Multiple sequence alignment - TraesCS7A01G071300

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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 TraesCS7A01G071300 chr7A 100.000 2549 0 0 1 2549 36945599 36948147 0.000000e+00 4708
1 TraesCS7A01G071300 chr2A 96.366 1954 61 7 602 2549 677958469 677956520 0.000000e+00 3206
2 TraesCS7A01G071300 chr2A 96.315 1954 63 7 602 2549 744582029 744583979 0.000000e+00 3201
3 TraesCS7A01G071300 chr2A 95.077 1950 88 8 600 2545 677413608 677411663 0.000000e+00 3062
4 TraesCS7A01G071300 chr2A 93.093 1969 111 19 596 2549 213959522 213957564 0.000000e+00 2859
5 TraesCS7A01G071300 chr2A 97.639 847 20 0 292 1138 695807062 695806216 0.000000e+00 1454
6 TraesCS7A01G071300 chr5A 96.101 1949 66 6 602 2547 689446507 689444566 0.000000e+00 3169
7 TraesCS7A01G071300 chr5B 95.801 1953 77 3 602 2549 3450172 3448220 0.000000e+00 3147
8 TraesCS7A01G071300 chr1B 95.363 1941 69 7 602 2536 645321437 645323362 0.000000e+00 3066
9 TraesCS7A01G071300 chr7D 94.898 1960 80 15 599 2549 63995387 63997335 0.000000e+00 3048
10 TraesCS7A01G071300 chr7D 94.343 601 34 0 1 601 626916160 626916760 0.000000e+00 922
11 TraesCS7A01G071300 chr7D 81.833 611 106 5 1 608 614834286 614834894 2.260000e-140 508
12 TraesCS7A01G071300 chr3D 94.836 1956 83 14 602 2549 475106681 475108626 0.000000e+00 3037
13 TraesCS7A01G071300 chr2D 92.939 609 41 2 1 608 606042814 606042207 0.000000e+00 885
14 TraesCS7A01G071300 chr2D 92.623 610 43 2 1 608 9864442 9865051 0.000000e+00 876
15 TraesCS7A01G071300 chr2D 83.306 605 100 1 1 605 63223011 63223614 7.970000e-155 556
16 TraesCS7A01G071300 chr5D 86.371 609 82 1 1 608 225508594 225509202 0.000000e+00 664
17 TraesCS7A01G071300 chr1D 84.628 605 92 1 1 605 375250351 375249748 3.630000e-168 601
18 TraesCS7A01G071300 chr6B 82.516 612 98 9 1 608 714217139 714216533 1.740000e-146 529


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 TraesCS7A01G071300 chr7A 36945599 36948147 2548 False 4708 4708 100.000 1 2549 1 chr7A.!!$F1 2548
1 TraesCS7A01G071300 chr2A 677956520 677958469 1949 True 3206 3206 96.366 602 2549 1 chr2A.!!$R3 1947
2 TraesCS7A01G071300 chr2A 744582029 744583979 1950 False 3201 3201 96.315 602 2549 1 chr2A.!!$F1 1947
3 TraesCS7A01G071300 chr2A 677411663 677413608 1945 True 3062 3062 95.077 600 2545 1 chr2A.!!$R2 1945
4 TraesCS7A01G071300 chr2A 213957564 213959522 1958 True 2859 2859 93.093 596 2549 1 chr2A.!!$R1 1953
5 TraesCS7A01G071300 chr2A 695806216 695807062 846 True 1454 1454 97.639 292 1138 1 chr2A.!!$R4 846
6 TraesCS7A01G071300 chr5A 689444566 689446507 1941 True 3169 3169 96.101 602 2547 1 chr5A.!!$R1 1945
7 TraesCS7A01G071300 chr5B 3448220 3450172 1952 True 3147 3147 95.801 602 2549 1 chr5B.!!$R1 1947
8 TraesCS7A01G071300 chr1B 645321437 645323362 1925 False 3066 3066 95.363 602 2536 1 chr1B.!!$F1 1934
9 TraesCS7A01G071300 chr7D 63995387 63997335 1948 False 3048 3048 94.898 599 2549 1 chr7D.!!$F1 1950
10 TraesCS7A01G071300 chr7D 626916160 626916760 600 False 922 922 94.343 1 601 1 chr7D.!!$F3 600
11 TraesCS7A01G071300 chr7D 614834286 614834894 608 False 508 508 81.833 1 608 1 chr7D.!!$F2 607
12 TraesCS7A01G071300 chr3D 475106681 475108626 1945 False 3037 3037 94.836 602 2549 1 chr3D.!!$F1 1947
13 TraesCS7A01G071300 chr2D 606042207 606042814 607 True 885 885 92.939 1 608 1 chr2D.!!$R1 607
14 TraesCS7A01G071300 chr2D 9864442 9865051 609 False 876 876 92.623 1 608 1 chr2D.!!$F1 607
15 TraesCS7A01G071300 chr2D 63223011 63223614 603 False 556 556 83.306 1 605 1 chr2D.!!$F2 604
16 TraesCS7A01G071300 chr5D 225508594 225509202 608 False 664 664 86.371 1 608 1 chr5D.!!$F1 607
17 TraesCS7A01G071300 chr1D 375249748 375250351 603 True 601 601 84.628 1 605 1 chr1D.!!$R1 604
18 TraesCS7A01G071300 chr6B 714216533 714217139 606 True 529 529 82.516 1 608 1 chr6B.!!$R1 607

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
883 887 1.665264 TATAAGCGGGCGACAACGGA 61.665 55.0 0.0 0.0 40.15 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2025 2050 1.093159 CCAGAGCTGAGGCACATTTC 58.907 55.0 0.0 0.0 41.7 2.17 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
53 54 4.644234 TGAGATTTCTAGCACTCTCCTCAG 59.356 45.833 7.17 0.0 34.54 3.35
118 119 2.919602 GCTTATCCCATTATCCCCCAGA 59.080 50.000 0.00 0.0 0.00 3.86
143 144 7.081857 TCAGTTAACACCCCTTTTACATAGT 57.918 36.000 8.61 0.0 0.00 2.12
155 156 5.705441 CCTTTTACATAGTCTGCCTGTTTGA 59.295 40.000 0.00 0.0 0.00 2.69
756 759 2.500229 CTTTTGACTCGGCCCTTACAA 58.500 47.619 0.00 0.0 0.00 2.41
824 827 2.776526 TGGCTTGTGGGACCCAGT 60.777 61.111 15.52 0.0 32.34 4.00
879 883 2.074547 GCTATATAAGCGGGCGACAA 57.925 50.000 0.00 0.0 42.53 3.18
883 887 1.665264 TATAAGCGGGCGACAACGGA 61.665 55.000 0.00 0.0 40.15 4.69
948 960 2.737376 GAGCACGACGGTGGGAAC 60.737 66.667 0.00 0.0 44.54 3.62
1078 1090 2.651361 CTGTCTTCGCCTGTCCGT 59.349 61.111 0.00 0.0 0.00 4.69
1118 1130 2.103153 TGGAGGGTTTCTCAGACACT 57.897 50.000 0.00 0.0 44.19 3.55
1120 1132 1.002544 GGAGGGTTTCTCAGACACTGG 59.997 57.143 0.00 0.0 44.19 4.00
1195 1207 1.460359 CAATTGCACCATTTTCGTGGC 59.540 47.619 0.00 0.0 43.27 5.01
1428 1441 4.397417 GCTGTTGAGCTTAGGATGTTGAAT 59.603 41.667 0.00 0.0 42.52 2.57
1490 1503 4.349342 ACCCATTTGCAAATACTTTTGGGA 59.651 37.500 36.19 7.3 42.09 4.37
1510 1523 7.214460 TGGGAATTTGTAGGTATGGTAATCA 57.786 36.000 0.00 0.0 0.00 2.57
2003 2028 8.240682 TCCAATTCAAATACACCGTGATTTAAG 58.759 33.333 5.28 0.0 0.00 1.85
2025 2050 4.281688 AGTCAAAGACCAAAATGTCATGGG 59.718 41.667 0.00 0.0 41.17 4.00
2219 2248 0.838554 TAGGGCTGCACTGGTAACCA 60.839 55.000 16.10 0.0 0.00 3.67
2407 2441 3.342719 TGTATGTTGCACTACCACATGG 58.657 45.455 10.54 0.0 42.17 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
98 99 4.790246 TGATCTGGGGGATAATGGGATAAG 59.210 45.833 0.00 0.0 34.33 1.73
118 119 7.696017 ACTATGTAAAAGGGGTGTTAACTGAT 58.304 34.615 7.22 0.0 0.00 2.90
143 144 7.004555 TCTTAGATAAAGTCAAACAGGCAGA 57.995 36.000 0.00 0.0 36.51 4.26
155 156 8.159344 GCATTGGCACTAATCTTAGATAAAGT 57.841 34.615 4.03 0.0 40.72 2.66
265 267 4.582656 CAGGTTGGTGTTAAGGTGAATGAA 59.417 41.667 0.00 0.0 0.00 2.57
824 827 1.098869 CTCTGCTCAACGGCTCTCTA 58.901 55.000 0.00 0.0 0.00 2.43
883 887 3.991051 CTGTCGCCGTGGTCACCT 61.991 66.667 0.00 0.0 0.00 4.00
919 923 2.402572 CGTGCTCTCTCTCTCGCCA 61.403 63.158 0.00 0.0 0.00 5.69
948 960 4.537433 GCGCCCTCCACTGCTAGG 62.537 72.222 0.00 0.0 0.00 3.02
1118 1130 1.895020 CGGACGATTCTGGTTCCCCA 61.895 60.000 0.00 0.0 38.87 4.96
1120 1132 0.036671 AACGGACGATTCTGGTTCCC 60.037 55.000 0.00 0.0 31.53 3.97
1195 1207 1.027357 CCATTGCTCAAAGATCCCGG 58.973 55.000 0.00 0.0 0.00 5.73
1355 1367 1.484240 CCATCTCTTCTTCCGGAGCTT 59.516 52.381 3.34 0.0 0.00 3.74
1428 1441 6.681729 TCTTCAAGCTTCCTAACCTTCTTA 57.318 37.500 0.00 0.0 0.00 2.10
1490 1503 7.556275 CCAGTGTGATTACCATACCTACAAATT 59.444 37.037 0.00 0.0 37.58 1.82
1510 1523 6.872920 ACATTTTCAACATTACAACCAGTGT 58.127 32.000 0.00 0.0 44.82 3.55
2003 2028 4.280677 TCCCATGACATTTTGGTCTTTGAC 59.719 41.667 0.00 0.0 38.61 3.18
2025 2050 1.093159 CCAGAGCTGAGGCACATTTC 58.907 55.000 0.00 0.0 41.70 2.17
2219 2248 2.826488 AGTCTTGCCATCTGTCCTAGT 58.174 47.619 0.00 0.0 0.00 2.57
2407 2441 1.680338 AGTGCCACTCTGACCAAAAC 58.320 50.000 0.00 0.0 0.00 2.43


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

AutoCloner maintained by Alex Coulton.