Multiple sequence alignment - TraesCS3B01G296400

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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 TraesCS3B01G296400 chr3B 100.000 2780 0 0 1 2780 474996355 474999134 0.000000e+00 5134.0
1 TraesCS3B01G296400 chr3B 78.824 170 32 1 255 420 238116882 238116713 8.140000e-21 111.0
2 TraesCS3B01G296400 chr3D 95.334 2079 54 13 472 2544 364733634 364735675 0.000000e+00 3262.0
3 TraesCS3B01G296400 chr3D 83.969 524 61 15 1 512 364733129 364733641 5.390000e-132 481.0
4 TraesCS3B01G296400 chr3D 94.089 203 9 1 2578 2780 364735675 364735874 3.480000e-79 305.0
5 TraesCS3B01G296400 chr3D 79.641 167 27 5 243 405 105497306 105497469 2.260000e-21 113.0
6 TraesCS3B01G296400 chr3A 94.448 1801 49 12 423 2218 486044064 486045818 0.000000e+00 2724.0
7 TraesCS3B01G296400 chr3A 94.297 491 19 3 2275 2765 486045818 486046299 0.000000e+00 743.0
8 TraesCS3B01G296400 chr3A 85.612 417 55 4 1 412 486042108 486042524 1.530000e-117 433.0
9 TraesCS3B01G296400 chr1D 83.721 172 21 4 256 421 489752289 489752119 3.710000e-34 156.0
10 TraesCS3B01G296400 chr5B 80.723 166 28 1 256 417 376023377 376023542 2.910000e-25 126.0
11 TraesCS3B01G296400 chr7B 81.410 156 24 2 254 405 446189572 446189418 3.760000e-24 122.0
12 TraesCS3B01G296400 chr2A 79.191 173 32 2 253 421 690720022 690719850 1.750000e-22 117.0
13 TraesCS3B01G296400 chr2B 79.070 172 32 3 253 420 356305689 356305518 6.290000e-22 115.0
14 TraesCS3B01G296400 chr7A 82.051 117 11 7 57 173 279124104 279123998 1.060000e-14 91.6
15 TraesCS3B01G296400 chr6A 90.476 42 4 0 53 94 432710176 432710217 3.870000e-04 56.5
16 TraesCS3B01G296400 chr7D 100.000 28 0 0 57 84 258188483 258188456 5.000000e-03 52.8


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 TraesCS3B01G296400 chr3B 474996355 474999134 2779 False 5134.000000 5134 100.000000 1 2780 1 chr3B.!!$F1 2779
1 TraesCS3B01G296400 chr3D 364733129 364735874 2745 False 1349.333333 3262 91.130667 1 2780 3 chr3D.!!$F2 2779
2 TraesCS3B01G296400 chr3A 486042108 486046299 4191 False 1300.000000 2724 91.452333 1 2765 3 chr3A.!!$F1 2764

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
101 102 0.250234 CCATCCGTGTCCACATGTCT 59.750 55.0 0.0 0.0 0.00 3.41 F
427 1961 0.401395 TGGTGGACTGGGACTTTCCT 60.401 55.0 0.0 0.0 36.57 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1643 3218 1.218316 GAGTCCGGCGTCAAATCCT 59.782 57.895 6.01 0.0 0.0 3.24 R
2344 3920 0.664166 GCAATGCAACAGGTCCAACG 60.664 55.000 0.00 0.0 0.0 4.10 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
28 29 4.932200 GTCTGACAACATTTCTTCTCCGAT 59.068 41.667 2.24 0.00 0.00 4.18
50 51 1.668826 TGAAGGGGCTAGGACATGTT 58.331 50.000 0.00 0.00 0.00 2.71
51 52 1.992557 TGAAGGGGCTAGGACATGTTT 59.007 47.619 0.00 0.00 0.00 2.83
101 102 0.250234 CCATCCGTGTCCACATGTCT 59.750 55.000 0.00 0.00 0.00 3.41
108 109 2.807967 CGTGTCCACATGTCTGTTTGAT 59.192 45.455 0.00 0.00 31.62 2.57
119 120 3.258123 TGTCTGTTTGATGACTCGGATGA 59.742 43.478 0.00 0.00 34.57 2.92
213 215 5.238432 ACACAATACAATCAAAGTCGCTCAA 59.762 36.000 0.00 0.00 0.00 3.02
218 220 5.940192 ACAATCAAAGTCGCTCAAATACA 57.060 34.783 0.00 0.00 0.00 2.29
220 222 4.946784 ATCAAAGTCGCTCAAATACACC 57.053 40.909 0.00 0.00 0.00 4.16
304 306 4.771590 TTTACGAAGTCACCATAGACGT 57.228 40.909 0.00 0.00 43.93 4.34
316 318 1.062148 CATAGACGTCTCGCAGTCGAA 59.938 52.381 23.89 0.52 44.98 3.71
318 320 0.522180 AGACGTCTCGCAGTCGAAAT 59.478 50.000 13.58 0.00 44.98 2.17
346 352 3.469008 TTCACTGAACGAACATCACCT 57.531 42.857 0.00 0.00 0.00 4.00
350 356 3.559655 CACTGAACGAACATCACCTGAAA 59.440 43.478 0.00 0.00 0.00 2.69
360 366 6.094048 CGAACATCACCTGAAACCTGAAATAT 59.906 38.462 0.00 0.00 0.00 1.28
361 367 6.764308 ACATCACCTGAAACCTGAAATATG 57.236 37.500 0.00 0.00 0.00 1.78
376 382 8.621286 ACCTGAAATATGTTTAGGAATAAAGCG 58.379 33.333 13.49 0.00 32.86 4.68
386 392 4.150897 AGGAATAAAGCGAGCACCAATA 57.849 40.909 0.00 0.00 0.00 1.90
397 403 4.786609 GCGAGCACCAATATCAAGTTTAGC 60.787 45.833 0.00 0.00 0.00 3.09
415 421 3.733443 AGCACTTGAATTTTGGTGGAC 57.267 42.857 0.00 0.00 0.00 4.02
416 422 3.299503 AGCACTTGAATTTTGGTGGACT 58.700 40.909 0.00 0.00 0.00 3.85
417 423 3.068590 AGCACTTGAATTTTGGTGGACTG 59.931 43.478 0.00 0.00 0.00 3.51
418 424 3.799917 GCACTTGAATTTTGGTGGACTGG 60.800 47.826 0.00 0.00 0.00 4.00
419 425 2.965147 ACTTGAATTTTGGTGGACTGGG 59.035 45.455 0.00 0.00 0.00 4.45
420 426 3.230134 CTTGAATTTTGGTGGACTGGGA 58.770 45.455 0.00 0.00 0.00 4.37
425 1959 2.358322 TTTGGTGGACTGGGACTTTC 57.642 50.000 0.00 0.00 0.00 2.62
427 1961 0.401395 TGGTGGACTGGGACTTTCCT 60.401 55.000 0.00 0.00 36.57 3.36
430 1964 1.700186 GTGGACTGGGACTTTCCTTCT 59.300 52.381 0.00 0.00 36.57 2.85
431 1965 1.978580 TGGACTGGGACTTTCCTTCTC 59.021 52.381 0.00 0.00 36.57 2.87
435 1969 4.006319 GACTGGGACTTTCCTTCTCAATG 58.994 47.826 0.00 0.00 36.57 2.82
442 1976 5.152623 ACTTTCCTTCTCAATGATCGTCA 57.847 39.130 0.00 0.00 0.00 4.35
452 1986 5.578336 TCTCAATGATCGTCACATGTCTTTC 59.422 40.000 0.00 0.00 0.00 2.62
837 2408 6.015095 CAGCAGGGGTAGAAAAGAAGAAATTT 60.015 38.462 0.00 0.00 0.00 1.82
1596 3171 4.844522 GGCGTCTTATTCGAGTTTTTGTTC 59.155 41.667 0.00 0.00 0.00 3.18
1619 3194 6.815089 TCTTGTTATTGTTGGAATTGCAGTT 58.185 32.000 0.00 0.00 0.00 3.16
1643 3218 0.044092 TGCCCTGGATTGTCCCTAGA 59.956 55.000 0.00 0.00 35.03 2.43
1701 3277 3.721087 AGGAACAAGGGATCGTTTGAT 57.279 42.857 12.98 3.27 37.60 2.57
1702 3278 4.034285 AGGAACAAGGGATCGTTTGATT 57.966 40.909 12.98 5.54 34.09 2.57
1724 3300 1.872388 TCTTGTCGCAATTCGGTTCA 58.128 45.000 0.00 0.00 39.05 3.18
1991 3567 9.112725 GGAGTTGGTGAGTAGTTTAAAGTTAAA 57.887 33.333 0.00 0.00 0.00 1.52
2155 3731 2.418197 GCTTCATTGTAGCGGTGAGGTA 60.418 50.000 0.00 0.00 0.00 3.08
2170 3746 6.369615 GCGGTGAGGTATTTTAAGTGTTCTTA 59.630 38.462 0.00 0.00 35.36 2.10
2196 3772 6.583427 TGCATTGATCACATTTCTTTTCTTCG 59.417 34.615 0.00 0.00 0.00 3.79
2415 3991 5.131475 TGATCCTTATTAGGTGGGGTGTAAC 59.869 44.000 0.00 0.00 42.60 2.50
2449 4027 2.297701 ACATGGGCATTAATCCGTGAC 58.702 47.619 17.93 0.00 41.33 3.67
2450 4028 2.092429 ACATGGGCATTAATCCGTGACT 60.092 45.455 17.93 0.00 41.33 3.41
2470 4048 9.825972 CGTGACTGTTTCTTATATGAAATTGTT 57.174 29.630 14.74 3.33 38.09 2.83
2569 4147 4.852134 TTGCTTGTTGTGATTGCATACT 57.148 36.364 0.00 0.00 33.50 2.12
2570 4148 4.852134 TGCTTGTTGTGATTGCATACTT 57.148 36.364 0.00 0.00 0.00 2.24
2571 4149 5.199024 TGCTTGTTGTGATTGCATACTTT 57.801 34.783 0.00 0.00 0.00 2.66
2572 4150 5.221880 TGCTTGTTGTGATTGCATACTTTC 58.778 37.500 0.00 0.00 0.00 2.62
2573 4151 4.622740 GCTTGTTGTGATTGCATACTTTCC 59.377 41.667 0.00 0.00 0.00 3.13
2602 4180 7.594714 TCGGCTTAGCAAACATAAAACAATAA 58.405 30.769 6.53 0.00 0.00 1.40
2672 4250 8.033038 TGTACTCTGATAGGTTACACATGTTTC 58.967 37.037 0.00 0.00 0.00 2.78
2765 4344 1.635487 TGGCCATCTCCTAGTTTTGCT 59.365 47.619 0.00 0.00 0.00 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 4.893608 TCATCGGAGAAGAAATGTTGTCA 58.106 39.130 0.00 0.00 43.58 3.58
28 29 1.770658 CATGTCCTAGCCCCTTCATCA 59.229 52.381 0.00 0.00 0.00 3.07
50 51 2.630580 GGTGCTACCCCATTTGAAACAA 59.369 45.455 0.00 0.00 30.04 2.83
51 52 2.243810 GGTGCTACCCCATTTGAAACA 58.756 47.619 0.00 0.00 30.04 2.83
101 102 4.001618 TGTTCATCCGAGTCATCAAACA 57.998 40.909 0.00 0.00 0.00 2.83
133 135 2.037511 AGACCCAAACGGACACGAAATA 59.962 45.455 0.00 0.00 44.60 1.40
213 215 2.171870 CGTTCATAGGGGTGGGTGTATT 59.828 50.000 0.00 0.00 0.00 1.89
218 220 1.921346 TGCGTTCATAGGGGTGGGT 60.921 57.895 0.00 0.00 0.00 4.51
220 222 1.813753 CGTGCGTTCATAGGGGTGG 60.814 63.158 0.00 0.00 0.00 4.61
252 254 5.825679 AGATGCTATGTCGACTTAGTCTCTT 59.174 40.000 28.88 16.30 0.00 2.85
316 318 5.584649 TGTTCGTTCAGTGAAAGAAGACATT 59.415 36.000 27.57 0.00 39.71 2.71
318 320 4.500127 TGTTCGTTCAGTGAAAGAAGACA 58.500 39.130 27.57 22.09 39.71 3.41
350 356 8.621286 CGCTTTATTCCTAAACATATTTCAGGT 58.379 33.333 0.00 0.00 0.00 4.00
360 366 3.687698 GGTGCTCGCTTTATTCCTAAACA 59.312 43.478 0.00 0.00 0.00 2.83
361 367 3.687698 TGGTGCTCGCTTTATTCCTAAAC 59.312 43.478 0.00 0.00 0.00 2.01
373 379 2.698855 ACTTGATATTGGTGCTCGCT 57.301 45.000 0.00 0.00 0.00 4.93
376 382 5.355350 AGTGCTAAACTTGATATTGGTGCTC 59.645 40.000 0.00 0.00 34.57 4.26
397 403 3.243839 CCCAGTCCACCAAAATTCAAGTG 60.244 47.826 0.00 0.00 0.00 3.16
405 411 2.661718 GAAAGTCCCAGTCCACCAAAA 58.338 47.619 0.00 0.00 0.00 2.44
407 413 0.476771 GGAAAGTCCCAGTCCACCAA 59.523 55.000 0.00 0.00 0.00 3.67
412 418 1.978580 TGAGAAGGAAAGTCCCAGTCC 59.021 52.381 0.00 0.00 37.19 3.85
415 421 4.292186 TCATTGAGAAGGAAAGTCCCAG 57.708 45.455 0.00 0.00 37.19 4.45
416 422 4.623886 CGATCATTGAGAAGGAAAGTCCCA 60.624 45.833 0.00 0.00 37.19 4.37
417 423 3.873952 CGATCATTGAGAAGGAAAGTCCC 59.126 47.826 0.00 0.00 37.19 4.46
418 424 4.508662 ACGATCATTGAGAAGGAAAGTCC 58.491 43.478 0.00 0.00 36.58 3.85
419 425 5.062809 GTGACGATCATTGAGAAGGAAAGTC 59.937 44.000 0.00 0.00 34.54 3.01
420 426 4.932200 GTGACGATCATTGAGAAGGAAAGT 59.068 41.667 0.00 0.00 0.00 2.66
425 1959 4.186926 ACATGTGACGATCATTGAGAAGG 58.813 43.478 0.00 0.00 0.00 3.46
427 1961 5.077134 AGACATGTGACGATCATTGAGAA 57.923 39.130 1.15 0.00 0.00 2.87
430 1964 5.120674 GTGAAAGACATGTGACGATCATTGA 59.879 40.000 1.15 0.00 0.00 2.57
431 1965 5.319139 GTGAAAGACATGTGACGATCATTG 58.681 41.667 1.15 0.00 0.00 2.82
435 1969 2.673368 GGGTGAAAGACATGTGACGATC 59.327 50.000 1.15 0.00 0.00 3.69
442 1976 2.999185 ATTGGGGGTGAAAGACATGT 57.001 45.000 0.00 0.00 0.00 3.21
452 1986 2.478831 CACAACGAAAAATTGGGGGTG 58.521 47.619 0.00 0.00 0.00 4.61
837 2408 2.227194 GAAAGGCCAGTTTCTTCCGAA 58.773 47.619 5.01 0.00 34.19 4.30
912 2483 1.811679 CGGAAGGAAGCGAGGAAGC 60.812 63.158 0.00 0.00 37.41 3.86
916 2487 4.840005 GGGCGGAAGGAAGCGAGG 62.840 72.222 0.00 0.00 0.00 4.63
1047 2622 2.124653 GAGGGAGACGGCGAGAGA 60.125 66.667 16.62 0.00 0.00 3.10
1596 3171 6.564499 GCAACTGCAATTCCAACAATAACAAG 60.564 38.462 0.00 0.00 41.59 3.16
1619 3194 1.303561 GACAATCCAGGGCACAGCA 60.304 57.895 0.00 0.00 0.00 4.41
1643 3218 1.218316 GAGTCCGGCGTCAAATCCT 59.782 57.895 6.01 0.00 0.00 3.24
1701 3277 2.489971 ACCGAATTGCGACAAGAAGAA 58.510 42.857 0.00 0.00 44.57 2.52
1702 3278 2.163818 ACCGAATTGCGACAAGAAGA 57.836 45.000 0.00 0.00 44.57 2.87
1724 3300 6.906157 TCTTCAGAGCCAAATCAAAGAAAT 57.094 33.333 0.00 0.00 0.00 2.17
1991 3567 5.422012 CCTACAAGCCCAATAACCAAATTCT 59.578 40.000 0.00 0.00 0.00 2.40
2170 3746 7.274904 CGAAGAAAAGAAATGTGATCAATGCAT 59.725 33.333 0.00 0.00 0.00 3.96
2220 3796 7.095144 CCACAACAACACCACTTACGAATTATA 60.095 37.037 0.00 0.00 0.00 0.98
2228 3804 3.630312 ACATCCACAACAACACCACTTAC 59.370 43.478 0.00 0.00 0.00 2.34
2240 3816 8.556213 TGTACCTTATCTAAAACATCCACAAC 57.444 34.615 0.00 0.00 0.00 3.32
2344 3920 0.664166 GCAATGCAACAGGTCCAACG 60.664 55.000 0.00 0.00 0.00 4.10
2398 3974 3.776417 GGACAGTTACACCCCACCTAATA 59.224 47.826 0.00 0.00 0.00 0.98
2399 3975 2.574824 GGACAGTTACACCCCACCTAAT 59.425 50.000 0.00 0.00 0.00 1.73
2400 3976 1.980036 GGACAGTTACACCCCACCTAA 59.020 52.381 0.00 0.00 0.00 2.69
2415 3991 4.269183 TGCCCATGTAAATAACAGGACAG 58.731 43.478 0.00 0.00 42.55 3.51
2573 4151 4.530094 TTATGTTTGCTAAGCCGATTCG 57.470 40.909 0.00 0.00 0.00 3.34


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

AutoCloner maintained by Alex Coulton.