Multiple sequence alignment - TraesCS6A01G128500

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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 TraesCS6A01G128500 chr6A 100.000 3524 0 0 1 3524 100759985 100763508 0.000000e+00 6508.0
1 TraesCS6A01G128500 chr6A 97.166 3317 73 6 1 3316 100802063 100805359 0.000000e+00 5585.0
2 TraesCS6A01G128500 chr6A 92.190 2612 172 23 937 3524 100185143 100182540 0.000000e+00 3664.0
3 TraesCS6A01G128500 chr6A 85.408 2145 288 19 984 3120 100087886 100085759 0.000000e+00 2204.0
4 TraesCS6A01G128500 chr6A 99.434 883 5 0 2642 3524 100809263 100810145 0.000000e+00 1604.0
5 TraesCS6A01G128500 chr6A 90.205 633 51 8 319 943 100186501 100185872 0.000000e+00 815.0
6 TraesCS6A01G128500 chr6A 94.779 249 13 0 3276 3524 100805365 100805613 4.270000e-104 388.0
7 TraesCS6A01G128500 chr6A 80.672 238 17 9 304 539 100185395 100185185 1.310000e-34 158.0
8 TraesCS6A01G128500 chr6D 96.635 2556 78 7 742 3296 83540355 83542903 0.000000e+00 4237.0
9 TraesCS6A01G128500 chr6D 93.267 2614 148 9 937 3524 83124785 83122174 0.000000e+00 3827.0
10 TraesCS6A01G128500 chr6D 86.210 2190 277 16 943 3122 83057981 83055807 0.000000e+00 2348.0
11 TraesCS6A01G128500 chr6D 85.494 2137 291 17 994 3122 83046865 83044740 0.000000e+00 2211.0
12 TraesCS6A01G128500 chr6D 89.508 1077 77 21 2478 3524 83105907 83104837 0.000000e+00 1330.0
13 TraesCS6A01G128500 chr6D 90.190 632 47 11 319 943 83126185 83125562 0.000000e+00 809.0
14 TraesCS6A01G128500 chr6D 95.562 338 14 1 406 743 83827352 83827688 1.110000e-149 540.0
15 TraesCS6A01G128500 chr6D 92.330 339 13 3 406 743 83540000 83540326 1.480000e-128 470.0
16 TraesCS6A01G128500 chr6D 87.283 346 35 3 69 409 83539696 83540037 1.530000e-103 387.0
17 TraesCS6A01G128500 chr6D 92.369 249 19 0 3276 3524 83542928 83543176 4.330000e-94 355.0
18 TraesCS6A01G128500 chr6D 90.541 222 17 4 43 261 83820875 83821095 1.240000e-74 291.0
19 TraesCS6A01G128500 chr6D 92.105 152 12 0 258 409 83827238 83827389 7.660000e-52 215.0
20 TraesCS6A01G128500 chr6D 79.608 255 21 12 304 556 83125093 83124868 1.690000e-33 154.0
21 TraesCS6A01G128500 chr6B 96.318 2580 85 9 742 3316 159401817 159404391 0.000000e+00 4229.0
22 TraesCS6A01G128500 chr6B 93.529 2380 152 2 937 3316 158149854 158147477 0.000000e+00 3541.0
23 TraesCS6A01G128500 chr6B 85.216 2178 297 15 943 3110 158103940 158101778 0.000000e+00 2215.0
24 TraesCS6A01G128500 chr6B 90.751 746 59 6 1 743 159401052 159401790 0.000000e+00 987.0
25 TraesCS6A01G128500 chr6B 90.339 383 32 3 322 700 158151230 158150849 6.790000e-137 497.0
26 TraesCS6A01G128500 chr6B 96.386 249 9 0 3276 3524 159404397 159404645 9.100000e-111 411.0
27 TraesCS6A01G128500 chr6B 94.779 249 13 0 3276 3524 158147471 158147223 4.270000e-104 388.0
28 TraesCS6A01G128500 chr3A 94.595 37 1 1 273 309 46737244 46737209 4.910000e-04 56.5
29 TraesCS6A01G128500 chr1D 100.000 28 0 0 277 304 303021480 303021507 6.000000e-03 52.8


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 TraesCS6A01G128500 chr6A 100759985 100763508 3523 False 6508.000000 6508 100.000000 1 3524 1 chr6A.!!$F1 3523
1 TraesCS6A01G128500 chr6A 100802063 100810145 8082 False 2525.666667 5585 97.126333 1 3524 3 chr6A.!!$F2 3523
2 TraesCS6A01G128500 chr6A 100085759 100087886 2127 True 2204.000000 2204 85.408000 984 3120 1 chr6A.!!$R1 2136
3 TraesCS6A01G128500 chr6A 100182540 100186501 3961 True 1545.666667 3664 87.689000 304 3524 3 chr6A.!!$R2 3220
4 TraesCS6A01G128500 chr6D 83055807 83057981 2174 True 2348.000000 2348 86.210000 943 3122 1 chr6D.!!$R2 2179
5 TraesCS6A01G128500 chr6D 83044740 83046865 2125 True 2211.000000 2211 85.494000 994 3122 1 chr6D.!!$R1 2128
6 TraesCS6A01G128500 chr6D 83122174 83126185 4011 True 1596.666667 3827 87.688333 304 3524 3 chr6D.!!$R4 3220
7 TraesCS6A01G128500 chr6D 83539696 83543176 3480 False 1362.250000 4237 92.154250 69 3524 4 chr6D.!!$F2 3455
8 TraesCS6A01G128500 chr6D 83104837 83105907 1070 True 1330.000000 1330 89.508000 2478 3524 1 chr6D.!!$R3 1046
9 TraesCS6A01G128500 chr6B 158101778 158103940 2162 True 2215.000000 2215 85.216000 943 3110 1 chr6B.!!$R1 2167
10 TraesCS6A01G128500 chr6B 159401052 159404645 3593 False 1875.666667 4229 94.485000 1 3524 3 chr6B.!!$F1 3523
11 TraesCS6A01G128500 chr6B 158147223 158151230 4007 True 1475.333333 3541 92.882333 322 3524 3 chr6B.!!$R2 3202

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
265 269 4.651045 ACTATGCTCACAGACACATATCCA 59.349 41.667 0.0 0.0 0.0 3.41 F
1498 3081 0.615331 GGTGATGAAGAGCCTGGTCA 59.385 55.000 0.0 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1547 3130 0.744414 AGATGGCGCGCTAACACATT 60.744 50.0 32.29 8.67 0.00 2.71 R
3493 5163 0.459078 GGGCGAGACACCCTACTTAC 59.541 60.0 0.00 0.00 44.68 2.34 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
265 269 4.651045 ACTATGCTCACAGACACATATCCA 59.349 41.667 0.00 0.00 0.00 3.41
523 565 7.762159 TGTCATGCTTCTGTACGTCATAATAAA 59.238 33.333 0.00 0.00 0.00 1.40
929 1012 9.883142 AGGAAACTGTCAAACAAAAATATTCAA 57.117 25.926 0.00 0.00 41.13 2.69
975 1103 6.982141 CACCATGCAGCAACTATTTTTCATAT 59.018 34.615 0.00 0.00 0.00 1.78
1447 3030 2.486982 CTCAACATCTCAAGCAACTGGG 59.513 50.000 0.00 0.00 0.00 4.45
1465 3048 4.787551 CTGGGTTACAGGCATATTACCAA 58.212 43.478 0.00 0.00 43.70 3.67
1466 3049 5.385198 CTGGGTTACAGGCATATTACCAAT 58.615 41.667 0.00 0.00 43.70 3.16
1498 3081 0.615331 GGTGATGAAGAGCCTGGTCA 59.385 55.000 0.00 0.00 0.00 4.02
1571 3154 0.168128 GTTAGCGCGCCATCTTTTGT 59.832 50.000 30.33 8.40 0.00 2.83
1648 3231 1.603456 TTGCTCGGTGCTGAAATTGA 58.397 45.000 3.53 0.00 43.37 2.57
1677 3260 1.202348 GGCTACAACAACCTCAATGGC 59.798 52.381 0.00 0.00 40.22 4.40
1680 3263 0.667993 ACAACAACCTCAATGGCACG 59.332 50.000 0.00 0.00 40.22 5.34
1687 3270 1.243342 CCTCAATGGCACGCTTCCAA 61.243 55.000 0.00 0.00 37.13 3.53
1858 3442 4.618635 AGGTGATCTGAAGAGATTGGAGA 58.381 43.478 0.00 0.00 39.19 3.71
2076 3660 2.357881 TCCTGCAGCAAGCTGACG 60.358 61.111 25.03 13.80 46.30 4.35
2353 3937 4.021544 TGTGTGGAAAAATACCTGATTGGC 60.022 41.667 0.00 0.00 40.22 4.52
2522 4106 3.483421 TGGAGATGCCAATGCTAGAATG 58.517 45.455 0.00 0.00 45.87 2.67
2991 4579 2.065799 AGTCCAGTTTCCATTGACCCT 58.934 47.619 0.00 0.00 0.00 4.34
3124 4712 4.081752 ACCATGTAACCGTTATCACCGTTA 60.082 41.667 0.00 0.00 0.00 3.18
3296 4885 3.465871 CTCTCCTGCCTAAAGCTGATTC 58.534 50.000 0.00 0.00 42.76 2.52
3420 5083 0.401738 AGCTAACCAGAAGCCTTGCA 59.598 50.000 0.00 0.00 41.02 4.08
3441 5104 4.202050 GCAAATCAGACCAACTTTGTGTCT 60.202 41.667 7.08 7.08 38.42 3.41
3493 5163 3.619038 GGCTGACTTCATTTCTTCCTACG 59.381 47.826 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
265 269 2.443255 ACCCCTCAAACTGTCAGTTGAT 59.557 45.455 18.84 1.40 38.66 2.57
929 1012 0.105760 TGTGGTGGAACTGCCCATTT 60.106 50.000 0.00 0.00 38.66 2.32
975 1103 5.472137 GTGAAATTTCTTGGTGTACCTGCTA 59.528 40.000 18.64 0.00 36.82 3.49
1139 2722 3.606662 AGCAGTCGGTGTCGTGCT 61.607 61.111 0.00 0.00 41.70 4.40
1447 3030 6.935741 TGTGATTGGTAATATGCCTGTAAC 57.064 37.500 0.00 0.00 0.00 2.50
1465 3048 2.577563 TCATCACCTCCCATGTTGTGAT 59.422 45.455 9.52 9.52 46.41 3.06
1466 3049 1.984424 TCATCACCTCCCATGTTGTGA 59.016 47.619 6.38 6.38 41.52 3.58
1498 3081 8.814038 AATCTGTTGGAACTAGCATTAAGAAT 57.186 30.769 0.00 0.00 0.00 2.40
1547 3130 0.744414 AGATGGCGCGCTAACACATT 60.744 50.000 32.29 8.67 0.00 2.71
1571 3154 2.642427 TGAAACTGAGCTCAAGCACAA 58.358 42.857 18.85 0.00 45.16 3.33
1677 3260 3.250762 TGAAGAGTTCATTTGGAAGCGTG 59.749 43.478 0.00 0.00 35.82 5.34
1680 3263 4.222114 CGTTGAAGAGTTCATTTGGAAGC 58.778 43.478 0.00 0.00 39.84 3.86
1687 3270 4.210537 CGTGGTTACGTTGAAGAGTTCATT 59.789 41.667 0.00 0.00 44.99 2.57
1858 3442 2.168106 TGTTGTGTTCCAAATGCAGCTT 59.832 40.909 0.00 0.00 34.07 3.74
2029 3613 1.003355 CTGGAACTGTGCCGGTGAT 60.003 57.895 5.38 0.00 0.00 3.06
2076 3660 3.447918 TTGTAAGATAGCCGTAGTGCC 57.552 47.619 0.00 0.00 0.00 5.01
2333 3917 6.321181 TGATAGCCAATCAGGTATTTTTCCAC 59.679 38.462 0.00 0.00 39.77 4.02
2353 3937 4.275936 CCCCAAATTCGGTAGCTTTGATAG 59.724 45.833 0.00 0.00 32.83 2.08
2522 4106 7.934120 AGAATACCTTTGGTGCAGTATTATCTC 59.066 37.037 6.72 0.00 35.96 2.75
2991 4579 6.069905 TGGCCTCACTACCAATCTGTTTTATA 60.070 38.462 3.32 0.00 31.46 0.98
3189 4777 7.001674 TGTGCTTTCCCTGTAGATTTTCTTTA 58.998 34.615 0.00 0.00 0.00 1.85
3249 4838 7.363268 GGCTACAAAGGAGATGAAAAATGACAT 60.363 37.037 0.00 0.00 0.00 3.06
3420 5083 5.297776 CAGAGACACAAAGTTGGTCTGATTT 59.702 40.000 15.47 0.00 38.18 2.17
3493 5163 0.459078 GGGCGAGACACCCTACTTAC 59.541 60.000 0.00 0.00 44.68 2.34


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

AutoCloner maintained by Alex Coulton.