Multiple sequence alignment - TraesCS2B01G295700

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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 TraesCS2B01G295700 chr2B 100.000 5577 0 0 1 5577 412743421 412748997 0.000000e+00 10299.0
1 TraesCS2B01G295700 chr2D 97.160 4190 96 13 1395 5577 347455191 347459364 0.000000e+00 7057.0
2 TraesCS2B01G295700 chr2D 93.343 1412 52 9 1 1401 347453780 347455160 0.000000e+00 2049.0
3 TraesCS2B01G295700 chr2A 93.665 1626 73 13 2119 3740 461030621 461032220 0.000000e+00 2405.0
4 TraesCS2B01G295700 chr2A 91.835 1433 59 13 1 1401 461028362 461029768 0.000000e+00 1945.0
5 TraesCS2B01G295700 chr2A 94.211 1261 51 10 3822 5076 461032219 461033463 0.000000e+00 1905.0
6 TraesCS2B01G295700 chr2A 94.085 710 23 2 1391 2082 461029795 461030503 0.000000e+00 1061.0
7 TraesCS2B01G295700 chr2A 96.471 85 3 0 3739 3823 703709094 703709010 2.090000e-29 141.0
8 TraesCS2B01G295700 chr2A 95.294 85 4 0 3739 3823 51498555 51498639 9.750000e-28 135.0
9 TraesCS2B01G295700 chr3B 89.899 396 33 3 3350 3740 769543861 769544254 2.320000e-138 503.0
10 TraesCS2B01G295700 chr7D 96.512 86 3 0 3738 3823 474349061 474349146 5.820000e-30 143.0
11 TraesCS2B01G295700 chr7D 94.186 86 5 0 3738 3823 164195994 164195909 1.260000e-26 132.0
12 TraesCS2B01G295700 chr7D 86.585 82 7 3 3163 3244 63446949 63446872 2.770000e-13 87.9
13 TraesCS2B01G295700 chr5D 95.349 86 4 0 3739 3824 434549396 434549311 2.710000e-28 137.0
14 TraesCS2B01G295700 chr6A 95.294 85 4 0 3739 3823 40525460 40525376 9.750000e-28 135.0
15 TraesCS2B01G295700 chr1D 95.294 85 4 0 3739 3823 307830103 307830187 9.750000e-28 135.0
16 TraesCS2B01G295700 chr3A 93.333 90 5 1 3735 3824 489193172 489193084 1.260000e-26 132.0
17 TraesCS2B01G295700 chr7B 82.812 128 16 4 3163 3289 3851049 3850927 5.910000e-20 110.0
18 TraesCS2B01G295700 chr7A 83.871 124 11 7 3163 3284 66237048 66236932 5.910000e-20 110.0


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 TraesCS2B01G295700 chr2B 412743421 412748997 5576 False 10299 10299 100.0000 1 5577 1 chr2B.!!$F1 5576
1 TraesCS2B01G295700 chr2D 347453780 347459364 5584 False 4553 7057 95.2515 1 5577 2 chr2D.!!$F1 5576
2 TraesCS2B01G295700 chr2A 461028362 461033463 5101 False 1829 2405 93.4490 1 5076 4 chr2A.!!$F2 5075

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
50 53 1.414527 GCGTGCTTACTTCGAGAGCC 61.415 60.000 8.89 2.19 35.59 4.70 F
447 477 3.903090 TGAATGATGGTTTGCCTCCTTTT 59.097 39.130 0.00 0.00 35.27 2.27 F
1053 1087 1.200948 GCCACATCCTCAAGTGCTTTC 59.799 52.381 0.00 0.00 34.48 2.62 F
1272 1307 2.054232 TAGGTTCTGGAGGCTACTCG 57.946 55.000 0.00 0.00 44.93 4.18 F
2199 2371 2.061061 AGGGCTCAGGAATATCTTGGG 58.939 52.381 0.00 0.00 0.00 4.12 F
3364 3540 1.907255 TGCCAATTGCCATTCATCCAA 59.093 42.857 0.00 0.00 40.16 3.53 F
3953 4129 0.602638 TTGCATCTTTCGAGCACGGT 60.603 50.000 3.11 0.00 38.11 4.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1041 1075 5.220815 GCTAGATCCAATGAAAGCACTTGAG 60.221 44.000 0.00 0.0 0.00 3.02 R
2018 2108 5.698832 ACACATGGTCACAATTAACATTCG 58.301 37.500 0.00 0.0 0.00 3.34 R
2486 2659 4.230745 ACTTTCTTGGTGGTGTAACAGT 57.769 40.909 0.00 0.0 39.98 3.55 R
2487 2660 6.147821 CAGATACTTTCTTGGTGGTGTAACAG 59.852 42.308 0.00 0.0 31.84 3.16 R
3553 3729 2.164624 ACAAAACTGTTGCCGCAAAGTA 59.835 40.909 7.54 0.0 0.00 2.24 R
4535 4712 2.094286 CACAGTCCGCTCTCAGAGAATT 60.094 50.000 5.62 0.0 0.00 2.17 R
5017 5199 2.824936 TGATTCGCATGGTTGATGGTTT 59.175 40.909 0.00 0.0 31.99 3.27 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 7.661536 TTGGCTACTCATCTAGTTAGATTGT 57.338 36.000 0.00 4.88 40.91 2.71
31 32 7.013750 TGGCTACTCATCTAGTTAGATTGTCTG 59.986 40.741 0.00 1.90 40.91 3.51
50 53 1.414527 GCGTGCTTACTTCGAGAGCC 61.415 60.000 8.89 2.19 35.59 4.70
199 213 4.142881 GGCTTCCAAGTAGAAACGAATCAC 60.143 45.833 0.00 0.00 0.00 3.06
297 327 5.010282 ACTAAGGTTCAGCAAATTAGTGGG 58.990 41.667 0.00 0.00 35.82 4.61
447 477 3.903090 TGAATGATGGTTTGCCTCCTTTT 59.097 39.130 0.00 0.00 35.27 2.27
597 629 8.082672 ACATAATATATACATGAGCTGGAGCA 57.917 34.615 0.00 0.00 45.16 4.26
659 691 9.628500 AAACTAAAACAACTTACTCTTGAGGAT 57.372 29.630 2.55 0.00 0.00 3.24
714 747 9.109393 GATTGTTCTTGTATTGCCATCTTAGTA 57.891 33.333 0.00 0.00 0.00 1.82
718 751 8.893727 GTTCTTGTATTGCCATCTTAGTATTGT 58.106 33.333 0.00 0.00 0.00 2.71
783 816 9.274065 CTTATACTTTTAAGAATTTGGACGCAC 57.726 33.333 0.00 0.00 32.02 5.34
898 932 6.536582 CCTAGTGTTCCAGTGAATATGTTCAG 59.463 42.308 4.98 0.00 44.58 3.02
1041 1075 2.214387 GCTTTGCATTAGCCACATCC 57.786 50.000 9.56 0.00 41.13 3.51
1053 1087 1.200948 GCCACATCCTCAAGTGCTTTC 59.799 52.381 0.00 0.00 34.48 2.62
1185 1219 8.365399 TCGCATACAAGGTGATTTAAAGATAG 57.635 34.615 0.00 0.00 0.00 2.08
1272 1307 2.054232 TAGGTTCTGGAGGCTACTCG 57.946 55.000 0.00 0.00 44.93 4.18
1369 1404 2.853731 TTGGCGTTACAACAAAGGTG 57.146 45.000 0.00 0.00 0.00 4.00
1392 1464 6.535508 GTGCTCAGTAAAGATACTAACCCAAG 59.464 42.308 0.00 0.00 40.44 3.61
1405 1477 5.014202 ACTAACCCAAGTGACTTTTGTTGT 58.986 37.500 15.59 10.48 0.00 3.32
1482 1554 4.279145 AGATGTCAGGTACGGATAGTGTT 58.721 43.478 0.00 0.00 33.60 3.32
1755 1845 5.437060 TCTAAGCCATAATTCTGGTGAACC 58.563 41.667 11.20 0.00 38.63 3.62
1968 2058 5.241728 GCAACTGAACCAGGTATCTCTTTTT 59.758 40.000 0.00 0.00 35.51 1.94
2018 2108 9.639601 CCATTTCTCATAGTTTTCCCTTTAAAC 57.360 33.333 0.00 0.00 36.08 2.01
2097 2187 5.231702 ACCATCAATGCTGGTTTGAAATT 57.768 34.783 2.47 0.00 44.67 1.82
2162 2333 4.957296 TCACCAGAGTTTTCCAGTTAGTC 58.043 43.478 0.00 0.00 0.00 2.59
2199 2371 2.061061 AGGGCTCAGGAATATCTTGGG 58.939 52.381 0.00 0.00 0.00 4.12
2400 2572 3.194329 TGTTTCTGTGGACAAAACATGCA 59.806 39.130 12.33 0.00 37.82 3.96
2842 3016 3.257393 CGCCCTGATGAAGTGCTATATC 58.743 50.000 0.00 0.00 0.00 1.63
3097 3272 5.866633 TCCGCAAAAACAATTGATATGGAAC 59.133 36.000 13.59 0.00 31.84 3.62
3296 3472 5.504853 TGCATCCCAAACTACATGAATGTA 58.495 37.500 0.00 3.27 41.97 2.29
3308 3484 9.461312 AACTACATGAATGTACAATGGTTGTAT 57.539 29.630 0.00 0.00 46.73 2.29
3316 3492 6.767524 TGTACAATGGTTGTATTTCCCATC 57.232 37.500 5.90 0.00 46.73 3.51
3364 3540 1.907255 TGCCAATTGCCATTCATCCAA 59.093 42.857 0.00 0.00 40.16 3.53
3460 3636 7.469537 TTTGGAGTTCTCCTGTTTGTAAAAA 57.530 32.000 18.07 5.95 0.00 1.94
3553 3729 5.609533 ACAAGTAGTGTACTGAACCTTGT 57.390 39.130 10.57 10.57 39.29 3.16
3667 3843 5.928153 ACATCTAAGCGTTCTAAAGTTTGC 58.072 37.500 0.00 0.00 0.00 3.68
3759 3935 7.069578 TGAGCTACTCCTTCCGTAAAGAAATAT 59.930 37.037 0.00 0.00 37.12 1.28
3779 3955 8.958119 AAATATAAGAGCGTTTGGATCACTAA 57.042 30.769 0.00 0.00 32.03 2.24
3780 3956 8.958119 AATATAAGAGCGTTTGGATCACTAAA 57.042 30.769 0.00 0.00 32.03 1.85
3781 3957 6.910536 ATAAGAGCGTTTGGATCACTAAAG 57.089 37.500 0.00 0.00 32.03 1.85
3953 4129 0.602638 TTGCATCTTTCGAGCACGGT 60.603 50.000 3.11 0.00 38.11 4.83
4157 4333 6.976925 GCAATAGCTTTTAGCAGTTTCATGAT 59.023 34.615 0.00 0.00 45.56 2.45
4323 4499 6.768381 ACTCGAAATTCCATTCTAAATCCTCC 59.232 38.462 0.00 0.00 0.00 4.30
4534 4711 1.217882 GGAACACACAACCTGACTCG 58.782 55.000 0.00 0.00 0.00 4.18
4535 4712 1.202486 GGAACACACAACCTGACTCGA 60.202 52.381 0.00 0.00 0.00 4.04
4922 5099 4.201647 CGACCGTAATGTGTCGCTAAATTT 60.202 41.667 0.00 0.00 46.41 1.82
4954 5131 6.989155 AACATCGGGGTAGTAATTCTGATA 57.011 37.500 0.00 0.00 0.00 2.15
5017 5199 5.163468 TGGAGTTTTTGCTTGTTTAGATGCA 60.163 36.000 0.00 0.00 0.00 3.96
5056 5238 6.896613 GCGAATCATGCATCATTTATAGTACG 59.103 38.462 0.00 0.00 0.00 3.67
5112 5294 8.075593 ACACATTGTGATAAAGCAAACATTTC 57.924 30.769 23.12 0.00 36.96 2.17
5142 5324 4.976864 AGCACATGCCATCAATATGTAGA 58.023 39.130 0.00 0.00 43.38 2.59
5146 5328 5.761726 CACATGCCATCAATATGTAGACACT 59.238 40.000 0.00 0.00 33.57 3.55
5272 5458 6.392625 TGTCTAGGACAAGTATATCTGTGC 57.607 41.667 0.00 1.80 39.78 4.57
5278 5464 9.416794 CTAGGACAAGTATATCTGTGCATTAAG 57.583 37.037 10.07 0.00 0.00 1.85
5313 5499 2.723273 ACATTAAGAAAAGCTCGGGGG 58.277 47.619 0.00 0.00 0.00 5.40
5322 5508 1.349067 AAGCTCGGGGGTATGGATAC 58.651 55.000 0.00 0.00 0.00 2.24
5447 5633 7.864108 TGTTTATGTCTTTAGATCATGTGGG 57.136 36.000 0.00 0.00 0.00 4.61
5458 5644 4.074970 AGATCATGTGGGTTTTCAGTGTC 58.925 43.478 0.00 0.00 0.00 3.67
5462 5648 2.582052 TGTGGGTTTTCAGTGTCCATC 58.418 47.619 0.00 0.00 0.00 3.51
5463 5649 1.535462 GTGGGTTTTCAGTGTCCATCG 59.465 52.381 0.00 0.00 0.00 3.84
5475 5661 1.134128 TGTCCATCGCAATGCCATACT 60.134 47.619 0.00 0.00 0.00 2.12
5522 5708 6.845302 TGACATGCAATTAAACTAGAAGCTG 58.155 36.000 0.00 0.00 0.00 4.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 0.879090 TCTCGAAGTAAGCACGCAGA 59.121 50.000 0.00 0.00 0.00 4.26
31 32 1.414527 GGCTCTCGAAGTAAGCACGC 61.415 60.000 9.93 0.00 37.74 5.34
297 327 5.009310 CCAGGACAACAAAAGTAAAGGTACC 59.991 44.000 2.73 2.73 0.00 3.34
411 441 4.142093 CCATCATTCACCCCAAATGTCTTC 60.142 45.833 0.00 0.00 35.92 2.87
447 477 2.529780 ACAACGACGTAACCAATCCA 57.470 45.000 0.00 0.00 0.00 3.41
570 602 9.469807 GCTCCAGCTCATGTATATATTATGTAC 57.530 37.037 4.18 4.18 38.21 2.90
571 603 9.200817 TGCTCCAGCTCATGTATATATTATGTA 57.799 33.333 0.00 0.00 42.66 2.29
572 604 8.082672 TGCTCCAGCTCATGTATATATTATGT 57.917 34.615 0.00 0.00 42.66 2.29
573 605 8.590719 CTGCTCCAGCTCATGTATATATTATG 57.409 38.462 0.00 0.00 42.66 1.90
597 629 7.619302 TCAGAAAAGTATTGGGATAAAATGGCT 59.381 33.333 0.00 0.00 0.00 4.75
659 691 4.600062 TGCTACTGATAGAGAACCTGACA 58.400 43.478 0.00 0.00 0.00 3.58
714 747 3.387374 TGGGCTGTCACAAAAATCACAAT 59.613 39.130 0.00 0.00 0.00 2.71
718 751 2.361757 CTGTGGGCTGTCACAAAAATCA 59.638 45.455 8.78 0.00 45.60 2.57
763 796 6.306356 CAGATGTGCGTCCAAATTCTTAAAAG 59.694 38.462 0.00 0.00 0.00 2.27
772 805 5.415701 AGAATTAACAGATGTGCGTCCAAAT 59.584 36.000 0.00 0.00 0.00 2.32
1041 1075 5.220815 GCTAGATCCAATGAAAGCACTTGAG 60.221 44.000 0.00 0.00 0.00 3.02
1053 1087 6.541278 TCTTGATCACAAAGCTAGATCCAATG 59.459 38.462 0.00 0.00 37.86 2.82
1361 1396 6.115448 AGTATCTTTACTGAGCACCTTTGT 57.885 37.500 0.00 0.00 37.28 2.83
1368 1403 6.212791 ACTTGGGTTAGTATCTTTACTGAGCA 59.787 38.462 8.67 0.00 41.63 4.26
1369 1404 6.535508 CACTTGGGTTAGTATCTTTACTGAGC 59.464 42.308 0.00 0.00 40.07 4.26
1405 1477 9.034544 CACATCTATTCGAAGATATTTGTGTGA 57.965 33.333 3.35 0.00 34.40 3.58
1968 2058 7.125204 TGGCAGCTAGAACTATTTAAGGACTTA 59.875 37.037 0.00 0.00 0.00 2.24
2018 2108 5.698832 ACACATGGTCACAATTAACATTCG 58.301 37.500 0.00 0.00 0.00 3.34
2400 2572 8.768397 TGGTATTAAATCCAGTAGAATGACACT 58.232 33.333 0.00 0.00 0.00 3.55
2481 2654 4.444536 TCTTGGTGGTGTAACAGTAACAC 58.555 43.478 0.00 0.00 45.21 3.32
2482 2655 4.757019 TCTTGGTGGTGTAACAGTAACA 57.243 40.909 0.00 0.00 39.98 2.41
2483 2656 5.587443 ACTTTCTTGGTGGTGTAACAGTAAC 59.413 40.000 0.00 0.00 39.98 2.50
2484 2657 5.747342 ACTTTCTTGGTGGTGTAACAGTAA 58.253 37.500 0.00 0.00 39.98 2.24
2485 2658 5.362105 ACTTTCTTGGTGGTGTAACAGTA 57.638 39.130 0.00 0.00 39.98 2.74
2486 2659 4.230745 ACTTTCTTGGTGGTGTAACAGT 57.769 40.909 0.00 0.00 39.98 3.55
2487 2660 6.147821 CAGATACTTTCTTGGTGGTGTAACAG 59.852 42.308 0.00 0.00 31.84 3.16
2546 2720 7.088272 GGGATAGAAAACATAACCACAAACAC 58.912 38.462 0.00 0.00 0.00 3.32
2842 3016 6.348540 GCTTTAACACTGATAACCTGTTCCAG 60.349 42.308 9.43 9.43 32.93 3.86
3097 3272 7.592938 TGTTCTAGTGACAAAAATATTGGCAG 58.407 34.615 0.00 0.00 38.25 4.85
3296 3472 4.981806 CGATGGGAAATACAACCATTGT 57.018 40.909 0.00 0.00 44.62 2.71
3308 3484 5.687166 AACAGACCTATTACGATGGGAAA 57.313 39.130 0.00 0.00 37.35 3.13
3316 3492 7.465513 GCATCCTTTGTTAACAGACCTATTACG 60.466 40.741 8.56 0.00 0.00 3.18
3364 3540 9.396022 TCAAACTTTACTTCTCAGAAAATGTCT 57.604 29.630 0.00 0.00 36.88 3.41
3426 3602 4.866682 GAGAACTCCAAAATCGATGTCC 57.133 45.455 0.00 0.00 0.00 4.02
3462 3638 9.886132 CAGTACTACTTTCCAAGTAATTACCAT 57.114 33.333 12.05 0.00 42.99 3.55
3553 3729 2.164624 ACAAAACTGTTGCCGCAAAGTA 59.835 40.909 7.54 0.00 0.00 2.24
3646 3822 4.689345 ACGCAAACTTTAGAACGCTTAGAT 59.311 37.500 0.00 0.00 0.00 1.98
3759 3935 5.790593 ACTTTAGTGATCCAAACGCTCTTA 58.209 37.500 0.00 0.00 0.00 2.10
3779 3955 3.963428 AGAGCGTTTGGATCACTACTT 57.037 42.857 0.00 0.00 32.03 2.24
3780 3956 3.963428 AAGAGCGTTTGGATCACTACT 57.037 42.857 0.00 0.00 32.03 2.57
3781 3957 7.948278 AATATAAGAGCGTTTGGATCACTAC 57.052 36.000 0.00 0.00 32.03 2.73
4363 4539 5.047306 TGCTATCCCTGTCGTATTCATAAGG 60.047 44.000 0.00 0.00 0.00 2.69
4534 4711 2.165437 ACAGTCCGCTCTCAGAGAATTC 59.835 50.000 5.62 0.00 0.00 2.17
4535 4712 2.094286 CACAGTCCGCTCTCAGAGAATT 60.094 50.000 5.62 0.00 0.00 2.17
5017 5199 2.824936 TGATTCGCATGGTTGATGGTTT 59.175 40.909 0.00 0.00 31.99 3.27
5056 5238 7.364970 TCCCGCAAAAGAAAGAAAATACTAAC 58.635 34.615 0.00 0.00 0.00 2.34
5062 5244 4.058124 GCTTCCCGCAAAAGAAAGAAAAT 58.942 39.130 0.00 0.00 38.92 1.82
5112 5294 3.544684 TGATGGCATGTGCTAGGTAAAG 58.455 45.455 3.81 0.00 41.70 1.85
5142 5324 3.981375 AGAAGAGTAGGGGGAAAAAGTGT 59.019 43.478 0.00 0.00 0.00 3.55
5146 5328 4.587262 GCAAAAGAAGAGTAGGGGGAAAAA 59.413 41.667 0.00 0.00 0.00 1.94
5418 5604 8.450964 ACATGATCTAAAGACATAAACAAACCG 58.549 33.333 0.00 0.00 0.00 4.44
5419 5605 9.559958 CACATGATCTAAAGACATAAACAAACC 57.440 33.333 0.00 0.00 0.00 3.27
5447 5633 3.236816 CATTGCGATGGACACTGAAAAC 58.763 45.455 5.98 0.00 0.00 2.43


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

AutoCloner maintained by Alex Coulton.