Multiple sequence alignment - TraesCS6A01G027800

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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 TraesCS6A01G027800 chr6A 100.000 3218 0 0 1 3218 14179560 14182777 0.000000e+00 5943
1 TraesCS6A01G027800 chr3A 97.994 3240 43 2 1 3218 26464628 26461389 0.000000e+00 5603
2 TraesCS6A01G027800 chr3A 87.584 2239 256 14 305 2534 700385701 700383476 0.000000e+00 2575
3 TraesCS6A01G027800 chr3A 87.032 2244 266 17 301 2534 724158923 724161151 0.000000e+00 2508
4 TraesCS6A01G027800 chr3A 87.307 1623 185 12 920 2534 730308843 730307234 0.000000e+00 1836
5 TraesCS6A01G027800 chr1B 96.464 2998 52 7 130 3105 67032126 67029161 0.000000e+00 4900
6 TraesCS6A01G027800 chr1B 95.785 2752 89 7 304 3030 25486650 25483901 0.000000e+00 4414
7 TraesCS6A01G027800 chr1B 93.060 2752 93 12 304 3030 639040555 639043233 0.000000e+00 3934
8 TraesCS6A01G027800 chr1B 88.125 320 31 4 2903 3218 25483963 25483647 1.090000e-99 374
9 TraesCS6A01G027800 chr1B 97.531 162 4 0 125 286 25501766 25501605 8.790000e-71 278
10 TraesCS6A01G027800 chr1B 97.531 162 4 0 125 286 639039588 639039749 8.790000e-71 278
11 TraesCS6A01G027800 chr1B 98.387 124 2 0 1 124 67032316 67032193 5.410000e-53 219
12 TraesCS6A01G027800 chr1B 96.899 129 4 0 3090 3218 67029139 67029011 1.940000e-52 217
13 TraesCS6A01G027800 chr1B 96.774 124 3 1 1 124 25502006 25501884 4.210000e-49 206
14 TraesCS6A01G027800 chr1B 95.238 126 3 3 1 124 639039338 639039462 2.530000e-46 196
15 TraesCS6A01G027800 chr6B 96.309 2709 75 5 304 2988 63985512 63988219 0.000000e+00 4425
16 TraesCS6A01G027800 chr6B 85.817 1812 216 27 934 2726 707822572 707824361 0.000000e+00 1884
17 TraesCS6A01G027800 chr6B 93.772 1140 65 5 2085 3218 16952288 16953427 0.000000e+00 1707
18 TraesCS6A01G027800 chr6B 88.308 402 36 7 2745 3138 9981842 9981444 3.760000e-129 472
19 TraesCS6A01G027800 chr6B 90.196 255 25 0 2964 3218 63988249 63988503 1.850000e-87 333
20 TraesCS6A01G027800 chr6B 96.914 162 5 0 125 286 63984543 63984704 4.090000e-69 272
21 TraesCS6A01G027800 chr6B 96.774 124 3 1 1 124 63984305 63984427 4.210000e-49 206
22 TraesCS6A01G027800 chr2B 86.737 2360 264 21 301 2631 46336696 46339035 0.000000e+00 2579
23 TraesCS6A01G027800 chrUn 85.912 1810 219 24 934 2726 47563422 47565212 0.000000e+00 1897
24 TraesCS6A01G027800 chrUn 88.308 402 36 7 2745 3138 75929172 75929570 3.760000e-129 472
25 TraesCS6A01G027800 chr5A 97.720 614 14 0 2492 3105 512821832 512822445 0.000000e+00 1057
26 TraesCS6A01G027800 chr5A 96.124 129 5 0 3090 3218 512822468 512822596 9.040000e-51 211
27 TraesCS6A01G027800 chr5B 83.071 254 36 5 2901 3150 682694113 682694363 1.160000e-54 224
28 TraesCS6A01G027800 chr4A 92.248 129 10 0 127 255 732529660 732529532 1.970000e-42 183


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 TraesCS6A01G027800 chr6A 14179560 14182777 3217 False 5943.000000 5943 100.000000 1 3218 1 chr6A.!!$F1 3217
1 TraesCS6A01G027800 chr3A 26461389 26464628 3239 True 5603.000000 5603 97.994000 1 3218 1 chr3A.!!$R1 3217
2 TraesCS6A01G027800 chr3A 700383476 700385701 2225 True 2575.000000 2575 87.584000 305 2534 1 chr3A.!!$R2 2229
3 TraesCS6A01G027800 chr3A 724158923 724161151 2228 False 2508.000000 2508 87.032000 301 2534 1 chr3A.!!$F1 2233
4 TraesCS6A01G027800 chr3A 730307234 730308843 1609 True 1836.000000 1836 87.307000 920 2534 1 chr3A.!!$R3 1614
5 TraesCS6A01G027800 chr1B 25483647 25486650 3003 True 2394.000000 4414 91.955000 304 3218 2 chr1B.!!$R1 2914
6 TraesCS6A01G027800 chr1B 67029011 67032316 3305 True 1778.666667 4900 97.250000 1 3218 3 chr1B.!!$R3 3217
7 TraesCS6A01G027800 chr1B 639039338 639043233 3895 False 1469.333333 3934 95.276333 1 3030 3 chr1B.!!$F1 3029
8 TraesCS6A01G027800 chr6B 707822572 707824361 1789 False 1884.000000 1884 85.817000 934 2726 1 chr6B.!!$F2 1792
9 TraesCS6A01G027800 chr6B 16952288 16953427 1139 False 1707.000000 1707 93.772000 2085 3218 1 chr6B.!!$F1 1133
10 TraesCS6A01G027800 chr6B 63984305 63988503 4198 False 1309.000000 4425 95.048250 1 3218 4 chr6B.!!$F3 3217
11 TraesCS6A01G027800 chr2B 46336696 46339035 2339 False 2579.000000 2579 86.737000 301 2631 1 chr2B.!!$F1 2330
12 TraesCS6A01G027800 chrUn 47563422 47565212 1790 False 1897.000000 1897 85.912000 934 2726 1 chrUn.!!$F1 1792
13 TraesCS6A01G027800 chr5A 512821832 512822596 764 False 634.000000 1057 96.922000 2492 3218 2 chr5A.!!$F1 726

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
663 1584 0.927767 ATAGGAGACGGTGAGGAGGT 59.072 55.000 0.00 0.00 0.00 3.85 F
700 1621 2.357517 CACTGGAAACGCGCTCCT 60.358 61.111 23.78 6.58 33.77 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1688 2614 1.483827 CAATAGCAGGACCTGAGCTCA 59.516 52.381 26.25 17.19 39.68 4.26 R
2667 3677 2.450476 GGCCATGAGTTCAAAGTCCAT 58.550 47.619 0.00 0.00 0.00 3.41 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
273 401 7.353414 TCTCTGTCTTCCAGGATATTAAGTG 57.647 40.000 0.00 0.00 41.83 3.16
280 408 9.232473 GTCTTCCAGGATATTAAGTGAACTTTT 57.768 33.333 0.21 0.00 37.40 2.27
663 1584 0.927767 ATAGGAGACGGTGAGGAGGT 59.072 55.000 0.00 0.00 0.00 3.85
700 1621 2.357517 CACTGGAAACGCGCTCCT 60.358 61.111 23.78 6.58 33.77 3.69
1091 2015 8.133024 TCCATTTAATTACTTGTGATTGCCTT 57.867 30.769 1.74 0.00 0.00 4.35
1961 2950 5.625197 GCAGGAATTCATGGTTAAACAGCAT 60.625 40.000 20.68 0.00 44.90 3.79
2495 3495 7.118245 GGAAATTCTTACTTGGCTTCAATTTGG 59.882 37.037 0.00 0.00 0.00 3.28
2585 3585 5.644644 CATCTTTTAGGTTGAACTCATGCC 58.355 41.667 0.00 0.00 0.00 4.40
2667 3677 5.736813 ACCCTTGTTGAATATGTACGCTTA 58.263 37.500 0.00 0.00 0.00 3.09
3107 4225 5.625568 AGCCCTCGGTTTACATATAAACT 57.374 39.130 6.58 0.00 46.42 2.66
3135 4253 1.382146 TCCTCGGCCCTCGGTTTAT 60.382 57.895 0.00 0.00 39.77 1.40
3213 4331 3.583276 TAGTGTCCGGCTGCCGTTG 62.583 63.158 35.82 23.41 46.80 4.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
80 81 9.959721 ACTCATTAAAAGCTTTTACTCTGGATA 57.040 29.630 27.22 13.24 32.77 2.59
273 401 7.096065 GCACATGTTAGTCAATCCAAAAAGTTC 60.096 37.037 0.00 0.00 0.00 3.01
280 408 3.758023 CCTGCACATGTTAGTCAATCCAA 59.242 43.478 0.00 0.00 0.00 3.53
286 414 2.234661 CTCCTCCTGCACATGTTAGTCA 59.765 50.000 0.00 0.00 0.00 3.41
364 1285 7.273917 CCAGATTTTGGTCTCCTGAGGAACT 62.274 48.000 1.41 0.00 42.18 3.01
569 1490 4.321966 TCGTGGCGGGATTGTGCA 62.322 61.111 0.00 0.00 0.00 4.57
663 1584 2.115910 CCCAAGACCAAGCTGGCA 59.884 61.111 0.00 0.00 42.67 4.92
700 1621 4.900684 TGTCCCAATTGTCTTTCGTATCA 58.099 39.130 4.43 0.00 0.00 2.15
1617 2543 5.105567 TGGAACCGTCACCAACATATAAT 57.894 39.130 0.00 0.00 32.93 1.28
1688 2614 1.483827 CAATAGCAGGACCTGAGCTCA 59.516 52.381 26.25 17.19 39.68 4.26
2495 3495 4.873827 TCCACGATGCAAACCTATAAGTTC 59.126 41.667 0.00 0.00 0.00 3.01
2585 3585 2.917933 TGAGTTCCAAGTTCACACCTG 58.082 47.619 0.00 0.00 0.00 4.00
2667 3677 2.450476 GGCCATGAGTTCAAAGTCCAT 58.550 47.619 0.00 0.00 0.00 3.41
3135 4253 1.553248 AGCGAGCACAGGGTTTACATA 59.447 47.619 0.00 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.