Multiple sequence alignment - TraesCS4D01G151900

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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 TraesCS4D01G151900 chr4D 100.000 4077 0 0 1 4077 179311460 179315536 0.000000e+00 7529.0
1 TraesCS4D01G151900 chr4B 96.851 2604 59 9 753 3353 199189935 199192518 0.000000e+00 4333.0
2 TraesCS4D01G151900 chr4B 94.286 735 30 5 1 726 510850337 510849606 0.000000e+00 1114.0
3 TraesCS4D01G151900 chr4B 85.442 419 24 11 3683 4070 199209474 199209886 6.350000e-108 401.0
4 TraesCS4D01G151900 chr4B 93.583 187 10 2 3355 3540 199208285 199208470 1.120000e-70 278.0
5 TraesCS4D01G151900 chr4B 95.604 91 3 1 3471 3561 199208487 199208576 1.180000e-30 145.0
6 TraesCS4D01G151900 chr4A 94.944 2591 82 18 763 3330 409035340 409037904 0.000000e+00 4013.0
7 TraesCS4D01G151900 chr4A 91.064 761 51 7 1 757 82618224 82618971 0.000000e+00 1013.0
8 TraesCS4D01G151900 chr4A 88.052 770 64 16 3327 4077 409038226 409038986 0.000000e+00 887.0
9 TraesCS4D01G151900 chr4A 93.605 516 20 5 1 504 647948197 647948711 0.000000e+00 758.0
10 TraesCS4D01G151900 chr4A 92.251 271 16 2 491 757 647948727 647948996 2.970000e-101 379.0
11 TraesCS4D01G151900 chr2D 93.247 770 46 5 1 765 487939908 487939140 0.000000e+00 1129.0
12 TraesCS4D01G151900 chr2D 93.182 308 21 0 1041 1348 126739433 126739126 1.730000e-123 453.0
13 TraesCS4D01G151900 chr2D 80.806 521 79 14 2095 2612 126737678 126737176 4.940000e-104 388.0
14 TraesCS4D01G151900 chr2D 85.430 302 40 4 2730 3029 628412146 628412445 1.100000e-80 311.0
15 TraesCS4D01G151900 chr2D 83.784 74 12 0 4004 4077 111991490 111991417 2.030000e-08 71.3
16 TraesCS4D01G151900 chr2B 92.857 770 43 7 1 761 57097133 57096367 0.000000e+00 1107.0
17 TraesCS4D01G151900 chr2B 93.506 308 20 0 1041 1348 180423774 180423467 3.710000e-125 459.0
18 TraesCS4D01G151900 chr2B 80.422 521 81 14 2095 2612 180421914 180421412 1.070000e-100 377.0
19 TraesCS4D01G151900 chr3B 91.536 768 52 6 1 757 700971061 700971826 0.000000e+00 1046.0
20 TraesCS4D01G151900 chr3B 92.810 306 20 2 1044 1348 539561499 539561195 3.740000e-120 442.0
21 TraesCS4D01G151900 chr3B 86.093 302 39 3 2730 3029 539560564 539560264 5.080000e-84 322.0
22 TraesCS4D01G151900 chr3B 80.569 211 33 7 3659 3868 503028488 503028285 5.460000e-34 156.0
23 TraesCS4D01G151900 chr2A 90.423 355 31 3 404 757 431522584 431522232 7.980000e-127 464.0
24 TraesCS4D01G151900 chr2A 92.532 308 23 0 1041 1348 133346365 133346058 3.740000e-120 442.0
25 TraesCS4D01G151900 chr2A 80.038 521 83 15 2095 2612 133344675 133344173 2.320000e-97 366.0
26 TraesCS4D01G151900 chr2A 84.437 302 40 5 2730 3029 616455461 616455165 1.430000e-74 291.0
27 TraesCS4D01G151900 chr2A 78.328 323 44 18 3652 3967 652608021 652607718 6.960000e-43 185.0
28 TraesCS4D01G151900 chr3D 92.557 309 21 2 1044 1351 412786139 412785832 3.740000e-120 442.0
29 TraesCS4D01G151900 chr3D 86.093 302 39 3 2730 3029 412785189 412784889 5.080000e-84 322.0
30 TraesCS4D01G151900 chr3D 82.511 223 32 6 3647 3867 386739305 386739088 5.380000e-44 189.0
31 TraesCS4D01G151900 chr3A 91.803 305 25 0 1044 1348 537507638 537507942 3.770000e-115 425.0
32 TraesCS4D01G151900 chr3A 85.430 302 41 3 2730 3029 537508547 537508847 1.100000e-80 311.0
33 TraesCS4D01G151900 chr3A 81.043 211 34 3 3659 3868 508206487 508206282 3.260000e-36 163.0
34 TraesCS4D01G151900 chr3A 81.707 82 13 2 3993 4072 340410263 340410182 2.630000e-07 67.6
35 TraesCS4D01G151900 chr5B 84.106 302 44 4 2730 3029 139002632 139002931 5.160000e-74 289.0
36 TraesCS4D01G151900 chr5B 85.135 74 11 0 4004 4077 72464224 72464297 4.370000e-10 76.8
37 TraesCS4D01G151900 chr1A 83.775 302 42 5 2730 3029 465252284 465252580 3.100000e-71 279.0
38 TraesCS4D01G151900 chr1A 83.036 224 28 9 3647 3867 534616525 534616309 1.160000e-45 195.0
39 TraesCS4D01G151900 chr5D 77.469 324 52 20 3565 3876 435022420 435022734 1.510000e-39 174.0
40 TraesCS4D01G151900 chr6D 79.556 225 28 13 3647 3868 8893139 8892930 1.180000e-30 145.0
41 TraesCS4D01G151900 chr6D 85.333 75 11 0 4003 4077 60383270 60383196 1.210000e-10 78.7
42 TraesCS4D01G151900 chr7A 85.135 74 11 0 4004 4077 675073519 675073592 4.370000e-10 76.8
43 TraesCS4D01G151900 chrUn 83.333 78 12 1 4001 4077 57820061 57820138 2.030000e-08 71.3
44 TraesCS4D01G151900 chr6B 83.784 74 12 0 4004 4077 43318082 43318009 2.030000e-08 71.3
45 TraesCS4D01G151900 chr7B 83.117 77 12 1 3997 4072 250369312 250369236 7.310000e-08 69.4


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 TraesCS4D01G151900 chr4D 179311460 179315536 4076 False 7529.000000 7529 100.0000 1 4077 1 chr4D.!!$F1 4076
1 TraesCS4D01G151900 chr4B 199189935 199192518 2583 False 4333.000000 4333 96.8510 753 3353 1 chr4B.!!$F1 2600
2 TraesCS4D01G151900 chr4B 510849606 510850337 731 True 1114.000000 1114 94.2860 1 726 1 chr4B.!!$R1 725
3 TraesCS4D01G151900 chr4B 199208285 199209886 1601 False 274.666667 401 91.5430 3355 4070 3 chr4B.!!$F2 715
4 TraesCS4D01G151900 chr4A 409035340 409038986 3646 False 2450.000000 4013 91.4980 763 4077 2 chr4A.!!$F2 3314
5 TraesCS4D01G151900 chr4A 82618224 82618971 747 False 1013.000000 1013 91.0640 1 757 1 chr4A.!!$F1 756
6 TraesCS4D01G151900 chr4A 647948197 647948996 799 False 568.500000 758 92.9280 1 757 2 chr4A.!!$F3 756
7 TraesCS4D01G151900 chr2D 487939140 487939908 768 True 1129.000000 1129 93.2470 1 765 1 chr2D.!!$R2 764
8 TraesCS4D01G151900 chr2D 126737176 126739433 2257 True 420.500000 453 86.9940 1041 2612 2 chr2D.!!$R3 1571
9 TraesCS4D01G151900 chr2B 57096367 57097133 766 True 1107.000000 1107 92.8570 1 761 1 chr2B.!!$R1 760
10 TraesCS4D01G151900 chr2B 180421412 180423774 2362 True 418.000000 459 86.9640 1041 2612 2 chr2B.!!$R2 1571
11 TraesCS4D01G151900 chr3B 700971061 700971826 765 False 1046.000000 1046 91.5360 1 757 1 chr3B.!!$F1 756
12 TraesCS4D01G151900 chr3B 539560264 539561499 1235 True 382.000000 442 89.4515 1044 3029 2 chr3B.!!$R2 1985
13 TraesCS4D01G151900 chr2A 133344173 133346365 2192 True 404.000000 442 86.2850 1041 2612 2 chr2A.!!$R4 1571
14 TraesCS4D01G151900 chr3D 412784889 412786139 1250 True 382.000000 442 89.3250 1044 3029 2 chr3D.!!$R2 1985
15 TraesCS4D01G151900 chr3A 537507638 537508847 1209 False 368.000000 425 88.6165 1044 3029 2 chr3A.!!$F1 1985

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
100 101 0.802494 CCACACGGCTCCACAAATAC 59.198 55.000 0.0 0.0 0.00 1.89 F
598 647 1.376037 GTTTGCAGAGTAGCGGCCT 60.376 57.895 0.0 0.0 36.83 5.19 F
1649 2398 0.034337 CTTGCTTGCATTGGCTGGTT 59.966 50.000 0.0 0.0 41.91 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1649 2398 5.362143 CAGAGATCACTTTACTGGATCCTCA 59.638 44.000 14.23 0.0 38.52 3.86 R
2367 3513 2.835027 CTGATTAGCAGCAGATCAGCA 58.165 47.619 19.26 0.0 40.00 4.41 R
3093 4287 1.282157 GCCCCAACCATACACTCTTCT 59.718 52.381 0.00 0.0 0.00 2.85 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
34 35 6.934048 TGCATAATCGTGGTGAATTCATTA 57.066 33.333 12.12 5.46 0.00 1.90
100 101 0.802494 CCACACGGCTCCACAAATAC 59.198 55.000 0.00 0.00 0.00 1.89
112 114 6.183360 GGCTCCACAAATACTGTACAACATAC 60.183 42.308 0.00 0.00 36.10 2.39
141 147 4.028383 CGAAATCAACATCAATACACGGC 58.972 43.478 0.00 0.00 0.00 5.68
148 154 2.092968 ACATCAATACACGGCATGAGGT 60.093 45.455 0.00 0.00 32.56 3.85
196 202 1.555075 CACTACCTGTATGTGGCCTGT 59.445 52.381 3.32 0.00 0.00 4.00
278 292 1.850345 TCTTTGGGTGTCCTTCCTTGT 59.150 47.619 0.00 0.00 0.00 3.16
283 297 4.069312 TGGGTGTCCTTCCTTGTATCTA 57.931 45.455 0.00 0.00 0.00 1.98
287 301 4.101741 GGTGTCCTTCCTTGTATCTAGCAT 59.898 45.833 0.00 0.00 0.00 3.79
428 448 3.288092 GTTATGGAAGGGAGGCGAAAAT 58.712 45.455 0.00 0.00 0.00 1.82
530 579 2.808543 GTCATCCTCTCGCAACAAACTT 59.191 45.455 0.00 0.00 0.00 2.66
598 647 1.376037 GTTTGCAGAGTAGCGGCCT 60.376 57.895 0.00 0.00 36.83 5.19
696 749 5.163499 GGACTCTCAGTAAGTTTGATCGGAT 60.163 44.000 0.00 0.00 0.00 4.18
721 774 3.534554 TGAGGATGTCAAATCGATGTGG 58.465 45.455 15.60 0.40 29.64 4.17
924 979 1.843421 CCCAAACCCACACCTCTCA 59.157 57.895 0.00 0.00 0.00 3.27
1236 1291 1.808411 ACGACATCAACCGCATTCTT 58.192 45.000 0.00 0.00 0.00 2.52
1377 1965 2.301346 ACTTTCCCTCTGTGCACAAAG 58.699 47.619 21.98 20.82 0.00 2.77
1542 2291 1.648467 GGAACCCGCAATCAGTCAGC 61.648 60.000 0.00 0.00 0.00 4.26
1649 2398 0.034337 CTTGCTTGCATTGGCTGGTT 59.966 50.000 0.00 0.00 41.91 3.67
1920 2792 8.429641 AGGTCAATTTCAGTTTAGTCTCTGTAA 58.570 33.333 0.00 0.00 33.89 2.41
2019 3052 3.349927 CTGATGAAGCAATCAAGTGGGA 58.650 45.455 0.00 0.00 42.54 4.37
2170 3316 2.997315 CTCCTCAGCCCGTCCACA 60.997 66.667 0.00 0.00 0.00 4.17
2367 3513 5.982890 AGGTACTGCATTTTGTTAGCAAT 57.017 34.783 0.00 0.00 37.18 3.56
2368 3514 5.713025 AGGTACTGCATTTTGTTAGCAATG 58.287 37.500 0.00 0.00 37.18 2.82
3272 4466 6.454795 TGTATTTTTGAGAAATCAAGCACCC 58.545 36.000 0.00 0.00 0.00 4.61
3282 4476 6.458210 AGAAATCAAGCACCCTTTGTTATTG 58.542 36.000 0.00 0.00 0.00 1.90
3344 4863 5.890424 TTGGCTTAATTTTCCCTAACGAG 57.110 39.130 0.00 0.00 0.00 4.18
3467 4988 1.974265 TGGTGCAATTCCGTTCTTCA 58.026 45.000 0.00 0.00 0.00 3.02
3545 5152 5.222254 TGACTCCCCAGCCTTTTACTTTTAT 60.222 40.000 0.00 0.00 0.00 1.40
3546 5153 5.262009 ACTCCCCAGCCTTTTACTTTTATC 58.738 41.667 0.00 0.00 0.00 1.75
3561 5168 4.021192 ACTTTTATCGAAGGGTTGGACGTA 60.021 41.667 0.00 0.00 0.00 3.57
3589 5196 6.709643 TGTTGCGGTTTTCATAATGTTTTTG 58.290 32.000 0.00 0.00 0.00 2.44
3751 6206 9.878667 TTTATTTAGTAGAATCGTGGATGTTGA 57.121 29.630 0.00 0.00 0.00 3.18
3758 6213 8.085296 AGTAGAATCGTGGATGTTGAGATATTC 58.915 37.037 0.00 0.00 0.00 1.75
3859 6315 4.699637 AGTATTTCGTTTGGTGAGTGTGA 58.300 39.130 0.00 0.00 0.00 3.58
3895 6374 1.892474 GCAGTGTTTTGATGGGCCTTA 59.108 47.619 4.53 0.00 0.00 2.69
3904 6387 6.667414 TGTTTTGATGGGCCTTAGTATGATTT 59.333 34.615 4.53 0.00 0.00 2.17
3941 6424 7.545965 GCTAATCAATCTATACTTATGTGCGGT 59.454 37.037 0.00 0.00 0.00 5.68
3980 6465 5.173312 CGGTGTCTGCACTTACTATATTTCG 59.827 44.000 0.00 0.00 44.65 3.46
4073 6560 5.975693 TTCACAATCCAAGGTACATTTCC 57.024 39.130 0.00 0.00 0.00 3.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 0.465287 CAACTGGCTGCCTTGGTTTT 59.535 50.000 21.03 1.01 0.00 2.43
100 101 8.661257 TGATTTCGTTTATGGTATGTTGTACAG 58.339 33.333 0.00 0.00 0.00 2.74
112 114 9.009327 GTGTATTGATGTTGATTTCGTTTATGG 57.991 33.333 0.00 0.00 0.00 2.74
141 147 2.480416 GCTCTAACGGTCTCACCTCATG 60.480 54.545 0.00 0.00 35.66 3.07
148 154 0.607217 TCGGTGCTCTAACGGTCTCA 60.607 55.000 0.00 0.00 0.00 3.27
278 292 3.944087 TCTCAGCGAGCTATGCTAGATA 58.056 45.455 12.22 4.06 41.72 1.98
283 297 1.110442 ACTTCTCAGCGAGCTATGCT 58.890 50.000 7.11 7.11 45.31 3.79
287 301 1.398739 CGAGAACTTCTCAGCGAGCTA 59.601 52.381 17.23 0.00 43.55 3.32
428 448 0.109532 TGGTTCAAACGCATCTCCCA 59.890 50.000 0.00 0.00 0.00 4.37
495 515 0.169009 GATGACGCACCAAAGCTTCC 59.831 55.000 0.00 0.00 32.35 3.46
530 579 0.181114 GACATCCTATGTGGGCTGCA 59.819 55.000 0.50 0.00 45.03 4.41
586 635 0.753262 CATAACCAGGCCGCTACTCT 59.247 55.000 0.00 0.00 0.00 3.24
598 647 1.001887 GGACGGCCCAACATAACCA 60.002 57.895 0.00 0.00 34.14 3.67
696 749 3.694043 TCGATTTGACATCCTCAACCA 57.306 42.857 0.00 0.00 38.70 3.67
716 769 0.753262 CTAGCTACGCCTTCCCACAT 59.247 55.000 0.00 0.00 0.00 3.21
721 774 0.031449 CTCAGCTAGCTACGCCTTCC 59.969 60.000 18.86 0.00 0.00 3.46
924 979 0.042281 GTGGTAGGGGTGGGAGTAGT 59.958 60.000 0.00 0.00 0.00 2.73
1475 2224 5.995565 TCTGGAGAAATTAGAACGAAGGA 57.004 39.130 0.00 0.00 0.00 3.36
1542 2291 5.700832 TGACAGGCTACACTTTATTGTTGAG 59.299 40.000 0.00 0.00 0.00 3.02
1649 2398 5.362143 CAGAGATCACTTTACTGGATCCTCA 59.638 44.000 14.23 0.00 38.52 3.86
1749 2614 9.877178 ATCACATAAACTAGAACTTCTAACCAG 57.123 33.333 0.00 0.00 0.00 4.00
1758 2627 6.034591 CGACCGAATCACATAAACTAGAACT 58.965 40.000 0.00 0.00 0.00 3.01
1924 2796 9.684448 TGAAGCATTGTTATTTTACAATCGAAA 57.316 25.926 0.00 0.00 44.64 3.46
2170 3316 3.508402 ACAAGGTGTTGAAGAAAAACGGT 59.492 39.130 0.00 0.00 37.10 4.83
2367 3513 2.835027 CTGATTAGCAGCAGATCAGCA 58.165 47.619 19.26 0.00 40.00 4.41
2687 3881 7.645058 TCAGTTTCATTTCTTCAGTTCCTTT 57.355 32.000 0.00 0.00 0.00 3.11
3092 4286 2.290960 GCCCCAACCATACACTCTTCTT 60.291 50.000 0.00 0.00 0.00 2.52
3093 4287 1.282157 GCCCCAACCATACACTCTTCT 59.718 52.381 0.00 0.00 0.00 2.85
3094 4288 1.682087 GGCCCCAACCATACACTCTTC 60.682 57.143 0.00 0.00 0.00 2.87
3252 4446 5.612725 AAGGGTGCTTGATTTCTCAAAAA 57.387 34.783 0.00 0.00 40.78 1.94
3282 4476 5.849081 TGCTCAACGAAAATAATTTCACGAC 59.151 36.000 4.24 0.00 44.24 4.34
3467 4988 3.369576 GCTGGGGAGTCGAGAATAAAAGT 60.370 47.826 0.00 0.00 0.00 2.66
3545 5152 1.331214 AAGTACGTCCAACCCTTCGA 58.669 50.000 0.00 0.00 0.00 3.71
3546 5153 1.796459 CAAAGTACGTCCAACCCTTCG 59.204 52.381 0.00 0.00 0.00 3.79
3561 5168 5.596845 ACATTATGAAAACCGCAACAAAGT 58.403 33.333 0.00 0.00 0.00 2.66
3589 5196 7.595130 CACTTTACATTTTAAAACAGAGGGAGC 59.405 37.037 1.97 0.00 0.00 4.70
3750 6205 6.151817 ACCAAGTTCAAAGCCAAGAATATCTC 59.848 38.462 0.00 0.00 0.00 2.75
3751 6206 6.012745 ACCAAGTTCAAAGCCAAGAATATCT 58.987 36.000 0.00 0.00 0.00 1.98
3758 6213 3.799281 TTGACCAAGTTCAAAGCCAAG 57.201 42.857 0.00 0.00 32.42 3.61
3831 6286 4.951254 TCACCAAACGAAATACTCACTCA 58.049 39.130 0.00 0.00 0.00 3.41
3832 6287 4.989168 ACTCACCAAACGAAATACTCACTC 59.011 41.667 0.00 0.00 0.00 3.51
3833 6288 4.750098 CACTCACCAAACGAAATACTCACT 59.250 41.667 0.00 0.00 0.00 3.41
3844 6300 2.509052 TCTCTCACACTCACCAAACG 57.491 50.000 0.00 0.00 0.00 3.60
3859 6315 4.586884 ACACTGCACATTTCATCATCTCT 58.413 39.130 0.00 0.00 0.00 3.10
3938 6421 1.850441 CCGACGCAGAAACTTATACCG 59.150 52.381 0.00 0.00 0.00 4.02
3941 6424 3.192001 AGACACCGACGCAGAAACTTATA 59.808 43.478 0.00 0.00 0.00 0.98
3942 6425 2.029290 AGACACCGACGCAGAAACTTAT 60.029 45.455 0.00 0.00 0.00 1.73


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

AutoCloner maintained by Alex Coulton.