Multiple sequence alignment - TraesCS3D01G304300

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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 TraesCS3D01G304300 chr3D 100.000 3967 0 0 1 3967 418713394 418709428 0.000000e+00 7326
1 TraesCS3D01G304300 chr7D 98.799 3579 42 1 389 3967 136701765 136698188 0.000000e+00 6370
2 TraesCS3D01G304300 chr7D 88.743 1066 110 8 966 2022 199528749 199529813 0.000000e+00 1295
3 TraesCS3D01G304300 chr7D 98.555 346 5 0 1 346 136702106 136701761 2.620000e-171 612
4 TraesCS3D01G304300 chr7D 81.800 489 69 14 1 473 99608973 99609457 3.720000e-105 392
5 TraesCS3D01G304300 chr3A 94.158 2328 118 8 797 3111 667164531 667162209 0.000000e+00 3530
6 TraesCS3D01G304300 chr3A 92.216 668 36 7 3309 3967 667161648 667160988 0.000000e+00 931
7 TraesCS3D01G304300 chr3A 88.889 180 19 1 3124 3303 667161894 667161716 1.860000e-53 220
8 TraesCS3D01G304300 chr6A 89.335 2119 206 10 998 3099 563488593 563490708 0.000000e+00 2643
9 TraesCS3D01G304300 chr6A 85.813 2171 268 24 906 3054 591517121 591519273 0.000000e+00 2266
10 TraesCS3D01G304300 chr6A 83.585 597 69 13 3371 3967 563490905 563491472 2.100000e-147 532
11 TraesCS3D01G304300 chr4B 88.910 2119 215 15 998 3099 168270921 168268806 0.000000e+00 2593
12 TraesCS3D01G304300 chr4B 97.538 325 8 0 474 798 37852231 37852555 1.250000e-154 556
13 TraesCS3D01G304300 chr4B 82.820 617 74 12 3372 3967 168268609 168268004 1.260000e-144 523
14 TraesCS3D01G304300 chr2A 83.034 2281 343 32 797 3045 291665829 291668097 0.000000e+00 2028
15 TraesCS3D01G304300 chr2A 82.991 2287 336 34 797 3045 556948891 556951162 0.000000e+00 2019
16 TraesCS3D01G304300 chr2A 88.453 1325 134 14 1792 3099 21940840 21939518 0.000000e+00 1581
17 TraesCS3D01G304300 chr2A 83.082 597 72 10 3371 3967 21939322 21938755 2.110000e-142 516
18 TraesCS3D01G304300 chr2A 80.795 453 76 8 3517 3967 291668972 291669415 1.060000e-90 344
19 TraesCS3D01G304300 chr2A 79.249 453 82 10 3517 3967 556952044 556952486 4.980000e-79 305
20 TraesCS3D01G304300 chr6D 94.412 1038 50 6 2080 3111 318068901 318067866 0.000000e+00 1589
21 TraesCS3D01G304300 chr6D 89.556 450 37 3 3527 3967 318053803 318053355 2.680000e-156 562
22 TraesCS3D01G304300 chr6D 93.436 259 12 2 3306 3562 318053984 318053729 2.890000e-101 379
23 TraesCS3D01G304300 chr6D 90.769 195 17 1 3113 3306 318054308 318054114 3.930000e-65 259
24 TraesCS3D01G304300 chr7A 88.452 1247 126 8 998 2228 106410298 106409054 0.000000e+00 1489
25 TraesCS3D01G304300 chr2D 95.106 899 36 4 797 1692 646281439 646280546 0.000000e+00 1410
26 TraesCS3D01G304300 chr2D 92.708 672 36 6 3305 3967 646280364 646279697 0.000000e+00 957
27 TraesCS3D01G304300 chr2D 88.333 120 13 1 3184 3303 646280546 646280428 4.130000e-30 143
28 TraesCS3D01G304300 chr5A 93.490 891 19 6 45 934 35278203 35277351 0.000000e+00 1288
29 TraesCS3D01G304300 chr5A 81.879 1352 206 27 1731 3054 341511683 341510343 0.000000e+00 1103
30 TraesCS3D01G304300 chr5A 79.912 453 80 9 3517 3967 341509477 341509034 4.950000e-84 322
31 TraesCS3D01G304300 chr1B 83.120 1404 202 24 797 2177 502774440 502775831 0.000000e+00 1247
32 TraesCS3D01G304300 chr5B 88.967 707 77 1 2394 3099 551736890 551736184 0.000000e+00 872
33 TraesCS3D01G304300 chr5B 83.615 592 70 8 3397 3967 551735969 551735384 7.550000e-147 531
34 TraesCS3D01G304300 chr1A 91.509 530 39 3 2387 2915 567513317 567512793 0.000000e+00 725
35 TraesCS3D01G304300 chr1A 82.039 618 78 15 3371 3967 13160899 13161504 2.750000e-136 496
36 TraesCS3D01G304300 chr1A 82.578 287 42 6 168 449 567514244 567513961 3.060000e-61 246
37 TraesCS3D01G304300 chr4A 97.538 325 8 0 474 798 577543963 577543639 1.250000e-154 556
38 TraesCS3D01G304300 chr4D 95.385 325 15 0 474 798 25488288 25488612 5.880000e-143 518
39 TraesCS3D01G304300 chr6B 84.802 454 57 8 3 448 494099814 494099365 2.810000e-121 446


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 TraesCS3D01G304300 chr3D 418709428 418713394 3966 True 7326.000000 7326 100.000000 1 3967 1 chr3D.!!$R1 3966
1 TraesCS3D01G304300 chr7D 136698188 136702106 3918 True 3491.000000 6370 98.677000 1 3967 2 chr7D.!!$R1 3966
2 TraesCS3D01G304300 chr7D 199528749 199529813 1064 False 1295.000000 1295 88.743000 966 2022 1 chr7D.!!$F2 1056
3 TraesCS3D01G304300 chr3A 667160988 667164531 3543 True 1560.333333 3530 91.754333 797 3967 3 chr3A.!!$R1 3170
4 TraesCS3D01G304300 chr6A 591517121 591519273 2152 False 2266.000000 2266 85.813000 906 3054 1 chr6A.!!$F1 2148
5 TraesCS3D01G304300 chr6A 563488593 563491472 2879 False 1587.500000 2643 86.460000 998 3967 2 chr6A.!!$F2 2969
6 TraesCS3D01G304300 chr4B 168268004 168270921 2917 True 1558.000000 2593 85.865000 998 3967 2 chr4B.!!$R1 2969
7 TraesCS3D01G304300 chr2A 291665829 291669415 3586 False 1186.000000 2028 81.914500 797 3967 2 chr2A.!!$F1 3170
8 TraesCS3D01G304300 chr2A 556948891 556952486 3595 False 1162.000000 2019 81.120000 797 3967 2 chr2A.!!$F2 3170
9 TraesCS3D01G304300 chr2A 21938755 21940840 2085 True 1048.500000 1581 85.767500 1792 3967 2 chr2A.!!$R1 2175
10 TraesCS3D01G304300 chr6D 318067866 318068901 1035 True 1589.000000 1589 94.412000 2080 3111 1 chr6D.!!$R1 1031
11 TraesCS3D01G304300 chr6D 318053355 318054308 953 True 400.000000 562 91.253667 3113 3967 3 chr6D.!!$R2 854
12 TraesCS3D01G304300 chr7A 106409054 106410298 1244 True 1489.000000 1489 88.452000 998 2228 1 chr7A.!!$R1 1230
13 TraesCS3D01G304300 chr2D 646279697 646281439 1742 True 836.666667 1410 92.049000 797 3967 3 chr2D.!!$R1 3170
14 TraesCS3D01G304300 chr5A 35277351 35278203 852 True 1288.000000 1288 93.490000 45 934 1 chr5A.!!$R1 889
15 TraesCS3D01G304300 chr5A 341509034 341511683 2649 True 712.500000 1103 80.895500 1731 3967 2 chr5A.!!$R2 2236
16 TraesCS3D01G304300 chr1B 502774440 502775831 1391 False 1247.000000 1247 83.120000 797 2177 1 chr1B.!!$F1 1380
17 TraesCS3D01G304300 chr5B 551735384 551736890 1506 True 701.500000 872 86.291000 2394 3967 2 chr5B.!!$R1 1573
18 TraesCS3D01G304300 chr1A 13160899 13161504 605 False 496.000000 496 82.039000 3371 3967 1 chr1A.!!$F1 596
19 TraesCS3D01G304300 chr1A 567512793 567514244 1451 True 485.500000 725 87.043500 168 2915 2 chr1A.!!$R1 2747

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
314 317 1.889530 GAGCACAGGACGGTAGGCTT 61.890 60.000 0.00 0.0 0.0 4.35 F
368 384 4.334759 CCTCTCCAATTGAATAGCACACTG 59.665 45.833 7.12 0.0 0.0 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2305 2358 1.525077 GCCTCACCACGTGGAACAA 60.525 57.895 40.21 19.88 44.16 2.83 R
2966 3042 6.181908 TGTAAAACCTTTGCCGGAGTATATT 58.818 36.000 5.05 0.00 0.00 1.28 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
314 317 1.889530 GAGCACAGGACGGTAGGCTT 61.890 60.000 0.00 0.00 0.0 4.35
354 370 4.472833 AGCTGTATGTTCTTCCTCTCCAAT 59.527 41.667 0.00 0.00 0.0 3.16
355 371 5.045286 AGCTGTATGTTCTTCCTCTCCAATT 60.045 40.000 0.00 0.00 0.0 2.32
356 372 5.065731 GCTGTATGTTCTTCCTCTCCAATTG 59.934 44.000 0.00 0.00 0.0 2.32
357 373 6.373005 TGTATGTTCTTCCTCTCCAATTGA 57.627 37.500 7.12 0.00 0.0 2.57
358 374 6.778821 TGTATGTTCTTCCTCTCCAATTGAA 58.221 36.000 7.12 0.00 0.0 2.69
359 375 7.405292 TGTATGTTCTTCCTCTCCAATTGAAT 58.595 34.615 7.12 0.00 0.0 2.57
360 376 8.548025 TGTATGTTCTTCCTCTCCAATTGAATA 58.452 33.333 7.12 0.00 0.0 1.75
361 377 9.050601 GTATGTTCTTCCTCTCCAATTGAATAG 57.949 37.037 7.12 1.61 0.0 1.73
362 378 5.882557 TGTTCTTCCTCTCCAATTGAATAGC 59.117 40.000 7.12 0.00 0.0 2.97
363 379 5.698741 TCTTCCTCTCCAATTGAATAGCA 57.301 39.130 7.12 0.00 0.0 3.49
368 384 4.334759 CCTCTCCAATTGAATAGCACACTG 59.665 45.833 7.12 0.00 0.0 3.66
369 385 4.910195 TCTCCAATTGAATAGCACACTGT 58.090 39.130 7.12 0.00 0.0 3.55
371 387 6.108687 TCTCCAATTGAATAGCACACTGTAG 58.891 40.000 7.12 0.00 0.0 2.74
537 559 5.820131 TGCCGAGATTAAAAGCAATGTATG 58.180 37.500 0.00 0.00 0.0 2.39
908 935 9.829507 AGAGAGAATATGATTTACTGAGGTTTG 57.170 33.333 0.00 0.00 0.0 2.93
1044 1077 9.812347 TTTAGTGATTTATTATGGATGCCTCAT 57.188 29.630 0.00 0.00 0.0 2.90
2305 2358 6.351286 GGATTAAGACAATGCATTCCACCTTT 60.351 38.462 9.53 1.69 0.0 3.11
2966 3042 7.175467 AGCAACTCTGATGTGTTTAATGAATGA 59.825 33.333 0.00 0.00 0.0 2.57
3029 3106 3.376218 GCAGTGAGCGATGGAGAAT 57.624 52.632 0.00 0.00 0.0 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 59 2.801631 GGTGGGCGAGAGATGAGGG 61.802 68.421 0.00 0.00 0.00 4.30
314 317 3.117663 ACAGCTTGAGGGGAAAACTACAA 60.118 43.478 0.00 0.00 0.00 2.41
354 370 6.042777 GCATCTACTACAGTGTGCTATTCAA 58.957 40.000 5.88 0.00 35.49 2.69
355 371 5.360999 AGCATCTACTACAGTGTGCTATTCA 59.639 40.000 5.88 0.00 41.89 2.57
356 372 5.837437 AGCATCTACTACAGTGTGCTATTC 58.163 41.667 5.88 0.00 41.89 1.75
357 373 5.860941 AGCATCTACTACAGTGTGCTATT 57.139 39.130 5.88 0.00 41.89 1.73
358 374 6.299922 TCTAGCATCTACTACAGTGTGCTAT 58.700 40.000 18.11 0.00 42.74 2.97
359 375 5.681639 TCTAGCATCTACTACAGTGTGCTA 58.318 41.667 5.88 17.38 42.81 3.49
360 376 4.527944 TCTAGCATCTACTACAGTGTGCT 58.472 43.478 5.88 17.12 44.10 4.40
361 377 4.902443 TCTAGCATCTACTACAGTGTGC 57.098 45.455 5.88 0.00 37.29 4.57
362 378 9.973450 ATATTTTCTAGCATCTACTACAGTGTG 57.027 33.333 5.88 0.00 0.00 3.82
537 559 7.731882 AGGTTCTCTTTGCTAACTTTCTTAC 57.268 36.000 0.00 0.00 0.00 2.34
636 658 4.449743 TGGAAACGTAGCAAATACAGTCAC 59.550 41.667 0.00 0.00 33.65 3.67
677 700 2.905959 TGCAGCAACGATGAATTCAG 57.094 45.000 14.54 3.71 0.00 3.02
2305 2358 1.525077 GCCTCACCACGTGGAACAA 60.525 57.895 40.21 19.88 44.16 2.83
2966 3042 6.181908 TGTAAAACCTTTGCCGGAGTATATT 58.818 36.000 5.05 0.00 0.00 1.28
3029 3106 6.041637 ACTTGACCTACATCTTGTGTTGTAGA 59.958 38.462 10.77 0.00 43.73 2.59
3418 4149 1.130561 GGACGTGCTTACTGATTTGCC 59.869 52.381 0.00 0.00 0.00 4.52
3745 4848 2.239124 GCCCGACGTTCGACAACAA 61.239 57.895 8.63 0.00 43.74 2.83


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

AutoCloner maintained by Alex Coulton.