Multiple sequence alignment - TraesCS6D01G383100

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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 TraesCS6D01G383100 chr6D 100.000 2883 0 0 1 2883 462410448 462407566 0.000000e+00 5325
1 TraesCS6D01G383100 chr6D 97.510 2088 44 6 802 2883 452082176 452080091 0.000000e+00 3561
2 TraesCS6D01G383100 chr6D 81.240 629 82 21 1357 1956 449817224 449816603 2.600000e-130 475
3 TraesCS6D01G383100 chr6D 82.479 468 62 14 802 1253 449843902 449843439 2.690000e-105 392
4 TraesCS6D01G383100 chr6D 78.450 645 99 22 1331 1954 450168065 450167440 4.510000e-103 385
5 TraesCS6D01G383100 chr6D 85.379 383 36 9 1 380 452085088 452084723 2.100000e-101 379
6 TraesCS6D01G383100 chr6D 80.159 378 38 16 419 767 452084317 452083948 6.170000e-62 248
7 TraesCS6D01G383100 chr6A 94.320 2095 83 18 802 2883 609162819 609160748 0.000000e+00 3177
8 TraesCS6D01G383100 chr6A 92.327 391 25 5 1 387 609165017 609164628 4.200000e-153 551
9 TraesCS6D01G383100 chr6A 85.055 542 37 20 294 801 609164676 609164145 1.980000e-141 512
10 TraesCS6D01G383100 chr6A 79.154 638 95 22 1331 1947 595663709 595663089 9.620000e-110 407
11 TraesCS6D01G383100 chr6A 80.818 318 45 13 802 1105 595489293 595488978 4.800000e-58 235
12 TraesCS6D01G383100 chr6B 93.555 2110 92 14 802 2883 704861471 704859378 0.000000e+00 3103
13 TraesCS6D01G383100 chr6B 80.159 630 92 16 1357 1956 681929511 681928885 9.480000e-120 440
14 TraesCS6D01G383100 chr6B 78.683 638 98 22 1331 1947 682660970 682660350 9.690000e-105 390
15 TraesCS6D01G383100 chr6B 82.013 467 66 12 802 1253 682418547 682419010 5.830000e-102 381
16 TraesCS6D01G383100 chr6B 82.879 257 34 8 1004 1253 681929816 681929563 3.740000e-54 222
17 TraesCS6D01G383100 chr6B 77.273 396 49 17 1 389 704873488 704873127 8.150000e-46 195
18 TraesCS6D01G383100 chr6B 78.878 303 50 11 802 1092 681930116 681929816 2.930000e-45 193


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 TraesCS6D01G383100 chr6D 462407566 462410448 2882 True 5325.000000 5325 100.000000 1 2883 1 chr6D.!!$R4 2882
1 TraesCS6D01G383100 chr6D 452080091 452085088 4997 True 1396.000000 3561 87.682667 1 2883 3 chr6D.!!$R5 2882
2 TraesCS6D01G383100 chr6D 449816603 449817224 621 True 475.000000 475 81.240000 1357 1956 1 chr6D.!!$R1 599
3 TraesCS6D01G383100 chr6D 450167440 450168065 625 True 385.000000 385 78.450000 1331 1954 1 chr6D.!!$R3 623
4 TraesCS6D01G383100 chr6A 609160748 609165017 4269 True 1413.333333 3177 90.567333 1 2883 3 chr6A.!!$R3 2882
5 TraesCS6D01G383100 chr6A 595663089 595663709 620 True 407.000000 407 79.154000 1331 1947 1 chr6A.!!$R2 616
6 TraesCS6D01G383100 chr6B 704859378 704861471 2093 True 3103.000000 3103 93.555000 802 2883 1 chr6B.!!$R2 2081
7 TraesCS6D01G383100 chr6B 682660350 682660970 620 True 390.000000 390 78.683000 1331 1947 1 chr6B.!!$R1 616
8 TraesCS6D01G383100 chr6B 681928885 681930116 1231 True 285.000000 440 80.638667 802 1956 3 chr6B.!!$R4 1154

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
601 1003 0.179045 ACGAGGAGTTGTTGCTGCTT 60.179 50.0 0.0 0.0 37.29 3.91 F
786 1218 0.319986 GTAGGAGGAGCTAATGCGGC 60.320 60.0 0.0 0.0 45.42 6.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1837 4303 1.908340 GCACTCCATGGGCAGAGAGT 61.908 60.000 13.02 3.54 46.29 3.24 R
2055 4537 2.190161 CACGGATTGAAATGCATGCTG 58.810 47.619 20.33 0.00 0.00 4.41 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
208 212 7.382218 AGGAAATTGTTCGCTCATTTGTAAAAG 59.618 33.333 0.00 0.00 34.28 2.27
459 858 1.818674 CATCAGTAACCTTGGCCAACC 59.181 52.381 16.05 0.01 0.00 3.77
473 872 1.052617 CCAACCCCCGAAACCAAAAT 58.947 50.000 0.00 0.00 0.00 1.82
518 919 2.416972 GCGACAGGACGATTACCTTTCT 60.417 50.000 0.00 0.00 35.35 2.52
523 924 3.702045 CAGGACGATTACCTTTCTCCTCT 59.298 47.826 0.00 0.00 35.35 3.69
548 949 4.058817 CGCTCGGCTTCCTAAAGATTAAT 58.941 43.478 0.00 0.00 34.14 1.40
549 950 4.084328 CGCTCGGCTTCCTAAAGATTAATG 60.084 45.833 0.00 0.00 34.14 1.90
550 951 4.319839 GCTCGGCTTCCTAAAGATTAATGC 60.320 45.833 0.00 0.00 34.14 3.56
551 952 4.776349 TCGGCTTCCTAAAGATTAATGCA 58.224 39.130 0.00 0.00 34.14 3.96
576 978 6.413892 TGCAGATGGTGTAGTCAATATTCAA 58.586 36.000 0.00 0.00 0.00 2.69
601 1003 0.179045 ACGAGGAGTTGTTGCTGCTT 60.179 50.000 0.00 0.00 37.29 3.91
602 1004 1.070134 ACGAGGAGTTGTTGCTGCTTA 59.930 47.619 0.00 0.00 37.29 3.09
708 1140 0.458543 AGCAACTGACTATGGCGACG 60.459 55.000 0.00 0.00 0.00 5.12
740 1172 2.589798 TTTCGAGACAACAGTTCGGT 57.410 45.000 0.00 0.00 35.21 4.69
741 1173 2.129823 TTCGAGACAACAGTTCGGTC 57.870 50.000 0.00 0.00 35.21 4.79
754 1186 4.633126 ACAGTTCGGTCATCATCAAAGATG 59.367 41.667 0.62 0.62 45.28 2.90
759 1191 5.836347 TCGGTCATCATCAAAGATGTAGAG 58.164 41.667 6.86 0.00 44.46 2.43
767 1199 3.889815 TCAAAGATGTAGAGGCCAATGG 58.110 45.455 5.01 0.00 0.00 3.16
769 1201 4.473196 TCAAAGATGTAGAGGCCAATGGTA 59.527 41.667 5.01 0.00 0.00 3.25
786 1218 0.319986 GTAGGAGGAGCTAATGCGGC 60.320 60.000 0.00 0.00 45.42 6.53
792 1224 2.511600 AGCTAATGCGGCGGTGAC 60.512 61.111 9.78 0.00 45.42 3.67
857 3176 2.694065 GCTTGATAGCATGCCGTCA 58.306 52.632 15.66 15.97 46.95 4.35
984 3309 2.159462 GGCTTGTCTGCTGCTACAAATC 60.159 50.000 17.46 13.18 35.32 2.17
1161 3587 7.714703 TCACATGTTTGAATCTTGATGTTTCA 58.285 30.769 0.00 0.00 33.88 2.69
1164 3590 9.550406 ACATGTTTGAATCTTGATGTTTCAATT 57.450 25.926 0.00 0.00 41.31 2.32
1174 3600 7.796838 TCTTGATGTTTCAATTTACTCGTCTG 58.203 34.615 0.00 0.00 40.95 3.51
1447 3895 4.202441 CCCCTTCATTCTGTCCAGTTATG 58.798 47.826 0.00 1.07 0.00 1.90
1761 4224 4.772100 CCCAAAGGAACAATCACCACTATT 59.228 41.667 0.00 0.00 33.47 1.73
1956 4438 9.586435 TTATATCTTTGATAGTCGGCATATGTG 57.414 33.333 4.29 0.00 0.00 3.21
1977 4459 3.116300 GTGTACATAGTGTGCTCGGATG 58.884 50.000 0.00 0.00 33.97 3.51
1989 4471 5.182570 GTGTGCTCGGATGTATATAGTACCA 59.817 44.000 0.00 0.00 0.00 3.25
2055 4537 1.670811 CATTTCTACACCCGCCATGAC 59.329 52.381 0.00 0.00 0.00 3.06
2206 4688 3.589988 AGACTTTGCAAGTGTCTATCCG 58.410 45.455 25.62 1.45 43.03 4.18
2420 4910 5.652014 TCCAATAACCATCCAATCAGTGAAC 59.348 40.000 0.00 0.00 0.00 3.18
2622 5120 3.376636 TCCCCGTGTCCTGTTCATATAA 58.623 45.455 0.00 0.00 0.00 0.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
232 236 9.523730 GTGAACATTTTTAAACACAAGTTGAAC 57.476 29.630 10.54 0.00 38.17 3.18
459 858 3.192633 AGAATTCGATTTTGGTTTCGGGG 59.807 43.478 0.00 0.00 36.08 5.73
473 872 0.518636 GCACTTGCAGCAGAATTCGA 59.481 50.000 0.00 0.00 41.59 3.71
505 904 2.168728 GGCAGAGGAGAAAGGTAATCGT 59.831 50.000 0.00 0.00 0.00 3.73
548 949 1.278699 TGACTACACCATCTGCATGCA 59.721 47.619 21.29 21.29 0.00 3.96
549 950 2.028420 TGACTACACCATCTGCATGC 57.972 50.000 11.82 11.82 0.00 4.06
550 951 6.484308 TGAATATTGACTACACCATCTGCATG 59.516 38.462 0.00 0.00 0.00 4.06
551 952 6.594744 TGAATATTGACTACACCATCTGCAT 58.405 36.000 0.00 0.00 0.00 3.96
576 978 2.207924 AACAACTCCTCGTCCGCCT 61.208 57.895 0.00 0.00 0.00 5.52
602 1004 9.781425 AGAGTAATAGATGAGATCCCATGTATT 57.219 33.333 19.17 19.17 42.20 1.89
708 1140 7.748847 TGTTGTCTCGAAAAATAAGAATAGGC 58.251 34.615 0.00 0.00 0.00 3.93
740 1172 4.409901 TGGCCTCTACATCTTTGATGATGA 59.590 41.667 13.63 9.65 44.71 2.92
741 1173 4.711399 TGGCCTCTACATCTTTGATGATG 58.289 43.478 13.63 6.52 46.61 3.07
754 1186 1.694696 CCTCCTACCATTGGCCTCTAC 59.305 57.143 3.32 0.00 0.00 2.59
759 1191 1.149401 GCTCCTCCTACCATTGGCC 59.851 63.158 1.54 0.00 0.00 5.36
767 1199 0.319986 GCCGCATTAGCTCCTCCTAC 60.320 60.000 0.00 0.00 39.10 3.18
769 1201 2.825264 GCCGCATTAGCTCCTCCT 59.175 61.111 0.00 0.00 39.10 3.69
786 1218 0.035458 AAGCTCCTCTTTGGTCACCG 59.965 55.000 0.00 0.00 37.07 4.94
792 1224 3.438434 GCTAGTTTCAAGCTCCTCTTTGG 59.562 47.826 0.00 0.00 37.01 3.28
984 3309 5.583854 CCTGATCATCACTTGTTAACTCCAG 59.416 44.000 7.22 3.11 0.00 3.86
1047 3467 9.331282 GGATACAAACATAAAAGACTAGCTCAT 57.669 33.333 0.00 0.00 0.00 2.90
1048 3468 8.718102 GGATACAAACATAAAAGACTAGCTCA 57.282 34.615 0.00 0.00 0.00 4.26
1161 3587 4.881273 TGCATATTGCCAGACGAGTAAATT 59.119 37.500 0.00 0.00 44.23 1.82
1164 3590 3.535280 TGCATATTGCCAGACGAGTAA 57.465 42.857 0.00 0.00 44.23 2.24
1174 3600 5.551233 TCAAGTAGAGGTATGCATATTGCC 58.449 41.667 10.16 6.71 44.23 4.52
1447 3895 9.657419 ACCATTTCAAATCCATTCTGAAAATAC 57.343 29.630 0.00 0.00 41.14 1.89
1643 4094 4.074970 AGGTACATGGCAACTTCAAAGAG 58.925 43.478 0.00 0.00 37.61 2.85
1761 4224 4.890158 TTGACTACCTTGAGATGCTTCA 57.110 40.909 2.07 0.00 0.00 3.02
1837 4303 1.908340 GCACTCCATGGGCAGAGAGT 61.908 60.000 13.02 3.54 46.29 3.24
1956 4438 2.933495 TCCGAGCACACTATGTACAC 57.067 50.000 0.00 0.00 0.00 2.90
1977 4459 7.751768 AACTAGGTCGGTTGGTACTATATAC 57.248 40.000 0.00 0.00 0.00 1.47
1989 4471 2.767505 CTGCTTCAAACTAGGTCGGTT 58.232 47.619 0.00 0.00 0.00 4.44
2055 4537 2.190161 CACGGATTGAAATGCATGCTG 58.810 47.619 20.33 0.00 0.00 4.41
2147 4629 2.741878 GCCTGCCTTTAGTTCGCATCTA 60.742 50.000 0.00 0.00 0.00 1.98
2206 4688 5.809051 ACCAATCCTATTACGAAGACGAAAC 59.191 40.000 0.00 0.00 42.66 2.78
2420 4910 5.067023 GCAGGGGAAACTTTATGAGAGATTG 59.933 44.000 0.00 0.00 0.00 2.67


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

AutoCloner maintained by Alex Coulton.