Multiple sequence alignment - TraesCS6A01G127000

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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 TraesCS6A01G127000 chr6A 100.000 2957 0 0 1 2957 100241610 100244566 0.000000e+00 5461
1 TraesCS6A01G127000 chr6B 94.906 2827 125 11 1 2826 471161268 471164076 0.000000e+00 4405
2 TraesCS6A01G127000 chr1A 94.798 1884 90 4 1074 2957 530689265 530691140 0.000000e+00 2929
3 TraesCS6A01G127000 chr1A 93.426 867 54 3 1 866 530620058 530620922 0.000000e+00 1282
4 TraesCS6A01G127000 chr1A 95.906 342 14 0 1074 1415 530672910 530673251 3.330000e-154 555
5 TraesCS6A01G127000 chr1A 91.743 218 18 0 861 1078 530671275 530671492 1.330000e-78 303
6 TraesCS6A01G127000 chr4D 78.462 195 32 9 7 196 475031740 475031929 5.180000e-23 119
7 TraesCS6A01G127000 chr3D 79.235 183 27 10 25 203 597450945 597450770 1.860000e-22 117
8 TraesCS6A01G127000 chr5A 75.200 250 45 17 32 272 414047330 414047089 5.210000e-18 102


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 TraesCS6A01G127000 chr6A 100241610 100244566 2956 False 5461 5461 100.0000 1 2957 1 chr6A.!!$F1 2956
1 TraesCS6A01G127000 chr6B 471161268 471164076 2808 False 4405 4405 94.9060 1 2826 1 chr6B.!!$F1 2825
2 TraesCS6A01G127000 chr1A 530689265 530691140 1875 False 2929 2929 94.7980 1074 2957 1 chr1A.!!$F2 1883
3 TraesCS6A01G127000 chr1A 530620058 530620922 864 False 1282 1282 93.4260 1 866 1 chr1A.!!$F1 865
4 TraesCS6A01G127000 chr1A 530671275 530673251 1976 False 429 555 93.8245 861 1415 2 chr1A.!!$F3 554

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
709 710 0.179 GCTCCCACATCCGTTCTGAT 59.821 55.0 0.0 0.0 0.00 2.90 F
1672 3096 0.179 CCATCCTGTACTGTCCCAGC 59.821 60.0 0.0 0.0 34.37 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1719 3143 0.039035 ACAATGTTATGCGGGGGTGT 59.961 50.000 0.0 0.0 0.0 4.16 R
2856 4280 1.227438 CCCAGTATTACCACCCGCG 60.227 63.158 0.0 0.0 0.0 6.46 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
37 38 5.471116 CCATGATGGAATTTTCGAGCATCTA 59.529 40.000 5.27 0.00 39.45 1.98
42 43 7.500227 TGATGGAATTTTCGAGCATCTATTCTT 59.500 33.333 0.00 0.00 30.01 2.52
48 49 6.707440 TTTCGAGCATCTATTCTTCTCTCT 57.293 37.500 0.00 0.00 0.00 3.10
114 115 1.001597 GACTGATTAGACGCTACCGGG 60.002 57.143 6.32 0.00 39.22 5.73
116 117 1.006454 GATTAGACGCTACCGGGCC 60.006 63.158 6.32 0.00 39.22 5.80
117 118 2.431805 GATTAGACGCTACCGGGCCC 62.432 65.000 13.57 13.57 39.22 5.80
416 417 0.889994 GTTCCTTGCCATGCATGACA 59.110 50.000 28.31 20.53 38.76 3.58
419 420 2.181125 TCCTTGCCATGCATGACAAAT 58.819 42.857 28.31 0.00 38.76 2.32
443 444 3.057019 TGTTCGGACACAAATCTTCTCG 58.943 45.455 0.00 0.00 0.00 4.04
670 671 0.895530 CTTTCGCCTCACCACCTCTA 59.104 55.000 0.00 0.00 0.00 2.43
698 699 4.704833 GGCTTGCTCGCTCCCACA 62.705 66.667 0.00 0.00 0.00 4.17
705 706 1.519455 CTCGCTCCCACATCCGTTC 60.519 63.158 0.00 0.00 0.00 3.95
709 710 0.179000 GCTCCCACATCCGTTCTGAT 59.821 55.000 0.00 0.00 0.00 2.90
710 711 1.407437 GCTCCCACATCCGTTCTGATT 60.407 52.381 0.00 0.00 0.00 2.57
807 808 2.818132 GACCGGCAGCAGCTCTAT 59.182 61.111 0.00 0.00 41.70 1.98
881 882 1.278985 ACGATCCAAGCAATGAGTCCA 59.721 47.619 0.00 0.00 0.00 4.02
949 950 3.309954 GGATAGTGAATGAAGTCGTTGCC 59.690 47.826 0.00 0.00 0.00 4.52
1038 1040 3.650139 ACTTGTGAACATAGACCGTCAC 58.350 45.455 0.40 0.00 0.00 3.67
1047 1049 5.464030 ACATAGACCGTCACTACAGTTTT 57.536 39.130 0.40 0.00 0.00 2.43
1092 2516 3.075148 GGTTAGGAAAACAGTCAGGCTC 58.925 50.000 0.00 0.00 0.00 4.70
1112 2536 1.078848 GTGATGGCAGTTCTCGGCT 60.079 57.895 0.00 0.00 35.25 5.52
1156 2580 0.994247 TGTAGTAGGTCTGGGGACGA 59.006 55.000 0.00 0.00 42.97 4.20
1188 2612 2.697644 CCCTTCCCCCATGAGCCT 60.698 66.667 0.00 0.00 0.00 4.58
1260 2684 6.477253 ACTAGATGAGACGCTGGATAAGATA 58.523 40.000 0.00 0.00 0.00 1.98
1323 2747 6.809196 GTGATCTAAGTGTCGATTTTGAGTCT 59.191 38.462 0.00 0.00 0.00 3.24
1327 2751 7.088905 TCTAAGTGTCGATTTTGAGTCTAACC 58.911 38.462 0.00 0.00 0.00 2.85
1346 2770 0.668096 CGGCAATGTGCTGCATTTGT 60.668 50.000 21.49 2.29 44.82 2.83
1420 2844 1.079127 ATCAGCCCGGAAGTGTTCG 60.079 57.895 0.73 0.00 0.00 3.95
1424 2848 2.943653 CCCGGAAGTGTTCGTTGC 59.056 61.111 0.73 0.00 0.00 4.17
1640 3064 4.694512 TGCATACCTATCCCATAAGGCTA 58.305 43.478 0.00 0.00 34.51 3.93
1655 3079 4.953940 AAGGCTAAATTGTTGCTTTCCA 57.046 36.364 0.00 0.00 0.00 3.53
1672 3096 0.179000 CCATCCTGTACTGTCCCAGC 59.821 60.000 0.00 0.00 34.37 4.85
1807 3231 2.084546 GAAGTATTGGTGGACACAGGC 58.915 52.381 4.69 0.00 0.00 4.85
1836 3260 0.966370 AGGCGAGGGTGAGTAGACAC 60.966 60.000 0.00 0.00 39.70 3.67
1898 3322 3.435590 CACATATGCTTGCCCCCG 58.564 61.111 1.58 0.00 0.00 5.73
1900 3324 2.598394 CATATGCTTGCCCCCGGG 60.598 66.667 15.80 15.80 38.57 5.73
1912 3336 1.816572 GCCCCCGGGTGTTGTATTATC 60.817 57.143 21.85 0.00 37.65 1.75
1915 3339 1.772453 CCCGGGTGTTGTATTATCCCT 59.228 52.381 14.18 0.00 36.30 4.20
1925 3349 7.942341 GGTGTTGTATTATCCCTATTTGATCCA 59.058 37.037 0.00 0.00 0.00 3.41
1939 3363 2.886913 TGATCCACATTTCCTTGCCAA 58.113 42.857 0.00 0.00 0.00 4.52
1983 3407 2.565645 CCATAGGGGACTCGGCGAG 61.566 68.421 33.42 33.42 43.67 5.03
2146 3570 1.153549 GTCTTGCCGCTCCCTACTG 60.154 63.158 0.00 0.00 0.00 2.74
2209 3633 3.814842 TGGTTGACTATTTGAGTGCAGTG 59.185 43.478 0.00 0.00 39.06 3.66
2512 3936 2.380084 TCAGATTCTAACACGGGTGC 57.620 50.000 0.00 0.00 0.00 5.01
2530 3954 1.242076 GCTGTGCCTGATGTCAAAGT 58.758 50.000 0.00 0.00 0.00 2.66
2547 3971 4.832266 TCAAAGTGAAAAGCCATGTACCAT 59.168 37.500 0.00 0.00 0.00 3.55
2591 4015 2.685897 GTTGTCAGCTTTGTGTGGGTTA 59.314 45.455 0.00 0.00 0.00 2.85
2614 4038 6.723298 AAGTTGGTTATTTGTTGTGATGGA 57.277 33.333 0.00 0.00 0.00 3.41
2626 4050 1.617850 TGTGATGGATTGTGGCAAACC 59.382 47.619 0.00 1.85 0.00 3.27
2628 4052 0.173255 GATGGATTGTGGCAAACCGG 59.827 55.000 0.00 0.00 39.70 5.28
2658 4082 0.692476 CCCTTGTGACAGGTCCATCA 59.308 55.000 0.00 0.00 30.96 3.07
2679 4103 0.895530 CTTCTAGGCTCGTGAACCCA 59.104 55.000 0.00 0.00 0.00 4.51
2731 4155 4.047059 CAAGCTTGGGTGCTGCCG 62.047 66.667 19.14 0.00 43.24 5.69
2821 4245 1.537990 GGTGGTCAAGCGTGCATTTTT 60.538 47.619 0.00 0.00 0.00 1.94
2874 4298 1.227438 CGCGGGTGGTAATACTGGG 60.227 63.158 0.00 0.00 0.00 4.45
2931 4355 2.406002 GACCGTTCCCAAGCCCAGAA 62.406 60.000 0.00 0.00 0.00 3.02
2949 4373 1.947456 GAAAGCCTTGACTTGAACCGT 59.053 47.619 0.00 0.00 0.00 4.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 8.203485 AGAGAGAAGAATAGATGCTCGAAAATT 58.797 33.333 0.00 0.00 0.00 1.82
37 38 2.233431 AGCTGTTGCGAGAGAGAAGAAT 59.767 45.455 1.37 0.00 45.42 2.40
42 43 0.448197 CGTAGCTGTTGCGAGAGAGA 59.552 55.000 1.37 0.00 45.42 3.10
48 49 1.444383 CTGCTCGTAGCTGTTGCGA 60.444 57.895 4.57 4.57 42.97 5.10
95 96 1.030457 CCCGGTAGCGTCTAATCAGT 58.970 55.000 13.99 0.00 0.00 3.41
114 115 2.960129 CGCAAGGACGTATCGGGC 60.960 66.667 0.00 0.00 0.00 6.13
116 117 2.514013 GCACGCAAGGACGTATCGG 61.514 63.158 0.00 0.00 46.34 4.18
117 118 1.742900 CTGCACGCAAGGACGTATCG 61.743 60.000 0.00 0.00 46.34 2.92
119 120 0.175760 ATCTGCACGCAAGGACGTAT 59.824 50.000 0.00 0.00 46.34 3.06
197 198 1.011904 CAATCGTTGCGATGCGAGG 60.012 57.895 4.75 0.00 46.30 4.63
310 311 7.769272 TTTTCTGAAAGGTTACTTTTGCATG 57.231 32.000 2.75 0.00 46.51 4.06
438 439 0.522180 GGAAGACGACAGAGCGAGAA 59.478 55.000 0.00 0.00 34.83 2.87
443 444 1.195674 GCTTTTGGAAGACGACAGAGC 59.804 52.381 0.00 0.00 34.71 4.09
635 636 2.027688 CGAAAGACGATACCTTGCGTTC 59.972 50.000 0.00 0.00 45.77 3.95
670 671 4.060038 GCAAGCCAGCGCCAACAT 62.060 61.111 2.29 0.00 34.57 2.71
698 699 2.346803 CACGAACCAATCAGAACGGAT 58.653 47.619 0.00 0.00 0.00 4.18
705 706 1.154413 GCGTGCACGAACCAATCAG 60.154 57.895 41.19 10.08 43.02 2.90
709 710 1.649390 AACAAGCGTGCACGAACCAA 61.649 50.000 41.19 0.00 43.02 3.67
710 711 2.042520 GAACAAGCGTGCACGAACCA 62.043 55.000 41.19 0.00 43.02 3.67
854 855 0.317160 TTGCTTGGATCGTCGTCTGT 59.683 50.000 0.00 0.00 0.00 3.41
881 882 0.604578 ATCTTGCCGCAGTTTGCATT 59.395 45.000 1.69 0.00 45.36 3.56
949 950 3.818121 TTGTGGTTCCGTCAGGGCG 62.818 63.158 0.00 0.00 38.33 6.13
972 973 1.587043 GGCCCCTCTCAACGAAAAGC 61.587 60.000 0.00 0.00 0.00 3.51
975 977 0.250727 CAAGGCCCCTCTCAACGAAA 60.251 55.000 0.00 0.00 0.00 3.46
978 980 2.045926 CCAAGGCCCCTCTCAACG 60.046 66.667 0.00 0.00 0.00 4.10
1038 1040 7.103641 TCCTAGTAGCATTCCAAAAACTGTAG 58.896 38.462 0.00 0.00 0.00 2.74
1047 1049 5.419155 CGGATCTATCCTAGTAGCATTCCAA 59.581 44.000 7.39 0.00 44.93 3.53
1092 2516 1.811266 CCGAGAACTGCCATCACCG 60.811 63.158 0.00 0.00 0.00 4.94
1112 2536 2.048597 CAGCGTTAGCCGTCACCA 60.049 61.111 0.00 0.00 46.67 4.17
1188 2612 1.223187 TATCACGATCGACGCAGCTA 58.777 50.000 24.34 0.51 46.94 3.32
1323 2747 0.964860 ATGCAGCACATTGCCGGTTA 60.965 50.000 1.90 0.00 46.52 2.85
1420 2844 0.097674 GATGGATCACGCACAGCAAC 59.902 55.000 0.00 0.00 0.00 4.17
1424 2848 0.926155 CTTCGATGGATCACGCACAG 59.074 55.000 0.00 0.00 0.00 3.66
1573 2997 6.820335 TGAAACATAGTATGTGAGATGAGGG 58.180 40.000 16.46 0.00 44.07 4.30
1640 3064 4.961438 ACAGGATGGAAAGCAACAATTT 57.039 36.364 0.00 0.00 43.62 1.82
1672 3096 5.751509 CCACCATTGCATCAAATGTGATTAG 59.248 40.000 0.00 0.00 42.03 1.73
1719 3143 0.039035 ACAATGTTATGCGGGGGTGT 59.961 50.000 0.00 0.00 0.00 4.16
1722 3146 2.045561 TGTACAATGTTATGCGGGGG 57.954 50.000 0.00 0.00 0.00 5.40
1807 3231 1.006102 CCCTCGCCTTGCCGTATAG 60.006 63.158 0.00 0.00 0.00 1.31
1836 3260 6.352016 ACAGCTATCCCATATGACAGTAAG 57.648 41.667 3.65 0.00 0.00 2.34
1898 3322 7.393515 GGATCAAATAGGGATAATACAACACCC 59.606 40.741 0.00 0.00 40.71 4.61
1900 3324 8.784043 GTGGATCAAATAGGGATAATACAACAC 58.216 37.037 0.00 0.00 0.00 3.32
1912 3336 5.452356 GCAAGGAAATGTGGATCAAATAGGG 60.452 44.000 0.00 0.00 0.00 3.53
1915 3339 5.022122 TGGCAAGGAAATGTGGATCAAATA 58.978 37.500 0.00 0.00 0.00 1.40
1925 3349 5.047092 CAGACCTTATTTGGCAAGGAAATGT 60.047 40.000 9.88 4.81 44.59 2.71
1939 3363 2.904434 ACCTTCACCGACAGACCTTATT 59.096 45.455 0.00 0.00 0.00 1.40
1983 3407 4.748144 CAGGAGGCAACCCCTGGC 62.748 72.222 11.32 0.00 46.60 4.85
2106 3530 3.126858 CACGCCGGCAGCAAAATATATAT 59.873 43.478 28.98 0.00 44.04 0.86
2146 3570 5.106396 GCTCATCCCATTAGTGATTATGCAC 60.106 44.000 0.00 0.00 39.05 4.57
2183 3607 3.189287 GCACTCAAATAGTCAACCACCTG 59.811 47.826 0.00 0.00 35.76 4.00
2209 3633 3.001026 CAGACGAGATGTGTGCATTCATC 59.999 47.826 19.52 19.52 40.21 2.92
2483 3907 6.128661 CCGTGTTAGAATCTGAAACGAAATCA 60.129 38.462 17.74 0.00 0.00 2.57
2485 3909 5.121768 CCCGTGTTAGAATCTGAAACGAAAT 59.878 40.000 17.74 0.00 0.00 2.17
2512 3936 2.497138 TCACTTTGACATCAGGCACAG 58.503 47.619 0.00 0.00 0.00 3.66
2547 3971 2.354704 GCACACACATACCTTCTGCCTA 60.355 50.000 0.00 0.00 0.00 3.93
2591 4015 6.723298 TCCATCACAACAAATAACCAACTT 57.277 33.333 0.00 0.00 0.00 2.66
2614 4038 1.261480 TTATGCCGGTTTGCCACAAT 58.739 45.000 1.90 0.00 34.09 2.71
2626 4050 4.173256 GTCACAAGGGAAAATTTATGCCG 58.827 43.478 0.00 0.00 32.81 5.69
2628 4052 5.170748 CCTGTCACAAGGGAAAATTTATGC 58.829 41.667 0.00 0.00 33.28 3.14
2637 4061 1.351017 GATGGACCTGTCACAAGGGAA 59.649 52.381 0.00 0.00 42.11 3.97
2658 4082 1.275573 GGGTTCACGAGCCTAGAAGTT 59.724 52.381 0.00 0.00 42.81 2.66
2679 4103 2.623416 GCCAAGCCGCTTCCTAATATTT 59.377 45.455 1.56 0.00 0.00 1.40
2771 4195 5.221783 TGGCTGACATTCTCATATAGCATGT 60.222 40.000 0.00 0.00 43.63 3.21
2821 4245 3.135225 GCACAACACCTACACACACATA 58.865 45.455 0.00 0.00 0.00 2.29
2856 4280 1.227438 CCCAGTATTACCACCCGCG 60.227 63.158 0.00 0.00 0.00 6.46
2861 4285 1.806623 CGCTCTGCCCAGTATTACCAC 60.807 57.143 0.00 0.00 0.00 4.16
2874 4298 4.040068 GGGATCACATCGCTCTGC 57.960 61.111 0.00 0.00 38.98 4.26
2931 4355 2.550208 CCTACGGTTCAAGTCAAGGCTT 60.550 50.000 0.00 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.