Multiple sequence alignment - TraesCS5B01G142700

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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 TraesCS5B01G142700 chr5B 100.000 2549 0 0 1 2549 269388907 269391455 0 4708
1 TraesCS5B01G142700 chr5B 96.322 1985 68 4 567 2549 446193254 446191273 0 3256
2 TraesCS5B01G142700 chr1B 96.588 1993 64 4 559 2549 663786486 663788476 0 3301
3 TraesCS5B01G142700 chr2B 96.540 1994 57 9 560 2549 543889479 543887494 0 3290
4 TraesCS5B01G142700 chr2B 96.479 1988 65 5 566 2549 602077186 602075200 0 3278
5 TraesCS5B01G142700 chr2B 96.389 1994 60 9 560 2549 544319650 544317665 0 3273
6 TraesCS5B01G142700 chr2B 96.281 1990 68 5 564 2549 596962065 596964052 0 3260
7 TraesCS5B01G142700 chr7B 96.477 1987 62 5 565 2549 718488476 718486496 0 3275
8 TraesCS5B01G142700 chr7B 96.291 1995 69 5 558 2549 621924182 621926174 0 3269
9 TraesCS5B01G142700 chr3B 96.373 1985 65 6 566 2549 703251168 703253146 0 3260
10 TraesCS5B01G142700 chr5D 93.838 568 30 4 1 566 235772274 235771710 0 850
11 TraesCS5B01G142700 chr5D 92.430 568 39 4 1 566 43663689 43664254 0 808
12 TraesCS5B01G142700 chr3D 92.769 567 36 4 1 566 439009723 439009161 0 815
13 TraesCS5B01G142700 chr3D 92.416 567 39 3 1 566 338188392 338187829 0 806
14 TraesCS5B01G142700 chr2D 92.593 567 38 3 1 566 441467379 441467942 0 811
15 TraesCS5B01G142700 chr2D 92.416 567 39 3 1 566 441468886 441469449 0 806
16 TraesCS5B01G142700 chr6D 92.456 570 35 7 1 566 64012274 64011709 0 808
17 TraesCS5B01G142700 chr4D 92.281 570 38 5 1 566 486988646 486988079 0 804
18 TraesCS5B01G142700 chr1D 92.403 566 39 3 2 566 296207870 296207308 0 804


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 TraesCS5B01G142700 chr5B 269388907 269391455 2548 False 4708.0 4708 100.0000 1 2549 1 chr5B.!!$F1 2548
1 TraesCS5B01G142700 chr5B 446191273 446193254 1981 True 3256.0 3256 96.3220 567 2549 1 chr5B.!!$R1 1982
2 TraesCS5B01G142700 chr1B 663786486 663788476 1990 False 3301.0 3301 96.5880 559 2549 1 chr1B.!!$F1 1990
3 TraesCS5B01G142700 chr2B 543887494 543889479 1985 True 3290.0 3290 96.5400 560 2549 1 chr2B.!!$R1 1989
4 TraesCS5B01G142700 chr2B 602075200 602077186 1986 True 3278.0 3278 96.4790 566 2549 1 chr2B.!!$R3 1983
5 TraesCS5B01G142700 chr2B 544317665 544319650 1985 True 3273.0 3273 96.3890 560 2549 1 chr2B.!!$R2 1989
6 TraesCS5B01G142700 chr2B 596962065 596964052 1987 False 3260.0 3260 96.2810 564 2549 1 chr2B.!!$F1 1985
7 TraesCS5B01G142700 chr7B 718486496 718488476 1980 True 3275.0 3275 96.4770 565 2549 1 chr7B.!!$R1 1984
8 TraesCS5B01G142700 chr7B 621924182 621926174 1992 False 3269.0 3269 96.2910 558 2549 1 chr7B.!!$F1 1991
9 TraesCS5B01G142700 chr3B 703251168 703253146 1978 False 3260.0 3260 96.3730 566 2549 1 chr3B.!!$F1 1983
10 TraesCS5B01G142700 chr5D 235771710 235772274 564 True 850.0 850 93.8380 1 566 1 chr5D.!!$R1 565
11 TraesCS5B01G142700 chr5D 43663689 43664254 565 False 808.0 808 92.4300 1 566 1 chr5D.!!$F1 565
12 TraesCS5B01G142700 chr3D 439009161 439009723 562 True 815.0 815 92.7690 1 566 1 chr3D.!!$R2 565
13 TraesCS5B01G142700 chr3D 338187829 338188392 563 True 806.0 806 92.4160 1 566 1 chr3D.!!$R1 565
14 TraesCS5B01G142700 chr2D 441467379 441469449 2070 False 808.5 811 92.5045 1 566 2 chr2D.!!$F1 565
15 TraesCS5B01G142700 chr6D 64011709 64012274 565 True 808.0 808 92.4560 1 566 1 chr6D.!!$R1 565
16 TraesCS5B01G142700 chr4D 486988079 486988646 567 True 804.0 804 92.2810 1 566 1 chr4D.!!$R1 565
17 TraesCS5B01G142700 chr1D 296207308 296207870 562 True 804.0 804 92.4030 2 566 1 chr1D.!!$R1 564

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
22 23 0.039256 CAAACATCGGGGCACTGTTG 60.039 55.0 4.22 4.22 33.6 3.33 F
1009 2526 0.041238 TCCGAGGTCCATGTCTTCCT 59.959 55.0 0.00 0.00 0.0 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1060 2577 0.098200 CGCGGACAGACGAAGACATA 59.902 55.000 0.0 0.0 35.47 2.29 R
2171 3694 1.406887 CGCAGCCCTAAACACCACTAT 60.407 52.381 0.0 0.0 0.00 2.12 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
22 23 0.039256 CAAACATCGGGGCACTGTTG 60.039 55.000 4.22 4.22 33.60 3.33
174 679 7.291566 CCATTTGGTGTAGGTTTGGGTATATA 58.708 38.462 0.00 0.00 0.00 0.86
206 711 2.149578 CCAGAGCTTCTCACAACAAGG 58.850 52.381 0.00 0.00 32.06 3.61
307 1822 9.985730 AAAAATCATGTGTCAACATAGAACAAT 57.014 25.926 0.00 0.00 45.50 2.71
317 1832 8.590204 TGTCAACATAGAACAATAGGAGTGTTA 58.410 33.333 0.00 0.00 39.29 2.41
445 1961 5.421693 TGCTCCAGTGCATATAAATTGGTTT 59.578 36.000 0.00 0.00 38.12 3.27
474 1990 0.831711 ATTTGGGTCCTTGGGTGCAC 60.832 55.000 8.80 8.80 0.00 4.57
481 1997 0.759959 TCCTTGGGTGCACGTTTAGA 59.240 50.000 11.45 1.95 0.00 2.10
504 2020 2.557317 CCATGCAAGAAATGGGAATGC 58.443 47.619 0.00 0.00 40.86 3.56
734 2251 1.462432 TTACAGGTGGGACCAGGCA 60.462 57.895 0.00 0.00 41.95 4.75
930 2447 1.679898 GTGGGAAGCTAGCTGTGGT 59.320 57.895 20.16 1.15 0.00 4.16
937 2454 4.087892 CTAGCTGTGGTGGGCGCT 62.088 66.667 7.64 0.00 36.56 5.92
953 2470 1.599047 GCTGCAGTGGGAAGCTAGA 59.401 57.895 16.64 0.00 34.05 2.43
1009 2526 0.041238 TCCGAGGTCCATGTCTTCCT 59.959 55.000 0.00 0.00 0.00 3.36
1060 2577 2.347490 GGGTGCGTGTGGAGATGT 59.653 61.111 0.00 0.00 0.00 3.06
1061 2578 1.594833 GGGTGCGTGTGGAGATGTA 59.405 57.895 0.00 0.00 0.00 2.29
1110 2627 1.347707 AGCGTTGATCAGAGGGTTTCA 59.652 47.619 0.00 0.00 0.00 2.69
1270 2787 3.140325 TCTTTCTTTGGGTCGATGCTT 57.860 42.857 0.00 0.00 0.00 3.91
1495 3012 6.705863 TTTGCAAATACTTTTGGGCATTTT 57.294 29.167 8.05 0.00 42.09 1.82
1868 3387 5.337571 CCTCAGCTCTGGTAGATGTTTACAA 60.338 44.000 0.00 0.00 42.45 2.41
2313 3837 1.436195 ATGTTTGCACACGCGTGAGT 61.436 50.000 42.94 21.60 46.80 3.41
2352 3877 3.838565 TGCACTGAAATTTTGGAGGGTA 58.161 40.909 0.00 0.00 0.00 3.69
2422 3947 2.882137 TGGCACTTGGTTTAGTGTTAGC 59.118 45.455 5.75 0.00 45.76 3.09
2428 3953 4.038883 ACTTGGTTTAGTGTTAGCGTCTCT 59.961 41.667 0.00 0.00 0.00 3.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 1.303236 CAATCCAACAGTGCCCCGA 60.303 57.895 0.00 0.00 0.00 5.14
22 23 0.179129 CAATGTCTTGCCGGCAATCC 60.179 55.000 40.03 30.93 35.20 3.01
174 679 3.135530 AGAAGCTCTGGTTTGTGAGAAGT 59.864 43.478 0.00 0.00 32.44 3.01
206 711 3.203716 GTTCCCTACCGAAACCATCATC 58.796 50.000 0.00 0.00 0.00 2.92
284 1797 8.896744 CCTATTGTTCTATGTTGACACATGATT 58.103 33.333 0.00 0.00 43.92 2.57
285 1798 8.267183 TCCTATTGTTCTATGTTGACACATGAT 58.733 33.333 0.00 0.00 43.92 2.45
288 1801 7.550551 CACTCCTATTGTTCTATGTTGACACAT 59.449 37.037 0.00 0.00 46.07 3.21
307 1822 8.684386 TCACAAAAATTGACATAACACTCCTA 57.316 30.769 0.00 0.00 0.00 2.94
317 1832 6.204495 CCCCGAAAAATCACAAAAATTGACAT 59.796 34.615 0.00 0.00 0.00 3.06
445 1961 6.101881 ACCCAAGGACCCAAATTTGATTTTTA 59.898 34.615 19.86 0.00 0.00 1.52
457 1973 2.197324 GTGCACCCAAGGACCCAA 59.803 61.111 5.22 0.00 0.00 4.12
474 1990 4.963276 TTTCTTGCATGGGATCTAAACG 57.037 40.909 0.00 0.00 0.00 3.60
504 2020 2.166829 TGGTCCCCGATGTTTGAAATG 58.833 47.619 0.00 0.00 0.00 2.32
734 2251 0.323360 TAAAATTGGCCGCCTCTGCT 60.323 50.000 11.61 0.00 34.43 4.24
813 2330 2.638480 ATATAGCACACACCCGCAAT 57.362 45.000 0.00 0.00 0.00 3.56
850 2367 3.207547 CTCTGTCGCCGTGGTCACA 62.208 63.158 1.90 0.00 0.00 3.58
937 2454 1.065926 CACATCTAGCTTCCCACTGCA 60.066 52.381 0.00 0.00 0.00 4.41
996 2513 2.626840 GAGCTTGAGGAAGACATGGAC 58.373 52.381 0.00 0.00 0.00 4.02
1026 2543 4.957684 CGGCTCTGCATCCGCGAT 62.958 66.667 8.23 0.00 42.97 4.58
1060 2577 0.098200 CGCGGACAGACGAAGACATA 59.902 55.000 0.00 0.00 35.47 2.29
1061 2578 1.154016 CGCGGACAGACGAAGACAT 60.154 57.895 0.00 0.00 35.47 3.06
1110 2627 1.145377 GTGGTTCCTCGGTGTGTGT 59.855 57.895 0.00 0.00 0.00 3.72
1226 2743 1.965930 GCCACCTGCATGAACACGA 60.966 57.895 0.00 0.00 40.77 4.35
1270 2787 5.178096 TCATTTATCAGAGTCTTGGCCAA 57.822 39.130 19.25 19.25 0.00 4.52
1495 3012 3.707611 ACCAGTGCGATTACCATACCTAA 59.292 43.478 0.00 0.00 0.00 2.69
1868 3387 9.777297 AAAATGTTCATTTATTTTGGCACTAGT 57.223 25.926 10.54 0.00 35.73 2.57
2171 3694 1.406887 CGCAGCCCTAAACACCACTAT 60.407 52.381 0.00 0.00 0.00 2.12
2313 3837 3.748568 GTGCAAAACAAAGGAAAACCACA 59.251 39.130 0.00 0.00 0.00 4.17
2352 3877 5.735070 GCAAACATACGTTTTCAACCTTCCT 60.735 40.000 0.00 0.00 42.82 3.36
2422 3947 7.411588 CGTTTAAATCCTAAACCAAGAGAGACG 60.412 40.741 0.00 0.00 34.81 4.18
2428 3953 9.517868 TTATTCCGTTTAAATCCTAAACCAAGA 57.482 29.630 0.00 0.00 34.81 3.02


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

AutoCloner maintained by Alex Coulton.