATTTATTGGGCCAA 59.572 36.000 23.33 23.33 42.23 4.52
5059 5779 9.569167 AAACTGCTAAAGAAACTACAGAAAAAC 57.431 29.630 0.00 0.00 0.00 2.43
5079 5800 8.244494 AGAAAAGAACTGAAAAAGAAAACTGC 57.756 30.769 0.00 0.00 0.00 4.40
5118 5839 7.908827 TTTTGAAAAGGGTAAAACCTGAAAC 57.091 32.000 0.00 0.00 40.87 2.78
5193 5915 8.622157 TCACCGTTTTTAATCTGTGAACATTTA 58.378 29.630 0.00 0.00 30.44 1.40
5407 6144 6.579666 TGCAGAAAAACAAGAGATGCTTAT 57.420 33.333 0.00 0.00 34.31 1.73
5409 6146 4.924305 TGCAGAAAAACAAGAGATGCTT 57.076 36.364 0.00 0.00 37.29 3.91
5410 6147 4.924305 TTGCAGAAAAACAAGAGATGCT 57.076 36.364 0.00 0.00 33.47 3.79
5411 6148 6.151691 TGTATTGCAGAAAAACAAGAGATGC 58.848 36.000 0.00 0.00 0.00 3.91
5412 6149 8.578308 TTTGTATTGCAGAAAAACAAGAGATG 57.422 30.769 0.00 0.00 32.18 2.90
5479 6218 2.622436 CCTAGATATTAGGGCAAGCGC 58.378 52.381 0.00 0.00 37.44 5.92


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

AutoCloner maintained by Alex Coulton.