Multiple sequence alignment - TraesCS7B01G264500

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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 TraesCS7B01G264500 chr7B 100.000 2324 0 0 1 2324 484928864 484926541 0.000000e+00 4292
1 TraesCS7B01G264500 chr7B 92.413 659 43 5 1671 2324 393363086 393363742 0.000000e+00 933
2 TraesCS7B01G264500 chr6B 96.318 1684 58 4 1 1684 18600449 18598770 0.000000e+00 2763
3 TraesCS7B01G264500 chr6B 95.779 1682 64 5 1 1679 573347663 573349340 0.000000e+00 2706
4 TraesCS7B01G264500 chr6B 92.273 660 43 4 1671 2324 580865177 580865834 0.000000e+00 929
5 TraesCS7B01G264500 chr5B 90.263 1674 155 7 1 1672 364099711 364098044 0.000000e+00 2182
6 TraesCS7B01G264500 chr3B 88.571 1680 178 13 2 1676 629908993 629910663 0.000000e+00 2026
7 TraesCS7B01G264500 chr3B 92.121 660 44 4 1671 2324 242962189 242962846 0.000000e+00 924
8 TraesCS7B01G264500 chr3B 92.109 659 45 5 1671 2324 310099808 310100464 0.000000e+00 922
9 TraesCS7B01G264500 chr4A 88.368 1685 181 14 1 1680 700975954 700977628 0.000000e+00 2012
10 TraesCS7B01G264500 chr4A 87.806 1673 196 8 1 1672 632630871 632632536 0.000000e+00 1953
11 TraesCS7B01G264500 chr3A 86.933 1676 206 9 1 1672 702515842 702514176 0.000000e+00 1869
12 TraesCS7B01G264500 chr2A 86.412 1678 214 11 1 1672 179276104 179277773 0.000000e+00 1823
13 TraesCS7B01G264500 chr2A 85.459 1678 231 13 1 1672 673275406 673273736 0.000000e+00 1735
14 TraesCS7B01G264500 chr2A 83.069 189 20 11 1487 1672 592002825 592003004 6.650000e-36 161
15 TraesCS7B01G264500 chr1B 92.553 658 40 6 1676 2324 509271736 509271079 0.000000e+00 935
16 TraesCS7B01G264500 chr1B 92.109 659 45 6 1671 2324 161947907 161948563 0.000000e+00 922
17 TraesCS7B01G264500 chr1B 91.933 657 48 3 1671 2324 409226089 409226743 0.000000e+00 915
18 TraesCS7B01G264500 chr2B 92.366 655 46 4 1671 2324 110163173 110163824 0.000000e+00 929
19 TraesCS7B01G264500 chr4B 92.249 658 45 4 1671 2324 94403752 94404407 0.000000e+00 928


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 TraesCS7B01G264500 chr7B 484926541 484928864 2323 True 4292 4292 100.000 1 2324 1 chr7B.!!$R1 2323
1 TraesCS7B01G264500 chr7B 393363086 393363742 656 False 933 933 92.413 1671 2324 1 chr7B.!!$F1 653
2 TraesCS7B01G264500 chr6B 18598770 18600449 1679 True 2763 2763 96.318 1 1684 1 chr6B.!!$R1 1683
3 TraesCS7B01G264500 chr6B 573347663 573349340 1677 False 2706 2706 95.779 1 1679 1 chr6B.!!$F1 1678
4 TraesCS7B01G264500 chr6B 580865177 580865834 657 False 929 929 92.273 1671 2324 1 chr6B.!!$F2 653
5 TraesCS7B01G264500 chr5B 364098044 364099711 1667 True 2182 2182 90.263 1 1672 1 chr5B.!!$R1 1671
6 TraesCS7B01G264500 chr3B 629908993 629910663 1670 False 2026 2026 88.571 2 1676 1 chr3B.!!$F3 1674
7 TraesCS7B01G264500 chr3B 242962189 242962846 657 False 924 924 92.121 1671 2324 1 chr3B.!!$F1 653
8 TraesCS7B01G264500 chr3B 310099808 310100464 656 False 922 922 92.109 1671 2324 1 chr3B.!!$F2 653
9 TraesCS7B01G264500 chr4A 700975954 700977628 1674 False 2012 2012 88.368 1 1680 1 chr4A.!!$F2 1679
10 TraesCS7B01G264500 chr4A 632630871 632632536 1665 False 1953 1953 87.806 1 1672 1 chr4A.!!$F1 1671
11 TraesCS7B01G264500 chr3A 702514176 702515842 1666 True 1869 1869 86.933 1 1672 1 chr3A.!!$R1 1671
12 TraesCS7B01G264500 chr2A 179276104 179277773 1669 False 1823 1823 86.412 1 1672 1 chr2A.!!$F1 1671
13 TraesCS7B01G264500 chr2A 673273736 673275406 1670 True 1735 1735 85.459 1 1672 1 chr2A.!!$R1 1671
14 TraesCS7B01G264500 chr1B 509271079 509271736 657 True 935 935 92.553 1676 2324 1 chr1B.!!$R1 648
15 TraesCS7B01G264500 chr1B 161947907 161948563 656 False 922 922 92.109 1671 2324 1 chr1B.!!$F1 653
16 TraesCS7B01G264500 chr1B 409226089 409226743 654 False 915 915 91.933 1671 2324 1 chr1B.!!$F2 653
17 TraesCS7B01G264500 chr2B 110163173 110163824 651 False 929 929 92.366 1671 2324 1 chr2B.!!$F1 653
18 TraesCS7B01G264500 chr4B 94403752 94404407 655 False 928 928 92.249 1671 2324 1 chr4B.!!$F1 653

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
274 276 1.902508 GTGTGAAGGATCTCCACAGGA 59.097 52.381 12.99 0.0 40.9 3.86 F
330 332 2.356125 GCTTGAGATGAAACAGGGGCTA 60.356 50.000 0.00 0.0 0.0 3.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1091 1093 0.032952 ACACAAAGCTGCAATGCCAG 59.967 50.0 1.53 1.39 35.93 4.85 R
1578 1586 0.606673 ACAGGAAAGAGGAAAGCGGC 60.607 55.0 0.00 0.00 0.00 6.53 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
35 36 3.717576 AGAGATGTGAATCTGGACTGGA 58.282 45.455 0.00 0.0 0.00 3.86
36 37 3.705579 AGAGATGTGAATCTGGACTGGAG 59.294 47.826 0.00 0.0 0.00 3.86
99 101 7.748691 TGCTAATATTTCTAGCATTGCATCA 57.251 32.000 11.91 0.0 45.24 3.07
164 166 7.093727 TGAGAGGTTAGATAAACACAGAAGGAG 60.094 40.741 0.00 0.0 40.08 3.69
261 263 4.191243 GGGGGTTTGGGTGTGAAG 57.809 61.111 0.00 0.0 0.00 3.02
274 276 1.902508 GTGTGAAGGATCTCCACAGGA 59.097 52.381 12.99 0.0 40.90 3.86
330 332 2.356125 GCTTGAGATGAAACAGGGGCTA 60.356 50.000 0.00 0.0 0.00 3.93
679 681 4.166144 AGATGATTTCCACGGTTAGGGAAT 59.834 41.667 0.00 0.0 42.44 3.01
772 774 8.499403 AGCTCTTTATGCTTACCTAGAAAAAG 57.501 34.615 0.00 0.0 37.52 2.27
847 849 7.718753 TGAAAATCCAAATTTTTATGTGGCAGT 59.281 29.630 0.00 0.0 43.48 4.40
939 941 3.435026 CCTTTTGTGGGGAGAGAGAAACA 60.435 47.826 0.00 0.0 0.00 2.83
946 948 2.998316 GGAGAGAGAAACATCCCAGG 57.002 55.000 0.00 0.0 0.00 4.45
1091 1093 2.033151 GTGGCGATGTTTTCTATACGGC 60.033 50.000 0.00 0.0 44.14 5.68
1218 1220 2.162681 CTTCTTTGTTACTGGGCAGGG 58.837 52.381 0.00 0.0 0.00 4.45
1249 1251 1.417145 AGGAGGATGCTGAGAAGATGC 59.583 52.381 0.00 0.0 32.93 3.91
1257 1259 1.005340 CTGAGAAGATGCGAGTTGGC 58.995 55.000 0.00 0.0 0.00 4.52
1356 1361 4.285863 CTGAGGACTAATGAAGAGGGAGT 58.714 47.826 0.00 0.0 0.00 3.85
1363 1368 6.070710 GGACTAATGAAGAGGGAGTAAGTTGT 60.071 42.308 0.00 0.0 0.00 3.32
1466 1474 1.202428 GCGTTGGCCTTTTGGTGTTAA 60.202 47.619 3.32 0.0 42.99 2.01
1470 1478 4.202030 CGTTGGCCTTTTGGTGTTAAACTA 60.202 41.667 3.32 0.0 42.99 2.24
1541 1549 3.321968 CCCATGGTGAGTAATCTCGATGA 59.678 47.826 15.71 0.0 43.09 2.92
1578 1586 1.305219 TTTCCCGGCGATGCTTGAAG 61.305 55.000 9.30 0.0 0.00 3.02
1595 1603 0.402121 AAGCCGCTTTCCTCTTTCCT 59.598 50.000 0.00 0.0 0.00 3.36
1667 1678 1.800681 GGATTCGCCCGGTTCAAAG 59.199 57.895 0.00 0.0 0.00 2.77
1864 1887 4.082787 ACAATGAAAAAGTATGAGCACCGG 60.083 41.667 0.00 0.0 0.00 5.28
1895 1918 4.816786 TGAGTGTGTGAACATGAATGTG 57.183 40.909 0.00 0.0 41.61 3.21
1912 1935 6.348498 TGAATGTGATGTCGGTGAGAAATAT 58.652 36.000 0.00 0.0 0.00 1.28
1964 1987 2.515429 AGTTGGTCTATGCCCATGGATT 59.485 45.455 15.22 0.0 30.97 3.01
1980 2003 4.265856 TGGATTGAAGCTACCCTCTCTA 57.734 45.455 0.00 0.0 0.00 2.43
2075 2098 1.072266 TATGGGTCAAGTGGTGGCTT 58.928 50.000 0.00 0.0 30.18 4.35
2090 2113 1.748500 GCTTTGGCTCAGGCTCTCC 60.749 63.158 0.00 0.0 38.73 3.71
2094 2117 2.129555 TTGGCTCAGGCTCTCCAACC 62.130 60.000 0.00 0.0 38.73 3.77
2147 2170 0.391130 GGCAAGATGAGGTACGTGCA 60.391 55.000 5.86 0.0 41.62 4.57
2178 2201 5.633655 TGTTAAACAAAGAGGGTGTAGGA 57.366 39.130 0.00 0.0 0.00 2.94
2313 2339 2.890945 GGGCAGCAACTTTTCCTCTTTA 59.109 45.455 0.00 0.0 0.00 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 0.760945 CCCCGAGGAGGCATTACTCT 60.761 60.000 3.19 0.00 39.21 3.24
36 37 1.749033 CCCCGAGGAGGCATTACTC 59.251 63.158 0.00 0.00 39.21 2.59
87 89 9.856162 ATGGACATATAATATGATGCAATGCTA 57.144 29.630 6.82 0.00 0.00 3.49
164 166 2.262423 AGTCACTTGCCAGAAGAACC 57.738 50.000 0.00 0.00 0.00 3.62
261 263 6.276091 GCAAATATTTTTCCTGTGGAGATCC 58.724 40.000 0.00 0.00 31.21 3.36
274 276 8.358895 CCATTTCACCAAAAGGCAAATATTTTT 58.641 29.630 0.00 0.00 0.00 1.94
330 332 2.028748 GGCTTTGACAATGTCTTGCCAT 60.029 45.455 26.38 0.00 39.97 4.40
483 485 1.583054 GATCATACCACAACCTCGCC 58.417 55.000 0.00 0.00 0.00 5.54
490 492 2.722094 GCCAACTGGATCATACCACAA 58.278 47.619 0.00 0.00 37.39 3.33
679 681 4.918588 TCACTATCCGCAGATATACAGGA 58.081 43.478 0.00 0.00 34.44 3.86
772 774 3.467803 GATAGTCACACCCAGCAATACC 58.532 50.000 0.00 0.00 0.00 2.73
774 776 2.483013 GCGATAGTCACACCCAGCAATA 60.483 50.000 0.00 0.00 39.35 1.90
847 849 4.430007 GTCAGTACCACATCTTGCGATAA 58.570 43.478 0.00 0.00 0.00 1.75
939 941 3.854994 AGGTGAAAAAGAGATCCTGGGAT 59.145 43.478 1.24 1.24 37.59 3.85
946 948 2.751806 CAGGGCAGGTGAAAAAGAGATC 59.248 50.000 0.00 0.00 0.00 2.75
1021 1023 1.656441 CCTGCCACAAGTTGTCAGC 59.344 57.895 17.05 17.05 0.00 4.26
1091 1093 0.032952 ACACAAAGCTGCAATGCCAG 59.967 50.000 1.53 1.39 35.93 4.85
1218 1220 1.674962 GCATCCTCCTGTTTCATCAGC 59.325 52.381 0.00 0.00 34.47 4.26
1246 1248 4.087892 AGCTCCGCCAACTCGCAT 62.088 61.111 0.00 0.00 0.00 4.73
1249 1251 2.507992 CAGAGCTCCGCCAACTCG 60.508 66.667 10.93 0.00 35.56 4.18
1257 1259 1.153667 GTCCTTCAGCAGAGCTCCG 60.154 63.158 10.93 0.00 36.40 4.63
1356 1361 5.457140 CAAAAGGCGCAATAGAACAACTTA 58.543 37.500 10.83 0.00 0.00 2.24
1466 1474 6.670027 AGGACTCCAACATCTAACTCATAGTT 59.330 38.462 0.00 0.00 41.97 2.24
1470 1478 4.163078 CCAGGACTCCAACATCTAACTCAT 59.837 45.833 0.00 0.00 0.00 2.90
1541 1549 1.768684 AACCCACCATGAGCACTCGT 61.769 55.000 0.00 0.00 0.00 4.18
1578 1586 0.606673 ACAGGAAAGAGGAAAGCGGC 60.607 55.000 0.00 0.00 0.00 6.53
1595 1603 2.355108 GCCAAGTTCAGCAGATAGGACA 60.355 50.000 0.00 0.00 0.00 4.02
1667 1678 6.099341 TCCTGTTCTTCTTTTGCTTGTTTTC 58.901 36.000 0.00 0.00 0.00 2.29
1716 1729 7.713734 ACTTTCCATGCTTGTAGTAGTAGTA 57.286 36.000 0.00 0.00 0.00 1.82
1778 1799 7.093992 TCTTGTGTGTTTGAAAACCCTTTAAG 58.906 34.615 3.59 3.22 38.11 1.85
1864 1887 4.511454 TGTTCACACACTCATTCTAGTTGC 59.489 41.667 0.00 0.00 0.00 4.17
1895 1918 5.921408 GGAGTACATATTTCTCACCGACATC 59.079 44.000 0.00 0.00 0.00 3.06
1912 1935 1.580059 CCTAAGCTTGGGGGAGTACA 58.420 55.000 20.71 0.00 0.00 2.90
1964 1987 3.741245 ACACTAGAGAGGGTAGCTTCA 57.259 47.619 6.82 0.00 37.64 3.02
1980 2003 1.000107 GGACCCTCCTCGGTACACT 60.000 63.158 0.00 0.00 36.65 3.55
2075 2098 1.376466 GTTGGAGAGCCTGAGCCAA 59.624 57.895 0.00 0.00 41.25 4.52
2090 2113 7.041721 TGCATACTAGAATCTAACACAGGTTG 58.958 38.462 0.00 0.00 37.88 3.77
2147 2170 8.576442 CACCCTCTTTGTTTAACATACTTTCAT 58.424 33.333 0.00 0.00 0.00 2.57
2284 2310 3.942130 AAAGTTGCTGCCCACTATTTC 57.058 42.857 0.00 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.