Multiple sequence alignment - TraesCS6A01G287400

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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 TraesCS6A01G287400 chr6A 100.000 2580 0 0 1 2580 519597283 519594704 0.000000e+00 4765
1 TraesCS6A01G287400 chr6A 80.395 607 58 30 714 1276 519950550 519949961 3.090000e-109 405
2 TraesCS6A01G287400 chr6D 94.580 1679 57 16 252 1909 377976198 377974533 0.000000e+00 2566
3 TraesCS6A01G287400 chr6D 89.947 378 29 5 1994 2362 377974519 377974142 1.800000e-131 479
4 TraesCS6A01G287400 chr6D 80.597 603 62 28 714 1276 378167944 378167357 5.140000e-112 414
5 TraesCS6A01G287400 chr6D 94.470 217 12 0 2364 2580 377973888 377973672 4.110000e-88 335
6 TraesCS6A01G287400 chr6B 92.295 1830 95 18 764 2580 564509353 564507557 0.000000e+00 2556
7 TraesCS6A01G287400 chr6B 94.595 407 14 3 333 734 564509753 564509350 7.840000e-175 623
8 TraesCS6A01G287400 chr6B 79.623 530 64 23 775 1276 564569175 564568662 8.840000e-90 340
9 TraesCS6A01G287400 chr6B 91.600 250 13 3 8 250 564510044 564509796 3.180000e-89 339


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 TraesCS6A01G287400 chr6A 519594704 519597283 2579 True 4765.000000 4765 100.000 1 2580 1 chr6A.!!$R1 2579
1 TraesCS6A01G287400 chr6A 519949961 519950550 589 True 405.000000 405 80.395 714 1276 1 chr6A.!!$R2 562
2 TraesCS6A01G287400 chr6D 377973672 377976198 2526 True 1126.666667 2566 92.999 252 2580 3 chr6D.!!$R2 2328
3 TraesCS6A01G287400 chr6D 378167357 378167944 587 True 414.000000 414 80.597 714 1276 1 chr6D.!!$R1 562
4 TraesCS6A01G287400 chr6B 564507557 564510044 2487 True 1172.666667 2556 92.830 8 2580 3 chr6B.!!$R2 2572
5 TraesCS6A01G287400 chr6B 564568662 564569175 513 True 340.000000 340 79.623 775 1276 1 chr6B.!!$R1 501

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
291 299 1.291132 GGCTCGCTGAACCACTAATC 58.709 55.0 0.00 0.00 0.00 1.75 F
1051 1110 0.683504 ACTGCTCCGGGAGATTACGT 60.684 55.0 27.95 12.27 34.86 3.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1373 1447 1.226435 GCTGGACGTAGCTGTCGAG 60.226 63.158 17.43 14.0 44.59 4.04 R
2519 2870 0.232303 GTTGCTTCAGTTCCGTCACG 59.768 55.000 0.00 0.0 0.00 4.35 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
57 58 6.824305 CAGTGGTGGAATCTTTCTTACAAT 57.176 37.500 0.00 0.00 0.00 2.71
58 59 7.921786 CAGTGGTGGAATCTTTCTTACAATA 57.078 36.000 0.00 0.00 0.00 1.90
59 60 7.978982 CAGTGGTGGAATCTTTCTTACAATAG 58.021 38.462 0.00 0.00 0.00 1.73
60 61 7.607991 CAGTGGTGGAATCTTTCTTACAATAGT 59.392 37.037 0.00 0.00 0.00 2.12
61 62 8.822805 AGTGGTGGAATCTTTCTTACAATAGTA 58.177 33.333 0.00 0.00 0.00 1.82
62 63 8.880750 GTGGTGGAATCTTTCTTACAATAGTAC 58.119 37.037 0.00 0.00 0.00 2.73
106 114 7.915293 TCACTAAATGTCCATAAAACGTCAT 57.085 32.000 0.00 0.00 0.00 3.06
175 183 9.614792 AACCAGATTAGAACAATAATACCTCAC 57.385 33.333 0.00 0.00 0.00 3.51
244 252 3.462205 AGTGGACTAAAGAGGGGTTGTTT 59.538 43.478 0.00 0.00 0.00 2.83
245 253 4.661709 AGTGGACTAAAGAGGGGTTGTTTA 59.338 41.667 0.00 0.00 0.00 2.01
246 254 5.001874 GTGGACTAAAGAGGGGTTGTTTAG 58.998 45.833 0.00 0.00 44.23 1.85
247 255 4.008330 GGACTAAAGAGGGGTTGTTTAGC 58.992 47.826 4.36 0.00 43.11 3.09
248 256 4.008330 GACTAAAGAGGGGTTGTTTAGCC 58.992 47.826 4.36 0.00 43.11 3.93
249 257 3.656264 ACTAAAGAGGGGTTGTTTAGCCT 59.344 43.478 4.36 0.00 43.11 4.58
250 258 4.848086 ACTAAAGAGGGGTTGTTTAGCCTA 59.152 41.667 4.36 0.00 43.11 3.93
251 259 4.948062 AAAGAGGGGTTGTTTAGCCTAT 57.052 40.909 0.00 0.00 44.17 2.57
252 260 4.948062 AAGAGGGGTTGTTTAGCCTATT 57.052 40.909 0.00 0.00 44.17 1.73
253 261 4.236527 AGAGGGGTTGTTTAGCCTATTG 57.763 45.455 0.00 0.00 44.17 1.90
254 262 3.850173 AGAGGGGTTGTTTAGCCTATTGA 59.150 43.478 0.00 0.00 44.17 2.57
255 263 4.478686 AGAGGGGTTGTTTAGCCTATTGAT 59.521 41.667 0.00 0.00 44.17 2.57
256 264 5.044105 AGAGGGGTTGTTTAGCCTATTGATT 60.044 40.000 0.00 0.00 44.17 2.57
291 299 1.291132 GGCTCGCTGAACCACTAATC 58.709 55.000 0.00 0.00 0.00 1.75
294 302 3.492656 GGCTCGCTGAACCACTAATCATA 60.493 47.826 0.00 0.00 0.00 2.15
298 306 5.049828 TCGCTGAACCACTAATCATACATG 58.950 41.667 0.00 0.00 0.00 3.21
303 311 5.817296 TGAACCACTAATCATACATGCTCAC 59.183 40.000 0.00 0.00 0.00 3.51
315 323 9.955102 ATCATACATGCTCACAGTATATGAATT 57.045 29.630 0.00 0.00 34.28 2.17
402 422 1.767759 ATTGAAATTGAGGCGAGGGG 58.232 50.000 0.00 0.00 0.00 4.79
490 510 2.092914 CCGACCTCTTAATTTCCAGGCT 60.093 50.000 0.00 0.00 0.00 4.58
631 651 3.322828 TCAGTTACCACCCAGACAGTAAC 59.677 47.826 0.00 0.00 43.05 2.50
646 666 5.080969 ACAGTAACCGCTTGCTAAAGATA 57.919 39.130 0.00 0.00 35.19 1.98
829 861 1.878656 CGGCCTCAACTCGTTCTCCT 61.879 60.000 0.00 0.00 0.00 3.69
939 978 3.064324 GCCACAAGCCGCTTCCAT 61.064 61.111 1.56 0.00 34.35 3.41
948 995 1.889105 CCGCTTCCATCCCATCACG 60.889 63.158 0.00 0.00 0.00 4.35
1008 1061 1.080354 AGGTTGGACGATGGGAGGA 59.920 57.895 0.00 0.00 0.00 3.71
1051 1110 0.683504 ACTGCTCCGGGAGATTACGT 60.684 55.000 27.95 12.27 34.86 3.57
1058 1118 1.542544 CGGGAGATTACGTCACGTTC 58.457 55.000 8.85 0.00 41.54 3.95
1076 1136 4.748600 ACGTTCAAAACCAGAGTTACTAGC 59.251 41.667 0.00 0.00 34.19 3.42
1397 1471 2.897350 GCTACGTCCAGCCCATGC 60.897 66.667 0.00 0.00 35.40 4.06
1410 1484 0.982852 CCCATGCAGACCTACCTCCA 60.983 60.000 0.00 0.00 0.00 3.86
1411 1485 0.911769 CCATGCAGACCTACCTCCAA 59.088 55.000 0.00 0.00 0.00 3.53
1670 1756 3.437845 CGCCAATATGTAGCGTTGC 57.562 52.632 6.21 0.00 44.65 4.17
1752 1839 2.524569 TCAGTGTGCGAATGTCTTCA 57.475 45.000 0.00 0.00 0.00 3.02
1777 1864 4.720649 AGATATAATCGATCACCCACGG 57.279 45.455 0.00 0.00 0.00 4.94
1895 1982 9.877178 GTATATTTGGGAGGTGATATTCTACAG 57.123 37.037 0.00 0.00 0.00 2.74
1901 1988 5.305644 GGGAGGTGATATTCTACAGACATGT 59.694 44.000 0.00 0.00 43.76 3.21
1902 1989 6.219473 GGAGGTGATATTCTACAGACATGTG 58.781 44.000 1.15 0.00 40.79 3.21
1909 1996 8.236586 TGATATTCTACAGACATGTGCAAAAAC 58.763 33.333 1.15 0.00 40.79 2.43
1967 2054 7.958053 AAGAAAGAAAATCCAAGCAATGAAG 57.042 32.000 0.00 0.00 0.00 3.02
1976 2063 2.486982 CCAAGCAATGAAGAGTGACAGG 59.513 50.000 0.00 0.00 0.00 4.00
1986 2073 2.358615 GTGACAGGCGGTGCATCA 60.359 61.111 0.00 0.00 0.00 3.07
1992 2079 1.484653 ACAGGCGGTGCATCACTATTA 59.515 47.619 0.00 0.00 34.40 0.98
2114 2205 7.652727 AGAGAATTCTTTGGAAAGCACTAAAC 58.347 34.615 9.87 0.00 35.99 2.01
2192 2286 6.487668 TCGGTTATAGGAATGTCTATGAACGA 59.512 38.462 12.98 12.98 46.11 3.85
2244 2343 0.879839 TGTCACACGTGATGCAGTGG 60.880 55.000 25.01 1.05 42.18 4.00
2258 2357 1.068816 GCAGTGGGCGTTTATTCGTTT 60.069 47.619 0.00 0.00 0.00 3.60
2432 2783 2.628106 CGATTCGCTGCCGATTGG 59.372 61.111 0.00 0.00 43.97 3.16
2433 2784 1.882625 CGATTCGCTGCCGATTGGA 60.883 57.895 1.98 0.00 43.97 3.53
2457 2808 1.611491 GGTCAAAACATTCGAGGGCAA 59.389 47.619 0.00 0.00 0.00 4.52
2464 2815 3.350031 ATTCGAGGGCAAGGCAGGG 62.350 63.158 0.00 0.00 0.00 4.45
2519 2870 2.595386 GATGAACGCATTTTGGTGGAC 58.405 47.619 0.00 0.00 34.11 4.02
2574 2925 0.322322 TGGTACCCACGTGCCTAAAG 59.678 55.000 10.91 0.00 44.62 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 8.816894 ACTGGTTGAATCGGATTATATCAGTAT 58.183 33.333 20.33 5.81 0.00 2.12
12 13 8.088365 CACTGGTTGAATCGGATTATATCAGTA 58.912 37.037 20.86 0.00 0.00 2.74
13 14 6.931281 CACTGGTTGAATCGGATTATATCAGT 59.069 38.462 17.87 17.87 0.00 3.41
14 15 6.369890 CCACTGGTTGAATCGGATTATATCAG 59.630 42.308 16.97 16.97 0.00 2.90
31 32 3.884037 AGAAAGATTCCACCACTGGTT 57.116 42.857 0.00 0.00 38.90 3.67
36 37 7.923414 ACTATTGTAAGAAAGATTCCACCAC 57.077 36.000 0.00 0.00 0.00 4.16
58 59 9.256228 TGAAGTCTCCATAATTTCACTAGTACT 57.744 33.333 0.00 0.00 0.00 2.73
59 60 9.303537 GTGAAGTCTCCATAATTTCACTAGTAC 57.696 37.037 0.00 0.00 42.51 2.73
226 234 4.008330 GGCTAAACAACCCCTCTTTAGTC 58.992 47.826 0.00 0.00 32.34 2.59
246 254 4.821805 TGCACTAAGGCTAAATCAATAGGC 59.178 41.667 0.00 0.08 45.95 3.93
247 255 7.365741 CAATGCACTAAGGCTAAATCAATAGG 58.634 38.462 0.00 0.00 34.04 2.57
248 256 7.365741 CCAATGCACTAAGGCTAAATCAATAG 58.634 38.462 0.00 0.00 34.04 1.73
249 257 6.239008 GCCAATGCACTAAGGCTAAATCAATA 60.239 38.462 11.91 0.00 43.70 1.90
250 258 5.452356 GCCAATGCACTAAGGCTAAATCAAT 60.452 40.000 11.91 0.00 43.70 2.57
251 259 4.142182 GCCAATGCACTAAGGCTAAATCAA 60.142 41.667 11.91 0.00 43.70 2.57
252 260 3.381272 GCCAATGCACTAAGGCTAAATCA 59.619 43.478 11.91 0.00 43.70 2.57
253 261 3.969899 GCCAATGCACTAAGGCTAAATC 58.030 45.455 11.91 0.00 43.70 2.17
291 299 9.211485 TCAATTCATATACTGTGAGCATGTATG 57.789 33.333 0.00 0.00 0.00 2.39
294 302 8.687292 AATCAATTCATATACTGTGAGCATGT 57.313 30.769 0.00 0.00 0.00 3.21
315 323 7.800155 TGCGTATTAGGAAATCAATGAATCA 57.200 32.000 0.00 0.00 0.00 2.57
374 394 7.809806 CCTCGCCTCAATTTCAATTTATATTCC 59.190 37.037 0.00 0.00 0.00 3.01
402 422 0.179045 ATGAACCGCACTATCTGCCC 60.179 55.000 0.00 0.00 43.84 5.36
404 424 1.656652 ACATGAACCGCACTATCTGC 58.343 50.000 0.00 0.00 43.21 4.26
449 469 0.599558 ACCGCTTGCGTAGTTGACTA 59.400 50.000 13.97 0.00 0.00 2.59
631 651 6.422776 TCTCTTTTTATCTTTAGCAAGCGG 57.577 37.500 0.00 0.00 0.00 5.52
646 666 4.527564 CGTTCGCAGTCAAATCTCTTTTT 58.472 39.130 0.00 0.00 0.00 1.94
761 781 2.169146 CGTTACCGGCGGGCTTTAG 61.169 63.158 31.78 12.24 36.48 1.85
858 890 3.049674 CTGGACGCACGTGCCATT 61.050 61.111 33.23 18.71 37.91 3.16
935 974 2.355193 TGCGTCGTGATGGGATGGA 61.355 57.895 0.00 0.00 0.00 3.41
936 975 2.173669 GTGCGTCGTGATGGGATGG 61.174 63.158 0.00 0.00 0.00 3.51
937 976 1.447663 TGTGCGTCGTGATGGGATG 60.448 57.895 0.00 0.00 0.00 3.51
938 977 1.447838 GTGTGCGTCGTGATGGGAT 60.448 57.895 0.00 0.00 0.00 3.85
939 978 2.048597 GTGTGCGTCGTGATGGGA 60.049 61.111 0.00 0.00 0.00 4.37
948 995 1.787155 CTTACTCAGTGTGTGTGCGTC 59.213 52.381 8.09 0.00 0.00 5.19
1008 1061 1.961793 TACCACGTTTCTTGCTGCTT 58.038 45.000 0.00 0.00 0.00 3.91
1051 1110 4.761975 AGTAACTCTGGTTTTGAACGTGA 58.238 39.130 0.00 0.00 36.92 4.35
1058 1118 5.758296 TGAACAGCTAGTAACTCTGGTTTTG 59.242 40.000 0.00 0.00 36.92 2.44
1076 1136 5.277974 CCAGTGACAAAACTACCATGAACAG 60.278 44.000 0.00 0.00 0.00 3.16
1373 1447 1.226435 GCTGGACGTAGCTGTCGAG 60.226 63.158 17.43 14.00 44.59 4.04
1397 1471 1.757699 GTAGCCTTGGAGGTAGGTCTG 59.242 57.143 0.00 0.00 37.80 3.51
1410 1484 1.746615 TCGTACTCGCGGTAGCCTT 60.747 57.895 6.13 0.00 41.18 4.35
1411 1485 2.124983 TCGTACTCGCGGTAGCCT 60.125 61.111 6.13 0.00 41.18 4.58
1670 1756 4.503741 TCGGGATTTTCTTCAAGCAAAG 57.496 40.909 0.00 0.00 0.00 2.77
1733 1820 2.524569 TGAAGACATTCGCACACTGA 57.475 45.000 0.00 0.00 38.34 3.41
1752 1839 6.426937 CCGTGGGTGATCGATTATATCTTTTT 59.573 38.462 0.00 0.00 0.00 1.94
1895 1982 4.803088 TGCACTTTAGTTTTTGCACATGTC 59.197 37.500 0.00 0.00 40.01 3.06
1901 1988 5.414360 TGATTGTGCACTTTAGTTTTTGCA 58.586 33.333 19.41 0.00 42.60 4.08
1902 1989 5.964887 TGATTGTGCACTTTAGTTTTTGC 57.035 34.783 19.41 0.00 35.45 3.68
1909 1996 7.095523 CCAAAGGATTTTGATTGTGCACTTTAG 60.096 37.037 19.41 0.00 45.21 1.85
1967 2054 2.046892 ATGCACCGCCTGTCACTC 60.047 61.111 0.00 0.00 0.00 3.51
1976 2063 5.666969 TTACATTAATAGTGATGCACCGC 57.333 39.130 0.00 0.00 34.49 5.68
2087 2177 6.081872 AGTGCTTTCCAAAGAATTCTCTTG 57.918 37.500 8.78 14.12 41.23 3.02
2088 2178 7.823745 TTAGTGCTTTCCAAAGAATTCTCTT 57.176 32.000 8.78 2.95 44.11 2.85
2170 2261 9.790389 CCTATCGTTCATAGACATTCCTATAAC 57.210 37.037 0.00 0.00 37.27 1.89
2181 2275 5.180492 CCTCTCTCACCTATCGTTCATAGAC 59.820 48.000 0.00 0.00 37.27 2.59
2244 2343 7.974243 AACCATAAATAAACGAATAAACGCC 57.026 32.000 0.00 0.00 36.70 5.68
2299 2398 6.481954 AAAAATCTACTCACAACTAAGCGG 57.518 37.500 0.00 0.00 0.00 5.52
2424 2775 2.396590 TTTGACCTACTCCAATCGGC 57.603 50.000 0.00 0.00 0.00 5.54
2428 2779 5.556915 TCGAATGTTTTGACCTACTCCAAT 58.443 37.500 0.00 0.00 0.00 3.16
2432 2783 3.933332 CCCTCGAATGTTTTGACCTACTC 59.067 47.826 0.00 0.00 0.00 2.59
2433 2784 3.868754 GCCCTCGAATGTTTTGACCTACT 60.869 47.826 0.00 0.00 0.00 2.57
2457 2808 2.930562 GTCACACCCTCCCTGCCT 60.931 66.667 0.00 0.00 0.00 4.75
2464 2815 3.384668 CATCATATGTCGTCACACCCTC 58.615 50.000 1.90 0.00 34.48 4.30
2519 2870 0.232303 GTTGCTTCAGTTCCGTCACG 59.768 55.000 0.00 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.