Multiple sequence alignment - TraesCS5D01G262000

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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 TraesCS5D01G262000 chr5D 100.000 3248 0 0 1 3248 368078027 368081274 0.000000e+00 5999
1 TraesCS5D01G262000 chr5D 91.375 3084 212 23 193 3248 368029073 368032130 0.000000e+00 4172
2 TraesCS5D01G262000 chr5D 89.606 1982 191 9 632 2602 368244606 368246583 0.000000e+00 2505
3 TraesCS5D01G262000 chr5D 84.388 2498 310 50 375 2829 368285798 368288258 0.000000e+00 2379
4 TraesCS5D01G262000 chr5D 80.846 402 44 25 73 450 368244033 368244425 5.300000e-73 285
5 TraesCS5D01G262000 chr5D 85.315 143 9 4 52 183 367990258 367990399 1.570000e-28 137
6 TraesCS5D01G262000 chr5B 91.555 3292 206 25 1 3248 436152102 436155365 0.000000e+00 4473
7 TraesCS5D01G262000 chr5B 92.776 2118 119 14 193 2284 436095574 436097683 0.000000e+00 3033
8 TraesCS5D01G262000 chr5B 83.908 2815 377 38 476 3246 436209055 436211837 0.000000e+00 2619
9 TraesCS5D01G262000 chr5B 89.248 1981 197 8 632 2602 436162916 436164890 0.000000e+00 2464
10 TraesCS5D01G262000 chr5B 87.015 824 75 10 2429 3248 436097691 436098486 0.000000e+00 900
11 TraesCS5D01G262000 chr5B 80.743 296 34 19 76 367 436162045 436162321 3.280000e-50 209
12 TraesCS5D01G262000 chr5B 75.688 436 84 14 2829 3247 435773931 435774361 7.110000e-47 198
13 TraesCS5D01G262000 chr5B 89.247 93 10 0 382 474 436208933 436209025 2.050000e-22 117
14 TraesCS5D01G262000 chr5A 92.042 2777 190 8 476 3248 470076442 470079191 0.000000e+00 3875
15 TraesCS5D01G262000 chr5A 84.409 2790 379 36 476 3246 470170324 470173076 0.000000e+00 2691
16 TraesCS5D01G262000 chr5A 83.030 165 11 6 52 200 470037805 470037968 2.030000e-27 134
17 TraesCS5D01G262000 chr5A 86.957 92 12 0 383 474 470170203 470170294 1.590000e-18 104


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 TraesCS5D01G262000 chr5D 368078027 368081274 3247 False 5999.0 5999 100.0000 1 3248 1 chr5D.!!$F3 3247
1 TraesCS5D01G262000 chr5D 368029073 368032130 3057 False 4172.0 4172 91.3750 193 3248 1 chr5D.!!$F2 3055
2 TraesCS5D01G262000 chr5D 368285798 368288258 2460 False 2379.0 2379 84.3880 375 2829 1 chr5D.!!$F4 2454
3 TraesCS5D01G262000 chr5D 368244033 368246583 2550 False 1395.0 2505 85.2260 73 2602 2 chr5D.!!$F5 2529
4 TraesCS5D01G262000 chr5B 436152102 436155365 3263 False 4473.0 4473 91.5550 1 3248 1 chr5B.!!$F2 3247
5 TraesCS5D01G262000 chr5B 436095574 436098486 2912 False 1966.5 3033 89.8955 193 3248 2 chr5B.!!$F3 3055
6 TraesCS5D01G262000 chr5B 436208933 436211837 2904 False 1368.0 2619 86.5775 382 3246 2 chr5B.!!$F5 2864
7 TraesCS5D01G262000 chr5B 436162045 436164890 2845 False 1336.5 2464 84.9955 76 2602 2 chr5B.!!$F4 2526
8 TraesCS5D01G262000 chr5A 470076442 470079191 2749 False 3875.0 3875 92.0420 476 3248 1 chr5A.!!$F2 2772
9 TraesCS5D01G262000 chr5A 470170203 470173076 2873 False 1397.5 2691 85.6830 383 3246 2 chr5A.!!$F3 2863

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
236 239 0.673985 GTTTCCTGGTTTGCAGGTCC 59.326 55.0 0.0 0.0 40.59 4.46 F
1351 1787 0.609151 TGGTTCATGCAATGGGCTTG 59.391 50.0 0.0 0.0 46.73 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1935 2372 0.040058 TGTACTTCCGGCTCCACCTA 59.960 55.0 0.0 0.0 35.61 3.08 R
2424 2861 0.108186 TGCGGCAGTAGACCATTGAG 60.108 55.0 0.0 0.0 0.00 3.02 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
46 47 2.919856 CGGGGGCTGAGGATCGAT 60.920 66.667 0.00 0.00 38.61 3.59
47 48 2.936912 CGGGGGCTGAGGATCGATC 61.937 68.421 17.36 17.36 38.61 3.69
236 239 0.673985 GTTTCCTGGTTTGCAGGTCC 59.326 55.000 0.00 0.00 40.59 4.46
300 315 2.202096 CGCACTCGCAAGCTTTCG 60.202 61.111 12.50 12.50 38.40 3.46
308 323 2.786578 CTCGCAAGCTTTCGATCTACTC 59.213 50.000 21.08 0.00 33.98 2.59
367 395 2.165437 TCCTTCGCTTGTTTTGCTGTTT 59.835 40.909 0.00 0.00 0.00 2.83
373 413 4.036262 TCGCTTGTTTTGCTGTTTCTACAT 59.964 37.500 0.00 0.00 32.86 2.29
378 418 6.691754 TGTTTTGCTGTTTCTACATCAGAA 57.308 33.333 0.00 0.00 41.66 3.02
402 446 9.708222 GAAAACTGTTTATACATCTGCATACTG 57.292 33.333 6.16 0.00 32.86 2.74
406 450 1.800805 ATACATCTGCATACTGCCGC 58.199 50.000 0.00 0.00 44.23 6.53
453 506 2.939103 AGAAATTGCTGTCTATGACCGC 59.061 45.455 7.07 7.07 41.82 5.68
562 658 1.519408 AGTTGTATGGTTGTCGCACC 58.481 50.000 0.00 0.00 37.34 5.01
617 1029 1.153823 GCGTGTCGTGTGGCTAGAT 60.154 57.895 0.00 0.00 0.00 1.98
716 1130 6.642707 TGCTTTTAGTTTTAAGCCAGCTTA 57.357 33.333 8.01 8.01 44.72 3.09
748 1162 6.808008 ACTTTGCAGGCATCATATGTATAC 57.192 37.500 1.90 0.00 0.00 1.47
903 1325 9.638239 TTCATGTTATTTTCCTGCAAATTACTC 57.362 29.630 0.00 0.00 30.42 2.59
968 1391 4.863131 GTGTCTACAGAAGGATTTGGTACG 59.137 45.833 0.00 0.00 0.00 3.67
1351 1787 0.609151 TGGTTCATGCAATGGGCTTG 59.391 50.000 0.00 0.00 46.73 4.01
1517 1953 8.507249 AGAATACAAGATTACACACTTTCTTGC 58.493 33.333 10.53 0.00 45.66 4.01
1566 2002 7.108847 GCTCCCATAATAATAGCAGATTCAGT 58.891 38.462 0.00 0.00 33.38 3.41
1758 2194 7.281040 TGATCTCAATGAAGAAAGTTTTGCT 57.719 32.000 0.00 0.00 0.00 3.91
1770 2206 8.677148 AAGAAAGTTTTGCTCAGATACAACTA 57.323 30.769 0.00 0.00 0.00 2.24
1825 2261 2.496291 CCCCGTCGGTACTGGATCC 61.496 68.421 11.06 4.20 31.92 3.36
1872 2308 1.302033 AACAGCTCAAGCCTGTCCG 60.302 57.895 0.00 0.00 43.38 4.79
1935 2372 3.214328 ACTTGAGAACAAAACGGAGCAT 58.786 40.909 0.00 0.00 35.49 3.79
1946 2383 2.423446 GGAGCATAGGTGGAGCCG 59.577 66.667 0.00 0.00 43.70 5.52
1982 2419 4.645136 TCAGTACTCGCCAGATTACATTCT 59.355 41.667 0.00 0.00 35.66 2.40
2017 2454 6.378661 TGGTTCATGGGGATAAGATCATAG 57.621 41.667 0.00 0.00 0.00 2.23
2021 2458 4.225942 TCATGGGGATAAGATCATAGTGCC 59.774 45.833 0.00 0.00 0.00 5.01
2023 2460 4.178339 TGGGGATAAGATCATAGTGCCAT 58.822 43.478 0.00 0.00 0.00 4.40
2046 2483 2.299013 TCGCGATGGCAACCTATATTCT 59.701 45.455 3.71 0.00 39.92 2.40
2168 2605 3.861113 TGTGTGAAGTCACTTGTACGTTC 59.139 43.478 12.43 0.00 46.55 3.95
2174 2611 3.318017 AGTCACTTGTACGTTCAGATGC 58.682 45.455 0.00 0.00 0.00 3.91
2193 2630 1.336125 GCATACAAGAAGGCTGGCATC 59.664 52.381 3.38 0.22 0.00 3.91
2194 2631 2.646930 CATACAAGAAGGCTGGCATCA 58.353 47.619 9.14 0.00 0.00 3.07
2212 2649 1.070105 ACGCGTAGGCCAAAACAGA 59.930 52.632 11.67 0.00 35.02 3.41
2218 2655 2.618045 CGTAGGCCAAAACAGAGGGAAT 60.618 50.000 5.01 0.00 0.00 3.01
2246 2683 1.344065 TTGAAGAAGTGGGAGGCGTA 58.656 50.000 0.00 0.00 0.00 4.42
2251 2688 0.971447 GAAGTGGGAGGCGTAGGAGT 60.971 60.000 0.00 0.00 0.00 3.85
2284 2721 6.826668 TCTGAGAATGAAAAACTGTGGACTA 58.173 36.000 0.00 0.00 0.00 2.59
2290 2727 8.695456 AGAATGAAAAACTGTGGACTAACATTT 58.305 29.630 0.00 0.00 0.00 2.32
2343 2780 8.721478 TGTTAGCTGAACTCAAATTTAGCTTAG 58.279 33.333 14.34 1.04 46.22 2.18
2347 2784 6.165659 TGAACTCAAATTTAGCTTAGCGAC 57.834 37.500 0.00 0.00 0.00 5.19
2400 2837 5.300286 GGTTGAGTTGCTATTTGATAGGCAT 59.700 40.000 0.00 0.00 33.43 4.40
2424 2861 2.855953 GCAGAACGCAATGGCATATCAC 60.856 50.000 0.00 0.00 41.79 3.06
2468 2905 2.531522 TGGATGATGCGATTCGACAT 57.468 45.000 10.88 12.37 0.00 3.06
2472 2909 3.181523 GGATGATGCGATTCGACATGATG 60.182 47.826 10.88 0.00 0.00 3.07
2607 3046 8.048534 TGATCATTTGAAAAGGAGAAGATGTC 57.951 34.615 0.00 0.00 31.76 3.06
2623 3064 7.533426 AGAAGATGTCATGATTGTTTAAGTGC 58.467 34.615 0.00 0.00 0.00 4.40
2636 3077 5.565509 TGTTTAAGTGCACCCTCATCATTA 58.434 37.500 14.63 0.00 0.00 1.90
2678 3125 3.966543 CAACCAAGGCCCCTCCGT 61.967 66.667 0.00 0.00 40.77 4.69
2699 3146 2.152078 GCTTAATTGTGTGGCGCGC 61.152 57.895 25.94 25.94 0.00 6.86
2790 3238 9.087424 GTTTTAAATTTACAGGCCAGATCATTC 57.913 33.333 5.01 0.00 0.00 2.67
2857 3327 1.133325 ACAGACATCGAGGGAGGCTAT 60.133 52.381 0.69 0.00 0.00 2.97
2859 3329 1.133325 AGACATCGAGGGAGGCTATGT 60.133 52.381 0.69 0.00 33.63 2.29
2863 3333 4.673968 ACATCGAGGGAGGCTATGTATAA 58.326 43.478 0.69 0.00 0.00 0.98
2894 3364 6.542574 AGTATGATACGTAGTGCTGTAGAC 57.457 41.667 0.08 0.00 45.73 2.59
2913 3383 7.970102 TGTAGACAATCAGGTAAAGGTTTACT 58.030 34.615 11.43 0.00 42.00 2.24
2973 3443 2.733858 GCTCGCTAGTTCTTGTCTCCTG 60.734 54.545 0.00 0.00 0.00 3.86
3038 3508 8.404000 AGCTTCTTTTGAACTATAAGCATGATG 58.596 33.333 0.00 0.00 41.31 3.07
3121 3592 8.542080 CCATCCCATATTTTAATATTGGCATGT 58.458 33.333 0.00 0.00 35.31 3.21
3122 3593 9.373603 CATCCCATATTTTAATATTGGCATGTG 57.626 33.333 0.00 0.00 35.31 3.21
3129 3600 0.740149 ATATTGGCATGTGCGTGTGG 59.260 50.000 0.00 0.00 43.26 4.17
3143 3614 4.034279 GTGCGTGTGGTTTAGTTCTTTGTA 59.966 41.667 0.00 0.00 0.00 2.41
3145 3616 4.553351 GCGTGTGGTTTAGTTCTTTGTACC 60.553 45.833 0.00 0.00 0.00 3.34
3156 3627 6.031751 AGTTCTTTGTACCAACTTTGCAAA 57.968 33.333 12.14 12.14 0.00 3.68
3157 3628 5.867174 AGTTCTTTGTACCAACTTTGCAAAC 59.133 36.000 8.05 0.00 0.00 2.93
3160 3631 3.157932 TGTACCAACTTTGCAAACTGC 57.842 42.857 8.05 0.00 45.29 4.40
3218 3691 3.696051 GCCCACAGTCAACATATCACATT 59.304 43.478 0.00 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 46 2.237751 GCGGTTCGCGCACTATGAT 61.238 57.895 8.75 0.00 44.55 2.45
46 47 2.883730 GCGGTTCGCGCACTATGA 60.884 61.111 8.75 0.00 44.55 2.15
250 253 4.678743 GGGCGGCAAAAGAGGGGT 62.679 66.667 12.47 0.00 0.00 4.95
256 271 1.431496 CAATTTGAGGGCGGCAAAAG 58.569 50.000 12.47 0.00 38.57 2.27
343 371 1.120437 GCAAAACAAGCGAAGGAACG 58.880 50.000 0.00 0.00 0.00 3.95
402 446 1.234615 TAAGTTTCAGTGGCTGCGGC 61.235 55.000 9.72 9.72 37.82 6.53
406 450 3.499918 CCTTCTGTAAGTTTCAGTGGCTG 59.500 47.826 9.08 0.00 34.86 4.85
453 506 1.424493 GCATCGGCGACAAAGAGGAG 61.424 60.000 13.76 0.00 0.00 3.69
562 658 3.756780 CACAACAAAATGTGTGCATCG 57.243 42.857 0.00 0.00 44.46 3.84
748 1162 7.270757 TGATCCATAACCATAAACAAATCGG 57.729 36.000 0.00 0.00 0.00 4.18
767 1181 1.678101 GCCCTGTGTTGCTATTGATCC 59.322 52.381 0.00 0.00 0.00 3.36
968 1391 0.612744 AGTCTCTTGAGGAAGCCTGC 59.387 55.000 0.00 0.00 31.76 4.85
1351 1787 8.556194 TGTTGATGACTTTGTGTATAAGACAAC 58.444 33.333 0.00 0.00 40.66 3.32
1512 1948 2.846206 ACCCACAATAGGATCAGCAAGA 59.154 45.455 0.00 0.00 0.00 3.02
1517 1953 1.541233 GGCGACCCACAATAGGATCAG 60.541 57.143 0.00 0.00 0.00 2.90
1539 1975 6.881065 TGAATCTGCTATTATTATGGGAGCAC 59.119 38.462 0.00 0.00 38.20 4.40
1729 2165 6.264841 ACTTTCTTCATTGAGATCAAAGGC 57.735 37.500 0.00 0.00 39.55 4.35
1758 2194 4.283467 ACAGTTGCTGGTAGTTGTATCTGA 59.717 41.667 1.08 0.00 35.51 3.27
1770 2206 3.769739 TCTTCATGTACAGTTGCTGGT 57.230 42.857 0.33 0.00 35.51 4.00
1834 2270 7.162082 GCTGTTGCTATACATACCTTCCTATT 58.838 38.462 0.00 0.00 36.03 1.73
1857 2293 1.882989 GAGACGGACAGGCTTGAGCT 61.883 60.000 1.40 0.00 39.26 4.09
1872 2308 1.349357 ACAAGCCTTCTGGGAAGAGAC 59.651 52.381 8.64 0.00 37.23 3.36
1935 2372 0.040058 TGTACTTCCGGCTCCACCTA 59.960 55.000 0.00 0.00 35.61 3.08
1946 2383 5.690857 GGCGAGTACTGAATATTGTACTTCC 59.309 44.000 15.85 15.37 46.23 3.46
2046 2483 1.860641 TCTCCCCGAGCAACTCATAA 58.139 50.000 0.00 0.00 0.00 1.90
2168 2605 2.617308 CCAGCCTTCTTGTATGCATCTG 59.383 50.000 0.19 0.41 0.00 2.90
2174 2611 2.357009 GTGATGCCAGCCTTCTTGTATG 59.643 50.000 0.00 0.00 0.00 2.39
2193 2630 1.206578 CTGTTTTGGCCTACGCGTG 59.793 57.895 24.59 11.90 35.02 5.34
2194 2631 0.949105 CTCTGTTTTGGCCTACGCGT 60.949 55.000 19.17 19.17 35.02 6.01
2212 2649 2.312741 TCTTCAATTCCCAGCATTCCCT 59.687 45.455 0.00 0.00 0.00 4.20
2218 2655 2.517959 CCACTTCTTCAATTCCCAGCA 58.482 47.619 0.00 0.00 0.00 4.41
2246 2683 1.919654 TCTCAGAGAGCTGGTACTCCT 59.080 52.381 0.00 0.00 42.53 3.69
2251 2688 5.745312 TTTTCATTCTCAGAGAGCTGGTA 57.255 39.130 0.00 0.00 42.53 3.25
2284 2721 5.826737 CCTCATGCTCTTCTCCATAAATGTT 59.173 40.000 0.00 0.00 0.00 2.71
2290 2727 3.334910 TCCCTCATGCTCTTCTCCATA 57.665 47.619 0.00 0.00 0.00 2.74
2378 2815 7.259882 CAAATGCCTATCAAATAGCAACTCAA 58.740 34.615 0.00 0.00 0.00 3.02
2415 2852 4.993584 CAGTAGACCATTGAGTGATATGCC 59.006 45.833 0.00 0.00 0.00 4.40
2424 2861 0.108186 TGCGGCAGTAGACCATTGAG 60.108 55.000 0.00 0.00 0.00 3.02
2468 2905 9.878667 ATTTGATTGATTTTCATGCTTACATCA 57.121 25.926 0.00 0.00 32.87 3.07
2497 2934 2.579860 ACCTGATCTGGAAAGCTTGGAT 59.420 45.455 24.13 1.93 0.00 3.41
2607 3046 4.218200 TGAGGGTGCACTTAAACAATCATG 59.782 41.667 17.98 0.00 0.00 3.07
2623 3064 6.477688 GCAAAACATGAATAATGATGAGGGTG 59.522 38.462 0.00 0.00 38.72 4.61
2678 3125 1.917782 GCGCCACACAATTAAGCCGA 61.918 55.000 0.00 0.00 0.00 5.54
2699 3146 7.520614 GCAGATAAATTTTCCCTATCTCGGTTG 60.521 40.741 0.00 0.00 31.45 3.77
2702 3149 6.234177 AGCAGATAAATTTTCCCTATCTCGG 58.766 40.000 0.00 0.00 31.45 4.63
2704 3151 6.931840 ACGAGCAGATAAATTTTCCCTATCTC 59.068 38.462 0.00 2.07 31.45 2.75
2762 3210 8.133024 TGATCTGGCCTGTAAATTTAAAACAT 57.867 30.769 3.32 0.00 0.00 2.71
2778 3226 2.725221 AAGTCCTGAATGATCTGGCC 57.275 50.000 0.00 0.00 42.71 5.36
2841 3311 2.677542 TACATAGCCTCCCTCGATGT 57.322 50.000 0.00 0.00 34.83 3.06
2881 3351 4.457834 ACCTGATTGTCTACAGCACTAC 57.542 45.455 0.00 0.00 33.40 2.73
2894 3364 7.722363 ACCAAAAGTAAACCTTTACCTGATTG 58.278 34.615 4.61 5.48 42.62 2.67
2938 3408 3.760580 AGCGAGCTATAGCAGGAAAAT 57.239 42.857 26.07 3.69 45.16 1.82
2940 3410 3.223435 ACTAGCGAGCTATAGCAGGAAA 58.777 45.455 26.07 8.03 45.16 3.13
2943 3413 2.817258 AGAACTAGCGAGCTATAGCAGG 59.183 50.000 26.07 17.39 45.16 4.85
3034 3504 9.256228 GTATGAAGGGAGGTAATAGTATCATCA 57.744 37.037 0.00 0.00 0.00 3.07
3038 3508 9.091220 ACTTGTATGAAGGGAGGTAATAGTATC 57.909 37.037 0.00 0.00 0.00 2.24
3042 3512 7.361457 TCACTTGTATGAAGGGAGGTAATAG 57.639 40.000 0.00 0.00 0.00 1.73
3112 3583 1.462731 AACCACACGCACATGCCAAT 61.463 50.000 0.00 0.00 37.91 3.16
3114 3585 0.819666 TAAACCACACGCACATGCCA 60.820 50.000 0.00 0.00 37.91 4.92
3115 3586 0.109781 CTAAACCACACGCACATGCC 60.110 55.000 0.00 0.00 37.91 4.40
3121 3592 3.011119 ACAAAGAACTAAACCACACGCA 58.989 40.909 0.00 0.00 0.00 5.24
3122 3593 3.685836 ACAAAGAACTAAACCACACGC 57.314 42.857 0.00 0.00 0.00 5.34
3156 3627 4.891992 ATGAACACAGTAACTAGGCAGT 57.108 40.909 0.00 0.00 36.19 4.40
3157 3628 4.393062 CCAATGAACACAGTAACTAGGCAG 59.607 45.833 0.00 0.00 0.00 4.85
3160 3631 3.689649 GCCCAATGAACACAGTAACTAGG 59.310 47.826 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.