Multiple sequence alignment - TraesCS7D01G321300

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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 TraesCS7D01G321300 chr7D 100.000 2267 0 0 1 2267 411315790 411313524 0.000000e+00 4187
1 TraesCS7D01G321300 chr5D 94.536 1940 94 8 3 1932 522787157 522789094 0.000000e+00 2985
2 TraesCS7D01G321300 chr5D 93.679 1946 99 2 1 1946 517098992 517100913 0.000000e+00 2891
3 TraesCS7D01G321300 chr5D 92.027 301 24 0 1918 2218 517100921 517101221 7.490000e-115 424
4 TraesCS7D01G321300 chr5D 88.589 333 37 1 1918 2249 452399582 452399250 9.750000e-109 403
5 TraesCS7D01G321300 chr5D 86.826 334 41 3 1918 2249 522789115 522789447 9.890000e-99 370
6 TraesCS7D01G321300 chr3B 93.172 1860 101 12 1 1858 738417837 738419672 0.000000e+00 2708
7 TraesCS7D01G321300 chr3B 89.785 1958 175 16 1 1946 213720125 213718181 0.000000e+00 2484
8 TraesCS7D01G321300 chr1D 91.735 1960 131 18 1 1946 92054250 92056192 0.000000e+00 2693
9 TraesCS7D01G321300 chr1D 87.537 337 38 3 1918 2253 20009089 20008756 9.820000e-104 387
10 TraesCS7D01G321300 chr2B 91.135 1929 153 6 1 1920 747523227 747525146 0.000000e+00 2599
11 TraesCS7D01G321300 chr2B 91.374 684 56 3 1178 1859 82426783 82426101 0.000000e+00 933
12 TraesCS7D01G321300 chr2B 87.132 272 24 9 1982 2249 669246404 669246668 4.730000e-77 298
13 TraesCS7D01G321300 chr2B 90.265 226 19 2 2042 2267 669246362 669246584 2.200000e-75 292
14 TraesCS7D01G321300 chr2D 92.266 1836 107 12 116 1946 314480299 314478494 0.000000e+00 2571
15 TraesCS7D01G321300 chr2D 89.458 332 35 0 1918 2249 314478486 314478155 9.680000e-114 420
16 TraesCS7D01G321300 chr7B 89.223 1828 162 14 1 1820 122756886 122758686 0.000000e+00 2252
17 TraesCS7D01G321300 chr4D 86.722 1800 191 28 1 1789 343945635 343947397 0.000000e+00 1956
18 TraesCS7D01G321300 chr6D 91.462 773 42 5 1174 1946 421611652 421612400 0.000000e+00 1040
19 TraesCS7D01G321300 chr1A 92.308 221 16 1 2029 2249 215652745 215652526 1.690000e-81 313
20 TraesCS7D01G321300 chr3D 87.069 232 27 3 1918 2148 416000446 416000675 2.230000e-65 259
21 TraesCS7D01G321300 chr5B 79.511 327 58 9 1921 2243 595180348 595180027 8.150000e-55 224


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 TraesCS7D01G321300 chr7D 411313524 411315790 2266 True 4187.0 4187 100.000 1 2267 1 chr7D.!!$R1 2266
1 TraesCS7D01G321300 chr5D 522787157 522789447 2290 False 1677.5 2985 90.681 3 2249 2 chr5D.!!$F2 2246
2 TraesCS7D01G321300 chr5D 517098992 517101221 2229 False 1657.5 2891 92.853 1 2218 2 chr5D.!!$F1 2217
3 TraesCS7D01G321300 chr3B 738417837 738419672 1835 False 2708.0 2708 93.172 1 1858 1 chr3B.!!$F1 1857
4 TraesCS7D01G321300 chr3B 213718181 213720125 1944 True 2484.0 2484 89.785 1 1946 1 chr3B.!!$R1 1945
5 TraesCS7D01G321300 chr1D 92054250 92056192 1942 False 2693.0 2693 91.735 1 1946 1 chr1D.!!$F1 1945
6 TraesCS7D01G321300 chr2B 747523227 747525146 1919 False 2599.0 2599 91.135 1 1920 1 chr2B.!!$F1 1919
7 TraesCS7D01G321300 chr2B 82426101 82426783 682 True 933.0 933 91.374 1178 1859 1 chr2B.!!$R1 681
8 TraesCS7D01G321300 chr2D 314478155 314480299 2144 True 1495.5 2571 90.862 116 2249 2 chr2D.!!$R1 2133
9 TraesCS7D01G321300 chr7B 122756886 122758686 1800 False 2252.0 2252 89.223 1 1820 1 chr7B.!!$F1 1819
10 TraesCS7D01G321300 chr4D 343945635 343947397 1762 False 1956.0 1956 86.722 1 1789 1 chr4D.!!$F1 1788
11 TraesCS7D01G321300 chr6D 421611652 421612400 748 False 1040.0 1040 91.462 1174 1946 1 chr6D.!!$F1 772

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
392 393 0.174389 CCTCGATCAGTCACAGTGGG 59.826 60.0 0.0 0.0 0.0 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2116 2277 0.322098 CAACCCTACCGCCATGAACA 60.322 55.0 0.0 0.0 0.0 3.18 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
392 393 0.174389 CCTCGATCAGTCACAGTGGG 59.826 60.000 0.00 0.00 0.00 4.61
395 396 0.817654 CGATCAGTCACAGTGGGCTA 59.182 55.000 0.00 0.00 0.00 3.93
420 421 2.257409 GATGGGCCACACATCGTCCT 62.257 60.000 9.28 0.00 35.84 3.85
453 457 2.311542 TCATGGTGCCTACAAAGGGAAT 59.688 45.455 0.00 0.00 46.04 3.01
493 500 1.773052 AGGGGTGACATGGATGATCTG 59.227 52.381 0.00 0.00 0.00 2.90
783 796 2.894765 GAGGAGACACTATTAGAGGGCC 59.105 54.545 0.00 0.00 27.73 5.80
804 817 0.967380 GGGGGACGGTCGACTCTTAA 60.967 60.000 16.46 0.00 0.00 1.85
871 884 3.205784 AGGCCTATTGACATCTTGCTC 57.794 47.619 1.29 0.00 0.00 4.26
878 891 0.684535 TGACATCTTGCTCAACCCGA 59.315 50.000 0.00 0.00 0.00 5.14
907 921 7.959109 GGTTGAAATAATGTGAACGGTACTTAC 59.041 37.037 0.00 0.00 0.00 2.34
1064 1085 1.336887 CGAGGACATGTCGGACAAGTT 60.337 52.381 18.72 5.53 29.32 2.66
1069 1090 4.162320 AGGACATGTCGGACAAGTTGATAT 59.838 41.667 18.72 3.12 29.32 1.63
1255 1276 2.027625 GCCTATGATGTACCGCCGC 61.028 63.158 0.00 0.00 0.00 6.53
1275 1296 5.519722 CCGCTAAGTTGTTGAAGTTCAAAT 58.480 37.500 19.63 7.02 38.22 2.32
1328 1350 8.768397 ACCTATCTTACTAATGACCACATTTGA 58.232 33.333 10.19 0.00 43.17 2.69
1530 1559 3.576118 TGAAAGAAGTGTGAGGAGGAGAG 59.424 47.826 0.00 0.00 0.00 3.20
1634 1667 2.726241 GCATGCGACAAGAAAGGAAAAC 59.274 45.455 0.00 0.00 0.00 2.43
1636 1669 2.011222 TGCGACAAGAAAGGAAAACGT 58.989 42.857 0.00 0.00 0.00 3.99
1908 2022 4.272504 CACGAGGAAAAACAGAGCAAACTA 59.727 41.667 0.00 0.00 0.00 2.24
1931 2055 1.175983 TTTGCACCCTACCGCCAAAG 61.176 55.000 0.00 0.00 0.00 2.77
1967 2127 1.663739 CCGAACTGTCCTGGAACGA 59.336 57.895 0.00 0.00 0.00 3.85
2053 2214 1.550327 CACCCTACTGTCTGCTCTGA 58.450 55.000 0.00 0.00 0.00 3.27
2086 2247 2.482336 TGACCAAATCGGACACATTTCG 59.518 45.455 0.00 0.00 34.28 3.46
2159 2320 2.127869 CCTACGGCCTGCTCTGCTA 61.128 63.158 0.00 0.00 0.00 3.49
2168 2329 1.686428 CCTGCTCTGCTACCTGTCCTA 60.686 57.143 0.00 0.00 0.00 2.94
2189 2350 1.543802 TGACCAAATCGGCCACATTTC 59.456 47.619 2.24 0.00 39.03 2.17
2258 2419 4.567318 CCACCCTATGGCTTGCTC 57.433 61.111 0.00 0.00 43.24 4.26
2259 2420 1.918253 CCACCCTATGGCTTGCTCT 59.082 57.895 0.00 0.00 43.24 4.09
2260 2421 0.465097 CCACCCTATGGCTTGCTCTG 60.465 60.000 0.00 0.00 43.24 3.35
2261 2422 1.099879 CACCCTATGGCTTGCTCTGC 61.100 60.000 0.00 0.00 33.59 4.26
2262 2423 1.277580 ACCCTATGGCTTGCTCTGCT 61.278 55.000 0.00 0.00 33.59 4.24
2263 2424 0.818445 CCCTATGGCTTGCTCTGCTG 60.818 60.000 0.00 0.00 0.00 4.41
2264 2425 1.445716 CCTATGGCTTGCTCTGCTGC 61.446 60.000 0.00 0.00 0.00 5.25
2265 2426 1.445716 CTATGGCTTGCTCTGCTGCC 61.446 60.000 15.75 15.75 44.20 4.85
2266 2427 1.918467 TATGGCTTGCTCTGCTGCCT 61.918 55.000 20.30 12.46 44.23 4.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
119 120 5.116180 CGGCTCATTGACTTGGTAGATTTA 58.884 41.667 0.00 0.00 0.00 1.40
392 393 2.222027 GTGTGGCCCATCATACTTAGC 58.778 52.381 0.00 0.00 0.00 3.09
395 396 2.746142 CGATGTGTGGCCCATCATACTT 60.746 50.000 17.41 0.00 38.90 2.24
420 421 1.608336 ACCATGAGTTCGGGGTCGA 60.608 57.895 0.00 0.00 44.44 4.20
453 457 6.561454 ACCCCTAAACCTCTTCTTTCTTCTTA 59.439 38.462 0.00 0.00 0.00 2.10
493 500 3.746045 TTCATTCCGGTGTATCTAGCC 57.254 47.619 0.00 0.00 0.00 3.93
692 699 1.321074 CCTCGTCCACTACCACTCCC 61.321 65.000 0.00 0.00 0.00 4.30
783 796 3.450115 GAGTCGACCGTCCCCCAG 61.450 72.222 13.01 0.00 0.00 4.45
804 817 4.003788 CACGACCACCGGCTCCTT 62.004 66.667 0.00 0.00 43.93 3.36
878 891 6.339587 ACCGTTCACATTATTTCAACCATT 57.660 33.333 0.00 0.00 0.00 3.16
907 921 7.257722 ACAAGACCGAATTAAGCCAATAAATG 58.742 34.615 0.00 0.00 0.00 2.32
1064 1085 4.082408 CCTTATCCAACTCGGCGTATATCA 60.082 45.833 6.85 0.00 33.14 2.15
1069 1090 1.135527 CACCTTATCCAACTCGGCGTA 59.864 52.381 6.85 0.00 33.14 4.42
1275 1296 5.786311 AGTTGTAGCAACGGTTGAATACTA 58.214 37.500 24.20 17.32 0.00 1.82
1328 1350 4.531332 GGCGACTACGTACGAATAAAGAT 58.469 43.478 24.41 0.00 41.98 2.40
1530 1559 1.815003 CAATCTTCTCCTTGTGTGCCC 59.185 52.381 0.00 0.00 0.00 5.36
1634 1667 0.528924 TATTGGGTCACACGAGGACG 59.471 55.000 0.00 0.00 45.75 4.79
1636 1669 1.553248 CCTTATTGGGTCACACGAGGA 59.447 52.381 0.00 0.00 0.00 3.71
1908 2022 2.046285 GCGGTAGGGTGCAAAGCAT 61.046 57.895 0.00 0.00 41.91 3.79
1931 2055 2.044946 CAACCTACTGCCAGGCCC 60.045 66.667 9.64 0.00 39.53 5.80
1967 2127 1.260544 GCAGAACAGGGGAGCATTTT 58.739 50.000 0.00 0.00 0.00 1.82
2044 2205 0.616964 AGGACAGGCATCAGAGCAGA 60.617 55.000 0.00 0.00 35.83 4.26
2053 2214 0.478072 TTTGGTCACAGGACAGGCAT 59.522 50.000 0.00 0.00 46.17 4.40
2086 2247 4.338710 TGGCCAACCCTACCGCAC 62.339 66.667 0.61 0.00 33.59 5.34
2116 2277 0.322098 CAACCCTACCGCCATGAACA 60.322 55.000 0.00 0.00 0.00 3.18
2159 2320 2.170607 CCGATTTGGTCATAGGACAGGT 59.829 50.000 10.08 0.00 46.17 4.00
2219 2380 2.192175 CCCTACCGCCATGAACCC 59.808 66.667 0.00 0.00 0.00 4.11
2220 2381 1.029947 CAACCCTACCGCCATGAACC 61.030 60.000 0.00 0.00 0.00 3.62
2223 2384 2.994699 CCAACCCTACCGCCATGA 59.005 61.111 0.00 0.00 0.00 3.07


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

AutoCloner maintained by Alex Coulton.