Multiple sequence alignment - TraesCS2B01G142400

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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 TraesCS2B01G142400 chr2B 100.000 4580 0 0 1 4580 109184687 109180108 0.000000e+00 8458
1 TraesCS2B01G142400 chr2B 97.104 4247 98 7 1 4242 109873062 109868836 0.000000e+00 7138
2 TraesCS2B01G142400 chr2B 95.527 2638 90 6 1 2632 109093662 109091047 0.000000e+00 4193
3 TraesCS2B01G142400 chr2B 95.399 1304 50 3 2786 4079 109085401 109084098 0.000000e+00 2067
4 TraesCS2B01G142400 chr2B 92.695 972 66 5 2628 3596 109359520 109358551 0.000000e+00 1397
5 TraesCS2B01G142400 chr2B 97.569 288 6 1 4293 4580 109868816 109868530 4.120000e-135 492
6 TraesCS2B01G142400 chr2B 91.732 254 18 3 4330 4580 762029180 762029433 2.620000e-92 350
7 TraesCS2B01G142400 chr2B 85.551 263 14 4 4098 4337 109083887 109083626 2.110000e-63 254
8 TraesCS2B01G142400 chrUn 96.544 2633 83 6 1 2632 235541352 235543977 0.000000e+00 4351
9 TraesCS2B01G142400 chrUn 96.544 2633 83 6 1 2632 256966687 256964062 0.000000e+00 4351
10 TraesCS2B01G142400 chrUn 96.544 2633 83 6 1 2632 271157732 271155107 0.000000e+00 4351
11 TraesCS2B01G142400 chrUn 92.657 2642 130 27 2 2632 289663181 289660593 0.000000e+00 3746
12 TraesCS2B01G142400 chrUn 93.705 1382 70 9 2628 3993 289660540 289659160 0.000000e+00 2054
13 TraesCS2B01G142400 chr2D 95.211 2506 102 8 142 2632 72376580 72374078 0.000000e+00 3947
14 TraesCS2B01G142400 chr2D 94.923 2521 97 8 142 2632 72657078 72654559 0.000000e+00 3917
15 TraesCS2B01G142400 chr2D 95.497 1732 55 6 2628 4337 72654506 72652776 0.000000e+00 2745
16 TraesCS2B01G142400 chr2D 94.175 1734 53 9 2628 4337 72374025 72372316 0.000000e+00 2599
17 TraesCS2B01G142400 chr2D 91.165 249 12 5 4338 4578 482383890 482384136 3.420000e-86 329
18 TraesCS2B01G142400 chr2D 88.618 123 7 6 4334 4449 574938978 574939100 4.780000e-30 143
19 TraesCS2B01G142400 chr2A 92.771 2642 127 29 2 2632 71214815 71212227 0.000000e+00 3762
20 TraesCS2B01G142400 chr2A 91.408 2642 141 32 2 2632 71162033 71159467 0.000000e+00 3542
21 TraesCS2B01G142400 chr2A 95.226 1529 67 5 1105 2632 71315305 71313782 0.000000e+00 2414
22 TraesCS2B01G142400 chr2A 96.779 1428 40 3 2629 4055 71115661 71114239 0.000000e+00 2377
23 TraesCS2B01G142400 chr2A 93.777 1382 69 7 2628 3993 71212174 71210794 0.000000e+00 2060
24 TraesCS2B01G142400 chr2A 93.415 1382 74 7 2628 3993 71159414 71158034 0.000000e+00 2032
25 TraesCS2B01G142400 chr2A 93.271 1382 74 9 2628 3993 71313729 71312351 0.000000e+00 2019
26 TraesCS2B01G142400 chr2A 85.080 1756 199 35 918 2632 71155769 71154036 0.000000e+00 1733
27 TraesCS2B01G142400 chr2A 88.941 1058 72 23 2 1046 71316345 71315320 0.000000e+00 1264
28 TraesCS2B01G142400 chr2A 92.063 315 18 1 3686 3993 71263737 71263423 1.960000e-118 436
29 TraesCS2B01G142400 chr2A 88.487 304 13 5 4055 4337 71113828 71113526 9.430000e-92 348
30 TraesCS2B01G142400 chr2A 82.759 377 36 12 3987 4335 71079300 71078925 4.450000e-80 309
31 TraesCS2B01G142400 chr7A 91.667 252 15 5 4334 4580 625509948 625510198 1.220000e-90 344
32 TraesCS2B01G142400 chr6A 87.805 246 20 7 4338 4578 115748073 115747833 3.490000e-71 279
33 TraesCS2B01G142400 chr3D 93.651 189 8 3 4396 4580 537696857 537696669 3.490000e-71 279
34 TraesCS2B01G142400 chr5B 93.548 186 10 2 4394 4578 393673984 393674168 4.510000e-70 276
35 TraesCS2B01G142400 chr1A 92.896 183 11 2 4400 4580 44404756 44404574 9.770000e-67 265
36 TraesCS2B01G142400 chr4D 92.473 186 10 4 4396 4578 490616245 490616429 3.510000e-66 263
37 TraesCS2B01G142400 chr4A 89.831 118 10 2 4334 4449 152834039 152833922 2.850000e-32 150


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 TraesCS2B01G142400 chr2B 109180108 109184687 4579 True 8458.000000 8458 100.000000 1 4580 1 chr2B.!!$R2 4579
1 TraesCS2B01G142400 chr2B 109091047 109093662 2615 True 4193.000000 4193 95.527000 1 2632 1 chr2B.!!$R1 2631
2 TraesCS2B01G142400 chr2B 109868530 109873062 4532 True 3815.000000 7138 97.336500 1 4580 2 chr2B.!!$R5 4579
3 TraesCS2B01G142400 chr2B 109358551 109359520 969 True 1397.000000 1397 92.695000 2628 3596 1 chr2B.!!$R3 968
4 TraesCS2B01G142400 chr2B 109083626 109085401 1775 True 1160.500000 2067 90.475000 2786 4337 2 chr2B.!!$R4 1551
5 TraesCS2B01G142400 chrUn 235541352 235543977 2625 False 4351.000000 4351 96.544000 1 2632 1 chrUn.!!$F1 2631
6 TraesCS2B01G142400 chrUn 256964062 256966687 2625 True 4351.000000 4351 96.544000 1 2632 1 chrUn.!!$R1 2631
7 TraesCS2B01G142400 chrUn 271155107 271157732 2625 True 4351.000000 4351 96.544000 1 2632 1 chrUn.!!$R2 2631
8 TraesCS2B01G142400 chrUn 289659160 289663181 4021 True 2900.000000 3746 93.181000 2 3993 2 chrUn.!!$R3 3991
9 TraesCS2B01G142400 chr2D 72652776 72657078 4302 True 3331.000000 3917 95.210000 142 4337 2 chr2D.!!$R2 4195
10 TraesCS2B01G142400 chr2D 72372316 72376580 4264 True 3273.000000 3947 94.693000 142 4337 2 chr2D.!!$R1 4195
11 TraesCS2B01G142400 chr2A 71210794 71214815 4021 True 2911.000000 3762 93.274000 2 3993 2 chr2A.!!$R5 3991
12 TraesCS2B01G142400 chr2A 71154036 71162033 7997 True 2435.666667 3542 89.967667 2 3993 3 chr2A.!!$R4 3991
13 TraesCS2B01G142400 chr2A 71312351 71316345 3994 True 1899.000000 2414 92.479333 2 3993 3 chr2A.!!$R6 3991
14 TraesCS2B01G142400 chr2A 71113526 71115661 2135 True 1362.500000 2377 92.633000 2629 4337 2 chr2A.!!$R3 1708

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
317 324 1.611673 CCATCTCCCTTGTTGCTTCGT 60.612 52.381 0.0 0.0 0.00 3.85 F
1608 1648 0.756294 TGTCCGCCTCTTTGAAGACA 59.244 50.000 0.0 0.0 32.15 3.41 F
2008 2048 3.904800 ATGGTGGTGATATCGACAACA 57.095 42.857 16.5 16.5 34.71 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1930 1970 1.879380 TCCTTCAGCAAAACCATGTCG 59.121 47.619 0.0 0.0 0.0 4.35 R
3095 3219 4.712829 TGATCTTCCCCGTAGTTTGATACA 59.287 41.667 0.0 0.0 0.0 2.29 R
3979 4127 2.238646 ACATTCCCAGCACCGAAATCTA 59.761 45.455 0.0 0.0 0.0 1.98 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
249 256 3.150335 CTCTAGAGCGCAGGGGCA 61.150 66.667 11.47 0.0 41.24 5.36
317 324 1.611673 CCATCTCCCTTGTTGCTTCGT 60.612 52.381 0.00 0.0 0.00 3.85
339 346 4.148825 GCGCTCCAGATCCGGTGT 62.149 66.667 0.00 0.0 0.00 4.16
433 445 2.355837 GCAACTGGCTGTCGTCGA 60.356 61.111 0.00 0.0 40.25 4.20
615 637 3.138128 GCAACGCCGCCCCTAATT 61.138 61.111 0.00 0.0 0.00 1.40
876 908 1.667724 CAGTTTAGGCCATCTCAAGCG 59.332 52.381 5.01 0.0 0.00 4.68
1286 1326 1.819903 GCTCTTCCTCCTACGTGAAGT 59.180 52.381 11.11 0.0 37.39 3.01
1292 1332 1.202582 CCTCCTACGTGAAGTGTCAGG 59.797 57.143 0.00 0.0 43.77 3.86
1314 1354 2.900273 GTGGTCATGCTCCGCCTA 59.100 61.111 8.48 0.0 0.00 3.93
1421 1461 3.254024 ATCTCACCGGGCGTTGCTT 62.254 57.895 6.32 0.0 0.00 3.91
1608 1648 0.756294 TGTCCGCCTCTTTGAAGACA 59.244 50.000 0.00 0.0 32.15 3.41
2008 2048 3.904800 ATGGTGGTGATATCGACAACA 57.095 42.857 16.50 16.5 34.71 3.33
3095 3219 3.278668 CCAGAGAGGCATCAGAAACAT 57.721 47.619 0.00 0.0 0.00 2.71
3440 3565 5.769662 TCTGCTTAATGTCTTGTCACCATTT 59.230 36.000 0.00 0.0 31.63 2.32
3448 3573 8.419076 AATGTCTTGTCACCATTTTGTTAAAC 57.581 30.769 0.00 0.0 0.00 2.01
3488 3613 7.602644 TGCTAACTTAACTATGTTCCTTCTGTG 59.397 37.037 0.00 0.0 0.00 3.66
3845 3986 0.588252 GTCTGTCATGCGTTGTGCTT 59.412 50.000 0.00 0.0 46.63 3.91
4094 5808 7.331440 TGGCTCAAATAAACACAAATATGCTTG 59.669 33.333 0.00 0.0 0.00 4.01
4116 5830 3.705934 TTCACTGCAACCGGCCACA 62.706 57.895 0.00 0.0 43.89 4.17
4440 6177 2.750237 CCCGCCAGTTTACCAGGC 60.750 66.667 0.00 0.0 44.89 4.85
4493 6511 2.030562 CCCCACGACGCACTTTCT 59.969 61.111 0.00 0.0 0.00 2.52
4495 6513 0.736325 CCCCACGACGCACTTTCTAG 60.736 60.000 0.00 0.0 0.00 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
130 131 3.697045 TCGGATCAAACCAAAAACACTGT 59.303 39.130 0.00 0.00 0.00 3.55
249 256 4.946160 TCCTGAAATAAGAACCATGGGT 57.054 40.909 18.09 10.33 37.65 4.51
254 261 5.418840 GGAGCAAATCCTGAAATAAGAACCA 59.581 40.000 0.00 0.00 45.64 3.67
339 346 0.034186 AATGGAAGGGATGCGCTTGA 60.034 50.000 9.73 0.00 36.78 3.02
433 445 3.991051 CCGTGGAGCTCACCGTGT 61.991 66.667 17.19 0.00 43.23 4.49
556 568 2.598394 GGCCACCTTGCAGCTTGA 60.598 61.111 0.00 0.00 0.00 3.02
876 908 6.049790 GGAACATAACATACCAAGAGAGACC 58.950 44.000 0.00 0.00 0.00 3.85
1421 1461 2.180769 CCAACGACGCGATCTCCA 59.819 61.111 15.93 0.00 0.00 3.86
1930 1970 1.879380 TCCTTCAGCAAAACCATGTCG 59.121 47.619 0.00 0.00 0.00 4.35
2008 2048 7.508687 TCACTGTATGCATAGGTATTGTCATT 58.491 34.615 6.67 0.00 0.00 2.57
3095 3219 4.712829 TGATCTTCCCCGTAGTTTGATACA 59.287 41.667 0.00 0.00 0.00 2.29
3252 3377 6.267699 TCTGAAGAGAAGGTATGACTCACAAA 59.732 38.462 0.00 0.00 33.69 2.83
3440 3565 7.777095 AGCAAAACATACTTCCAGTTTAACAA 58.223 30.769 0.00 0.00 34.64 2.83
3448 3573 8.784043 AGTTAAGTTAGCAAAACATACTTCCAG 58.216 33.333 0.00 0.00 31.94 3.86
3488 3613 4.927978 AGTGTGTAGTCTAGGATCATGC 57.072 45.455 0.00 0.00 0.00 4.06
3979 4127 2.238646 ACATTCCCAGCACCGAAATCTA 59.761 45.455 0.00 0.00 0.00 1.98
4081 4690 5.396484 CAGTGAAGACCAAGCATATTTGTG 58.604 41.667 0.00 0.00 0.00 3.33
4082 4691 4.082571 GCAGTGAAGACCAAGCATATTTGT 60.083 41.667 0.00 0.00 0.00 2.83
4094 5808 2.617274 GCCGGTTGCAGTGAAGACC 61.617 63.158 1.90 0.00 40.77 3.85
4116 5830 2.943978 CGTTCGCTTCCACCCTCCT 61.944 63.158 0.00 0.00 0.00 3.69
4178 5892 2.482721 CGTCTATGGTTGCTCGGTTTTT 59.517 45.455 0.00 0.00 0.00 1.94
4431 6168 1.219664 CGGTGATCGGCCTGGTAAA 59.780 57.895 0.00 0.00 34.75 2.01
4440 6177 1.520787 GGCCTTGTACGGTGATCGG 60.521 63.158 0.00 0.00 44.45 4.18
4488 6506 3.623510 GGGGAAAGTTGCGATCTAGAAAG 59.376 47.826 0.00 0.00 0.00 2.62
4493 6511 1.065709 GTGGGGGAAAGTTGCGATCTA 60.066 52.381 0.00 0.00 0.00 1.98
4495 6513 1.313091 GGTGGGGGAAAGTTGCGATC 61.313 60.000 0.00 0.00 0.00 3.69


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

AutoCloner maintained by Alex Coulton.