Multiple sequence alignment - TraesCS5D01G350200

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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 TraesCS5D01G350200 chr5D 100.000 2288 0 0 1 2288 434568394 434570681 0.000000e+00 4226.0
1 TraesCS5D01G350200 chr5D 93.074 2310 92 21 1 2288 434656392 434654129 0.000000e+00 3317.0
2 TraesCS5D01G350200 chr5D 84.513 904 103 27 643 1528 434575682 434576566 0.000000e+00 859.0
3 TraesCS5D01G350200 chr5D 83.846 910 110 19 453 1352 434663328 434662446 0.000000e+00 832.0
4 TraesCS5D01G350200 chr5D 80.068 878 142 25 574 1429 434331046 434331912 2.500000e-174 621.0
5 TraesCS5D01G350200 chr5D 79.490 785 132 21 665 1429 434382263 434381488 4.330000e-147 531.0
6 TraesCS5D01G350200 chr5D 82.902 579 66 12 1551 2110 434662208 434661644 7.350000e-135 490.0
7 TraesCS5D01G350200 chr5D 81.250 448 61 13 1638 2075 434712829 434712395 7.830000e-90 340.0
8 TraesCS5D01G350200 chr5D 92.488 213 9 3 44 249 434678489 434678277 4.780000e-77 298.0
9 TraesCS5D01G350200 chr5D 87.662 154 13 4 453 605 434575531 434575679 8.400000e-40 174.0
10 TraesCS5D01G350200 chr5D 94.118 102 5 1 1816 1917 434604642 434604742 1.090000e-33 154.0
11 TraesCS5D01G350200 chr5D 83.099 71 7 3 273 341 434674635 434674568 2.450000e-05 60.2
12 TraesCS5D01G350200 chr5B 95.810 2291 79 10 1 2288 527606949 527609225 0.000000e+00 3683.0
13 TraesCS5D01G350200 chr5B 95.635 1558 58 5 1 1555 527785831 527787381 0.000000e+00 2492.0
14 TraesCS5D01G350200 chr5B 93.708 747 35 3 1550 2288 527787418 527788160 0.000000e+00 1109.0
15 TraesCS5D01G350200 chr5B 80.046 872 142 23 577 1429 527040340 527039482 3.230000e-173 617.0
16 TraesCS5D01G350200 chr5B 78.480 855 136 31 604 1429 527061056 527060221 1.210000e-142 516.0
17 TraesCS5D01G350200 chr5B 79.552 670 120 15 773 1431 527059025 527058362 1.600000e-126 462.0
18 TraesCS5D01G350200 chr5B 79.760 499 56 15 1796 2286 527774106 527774567 1.020000e-83 320.0
19 TraesCS5D01G350200 chr5B 81.022 137 20 2 1651 1787 527495774 527495904 1.120000e-18 104.0
20 TraesCS5D01G350200 chr5B 84.507 71 6 3 273 341 527494966 527495033 5.280000e-07 65.8
21 TraesCS5D01G350200 chr5A 80.206 874 142 24 577 1429 548226986 548226123 5.370000e-176 627.0


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 TraesCS5D01G350200 chr5D 434568394 434570681 2287 False 4226.0 4226 100.0000 1 2288 1 chr5D.!!$F2 2287
1 TraesCS5D01G350200 chr5D 434654129 434656392 2263 True 3317.0 3317 93.0740 1 2288 1 chr5D.!!$R2 2287
2 TraesCS5D01G350200 chr5D 434661644 434663328 1684 True 661.0 832 83.3740 453 2110 2 chr5D.!!$R4 1657
3 TraesCS5D01G350200 chr5D 434331046 434331912 866 False 621.0 621 80.0680 574 1429 1 chr5D.!!$F1 855
4 TraesCS5D01G350200 chr5D 434381488 434382263 775 True 531.0 531 79.4900 665 1429 1 chr5D.!!$R1 764
5 TraesCS5D01G350200 chr5D 434575531 434576566 1035 False 516.5 859 86.0875 453 1528 2 chr5D.!!$F4 1075
6 TraesCS5D01G350200 chr5B 527606949 527609225 2276 False 3683.0 3683 95.8100 1 2288 1 chr5B.!!$F1 2287
7 TraesCS5D01G350200 chr5B 527785831 527788160 2329 False 1800.5 2492 94.6715 1 2288 2 chr5B.!!$F4 2287
8 TraesCS5D01G350200 chr5B 527039482 527040340 858 True 617.0 617 80.0460 577 1429 1 chr5B.!!$R1 852
9 TraesCS5D01G350200 chr5B 527058362 527061056 2694 True 489.0 516 79.0160 604 1431 2 chr5B.!!$R2 827
10 TraesCS5D01G350200 chr5A 548226123 548226986 863 True 627.0 627 80.2060 577 1429 1 chr5A.!!$R1 852

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
599 611 0.179045 ACCGCTATTGGATCCAGCAC 60.179 55.0 20.77 9.83 34.94 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2118 4209 1.00358 CTATCAAGGTGTGCCCTGTGT 59.996 52.381 0.0 0.0 45.47 3.72 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
32 33 3.314635 CACAGGAGCTTTGCCTATCATTC 59.685 47.826 0.00 0.00 33.51 2.67
89 90 7.312154 TGCATACCACATGAGTTTAACAAATC 58.688 34.615 0.00 0.00 0.00 2.17
168 170 1.467734 CACCTGCAGATTGAGCAACTC 59.532 52.381 17.39 0.00 42.17 3.01
299 309 3.790089 ACTTAGAAGTCAAACTGGGGG 57.210 47.619 0.00 0.00 32.86 5.40
599 611 0.179045 ACCGCTATTGGATCCAGCAC 60.179 55.000 20.77 9.83 34.94 4.40
754 787 5.428253 TCCTCTCGGAAATAAATTCAGTGG 58.572 41.667 0.00 0.00 39.98 4.00
984 1036 1.134877 GCAGCATCTCTGTAGCAGTCA 60.135 52.381 0.00 0.00 44.66 3.41
1127 1179 1.322637 CGATGACAAGATCACACTGCG 59.677 52.381 0.00 0.00 41.24 5.18
1352 3270 6.877322 TGTTTTCTGTAGTTTACCTGGATAGC 59.123 38.462 0.00 0.00 0.00 2.97
1442 3367 0.036010 AAGCAGCAACGCCAGTAGAT 60.036 50.000 0.00 0.00 0.00 1.98
1520 3446 6.623486 CAACTGTTCATTCAGATGCCAATAA 58.377 36.000 0.65 0.00 38.63 1.40
1597 3669 1.497309 AAGGGCCATCGGGACTTTGA 61.497 55.000 6.18 0.00 40.64 2.69
1793 3872 2.423577 ACTCAAGGACAATTACGCCAC 58.576 47.619 0.00 0.00 0.00 5.01
1935 4017 7.041635 TCAATGTCAATTTGTTCATGTCAGT 57.958 32.000 0.00 0.00 0.00 3.41
1936 4018 6.919115 TCAATGTCAATTTGTTCATGTCAGTG 59.081 34.615 0.00 0.00 32.36 3.66
1976 4067 9.911788 ATGTATCTTCATCAAACTAAAGGACAT 57.088 29.630 0.00 0.00 0.00 3.06
2115 4206 8.657074 TGTACAAAATTAGTTATAGCGAGCAT 57.343 30.769 0.00 0.00 0.00 3.79
2118 4209 6.038161 ACAAAATTAGTTATAGCGAGCATGCA 59.962 34.615 21.98 0.00 37.31 3.96
2130 4221 2.646719 CATGCACACAGGGCACAC 59.353 61.111 0.00 0.00 45.23 3.82
2230 4329 1.668751 GTTGTTCTTGGCTCGACAACA 59.331 47.619 16.13 3.93 46.72 3.33
2248 4347 3.476295 ACAATGATGCAGCAAACTACG 57.524 42.857 9.54 0.00 0.00 3.51
2257 4356 3.243941 TGCAGCAAACTACGTAAGGAAGA 60.244 43.478 0.00 0.00 46.39 2.87
2261 4360 4.748600 AGCAAACTACGTAAGGAAGACAAC 59.251 41.667 0.00 0.00 46.39 3.32
2263 4362 5.922544 GCAAACTACGTAAGGAAGACAACTA 59.077 40.000 0.00 0.00 46.39 2.24
2277 4376 7.181125 AGGAAGACAACTAAGGATACATCAACT 59.819 37.037 0.00 0.00 41.41 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 2.021457 ACACCCTCTGTTTTTCCGTTG 58.979 47.619 0.00 0.00 0.00 4.10
89 90 8.424918 TCTTTCATCTAATTCTAGGCAGGTAAG 58.575 37.037 0.00 0.00 0.00 2.34
168 170 7.548196 TTCAAGTGTTTGGTAACTAGTTCTG 57.452 36.000 12.39 0.00 35.24 3.02
299 309 3.753797 GTGGTCTCCATTTCACTCTTTCC 59.246 47.826 0.00 0.00 35.28 3.13
300 310 4.389374 TGTGGTCTCCATTTCACTCTTTC 58.611 43.478 0.00 0.00 35.28 2.62
365 375 3.753815 TCCATTTGCTCAACAGATGTCA 58.246 40.909 0.00 0.00 38.83 3.58
754 787 0.391130 TGGTGTTGAGCATAGCCGTC 60.391 55.000 0.00 0.00 0.00 4.79
984 1036 0.185901 ACATGACACAGTGGCCCTTT 59.814 50.000 3.17 0.00 0.00 3.11
1127 1179 0.729116 CATCACTCCGGCATCACAAC 59.271 55.000 0.00 0.00 0.00 3.32
1352 3270 8.663025 TCCGTTGCTTATATCTAACTATCTACG 58.337 37.037 0.00 0.00 0.00 3.51
1375 3298 2.554032 ACACAGCAATTTTCCTTCTCCG 59.446 45.455 0.00 0.00 0.00 4.63
1442 3367 9.278978 TGTATATCTACAAGAAAAACAACTGCA 57.721 29.630 0.00 0.00 34.92 4.41
1520 3446 4.292306 CCCCTAATAACCTGGCTATGGAAT 59.708 45.833 0.00 0.00 0.00 3.01
1758 3830 2.877097 TGAGTATTTTCAGGCTGCCA 57.123 45.000 22.65 0.00 0.00 4.92
1793 3872 2.884012 TGAGTAACAAACACATGCCAGG 59.116 45.455 0.00 0.00 0.00 4.45
1935 4017 8.614469 TGAAGATACATACAAATGTTCACACA 57.386 30.769 0.00 0.00 44.07 3.72
1936 4018 9.708222 GATGAAGATACATACAAATGTTCACAC 57.292 33.333 0.00 0.00 44.07 3.82
1976 4067 6.623486 GCACCATGCATCTATATATTTTGCA 58.377 36.000 15.12 15.12 46.22 4.08
2115 4206 3.357444 AAGGTGTGCCCTGTGTGCA 62.357 57.895 0.00 0.00 45.47 4.57
2118 4209 1.003580 CTATCAAGGTGTGCCCTGTGT 59.996 52.381 0.00 0.00 45.47 3.72
2230 4329 4.094887 CCTTACGTAGTTTGCTGCATCATT 59.905 41.667 1.84 0.00 37.78 2.57
2248 4347 8.475639 TGATGTATCCTTAGTTGTCTTCCTTAC 58.524 37.037 0.00 0.00 0.00 2.34
2257 4356 6.672657 AGGGTAGTTGATGTATCCTTAGTTGT 59.327 38.462 0.00 0.00 24.71 3.32
2261 4360 6.078664 AGGAGGGTAGTTGATGTATCCTTAG 58.921 44.000 0.00 0.00 30.53 2.18
2263 4362 4.897051 AGGAGGGTAGTTGATGTATCCTT 58.103 43.478 0.00 0.00 30.53 3.36


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

AutoCloner maintained by Alex Coulton.