Multiple sequence alignment - TraesCS7B01G128100

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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 TraesCS7B01G128100 chr7B 100.000 3327 0 0 1 3327 153439394 153436068 0.000000e+00 6144
1 TraesCS7B01G128100 chr7D 94.466 3361 115 23 1 3327 184188335 184185012 0.000000e+00 5110
2 TraesCS7B01G128100 chr7A 96.145 2620 77 15 2 2605 186530327 186532938 0.000000e+00 4257
3 TraesCS7B01G128100 chr7A 94.851 738 34 2 2593 3327 186533203 186533939 0.000000e+00 1149
4 TraesCS7B01G128100 chr7A 86.835 357 42 3 2974 3327 512186889 512187243 8.650000e-106 394
5 TraesCS7B01G128100 chr1D 89.504 343 33 1 2988 3327 197732956 197732614 6.590000e-117 431
6 TraesCS7B01G128100 chr6D 89.181 342 33 2 2986 3324 48674767 48675107 1.100000e-114 424
7 TraesCS7B01G128100 chr6A 88.986 345 33 3 2986 3327 65859170 65858828 3.970000e-114 422
8 TraesCS7B01G128100 chr4B 88.439 346 35 3 2986 3327 181507807 181508151 2.390000e-111 412
9 TraesCS7B01G128100 chr2D 88.047 343 36 3 2988 3327 136674717 136674377 5.170000e-108 401
10 TraesCS7B01G128100 chr2A 87.288 354 38 5 2977 3327 415262127 415261778 6.690000e-107 398


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 TraesCS7B01G128100 chr7B 153436068 153439394 3326 True 6144 6144 100.000 1 3327 1 chr7B.!!$R1 3326
1 TraesCS7B01G128100 chr7D 184185012 184188335 3323 True 5110 5110 94.466 1 3327 1 chr7D.!!$R1 3326
2 TraesCS7B01G128100 chr7A 186530327 186533939 3612 False 2703 4257 95.498 2 3327 2 chr7A.!!$F2 3325

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
314 316 0.396695 AGCCGATCCCCTAAGTCGAA 60.397 55.000 0.0 0.0 37.55 3.71 F
442 462 0.656259 CTCGACGTGCCTCGAAGATA 59.344 55.000 0.0 0.0 42.00 1.98 F
946 972 1.206849 CAAACAAACACAGTTGGCCCT 59.793 47.619 0.0 0.0 32.50 5.19 F
1117 1145 2.693069 CCTCCATCGCCATCTTGTATC 58.307 52.381 0.0 0.0 0.00 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1134 1162 0.107703 TCGCTGGTTAGGAGGCAATG 60.108 55.000 0.00 0.00 0.00 2.82 R
1680 1712 1.186200 CGGTCAGAATCTCAGGGTCA 58.814 55.000 0.00 0.00 0.00 4.02 R
1882 1914 1.968017 CTTTGCTGAGCCTCGCCAA 60.968 57.895 0.23 0.37 0.00 4.52 R
2676 2990 2.725221 CCTATCTGAGGGCAAGCTTT 57.275 50.000 0.00 0.00 42.39 3.51 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
23 24 4.694339 GAGTTTACCACCGCAAGATCTAT 58.306 43.478 0.00 0.00 43.02 1.98
101 102 2.497273 GCTATTTTGTCCAACCCAGCAT 59.503 45.455 0.00 0.00 0.00 3.79
128 129 1.035385 TTCGCTGATCGCCTAGGTCA 61.035 55.000 11.31 5.49 37.72 4.02
185 186 2.364317 TCTCGGAGCCCCCTCAAG 60.364 66.667 0.00 0.00 39.96 3.02
313 315 0.822532 GAGCCGATCCCCTAAGTCGA 60.823 60.000 0.00 0.00 37.55 4.20
314 316 0.396695 AGCCGATCCCCTAAGTCGAA 60.397 55.000 0.00 0.00 37.55 3.71
341 343 1.147557 ACGGACCACAACGACGAAAC 61.148 55.000 0.00 0.00 0.00 2.78
342 344 1.146957 CGGACCACAACGACGAAACA 61.147 55.000 0.00 0.00 0.00 2.83
350 369 4.159857 CACAACGACGAAACAAAAAGGAA 58.840 39.130 0.00 0.00 0.00 3.36
442 462 0.656259 CTCGACGTGCCTCGAAGATA 59.344 55.000 0.00 0.00 42.00 1.98
582 603 1.815421 GCGTGGCGTTGATGAGGAT 60.815 57.895 0.00 0.00 0.00 3.24
844 868 3.833645 CGACGATCTCCGGCCCAA 61.834 66.667 0.00 0.00 45.44 4.12
935 961 2.037772 AGCCCAAACACACAAACAAACA 59.962 40.909 0.00 0.00 0.00 2.83
946 972 1.206849 CAAACAAACACAGTTGGCCCT 59.793 47.619 0.00 0.00 32.50 5.19
1117 1145 2.693069 CCTCCATCGCCATCTTGTATC 58.307 52.381 0.00 0.00 0.00 2.24
1122 1150 3.494924 CCATCGCCATCTTGTATCTTGGA 60.495 47.826 0.00 0.00 0.00 3.53
1310 1338 3.547249 GACGCTGAACACGGACGGA 62.547 63.158 0.00 0.00 34.00 4.69
1495 1523 5.133941 AGTCAGGATAAGATACAAGCTCGA 58.866 41.667 0.00 0.00 0.00 4.04
1502 1530 6.201234 GGATAAGATACAAGCTCGAAAAGGTC 59.799 42.308 0.00 0.00 33.60 3.85
1503 1531 4.537135 AGATACAAGCTCGAAAAGGTCA 57.463 40.909 0.00 0.00 33.60 4.02
1570 1602 6.544928 TGTATAGTTGAGGAGAAATGCTGA 57.455 37.500 0.00 0.00 0.00 4.26
1882 1914 2.683867 GTGTATGAGTACGCAGAGGAGT 59.316 50.000 5.33 0.00 40.29 3.85
2018 2050 7.984050 TCTTTCTAAGCAGAAGGTAATCATCAG 59.016 37.037 0.00 0.00 41.75 2.90
2075 2107 6.634805 TGGTACTCTTTTTCTATCTGAGCAG 58.365 40.000 0.00 0.00 0.00 4.24
2085 2117 5.933187 TCTATCTGAGCAGACTATCGTTC 57.067 43.478 1.71 0.00 40.75 3.95
2101 2133 3.601435 TCGTTCAGTTGGTTCAGTTGAA 58.399 40.909 0.00 0.00 0.00 2.69
2289 2322 6.705302 AGCAAATCAGTAATGAAGACTCTGA 58.295 36.000 0.00 0.00 39.05 3.27
2360 2393 7.935755 TCTTCCTCAATTGACATCTCATATTCC 59.064 37.037 3.38 0.00 0.00 3.01
2361 2394 6.226052 TCCTCAATTGACATCTCATATTCCG 58.774 40.000 3.38 0.00 0.00 4.30
2408 2445 7.784037 TCGCTACCCTAAAAACTTATGTCATA 58.216 34.615 0.00 0.00 0.00 2.15
2612 2926 1.064758 ACCTGTGGCACAAAAGTGAGA 60.065 47.619 22.31 0.00 44.16 3.27
2755 3069 4.084287 TCAGGTAGAAAAAGAGCGGTAGA 58.916 43.478 0.00 0.00 0.00 2.59
2850 3164 2.154462 GTGTCTTGATGTGGTCTTGGG 58.846 52.381 0.00 0.00 0.00 4.12
2880 3194 9.837525 GATACATCCATTTAATGAAAGATCTGC 57.162 33.333 6.50 0.00 0.00 4.26
3145 3462 5.645929 TCCGTTAGATGCTTGCTCAAAAATA 59.354 36.000 0.00 0.00 0.00 1.40
3172 3489 0.313043 ACACCGTTACTGTCAGGTCG 59.687 55.000 4.53 5.80 34.25 4.79
3185 3502 2.735857 GGTCGAACCCGTTGACCG 60.736 66.667 11.07 0.00 42.42 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
81 82 4.806640 AATGCTGGGTTGGACAAAATAG 57.193 40.909 0.00 0.00 0.00 1.73
185 186 0.248784 GCAATCCATTCAGCTTCGCC 60.249 55.000 0.00 0.00 0.00 5.54
341 343 4.692228 TGTGCTTTTAGCCTTCCTTTTTG 58.308 39.130 0.00 0.00 41.51 2.44
342 344 5.551305 ATGTGCTTTTAGCCTTCCTTTTT 57.449 34.783 0.00 0.00 41.51 1.94
350 369 7.703058 ATTTAAGTGTATGTGCTTTTAGCCT 57.297 32.000 0.00 0.00 41.51 4.58
1122 1150 7.015584 GGTTAGGAGGCAATGGATAAATCAAAT 59.984 37.037 0.00 0.00 0.00 2.32
1134 1162 0.107703 TCGCTGGTTAGGAGGCAATG 60.108 55.000 0.00 0.00 0.00 2.82
1135 1163 0.839946 ATCGCTGGTTAGGAGGCAAT 59.160 50.000 0.00 0.00 0.00 3.56
1310 1338 3.426568 GAGAAGCGCGCAAAGCCT 61.427 61.111 35.10 20.79 44.76 4.58
1375 1403 4.249661 GGACATCTTCTTCTTCTTCGCTT 58.750 43.478 0.00 0.00 0.00 4.68
1376 1404 3.259374 TGGACATCTTCTTCTTCTTCGCT 59.741 43.478 0.00 0.00 0.00 4.93
1379 1407 6.934083 ACTTCTTGGACATCTTCTTCTTCTTC 59.066 38.462 0.00 0.00 0.00 2.87
1380 1408 6.836242 ACTTCTTGGACATCTTCTTCTTCTT 58.164 36.000 0.00 0.00 0.00 2.52
1381 1409 6.432403 ACTTCTTGGACATCTTCTTCTTCT 57.568 37.500 0.00 0.00 0.00 2.85
1495 1523 5.128663 ACATGCTAAAACCAAGTGACCTTTT 59.871 36.000 0.00 0.00 0.00 2.27
1502 1530 9.730420 GGTAATATAACATGCTAAAACCAAGTG 57.270 33.333 0.00 0.00 0.00 3.16
1503 1531 9.469097 TGGTAATATAACATGCTAAAACCAAGT 57.531 29.630 0.00 0.00 30.72 3.16
1570 1602 5.992829 TGAGAAATTGACAATGCAGCATTTT 59.007 32.000 18.48 12.48 31.05 1.82
1680 1712 1.186200 CGGTCAGAATCTCAGGGTCA 58.814 55.000 0.00 0.00 0.00 4.02
1882 1914 1.968017 CTTTGCTGAGCCTCGCCAA 60.968 57.895 0.23 0.37 0.00 4.52
2018 2050 5.009811 AGCAGATTTGTCGGTATAGGACTAC 59.990 44.000 5.68 0.00 35.45 2.73
2085 2117 5.247507 TGTCAATTCAACTGAACCAACTG 57.752 39.130 0.00 0.00 36.80 3.16
2289 2322 3.369892 GCTAGTTGTGAGGTCATCCACAT 60.370 47.826 0.00 0.00 42.13 3.21
2360 2393 5.174395 AGATCTTCTCAAACCTTCATCACG 58.826 41.667 0.00 0.00 0.00 4.35
2361 2394 5.290643 CGAGATCTTCTCAAACCTTCATCAC 59.709 44.000 0.00 0.00 43.55 3.06
2408 2445 9.671279 AAACATTTGGAAGAGTGAAAAGAAAAT 57.329 25.926 0.00 0.00 0.00 1.82
2612 2926 5.366186 TGTTTGGCTGCCATCCATAAATTAT 59.634 36.000 24.03 0.00 31.53 1.28
2676 2990 2.725221 CCTATCTGAGGGCAAGCTTT 57.275 50.000 0.00 0.00 42.39 3.51
2784 3098 7.516450 AGTACCTACTAACTACCCAGACTAA 57.484 40.000 0.00 0.00 34.13 2.24
2799 3113 7.312415 AGAACATTTGTACCAAGTACCTACT 57.688 36.000 2.63 0.00 38.14 2.57
2902 3219 3.887110 CAGCCCTATGAAGATCAAATGCA 59.113 43.478 0.00 0.00 0.00 3.96
3119 3436 2.621338 TGAGCAAGCATCTAACGGAAG 58.379 47.619 0.00 0.00 0.00 3.46
3145 3462 5.394224 CCTGACAGTAACGGTGTCTAATGAT 60.394 44.000 0.93 0.00 44.02 2.45
3185 3502 8.434392 TCTAGGGGTATTTTGGTCATATAACAC 58.566 37.037 0.00 0.00 0.00 3.32


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

AutoCloner maintained by Alex Coulton.