Multiple sequence alignment - TraesCS1D01G438100

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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 TraesCS1D01G438100 chr1D 100.000 3395 0 0 1 3395 485157613 485161007 0.000000e+00 6270
1 TraesCS1D01G438100 chr2A 96.709 3403 88 11 1 3394 17677504 17674117 0.000000e+00 5642
2 TraesCS1D01G438100 chr2A 93.107 3235 145 38 206 3393 719453996 719457199 0.000000e+00 4667
3 TraesCS1D01G438100 chr2D 96.618 3193 97 10 206 3395 617164825 617161641 0.000000e+00 5288
4 TraesCS1D01G438100 chr2D 95.215 209 7 2 6 213 617165117 617164911 9.080000e-86 327
5 TraesCS1D01G438100 chr5B 93.414 3234 139 30 210 3395 420717407 420720614 0.000000e+00 4724
6 TraesCS1D01G438100 chr5B 93.049 3237 147 37 206 3395 179227221 179230426 0.000000e+00 4660
7 TraesCS1D01G438100 chr5B 93.031 2554 142 18 848 3395 445131717 445134240 0.000000e+00 3698
8 TraesCS1D01G438100 chr5B 91.628 215 12 5 1 212 179226927 179227138 3.310000e-75 292
9 TraesCS1D01G438100 chr5B 91.163 215 15 3 1 212 406870690 406870477 4.290000e-74 289
10 TraesCS1D01G438100 chr6B 93.232 3236 143 30 206 3395 408662163 408665368 0.000000e+00 4693
11 TraesCS1D01G438100 chr6B 93.020 3238 148 44 206 3395 704850483 704847276 0.000000e+00 4656
12 TraesCS1D01G438100 chr6B 91.628 215 13 4 1 212 704850778 704850566 3.310000e-75 292
13 TraesCS1D01G438100 chr6B 91.204 216 13 5 1 212 408661867 408662080 4.290000e-74 289
14 TraesCS1D01G438100 chr7B 93.232 3236 142 37 206 3395 528879704 528882908 0.000000e+00 4691
15 TraesCS1D01G438100 chr7B 93.484 3177 149 28 267 3395 68097667 68100833 0.000000e+00 4667
16 TraesCS1D01G438100 chr3B 93.105 3234 144 35 206 3395 552478358 552481556 0.000000e+00 4663
17 TraesCS1D01G438100 chr3B 92.093 215 13 3 1 212 552478062 552478275 1.980000e-77 300
18 TraesCS1D01G438100 chr4B 92.932 3240 149 43 206 3395 194219358 194222567 0.000000e+00 4641
19 TraesCS1D01G438100 chr4B 93.935 1995 107 12 848 2834 602292490 602290502 0.000000e+00 3001
20 TraesCS1D01G438100 chr4B 94.416 591 27 5 206 793 602293075 602292488 0.000000e+00 904
21 TraesCS1D01G438100 chr4B 91.204 216 12 6 1 212 194219063 194219275 1.540000e-73 287
22 TraesCS1D01G438100 chr7A 92.467 3239 147 40 206 3395 171418852 171422042 0.000000e+00 4540
23 TraesCS1D01G438100 chr7A 91.667 216 11 6 1 212 171418557 171418769 3.310000e-75 292
24 TraesCS1D01G438100 chr1A 93.942 2839 123 27 600 3395 567477552 567474720 0.000000e+00 4244
25 TraesCS1D01G438100 chr6D 93.659 2555 127 17 848 3395 14046416 14048942 0.000000e+00 3788
26 TraesCS1D01G438100 chr5D 92.913 2554 125 21 848 3395 373748569 373751072 0.000000e+00 3663
27 TraesCS1D01G438100 chr5D 92.061 592 36 8 213 796 373747979 373748567 0.000000e+00 822


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 TraesCS1D01G438100 chr1D 485157613 485161007 3394 False 6270.0 6270 100.0000 1 3395 1 chr1D.!!$F1 3394
1 TraesCS1D01G438100 chr2A 17674117 17677504 3387 True 5642.0 5642 96.7090 1 3394 1 chr2A.!!$R1 3393
2 TraesCS1D01G438100 chr2A 719453996 719457199 3203 False 4667.0 4667 93.1070 206 3393 1 chr2A.!!$F1 3187
3 TraesCS1D01G438100 chr2D 617161641 617165117 3476 True 2807.5 5288 95.9165 6 3395 2 chr2D.!!$R1 3389
4 TraesCS1D01G438100 chr5B 420717407 420720614 3207 False 4724.0 4724 93.4140 210 3395 1 chr5B.!!$F1 3185
5 TraesCS1D01G438100 chr5B 445131717 445134240 2523 False 3698.0 3698 93.0310 848 3395 1 chr5B.!!$F2 2547
6 TraesCS1D01G438100 chr5B 179226927 179230426 3499 False 2476.0 4660 92.3385 1 3395 2 chr5B.!!$F3 3394
7 TraesCS1D01G438100 chr6B 408661867 408665368 3501 False 2491.0 4693 92.2180 1 3395 2 chr6B.!!$F1 3394
8 TraesCS1D01G438100 chr6B 704847276 704850778 3502 True 2474.0 4656 92.3240 1 3395 2 chr6B.!!$R1 3394
9 TraesCS1D01G438100 chr7B 528879704 528882908 3204 False 4691.0 4691 93.2320 206 3395 1 chr7B.!!$F2 3189
10 TraesCS1D01G438100 chr7B 68097667 68100833 3166 False 4667.0 4667 93.4840 267 3395 1 chr7B.!!$F1 3128
11 TraesCS1D01G438100 chr3B 552478062 552481556 3494 False 2481.5 4663 92.5990 1 3395 2 chr3B.!!$F1 3394
12 TraesCS1D01G438100 chr4B 194219063 194222567 3504 False 2464.0 4641 92.0680 1 3395 2 chr4B.!!$F1 3394
13 TraesCS1D01G438100 chr4B 602290502 602293075 2573 True 1952.5 3001 94.1755 206 2834 2 chr4B.!!$R1 2628
14 TraesCS1D01G438100 chr7A 171418557 171422042 3485 False 2416.0 4540 92.0670 1 3395 2 chr7A.!!$F1 3394
15 TraesCS1D01G438100 chr1A 567474720 567477552 2832 True 4244.0 4244 93.9420 600 3395 1 chr1A.!!$R1 2795
16 TraesCS1D01G438100 chr6D 14046416 14048942 2526 False 3788.0 3788 93.6590 848 3395 1 chr6D.!!$F1 2547
17 TraesCS1D01G438100 chr5D 373747979 373751072 3093 False 2242.5 3663 92.4870 213 3395 2 chr5D.!!$F1 3182

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
257 361 6.591935 TCCAATAAGGTCTAGGTTGCATTAG 58.408 40.0 0.00 0.0 39.02 1.73 F
1006 1167 5.709631 TGCACAGGCTGTAAAAAGATGATTA 59.290 36.0 21.59 0.0 41.91 1.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1174 1335 4.285517 ACCATCAGTCTCAGATTCTTGTGT 59.714 41.667 0.00 0.0 0.0 3.72 R
2634 2845 4.201950 GCAATCATGATAAGCTTCCACGTT 60.202 41.667 20.11 0.0 0.0 3.99 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
150 157 6.999950 TGTGAACACTAGGCAAGAAATACTA 58.000 36.000 6.51 0.0 0.00 1.82
163 172 7.362920 GGCAAGAAATACTATGAAAGAGGCAAA 60.363 37.037 0.00 0.0 0.00 3.68
257 361 6.591935 TCCAATAAGGTCTAGGTTGCATTAG 58.408 40.000 0.00 0.0 39.02 1.73
483 627 7.387948 ACAGATTACTTGAAAAAGCGACTACAT 59.612 33.333 0.00 0.0 0.00 2.29
1006 1167 5.709631 TGCACAGGCTGTAAAAAGATGATTA 59.290 36.000 21.59 0.0 41.91 1.75
1040 1201 7.024345 AGGAAGCACATGATATGGATATTGA 57.976 36.000 0.00 0.0 33.60 2.57
1174 1335 0.251033 AGATGAGCAAGCACCTGCAA 60.251 50.000 8.00 0.0 45.18 4.08
1916 2082 2.101082 TGCAACATGTGTGTGATTTGCT 59.899 40.909 14.11 0.0 38.53 3.91
2552 2763 5.697082 AAGATCAGCAAAGAGAAGATCCT 57.303 39.130 0.00 0.0 36.61 3.24
2634 2845 2.202395 GGTGCAGCAAGGAAGGCAA 61.202 57.895 11.86 0.0 38.10 4.52
2874 3085 0.742505 CCAAGACATCGCAATGGCAT 59.257 50.000 0.00 0.0 44.06 4.40
2925 3136 3.923864 ACCGCTGTTGTCGCTGGA 61.924 61.111 0.00 0.0 0.00 3.86
3072 3283 5.128335 TGTGAGCTGATGATGAAGTATGAGT 59.872 40.000 0.00 0.0 0.00 3.41
3117 3328 7.171167 TCGAGAATCTATACAAGTACCGAGAAG 59.829 40.741 0.00 0.0 0.00 2.85
3126 3337 0.535335 GTACCGAGAAGCATGGGTGA 59.465 55.000 0.00 0.0 32.92 4.02
3203 3414 2.223745 GGGTTCAACGCTGTCCTTAAA 58.776 47.619 0.00 0.0 0.00 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
150 157 3.132289 CAGCCATGATTTGCCTCTTTCAT 59.868 43.478 0.00 0.00 0.00 2.57
257 361 4.613925 TGTAGGATCATGCTGAAGGATC 57.386 45.455 1.58 1.58 37.34 3.36
483 627 8.081633 CAGCAACTTTGGTTATCATTGTCTTTA 58.918 33.333 0.00 0.00 36.65 1.85
735 884 7.608308 TTATCATTTTAAAATGCAGGCAACC 57.392 32.000 28.54 0.00 44.15 3.77
898 1055 5.066893 CCCAGGTAATCACAACTGAATGATG 59.933 44.000 0.00 0.00 35.71 3.07
1006 1167 4.922206 TCATGTGCTTCCTCATTTAGGTT 58.078 39.130 0.00 0.00 46.62 3.50
1021 1182 7.501225 TGGATCATCAATATCCATATCATGTGC 59.499 37.037 0.67 0.00 46.29 4.57
1040 1201 5.012046 TGTTGTGTAGAGTTCACTGGATCAT 59.988 40.000 0.00 0.00 36.83 2.45
1174 1335 4.285517 ACCATCAGTCTCAGATTCTTGTGT 59.714 41.667 0.00 0.00 0.00 3.72
1593 1759 6.174720 TCTCTCTTTTGTTTCTTGCTCCTA 57.825 37.500 0.00 0.00 0.00 2.94
1916 2082 7.214381 ACAAGCATGTTTGTGTACTTAGTCTA 58.786 34.615 24.84 0.00 39.68 2.59
1998 2168 5.596836 TTGTTTTCTGATCAAAAGCAGGT 57.403 34.783 14.46 0.00 39.44 4.00
2336 2534 5.409520 GGTTAACCCTTGTTACCTAAGAACG 59.590 44.000 14.16 0.00 36.69 3.95
2634 2845 4.201950 GCAATCATGATAAGCTTCCACGTT 60.202 41.667 20.11 0.00 0.00 3.99
2874 3085 9.488762 TGTAGGGAAGATCTTCTTAATTGACTA 57.511 33.333 29.64 17.05 36.73 2.59
2925 3136 7.792374 TCTCTTGCGCTTTCTTCATAATATT 57.208 32.000 9.73 0.00 0.00 1.28
3072 3283 3.017442 CGAAGTGGGAGTCAGTCATAGA 58.983 50.000 0.00 0.00 0.00 1.98
3117 3328 2.084546 GAAGTAACAGGTCACCCATGC 58.915 52.381 0.00 0.00 0.00 4.06
3126 3337 6.006449 AGAATTGATGCTTGAAGTAACAGGT 58.994 36.000 0.00 0.00 0.00 4.00
3328 3539 5.095490 GCTTTTCAATTGGGTAAGATGACG 58.905 41.667 5.42 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.