Multiple sequence alignment - TraesCS7D01G207500

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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 TraesCS7D01G207500 chr7D 100.000 2689 0 0 1 2689 164868000 164870688 0.000000e+00 4966.0
1 TraesCS7D01G207500 chr7D 87.838 74 8 1 1406 1479 447035348 447035420 4.770000e-13 86.1
2 TraesCS7D01G207500 chr7B 93.178 2712 123 29 9 2689 128301695 128304375 0.000000e+00 3927.0
3 TraesCS7D01G207500 chr7A 88.553 2682 179 63 75 2678 166745363 166747994 0.000000e+00 3134.0
4 TraesCS7D01G207500 chr3D 90.000 80 7 1 1401 1480 562472333 562472255 4.740000e-18 102.0
5 TraesCS7D01G207500 chr6D 94.231 52 3 0 1632 1683 384444900 384444849 2.220000e-11 80.5
6 TraesCS7D01G207500 chr6B 94.231 52 3 0 1632 1683 574724809 574724758 2.220000e-11 80.5
7 TraesCS7D01G207500 chr6A 94.231 52 3 0 1632 1683 529025052 529025001 2.220000e-11 80.5
8 TraesCS7D01G207500 chr3B 89.062 64 6 1 1416 1479 157241609 157241671 7.980000e-11 78.7
9 TraesCS7D01G207500 chr3A 89.062 64 6 1 1416 1479 550423794 550423732 7.980000e-11 78.7


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 TraesCS7D01G207500 chr7D 164868000 164870688 2688 False 4966 4966 100.000 1 2689 1 chr7D.!!$F1 2688
1 TraesCS7D01G207500 chr7B 128301695 128304375 2680 False 3927 3927 93.178 9 2689 1 chr7B.!!$F1 2680
2 TraesCS7D01G207500 chr7A 166745363 166747994 2631 False 3134 3134 88.553 75 2678 1 chr7A.!!$F1 2603

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
46 47 1.003118 GACAGTATGCAGTTGGTGGGA 59.997 52.381 0.00 0.0 42.53 4.37 F
1026 1067 0.659427 TCGACGACGACATGATACCC 59.341 55.000 5.75 0.0 43.81 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1094 1135 2.436646 CTAACCGCACCCAGCCAG 60.437 66.667 0.00 0.0 41.38 4.85 R
2503 2605 0.536460 TGAAACCGGAAGCAACTCCC 60.536 55.000 9.46 0.0 31.03 4.30 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
33 34 9.764363 TTTGCATCTATAAAATCGAGACAGTAT 57.236 29.630 0.00 0.00 0.00 2.12
35 36 7.329471 TGCATCTATAAAATCGAGACAGTATGC 59.671 37.037 0.00 0.00 42.53 3.14
39 40 8.414003 TCTATAAAATCGAGACAGTATGCAGTT 58.586 33.333 0.00 0.00 42.53 3.16
46 47 1.003118 GACAGTATGCAGTTGGTGGGA 59.997 52.381 0.00 0.00 42.53 4.37
54 55 1.930656 AGTTGGTGGGATGGGGAGG 60.931 63.158 0.00 0.00 0.00 4.30
55 56 2.616893 TTGGTGGGATGGGGAGGG 60.617 66.667 0.00 0.00 0.00 4.30
269 270 3.247173 GCCTCGACATTGCTAATCTTCAG 59.753 47.826 0.00 0.00 0.00 3.02
382 384 4.562143 GCAAAGTTGGAAATGGAGCATCTT 60.562 41.667 0.00 0.00 33.73 2.40
383 385 5.336690 GCAAAGTTGGAAATGGAGCATCTTA 60.337 40.000 0.00 0.00 33.73 2.10
384 386 6.327934 CAAAGTTGGAAATGGAGCATCTTAG 58.672 40.000 0.00 0.00 33.73 2.18
385 387 5.184892 AGTTGGAAATGGAGCATCTTAGT 57.815 39.130 0.00 0.00 33.73 2.24
386 388 6.313519 AGTTGGAAATGGAGCATCTTAGTA 57.686 37.500 0.00 0.00 33.73 1.82
387 389 6.904626 AGTTGGAAATGGAGCATCTTAGTAT 58.095 36.000 0.00 0.00 33.73 2.12
388 390 6.995091 AGTTGGAAATGGAGCATCTTAGTATC 59.005 38.462 0.00 0.00 33.73 2.24
389 391 6.753913 TGGAAATGGAGCATCTTAGTATCT 57.246 37.500 0.00 0.00 33.73 1.98
513 518 3.589988 ACGGAACATTCTGATGTCACTC 58.410 45.455 7.45 0.00 45.58 3.51
533 538 3.340928 TCATCAGTCAATCACAGGCTTG 58.659 45.455 0.00 0.00 0.00 4.01
546 551 3.188048 CACAGGCTTGTTCAGATCAAGTC 59.812 47.826 15.43 15.43 44.65 3.01
547 552 2.746362 CAGGCTTGTTCAGATCAAGTCC 59.254 50.000 18.41 18.25 45.19 3.85
564 576 6.180472 TCAAGTCCTAGACCCATTTGAAATC 58.820 40.000 0.00 0.00 32.18 2.17
569 581 3.833559 AGACCCATTTGAAATCCTGGT 57.166 42.857 3.69 3.69 0.00 4.00
576 588 5.170748 CCATTTGAAATCCTGGTAACTTGC 58.829 41.667 0.00 0.00 37.61 4.01
583 595 2.660572 TCCTGGTAACTTGCTGCAAAA 58.339 42.857 16.74 2.19 37.61 2.44
594 606 7.551035 AACTTGCTGCAAAATTTACATGAAA 57.449 28.000 16.74 0.00 0.00 2.69
657 669 3.773119 TGACACAAGACCCCTTCCTATAC 59.227 47.826 0.00 0.00 0.00 1.47
667 679 5.793967 ACCCCTTCCTATACAGAAGAAGAT 58.206 41.667 8.68 0.00 42.80 2.40
683 695 7.487189 CAGAAGAAGATATCCAAATGTTGCAAC 59.513 37.037 22.83 22.83 0.00 4.17
691 703 1.722464 CAAATGTTGCAACGGAGCATG 59.278 47.619 23.79 12.77 45.19 4.06
726 750 2.121116 ATGTACATGCTCGTACGCTC 57.879 50.000 11.24 4.99 43.89 5.03
948 978 1.305381 CGTCTTCCTCCTCCCACCT 60.305 63.158 0.00 0.00 0.00 4.00
991 1032 4.707768 TCTCCCCCTTTCCGCCGA 62.708 66.667 0.00 0.00 0.00 5.54
1026 1067 0.659427 TCGACGACGACATGATACCC 59.341 55.000 5.75 0.00 43.81 3.69
1031 1072 4.060900 GACGACGACATGATACCCTACTA 58.939 47.826 0.00 0.00 0.00 1.82
1033 1074 3.120752 CGACGACATGATACCCTACTACG 60.121 52.174 0.00 0.00 0.00 3.51
1094 1135 4.743644 CACCGAGGTAGTTATCGAATTTCC 59.256 45.833 0.00 0.00 41.40 3.13
1122 1163 0.958091 TGCGGTTAGTTGCATTTGCT 59.042 45.000 3.94 0.00 42.66 3.91
1123 1164 1.068610 TGCGGTTAGTTGCATTTGCTC 60.069 47.619 3.94 0.00 42.66 4.26
1165 1206 2.032924 CGGAGTTGTTGGTTTTGGTCTC 59.967 50.000 0.00 0.00 0.00 3.36
1806 1858 1.299773 CGGATTCTCTCTGCCGCTC 60.300 63.158 0.00 0.00 37.08 5.03
1820 1872 1.680249 GCCGCTCCATTTCTCCTTTCT 60.680 52.381 0.00 0.00 0.00 2.52
1983 2045 7.721286 AGTGACAAAACTATGTTCTCTTCTG 57.279 36.000 0.00 0.00 32.57 3.02
2013 2075 3.135994 GACTTGTTGTTACACCCGTCAT 58.864 45.455 0.00 0.00 32.98 3.06
2018 2080 6.095160 ACTTGTTGTTACACCCGTCATTTTTA 59.905 34.615 0.00 0.00 32.98 1.52
2019 2081 6.636562 TGTTGTTACACCCGTCATTTTTAT 57.363 33.333 0.00 0.00 0.00 1.40
2020 2082 6.670233 TGTTGTTACACCCGTCATTTTTATC 58.330 36.000 0.00 0.00 0.00 1.75
2021 2083 6.487331 TGTTGTTACACCCGTCATTTTTATCT 59.513 34.615 0.00 0.00 0.00 1.98
2022 2084 6.730960 TGTTACACCCGTCATTTTTATCTC 57.269 37.500 0.00 0.00 0.00 2.75
2023 2085 6.231951 TGTTACACCCGTCATTTTTATCTCA 58.768 36.000 0.00 0.00 0.00 3.27
2024 2086 6.882140 TGTTACACCCGTCATTTTTATCTCAT 59.118 34.615 0.00 0.00 0.00 2.90
2090 2157 2.624169 GCAGTGGGCAACGTAAAGA 58.376 52.632 0.00 0.00 43.97 2.52
2181 2249 5.336531 GCAGTAAGTGTATCACCAGTACAGT 60.337 44.000 0.00 0.00 37.32 3.55
2182 2250 6.127814 GCAGTAAGTGTATCACCAGTACAGTA 60.128 42.308 0.00 0.00 35.29 2.74
2183 2251 7.249147 CAGTAAGTGTATCACCAGTACAGTAC 58.751 42.308 2.05 2.05 35.29 2.73
2184 2252 6.944290 AGTAAGTGTATCACCAGTACAGTACA 59.056 38.462 13.37 0.00 35.29 2.90
2185 2253 6.852420 AAGTGTATCACCAGTACAGTACAT 57.148 37.500 13.37 0.05 35.29 2.29
2193 2261 1.807981 GTACAGTACATGCGCGGCA 60.808 57.895 8.83 7.01 44.86 5.69
2222 2290 0.318441 TTTCTCTCCTGTCCGTGCAG 59.682 55.000 0.00 0.00 36.31 4.41
2223 2291 2.125753 CTCTCCTGTCCGTGCAGC 60.126 66.667 0.00 0.00 35.28 5.25
2297 2365 4.056125 CGAGTGCCAGCTGACCGA 62.056 66.667 17.39 0.00 0.00 4.69
2305 2380 3.805307 AGCTGACCGACGAGAGCG 61.805 66.667 0.00 0.00 44.79 5.03
2348 2423 3.342627 CGAACCTTTGCACGGCGA 61.343 61.111 16.62 0.00 0.00 5.54
2378 2453 2.537560 CGCCGCATGGGTTCATCTC 61.538 63.158 9.14 0.00 38.44 2.75
2503 2605 1.611519 GAGGAGGAGGAGATGTACCG 58.388 60.000 0.00 0.00 0.00 4.02
2521 2623 2.254471 GGGAGTTGCTTCCGGTTTC 58.746 57.895 0.00 0.00 38.17 2.78
2639 2747 4.977963 CACACATGTTTAACCTGAAGCTTG 59.022 41.667 2.10 0.00 0.00 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.373048 TCGATTTTATAGATGCAAATTACCGT 57.627 30.769 0.00 0.00 0.00 4.83
1 2 8.708742 TCTCGATTTTATAGATGCAAATTACCG 58.291 33.333 0.00 0.00 0.00 4.02
2 3 9.813080 GTCTCGATTTTATAGATGCAAATTACC 57.187 33.333 0.00 0.00 0.00 2.85
5 6 9.113838 ACTGTCTCGATTTTATAGATGCAAATT 57.886 29.630 0.00 0.00 0.00 1.82
6 7 8.668510 ACTGTCTCGATTTTATAGATGCAAAT 57.331 30.769 0.00 0.00 0.00 2.32
7 8 9.764363 ATACTGTCTCGATTTTATAGATGCAAA 57.236 29.630 0.00 0.00 0.00 3.68
24 25 2.350522 CCACCAACTGCATACTGTCTC 58.649 52.381 0.00 0.00 0.00 3.36
33 34 2.440147 CCCATCCCACCAACTGCA 59.560 61.111 0.00 0.00 0.00 4.41
35 36 1.304282 CTCCCCATCCCACCAACTG 59.696 63.158 0.00 0.00 0.00 3.16
39 40 4.777546 CCCCTCCCCATCCCACCA 62.778 72.222 0.00 0.00 0.00 4.17
54 55 7.996644 TCATGAACTACATATTTTTACTCCCCC 59.003 37.037 0.00 0.00 37.46 5.40
55 56 8.974060 TCATGAACTACATATTTTTACTCCCC 57.026 34.615 0.00 0.00 37.46 4.81
269 270 6.425114 TCATTGTCTAGTTGTCTCTTCTTTGC 59.575 38.462 0.00 0.00 0.00 3.68
513 518 3.079578 ACAAGCCTGTGATTGACTGATG 58.920 45.455 0.00 0.00 40.30 3.07
523 528 3.181451 ACTTGATCTGAACAAGCCTGTGA 60.181 43.478 22.70 0.00 45.66 3.58
533 538 3.769844 TGGGTCTAGGACTTGATCTGAAC 59.230 47.826 0.00 0.00 32.47 3.18
546 551 4.210331 CCAGGATTTCAAATGGGTCTAGG 58.790 47.826 0.00 0.00 0.00 3.02
547 552 4.860022 ACCAGGATTTCAAATGGGTCTAG 58.140 43.478 0.00 0.00 37.13 2.43
564 576 3.665745 ATTTTGCAGCAAGTTACCAGG 57.334 42.857 8.12 0.00 0.00 4.45
569 581 8.654230 TTTCATGTAAATTTTGCAGCAAGTTA 57.346 26.923 8.12 6.00 0.00 2.24
625 637 3.433173 GGGTCTTGTGTCACTAAACCAGT 60.433 47.826 11.33 0.00 38.32 4.00
626 638 3.139077 GGGTCTTGTGTCACTAAACCAG 58.861 50.000 11.33 0.00 0.00 4.00
657 669 7.092137 TGCAACATTTGGATATCTTCTTCTG 57.908 36.000 2.05 0.00 0.00 3.02
667 679 2.163412 GCTCCGTTGCAACATTTGGATA 59.837 45.455 28.01 6.45 0.00 2.59
679 691 2.870372 GTGACCATGCTCCGTTGC 59.130 61.111 0.00 0.00 0.00 4.17
691 703 0.748005 ACATTATGCAGCCCGTGACC 60.748 55.000 0.00 0.00 0.00 4.02
726 750 2.774126 CGCGCATATGCTCCATCG 59.226 61.111 24.56 15.13 39.32 3.84
948 978 1.602323 GGCGGTGGTGAATGGTGAA 60.602 57.895 0.00 0.00 0.00 3.18
976 1017 3.712907 CTTCGGCGGAAAGGGGGA 61.713 66.667 7.21 0.00 0.00 4.81
991 1032 1.448540 CGAGGTCCATTGCTCGCTT 60.449 57.895 0.00 0.00 32.62 4.68
1094 1135 2.436646 CTAACCGCACCCAGCCAG 60.437 66.667 0.00 0.00 41.38 4.85
1122 1163 2.629210 CGCACGCAAGAAAACGGA 59.371 55.556 0.00 0.00 43.62 4.69
1123 1164 3.091022 GCGCACGCAAGAAAACGG 61.091 61.111 10.65 0.00 41.49 4.44
1165 1206 3.934391 GACCCCGTCGACTGCCAAG 62.934 68.421 14.70 0.00 0.00 3.61
1983 2045 5.028375 GTGTAACAACAAGTCAACAAGAGC 58.972 41.667 0.00 0.00 36.32 4.09
2018 2080 7.914427 TGGTATTTACAGGAGTACATGAGAT 57.086 36.000 0.00 0.00 0.00 2.75
2019 2081 7.727578 TTGGTATTTACAGGAGTACATGAGA 57.272 36.000 0.00 0.00 0.00 3.27
2020 2082 8.786826 TTTTGGTATTTACAGGAGTACATGAG 57.213 34.615 0.00 0.00 0.00 2.90
2021 2083 8.380099 ACTTTTGGTATTTACAGGAGTACATGA 58.620 33.333 0.00 0.00 0.00 3.07
2022 2084 8.561738 ACTTTTGGTATTTACAGGAGTACATG 57.438 34.615 0.00 0.00 0.00 3.21
2102 2169 6.252869 AGCACGAAATAGTACAGACAAATACG 59.747 38.462 0.00 0.00 0.00 3.06
2193 2261 0.693049 AGGAGAGAAAATGCCACGGT 59.307 50.000 0.00 0.00 0.00 4.83
2297 2365 1.371389 GTTTCGTGTCCGCTCTCGT 60.371 57.895 0.00 0.00 0.00 4.18
2305 2380 2.735857 CGTCGGGGTTTCGTGTCC 60.736 66.667 0.00 0.00 0.00 4.02
2378 2453 3.187699 CTCCGAGAGCGACCGATGG 62.188 68.421 0.00 0.00 40.82 3.51
2503 2605 0.536460 TGAAACCGGAAGCAACTCCC 60.536 55.000 9.46 0.00 31.03 4.30
2639 2747 1.450531 CCAGAGCGGCCATCCAATTC 61.451 60.000 2.24 0.00 0.00 2.17


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

AutoCloner maintained by Alex Coulton.