Multiple sequence alignment - TraesCS6D01G210300

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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 TraesCS6D01G210300 chr6D 100.000 2906 0 0 1 2906 296859770 296862675 0.000000e+00 5367.0
1 TraesCS6D01G210300 chr6A 93.783 2799 127 24 1 2768 424086476 424089258 0.000000e+00 4161.0
2 TraesCS6D01G210300 chr6B 94.709 2287 72 22 638 2906 460092485 460090230 0.000000e+00 3507.0
3 TraesCS6D01G210300 chr6B 86.790 651 59 13 1 639 460093909 460093274 0.000000e+00 701.0
4 TraesCS6D01G210300 chr3B 98.755 241 3 0 1796 2036 242897778 242897538 2.070000e-116 429.0
5 TraesCS6D01G210300 chr4B 98.404 188 3 0 1849 2036 241353741 241353928 6.000000e-87 331.0
6 TraesCS6D01G210300 chr2A 98.404 188 3 0 1849 2036 135190494 135190307 6.000000e-87 331.0
7 TraesCS6D01G210300 chr2A 98.404 188 3 0 1849 2036 160160122 160160309 6.000000e-87 331.0
8 TraesCS6D01G210300 chr2A 98.907 183 2 0 1854 2036 135189496 135189314 7.760000e-86 327.0
9 TraesCS6D01G210300 chr2A 96.000 75 2 1 1962 2036 159927832 159927905 1.410000e-23 121.0
10 TraesCS6D01G210300 chr7B 94.444 36 0 2 598 633 636877600 636877633 1.000000e-03 54.7


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 TraesCS6D01G210300 chr6D 296859770 296862675 2905 False 5367 5367 100.0000 1 2906 1 chr6D.!!$F1 2905
1 TraesCS6D01G210300 chr6A 424086476 424089258 2782 False 4161 4161 93.7830 1 2768 1 chr6A.!!$F1 2767
2 TraesCS6D01G210300 chr6B 460090230 460093909 3679 True 2104 3507 90.7495 1 2906 2 chr6B.!!$R1 2905
3 TraesCS6D01G210300 chr2A 135189314 135190494 1180 True 329 331 98.6555 1849 2036 2 chr2A.!!$R1 187

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
918 1728 0.669318 GAGTGACCACGGCGAATCAA 60.669 55.0 16.62 0.0 36.2 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2633 3455 0.036294 ACTTCGGGCTGTTCTAAGGC 60.036 55.0 0.0 0.0 41.86 4.35 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
36 37 6.234177 CCTAGCATCTAATCGGGAGAATTTT 58.766 40.000 0.00 0.00 45.37 1.82
66 67 3.949113 TCTTTTTCAGGTTTGTAAGCGGT 59.051 39.130 0.00 0.00 0.00 5.68
185 197 3.010200 AGGGCCTAAAGAATCTGCTTG 57.990 47.619 2.82 0.00 0.00 4.01
398 411 0.934496 CTCGCACAAGAAACCGTTCA 59.066 50.000 0.00 0.00 36.09 3.18
431 444 4.938129 ACACTTTAGTAAAATTCGTCGCG 58.062 39.130 0.00 0.00 0.00 5.87
447 460 0.726827 CGCGTATTCACCACATGCTT 59.273 50.000 0.00 0.00 0.00 3.91
578 592 8.015185 TGAAACTAAGAAAGTAGTGTACCTGT 57.985 34.615 0.00 0.00 37.50 4.00
687 1489 2.450476 CAGCTAGGTGGAGGCAAAAAT 58.550 47.619 14.29 0.00 0.00 1.82
918 1728 0.669318 GAGTGACCACGGCGAATCAA 60.669 55.000 16.62 0.00 36.20 2.57
1230 2040 3.244249 TGGTTTCGACATGGACACATACA 60.244 43.478 0.00 0.00 34.99 2.29
1392 2202 3.585289 TCACCAGTGGCCTTTATGTTCTA 59.415 43.478 9.78 0.00 0.00 2.10
1416 2226 2.738743 CCAATTTGCCATACCCTCACT 58.261 47.619 0.00 0.00 0.00 3.41
1437 2247 5.026121 ACTAGGTCCATCAGTTCAGATTCA 58.974 41.667 0.00 0.00 0.00 2.57
1581 2391 0.861866 CGTCGATAGTGGCGTCTGTG 60.862 60.000 0.00 0.00 37.40 3.66
1791 2601 4.005650 TCTTCATTTTACTGCTGGCTCTG 58.994 43.478 0.00 0.00 0.00 3.35
2067 2877 3.691609 GCTACTGTGGCTCTAAATGCTTT 59.308 43.478 9.05 0.00 0.00 3.51
2080 2890 8.281893 GCTCTAAATGCTTTGCAAAATTTTGTA 58.718 29.630 27.13 22.18 43.62 2.41
2113 2923 3.136443 TGGTCTGGTGATGTGTTTTCTCT 59.864 43.478 0.00 0.00 0.00 3.10
2234 3044 6.091441 AGCAACACTGATTATTTTCTCTCGTC 59.909 38.462 0.00 0.00 0.00 4.20
2289 3099 3.825143 AAAAGAAACAGCCTGTGCATT 57.175 38.095 0.00 0.00 41.13 3.56
2322 3132 3.071479 TCAGTTCTATGTTTGCGGGAAC 58.929 45.455 0.00 0.00 37.23 3.62
2362 3173 1.002888 ACTCTGCACTCTGTTGATGGG 59.997 52.381 0.00 0.00 0.00 4.00
2446 3257 3.849951 GCCGCCCTCTCCGATTCA 61.850 66.667 0.00 0.00 0.00 2.57
2465 3276 7.031372 CGATTCAAAATGACTGAAACCATCAT 58.969 34.615 0.00 0.00 37.44 2.45
2512 3323 2.691526 ACACACACTCGAACCTAAGACA 59.308 45.455 0.00 0.00 0.00 3.41
2513 3324 3.243434 ACACACACTCGAACCTAAGACAG 60.243 47.826 0.00 0.00 0.00 3.51
2623 3445 4.979197 GGAGTCTAAGACATGAACTATGCG 59.021 45.833 0.00 0.00 40.59 4.73
2628 3450 6.019479 GTCTAAGACATGAACTATGCGAAAGG 60.019 42.308 0.00 0.00 40.59 3.11
2648 3470 1.144057 ATCGCCTTAGAACAGCCCG 59.856 57.895 0.00 0.00 0.00 6.13
2659 3481 4.015872 AGAACAGCCCGAAGTATGAAAA 57.984 40.909 0.00 0.00 0.00 2.29
2660 3482 4.589908 AGAACAGCCCGAAGTATGAAAAT 58.410 39.130 0.00 0.00 0.00 1.82
2673 3495 5.874093 AGTATGAAAATAGCATAGGCAGCT 58.126 37.500 0.67 4.60 44.61 4.24
2680 3502 0.179089 AGCATAGGCAGCTGTCGAAG 60.179 55.000 16.64 7.51 44.61 3.79
2681 3503 0.460987 GCATAGGCAGCTGTCGAAGT 60.461 55.000 16.64 0.00 40.72 3.01
2699 3521 1.375140 TGAAGAAGCCAGCGAGCTG 60.375 57.895 17.44 17.44 44.11 4.24
2748 3570 1.592223 CCGAACTCCAGGTCTCCAC 59.408 63.158 0.00 0.00 0.00 4.02
2749 3571 1.592223 CGAACTCCAGGTCTCCACC 59.408 63.158 0.00 0.00 44.19 4.61
2783 3605 1.296727 GTACGCCTCATTTGCTACCC 58.703 55.000 0.00 0.00 0.00 3.69
2784 3606 0.179094 TACGCCTCATTTGCTACCCG 60.179 55.000 0.00 0.00 0.00 5.28
2785 3607 2.823829 CGCCTCATTTGCTACCCGC 61.824 63.158 0.00 0.00 39.77 6.13
2786 3608 1.452108 GCCTCATTTGCTACCCGCT 60.452 57.895 0.00 0.00 40.11 5.52
2787 3609 1.440145 GCCTCATTTGCTACCCGCTC 61.440 60.000 0.00 0.00 40.11 5.03
2788 3610 0.179000 CCTCATTTGCTACCCGCTCT 59.821 55.000 0.00 0.00 40.11 4.09
2789 3611 1.412710 CCTCATTTGCTACCCGCTCTA 59.587 52.381 0.00 0.00 40.11 2.43
2824 3646 0.527565 GCACGGACCAATCATTGCTT 59.472 50.000 0.00 0.00 33.39 3.91
2842 3664 6.768029 TTGCTTCAATTGCACATTAGTTTC 57.232 33.333 0.00 0.00 40.40 2.78
2858 3680 4.373156 AGTTTCACAAGCATCTTAGGGT 57.627 40.909 0.00 0.00 0.00 4.34
2861 3683 3.616956 TCACAAGCATCTTAGGGTCAG 57.383 47.619 0.00 0.00 0.00 3.51
2862 3684 2.906389 TCACAAGCATCTTAGGGTCAGT 59.094 45.455 0.00 0.00 0.00 3.41
2901 3724 7.493976 AAGATTATATCGTTTCTACATCGCG 57.506 36.000 0.00 0.00 0.00 5.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 6.693315 ACAAACCTGAAAAAGAAAGATCGA 57.307 33.333 0.00 0.00 0.00 3.59
66 67 2.224744 TGCTTTTGGTGATGCTAGTGGA 60.225 45.455 0.00 0.00 0.00 4.02
101 102 3.541996 TGATGAGATGCGTACCATTGT 57.458 42.857 0.00 0.00 33.29 2.71
103 104 3.251729 GCATTGATGAGATGCGTACCATT 59.748 43.478 0.00 0.00 40.30 3.16
106 107 2.957576 GCATTGATGAGATGCGTACC 57.042 50.000 0.00 0.00 40.30 3.34
163 174 3.010200 AGCAGATTCTTTAGGCCCTTG 57.990 47.619 0.00 0.00 0.00 3.61
185 197 0.177373 ACGGTTTATCGGGGCTTCTC 59.823 55.000 0.00 0.00 0.00 2.87
195 207 6.962686 ACAACCTCTGTAAAAACGGTTTATC 58.037 36.000 6.53 0.00 36.10 1.75
281 294 8.706492 TCGTACTGAACCGATACAAATAATTT 57.294 30.769 0.00 0.00 0.00 1.82
310 323 6.763610 AGTTCTTTCGTTTGAAGAGAGTTCAT 59.236 34.615 0.00 0.00 35.06 2.57
431 444 6.183360 TGTCGAATAAAGCATGTGGTGAATAC 60.183 38.462 0.00 0.00 0.00 1.89
587 601 7.874016 TGTAACTTTATTTATACCCGCGATCAT 59.126 33.333 8.23 0.00 0.00 2.45
646 1448 1.135944 GCACGCTTAAGAGTTTGAGCC 60.136 52.381 9.34 0.00 41.48 4.70
687 1489 2.091939 TGCAGGGCTGGCTCAAATATTA 60.092 45.455 0.00 0.00 0.00 0.98
918 1728 3.782443 GGTCCGGATTCGCACCCT 61.782 66.667 7.81 0.00 41.18 4.34
1071 1881 3.004002 CGGTGTAGTTATCATCGTAGCCA 59.996 47.826 0.00 0.00 35.13 4.75
1230 2040 1.086696 CGTCGATGGCCAAATTCAGT 58.913 50.000 10.96 0.00 0.00 3.41
1416 2226 6.385176 AGATTGAATCTGAACTGATGGACCTA 59.615 38.462 6.93 0.00 38.44 3.08
1437 2247 2.649831 CACAGCAAGTGCCCAGATT 58.350 52.632 0.00 0.00 42.15 2.40
1743 2553 0.389817 GATGCAGCTGGTACGTGACA 60.390 55.000 17.12 2.03 0.00 3.58
1779 2589 2.044806 AAACGACCAGAGCCAGCAGT 62.045 55.000 0.00 0.00 0.00 4.40
1791 2601 1.798813 ACAAGCGAGATGAAAACGACC 59.201 47.619 0.00 0.00 0.00 4.79
2067 2877 6.421501 CAGAGTGCAGAATACAAAATTTTGCA 59.578 34.615 26.94 17.41 43.69 4.08
2080 2890 1.002888 CACCAGACCAGAGTGCAGAAT 59.997 52.381 0.00 0.00 0.00 2.40
2188 2998 2.264455 AGAATGAGCAAGACACCCTCT 58.736 47.619 0.00 0.00 0.00 3.69
2190 3000 2.093235 GCTAGAATGAGCAAGACACCCT 60.093 50.000 0.00 0.00 42.36 4.34
2304 3114 3.071479 TCAGTTCCCGCAAACATAGAAC 58.929 45.455 0.00 0.00 37.65 3.01
2307 3117 3.074412 AGTTCAGTTCCCGCAAACATAG 58.926 45.455 1.71 0.00 0.00 2.23
2322 3132 1.972872 AGGGTTGAGTTGCAGTTCAG 58.027 50.000 2.98 0.00 0.00 3.02
2362 3173 1.271597 ACAGGAGATTGTGGAGCCAAC 60.272 52.381 0.00 0.00 0.00 3.77
2415 3226 1.098129 GGCGGCCTCTCTTTTGATCC 61.098 60.000 12.87 0.00 0.00 3.36
2446 3257 4.529377 AGGCATGATGGTTTCAGTCATTTT 59.471 37.500 0.00 0.00 37.89 1.82
2465 3276 3.138653 TGGGTTTGTAGTTCCTTAAGGCA 59.861 43.478 17.32 2.48 34.44 4.75
2512 3323 4.523173 TGGTCTGTAATTTGTCTCGACTCT 59.477 41.667 0.00 0.00 0.00 3.24
2513 3324 4.806330 TGGTCTGTAATTTGTCTCGACTC 58.194 43.478 0.00 0.00 0.00 3.36
2584 3406 4.107072 AGACTCCTCTGAATTTGGGATCA 58.893 43.478 0.00 0.00 0.00 2.92
2628 3450 1.440145 GGGCTGTTCTAAGGCGATGC 61.440 60.000 0.00 0.00 43.45 3.91
2633 3455 0.036294 ACTTCGGGCTGTTCTAAGGC 60.036 55.000 0.00 0.00 41.86 4.35
2635 3457 4.386867 TCATACTTCGGGCTGTTCTAAG 57.613 45.455 0.00 0.00 0.00 2.18
2648 3470 6.429385 AGCTGCCTATGCTATTTTCATACTTC 59.571 38.462 0.00 0.00 39.21 3.01
2659 3481 1.332195 TCGACAGCTGCCTATGCTAT 58.668 50.000 15.27 0.00 38.92 2.97
2660 3482 1.067669 CTTCGACAGCTGCCTATGCTA 59.932 52.381 15.27 0.00 38.92 3.49
2673 3495 1.873903 GCTGGCTTCTTCACTTCGACA 60.874 52.381 0.00 0.00 0.00 4.35
2680 3502 1.375268 AGCTCGCTGGCTTCTTCAC 60.375 57.895 0.00 0.00 39.86 3.18
2681 3503 1.375140 CAGCTCGCTGGCTTCTTCA 60.375 57.895 10.98 0.00 41.00 3.02
2699 3521 2.010582 CTGACGGGACCTAGAGCAGC 62.011 65.000 0.00 0.00 0.00 5.25
2749 3571 4.155733 TACCACGCATCGCAGGGG 62.156 66.667 0.00 0.00 33.35 4.79
2785 3607 0.615331 TGGGAGCAAAGCTGGTAGAG 59.385 55.000 0.00 0.00 39.88 2.43
2786 3608 0.615331 CTGGGAGCAAAGCTGGTAGA 59.385 55.000 0.00 0.00 39.88 2.59
2787 3609 1.028868 GCTGGGAGCAAAGCTGGTAG 61.029 60.000 0.00 0.00 41.89 3.18
2788 3610 1.002134 GCTGGGAGCAAAGCTGGTA 60.002 57.895 0.00 0.00 41.89 3.25
2789 3611 2.282745 GCTGGGAGCAAAGCTGGT 60.283 61.111 0.00 0.00 41.89 4.00
2824 3646 5.691305 GCTTGTGAAACTAATGTGCAATTGA 59.309 36.000 10.34 0.00 38.04 2.57
2842 3664 3.340814 ACTGACCCTAAGATGCTTGTG 57.659 47.619 0.00 0.00 0.00 3.33


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

AutoCloner maintained by Alex Coulton.