Multiple sequence alignment - TraesCS6D01G168100

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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 TraesCS6D01G168100 chr6D 100.000 2361 0 0 2126 4486 152264927 152267287 0.000000e+00 4361.0
1 TraesCS6D01G168100 chr6D 100.000 1628 0 0 1 1628 152262802 152264429 0.000000e+00 3007.0
2 TraesCS6D01G168100 chr6B 95.443 1580 54 8 2600 4175 276741155 276742720 0.000000e+00 2503.0
3 TraesCS6D01G168100 chr6B 93.042 1394 61 19 257 1625 276739215 276740597 0.000000e+00 2004.0
4 TraesCS6D01G168100 chr6B 96.735 490 13 2 2126 2614 276740636 276741123 0.000000e+00 813.0
5 TraesCS6D01G168100 chr6B 90.830 229 16 4 1 226 276738995 276739221 7.290000e-78 302.0
6 TraesCS6D01G168100 chr6B 93.197 147 9 1 4322 4467 276743184 276743330 9.770000e-52 215.0
7 TraesCS6D01G168100 chr6A 94.471 1465 49 9 2600 4042 190598414 190596960 0.000000e+00 2228.0
8 TraesCS6D01G168100 chr6A 90.852 1585 74 30 66 1628 190600608 190599073 0.000000e+00 2058.0
9 TraesCS6D01G168100 chr6A 93.333 270 17 1 2346 2614 190598715 190598446 9.040000e-107 398.0
10 TraesCS6D01G168100 chr6A 94.495 218 8 2 2126 2342 190599037 190598823 2.590000e-87 333.0
11 TraesCS6D01G168100 chr6A 93.701 127 8 0 4356 4482 190595237 190595111 1.650000e-44 191.0
12 TraesCS6D01G168100 chr6A 82.927 205 9 7 4188 4373 190596963 190596766 1.290000e-35 161.0
13 TraesCS6D01G168100 chr4A 98.914 1197 9 2 2126 3322 642774372 642773180 0.000000e+00 2135.0
14 TraesCS6D01G168100 chr3B 98.832 1113 10 1 2126 3238 14725822 14726931 0.000000e+00 1980.0
15 TraesCS6D01G168100 chr3D 96.825 63 2 0 1085 1147 90369683 90369745 6.140000e-19 106.0
16 TraesCS6D01G168100 chr3A 96.825 63 2 0 1085 1147 106657718 106657780 6.140000e-19 106.0
17 TraesCS6D01G168100 chr1D 85.870 92 11 2 1058 1147 112771715 112771624 3.690000e-16 97.1
18 TraesCS6D01G168100 chr1D 93.750 48 3 0 294 341 357456107 357456154 6.220000e-09 73.1
19 TraesCS6D01G168100 chr1B 93.651 63 4 0 1085 1147 172387999 172387937 1.330000e-15 95.3
20 TraesCS6D01G168100 chr1A 93.651 63 4 0 1085 1147 120012480 120012418 1.330000e-15 95.3


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 TraesCS6D01G168100 chr6D 152262802 152267287 4485 False 3684.000000 4361 100.000000 1 4486 2 chr6D.!!$F1 4485
1 TraesCS6D01G168100 chr6B 276738995 276743330 4335 False 1167.400000 2503 93.849400 1 4467 5 chr6B.!!$F1 4466
2 TraesCS6D01G168100 chr6A 190595111 190600608 5497 True 894.833333 2228 91.629833 66 4482 6 chr6A.!!$R1 4416
3 TraesCS6D01G168100 chr4A 642773180 642774372 1192 True 2135.000000 2135 98.914000 2126 3322 1 chr4A.!!$R1 1196
4 TraesCS6D01G168100 chr3B 14725822 14726931 1109 False 1980.000000 1980 98.832000 2126 3238 1 chr3B.!!$F1 1112

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
262 267 0.320771 GCTCACAACGACATGGTCCT 60.321 55.0 0.00 0.00 0.00 3.85 F
616 623 0.400213 TCACAAGCCCGGTCTGAAAT 59.600 50.0 0.00 0.00 0.00 2.17 F
1527 1553 1.673760 GCCGTATGCATTTGCGTATG 58.326 50.0 3.54 14.39 43.52 2.39 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2223 2252 0.391661 CACAACCAGGTGGGAGATCG 60.392 60.0 0.00 0.0 41.15 3.69 R
3099 3280 1.498865 CCGCAACAGTCACCACAGTC 61.499 60.0 0.00 0.0 0.00 3.51 R
3682 3863 0.168788 AATGCACGCGAGGACAAATG 59.831 50.0 15.93 0.0 0.00 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
131 133 5.772825 AAACATCCATTCCGAACATATGG 57.227 39.130 7.80 0.00 40.14 2.74
228 233 4.825085 TGAAAAATCACCACTGGTCCTAAC 59.175 41.667 0.00 0.00 31.02 2.34
243 248 2.632996 TCCTAACATAAGATGCCCTCCG 59.367 50.000 0.00 0.00 0.00 4.63
252 257 3.958147 ATGCCCTCCGCTCACAACG 62.958 63.158 0.00 0.00 38.78 4.10
258 263 1.354337 CTCCGCTCACAACGACATGG 61.354 60.000 0.00 0.00 0.00 3.66
261 266 1.626654 CGCTCACAACGACATGGTCC 61.627 60.000 0.00 0.00 0.00 4.46
262 267 0.320771 GCTCACAACGACATGGTCCT 60.321 55.000 0.00 0.00 0.00 3.85
263 268 1.878102 GCTCACAACGACATGGTCCTT 60.878 52.381 0.00 0.00 0.00 3.36
287 292 2.701423 GAGTTAGGAACTGGATCCCCTC 59.299 54.545 9.90 2.71 43.03 4.30
289 294 1.330155 TAGGAACTGGATCCCCTCCT 58.670 55.000 23.04 23.04 45.21 3.69
290 295 0.423544 AGGAACTGGATCCCCTCCTT 59.576 55.000 16.92 5.66 45.21 3.36
362 367 7.884877 AGGACTTGTGATTAAACTTGATCATGA 59.115 33.333 15.03 0.00 35.92 3.07
527 533 1.683385 GGTTTTCAGGCTTCAAGCTGT 59.317 47.619 9.83 0.00 41.99 4.40
564 570 6.390721 GCTCGGACATGAGAAAATAGCTATA 58.609 40.000 6.68 0.00 38.28 1.31
581 588 3.435026 GCTATATTTGGTCTTGGGCCAGA 60.435 47.826 6.23 3.75 37.31 3.86
616 623 0.400213 TCACAAGCCCGGTCTGAAAT 59.600 50.000 0.00 0.00 0.00 2.17
663 670 8.570096 TGAAGTTTGCGTGTGATAGTATATAC 57.430 34.615 4.60 4.60 0.00 1.47
776 797 3.006967 AGCTGAACACCGTCTATTTCAGT 59.993 43.478 10.88 0.00 44.54 3.41
778 799 4.810790 CTGAACACCGTCTATTTCAGTCT 58.189 43.478 0.00 0.00 39.99 3.24
781 802 5.694910 TGAACACCGTCTATTTCAGTCTTTC 59.305 40.000 0.00 0.00 0.00 2.62
823 845 4.459089 GGGCCAGACTCCGACTGC 62.459 72.222 4.39 0.00 34.47 4.40
824 846 3.695606 GGCCAGACTCCGACTGCA 61.696 66.667 0.00 0.00 34.47 4.41
825 847 2.343758 GCCAGACTCCGACTGCAA 59.656 61.111 0.00 0.00 34.47 4.08
839 861 3.304057 CGACTGCAAGAAGAGGGAAAAAC 60.304 47.826 0.00 0.00 37.43 2.43
894 916 2.467566 TAAAACCCCGAAGCTGAGAC 57.532 50.000 0.00 0.00 0.00 3.36
960 982 2.732619 CCCTCAAGTCCCCGTAGCC 61.733 68.421 0.00 0.00 0.00 3.93
1152 1174 2.221918 CCTCGCCAAGGTAGGGAAT 58.778 57.895 2.68 0.00 40.67 3.01
1452 1476 3.535561 CATGGGTAAATCTTCACTCGCT 58.464 45.455 0.00 0.00 0.00 4.93
1527 1553 1.673760 GCCGTATGCATTTGCGTATG 58.326 50.000 3.54 14.39 43.52 2.39
1536 1563 4.165036 TGCATTTGCGTATGAATGTTGAC 58.835 39.130 2.33 0.00 45.83 3.18
1580 1607 2.430465 TCTTTCTGCTTGTCCATGAGC 58.570 47.619 0.00 0.00 39.33 4.26
1604 1633 5.065988 CGGCATTTTATTACCTGCTAACTGT 59.934 40.000 0.00 0.00 35.03 3.55
1625 1654 4.142071 TGTGGTTGTTGCAGCTCATTTAAA 60.142 37.500 1.17 0.00 0.00 1.52
2720 2901 7.507277 AGTCATCTAGCTCTGGACATGTAATAA 59.493 37.037 0.00 0.00 0.00 1.40
3099 3280 3.189287 ACTTTGTCCTTTCAGCTATTGCG 59.811 43.478 0.00 0.00 45.42 4.85
3532 3713 7.751768 AGCTTAATTTTACTGTTCTTCTGCT 57.248 32.000 0.00 0.00 0.00 4.24
3533 3714 7.588512 AGCTTAATTTTACTGTTCTTCTGCTG 58.411 34.615 0.00 0.00 0.00 4.41
3550 3731 4.027572 TGCTGTTTGCTGTGTTTTAGTC 57.972 40.909 0.00 0.00 43.37 2.59
3552 3733 4.878971 TGCTGTTTGCTGTGTTTTAGTCTA 59.121 37.500 0.00 0.00 43.37 2.59
3682 3863 6.090129 GGATTATGAGTCTGATACGCTCTTC 58.910 44.000 0.00 0.00 0.00 2.87
3867 4066 7.040892 GCAGCTTAGATCATTATTGGATGAACA 60.041 37.037 0.00 0.00 39.33 3.18
3868 4067 8.843262 CAGCTTAGATCATTATTGGATGAACAA 58.157 33.333 0.00 0.00 39.33 2.83
3956 4159 5.887754 TCCCCAGGATTTTGGCTAATATAC 58.112 41.667 0.00 0.00 36.88 1.47
3972 4175 4.672587 ATATACCGTCAATGTGAGCTGT 57.327 40.909 0.00 0.00 0.00 4.40
3973 4176 2.831685 TACCGTCAATGTGAGCTGTT 57.168 45.000 0.00 0.00 0.00 3.16
4013 4216 4.816925 GGGTCTATGTCAGCTGGTTTTATC 59.183 45.833 15.13 0.54 0.00 1.75
4022 4225 5.232414 GTCAGCTGGTTTTATCGATGTAGTC 59.768 44.000 15.13 0.00 0.00 2.59
4041 4244 1.071605 CGCCACAGACAAGAGTAAGC 58.928 55.000 0.00 0.00 0.00 3.09
4087 4290 6.811170 TCTTTTATTCCATTTCATTCGTTGCC 59.189 34.615 0.00 0.00 0.00 4.52
4102 4305 2.737359 CGTTGCCGAACTAGATAGCCAA 60.737 50.000 0.00 0.00 35.63 4.52
4109 4312 2.074729 ACTAGATAGCCAACGAGCCT 57.925 50.000 0.00 0.00 0.00 4.58
4138 4341 3.742385 AGCTATCCTCTACTCACGGTAC 58.258 50.000 0.00 0.00 0.00 3.34
4141 4344 4.519730 GCTATCCTCTACTCACGGTACAAT 59.480 45.833 0.00 0.00 0.00 2.71
4151 4354 4.253685 CTCACGGTACAATTCACAGGAAT 58.746 43.478 0.00 0.00 45.57 3.01
4175 4378 1.004440 ACAGCCTCTTCTTGACGCC 60.004 57.895 0.00 0.00 0.00 5.68
4176 4379 2.097038 CAGCCTCTTCTTGACGCCG 61.097 63.158 0.00 0.00 0.00 6.46
4177 4380 3.491652 GCCTCTTCTTGACGCCGC 61.492 66.667 0.00 0.00 0.00 6.53
4178 4381 2.815647 CCTCTTCTTGACGCCGCC 60.816 66.667 0.00 0.00 0.00 6.13
4212 4415 1.007271 GTCCGACGATGATGCCGAT 60.007 57.895 0.00 0.00 0.00 4.18
4261 4464 1.003355 CAGCATCCCCTTGACGTGT 60.003 57.895 0.00 0.00 0.00 4.49
4280 4483 1.195674 GTCTGCCTTGTCTTCTTTCGC 59.804 52.381 0.00 0.00 0.00 4.70
4284 4487 1.935300 GCCTTGTCTTCTTTCGCTCGA 60.935 52.381 0.00 0.00 0.00 4.04
4286 4489 2.996621 CCTTGTCTTCTTTCGCTCGAAT 59.003 45.455 5.50 0.00 33.79 3.34
4309 4532 1.955778 CTGATGCCCTTGTTGTGTTGA 59.044 47.619 0.00 0.00 0.00 3.18
4326 4892 2.521708 AGGCGCTGCTGGGTTTTT 60.522 55.556 7.64 0.00 0.00 1.94
4342 4908 0.250553 TTTTCTCGTGCCGGTGGATT 60.251 50.000 1.90 0.00 0.00 3.01
4388 6493 3.898627 AAGCTGAGCGTGTCCGTCG 62.899 63.158 0.00 0.00 36.15 5.12
4467 6572 6.144402 GCAACATGTTCTGTTTTACTCCATTG 59.856 38.462 8.48 0.00 45.98 2.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 58 7.177568 TCCTTTTTGCCTTGTATAAATACTGCA 59.822 33.333 2.07 5.43 34.08 4.41
100 102 7.175816 TGTTCGGAATGGATGTTTTCTGAATAA 59.824 33.333 9.41 1.24 44.62 1.40
131 133 4.008330 GGACTGTAGAAACTTTAAGGGCC 58.992 47.826 0.00 0.00 0.00 5.80
213 218 4.819105 TCTTATGTTAGGACCAGTGGTG 57.181 45.455 22.50 0.46 35.25 4.17
214 219 4.384208 GCATCTTATGTTAGGACCAGTGGT 60.384 45.833 16.70 16.70 39.44 4.16
243 248 0.320771 AGGACCATGTCGTTGTGAGC 60.321 55.000 0.00 0.00 32.65 4.26
252 257 5.871396 TCCTAACTCATAAGGACCATGTC 57.129 43.478 0.00 0.00 36.97 3.06
258 263 5.934402 TCCAGTTCCTAACTCATAAGGAC 57.066 43.478 0.00 0.00 41.63 3.85
261 266 5.221742 GGGGATCCAGTTCCTAACTCATAAG 60.222 48.000 15.23 0.00 40.46 1.73
262 267 4.658901 GGGGATCCAGTTCCTAACTCATAA 59.341 45.833 15.23 0.00 40.46 1.90
263 268 4.077982 AGGGGATCCAGTTCCTAACTCATA 60.078 45.833 15.23 0.00 40.46 2.15
287 292 6.806388 AAAATTGCATTCAAAGCCTTAAGG 57.194 33.333 17.81 17.81 35.56 2.69
456 462 3.734463 TGTGCAAGTCTGGTCGAAAATA 58.266 40.909 0.00 0.00 0.00 1.40
464 470 0.034756 TACGCATGTGCAAGTCTGGT 59.965 50.000 6.08 0.00 42.21 4.00
469 475 0.249120 TAGCCTACGCATGTGCAAGT 59.751 50.000 6.08 0.00 42.21 3.16
504 510 1.603931 GCTTGAAGCCTGAAAACCTGC 60.604 52.381 5.74 0.00 34.48 4.85
509 515 4.470334 AAAACAGCTTGAAGCCTGAAAA 57.530 36.364 14.45 0.00 43.77 2.29
544 550 9.289782 ACCAAATATAGCTATTTTCTCATGTCC 57.710 33.333 12.39 0.00 35.77 4.02
564 570 0.779997 AGTCTGGCCCAAGACCAAAT 59.220 50.000 17.40 0.00 46.51 2.32
581 588 6.224584 GGCTTGTGAAACTAGAAGACTAAGT 58.775 40.000 0.00 0.00 42.45 2.24
735 742 5.243730 TCAGCTAGATTTTCCCCAGTTTTTG 59.756 40.000 0.00 0.00 0.00 2.44
823 845 2.858745 TCCGGTTTTTCCCTCTTCTTG 58.141 47.619 0.00 0.00 0.00 3.02
824 846 3.220110 GTTCCGGTTTTTCCCTCTTCTT 58.780 45.455 0.00 0.00 0.00 2.52
825 847 2.173996 TGTTCCGGTTTTTCCCTCTTCT 59.826 45.455 0.00 0.00 0.00 2.85
839 861 2.989253 GGTTTGGGGCTGTTCCGG 60.989 66.667 0.00 0.00 34.94 5.14
1367 1391 2.228103 CTCTGCACACAAACAGCATCAT 59.772 45.455 0.00 0.00 37.68 2.45
1452 1476 8.447833 CCTAAACTGATACAAAAATACGCTTCA 58.552 33.333 0.00 0.00 0.00 3.02
1519 1543 3.322369 AGTCGTCAACATTCATACGCAA 58.678 40.909 0.00 0.00 35.40 4.85
1520 1544 2.954316 AGTCGTCAACATTCATACGCA 58.046 42.857 0.00 0.00 35.40 5.24
1523 1549 9.084164 AGTATAACAAGTCGTCAACATTCATAC 57.916 33.333 0.00 0.00 0.00 2.39
1527 1553 7.115805 TCACAGTATAACAAGTCGTCAACATTC 59.884 37.037 0.00 0.00 0.00 2.67
1536 1563 4.755411 ACCCATCACAGTATAACAAGTCG 58.245 43.478 0.00 0.00 0.00 4.18
1580 1607 5.065988 ACAGTTAGCAGGTAATAAAATGCCG 59.934 40.000 0.00 0.00 39.51 5.69
1604 1633 4.501229 CCTTTAAATGAGCTGCAACAACCA 60.501 41.667 1.02 0.00 0.00 3.67
2223 2252 0.391661 CACAACCAGGTGGGAGATCG 60.392 60.000 0.00 0.00 41.15 3.69
3099 3280 1.498865 CCGCAACAGTCACCACAGTC 61.499 60.000 0.00 0.00 0.00 3.51
3532 3713 7.148154 ACACAATAGACTAAAACACAGCAAACA 60.148 33.333 0.00 0.00 0.00 2.83
3533 3714 7.193595 ACACAATAGACTAAAACACAGCAAAC 58.806 34.615 0.00 0.00 0.00 2.93
3550 3731 5.117745 CACTTGTCTCTTGTCGACACAATAG 59.882 44.000 19.90 13.28 41.82 1.73
3552 3733 3.804325 CACTTGTCTCTTGTCGACACAAT 59.196 43.478 19.90 6.39 41.82 2.71
3682 3863 0.168788 AATGCACGCGAGGACAAATG 59.831 50.000 15.93 0.00 0.00 2.32
3867 4066 4.502105 AGTGAACTTGGGGCAAAATTTT 57.498 36.364 0.00 0.00 0.00 1.82
3868 4067 4.164030 AGAAGTGAACTTGGGGCAAAATTT 59.836 37.500 0.00 0.00 36.11 1.82
3924 4125 0.704664 AATCCTGGGGAGTCCAAACC 59.295 55.000 12.30 3.56 46.51 3.27
3956 4159 4.685169 ATAAAACAGCTCACATTGACGG 57.315 40.909 0.00 0.00 0.00 4.79
4022 4225 1.071605 GCTTACTCTTGTCTGTGGCG 58.928 55.000 0.00 0.00 0.00 5.69
4087 4290 2.386249 GCTCGTTGGCTATCTAGTTCG 58.614 52.381 0.00 0.00 0.00 3.95
4109 4312 5.767665 GTGAGTAGAGGATAGCTTCTCATGA 59.232 44.000 0.00 0.00 40.36 3.07
4151 4354 2.037772 GTCAAGAAGAGGCTGTGAGGAA 59.962 50.000 0.00 0.00 0.00 3.36
4186 4389 4.925576 ATCGTCGGACGGCGCATC 62.926 66.667 28.07 5.96 43.58 3.91
4212 4415 0.242286 GCTCAGACAGCTTCGACTGA 59.758 55.000 9.80 5.63 45.83 3.41
4261 4464 1.070758 AGCGAAAGAAGACAAGGCAGA 59.929 47.619 0.00 0.00 0.00 4.26
4280 4483 0.471617 AAGGGCATCAGGGATTCGAG 59.528 55.000 0.00 0.00 0.00 4.04
4284 4487 1.077663 ACAACAAGGGCATCAGGGATT 59.922 47.619 0.00 0.00 0.00 3.01
4286 4489 0.251297 CACAACAAGGGCATCAGGGA 60.251 55.000 0.00 0.00 0.00 4.20
4309 4532 2.521708 AAAAACCCAGCAGCGCCT 60.522 55.556 2.29 0.00 0.00 5.52
4342 4908 1.691219 GGCCCCCTTGATCAAGACA 59.309 57.895 32.49 0.41 40.79 3.41


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

AutoCloner maintained by Alex Coulton.