Multiple sequence alignment - TraesCS7D01G248000
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BLAST Results
BLAST Results - Input Sequence
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
TraesCS7D01G248000
chr7D
100.000
6365
0
0
1
6365
219290533
219296897
0.000000e+00
11755
1
TraesCS7D01G248000
chr7A
96.491
6212
121
40
206
6364
231543666
231549833
0.000000e+00
10174
2
TraesCS7D01G248000
chr7A
92.453
212
8
4
1
210
231542032
231542237
4.830000e-76
296
3
TraesCS7D01G248000
chr7B
96.548
5504
150
22
602
6083
181039170
181033685
0.000000e+00
9075
4
TraesCS7D01G248000
chr7B
85.294
612
34
28
1
573
181040017
181039423
1.190000e-161
580
5
TraesCS7D01G248000
chr7B
94.245
278
12
1
6087
6364
181033583
181033310
7.630000e-114
422
BLAST Results - HSPs grouped
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
TraesCS7D01G248000
chr7D
219290533
219296897
6364
False
11755
11755
100.000
1
6365
1
chr7D.!!$F1
6364
1
TraesCS7D01G248000
chr7A
231542032
231549833
7801
False
5235
10174
94.472
1
6364
2
chr7A.!!$F1
6363
2
TraesCS7D01G248000
chr7B
181033310
181040017
6707
True
3359
9075
92.029
1
6364
3
chr7B.!!$R1
6363
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.
Forward
Primers
Reverse
Primers
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
Orientation
311
1759
0.030369
CGGCATCAGTCGTACTACCC
59.970
60.000
0.0
0.0
38.25
3.69
F
312
1760
0.030369
GGCATCAGTCGTACTACCCG
59.970
60.000
0.0
0.0
0.00
5.28
F
934
2661
0.032403
TCGTCCGTTTTGATCCGTGT
59.968
50.000
0.0
0.0
0.00
4.49
F
1272
3002
1.152599
CCACCACCATCACCACCAA
59.847
57.895
0.0
0.0
0.00
3.67
F
1871
3602
2.877168
CCAATGCTTATGGTCTCTCTGC
59.123
50.000
0.0
0.0
33.08
4.26
F
3856
5587
1.700186
GTTGGTGGGAGAAAGACCTCT
59.300
52.381
0.0
0.0
33.79
3.69
F
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
Orientation
2307
4038
1.003580
TGATGGAGGAGACTTTGCCAC
59.996
52.381
0.00
0.00
44.43
5.01
R
3038
4769
7.396540
AATTACCTGTCCATCTGAATTTGAC
57.603
36.000
0.00
0.00
0.00
3.18
R
3466
5197
2.028404
GCATGCATTCGTTTTTGCTAGC
59.972
45.455
14.21
8.10
39.60
3.42
R
3856
5587
1.838112
TACGGCCCTTAAGAACGAGA
58.162
50.000
16.49
5.19
0.00
4.04
R
4068
5799
1.403780
CCCGGTAAGTCAAAGGTCTCG
60.404
57.143
0.00
0.00
0.00
4.04
R
6311
8170
0.611714
AAGGCATCGTTTCCTACCGT
59.388
50.000
0.00
0.00
31.24
4.83
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.
Forward
Primers
Reverse
Primers
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
307
1755
1.139734
CAGCGGCATCAGTCGTACT
59.860
57.895
1.45
0.00
46.51
2.73
308
1756
0.380733
CAGCGGCATCAGTCGTACTA
59.619
55.000
1.45
0.00
46.51
1.82
309
1757
0.381089
AGCGGCATCAGTCGTACTAC
59.619
55.000
1.45
0.00
46.51
2.73
311
1759
0.030369
CGGCATCAGTCGTACTACCC
59.970
60.000
0.00
0.00
38.25
3.69
312
1760
0.030369
GGCATCAGTCGTACTACCCG
59.970
60.000
0.00
0.00
0.00
5.28
313
1761
0.594284
GCATCAGTCGTACTACCCGC
60.594
60.000
0.00
0.00
0.00
6.13
314
1762
0.736636
CATCAGTCGTACTACCCGCA
59.263
55.000
0.00
0.00
0.00
5.69
315
1763
0.737219
ATCAGTCGTACTACCCGCAC
59.263
55.000
0.00
0.00
0.00
5.34
316
1764
1.138247
CAGTCGTACTACCCGCACC
59.862
63.158
0.00
0.00
0.00
5.01
317
1765
1.303561
AGTCGTACTACCCGCACCA
60.304
57.895
0.00
0.00
0.00
4.17
318
1766
1.138247
GTCGTACTACCCGCACCAG
59.862
63.158
0.00
0.00
0.00
4.00
319
1767
2.202703
CGTACTACCCGCACCAGC
60.203
66.667
0.00
0.00
37.42
4.85
320
1768
2.975536
GTACTACCCGCACCAGCA
59.024
61.111
0.00
0.00
42.27
4.41
321
1769
1.447314
GTACTACCCGCACCAGCAC
60.447
63.158
0.00
0.00
42.27
4.40
322
1770
2.652095
TACTACCCGCACCAGCACC
61.652
63.158
0.00
0.00
42.27
5.01
323
1771
4.015406
CTACCCGCACCAGCACCA
62.015
66.667
0.00
0.00
42.27
4.17
324
1772
3.958147
CTACCCGCACCAGCACCAG
62.958
68.421
0.00
0.00
42.27
4.00
589
2083
4.142609
CTAGTTGAGCAGCTAATCCCAA
57.857
45.455
0.00
0.00
0.00
4.12
760
2478
1.534729
GCCGTTTCCACCATTTCTCT
58.465
50.000
0.00
0.00
0.00
3.10
799
2517
1.292223
CTCCTGTTTTCTCCGCGGA
59.708
57.895
29.03
29.03
0.00
5.54
893
2619
1.212616
CGACTGCTCCAATCGAATCC
58.787
55.000
0.00
0.00
38.10
3.01
899
2626
2.044806
CTCCAATCGAATCCCCCGCT
62.045
60.000
0.00
0.00
0.00
5.52
934
2661
0.032403
TCGTCCGTTTTGATCCGTGT
59.968
50.000
0.00
0.00
0.00
4.49
1140
2870
4.109675
CCGGAGAACGCCCCCATT
62.110
66.667
0.00
0.00
42.52
3.16
1272
3002
1.152599
CCACCACCATCACCACCAA
59.847
57.895
0.00
0.00
0.00
3.67
1790
3520
6.959639
TGATGCCACTTTTAGGGATTTATC
57.040
37.500
0.00
0.00
37.32
1.75
1856
3587
6.705863
AGAAATGGTTTCTCTATCCAATGC
57.294
37.500
0.00
0.00
46.62
3.56
1868
3599
6.210385
TCTCTATCCAATGCTTATGGTCTCTC
59.790
42.308
3.49
0.00
39.09
3.20
1871
3602
2.877168
CCAATGCTTATGGTCTCTCTGC
59.123
50.000
0.00
0.00
33.08
4.26
1992
3723
2.902423
AAGGCTTGCCGGACACAACA
62.902
55.000
5.05
0.00
0.00
3.33
2143
3874
3.264450
ACTTGATCCCCTACTGAACTTGG
59.736
47.826
0.00
0.00
0.00
3.61
2144
3875
3.199442
TGATCCCCTACTGAACTTGGA
57.801
47.619
0.00
0.00
0.00
3.53
2145
3876
3.736094
TGATCCCCTACTGAACTTGGAT
58.264
45.455
0.00
0.00
35.38
3.41
2146
3877
4.890988
TGATCCCCTACTGAACTTGGATA
58.109
43.478
0.00
0.00
32.91
2.59
2307
4038
5.883661
ACTCAATCAATAATGCAAACTCCG
58.116
37.500
0.00
0.00
0.00
4.63
3038
4769
3.251479
TCAGACCATTCTCCATCAACG
57.749
47.619
0.00
0.00
0.00
4.10
3070
4801
7.611770
TCAGATGGACAGGTAATTTATATCGG
58.388
38.462
0.00
0.00
0.00
4.18
3079
4810
5.001232
GGTAATTTATATCGGAGCTTGCCA
58.999
41.667
0.00
0.00
0.00
4.92
3466
5197
3.217599
TGAAGTAAGTCTGCTGCTACG
57.782
47.619
0.00
0.00
0.00
3.51
3856
5587
1.700186
GTTGGTGGGAGAAAGACCTCT
59.300
52.381
0.00
0.00
33.79
3.69
3975
5706
4.699257
GCTTGACCATTGACTCTGAATCTT
59.301
41.667
0.00
0.00
0.00
2.40
4068
5799
8.200792
GGTACCATATATGATGATTCAGGAGTC
58.799
40.741
14.54
0.00
34.73
3.36
4216
5947
9.891828
GTGATTACAACTTTGAATGTTCATACA
57.108
29.630
0.00
0.00
37.00
2.29
5537
7268
2.040545
TGGATAAAACCTTGCCGGAAGA
59.959
45.455
5.05
0.00
32.82
2.87
6093
7940
8.470657
TTTATAAATACAGTATGCAATGCCCA
57.529
30.769
1.53
0.00
42.53
5.36
6181
8028
1.434696
GGGCTTGTGATGCGAATGG
59.565
57.895
0.00
0.00
0.00
3.16
6311
8170
1.739196
GTGATCTGCACAGCTCGCA
60.739
57.895
9.52
7.12
46.91
5.10
6336
8195
1.654023
GGAAACGATGCCTTTCCCGG
61.654
60.000
0.00
0.00
40.59
5.73
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
13
14
9.512435
ACATGTGTAGTACGAGTATTCAAATAC
57.488
33.333
0.00
4.99
41.19
1.89
36
37
5.754782
TCATTATTGTACTTGGCCTGACAT
58.245
37.500
3.32
0.00
0.00
3.06
86
93
3.967335
CGCGATCGGGTCCTCCTC
61.967
72.222
22.77
0.00
0.00
3.71
293
1741
0.030369
CGGGTAGTACGACTGATGCC
59.970
60.000
6.07
0.00
0.00
4.40
307
1755
4.015406
CTGGTGCTGGTGCGGGTA
62.015
66.667
0.00
0.00
43.34
3.69
309
1757
4.015406
TACTGGTGCTGGTGCGGG
62.015
66.667
0.00
0.00
43.34
6.13
311
1759
2.742372
GGTACTGGTGCTGGTGCG
60.742
66.667
0.00
0.00
43.34
5.34
312
1760
1.672356
CTGGTACTGGTGCTGGTGC
60.672
63.158
0.00
0.00
40.20
5.01
313
1761
0.973632
TACTGGTACTGGTGCTGGTG
59.026
55.000
0.00
0.00
0.00
4.17
314
1762
0.974383
GTACTGGTACTGGTGCTGGT
59.026
55.000
3.89
0.00
33.45
4.00
315
1763
0.249398
GGTACTGGTACTGGTGCTGG
59.751
60.000
10.19
0.00
36.36
4.85
316
1764
0.973632
TGGTACTGGTACTGGTGCTG
59.026
55.000
10.19
0.00
36.36
4.41
317
1765
1.267121
CTGGTACTGGTACTGGTGCT
58.733
55.000
10.19
0.00
36.36
4.40
318
1766
0.974383
ACTGGTACTGGTACTGGTGC
59.026
55.000
10.19
0.00
36.36
5.01
319
1767
2.494870
GGTACTGGTACTGGTACTGGTG
59.505
54.545
19.84
2.61
37.93
4.17
320
1768
2.812658
GGTACTGGTACTGGTACTGGT
58.187
52.381
19.84
10.84
37.93
4.00
321
1769
1.747355
CGGTACTGGTACTGGTACTGG
59.253
57.143
20.04
13.05
39.18
4.00
322
1770
1.133790
GCGGTACTGGTACTGGTACTG
59.866
57.143
21.87
21.87
42.50
2.74
323
1771
1.467920
GCGGTACTGGTACTGGTACT
58.532
55.000
17.89
0.00
41.52
2.73
324
1772
0.457443
GGCGGTACTGGTACTGGTAC
59.543
60.000
17.89
15.45
41.52
3.34
325
1773
0.039472
TGGCGGTACTGGTACTGGTA
59.961
55.000
17.89
0.00
41.52
3.25
634
2347
1.440938
ATCGAGCCGAGACGAAGAGG
61.441
60.000
0.00
0.00
39.91
3.69
799
2517
3.023949
GCCTCACCTCATGTCGCCT
62.024
63.158
0.00
0.00
0.00
5.52
805
2523
0.609131
AAAACCCGCCTCACCTCATG
60.609
55.000
0.00
0.00
0.00
3.07
920
2647
1.924191
GCCACAACACGGATCAAAACG
60.924
52.381
0.00
0.00
0.00
3.60
1790
3520
1.586422
CAACCGGTGGCATCATAGAG
58.414
55.000
8.52
0.00
0.00
2.43
1856
3587
1.761784
AGCCTGCAGAGAGACCATAAG
59.238
52.381
17.39
0.00
0.00
1.73
1868
3599
1.174783
AAAATGCTCTCAGCCTGCAG
58.825
50.000
6.78
6.78
41.51
4.41
1871
3602
5.181748
AGTAACTAAAATGCTCTCAGCCTG
58.818
41.667
0.00
0.00
41.51
4.85
1992
3723
2.346365
GGTTTTCCTCCGCCGTCT
59.654
61.111
0.00
0.00
36.94
4.18
2143
3874
5.786401
ATCAACAAGTGAAAGAGCGTATC
57.214
39.130
0.00
0.00
40.50
2.24
2144
3875
6.560253
AAATCAACAAGTGAAAGAGCGTAT
57.440
33.333
0.00
0.00
40.50
3.06
2145
3876
7.485418
TTAAATCAACAAGTGAAAGAGCGTA
57.515
32.000
0.00
0.00
40.50
4.42
2146
3877
4.900635
AAATCAACAAGTGAAAGAGCGT
57.099
36.364
0.00
0.00
40.50
5.07
2307
4038
1.003580
TGATGGAGGAGACTTTGCCAC
59.996
52.381
0.00
0.00
44.43
5.01
3038
4769
7.396540
AATTACCTGTCCATCTGAATTTGAC
57.603
36.000
0.00
0.00
0.00
3.18
3070
4801
3.863142
ATCAACTGAAATGGCAAGCTC
57.137
42.857
0.00
0.00
0.00
4.09
3079
4810
6.209192
TGGCTTGTGACATAATCAACTGAAAT
59.791
34.615
0.00
0.00
39.72
2.17
3466
5197
2.028404
GCATGCATTCGTTTTTGCTAGC
59.972
45.455
14.21
8.10
39.60
3.42
3856
5587
1.838112
TACGGCCCTTAAGAACGAGA
58.162
50.000
16.49
5.19
0.00
4.04
4047
5778
7.914871
GTCTCGACTCCTGAATCATCATATATG
59.085
40.741
6.36
6.36
34.37
1.78
4068
5799
1.403780
CCCGGTAAGTCAAAGGTCTCG
60.404
57.143
0.00
0.00
0.00
4.04
4175
5906
6.614694
TGTAATCACCTTCCTAGTGCTAAA
57.385
37.500
0.00
0.00
35.14
1.85
4216
5947
2.158623
TGAACCTGTTCTCAACCTGCAT
60.159
45.455
11.03
0.00
40.14
3.96
5537
7268
7.353525
TGATTATCCCCACATATCAACACTTT
58.646
34.615
0.00
0.00
0.00
2.66
5757
7494
5.359576
AGATTCACACTTACACCAGCAAAAA
59.640
36.000
0.00
0.00
0.00
1.94
5864
7601
9.834628
CTAAACACAAGACAAAACAGTAAGAAA
57.165
29.630
0.00
0.00
0.00
2.52
5865
7602
9.221933
TCTAAACACAAGACAAAACAGTAAGAA
57.778
29.630
0.00
0.00
0.00
2.52
5866
7603
8.662141
GTCTAAACACAAGACAAAACAGTAAGA
58.338
33.333
0.00
0.00
42.43
2.10
6012
7760
3.081804
ACCCAGGCTTTCTATCAAAACG
58.918
45.455
0.00
0.00
0.00
3.60
6043
7792
2.991190
CAAGGAAATGCATGCACAGAAC
59.009
45.455
25.37
12.57
0.00
3.01
6093
7940
2.545526
CACGGAAGCGAATCAGCATAAT
59.454
45.455
0.00
0.00
40.15
1.28
6168
8015
1.102809
GGCATCCCATTCGCATCACA
61.103
55.000
0.00
0.00
0.00
3.58
6181
8028
3.514417
GGAAAAGCTCCGGCATCC
58.486
61.111
0.00
0.00
41.70
3.51
6272
8119
3.706373
TCTGGGTCCGGCTTCTGC
61.706
66.667
0.00
0.00
38.76
4.26
6273
8120
2.266055
GTCTGGGTCCGGCTTCTG
59.734
66.667
0.00
0.00
0.00
3.02
6311
8170
0.611714
AAGGCATCGTTTCCTACCGT
59.388
50.000
0.00
0.00
31.24
4.83
Based at the University of Bristol with support from BBSRC .
AutoCloner maintained by Alex Coulton.