Multiple sequence alignment - TraesCS6D01G354400

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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 TraesCS6D01G354400 chr6D 100.000 3719 0 0 1 3719 449845556 449841838 0.000000e+00 6868.0
1 TraesCS6D01G354400 chr6D 88.935 2178 195 23 870 3033 449818499 449816354 0.000000e+00 2645.0
2 TraesCS6D01G354400 chr6D 78.333 1080 177 34 1057 2118 452082762 452081722 0.000000e+00 645.0
3 TraesCS6D01G354400 chr6D 75.345 941 169 41 1867 2789 450168337 450167442 9.680000e-106 394.0
4 TraesCS6D01G354400 chr6D 82.479 468 62 14 1655 2118 462409647 462409196 3.480000e-105 392.0
5 TraesCS6D01G354400 chr6D 72.637 1312 283 54 1441 2709 450212096 450210818 7.590000e-97 364.0
6 TraesCS6D01G354400 chr6D 92.308 52 4 0 3029 3080 449815548 449815497 1.430000e-09 75.0
7 TraesCS6D01G354400 chr6D 93.182 44 2 1 1064 1107 380495624 380495666 3.100000e-06 63.9
8 TraesCS6D01G354400 chr6D 93.182 44 2 1 1064 1107 380565618 380565660 3.100000e-06 63.9
9 TraesCS6D01G354400 chr6B 94.504 3639 152 16 111 3719 682417004 682420624 0.000000e+00 5568.0
10 TraesCS6D01G354400 chr6B 89.918 1220 89 22 1863 3080 681929816 681928629 0.000000e+00 1541.0
11 TraesCS6D01G354400 chr6B 92.694 1054 77 0 902 1955 681930869 681929816 0.000000e+00 1520.0
12 TraesCS6D01G354400 chr6B 73.770 1971 395 82 870 2783 682662256 682660351 0.000000e+00 664.0
13 TraesCS6D01G354400 chr6B 87.821 312 13 6 111 416 681931191 681930899 3.560000e-90 342.0
14 TraesCS6D01G354400 chr6B 78.373 541 100 8 2173 2709 682707636 682707109 5.950000e-88 335.0
15 TraesCS6D01G354400 chr6B 93.182 44 2 1 1064 1107 567764986 567765028 3.100000e-06 63.9
16 TraesCS6D01G354400 chr6B 93.182 44 2 1 1064 1107 567844261 567844303 3.100000e-06 63.9
17 TraesCS6D01G354400 chr6A 94.646 1158 60 2 815 1970 595490133 595488976 0.000000e+00 1794.0
18 TraesCS6D01G354400 chr6A 86.704 1617 103 41 2122 3650 595488471 595486879 0.000000e+00 1692.0
19 TraesCS6D01G354400 chr6A 93.459 688 30 6 111 787 595490813 595490130 0.000000e+00 1007.0
20 TraesCS6D01G354400 chr6A 73.806 1779 351 77 1062 2783 595664810 595663090 6.870000e-167 597.0
21 TraesCS6D01G354400 chr6A 77.332 1072 171 31 1071 2127 609163391 609162377 5.390000e-158 568.0
22 TraesCS6D01G354400 chr6A 95.556 135 4 2 2007 2139 595488786 595488652 8.090000e-52 215.0
23 TraesCS6D01G354400 chr6A 93.182 44 2 1 1064 1107 522044537 522044579 3.100000e-06 63.9
24 TraesCS6D01G354400 chr3B 82.326 877 89 38 33 871 653623372 653622524 0.000000e+00 701.0
25 TraesCS6D01G354400 chr1A 93.277 119 8 0 109 227 583526054 583526172 3.820000e-40 176.0
26 TraesCS6D01G354400 chr1A 82.143 196 28 6 676 868 16760004 16760195 1.070000e-35 161.0
27 TraesCS6D01G354400 chr2B 78.061 196 25 10 676 868 32053338 32053518 1.410000e-19 108.0


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 TraesCS6D01G354400 chr6D 449841838 449845556 3718 True 6868.000000 6868 100.000000 1 3719 1 chr6D.!!$R1 3718
1 TraesCS6D01G354400 chr6D 449815497 449818499 3002 True 1360.000000 2645 90.621500 870 3080 2 chr6D.!!$R6 2210
2 TraesCS6D01G354400 chr6D 452081722 452082762 1040 True 645.000000 645 78.333000 1057 2118 1 chr6D.!!$R4 1061
3 TraesCS6D01G354400 chr6D 450167442 450168337 895 True 394.000000 394 75.345000 1867 2789 1 chr6D.!!$R2 922
4 TraesCS6D01G354400 chr6D 450210818 450212096 1278 True 364.000000 364 72.637000 1441 2709 1 chr6D.!!$R3 1268
5 TraesCS6D01G354400 chr6B 682417004 682420624 3620 False 5568.000000 5568 94.504000 111 3719 1 chr6B.!!$F3 3608
6 TraesCS6D01G354400 chr6B 681928629 681931191 2562 True 1134.333333 1541 90.144333 111 3080 3 chr6B.!!$R3 2969
7 TraesCS6D01G354400 chr6B 682660351 682662256 1905 True 664.000000 664 73.770000 870 2783 1 chr6B.!!$R1 1913
8 TraesCS6D01G354400 chr6B 682707109 682707636 527 True 335.000000 335 78.373000 2173 2709 1 chr6B.!!$R2 536
9 TraesCS6D01G354400 chr6A 595486879 595490813 3934 True 1177.000000 1794 92.591250 111 3650 4 chr6A.!!$R3 3539
10 TraesCS6D01G354400 chr6A 595663090 595664810 1720 True 597.000000 597 73.806000 1062 2783 1 chr6A.!!$R1 1721
11 TraesCS6D01G354400 chr6A 609162377 609163391 1014 True 568.000000 568 77.332000 1071 2127 1 chr6A.!!$R2 1056
12 TraesCS6D01G354400 chr3B 653622524 653623372 848 True 701.000000 701 82.326000 33 871 1 chr3B.!!$R1 838


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
368 416 0.596577 GGGGCACGGTTTTCTTCTTC 59.403 55.0 0.0 0.0 0.0 2.87 F
1529 1714 0.393537 AGCTGCCAGGTGTTAGATGC 60.394 55.0 0.0 0.0 0.0 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1779 1974 2.050144 TCTTCCCTAGTGCATCCATCC 58.950 52.381 0.00 0.00 0.00 3.51 R
3525 5162 0.607620 GGCAAAATACAGGCCTTGCA 59.392 50.000 22.83 3.81 44.72 4.08 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
80 81 3.260100 ACCTCCCTGCCCCTGTTG 61.260 66.667 0.00 0.00 0.00 3.33
305 353 1.006400 CTGAAATTGGGGCCTCTCCTT 59.994 52.381 3.07 0.00 34.39 3.36
368 416 0.596577 GGGGCACGGTTTTCTTCTTC 59.403 55.000 0.00 0.00 0.00 2.87
382 434 7.353497 GTTTTCTTCTTCTACTGCTAAACACC 58.647 38.462 0.00 0.00 0.00 4.16
399 491 8.947115 GCTAAACACCTGTCTGTCTATTTAATT 58.053 33.333 0.00 0.00 0.00 1.40
425 517 5.551760 ATGGCGAAATTAGAACTTGTCTG 57.448 39.130 0.00 0.00 37.12 3.51
426 518 3.188460 TGGCGAAATTAGAACTTGTCTGC 59.812 43.478 0.00 0.00 37.12 4.26
429 521 4.083271 GCGAAATTAGAACTTGTCTGCCTT 60.083 41.667 0.00 0.00 37.12 4.35
430 522 5.562890 GCGAAATTAGAACTTGTCTGCCTTT 60.563 40.000 0.00 0.00 37.12 3.11
484 621 3.549471 CGTGTCTGTCTATTCAGATGTGC 59.451 47.826 0.00 0.00 44.59 4.57
492 631 5.530543 TGTCTATTCAGATGTGCACAAAACA 59.469 36.000 25.72 11.65 32.09 2.83
501 640 3.175152 TGTGCACAAAACAAAGTTAGCG 58.825 40.909 19.28 0.00 0.00 4.26
507 646 4.028830 CACAAAACAAAGTTAGCGTGAACG 60.029 41.667 0.00 0.00 43.27 3.95
614 761 9.368674 CAATTTTCCATCTACATTTGCAATGTA 57.631 29.630 15.98 15.98 33.76 2.29
615 762 9.941325 AATTTTCCATCTACATTTGCAATGTAA 57.059 25.926 16.95 11.34 34.50 2.41
616 763 8.984891 TTTTCCATCTACATTTGCAATGTAAG 57.015 30.769 16.95 12.87 34.50 2.34
617 764 7.936496 TTCCATCTACATTTGCAATGTAAGA 57.064 32.000 16.95 15.85 34.50 2.10
618 765 7.936496 TCCATCTACATTTGCAATGTAAGAA 57.064 32.000 16.95 9.83 34.50 2.52
619 766 8.523915 TCCATCTACATTTGCAATGTAAGAAT 57.476 30.769 16.95 11.03 34.50 2.40
620 767 8.407832 TCCATCTACATTTGCAATGTAAGAATG 58.592 33.333 16.95 17.46 34.50 2.67
621 768 8.192774 CCATCTACATTTGCAATGTAAGAATGT 58.807 33.333 13.50 13.50 41.97 2.71
659 813 9.922305 GAATTTGTTACAGTGAGCATTATCTAC 57.078 33.333 0.00 0.00 0.00 2.59
868 1029 7.581213 TTGAATACACTGTGTTCAATTCCTT 57.419 32.000 23.05 0.93 44.36 3.36
910 1071 2.483876 GGGATGTGGTGATACGTGATG 58.516 52.381 0.00 0.00 0.00 3.07
1021 1182 0.962356 GGTCAGCACAAGGTCCATGG 60.962 60.000 4.97 4.97 0.00 3.66
1132 1293 1.913262 TCCTTCTTGCTCTCCCGCA 60.913 57.895 0.00 0.00 38.31 5.69
1268 1450 3.681835 GCGTCTCCGTGACCCAGT 61.682 66.667 1.10 0.00 42.49 4.00
1529 1714 0.393537 AGCTGCCAGGTGTTAGATGC 60.394 55.000 0.00 0.00 0.00 3.91
1779 1974 5.463286 TGTTTTGCTTTGCTATCATGTGAG 58.537 37.500 0.00 0.00 0.00 3.51
1907 2213 3.689161 TGATTCCTATTGCCGTTTGTCAG 59.311 43.478 0.00 0.00 0.00 3.51
2206 2917 7.060600 TCAAAGCATGTACTTTTGTATCTCG 57.939 36.000 0.00 0.00 37.78 4.04
2240 2951 8.258007 TCATGTACTTATGAAGGTAGTTCTTGG 58.742 37.037 0.00 0.00 34.32 3.61
2505 3221 1.073763 AGTTGCCATGTACCTTCTGCA 59.926 47.619 0.00 0.00 0.00 4.41
2631 3347 9.334947 CTCAAGATAGTCAAAATCATATGTGGT 57.665 33.333 1.90 0.00 0.00 4.16
2678 3394 2.028112 ACCGTGCTTTGAAGATGCTCTA 60.028 45.455 0.00 0.00 0.00 2.43
2915 3658 1.901159 CATTTCAATCCCTGGCACCAA 59.099 47.619 0.00 0.00 0.00 3.67
2919 3662 1.707989 TCAATCCCTGGCACCAAGTAA 59.292 47.619 0.00 0.00 0.00 2.24
3027 3770 1.404748 GTAGGAAGACTCGTGTAGGGC 59.595 57.143 0.00 0.00 0.00 5.19
3067 4620 3.056891 CGTAATGTGATTGGGGCAGTTTT 60.057 43.478 0.00 0.00 0.00 2.43
3107 4690 1.468520 CCGCCACCTGTCAATTAACAG 59.531 52.381 1.29 1.29 45.10 3.16
3141 4724 5.576384 TGTGTTCAGTTTCATGTCAAAAAGC 59.424 36.000 0.00 0.00 0.00 3.51
3147 4730 7.771183 TCAGTTTCATGTCAAAAAGCTACTTT 58.229 30.769 0.00 0.00 34.94 2.66
3225 4825 4.934797 TCCAATTGAATCTCCTCCTGTT 57.065 40.909 7.12 0.00 0.00 3.16
3233 4833 1.776662 TCTCCTCCTGTTGTATCCCG 58.223 55.000 0.00 0.00 0.00 5.14
3321 4931 3.194968 GTGGAGGCTTACTTACAGCTGTA 59.805 47.826 22.67 22.67 37.43 2.74
3342 4962 6.000219 TGTACTGGTCTACTTTCTCTACGTT 59.000 40.000 0.00 0.00 0.00 3.99
3351 4971 2.838386 TTCTCTACGTTCCCGAATCG 57.162 50.000 0.00 0.00 37.88 3.34
3381 5001 1.407258 GTTGCTGTGTTTTGCCTACCA 59.593 47.619 0.00 0.00 0.00 3.25
3421 5058 8.692710 TCCTATATTTGTATGACAGAACTCGTT 58.307 33.333 0.00 0.00 0.00 3.85
3468 5105 1.153568 GCAGCTGGAGCATGTCGTA 60.154 57.895 17.12 0.00 45.16 3.43
3480 5117 2.672874 GCATGTCGTAGCAGTTTCATCA 59.327 45.455 0.00 0.00 0.00 3.07
3486 5123 6.163476 TGTCGTAGCAGTTTCATCATAGTTT 58.837 36.000 0.00 0.00 0.00 2.66
3525 5162 2.173996 TCGTTTCCTGAACTTTCCCCTT 59.826 45.455 0.00 0.00 36.06 3.95
3586 5223 0.466739 TCCAGGATCGCGCTAGGTTA 60.467 55.000 5.56 0.00 0.00 2.85
3591 5228 2.628657 AGGATCGCGCTAGGTTATTTCT 59.371 45.455 5.56 0.00 0.00 2.52
3636 5273 5.163248 TGTGTCTCCTGTTACCAGAAAATCA 60.163 40.000 0.00 0.00 41.50 2.57
3714 5351 6.699204 ACTCGATCTGTTACTATGCTGATTTG 59.301 38.462 0.00 0.00 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 4.826274 TCGTCTCCTGGATCTGATTTTT 57.174 40.909 0.00 0.00 0.00 1.94
29 30 4.508662 GTTCGTCTCCTGGATCTGATTTT 58.491 43.478 0.00 0.00 0.00 1.82
30 31 3.118592 GGTTCGTCTCCTGGATCTGATTT 60.119 47.826 0.00 0.00 0.00 2.17
31 32 2.432510 GGTTCGTCTCCTGGATCTGATT 59.567 50.000 0.00 0.00 0.00 2.57
65 66 2.034687 CACAACAGGGGCAGGGAG 59.965 66.667 0.00 0.00 0.00 4.30
104 105 2.969238 CACATCCGATCGCCTGGC 60.969 66.667 10.32 9.11 0.00 4.85
278 326 1.546029 GGCCCCAATTTCAGAAGTGAC 59.454 52.381 0.00 0.00 32.82 3.67
368 416 4.021894 AGACAGACAGGTGTTTAGCAGTAG 60.022 45.833 0.00 0.00 0.00 2.57
399 491 8.826710 CAGACAAGTTCTAATTTCGCCATTATA 58.173 33.333 0.00 0.00 31.12 0.98
402 494 5.619981 GCAGACAAGTTCTAATTTCGCCATT 60.620 40.000 0.00 0.00 31.12 3.16
407 499 5.613358 AAGGCAGACAAGTTCTAATTTCG 57.387 39.130 0.00 0.00 31.12 3.46
450 542 4.945246 AGACAGACACGTGTTCAAACTAT 58.055 39.130 24.26 3.39 0.00 2.12
484 621 4.028830 CGTTCACGCTAACTTTGTTTTGTG 60.029 41.667 0.00 0.00 0.00 3.33
501 640 4.992381 AAATAGACAGACAAGCGTTCAC 57.008 40.909 0.00 0.00 0.00 3.18
530 669 6.364165 CGACTACAAACGAGTCCTAATTTCAA 59.636 38.462 0.00 0.00 40.25 2.69
540 679 5.213913 TCATAGTCGACTACAAACGAGTC 57.786 43.478 26.87 0.00 41.39 3.36
583 722 9.770097 TGCAAATGTAGATGGAAAATTGTAAAA 57.230 25.926 0.00 0.00 0.00 1.52
626 773 8.351495 TGCTCACTGTAACAAATTCAAAATTC 57.649 30.769 0.00 0.00 0.00 2.17
910 1071 4.819088 GGAATAGGCAGAGAAACCAAGATC 59.181 45.833 0.00 0.00 0.00 2.75
1021 1182 2.288395 TGTTTCCCTCGTTACGAAGACC 60.288 50.000 9.23 3.27 34.74 3.85
1217 1390 2.167693 ACGAACTTGTTGGAGTCAGTCA 59.832 45.455 2.69 0.00 0.00 3.41
1268 1450 2.772287 TGTCACATACGTTCAATGGCA 58.228 42.857 0.00 0.00 0.00 4.92
1529 1714 7.918033 AGATGTTACAATCTGTCATCTCTAACG 59.082 37.037 5.57 0.00 37.36 3.18
1779 1974 2.050144 TCTTCCCTAGTGCATCCATCC 58.950 52.381 0.00 0.00 0.00 3.51
2140 2623 8.251383 ACCAGATACCGATATTTATATCCCAG 57.749 38.462 4.58 0.00 36.62 4.45
2240 2951 7.712797 TGAAGAGGGTTAAACAAGAAACAATC 58.287 34.615 0.00 0.00 0.00 2.67
2631 3347 3.555966 TCTAGCATCGTCCTTCATCAGA 58.444 45.455 0.00 0.00 0.00 3.27
3027 3770 2.826428 ACGATGATGAAATGGACGGAG 58.174 47.619 0.00 0.00 0.00 4.63
3067 4620 3.614150 CGGCTTTGACTAGCAACTCACTA 60.614 47.826 0.00 0.00 43.02 2.74
3107 4690 5.956642 TGAAACTGAACACAAGGTTTAACC 58.043 37.500 5.91 5.91 40.63 2.85
3209 4809 4.164221 GGGATACAACAGGAGGAGATTCAA 59.836 45.833 0.00 0.00 39.74 2.69
3225 4825 2.026729 TGGAAGAAATGCACGGGATACA 60.027 45.455 0.00 0.00 39.74 2.29
3233 4833 4.730657 CTGAGAACATGGAAGAAATGCAC 58.269 43.478 0.00 0.00 29.34 4.57
3321 4931 4.458642 GGAACGTAGAGAAAGTAGACCAGT 59.541 45.833 0.00 0.00 0.00 4.00
3342 4962 1.138859 ACTTCATGATGCGATTCGGGA 59.861 47.619 8.34 0.00 0.00 5.14
3351 4971 3.293311 AACACAGCAACTTCATGATGC 57.707 42.857 11.10 11.10 40.28 3.91
3404 5024 6.982141 AGTTTACAAACGAGTTCTGTCATACA 59.018 34.615 0.00 0.00 43.51 2.29
3421 5058 5.063204 AGCAAGACATACAGCAGTTTACAA 58.937 37.500 0.00 0.00 0.00 2.41
3468 5105 5.972107 AGCAAAACTATGATGAAACTGCT 57.028 34.783 0.00 0.00 32.97 4.24
3480 5117 8.015658 CGAGCAAAACTAAACTAGCAAAACTAT 58.984 33.333 0.00 0.00 0.00 2.12
3486 5123 5.744666 AACGAGCAAAACTAAACTAGCAA 57.255 34.783 0.00 0.00 0.00 3.91
3525 5162 0.607620 GGCAAAATACAGGCCTTGCA 59.392 50.000 22.83 3.81 44.72 4.08



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

AutoCloner maintained by Alex Coulton.