Multiple sequence alignment - TraesCS7B01G188300

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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 TraesCS7B01G188300 chr7B 100.000 3206 0 0 1 3206 319716137 319719342 0.000000e+00 5921
1 TraesCS7B01G188300 chr7B 95.648 2918 103 18 302 3206 393237308 393234402 0.000000e+00 4663
2 TraesCS7B01G188300 chr7B 96.589 557 18 1 1 556 319734217 319734773 0.000000e+00 922
3 TraesCS7B01G188300 chr2B 94.911 2928 135 14 286 3206 386132470 386135390 0.000000e+00 4569
4 TraesCS7B01G188300 chr2B 92.405 2778 178 30 214 2977 320940807 320938049 0.000000e+00 3930
5 TraesCS7B01G188300 chr2B 85.549 1993 231 35 1 1975 298275220 298277173 0.000000e+00 2032
6 TraesCS7B01G188300 chr2B 80.507 513 77 13 1 507 298279548 298280043 3.910000e-99 372
7 TraesCS7B01G188300 chr1B 94.501 2928 148 12 286 3206 348700001 348697080 0.000000e+00 4503
8 TraesCS7B01G188300 chr1B 94.844 2812 128 16 403 3206 60863666 60860864 0.000000e+00 4373
9 TraesCS7B01G188300 chr1B 89.524 105 10 1 60 163 685555436 685555540 7.220000e-27 132
10 TraesCS7B01G188300 chr1B 88.571 105 11 1 60 163 685559943 685560047 3.360000e-25 126
11 TraesCS7B01G188300 chr4B 93.183 3051 184 23 169 3206 559209763 559206724 0.000000e+00 4460
12 TraesCS7B01G188300 chr4B 93.033 2928 144 33 290 3206 353677272 353680150 0.000000e+00 4222
13 TraesCS7B01G188300 chr4B 93.881 2582 145 13 404 2977 277835053 277832477 0.000000e+00 3880
14 TraesCS7B01G188300 chr4B 84.583 480 47 17 146 619 162547731 162548189 4.880000e-123 451
15 TraesCS7B01G188300 chr4B 84.539 401 37 15 146 541 162552303 162552683 1.090000e-99 374
16 TraesCS7B01G188300 chr4B 89.796 98 9 1 60 156 595408866 595408963 1.210000e-24 124
17 TraesCS7B01G188300 chr6B 94.045 2586 136 16 401 2977 48901237 48903813 0.000000e+00 3906
18 TraesCS7B01G188300 chr6B 91.011 89 7 1 60 147 471280342 471280430 5.620000e-23 119
19 TraesCS7B01G188300 chr6B 90.000 90 6 2 60 147 471275769 471275857 2.610000e-21 113
20 TraesCS7B01G188300 chr3B 91.116 1936 131 33 61 1975 71908110 71910025 0.000000e+00 2584
21 TraesCS7B01G188300 chr3B 93.258 89 5 1 60 147 261626723 261626811 2.600000e-26 130
22 TraesCS7B01G188300 chr3B 90.816 98 8 1 60 156 261631317 261631414 2.600000e-26 130
23 TraesCS7B01G188300 chr3A 89.772 1007 71 18 2206 3206 261864774 261863794 0.000000e+00 1260
24 TraesCS7B01G188300 chr4A 96.096 333 10 2 2877 3206 487351063 487350731 1.010000e-149 540


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 TraesCS7B01G188300 chr7B 319716137 319719342 3205 False 5921 5921 100.000 1 3206 1 chr7B.!!$F1 3205
1 TraesCS7B01G188300 chr7B 393234402 393237308 2906 True 4663 4663 95.648 302 3206 1 chr7B.!!$R1 2904
2 TraesCS7B01G188300 chr7B 319734217 319734773 556 False 922 922 96.589 1 556 1 chr7B.!!$F2 555
3 TraesCS7B01G188300 chr2B 386132470 386135390 2920 False 4569 4569 94.911 286 3206 1 chr2B.!!$F1 2920
4 TraesCS7B01G188300 chr2B 320938049 320940807 2758 True 3930 3930 92.405 214 2977 1 chr2B.!!$R1 2763
5 TraesCS7B01G188300 chr2B 298275220 298280043 4823 False 1202 2032 83.028 1 1975 2 chr2B.!!$F2 1974
6 TraesCS7B01G188300 chr1B 348697080 348700001 2921 True 4503 4503 94.501 286 3206 1 chr1B.!!$R2 2920
7 TraesCS7B01G188300 chr1B 60860864 60863666 2802 True 4373 4373 94.844 403 3206 1 chr1B.!!$R1 2803
8 TraesCS7B01G188300 chr4B 559206724 559209763 3039 True 4460 4460 93.183 169 3206 1 chr4B.!!$R2 3037
9 TraesCS7B01G188300 chr4B 353677272 353680150 2878 False 4222 4222 93.033 290 3206 1 chr4B.!!$F3 2916
10 TraesCS7B01G188300 chr4B 277832477 277835053 2576 True 3880 3880 93.881 404 2977 1 chr4B.!!$R1 2573
11 TraesCS7B01G188300 chr6B 48901237 48903813 2576 False 3906 3906 94.045 401 2977 1 chr6B.!!$F1 2576
12 TraesCS7B01G188300 chr3B 71908110 71910025 1915 False 2584 2584 91.116 61 1975 1 chr3B.!!$F1 1914
13 TraesCS7B01G188300 chr3A 261863794 261864774 980 True 1260 1260 89.772 2206 3206 1 chr3A.!!$R1 1000

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
298 314 4.631131 TGATGTTCTCCTGTGTTAGTGTG 58.369 43.478 0.0 0.0 0.00 3.82 F
914 945 6.672266 TTCTAGAGGCTATCCTTATGTTGG 57.328 41.667 0.0 0.0 44.46 3.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1135 1166 1.134371 GTGGCTCTCCTCATTGTACCC 60.134 57.143 0.0 0.0 0.0 3.69 R
2865 3249 4.344104 CCAAAGGAACATACCACCAATCT 58.656 43.478 0.0 0.0 0.0 2.40 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
298 314 4.631131 TGATGTTCTCCTGTGTTAGTGTG 58.369 43.478 0.00 0.00 0.00 3.82
914 945 6.672266 TTCTAGAGGCTATCCTTATGTTGG 57.328 41.667 0.00 0.00 44.46 3.77
1135 1166 8.853077 TTCTAGTAATCATATGCAGGGATTTG 57.147 34.615 13.39 5.24 33.59 2.32
1165 1196 1.842562 AGGAGAGCCACAACTATGCAT 59.157 47.619 3.79 3.79 36.29 3.96
1300 1340 0.754587 TCATGTGCAAGTGCCCACAA 60.755 50.000 0.00 0.00 44.22 3.33
1330 1370 4.400884 AGTTCGATGACATAGACAAGCTCT 59.599 41.667 0.00 0.00 0.00 4.09
1397 1437 6.893005 CCTATCAGGAAGGTTATACTAGAGGG 59.107 46.154 0.00 0.00 37.67 4.30
1534 1574 1.133792 CCCTTGAGGTGTGTGAGGTTT 60.134 52.381 0.00 0.00 0.00 3.27
1541 1581 2.026262 AGGTGTGTGAGGTTTCAACACT 60.026 45.455 15.58 0.00 40.79 3.55
1567 1607 1.931906 TTCAGCTGAGCAAGATAGCG 58.068 50.000 17.43 0.00 42.10 4.26
2451 2780 6.927294 ACTAAAACTATGCAGCTGTATTCC 57.073 37.500 22.76 1.65 0.00 3.01
2556 2885 6.968904 CCTACTAATGAATTGATGTGTTGTGC 59.031 38.462 0.00 0.00 0.00 4.57
2561 2890 3.827876 TGAATTGATGTGTTGTGCCTGAT 59.172 39.130 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
242 257 7.601886 AGAGAATCAACAAGACTAGAACACATG 59.398 37.037 0.00 0.00 37.82 3.21
331 347 7.545362 AGGTTCAGATTATCTTCAACAATCG 57.455 36.000 12.99 0.00 34.55 3.34
563 591 4.077184 CGCTAGTCCCCGGCAACA 62.077 66.667 0.00 0.00 0.00 3.33
660 688 5.400870 ACTAACTAGAACAGGGGTTAGTGT 58.599 41.667 14.00 0.00 46.75 3.55
914 945 3.118038 TCCACAAATATGGCAGGTAGGAC 60.118 47.826 0.00 0.00 39.85 3.85
1135 1166 1.134371 GTGGCTCTCCTCATTGTACCC 60.134 57.143 0.00 0.00 0.00 3.69
1165 1196 4.834496 AGGAGCTGAATGGAATTGTTTTGA 59.166 37.500 0.00 0.00 36.07 2.69
1300 1340 6.867550 TGTCTATGTCATCGAACTCATCTTT 58.132 36.000 0.00 0.00 0.00 2.52
1330 1370 4.098044 AGTGAACTCGAGACTCAAAAGTGA 59.902 41.667 21.68 0.00 35.28 3.41
1377 1417 6.782988 TCATTCCCTCTAGTATAACCTTCCTG 59.217 42.308 0.00 0.00 0.00 3.86
1397 1437 8.672815 CCTTTCCACTCTTAATCTTCTTCATTC 58.327 37.037 0.00 0.00 0.00 2.67
1516 1556 2.917933 TGAAACCTCACACACCTCAAG 58.082 47.619 0.00 0.00 0.00 3.02
1521 1561 2.097466 CAGTGTTGAAACCTCACACACC 59.903 50.000 4.60 0.00 40.57 4.16
1522 1562 2.747446 ACAGTGTTGAAACCTCACACAC 59.253 45.455 4.60 7.06 40.31 3.82
1523 1563 3.006940 GACAGTGTTGAAACCTCACACA 58.993 45.455 0.00 0.00 36.69 3.72
1524 1564 3.006940 TGACAGTGTTGAAACCTCACAC 58.993 45.455 0.00 0.00 35.53 3.82
1534 1574 2.874086 CAGCTGAATGTGACAGTGTTGA 59.126 45.455 8.42 0.00 37.64 3.18
1541 1581 2.148768 CTTGCTCAGCTGAATGTGACA 58.851 47.619 18.85 6.50 0.00 3.58
1567 1607 4.141251 AGGTATCTCTTCCTCTGGACTCTC 60.141 50.000 0.00 0.00 0.00 3.20
2865 3249 4.344104 CCAAAGGAACATACCACCAATCT 58.656 43.478 0.00 0.00 0.00 2.40
2945 3331 0.462789 AACATACCACCGATCCCGAC 59.537 55.000 0.00 0.00 38.22 4.79
3108 5035 5.598754 TGGGACCCCAAAATCAATTAGAAT 58.401 37.500 8.45 0.00 44.12 2.40


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

AutoCloner maintained by Alex Coulton.