Multiple sequence alignment - TraesCS7D01G477800

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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 TraesCS7D01G477800 chr7D 100.000 2276 0 0 1 2276 588679846 588677571 0.000000e+00 4204.0
1 TraesCS7D01G477800 chr7D 90.111 718 43 14 858 1568 354527415 354528111 0.000000e+00 907.0
2 TraesCS7D01G477800 chr7D 89.847 719 44 16 858 1568 195395634 195396331 0.000000e+00 896.0
3 TraesCS7D01G477800 chr7D 90.415 699 38 15 878 1568 346184965 346184288 0.000000e+00 893.0
4 TraesCS7D01G477800 chr7D 89.759 332 13 11 1448 1762 588841162 588841489 2.720000e-109 405.0
5 TraesCS7D01G477800 chr7D 84.524 252 37 1 1957 2206 8275912 8275661 4.850000e-62 248.0
6 TraesCS7D01G477800 chr7D 81.498 227 30 10 1479 1698 588840924 588841145 2.320000e-40 176.0
7 TraesCS7D01G477800 chr7B 90.884 1843 79 41 62 1855 663106894 663108696 0.000000e+00 2390.0
8 TraesCS7D01G477800 chr7B 88.843 726 52 16 852 1568 253264517 253263812 0.000000e+00 865.0
9 TraesCS7D01G477800 chr7B 86.777 242 32 0 1957 2198 663109023 663109264 1.040000e-68 270.0
10 TraesCS7D01G477800 chr7B 81.013 237 18 7 1643 1855 663111905 663112138 1.810000e-36 163.0
11 TraesCS7D01G477800 chr7A 88.836 1899 105 52 1 1863 680405820 680407647 0.000000e+00 2233.0
12 TraesCS7D01G477800 chr7A 86.349 315 43 0 1951 2265 680407970 680408284 6.020000e-91 344.0
13 TraesCS7D01G477800 chr7A 80.503 318 54 7 1962 2276 8686189 8686501 1.050000e-58 237.0
14 TraesCS7D01G477800 chr4B 88.873 719 51 14 858 1568 141080065 141080762 0.000000e+00 857.0
15 TraesCS7D01G477800 chr2B 88.456 719 55 17 858 1568 311334515 311335213 0.000000e+00 843.0
16 TraesCS7D01G477800 chr2B 88.235 51 6 0 1905 1955 103694564 103694514 6.790000e-06 62.1
17 TraesCS7D01G477800 chr1D 82.965 317 51 1 1958 2274 430423234 430423547 1.330000e-72 283.0
18 TraesCS7D01G477800 chr1D 80.000 305 52 6 1964 2267 347302535 347302831 1.370000e-52 217.0
19 TraesCS7D01G477800 chr2A 84.783 276 41 1 1986 2261 83777147 83777421 2.230000e-70 276.0
20 TraesCS7D01G477800 chr5B 82.818 291 47 3 1957 2246 130400738 130401026 8.070000e-65 257.0
21 TraesCS7D01G477800 chr4D 81.648 267 41 8 1953 2216 400892520 400892781 4.920000e-52 215.0
22 TraesCS7D01G477800 chr1B 90.196 51 5 0 1905 1955 469120553 469120603 1.460000e-07 67.6
23 TraesCS7D01G477800 chr1A 89.796 49 5 0 1905 1953 464090482 464090434 1.890000e-06 63.9
24 TraesCS7D01G477800 chr1A 94.118 34 2 0 1905 1938 574501913 574501880 4.000000e-03 52.8
25 TraesCS7D01G477800 chr4A 89.583 48 5 0 1905 1952 686533671 686533624 6.790000e-06 62.1


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 TraesCS7D01G477800 chr7D 588677571 588679846 2275 True 4204.0 4204 100.000000 1 2276 1 chr7D.!!$R3 2275
1 TraesCS7D01G477800 chr7D 354527415 354528111 696 False 907.0 907 90.111000 858 1568 1 chr7D.!!$F2 710
2 TraesCS7D01G477800 chr7D 195395634 195396331 697 False 896.0 896 89.847000 858 1568 1 chr7D.!!$F1 710
3 TraesCS7D01G477800 chr7D 346184288 346184965 677 True 893.0 893 90.415000 878 1568 1 chr7D.!!$R2 690
4 TraesCS7D01G477800 chr7D 588840924 588841489 565 False 290.5 405 85.628500 1448 1762 2 chr7D.!!$F3 314
5 TraesCS7D01G477800 chr7B 663106894 663112138 5244 False 941.0 2390 86.224667 62 2198 3 chr7B.!!$F1 2136
6 TraesCS7D01G477800 chr7B 253263812 253264517 705 True 865.0 865 88.843000 852 1568 1 chr7B.!!$R1 716
7 TraesCS7D01G477800 chr7A 680405820 680408284 2464 False 1288.5 2233 87.592500 1 2265 2 chr7A.!!$F2 2264
8 TraesCS7D01G477800 chr4B 141080065 141080762 697 False 857.0 857 88.873000 858 1568 1 chr4B.!!$F1 710
9 TraesCS7D01G477800 chr2B 311334515 311335213 698 False 843.0 843 88.456000 858 1568 1 chr2B.!!$F1 710

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
972 1009 0.523072 CACAGCACCCTTCGATTTGG 59.477 55.0 0.0 0.0 0.0 3.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1924 2091 0.59117 CGAGTGTTTGATGCCCGTTT 59.409 50.0 0.0 0.0 0.0 3.6 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
125 130 0.645868 GATGCCGAAGCTTGTACGTC 59.354 55.000 2.10 0.00 40.80 4.34
175 180 4.778415 ACGCACGCACCTCGCTAG 62.778 66.667 0.00 0.00 43.23 3.42
197 206 3.055819 GGCGTCCAGATACATACATGGAT 60.056 47.826 0.00 0.00 43.42 3.41
334 343 3.711704 ACCACAGATTTCGGGACATATCT 59.288 43.478 0.00 0.00 0.00 1.98
595 613 1.759293 CGCGGTGAGATGCATGTGAG 61.759 60.000 2.46 0.00 0.00 3.51
596 614 0.742281 GCGGTGAGATGCATGTGAGT 60.742 55.000 2.46 0.00 0.00 3.41
597 615 1.004595 CGGTGAGATGCATGTGAGTG 58.995 55.000 2.46 0.00 0.00 3.51
598 616 1.404583 CGGTGAGATGCATGTGAGTGA 60.405 52.381 2.46 0.00 0.00 3.41
692 710 1.406069 CCCAGCTAAATGACAGCGTCT 60.406 52.381 9.49 0.00 43.97 4.18
819 842 2.278271 GAGAGGTAGCTCGCGTGC 60.278 66.667 24.56 24.56 0.00 5.34
832 855 2.049526 CGTGCTGGTGAGTGCGTA 60.050 61.111 0.00 0.00 0.00 4.42
941 973 1.968017 CCAAGAAAGCAGAGCGGCA 60.968 57.895 1.45 0.00 35.83 5.69
972 1009 0.523072 CACAGCACCCTTCGATTTGG 59.477 55.000 0.00 0.00 0.00 3.28
973 1010 1.244019 ACAGCACCCTTCGATTTGGC 61.244 55.000 0.00 0.00 0.00 4.52
974 1011 1.074775 AGCACCCTTCGATTTGGCA 59.925 52.632 0.00 0.00 0.00 4.92
975 1012 0.962356 AGCACCCTTCGATTTGGCAG 60.962 55.000 0.00 0.00 0.00 4.85
976 1013 1.508088 CACCCTTCGATTTGGCAGC 59.492 57.895 0.00 0.00 0.00 5.25
977 1014 2.040544 ACCCTTCGATTTGGCAGCG 61.041 57.895 0.00 0.00 0.00 5.18
1266 1312 1.001393 CACCTACCCCGCCATTGTT 60.001 57.895 0.00 0.00 0.00 2.83
1464 1516 7.360185 CGATCTTGATTTGGATATCTGCTTGAG 60.360 40.741 2.05 0.00 0.00 3.02
1547 1631 2.159234 CAGTTCTTCTTACTGCTGCTGC 59.841 50.000 8.89 8.89 36.88 5.25
1554 1639 0.393402 TTACTGCTGCTGCTGATGGG 60.393 55.000 25.33 8.12 40.66 4.00
1560 1645 0.107361 CTGCTGCTGATGGGTGATGA 60.107 55.000 0.00 0.00 0.00 2.92
1664 1749 2.542178 CGACGTGTCTGAAATGGTTTCA 59.458 45.455 0.00 5.17 46.68 2.69
1732 1823 0.547553 TGCTGATGCTGATTGCCCTA 59.452 50.000 0.00 0.00 42.00 3.53
1795 1897 3.143728 TGTAGCAGAGTCGTCACAAGTA 58.856 45.455 0.00 0.00 0.00 2.24
1819 1921 1.909532 GATCGCCGTAATAATCGACCG 59.090 52.381 0.00 0.00 33.59 4.79
1863 1965 5.515106 AGGACAGTCTAAGAGTAAGAGCAT 58.485 41.667 0.00 0.00 0.00 3.79
1864 1966 5.592688 AGGACAGTCTAAGAGTAAGAGCATC 59.407 44.000 0.00 0.00 0.00 3.91
1865 1967 5.221165 GGACAGTCTAAGAGTAAGAGCATCC 60.221 48.000 0.00 0.00 33.66 3.51
1866 1968 5.515106 ACAGTCTAAGAGTAAGAGCATCCT 58.485 41.667 0.00 0.00 33.66 3.24
1868 1970 4.819630 AGTCTAAGAGTAAGAGCATCCTCG 59.180 45.833 0.00 0.00 43.05 4.63
1869 1971 4.023536 GTCTAAGAGTAAGAGCATCCTCGG 60.024 50.000 0.00 0.00 43.05 4.63
1871 1973 0.032815 GAGTAAGAGCATCCTCGGGC 59.967 60.000 0.00 0.00 43.05 6.13
1873 1975 2.498941 TAAGAGCATCCTCGGGCGG 61.499 63.158 0.00 0.00 43.05 6.13
1918 2085 2.781681 AAAAATCGACCCAGACGGAT 57.218 45.000 0.00 0.00 34.64 4.18
1924 2091 2.284625 ACCCAGACGGATGCCTCA 60.285 61.111 0.00 0.00 34.64 3.86
1939 2106 0.958091 CCTCAAACGGGCATCAAACA 59.042 50.000 0.00 0.00 0.00 2.83
1940 2107 1.335872 CCTCAAACGGGCATCAAACAC 60.336 52.381 0.00 0.00 0.00 3.32
1941 2108 1.608590 CTCAAACGGGCATCAAACACT 59.391 47.619 0.00 0.00 0.00 3.55
1952 2119 1.116308 TCAAACACTCGGACTGACCA 58.884 50.000 0.00 0.00 38.90 4.02
1955 2333 1.115930 AACACTCGGACTGACCAGCT 61.116 55.000 0.00 0.00 38.90 4.24
1975 2353 3.006728 CGTCCCCCAACCCTAGCA 61.007 66.667 0.00 0.00 0.00 3.49
1993 2371 2.050144 GCAACATCCATCTCCTCCCTA 58.950 52.381 0.00 0.00 0.00 3.53
1998 2376 3.143741 ACATCCATCTCCTCCCTATCTGT 59.856 47.826 0.00 0.00 0.00 3.41
2028 2406 1.828768 GAGCCCATCCACCTCTCTG 59.171 63.158 0.00 0.00 0.00 3.35
2034 2412 1.992277 ATCCACCTCTCTGCCGCTT 60.992 57.895 0.00 0.00 0.00 4.68
2056 2434 2.342648 GTTCTTCCCACGCCGTCT 59.657 61.111 0.00 0.00 0.00 4.18
2104 2482 5.479124 AGATGACATATGCTATGCTCACA 57.521 39.130 1.58 0.00 0.00 3.58
2210 2588 2.520741 CGGAGGAGGAGGAGGAGC 60.521 72.222 0.00 0.00 0.00 4.70
2213 2591 4.150454 AGGAGGAGGAGGAGCCGG 62.150 72.222 0.00 0.00 43.43 6.13
2229 2607 4.400961 GGAGCAGCAGCCGGTTCT 62.401 66.667 1.90 0.00 43.56 3.01
2230 2608 3.123620 GAGCAGCAGCCGGTTCTG 61.124 66.667 1.90 9.29 43.56 3.02
2238 2616 2.514824 GCCGGTTCTGATGGAGGC 60.515 66.667 1.90 0.00 37.61 4.70
2257 2635 1.520666 GGCGGATTCGAAGGAGGAA 59.479 57.895 3.35 0.00 39.00 3.36
2265 2643 0.408309 TCGAAGGAGGAAGAGGTGGA 59.592 55.000 0.00 0.00 0.00 4.02
2268 2646 2.620886 CGAAGGAGGAAGAGGTGGAGTA 60.621 54.545 0.00 0.00 0.00 2.59
2270 2648 1.116308 GGAGGAAGAGGTGGAGTAGC 58.884 60.000 0.00 0.00 0.00 3.58
2272 2650 0.684805 AGGAAGAGGTGGAGTAGCCG 60.685 60.000 0.00 0.00 40.66 5.52
2274 2652 0.683504 GAAGAGGTGGAGTAGCCGGA 60.684 60.000 5.05 0.00 40.66 5.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 60 2.671177 CCGCTGGCGTCTTCTGTTG 61.671 63.158 13.84 0.00 37.81 3.33
125 130 2.182842 GCCTTATCGCACTGGGCTG 61.183 63.158 0.00 0.00 41.67 4.85
171 176 2.557056 TGTATGTATCTGGACGCCTAGC 59.443 50.000 0.00 0.00 0.00 3.42
175 180 2.299013 TCCATGTATGTATCTGGACGCC 59.701 50.000 0.00 0.00 32.92 5.68
274 283 3.373565 CTTGGCTTGTTCCGGGGC 61.374 66.667 0.00 0.00 0.00 5.80
334 343 1.372997 GACTCGAGAAACGCCTGCA 60.373 57.895 21.68 0.00 42.26 4.41
517 531 1.669115 CCAGTGCTCCGTGACAAGG 60.669 63.158 0.22 0.22 0.00 3.61
584 602 2.969990 AGTCACTCACTCACATGCATC 58.030 47.619 0.00 0.00 0.00 3.91
595 613 1.523758 AATTTGGGCGAGTCACTCAC 58.476 50.000 5.45 0.00 0.00 3.51
596 614 1.879380 CAAATTTGGGCGAGTCACTCA 59.121 47.619 10.49 0.00 0.00 3.41
597 615 1.200020 CCAAATTTGGGCGAGTCACTC 59.800 52.381 26.87 0.00 44.70 3.51
598 616 1.247567 CCAAATTTGGGCGAGTCACT 58.752 50.000 26.87 0.00 44.70 3.41
639 657 4.736896 GGACACGACGGACAGGGC 62.737 72.222 0.00 0.00 0.00 5.19
851 879 3.436924 GGGCGGTGGGCTTTAACG 61.437 66.667 0.00 0.00 42.94 3.18
941 973 2.142761 TGCTGTGCTGGTCAGGAGT 61.143 57.895 0.00 0.00 33.98 3.85
990 1027 3.610669 CCCTCCATCTCGCCCTCG 61.611 72.222 0.00 0.00 0.00 4.63
992 1035 4.095400 ACCCCTCCATCTCGCCCT 62.095 66.667 0.00 0.00 0.00 5.19
995 1038 3.140225 GACGACCCCTCCATCTCGC 62.140 68.421 0.00 0.00 0.00 5.03
999 1042 2.806237 GACGACGACCCCTCCATC 59.194 66.667 0.00 0.00 0.00 3.51
1301 1347 4.003648 GGGCGGAGAATGAAATAGTATGG 58.996 47.826 0.00 0.00 0.00 2.74
1438 1490 6.426025 TCAAGCAGATATCCAAATCAAGATCG 59.574 38.462 0.00 0.00 0.00 3.69
1464 1516 6.150140 ACATCTAGCCAGAATCAAGAAAACAC 59.850 38.462 0.00 0.00 33.50 3.32
1547 1631 3.899980 TCCTGTATCTCATCACCCATCAG 59.100 47.826 0.00 0.00 0.00 2.90
1554 1639 4.202101 CCTGTCAGTCCTGTATCTCATCAC 60.202 50.000 0.00 0.00 0.00 3.06
1560 1645 2.952702 GCTCCCTGTCAGTCCTGTATCT 60.953 54.545 0.00 0.00 0.00 1.98
1732 1823 5.122396 GCACGAATGTTCTATTTCCAGACTT 59.878 40.000 0.00 0.00 0.00 3.01
1795 1897 1.731424 CGATTATTACGGCGATCGGCT 60.731 52.381 34.57 24.40 44.45 5.52
1819 1921 9.832445 TGTCCTTCTCCACTAAAATCATAATAC 57.168 33.333 0.00 0.00 0.00 1.89
1835 1937 6.181908 TCTTACTCTTAGACTGTCCTTCTCC 58.818 44.000 3.76 0.00 0.00 3.71
1910 2077 1.361668 CCGTTTGAGGCATCCGTCTG 61.362 60.000 0.00 0.00 0.00 3.51
1924 2091 0.591170 CGAGTGTTTGATGCCCGTTT 59.409 50.000 0.00 0.00 0.00 3.60
1939 2106 2.279069 CCAGCTGGTCAGTCCGAGT 61.279 63.158 25.53 0.00 39.52 4.18
1940 2107 2.575993 CCAGCTGGTCAGTCCGAG 59.424 66.667 25.53 0.00 39.52 4.63
1941 2108 3.695606 GCCAGCTGGTCAGTCCGA 61.696 66.667 32.81 0.00 39.52 4.55
1955 2333 4.660611 TAGGGTTGGGGGACGCCA 62.661 66.667 11.16 3.74 42.25 5.69
1975 2353 4.166539 CAGATAGGGAGGAGATGGATGTT 58.833 47.826 0.00 0.00 0.00 2.71
2062 2440 2.203552 TTTTGCCGGGCCATGACA 60.204 55.556 17.97 0.00 0.00 3.58
2064 2442 1.228706 TTCTTTTGCCGGGCCATGA 60.229 52.632 17.97 8.09 0.00 3.07
2114 2492 2.191400 CTCCTCCTCAATCTGGAACCA 58.809 52.381 0.00 0.00 32.61 3.67
2201 2579 3.535962 CTGCTCCGGCTCCTCCTC 61.536 72.222 0.00 0.00 39.59 3.71
2213 2591 2.866085 ATCAGAACCGGCTGCTGCTC 62.866 60.000 15.64 5.05 39.59 4.26
2217 2595 2.249413 CTCCATCAGAACCGGCTGCT 62.249 60.000 0.00 0.00 35.86 4.24
2229 2607 3.460672 GAATCCGCCGCCTCCATCA 62.461 63.158 0.00 0.00 0.00 3.07
2230 2608 2.666526 GAATCCGCCGCCTCCATC 60.667 66.667 0.00 0.00 0.00 3.51
2238 2616 2.279517 CCTCCTTCGAATCCGCCG 60.280 66.667 0.00 0.00 35.37 6.46
2257 2635 1.076632 CTCCGGCTACTCCACCTCT 60.077 63.158 0.00 0.00 34.01 3.69


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

AutoCloner maintained by Alex Coulton.