Multiple sequence alignment - TraesCS4B01G077300

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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 TraesCS4B01G077300 chr4B 100.000 2264 0 0 1 2264 74251912 74254175 0.000000e+00 4181
1 TraesCS4B01G077300 chr4B 89.305 187 9 2 1797 1973 563810392 563810577 8.140000e-55 224
2 TraesCS4B01G077300 chr2B 93.747 2287 108 18 1 2264 29754563 29752289 0.000000e+00 3398
3 TraesCS4B01G077300 chr2B 91.507 1413 102 7 573 1973 138732372 138733778 0.000000e+00 1929
4 TraesCS4B01G077300 chr2B 90.556 1440 111 9 546 1973 42193952 42195378 0.000000e+00 1882
5 TraesCS4B01G077300 chr2B 89.485 1398 101 28 589 1973 717652642 717654006 0.000000e+00 1725
6 TraesCS4B01G077300 chr2B 90.769 325 14 3 1940 2264 563915127 563914819 9.670000e-114 420
7 TraesCS4B01G077300 chr2B 83.832 334 31 8 1775 2098 440605722 440606042 1.700000e-76 296
8 TraesCS4B01G077300 chr2B 85.366 205 15 7 1775 1972 154583796 154583600 4.930000e-47 198
9 TraesCS4B01G077300 chr5B 96.749 2030 53 4 1 2019 548566799 548564772 0.000000e+00 3371
10 TraesCS4B01G077300 chr5B 92.596 2161 118 22 1 2124 428831263 428833418 0.000000e+00 3066
11 TraesCS4B01G077300 chr5B 93.842 1965 96 11 1 1942 428825812 428827774 0.000000e+00 2935
12 TraesCS4B01G077300 chr5B 92.295 1752 124 6 1 1744 454660902 454662650 0.000000e+00 2477
13 TraesCS4B01G077300 chr5B 94.662 281 12 3 1984 2264 428833480 428833757 1.240000e-117 433
14 TraesCS4B01G077300 chr7B 93.866 1989 97 11 1 1966 27326580 27328566 0.000000e+00 2974
15 TraesCS4B01G077300 chr7B 90.765 1646 106 15 573 2216 687041199 687042800 0.000000e+00 2156
16 TraesCS4B01G077300 chr7B 90.467 1626 112 14 593 2216 713543536 713541952 0.000000e+00 2104
17 TraesCS4B01G077300 chr7B 90.639 1613 102 17 606 2216 95041366 95039801 0.000000e+00 2097
18 TraesCS4B01G077300 chr7B 90.769 325 14 3 1940 2264 713542099 713541791 9.670000e-114 420
19 TraesCS4B01G077300 chr7B 90.462 325 15 3 1940 2264 27328622 27328930 4.500000e-112 414
20 TraesCS4B01G077300 chr7B 90.462 325 15 3 1940 2264 95039948 95039640 4.500000e-112 414
21 TraesCS4B01G077300 chr7B 89.538 325 18 3 1940 2264 687042653 687042961 4.530000e-107 398
22 TraesCS4B01G077300 chr7B 93.966 116 6 1 1983 2098 713541948 713541834 8.310000e-40 174
23 TraesCS4B01G077300 chr7B 86.164 159 11 2 1940 2098 95039830 95039683 6.470000e-36 161
24 TraesCS4B01G077300 chr6B 91.438 2114 147 21 1 2103 687514433 687512343 0.000000e+00 2870
25 TraesCS4B01G077300 chr6B 92.580 1752 118 7 1 1744 661051611 661053358 0.000000e+00 2505
26 TraesCS4B01G077300 chr6B 93.238 281 13 2 1984 2264 694765469 694765743 2.090000e-110 409
27 TraesCS4B01G077300 chr6A 92.278 1787 123 12 1 1779 74992227 74990448 0.000000e+00 2521
28 TraesCS4B01G077300 chr3B 91.323 1867 122 20 1 1860 16203486 16201653 0.000000e+00 2514
29 TraesCS4B01G077300 chr3B 92.040 1407 90 10 573 1966 28617502 28618899 0.000000e+00 1958
30 TraesCS4B01G077300 chr3B 90.769 325 14 3 1940 2264 16122419 16122111 9.670000e-114 420
31 TraesCS4B01G077300 chr3B 90.798 326 13 5 1940 2264 28618954 28619263 9.670000e-114 420
32 TraesCS4B01G077300 chr3B 88.679 159 7 2 1940 2098 16122301 16122154 1.380000e-42 183
33 TraesCS4B01G077300 chr1B 89.486 1674 116 22 546 2216 38183941 38185557 0.000000e+00 2061
34 TraesCS4B01G077300 chr5A 84.368 467 49 9 1775 2230 300956662 300957115 9.600000e-119 436


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 TraesCS4B01G077300 chr4B 74251912 74254175 2263 False 4181.000000 4181 100.000000 1 2264 1 chr4B.!!$F1 2263
1 TraesCS4B01G077300 chr2B 29752289 29754563 2274 True 3398.000000 3398 93.747000 1 2264 1 chr2B.!!$R1 2263
2 TraesCS4B01G077300 chr2B 138732372 138733778 1406 False 1929.000000 1929 91.507000 573 1973 1 chr2B.!!$F2 1400
3 TraesCS4B01G077300 chr2B 42193952 42195378 1426 False 1882.000000 1882 90.556000 546 1973 1 chr2B.!!$F1 1427
4 TraesCS4B01G077300 chr2B 717652642 717654006 1364 False 1725.000000 1725 89.485000 589 1973 1 chr2B.!!$F4 1384
5 TraesCS4B01G077300 chr5B 548564772 548566799 2027 True 3371.000000 3371 96.749000 1 2019 1 chr5B.!!$R1 2018
6 TraesCS4B01G077300 chr5B 454660902 454662650 1748 False 2477.000000 2477 92.295000 1 1744 1 chr5B.!!$F1 1743
7 TraesCS4B01G077300 chr5B 428825812 428833757 7945 False 2144.666667 3066 93.700000 1 2264 3 chr5B.!!$F2 2263
8 TraesCS4B01G077300 chr7B 27326580 27328930 2350 False 1694.000000 2974 92.164000 1 2264 2 chr7B.!!$F1 2263
9 TraesCS4B01G077300 chr7B 687041199 687042961 1762 False 1277.000000 2156 90.151500 573 2264 2 chr7B.!!$F2 1691
10 TraesCS4B01G077300 chr7B 713541791 713543536 1745 True 899.333333 2104 91.734000 593 2264 3 chr7B.!!$R2 1671
11 TraesCS4B01G077300 chr7B 95039640 95041366 1726 True 890.666667 2097 89.088333 606 2264 3 chr7B.!!$R1 1658
12 TraesCS4B01G077300 chr6B 687512343 687514433 2090 True 2870.000000 2870 91.438000 1 2103 1 chr6B.!!$R1 2102
13 TraesCS4B01G077300 chr6B 661051611 661053358 1747 False 2505.000000 2505 92.580000 1 1744 1 chr6B.!!$F1 1743
14 TraesCS4B01G077300 chr6A 74990448 74992227 1779 True 2521.000000 2521 92.278000 1 1779 1 chr6A.!!$R1 1778
15 TraesCS4B01G077300 chr3B 16201653 16203486 1833 True 2514.000000 2514 91.323000 1 1860 1 chr3B.!!$R1 1859
16 TraesCS4B01G077300 chr3B 28617502 28619263 1761 False 1189.000000 1958 91.419000 573 2264 2 chr3B.!!$F1 1691
17 TraesCS4B01G077300 chr1B 38183941 38185557 1616 False 2061.000000 2061 89.486000 546 2216 1 chr1B.!!$F1 1670

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
726 6253 0.178932 AGTGCTAGAGGTGGTGGTCA 60.179 55.0 0.0 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2029 7641 1.892819 ATGGTGTCTGGTCTCCTGCG 61.893 60.0 0.0 0.0 0.0 5.18 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
405 406 3.366883 GGCATGAAACAATTTGGTAGCGA 60.367 43.478 0.00 0.00 0.00 4.93
558 598 1.746517 GTGGAAGAGGTGACGGTGT 59.253 57.895 0.00 0.00 0.00 4.16
599 639 1.692519 GTGTCAGAGGTGGTAGTGGTT 59.307 52.381 0.00 0.00 0.00 3.67
726 6253 0.178932 AGTGCTAGAGGTGGTGGTCA 60.179 55.000 0.00 0.00 0.00 4.02
756 6349 1.006102 GTGTCAGAGGTGGTGGTCG 60.006 63.158 0.00 0.00 0.00 4.79
858 6451 5.123227 GGTTGATAATGGATCGGTCTTTGA 58.877 41.667 0.00 0.00 37.38 2.69
898 6491 8.378565 CCAGATGGTTGATCTAGTAATAATGGT 58.621 37.037 0.00 0.00 39.64 3.55
1054 6649 1.296715 GCGGACCAAGAGGACATGT 59.703 57.895 0.00 0.00 38.69 3.21
1226 6821 3.982475 ACTATGCACATGATCGTCGAAT 58.018 40.909 0.00 0.00 0.00 3.34
1428 7024 2.100916 GAGATTACTTACGGAGGCAGCA 59.899 50.000 0.00 0.00 0.00 4.41
1539 7135 0.036952 CGCAAAGAGAAGGAGGCTCA 60.037 55.000 17.69 0.00 34.85 4.26
1549 7145 3.197549 AGAAGGAGGCTCATCAAGAAGAC 59.802 47.826 17.69 0.00 0.00 3.01
1664 7262 0.109532 TGGAAAAGGCACCGACATCA 59.890 50.000 0.00 0.00 0.00 3.07
1680 7278 4.259970 CGACATCAATGATGGACTTTCGAC 60.260 45.833 24.99 6.07 43.60 4.20
1744 7344 8.892723 GTGGTCATGAACTATTTATGTCATTCA 58.107 33.333 12.94 0.00 0.00 2.57
1773 7373 7.602644 ACATCGTGTATGATGAACTTGTAAGTT 59.397 33.333 18.26 9.59 46.98 2.66
1957 7569 2.358737 CACCCAGACGCCAAGGTC 60.359 66.667 0.00 0.00 37.19 3.85
1969 7581 1.080569 CAAGGTCCATGGCGTTTGC 60.081 57.895 6.96 0.00 41.71 3.68
1980 7592 2.983592 CGTTTGCCTCCCACACCC 60.984 66.667 0.00 0.00 0.00 4.61
1982 7594 1.903404 GTTTGCCTCCCACACCCAG 60.903 63.158 0.00 0.00 0.00 4.45
1983 7595 3.808218 TTTGCCTCCCACACCCAGC 62.808 63.158 0.00 0.00 0.00 4.85
1986 7598 4.351054 CCTCCCACACCCAGCCAC 62.351 72.222 0.00 0.00 0.00 5.01
1987 7599 3.569210 CTCCCACACCCAGCCACA 61.569 66.667 0.00 0.00 0.00 4.17
1988 7600 3.850098 CTCCCACACCCAGCCACAC 62.850 68.421 0.00 0.00 0.00 3.82
2029 7641 0.179179 GTCTGGCTCATTTTGCTCGC 60.179 55.000 0.00 0.00 0.00 5.03
2047 7659 2.574018 CGCAGGAGACCAGACACCA 61.574 63.158 0.00 0.00 0.00 4.17
2048 7660 1.892819 CGCAGGAGACCAGACACCAT 61.893 60.000 0.00 0.00 0.00 3.55
2143 8424 1.507141 CTGGCGTCTGGCTCGTTTTT 61.507 55.000 0.00 0.00 42.94 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
405 406 4.166725 TGTCAGGAGCCTCCATAAAATGAT 59.833 41.667 14.46 0.00 39.61 2.45
527 528 1.972075 TCTTCCACCACGTTCACCATA 59.028 47.619 0.00 0.00 0.00 2.74
538 539 1.458777 ACCGTCACCTCTTCCACCA 60.459 57.895 0.00 0.00 0.00 4.17
558 598 0.393132 TGTGCTTGTTCGACCACCAA 60.393 50.000 0.00 0.00 0.00 3.67
599 639 3.079578 CACTTGTACTCCCTCTACGACA 58.920 50.000 0.00 0.00 0.00 4.35
726 6253 1.945394 CTCTGACACTTGTGCTTGCTT 59.055 47.619 0.10 0.00 0.00 3.91
858 6451 8.537728 TCAACCATCTGGATTAAGCAAATAAT 57.462 30.769 2.55 0.00 38.94 1.28
1054 6649 1.945354 GCCTCCATCCACGTCTTCGA 61.945 60.000 0.00 0.00 40.62 3.71
1226 6821 2.979240 TGTCATATGCGTTAGTTGGCA 58.021 42.857 0.00 0.00 44.29 4.92
1428 7024 3.330701 TGCAAAGGACTCCTCAAATAGGT 59.669 43.478 0.00 0.00 46.62 3.08
1539 7135 3.795688 TTCTTGCCCTGTCTTCTTGAT 57.204 42.857 0.00 0.00 0.00 2.57
1574 7170 2.780094 CCTCCTCTCGTGCATCGCT 61.780 63.158 0.00 0.00 39.67 4.93
1664 7262 4.821805 ACAAAGTGTCGAAAGTCCATCATT 59.178 37.500 0.00 0.00 0.00 2.57
1744 7344 5.700832 ACAAGTTCATCATACACGATGTGTT 59.299 36.000 8.00 0.00 45.08 3.32
1773 7373 8.668353 GTTTGCACATAATCTCAAATAGTCTCA 58.332 33.333 0.00 0.00 32.07 3.27
1966 7578 4.284550 GCTGGGTGTGGGAGGCAA 62.285 66.667 0.00 0.00 0.00 4.52
1969 7581 4.351054 GTGGCTGGGTGTGGGAGG 62.351 72.222 0.00 0.00 0.00 4.30
1973 7585 4.974721 GGGTGTGGCTGGGTGTGG 62.975 72.222 0.00 0.00 0.00 4.17
1974 7586 4.202574 TGGGTGTGGCTGGGTGTG 62.203 66.667 0.00 0.00 0.00 3.82
1975 7587 3.889692 CTGGGTGTGGCTGGGTGT 61.890 66.667 0.00 0.00 0.00 4.16
1977 7589 3.570212 GTCTGGGTGTGGCTGGGT 61.570 66.667 0.00 0.00 0.00 4.51
1978 7590 4.704833 CGTCTGGGTGTGGCTGGG 62.705 72.222 0.00 0.00 0.00 4.45
1983 7595 4.704833 CCTGGCGTCTGGGTGTGG 62.705 72.222 4.79 0.00 0.00 4.17
1984 7596 4.704833 CCCTGGCGTCTGGGTGTG 62.705 72.222 22.99 0.00 44.42 3.82
2029 7641 1.892819 ATGGTGTCTGGTCTCCTGCG 61.893 60.000 0.00 0.00 0.00 5.18
2047 7659 4.134379 GTCCATCAGACACATCAGACAT 57.866 45.455 0.00 0.00 45.55 3.06
2048 7660 3.599730 GTCCATCAGACACATCAGACA 57.400 47.619 0.00 0.00 45.55 3.41
2070 7682 4.410400 GGACCTTGGCGTCTGGGG 62.410 72.222 4.80 0.00 33.07 4.96
2071 7683 2.971598 ATGGACCTTGGCGTCTGGG 61.972 63.158 4.80 1.36 33.07 4.45
2143 8424 3.443925 CTGGTCTCCTGCGCGAGA 61.444 66.667 12.10 10.50 36.53 4.04


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

AutoCloner maintained by Alex Coulton.