Multiple sequence alignment - TraesCS3D01G403500
Loading Multiple Alignment...
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
TraesCS3D01G403500
chr3D
100.000
3474
0
0
1
3474
517487139
517490612
0.000000e+00
6416
1
TraesCS3D01G403500
chr3D
86.364
110
14
1
645
753
46257311
46257202
6.090000e-23
119
2
TraesCS3D01G403500
chr3B
92.048
2427
104
33
379
2750
681209804
681212196
0.000000e+00
3330
3
TraesCS3D01G403500
chr3B
89.959
727
52
12
2753
3474
681493922
681494632
0.000000e+00
918
4
TraesCS3D01G403500
chr3B
88.580
324
24
11
1
315
681209204
681209523
7.040000e-102
381
5
TraesCS3D01G403500
chr3B
88.591
298
26
7
141
431
681209522
681209818
4.260000e-94
355
6
TraesCS3D01G403500
chr3B
87.273
110
13
1
645
753
72457562
72457453
1.310000e-24
124
7
TraesCS3D01G403500
chr3A
92.784
1857
69
26
824
2647
653330721
653332545
0.000000e+00
2627
8
TraesCS3D01G403500
chr3A
88.401
638
24
12
2843
3474
653332814
653333407
0.000000e+00
723
9
TraesCS3D01G403500
chr3A
87.021
339
30
11
3
330
653329775
653330110
1.520000e-98
370
10
TraesCS3D01G403500
chr3A
87.786
262
22
8
180
432
653330113
653330373
7.290000e-77
298
11
TraesCS3D01G403500
chr3A
79.635
329
43
17
2714
3038
72287771
72287463
7.550000e-52
215
12
TraesCS3D01G403500
chr7D
81.271
598
80
19
2714
3304
571875068
571874496
4.090000e-124
455
13
TraesCS3D01G403500
chr7B
82.172
488
69
15
2714
3197
628461783
628461310
1.500000e-108
403
14
TraesCS3D01G403500
chr2A
76.690
562
94
31
1802
2334
580385010
580385563
9.500000e-71
278
15
TraesCS3D01G403500
chr2D
77.200
500
82
28
1802
2276
413353626
413354118
2.660000e-66
263
16
TraesCS3D01G403500
chr2B
75.593
590
105
32
1715
2276
486843653
486844231
4.450000e-64
255
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
TraesCS3D01G403500
chr3D
517487139
517490612
3473
False
6416.000000
6416
100.000000
1
3474
1
chr3D.!!$F1
3473
1
TraesCS3D01G403500
chr3B
681209204
681212196
2992
False
1355.333333
3330
89.739667
1
2750
3
chr3B.!!$F2
2749
2
TraesCS3D01G403500
chr3B
681493922
681494632
710
False
918.000000
918
89.959000
2753
3474
1
chr3B.!!$F1
721
3
TraesCS3D01G403500
chr3A
653329775
653333407
3632
False
1004.500000
2627
88.998000
3
3474
4
chr3A.!!$F1
3471
4
TraesCS3D01G403500
chr7D
571874496
571875068
572
True
455.000000
455
81.271000
2714
3304
1
chr7D.!!$R1
590
5
TraesCS3D01G403500
chr2A
580385010
580385563
553
False
278.000000
278
76.690000
1802
2334
1
chr2A.!!$F1
532
6
TraesCS3D01G403500
chr2B
486843653
486844231
578
False
255.000000
255
75.593000
1715
2276
1
chr2B.!!$F1
561
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
892
1256
0.040058
AACCTGCATGGATCAAGGCA
59.96
50.0
9.46
9.46
39.71
4.75
F
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
Orientation
2486
2934
1.207791
GAGACATGACATGAGGGGGT
58.792
55.0
22.19
0.0
0.0
4.95
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
67
69
2.159114
GCACCCGGATAAACAAATGCAT
60.159
45.455
0.73
0.00
0.00
3.96
73
75
6.603997
ACCCGGATAAACAAATGCATAAGTAA
59.396
34.615
0.73
0.00
0.00
2.24
110
112
4.881273
ACATGTTCACTTGTTCTAGTTGCA
59.119
37.500
0.00
0.00
31.23
4.08
167
352
8.336080
GTTGCTCCATAAAAACTATAGTGCTAC
58.664
37.037
6.06
5.65
0.00
3.58
168
353
6.700081
TGCTCCATAAAAACTATAGTGCTACG
59.300
38.462
6.06
0.00
0.00
3.51
228
415
3.213506
TCTCAGACCACCACAAATGTTG
58.786
45.455
0.00
0.00
0.00
3.33
280
467
7.435068
AACAAGCATACAAGTTAGTTACCAG
57.565
36.000
0.00
0.00
0.00
4.00
286
473
9.953565
AGCATACAAGTTAGTTACCAGAAAATA
57.046
29.630
0.00
0.00
0.00
1.40
340
534
2.746277
GTCCATCCGGGTGCACAC
60.746
66.667
20.43
15.50
38.11
3.82
415
647
6.183361
ACACTAAGAGGATGGTTTGTAAGGTT
60.183
38.462
0.00
0.00
0.00
3.50
419
651
5.701224
AGAGGATGGTTTGTAAGGTTGAAA
58.299
37.500
0.00
0.00
0.00
2.69
446
678
5.384063
TTGCACAAACCGATATTGTCAAT
57.616
34.783
3.06
3.06
38.90
2.57
557
789
8.937207
ACTCCCTCTGTAACTTAATATACGAT
57.063
34.615
0.00
0.00
0.00
3.73
561
793
7.749570
CCCTCTGTAACTTAATATACGATGTCG
59.250
40.741
0.11
0.11
46.33
4.35
674
908
4.065088
TGTCAGAGCAATTAGTCGCTTTT
58.935
39.130
0.00
0.00
38.99
2.27
686
920
1.662446
CGCTTTTGGCAGTGGCTTG
60.662
57.895
18.53
6.37
41.91
4.01
697
937
0.392998
AGTGGCTTGCATTCCCTACG
60.393
55.000
0.00
0.00
0.00
3.51
698
938
1.748879
TGGCTTGCATTCCCTACGC
60.749
57.895
0.00
0.00
0.00
4.42
699
939
1.748879
GGCTTGCATTCCCTACGCA
60.749
57.895
0.00
0.00
0.00
5.24
744
1092
4.632153
AGCAGTGATTTTCAAGTAGTCGT
58.368
39.130
0.00
0.00
0.00
4.34
793
1141
1.755179
CAGCAAAATGATCCGAGGGT
58.245
50.000
0.00
0.00
0.00
4.34
858
1222
6.401477
CGTTTTTCACGTAACAGTCAAATC
57.599
37.500
0.00
0.00
44.49
2.17
859
1223
6.189567
CGTTTTTCACGTAACAGTCAAATCT
58.810
36.000
0.00
0.00
44.49
2.40
881
1245
1.812571
GTGGTTCGATTCAACCTGCAT
59.187
47.619
14.81
0.00
45.54
3.96
892
1256
0.040058
AACCTGCATGGATCAAGGCA
59.960
50.000
9.46
9.46
39.71
4.75
916
1281
3.005897
CGTCTGTTATCCGATCCATCCTT
59.994
47.826
0.00
0.00
0.00
3.36
962
1327
2.165437
CTCTCTCTGGAGTGCTAACCAC
59.835
54.545
0.00
0.00
45.01
4.16
974
1339
4.140663
AGTGCTAACCACCCTCCTCTATAT
60.141
45.833
0.00
0.00
45.83
0.86
1217
1607
3.095347
GCCACCATCCTCTCCGTCC
62.095
68.421
0.00
0.00
0.00
4.79
1219
1609
1.753078
CACCATCCTCTCCGTCCGA
60.753
63.158
0.00
0.00
0.00
4.55
1253
1643
0.103208
CGGTACTGGCTGCTCTTAGG
59.897
60.000
0.00
0.00
0.00
2.69
1300
1699
3.058450
GTTGAGATGGAGATGCTGATCG
58.942
50.000
0.00
0.00
33.34
3.69
1370
1769
4.667519
GTACAAGACCATCGGAGGTTAT
57.332
45.455
1.25
0.00
43.38
1.89
1399
1798
3.304257
CGCTGCTTGATCTTGAACTGTTT
60.304
43.478
0.00
0.00
0.00
2.83
1400
1799
4.083855
CGCTGCTTGATCTTGAACTGTTTA
60.084
41.667
0.00
0.00
0.00
2.01
1446
1849
1.062525
GTGCCGCCGACATTGATTC
59.937
57.895
0.00
0.00
0.00
2.52
1467
1870
7.647715
TGATTCGTTTGTTTGATCCTTTCTTTC
59.352
33.333
0.00
0.00
0.00
2.62
1470
1873
7.543756
TCGTTTGTTTGATCCTTTCTTTCTTT
58.456
30.769
0.00
0.00
0.00
2.52
2369
2808
3.682792
GGATCCGATCCGATCCGT
58.317
61.111
22.21
0.00
46.73
4.69
2486
2934
3.751246
CGTTACGGCCGGTGAGGA
61.751
66.667
31.76
5.12
45.00
3.71
2507
2955
1.140452
CCCCCTCATGTCATGTCTCAG
59.860
57.143
12.54
2.83
0.00
3.35
2514
2962
1.247567
TGTCATGTCTCAGTCGCTCA
58.752
50.000
0.00
0.00
0.00
4.26
2589
3037
1.740025
GCTTGGTGTCTAGGATTGTGC
59.260
52.381
0.00
0.00
0.00
4.57
2638
3086
6.838090
TGGGCATCCATATTTTAGAATTCACA
59.162
34.615
8.44
0.00
38.32
3.58
2641
3089
8.579006
GGCATCCATATTTTAGAATTCACATCA
58.421
33.333
8.44
0.00
0.00
3.07
2660
3108
6.048509
ACATCAATTGTGTCTCGCATATACA
58.951
36.000
5.13
0.00
37.11
2.29
2664
3112
6.202762
TCAATTGTGTCTCGCATATACATTCC
59.797
38.462
5.13
0.00
0.00
3.01
2669
3117
3.086282
TCTCGCATATACATTCCGCCTA
58.914
45.455
0.00
0.00
0.00
3.93
2670
3118
3.119602
TCTCGCATATACATTCCGCCTAC
60.120
47.826
0.00
0.00
0.00
3.18
2676
3124
6.210078
GCATATACATTCCGCCTACTATCTC
58.790
44.000
0.00
0.00
0.00
2.75
2677
3125
6.039941
GCATATACATTCCGCCTACTATCTCT
59.960
42.308
0.00
0.00
0.00
3.10
2678
3126
5.906113
ATACATTCCGCCTACTATCTCTG
57.094
43.478
0.00
0.00
0.00
3.35
2680
3128
3.823873
ACATTCCGCCTACTATCTCTGAG
59.176
47.826
0.00
0.00
0.00
3.35
2681
3129
3.859061
TTCCGCCTACTATCTCTGAGA
57.141
47.619
10.23
10.23
0.00
3.27
2710
3259
6.056236
GTCTCCCCAATCTAATCTTACCAAC
58.944
44.000
0.00
0.00
0.00
3.77
2730
3281
2.198304
CTCCCTTACACTGCCACCCC
62.198
65.000
0.00
0.00
0.00
4.95
2750
3301
3.987220
CCCCACACTTTGAATTTAAAGCG
59.013
43.478
19.50
14.07
40.48
4.68
2758
3309
9.632807
ACACTTTGAATTTAAAGCGCATAATTA
57.367
25.926
19.50
0.06
40.48
1.40
2946
3500
3.760684
GAGCTCACAAAATGGACCTGAAT
59.239
43.478
9.40
0.00
0.00
2.57
3039
3599
4.335594
AGCAAATCGGTAGTTAAATGCTCC
59.664
41.667
0.00
0.00
38.42
4.70
3129
3693
5.122239
CCTTTGCATAGAACATTCGTCTTCA
59.878
40.000
5.65
0.00
0.00
3.02
3160
3724
0.751277
TGGGTCAATATGGCTTGGCG
60.751
55.000
0.00
0.00
31.42
5.69
3249
3813
6.849305
GCCGAATATTTTATTTCCGTGTACTG
59.151
38.462
0.00
0.00
0.00
2.74
3306
3872
9.405587
GATGTCGGACAATAAAATTGAAAAAGA
57.594
29.630
15.72
0.00
0.00
2.52
3361
3928
2.952310
GTTTTGTGCCAGAAGAAGACCT
59.048
45.455
0.00
0.00
0.00
3.85
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
16
17
0.467290
AGGAGCCAAAACTTCGCCAA
60.467
50.000
0.00
0.00
0.00
4.52
73
75
9.912634
CAAGTGAACATGTTTATTGTTAATCCT
57.087
29.630
13.36
0.00
37.43
3.24
97
99
6.760298
TGAAAATTTGCATGCAACTAGAACAA
59.240
30.769
31.99
15.70
35.46
2.83
110
112
7.218614
TGTCATTTCTCCTTGAAAATTTGCAT
58.781
30.769
0.00
0.00
46.32
3.96
228
415
5.351189
ACTGTGCAAAAATTGGTGAAGAAAC
59.649
36.000
0.00
0.00
0.00
2.78
340
534
8.799695
AGAAATTCAATTCTAAGCCTGAGCTCG
61.800
40.741
9.64
3.88
40.79
5.03
352
546
9.393249
CGTGCTTTTAACAGAAATTCAATTCTA
57.607
29.630
0.00
0.00
37.56
2.10
375
569
6.199154
CCTCTTAGTGTGCAATATAGTTCGTG
59.801
42.308
0.00
0.00
0.00
4.35
376
570
6.096423
TCCTCTTAGTGTGCAATATAGTTCGT
59.904
38.462
0.00
0.00
0.00
3.85
415
647
9.676195
CAATATCGGTTTGTGCAATATATTTCA
57.324
29.630
0.00
0.00
0.00
2.69
419
651
8.389779
TGACAATATCGGTTTGTGCAATATAT
57.610
30.769
0.00
0.00
37.43
0.86
494
726
4.941263
TGCGATTGTATTTTTAGCAGGAGT
59.059
37.500
0.00
0.00
0.00
3.85
631
864
9.533253
CTGACAATCATGTATGTATCTGTAACA
57.467
33.333
6.20
0.00
40.74
2.41
634
867
8.084684
GCTCTGACAATCATGTATGTATCTGTA
58.915
37.037
6.20
0.00
40.74
2.74
642
875
8.151141
ACTAATTGCTCTGACAATCATGTATG
57.849
34.615
0.00
0.00
40.74
2.39
644
877
6.476706
CGACTAATTGCTCTGACAATCATGTA
59.523
38.462
0.00
0.00
40.74
2.29
645
878
5.292834
CGACTAATTGCTCTGACAATCATGT
59.707
40.000
0.00
0.00
44.25
3.21
646
879
5.735324
CGACTAATTGCTCTGACAATCATG
58.265
41.667
6.12
0.00
39.32
3.07
653
887
4.398247
CAAAAGCGACTAATTGCTCTGAC
58.602
43.478
0.00
0.00
45.59
3.51
674
908
2.277591
GGAATGCAAGCCACTGCCA
61.278
57.895
0.00
0.00
41.90
4.92
686
920
1.090052
GGTCACTGCGTAGGGAATGC
61.090
60.000
7.16
0.00
38.28
3.56
699
939
3.558931
TTGTTCACATCACAGGTCACT
57.441
42.857
0.00
0.00
0.00
3.41
714
954
7.294676
ACTTGAAAATCACTGCTTTTTGTTC
57.705
32.000
0.00
0.00
0.00
3.18
811
1159
4.524714
GCAACTATCAGGCTCTACTCCATA
59.475
45.833
0.00
0.00
0.00
2.74
858
1222
1.806542
CAGGTTGAATCGAACCACCAG
59.193
52.381
14.99
6.62
46.94
4.00
859
1223
1.890876
CAGGTTGAATCGAACCACCA
58.109
50.000
14.99
0.00
46.94
4.17
881
1245
1.078918
CAGACGCTGCCTTGATCCA
60.079
57.895
0.00
0.00
0.00
3.41
892
1256
1.399714
TGGATCGGATAACAGACGCT
58.600
50.000
0.00
0.00
0.00
5.07
974
1339
6.205464
CGTATACTCTTGTTTCCTCCGGTATA
59.795
42.308
0.00
0.00
0.00
1.47
984
1349
4.174009
TCAGCTGCGTATACTCTTGTTTC
58.826
43.478
9.47
0.00
0.00
2.78
1015
1380
3.881688
CCGCCATGATTCTCTCTCAAAAT
59.118
43.478
0.00
0.00
0.00
1.82
1019
1409
0.105593
GCCGCCATGATTCTCTCTCA
59.894
55.000
0.00
0.00
0.00
3.27
1217
1607
1.443872
CGTTCTTGTCGGGGAGTCG
60.444
63.158
0.00
0.00
0.00
4.18
1219
1609
3.057337
CCGTTCTTGTCGGGGAGT
58.943
61.111
0.00
0.00
43.68
3.85
1253
1643
7.787725
AGAAACATAATCAAGGGAATACGTC
57.212
36.000
0.00
0.00
0.00
4.34
1270
1660
5.125097
GCATCTCCATCTCAACAAGAAACAT
59.875
40.000
0.00
0.00
37.61
2.71
1300
1699
3.069872
TGCCAATTAACCATGGATGCATC
59.930
43.478
21.47
18.81
39.12
3.91
1370
1769
2.281692
ATCAAGCAGCGCACCACA
60.282
55.556
11.47
0.00
0.00
4.17
1415
1814
3.884774
GGCACCACCAGTCCACCA
61.885
66.667
0.00
0.00
38.86
4.17
1446
1849
7.755582
AAAGAAAGAAAGGATCAAACAAACG
57.244
32.000
0.00
0.00
0.00
3.60
1470
1873
3.558006
TCATTCTGCGTCGTCAAGAAAAA
59.442
39.130
9.97
1.83
0.00
1.94
1473
1876
2.058798
GTCATTCTGCGTCGTCAAGAA
58.941
47.619
8.81
8.81
0.00
2.52
1474
1877
1.000717
TGTCATTCTGCGTCGTCAAGA
60.001
47.619
0.00
0.00
0.00
3.02
1475
1878
1.125021
GTGTCATTCTGCGTCGTCAAG
59.875
52.381
0.00
0.00
0.00
3.02
1477
1880
0.666274
GGTGTCATTCTGCGTCGTCA
60.666
55.000
0.00
0.00
0.00
4.35
1479
1882
0.944311
GTGGTGTCATTCTGCGTCGT
60.944
55.000
0.00
0.00
0.00
4.34
1480
1883
1.626654
GGTGGTGTCATTCTGCGTCG
61.627
60.000
0.00
0.00
0.00
5.12
1481
1884
0.320771
AGGTGGTGTCATTCTGCGTC
60.321
55.000
0.00
0.00
0.00
5.19
1482
1885
0.973632
TAGGTGGTGTCATTCTGCGT
59.026
50.000
0.00
0.00
0.00
5.24
2353
2788
1.507174
GGACGGATCGGATCGGATC
59.493
63.158
26.93
26.93
41.67
3.36
2354
2789
2.333417
CGGACGGATCGGATCGGAT
61.333
63.158
26.28
15.03
34.17
4.18
2355
2790
2.976350
CGGACGGATCGGATCGGA
60.976
66.667
26.28
5.34
34.17
4.55
2369
2808
1.265635
CATCGAAAACTTGTTGCCGGA
59.734
47.619
5.05
0.00
0.00
5.14
2486
2934
1.207791
GAGACATGACATGAGGGGGT
58.792
55.000
22.19
0.00
0.00
4.95
2507
2955
2.105128
CACGGGAGGATGAGCGAC
59.895
66.667
0.00
0.00
0.00
5.19
2589
3037
3.817647
CTGAGGTTCTGAACAAAAGAGGG
59.182
47.826
21.01
0.82
0.00
4.30
2638
3086
7.095060
GGAATGTATATGCGAGACACAATTGAT
60.095
37.037
13.59
0.00
30.44
2.57
2641
3089
5.177511
CGGAATGTATATGCGAGACACAATT
59.822
40.000
0.00
0.00
30.44
2.32
2660
3108
4.076394
GTCTCAGAGATAGTAGGCGGAAT
58.924
47.826
2.64
0.00
0.00
3.01
2664
3112
3.071479
GGAGTCTCAGAGATAGTAGGCG
58.929
54.545
2.64
0.00
0.00
5.52
2710
3259
1.299976
GGTGGCAGTGTAAGGGAGG
59.700
63.158
0.00
0.00
0.00
4.30
2730
3281
4.047822
TGCGCTTTAAATTCAAAGTGTGG
58.952
39.130
14.60
0.00
44.29
4.17
2878
3432
7.446106
TTTCTAGACCAATATTAGCTTCCCA
57.554
36.000
0.00
0.00
0.00
4.37
2879
3433
8.747538
TTTTTCTAGACCAATATTAGCTTCCC
57.252
34.615
0.00
0.00
0.00
3.97
2880
3434
9.397280
ACTTTTTCTAGACCAATATTAGCTTCC
57.603
33.333
0.00
0.00
0.00
3.46
3013
3573
7.255139
GGAGCATTTAACTACCGATTTGCTTAT
60.255
37.037
0.00
0.00
39.15
1.73
3039
3599
2.968675
ACTCGGGAAAGTTGGTTATCG
58.031
47.619
0.00
0.00
0.00
2.92
3080
3641
7.758076
GGCTATTGTTTTAAGGATGGTGTAAAC
59.242
37.037
0.00
0.00
0.00
2.01
3101
3665
5.126067
ACGAATGTTCTATGCAAAGGCTAT
58.874
37.500
0.00
0.00
41.91
2.97
3147
3711
0.684153
AAGTGCCGCCAAGCCATATT
60.684
50.000
0.00
0.00
0.00
1.28
3249
3813
8.181904
TCCTTCCTCCAATAATATGAAAATGC
57.818
34.615
0.00
0.00
0.00
3.56
3306
3872
8.504005
CCTATTGTCGTTTTATTGTTTCTCAGT
58.496
33.333
0.00
0.00
0.00
3.41
3392
3959
3.766691
GGTCGCTTAGGCCGTCCA
61.767
66.667
0.00
0.00
33.32
4.02
Based at the University of Bristol with support from BBSRC .
AutoCloner maintained by Alex Coulton.