Multiple sequence alignment - TraesCS5B01G121400

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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 TraesCS5B01G121400 chr5B 100.000 4758 0 0 1 4758 216649268 216654025 0.000000e+00 8787
1 TraesCS5B01G121400 chr5B 88.199 161 18 1 1 160 327750360 327750200 1.750000e-44 191
2 TraesCS5B01G121400 chr5D 97.683 3021 53 5 1749 4758 193631241 193634255 0.000000e+00 5175
3 TraesCS5B01G121400 chr5D 93.983 1180 42 10 592 1750 193613665 193614836 0.000000e+00 1759
4 TraesCS5B01G121400 chr5A 97.355 2193 42 5 1749 3931 253607294 253605108 0.000000e+00 3714
5 TraesCS5B01G121400 chr5A 94.553 1175 40 5 592 1753 253608524 253607361 0.000000e+00 1794
6 TraesCS5B01G121400 chr5A 98.186 827 14 1 3933 4758 253602501 253601675 0.000000e+00 1443
7 TraesCS5B01G121400 chr5A 90.265 113 11 0 476 588 597081440 597081552 1.070000e-31 148
8 TraesCS5B01G121400 chr5A 86.992 123 16 0 479 601 314941922 314942044 6.420000e-29 139
9 TraesCS5B01G121400 chr4B 94.831 2070 44 18 592 2641 66102875 66104901 0.000000e+00 3171
10 TraesCS5B01G121400 chr4B 96.283 1695 23 16 2636 4325 66104854 66106513 0.000000e+00 2745
11 TraesCS5B01G121400 chr4B 95.485 598 24 2 1 597 634413274 634412679 0.000000e+00 952
12 TraesCS5B01G121400 chr4B 93.600 125 8 0 1 125 451219922 451219798 2.260000e-43 187
13 TraesCS5B01G121400 chr4B 87.421 159 20 0 1 159 352135635 352135477 2.920000e-42 183
14 TraesCS5B01G121400 chr7B 94.353 549 27 3 1 548 612297672 612298217 0.000000e+00 839
15 TraesCS5B01G121400 chr7B 87.817 197 18 3 392 588 1363411 1363601 4.790000e-55 226
16 TraesCS5B01G121400 chr7B 88.496 113 13 0 476 588 593070862 593070974 2.310000e-28 137
17 TraesCS5B01G121400 chr7A 82.521 841 81 29 3952 4758 62529710 62528902 0.000000e+00 678
18 TraesCS5B01G121400 chr7A 88.325 197 18 2 395 588 150445557 150445363 1.030000e-56 231
19 TraesCS5B01G121400 chr7A 84.236 203 27 2 390 588 506681927 506682128 4.860000e-45 193
20 TraesCS5B01G121400 chr7A 86.719 128 16 1 476 603 153262086 153262212 1.790000e-29 141
21 TraesCS5B01G121400 chr4A 81.797 846 85 31 3954 4758 674604942 674604125 0.000000e+00 645
22 TraesCS5B01G121400 chr4A 90.492 305 27 2 4455 4758 674556368 674556065 7.420000e-108 401
23 TraesCS5B01G121400 chr4A 84.472 161 21 4 1 159 503630430 503630588 6.380000e-34 156
24 TraesCS5B01G121400 chr4A 89.655 116 12 0 479 594 490857541 490857426 1.070000e-31 148
25 TraesCS5B01G121400 chrUn 90.096 313 27 4 4447 4758 91245779 91246088 2.060000e-108 403
26 TraesCS5B01G121400 chrUn 92.969 128 7 2 1 127 356042922 356043048 8.130000e-43 185
27 TraesCS5B01G121400 chr6B 94.954 218 8 2 371 588 632524397 632524183 5.900000e-89 339
28 TraesCS5B01G121400 chr6B 94.326 141 5 1 230 370 632524656 632524519 3.730000e-51 213
29 TraesCS5B01G121400 chr6B 86.508 126 16 1 479 603 233170363 233170238 2.310000e-28 137
30 TraesCS5B01G121400 chr3B 80.249 481 67 12 4274 4753 4450183 4449730 2.120000e-88 337
31 TraesCS5B01G121400 chr1B 89.238 223 17 2 370 591 684284553 684284337 6.070000e-69 272
32 TraesCS5B01G121400 chr1B 88.584 219 19 1 370 588 483592026 483592238 1.310000e-65 261
33 TraesCS5B01G121400 chr1B 84.756 164 23 2 1 163 41091148 41090986 3.810000e-36 163
34 TraesCS5B01G121400 chr3A 84.018 219 25 4 374 588 33428338 33428126 8.070000e-48 202
35 TraesCS5B01G121400 chr3A 87.805 123 15 0 479 601 435916718 435916840 1.380000e-30 145
36 TraesCS5B01G121400 chr3A 86.508 126 17 0 476 601 429149074 429149199 6.420000e-29 139
37 TraesCS5B01G121400 chr3D 88.050 159 18 1 2 159 382748007 382747849 2.260000e-43 187
38 TraesCS5B01G121400 chr3D 92.857 126 7 2 1 125 267286413 267286537 1.050000e-41 182
39 TraesCS5B01G121400 chr3D 88.591 149 16 1 1 149 614251096 614251243 3.780000e-41 180
40 TraesCS5B01G121400 chr3D 81.152 191 26 7 4077 4263 2258276 2258092 1.380000e-30 145
41 TraesCS5B01G121400 chr6D 92.135 89 6 1 72 159 312136308 312136220 1.800000e-24 124


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 TraesCS5B01G121400 chr5B 216649268 216654025 4757 False 8787 8787 100.000 1 4758 1 chr5B.!!$F1 4757
1 TraesCS5B01G121400 chr5D 193631241 193634255 3014 False 5175 5175 97.683 1749 4758 1 chr5D.!!$F2 3009
2 TraesCS5B01G121400 chr5D 193613665 193614836 1171 False 1759 1759 93.983 592 1750 1 chr5D.!!$F1 1158
3 TraesCS5B01G121400 chr5A 253601675 253608524 6849 True 2317 3714 96.698 592 4758 3 chr5A.!!$R1 4166
4 TraesCS5B01G121400 chr4B 66102875 66106513 3638 False 2958 3171 95.557 592 4325 2 chr4B.!!$F1 3733
5 TraesCS5B01G121400 chr4B 634412679 634413274 595 True 952 952 95.485 1 597 1 chr4B.!!$R3 596
6 TraesCS5B01G121400 chr7B 612297672 612298217 545 False 839 839 94.353 1 548 1 chr7B.!!$F3 547
7 TraesCS5B01G121400 chr7A 62528902 62529710 808 True 678 678 82.521 3952 4758 1 chr7A.!!$R1 806
8 TraesCS5B01G121400 chr4A 674604125 674604942 817 True 645 645 81.797 3954 4758 1 chr4A.!!$R3 804

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
605 607 0.179089 CTGTGAGCTCCCATCCTTCG 60.179 60.000 12.15 0.0 0.00 3.79 F
1137 1154 1.152333 GGACCAAAGCAGGGGGTTT 60.152 57.895 0.00 0.0 45.04 3.27 F
1451 1492 1.898330 TTCAGGATGCTGCGCCTACA 61.898 55.000 9.76 0.0 34.76 2.74 F
2756 2868 1.073897 GCTCCCTCAAGCTGTTGGT 59.926 57.895 0.00 0.0 39.27 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2386 2498 1.339929 TCCGGCCAAGAAAAGAAAAGC 59.660 47.619 2.24 0.0 0.00 3.51 R
2756 2868 3.181457 CCATCTTGAGAGAATAGGCAGCA 60.181 47.826 0.00 0.0 35.07 4.41 R
2870 2982 3.181480 GCTGTCAGAGAGATCTGGTTACC 60.181 52.174 0.00 0.0 38.23 2.85 R
4110 6888 3.222173 TGCCACACCTTATTCACACTT 57.778 42.857 0.00 0.0 0.00 3.16 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
146 147 6.805713 ACAAAGTTGAGACACTTATTTTGGG 58.194 36.000 0.00 0.00 35.87 4.12
174 175 3.130869 GGAAGTATGTGGCAATGCATTGA 59.869 43.478 37.36 20.29 40.14 2.57
188 190 1.535462 GCATTGACGTGCAGGTTAACT 59.465 47.619 17.53 6.15 44.43 2.24
385 387 6.741992 TGATGTAGTTAGAAACCAATGCAG 57.258 37.500 0.00 0.00 0.00 4.41
496 498 9.015367 ACGTTCTATATATAGACATTCTGCTGT 57.985 33.333 19.94 7.29 39.00 4.40
575 577 3.258123 AGACACCCAAATTTACACATGCC 59.742 43.478 0.00 0.00 0.00 4.40
588 590 1.028330 ACATGCCGTTGGAGATGCTG 61.028 55.000 0.00 0.00 0.00 4.41
589 591 1.028330 CATGCCGTTGGAGATGCTGT 61.028 55.000 0.00 0.00 0.00 4.40
590 592 1.028330 ATGCCGTTGGAGATGCTGTG 61.028 55.000 0.00 0.00 0.00 3.66
605 607 0.179089 CTGTGAGCTCCCATCCTTCG 60.179 60.000 12.15 0.00 0.00 3.79
679 684 3.499737 CCACGCGCCATCCTTCAC 61.500 66.667 5.73 0.00 0.00 3.18
1005 1022 8.067751 AGATAATCACGTACATATACATGGCT 57.932 34.615 0.00 0.00 36.39 4.75
1008 1025 3.068873 TCACGTACATATACATGGCTGCA 59.931 43.478 0.50 0.00 36.39 4.41
1097 1114 4.104417 GAGCTCGTCGACGGTGCT 62.104 66.667 38.40 38.40 45.85 4.40
1137 1154 1.152333 GGACCAAAGCAGGGGGTTT 60.152 57.895 0.00 0.00 45.04 3.27
1268 1290 2.305009 GGTACATACAGTAGGACGGCT 58.695 52.381 0.00 0.00 32.19 5.52
1297 1319 7.539436 TCTAGACATGTGTGTTCTACAGAATC 58.461 38.462 1.15 0.00 40.69 2.52
1339 1371 7.534723 AGTACCACGAATATTTAGGATGCTA 57.465 36.000 8.28 0.00 0.00 3.49
1371 1403 8.322906 TGAAGATTACATTATATTTCCCGCAG 57.677 34.615 0.00 0.00 0.00 5.18
1451 1492 1.898330 TTCAGGATGCTGCGCCTACA 61.898 55.000 9.76 0.00 34.76 2.74
1494 1535 9.423061 CCTTGATTAAAGAAAATTTAGTGTGGG 57.577 33.333 0.00 0.00 38.24 4.61
2756 2868 1.073897 GCTCCCTCAAGCTGTTGGT 59.926 57.895 0.00 0.00 39.27 3.67
2839 2951 1.299468 GCACGAGCGAGGTAGATGG 60.299 63.158 0.00 0.00 0.00 3.51
2870 2982 8.075574 TCATTGATTGCTTACTTACAACTTGTG 58.924 33.333 4.57 0.00 0.00 3.33
2871 2983 6.312399 TGATTGCTTACTTACAACTTGTGG 57.688 37.500 4.57 0.65 0.00 4.17
2872 2984 5.825679 TGATTGCTTACTTACAACTTGTGGT 59.174 36.000 4.57 6.21 0.00 4.16
3004 3116 3.505790 AATCAGCACCCCAACCGCA 62.506 57.895 0.00 0.00 0.00 5.69
3239 3353 3.251004 GGCCTATTTTAATCGAGGTGCAG 59.749 47.826 0.00 0.00 0.00 4.41
3942 6690 2.254546 TGGCTGTTACTCACACAAGG 57.745 50.000 0.00 0.00 0.00 3.61
4106 6883 5.522097 CCCAACAAAAAGGTCATTTACACAC 59.478 40.000 0.00 0.00 0.00 3.82
4108 6886 6.255453 CCAACAAAAAGGTCATTTACACACAG 59.745 38.462 0.00 0.00 0.00 3.66
4110 6888 7.164230 ACAAAAAGGTCATTTACACACAGAA 57.836 32.000 0.00 0.00 0.00 3.02
4309 7098 5.278660 GCCTGTGTCAACATCAAGAAATCTT 60.279 40.000 0.00 0.00 35.22 2.40
4383 7172 1.670791 TCTGGGGAACACACGAAAAC 58.329 50.000 0.00 0.00 0.00 2.43
4385 7174 0.392729 TGGGGAACACACGAAAACGT 60.393 50.000 0.00 0.00 0.00 3.99
4389 7178 3.546616 GGGGAACACACGAAAACGTAAAG 60.547 47.826 0.00 0.00 0.00 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 7.165460 TGTAAGACAAGAATTATGAGACGGA 57.835 36.000 0.00 0.00 0.00 4.69
48 49 9.926158 TGTAACAAGTATCGTTTTGGTATTAGA 57.074 29.630 0.00 0.00 30.00 2.10
64 65 6.699366 TGTCCAAATACGGATGTAACAAGTA 58.301 36.000 0.00 0.00 37.41 2.24
70 71 9.104965 CTTAGATTTGTCCAAATACGGATGTAA 57.895 33.333 5.29 0.00 40.77 2.41
146 147 0.535335 TGCCACATACTTCCTCCGTC 59.465 55.000 0.00 0.00 0.00 4.79
174 175 4.575885 ACATATTCAGTTAACCTGCACGT 58.424 39.130 0.88 0.00 41.25 4.49
326 328 5.620206 AGTACCATCAATATCAATTCGCCA 58.380 37.500 0.00 0.00 0.00 5.69
327 329 6.313905 CCTAGTACCATCAATATCAATTCGCC 59.686 42.308 0.00 0.00 0.00 5.54
575 577 0.390866 AGCTCACAGCATCTCCAACG 60.391 55.000 0.00 0.00 45.56 4.10
588 590 4.844420 CGAAGGATGGGAGCTCAC 57.156 61.111 17.19 13.72 0.00 3.51
1071 1088 2.586792 GACGAGCTCAAGGGCCAT 59.413 61.111 15.40 0.00 0.00 4.40
1097 1114 2.933287 ATGGCACCCCGAGAACCA 60.933 61.111 0.00 0.00 34.28 3.67
1268 1290 4.607293 AGAACACACATGTCTAGAAGCA 57.393 40.909 0.00 0.00 38.45 3.91
1297 1319 5.874892 GTACTACGTACCACTACTAGACG 57.125 47.826 0.00 0.00 39.37 4.18
1451 1492 9.690913 TTAATCAAGGAGAAAGATCACATGATT 57.309 29.630 0.00 0.00 37.64 2.57
1578 1619 7.199766 TCCACAATTGTCATGTGTTAAAGTTC 58.800 34.615 8.48 0.00 45.23 3.01
1663 1704 2.034221 GTGAAGTCCCACCAGCCC 59.966 66.667 0.00 0.00 0.00 5.19
1890 2002 9.029243 CAATCAAAATTAAGTTAGTTGTGCACA 57.971 29.630 17.42 17.42 0.00 4.57
2247 2359 7.336931 GCTTCTTCACCATTGGAAGTTAGATAA 59.663 37.037 10.37 0.00 41.88 1.75
2386 2498 1.339929 TCCGGCCAAGAAAAGAAAAGC 59.660 47.619 2.24 0.00 0.00 3.51
2673 2785 7.517321 TCACTTGCACAACATTTTTCTTTTTC 58.483 30.769 0.00 0.00 0.00 2.29
2756 2868 3.181457 CCATCTTGAGAGAATAGGCAGCA 60.181 47.826 0.00 0.00 35.07 4.41
2870 2982 3.181480 GCTGTCAGAGAGATCTGGTTACC 60.181 52.174 0.00 0.00 38.23 2.85
2871 2983 3.699038 AGCTGTCAGAGAGATCTGGTTAC 59.301 47.826 0.00 0.00 38.23 2.50
2872 2984 3.698539 CAGCTGTCAGAGAGATCTGGTTA 59.301 47.826 5.25 0.00 38.23 2.85
3004 3116 7.308229 GCACAATTCATACTTCTGAACTGTTCT 60.308 37.037 20.18 3.56 41.36 3.01
4106 6883 4.320494 GCCACACCTTATTCACACTTTCTG 60.320 45.833 0.00 0.00 0.00 3.02
4108 6886 3.568007 TGCCACACCTTATTCACACTTTC 59.432 43.478 0.00 0.00 0.00 2.62
4110 6888 3.222173 TGCCACACCTTATTCACACTT 57.778 42.857 0.00 0.00 0.00 3.16
4309 7098 5.073311 ACGATCTTGATTTCTCGAAAGGA 57.927 39.130 0.00 0.00 35.24 3.36


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

AutoCloner maintained by Alex Coulton.