Multiple sequence alignment - TraesCS6D01G193400

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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 TraesCS6D01G193400 chr6D 100.000 4698 0 0 1 4698 267528400 267523703 0.000000e+00 8676
1 TraesCS6D01G193400 chr6A 94.532 3438 105 30 609 4001 381083442 381080043 0.000000e+00 5230
2 TraesCS6D01G193400 chr6A 91.270 630 31 7 5 610 381084151 381083522 0.000000e+00 837
3 TraesCS6D01G193400 chr6A 81.062 697 120 6 4009 4695 206910259 206910953 3.200000e-151 545
4 TraesCS6D01G193400 chr6A 96.815 157 4 1 3846 4001 381035779 381035623 1.300000e-65 261
5 TraesCS6D01G193400 chr6B 90.069 3635 206 67 1 3554 415874039 415870479 0.000000e+00 4569
6 TraesCS6D01G193400 chr6B 82.982 711 105 12 4001 4698 602556928 602556221 3.090000e-176 628
7 TraesCS6D01G193400 chr6B 88.272 324 22 5 3550 3873 415870447 415870140 1.600000e-99 374
8 TraesCS6D01G193400 chr6B 93.506 154 6 3 3859 4008 415870120 415869967 4.730000e-55 226
9 TraesCS6D01G193400 chr2D 93.247 696 39 2 4010 4698 571173489 571174183 0.000000e+00 1018
10 TraesCS6D01G193400 chr2D 88.023 693 75 2 4010 4695 323106912 323106221 0.000000e+00 813
11 TraesCS6D01G193400 chr3D 92.857 700 28 9 4010 4698 1492530 1493218 0.000000e+00 996
12 TraesCS6D01G193400 chr2A 92.249 658 41 3 4048 4698 55932082 55931428 0.000000e+00 924
13 TraesCS6D01G193400 chr7A 89.899 594 49 8 3424 4009 7136824 7136234 0.000000e+00 754
14 TraesCS6D01G193400 chr5B 86.291 693 85 4 4012 4696 355895942 355896632 0.000000e+00 745
15 TraesCS6D01G193400 chr2B 84.801 704 99 5 3999 4695 454444092 454444794 0.000000e+00 701
16 TraesCS6D01G193400 chr2B 84.870 694 97 5 4009 4695 454468445 454469137 0.000000e+00 693
17 TraesCS6D01G193400 chr2B 82.640 697 109 10 4012 4698 554592944 554592250 1.450000e-169 606
18 TraesCS6D01G193400 chr2B 96.923 65 1 1 4008 4071 520210338 520210274 1.790000e-19 108
19 TraesCS6D01G193400 chr7B 84.072 609 69 8 4095 4696 678906925 678906338 3.170000e-156 562
20 TraesCS6D01G193400 chr1D 84.286 490 49 14 3 473 30103552 30104032 1.990000e-123 453
21 TraesCS6D01G193400 chr1A 84.310 478 57 11 11 473 30193009 30193483 7.170000e-123 451
22 TraesCS6D01G193400 chr1B 83.673 490 52 14 3 473 48279483 48279963 2.010000e-118 436
23 TraesCS6D01G193400 chr3B 89.766 342 22 5 4011 4352 682916787 682916459 4.350000e-115 425
24 TraesCS6D01G193400 chr3B 95.522 67 2 1 4007 4072 128675173 128675107 6.430000e-19 106


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 TraesCS6D01G193400 chr6D 267523703 267528400 4697 True 8676.0 8676 100.000000 1 4698 1 chr6D.!!$R1 4697
1 TraesCS6D01G193400 chr6A 381080043 381084151 4108 True 3033.5 5230 92.901000 5 4001 2 chr6A.!!$R2 3996
2 TraesCS6D01G193400 chr6A 206910259 206910953 694 False 545.0 545 81.062000 4009 4695 1 chr6A.!!$F1 686
3 TraesCS6D01G193400 chr6B 415869967 415874039 4072 True 1723.0 4569 90.615667 1 4008 3 chr6B.!!$R2 4007
4 TraesCS6D01G193400 chr6B 602556221 602556928 707 True 628.0 628 82.982000 4001 4698 1 chr6B.!!$R1 697
5 TraesCS6D01G193400 chr2D 571173489 571174183 694 False 1018.0 1018 93.247000 4010 4698 1 chr2D.!!$F1 688
6 TraesCS6D01G193400 chr2D 323106221 323106912 691 True 813.0 813 88.023000 4010 4695 1 chr2D.!!$R1 685
7 TraesCS6D01G193400 chr3D 1492530 1493218 688 False 996.0 996 92.857000 4010 4698 1 chr3D.!!$F1 688
8 TraesCS6D01G193400 chr2A 55931428 55932082 654 True 924.0 924 92.249000 4048 4698 1 chr2A.!!$R1 650
9 TraesCS6D01G193400 chr7A 7136234 7136824 590 True 754.0 754 89.899000 3424 4009 1 chr7A.!!$R1 585
10 TraesCS6D01G193400 chr5B 355895942 355896632 690 False 745.0 745 86.291000 4012 4696 1 chr5B.!!$F1 684
11 TraesCS6D01G193400 chr2B 454444092 454444794 702 False 701.0 701 84.801000 3999 4695 1 chr2B.!!$F1 696
12 TraesCS6D01G193400 chr2B 454468445 454469137 692 False 693.0 693 84.870000 4009 4695 1 chr2B.!!$F2 686
13 TraesCS6D01G193400 chr2B 554592250 554592944 694 True 606.0 606 82.640000 4012 4698 1 chr2B.!!$R2 686
14 TraesCS6D01G193400 chr7B 678906338 678906925 587 True 562.0 562 84.072000 4095 4696 1 chr7B.!!$R1 601

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
841 975 1.754234 GCACGCCCTTTCCATCCAT 60.754 57.895 0.00 0.0 0.00 3.41 F
1124 1258 1.359459 CTCCCTTCAAAGGTACGCGC 61.359 60.000 5.73 0.0 44.98 6.86 F
2523 2681 0.032540 CTTGCTGGCCTTTGTGGAAC 59.967 55.000 3.32 0.0 38.35 3.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1712 1866 0.546507 TCACCCAGGCCTGTGATACA 60.547 55.0 30.63 7.11 36.62 2.29 R
2625 2784 0.808453 TAAGAAGTGGTATGCGCCGC 60.808 55.0 4.18 0.00 39.22 6.53 R
4164 4441 0.317479 AGCTCACGGAGTTACCACAC 59.683 55.0 3.38 0.00 41.61 3.82 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
78 79 3.106738 GCATCCACATGGCTTAGCT 57.893 52.632 3.59 0.00 34.44 3.32
117 118 5.105997 GCTTGCAATGTTCCTCAATACTCTT 60.106 40.000 0.00 0.00 0.00 2.85
123 124 3.582647 TGTTCCTCAATACTCTTCCAGCA 59.417 43.478 0.00 0.00 0.00 4.41
168 169 4.908601 TCATGCTTTCCTCAAGGTAGAA 57.091 40.909 0.00 0.00 36.34 2.10
177 178 3.199946 TCCTCAAGGTAGAAATCCGCATT 59.800 43.478 0.00 0.00 36.34 3.56
178 179 3.313526 CCTCAAGGTAGAAATCCGCATTG 59.686 47.826 0.00 0.00 0.00 2.82
215 232 5.360999 TGACTATCTGTGTATGCAGCTAACT 59.639 40.000 0.00 0.00 36.49 2.24
228 245 3.679917 GCAGCTAACTAGGATTGTGCTCA 60.680 47.826 0.00 0.00 0.00 4.26
345 362 3.214328 AGCACAAGGTTCGAAAGTTCAT 58.786 40.909 0.00 0.00 0.00 2.57
558 582 2.933492 GCTGCGTGGGTGTAACTTATGA 60.933 50.000 0.00 0.00 36.74 2.15
648 754 3.254629 CACTTGGTGGAGGTCATGG 57.745 57.895 0.00 0.00 0.00 3.66
682 788 7.608761 TGTATGTACTGTGTGTCTGTACTATGA 59.391 37.037 13.17 0.00 45.42 2.15
699 805 2.435372 TGAGGTGCAAACCTTCTGTT 57.565 45.000 0.00 0.00 40.86 3.16
778 912 4.027572 TGTAGCACAAAACACTTGCTTC 57.972 40.909 0.00 0.00 44.26 3.86
783 917 3.549070 GCACAAAACACTTGCTTCTGAAG 59.451 43.478 13.02 13.02 33.26 3.02
838 972 1.926511 CTGTGCACGCCCTTTCCATC 61.927 60.000 13.13 0.00 0.00 3.51
839 973 2.361104 TGCACGCCCTTTCCATCC 60.361 61.111 0.00 0.00 0.00 3.51
840 974 2.361104 GCACGCCCTTTCCATCCA 60.361 61.111 0.00 0.00 0.00 3.41
841 975 1.754234 GCACGCCCTTTCCATCCAT 60.754 57.895 0.00 0.00 0.00 3.41
862 996 2.025605 TGCATCTCTTTCAGGCCTCAAT 60.026 45.455 0.00 0.00 0.00 2.57
888 1022 2.995574 AGTTCTCCGGTCCCCACG 60.996 66.667 0.00 0.00 0.00 4.94
952 1086 5.334421 AGTACGAGATGGGGATAAAGCTAT 58.666 41.667 0.00 0.00 0.00 2.97
953 1087 4.810191 ACGAGATGGGGATAAAGCTATC 57.190 45.455 0.00 0.00 34.25 2.08
954 1088 4.421131 ACGAGATGGGGATAAAGCTATCT 58.579 43.478 0.00 0.00 35.23 1.98
955 1089 5.580998 ACGAGATGGGGATAAAGCTATCTA 58.419 41.667 0.00 0.00 35.23 1.98
980 1114 4.079970 GCTAAAAGCCTAAAACCTCCTGT 58.920 43.478 0.00 0.00 34.48 4.00
1124 1258 1.359459 CTCCCTTCAAAGGTACGCGC 61.359 60.000 5.73 0.00 44.98 6.86
1458 1602 5.619981 GCTTTGTAGTTTGAATTCGGCATCT 60.620 40.000 0.04 0.00 0.00 2.90
1459 1603 4.944962 TGTAGTTTGAATTCGGCATCTG 57.055 40.909 0.04 0.00 0.00 2.90
1460 1604 2.927553 AGTTTGAATTCGGCATCTGC 57.072 45.000 0.04 0.00 41.14 4.26
1511 1659 4.157656 TGAACTGCTGTTATTTGTATGGCC 59.842 41.667 9.14 0.00 36.39 5.36
1654 1802 2.158579 TCAAAAGGTTGGTGGTAGGACC 60.159 50.000 0.00 0.00 35.54 4.46
1712 1866 3.960102 TCACATTTTCCTGTCCTTTGCTT 59.040 39.130 0.00 0.00 0.00 3.91
1718 1872 4.365514 TTCCTGTCCTTTGCTTGTATCA 57.634 40.909 0.00 0.00 0.00 2.15
1924 2078 8.835467 TGTTCGCACTATTTCATTATAAAAGC 57.165 30.769 0.00 0.00 0.00 3.51
2516 2674 1.413812 CTTTTCACCTTGCTGGCCTTT 59.586 47.619 3.32 0.00 40.22 3.11
2523 2681 0.032540 CTTGCTGGCCTTTGTGGAAC 59.967 55.000 3.32 0.00 38.35 3.62
2552 2710 9.504708 AAATCATCTCATCATCCTATGTTCTTC 57.495 33.333 0.00 0.00 0.00 2.87
2625 2784 1.272490 TCTCTACCGTTTGCTGGACAG 59.728 52.381 0.00 0.00 0.00 3.51
2695 2855 7.543947 TCATACACACAAGATGCTATTTCAG 57.456 36.000 0.00 0.00 0.00 3.02
2769 2950 4.514441 CACTCTTTCAGTCATTGCACTCTT 59.486 41.667 0.00 0.00 30.26 2.85
2789 2970 7.538678 CACTCTTGTAATTTAAGGTTGCATGTC 59.461 37.037 0.00 0.00 0.00 3.06
2835 3017 7.824704 CTACATCTTGTAGCATCCATCATAC 57.175 40.000 2.01 0.00 43.11 2.39
2922 3104 2.104267 CAGATCAATTGCTGCCGCT 58.896 52.632 0.00 0.00 36.97 5.52
3258 3449 7.800092 AGATTTTCCTGTGAGATACAAGCTAT 58.200 34.615 0.00 0.00 39.20 2.97
3273 3464 1.285962 AGCTATGACCTTGCCACCAAT 59.714 47.619 0.00 0.00 0.00 3.16
3377 3568 7.148540 CCAAATATGTTTCAGCATTCCACAAAG 60.149 37.037 0.00 0.00 0.00 2.77
3412 3603 8.896744 CATTGTTAGTGAAATGACATCCACTAT 58.103 33.333 21.44 11.62 40.48 2.12
3723 3957 1.224965 GATTCCGAGGAAGATGCTGC 58.775 55.000 10.56 0.00 37.56 5.25
3766 4000 2.628106 CATTTCGGCCGCTCATCG 59.372 61.111 23.51 2.10 38.08 3.84
3767 4001 1.882625 CATTTCGGCCGCTCATCGA 60.883 57.895 23.51 0.00 41.67 3.59
3979 4249 7.759433 TCCTGTTGAAAATTCTGTTGAGAAAAC 59.241 33.333 0.00 0.00 41.64 2.43
4120 4394 1.266175 CACAAGTAGTCACGACTCGGT 59.734 52.381 2.26 0.00 42.54 4.69
4146 4420 4.828939 TCGAAACTCCACTCCTACAACTAA 59.171 41.667 0.00 0.00 0.00 2.24
4209 4486 2.224606 CGATGCCCAAGTATGCAGATT 58.775 47.619 0.00 0.00 41.46 2.40
4327 4608 1.144969 GCATGACAACCGAGTCGAAA 58.855 50.000 15.64 0.00 41.41 3.46
4355 4637 0.700564 AGCCTCTTTTGGGATCTGCA 59.299 50.000 0.00 0.00 0.00 4.41
4386 4675 2.414559 GCAACCACCAATCTTGTCATCG 60.415 50.000 0.00 0.00 0.00 3.84
4501 4790 1.390565 CGTATCCTCCTCTTGGTCGT 58.609 55.000 0.00 0.00 34.23 4.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
78 79 1.961435 GCAAGCCATTTCCATCCCTCA 60.961 52.381 0.00 0.00 0.00 3.86
117 118 2.233566 AGTGGCTGGGATTGCTGGA 61.234 57.895 0.00 0.00 0.00 3.86
144 145 2.800250 ACCTTGAGGAAAGCATGAAGG 58.200 47.619 3.59 0.00 38.94 3.46
177 178 4.275689 CAGATAGTCAAACACAAAGCACCA 59.724 41.667 0.00 0.00 0.00 4.17
178 179 4.275936 ACAGATAGTCAAACACAAAGCACC 59.724 41.667 0.00 0.00 0.00 5.01
183 192 6.484977 TGCATACACAGATAGTCAAACACAAA 59.515 34.615 0.00 0.00 0.00 2.83
190 199 4.743057 AGCTGCATACACAGATAGTCAA 57.257 40.909 1.02 0.00 40.25 3.18
215 232 5.192927 CCACCTAAAATGAGCACAATCCTA 58.807 41.667 0.00 0.00 0.00 2.94
228 245 2.288763 CGCAAAACCAGCCACCTAAAAT 60.289 45.455 0.00 0.00 0.00 1.82
345 362 7.241628 TCTGTAGATTATTGATAGCCTCTGGA 58.758 38.462 0.00 0.00 0.00 3.86
558 582 6.231211 TCTTCAAGACGATTTTAGGCTTCTT 58.769 36.000 0.00 0.00 34.11 2.52
648 754 6.426937 AGACACACAGTACATACAACAAATCC 59.573 38.462 0.00 0.00 0.00 3.01
699 805 6.900189 TCAAAACAACGTTGAGTTCAAACTA 58.100 32.000 33.66 6.30 42.02 2.24
708 814 5.640218 ATTGCATTCAAAACAACGTTGAG 57.360 34.783 33.66 19.04 36.41 3.02
778 912 3.926527 TGCTGCGACTAACAATACTTCAG 59.073 43.478 0.00 0.00 0.00 3.02
783 917 2.343101 TGGTGCTGCGACTAACAATAC 58.657 47.619 0.00 0.00 0.00 1.89
838 972 1.030457 GGCCTGAAAGAGATGCATGG 58.970 55.000 2.46 0.00 34.07 3.66
839 973 1.948145 GAGGCCTGAAAGAGATGCATG 59.052 52.381 12.00 0.00 34.07 4.06
840 974 1.562942 TGAGGCCTGAAAGAGATGCAT 59.437 47.619 12.00 0.00 34.07 3.96
841 975 0.986527 TGAGGCCTGAAAGAGATGCA 59.013 50.000 12.00 0.00 34.07 3.96
862 996 2.376109 GACCGGAGAACTGGACTGATA 58.624 52.381 9.46 0.00 44.87 2.15
980 1114 4.763793 CCATTTTCTTGCTTTCCTCTCAGA 59.236 41.667 0.00 0.00 0.00 3.27
1124 1258 2.618709 AGGAAAACGCAGGAGACAAAAG 59.381 45.455 0.00 0.00 0.00 2.27
1441 1585 1.131126 CGCAGATGCCGAATTCAAACT 59.869 47.619 6.22 0.00 37.91 2.66
1459 1603 3.744942 AGAGATTCATACATGCATCACGC 59.255 43.478 0.00 0.00 42.89 5.34
1460 1604 7.412137 TTTAGAGATTCATACATGCATCACG 57.588 36.000 0.00 0.00 33.70 4.35
1511 1659 1.129998 CTTCAAGCAGAGCATTCCACG 59.870 52.381 0.00 0.00 0.00 4.94
1712 1866 0.546507 TCACCCAGGCCTGTGATACA 60.547 55.000 30.63 7.11 36.62 2.29
1718 1872 1.655114 AACCTTTCACCCAGGCCTGT 61.655 55.000 30.63 11.35 34.32 4.00
1924 2078 4.422073 TGTTATGGTCCTTCTATGGCAG 57.578 45.455 0.00 0.00 0.00 4.85
1989 2143 5.122869 ACTGTGTTTGATGCACTATTAGCTG 59.877 40.000 0.00 0.00 37.70 4.24
2073 2227 9.042008 AGTTGACATATTACAAACGATGGTATC 57.958 33.333 0.00 0.00 0.00 2.24
2437 2593 3.606595 TCCAGCATCAGAAAGTCAGAG 57.393 47.619 0.00 0.00 0.00 3.35
2516 2674 7.500227 GGATGATGAGATGATTTAAGTTCCACA 59.500 37.037 0.00 0.00 0.00 4.17
2625 2784 0.808453 TAAGAAGTGGTATGCGCCGC 60.808 55.000 4.18 0.00 39.22 6.53
2695 2855 7.573968 ATCATTTGTCCAAGATTTAGGTAGC 57.426 36.000 0.00 0.00 0.00 3.58
2769 2950 4.464597 GGGGACATGCAACCTTAAATTACA 59.535 41.667 0.00 0.00 0.00 2.41
2825 3007 6.039605 TGAATCGCAAATGTTGTATGATGGAT 59.960 34.615 0.00 0.00 0.00 3.41
2835 3017 2.656422 GGACGTTGAATCGCAAATGTTG 59.344 45.455 0.00 0.00 38.44 3.33
2922 3104 2.030007 GCCAGCATTGTAAAGTTGCTCA 60.030 45.455 0.00 0.00 39.96 4.26
3057 3240 4.372656 CGCTCAAAGTCCTATAAAGAGGG 58.627 47.826 0.00 0.00 37.20 4.30
3058 3241 4.372656 CCGCTCAAAGTCCTATAAAGAGG 58.627 47.826 0.00 0.00 38.03 3.69
3258 3449 2.642311 TCTTAGATTGGTGGCAAGGTCA 59.358 45.455 0.00 0.00 0.00 4.02
3273 3464 5.843673 AATCTGATCGCTCAAGTCTTAGA 57.156 39.130 0.00 0.00 0.00 2.10
3377 3568 4.439305 TTCACTAACAATGCTGAATGCC 57.561 40.909 0.00 0.00 42.00 4.40
3412 3603 9.436957 GTCAGAAAAGATTCAGGATTAGTAACA 57.563 33.333 0.00 0.00 38.06 2.41
3434 3625 2.033801 CCAGCTGAAACCAAGTTGTCAG 59.966 50.000 17.39 14.59 35.69 3.51
3757 3991 0.586319 GTCTCTCTCTCGATGAGCGG 59.414 60.000 9.81 6.45 42.38 5.52
3760 3994 2.340210 TGGGTCTCTCTCTCGATGAG 57.660 55.000 8.70 8.70 43.96 2.90
3766 4000 4.061596 CAGTTGTTTTGGGTCTCTCTCTC 58.938 47.826 0.00 0.00 0.00 3.20
3767 4001 3.745797 GCAGTTGTTTTGGGTCTCTCTCT 60.746 47.826 0.00 0.00 0.00 3.10
3979 4249 8.498054 ACACATGTGATATTTTGAGACTAAGG 57.502 34.615 31.94 0.00 0.00 2.69
4120 4394 2.224942 TGTAGGAGTGGAGTTTCGAGGA 60.225 50.000 0.00 0.00 0.00 3.71
4146 4420 7.778185 ACCACACTTTATGAGTAGTAGAGTT 57.222 36.000 0.00 0.00 36.65 3.01
4164 4441 0.317479 AGCTCACGGAGTTACCACAC 59.683 55.000 3.38 0.00 41.61 3.82
4327 4608 1.545651 CCAAAAGAGGCTCGGAAAGGT 60.546 52.381 9.22 0.00 0.00 3.50
4355 4637 2.259204 GTGGTTGCATGTGCGCAT 59.741 55.556 15.91 7.01 45.83 4.73
4369 4658 2.009774 GTCCGATGACAAGATTGGTGG 58.990 52.381 0.00 0.00 41.37 4.61
4371 4660 1.275291 ACGTCCGATGACAAGATTGGT 59.725 47.619 0.00 0.00 41.85 3.67
4372 4661 1.660607 CACGTCCGATGACAAGATTGG 59.339 52.381 0.00 0.00 41.85 3.16
4386 4675 1.304713 TGACCTAGTCCCCACGTCC 60.305 63.158 0.00 0.00 0.00 4.79
4460 4749 3.058639 GGTTGATCATATCTTGCTTCGCC 60.059 47.826 0.00 0.00 0.00 5.54
4501 4790 4.202192 CCAGACATCTGCTTGCTACATCTA 60.202 45.833 3.18 0.00 42.47 1.98


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

AutoCloner maintained by Alex Coulton.