Multiple sequence alignment - TraesCS4A01G440500

Loading Multiple Alignment...

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 TraesCS4A01G440500 chr4A 100.000 5904 0 0 1 5904 709423229 709417326 0.000000e+00 10903.0
1 TraesCS4A01G440500 chr4A 99.339 5904 25 4 1 5904 709570845 709564956 0.000000e+00 10674.0
2 TraesCS4A01G440500 chr4A 99.387 4892 25 4 1 4892 709276894 709272008 0.000000e+00 8863.0
3 TraesCS4A01G440500 chr4A 94.697 4507 181 29 398 4868 709616923 709612439 0.000000e+00 6946.0
4 TraesCS4A01G440500 chr4A 84.335 1730 220 16 3237 4965 709207285 709205606 0.000000e+00 1646.0
5 TraesCS4A01G440500 chr4A 78.591 1476 251 41 3298 4732 709717807 709716356 0.000000e+00 915.0
6 TraesCS4A01G440500 chr4A 95.491 377 13 2 5529 5904 709612384 709612011 3.040000e-167 599.0
7 TraesCS4A01G440500 chr4A 93.684 380 20 2 5529 5904 709271988 709271609 3.090000e-157 566.0
8 TraesCS4A01G440500 chr4A 90.283 247 24 0 1238 1484 709209617 709209371 2.050000e-84 324.0
9 TraesCS4A01G440500 chr4A 97.143 70 2 0 4901 4970 709612446 709612377 1.040000e-22 119.0
10 TraesCS4A01G440500 chr4A 100.000 34 0 0 1950 1983 709615431 709615398 4.940000e-06 63.9
11 TraesCS4A01G440500 chr4A 86.538 52 4 3 1755 1804 554837524 554837474 3.000000e-03 54.7
12 TraesCS4A01G440500 chr4A 100.000 28 0 0 4943 4970 709272008 709271981 1.100000e-02 52.8
13 TraesCS4A01G440500 chr7A 89.492 3940 287 60 858 4751 26105913 26102055 0.000000e+00 4865.0
14 TraesCS4A01G440500 chr7A 89.227 854 50 19 1 821 26106896 26106052 0.000000e+00 1029.0
15 TraesCS4A01G440500 chr7A 79.823 1467 232 43 3298 4732 26241110 26239676 0.000000e+00 1011.0
16 TraesCS4A01G440500 chr7A 87.708 781 89 4 3936 4713 26057509 26056733 0.000000e+00 904.0
17 TraesCS4A01G440500 chr7A 88.525 244 28 0 1241 1484 26060126 26059883 4.470000e-76 296.0
18 TraesCS4A01G440500 chrUn 100.000 2275 0 0 269 2543 346599310 346601584 0.000000e+00 4202.0
19 TraesCS4A01G440500 chrUn 99.862 2180 2 1 1894 4073 350559109 350561287 0.000000e+00 4008.0
20 TraesCS4A01G440500 chr7D 90.903 3023 213 31 1972 4970 25291073 25288089 0.000000e+00 4002.0
21 TraesCS4A01G440500 chr7D 87.888 966 66 29 863 1784 25292115 25291157 0.000000e+00 1088.0
22 TraesCS4A01G440500 chr7D 92.483 745 44 6 1 737 25293099 25292359 0.000000e+00 1055.0
23 TraesCS4A01G440500 chr7D 86.018 565 73 5 4968 5528 418638718 418639280 8.470000e-168 601.0
24 TraesCS4A01G440500 chr7D 85.664 565 80 1 4965 5528 367585360 367585924 1.420000e-165 593.0
25 TraesCS4A01G440500 chr7D 89.388 245 26 0 1254 1498 25338520 25338276 5.750000e-80 309.0
26 TraesCS4A01G440500 chr7D 95.312 128 5 1 5530 5656 25288095 25287968 1.000000e-47 202.0
27 TraesCS4A01G440500 chr7D 89.041 73 5 3 1755 1824 117545281 117545209 2.930000e-13 87.9
28 TraesCS4A01G440500 chr1D 87.189 562 68 3 4971 5528 362791460 362792021 2.320000e-178 636.0
29 TraesCS4A01G440500 chr4D 86.348 564 73 3 4970 5532 230660606 230660046 3.910000e-171 612.0
30 TraesCS4A01G440500 chr4D 85.893 560 77 2 4971 5529 444274426 444274984 3.940000e-166 595.0
31 TraesCS4A01G440500 chr4D 87.027 185 23 1 5721 5904 117738562 117738378 2.160000e-49 207.0
32 TraesCS4A01G440500 chr2A 86.042 566 76 3 4971 5533 33314141 33313576 6.540000e-169 604.0
33 TraesCS4A01G440500 chr2B 86.018 565 76 3 4968 5529 410101733 410102297 2.350000e-168 603.0
34 TraesCS4A01G440500 chr7B 85.340 573 81 3 4965 5535 102688066 102688637 1.830000e-164 590.0
35 TraesCS4A01G440500 chr3D 89.595 173 17 1 5712 5883 366011118 366010946 9.960000e-53 219.0
36 TraesCS4A01G440500 chr3D 88.108 185 20 2 5721 5904 463117432 463117249 9.960000e-53 219.0
37 TraesCS4A01G440500 chr3D 86.154 195 24 3 5712 5904 443428501 443428308 2.160000e-49 207.0
38 TraesCS4A01G440500 chr6D 85.787 197 24 4 5709 5904 13965226 13965419 7.760000e-49 206.0
39 TraesCS4A01G440500 chr5B 86.082 194 24 3 5713 5904 513810008 513810200 7.760000e-49 206.0
40 TraesCS4A01G440500 chr5B 97.297 37 1 0 2378 2414 369484692 369484656 4.940000e-06 63.9
41 TraesCS4A01G440500 chr6B 95.238 42 1 1 2373 2414 669010947 669010907 1.370000e-06 65.8


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 TraesCS4A01G440500 chr4A 709417326 709423229 5903 True 10903.000 10903 100.000000 1 5904 1 chr4A.!!$R2 5903
1 TraesCS4A01G440500 chr4A 709564956 709570845 5889 True 10674.000 10674 99.339000 1 5904 1 chr4A.!!$R3 5903
2 TraesCS4A01G440500 chr4A 709271609 709276894 5285 True 3160.600 8863 97.690333 1 5904 3 chr4A.!!$R6 5903
3 TraesCS4A01G440500 chr4A 709612011 709616923 4912 True 1931.975 6946 96.832750 398 5904 4 chr4A.!!$R7 5506
4 TraesCS4A01G440500 chr4A 709205606 709209617 4011 True 985.000 1646 87.309000 1238 4965 2 chr4A.!!$R5 3727
5 TraesCS4A01G440500 chr4A 709716356 709717807 1451 True 915.000 915 78.591000 3298 4732 1 chr4A.!!$R4 1434
6 TraesCS4A01G440500 chr7A 26102055 26106896 4841 True 2947.000 4865 89.359500 1 4751 2 chr7A.!!$R3 4750
7 TraesCS4A01G440500 chr7A 26239676 26241110 1434 True 1011.000 1011 79.823000 3298 4732 1 chr7A.!!$R1 1434
8 TraesCS4A01G440500 chr7A 26056733 26060126 3393 True 600.000 904 88.116500 1241 4713 2 chr7A.!!$R2 3472
9 TraesCS4A01G440500 chrUn 346599310 346601584 2274 False 4202.000 4202 100.000000 269 2543 1 chrUn.!!$F1 2274
10 TraesCS4A01G440500 chrUn 350559109 350561287 2178 False 4008.000 4008 99.862000 1894 4073 1 chrUn.!!$F2 2179
11 TraesCS4A01G440500 chr7D 25287968 25293099 5131 True 1586.750 4002 91.646500 1 5656 4 chr7D.!!$R3 5655
12 TraesCS4A01G440500 chr7D 418638718 418639280 562 False 601.000 601 86.018000 4968 5528 1 chr7D.!!$F2 560
13 TraesCS4A01G440500 chr7D 367585360 367585924 564 False 593.000 593 85.664000 4965 5528 1 chr7D.!!$F1 563
14 TraesCS4A01G440500 chr1D 362791460 362792021 561 False 636.000 636 87.189000 4971 5528 1 chr1D.!!$F1 557
15 TraesCS4A01G440500 chr4D 230660046 230660606 560 True 612.000 612 86.348000 4970 5532 1 chr4D.!!$R2 562
16 TraesCS4A01G440500 chr4D 444274426 444274984 558 False 595.000 595 85.893000 4971 5529 1 chr4D.!!$F1 558
17 TraesCS4A01G440500 chr2A 33313576 33314141 565 True 604.000 604 86.042000 4971 5533 1 chr2A.!!$R1 562
18 TraesCS4A01G440500 chr2B 410101733 410102297 564 False 603.000 603 86.018000 4968 5529 1 chr2B.!!$F1 561
19 TraesCS4A01G440500 chr7B 102688066 102688637 571 False 590.000 590 85.340000 4965 5535 1 chr7B.!!$F1 570

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
1208 1358 3.307691 CCTCTCTGTCTGTCTGTCTCTCT 60.308 52.174 0.0 0.0 0.0 3.1 F
1209 1359 3.935203 CTCTCTGTCTGTCTGTCTCTCTC 59.065 52.174 0.0 0.0 0.0 3.2 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
4489 6067 2.242882 TGGGGAACTCCTGGTAGTAC 57.757 55.000 0.0 0.0 35.95 2.73 R
5712 7319 7.016296 AGGGTCAATCCTCCTTTTCAAAATAA 58.984 34.615 0.0 0.0 36.25 1.40 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
1208 1358 3.307691 CCTCTCTGTCTGTCTGTCTCTCT 60.308 52.174 0.0 0.0 0.0 3.1
1209 1359 3.935203 CTCTCTGTCTGTCTGTCTCTCTC 59.065 52.174 0.0 0.0 0.0 3.2
4987 6576 5.221048 GCACGACTAAGGATGGCAATTTTAT 60.221 40.000 0.0 0.0 0.0 1.4
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1208 1358 3.056536 CCATGAAAACACGGAGAGAGAGA 60.057 47.826 0.0 0.0 0.00 3.10
1209 1359 3.257393 CCATGAAAACACGGAGAGAGAG 58.743 50.000 0.0 0.0 0.00 3.20
4489 6067 2.242882 TGGGGAACTCCTGGTAGTAC 57.757 55.000 0.0 0.0 35.95 2.73
5710 7317 8.977412 GGGTCAATCCTCCTTTTCAAAATAATA 58.023 33.333 0.0 0.0 36.25 0.98
5711 7318 7.679881 AGGGTCAATCCTCCTTTTCAAAATAAT 59.320 33.333 0.0 0.0 36.25 1.28
5712 7319 7.016296 AGGGTCAATCCTCCTTTTCAAAATAA 58.984 34.615 0.0 0.0 36.25 1.40


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

AutoCloner maintained by Alex Coulton.