Multiple sequence alignment - TraesCS3D01G156600

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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 TraesCS3D01G156600 chr3D 100.000 1651 0 0 941 2591 124070379 124072029 0.000000e+00 3049.0
1 TraesCS3D01G156600 chr3D 96.771 929 19 4 941 1865 486147201 486146280 0.000000e+00 1539.0
2 TraesCS3D01G156600 chr3D 95.590 907 24 5 941 1843 338869964 338869070 0.000000e+00 1439.0
3 TraesCS3D01G156600 chr3D 95.455 858 24 6 1012 1865 363854795 363853949 0.000000e+00 1354.0
4 TraesCS3D01G156600 chr3D 100.000 297 0 0 1 297 124069439 124069735 1.360000e-152 549.0
5 TraesCS3D01G156600 chr3D 95.699 279 4 4 9 285 486147833 486147561 2.370000e-120 442.0
6 TraesCS3D01G156600 chr3D 93.836 292 13 2 9 295 601117365 601117074 3.960000e-118 435.0
7 TraesCS3D01G156600 chr3D 85.761 309 35 6 2282 2588 281088985 281089286 4.160000e-83 318.0
8 TraesCS3D01G156600 chr6D 94.714 927 38 4 941 1863 424649068 424648149 0.000000e+00 1430.0
9 TraesCS3D01G156600 chr5B 94.030 938 35 10 941 1865 56361527 56362456 0.000000e+00 1402.0
10 TraesCS3D01G156600 chr5B 93.818 922 38 8 956 1863 517572304 517571388 0.000000e+00 1369.0
11 TraesCS3D01G156600 chr5B 93.066 923 38 9 957 1866 297042230 297043139 0.000000e+00 1327.0
12 TraesCS3D01G156600 chr5B 84.665 313 35 8 2282 2591 330123593 330123291 1.510000e-77 300.0
13 TraesCS3D01G156600 chr7A 93.920 921 37 10 951 1866 700256716 700257622 0.000000e+00 1373.0
14 TraesCS3D01G156600 chr4D 94.283 892 36 9 984 1863 503905579 503906467 0.000000e+00 1351.0
15 TraesCS3D01G156600 chr4D 94.077 287 15 1 11 295 92671986 92671700 3.960000e-118 435.0
16 TraesCS3D01G156600 chr3A 92.838 377 22 1 2215 2591 131643081 131643452 2.270000e-150 542.0
17 TraesCS3D01G156600 chr3A 93.534 232 13 2 1922 2153 131642849 131643078 6.860000e-91 344.0
18 TraesCS3D01G156600 chr3A 85.065 308 38 5 2282 2589 159391946 159391647 9.010000e-80 307.0
19 TraesCS3D01G156600 chr3B 89.867 375 22 5 2218 2591 178257284 178257643 3.900000e-128 468.0
20 TraesCS3D01G156600 chr3B 93.581 296 17 2 1859 2153 178256985 178257279 8.510000e-120 440.0
21 TraesCS3D01G156600 chr3B 94.624 279 11 3 9 285 207205132 207204856 1.840000e-116 429.0
22 TraesCS3D01G156600 chr4B 96.751 277 5 3 11 285 577064128 577063854 2.350000e-125 459.0
23 TraesCS3D01G156600 chr4B 93.080 289 16 2 8 295 409267129 409267414 1.110000e-113 420.0
24 TraesCS3D01G156600 chr4A 96.970 264 8 0 9 272 274637187 274637450 6.580000e-121 444.0
25 TraesCS3D01G156600 chr6B 95.865 266 10 1 8 272 38933299 38933564 1.840000e-116 429.0
26 TraesCS3D01G156600 chr6B 85.161 310 35 7 2282 2588 157907578 157907879 9.010000e-80 307.0
27 TraesCS3D01G156600 chr5D 95.865 266 9 1 9 272 53755584 53755849 1.840000e-116 429.0
28 TraesCS3D01G156600 chr1A 85.806 310 35 6 2282 2589 493932274 493931972 1.160000e-83 320.0
29 TraesCS3D01G156600 chr7B 85.577 312 35 6 2282 2591 261954720 261955023 4.160000e-83 318.0
30 TraesCS3D01G156600 chr1D 85.484 310 34 8 2282 2588 163706470 163706169 1.940000e-81 313.0
31 TraesCS3D01G156600 chr1D 100.000 28 0 0 2157 2184 423047526 423047499 5.000000e-03 52.8
32 TraesCS3D01G156600 chr2A 87.160 257 30 3 1898 2153 724412640 724412894 3.260000e-74 289.0


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 TraesCS3D01G156600 chr3D 124069439 124072029 2590 False 1799.0 3049 100.000 1 2591 2 chr3D.!!$F2 2590
1 TraesCS3D01G156600 chr3D 338869070 338869964 894 True 1439.0 1439 95.590 941 1843 1 chr3D.!!$R1 902
2 TraesCS3D01G156600 chr3D 363853949 363854795 846 True 1354.0 1354 95.455 1012 1865 1 chr3D.!!$R2 853
3 TraesCS3D01G156600 chr3D 486146280 486147833 1553 True 990.5 1539 96.235 9 1865 2 chr3D.!!$R4 1856
4 TraesCS3D01G156600 chr6D 424648149 424649068 919 True 1430.0 1430 94.714 941 1863 1 chr6D.!!$R1 922
5 TraesCS3D01G156600 chr5B 56361527 56362456 929 False 1402.0 1402 94.030 941 1865 1 chr5B.!!$F1 924
6 TraesCS3D01G156600 chr5B 517571388 517572304 916 True 1369.0 1369 93.818 956 1863 1 chr5B.!!$R2 907
7 TraesCS3D01G156600 chr5B 297042230 297043139 909 False 1327.0 1327 93.066 957 1866 1 chr5B.!!$F2 909
8 TraesCS3D01G156600 chr7A 700256716 700257622 906 False 1373.0 1373 93.920 951 1866 1 chr7A.!!$F1 915
9 TraesCS3D01G156600 chr4D 503905579 503906467 888 False 1351.0 1351 94.283 984 1863 1 chr4D.!!$F1 879
10 TraesCS3D01G156600 chr3A 131642849 131643452 603 False 443.0 542 93.186 1922 2591 2 chr3A.!!$F1 669
11 TraesCS3D01G156600 chr3B 178256985 178257643 658 False 454.0 468 91.724 1859 2591 2 chr3B.!!$F1 732

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
233 236 0.168128 CCGCCACTTCATTTCCGTTC 59.832 55.0 0.0 0.0 0.0 3.95 F
234 237 0.168128 CGCCACTTCATTTCCGTTCC 59.832 55.0 0.0 0.0 0.0 3.62 F
235 238 0.526211 GCCACTTCATTTCCGTTCCC 59.474 55.0 0.0 0.0 0.0 3.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1298 1325 0.882927 GCCAGCACTAACGACAACCA 60.883 55.000 0.0 0.0 0.0 3.67 R
1505 1538 0.998945 CTCCTCCTCCTCCTCCTCCT 60.999 65.000 0.0 0.0 0.0 3.69 R
1966 2016 1.134068 GCCCAATCTTCCACCTCCTAC 60.134 57.143 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
149 152 4.320129 CGTGATGTAAAATGCAACACCTCA 60.320 41.667 0.00 0.00 36.64 3.86
233 236 0.168128 CCGCCACTTCATTTCCGTTC 59.832 55.000 0.00 0.00 0.00 3.95
234 237 0.168128 CGCCACTTCATTTCCGTTCC 59.832 55.000 0.00 0.00 0.00 3.62
235 238 0.526211 GCCACTTCATTTCCGTTCCC 59.474 55.000 0.00 0.00 0.00 3.97
236 239 0.802494 CCACTTCATTTCCGTTCCCG 59.198 55.000 0.00 0.00 0.00 5.14
240 243 2.360600 CATTTCCGTTCCCGCCCA 60.361 61.111 0.00 0.00 0.00 5.36
1271 1295 2.159366 ACATGAAGGAGATCACGACGAC 60.159 50.000 0.00 0.00 30.82 4.34
1298 1325 4.278975 AGAAGAAGATGAAGAAGCCGTT 57.721 40.909 0.00 0.00 0.00 4.44
1424 1457 0.617935 GAGCAGAAGAAGAAGGGGCT 59.382 55.000 0.00 0.00 0.00 5.19
1505 1538 1.228894 ACTGGGCAGACTTCTCGGA 60.229 57.895 0.00 0.00 0.00 4.55
1506 1539 1.254284 ACTGGGCAGACTTCTCGGAG 61.254 60.000 0.00 0.00 0.00 4.63
1580 1629 2.615262 GAGCAGTTCCGTAGCTCCGG 62.615 65.000 12.21 12.21 46.82 5.14
1884 1934 6.601332 TCTAAAAGTGTTCCCTTCAATCAGT 58.399 36.000 0.00 0.00 0.00 3.41
1899 1949 6.874278 TCAATCAGTCCTTCCTTCAAGATA 57.126 37.500 0.00 0.00 33.29 1.98
1959 2009 4.767928 ACTTCAGTTCCTACTCGAATCAGT 59.232 41.667 0.00 0.00 30.26 3.41
1966 2016 4.669318 TCCTACTCGAATCAGTTTTAGCG 58.331 43.478 0.00 0.00 0.00 4.26
2001 2051 2.514458 TGGGCCAAAATCTTCCTCTC 57.486 50.000 2.13 0.00 0.00 3.20
2025 2075 4.062991 ACGACTTCTATGTTTGGAACCAC 58.937 43.478 0.00 0.00 0.00 4.16
2122 2172 8.902540 ATTTTTATGCATTGCTGATTCATCAT 57.097 26.923 3.54 0.00 36.02 2.45
2153 2203 7.031372 ACAAAAGATATGTTGTGATGATGCAC 58.969 34.615 9.66 0.00 36.62 4.57
2161 2211 3.251479 TGTGATGATGCACAGTACTCC 57.749 47.619 0.00 0.00 43.35 3.85
2162 2212 2.093500 TGTGATGATGCACAGTACTCCC 60.093 50.000 0.00 0.00 43.35 4.30
2163 2213 2.169352 GTGATGATGCACAGTACTCCCT 59.831 50.000 0.00 0.00 38.63 4.20
2164 2214 2.432146 TGATGATGCACAGTACTCCCTC 59.568 50.000 0.00 0.00 0.00 4.30
2165 2215 2.238084 TGATGCACAGTACTCCCTCT 57.762 50.000 0.00 0.00 0.00 3.69
2166 2216 1.827344 TGATGCACAGTACTCCCTCTG 59.173 52.381 0.00 0.00 37.65 3.35
2167 2217 1.827969 GATGCACAGTACTCCCTCTGT 59.172 52.381 0.00 0.00 44.32 3.41
2168 2218 2.597578 TGCACAGTACTCCCTCTGTA 57.402 50.000 0.00 0.00 42.05 2.74
2169 2219 2.884320 TGCACAGTACTCCCTCTGTAA 58.116 47.619 0.00 0.00 42.05 2.41
2170 2220 3.236047 TGCACAGTACTCCCTCTGTAAA 58.764 45.455 0.00 0.00 42.05 2.01
2171 2221 3.258372 TGCACAGTACTCCCTCTGTAAAG 59.742 47.826 0.00 0.00 42.05 1.85
2172 2222 3.258622 GCACAGTACTCCCTCTGTAAAGT 59.741 47.826 0.00 0.00 42.05 2.66
2173 2223 4.461781 GCACAGTACTCCCTCTGTAAAGTA 59.538 45.833 0.00 0.00 42.05 2.24
2174 2224 5.127356 GCACAGTACTCCCTCTGTAAAGTAT 59.873 44.000 0.00 0.00 42.05 2.12
2175 2225 6.351117 GCACAGTACTCCCTCTGTAAAGTATT 60.351 42.308 0.00 0.00 42.05 1.89
2176 2226 7.147949 GCACAGTACTCCCTCTGTAAAGTATTA 60.148 40.741 0.00 0.00 42.05 0.98
2177 2227 8.915036 CACAGTACTCCCTCTGTAAAGTATTAT 58.085 37.037 0.00 0.00 42.05 1.28
2183 2233 8.848182 ACTCCCTCTGTAAAGTATTATAAGACG 58.152 37.037 4.66 0.00 0.00 4.18
2184 2234 8.985315 TCCCTCTGTAAAGTATTATAAGACGA 57.015 34.615 4.66 0.00 0.00 4.20
2185 2235 9.584008 TCCCTCTGTAAAGTATTATAAGACGAT 57.416 33.333 4.66 1.16 0.00 3.73
2330 2380 9.412460 TCTATCTCTATCAATTGCAAAATTGGT 57.588 29.630 1.71 3.20 39.84 3.67
2368 2418 5.235186 GTGGAGTGATATTGATTTGTCGAGG 59.765 44.000 0.00 0.00 0.00 4.63
2369 2419 4.212214 GGAGTGATATTGATTTGTCGAGGC 59.788 45.833 0.00 0.00 0.00 4.70
2421 2472 5.048083 GTCCACCTTCATGCATTTTAGTTGA 60.048 40.000 0.00 0.00 0.00 3.18
2422 2473 5.716228 TCCACCTTCATGCATTTTAGTTGAT 59.284 36.000 0.00 0.00 0.00 2.57
2451 2502 9.529325 ACTTACAAAAGTGAAGGAAAAATTAGC 57.471 29.630 0.00 0.00 44.40 3.09
2536 2587 3.114606 TCATCTTGCCCTCAACCAGATA 58.885 45.455 0.00 0.00 0.00 1.98
2537 2588 3.523157 TCATCTTGCCCTCAACCAGATAA 59.477 43.478 0.00 0.00 0.00 1.75
2538 2589 3.634397 TCTTGCCCTCAACCAGATAAG 57.366 47.619 0.00 0.00 0.00 1.73
2539 2590 3.181329 TCTTGCCCTCAACCAGATAAGA 58.819 45.455 0.00 0.00 0.00 2.10
2540 2591 3.782523 TCTTGCCCTCAACCAGATAAGAT 59.217 43.478 0.00 0.00 0.00 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
81 82 2.826428 CATATGGACCGTCTGTTGGAG 58.174 52.381 0.00 0.00 0.00 3.86
149 152 5.528870 TCTCGTGATGTATATTTGCATCGT 58.471 37.500 9.07 0.00 45.03 3.73
1271 1295 5.063312 GGCTTCTTCATCTTCTTCTTCTTCG 59.937 44.000 0.00 0.00 0.00 3.79
1298 1325 0.882927 GCCAGCACTAACGACAACCA 60.883 55.000 0.00 0.00 0.00 3.67
1375 1405 2.498078 GCTTCCAGTAGTACTCCAGCTT 59.502 50.000 0.00 0.00 0.00 3.74
1424 1457 1.207791 GGCCTCATCCTCCTTCTTCA 58.792 55.000 0.00 0.00 0.00 3.02
1505 1538 0.998945 CTCCTCCTCCTCCTCCTCCT 60.999 65.000 0.00 0.00 0.00 3.69
1506 1539 1.541672 CTCCTCCTCCTCCTCCTCC 59.458 68.421 0.00 0.00 0.00 4.30
1580 1629 6.702716 ACTGCTAGATAAACTACTCCTCAC 57.297 41.667 0.00 0.00 0.00 3.51
1801 1851 7.039363 TCCAAAATCGGAGATGTAAAATTTGGT 60.039 33.333 15.44 0.00 45.12 3.67
1899 1949 6.153340 AGCACAATCAACAGCTAATACCAAAT 59.847 34.615 0.00 0.00 35.19 2.32
1959 2009 3.167485 TCTTCCACCTCCTACGCTAAAA 58.833 45.455 0.00 0.00 0.00 1.52
1966 2016 1.134068 GCCCAATCTTCCACCTCCTAC 60.134 57.143 0.00 0.00 0.00 3.18
2001 2051 5.347907 GTGGTTCCAAACATAGAAGTCGTAG 59.652 44.000 0.00 0.00 0.00 3.51
2025 2075 1.915141 AAGATCCCCAACTTGCACTG 58.085 50.000 0.00 0.00 0.00 3.66
2122 2172 9.936759 TCATCACAACATATCTTTTGTAGTACA 57.063 29.630 0.00 0.00 34.12 2.90
2137 2187 4.582869 AGTACTGTGCATCATCACAACAT 58.417 39.130 0.00 0.00 45.22 2.71
2157 2207 8.848182 CGTCTTATAATACTTTACAGAGGGAGT 58.152 37.037 0.21 0.00 0.00 3.85
2158 2208 9.064706 TCGTCTTATAATACTTTACAGAGGGAG 57.935 37.037 0.21 0.00 0.00 4.30
2159 2209 8.985315 TCGTCTTATAATACTTTACAGAGGGA 57.015 34.615 0.21 0.00 0.00 4.20
2330 2380 6.560003 ATCACTCCACAAATGATAGGTGTA 57.440 37.500 0.00 0.00 31.26 2.90
2368 2418 4.274421 GGTAGCAAACCTTTCGATAAGC 57.726 45.455 1.14 0.00 45.75 3.09
2398 2448 5.076182 TCAACTAAAATGCATGAAGGTGGA 58.924 37.500 16.79 8.17 0.00 4.02
2434 2485 6.319911 GCTATCCAGCTAATTTTTCCTTCACT 59.680 38.462 0.00 0.00 44.93 3.41
2451 2502 1.035923 TTCTCAGCCGAGCTATCCAG 58.964 55.000 0.00 0.00 36.40 3.86
2514 2565 1.003580 TCTGGTTGAGGGCAAGATGAC 59.996 52.381 0.00 0.00 34.01 3.06
2536 2587 7.814264 AAGTGAGTCAAAGAACATGAATCTT 57.186 32.000 0.00 6.20 41.23 2.40
2537 2588 7.814264 AAAGTGAGTCAAAGAACATGAATCT 57.186 32.000 0.00 0.00 41.23 2.40
2538 2589 7.592903 GGAAAAGTGAGTCAAAGAACATGAATC 59.407 37.037 0.00 0.00 41.08 2.52
2539 2590 7.068593 TGGAAAAGTGAGTCAAAGAACATGAAT 59.931 33.333 0.00 0.00 0.00 2.57
2540 2591 6.376864 TGGAAAAGTGAGTCAAAGAACATGAA 59.623 34.615 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.