Multiple sequence alignment - TraesCS6D01G258700

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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 TraesCS6D01G258700 chr6D 100.000 2666 0 0 1 2666 364850812 364848147 0.000000e+00 4924
1 TraesCS6D01G258700 chr6D 91.290 620 35 13 2016 2631 98077527 98078131 0.000000e+00 828
2 TraesCS6D01G258700 chr6D 95.789 380 14 1 2011 2388 49185689 49185310 1.750000e-171 612
3 TraesCS6D01G258700 chr6A 90.387 1602 83 35 462 2019 506185836 506184262 0.000000e+00 2039
4 TraesCS6D01G258700 chr6A 89.560 182 13 4 140 316 506186598 506186418 2.670000e-55 226
5 TraesCS6D01G258700 chr6A 95.833 72 3 0 67 138 506186718 506186647 1.680000e-22 117
6 TraesCS6D01G258700 chr6B 92.482 1277 53 15 771 2019 578688895 578687634 0.000000e+00 1786
7 TraesCS6D01G258700 chr6B 91.972 1283 54 15 771 2019 549714595 549713328 0.000000e+00 1753
8 TraesCS6D01G258700 chr6B 90.939 607 27 11 140 733 549716260 549715669 0.000000e+00 791
9 TraesCS6D01G258700 chr6B 93.077 130 8 1 14 142 549716434 549716305 3.500000e-44 189
10 TraesCS6D01G258700 chr3D 91.807 476 24 9 2015 2488 612020075 612019613 0.000000e+00 649
11 TraesCS6D01G258700 chr3D 90.737 475 27 11 2017 2488 325186140 325185680 3.770000e-173 617
12 TraesCS6D01G258700 chr3D 95.733 375 14 1 2016 2388 154427798 154427424 1.060000e-168 603
13 TraesCS6D01G258700 chr3D 96.429 280 8 2 2389 2666 612019660 612019381 6.720000e-126 460
14 TraesCS6D01G258700 chr3D 95.714 280 9 3 2389 2666 12056120 12055842 5.240000e-122 448
15 TraesCS6D01G258700 chr3D 95.018 281 9 5 2389 2666 461319982 461320260 1.130000e-118 436
16 TraesCS6D01G258700 chr4D 96.011 376 11 3 2016 2388 35124711 35124337 2.270000e-170 608
17 TraesCS6D01G258700 chr4D 90.234 471 30 10 2017 2485 364026895 364026439 3.800000e-168 601
18 TraesCS6D01G258700 chr4D 95.341 279 10 3 2390 2666 398675033 398675310 8.760000e-120 440
19 TraesCS6D01G258700 chr1D 96.011 376 11 3 2016 2388 463249903 463250277 2.270000e-170 608
20 TraesCS6D01G258700 chr2D 95.515 379 14 2 2012 2388 321080992 321081369 1.060000e-168 603
21 TraesCS6D01G258700 chr2D 95.341 279 10 3 2389 2666 539164732 539165008 8.760000e-120 440
22 TraesCS6D01G258700 chr7D 95.699 279 10 2 2389 2666 613487626 613487349 5.240000e-122 448
23 TraesCS6D01G258700 chr7D 95.357 280 9 4 2389 2666 510702465 510702188 2.440000e-120 442
24 TraesCS6D01G258700 chr7D 94.982 279 11 3 2389 2666 215100385 215100661 4.080000e-118 435
25 TraesCS6D01G258700 chr5D 95.357 280 10 3 2389 2666 432006538 432006260 2.440000e-120 442


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 TraesCS6D01G258700 chr6D 364848147 364850812 2665 True 4924.0 4924 100.000000 1 2666 1 chr6D.!!$R2 2665
1 TraesCS6D01G258700 chr6D 98077527 98078131 604 False 828.0 828 91.290000 2016 2631 1 chr6D.!!$F1 615
2 TraesCS6D01G258700 chr6A 506184262 506186718 2456 True 794.0 2039 91.926667 67 2019 3 chr6A.!!$R1 1952
3 TraesCS6D01G258700 chr6B 578687634 578688895 1261 True 1786.0 1786 92.482000 771 2019 1 chr6B.!!$R1 1248
4 TraesCS6D01G258700 chr6B 549713328 549716434 3106 True 911.0 1753 91.996000 14 2019 3 chr6B.!!$R2 2005
5 TraesCS6D01G258700 chr3D 612019381 612020075 694 True 554.5 649 94.118000 2015 2666 2 chr3D.!!$R4 651

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
714 1211 0.034896 CCAGTAGTGCTTGGTCCGTT 59.965 55.0 0.0 0.0 0.0 4.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1682 3261 0.111045 CGAGACTCCATCGACGATCG 60.111 60.0 14.88 14.88 42.76 3.69 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
174 222 0.037303 TCCGGACCTCTACTTGTCGT 59.963 55.000 0.00 0.00 32.19 4.34
187 235 6.484540 TCTACTTGTCGTTCGCTAATCTTAG 58.515 40.000 0.00 0.00 0.00 2.18
271 319 7.386851 ACTGATTTTCATCTACGGAGAAGAAA 58.613 34.615 21.13 21.13 43.92 2.52
277 325 6.531503 TCATCTACGGAGAAGAAAATCACT 57.468 37.500 0.00 0.00 34.61 3.41
280 328 5.955488 TCTACGGAGAAGAAAATCACTGAG 58.045 41.667 0.00 0.00 0.00 3.35
333 386 4.082523 GCGGTGACCAGCAGGCTA 62.083 66.667 12.33 0.00 39.06 3.93
334 387 2.125512 CGGTGACCAGCAGGCTAC 60.126 66.667 1.11 0.00 39.06 3.58
335 388 2.269241 GGTGACCAGCAGGCTACC 59.731 66.667 0.00 5.78 39.06 3.18
336 389 2.592993 GGTGACCAGCAGGCTACCA 61.593 63.158 14.26 0.00 41.47 3.25
352 405 3.381908 GCTACCACTAGCAGTGTATCACT 59.618 47.826 13.06 0.00 46.51 3.41
605 1094 5.569413 GTTAATTCAGATTAACCACCAGCG 58.431 41.667 9.71 0.00 46.15 5.18
606 1095 2.851263 TTCAGATTAACCACCAGCGT 57.149 45.000 0.00 0.00 0.00 5.07
607 1096 2.093306 TCAGATTAACCACCAGCGTG 57.907 50.000 0.00 0.00 39.91 5.34
608 1097 1.621317 TCAGATTAACCACCAGCGTGA 59.379 47.619 0.00 0.00 43.14 4.35
714 1211 0.034896 CCAGTAGTGCTTGGTCCGTT 59.965 55.000 0.00 0.00 0.00 4.44
735 1232 2.208619 TCGACCGCCCAACCTGTTA 61.209 57.895 0.00 0.00 0.00 2.41
769 1287 0.599558 GCACACTACGAGGTACACCA 59.400 55.000 0.38 0.00 38.89 4.17
843 2385 0.255890 TAATGCCTTCTCCCCAGCAC 59.744 55.000 0.00 0.00 38.21 4.40
888 2430 0.541392 TGATCTTGTCATGTCCCGGG 59.459 55.000 16.85 16.85 0.00 5.73
889 2431 0.541863 GATCTTGTCATGTCCCGGGT 59.458 55.000 22.86 0.00 0.00 5.28
1029 2589 2.169144 ACCAGAATCAGATCATCACGCA 59.831 45.455 0.00 0.00 0.00 5.24
1032 2592 3.619929 CAGAATCAGATCATCACGCACAA 59.380 43.478 0.00 0.00 0.00 3.33
1106 2668 1.238439 ATTGGTGAACAGAACAGGCG 58.762 50.000 0.00 0.00 0.00 5.52
1185 2747 4.530857 ATCGGCTTCGGCTTCGGG 62.531 66.667 0.00 0.00 41.44 5.14
1273 2835 2.253758 GCCAAGCTGCTGACGTTCA 61.254 57.895 1.35 0.00 0.00 3.18
1275 2837 0.445436 CCAAGCTGCTGACGTTCATC 59.555 55.000 1.35 0.00 0.00 2.92
1628 3207 3.053291 GTTTGGATCGCGTGGGCA 61.053 61.111 5.77 0.00 39.92 5.36
1702 3281 0.236187 GATCGTCGATGGAGTCTCGG 59.764 60.000 13.54 0.00 36.78 4.63
1717 3296 2.166664 GTCTCGGGATGTGAAACTAGCT 59.833 50.000 0.00 0.00 38.04 3.32
1718 3297 3.380637 GTCTCGGGATGTGAAACTAGCTA 59.619 47.826 0.00 0.00 38.04 3.32
1719 3298 3.632604 TCTCGGGATGTGAAACTAGCTAG 59.367 47.826 19.44 19.44 38.04 3.42
1720 3299 2.100916 TCGGGATGTGAAACTAGCTAGC 59.899 50.000 20.91 6.62 38.04 3.42
1721 3300 2.159099 CGGGATGTGAAACTAGCTAGCA 60.159 50.000 20.91 10.34 38.04 3.49
1880 3464 6.228258 TCTTGTACATTTCCAGGTGTAAGAC 58.772 40.000 0.00 0.00 33.05 3.01
1931 3515 2.061773 CACAACTAAGGTCTGACTGCG 58.938 52.381 7.85 0.00 0.00 5.18
2133 3720 2.353269 CAGTTTTTGTGTGCCACGTAGA 59.647 45.455 0.00 0.00 37.14 2.59
2285 3872 1.014352 GCGTTTATCACTTCGCCCAT 58.986 50.000 0.00 0.00 42.33 4.00
2317 3904 1.422977 TAGCCCACACCCAAAGCTGA 61.423 55.000 0.00 0.00 35.03 4.26
2353 3940 5.012251 TGTTTCTACAGGTACATGGCAACTA 59.988 40.000 12.79 0.00 37.61 2.24
2403 4029 0.179124 CTCTCAACTGCCCTAGCGTC 60.179 60.000 0.00 0.00 44.31 5.19
2559 4187 2.028876 GTGTTTAGTGGGTGGCAACTT 58.971 47.619 0.97 0.00 37.61 2.66
2607 4235 3.384789 GCAGTAGACCAGACCATACATGA 59.615 47.826 0.00 0.00 0.00 3.07
2614 4242 3.327757 ACCAGACCATACATGACAACTGT 59.672 43.478 0.00 0.00 0.00 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 3.470567 CGAGGTTGTCGTCGCTGC 61.471 66.667 0.00 0.00 44.20 5.25
151 199 1.001145 AAGTAGAGGTCCGGAGCGT 60.001 57.895 26.86 20.33 0.00 5.07
220 268 1.737793 GAATTCGATTGCTTCCCACGT 59.262 47.619 0.00 0.00 0.00 4.49
271 319 1.211457 GGGGTGATCTGCTCAGTGATT 59.789 52.381 0.00 0.00 33.51 2.57
277 325 2.060383 CCTCGGGGTGATCTGCTCA 61.060 63.158 0.00 0.00 0.00 4.26
280 328 4.554036 GCCCTCGGGGTGATCTGC 62.554 72.222 0.00 0.00 46.51 4.26
352 405 1.643310 CCCAGGCCAAATCTTTTCCA 58.357 50.000 5.01 0.00 0.00 3.53
384 438 4.648626 TGGTGTCCAGCTGCTGCC 62.649 66.667 23.86 18.74 40.80 4.85
602 1091 1.008424 CGACACAGTCACTCACGCT 60.008 57.895 0.00 0.00 32.09 5.07
604 1093 0.660595 GGTCGACACAGTCACTCACG 60.661 60.000 18.91 0.00 32.09 4.35
605 1094 0.660595 CGGTCGACACAGTCACTCAC 60.661 60.000 18.91 0.00 32.09 3.51
606 1095 1.099295 ACGGTCGACACAGTCACTCA 61.099 55.000 18.91 0.00 32.09 3.41
607 1096 0.385723 GACGGTCGACACAGTCACTC 60.386 60.000 23.79 3.57 44.59 3.51
608 1097 1.653115 GACGGTCGACACAGTCACT 59.347 57.895 23.79 0.91 44.59 3.41
769 1287 3.756434 CCGTGTAAAATGTGATGGGAACT 59.244 43.478 0.00 0.00 0.00 3.01
843 2385 2.014128 CCCATTAGTTTACGGTGCTGG 58.986 52.381 0.00 0.00 0.00 4.85
1029 2589 2.530151 TCCTCCTGGCTGGCTTGT 60.530 61.111 5.39 0.00 35.26 3.16
1073 2635 4.844065 CAATACGTGGCGTGCGCG 62.844 66.667 16.86 16.86 41.39 6.86
1074 2636 4.514569 CCAATACGTGGCGTGCGC 62.515 66.667 8.17 8.17 41.72 6.09
1088 2650 1.444119 GCGCCTGTTCTGTTCACCAA 61.444 55.000 0.00 0.00 0.00 3.67
1266 2828 1.872679 GACGAGGCCGATGAACGTC 60.873 63.158 16.93 16.93 44.19 4.34
1315 2877 2.841988 GCCGCCTCTCCTGGAGAT 60.842 66.667 25.82 0.00 44.45 2.75
1458 3032 2.471255 GGAGTTGGTCCGCATGAAG 58.529 57.895 0.00 0.00 34.84 3.02
1628 3207 2.438021 TGTTCCAGCTAGTTGTTCCACT 59.562 45.455 5.81 0.00 0.00 4.00
1682 3261 0.111045 CGAGACTCCATCGACGATCG 60.111 60.000 14.88 14.88 42.76 3.69
1683 3262 0.236187 CCGAGACTCCATCGACGATC 59.764 60.000 7.54 0.00 42.76 3.69
1684 3263 1.167155 CCCGAGACTCCATCGACGAT 61.167 60.000 4.05 4.05 42.76 3.73
1702 3281 5.694006 CACTATGCTAGCTAGTTTCACATCC 59.306 44.000 21.62 2.71 0.00 3.51
1739 3318 3.223435 CACCTCTGTACTCCATCGGTAT 58.777 50.000 0.00 0.00 0.00 2.73
1743 3322 4.082408 TGTTTACACCTCTGTACTCCATCG 60.082 45.833 0.00 0.00 32.28 3.84
1880 3464 3.132646 AGAGCCTCATGCAGAAAGTCTAG 59.867 47.826 0.00 0.00 44.83 2.43
1931 3515 6.255596 TCTATCGTGTAGTAGAATCCATGC 57.744 41.667 0.00 0.00 0.00 4.06
2133 3720 0.537371 GCCCACACACCAGCTTAGTT 60.537 55.000 0.00 0.00 0.00 2.24
2196 3783 0.534203 CTAAACGCCCACACACCAGT 60.534 55.000 0.00 0.00 0.00 4.00
2222 3809 0.746563 CGTGAAACTGGTGTGTGGGT 60.747 55.000 0.00 0.00 31.75 4.51
2285 3872 2.517875 GGCTAGGAGACGGGCGTA 60.518 66.667 0.00 0.00 34.43 4.42
2317 3904 3.550820 TGTAGAAACACATGGCAACTGT 58.449 40.909 0.00 0.00 37.61 3.55
2403 4029 5.312120 AGAGTTGACATCTACTTACGTGG 57.688 43.478 0.00 0.00 32.36 4.94
2418 4044 6.707440 TGCCATGTAAAAAGAAAGAGTTGA 57.293 33.333 0.00 0.00 0.00 3.18
2559 4187 7.652909 CAGTTGCCATGATTTCAAAACTTTAGA 59.347 33.333 0.00 0.00 0.00 2.10
2614 4242 4.202419 ACAGTTGCCATGGTTACTCAACTA 60.202 41.667 25.16 0.00 43.59 2.24
2643 4271 1.375396 CTTCGGTTGCCATGACGGA 60.375 57.895 0.00 0.00 36.56 4.69


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

AutoCloner maintained by Alex Coulton.