Multiple sequence alignment - TraesCS5B01G109700

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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 TraesCS5B01G109700 chr5B 100.000 2528 0 0 1 2528 155708356 155705829 0.000000e+00 4669.0
1 TraesCS5B01G109700 chr5B 97.095 964 23 3 93 1052 130348386 130347424 0.000000e+00 1620.0
2 TraesCS5B01G109700 chr5B 85.265 509 40 10 1956 2457 403750926 403750446 2.260000e-135 492.0
3 TraesCS5B01G109700 chr5B 81.092 238 36 9 1 230 130348522 130348286 5.560000e-42 182.0
4 TraesCS5B01G109700 chr5B 93.651 63 3 1 131 193 155708188 155708127 2.680000e-15 93.5
5 TraesCS5B01G109700 chr5B 93.651 63 3 1 169 230 155708226 155708164 2.680000e-15 93.5
6 TraesCS5B01G109700 chr5B 92.063 63 4 1 131 193 130348310 130348249 1.250000e-13 87.9
7 TraesCS5B01G109700 chr5B 94.872 39 1 1 1572 1609 155706642 155706604 2.720000e-05 60.2
8 TraesCS5B01G109700 chr5B 94.872 39 1 1 1715 1753 155706785 155706748 2.720000e-05 60.2
9 TraesCS5B01G109700 chr5B 96.970 33 1 0 1606 1638 155706700 155706668 3.510000e-04 56.5
10 TraesCS5B01G109700 chr5B 96.970 33 1 0 1657 1689 155706751 155706719 3.510000e-04 56.5
11 TraesCS5B01G109700 chr1B 98.183 2311 27 3 169 2466 236966063 236968371 0.000000e+00 4021.0
12 TraesCS5B01G109700 chr1B 87.738 1468 146 22 93 1539 95395294 95396748 0.000000e+00 1683.0
13 TraesCS5B01G109700 chr1B 88.710 558 39 9 1956 2506 95397355 95397895 0.000000e+00 660.0
14 TraesCS5B01G109700 chr1B 88.551 559 40 8 1956 2506 95392028 95392570 0.000000e+00 656.0
15 TraesCS5B01G109700 chr1B 89.813 481 28 6 2032 2506 95389472 95389937 4.650000e-167 597.0
16 TraesCS5B01G109700 chr1B 95.349 86 4 0 1 86 95381248 95381333 1.220000e-28 137.0
17 TraesCS5B01G109700 chr1B 95.349 86 4 0 1 86 95395117 95395202 1.220000e-28 137.0
18 TraesCS5B01G109700 chr1B 90.476 105 8 2 89 193 236966022 236966124 1.220000e-28 137.0
19 TraesCS5B01G109700 chr1B 100.000 34 0 0 1538 1571 95391797 95391830 2.100000e-06 63.9
20 TraesCS5B01G109700 chr1B 94.872 39 1 1 1715 1753 236967465 236967502 2.720000e-05 60.2
21 TraesCS5B01G109700 chr1B 94.872 39 1 1 1572 1609 236967621 236967659 2.720000e-05 60.2
22 TraesCS5B01G109700 chr1B 96.970 33 1 0 1606 1638 236967563 236967595 3.510000e-04 56.5
23 TraesCS5B01G109700 chr6B 87.918 1465 146 21 93 1539 719347398 719348849 0.000000e+00 1696.0
24 TraesCS5B01G109700 chr6B 88.839 224 13 4 1 223 491688088 491687876 5.360000e-67 265.0
25 TraesCS5B01G109700 chr6B 90.141 142 9 3 130 267 491687838 491687698 2.000000e-41 180.0
26 TraesCS5B01G109700 chr6B 94.186 86 5 0 1 86 719347233 719347318 5.670000e-27 132.0
27 TraesCS5B01G109700 chr6B 95.000 60 3 0 131 190 491687892 491687833 7.450000e-16 95.3
28 TraesCS5B01G109700 chr4B 89.353 1268 121 5 276 1539 239435378 239436635 0.000000e+00 1581.0
29 TraesCS5B01G109700 chr4B 89.748 556 40 5 1956 2504 239437180 239437725 0.000000e+00 695.0
30 TraesCS5B01G109700 chr4B 88.550 131 13 2 1739 1869 464165497 464165369 9.360000e-35 158.0
31 TraesCS5B01G109700 chr4B 100.000 34 0 0 1538 1571 239436949 239436982 2.100000e-06 63.9
32 TraesCS5B01G109700 chr6D 91.719 1123 87 4 420 1538 459686409 459687529 0.000000e+00 1554.0
33 TraesCS5B01G109700 chr7A 86.075 1465 165 29 93 1539 638647344 638648787 0.000000e+00 1539.0
34 TraesCS5B01G109700 chr1D 87.611 1235 141 7 311 1538 41174493 41173264 0.000000e+00 1423.0
35 TraesCS5B01G109700 chr2B 85.545 1266 165 7 287 1538 442603011 442604272 0.000000e+00 1308.0
36 TraesCS5B01G109700 chr2B 92.407 777 41 8 1689 2465 594187940 594187182 0.000000e+00 1092.0
37 TraesCS5B01G109700 chr2B 80.755 556 67 19 1961 2507 442604701 442605225 5.070000e-107 398.0
38 TraesCS5B01G109700 chr2B 87.129 101 8 5 93 190 477562088 477562186 2.660000e-20 110.0
39 TraesCS5B01G109700 chr2B 84.848 99 6 5 95 190 442602831 442602923 9.630000e-15 91.6
40 TraesCS5B01G109700 chr7D 85.075 1206 158 12 297 1494 45103630 45104821 0.000000e+00 1210.0
41 TraesCS5B01G109700 chr5A 88.968 562 41 10 1956 2507 479751906 479751356 0.000000e+00 675.0
42 TraesCS5B01G109700 chr5A 100.000 34 0 0 1538 1571 479752137 479752104 2.100000e-06 63.9
43 TraesCS5B01G109700 chrUn 88.372 559 40 9 1956 2506 6207261 6206720 0.000000e+00 649.0
44 TraesCS5B01G109700 chrUn 89.813 481 28 6 2032 2506 358405122 358404657 4.650000e-167 597.0
45 TraesCS5B01G109700 chrUn 89.813 481 28 6 2032 2506 399533096 399533561 4.650000e-167 597.0
46 TraesCS5B01G109700 chrUn 92.632 95 7 0 1 95 6210861 6210767 1.220000e-28 137.0
47 TraesCS5B01G109700 chrUn 95.349 86 4 0 1 86 364130424 364130509 1.220000e-28 137.0
48 TraesCS5B01G109700 chrUn 92.632 95 7 0 1 95 365288719 365288625 1.220000e-28 137.0
49 TraesCS5B01G109700 chrUn 100.000 34 0 0 1538 1571 6207492 6207459 2.100000e-06 63.9
50 TraesCS5B01G109700 chrUn 100.000 34 0 0 1538 1571 180896435 180896402 2.100000e-06 63.9
51 TraesCS5B01G109700 chrUn 100.000 34 0 0 1538 1571 387850483 387850450 2.100000e-06 63.9
52 TraesCS5B01G109700 chr3D 87.818 550 41 7 1956 2504 184584922 184585446 2.760000e-174 621.0
53 TraesCS5B01G109700 chr3D 100.000 34 0 0 1538 1571 184489849 184489816 2.100000e-06 63.9
54 TraesCS5B01G109700 chr4A 92.308 104 7 1 1763 1866 87407335 87407437 2.030000e-31 147.0


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 TraesCS5B01G109700 chr5B 155705829 155708356 2527 True 727.057143 4669 95.855143 1 2528 7 chr5B.!!$R3 2527
1 TraesCS5B01G109700 chr5B 130347424 130348522 1098 True 629.966667 1620 90.083333 1 1052 3 chr5B.!!$R2 1051
2 TraesCS5B01G109700 chr1B 236966022 236968371 2349 False 866.980000 4021 95.074600 89 2466 5 chr1B.!!$F3 2377
3 TraesCS5B01G109700 chr1B 95389472 95397895 8423 False 632.816667 1683 91.693500 1 2506 6 chr1B.!!$F2 2505
4 TraesCS5B01G109700 chr6B 719347233 719348849 1616 False 914.000000 1696 91.052000 1 1539 2 chr6B.!!$F1 1538
5 TraesCS5B01G109700 chr4B 239435378 239437725 2347 False 779.966667 1581 93.033667 276 2504 3 chr4B.!!$F1 2228
6 TraesCS5B01G109700 chr6D 459686409 459687529 1120 False 1554.000000 1554 91.719000 420 1538 1 chr6D.!!$F1 1118
7 TraesCS5B01G109700 chr7A 638647344 638648787 1443 False 1539.000000 1539 86.075000 93 1539 1 chr7A.!!$F1 1446
8 TraesCS5B01G109700 chr1D 41173264 41174493 1229 True 1423.000000 1423 87.611000 311 1538 1 chr1D.!!$R1 1227
9 TraesCS5B01G109700 chr2B 594187182 594187940 758 True 1092.000000 1092 92.407000 1689 2465 1 chr2B.!!$R1 776
10 TraesCS5B01G109700 chr2B 442602831 442605225 2394 False 599.200000 1308 83.716000 95 2507 3 chr2B.!!$F2 2412
11 TraesCS5B01G109700 chr7D 45103630 45104821 1191 False 1210.000000 1210 85.075000 297 1494 1 chr7D.!!$F1 1197
12 TraesCS5B01G109700 chr5A 479751356 479752137 781 True 369.450000 675 94.484000 1538 2507 2 chr5A.!!$R1 969
13 TraesCS5B01G109700 chrUn 6206720 6210861 4141 True 283.300000 649 93.668000 1 2506 3 chrUn.!!$R5 2505
14 TraesCS5B01G109700 chr3D 184584922 184585446 524 False 621.000000 621 87.818000 1956 2504 1 chr3D.!!$F1 548

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
910 6710 0.244721 GCACCTGAAGAACCATTGGC 59.755 55.0 1.54 0.0 0.0 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2479 10130 2.304092 CATGTACAATGGAGGCAGCAT 58.696 47.619 0.0 0.0 0.0 3.79 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
30 5676 2.404789 CGGTCCATGCACAATCGC 59.595 61.111 0.00 0.0 0.00 4.58
86 5732 6.835914 AGAAATTCAGCGAAGATACAAACAG 58.164 36.000 0.00 0.0 0.00 3.16
249 5985 7.061054 AGTGTACTCTAGATGCATACCACTTA 58.939 38.462 0.00 0.0 0.00 2.24
255 5991 7.069950 ACTCTAGATGCATACCACTTATGTTCA 59.930 37.037 0.00 0.0 40.02 3.18
559 6350 5.129980 TGTGGAAGCAGATGATGAAGATAGT 59.870 40.000 0.00 0.0 0.00 2.12
910 6710 0.244721 GCACCTGAAGAACCATTGGC 59.755 55.000 1.54 0.0 0.00 4.52
1056 6859 5.692115 ATGGACACCAGTTCATGTATGTA 57.308 39.130 0.00 0.0 42.47 2.29
1063 6866 4.640201 ACCAGTTCATGTATGTACATTGGC 59.360 41.667 14.77 5.8 43.99 4.52
1500 7309 1.618837 GTGAGGGCTGTCACAAGACTA 59.381 52.381 13.48 0.0 45.34 2.59
2507 10158 4.473444 CCTCCATTGTACATGCCCTAATT 58.527 43.478 0.00 0.0 0.00 1.40
2508 10159 4.895297 CCTCCATTGTACATGCCCTAATTT 59.105 41.667 0.00 0.0 0.00 1.82
2509 10160 5.363580 CCTCCATTGTACATGCCCTAATTTT 59.636 40.000 0.00 0.0 0.00 1.82
2510 10161 6.219417 TCCATTGTACATGCCCTAATTTTG 57.781 37.500 0.00 0.0 0.00 2.44
2511 10162 5.719085 TCCATTGTACATGCCCTAATTTTGT 59.281 36.000 0.00 0.0 0.00 2.83
2512 10163 6.892456 TCCATTGTACATGCCCTAATTTTGTA 59.108 34.615 0.00 0.0 0.00 2.41
2513 10164 7.068103 TCCATTGTACATGCCCTAATTTTGTAG 59.932 37.037 0.00 0.0 0.00 2.74
2514 10165 6.767524 TTGTACATGCCCTAATTTTGTAGG 57.232 37.500 0.00 0.0 40.48 3.18
2515 10166 5.822204 TGTACATGCCCTAATTTTGTAGGT 58.178 37.500 0.00 0.0 39.33 3.08
2516 10167 5.650266 TGTACATGCCCTAATTTTGTAGGTG 59.350 40.000 0.00 0.0 39.33 4.00
2517 10168 4.023291 ACATGCCCTAATTTTGTAGGTGG 58.977 43.478 0.00 0.0 39.33 4.61
2518 10169 2.452505 TGCCCTAATTTTGTAGGTGGC 58.547 47.619 0.00 0.0 39.33 5.01
2519 10170 2.225142 TGCCCTAATTTTGTAGGTGGCA 60.225 45.455 0.00 0.0 39.33 4.92
2520 10171 3.031013 GCCCTAATTTTGTAGGTGGCAT 58.969 45.455 0.00 0.0 39.33 4.40
2521 10172 3.450817 GCCCTAATTTTGTAGGTGGCATT 59.549 43.478 0.00 0.0 39.33 3.56
2522 10173 4.647399 GCCCTAATTTTGTAGGTGGCATTA 59.353 41.667 0.00 0.0 39.33 1.90
2523 10174 5.221244 GCCCTAATTTTGTAGGTGGCATTAG 60.221 44.000 0.00 0.0 39.33 1.73
2524 10175 5.891551 CCCTAATTTTGTAGGTGGCATTAGT 59.108 40.000 0.00 0.0 39.33 2.24
2525 10176 6.379988 CCCTAATTTTGTAGGTGGCATTAGTT 59.620 38.462 0.00 0.0 39.33 2.24
2526 10177 7.093509 CCCTAATTTTGTAGGTGGCATTAGTTT 60.094 37.037 0.00 0.0 39.33 2.66
2527 10178 7.759433 CCTAATTTTGTAGGTGGCATTAGTTTG 59.241 37.037 0.00 0.0 36.62 2.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 5676 3.675228 GCTCAACCAAATCATGCTTGAGG 60.675 47.826 8.4 6.63 45.69 3.86
86 5732 4.368315 TCTCACACACACACACATCTAAC 58.632 43.478 0.0 0.00 0.00 2.34
249 5985 4.516698 CCAGAACAAGCAAGTACTGAACAT 59.483 41.667 0.0 0.00 0.00 2.71
255 5991 1.142870 TGCCCAGAACAAGCAAGTACT 59.857 47.619 0.0 0.00 32.56 2.73
582 6373 6.043243 GGGACTTACCAATCTGATATCCTCAA 59.957 42.308 0.0 0.00 41.20 3.02
680 6475 8.440771 CAGGAGTATAAAAATAGGAGAACCCAT 58.559 37.037 0.0 0.00 37.41 4.00
910 6710 6.394809 AGGTTACCTTCTTTGTTGTTTTGTG 58.605 36.000 0.0 0.00 0.00 3.33
1056 6859 1.973281 CACAGCTTCCCGCCAATGT 60.973 57.895 0.0 0.00 40.39 2.71
1063 6866 1.160137 CTTTCCTTCACAGCTTCCCG 58.840 55.000 0.0 0.00 0.00 5.14
1500 7309 4.044571 TCATCCTTGAAAAGTTGATCCCCT 59.955 41.667 0.0 0.00 44.25 4.79
1876 9446 9.911788 AAGAAACAGAATTATCACCATAGACAT 57.088 29.630 0.0 0.00 0.00 3.06
2257 9907 5.804473 CACACTGAAAAACAAGCATACACAA 59.196 36.000 0.0 0.00 0.00 3.33
2479 10130 2.304092 CATGTACAATGGAGGCAGCAT 58.696 47.619 0.0 0.00 0.00 3.79


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

AutoCloner maintained by Alex Coulton.