Multiple sequence alignment - TraesCS6B01G175500

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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 TraesCS6B01G175500 chr6B 100.000 2715 0 0 1 2715 191530788 191533502 0.000000e+00 5014
1 TraesCS6B01G175500 chr6A 93.596 2764 95 32 1 2715 127181665 127184395 0.000000e+00 4048
2 TraesCS6B01G175500 chr6D 95.171 1139 34 11 1581 2715 104979660 104980781 0.000000e+00 1779
3 TraesCS6B01G175500 chr6D 94.153 1163 39 11 395 1538 104978269 104979421 0.000000e+00 1744
4 TraesCS6B01G175500 chr6D 85.117 383 44 9 1 379 104977911 104978284 1.970000e-101 379


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 TraesCS6B01G175500 chr6B 191530788 191533502 2714 False 5014.000000 5014 100.000000 1 2715 1 chr6B.!!$F1 2714
1 TraesCS6B01G175500 chr6A 127181665 127184395 2730 False 4048.000000 4048 93.596000 1 2715 1 chr6A.!!$F1 2714
2 TraesCS6B01G175500 chr6D 104977911 104980781 2870 False 1300.666667 1779 91.480333 1 2715 3 chr6D.!!$F1 2714

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
636 648 0.249489 CGCAGCATGGGTACTACTCC 60.249 60.0 0.00 0.00 44.98 3.85 F
688 700 0.614979 AGCACTGGAGGTACGACCAT 60.615 55.0 9.51 0.18 41.95 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1494 1536 0.391661 CAGTGTACCGGCAGCATCTT 60.392 55.000 0.0 0.0 0.00 2.4 R
1796 2062 1.202663 TGCACCCTTTTACAGCGTGTA 60.203 47.619 0.0 0.0 34.21 2.9 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
27 28 7.615582 TCAATCCATTATGAATTATCTCCGC 57.384 36.000 0.00 0.00 0.00 5.54
83 84 6.949578 GCTGATTAGTCTGCTTGATATCTC 57.050 41.667 9.44 0.00 43.57 2.75
126 136 1.019278 TCGATGCCGGCAGTTTCTTC 61.019 55.000 35.36 23.98 36.24 2.87
128 138 1.739035 CGATGCCGGCAGTTTCTTCTA 60.739 52.381 35.36 6.78 0.00 2.10
159 169 1.750022 TACAAAACAGGTAGGGGGCT 58.250 50.000 0.00 0.00 0.00 5.19
268 279 1.268625 TGGTATACACGATAGCCAGCG 59.731 52.381 5.01 0.00 37.67 5.18
303 314 3.350219 TCAAACCAGATACTCTTGGCC 57.650 47.619 0.00 0.00 0.00 5.36
361 372 6.387192 TCCAGATTTAATTCCCAAGAGACA 57.613 37.500 0.00 0.00 0.00 3.41
362 373 6.789268 TCCAGATTTAATTCCCAAGAGACAA 58.211 36.000 0.00 0.00 0.00 3.18
363 374 7.237982 TCCAGATTTAATTCCCAAGAGACAAA 58.762 34.615 0.00 0.00 0.00 2.83
364 375 7.728083 TCCAGATTTAATTCCCAAGAGACAAAA 59.272 33.333 0.00 0.00 0.00 2.44
365 376 8.367156 CCAGATTTAATTCCCAAGAGACAAAAA 58.633 33.333 0.00 0.00 0.00 1.94
455 466 9.694137 ATTATAAAGCCTCGTTTGAGATACTAC 57.306 33.333 0.00 0.00 45.57 2.73
464 475 8.505625 CCTCGTTTGAGATACTACCTATAGTTC 58.494 40.741 0.00 0.00 45.57 3.01
475 486 9.921637 ATACTACCTATAGTTCTGACGTACTAC 57.078 37.037 0.00 0.00 41.99 2.73
502 514 6.665465 ACAGTGCTAGGTTTAATTCGTTTTC 58.335 36.000 0.00 0.00 0.00 2.29
636 648 0.249489 CGCAGCATGGGTACTACTCC 60.249 60.000 0.00 0.00 44.98 3.85
637 649 1.123928 GCAGCATGGGTACTACTCCT 58.876 55.000 0.00 0.00 35.86 3.69
638 650 1.069358 GCAGCATGGGTACTACTCCTC 59.931 57.143 0.00 0.00 35.86 3.71
688 700 0.614979 AGCACTGGAGGTACGACCAT 60.615 55.000 9.51 0.18 41.95 3.55
823 836 3.891366 CTCTCCCATTTCCTGTTGTGTTT 59.109 43.478 0.00 0.00 0.00 2.83
824 837 3.888930 TCTCCCATTTCCTGTTGTGTTTC 59.111 43.478 0.00 0.00 0.00 2.78
853 866 5.907866 TTATTTGGGTTTCCTTTCGGATC 57.092 39.130 0.00 0.00 39.58 3.36
864 878 2.890945 CCTTTCGGATCTTTGGGTTGTT 59.109 45.455 0.00 0.00 0.00 2.83
865 879 3.320826 CCTTTCGGATCTTTGGGTTGTTT 59.679 43.478 0.00 0.00 0.00 2.83
866 880 4.521256 CCTTTCGGATCTTTGGGTTGTTTA 59.479 41.667 0.00 0.00 0.00 2.01
867 881 5.010213 CCTTTCGGATCTTTGGGTTGTTTAA 59.990 40.000 0.00 0.00 0.00 1.52
938 952 1.656587 ATGTTAGCTCCTGGTGTGGA 58.343 50.000 0.00 0.00 34.52 4.02
1094 1108 4.348168 GATCCACTGGTGGGTATGTAGAAT 59.652 45.833 18.26 2.78 45.85 2.40
1198 1213 4.646492 AGCCACAAAAGAAAGACAGAACAT 59.354 37.500 0.00 0.00 0.00 2.71
1415 1457 9.778741 TGTAGTACTGGAATAAATGATTGGATC 57.221 33.333 5.39 0.00 0.00 3.36
1494 1536 1.409241 GCCTTGGGAGCTGAATCATGA 60.409 52.381 0.00 0.00 0.00 3.07
1533 1582 1.612726 GCAACATGCACCCTCTCTCTT 60.613 52.381 0.00 0.00 44.26 2.85
1544 1593 3.077695 ACCCTCTCTCTTTCTCACCCTAA 59.922 47.826 0.00 0.00 0.00 2.69
1546 1595 4.349365 CCTCTCTCTTTCTCACCCTAACT 58.651 47.826 0.00 0.00 0.00 2.24
1579 1826 3.766591 TCTTTCCTGTTGCCTTGTTTTCA 59.233 39.130 0.00 0.00 0.00 2.69
1796 2062 3.012274 TCTCTCTCCTTCCTGTTCCTCAT 59.988 47.826 0.00 0.00 0.00 2.90
1876 2142 5.570589 GCTTGCTTATGTCTGTTTGCTTTAG 59.429 40.000 0.00 0.00 0.00 1.85
1882 2148 7.862873 GCTTATGTCTGTTTGCTTTAGTTTTCT 59.137 33.333 0.00 0.00 0.00 2.52
1886 2152 8.825667 TGTCTGTTTGCTTTAGTTTTCTTTTT 57.174 26.923 0.00 0.00 0.00 1.94
1963 2229 3.123050 GGTTTGCACCTTGTTTGTGATC 58.877 45.455 0.00 0.00 40.44 2.92
1979 2245 4.448537 GTGATCTTCACTGCTACTCACT 57.551 45.455 0.45 0.00 43.73 3.41
1986 2252 2.899900 TCACTGCTACTCACTGGTGATT 59.100 45.455 3.80 1.63 39.13 2.57
2101 2368 3.659841 TGGTTTCTTTAGCCCCCTTTTT 58.340 40.909 0.00 0.00 0.00 1.94
2189 2456 5.255687 AGATGTGTTATTGGTTGCATCTGA 58.744 37.500 0.00 0.00 40.72 3.27
2217 2484 8.196802 ACAATTTAGTTTTTCTTGCTTTGACC 57.803 30.769 0.00 0.00 0.00 4.02
2414 2683 5.068198 CCTAAGCACAGCCATATCAATTTGT 59.932 40.000 0.00 0.00 0.00 2.83
2424 2693 6.038356 GCCATATCAATTTGTGTGGAGAAAG 58.962 40.000 16.19 0.00 0.00 2.62
2443 2712 7.384387 GGAGAAAGAAGTGACACGTAGTAAAAT 59.616 37.037 0.00 0.00 41.61 1.82
2511 2780 7.464358 CACGCTTTAGACAAGTTAATTGCTAT 58.536 34.615 0.00 0.00 43.15 2.97
2582 2851 8.915871 AAATCATTAAATTGTCAACATCCTCG 57.084 30.769 0.00 0.00 0.00 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 8.077991 CACAATGGCAATAATACATAACAGAGG 58.922 37.037 0.00 0.00 0.00 3.69
79 80 7.275920 GTCCTACATCAAATGTGTAAGGAGAT 58.724 38.462 9.34 0.00 44.60 2.75
83 84 4.570772 CCGTCCTACATCAAATGTGTAAGG 59.429 45.833 2.88 2.56 44.60 2.69
176 186 2.251818 CATCCATGATAGTCCCTCCGT 58.748 52.381 0.00 0.00 0.00 4.69
186 196 4.768448 GCATCCATGAAACCATCCATGATA 59.232 41.667 0.00 0.00 41.88 2.15
268 279 7.002250 TCTGGTTTGATCTCATGATATCCTC 57.998 40.000 16.13 8.07 32.19 3.71
303 314 2.176546 CGCCAGCCAATTCACACG 59.823 61.111 0.00 0.00 0.00 4.49
399 410 8.519799 TGTCTTCAGTCCATTTTACTTTTCTT 57.480 30.769 0.00 0.00 0.00 2.52
455 466 6.256539 TGTTCGTAGTACGTCAGAACTATAGG 59.743 42.308 21.38 5.11 43.14 2.57
464 475 2.095869 AGCACTGTTCGTAGTACGTCAG 60.096 50.000 29.39 29.39 43.14 3.51
475 486 4.387862 ACGAATTAAACCTAGCACTGTTCG 59.612 41.667 0.00 0.00 40.96 3.95
502 514 5.860182 CGTACATAGTACAAATATCCCACCG 59.140 44.000 7.93 0.00 0.00 4.94
636 648 4.806640 TGGTTTTAAGTAGTACCGGGAG 57.193 45.455 6.32 0.00 33.29 4.30
637 649 4.080975 CCATGGTTTTAAGTAGTACCGGGA 60.081 45.833 6.32 0.00 32.48 5.14
638 650 4.193865 CCATGGTTTTAAGTAGTACCGGG 58.806 47.826 6.32 0.00 33.29 5.73
688 700 3.820852 GCAGAGGAGATGGATGGGATAGA 60.821 52.174 0.00 0.00 0.00 1.98
823 836 4.732065 AGGAAACCCAAATAAAACCTCGA 58.268 39.130 0.00 0.00 0.00 4.04
824 837 5.462530 AAGGAAACCCAAATAAAACCTCG 57.537 39.130 0.00 0.00 0.00 4.63
853 866 4.379652 AGCAGCAATTAAACAACCCAAAG 58.620 39.130 0.00 0.00 0.00 2.77
864 878 3.316588 TCCGACACAAAAGCAGCAATTAA 59.683 39.130 0.00 0.00 0.00 1.40
865 879 2.881513 TCCGACACAAAAGCAGCAATTA 59.118 40.909 0.00 0.00 0.00 1.40
866 880 1.680735 TCCGACACAAAAGCAGCAATT 59.319 42.857 0.00 0.00 0.00 2.32
867 881 1.317613 TCCGACACAAAAGCAGCAAT 58.682 45.000 0.00 0.00 0.00 3.56
938 952 0.260230 TCAATCTCTCGAGGGCCTCT 59.740 55.000 29.81 8.49 0.00 3.69
1150 1165 3.634397 TCCTCTCATAAGCAGGGTTTG 57.366 47.619 0.00 0.00 0.00 2.93
1153 1168 2.769095 GAGTTCCTCTCATAAGCAGGGT 59.231 50.000 0.00 0.00 42.34 4.34
1198 1213 1.882625 GAGTACATGCCGCATGCGA 60.883 57.895 39.90 22.82 44.80 5.10
1437 1479 7.872483 GCAAAGGGAGAAGATAAAACAATTTGA 59.128 33.333 2.79 0.00 0.00 2.69
1494 1536 0.391661 CAGTGTACCGGCAGCATCTT 60.392 55.000 0.00 0.00 0.00 2.40
1533 1582 1.726352 AGGGGGTAGTTAGGGTGAGAA 59.274 52.381 0.00 0.00 0.00 2.87
1544 1593 2.913617 CAGGAAAGAAGAAGGGGGTAGT 59.086 50.000 0.00 0.00 0.00 2.73
1546 1595 2.999928 ACAGGAAAGAAGAAGGGGGTA 58.000 47.619 0.00 0.00 0.00 3.69
1579 1826 2.888212 TGGCTAAAACCTGCTTCCATT 58.112 42.857 0.00 0.00 0.00 3.16
1796 2062 1.202663 TGCACCCTTTTACAGCGTGTA 60.203 47.619 0.00 0.00 34.21 2.90
1845 2111 2.135189 AGACATAAGCAAGCCCCCATA 58.865 47.619 0.00 0.00 0.00 2.74
1979 2245 8.884124 AAAGAATAATGGAAGAAGAATCACCA 57.116 30.769 0.00 0.00 38.17 4.17
2101 2368 4.719773 AGGCACCAGATAGTATAACCAACA 59.280 41.667 0.00 0.00 0.00 3.33
2205 2472 4.350368 TCACATGTAGGTCAAAGCAAGA 57.650 40.909 0.00 0.00 0.00 3.02
2217 2484 7.267857 TCACTCATAGACCAAATCACATGTAG 58.732 38.462 0.00 0.00 0.00 2.74
2270 2539 7.987750 TCAGTTAACCAAGCACACATATTAA 57.012 32.000 0.88 0.00 0.00 1.40
2322 2591 5.129634 TCAACAACAAGCAAGATGGACTTA 58.870 37.500 0.00 0.00 37.03 2.24
2323 2592 3.953612 TCAACAACAAGCAAGATGGACTT 59.046 39.130 0.00 0.00 39.70 3.01
2414 2683 2.167693 ACGTGTCACTTCTTTCTCCACA 59.832 45.455 0.65 0.00 0.00 4.17
2424 2693 9.570488 AGATTAGATTTTACTACGTGTCACTTC 57.430 33.333 0.00 0.00 0.00 3.01
2443 2712 8.082672 TCAACCAGATCATTCAAGAGATTAGA 57.917 34.615 0.00 0.00 0.00 2.10
2516 2785 9.784531 AATGGGTCTATGCATATATATGTTAGC 57.215 33.333 21.10 16.25 36.11 3.09
2520 2789 9.632638 GGAAAATGGGTCTATGCATATATATGT 57.367 33.333 21.10 7.63 36.11 2.29
2521 2790 9.631257 TGGAAAATGGGTCTATGCATATATATG 57.369 33.333 17.01 17.01 36.78 1.78
2523 2792 9.685276 CTTGGAAAATGGGTCTATGCATATATA 57.315 33.333 6.92 0.00 0.00 0.86
2582 2851 3.443976 CCACCACAAACAAACTTAGCAC 58.556 45.455 0.00 0.00 0.00 4.40
2653 2923 8.055181 ACACAATGGATCCACAGAAATAACTAT 58.945 33.333 18.99 0.00 0.00 2.12


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

AutoCloner maintained by Alex Coulton.