Multiple sequence alignment - TraesCS2B01G332000

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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 TraesCS2B01G332000 chr2B 100.000 2216 0 0 1 2216 474936404 474938619 0.000000e+00 4093
1 TraesCS2B01G332000 chr2B 97.657 811 19 0 1 811 706860503 706859693 0.000000e+00 1393
2 TraesCS2B01G332000 chr2B 97.417 813 21 0 1 813 382708498 382707686 0.000000e+00 1386
3 TraesCS2B01G332000 chr2B 97.417 813 20 1 1 812 775518080 775518892 0.000000e+00 1384
4 TraesCS2B01G332000 chr2B 97.297 814 22 0 1 814 363371281 363370468 0.000000e+00 1382
5 TraesCS2B01G332000 chr2B 98.529 136 2 0 2081 2216 161762048 161762183 7.910000e-60 241
6 TraesCS2B01G332000 chr5D 98.017 1412 20 1 813 2216 483805419 483804008 0.000000e+00 2446
7 TraesCS2B01G332000 chr5D 97.240 1413 30 4 813 2216 6233891 6232479 0.000000e+00 2385
8 TraesCS2B01G332000 chr3B 97.734 1412 24 1 813 2216 201495360 201496771 0.000000e+00 2423
9 TraesCS2B01G332000 chr3B 97.654 810 19 0 1 810 564099354 564100163 0.000000e+00 1391
10 TraesCS2B01G332000 chr1D 97.527 1415 24 3 813 2216 254479335 254480749 0.000000e+00 2409
11 TraesCS2B01G332000 chr1D 96.549 1275 36 1 813 2079 180353389 180352115 0.000000e+00 2104
12 TraesCS2B01G332000 chr2D 97.864 1311 20 1 914 2216 643855801 643857111 0.000000e+00 2259
13 TraesCS2B01G332000 chr2D 98.427 1081 17 0 1136 2216 359632206 359631126 0.000000e+00 1903
14 TraesCS2B01G332000 chr2D 96.791 187 2 3 813 997 488281321 488281505 2.140000e-80 309
15 TraesCS2B01G332000 chr6D 95.113 1412 55 6 813 2216 210722992 210721587 0.000000e+00 2213
16 TraesCS2B01G332000 chr7A 93.670 1406 77 7 813 2210 352294454 352293053 0.000000e+00 2093
17 TraesCS2B01G332000 chrUn 97.933 1161 15 2 813 1965 407031753 407032912 0.000000e+00 2002
18 TraesCS2B01G332000 chrUn 97.594 1039 17 1 813 1843 386523382 386522344 0.000000e+00 1773
19 TraesCS2B01G332000 chr6B 97.660 812 19 0 1 812 188180783 188181594 0.000000e+00 1395
20 TraesCS2B01G332000 chr1B 97.414 812 21 0 1 812 403571598 403572409 0.000000e+00 1384
21 TraesCS2B01G332000 chr1B 97.414 812 21 0 1 812 474090051 474089240 0.000000e+00 1384
22 TraesCS2B01G332000 chr5B 97.414 812 19 1 1 812 334244763 334245572 0.000000e+00 1382
23 TraesCS2B01G332000 chr4B 97.387 574 7 1 813 1378 381290959 381290386 0.000000e+00 970
24 TraesCS2B01G332000 chr7B 98.883 179 2 0 813 991 40709491 40709669 9.870000e-84 320


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 TraesCS2B01G332000 chr2B 474936404 474938619 2215 False 4093 4093 100.000 1 2216 1 chr2B.!!$F2 2215
1 TraesCS2B01G332000 chr2B 706859693 706860503 810 True 1393 1393 97.657 1 811 1 chr2B.!!$R3 810
2 TraesCS2B01G332000 chr2B 382707686 382708498 812 True 1386 1386 97.417 1 813 1 chr2B.!!$R2 812
3 TraesCS2B01G332000 chr2B 775518080 775518892 812 False 1384 1384 97.417 1 812 1 chr2B.!!$F3 811
4 TraesCS2B01G332000 chr2B 363370468 363371281 813 True 1382 1382 97.297 1 814 1 chr2B.!!$R1 813
5 TraesCS2B01G332000 chr5D 483804008 483805419 1411 True 2446 2446 98.017 813 2216 1 chr5D.!!$R2 1403
6 TraesCS2B01G332000 chr5D 6232479 6233891 1412 True 2385 2385 97.240 813 2216 1 chr5D.!!$R1 1403
7 TraesCS2B01G332000 chr3B 201495360 201496771 1411 False 2423 2423 97.734 813 2216 1 chr3B.!!$F1 1403
8 TraesCS2B01G332000 chr3B 564099354 564100163 809 False 1391 1391 97.654 1 810 1 chr3B.!!$F2 809
9 TraesCS2B01G332000 chr1D 254479335 254480749 1414 False 2409 2409 97.527 813 2216 1 chr1D.!!$F1 1403
10 TraesCS2B01G332000 chr1D 180352115 180353389 1274 True 2104 2104 96.549 813 2079 1 chr1D.!!$R1 1266
11 TraesCS2B01G332000 chr2D 643855801 643857111 1310 False 2259 2259 97.864 914 2216 1 chr2D.!!$F2 1302
12 TraesCS2B01G332000 chr2D 359631126 359632206 1080 True 1903 1903 98.427 1136 2216 1 chr2D.!!$R1 1080
13 TraesCS2B01G332000 chr6D 210721587 210722992 1405 True 2213 2213 95.113 813 2216 1 chr6D.!!$R1 1403
14 TraesCS2B01G332000 chr7A 352293053 352294454 1401 True 2093 2093 93.670 813 2210 1 chr7A.!!$R1 1397
15 TraesCS2B01G332000 chrUn 407031753 407032912 1159 False 2002 2002 97.933 813 1965 1 chrUn.!!$F1 1152
16 TraesCS2B01G332000 chrUn 386522344 386523382 1038 True 1773 1773 97.594 813 1843 1 chrUn.!!$R1 1030
17 TraesCS2B01G332000 chr6B 188180783 188181594 811 False 1395 1395 97.660 1 812 1 chr6B.!!$F1 811
18 TraesCS2B01G332000 chr1B 403571598 403572409 811 False 1384 1384 97.414 1 812 1 chr1B.!!$F1 811
19 TraesCS2B01G332000 chr1B 474089240 474090051 811 True 1384 1384 97.414 1 812 1 chr1B.!!$R1 811
20 TraesCS2B01G332000 chr5B 334244763 334245572 809 False 1382 1382 97.414 1 812 1 chr5B.!!$F1 811
21 TraesCS2B01G332000 chr4B 381290386 381290959 573 True 970 970 97.387 813 1378 1 chr4B.!!$R1 565

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
98 99 1.464997 GCCGTGAAGTTTAGGCTTCTG 59.535 52.381 0.00 1.13 45.67 3.02 F
351 352 1.585006 CCGAACTGTGCGTCTAGGT 59.415 57.895 7.51 0.00 0.00 3.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1034 1044 2.031012 CAGCGGTTCTGTGGAGCA 59.969 61.111 0.0 0.0 38.02 4.26 R
1590 1602 2.688446 CCTCGACTATGTTACAGCCTCA 59.312 50.000 0.0 0.0 0.00 3.86 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
19 20 3.179265 GTCGTGCCCATCGTGACG 61.179 66.667 0.00 0.00 0.00 4.35
59 60 3.256879 GTGGCTCTGATCCATCGAAGATA 59.743 47.826 3.22 0.00 45.12 1.98
97 98 1.809684 GCCGTGAAGTTTAGGCTTCT 58.190 50.000 0.00 0.00 45.67 2.85
98 99 1.464997 GCCGTGAAGTTTAGGCTTCTG 59.535 52.381 0.00 1.13 45.67 3.02
195 196 2.460918 CGCCGAATACGAAGATCTGTT 58.539 47.619 0.00 0.00 42.66 3.16
208 209 2.010497 GATCTGTTCGGGGAGAAAAGC 58.990 52.381 0.00 0.00 42.63 3.51
351 352 1.585006 CCGAACTGTGCGTCTAGGT 59.415 57.895 7.51 0.00 0.00 3.08
405 406 3.787001 CCAGGTTCGGGCCCTCTC 61.787 72.222 22.43 9.34 0.00 3.20
453 454 8.789762 CCTGCTTGATTGATATTGATATTGTGA 58.210 33.333 0.00 0.00 0.00 3.58
1009 1019 7.093333 ACCCAGTTTTTCCTAAAATGATGATCC 60.093 37.037 0.00 0.00 35.80 3.36
1034 1044 8.621286 CCCATTATTAACTATTCTCGCAAAACT 58.379 33.333 0.00 0.00 0.00 2.66
1630 1642 7.507616 AGTCGAGGTTGAATCTAAAGGATCTAT 59.492 37.037 0.00 0.00 32.76 1.98
1672 1684 5.667626 TGGAAGCTAATCCTCTGGAAAGTAT 59.332 40.000 6.03 0.00 40.35 2.12
1746 1758 5.847111 ATCGTCTGCAGGTACATAAACTA 57.153 39.130 15.13 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 4.040461 GGGGACTTTATCTTCGATGGATCA 59.960 45.833 4.94 0.0 0.00 2.92
97 98 2.741092 GCCGTCAGGTCAGGTTCA 59.259 61.111 0.00 0.0 40.50 3.18
98 99 2.047179 GGCCGTCAGGTCAGGTTC 60.047 66.667 0.00 0.0 43.06 3.62
122 123 2.961741 TCTGGAGCAGATCGAAAGCTAT 59.038 45.455 9.22 0.0 39.02 2.97
195 196 1.677552 GTGAGGCTTTTCTCCCCGA 59.322 57.895 0.00 0.0 33.04 5.14
351 352 2.571653 CCTTGTCTCCTGTTACCATCCA 59.428 50.000 0.00 0.0 0.00 3.41
405 406 2.167075 ACGTAGGGTTTTACCTCCATCG 59.833 50.000 0.00 0.0 42.09 3.84
453 454 7.016153 TGGTAGATCCACTCTTGTAAACATT 57.984 36.000 0.00 0.0 41.93 2.71
1009 1019 9.438291 CAGTTTTGCGAGAATAGTTAATAATGG 57.562 33.333 0.00 0.0 0.00 3.16
1034 1044 2.031012 CAGCGGTTCTGTGGAGCA 59.969 61.111 0.00 0.0 38.02 4.26
1235 1245 6.688073 ACCTTAGAAGAGGAGAACAAATCA 57.312 37.500 0.00 0.0 39.25 2.57
1507 1519 9.827411 GTTACAAAGAACTTCAGGACATTATTC 57.173 33.333 0.00 0.0 0.00 1.75
1590 1602 2.688446 CCTCGACTATGTTACAGCCTCA 59.312 50.000 0.00 0.0 0.00 3.86
1630 1642 4.871871 TCCAAGGGTATTTATCCAGCAA 57.128 40.909 0.00 0.0 0.00 3.91
1672 1684 3.278574 GCACATTTGGATGCTACTACCA 58.721 45.455 0.00 0.0 38.84 3.25
1746 1758 7.604657 AGGGATCTATAACTTCGATTCAAGT 57.395 36.000 0.00 0.0 38.30 3.16


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

AutoCloner maintained by Alex Coulton.