Multiple sequence alignment - TraesCS5D01G442900

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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 TraesCS5D01G442900 chr5D 100.000 3068 0 0 1 3068 494760790 494763857 0.000000e+00 5666.0
1 TraesCS5D01G442900 chr5D 83.757 1299 187 12 784 2073 494684580 494685863 0.000000e+00 1208.0
2 TraesCS5D01G442900 chr5D 80.706 1389 183 42 983 2310 494773751 494775115 0.000000e+00 1002.0
3 TraesCS5D01G442900 chr5D 81.653 1101 185 15 984 2074 494654379 494655472 0.000000e+00 898.0
4 TraesCS5D01G442900 chr5D 90.175 285 27 1 2322 2605 497778989 497779273 1.340000e-98 370.0
5 TraesCS5D01G442900 chr5D 95.238 42 2 0 2609 2650 494775525 494775566 1.970000e-07 67.6
6 TraesCS5D01G442900 chr5A 92.659 2997 110 31 1 2947 618601723 618604659 0.000000e+00 4215.0
7 TraesCS5D01G442900 chr5A 83.719 1296 183 16 855 2132 618270423 618271708 0.000000e+00 1199.0
8 TraesCS5D01G442900 chr5A 85.152 889 129 2 1158 2043 618430316 618431204 0.000000e+00 907.0
9 TraesCS5D01G442900 chr5A 81.118 1091 191 7 984 2074 618273220 618274295 0.000000e+00 859.0
10 TraesCS5D01G442900 chr5A 91.166 283 24 1 2324 2605 621756472 621756754 1.730000e-102 383.0
11 TraesCS5D01G442900 chr5B 95.031 1630 55 7 607 2215 611322704 611324328 0.000000e+00 2538.0
12 TraesCS5D01G442900 chr5B 83.211 1358 192 18 784 2133 610922763 610924092 0.000000e+00 1212.0
13 TraesCS5D01G442900 chr5B 81.908 1216 190 21 985 2183 610965571 610966773 0.000000e+00 1000.0
14 TraesCS5D01G442900 chr5B 88.862 817 43 22 2299 3068 611326126 611326941 0.000000e+00 961.0
15 TraesCS5D01G442900 chr5B 81.818 1166 179 14 607 1761 610957976 610959119 0.000000e+00 948.0
16 TraesCS5D01G442900 chr5B 79.468 1354 238 28 736 2074 610873834 610875162 0.000000e+00 924.0
17 TraesCS5D01G442900 chr5B 80.823 1142 197 15 882 2013 611045279 611046408 0.000000e+00 876.0
18 TraesCS5D01G442900 chr5B 79.644 1125 173 25 984 2071 610882870 610883975 0.000000e+00 758.0
19 TraesCS5D01G442900 chr5B 91.553 438 35 2 41 476 611321913 611322350 1.220000e-168 603.0
20 TraesCS5D01G442900 chr5B 90.526 285 26 1 2322 2605 616649301 616649585 2.890000e-100 375.0
21 TraesCS5D01G442900 chr5B 94.203 69 4 0 490 558 611322632 611322700 4.180000e-19 106.0
22 TraesCS5D01G442900 chr1D 80.423 1323 201 26 981 2252 491604286 491602971 0.000000e+00 955.0
23 TraesCS5D01G442900 chr7B 81.128 514 74 14 20 517 41648474 41648980 1.030000e-104 390.0
24 TraesCS5D01G442900 chr7D 78.947 437 71 11 203 619 603838866 603839301 8.380000e-71 278.0


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 TraesCS5D01G442900 chr5D 494760790 494763857 3067 False 5666.0 5666 100.00000 1 3068 1 chr5D.!!$F3 3067
1 TraesCS5D01G442900 chr5D 494684580 494685863 1283 False 1208.0 1208 83.75700 784 2073 1 chr5D.!!$F2 1289
2 TraesCS5D01G442900 chr5D 494654379 494655472 1093 False 898.0 898 81.65300 984 2074 1 chr5D.!!$F1 1090
3 TraesCS5D01G442900 chr5D 494773751 494775566 1815 False 534.8 1002 87.97200 983 2650 2 chr5D.!!$F5 1667
4 TraesCS5D01G442900 chr5A 618601723 618604659 2936 False 4215.0 4215 92.65900 1 2947 1 chr5A.!!$F2 2946
5 TraesCS5D01G442900 chr5A 618270423 618274295 3872 False 1029.0 1199 82.41850 855 2132 2 chr5A.!!$F4 1277
6 TraesCS5D01G442900 chr5A 618430316 618431204 888 False 907.0 907 85.15200 1158 2043 1 chr5A.!!$F1 885
7 TraesCS5D01G442900 chr5B 610922763 610924092 1329 False 1212.0 1212 83.21100 784 2133 1 chr5B.!!$F3 1349
8 TraesCS5D01G442900 chr5B 611321913 611326941 5028 False 1052.0 2538 92.41225 41 3068 4 chr5B.!!$F8 3027
9 TraesCS5D01G442900 chr5B 610965571 610966773 1202 False 1000.0 1000 81.90800 985 2183 1 chr5B.!!$F5 1198
10 TraesCS5D01G442900 chr5B 610957976 610959119 1143 False 948.0 948 81.81800 607 1761 1 chr5B.!!$F4 1154
11 TraesCS5D01G442900 chr5B 610873834 610875162 1328 False 924.0 924 79.46800 736 2074 1 chr5B.!!$F1 1338
12 TraesCS5D01G442900 chr5B 611045279 611046408 1129 False 876.0 876 80.82300 882 2013 1 chr5B.!!$F6 1131
13 TraesCS5D01G442900 chr5B 610882870 610883975 1105 False 758.0 758 79.64400 984 2071 1 chr5B.!!$F2 1087
14 TraesCS5D01G442900 chr1D 491602971 491604286 1315 True 955.0 955 80.42300 981 2252 1 chr1D.!!$R1 1271
15 TraesCS5D01G442900 chr7B 41648474 41648980 506 False 390.0 390 81.12800 20 517 1 chr7B.!!$F1 497

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
731 1017 1.388547 CAGTCCTCTCTCTCCCTTCG 58.611 60.0 0.0 0.0 0.0 3.79 F
1742 2157 0.679002 CCTCCAGTGCTTGATGTGGG 60.679 60.0 0.0 0.0 0.0 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1767 2182 1.337728 CCGATGTTGTACCTGTCAGCA 60.338 52.381 0.0 0.0 0.0 4.41 R
2890 5215 1.859302 AACCAAAGCCCTGTCACAAA 58.141 45.000 0.0 0.0 0.0 2.83 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
110 113 1.446907 CAGTTGAGAAGCCGCTGAAT 58.553 50.000 0.00 0.00 0.00 2.57
180 187 3.402681 CAGGGGTGGCGGTGAGAT 61.403 66.667 0.00 0.00 0.00 2.75
293 302 4.415332 CTCCACCGTACGCGCAGT 62.415 66.667 10.49 9.29 36.67 4.40
328 337 3.127533 GCCACACAAGCGCCCTAG 61.128 66.667 2.29 0.00 0.00 3.02
329 338 2.347490 CCACACAAGCGCCCTAGT 59.653 61.111 2.29 0.00 0.00 2.57
366 376 1.673009 CCTCGGCGGCCACTAAAAA 60.673 57.895 20.71 0.00 0.00 1.94
427 437 4.579384 CCGGCCACACCCACACTT 62.579 66.667 2.24 0.00 33.26 3.16
430 440 1.454539 GGCCACACCCACACTTAGT 59.545 57.895 0.00 0.00 0.00 2.24
476 486 2.257207 CTAAAGACCCCACCTGTCAGA 58.743 52.381 0.00 0.00 35.15 3.27
477 487 1.747444 AAAGACCCCACCTGTCAGAT 58.253 50.000 0.00 0.00 35.15 2.90
559 837 1.895707 CGGCCAGGATTGCTCCATC 60.896 63.158 2.24 0.00 44.79 3.51
731 1017 1.388547 CAGTCCTCTCTCTCCCTTCG 58.611 60.000 0.00 0.00 0.00 3.79
803 1104 3.760035 GAGCTCCCGCCGTCAAGA 61.760 66.667 0.87 0.00 36.60 3.02
1052 1398 5.398353 CCATGGTATCTGAGGAAAGGTCATT 60.398 44.000 2.57 0.00 0.00 2.57
1216 1574 7.515004 AGGAATCATGCCTATTACATATCCA 57.485 36.000 0.00 0.00 32.92 3.41
1380 1748 2.615747 GGGCTACCCTGACTTCTTCAAC 60.616 54.545 0.00 0.00 41.34 3.18
1742 2157 0.679002 CCTCCAGTGCTTGATGTGGG 60.679 60.000 0.00 0.00 0.00 4.61
2074 2489 4.184629 GACAATGTGGAAGTAGTGCCTAG 58.815 47.826 0.00 0.00 0.00 3.02
2255 4399 1.419762 TGTATGGTTGGATGGATCGGG 59.580 52.381 0.00 0.00 0.00 5.14
2477 4668 1.202698 GGAGAGATTCCATCAACGGGG 60.203 57.143 0.00 0.00 46.01 5.73
2537 4732 6.412214 ACGCTGTTTAAAGGTGTATAAGGAT 58.588 36.000 5.76 0.00 0.00 3.24
2654 4932 7.682787 AATAGAATCAGTCACCTCTGGTATT 57.317 36.000 0.00 0.00 32.11 1.89
2663 4941 5.046520 AGTCACCTCTGGTATTGTCCTTAAC 60.047 44.000 0.00 0.00 32.11 2.01
2748 5032 4.620723 TGTCTATGTGGACCTTGGTATCT 58.379 43.478 0.00 0.00 35.54 1.98
2890 5215 1.103803 CTGCATGCAATCCTCAAGCT 58.896 50.000 22.88 0.00 0.00 3.74
2898 5260 2.294233 GCAATCCTCAAGCTTTGTGACA 59.706 45.455 0.00 0.00 0.00 3.58
2936 5298 3.031013 TCCCTCTGAATATTGCTCGTCA 58.969 45.455 0.00 0.00 0.00 4.35
2947 5309 1.739196 GCTCGTCATGCAGCTGTGA 60.739 57.895 16.64 9.36 32.48 3.58
2970 5344 2.363306 TGTCATGCTGTTGAGGGTTT 57.637 45.000 0.00 0.00 0.00 3.27
2996 5370 3.120304 GGATTCAGTTTTCGGAAAGTCGG 60.120 47.826 3.09 3.14 37.52 4.79
3028 5402 3.409570 GTTGTAGGGGAAAACAGGACTC 58.590 50.000 0.00 0.00 0.00 3.36
3052 5427 4.614946 AGTTTTCTGATGAGCAAAACTGC 58.385 39.130 15.86 0.00 44.74 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 3.880047 TGGTAGACCACGACCTAAATG 57.120 47.619 0.00 0.00 42.01 2.32
34 35 0.805614 CGAGAGAGAGCGAGGTTGAA 59.194 55.000 0.00 0.00 0.00 2.69
110 113 2.122729 CCTCCCCTGGACTGGTCA 59.877 66.667 0.00 0.00 0.00 4.02
293 302 3.399181 GTCCCGTGGATGGCTGGA 61.399 66.667 0.00 0.00 32.73 3.86
328 337 2.225727 GGGTTGTTCCGAGATTTCACAC 59.774 50.000 0.00 0.00 37.00 3.82
329 338 2.105821 AGGGTTGTTCCGAGATTTCACA 59.894 45.455 0.00 0.00 37.00 3.58
366 376 4.849310 ATGCCACCGCGCCGTAAT 62.849 61.111 0.00 0.00 38.08 1.89
427 437 2.416836 GCCGCTACTGTCATTGACACTA 60.417 50.000 15.41 10.05 37.67 2.74
430 440 0.391130 GGCCGCTACTGTCATTGACA 60.391 55.000 18.08 18.08 40.50 3.58
511 789 2.813754 ACTTCGATGTGACAACCAATGG 59.186 45.455 2.72 0.00 0.00 3.16
559 837 2.203567 TGGCCCTCCGGTTTTTGG 60.204 61.111 0.00 0.00 34.14 3.28
800 1101 2.131023 GGAATGGAGGAGGTGGATCTT 58.869 52.381 0.00 0.00 0.00 2.40
803 1104 0.699231 GGGGAATGGAGGAGGTGGAT 60.699 60.000 0.00 0.00 0.00 3.41
1052 1398 1.428370 GAGCACATATGACCGCGCAA 61.428 55.000 10.38 0.00 0.00 4.85
1216 1574 6.650807 TCAGCAGATTCAAGACGTAGAAAAAT 59.349 34.615 0.00 0.00 0.00 1.82
1380 1748 0.106335 ATCGCTCCAGATCAGCCTTG 59.894 55.000 0.00 0.00 32.83 3.61
1498 1887 0.251033 TTCTCGAGGAGGTCACCGAA 60.251 55.000 13.56 0.00 34.73 4.30
1767 2182 1.337728 CCGATGTTGTACCTGTCAGCA 60.338 52.381 0.00 0.00 0.00 4.41
1857 2272 1.380524 CATGCTGCTCTGCTAAAGCT 58.619 50.000 0.00 0.00 42.66 3.74
2198 2629 8.515414 GCATAACCATTAAAACAAGACTCTCTT 58.485 33.333 0.00 0.00 37.14 2.85
2200 2631 7.816640 TGCATAACCATTAAAACAAGACTCTC 58.183 34.615 0.00 0.00 0.00 3.20
2285 4432 3.704566 ACCATTCTACTCGCCTGAACATA 59.295 43.478 0.00 0.00 0.00 2.29
2286 4433 2.501723 ACCATTCTACTCGCCTGAACAT 59.498 45.455 0.00 0.00 0.00 2.71
2289 4436 3.362706 AGTACCATTCTACTCGCCTGAA 58.637 45.455 0.00 0.00 0.00 3.02
2290 4437 3.014304 AGTACCATTCTACTCGCCTGA 57.986 47.619 0.00 0.00 0.00 3.86
2291 4438 3.802948 AAGTACCATTCTACTCGCCTG 57.197 47.619 0.00 0.00 0.00 4.85
2292 4439 5.138276 TGATAAGTACCATTCTACTCGCCT 58.862 41.667 0.00 0.00 0.00 5.52
2294 4441 7.145985 TGATTGATAAGTACCATTCTACTCGC 58.854 38.462 0.00 0.00 0.00 5.03
2295 4442 9.698309 AATGATTGATAAGTACCATTCTACTCG 57.302 33.333 0.00 0.00 0.00 4.18
2502 4693 6.708949 ACCTTTAAACAGCGTTCAAGAATAGA 59.291 34.615 11.46 0.00 0.00 1.98
2537 4732 2.193993 GGACCTAAGCCCTCCAGTTTA 58.806 52.381 0.00 0.00 0.00 2.01
2654 4932 4.832248 CTGCTAATGGAGTGTTAAGGACA 58.168 43.478 0.00 0.00 35.42 4.02
2663 4941 2.391616 TGAGTGCTGCTAATGGAGTG 57.608 50.000 0.00 0.00 33.91 3.51
2890 5215 1.859302 AACCAAAGCCCTGTCACAAA 58.141 45.000 0.00 0.00 0.00 2.83
2898 5260 4.482398 AGAGGGAATAATAACCAAAGCCCT 59.518 41.667 0.00 0.00 46.86 5.19
2936 5298 1.971481 TGACAAGTTCACAGCTGCAT 58.029 45.000 15.27 0.00 0.00 3.96
2947 5309 2.233271 CCCTCAACAGCATGACAAGTT 58.767 47.619 0.00 0.00 39.69 2.66
2970 5344 6.215495 ACTTTCCGAAAACTGAATCCAAAA 57.785 33.333 0.00 0.00 0.00 2.44
2996 5370 6.964807 TTTCCCCTACAACCTCTTTAAAAC 57.035 37.500 0.00 0.00 0.00 2.43
3028 5402 5.855395 GCAGTTTTGCTCATCAGAAAACTAG 59.145 40.000 0.00 0.00 44.31 2.57


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

AutoCloner maintained by Alex Coulton.