Multiple sequence alignment - TraesCS6D01G292200

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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 TraesCS6D01G292200 chr6D 100.000 3365 0 0 1 3365 402878865 402882229 0.000000e+00 6215
1 TraesCS6D01G292200 chr6B 90.047 2984 151 56 14 2939 603770570 603773465 0.000000e+00 3731
2 TraesCS6D01G292200 chr6A 93.750 2352 100 26 252 2583 549321135 549323459 0.000000e+00 3485
3 TraesCS6D01G292200 chr6A 91.630 454 22 8 2630 3077 549323768 549324211 6.170000e-172 614
4 TraesCS6D01G292200 chr6A 97.115 312 9 0 3054 3365 549324216 549324527 8.270000e-146 527
5 TraesCS6D01G292200 chr1D 94.068 118 7 0 3248 3365 285439753 285439636 2.670000e-41 180
6 TraesCS6D01G292200 chr5D 93.333 120 8 0 3246 3365 33047507 33047388 9.590000e-41 178
7 TraesCS6D01G292200 chr5D 93.966 116 7 0 3246 3361 37048310 37048425 3.450000e-40 176
8 TraesCS6D01G292200 chr5A 93.333 120 7 1 3246 3365 22058161 22058043 3.450000e-40 176
9 TraesCS6D01G292200 chr3B 92.000 125 10 0 3241 3365 538815838 538815962 3.450000e-40 176
10 TraesCS6D01G292200 chr3A 92.500 120 9 0 3246 3365 179503204 179503085 4.460000e-39 172
11 TraesCS6D01G292200 chr1B 91.339 127 10 1 3240 3365 415552102 415551976 4.460000e-39 172
12 TraesCS6D01G292200 chr4B 91.200 125 9 2 3242 3365 71704410 71704533 5.770000e-38 169


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 TraesCS6D01G292200 chr6D 402878865 402882229 3364 False 6215 6215 100.000 1 3365 1 chr6D.!!$F1 3364
1 TraesCS6D01G292200 chr6B 603770570 603773465 2895 False 3731 3731 90.047 14 2939 1 chr6B.!!$F1 2925
2 TraesCS6D01G292200 chr6A 549321135 549324527 3392 False 1542 3485 94.165 252 3365 3 chr6A.!!$F1 3113

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
112 119 0.478072 CCCATGGTAGCCCTATTGCA 59.522 55.0 11.73 0.0 0.0 4.08 F
996 1060 0.527817 ATCGCCGCTTTCTTCTACCG 60.528 55.0 0.00 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1806 1883 1.497991 CGTATATGCCGGTGGTCTTG 58.502 55.0 1.90 0.0 0.00 3.02 R
2688 3031 0.744281 ACTCCACAAAGGGTTTTGCG 59.256 50.0 0.25 0.0 46.05 4.85 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
56 57 4.473520 CAACCCGGCTCGATGGCT 62.474 66.667 0.00 0.00 39.32 4.75
73 74 2.622942 TGGCTTGCTAAAACCTTGACAG 59.377 45.455 0.00 0.00 0.00 3.51
89 90 4.299586 TGACAGTTGGGCTATGATTTGA 57.700 40.909 0.00 0.00 0.00 2.69
92 93 5.716228 TGACAGTTGGGCTATGATTTGATTT 59.284 36.000 0.00 0.00 0.00 2.17
94 95 5.127682 ACAGTTGGGCTATGATTTGATTTCC 59.872 40.000 0.00 0.00 0.00 3.13
106 113 1.607225 TGATTTCCCATGGTAGCCCT 58.393 50.000 11.73 0.00 0.00 5.19
107 114 2.782922 TGATTTCCCATGGTAGCCCTA 58.217 47.619 11.73 0.00 0.00 3.53
108 115 3.335748 TGATTTCCCATGGTAGCCCTAT 58.664 45.455 11.73 0.00 0.00 2.57
109 116 3.726859 TGATTTCCCATGGTAGCCCTATT 59.273 43.478 11.73 0.00 0.00 1.73
110 117 3.593442 TTTCCCATGGTAGCCCTATTG 57.407 47.619 11.73 0.00 0.00 1.90
111 118 0.771127 TCCCATGGTAGCCCTATTGC 59.229 55.000 11.73 0.00 0.00 3.56
112 119 0.478072 CCCATGGTAGCCCTATTGCA 59.522 55.000 11.73 0.00 0.00 4.08
113 120 1.133513 CCCATGGTAGCCCTATTGCAA 60.134 52.381 11.73 0.00 0.00 4.08
114 121 2.665165 CCATGGTAGCCCTATTGCAAA 58.335 47.619 1.71 0.00 0.00 3.68
115 122 3.030291 CCATGGTAGCCCTATTGCAAAA 58.970 45.455 1.71 0.00 0.00 2.44
116 123 3.068590 CCATGGTAGCCCTATTGCAAAAG 59.931 47.826 1.71 0.00 0.00 2.27
117 124 3.449746 TGGTAGCCCTATTGCAAAAGT 57.550 42.857 1.71 0.00 0.00 2.66
118 125 3.773560 TGGTAGCCCTATTGCAAAAGTT 58.226 40.909 1.71 0.00 0.00 2.66
119 126 4.156477 TGGTAGCCCTATTGCAAAAGTTT 58.844 39.130 1.71 0.00 0.00 2.66
120 127 4.591072 TGGTAGCCCTATTGCAAAAGTTTT 59.409 37.500 1.71 0.00 0.00 2.43
121 128 5.071115 TGGTAGCCCTATTGCAAAAGTTTTT 59.929 36.000 1.71 0.00 0.00 1.94
261 272 7.739498 AATATAATACTACTTGTTTGGCCCG 57.261 36.000 0.00 0.00 0.00 6.13
268 280 4.531426 TGTTTGGCCCGGCTTGGT 62.531 61.111 9.86 0.00 35.15 3.67
275 287 1.890510 GCCCGGCTTGGTATTACCG 60.891 63.158 0.71 0.00 42.58 4.02
315 328 3.056179 CCGCCCAAAGAACCATGTTTATT 60.056 43.478 0.00 0.00 0.00 1.40
321 334 5.410067 CAAAGAACCATGTTTATTGGCGAT 58.590 37.500 0.00 0.00 37.81 4.58
370 407 8.885346 TCCACCATTTTTAAATAAAATCCCACT 58.115 29.630 0.00 0.00 35.36 4.00
371 408 8.945057 CCACCATTTTTAAATAAAATCCCACTG 58.055 33.333 0.00 0.00 35.36 3.66
399 437 5.638234 GTCGAAACACTAAAGTTAGCCTCAT 59.362 40.000 0.00 0.00 34.09 2.90
409 447 9.000486 ACTAAAGTTAGCCTCATGAACTTAAAC 58.000 33.333 9.55 6.57 41.39 2.01
463 505 9.575868 TTTAATTCAGGTAGTTTGTTCACCATA 57.424 29.630 0.00 0.00 34.62 2.74
531 574 1.819208 CCAAGATGCCGATTCGCCA 60.819 57.895 0.00 0.00 0.00 5.69
553 596 5.382303 CAGTTCAATTTACATGTGGACGAC 58.618 41.667 9.11 0.00 0.00 4.34
571 614 3.004315 ACGACGAAACATTTCAAATGCCT 59.996 39.130 10.21 0.00 37.01 4.75
579 622 5.549742 ACATTTCAAATGCCTTCTTCCAA 57.450 34.783 10.21 0.00 0.00 3.53
580 623 5.927819 ACATTTCAAATGCCTTCTTCCAAA 58.072 33.333 10.21 0.00 0.00 3.28
581 624 6.355747 ACATTTCAAATGCCTTCTTCCAAAA 58.644 32.000 10.21 0.00 0.00 2.44
582 625 6.260714 ACATTTCAAATGCCTTCTTCCAAAAC 59.739 34.615 10.21 0.00 0.00 2.43
583 626 5.350504 TTCAAATGCCTTCTTCCAAAACA 57.649 34.783 0.00 0.00 0.00 2.83
584 627 5.350504 TCAAATGCCTTCTTCCAAAACAA 57.649 34.783 0.00 0.00 0.00 2.83
585 628 5.738909 TCAAATGCCTTCTTCCAAAACAAA 58.261 33.333 0.00 0.00 0.00 2.83
586 629 6.176183 TCAAATGCCTTCTTCCAAAACAAAA 58.824 32.000 0.00 0.00 0.00 2.44
587 630 6.093357 TCAAATGCCTTCTTCCAAAACAAAAC 59.907 34.615 0.00 0.00 0.00 2.43
588 631 4.543590 TGCCTTCTTCCAAAACAAAACA 57.456 36.364 0.00 0.00 0.00 2.83
759 807 2.997315 CAGTCAGTCTCCGCCCCA 60.997 66.667 0.00 0.00 0.00 4.96
760 808 2.997897 AGTCAGTCTCCGCCCCAC 60.998 66.667 0.00 0.00 0.00 4.61
761 809 4.083862 GTCAGTCTCCGCCCCACC 62.084 72.222 0.00 0.00 0.00 4.61
912 976 2.223876 CCCATCCAAAAGGCAATCATCG 60.224 50.000 0.00 0.00 0.00 3.84
913 977 2.223876 CCATCCAAAAGGCAATCATCGG 60.224 50.000 0.00 0.00 0.00 4.18
914 978 2.214376 TCCAAAAGGCAATCATCGGT 57.786 45.000 0.00 0.00 0.00 4.69
915 979 2.091541 TCCAAAAGGCAATCATCGGTC 58.908 47.619 0.00 0.00 0.00 4.79
995 1059 1.209998 GATCGCCGCTTTCTTCTACC 58.790 55.000 0.00 0.00 0.00 3.18
996 1060 0.527817 ATCGCCGCTTTCTTCTACCG 60.528 55.000 0.00 0.00 0.00 4.02
997 1061 1.445582 CGCCGCTTTCTTCTACCGT 60.446 57.895 0.00 0.00 0.00 4.83
999 1063 1.411493 GCCGCTTTCTTCTACCGTCG 61.411 60.000 0.00 0.00 0.00 5.12
1083 1157 2.353607 GAGATACCGCTCGCCGTG 60.354 66.667 0.00 0.00 34.38 4.94
1431 1508 2.415608 CGAGCTTCTGGAGGCGGTA 61.416 63.158 0.00 0.00 38.56 4.02
1727 1804 2.870035 ATCCTCTCCCACAGCGAGCT 62.870 60.000 0.00 0.00 0.00 4.09
2121 2198 2.048222 CACGTGTCCGACATGGCT 60.048 61.111 21.96 2.32 39.36 4.75
2438 2516 9.041354 AGACACAATTAGGTTTAGATTCTCTCT 57.959 33.333 0.00 0.00 38.06 3.10
2439 2517 9.308318 GACACAATTAGGTTTAGATTCTCTCTC 57.692 37.037 0.00 0.00 35.28 3.20
2520 2598 5.813080 ATACGGTTCCACTCAAAATTAGC 57.187 39.130 0.00 0.00 0.00 3.09
2522 2600 2.817258 CGGTTCCACTCAAAATTAGCCA 59.183 45.455 0.00 0.00 0.00 4.75
2523 2601 3.254657 CGGTTCCACTCAAAATTAGCCAA 59.745 43.478 0.00 0.00 0.00 4.52
2596 2674 2.878406 TGCAACAGGTAGAAACTTGAGC 59.122 45.455 0.00 0.09 36.27 4.26
2600 2678 3.744660 ACAGGTAGAAACTTGAGCTTGG 58.255 45.455 0.00 0.00 36.27 3.61
2688 3031 9.157259 CAAACTGTGCAATAAAATACAAAAAGC 57.843 29.630 0.00 0.00 0.00 3.51
2706 3049 3.568093 CGCAAAACCCTTTGTGGAG 57.432 52.632 3.74 0.00 45.37 3.86
2980 3333 5.189539 AGCCAAACCAAATTACAGGCATATT 59.810 36.000 0.00 0.00 42.90 1.28
3025 3379 7.123697 GGGTAAAAATTTAGGCTCACCACTAAT 59.876 37.037 0.00 0.00 39.06 1.73
3031 3385 6.553953 TTTAGGCTCACCACTAATCATACA 57.446 37.500 0.00 0.00 39.06 2.29
3040 3394 6.384015 TCACCACTAATCATACACTTGAGGAT 59.616 38.462 0.00 0.00 0.00 3.24
3191 3573 2.811431 GTTGTTGAACGATGGATGGACA 59.189 45.455 0.00 0.00 0.00 4.02
3199 3581 3.104512 ACGATGGATGGACAAGGAGTTA 58.895 45.455 0.00 0.00 0.00 2.24
3251 3633 4.142609 TCTTGGAGCAATGGATGTACTC 57.857 45.455 0.00 0.00 0.00 2.59
3272 3654 2.277084 CCTCCGGTCATTTTTACTCCG 58.723 52.381 0.00 0.00 40.72 4.63
3293 3675 5.350365 TCCGTGTATTAGATTTGTGTCAAGC 59.650 40.000 0.00 0.00 0.00 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.255642 GCCTAGAATGGTTGCTCAAAACA 59.744 43.478 0.00 0.00 40.59 2.83
1 2 3.507622 AGCCTAGAATGGTTGCTCAAAAC 59.492 43.478 0.00 0.00 0.00 2.43
2 3 3.766545 AGCCTAGAATGGTTGCTCAAAA 58.233 40.909 0.00 0.00 0.00 2.44
3 4 3.439857 AGCCTAGAATGGTTGCTCAAA 57.560 42.857 0.00 0.00 0.00 2.69
4 5 3.263170 TGTAGCCTAGAATGGTTGCTCAA 59.737 43.478 0.00 0.00 33.63 3.02
5 6 2.837591 TGTAGCCTAGAATGGTTGCTCA 59.162 45.455 0.00 0.00 33.63 4.26
6 7 3.198872 GTGTAGCCTAGAATGGTTGCTC 58.801 50.000 0.00 0.00 33.63 4.26
7 8 2.092914 GGTGTAGCCTAGAATGGTTGCT 60.093 50.000 0.00 0.00 36.11 3.91
8 9 2.289565 GGTGTAGCCTAGAATGGTTGC 58.710 52.381 0.00 0.00 0.00 4.17
44 45 1.089481 TTTAGCAAGCCATCGAGCCG 61.089 55.000 0.00 0.00 0.00 5.52
46 47 1.202188 GGTTTTAGCAAGCCATCGAGC 60.202 52.381 0.00 0.00 33.44 5.03
55 56 4.499696 CCCAACTGTCAAGGTTTTAGCAAG 60.500 45.833 0.00 0.00 0.00 4.01
56 57 3.383185 CCCAACTGTCAAGGTTTTAGCAA 59.617 43.478 0.00 0.00 0.00 3.91
73 74 4.405358 TGGGAAATCAAATCATAGCCCAAC 59.595 41.667 0.00 0.00 41.10 3.77
89 90 3.755155 GCAATAGGGCTACCATGGGAAAT 60.755 47.826 18.09 0.00 40.13 2.17
92 93 0.771127 GCAATAGGGCTACCATGGGA 59.229 55.000 18.09 6.59 40.13 4.37
94 95 2.363306 TTGCAATAGGGCTACCATGG 57.637 50.000 11.19 11.19 40.13 3.66
120 127 7.420184 GCTTTTGCAATAAGGAGCTTAAAAA 57.580 32.000 17.37 0.00 46.58 1.94
248 259 2.123468 AAGCCGGGCCAAACAAGT 60.123 55.556 17.02 0.00 0.00 3.16
249 260 2.339712 CAAGCCGGGCCAAACAAG 59.660 61.111 17.02 0.00 0.00 3.16
250 261 2.642183 TACCAAGCCGGGCCAAACAA 62.642 55.000 17.02 0.00 40.22 2.83
261 272 2.400911 GGCACGGTAATACCAAGCC 58.599 57.895 21.23 21.23 46.11 4.35
268 280 2.863132 ACAAACCTGGCACGGTAATA 57.137 45.000 8.70 0.00 34.48 0.98
275 287 2.924880 GCGGATTTTACAAACCTGGCAC 60.925 50.000 0.00 0.00 0.00 5.01
347 383 7.609918 GGCAGTGGGATTTTATTTAAAAATGGT 59.390 33.333 0.71 0.00 38.50 3.55
370 407 1.202557 ACTTTAGTGTTTCGACGGGCA 60.203 47.619 0.00 0.00 0.00 5.36
371 408 1.505425 ACTTTAGTGTTTCGACGGGC 58.495 50.000 0.00 0.00 0.00 6.13
463 505 6.461110 CATGGCTTGGATTGAGAAAACTAT 57.539 37.500 0.00 0.00 0.00 2.12
531 574 4.151689 CGTCGTCCACATGTAAATTGAACT 59.848 41.667 0.00 0.00 0.00 3.01
553 596 5.119125 GGAAGAAGGCATTTGAAATGTTTCG 59.881 40.000 18.12 0.00 40.01 3.46
571 614 9.855021 TTTTTGTTTTGTTTTGTTTTGGAAGAA 57.145 22.222 0.00 0.00 0.00 2.52
580 623 9.923786 GTGTTCTAGTTTTTGTTTTGTTTTGTT 57.076 25.926 0.00 0.00 0.00 2.83
581 624 9.099454 TGTGTTCTAGTTTTTGTTTTGTTTTGT 57.901 25.926 0.00 0.00 0.00 2.83
582 625 9.922305 TTGTGTTCTAGTTTTTGTTTTGTTTTG 57.078 25.926 0.00 0.00 0.00 2.44
584 627 9.923786 GTTTGTGTTCTAGTTTTTGTTTTGTTT 57.076 25.926 0.00 0.00 0.00 2.83
585 628 8.270111 CGTTTGTGTTCTAGTTTTTGTTTTGTT 58.730 29.630 0.00 0.00 0.00 2.83
586 629 7.648510 TCGTTTGTGTTCTAGTTTTTGTTTTGT 59.351 29.630 0.00 0.00 0.00 2.83
587 630 7.998141 TCGTTTGTGTTCTAGTTTTTGTTTTG 58.002 30.769 0.00 0.00 0.00 2.44
588 631 7.327518 CCTCGTTTGTGTTCTAGTTTTTGTTTT 59.672 33.333 0.00 0.00 0.00 2.43
996 1060 4.796231 AGCGGCGTGACCATCGAC 62.796 66.667 9.37 0.00 39.03 4.20
997 1061 4.794439 CAGCGGCGTGACCATCGA 62.794 66.667 9.37 0.00 39.03 3.59
1687 1764 3.554692 CACGACGGATTCCAGCGC 61.555 66.667 0.00 0.00 0.00 5.92
1806 1883 1.497991 CGTATATGCCGGTGGTCTTG 58.502 55.000 1.90 0.00 0.00 3.02
1960 2037 2.125753 CACCAGCAGCTCGAGGAC 60.126 66.667 15.58 0.00 0.00 3.85
2438 2516 5.712917 GGTAGTTCTTCCAAAGAGAGAGAGA 59.287 44.000 0.00 0.00 39.03 3.10
2439 2517 5.392595 CGGTAGTTCTTCCAAAGAGAGAGAG 60.393 48.000 0.00 0.00 39.03 3.20
2558 2636 6.288941 TGTTGCATGGATGATTCTTTTCAT 57.711 33.333 0.00 0.00 39.04 2.57
2559 2637 5.336929 CCTGTTGCATGGATGATTCTTTTCA 60.337 40.000 0.00 0.00 0.00 2.69
2627 2708 3.373439 TGTGCTTTTGTTTTGCCAACATC 59.627 39.130 0.00 0.00 0.00 3.06
2688 3031 0.744281 ACTCCACAAAGGGTTTTGCG 59.256 50.000 0.25 0.00 46.05 4.85
2908 3261 7.923878 GCAAGGAGGTTGTATTTTCAGTAAAAA 59.076 33.333 0.00 0.00 38.56 1.94
2910 3263 6.775629 AGCAAGGAGGTTGTATTTTCAGTAAA 59.224 34.615 0.00 0.00 38.55 2.01
2911 3264 6.303839 AGCAAGGAGGTTGTATTTTCAGTAA 58.696 36.000 0.00 0.00 38.55 2.24
2980 3333 7.640577 TTACCCCATTTACATCCATGATCTA 57.359 36.000 0.00 0.00 0.00 1.98
3046 3400 2.576615 AGGAGAACTTTGTTGGCACTC 58.423 47.619 0.00 0.00 0.00 3.51
3047 3401 2.736670 AGGAGAACTTTGTTGGCACT 57.263 45.000 0.00 0.00 0.00 4.40
3049 3403 2.091885 AGGAAGGAGAACTTTGTTGGCA 60.092 45.455 0.00 0.00 40.21 4.92
3050 3404 2.294512 CAGGAAGGAGAACTTTGTTGGC 59.705 50.000 0.00 0.00 40.21 4.52
3051 3405 3.555966 ACAGGAAGGAGAACTTTGTTGG 58.444 45.455 0.00 0.00 40.21 3.77
3053 3407 5.104318 AGAGAACAGGAAGGAGAACTTTGTT 60.104 40.000 0.00 0.00 40.84 2.83
3055 3409 4.967036 AGAGAACAGGAAGGAGAACTTTG 58.033 43.478 0.00 0.00 40.21 2.77
3191 3573 0.963962 TCACCGTCGCTTAACTCCTT 59.036 50.000 0.00 0.00 0.00 3.36
3199 3581 2.049433 CCTTCGTCACCGTCGCTT 60.049 61.111 0.00 0.00 35.01 4.68
3272 3654 6.494893 TGGCTTGACACAAATCTAATACAC 57.505 37.500 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.