Multiple sequence alignment - TraesCS7B01G139200

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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 TraesCS7B01G139200 chr7B 100.000 4299 0 0 1 4299 175722668 175718370 0.000000e+00 7939
1 TraesCS7B01G139200 chr7B 96.086 3449 78 14 865 4299 175614433 175611028 0.000000e+00 5568
2 TraesCS7B01G139200 chr7B 98.421 570 9 0 1 570 175616703 175616134 0.000000e+00 1003
3 TraesCS7B01G139200 chr7B 88.720 461 32 5 3680 4140 175197389 175197829 2.920000e-151 545
4 TraesCS7B01G139200 chr7B 98.322 298 5 0 569 866 175616051 175615754 1.370000e-144 523
5 TraesCS7B01G139200 chr7B 94.203 345 14 3 2973 3315 175196766 175197106 4.930000e-144 521
6 TraesCS7B01G139200 chr7A 96.780 2981 73 9 1 2961 236079451 236082428 0.000000e+00 4951
7 TraesCS7B01G139200 chr7A 96.777 2979 73 9 1 2959 236323256 236326231 0.000000e+00 4948
8 TraesCS7B01G139200 chr7A 93.204 1339 51 18 2958 4294 236082456 236083756 0.000000e+00 1932
9 TraesCS7B01G139200 chr7A 88.773 1345 85 32 2958 4293 236377137 236378424 0.000000e+00 1587
10 TraesCS7B01G139200 chr7A 90.239 1004 72 8 3294 4293 236431435 236432416 0.000000e+00 1288
11 TraesCS7B01G139200 chr7A 90.399 802 41 17 2958 3753 236351679 236352450 0.000000e+00 1022
12 TraesCS7B01G139200 chr7A 92.211 719 33 6 3577 4293 236461490 236462187 0.000000e+00 996
13 TraesCS7B01G139200 chr7A 94.934 533 21 2 3467 3997 236328187 236328715 0.000000e+00 830
14 TraesCS7B01G139200 chr7A 90.000 520 18 16 2958 3477 236326261 236326746 3.620000e-180 641
15 TraesCS7B01G139200 chr7A 94.595 296 8 2 1 289 236348750 236349044 6.560000e-123 451
16 TraesCS7B01G139200 chr7A 95.299 234 8 2 4063 4294 236328715 236328947 6.790000e-98 368
17 TraesCS7B01G139200 chr7A 93.305 239 14 2 2718 2956 236376868 236377104 6.840000e-93 351
18 TraesCS7B01G139200 chr7A 92.562 242 16 2 2718 2959 236458799 236459038 3.180000e-91 346
19 TraesCS7B01G139200 chr7D 96.377 2539 69 8 435 2961 221296571 221299098 0.000000e+00 4157
20 TraesCS7B01G139200 chr7D 94.556 2535 128 8 435 2964 221697435 221694906 0.000000e+00 3908
21 TraesCS7B01G139200 chr7D 94.774 1722 82 6 889 2603 221686008 221687728 0.000000e+00 2675
22 TraesCS7B01G139200 chr7D 94.541 1722 84 8 889 2603 221581570 221583288 0.000000e+00 2651
23 TraesCS7B01G139200 chr7D 93.202 1324 51 18 2973 4294 221583810 221585096 0.000000e+00 1910
24 TraesCS7B01G139200 chr7D 95.713 1003 40 2 3292 4294 221688536 221689535 0.000000e+00 1611
25 TraesCS7B01G139200 chr7D 94.821 1004 50 2 3292 4294 221299426 221300428 0.000000e+00 1565
26 TraesCS7B01G139200 chr7D 94.530 914 40 3 1 904 221580640 221581553 0.000000e+00 1402
27 TraesCS7B01G139200 chr7D 94.311 914 42 3 1 904 221685083 221685996 0.000000e+00 1391
28 TraesCS7B01G139200 chr7D 95.616 365 11 5 2958 3320 221299126 221299487 8.010000e-162 580
29 TraesCS7B01G139200 chr7D 96.501 343 11 1 2973 3315 221688249 221688590 2.240000e-157 566
30 TraesCS7B01G139200 chr7D 93.733 367 15 6 2958 3320 221694881 221694519 1.050000e-150 544
31 TraesCS7B01G139200 chr7D 96.541 318 11 0 2644 2961 221687728 221688045 1.060000e-145 527
32 TraesCS7B01G139200 chr7D 95.298 319 14 1 2644 2961 221583288 221583606 4.960000e-139 505
33 TraesCS7B01G139200 chr7D 92.920 339 21 2 3292 3628 221694580 221694243 1.390000e-134 490
34 TraesCS7B01G139200 chr7D 91.892 296 16 2 1 289 221296276 221296570 1.440000e-109 407


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 TraesCS7B01G139200 chr7B 175718370 175722668 4298 True 7939.000000 7939 100.000000 1 4299 1 chr7B.!!$R1 4298
1 TraesCS7B01G139200 chr7B 175611028 175616703 5675 True 2364.666667 5568 97.609667 1 4299 3 chr7B.!!$R2 4298
2 TraesCS7B01G139200 chr7B 175196766 175197829 1063 False 533.000000 545 91.461500 2973 4140 2 chr7B.!!$F1 1167
3 TraesCS7B01G139200 chr7A 236079451 236083756 4305 False 3441.500000 4951 94.992000 1 4294 2 chr7A.!!$F2 4293
4 TraesCS7B01G139200 chr7A 236323256 236328947 5691 False 1696.750000 4948 94.252500 1 4294 4 chr7A.!!$F3 4293
5 TraesCS7B01G139200 chr7A 236431435 236432416 981 False 1288.000000 1288 90.239000 3294 4293 1 chr7A.!!$F1 999
6 TraesCS7B01G139200 chr7A 236376868 236378424 1556 False 969.000000 1587 91.039000 2718 4293 2 chr7A.!!$F5 1575
7 TraesCS7B01G139200 chr7A 236348750 236352450 3700 False 736.500000 1022 92.497000 1 3753 2 chr7A.!!$F4 3752
8 TraesCS7B01G139200 chr7A 236458799 236462187 3388 False 671.000000 996 92.386500 2718 4293 2 chr7A.!!$F6 1575
9 TraesCS7B01G139200 chr7D 221296276 221300428 4152 False 1677.250000 4157 94.676500 1 4294 4 chr7D.!!$F1 4293
10 TraesCS7B01G139200 chr7D 221694243 221697435 3192 True 1647.333333 3908 93.736333 435 3628 3 chr7D.!!$R1 3193
11 TraesCS7B01G139200 chr7D 221580640 221585096 4456 False 1617.000000 2651 94.392750 1 4294 4 chr7D.!!$F2 4293
12 TraesCS7B01G139200 chr7D 221685083 221689535 4452 False 1354.000000 2675 95.568000 1 4294 5 chr7D.!!$F3 4293

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
645 774 3.963428 AGTGATGAGGCGTTAAGTTCT 57.037 42.857 0.0 0.0 0.0 3.01 F
1749 3234 0.250510 TGCTTGCCATTCCGTGTACA 60.251 50.000 0.0 0.0 0.0 2.90 F
3275 4989 2.234661 CAAGTACCAGTGATGCTCTCCA 59.765 50.000 0.0 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2551 4053 0.115349 AGCTCACCACCTGTCCTACT 59.885 55.0 0.0 0.0 0.00 2.57 R
3289 5003 1.067295 TGGAGGAGCATCACTGGTTT 58.933 50.0 0.0 0.0 36.25 3.27 R
4204 9248 7.177832 TCCCGTTATTATGTCAAGAGAAAGA 57.822 36.0 0.0 0.0 0.00 2.52 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
645 774 3.963428 AGTGATGAGGCGTTAAGTTCT 57.037 42.857 0.00 0.00 0.00 3.01
708 837 6.267928 AGGGATCTCATAACATTACGTAAGCT 59.732 38.462 14.25 3.28 45.62 3.74
1293 2777 7.767198 CCATCCAAACTGAAATATGAGCAAATT 59.233 33.333 0.00 0.00 0.00 1.82
1749 3234 0.250510 TGCTTGCCATTCCGTGTACA 60.251 50.000 0.00 0.00 0.00 2.90
2040 3529 7.228590 TCAATGGCTCAATGATCATATGAAGA 58.771 34.615 9.99 0.00 0.00 2.87
2043 3532 6.598503 TGGCTCAATGATCATATGAAGAACT 58.401 36.000 9.99 0.00 0.00 3.01
2493 3988 3.210227 TCGGATTGCTTTGTCAACTGAA 58.790 40.909 0.00 0.00 0.00 3.02
3090 4800 5.140177 GCGTTCTATTCACTCTTTGTGTTG 58.860 41.667 0.00 0.00 46.27 3.33
3264 4978 8.273605 AGTTATACTAGCTCTACAAGTACCAGT 58.726 37.037 0.00 0.00 0.00 4.00
3265 4979 6.945938 ATACTAGCTCTACAAGTACCAGTG 57.054 41.667 0.00 0.00 0.00 3.66
3266 4980 4.919793 ACTAGCTCTACAAGTACCAGTGA 58.080 43.478 0.00 0.00 0.00 3.41
3267 4981 5.511363 ACTAGCTCTACAAGTACCAGTGAT 58.489 41.667 0.00 0.00 0.00 3.06
3268 4982 4.727507 AGCTCTACAAGTACCAGTGATG 57.272 45.455 0.00 0.00 0.00 3.07
3269 4983 3.118956 AGCTCTACAAGTACCAGTGATGC 60.119 47.826 0.00 0.00 0.00 3.91
3270 4984 3.118956 GCTCTACAAGTACCAGTGATGCT 60.119 47.826 0.00 0.00 0.00 3.79
3271 4985 4.677584 CTCTACAAGTACCAGTGATGCTC 58.322 47.826 0.00 0.00 0.00 4.26
3272 4986 4.344978 TCTACAAGTACCAGTGATGCTCT 58.655 43.478 0.00 0.00 0.00 4.09
3273 4987 3.601443 ACAAGTACCAGTGATGCTCTC 57.399 47.619 0.00 0.00 0.00 3.20
3274 4988 2.234908 ACAAGTACCAGTGATGCTCTCC 59.765 50.000 0.00 0.00 0.00 3.71
3275 4989 2.234661 CAAGTACCAGTGATGCTCTCCA 59.765 50.000 0.00 0.00 0.00 3.86
3276 4990 2.540383 AGTACCAGTGATGCTCTCCAA 58.460 47.619 0.00 0.00 0.00 3.53
3277 4991 2.906389 AGTACCAGTGATGCTCTCCAAA 59.094 45.455 0.00 0.00 0.00 3.28
3278 4992 2.957402 ACCAGTGATGCTCTCCAAAA 57.043 45.000 0.00 0.00 0.00 2.44
3279 4993 3.228188 ACCAGTGATGCTCTCCAAAAA 57.772 42.857 0.00 0.00 0.00 1.94
3280 4994 3.152341 ACCAGTGATGCTCTCCAAAAAG 58.848 45.455 0.00 0.00 0.00 2.27
3281 4995 3.181440 ACCAGTGATGCTCTCCAAAAAGA 60.181 43.478 0.00 0.00 0.00 2.52
3282 4996 3.439476 CCAGTGATGCTCTCCAAAAAGAG 59.561 47.826 0.00 0.00 44.69 2.85
3283 4997 4.321718 CAGTGATGCTCTCCAAAAAGAGA 58.678 43.478 5.13 0.00 44.67 3.10
3284 4998 4.758674 CAGTGATGCTCTCCAAAAAGAGAA 59.241 41.667 5.13 0.00 44.67 2.87
3285 4999 5.240183 CAGTGATGCTCTCCAAAAAGAGAAA 59.760 40.000 5.13 0.00 44.67 2.52
3286 5000 5.829924 AGTGATGCTCTCCAAAAAGAGAAAA 59.170 36.000 5.13 0.00 44.67 2.29
3287 5001 6.016443 AGTGATGCTCTCCAAAAAGAGAAAAG 60.016 38.462 5.13 0.00 44.67 2.27
3288 5002 5.829924 TGATGCTCTCCAAAAAGAGAAAAGT 59.170 36.000 5.13 0.00 44.67 2.66
3289 5003 6.998074 TGATGCTCTCCAAAAAGAGAAAAGTA 59.002 34.615 5.13 0.00 44.67 2.24
3290 5004 7.502226 TGATGCTCTCCAAAAAGAGAAAAGTAA 59.498 33.333 5.13 0.00 44.67 2.24
3291 5005 7.639113 TGCTCTCCAAAAAGAGAAAAGTAAA 57.361 32.000 5.13 0.00 44.67 2.01
3292 5006 7.480810 TGCTCTCCAAAAAGAGAAAAGTAAAC 58.519 34.615 5.13 0.00 44.67 2.01
3303 5017 5.703130 AGAGAAAAGTAAACCAGTGATGCTC 59.297 40.000 0.00 0.00 0.00 4.26
3320 5034 5.242393 TGATGCTCCTCCAAAAAGAGAAAAG 59.758 40.000 0.00 0.00 35.82 2.27
3415 5135 7.307493 TGTGCTAGTTTGCTGTATTATCTTG 57.693 36.000 0.00 0.00 0.00 3.02
3503 6676 4.437682 ACTGAGAGTTTTTGGGACATCA 57.562 40.909 0.00 0.00 39.30 3.07
3712 8717 1.976474 TTTCTGCCACGCCCATTCC 60.976 57.895 0.00 0.00 0.00 3.01
4001 9008 4.523943 ACTGGCATGACAAAATTTCAGCTA 59.476 37.500 1.11 0.00 0.00 3.32
4110 9119 7.765695 AGATGCAGGAACAAGAAAAATTCTA 57.234 32.000 0.00 0.00 39.61 2.10
4135 9175 3.844211 TGAGGTCAAATAGCCCTTGTACT 59.156 43.478 0.00 0.00 0.00 2.73
4184 9226 8.437575 TCTCCAAAACTTACTGAAAATCCTACT 58.562 33.333 0.00 0.00 0.00 2.57
4187 9229 8.846211 CCAAAACTTACTGAAAATCCTACTGAA 58.154 33.333 0.00 0.00 0.00 3.02
4204 9248 9.851686 TCCTACTGAACATTTGCTCATTATATT 57.148 29.630 0.00 0.00 0.00 1.28
4294 9338 1.139989 GATCGCATGGTCCATACGTG 58.860 55.000 21.27 9.84 33.05 4.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
176 185 4.833478 AGCCCTAGCATGGTAATCTATG 57.167 45.455 6.04 0.00 43.56 2.23
226 235 9.790389 ATCTACTACGTGTAAAATCTCTGAAAG 57.210 33.333 0.00 0.00 0.00 2.62
645 774 1.695242 TCCGTTAGGAACAGAAAGGCA 59.305 47.619 0.00 0.00 45.12 4.75
795 925 6.045698 GATATCAAGATATCGCTGGCATTG 57.954 41.667 12.77 0.00 39.94 2.82
947 2431 4.519906 AAAGTTTCAGACTGGGAAAGGA 57.480 40.909 1.81 0.00 39.00 3.36
1749 3234 8.997621 AGTGTTACGAAACAGTCATACAATAT 57.002 30.769 0.00 0.00 44.28 1.28
2040 3529 3.160679 AGCCTAAATGCTGGTTGAGTT 57.839 42.857 0.00 0.00 40.90 3.01
2043 3532 3.016736 GCTAAGCCTAAATGCTGGTTGA 58.983 45.455 0.00 0.00 41.80 3.18
2160 3653 2.170166 GGCAGATTGAACCACATGGAA 58.830 47.619 4.53 0.00 38.94 3.53
2551 4053 0.115349 AGCTCACCACCTGTCCTACT 59.885 55.000 0.00 0.00 0.00 2.57
3090 4800 5.105797 TGTCAAATTATCAGATGGTTGCACC 60.106 40.000 0.00 0.00 39.22 5.01
3264 4978 5.829924 ACTTTTCTCTTTTTGGAGAGCATCA 59.170 36.000 0.00 0.00 42.37 3.07
3265 4979 6.324561 ACTTTTCTCTTTTTGGAGAGCATC 57.675 37.500 0.00 0.00 42.37 3.91
3266 4980 7.823745 TTACTTTTCTCTTTTTGGAGAGCAT 57.176 32.000 0.00 0.00 42.37 3.79
3267 4981 7.416326 GGTTTACTTTTCTCTTTTTGGAGAGCA 60.416 37.037 0.00 0.00 42.37 4.26
3268 4982 6.918569 GGTTTACTTTTCTCTTTTTGGAGAGC 59.081 38.462 0.00 0.00 42.37 4.09
3269 4983 7.996385 TGGTTTACTTTTCTCTTTTTGGAGAG 58.004 34.615 0.00 0.00 42.37 3.20
3270 4984 7.614192 ACTGGTTTACTTTTCTCTTTTTGGAGA 59.386 33.333 0.00 0.00 40.16 3.71
3271 4985 7.702348 CACTGGTTTACTTTTCTCTTTTTGGAG 59.298 37.037 0.00 0.00 34.88 3.86
3272 4986 7.394923 TCACTGGTTTACTTTTCTCTTTTTGGA 59.605 33.333 0.00 0.00 0.00 3.53
3273 4987 7.543756 TCACTGGTTTACTTTTCTCTTTTTGG 58.456 34.615 0.00 0.00 0.00 3.28
3274 4988 9.023967 CATCACTGGTTTACTTTTCTCTTTTTG 57.976 33.333 0.00 0.00 0.00 2.44
3275 4989 7.706607 GCATCACTGGTTTACTTTTCTCTTTTT 59.293 33.333 0.00 0.00 0.00 1.94
3276 4990 7.068716 AGCATCACTGGTTTACTTTTCTCTTTT 59.931 33.333 0.00 0.00 0.00 2.27
3277 4991 6.547510 AGCATCACTGGTTTACTTTTCTCTTT 59.452 34.615 0.00 0.00 0.00 2.52
3278 4992 6.064717 AGCATCACTGGTTTACTTTTCTCTT 58.935 36.000 0.00 0.00 0.00 2.85
3279 4993 5.625150 AGCATCACTGGTTTACTTTTCTCT 58.375 37.500 0.00 0.00 0.00 3.10
3280 4994 5.106515 GGAGCATCACTGGTTTACTTTTCTC 60.107 44.000 0.00 0.00 36.25 2.87
3281 4995 4.762251 GGAGCATCACTGGTTTACTTTTCT 59.238 41.667 0.00 0.00 36.25 2.52
3282 4996 4.762251 AGGAGCATCACTGGTTTACTTTTC 59.238 41.667 0.00 0.00 36.25 2.29
3283 4997 4.729868 AGGAGCATCACTGGTTTACTTTT 58.270 39.130 0.00 0.00 36.25 2.27
3284 4998 4.327680 GAGGAGCATCACTGGTTTACTTT 58.672 43.478 0.00 0.00 36.25 2.66
3285 4999 3.307762 GGAGGAGCATCACTGGTTTACTT 60.308 47.826 0.00 0.00 36.25 2.24
3286 5000 2.237392 GGAGGAGCATCACTGGTTTACT 59.763 50.000 0.00 0.00 36.25 2.24
3287 5001 2.027192 TGGAGGAGCATCACTGGTTTAC 60.027 50.000 0.00 0.00 36.25 2.01
3288 5002 2.265367 TGGAGGAGCATCACTGGTTTA 58.735 47.619 0.00 0.00 36.25 2.01
3289 5003 1.067295 TGGAGGAGCATCACTGGTTT 58.933 50.000 0.00 0.00 36.25 3.27
3290 5004 1.067295 TTGGAGGAGCATCACTGGTT 58.933 50.000 0.00 0.00 36.25 3.67
3291 5005 1.067295 TTTGGAGGAGCATCACTGGT 58.933 50.000 0.00 0.00 36.25 4.00
3292 5006 2.205022 TTTTGGAGGAGCATCACTGG 57.795 50.000 0.00 0.00 36.25 4.00
3303 5017 7.107639 TGGTTTACTTTTCTCTTTTTGGAGG 57.892 36.000 0.00 0.00 34.39 4.30
3320 5034 3.055819 TCTGGAGAGCATCACTGGTTTAC 60.056 47.826 0.00 0.00 37.82 2.01
3415 5135 7.254488 GCTTAGCTAAGGTAGAACATTAACAGC 60.254 40.741 29.93 10.39 33.95 4.40
3712 8717 7.933396 TGCATATAATGTGATCTTTGGTCTTG 58.067 34.615 0.00 0.00 0.00 3.02
4001 9008 1.410224 GGCTAATAAAGGTGGCAGCCT 60.410 52.381 14.15 7.94 44.15 4.58
4204 9248 7.177832 TCCCGTTATTATGTCAAGAGAAAGA 57.822 36.000 0.00 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.