Multiple sequence alignment - TraesCS3B01G141900

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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 TraesCS3B01G141900 chr3B 100.000 2549 0 0 1 2549 129333303 129330755 0.000000e+00 4708
1 TraesCS3B01G141900 chr3B 95.796 1998 75 4 561 2549 734815232 734817229 0.000000e+00 3216
2 TraesCS3B01G141900 chr3B 93.617 141 8 1 427 566 683615902 683615762 2.570000e-50 209
3 TraesCS3B01G141900 chr7B 96.427 1987 66 4 567 2549 718488474 718486489 0.000000e+00 3271
4 TraesCS3B01G141900 chr7B 86.690 571 66 8 1 566 29089641 29089076 2.150000e-175 625
5 TraesCS3B01G141900 chr2B 96.326 1987 66 6 567 2549 543889470 543887487 0.000000e+00 3258
6 TraesCS3B01G141900 chr2B 96.276 1987 67 6 567 2549 544319641 544317658 0.000000e+00 3253
7 TraesCS3B01G141900 chr2B 95.838 1994 71 7 567 2549 602077185 602075193 0.000000e+00 3212
8 TraesCS3B01G141900 chr1B 96.283 1991 65 7 565 2549 490563564 490561577 0.000000e+00 3258
9 TraesCS3B01G141900 chr1B 96.181 1990 68 7 566 2549 232740733 232742720 0.000000e+00 3247
10 TraesCS3B01G141900 chr1B 95.982 1991 70 7 567 2549 663786495 663788483 0.000000e+00 3225
11 TraesCS3B01G141900 chr5B 96.032 1991 70 6 567 2549 269389473 269391462 0.000000e+00 3230
12 TraesCS3B01G141900 chr5B 85.133 565 81 2 5 566 640981555 640982119 2.200000e-160 575
13 TraesCS3B01G141900 chr5B 85.598 493 66 5 5 495 233123140 233123629 1.750000e-141 512
14 TraesCS3B01G141900 chr5D 84.480 567 83 5 1 564 393669430 393668866 2.870000e-154 555
15 TraesCS3B01G141900 chr5D 84.071 565 85 5 1 562 393694674 393694112 8.020000e-150 540
16 TraesCS3B01G141900 chr1A 84.779 565 70 14 7 562 358799708 358799151 1.030000e-153 553
17 TraesCS3B01G141900 chr3D 83.688 564 84 8 5 564 420145984 420146543 2.250000e-145 525
18 TraesCS3B01G141900 chr6D 83.101 574 79 12 1 564 94951928 94952493 8.140000e-140 507
19 TraesCS3B01G141900 chr4D 82.312 571 90 9 1 564 468637531 468636965 3.810000e-133 484


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 TraesCS3B01G141900 chr3B 129330755 129333303 2548 True 4708 4708 100.000 1 2549 1 chr3B.!!$R1 2548
1 TraesCS3B01G141900 chr3B 734815232 734817229 1997 False 3216 3216 95.796 561 2549 1 chr3B.!!$F1 1988
2 TraesCS3B01G141900 chr7B 718486489 718488474 1985 True 3271 3271 96.427 567 2549 1 chr7B.!!$R2 1982
3 TraesCS3B01G141900 chr7B 29089076 29089641 565 True 625 625 86.690 1 566 1 chr7B.!!$R1 565
4 TraesCS3B01G141900 chr2B 543887487 543889470 1983 True 3258 3258 96.326 567 2549 1 chr2B.!!$R1 1982
5 TraesCS3B01G141900 chr2B 544317658 544319641 1983 True 3253 3253 96.276 567 2549 1 chr2B.!!$R2 1982
6 TraesCS3B01G141900 chr2B 602075193 602077185 1992 True 3212 3212 95.838 567 2549 1 chr2B.!!$R3 1982
7 TraesCS3B01G141900 chr1B 490561577 490563564 1987 True 3258 3258 96.283 565 2549 1 chr1B.!!$R1 1984
8 TraesCS3B01G141900 chr1B 232740733 232742720 1987 False 3247 3247 96.181 566 2549 1 chr1B.!!$F1 1983
9 TraesCS3B01G141900 chr1B 663786495 663788483 1988 False 3225 3225 95.982 567 2549 1 chr1B.!!$F2 1982
10 TraesCS3B01G141900 chr5B 269389473 269391462 1989 False 3230 3230 96.032 567 2549 1 chr5B.!!$F2 1982
11 TraesCS3B01G141900 chr5B 640981555 640982119 564 False 575 575 85.133 5 566 1 chr5B.!!$F3 561
12 TraesCS3B01G141900 chr5D 393668866 393669430 564 True 555 555 84.480 1 564 1 chr5D.!!$R1 563
13 TraesCS3B01G141900 chr5D 393694112 393694674 562 True 540 540 84.071 1 562 1 chr5D.!!$R2 561
14 TraesCS3B01G141900 chr1A 358799151 358799708 557 True 553 553 84.779 7 562 1 chr1A.!!$R1 555
15 TraesCS3B01G141900 chr3D 420145984 420146543 559 False 525 525 83.688 5 564 1 chr3D.!!$F1 559
16 TraesCS3B01G141900 chr6D 94951928 94952493 565 False 507 507 83.101 1 564 1 chr6D.!!$F1 563
17 TraesCS3B01G141900 chr4D 468636965 468637531 566 True 484 484 82.312 1 564 1 chr4D.!!$R1 563

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
936 951 0.838122 AAGCTAGCTGTGGAGGGTGT 60.838 55.0 20.16 0.0 0.0 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2026 2047 1.483827 CTCTTGCCATCTGTCCTAGCA 59.516 52.381 0.0 0.0 0.0 3.49 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
182 188 4.882842 AAAGCCCGTAAACATCCAAAAT 57.117 36.364 0.00 0.00 0.00 1.82
258 269 7.861372 CGTATAAGTTTACATCAGGTCTGGTAG 59.139 40.741 0.00 0.00 0.00 3.18
275 286 5.365314 TCTGGTAGACAACATGGCATACATA 59.635 40.000 0.00 0.00 37.84 2.29
281 292 7.969536 AGACAACATGGCATACATAATAGAC 57.030 36.000 0.00 0.00 37.84 2.59
351 363 1.079127 ATGGTCGGGCTTTGAGTCG 60.079 57.895 0.00 0.00 0.00 4.18
353 366 2.027625 GGTCGGGCTTTGAGTCGTG 61.028 63.158 0.00 0.00 0.00 4.35
420 433 6.484977 GGACTGATCCATATTGAACTTCTTCC 59.515 42.308 0.00 0.00 45.47 3.46
422 435 7.580910 ACTGATCCATATTGAACTTCTTCCAT 58.419 34.615 0.00 0.00 0.00 3.41
458 472 5.633830 ATGTGCTTTGTGAAAGACCTATG 57.366 39.130 0.16 0.00 41.02 2.23
460 474 4.756642 TGTGCTTTGTGAAAGACCTATGAG 59.243 41.667 0.16 0.00 41.02 2.90
479 493 5.888691 TGAGGCGTCTTGATCTATATCTC 57.111 43.478 8.06 0.00 32.93 2.75
515 529 5.743130 GCCTAATATGTAAGCAGCTTCTCCA 60.743 44.000 12.07 7.71 0.00 3.86
533 547 4.827284 TCTCCAAGGTCCTTCATTGAAAAC 59.173 41.667 0.00 2.34 39.79 2.43
534 548 4.541705 TCCAAGGTCCTTCATTGAAAACA 58.458 39.130 0.00 0.00 39.79 2.83
660 675 3.849951 CCCCTAGTCCGTGCGCAT 61.850 66.667 15.91 0.00 0.00 4.73
700 715 1.215647 GCGTCTCCGTCAGGTCAAT 59.784 57.895 0.00 0.00 39.05 2.57
706 721 4.312443 GTCTCCGTCAGGTCAATGTTTTA 58.688 43.478 0.00 0.00 39.05 1.52
829 844 2.256158 CATTGCGGGTGTGTGCTG 59.744 61.111 0.00 0.00 0.00 4.41
936 951 0.838122 AAGCTAGCTGTGGAGGGTGT 60.838 55.000 20.16 0.00 0.00 4.16
1042 1057 2.185350 CCTCGCGGATGCAGAGTT 59.815 61.111 6.13 0.00 42.97 3.01
1056 1071 1.302511 GAGTTGGGTGCGTGTGGAT 60.303 57.895 0.00 0.00 0.00 3.41
1125 1140 2.135933 GTTTCTCACACACCGAGGAAG 58.864 52.381 0.00 0.00 28.39 3.46
1228 1243 2.026822 AGCAATCGGTTGATCTGTTCCT 60.027 45.455 13.85 0.00 37.53 3.36
1348 1363 2.521465 CCCAAACTGCAGTGGCCA 60.521 61.111 22.49 0.00 40.13 5.36
1762 1780 8.056407 AGGTTAGAAATTATTTGGAGCTGTTC 57.944 34.615 0.00 0.00 0.00 3.18
1860 1878 2.311463 GTGCCTCAGCTCTGGTAGATA 58.689 52.381 3.75 0.00 40.80 1.98
1965 1986 4.946157 TGGAAAATGCACAAAAATTGGTGT 59.054 33.333 2.82 0.00 37.35 4.16
2026 2047 1.550130 TTAGGGCTGCGCTGGTAACT 61.550 55.000 27.01 3.65 37.61 2.24
2130 2154 5.884792 TGAAGGTTGGAAAATGCACAAAAAT 59.115 32.000 0.00 0.00 0.00 1.82
2357 2384 2.080654 TTTTGGAGGGTTGGAAGGTG 57.919 50.000 0.00 0.00 0.00 4.00
2382 2409 0.590682 CGTATGTTTGCACTGCCACA 59.409 50.000 5.77 5.77 0.00 4.17
2435 2462 7.304497 AGTGTTAGAGTCTCACTTGGTTTAT 57.696 36.000 8.35 0.00 39.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 3.365969 GGAGCGTGATTTTTGGAACGAAT 60.366 43.478 0.00 0.00 38.27 3.34
237 243 5.542635 TGTCTACCAGACCTGATGTAAACTT 59.457 40.000 3.97 0.00 44.44 2.66
258 269 6.149474 GGGTCTATTATGTATGCCATGTTGTC 59.851 42.308 0.00 0.00 34.86 3.18
275 286 1.981495 GCCTCAGCCATAGGGTCTATT 59.019 52.381 0.00 0.00 34.46 1.73
281 292 0.617413 CCTATGCCTCAGCCATAGGG 59.383 60.000 13.18 0.00 41.59 3.53
351 363 1.198637 GCAAGGTGTGAGATTGAGCAC 59.801 52.381 0.00 0.00 35.63 4.40
353 366 1.527034 TGCAAGGTGTGAGATTGAGC 58.473 50.000 0.00 0.00 0.00 4.26
360 373 1.536709 GCCTGTTTTGCAAGGTGTGAG 60.537 52.381 0.00 0.00 0.00 3.51
420 433 9.060347 ACAAAGCACATACCTTGATAAGATATG 57.940 33.333 2.17 2.17 0.00 1.78
422 435 8.264347 TCACAAAGCACATACCTTGATAAGATA 58.736 33.333 0.00 0.00 0.00 1.98
458 472 7.045416 TCTAGAGATATAGATCAAGACGCCTC 58.955 42.308 0.00 0.00 34.17 4.70
460 474 7.801716 ATCTAGAGATATAGATCAAGACGCC 57.198 40.000 0.00 0.00 37.90 5.68
479 493 9.311916 GCTTACATATTAGGCATCAAGATCTAG 57.688 37.037 0.00 0.00 0.00 2.43
515 529 7.839680 ATAAGTGTTTTCAATGAAGGACCTT 57.160 32.000 6.40 6.40 0.00 3.50
533 547 6.543831 AGCATAAAGGCCTACTTGAATAAGTG 59.456 38.462 5.16 0.00 46.28 3.16
547 562 2.093500 CCCTTTGGAAAGCATAAAGGCC 60.093 50.000 8.98 0.00 45.72 5.19
628 643 1.109323 AGGGGCAAAACTGAGCACAC 61.109 55.000 0.00 0.00 35.37 3.82
660 675 4.058124 CCAAAGTTCACAGAATGAGTCGA 58.942 43.478 0.00 0.00 39.69 4.20
700 715 3.404899 CTGTAAGGGCCGAGTTAAAACA 58.595 45.455 0.00 0.00 0.00 2.83
829 844 0.318784 CCGCTGTCTCCCGCTAATAC 60.319 60.000 0.00 0.00 0.00 1.89
936 951 4.096003 GCTAGCTTCCCACCGCCA 62.096 66.667 7.70 0.00 0.00 5.69
1042 1057 1.451207 GCATATCCACACGCACCCA 60.451 57.895 0.00 0.00 0.00 4.51
1056 1071 1.476891 GGACAGACGAAGACAGGCATA 59.523 52.381 0.00 0.00 0.00 3.14
1125 1140 0.638746 CGTAGAACGGACGATTGTGC 59.361 55.000 0.00 0.00 42.98 4.57
1251 1266 3.012518 CAGAGCATCGACCCAAAGAAAT 58.987 45.455 0.00 0.00 42.67 2.17
1348 1363 1.006102 CTTCCGGAGCTCGTGTTGT 60.006 57.895 3.34 0.00 37.11 3.32
1388 1403 1.818060 CAGCTAGCTCTCTGTCAGTGT 59.182 52.381 16.15 0.00 0.00 3.55
1860 1878 9.030452 TCATTTATTTTGGCACTAGGTGTAAAT 57.970 29.630 0.00 0.00 35.75 1.40
1965 1986 3.319198 GGTTCGAGTCCCCAGCCA 61.319 66.667 0.00 0.00 0.00 4.75
2026 2047 1.483827 CTCTTGCCATCTGTCCTAGCA 59.516 52.381 0.00 0.00 0.00 3.49
2112 2136 6.327934 CACCAAATTTTTGTGCATTTTCCAA 58.672 32.000 0.00 0.00 36.45 3.53
2130 2154 4.966787 GTCCCCAGCCGCACCAAA 62.967 66.667 0.00 0.00 0.00 3.28
2305 2332 6.340522 CAAAACAAAGGAAAACCACTCTCAT 58.659 36.000 0.00 0.00 0.00 2.90
2357 2384 2.724174 GCAGTGCAAACATACGTTTTCC 59.276 45.455 11.09 0.00 42.82 3.13
2382 2409 2.890945 GTGCCACTCTAACCAAAACCAT 59.109 45.455 0.00 0.00 0.00 3.55
2435 2462 9.429359 ACATGCAAATTTATTCCGTTTAAATCA 57.571 25.926 0.00 0.00 30.79 2.57


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

AutoCloner maintained by Alex Coulton.