Multiple sequence alignment - TraesCS1D01G402600

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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 TraesCS1D01G402600 chr1D 100.000 2647 0 0 1 2647 467663369 467660723 0 4889
1 TraesCS1D01G402600 chr1D 96.328 708 24 2 1940 2647 391096741 391097446 0 1162
2 TraesCS1D01G402600 chr1A 93.630 1978 62 26 1 1940 560247930 560249881 0 2896
3 TraesCS1D01G402600 chr1B 90.927 1984 104 42 15 1940 645573008 645571043 0 2597
4 TraesCS1D01G402600 chr4D 96.328 708 25 1 1940 2647 502968940 502968234 0 1162
5 TraesCS1D01G402600 chr4D 96.056 710 27 1 1938 2647 5529308 5528600 0 1155
6 TraesCS1D01G402600 chr4D 95.152 722 33 2 1927 2647 3385010 3384290 0 1138
7 TraesCS1D01G402600 chr7D 96.203 711 21 4 1938 2647 634662895 634663600 0 1158
8 TraesCS1D01G402600 chr6D 96.056 710 27 1 1938 2647 44234989 44235697 0 1155
9 TraesCS1D01G402600 chr5D 96.045 708 26 2 1940 2647 108112585 108111880 0 1151
10 TraesCS1D01G402600 chr2D 96.045 708 27 1 1940 2647 586927314 586926608 0 1151
11 TraesCS1D01G402600 chrUn 95.915 710 28 1 1938 2647 90496981 90496273 0 1149


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 TraesCS1D01G402600 chr1D 467660723 467663369 2646 True 4889 4889 100.000 1 2647 1 chr1D.!!$R1 2646
1 TraesCS1D01G402600 chr1D 391096741 391097446 705 False 1162 1162 96.328 1940 2647 1 chr1D.!!$F1 707
2 TraesCS1D01G402600 chr1A 560247930 560249881 1951 False 2896 2896 93.630 1 1940 1 chr1A.!!$F1 1939
3 TraesCS1D01G402600 chr1B 645571043 645573008 1965 True 2597 2597 90.927 15 1940 1 chr1B.!!$R1 1925
4 TraesCS1D01G402600 chr4D 502968234 502968940 706 True 1162 1162 96.328 1940 2647 1 chr4D.!!$R3 707
5 TraesCS1D01G402600 chr4D 5528600 5529308 708 True 1155 1155 96.056 1938 2647 1 chr4D.!!$R2 709
6 TraesCS1D01G402600 chr4D 3384290 3385010 720 True 1138 1138 95.152 1927 2647 1 chr4D.!!$R1 720
7 TraesCS1D01G402600 chr7D 634662895 634663600 705 False 1158 1158 96.203 1938 2647 1 chr7D.!!$F1 709
8 TraesCS1D01G402600 chr6D 44234989 44235697 708 False 1155 1155 96.056 1938 2647 1 chr6D.!!$F1 709
9 TraesCS1D01G402600 chr5D 108111880 108112585 705 True 1151 1151 96.045 1940 2647 1 chr5D.!!$R1 707
10 TraesCS1D01G402600 chr2D 586926608 586927314 706 True 1151 1151 96.045 1940 2647 1 chr2D.!!$R1 707
11 TraesCS1D01G402600 chrUn 90496273 90496981 708 True 1149 1149 95.915 1938 2647 1 chrUn.!!$R1 709

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
659 677 0.460987 CAGCCACTGCCTGCTACTAC 60.461 60.0 0.0 0.0 38.69 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2159 2257 0.546747 CCTGGTTGGGACCTCAGGTA 60.547 60.0 0.0 0.0 46.66 3.08 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
75 76 3.711190 TCATCTCAGCCTACTTGCCATTA 59.289 43.478 0.00 0.00 0.00 1.90
103 107 5.869344 ACACTCAAAGGTTTGCTTTTCTTTC 59.131 36.000 0.00 0.00 38.05 2.62
113 117 5.759506 TTGCTTTTCTTTCGAACCATGTA 57.240 34.783 0.00 0.00 0.00 2.29
365 373 6.246420 GCACATGGTATGCTCCTAATAAAG 57.754 41.667 0.00 0.00 40.08 1.85
659 677 0.460987 CAGCCACTGCCTGCTACTAC 60.461 60.000 0.00 0.00 38.69 2.73
663 681 2.103263 GCCACTGCCTGCTACTACTAAT 59.897 50.000 0.00 0.00 0.00 1.73
664 682 3.321111 GCCACTGCCTGCTACTACTAATA 59.679 47.826 0.00 0.00 0.00 0.98
665 683 4.202223 GCCACTGCCTGCTACTACTAATAA 60.202 45.833 0.00 0.00 0.00 1.40
935 961 2.125350 GAGGCCTCTGCTTCACCG 60.125 66.667 26.25 0.00 42.78 4.94
955 981 2.668889 ACCTCGAGCGTCTGACGT 60.669 61.111 28.38 16.68 44.73 4.34
991 1017 0.815734 TGCGTTACTACTGAGGGAGC 59.184 55.000 0.00 0.00 0.00 4.70
1114 1146 1.498865 GGCAGGTTCGTGTGACTGTG 61.499 60.000 0.00 0.00 33.62 3.66
1115 1147 1.934463 CAGGTTCGTGTGACTGTGC 59.066 57.895 0.00 0.00 0.00 4.57
1119 1151 1.006832 GTTCGTGTGACTGTGCTGTT 58.993 50.000 0.00 0.00 0.00 3.16
1198 1234 4.273148 TCTAGTTTCCTCCTGCTTCAAC 57.727 45.455 0.00 0.00 0.00 3.18
1200 1236 1.777272 AGTTTCCTCCTGCTTCAACCT 59.223 47.619 0.00 0.00 0.00 3.50
1312 1370 7.061094 GCTTCTTACTGTTACAAATGCATCAAC 59.939 37.037 0.00 3.20 0.00 3.18
1334 1396 4.219288 ACAGATTTGAAGGGAACAAGATGC 59.781 41.667 0.00 0.00 0.00 3.91
1342 1404 0.674895 GGAACAAGATGCCGAGCTGT 60.675 55.000 0.00 0.00 0.00 4.40
1365 1428 7.526041 TGTGGCTTAATAATTAGGTGATCCAT 58.474 34.615 0.00 0.00 35.89 3.41
1413 1483 5.824624 AGAAAACAGATGCACTTTCTTCTGA 59.175 36.000 17.39 0.00 39.32 3.27
1417 1487 4.514441 ACAGATGCACTTTCTTCTGAGTTG 59.486 41.667 17.39 0.00 39.32 3.16
1423 1493 4.319839 GCACTTTCTTCTGAGTTGTTAGGC 60.320 45.833 0.00 0.00 0.00 3.93
1656 1738 1.513858 ACCCAACTGAACACACCCTA 58.486 50.000 0.00 0.00 0.00 3.53
1657 1739 1.142262 ACCCAACTGAACACACCCTAC 59.858 52.381 0.00 0.00 0.00 3.18
1660 1742 2.494059 CAACTGAACACACCCTACCTG 58.506 52.381 0.00 0.00 0.00 4.00
1661 1743 2.097110 ACTGAACACACCCTACCTGA 57.903 50.000 0.00 0.00 0.00 3.86
1662 1744 2.621070 ACTGAACACACCCTACCTGAT 58.379 47.619 0.00 0.00 0.00 2.90
1663 1745 3.786553 ACTGAACACACCCTACCTGATA 58.213 45.455 0.00 0.00 0.00 2.15
1982 2080 3.790437 CGGCCTCTGCATCTGGGT 61.790 66.667 0.00 0.00 40.13 4.51
2097 2195 4.687948 CGCTACACCTATCCAATTGATGAG 59.312 45.833 7.12 0.33 34.76 2.90
2099 2197 5.221722 GCTACACCTATCCAATTGATGAGGA 60.222 44.000 20.07 5.41 34.76 3.71
2159 2257 4.096382 CGCAGCCAAACCTAAACATCTAAT 59.904 41.667 0.00 0.00 0.00 1.73
2302 2400 4.081476 TCAGAGCTGTACTGTTGCATGTAT 60.081 41.667 0.00 0.00 36.81 2.29
2331 2429 3.781770 CTCTCTGCCATCGACGCCC 62.782 68.421 4.01 0.00 0.00 6.13
2402 2500 1.670087 CGAACTCCGAATCTGCACTGT 60.670 52.381 0.00 0.00 41.76 3.55
2406 2504 2.743752 CCGAATCTGCACTGTGCCG 61.744 63.158 28.17 22.45 44.23 5.69
2426 2524 1.153901 GCCGTCAAAGATCCGTCGA 60.154 57.895 0.00 0.00 0.00 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 1.031235 CATTGTTCAGGGTGTGTGCA 58.969 50.000 0.00 0.00 0.00 4.57
75 76 7.555965 AGAAAAGCAAACCTTTGAGTGTTAAT 58.444 30.769 1.81 0.00 42.82 1.40
113 117 8.519526 TCATACGAGATAAAAAGCAAACCATTT 58.480 29.630 0.00 0.00 0.00 2.32
361 369 6.669591 GGGGTAACTTAACTCTAGGGTCTTTA 59.330 42.308 0.00 0.00 0.00 1.85
362 370 5.486775 GGGGTAACTTAACTCTAGGGTCTTT 59.513 44.000 0.00 0.00 0.00 2.52
363 371 5.028802 GGGGTAACTTAACTCTAGGGTCTT 58.971 45.833 0.00 0.00 0.00 3.01
364 372 4.046360 TGGGGTAACTTAACTCTAGGGTCT 59.954 45.833 0.00 0.00 0.00 3.85
365 373 4.356436 TGGGGTAACTTAACTCTAGGGTC 58.644 47.826 0.00 0.00 0.00 4.46
425 433 3.587498 TCCCGGGTTCAGAATCAGATAT 58.413 45.455 22.86 0.00 0.00 1.63
659 677 8.821894 GTTTTCAGCTCTGATAGTGGTTATTAG 58.178 37.037 0.00 0.00 39.64 1.73
663 681 5.047590 TCGTTTTCAGCTCTGATAGTGGTTA 60.048 40.000 0.00 0.00 39.64 2.85
664 682 3.997021 CGTTTTCAGCTCTGATAGTGGTT 59.003 43.478 0.00 0.00 39.64 3.67
665 683 3.258372 TCGTTTTCAGCTCTGATAGTGGT 59.742 43.478 0.00 0.00 39.64 4.16
935 961 1.154188 GTCAGACGCTCGAGGTGAC 60.154 63.158 15.58 10.78 0.00 3.67
955 981 1.523154 GCATGGAAGGCGTGAACCAA 61.523 55.000 0.00 0.00 29.35 3.67
1074 1102 1.744741 GGAAGTGGAGAGCAGCAGC 60.745 63.158 0.00 0.00 42.56 5.25
1114 1146 4.045783 GGCTATCTAGAACGAAGAACAGC 58.954 47.826 0.00 0.55 35.74 4.40
1115 1147 5.250235 TGGCTATCTAGAACGAAGAACAG 57.750 43.478 0.00 0.00 0.00 3.16
1119 1151 4.166246 TCCTGGCTATCTAGAACGAAGA 57.834 45.455 0.00 0.00 0.00 2.87
1198 1234 4.449131 ACATCACATGTAGATGCAAGAGG 58.551 43.478 25.37 11.51 45.19 3.69
1225 1281 2.932614 GGAACTGCACTGCACTATACTG 59.067 50.000 0.00 0.00 33.79 2.74
1312 1370 4.381292 GGCATCTTGTTCCCTTCAAATCTG 60.381 45.833 0.00 0.00 0.00 2.90
1342 1404 6.434028 GCATGGATCACCTAATTATTAAGCCA 59.566 38.462 0.00 0.00 37.04 4.75
1365 1428 2.034532 CCAGACCCACAGCATGCA 59.965 61.111 21.98 0.00 42.53 3.96
1413 1483 6.785337 AACCTTGTAAAAAGCCTAACAACT 57.215 33.333 0.00 0.00 0.00 3.16
1417 1487 6.645003 CCATCAAACCTTGTAAAAAGCCTAAC 59.355 38.462 0.00 0.00 0.00 2.34
1423 1493 9.143631 GAATCATCCATCAAACCTTGTAAAAAG 57.856 33.333 0.00 0.00 0.00 2.27
1772 1865 3.424565 CGTACTCACCTCACGTCTACAAG 60.425 52.174 0.00 0.00 0.00 3.16
1982 2080 2.700722 TAAAGTGGCCGTATGCATCA 57.299 45.000 0.19 0.00 43.89 3.07
2025 2123 4.651778 AGTCTTGCTGTTGTATGGCTTTA 58.348 39.130 0.00 0.00 0.00 1.85
2097 2195 1.365633 CCAGACTATCTGCGCCTCC 59.634 63.158 4.18 0.00 42.98 4.30
2099 2197 2.801631 GCCCAGACTATCTGCGCCT 61.802 63.158 4.18 0.00 41.19 5.52
2159 2257 0.546747 CCTGGTTGGGACCTCAGGTA 60.547 60.000 0.00 0.00 46.66 3.08
2302 2400 2.640302 GCAGAGAGACCTGGCACGA 61.640 63.158 0.00 0.00 34.82 4.35
2406 2504 2.799540 GACGGATCTTTGACGGCGC 61.800 63.158 6.90 0.00 0.00 6.53
2414 2512 2.231478 ACACTGATGTCGACGGATCTTT 59.769 45.455 11.62 0.00 31.55 2.52
2426 2524 3.261643 TGCTTCATCCTACACACTGATGT 59.738 43.478 0.00 0.00 40.80 3.06


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

AutoCloner maintained by Alex Coulton.