Multiple sequence alignment - TraesCS7D01G226700

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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 TraesCS7D01G226700 chr7D 100.000 2207 0 0 1 2207 186828145 186830351 0 4076
1 TraesCS7D01G226700 chr7D 98.594 569 2 3 1 564 123460068 123460635 0 1002
2 TraesCS7D01G226700 chr7D 98.418 569 3 3 1 564 100459881 100460448 0 996
3 TraesCS7D01G226700 chr7D 98.063 568 5 3 1 563 156769462 156768896 0 983
4 TraesCS7D01G226700 chr7D 97.891 569 6 3 1 564 81794247 81794814 0 979
5 TraesCS7D01G226700 chr7B 96.138 1657 51 8 564 2207 329795518 329797174 0 2693
6 TraesCS7D01G226700 chr7A 92.408 1607 59 26 643 2207 198191468 198189883 0 2233
7 TraesCS7D01G226700 chr7A 94.294 701 31 7 1511 2207 198026689 198025994 0 1064
8 TraesCS7D01G226700 chr6D 98.421 570 3 3 1 565 20133107 20133675 0 998
9 TraesCS7D01G226700 chr6D 98.090 576 4 4 1 571 426894078 426893505 0 996
10 TraesCS7D01G226700 chr1D 98.246 570 4 4 1 565 296591407 296591975 0 992
11 TraesCS7D01G226700 chr3D 98.063 568 5 3 1 563 97274278 97274844 0 983
12 TraesCS7D01G226700 chr5D 97.387 574 7 5 1 569 275577323 275576753 0 970


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 TraesCS7D01G226700 chr7D 186828145 186830351 2206 False 4076 4076 100.000 1 2207 1 chr7D.!!$F4 2206
1 TraesCS7D01G226700 chr7D 123460068 123460635 567 False 1002 1002 98.594 1 564 1 chr7D.!!$F3 563
2 TraesCS7D01G226700 chr7D 100459881 100460448 567 False 996 996 98.418 1 564 1 chr7D.!!$F2 563
3 TraesCS7D01G226700 chr7D 156768896 156769462 566 True 983 983 98.063 1 563 1 chr7D.!!$R1 562
4 TraesCS7D01G226700 chr7D 81794247 81794814 567 False 979 979 97.891 1 564 1 chr7D.!!$F1 563
5 TraesCS7D01G226700 chr7B 329795518 329797174 1656 False 2693 2693 96.138 564 2207 1 chr7B.!!$F1 1643
6 TraesCS7D01G226700 chr7A 198189883 198191468 1585 True 2233 2233 92.408 643 2207 1 chr7A.!!$R2 1564
7 TraesCS7D01G226700 chr7A 198025994 198026689 695 True 1064 1064 94.294 1511 2207 1 chr7A.!!$R1 696
8 TraesCS7D01G226700 chr6D 20133107 20133675 568 False 998 998 98.421 1 565 1 chr6D.!!$F1 564
9 TraesCS7D01G226700 chr6D 426893505 426894078 573 True 996 996 98.090 1 571 1 chr6D.!!$R1 570
10 TraesCS7D01G226700 chr1D 296591407 296591975 568 False 992 992 98.246 1 565 1 chr1D.!!$F1 564
11 TraesCS7D01G226700 chr3D 97274278 97274844 566 False 983 983 98.063 1 563 1 chr3D.!!$F1 562
12 TraesCS7D01G226700 chr5D 275576753 275577323 570 True 970 970 97.387 1 569 1 chr5D.!!$R1 568

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
848 869 0.981277 TCTTCAACCTCCGATCCCCC 60.981 60.0 0.0 0.0 0.0 5.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2137 2189 0.313043 ATACTCGATTGTACCCGCCG 59.687 55.0 0.0 0.0 0.0 6.46 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
231 232 3.558099 CTGTGCTGCGGTCGACTGA 62.558 63.158 28.38 11.88 0.00 3.41
549 550 2.031258 TCCGTGACAAGTTCAAGCAA 57.969 45.000 0.00 0.00 35.39 3.91
776 793 1.146041 GCCGCCCACTCATATCACA 59.854 57.895 0.00 0.00 0.00 3.58
840 861 3.142174 CACCAACTCTTCTTCAACCTCC 58.858 50.000 0.00 0.00 0.00 4.30
843 864 3.307059 CCAACTCTTCTTCAACCTCCGAT 60.307 47.826 0.00 0.00 0.00 4.18
848 869 0.981277 TCTTCAACCTCCGATCCCCC 60.981 60.000 0.00 0.00 0.00 5.40
883 904 1.336609 GCTAACCCGGGCTATAAGACG 60.337 57.143 24.08 0.10 0.00 4.18
1336 1361 7.209475 ACATGTACCTTTGATTTGGTTTGAAG 58.791 34.615 0.00 0.00 37.74 3.02
1371 1396 7.901283 TGACCATATGTTGATTGATCCATTT 57.099 32.000 1.24 0.00 0.00 2.32
1436 1462 4.143179 CCTTTCTTACCGTCGTGAATTGAC 60.143 45.833 0.00 0.00 0.00 3.18
1446 1472 5.396484 CGTCGTGAATTGACCTCTAACTTA 58.604 41.667 0.00 0.00 32.68 2.24
1447 1473 6.034591 CGTCGTGAATTGACCTCTAACTTAT 58.965 40.000 0.00 0.00 32.68 1.73
1448 1474 7.191551 CGTCGTGAATTGACCTCTAACTTATA 58.808 38.462 0.00 0.00 32.68 0.98
1491 1532 7.936847 AGATTTTGGTTGTTCTACTGTATCACA 59.063 33.333 0.00 0.00 0.00 3.58
1495 1536 8.458573 TTGGTTGTTCTACTGTATCACATTTT 57.541 30.769 1.37 0.00 0.00 1.82
1576 1622 8.103305 AGAAAACATCTGCTTACAAGATCCTAA 58.897 33.333 0.00 0.00 36.88 2.69
1824 1876 2.099098 GGCATCTTGGGGAACGTAAATG 59.901 50.000 0.00 0.00 0.00 2.32
1938 1990 0.319986 TGCATGCACAGCAACAATGG 60.320 50.000 18.46 0.00 43.62 3.16
1982 2034 5.065090 ACACCTTAACAAAAACAGTACGGTC 59.935 40.000 0.00 0.00 0.00 4.79
2079 2131 2.359230 GTGACAGGGGAGCTGCAC 60.359 66.667 7.79 2.32 0.00 4.57
2099 2151 4.000325 CACGTCCTTTCAACATGGTATGA 59.000 43.478 0.00 0.00 0.00 2.15
2135 2187 4.878397 ACTTTCTTCTGTTGTGTGGAAGAG 59.122 41.667 0.00 0.00 43.78 2.85
2136 2188 4.753516 TTCTTCTGTTGTGTGGAAGAGA 57.246 40.909 0.00 0.00 43.78 3.10
2137 2189 4.060038 TCTTCTGTTGTGTGGAAGAGAC 57.940 45.455 0.00 0.00 39.99 3.36
2138 2190 2.509052 TCTGTTGTGTGGAAGAGACG 57.491 50.000 0.00 0.00 0.00 4.18
2152 2206 1.996786 GAGACGGCGGGTACAATCGA 61.997 60.000 13.24 0.00 0.00 3.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
506 507 7.389607 GGATGTTCACTTTAGTGCCTAAACTTA 59.610 37.037 5.00 0.00 45.25 2.24
587 593 6.113411 GGCTATACTTGTCTGGAAGCTAAAA 58.887 40.000 0.00 0.00 0.00 1.52
627 633 6.100004 CGGTTCAGAAGATAGCTACTTTCAA 58.900 40.000 16.93 5.34 0.00 2.69
633 639 4.995124 TGAACGGTTCAGAAGATAGCTAC 58.005 43.478 19.07 0.00 34.08 3.58
776 793 1.404035 TCTCTACGTGCGTGCATGTAT 59.596 47.619 22.99 5.11 44.38 2.29
840 861 1.205893 GCTAGCTAATCTGGGGGATCG 59.794 57.143 7.70 0.00 32.76 3.69
843 864 0.568192 AGGCTAGCTAATCTGGGGGA 59.432 55.000 15.72 0.00 0.00 4.81
1336 1361 5.822519 TCAACATATGGTCAAGTAATCCAGC 59.177 40.000 7.80 0.00 34.62 4.85
1388 1413 7.548075 GGCAATCAAATGAATGAAGAGTGAAAT 59.452 33.333 2.71 0.00 32.06 2.17
1447 1473 9.093970 CCAAAATCTCACATCGTTTACATAGTA 57.906 33.333 0.00 0.00 0.00 1.82
1448 1474 7.606456 ACCAAAATCTCACATCGTTTACATAGT 59.394 33.333 0.00 0.00 0.00 2.12
1551 1597 6.749923 AGGATCTTGTAAGCAGATGTTTTC 57.250 37.500 0.00 0.00 0.00 2.29
1824 1876 1.153349 GAGACCTTCCACCGATGCC 60.153 63.158 0.00 0.00 0.00 4.40
1930 1982 9.434420 AAACCACATTGTAATAATCCATTGTTG 57.566 29.630 0.00 0.00 0.00 3.33
1960 2012 5.184711 TGACCGTACTGTTTTTGTTAAGGT 58.815 37.500 0.00 0.00 0.00 3.50
1961 2013 5.738118 TGACCGTACTGTTTTTGTTAAGG 57.262 39.130 0.00 0.00 0.00 2.69
2079 2131 4.000325 TGTCATACCATGTTGAAAGGACG 59.000 43.478 0.00 0.00 0.00 4.79
2099 2151 5.594317 ACAGAAGAAAGTTTAGCAACCATGT 59.406 36.000 0.00 0.00 32.70 3.21
2135 2187 1.588139 CTCGATTGTACCCGCCGTC 60.588 63.158 0.00 0.00 0.00 4.79
2136 2188 1.031571 TACTCGATTGTACCCGCCGT 61.032 55.000 0.00 0.00 0.00 5.68
2137 2189 0.313043 ATACTCGATTGTACCCGCCG 59.687 55.000 0.00 0.00 0.00 6.46
2138 2190 2.521105 AATACTCGATTGTACCCGCC 57.479 50.000 0.00 0.00 0.00 6.13
2171 2225 8.718102 ATGCATTAACGAGTCACTTAATTACT 57.282 30.769 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.