Multiple sequence alignment - TraesCS6D01G080600

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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 TraesCS6D01G080600 chr6D 100.000 2827 0 0 1 2827 46442319 46445145 0.000000e+00 5221.0
1 TraesCS6D01G080600 chr6D 81.397 1317 224 16 1096 2408 46778330 46779629 0.000000e+00 1055.0
2 TraesCS6D01G080600 chr6D 83.333 222 31 4 548 765 46777517 46777736 1.720000e-47 200.0
3 TraesCS6D01G080600 chr6D 74.309 362 79 13 1991 2344 10441397 10441752 1.060000e-29 141.0
4 TraesCS6D01G080600 chr6B 95.453 2397 92 3 1 2396 115524339 115526719 0.000000e+00 3807.0
5 TraesCS6D01G080600 chr6B 94.163 2073 113 5 761 2827 114879949 114882019 0.000000e+00 3151.0
6 TraesCS6D01G080600 chr6B 93.170 2079 120 10 761 2827 115060418 115062486 0.000000e+00 3033.0
7 TraesCS6D01G080600 chr6B 96.118 1597 58 4 1232 2827 115022557 115024150 0.000000e+00 2603.0
8 TraesCS6D01G080600 chr6B 95.468 993 44 1 244 1236 115012563 115013554 0.000000e+00 1583.0
9 TraesCS6D01G080600 chr6B 88.429 700 64 7 37 734 115059614 115060298 0.000000e+00 828.0
10 TraesCS6D01G080600 chr6B 94.074 540 30 2 36 574 115057783 115058321 0.000000e+00 819.0
11 TraesCS6D01G080600 chr6B 87.161 701 72 9 36 734 114879145 114879829 0.000000e+00 780.0
12 TraesCS6D01G080600 chr6B 92.841 433 10 3 2394 2826 115535372 115535783 2.410000e-170 608.0
13 TraesCS6D01G080600 chr6B 94.378 249 14 0 1 249 114976714 114976962 1.590000e-102 383.0
14 TraesCS6D01G080600 chr6B 72.508 622 128 30 1755 2344 71356563 71355953 8.100000e-36 161.0
15 TraesCS6D01G080600 chr6B 71.652 702 155 30 1676 2344 71496088 71495398 1.360000e-33 154.0
16 TraesCS6D01G080600 chr3D 80.516 1704 279 36 1120 2784 569895117 569896806 0.000000e+00 1258.0
17 TraesCS6D01G080600 chr3D 80.070 1716 282 42 1112 2784 567412542 567410844 0.000000e+00 1219.0
18 TraesCS6D01G080600 chrUn 82.500 240 35 5 2318 2555 370311621 370311387 1.330000e-48 204.0
19 TraesCS6D01G080600 chrUn 79.290 169 31 3 1214 1380 30120743 30120909 6.400000e-22 115.0
20 TraesCS6D01G080600 chr4B 81.765 170 27 2 1213 1380 667351720 667351553 3.800000e-29 139.0
21 TraesCS6D01G080600 chr3B 86.022 93 8 5 896 987 756606695 756606783 8.340000e-16 95.3


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 TraesCS6D01G080600 chr6D 46442319 46445145 2826 False 5221.0 5221 100.000 1 2827 1 chr6D.!!$F2 2826
1 TraesCS6D01G080600 chr6D 46777517 46779629 2112 False 627.5 1055 82.365 548 2408 2 chr6D.!!$F3 1860
2 TraesCS6D01G080600 chr6B 115524339 115526719 2380 False 3807.0 3807 95.453 1 2396 1 chr6B.!!$F4 2395
3 TraesCS6D01G080600 chr6B 115022557 115024150 1593 False 2603.0 2603 96.118 1232 2827 1 chr6B.!!$F3 1595
4 TraesCS6D01G080600 chr6B 114879145 114882019 2874 False 1965.5 3151 90.662 36 2827 2 chr6B.!!$F6 2791
5 TraesCS6D01G080600 chr6B 115012563 115013554 991 False 1583.0 1583 95.468 244 1236 1 chr6B.!!$F2 992
6 TraesCS6D01G080600 chr6B 115057783 115062486 4703 False 1560.0 3033 91.891 36 2827 3 chr6B.!!$F7 2791
7 TraesCS6D01G080600 chr3D 569895117 569896806 1689 False 1258.0 1258 80.516 1120 2784 1 chr3D.!!$F1 1664
8 TraesCS6D01G080600 chr3D 567410844 567412542 1698 True 1219.0 1219 80.070 1112 2784 1 chr3D.!!$R1 1672

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
484 487 1.333636 CGAGCTTCTCCACCCATCCT 61.334 60.0 0.0 0.0 0.0 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2280 4515 1.114627 GAATGTGGGAGGCCAAATCC 58.885 55.0 5.01 2.48 35.99 3.01 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 6.655003 CACCATTGTTTCATAGGTCTGTTAGT 59.345 38.462 0.00 0.00 0.00 2.24
207 210 4.094442 GGTACCACGACAAAAATCATCTCC 59.906 45.833 7.15 0.00 0.00 3.71
218 221 2.765689 ATCATCTCCCCTCTCGTCTT 57.234 50.000 0.00 0.00 0.00 3.01
219 222 3.885976 ATCATCTCCCCTCTCGTCTTA 57.114 47.619 0.00 0.00 0.00 2.10
241 244 2.432510 CTCTCTCTGGCGATTAGGGTTT 59.567 50.000 0.00 0.00 0.00 3.27
484 487 1.333636 CGAGCTTCTCCACCCATCCT 61.334 60.000 0.00 0.00 0.00 3.24
651 2472 7.426929 ACACACACAAAAAGCAAACAAAATA 57.573 28.000 0.00 0.00 0.00 1.40
679 2500 7.133891 GGTATAGCACATACCAATCACATTC 57.866 40.000 18.07 0.00 42.68 2.67
987 3102 1.839894 GGGTGCTGAGATAAGGGGG 59.160 63.158 0.00 0.00 0.00 5.40
1008 3123 3.100671 GGGTAGATAGGCGATGAATCCT 58.899 50.000 0.00 0.00 36.51 3.24
1142 3357 2.346803 TGCTGCTATTTCAGGTTCGAC 58.653 47.619 0.00 0.00 34.74 4.20
1314 3529 0.375454 CGTCTGCAAACGTTGGTTCA 59.625 50.000 3.92 0.00 37.86 3.18
1350 3565 2.985456 CCTTCCTCTGCCGCTTCT 59.015 61.111 0.00 0.00 0.00 2.85
1356 3571 1.375140 CTCTGCCGCTTCTGCAAGA 60.375 57.895 0.00 0.00 44.68 3.02
1402 3617 2.691409 TATTTCAAGACCAGGGCGAG 57.309 50.000 0.00 0.00 0.00 5.03
1644 3877 0.902984 ATGCTACGGACACCAGGACA 60.903 55.000 0.00 0.00 0.00 4.02
1663 3896 7.363880 CCAGGACAGCTATTTCTACAAGTTCTA 60.364 40.741 0.00 0.00 0.00 2.10
1691 3924 5.659079 ACTCCTATTCGAAGAAGAAGGTGAT 59.341 40.000 3.35 0.00 45.90 3.06
1824 4057 1.377725 CAGCTTCCTTGTCGGCCAT 60.378 57.895 2.24 0.00 0.00 4.40
1843 4076 5.532406 GGCCATAGATACTGAATTCTTTGCA 59.468 40.000 7.05 0.00 0.00 4.08
1851 4084 4.539870 ACTGAATTCTTTGCATGTTGACG 58.460 39.130 7.05 0.00 0.00 4.35
1873 4106 2.071778 AAAATCTACATGGCGGCCAT 57.928 45.000 28.37 28.37 46.37 4.40
1893 4126 4.687483 CCATCCAAACTGAAATTCTTGTGC 59.313 41.667 0.00 0.00 0.00 4.57
2124 4358 5.397360 TGAGGATGCCTGATCTTACAGATA 58.603 41.667 0.00 0.00 39.94 1.98
2148 4382 2.241176 GTGTGGATAAATCAGGTGGGGA 59.759 50.000 0.00 0.00 0.00 4.81
2280 4515 3.448686 GTCGTGTCCATCCTTGTATGAG 58.551 50.000 0.00 0.00 0.00 2.90
2382 4617 2.483583 TGTTTTTGTGTGGTCGCATC 57.516 45.000 0.00 0.00 33.92 3.91
2555 4791 7.599621 CCTCAAGATATCATGTCTCAGATTGTC 59.400 40.741 5.32 0.00 0.00 3.18
2571 4807 7.211573 TCAGATTGTCAATGCTGATTGTTTTT 58.788 30.769 16.97 0.00 40.09 1.94
2606 4842 9.038803 GTCGTATAATAGAGTTAAGGGGTTTTG 57.961 37.037 0.00 0.00 0.00 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 4.404715 GCTTCCACCATACTAACAGACCTA 59.595 45.833 0.00 0.00 0.00 3.08
28 29 4.156922 CGTGTATTTTTGGCTTCCACCATA 59.843 41.667 0.00 0.00 40.13 2.74
207 210 3.202906 CAGAGAGAGTAAGACGAGAGGG 58.797 54.545 0.00 0.00 0.00 4.30
218 221 2.175069 ACCCTAATCGCCAGAGAGAGTA 59.825 50.000 0.00 0.00 0.00 2.59
219 222 1.063567 ACCCTAATCGCCAGAGAGAGT 60.064 52.381 0.00 0.00 0.00 3.24
484 487 4.408821 CTTGCGGTGGGGCAGCTA 62.409 66.667 0.00 0.00 44.94 3.32
614 2435 1.871039 GTGTGTGTAGCAATCAACGGT 59.129 47.619 0.00 0.00 0.00 4.83
623 2444 3.857549 TTGCTTTTTGTGTGTGTAGCA 57.142 38.095 0.00 0.00 36.90 3.49
987 3102 3.100671 AGGATTCATCGCCTATCTACCC 58.899 50.000 0.00 0.00 31.31 3.69
1008 3123 1.444933 ACCAGTGGGGAATCTCAACA 58.555 50.000 15.21 0.00 41.15 3.33
1115 3330 0.038021 TGAAATAGCAGCAGCCACCA 59.962 50.000 0.00 0.00 43.56 4.17
1142 3357 1.302511 CACTGAGTTGGGAACGGGG 60.303 63.158 0.00 0.00 36.23 5.73
1350 3565 4.424711 GGGCGGGTGGATCTTGCA 62.425 66.667 0.00 0.00 0.00 4.08
1663 3896 7.982354 CACCTTCTTCTTCGAATAGGAGTTTAT 59.018 37.037 0.00 0.00 0.00 1.40
1691 3924 4.245660 GCACACAGAAGTATGACAAGCTA 58.754 43.478 0.00 0.00 0.00 3.32
1824 4057 8.668353 GTCAACATGCAAAGAATTCAGTATCTA 58.332 33.333 8.44 0.00 0.00 1.98
1843 4076 6.292865 CGCCATGTAGATTTTATCGTCAACAT 60.293 38.462 0.00 0.00 0.00 2.71
1851 4084 3.146066 TGGCCGCCATGTAGATTTTATC 58.854 45.455 8.43 0.00 0.00 1.75
1873 4106 4.202141 CCAGCACAAGAATTTCAGTTTGGA 60.202 41.667 12.31 0.00 0.00 3.53
1893 4126 2.787994 ACTTGAGGCTGTCAAATCCAG 58.212 47.619 0.00 0.00 44.83 3.86
2124 4358 2.242196 CCACCTGATTTATCCACACCCT 59.758 50.000 0.00 0.00 0.00 4.34
2148 4382 7.869429 CCTCAAGAAAACAAACTCAGCATTTAT 59.131 33.333 0.00 0.00 0.00 1.40
2280 4515 1.114627 GAATGTGGGAGGCCAAATCC 58.885 55.000 5.01 2.48 35.99 3.01
2555 4791 7.911205 ACAACATTTCAAAAACAATCAGCATTG 59.089 29.630 0.00 0.00 44.57 2.82
2606 4842 1.251251 ACACAAGAATGCTTCCAGGC 58.749 50.000 0.00 0.00 30.14 4.85
2659 4907 6.541278 TCTCAATCAGAAGACATGCATAAAGG 59.459 38.462 0.00 0.00 0.00 3.11
2660 4908 7.549615 TCTCAATCAGAAGACATGCATAAAG 57.450 36.000 0.00 0.00 0.00 1.85
2670 4918 5.527951 AGCGATACATCTCAATCAGAAGAC 58.472 41.667 0.00 0.00 33.62 3.01


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

AutoCloner maintained by Alex Coulton.