Multiple sequence alignment - TraesCS7B01G117800

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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 TraesCS7B01G117800 chr7B 100.000 3113 0 0 1 3113 137678278 137681390 0.000000e+00 5749
1 TraesCS7B01G117800 chr5D 98.079 3123 46 4 1 3113 6261491 6258373 0.000000e+00 5422
2 TraesCS7B01G117800 chr5D 98.046 3122 48 3 1 3113 503305284 503308401 0.000000e+00 5415
3 TraesCS7B01G117800 chr5D 98.942 2646 23 2 469 3113 512404801 512407442 0.000000e+00 4726
4 TraesCS7B01G117800 chr5D 97.537 1705 30 2 1 1697 6163498 6161798 0.000000e+00 2905
5 TraesCS7B01G117800 chr5D 90.217 92 1 1 1 84 329150435 329150344 2.540000e-21 113
6 TraesCS7B01G117800 chr6B 97.181 3122 57 4 1 3113 18746650 18743551 0.000000e+00 5249
7 TraesCS7B01G117800 chr1D 96.861 3122 49 10 1 3113 254448452 254451533 0.000000e+00 5177
8 TraesCS7B01G117800 chr1D 97.608 2717 57 4 404 3113 51839940 51837225 0.000000e+00 4650
9 TraesCS7B01G117800 chr4D 97.116 3051 78 5 69 3113 19881916 19884962 0.000000e+00 5138
10 TraesCS7B01G117800 chr4D 95.171 1201 48 5 1 1193 206977949 206976751 0.000000e+00 1888
11 TraesCS7B01G117800 chr4A 97.030 2357 64 5 762 3113 309454023 309451668 0.000000e+00 3960
12 TraesCS7B01G117800 chr2D 94.188 2512 110 12 602 3110 408662496 408664974 0.000000e+00 3797
13 TraesCS7B01G117800 chr7A 94.458 2093 79 10 1 2077 352358397 352356326 0.000000e+00 3188
14 TraesCS7B01G117800 chr1A 98.641 1619 20 2 119 1736 241516584 241518201 0.000000e+00 2867
15 TraesCS7B01G117800 chr3D 97.031 1381 24 5 1 1368 596658229 596659605 0.000000e+00 2307
16 TraesCS7B01G117800 chr3D 100.000 53 0 0 1 53 527409034 527408982 7.100000e-17 99
17 TraesCS7B01G117800 chr7D 95.238 294 6 1 1 286 530797173 530796880 2.830000e-125 459
18 TraesCS7B01G117800 chr7D 90.361 83 0 1 1 75 566651971 566651889 5.490000e-18 102
19 TraesCS7B01G117800 chr2B 83.562 146 16 5 2970 3113 120718992 120719131 2.520000e-26 130
20 TraesCS7B01G117800 chr2A 100.000 53 0 0 1 53 117560048 117559996 7.100000e-17 99


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 TraesCS7B01G117800 chr7B 137678278 137681390 3112 False 5749 5749 100.000 1 3113 1 chr7B.!!$F1 3112
1 TraesCS7B01G117800 chr5D 6258373 6261491 3118 True 5422 5422 98.079 1 3113 1 chr5D.!!$R2 3112
2 TraesCS7B01G117800 chr5D 503305284 503308401 3117 False 5415 5415 98.046 1 3113 1 chr5D.!!$F1 3112
3 TraesCS7B01G117800 chr5D 512404801 512407442 2641 False 4726 4726 98.942 469 3113 1 chr5D.!!$F2 2644
4 TraesCS7B01G117800 chr5D 6161798 6163498 1700 True 2905 2905 97.537 1 1697 1 chr5D.!!$R1 1696
5 TraesCS7B01G117800 chr6B 18743551 18746650 3099 True 5249 5249 97.181 1 3113 1 chr6B.!!$R1 3112
6 TraesCS7B01G117800 chr1D 254448452 254451533 3081 False 5177 5177 96.861 1 3113 1 chr1D.!!$F1 3112
7 TraesCS7B01G117800 chr1D 51837225 51839940 2715 True 4650 4650 97.608 404 3113 1 chr1D.!!$R1 2709
8 TraesCS7B01G117800 chr4D 19881916 19884962 3046 False 5138 5138 97.116 69 3113 1 chr4D.!!$F1 3044
9 TraesCS7B01G117800 chr4D 206976751 206977949 1198 True 1888 1888 95.171 1 1193 1 chr4D.!!$R1 1192
10 TraesCS7B01G117800 chr4A 309451668 309454023 2355 True 3960 3960 97.030 762 3113 1 chr4A.!!$R1 2351
11 TraesCS7B01G117800 chr2D 408662496 408664974 2478 False 3797 3797 94.188 602 3110 1 chr2D.!!$F1 2508
12 TraesCS7B01G117800 chr7A 352356326 352358397 2071 True 3188 3188 94.458 1 2077 1 chr7A.!!$R1 2076
13 TraesCS7B01G117800 chr1A 241516584 241518201 1617 False 2867 2867 98.641 119 1736 1 chr1A.!!$F1 1617
14 TraesCS7B01G117800 chr3D 596658229 596659605 1376 False 2307 2307 97.031 1 1368 1 chr3D.!!$F1 1367

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
96 106 0.032912 TGCGGGGACATCCTGTACTA 60.033 55.000 0.0 0.00 43.94 1.82 F
1278 1339 0.544223 ATTATGGGGCTGTACACGCA 59.456 50.000 15.9 11.33 0.00 5.24 F
1849 1923 2.227865 GCCTTTCGAGCACAACCATTTA 59.772 45.455 0.0 0.00 0.00 1.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1951 2027 1.633945 ACCTACGGCTTCTCCCAATTT 59.366 47.619 0.0 0.0 0.0 1.82 R
2111 2187 0.677842 GGTACGTGTGGAGTGAACCT 59.322 55.000 0.0 0.0 0.0 3.50 R
2867 2950 6.548321 TCTAGGGTCTCATATTCCTCTTCTC 58.452 44.000 0.0 0.0 0.0 2.87 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
96 106 0.032912 TGCGGGGACATCCTGTACTA 60.033 55.000 0.00 0.00 43.94 1.82
135 145 4.350816 ACCCTGCATAGATTAGGCATACAA 59.649 41.667 0.00 0.00 45.06 2.41
563 583 3.844211 AGTTTAGATAGTCCCTTGTGGCA 59.156 43.478 0.00 0.00 0.00 4.92
877 909 4.821260 AGTATCATCATTATTTGCCACGCA 59.179 37.500 0.00 0.00 36.47 5.24
1232 1293 1.952133 TCCAAGACGCGGAACAACG 60.952 57.895 12.47 0.00 0.00 4.10
1278 1339 0.544223 ATTATGGGGCTGTACACGCA 59.456 50.000 15.90 11.33 0.00 5.24
1433 1497 3.063997 GGAAATGCATCTCAAGTACACCG 59.936 47.826 0.00 0.00 0.00 4.94
1849 1923 2.227865 GCCTTTCGAGCACAACCATTTA 59.772 45.455 0.00 0.00 0.00 1.40
1951 2027 5.103898 AGTCCTACTCATAGTGATCTGGTCA 60.104 44.000 0.00 0.00 0.00 4.02
1991 2067 6.699575 AGGTATTATTGCAGGTCAATCAAC 57.300 37.500 0.00 0.00 43.90 3.18
2867 2950 1.137825 GGACTCGAGCGGAAGACTG 59.862 63.158 13.61 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
96 106 4.412199 TGCAGGGTAGGTGCTCTATTTAAT 59.588 41.667 0.00 0.0 41.78 1.40
135 145 3.595190 ACTAAAGTGGGTTGAAAGGCT 57.405 42.857 0.00 0.0 0.00 4.58
231 241 5.914033 TCCAAGGATAAAGGTAGATGAACG 58.086 41.667 0.00 0.0 0.00 3.95
563 583 2.711542 GTTGATCCAGGTTCCATCGTT 58.288 47.619 0.00 0.0 0.00 3.85
877 909 4.863548 TGCCTCAATCTCAATCTGGATTT 58.136 39.130 0.00 0.0 30.81 2.17
1278 1339 7.174253 TCAACAGATTGGCGTAATTTTTCTACT 59.826 33.333 0.00 0.0 36.39 2.57
1849 1923 9.726438 GGTTCTAATATATATTGGTTGTGCTCT 57.274 33.333 16.72 0.0 0.00 4.09
1951 2027 1.633945 ACCTACGGCTTCTCCCAATTT 59.366 47.619 0.00 0.0 0.00 1.82
2111 2187 0.677842 GGTACGTGTGGAGTGAACCT 59.322 55.000 0.00 0.0 0.00 3.50
2552 2629 1.754226 TGGACATGATTCGATCCGACA 59.246 47.619 0.00 0.0 34.89 4.35
2867 2950 6.548321 TCTAGGGTCTCATATTCCTCTTCTC 58.452 44.000 0.00 0.0 0.00 2.87


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

AutoCloner maintained by Alex Coulton.