Multiple sequence alignment - TraesCS2D01G081700

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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 TraesCS2D01G081700 chr2D 100.000 2019 0 0 343 2361 35082180 35080162 0.000000e+00 3729.0
1 TraesCS2D01G081700 chr2D 100.000 163 0 0 1 163 35082522 35082360 3.810000e-78 302.0
2 TraesCS2D01G081700 chr2D 85.526 76 11 0 512 587 14764606 14764681 1.950000e-11 80.5
3 TraesCS2D01G081700 chr2B 94.671 1670 47 17 343 1974 58075409 58073744 0.000000e+00 2553.0
4 TraesCS2D01G081700 chr2B 96.367 523 16 1 1842 2361 58073476 58072954 0.000000e+00 857.0
5 TraesCS2D01G081700 chr2B 96.070 229 8 1 2087 2315 58073739 58073512 2.870000e-99 372.0
6 TraesCS2D01G081700 chr2B 96.988 166 2 1 1 163 58075719 58075554 2.310000e-70 276.0
7 TraesCS2D01G081700 chr2B 81.761 159 28 1 5 163 773872333 773872490 5.290000e-27 132.0
8 TraesCS2D01G081700 chr3A 91.480 1432 84 17 343 1745 750617289 750618711 0.000000e+00 1934.0
9 TraesCS2D01G081700 chr3A 90.152 396 26 1 1766 2148 750631324 750631719 9.740000e-139 503.0
10 TraesCS2D01G081700 chr3A 96.951 164 4 1 1 163 750611171 750611334 8.310000e-70 274.0
11 TraesCS2D01G081700 chr3A 82.622 328 28 17 1589 1903 365941858 365941547 1.800000e-66 263.0
12 TraesCS2D01G081700 chr3A 76.852 324 26 17 1387 1705 750619375 750619654 1.140000e-28 137.0
13 TraesCS2D01G081700 chr3A 81.098 164 29 2 1 163 110464396 110464558 1.900000e-26 130.0
14 TraesCS2D01G081700 chr3A 94.915 59 3 0 2242 2300 365582155 365582213 2.500000e-15 93.5
15 TraesCS2D01G081700 chr3A 93.220 59 4 0 2242 2300 365589188 365589246 1.160000e-13 87.9
16 TraesCS2D01G081700 chr3A 83.333 96 13 3 489 582 726204487 726204581 4.180000e-13 86.1
17 TraesCS2D01G081700 chr3A 97.297 37 1 0 2278 2314 365582158 365582122 1.960000e-06 63.9
18 TraesCS2D01G081700 chr3A 97.297 37 1 0 2278 2314 365589191 365589155 1.960000e-06 63.9
19 TraesCS2D01G081700 chr3B 90.249 1405 85 21 343 1718 823761234 823762615 0.000000e+00 1788.0
20 TraesCS2D01G081700 chr3B 90.397 479 28 4 1750 2210 823762613 823763091 4.310000e-172 614.0
21 TraesCS2D01G081700 chr3B 91.411 163 10 2 1 163 823760932 823761090 1.100000e-53 220.0
22 TraesCS2D01G081700 chr1B 82.209 163 26 3 2 163 376076008 376076168 1.140000e-28 137.0
23 TraesCS2D01G081700 chr7D 82.069 145 24 2 20 163 602267499 602267356 3.190000e-24 122.0
24 TraesCS2D01G081700 chr4D 80.488 164 29 3 1 163 50807566 50807405 3.190000e-24 122.0
25 TraesCS2D01G081700 chr5B 79.878 164 31 2 1 163 10078051 10077889 4.120000e-23 119.0
26 TraesCS2D01G081700 chr1A 90.278 72 6 1 512 582 325033890 325033819 2.500000e-15 93.5
27 TraesCS2D01G081700 chr5A 86.076 79 10 1 505 582 400880535 400880613 1.500000e-12 84.2
28 TraesCS2D01G081700 chr4A 86.842 76 9 1 513 587 39580931 39580856 1.500000e-12 84.2
29 TraesCS2D01G081700 chr6D 86.301 73 10 0 510 582 11786496 11786568 1.950000e-11 80.5


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 TraesCS2D01G081700 chr2D 35080162 35082522 2360 True 2015.5 3729 100.000000 1 2361 2 chr2D.!!$R1 2360
1 TraesCS2D01G081700 chr2B 58072954 58075719 2765 True 1014.5 2553 96.024000 1 2361 4 chr2B.!!$R1 2360
2 TraesCS2D01G081700 chr3A 750617289 750619654 2365 False 1035.5 1934 84.166000 343 1745 2 chr3A.!!$F7 1402
3 TraesCS2D01G081700 chr3B 823760932 823763091 2159 False 874.0 1788 90.685667 1 2210 3 chr3B.!!$F1 2209

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
985 1005 4.244066 TCGCATCCAACAATTTCATTTGG 58.756 39.13 0.0 0.0 41.12 3.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2319 2809 2.096218 CGTGCTCTACAAAACTTGGAGC 60.096 50.0 0.0 0.0 41.56 4.7 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
501 517 9.979578 AGTAGAGATTGATCAATGATAACTGAC 57.020 33.333 25.37 14.01 0.00 3.51
515 531 7.603180 TGATAACTGACTTGCACCTATATCT 57.397 36.000 0.00 0.00 0.00 1.98
516 532 8.706322 TGATAACTGACTTGCACCTATATCTA 57.294 34.615 0.00 0.00 0.00 1.98
587 604 7.043565 GCCATCAAATTAGGTCAATCAAATGT 58.956 34.615 0.00 0.00 0.00 2.71
588 605 7.550196 GCCATCAAATTAGGTCAATCAAATGTT 59.450 33.333 0.00 0.00 0.00 2.71
589 606 9.439500 CCATCAAATTAGGTCAATCAAATGTTT 57.561 29.630 0.00 0.00 0.00 2.83
593 610 7.656707 AATTAGGTCAATCAAATGTTTGTGC 57.343 32.000 5.48 0.00 39.18 4.57
595 612 5.280654 AGGTCAATCAAATGTTTGTGCTT 57.719 34.783 5.48 0.00 39.18 3.91
597 614 6.996509 AGGTCAATCAAATGTTTGTGCTTAT 58.003 32.000 5.48 0.00 39.18 1.73
598 615 7.092716 AGGTCAATCAAATGTTTGTGCTTATC 58.907 34.615 5.48 0.00 39.18 1.75
599 616 7.039504 AGGTCAATCAAATGTTTGTGCTTATCT 60.040 33.333 5.48 0.00 39.18 1.98
600 617 7.274250 GGTCAATCAAATGTTTGTGCTTATCTC 59.726 37.037 5.48 0.00 39.18 2.75
601 618 7.809331 GTCAATCAAATGTTTGTGCTTATCTCA 59.191 33.333 5.48 0.00 39.18 3.27
602 619 7.809331 TCAATCAAATGTTTGTGCTTATCTCAC 59.191 33.333 5.48 0.00 39.18 3.51
983 1003 4.871557 CCATCGCATCCAACAATTTCATTT 59.128 37.500 0.00 0.00 0.00 2.32
985 1005 4.244066 TCGCATCCAACAATTTCATTTGG 58.756 39.130 0.00 0.00 41.12 3.28
1007 1027 0.099436 GAGCAATTGGTCATGGCGTC 59.901 55.000 28.19 3.11 41.81 5.19
1282 1302 4.235360 ACAATACGGCTATCTGCGATAAC 58.765 43.478 0.00 0.00 44.05 1.89
1496 1549 1.874345 AACCGCGGATCGTGTCTTCT 61.874 55.000 35.90 0.00 35.46 2.85
1501 1554 1.404315 GCGGATCGTGTCTTCTCCTTT 60.404 52.381 0.00 0.00 0.00 3.11
1526 1579 0.526739 TTCTCGTCCGTGTGTGTGTG 60.527 55.000 0.00 0.00 0.00 3.82
1527 1580 1.226859 CTCGTCCGTGTGTGTGTGT 60.227 57.895 0.00 0.00 0.00 3.72
2133 2623 7.288810 TGCCTCAGATTTTGTTAAGAAATGT 57.711 32.000 0.00 0.00 0.00 2.71
2177 2667 2.159099 CCTACATCAAGCAGCGTCCTTA 60.159 50.000 0.00 0.00 0.00 2.69
2225 2715 2.673368 GGTCTCGTACAGCTGAAATTGG 59.327 50.000 23.35 5.90 0.00 3.16
2227 2717 3.746492 GTCTCGTACAGCTGAAATTGGTT 59.254 43.478 23.35 0.00 0.00 3.67
2269 2759 8.615878 TCATACGGGGATAGAAAATGTTATTG 57.384 34.615 0.00 0.00 0.00 1.90
2311 2801 3.849563 AGCACCGGTAGGCAATTATAA 57.150 42.857 18.19 0.00 42.76 0.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
589 606 8.575589 ACAAACATTAATTGTGAGATAAGCACA 58.424 29.630 0.00 0.00 43.89 4.57
590 607 8.970691 ACAAACATTAATTGTGAGATAAGCAC 57.029 30.769 0.00 0.00 39.43 4.40
601 618 8.575589 TGTGAGATAAGCACAAACATTAATTGT 58.424 29.630 0.00 0.00 42.75 2.71
602 619 8.969121 TGTGAGATAAGCACAAACATTAATTG 57.031 30.769 0.00 0.00 42.75 2.32
747 767 0.105964 ACAAAGGTCGCTAGTGTGCA 59.894 50.000 2.66 0.00 0.00 4.57
983 1003 1.452110 CATGACCAATTGCTCGACCA 58.548 50.000 0.00 0.00 0.00 4.02
985 1005 0.099436 GCCATGACCAATTGCTCGAC 59.901 55.000 0.00 0.00 0.00 4.20
1007 1027 1.789078 AAGCAGTTGAGCGCTGTTGG 61.789 55.000 18.48 0.71 38.82 3.77
1289 1309 4.742201 TCCGCTGTCTTCGCTGGC 62.742 66.667 0.00 0.00 0.00 4.85
1496 1549 1.540267 CGGACGAGAACAGAGAAAGGA 59.460 52.381 0.00 0.00 0.00 3.36
1501 1554 0.591659 CACACGGACGAGAACAGAGA 59.408 55.000 0.00 0.00 0.00 3.10
1526 1579 7.497579 GGAATGGATTAGAGAAAGGAGAAGAAC 59.502 40.741 0.00 0.00 0.00 3.01
1527 1580 7.404396 AGGAATGGATTAGAGAAAGGAGAAGAA 59.596 37.037 0.00 0.00 0.00 2.52
2133 2623 5.758296 GGCAATTCTGATTAACATAGACGGA 59.242 40.000 0.00 0.00 0.00 4.69
2177 2667 4.392047 TGCTTGATGTCACAGAATTCAGT 58.608 39.130 8.44 2.42 0.00 3.41
2225 2715 8.064222 CCGTATGATGAATAATGTTGTCTGAAC 58.936 37.037 0.00 0.00 0.00 3.18
2227 2717 6.705825 CCCGTATGATGAATAATGTTGTCTGA 59.294 38.462 0.00 0.00 0.00 3.27
2269 2759 7.795272 GTGCTTGTGAAAATGTCATTCAAAATC 59.205 33.333 0.00 0.00 38.44 2.17
2319 2809 2.096218 CGTGCTCTACAAAACTTGGAGC 60.096 50.000 0.00 0.00 41.56 4.70


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

AutoCloner maintained by Alex Coulton.