Multiple sequence alignment - TraesCS5B01G142400

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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 TraesCS5B01G142400 chr5B 100.000 2409 0 0 1 2409 268438190 268440598 0 4449
1 TraesCS5B01G142400 chr5B 91.929 954 47 8 1473 2407 268492826 268493768 0 1308
2 TraesCS5B01G142400 chr7D 93.809 1486 79 3 1 1473 433075869 433077354 0 2222
3 TraesCS5B01G142400 chr7D 93.414 1488 77 5 1 1473 561525254 561523773 0 2185
4 TraesCS5B01G142400 chr7A 93.801 1484 81 6 1 1473 141058464 141056981 0 2220
5 TraesCS5B01G142400 chr7A 93.733 1484 82 4 1 1473 141903737 141902254 0 2215
6 TraesCS5B01G142400 chr7A 93.531 1484 85 8 1 1473 141312635 141311152 0 2198
7 TraesCS5B01G142400 chr4A 93.464 1484 86 6 1 1473 588660164 588658681 0 2193
8 TraesCS5B01G142400 chr4A 92.809 1488 87 15 1 1473 418073027 418071545 0 2137
9 TraesCS5B01G142400 chr4A 89.840 935 83 11 1474 2402 11832145 11833073 0 1190
10 TraesCS5B01G142400 chr5D 92.862 1485 83 9 1 1473 492732845 492731372 0 2134
11 TraesCS5B01G142400 chr3D 92.737 1487 90 9 1 1473 93187986 93189468 0 2132
12 TraesCS5B01G142400 chr3D 92.565 955 45 9 1473 2407 55045317 55044369 0 1347
13 TraesCS5B01G142400 chr1D 92.356 955 46 8 1473 2407 283670319 283669372 0 1334
14 TraesCS5B01G142400 chr1D 92.042 955 47 12 1474 2407 283688134 283687188 0 1315
15 TraesCS5B01G142400 chr1D 90.705 936 75 9 1476 2405 170342217 170341288 0 1236
16 TraesCS5B01G142400 chr1D 91.125 631 36 11 1797 2407 197462865 197463495 0 837
17 TraesCS5B01G142400 chr6D 91.295 919 69 7 1473 2388 274920422 274921332 0 1243
18 TraesCS5B01G142400 chr2D 90.622 949 62 10 1473 2400 184416228 184415286 0 1234
19 TraesCS5B01G142400 chr3A 89.915 942 78 15 1474 2405 742763352 742762418 0 1197


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 TraesCS5B01G142400 chr5B 268438190 268440598 2408 False 4449 4449 100.000 1 2409 1 chr5B.!!$F1 2408
1 TraesCS5B01G142400 chr5B 268492826 268493768 942 False 1308 1308 91.929 1473 2407 1 chr5B.!!$F2 934
2 TraesCS5B01G142400 chr7D 433075869 433077354 1485 False 2222 2222 93.809 1 1473 1 chr7D.!!$F1 1472
3 TraesCS5B01G142400 chr7D 561523773 561525254 1481 True 2185 2185 93.414 1 1473 1 chr7D.!!$R1 1472
4 TraesCS5B01G142400 chr7A 141056981 141058464 1483 True 2220 2220 93.801 1 1473 1 chr7A.!!$R1 1472
5 TraesCS5B01G142400 chr7A 141902254 141903737 1483 True 2215 2215 93.733 1 1473 1 chr7A.!!$R3 1472
6 TraesCS5B01G142400 chr7A 141311152 141312635 1483 True 2198 2198 93.531 1 1473 1 chr7A.!!$R2 1472
7 TraesCS5B01G142400 chr4A 588658681 588660164 1483 True 2193 2193 93.464 1 1473 1 chr4A.!!$R2 1472
8 TraesCS5B01G142400 chr4A 418071545 418073027 1482 True 2137 2137 92.809 1 1473 1 chr4A.!!$R1 1472
9 TraesCS5B01G142400 chr4A 11832145 11833073 928 False 1190 1190 89.840 1474 2402 1 chr4A.!!$F1 928
10 TraesCS5B01G142400 chr5D 492731372 492732845 1473 True 2134 2134 92.862 1 1473 1 chr5D.!!$R1 1472
11 TraesCS5B01G142400 chr3D 93187986 93189468 1482 False 2132 2132 92.737 1 1473 1 chr3D.!!$F1 1472
12 TraesCS5B01G142400 chr3D 55044369 55045317 948 True 1347 1347 92.565 1473 2407 1 chr3D.!!$R1 934
13 TraesCS5B01G142400 chr1D 283669372 283670319 947 True 1334 1334 92.356 1473 2407 1 chr1D.!!$R2 934
14 TraesCS5B01G142400 chr1D 283687188 283688134 946 True 1315 1315 92.042 1474 2407 1 chr1D.!!$R3 933
15 TraesCS5B01G142400 chr1D 170341288 170342217 929 True 1236 1236 90.705 1476 2405 1 chr1D.!!$R1 929
16 TraesCS5B01G142400 chr1D 197462865 197463495 630 False 837 837 91.125 1797 2407 1 chr1D.!!$F1 610
17 TraesCS5B01G142400 chr6D 274920422 274921332 910 False 1243 1243 91.295 1473 2388 1 chr6D.!!$F1 915
18 TraesCS5B01G142400 chr2D 184415286 184416228 942 True 1234 1234 90.622 1473 2400 1 chr2D.!!$R1 927
19 TraesCS5B01G142400 chr3A 742762418 742763352 934 True 1197 1197 89.915 1474 2405 1 chr3A.!!$R1 931

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
154 164 0.462047 GGTTGATCTGCCAGGTACGG 60.462 60.0 0.0 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1474 1514 1.067821 AGGTCCATCTCGATCGCTTTC 59.932 52.381 11.09 0.0 0.0 2.62 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 31 4.357947 GACACCGGCTCACTGCGA 62.358 66.667 0.00 0.00 44.05 5.10
91 92 4.927049 TGGCCTTCATCTTCTTCTTCATT 58.073 39.130 3.32 0.00 0.00 2.57
154 164 0.462047 GGTTGATCTGCCAGGTACGG 60.462 60.000 0.00 0.00 0.00 4.02
225 241 1.905215 CTTAGGCTCCCCATCGATGAT 59.095 52.381 26.86 5.92 0.00 2.45
234 250 2.356313 ATCGATGATCGCCGGCAC 60.356 61.111 28.98 17.34 40.21 5.01
318 334 2.224402 ACTTGCACCACTTCTTCCTCTC 60.224 50.000 0.00 0.00 0.00 3.20
325 341 3.904339 ACCACTTCTTCCTCTCTTTAGCA 59.096 43.478 0.00 0.00 0.00 3.49
331 347 3.381908 TCTTCCTCTCTTTAGCATCGTCC 59.618 47.826 0.00 0.00 0.00 4.79
348 364 1.519455 CCGAGACGGCCTGATTCAC 60.519 63.158 0.00 0.00 41.17 3.18
357 373 2.825836 CTGATTCACGGCCCAGCC 60.826 66.667 0.00 0.00 46.75 4.85
463 479 4.820716 GCATTAGATTCCTTCTGCATGTCT 59.179 41.667 0.00 0.00 35.79 3.41
464 480 5.298777 GCATTAGATTCCTTCTGCATGTCTT 59.701 40.000 0.00 0.00 35.79 3.01
713 744 3.509575 GGAGAGAAGAGTGACAGTCATGT 59.490 47.826 6.51 0.00 44.31 3.21
810 841 0.622136 AGAGCAATGAGATGGGCACA 59.378 50.000 0.00 0.00 0.00 4.57
928 959 3.680786 CTGAGGGTGGCGACGACA 61.681 66.667 0.00 0.00 0.00 4.35
1141 1176 2.354259 GAAGGTGATGGTGAAGCTGAG 58.646 52.381 0.00 0.00 0.00 3.35
1357 1397 3.255634 GGGCCTCCCTAAGTACTATCA 57.744 52.381 0.84 0.00 41.34 2.15
1387 1427 8.925161 TGCTTTGAACTATTTATGTTTATGGC 57.075 30.769 0.00 0.00 0.00 4.40
1474 1514 6.214191 TCCTCTGTTTATACTCTGCTCTTG 57.786 41.667 0.00 0.00 0.00 3.02
1479 1519 6.591834 TCTGTTTATACTCTGCTCTTGAAAGC 59.408 38.462 0.00 0.00 42.82 3.51
1574 1621 8.918202 TTTAGGAAATAGTGCGGAATATGAAT 57.082 30.769 0.00 0.00 0.00 2.57
1709 1756 4.399483 ACCACAAGTAGAGAGTTAGGGA 57.601 45.455 0.00 0.00 0.00 4.20
1727 1774 3.458487 AGGGATAGGAATAACCGCAACTT 59.542 43.478 0.00 0.00 44.74 2.66
1805 1854 4.099573 CGTTAGAGAGGTGGATGTTACCAT 59.900 45.833 0.00 0.00 42.17 3.55
1815 1864 2.684881 GGATGTTACCATGAAGGCACAG 59.315 50.000 0.00 0.00 43.14 3.66
1844 1893 1.757118 CGAAGGCTCACCCTATTCTCA 59.243 52.381 0.00 0.00 45.62 3.27
1865 1914 2.285083 CTTTGAGACAACACCACGGAA 58.715 47.619 0.00 0.00 0.00 4.30
1884 1934 3.808174 GGAAGCGTTTCTCAACACTAGTT 59.192 43.478 11.94 0.00 34.33 2.24
1914 1964 1.134438 GGGTGGTCTCCAAACCCTCT 61.134 60.000 2.78 0.00 37.01 3.69
1923 1973 5.374071 GTCTCCAAACCCTCTCAAACTTTA 58.626 41.667 0.00 0.00 0.00 1.85
1929 1979 1.626825 CCCTCTCAAACTTTACCGGGA 59.373 52.381 6.32 0.00 32.10 5.14
1944 1994 2.307686 ACCGGGAGTAATCACAATGGTT 59.692 45.455 6.32 0.00 0.00 3.67
1990 2040 1.342574 GCCTAGGAGTCTCCAACCTCT 60.343 57.143 21.26 1.44 39.61 3.69
2025 2079 3.486383 ACGATGGGAAAAGCTCAAGAAA 58.514 40.909 0.00 0.00 0.00 2.52
2273 2330 3.762407 TTGAGCCACTTAAGTGCACTA 57.238 42.857 27.05 15.54 44.34 2.74
2306 2381 1.407979 GTCCGGTGGTACAGATAGGTG 59.592 57.143 0.00 0.00 41.80 4.00
2371 2446 1.431440 GCCACGAAACAGCACACAA 59.569 52.632 0.00 0.00 0.00 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
176 186 1.970917 GAACCGATGCAGACGCCAAG 61.971 60.000 10.00 0.87 37.32 3.61
177 187 2.031919 AACCGATGCAGACGCCAA 59.968 55.556 10.00 0.00 37.32 4.52
182 192 1.646189 GAGGAAGAACCGATGCAGAC 58.354 55.000 0.00 0.00 44.74 3.51
269 285 2.292918 ACTACTGGGCTCCTAATGACCA 60.293 50.000 0.00 0.00 0.00 4.02
331 347 1.874019 CGTGAATCAGGCCGTCTCG 60.874 63.158 0.00 3.04 0.00 4.04
463 479 1.298157 CGAACTTCGGCTCCATGCAA 61.298 55.000 3.06 0.00 45.15 4.08
464 480 1.741401 CGAACTTCGGCTCCATGCA 60.741 57.895 3.06 0.00 45.15 3.96
829 860 2.340427 GCTGCTTGCCCTTGTTGTA 58.660 52.632 0.00 0.00 35.15 2.41
963 996 2.691526 CTGATGGTAGTGGCCGTAGTTA 59.308 50.000 0.00 0.00 0.00 2.24
1084 1119 1.768275 TGTTCCTGAGCTTGAACTCCA 59.232 47.619 19.17 0.00 41.10 3.86
1141 1176 2.043953 GGGTCACCCTGCCATTCC 60.044 66.667 5.22 0.00 41.34 3.01
1188 1223 9.636879 CATGTAGTCGATCTTTATCTGATGAAT 57.363 33.333 0.00 0.00 0.00 2.57
1387 1427 7.275779 ACACTTCATAACAGTTCTACGCATAAG 59.724 37.037 0.00 0.00 0.00 1.73
1474 1514 1.067821 AGGTCCATCTCGATCGCTTTC 59.932 52.381 11.09 0.00 0.00 2.62
1479 1519 2.080693 CCTCTAGGTCCATCTCGATCG 58.919 57.143 9.36 9.36 0.00 3.69
1555 1602 6.293626 GCTCACATTCATATTCCGCACTATTT 60.294 38.462 0.00 0.00 0.00 1.40
1574 1621 3.485394 TCTTGCAATTGTTAGGCTCACA 58.515 40.909 7.40 0.00 0.00 3.58
1709 1756 3.463944 CCGAAGTTGCGGTTATTCCTAT 58.536 45.455 0.00 0.00 46.07 2.57
1727 1774 1.605753 CATACATCCTCGTCTCCCGA 58.394 55.000 0.00 0.00 45.00 5.14
1844 1893 1.208535 TCCGTGGTGTTGTCTCAAAGT 59.791 47.619 0.00 0.00 0.00 2.66
1884 1934 1.975680 GAGACCACCCCAAAGTCTACA 59.024 52.381 0.00 0.00 40.87 2.74
1914 1964 5.221682 TGTGATTACTCCCGGTAAAGTTTGA 60.222 40.000 0.00 0.00 42.74 2.69
1923 1973 1.913419 ACCATTGTGATTACTCCCGGT 59.087 47.619 0.00 0.00 0.00 5.28
1929 1979 6.725364 AGAGGAATCAACCATTGTGATTACT 58.275 36.000 12.32 12.32 0.00 2.24
1944 1994 2.761208 GGAGTCTTTCGGAGAGGAATCA 59.239 50.000 0.00 0.00 37.10 2.57
1990 2040 5.988310 TCCCATCGTTCTTGTTACTCTTA 57.012 39.130 0.00 0.00 0.00 2.10
2025 2079 5.649782 AAGGAATTCGTGATTTGAGCAAT 57.350 34.783 0.58 0.00 0.00 3.56
2295 2370 1.019673 GACGTCCGCACCTATCTGTA 58.980 55.000 3.51 0.00 0.00 2.74
2330 2405 0.540597 TGGATCTCCAGCGATCGGAT 60.541 55.000 18.30 10.32 42.01 4.18


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

AutoCloner maintained by Alex Coulton.