Multiple sequence alignment - TraesCS5D01G094700

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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 TraesCS5D01G094700 chr5D 100.000 3803 0 0 1 3803 104257870 104254068 0.000000e+00 7023
1 TraesCS5D01G094700 chr5D 81.556 1285 194 19 330 1587 425838939 425840207 0.000000e+00 1020
2 TraesCS5D01G094700 chr5B 98.537 2256 31 1 1548 3803 113676934 113674681 0.000000e+00 3982
3 TraesCS5D01G094700 chr5B 96.987 1560 34 5 1 1554 113683983 113682431 0.000000e+00 2608
4 TraesCS5D01G094700 chr5B 83.243 1653 231 25 1495 3120 14705917 14707550 0.000000e+00 1476
5 TraesCS5D01G094700 chr5B 81.598 1402 211 24 213 1587 515184000 515185381 0.000000e+00 1116
6 TraesCS5D01G094700 chr5B 79.673 551 87 15 80 615 14703148 14703688 1.290000e-99 374
7 TraesCS5D01G094700 chr5B 86.538 156 21 0 3536 3691 506313448 506313293 5.050000e-39 172
8 TraesCS5D01G094700 chr5B 85.806 155 22 0 3537 3691 707871823 707871669 8.450000e-37 165
9 TraesCS5D01G094700 chrUn 85.109 2834 352 47 55 2843 47549307 47546499 0.000000e+00 2832
10 TraesCS5D01G094700 chr4D 82.287 3201 488 47 1 3155 1995021 1998188 0.000000e+00 2697
11 TraesCS5D01G094700 chr3A 81.999 2922 415 64 1 2847 44709505 44712390 0.000000e+00 2379
12 TraesCS5D01G094700 chr3A 81.315 2906 448 45 1 2835 44639178 44642059 0.000000e+00 2270
13 TraesCS5D01G094700 chr3A 89.600 125 10 3 3680 3803 736150979 736150857 5.090000e-34 156
14 TraesCS5D01G094700 chr3B 81.139 2932 455 49 1 2858 54793975 54796882 0.000000e+00 2261
15 TraesCS5D01G094700 chr3B 84.838 1108 149 16 1766 2858 54786223 54787326 0.000000e+00 1098
16 TraesCS5D01G094700 chr3D 81.051 2950 431 69 1 2858 32299256 32302169 0.000000e+00 2233
17 TraesCS5D01G094700 chr3D 89.423 104 11 0 3695 3798 565791203 565791100 8.570000e-27 132
18 TraesCS5D01G094700 chr3D 85.321 109 14 2 3695 3802 1167195 1167088 1.120000e-20 111
19 TraesCS5D01G094700 chr4B 84.430 1201 157 18 1770 2950 2336122 2334932 0.000000e+00 1155
20 TraesCS5D01G094700 chr4B 82.284 1287 188 22 166 1425 2337404 2336131 0.000000e+00 1077
21 TraesCS5D01G094700 chr4B 89.474 114 12 0 3690 3803 661746595 661746482 1.100000e-30 145
22 TraesCS5D01G094700 chr5A 80.654 1406 218 32 212 1587 540051884 540053265 0.000000e+00 1040
23 TraesCS5D01G094700 chr5A 86.792 159 19 2 3533 3691 697731782 697731938 3.900000e-40 176
24 TraesCS5D01G094700 chr7B 87.421 159 19 1 3533 3691 683841343 683841500 8.390000e-42 182
25 TraesCS5D01G094700 chr7B 86.452 155 21 0 3537 3691 697617283 697617437 1.820000e-38 171
26 TraesCS5D01G094700 chr7B 86.111 108 15 0 3695 3802 745144865 745144972 2.400000e-22 117
27 TraesCS5D01G094700 chr2B 87.838 148 16 2 3537 3684 29217861 29218006 5.050000e-39 172
28 TraesCS5D01G094700 chr2B 85.535 159 22 1 3533 3691 793278081 793277924 8.450000e-37 165
29 TraesCS5D01G094700 chr1B 85.276 163 23 1 3525 3687 87965098 87964937 2.350000e-37 167
30 TraesCS5D01G094700 chr6B 87.156 109 14 0 3695 3803 504133213 504133105 1.430000e-24 124
31 TraesCS5D01G094700 chr6A 86.239 109 15 0 3695 3803 17407335 17407443 6.670000e-23 119
32 TraesCS5D01G094700 chr6D 87.037 108 9 5 3695 3800 449103305 449103409 2.400000e-22 117


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 TraesCS5D01G094700 chr5D 104254068 104257870 3802 True 7023 7023 100.000 1 3803 1 chr5D.!!$R1 3802
1 TraesCS5D01G094700 chr5D 425838939 425840207 1268 False 1020 1020 81.556 330 1587 1 chr5D.!!$F1 1257
2 TraesCS5D01G094700 chr5B 113674681 113676934 2253 True 3982 3982 98.537 1548 3803 1 chr5B.!!$R1 2255
3 TraesCS5D01G094700 chr5B 113682431 113683983 1552 True 2608 2608 96.987 1 1554 1 chr5B.!!$R2 1553
4 TraesCS5D01G094700 chr5B 515184000 515185381 1381 False 1116 1116 81.598 213 1587 1 chr5B.!!$F1 1374
5 TraesCS5D01G094700 chr5B 14703148 14707550 4402 False 925 1476 81.458 80 3120 2 chr5B.!!$F2 3040
6 TraesCS5D01G094700 chrUn 47546499 47549307 2808 True 2832 2832 85.109 55 2843 1 chrUn.!!$R1 2788
7 TraesCS5D01G094700 chr4D 1995021 1998188 3167 False 2697 2697 82.287 1 3155 1 chr4D.!!$F1 3154
8 TraesCS5D01G094700 chr3A 44709505 44712390 2885 False 2379 2379 81.999 1 2847 1 chr3A.!!$F2 2846
9 TraesCS5D01G094700 chr3A 44639178 44642059 2881 False 2270 2270 81.315 1 2835 1 chr3A.!!$F1 2834
10 TraesCS5D01G094700 chr3B 54793975 54796882 2907 False 2261 2261 81.139 1 2858 1 chr3B.!!$F2 2857
11 TraesCS5D01G094700 chr3B 54786223 54787326 1103 False 1098 1098 84.838 1766 2858 1 chr3B.!!$F1 1092
12 TraesCS5D01G094700 chr3D 32299256 32302169 2913 False 2233 2233 81.051 1 2858 1 chr3D.!!$F1 2857
13 TraesCS5D01G094700 chr4B 2334932 2337404 2472 True 1116 1155 83.357 166 2950 2 chr4B.!!$R2 2784
14 TraesCS5D01G094700 chr5A 540051884 540053265 1381 False 1040 1040 80.654 212 1587 1 chr5A.!!$F1 1375

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
836 895 0.875059 GCTTGGACCTCACCTTTTCG 59.125 55.0 0.00 0.0 0.0 3.46 F
1356 1436 0.106708 ACAACCAGACAGCGTGTGAT 59.893 50.0 7.26 0.0 0.0 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2565 4274 1.203928 CACATTTCTCCGCTAGCTCG 58.796 55.0 13.93 2.52 0.00 5.03 R
3138 4907 0.825010 ACAACTCCTGGCAAGCCAAG 60.825 55.0 15.55 12.73 46.63 3.61 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
278 297 3.117963 GCTCCTAGAGACACCCTGTAGTA 60.118 52.174 0.00 0.00 37.12 1.82
352 384 1.061546 GTGTTCCCAACCCTACCAGA 58.938 55.000 0.00 0.00 0.00 3.86
797 853 1.705873 ACCTTGTCCGTGAGTTCTCT 58.294 50.000 1.53 0.00 0.00 3.10
836 895 0.875059 GCTTGGACCTCACCTTTTCG 59.125 55.000 0.00 0.00 0.00 3.46
1171 1251 2.430694 ACAGCGCCACTTGATGTCTATA 59.569 45.455 2.29 0.00 0.00 1.31
1172 1252 2.797156 CAGCGCCACTTGATGTCTATAC 59.203 50.000 2.29 0.00 0.00 1.47
1295 1375 7.429374 TCCATTTCTGTGAGATTCAGTCTAT 57.571 36.000 0.00 0.00 37.29 1.98
1356 1436 0.106708 ACAACCAGACAGCGTGTGAT 59.893 50.000 7.26 0.00 0.00 3.06
1530 3188 4.008074 TGGTCTTGAGGTCTTTAAGCTG 57.992 45.455 0.00 0.00 35.33 4.24
1598 3262 2.086869 ACAAAAGCCTGATGTGGATCG 58.913 47.619 0.00 0.00 0.00 3.69
2565 4274 4.374399 CAAAATGCCTCAGGATATTTGCC 58.626 43.478 0.00 0.00 0.00 4.52
3138 4907 1.305201 TGCACTCTCCACCGTTTTTC 58.695 50.000 0.00 0.00 0.00 2.29
3194 4963 3.244044 GGAGTAGCAGATTAAGGAGGCAG 60.244 52.174 0.00 0.00 0.00 4.85
3219 4988 4.275810 ACTTTCATGGATCCAAGGATGTG 58.724 43.478 20.67 11.59 34.60 3.21
3236 5005 6.186957 AGGATGTGTATGTTAAATTCCTGCA 58.813 36.000 0.00 0.00 31.32 4.41
3277 5046 0.992072 CAGCGTACCACTTGTCATCG 59.008 55.000 0.00 0.00 0.00 3.84
3284 5053 2.742372 ACTTGTCATCGCCGGCAC 60.742 61.111 28.98 17.73 0.00 5.01
3340 5109 3.423539 AGGCTTGTGAATAGTGCAGAA 57.576 42.857 0.00 0.00 0.00 3.02
3542 5311 2.787601 CATGCATGCATGTTACTCCC 57.212 50.000 40.30 9.65 46.20 4.30
3560 5329 4.720273 ACTCCCTCCGTTCCTAAATACAAT 59.280 41.667 0.00 0.00 0.00 2.71
3593 5362 7.851228 AGAGATTTCACTATGAACCACATACA 58.149 34.615 0.00 0.00 35.89 2.29
3664 5433 9.778741 TCCATATATTGTTTGTAGTGGAATCTC 57.221 33.333 0.00 0.00 32.02 2.75
3673 5442 8.088981 TGTTTGTAGTGGAATCTCTAGAAAGAC 58.911 37.037 0.00 2.37 34.87 3.01
3735 5504 3.710722 CGGGTGCCAGGCTCTTCT 61.711 66.667 14.15 0.00 0.00 2.85
3736 5505 2.759795 GGGTGCCAGGCTCTTCTT 59.240 61.111 14.15 0.00 0.00 2.52
3775 5544 1.986378 CACTCGGCAAAGTAAGAGACG 59.014 52.381 0.00 0.00 34.98 4.18
3777 5546 0.389426 TCGGCAAAGTAAGAGACGCC 60.389 55.000 0.00 0.00 36.16 5.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
352 384 6.875972 AGAGAACTAACAACATGAGGGTAT 57.124 37.500 0.00 0.00 0.00 2.73
797 853 7.014134 TCCAAGCTATGTGAAGAAACATTCAAA 59.986 33.333 0.00 0.00 40.72 2.69
836 895 2.429610 ACCATTCTGAAATGCTGATGGC 59.570 45.455 0.00 0.00 40.85 4.40
1142 1222 1.535028 CAAGTGGCGCTGTGTAATTCA 59.465 47.619 7.64 0.00 0.00 2.57
1171 1251 1.384989 CCCATCGACCGAGCTGTAGT 61.385 60.000 0.00 0.00 0.00 2.73
1172 1252 1.360551 CCCATCGACCGAGCTGTAG 59.639 63.158 0.00 0.00 0.00 2.74
1295 1375 7.066781 AGTCCTCTGATTTTCCAAGGTAAAAA 58.933 34.615 0.00 0.00 30.20 1.94
1356 1436 3.459227 TCCAGAAGATTACATCCATGGCA 59.541 43.478 6.96 0.00 30.76 4.92
1419 1499 2.267961 CCGGAACCACTAGCCACC 59.732 66.667 0.00 0.00 0.00 4.61
1530 3188 1.810030 GTTCGATCCGTGACCCTGC 60.810 63.158 0.00 0.00 0.00 4.85
1598 3262 2.361438 ACACCGCTAGACAGCCTATTAC 59.639 50.000 0.00 0.00 45.64 1.89
1621 3285 6.183360 GCTAGTATGTCACCTTTGGATTTTCC 60.183 42.308 0.00 0.00 36.96 3.13
2565 4274 1.203928 CACATTTCTCCGCTAGCTCG 58.796 55.000 13.93 2.52 0.00 5.03
2831 4568 6.751514 AGGCAACGATGAACATGTAAATAA 57.248 33.333 0.00 0.00 46.39 1.40
3138 4907 0.825010 ACAACTCCTGGCAAGCCAAG 60.825 55.000 15.55 12.73 46.63 3.61
3194 4963 3.968265 TCCTTGGATCCATGAAAGTTCC 58.032 45.455 25.39 0.00 0.00 3.62
3219 4988 7.736447 AGCTATCTGCAGGAATTTAACATAC 57.264 36.000 15.13 0.00 45.94 2.39
3236 5005 0.958091 CTCTGCGTGGCTAGCTATCT 59.042 55.000 15.72 0.00 35.28 1.98
3284 5053 4.624024 ACATCATGTAGTACAAACGAACCG 59.376 41.667 7.16 1.62 0.00 4.44
3340 5109 1.269958 TCGCTGCAGGCCTCATATAT 58.730 50.000 17.12 0.00 37.74 0.86
3578 5347 8.761575 AATTTTGCTTTGTATGTGGTTCATAG 57.238 30.769 0.00 0.00 39.36 2.23
3650 5419 8.423906 AAGTCTTTCTAGAGATTCCACTACAA 57.576 34.615 0.00 0.00 0.00 2.41
3735 5504 2.314647 CCGCGTTTTGGCTCTCGAA 61.315 57.895 4.92 0.00 0.00 3.71
3736 5505 2.736995 CCGCGTTTTGGCTCTCGA 60.737 61.111 4.92 0.00 0.00 4.04


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

AutoCloner maintained by Alex Coulton.