Multiple sequence alignment - TraesCS6A01G129900

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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 TraesCS6A01G129900 chr6A 100.000 4145 0 0 1 4145 101563638 101559494 0.000000e+00 7655.0
1 TraesCS6A01G129900 chr6A 88.512 2594 263 22 563 3147 101865794 101863227 0.000000e+00 3107.0
2 TraesCS6A01G129900 chr6A 88.165 2594 277 20 563 3147 101548587 101546015 0.000000e+00 3062.0
3 TraesCS6A01G129900 chr6A 86.304 2373 312 9 819 3185 101554927 101552562 0.000000e+00 2569.0
4 TraesCS6A01G129900 chr6A 86.080 352 24 9 1 336 101866577 101866235 5.100000e-94 355.0
5 TraesCS6A01G129900 chr6A 85.237 359 28 10 1 336 101549381 101549025 3.070000e-91 346.0
6 TraesCS6A01G129900 chr6A 83.237 346 35 13 9 336 101846518 101846178 3.130000e-76 296.0
7 TraesCS6A01G129900 chr6A 81.897 116 18 3 90 202 101852636 101852521 1.230000e-15 95.3
8 TraesCS6A01G129900 chr6B 97.336 3603 68 13 549 4145 159990247 159986667 0.000000e+00 6096.0
9 TraesCS6A01G129900 chr6B 87.346 2600 292 25 563 3146 160663608 160661030 0.000000e+00 2944.0
10 TraesCS6A01G129900 chr6B 87.446 2541 280 26 779 3298 160683340 160680818 0.000000e+00 2889.0
11 TraesCS6A01G129900 chr6B 86.607 2240 281 13 921 3152 160717020 160714792 0.000000e+00 2457.0
12 TraesCS6A01G129900 chr6B 85.436 2259 288 27 914 3147 160912215 160909973 0.000000e+00 2311.0
13 TraesCS6A01G129900 chr6B 97.446 509 10 2 1 507 159991864 159991357 0.000000e+00 865.0
14 TraesCS6A01G129900 chr6B 84.439 784 101 8 2517 3299 160685827 160685064 0.000000e+00 752.0
15 TraesCS6A01G129900 chr6B 84.857 350 33 9 1 336 160906268 160905925 6.640000e-88 335.0
16 TraesCS6A01G129900 chr6B 86.325 117 8 1 1 109 160664171 160664055 2.020000e-23 121.0
17 TraesCS6A01G129900 chr6B 94.545 55 3 0 486 540 159991352 159991298 7.380000e-13 86.1
18 TraesCS6A01G129900 chr6D 96.395 3606 84 17 549 4145 84232269 84228701 0.000000e+00 5897.0
19 TraesCS6A01G129900 chr6D 87.211 2596 297 24 563 3147 84474448 84471877 0.000000e+00 2922.0
20 TraesCS6A01G129900 chr6D 86.824 2239 278 11 921 3152 84631062 84628834 0.000000e+00 2484.0
21 TraesCS6A01G129900 chr6D 95.034 443 10 4 81 514 84232829 84232390 0.000000e+00 686.0
22 TraesCS6A01G129900 chr6D 84.746 354 34 8 1 336 84219421 84219070 1.850000e-88 337.0
23 TraesCS6A01G129900 chr6D 100.000 82 0 0 1 82 84233584 84233503 7.180000e-33 152.0
24 TraesCS6A01G129900 chr6D 81.034 116 19 3 90 202 84623235 84623120 5.710000e-14 89.8
25 TraesCS6A01G129900 chr6D 94.444 54 3 0 487 540 84232390 84232337 2.660000e-12 84.2


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 TraesCS6A01G129900 chr6A 101559494 101563638 4144 True 7655.000000 7655 100.000000 1 4145 1 chr6A.!!$R1 4144
1 TraesCS6A01G129900 chr6A 101546015 101554927 8912 True 1992.333333 3062 86.568667 1 3185 3 chr6A.!!$R4 3184
2 TraesCS6A01G129900 chr6A 101863227 101866577 3350 True 1731.000000 3107 87.296000 1 3147 2 chr6A.!!$R5 3146
3 TraesCS6A01G129900 chr6B 160714792 160717020 2228 True 2457.000000 2457 86.607000 921 3152 1 chr6B.!!$R1 2231
4 TraesCS6A01G129900 chr6B 159986667 159991864 5197 True 2349.033333 6096 96.442333 1 4145 3 chr6B.!!$R2 4144
5 TraesCS6A01G129900 chr6B 160680818 160685827 5009 True 1820.500000 2889 85.942500 779 3299 2 chr6B.!!$R4 2520
6 TraesCS6A01G129900 chr6B 160661030 160664171 3141 True 1532.500000 2944 86.835500 1 3146 2 chr6B.!!$R3 3145
7 TraesCS6A01G129900 chr6B 160905925 160912215 6290 True 1323.000000 2311 85.146500 1 3147 2 chr6B.!!$R5 3146
8 TraesCS6A01G129900 chr6D 84471877 84474448 2571 True 2922.000000 2922 87.211000 563 3147 1 chr6D.!!$R2 2584
9 TraesCS6A01G129900 chr6D 84628834 84631062 2228 True 2484.000000 2484 86.824000 921 3152 1 chr6D.!!$R4 2231
10 TraesCS6A01G129900 chr6D 84228701 84233584 4883 True 1704.800000 5897 96.468250 1 4145 4 chr6D.!!$R5 4144

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
509 6887 4.326600 AAATTTAGGTTGGTACCCCCTC 57.673 45.455 20.48 3.9 46.28 4.30 F
1560 9062 0.035056 GCTTCAGTGGGCACATACCT 60.035 55.000 0.00 0.0 0.00 3.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1817 9319 2.106511 CTGTTCCCTCCAAGGTCAAGAA 59.893 50.000 0.0 0.0 31.93 2.52 R
3459 13644 1.480954 GATCTCGTTCAGGGTTGCCTA 59.519 52.381 0.0 0.0 0.00 3.93 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
224 6457 4.886579 TGTCTATCGCATATGCAGACAAT 58.113 39.130 31.59 18.3 43.76 2.71
278 6523 5.012768 AGGAAAATAACAAGAGGAGAACCGA 59.987 40.000 0.00 0.0 41.83 4.69
505 6883 5.921976 CGTTTCAAAATTTAGGTTGGTACCC 59.078 40.000 10.07 0.0 46.28 3.69
509 6887 4.326600 AAATTTAGGTTGGTACCCCCTC 57.673 45.455 20.48 3.9 46.28 4.30
737 8216 7.962441 TCCATGCATAACTAAGTGATAGCTTA 58.038 34.615 0.00 0.0 34.78 3.09
962 8454 4.714802 AGTACCACCACTACATGCATTCTA 59.285 41.667 0.00 0.0 0.00 2.10
997 8499 6.373759 ACAAGAAGGGGAAAGAAACACTAAT 58.626 36.000 0.00 0.0 0.00 1.73
1165 8667 2.933906 ACGTCTTGGTGTAATAATGGCG 59.066 45.455 0.00 0.0 0.00 5.69
1560 9062 0.035056 GCTTCAGTGGGCACATACCT 60.035 55.000 0.00 0.0 0.00 3.08
1576 9078 5.637810 CACATACCTTCTTCTCTTTGCGTTA 59.362 40.000 0.00 0.0 0.00 3.18
1817 9319 6.597832 AGTCAAACTCAGTAGTCTGCTTAT 57.402 37.500 0.00 0.0 41.10 1.73
2551 10067 4.098349 TGATGGAGATGGCAATGCTAAAAC 59.902 41.667 4.82 0.0 0.00 2.43
3182 10707 7.651304 CACTTCAGTGTAATCTGATCCAGTATC 59.349 40.741 0.00 0.0 42.84 2.24
3220 11722 6.533730 TCCAGTTATGTTGTTCACATCTCTT 58.466 36.000 0.00 0.0 43.17 2.85
3451 13636 3.055094 GGAGAAGGTTCAGGCTGTGAATA 60.055 47.826 15.27 0.0 46.99 1.75
3459 13644 5.127682 GGTTCAGGCTGTGAATAATGGATTT 59.872 40.000 15.27 0.0 46.99 2.17
3464 13649 4.584325 GGCTGTGAATAATGGATTTAGGCA 59.416 41.667 0.00 0.0 33.18 4.75
3484 13669 1.938585 ACCCTGAACGAGATCCTGAA 58.061 50.000 0.00 0.0 0.00 3.02
3669 13854 1.672356 CCACAAGCCGACAAGGGAG 60.672 63.158 0.00 0.0 41.48 4.30
3670 13855 1.672356 CACAAGCCGACAAGGGAGG 60.672 63.158 0.00 0.0 41.48 4.30
3671 13856 1.841556 ACAAGCCGACAAGGGAGGA 60.842 57.895 0.00 0.0 41.48 3.71
3672 13857 1.374947 CAAGCCGACAAGGGAGGAA 59.625 57.895 0.00 0.0 41.48 3.36
3674 13859 2.046217 GCCGACAAGGGAGGAACC 60.046 66.667 0.00 0.0 41.48 3.62
3675 13860 2.890766 GCCGACAAGGGAGGAACCA 61.891 63.158 0.00 0.0 41.48 3.67
3676 13861 1.991230 CCGACAAGGGAGGAACCAT 59.009 57.895 0.00 0.0 41.20 3.55
3879 14111 4.338012 AGATCAATGCCTGACATGTTTCA 58.662 39.130 0.00 0.0 39.60 2.69
3896 14128 8.820933 ACATGTTTCAAGATGTTAGATGTATCG 58.179 33.333 0.00 0.0 39.57 2.92
3899 14689 6.828502 TTCAAGATGTTAGATGTATCGTGC 57.171 37.500 0.00 0.0 32.68 5.34
4051 14887 4.346709 TGACTGTATTTGGTCAGGACTGAA 59.653 41.667 3.18 0.0 41.85 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
272 6517 4.750598 GCTTCAACTCCCTATATTCGGTTC 59.249 45.833 0.00 0.00 0.00 3.62
278 6523 5.358160 GCTTTGTGCTTCAACTCCCTATATT 59.642 40.000 0.00 0.00 38.95 1.28
359 6727 5.105554 TGAAAACTGCTTTATGGTTGTGTGT 60.106 36.000 0.00 0.00 0.00 3.72
509 6887 2.124320 CATTGGTACCCAGGGCCG 60.124 66.667 10.07 0.00 33.81 6.13
694 8172 7.293828 TGCATGGATGGATTAAATAGTTACCA 58.706 34.615 0.00 0.00 0.00 3.25
705 8184 7.744733 TCACTTAGTTATGCATGGATGGATTA 58.255 34.615 10.16 0.00 39.62 1.75
706 8185 6.604171 TCACTTAGTTATGCATGGATGGATT 58.396 36.000 10.16 0.00 39.62 3.01
707 8186 6.191657 TCACTTAGTTATGCATGGATGGAT 57.808 37.500 10.16 0.00 41.82 3.41
708 8187 5.628797 TCACTTAGTTATGCATGGATGGA 57.371 39.130 10.16 0.00 0.00 3.41
709 8188 6.093219 GCTATCACTTAGTTATGCATGGATGG 59.907 42.308 10.16 3.15 0.00 3.51
710 8189 6.877855 AGCTATCACTTAGTTATGCATGGATG 59.122 38.462 10.16 0.00 0.00 3.51
962 8454 2.168313 CCCCTTCTTGTTTTGCTGTTGT 59.832 45.455 0.00 0.00 0.00 3.32
1560 9062 2.987149 CGAGCTAACGCAAAGAGAAGAA 59.013 45.455 0.00 0.00 39.10 2.52
1817 9319 2.106511 CTGTTCCCTCCAAGGTCAAGAA 59.893 50.000 0.00 0.00 31.93 2.52
2551 10067 5.879223 CCAAATAGATGGCAGGCTTATCTAG 59.121 44.000 17.20 9.07 36.99 2.43
3182 10707 3.652057 AACTGGATACTGGACCATTGG 57.348 47.619 0.00 0.00 40.36 3.16
3451 13636 3.756082 TCAGGGTTGCCTAAATCCATT 57.244 42.857 0.00 0.00 42.17 3.16
3459 13644 1.480954 GATCTCGTTCAGGGTTGCCTA 59.519 52.381 0.00 0.00 0.00 3.93
3464 13649 1.938585 TCAGGATCTCGTTCAGGGTT 58.061 50.000 0.00 0.00 0.00 4.11
3507 13692 2.586792 GGAGACGGCCTTGATGCT 59.413 61.111 0.00 0.00 0.00 3.79
3879 14111 4.740205 CACGCACGATACATCTAACATCTT 59.260 41.667 0.00 0.00 0.00 2.40


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

AutoCloner maintained by Alex Coulton.