Multiple sequence alignment - TraesCS6D01G021300

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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 TraesCS6D01G021300 chr6D 100.000 2507 0 0 1 2507 8397506 8395000 0.000000e+00 4630.0
1 TraesCS6D01G021300 chr6D 91.403 1896 108 19 1 1885 8899178 8901029 0.000000e+00 2547.0
2 TraesCS6D01G021300 chr6D 86.166 1171 158 4 342 1509 8894044 8895213 0.000000e+00 1262.0
3 TraesCS6D01G021300 chr6D 91.483 634 26 5 1882 2507 8901109 8901722 0.000000e+00 846.0
4 TraesCS6D01G021300 chr6B 91.080 2074 144 26 1 2053 52568588 52566535 0.000000e+00 2767.0
5 TraesCS6D01G021300 chr6B 91.127 2006 151 16 256 2245 16428907 16430901 0.000000e+00 2693.0
6 TraesCS6D01G021300 chr6B 92.998 1471 73 15 1052 2507 52987888 52986433 0.000000e+00 2119.0
7 TraesCS6D01G021300 chr6B 86.842 1064 134 5 450 1509 15225632 15224571 0.000000e+00 1184.0
8 TraesCS6D01G021300 chr6B 78.739 1237 229 27 295 1507 15234922 15233696 0.000000e+00 797.0
9 TraesCS6D01G021300 chr6B 78.453 1267 229 27 273 1505 16320483 16321739 0.000000e+00 787.0
10 TraesCS6D01G021300 chr6B 77.891 1176 211 32 344 1504 16267380 16268521 0.000000e+00 686.0
11 TraesCS6D01G021300 chr6B 92.402 408 24 2 2106 2507 52566541 52566135 2.160000e-160 575.0
12 TraesCS6D01G021300 chr6B 95.053 283 7 2 2231 2507 16431101 16431382 2.960000e-119 438.0
13 TraesCS6D01G021300 chr6B 85.990 207 15 6 1 199 16252586 16252786 2.530000e-50 209.0
14 TraesCS6D01G021300 chr6B 87.500 72 4 2 2176 2247 15749301 15749235 7.430000e-11 78.7
15 TraesCS6D01G021300 chr6A 87.439 1234 136 13 742 1970 8804162 8802943 0.000000e+00 1402.0
16 TraesCS6D01G021300 chr1B 85.215 1231 159 17 295 1509 630644684 630645907 0.000000e+00 1243.0
17 TraesCS6D01G021300 chr1B 92.381 105 4 2 95 199 630644444 630644544 2.010000e-31 147.0
18 TraesCS6D01G021300 chr3A 84.184 1176 175 7 342 1508 45937987 45936814 0.000000e+00 1131.0
19 TraesCS6D01G021300 chr3D 83.904 1168 176 8 349 1507 33330498 33329334 0.000000e+00 1105.0
20 TraesCS6D01G021300 chr2B 86.494 348 38 6 343 688 89490671 89491011 8.470000e-100 374.0
21 TraesCS6D01G021300 chr2B 82.883 111 10 6 2161 2269 373066917 373066814 9.550000e-15 91.6
22 TraesCS6D01G021300 chr1D 90.588 85 7 1 2158 2242 416354728 416354645 7.330000e-21 111.0


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 TraesCS6D01G021300 chr6D 8395000 8397506 2506 True 4630.000000 4630 100.000 1 2507 1 chr6D.!!$R1 2506
1 TraesCS6D01G021300 chr6D 8894044 8901722 7678 False 1551.666667 2547 89.684 1 2507 3 chr6D.!!$F1 2506
2 TraesCS6D01G021300 chr6B 52986433 52987888 1455 True 2119.000000 2119 92.998 1052 2507 1 chr6B.!!$R4 1455
3 TraesCS6D01G021300 chr6B 52566135 52568588 2453 True 1671.000000 2767 91.741 1 2507 2 chr6B.!!$R5 2506
4 TraesCS6D01G021300 chr6B 16428907 16431382 2475 False 1565.500000 2693 93.090 256 2507 2 chr6B.!!$F4 2251
5 TraesCS6D01G021300 chr6B 15224571 15225632 1061 True 1184.000000 1184 86.842 450 1509 1 chr6B.!!$R1 1059
6 TraesCS6D01G021300 chr6B 15233696 15234922 1226 True 797.000000 797 78.739 295 1507 1 chr6B.!!$R2 1212
7 TraesCS6D01G021300 chr6B 16320483 16321739 1256 False 787.000000 787 78.453 273 1505 1 chr6B.!!$F3 1232
8 TraesCS6D01G021300 chr6B 16267380 16268521 1141 False 686.000000 686 77.891 344 1504 1 chr6B.!!$F2 1160
9 TraesCS6D01G021300 chr6A 8802943 8804162 1219 True 1402.000000 1402 87.439 742 1970 1 chr6A.!!$R1 1228
10 TraesCS6D01G021300 chr1B 630644444 630645907 1463 False 695.000000 1243 88.798 95 1509 2 chr1B.!!$F1 1414
11 TraesCS6D01G021300 chr3A 45936814 45937987 1173 True 1131.000000 1131 84.184 342 1508 1 chr3A.!!$R1 1166
12 TraesCS6D01G021300 chr3D 33329334 33330498 1164 True 1105.000000 1105 83.904 349 1507 1 chr3D.!!$R1 1158

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
934 6493 0.17668 CTGCGGGCTAGATGACACTT 59.823 55.0 0.0 0.0 0.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2116 7791 2.885135 AGTCCATGTCATCTTTGGCA 57.115 45.0 0.0 0.0 42.74 4.92 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
82 83 6.982852 TGGAGTATTCTGAACTCGATAATCC 58.017 40.000 7.25 7.25 43.55 3.01
134 135 7.944554 TGTTCTCCAACTTATTTTTCCTCATCT 59.055 33.333 0.00 0.00 33.17 2.90
222 235 4.570772 GCCCACCTGTTTTTCTTTTCTTTC 59.429 41.667 0.00 0.00 0.00 2.62
223 236 5.116180 CCCACCTGTTTTTCTTTTCTTTCC 58.884 41.667 0.00 0.00 0.00 3.13
338 416 2.123854 CCCCGTCGATCTCCTCCA 60.124 66.667 0.00 0.00 0.00 3.86
339 417 1.756950 CCCCGTCGATCTCCTCCAA 60.757 63.158 0.00 0.00 0.00 3.53
340 418 1.327690 CCCCGTCGATCTCCTCCAAA 61.328 60.000 0.00 0.00 0.00 3.28
645 6195 2.508663 GCCGCCCTCGTAGTCAAC 60.509 66.667 0.00 0.00 0.00 3.18
804 6354 2.094494 CGTCTCCAATCTGCAGTACTGT 60.094 50.000 23.44 1.04 0.00 3.55
886 6445 2.179517 CCGACCTCGAGACAGTGC 59.820 66.667 15.71 0.00 43.02 4.40
926 6485 4.143333 GCGTTCCTGCGGGCTAGA 62.143 66.667 6.73 0.00 0.00 2.43
931 6490 0.975556 TTCCTGCGGGCTAGATGACA 60.976 55.000 6.73 0.00 0.00 3.58
934 6493 0.176680 CTGCGGGCTAGATGACACTT 59.823 55.000 0.00 0.00 0.00 3.16
948 6507 3.221771 TGACACTTACATTGCCAAGCTT 58.778 40.909 0.00 0.00 0.00 3.74
960 6519 1.590932 CCAAGCTTAGCATCGCTCAT 58.409 50.000 7.07 0.00 40.44 2.90
1186 6748 1.930908 GCTTCCATCTGTGCTGGCAC 61.931 60.000 17.55 17.55 46.33 5.01
1320 6882 4.603131 GGATCATACCCCGGTACTATGTA 58.397 47.826 0.00 0.00 33.01 2.29
1530 7092 2.157834 TGGTAACAGTGCGGTAACAG 57.842 50.000 0.00 0.00 46.17 3.16
1531 7093 0.794473 GGTAACAGTGCGGTAACAGC 59.206 55.000 0.00 0.00 36.78 4.40
1534 7096 0.874390 AACAGTGCGGTAACAGCATG 59.126 50.000 1.19 4.50 45.12 4.06
1535 7097 0.034756 ACAGTGCGGTAACAGCATGA 59.965 50.000 0.00 0.00 45.12 3.07
1538 7100 2.009774 AGTGCGGTAACAGCATGATTC 58.990 47.619 0.00 0.00 45.12 2.52
1539 7101 1.737236 GTGCGGTAACAGCATGATTCA 59.263 47.619 0.00 0.00 45.12 2.57
1540 7102 2.161410 GTGCGGTAACAGCATGATTCAA 59.839 45.455 0.00 0.00 45.12 2.69
1541 7103 2.816672 TGCGGTAACAGCATGATTCAAA 59.183 40.909 0.00 0.00 39.69 2.69
1595 7157 4.440826 TTTGGTGTTCTTGGCCTAACTA 57.559 40.909 3.32 0.00 0.00 2.24
1654 7216 6.979465 TGTTTGTTACATGCTGATTTGATGA 58.021 32.000 0.00 0.00 0.00 2.92
1655 7217 6.862608 TGTTTGTTACATGCTGATTTGATGAC 59.137 34.615 0.00 0.00 0.00 3.06
1697 7262 9.729281 AATTGGCAATTTGATTTGAGAGTATTT 57.271 25.926 19.39 0.00 0.00 1.40
1885 7475 6.514947 TGTCAGAAAAAGCAATGCAAAGTAT 58.485 32.000 8.35 0.00 0.00 2.12
1918 7593 4.018506 TCTGACACATCCCCACAACATTAT 60.019 41.667 0.00 0.00 0.00 1.28
1927 7602 8.257306 ACATCCCCACAACATTATATTTGAAAC 58.743 33.333 0.00 0.00 0.00 2.78
2072 7747 7.649533 TCTCAAATGACCATAGCATTTTCAT 57.350 32.000 0.00 0.00 42.33 2.57
2116 7791 9.889128 TTTTCATGAAAGAAGGTTCTCATTTTT 57.111 25.926 19.64 0.00 36.28 1.94
2175 7850 4.062293 TGAAAGTATGTTTGTCACTCCCG 58.938 43.478 0.00 0.00 0.00 5.14
2277 8166 6.215845 AGCTTTGCTTATAAAACTGTTGTGG 58.784 36.000 0.00 0.00 33.89 4.17
2310 8199 8.080417 GTCATTGTGTACTACTCAGTAGTTTGA 58.920 37.037 22.67 12.66 45.68 2.69
2311 8200 8.297426 TCATTGTGTACTACTCAGTAGTTTGAG 58.703 37.037 22.67 7.30 45.68 3.02
2363 8253 5.376625 TGATGGCCTACTGGTTGATATTTC 58.623 41.667 3.32 0.00 35.27 2.17
2474 8370 2.027837 AGGCATTTTGGAGGCATTTGTC 60.028 45.455 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
134 135 6.950545 TCTTTCTTTTTATCGCTTCGTTCAA 58.049 32.000 0.00 0.00 0.00 2.69
223 236 2.744741 GAGCTCCTTTCCCTCGAAAAAG 59.255 50.000 0.87 7.34 37.53 2.27
369 448 2.603473 TGGGAGAGGACGGTGTGG 60.603 66.667 0.00 0.00 0.00 4.17
371 450 2.997897 GCTGGGAGAGGACGGTGT 60.998 66.667 0.00 0.00 0.00 4.16
374 453 3.151022 GGAGCTGGGAGAGGACGG 61.151 72.222 0.00 0.00 0.00 4.79
540 6090 3.334054 AGGTGGGAGAGCTTGGCC 61.334 66.667 0.00 0.00 0.00 5.36
639 6189 1.300697 GAACTGCGGGTCGTTGACT 60.301 57.895 0.00 0.00 32.47 3.41
641 6191 2.029964 GGAACTGCGGGTCGTTGA 59.970 61.111 4.06 0.00 0.00 3.18
645 6195 2.125912 CAGAGGAACTGCGGGTCG 60.126 66.667 4.06 0.00 41.55 4.79
886 6445 0.314935 AACGCAACATTGGGCTTGAG 59.685 50.000 8.46 0.00 44.05 3.02
931 6490 3.420893 TGCTAAGCTTGGCAATGTAAGT 58.579 40.909 32.21 0.00 41.85 2.24
948 6507 0.321034 GCCATGGATGAGCGATGCTA 60.321 55.000 18.40 0.00 39.88 3.49
960 6519 2.673200 GGAGGTGAGCAGCCATGGA 61.673 63.158 18.40 0.00 0.00 3.41
1074 6636 1.237285 TTTTCTCCTTGCTGAGGCGC 61.237 55.000 0.00 0.00 45.87 6.53
1186 6748 3.369381 CCAGCATCTGGTTAGACCG 57.631 57.895 4.74 0.00 45.82 4.79
1209 6771 3.702045 CGGAGATTAGGAACTCTGACCTT 59.298 47.826 0.00 0.00 40.67 3.50
1260 6822 0.820482 TGAGCAATGCCGGATGATGG 60.820 55.000 5.05 0.00 0.00 3.51
1320 6882 9.642343 AGTCCATTTTCCTTAAGAAACTTTACT 57.358 29.630 3.36 2.71 44.20 2.24
1521 7083 3.485947 TTTGAATCATGCTGTTACCGC 57.514 42.857 0.00 0.00 0.00 5.68
1527 7089 8.697846 CAGAATGTAAATTTGAATCATGCTGT 57.302 30.769 17.60 1.44 37.39 4.40
1654 7216 4.740934 GCCAATTTCATCCTAGACTAGCGT 60.741 45.833 3.76 0.00 0.00 5.07
1655 7217 3.743396 GCCAATTTCATCCTAGACTAGCG 59.257 47.826 3.76 0.00 0.00 4.26
1885 7475 3.055819 GGGATGTGTCAGAGAGTGCTTAA 60.056 47.826 0.00 0.00 0.00 1.85
1989 7664 5.728471 TGCTCTCACTCTCTTTAATTCCAG 58.272 41.667 0.00 0.00 0.00 3.86
2072 7747 5.559770 TGAAAAGATAGATTGAGGTGCACA 58.440 37.500 20.43 0.00 0.00 4.57
2116 7791 2.885135 AGTCCATGTCATCTTTGGCA 57.115 45.000 0.00 0.00 42.74 4.92
2175 7850 4.414337 ACTAGATCCAAACTGCATCCTC 57.586 45.455 0.00 0.00 0.00 3.71
2277 8166 5.926542 TGAGTAGTACACAATGACTTGCTTC 59.073 40.000 2.52 0.00 35.69 3.86
2310 8199 9.601810 AAAGAATATAAGGGGAAAAACTGAACT 57.398 29.630 0.00 0.00 0.00 3.01
2311 8200 9.639601 CAAAGAATATAAGGGGAAAAACTGAAC 57.360 33.333 0.00 0.00 0.00 3.18
2312 8201 9.594936 TCAAAGAATATAAGGGGAAAAACTGAA 57.405 29.630 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.