Multiple sequence alignment - TraesCS7D01G401100

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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 TraesCS7D01G401100 chr7D 100.000 3266 0 0 1 3266 518129537 518132802 0 6032
1 TraesCS7D01G401100 chr7D 96.326 3266 117 3 1 3266 610300223 610303485 0 5363
2 TraesCS7D01G401100 chr5D 97.061 3266 92 3 1 3266 539389230 539385969 0 5496
3 TraesCS7D01G401100 chr6D 96.880 3269 98 4 1 3266 411365372 411362105 0 5469
4 TraesCS7D01G401100 chr2D 96.572 3267 111 1 1 3266 534899897 534896631 0 5411
5 TraesCS7D01G401100 chr2D 96.541 3267 112 1 1 3266 536061444 536058178 0 5406
6 TraesCS7D01G401100 chr3D 96.509 3266 112 2 1 3266 335959059 335955796 0 5398
7 TraesCS7D01G401100 chr1D 96.454 3271 110 3 1 3266 366430891 366427622 0 5393
8 TraesCS7D01G401100 chr1D 96.330 3270 116 2 1 3266 466162874 466166143 0 5371
9 TraesCS7D01G401100 chr2A 94.645 3268 170 5 1 3266 307022426 307019162 0 5060


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 TraesCS7D01G401100 chr7D 518129537 518132802 3265 False 6032 6032 100.000 1 3266 1 chr7D.!!$F1 3265
1 TraesCS7D01G401100 chr7D 610300223 610303485 3262 False 5363 5363 96.326 1 3266 1 chr7D.!!$F2 3265
2 TraesCS7D01G401100 chr5D 539385969 539389230 3261 True 5496 5496 97.061 1 3266 1 chr5D.!!$R1 3265
3 TraesCS7D01G401100 chr6D 411362105 411365372 3267 True 5469 5469 96.880 1 3266 1 chr6D.!!$R1 3265
4 TraesCS7D01G401100 chr2D 534896631 534899897 3266 True 5411 5411 96.572 1 3266 1 chr2D.!!$R1 3265
5 TraesCS7D01G401100 chr2D 536058178 536061444 3266 True 5406 5406 96.541 1 3266 1 chr2D.!!$R2 3265
6 TraesCS7D01G401100 chr3D 335955796 335959059 3263 True 5398 5398 96.509 1 3266 1 chr3D.!!$R1 3265
7 TraesCS7D01G401100 chr1D 366427622 366430891 3269 True 5393 5393 96.454 1 3266 1 chr1D.!!$R1 3265
8 TraesCS7D01G401100 chr1D 466162874 466166143 3269 False 5371 5371 96.330 1 3266 1 chr1D.!!$F1 3265
9 TraesCS7D01G401100 chr2A 307019162 307022426 3264 True 5060 5060 94.645 1 3266 1 chr2A.!!$R1 3265

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
35 36 0.034198 TTTGTTGTGATCTCCGCCGA 59.966 50.0 0.0 0.0 0.00 5.54 F
913 921 0.882042 CTGCGATTCCATAGCCGCTT 60.882 55.0 0.0 0.0 46.77 4.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1158 1166 0.465705 CGGCTTCCTCAGGATTGCTA 59.534 55.0 16.09 0.0 33.98 3.49 R
2289 2304 0.178068 ACACAAGCAACTCCACGACT 59.822 50.0 0.00 0.0 0.00 4.18 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
35 36 0.034198 TTTGTTGTGATCTCCGCCGA 59.966 50.000 0.00 0.00 0.00 5.54
184 185 4.263771 GGGGAACTCTACTTGGAATTTGGA 60.264 45.833 0.00 0.00 0.00 3.53
197 198 3.606687 GAATTTGGACCCGTGTACTGAT 58.393 45.455 0.00 0.00 0.00 2.90
202 203 2.291735 TGGACCCGTGTACTGATCCTAA 60.292 50.000 0.00 0.00 0.00 2.69
266 271 2.499693 GTGGAAGAGAGGAAGGAAGAGG 59.500 54.545 0.00 0.00 0.00 3.69
517 524 4.274602 AGACTTACTCAGAGAGTCACGA 57.725 45.455 17.51 0.00 42.40 4.35
806 814 2.615618 CTCGACGCATAGCAACGC 59.384 61.111 0.00 0.00 0.00 4.84
899 907 1.732917 CACAAAAGGGCAACTGCGA 59.267 52.632 0.00 0.00 43.26 5.10
913 921 0.882042 CTGCGATTCCATAGCCGCTT 60.882 55.000 0.00 0.00 46.77 4.68
1150 1158 1.888512 GCAAGGAAAAGCTGGATGTCA 59.111 47.619 0.00 0.00 0.00 3.58
1158 1166 3.572632 AAGCTGGATGTCATATGCACT 57.427 42.857 0.00 0.00 0.00 4.40
1241 1249 0.108804 CCTCAGTACATCGGCGTTGT 60.109 55.000 24.79 24.79 0.00 3.32
1254 1262 2.730090 CGGCGTTGTTGTCGAGTATACT 60.730 50.000 4.68 4.68 39.90 2.12
1422 1430 7.903995 TCACCCTGAAATTTGATTAAATTGC 57.096 32.000 8.78 7.70 43.74 3.56
1423 1431 6.878389 TCACCCTGAAATTTGATTAAATTGCC 59.122 34.615 8.78 5.49 43.74 4.52
1506 1514 6.773638 ACTTGACTCACCAGATCAGTTTATT 58.226 36.000 0.00 0.00 0.00 1.40
1634 1642 7.107542 TGTTCCAGTGTAGTTTAGTTTCTTGT 58.892 34.615 0.00 0.00 0.00 3.16
2115 2130 2.242196 AGACCATAAACTGTGGGGGATG 59.758 50.000 0.00 0.00 41.14 3.51
2118 2133 2.509548 CCATAAACTGTGGGGGATGAGA 59.490 50.000 0.00 0.00 32.98 3.27
2135 2150 2.107378 TGAGACCACTGCCAAATTACCA 59.893 45.455 0.00 0.00 0.00 3.25
2177 2192 0.179119 GCGTACGCCACCTATGAGTT 60.179 55.000 29.51 0.00 34.56 3.01
2280 2295 5.229469 CGGATACTAGTGATGACGAAAACAC 59.771 44.000 5.39 0.00 0.00 3.32
2289 2304 6.537301 AGTGATGACGAAAACACAGAAAACTA 59.463 34.615 0.00 0.00 35.97 2.24
2385 2400 6.492007 AAGCAGTTTCTAATGTCATCTGTG 57.508 37.500 0.00 0.00 0.00 3.66
2639 2654 0.679505 ACGCAGTTAGAGAGGCACAA 59.320 50.000 0.00 0.00 37.78 3.33
2983 2999 2.852449 TGTGTTGGAATGCTCGGTTAA 58.148 42.857 0.00 0.00 0.00 2.01
3046 3062 0.172578 CCGCGACCATGTAAGAGTCA 59.827 55.000 8.23 0.00 0.00 3.41
3211 3227 1.269621 CCGAATACGCAGTTAGGGAGG 60.270 57.143 0.00 0.00 37.78 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 0.180406 AGCAAGGACTTCAACACCGT 59.820 50.000 0.00 0.00 0.00 4.83
184 185 3.288964 CTCTTAGGATCAGTACACGGGT 58.711 50.000 0.00 0.00 0.00 5.28
197 198 3.165875 CACACAAGGTCTCCTCTTAGGA 58.834 50.000 0.00 0.00 43.43 2.94
202 203 1.967066 CACTCACACAAGGTCTCCTCT 59.033 52.381 0.00 0.00 30.89 3.69
266 271 0.335361 TCTCTCCCACCTCCACTACC 59.665 60.000 0.00 0.00 0.00 3.18
517 524 6.586844 GCTCGTAACTCTAAAGACTTCACAAT 59.413 38.462 0.00 0.00 0.00 2.71
555 562 1.079543 GCATCACTCTCACGTGCCT 60.080 57.895 11.67 0.00 34.92 4.75
631 638 1.425066 ACTTCACACATGTGGACCCAT 59.575 47.619 28.64 4.62 45.65 4.00
689 696 4.697756 TGCTCGCACCTTTCCCGG 62.698 66.667 0.00 0.00 0.00 5.73
787 795 1.226575 CGTTGCTATGCGTCGAGGA 60.227 57.895 9.75 0.00 31.62 3.71
806 814 3.257561 CGGAAGACATGCGCTCGG 61.258 66.667 9.73 0.00 35.60 4.63
848 856 2.285368 TGGAGGAGGCGGTTGGAT 60.285 61.111 0.00 0.00 0.00 3.41
899 907 3.074412 CGGAATTAAGCGGCTATGGAAT 58.926 45.455 1.35 0.00 0.00 3.01
913 921 4.696402 ACGGCAATAGTGTTTTCGGAATTA 59.304 37.500 0.00 0.00 0.00 1.40
1158 1166 0.465705 CGGCTTCCTCAGGATTGCTA 59.534 55.000 16.09 0.00 33.98 3.49
1241 1249 4.712476 GTCCTCCCTAGTATACTCGACAA 58.288 47.826 9.12 0.00 0.00 3.18
1422 1430 8.722480 TTCACTGATACATCAAGTCAATAAGG 57.278 34.615 0.00 0.00 36.18 2.69
1423 1431 9.376075 ACTTCACTGATACATCAAGTCAATAAG 57.624 33.333 0.00 0.00 36.18 1.73
1634 1642 8.800370 TTCTTAGCCATGTTAACACATCAATA 57.200 30.769 11.22 0.00 42.14 1.90
1649 1657 9.381038 TCAATTACCTATCTACTTCTTAGCCAT 57.619 33.333 0.00 0.00 0.00 4.40
2115 2130 2.488153 GTGGTAATTTGGCAGTGGTCTC 59.512 50.000 0.00 0.00 0.00 3.36
2118 2133 2.373335 TGTGGTAATTTGGCAGTGGT 57.627 45.000 0.00 0.00 0.00 4.16
2135 2150 4.590850 TCTATCGCTGCATACTCAATGT 57.409 40.909 0.00 0.00 37.93 2.71
2177 2192 6.772233 TCTGATGTTTTCAATTCTCTTCCACA 59.228 34.615 0.00 0.00 32.78 4.17
2280 2295 3.184581 GCAACTCCACGACTAGTTTTCTG 59.815 47.826 0.00 0.00 33.72 3.02
2289 2304 0.178068 ACACAAGCAACTCCACGACT 59.822 50.000 0.00 0.00 0.00 4.18
2613 2628 2.287668 CCTCTCTAACTGCGTATTCCGG 60.288 54.545 0.00 0.00 36.94 5.14
2639 2654 2.028567 GTGGCTCTAGAGACTGCAAACT 60.029 50.000 25.95 0.00 37.35 2.66
2983 2999 3.988379 AACGTCACAACAATGCATCTT 57.012 38.095 0.00 0.00 0.00 2.40
3211 3227 0.320421 TAGAGGCTTCACAACCGTGC 60.320 55.000 0.00 0.00 43.28 5.34


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

AutoCloner maintained by Alex Coulton.