Multiple sequence alignment - TraesCS6D01G256000

Loading Multiple Alignment...

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 TraesCS6D01G256000 chr6D 100.000 3158 0 0 1 3158 361378651 361381808 0.000000e+00 5832.0
1 TraesCS6D01G256000 chr6D 97.782 496 11 0 2663 3158 361408654 361409149 0.000000e+00 856.0
2 TraesCS6D01G256000 chr6D 93.347 496 31 2 2663 3158 413140131 413140624 0.000000e+00 732.0
3 TraesCS6D01G256000 chr6A 94.990 2475 54 17 1 2433 502365117 502367563 0.000000e+00 3819.0
4 TraesCS6D01G256000 chr6A 97.175 177 5 0 2487 2663 502368032 502368208 1.840000e-77 300.0
5 TraesCS6D01G256000 chr6B 96.286 1804 28 8 699 2491 542584867 542586642 0.000000e+00 2924.0
6 TraesCS6D01G256000 chr6B 95.480 708 20 4 1 700 542584040 542584743 0.000000e+00 1120.0
7 TraesCS6D01G256000 chr6B 96.610 177 6 0 2487 2663 542586703 542586879 8.570000e-76 294.0
8 TraesCS6D01G256000 chr3D 94.862 506 24 2 2654 3158 186896502 186895998 0.000000e+00 789.0
9 TraesCS6D01G256000 chr3D 86.538 52 6 1 905 955 87339826 87339877 4.400000e-04 56.5
10 TraesCS6D01G256000 chr2D 94.970 497 23 2 2663 3158 335176120 335175625 0.000000e+00 778.0
11 TraesCS6D01G256000 chr2D 94.769 497 25 1 2663 3158 576687743 576688239 0.000000e+00 773.0
12 TraesCS6D01G256000 chr2D 94.366 497 26 2 2663 3158 335163366 335162871 0.000000e+00 761.0
13 TraesCS6D01G256000 chr2D 93.548 496 32 0 2663 3158 434215215 434214720 0.000000e+00 739.0
14 TraesCS6D01G256000 chr5D 93.548 496 31 1 2663 3158 84056295 84055801 0.000000e+00 737.0
15 TraesCS6D01G256000 chr1D 93.548 496 31 1 2663 3158 399753999 399753505 0.000000e+00 737.0
16 TraesCS6D01G256000 chr4D 78.916 498 99 6 1643 2137 101436892 101437386 1.820000e-87 333.0
17 TraesCS6D01G256000 chr4B 82.240 366 63 2 1773 2137 145371914 145372278 6.580000e-82 315.0
18 TraesCS6D01G256000 chr4B 79.286 140 23 6 408 544 53486721 53486585 3.350000e-15 93.5
19 TraesCS6D01G256000 chr4A 77.062 497 110 4 1652 2146 473946044 473945550 1.850000e-72 283.0


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 TraesCS6D01G256000 chr6D 361378651 361381808 3157 False 5832.0 5832 100.000000 1 3158 1 chr6D.!!$F1 3157
1 TraesCS6D01G256000 chr6A 502365117 502368208 3091 False 2059.5 3819 96.082500 1 2663 2 chr6A.!!$F1 2662
2 TraesCS6D01G256000 chr6B 542584040 542586879 2839 False 1446.0 2924 96.125333 1 2663 3 chr6B.!!$F1 2662
3 TraesCS6D01G256000 chr3D 186895998 186896502 504 True 789.0 789 94.862000 2654 3158 1 chr3D.!!$R1 504

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
435 467 0.109086 TTGCTAGTCTGCGAGTGCTC 60.109 55.0 0.0 0.0 43.34 4.26 F
1144 1321 0.322975 CACACACAAGGAGGAGGGAG 59.677 60.0 0.0 0.0 0.00 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1632 1809 3.326006 TGAAAGTGACATCTGCTTCCTCT 59.674 43.478 0.0 0.0 0.0 3.69 R
2925 3520 0.537188 GGAGTCGGCCTTCTTCATGA 59.463 55.000 0.0 0.0 0.0 3.07 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
267 299 0.938713 CTGACCTACTCGCCTAGTCG 59.061 60.000 0.00 0.00 39.80 4.18
286 318 4.193334 CGTCTGATCTCCGCCGCA 62.193 66.667 0.00 0.00 0.00 5.69
428 460 0.945743 TGCTGTGTTGCTAGTCTGCG 60.946 55.000 0.00 0.00 35.36 5.18
435 467 0.109086 TTGCTAGTCTGCGAGTGCTC 60.109 55.000 0.00 0.00 43.34 4.26
476 508 2.168521 ACTTGCGGCTCTAAATCTAGCA 59.831 45.455 0.00 0.00 40.61 3.49
688 728 3.002759 GGTTGTGTTCTTCTGCTCTGTTC 59.997 47.826 0.00 0.00 0.00 3.18
861 1026 0.543277 TATGGTCTGCTTGCTCCCAG 59.457 55.000 0.00 0.00 0.00 4.45
906 1071 7.872483 AGTTTTCACAAAATGTTGTTCTCTTGT 59.128 29.630 0.00 0.00 46.01 3.16
1016 1185 5.896678 AGCTGTCTATGTTCCTCTCTTATGT 59.103 40.000 0.00 0.00 0.00 2.29
1144 1321 0.322975 CACACACAAGGAGGAGGGAG 59.677 60.000 0.00 0.00 0.00 4.30
1203 1380 3.775316 AGGATATGGGTGTCGAGAAGTTT 59.225 43.478 0.00 0.00 0.00 2.66
1632 1809 2.032799 CGCAAAGCTGTTGGACACTAAA 59.967 45.455 9.63 0.00 0.00 1.85
2272 2452 5.560724 AGTGTAATAGCATGTGTGGAACTT 58.439 37.500 0.00 0.00 38.04 2.66
2335 2515 5.079643 ACAGTATCTTGTTGCTTTGGGAAT 58.920 37.500 0.00 0.00 0.00 3.01
2441 2621 7.040961 TCACATCATATACAATCTGGTGCATTG 60.041 37.037 0.00 0.00 37.29 2.82
2480 3010 1.393539 CGCATAATTATTCGAGGCCCG 59.606 52.381 11.43 2.55 40.25 6.13
2683 3278 1.078708 CGGAGTAAATGGCCACGGT 60.079 57.895 8.16 0.00 0.00 4.83
2727 3322 4.498177 GGCTCTTCGAAAAATTATCAGGCC 60.498 45.833 0.00 0.00 0.00 5.19
2732 3327 6.376864 TCTTCGAAAAATTATCAGGCCATTCA 59.623 34.615 5.01 0.00 0.00 2.57
2744 3339 0.457337 GCCATTCAAGCCTTCAAGCG 60.457 55.000 0.00 0.00 38.01 4.68
2755 3350 2.418628 GCCTTCAAGCGTACAAAGCATA 59.581 45.455 0.00 0.00 37.01 3.14
2758 3353 3.603158 TCAAGCGTACAAAGCATAGGA 57.397 42.857 0.00 0.00 37.01 2.94
2769 3364 2.444256 GCATAGGACCGCCTTCCCT 61.444 63.158 0.00 0.00 43.90 4.20
2770 3365 1.119574 GCATAGGACCGCCTTCCCTA 61.120 60.000 0.00 0.00 43.90 3.53
2804 3399 4.475135 GGCCGACTCCCAGAAGGC 62.475 72.222 0.00 0.00 46.51 4.35
2920 3515 0.836400 AGAAGGCCGACTCCCAGAAA 60.836 55.000 0.00 0.00 0.00 2.52
2925 3520 2.580601 CCGACTCCCAGAAACCGGT 61.581 63.158 0.00 0.00 33.02 5.28
2959 3554 3.984193 CTCCCAGAAGCCGGCCAAG 62.984 68.421 26.15 11.03 0.00 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
240 272 1.810532 GAGTAGGTCAGGCGTCTGG 59.189 63.158 18.55 0.00 41.23 3.86
267 299 2.024871 CGGCGGAGATCAGACGAC 59.975 66.667 1.73 2.68 45.38 4.34
428 460 4.391830 TCCAATTGTGTTAATCGAGCACTC 59.608 41.667 4.43 0.00 34.52 3.51
435 467 5.880054 AGTTCCTCCAATTGTGTTAATCG 57.120 39.130 4.43 0.00 0.00 3.34
861 1026 3.421844 ACTTCACAAACTAATGAGGGGC 58.578 45.455 0.00 0.00 0.00 5.80
906 1071 5.427036 AGTTGACGCGAATTTAGGAAAAA 57.573 34.783 15.93 0.00 0.00 1.94
1144 1321 1.063174 GGCGATCTCAAAGATGTGTGC 59.937 52.381 0.00 0.00 34.53 4.57
1632 1809 3.326006 TGAAAGTGACATCTGCTTCCTCT 59.674 43.478 0.00 0.00 0.00 3.69
2480 3010 3.350833 ACATTCATTCCTCACAGCTTCC 58.649 45.455 0.00 0.00 0.00 3.46
2523 3118 9.914834 AAATATAAGTACATCTAAGGGTTGCAA 57.085 29.630 0.00 0.00 0.00 4.08
2585 3180 7.373778 AGTGACCGAATAAATTGAGTAAACC 57.626 36.000 0.00 0.00 0.00 3.27
2636 3231 3.832490 GGTTTGGCCTTTGGAGTAAGATT 59.168 43.478 3.32 0.00 0.00 2.40
2683 3278 1.188863 GGGTGAGTCGGTTAGGCTAA 58.811 55.000 2.04 2.04 33.03 3.09
2699 3294 2.586648 ATTTTTCGAAGAGCCAGGGT 57.413 45.000 0.00 0.00 38.43 4.34
2727 3322 2.483877 TGTACGCTTGAAGGCTTGAATG 59.516 45.455 3.46 0.52 0.00 2.67
2732 3327 1.266989 GCTTTGTACGCTTGAAGGCTT 59.733 47.619 0.00 0.00 0.00 4.35
2741 3336 1.470979 CGGTCCTATGCTTTGTACGCT 60.471 52.381 0.00 0.00 0.00 5.07
2744 3339 1.134491 AGGCGGTCCTATGCTTTGTAC 60.134 52.381 0.00 0.00 42.06 2.90
2769 3364 1.155390 CCTGGGGATAGTCGGCCTA 59.845 63.158 0.00 0.00 0.00 3.93
2770 3365 2.122813 CCTGGGGATAGTCGGCCT 60.123 66.667 0.00 0.00 0.00 5.19
2776 3371 2.446036 GTCGGCCCTGGGGATAGT 60.446 66.667 16.03 0.00 37.50 2.12
2804 3399 1.344763 AGGTTTTCTGAGACTGGGTCG 59.655 52.381 0.00 0.00 37.67 4.79
2868 3463 0.612174 CTGGGAGTCGGTCCTCTTGA 60.612 60.000 4.92 0.00 46.06 3.02
2920 3515 1.299976 GGCCTTCTTCATGACCGGT 59.700 57.895 6.92 6.92 0.00 5.28
2925 3520 0.537188 GGAGTCGGCCTTCTTCATGA 59.463 55.000 0.00 0.00 0.00 3.07
2969 3564 3.214328 GTTATGTGGGCATAGTCTTGGG 58.786 50.000 0.00 0.00 38.64 4.12
2971 3566 2.872245 CCGTTATGTGGGCATAGTCTTG 59.128 50.000 0.00 0.00 38.64 3.02
2978 3573 2.224523 CCTATCACCGTTATGTGGGCAT 60.225 50.000 0.00 0.00 36.87 4.40


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

AutoCloner maintained by Alex Coulton.