Multiple sequence alignment - TraesCS4D01G153500

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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 TraesCS4D01G153500 chr4D 100.000 3033 0 0 1 3033 195023291 195020259 0.000000e+00 5602.0
1 TraesCS4D01G153500 chr4D 94.139 563 32 1 141 703 501080630 501080069 0.000000e+00 856.0
2 TraesCS4D01G153500 chr4D 94.526 548 28 2 156 702 50230987 50231533 0.000000e+00 845.0
3 TraesCS4D01G153500 chr4D 100.000 310 0 0 3515 3824 195019777 195019468 1.190000e-159 573.0
4 TraesCS4D01G153500 chr4B 96.603 2296 71 2 703 2991 150735005 150737300 0.000000e+00 3801.0
5 TraesCS4D01G153500 chr4B 98.065 310 6 0 3515 3824 150737312 150737621 1.210000e-149 540.0
6 TraesCS4D01G153500 chr4B 94.444 126 5 2 2 126 150732642 150732766 3.900000e-45 193.0
7 TraesCS4D01G153500 chr4B 97.727 44 0 1 110 153 150734969 150735011 1.470000e-09 75.0
8 TraesCS4D01G153500 chr4A 96.463 2290 79 2 703 2991 248836226 248833938 0.000000e+00 3779.0
9 TraesCS4D01G153500 chr4A 97.744 266 4 1 3515 3780 248833926 248833663 1.250000e-124 457.0
10 TraesCS4D01G153500 chr4A 94.079 152 1 3 2 153 248836363 248836220 1.380000e-54 224.0
11 TraesCS4D01G153500 chr1D 95.413 545 25 0 158 702 250740842 250741386 0.000000e+00 869.0
12 TraesCS4D01G153500 chr1D 94.679 545 29 0 158 702 19874692 19875236 0.000000e+00 846.0
13 TraesCS4D01G153500 chr5D 95.238 546 24 2 158 702 342526229 342525685 0.000000e+00 863.0
14 TraesCS4D01G153500 chr5D 95.064 547 21 5 158 702 397030347 397029805 0.000000e+00 856.0
15 TraesCS4D01G153500 chr1B 94.872 546 26 2 158 702 305284327 305284871 0.000000e+00 852.0
16 TraesCS4D01G153500 chr7D 94.033 553 32 1 151 702 521971260 521970708 0.000000e+00 837.0
17 TraesCS4D01G153500 chr6D 93.134 568 35 3 158 725 47270435 47269872 0.000000e+00 830.0
18 TraesCS4D01G153500 chr6D 100.000 44 0 0 2990 3033 436471947 436471990 8.800000e-12 82.4
19 TraesCS4D01G153500 chr7B 93.651 315 19 1 1733 2047 279842819 279843132 1.610000e-128 470.0
20 TraesCS4D01G153500 chr7A 100.000 43 0 0 2991 3033 105868412 105868370 3.170000e-11 80.5
21 TraesCS4D01G153500 chr7A 100.000 43 0 0 2991 3033 645908855 645908813 3.170000e-11 80.5
22 TraesCS4D01G153500 chr3B 100.000 43 0 0 2991 3033 450264827 450264785 3.170000e-11 80.5
23 TraesCS4D01G153500 chr3A 100.000 43 0 0 2991 3033 532327494 532327536 3.170000e-11 80.5
24 TraesCS4D01G153500 chr3A 100.000 42 0 0 2992 3033 469001978 469001937 1.140000e-10 78.7
25 TraesCS4D01G153500 chr6A 100.000 42 0 0 2992 3033 58708494 58708453 1.140000e-10 78.7
26 TraesCS4D01G153500 chr2A 100.000 42 0 0 2992 3033 743528777 743528818 1.140000e-10 78.7
27 TraesCS4D01G153500 chr2D 95.745 47 2 0 2987 3033 562213057 562213103 4.100000e-10 76.8


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 TraesCS4D01G153500 chr4D 195019468 195023291 3823 True 3087.500000 5602 100.000000 1 3824 2 chr4D.!!$R2 3823
1 TraesCS4D01G153500 chr4D 501080069 501080630 561 True 856.000000 856 94.139000 141 703 1 chr4D.!!$R1 562
2 TraesCS4D01G153500 chr4D 50230987 50231533 546 False 845.000000 845 94.526000 156 702 1 chr4D.!!$F1 546
3 TraesCS4D01G153500 chr4B 150732642 150737621 4979 False 1152.250000 3801 96.709750 2 3824 4 chr4B.!!$F1 3822
4 TraesCS4D01G153500 chr4A 248833663 248836363 2700 True 1486.666667 3779 96.095333 2 3780 3 chr4A.!!$R1 3778
5 TraesCS4D01G153500 chr1D 250740842 250741386 544 False 869.000000 869 95.413000 158 702 1 chr1D.!!$F2 544
6 TraesCS4D01G153500 chr1D 19874692 19875236 544 False 846.000000 846 94.679000 158 702 1 chr1D.!!$F1 544
7 TraesCS4D01G153500 chr5D 342525685 342526229 544 True 863.000000 863 95.238000 158 702 1 chr5D.!!$R1 544
8 TraesCS4D01G153500 chr5D 397029805 397030347 542 True 856.000000 856 95.064000 158 702 1 chr5D.!!$R2 544
9 TraesCS4D01G153500 chr1B 305284327 305284871 544 False 852.000000 852 94.872000 158 702 1 chr1B.!!$F1 544
10 TraesCS4D01G153500 chr7D 521970708 521971260 552 True 837.000000 837 94.033000 151 702 1 chr7D.!!$R1 551
11 TraesCS4D01G153500 chr6D 47269872 47270435 563 True 830.000000 830 93.134000 158 725 1 chr6D.!!$R1 567

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
645 2865 0.247537 GCCGCGTGAAATAGTTTCGG 60.248 55.000 4.92 0.0 42.55 4.30 F
1546 3773 0.677098 CCAGTGCTCTGCTGATGCTT 60.677 55.000 10.32 0.0 40.09 3.91 F
2217 4444 1.001181 GATGTTGCAAATGCCACCAGT 59.999 47.619 0.00 0.0 41.18 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2025 4252 0.250467 TCAGGCTGTCCAACTGCTTC 60.250 55.000 15.27 0.00 41.90 3.86 R
2631 4858 1.133199 TCTGCCTTCAACACCCCAATT 60.133 47.619 0.00 0.00 0.00 2.32 R
3611 5838 5.045505 TCCAACAGGCATGTAAGGTATGTAA 60.046 40.000 18.65 0.62 39.29 2.41 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
180 2399 5.563867 GCAAATTTGACCTGTGGACGAAATA 60.564 40.000 22.31 0.00 0.00 1.40
231 2450 1.214367 TTCACGCGACTGACCTTTTC 58.786 50.000 15.93 0.00 0.00 2.29
251 2470 2.659244 GTGACGCCCGACACGAAA 60.659 61.111 7.43 0.00 32.16 3.46
267 2486 2.924903 CGAAAGCGTCACACTACACTA 58.075 47.619 0.00 0.00 0.00 2.74
330 2549 1.623311 GCACCCCAAACTGCCTAAAAT 59.377 47.619 0.00 0.00 0.00 1.82
444 2663 4.644685 ACAAAATGAAGCAACCACTAGTGT 59.355 37.500 21.18 7.09 0.00 3.55
493 2712 6.968862 ACTATATAGTGTGGCGTCTAGCTCTT 60.969 42.308 14.71 0.00 39.62 2.85
529 2748 8.041323 ACACTGACTTAGTAATTTTCGGATCAT 58.959 33.333 0.00 0.00 37.60 2.45
644 2864 0.719465 AGCCGCGTGAAATAGTTTCG 59.281 50.000 4.92 0.00 42.55 3.46
645 2865 0.247537 GCCGCGTGAAATAGTTTCGG 60.248 55.000 4.92 0.00 42.55 4.30
703 2923 4.821260 GGTCAAATTTGTCAATTTTGCCCT 59.179 37.500 18.85 0.00 40.09 5.19
705 2925 4.749099 TCAAATTTGTCAATTTTGCCCTCG 59.251 37.500 20.61 4.60 40.09 4.63
706 2926 4.335400 AATTTGTCAATTTTGCCCTCGT 57.665 36.364 0.00 0.00 0.00 4.18
707 2927 3.363341 TTTGTCAATTTTGCCCTCGTC 57.637 42.857 0.00 0.00 0.00 4.20
708 2928 2.270352 TGTCAATTTTGCCCTCGTCT 57.730 45.000 0.00 0.00 0.00 4.18
1031 3258 5.014649 AGGGCAAGAATAAGAAGAAGAAGGT 59.985 40.000 0.00 0.00 0.00 3.50
1203 3430 2.747460 GGAGAACATGCTGCGCCA 60.747 61.111 4.18 0.00 0.00 5.69
1314 3541 3.419580 ATGCCCCCGGATTCAGCA 61.420 61.111 0.73 4.46 37.94 4.41
1357 3584 2.176273 CCTTCGATTGAGGCAGCCG 61.176 63.158 5.55 0.00 0.00 5.52
1546 3773 0.677098 CCAGTGCTCTGCTGATGCTT 60.677 55.000 10.32 0.00 40.09 3.91
1578 3805 2.111384 GATCTGGAGCCTGTGGTCTTA 58.889 52.381 0.00 0.00 39.02 2.10
1779 4006 4.516195 GAGCTCCTCCGCGGGAAC 62.516 72.222 27.83 11.14 34.66 3.62
2025 4252 4.440880 AGGAGAAGCTTGATGAGAAATCG 58.559 43.478 2.10 0.00 0.00 3.34
2047 4274 1.630369 AGCAGTTGGACAGCCTGATAA 59.370 47.619 0.00 0.00 30.21 1.75
2078 4305 2.565841 GGAAATGGAGGTGAAGATCCG 58.434 52.381 0.00 0.00 38.52 4.18
2217 4444 1.001181 GATGTTGCAAATGCCACCAGT 59.999 47.619 0.00 0.00 41.18 4.00
2631 4858 0.976641 ATGCTGAGAAGGACCGTGAA 59.023 50.000 0.00 0.00 0.00 3.18
2670 4897 3.503748 CAGAAGCACTAAACAAGGAAGGG 59.496 47.826 0.00 0.00 0.00 3.95
2778 5005 2.126071 CTGTGCCCTACCACGACG 60.126 66.667 0.00 0.00 38.55 5.12
2839 5066 3.495001 CCGGTGAACAGAGAACTCTTTTC 59.505 47.826 18.18 18.18 43.22 2.29
2853 5080 3.699538 ACTCTTTTCCTCGCCTTTTGTTT 59.300 39.130 0.00 0.00 0.00 2.83
2991 5218 5.296531 GTGTTTGCATGTTTTCCTGGAATTT 59.703 36.000 10.45 0.00 0.00 1.82
2992 5219 5.884792 TGTTTGCATGTTTTCCTGGAATTTT 59.115 32.000 10.45 0.00 0.00 1.82
2993 5220 6.376581 TGTTTGCATGTTTTCCTGGAATTTTT 59.623 30.769 10.45 0.00 0.00 1.94
3030 5257 5.778134 GCAAAAGTGCGTATCATTTCATTG 58.222 37.500 0.00 0.00 41.93 2.82
3031 5258 5.572511 GCAAAAGTGCGTATCATTTCATTGA 59.427 36.000 0.00 0.00 41.93 2.57
3032 5259 6.254157 GCAAAAGTGCGTATCATTTCATTGAT 59.746 34.615 0.00 0.00 41.93 2.57
3611 5838 6.323996 TGATAGGATAATGAGAACCTGTCGTT 59.676 38.462 0.00 0.00 41.37 3.85
3662 5889 7.224753 TCGGCTCTATAAACAAATCTGAATGTC 59.775 37.037 0.72 0.00 0.00 3.06
3811 6038 6.903883 TGTAGCTCGATTGGAAATAAAGTC 57.096 37.500 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
93 94 0.476771 TCGCTTCTTTTTCCCCCACT 59.523 50.000 0.00 0.00 0.00 4.00
100 101 0.450645 GTCGCCGTCGCTTCTTTTTC 60.451 55.000 0.00 0.00 35.26 2.29
180 2399 6.877611 ACGGACAGTTTATTCTGTGATTTT 57.122 33.333 4.06 0.00 46.81 1.82
220 2439 1.873591 GCGTCACATGAAAAGGTCAGT 59.126 47.619 0.00 0.00 40.43 3.41
231 2450 3.478394 CGTGTCGGGCGTCACATG 61.478 66.667 0.00 0.00 34.69 3.21
251 2470 1.544246 TGCATAGTGTAGTGTGACGCT 59.456 47.619 3.41 3.41 42.68 5.07
267 2486 3.325293 CCTATCTATGAGGCGTTGCAT 57.675 47.619 0.00 0.00 0.00 3.96
330 2549 3.058016 GCTCTGCACAATGACTTAGCAAA 60.058 43.478 0.00 0.00 34.45 3.68
493 2712 2.048222 GTCAGTGTGCAGCGCCTA 60.048 61.111 2.29 0.00 0.00 3.93
1057 3284 2.202703 GTCGCCGTTGACCGCTAT 60.203 61.111 0.00 0.00 32.61 2.97
1552 3779 2.522923 AGGCTCCAGATCGGCGAT 60.523 61.111 24.26 24.26 33.14 4.58
1800 4027 3.195396 CCAATTGGGTGACATTTTCGGAT 59.805 43.478 17.36 0.00 0.00 4.18
2025 4252 0.250467 TCAGGCTGTCCAACTGCTTC 60.250 55.000 15.27 0.00 41.90 3.86
2047 4274 1.002134 CCATTTCCGCCTCACTGGT 60.002 57.895 0.00 0.00 38.35 4.00
2217 4444 6.460537 CGTCAGCCACCACTATGTTATACTTA 60.461 42.308 0.00 0.00 0.00 2.24
2445 4672 1.444212 GGTACCGTTCAGCGCGTTA 60.444 57.895 8.43 0.00 39.71 3.18
2448 4675 2.098233 AATGGTACCGTTCAGCGCG 61.098 57.895 13.90 0.00 39.71 6.86
2552 4779 4.594920 TGTCTCCTTCAGATTTCTCCTTGT 59.405 41.667 0.00 0.00 32.08 3.16
2631 4858 1.133199 TCTGCCTTCAACACCCCAATT 60.133 47.619 0.00 0.00 0.00 2.32
2670 4897 1.506493 CATTCAGGCTACCGATCTGC 58.494 55.000 0.00 0.00 0.00 4.26
2778 5005 3.637030 GAAGCGGCGGCGATAACC 61.637 66.667 36.87 17.72 46.35 2.85
2839 5066 1.490621 CAAGCAAACAAAAGGCGAGG 58.509 50.000 0.00 0.00 0.00 4.63
2916 5143 1.668751 CCAAACGGTTCGTCATATGGG 59.331 52.381 2.13 0.00 39.99 4.00
3007 5234 5.572511 TCAATGAAATGATACGCACTTTTGC 59.427 36.000 0.00 0.00 46.21 3.68
3008 5235 7.745022 ATCAATGAAATGATACGCACTTTTG 57.255 32.000 0.00 0.00 38.25 2.44
3611 5838 5.045505 TCCAACAGGCATGTAAGGTATGTAA 60.046 40.000 18.65 0.62 39.29 2.41
3662 5889 8.655092 GTTCTCTCTTCATCTGTTTAACATGAG 58.345 37.037 0.00 1.20 0.00 2.90


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

AutoCloner maintained by Alex Coulton.