Multiple sequence alignment - TraesCS5B01G126100

Loading Multiple Alignment...

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 TraesCS5B01G126100 chr5B 100.000 3434 0 0 1 3434 230240138 230243571 0.000000e+00 6342
1 TraesCS5B01G126100 chr5A 96.604 3033 81 8 414 3434 282580386 282583408 0.000000e+00 5011
2 TraesCS5B01G126100 chr2D 95.153 2290 103 6 1133 3418 567487328 567485043 0.000000e+00 3607
3 TraesCS5B01G126100 chr2D 87.873 973 89 11 128 1088 567488284 567487329 0.000000e+00 1116
4 TraesCS5B01G126100 chr2B 94.803 2290 112 5 1133 3418 680204103 680201817 0.000000e+00 3563
5 TraesCS5B01G126100 chr2B 88.061 980 77 16 115 1088 680205049 680204104 0.000000e+00 1125
6 TraesCS5B01G126100 chr2A 94.227 2304 125 5 1133 3434 707003264 707000967 0.000000e+00 3511
7 TraesCS5B01G126100 chr2A 89.588 970 74 14 128 1088 707004216 707003265 0.000000e+00 1206
8 TraesCS5B01G126100 chr5D 97.318 1790 40 5 1647 3434 214913222 214915005 0.000000e+00 3033
9 TraesCS5B01G126100 chr5D 97.712 1355 22 5 303 1652 214909560 214910910 0.000000e+00 2322
10 TraesCS5B01G126100 chr5D 97.423 194 2 2 116 309 214907356 214907546 9.190000e-86 327
11 TraesCS5B01G126100 chr5D 93.137 102 6 1 1 101 214905691 214905792 7.680000e-32 148


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 TraesCS5B01G126100 chr5B 230240138 230243571 3433 False 6342.0 6342 100.0000 1 3434 1 chr5B.!!$F1 3433
1 TraesCS5B01G126100 chr5A 282580386 282583408 3022 False 5011.0 5011 96.6040 414 3434 1 chr5A.!!$F1 3020
2 TraesCS5B01G126100 chr2D 567485043 567488284 3241 True 2361.5 3607 91.5130 128 3418 2 chr2D.!!$R1 3290
3 TraesCS5B01G126100 chr2B 680201817 680205049 3232 True 2344.0 3563 91.4320 115 3418 2 chr2B.!!$R1 3303
4 TraesCS5B01G126100 chr2A 707000967 707004216 3249 True 2358.5 3511 91.9075 128 3434 2 chr2A.!!$R1 3306
5 TraesCS5B01G126100 chr5D 214905691 214915005 9314 False 1457.5 3033 96.3975 1 3434 4 chr5D.!!$F1 3433

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
74 75 0.603707 GCACAGTGCCTGTCTGCTTA 60.604 55.0 15.27 0.0 43.43 3.09 F
559 4138 0.615261 TACCACCTCCCGCACACATA 60.615 55.0 0.00 0.0 0.00 2.29 F
1484 5084 0.037232 CACCGAGAAGGGAGACAACC 60.037 60.0 0.00 0.0 46.96 3.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1426 5026 2.685388 TCAGAGCTTGTACATCCTCTCG 59.315 50.000 17.98 14.49 32.65 4.04 R
2204 8121 3.624777 ACCATGCAAGAATAGTGAAGGG 58.375 45.455 0.00 0.00 0.00 3.95 R
2789 8706 0.744414 AATGAATGACAGTCCCCGCG 60.744 55.000 0.00 0.00 0.00 6.46 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
74 75 0.603707 GCACAGTGCCTGTCTGCTTA 60.604 55.000 15.27 0.00 43.43 3.09
75 76 1.882912 CACAGTGCCTGTCTGCTTAA 58.117 50.000 5.02 0.00 43.43 1.85
83 84 4.818546 GTGCCTGTCTGCTTAATACATGAT 59.181 41.667 0.00 0.00 0.00 2.45
87 88 6.708054 GCCTGTCTGCTTAATACATGATACTT 59.292 38.462 0.00 0.00 0.00 2.24
88 89 7.227512 GCCTGTCTGCTTAATACATGATACTTT 59.772 37.037 0.00 0.00 0.00 2.66
278 1831 6.663093 TGGTACCTGATTTTAGATGCAAATGT 59.337 34.615 14.36 0.00 0.00 2.71
279 1832 7.178274 TGGTACCTGATTTTAGATGCAAATGTT 59.822 33.333 14.36 0.00 0.00 2.71
559 4138 0.615261 TACCACCTCCCGCACACATA 60.615 55.000 0.00 0.00 0.00 2.29
561 4140 1.295101 CACCTCCCGCACACATACA 59.705 57.895 0.00 0.00 0.00 2.29
847 4432 6.472887 TCAGGAATTTGTAAAGGTGGACTAG 58.527 40.000 0.00 0.00 0.00 2.57
1002 4588 8.781196 CCTTTTCAGTCATATTCTGGATGTATG 58.219 37.037 5.25 0.00 34.15 2.39
1056 4650 6.094325 CGTTTAACTACCCTGCCATAAATCAA 59.906 38.462 0.00 0.00 0.00 2.57
1142 4738 1.470805 GCGCAACCATAACAATTCCCC 60.471 52.381 0.30 0.00 0.00 4.81
1426 5026 6.338214 TGATTGCTGGATATACTCAGAGTC 57.662 41.667 6.27 0.00 33.11 3.36
1484 5084 0.037232 CACCGAGAAGGGAGACAACC 60.037 60.000 0.00 0.00 46.96 3.77
1581 5181 2.850060 CACTATTGCATTCAAGCTTGCG 59.150 45.455 21.99 13.03 41.80 4.85
1716 7633 0.804989 GGAGTTCATTGTTCGCAGGG 59.195 55.000 0.00 0.00 0.00 4.45
1935 7852 4.005650 CTCTTGTGGATGTGTATGCAAGT 58.994 43.478 0.00 0.00 36.34 3.16
2153 8070 2.504367 TGCAGGTTTAGTTGAAGAGGC 58.496 47.619 0.00 0.00 0.00 4.70
2160 8077 4.246458 GTTTAGTTGAAGAGGCTCGTCAT 58.754 43.478 29.09 19.54 35.00 3.06
2204 8121 2.695359 TCGGACTGTTGAACCTAATGC 58.305 47.619 0.00 0.00 0.00 3.56
2346 8263 5.414454 TGGGTCATGCAGAAACTACAATAAC 59.586 40.000 0.00 0.00 0.00 1.89
2433 8350 8.121305 ACCATGTTTTGCTCTCAAATGTATAA 57.879 30.769 0.00 0.00 41.37 0.98
2626 8543 9.573166 TGGAGGAAATTTATCACGATATGAAAT 57.427 29.630 0.00 0.00 41.93 2.17
2762 8679 7.726033 ATCAGCTTACCTCCTAATATACCAG 57.274 40.000 0.00 0.00 0.00 4.00
3062 8979 5.233957 TGCCATTCAAGTCAATAATGTCG 57.766 39.130 0.00 0.00 0.00 4.35
3339 9258 5.104776 TGAAGAAGTCTGCTATGCCACTTAT 60.105 40.000 4.63 0.38 32.98 1.73
3408 9334 1.281867 TGTGGTTCCAGCTCCTTATGG 59.718 52.381 0.00 0.00 37.97 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 3.337889 CGACCACACACGCACAGG 61.338 66.667 0.00 0.00 0.00 4.00
97 98 4.083643 AGCATCATATAACAAGCACATCGC 60.084 41.667 0.00 0.00 42.91 4.58
98 99 5.379827 CAGCATCATATAACAAGCACATCG 58.620 41.667 0.00 0.00 0.00 3.84
99 100 5.152097 GCAGCATCATATAACAAGCACATC 58.848 41.667 0.00 0.00 0.00 3.06
100 101 4.581409 TGCAGCATCATATAACAAGCACAT 59.419 37.500 0.00 0.00 0.00 3.21
101 102 3.946558 TGCAGCATCATATAACAAGCACA 59.053 39.130 0.00 0.00 0.00 4.57
102 103 4.285292 GTGCAGCATCATATAACAAGCAC 58.715 43.478 0.00 0.00 42.21 4.40
104 105 4.825546 AGTGCAGCATCATATAACAAGC 57.174 40.909 0.00 0.00 0.00 4.01
106 107 5.759763 CCACTAGTGCAGCATCATATAACAA 59.240 40.000 17.86 0.00 0.00 2.83
107 108 5.299949 CCACTAGTGCAGCATCATATAACA 58.700 41.667 17.86 0.00 0.00 2.41
108 109 4.153117 GCCACTAGTGCAGCATCATATAAC 59.847 45.833 17.86 0.00 0.00 1.89
109 110 4.202346 TGCCACTAGTGCAGCATCATATAA 60.202 41.667 19.15 0.00 34.05 0.98
110 111 3.324556 TGCCACTAGTGCAGCATCATATA 59.675 43.478 19.15 0.00 34.05 0.86
111 112 2.105306 TGCCACTAGTGCAGCATCATAT 59.895 45.455 19.15 0.00 34.05 1.78
112 113 1.485895 TGCCACTAGTGCAGCATCATA 59.514 47.619 19.15 1.00 34.05 2.15
113 114 0.253894 TGCCACTAGTGCAGCATCAT 59.746 50.000 19.15 0.00 34.05 2.45
559 4138 6.110543 GCTTCTTGCTTTTCAAACATTTGT 57.889 33.333 4.36 0.00 37.79 2.83
847 4432 2.436417 TGGCATGGCAACTTCTCTAAC 58.564 47.619 21.13 0.00 37.61 2.34
1002 4588 3.726607 CATCCATGGAAGACAGCTACTC 58.273 50.000 20.67 0.00 0.00 2.59
1056 4650 3.366052 ACACTTGGACACTTCCTGTTT 57.634 42.857 0.00 0.00 43.31 2.83
1142 4738 5.200483 TCCTACCATGCCTTTTATCCTTTG 58.800 41.667 0.00 0.00 0.00 2.77
1292 4891 9.399797 AGTTGATTAGAATATTGCATGTCAGAA 57.600 29.630 0.00 0.00 0.00 3.02
1337 4936 3.603532 ACATGACGAGCACAATCATTCT 58.396 40.909 0.00 0.00 30.58 2.40
1426 5026 2.685388 TCAGAGCTTGTACATCCTCTCG 59.315 50.000 17.98 14.49 32.65 4.04
1484 5084 6.092122 TGTGCTGGATAAAGTAAATTCAGTCG 59.908 38.462 0.00 0.00 33.19 4.18
1581 5181 3.782889 ACAAAGCTGTTTGAGTCCAAC 57.217 42.857 5.15 0.13 45.22 3.77
2153 8070 7.772332 ATTAGCAGGTTAAAGTAATGACGAG 57.228 36.000 0.00 0.00 0.00 4.18
2160 8077 9.692749 CGATCAGATATTAGCAGGTTAAAGTAA 57.307 33.333 0.00 0.00 0.00 2.24
2204 8121 3.624777 ACCATGCAAGAATAGTGAAGGG 58.375 45.455 0.00 0.00 0.00 3.95
2346 8263 4.118410 CAGCTATTCTGGCTAAGTCACTG 58.882 47.826 0.00 0.00 39.15 3.66
2433 8350 4.711949 CAGTTCCCGCTGGCAGCT 62.712 66.667 34.17 14.27 39.60 4.24
2678 8595 2.371658 AGCAGCTCCTCTTTTTGGTT 57.628 45.000 0.00 0.00 0.00 3.67
2789 8706 0.744414 AATGAATGACAGTCCCCGCG 60.744 55.000 0.00 0.00 0.00 6.46
3101 9018 6.628844 GCTTCCATTTCTGACAGGCAATAATT 60.629 38.462 1.81 0.00 0.00 1.40
3102 9019 5.163478 GCTTCCATTTCTGACAGGCAATAAT 60.163 40.000 1.81 0.00 0.00 1.28
3104 9021 3.696051 GCTTCCATTTCTGACAGGCAATA 59.304 43.478 1.81 0.00 0.00 1.90
3107 9024 1.202915 TGCTTCCATTTCTGACAGGCA 60.203 47.619 1.81 0.00 0.00 4.75
3108 9025 1.471684 CTGCTTCCATTTCTGACAGGC 59.528 52.381 1.81 0.00 0.00 4.85
3109 9026 3.063510 TCTGCTTCCATTTCTGACAGG 57.936 47.619 1.81 0.00 0.00 4.00
3111 9028 2.751259 GCATCTGCTTCCATTTCTGACA 59.249 45.455 0.00 0.00 38.21 3.58
3112 9029 2.751259 TGCATCTGCTTCCATTTCTGAC 59.249 45.455 3.53 0.00 42.66 3.51
3113 9030 3.076079 TGCATCTGCTTCCATTTCTGA 57.924 42.857 3.53 0.00 42.66 3.27
3114 9031 3.192844 ACTTGCATCTGCTTCCATTTCTG 59.807 43.478 3.53 0.00 42.66 3.02
3177 9095 4.776795 TGTAGCTCGTCATGTACAAGAA 57.223 40.909 1.69 0.00 0.00 2.52
3408 9334 4.935885 AGCATGACAAGAAAGATTCGAC 57.064 40.909 0.00 0.00 34.02 4.20


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

AutoCloner maintained by Alex Coulton.