Multiple sequence alignment - TraesCS6B01G122500

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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 TraesCS6B01G122500 chr6B 100.000 2483 0 0 1 2483 117706175 117708657 0.000000e+00 4586
1 TraesCS6B01G122500 chr6B 83.691 1257 192 12 353 1602 117771895 117773145 0.000000e+00 1173
2 TraesCS6B01G122500 chr6B 78.830 718 114 23 1767 2464 117752393 117753092 1.350000e-122 449
3 TraesCS6B01G122500 chr6B 78.356 730 112 26 1767 2479 117792404 117793104 4.910000e-117 431
4 TraesCS6B01G122500 chr6D 92.238 2087 106 12 5 2044 53775852 53773775 0.000000e+00 2905
5 TraesCS6B01G122500 chr6D 85.804 1268 160 14 365 1616 53681658 53680395 0.000000e+00 1327
6 TraesCS6B01G122500 chr6D 90.233 430 33 4 2060 2483 53771983 53771557 1.000000e-153 553
7 TraesCS6B01G122500 chr6A 91.851 1767 90 10 5 1753 61211255 61212985 0.000000e+00 2416
8 TraesCS6B01G122500 chr6A 86.093 1244 156 12 373 1604 61414620 61415858 0.000000e+00 1323
9 TraesCS6B01G122500 chr6A 85.782 1259 156 15 373 1612 61418302 61419556 0.000000e+00 1312
10 TraesCS6B01G122500 chr6A 85.691 1237 162 13 365 1591 61411488 61412719 0.000000e+00 1290
11 TraesCS6B01G122500 chr6A 83.159 1342 206 17 365 1694 61400208 61401541 0.000000e+00 1208
12 TraesCS6B01G122500 chr6A 84.801 1204 164 13 397 1587 61408453 61409650 0.000000e+00 1192
13 TraesCS6B01G122500 chr6A 89.583 528 30 9 1970 2477 61212989 61213511 0.000000e+00 647
14 TraesCS6B01G122500 chr6A 79.304 517 78 17 1978 2479 61405957 61406459 3.960000e-88 335
15 TraesCS6B01G122500 chrUn 84.475 219 29 3 1787 2004 77432657 77432443 6.960000e-51 211


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 TraesCS6B01G122500 chr6B 117706175 117708657 2482 False 4586.0 4586 100.0000 1 2483 1 chr6B.!!$F1 2482
1 TraesCS6B01G122500 chr6B 117771895 117773145 1250 False 1173.0 1173 83.6910 353 1602 1 chr6B.!!$F3 1249
2 TraesCS6B01G122500 chr6B 117752393 117753092 699 False 449.0 449 78.8300 1767 2464 1 chr6B.!!$F2 697
3 TraesCS6B01G122500 chr6B 117792404 117793104 700 False 431.0 431 78.3560 1767 2479 1 chr6B.!!$F4 712
4 TraesCS6B01G122500 chr6D 53771557 53775852 4295 True 1729.0 2905 91.2355 5 2483 2 chr6D.!!$R2 2478
5 TraesCS6B01G122500 chr6D 53680395 53681658 1263 True 1327.0 1327 85.8040 365 1616 1 chr6D.!!$R1 1251
6 TraesCS6B01G122500 chr6A 61211255 61213511 2256 False 1531.5 2416 90.7170 5 2477 2 chr6A.!!$F2 2472
7 TraesCS6B01G122500 chr6A 61400208 61401541 1333 False 1208.0 1208 83.1590 365 1694 1 chr6A.!!$F1 1329
8 TraesCS6B01G122500 chr6A 61405957 61419556 13599 False 1090.4 1323 84.3342 365 2479 5 chr6A.!!$F3 2114

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
916 3039 0.245813 GTGAGTTCCCCGGTGACTAC 59.754 60.0 0.0 0.0 0.0 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2049 14095 0.179045 CCCGTGAGAATGATGACCCC 60.179 60.0 0.0 0.0 0.0 4.95 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
172 177 5.416013 TCCAAATTTATGTGGTATCGTTGCA 59.584 36.000 0.00 0.00 36.23 4.08
215 223 4.836175 TCCAGCGGTCAATTCTACCATATA 59.164 41.667 7.17 0.00 36.78 0.86
216 224 5.483937 TCCAGCGGTCAATTCTACCATATAT 59.516 40.000 7.17 0.00 36.78 0.86
264 272 1.840635 GGAGTACATCAGGGCTTCCTT 59.159 52.381 0.00 0.00 39.29 3.36
495 2605 2.625790 GAGAGCAACATATCTCTCCGGT 59.374 50.000 0.00 0.00 45.85 5.28
526 2636 4.083590 GCGTCAAAGCTCAAGATTTCTCTT 60.084 41.667 0.00 0.00 42.59 2.85
625 2742 1.627834 CCCTCTCCTATCAAGCCATCC 59.372 57.143 0.00 0.00 0.00 3.51
626 2743 2.618794 CCTCTCCTATCAAGCCATCCT 58.381 52.381 0.00 0.00 0.00 3.24
634 2751 0.615331 TCAAGCCATCCTCACACTCC 59.385 55.000 0.00 0.00 0.00 3.85
636 2753 1.903877 AAGCCATCCTCACACTCCCG 61.904 60.000 0.00 0.00 0.00 5.14
654 2771 0.881796 CGCCTTTCTTTGAGAACCCC 59.118 55.000 0.00 0.00 33.26 4.95
700 2822 4.594854 ATGGCGGCAACCACCACA 62.595 61.111 18.31 0.00 44.17 4.17
765 2887 0.735471 CCATCGTCAGCTCTCTTCGA 59.265 55.000 0.00 0.00 33.19 3.71
885 3008 3.003173 CTCTGGTGAGCCCCCGAA 61.003 66.667 0.00 0.00 33.12 4.30
907 3030 2.663196 CTGACCGGTGAGTTCCCC 59.337 66.667 14.63 0.00 0.00 4.81
916 3039 0.245813 GTGAGTTCCCCGGTGACTAC 59.754 60.000 0.00 0.00 0.00 2.73
1007 3131 3.700970 TCGTTGGGCCATGCTCGA 61.701 61.111 7.26 12.93 0.00 4.04
1061 3185 0.586319 CGCAATGGTGTGAAGTTCGT 59.414 50.000 0.00 0.00 37.45 3.85
1069 3193 0.179234 TGTGAAGTTCGTTGAGGCCA 59.821 50.000 5.01 0.00 0.00 5.36
1101 3225 0.394565 CCGGCTCCCAGATCTTTAGG 59.605 60.000 0.00 0.00 0.00 2.69
1125 3249 2.572104 GGGTGGTCTTGACTATCTTGGT 59.428 50.000 0.61 0.00 0.00 3.67
1179 3303 1.488390 CTATTTGGGCATGCCAGGTT 58.512 50.000 36.56 20.65 37.98 3.50
1380 13380 4.568072 TGGCTTCTTTGTCCAAGCTATA 57.432 40.909 3.83 0.00 43.89 1.31
1499 13506 5.105064 GCAAGTAAGGTGTCTTGGGACTATA 60.105 44.000 6.96 0.00 42.54 1.31
1613 13623 1.855213 TTCCATGTCGCAGCTTGCAC 61.855 55.000 8.52 6.44 45.36 4.57
1620 13630 0.672091 TCGCAGCTTGCACCGATTTA 60.672 50.000 8.52 0.00 45.36 1.40
1670 13690 8.915654 CAATAACAGGAGCAAATAAACACTTTC 58.084 33.333 0.00 0.00 0.00 2.62
1731 13751 6.924060 AGACGAGTGGCAACTTATATAATCAC 59.076 38.462 0.00 1.50 36.52 3.06
1931 13976 5.005740 ACTGCAGCAGTGATTTTTCAGATA 58.994 37.500 27.73 0.00 43.63 1.98
2021 14067 1.070786 GACAAACCCTCTCGCCACA 59.929 57.895 0.00 0.00 0.00 4.17
2041 14087 4.565166 CACATATTCGTGTTCGGCTTCTAA 59.435 41.667 0.00 0.00 37.69 2.10
2049 14095 1.461127 GTTCGGCTTCTAAGTGCACAG 59.539 52.381 21.04 8.87 0.00 3.66
2066 15888 1.208052 ACAGGGGTCATCATTCTCACG 59.792 52.381 0.00 0.00 0.00 4.35
2072 15894 2.037772 GGTCATCATTCTCACGGGCTAT 59.962 50.000 0.00 0.00 0.00 2.97
2098 15920 5.357878 ACATCGTTAGATTTGTCCATTGCAT 59.642 36.000 0.00 0.00 34.23 3.96
2119 15941 1.141234 GTGCCTCCGTGCTACTACC 59.859 63.158 0.00 0.00 0.00 3.18
2276 16120 1.071471 CCCCTGTATCCCATGTCGC 59.929 63.158 0.00 0.00 0.00 5.19
2300 16144 2.202987 CACCCTCTCGGCTGATGC 60.203 66.667 0.00 0.00 38.76 3.91
2332 16179 5.367060 CCCCTAAACTAAGGCTATTCTGTCT 59.633 44.000 0.00 0.00 35.09 3.41
2391 16238 8.258007 TCTAGACATTTTTATACTGGTCCAGTG 58.742 37.037 31.23 15.93 45.01 3.66
2408 16255 4.037923 TCCAGTGCTTGAACCAATCTTTTC 59.962 41.667 0.00 0.00 0.00 2.29
2443 16291 8.093927 CCCAATTTCACCACACAACTAATATTT 58.906 33.333 0.00 0.00 0.00 1.40
2469 16317 7.194112 TCATTTTCACCTGATACATGACCTA 57.806 36.000 0.00 0.00 0.00 3.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
121 126 6.859017 ACAAAATGGTGGATACGGTTAATTC 58.141 36.000 0.00 0.0 42.51 2.17
123 128 6.844097 AACAAAATGGTGGATACGGTTAAT 57.156 33.333 0.00 0.0 42.51 1.40
125 130 6.294620 GGAAAACAAAATGGTGGATACGGTTA 60.295 38.462 0.00 0.0 42.51 2.85
126 131 5.510009 GGAAAACAAAATGGTGGATACGGTT 60.510 40.000 0.00 0.0 42.51 4.44
233 241 6.684613 GCCCTGATGTACTCCGTATCTTTTAA 60.685 42.308 0.00 0.0 0.00 1.52
264 272 6.073440 GCTCGTTGAAAGGAATTACTAACACA 60.073 38.462 0.00 0.0 0.00 3.72
344 359 5.412594 TGTGTTTCTGAGATCTGTTAATGGC 59.587 40.000 0.00 0.0 0.00 4.40
346 361 6.146184 ACGTGTGTTTCTGAGATCTGTTAATG 59.854 38.462 0.00 0.0 0.00 1.90
495 2605 1.271108 TGAGCTTTGACGCCATTGGTA 60.271 47.619 4.26 0.0 0.00 3.25
526 2636 5.819379 GCTGACAAGATCAACATGGATAGAA 59.181 40.000 0.00 0.0 36.69 2.10
625 2742 0.035458 AAGAAAGGCGGGAGTGTGAG 59.965 55.000 0.00 0.0 0.00 3.51
626 2743 0.472471 AAAGAAAGGCGGGAGTGTGA 59.528 50.000 0.00 0.0 0.00 3.58
634 2751 0.881796 GGGTTCTCAAAGAAAGGCGG 59.118 55.000 0.00 0.0 35.75 6.13
636 2753 2.294449 AGGGGTTCTCAAAGAAAGGC 57.706 50.000 0.00 0.0 35.75 4.35
654 2771 5.233988 AGCTAAGAAAAGTGTCTGCTGTAG 58.766 41.667 0.00 0.0 28.60 2.74
700 2822 0.996762 AGGTCGAGGAGGAGAGGGAT 60.997 60.000 0.00 0.0 0.00 3.85
776 2899 0.388907 GCAGTTTTGCGCATGGTCAT 60.389 50.000 12.75 0.0 41.13 3.06
840 2963 2.577593 GGTAGAGCACCCGGTCAC 59.422 66.667 0.00 0.0 42.07 3.67
907 3030 1.317431 TGTCCCATCCGTAGTCACCG 61.317 60.000 0.00 0.0 0.00 4.94
919 3042 1.562672 AAAGCCTAGCGGTGTCCCAT 61.563 55.000 0.00 0.0 0.00 4.00
1007 3131 2.024414 GGAAGACACAACCAAGTGCTT 58.976 47.619 0.00 0.0 43.23 3.91
1061 3185 2.301583 GCCTTAAACCAAATGGCCTCAA 59.698 45.455 3.32 0.0 39.32 3.02
1069 3193 1.182667 GAGCCGGCCTTAAACCAAAT 58.817 50.000 26.15 0.0 0.00 2.32
1101 3225 2.753247 AGATAGTCAAGACCACCCTCC 58.247 52.381 0.00 0.0 0.00 4.30
1125 3249 2.120940 TGGACGAGGCTGGGGTTA 59.879 61.111 0.51 0.0 0.00 2.85
1179 3303 3.490031 AACGGCACCCATGAGCACA 62.490 57.895 0.00 0.0 0.00 4.57
1242 13242 2.522436 CCGCCCGGGTATAGTGGA 60.522 66.667 24.63 0.0 32.75 4.02
1453 13453 1.652563 GGACAAAGTTGGTGGCGAC 59.347 57.895 0.00 0.0 0.00 5.19
1512 13520 3.185246 ACTCAGACCACAAGACAACAG 57.815 47.619 0.00 0.0 0.00 3.16
1631 13641 6.065976 TCCTGTTATTGTGATTGTGATCCT 57.934 37.500 0.00 0.0 0.00 3.24
1633 13643 5.355071 TGCTCCTGTTATTGTGATTGTGATC 59.645 40.000 0.00 0.0 0.00 2.92
1670 13690 5.471116 GGTAATAGTTAATTAAGCCCACCGG 59.529 44.000 0.00 0.0 31.82 5.28
1731 13751 1.600164 CCACAAATTCACCTGCACACG 60.600 52.381 0.00 0.0 0.00 4.49
1766 13810 9.638300 CAGAATATACACGAAACATAAAGCTTC 57.362 33.333 0.00 0.0 0.00 3.86
2007 14053 1.202533 CGAATATGTGGCGAGAGGGTT 60.203 52.381 0.00 0.0 0.00 4.11
2021 14067 4.804139 CACTTAGAAGCCGAACACGAATAT 59.196 41.667 0.00 0.0 0.00 1.28
2041 14087 0.700564 AATGATGACCCCTGTGCACT 59.299 50.000 19.41 0.0 0.00 4.40
2049 14095 0.179045 CCCGTGAGAATGATGACCCC 60.179 60.000 0.00 0.0 0.00 4.95
2066 15888 6.147328 GGACAAATCTAACGATGTTATAGCCC 59.853 42.308 0.00 0.0 0.00 5.19
2072 15894 6.372937 TGCAATGGACAAATCTAACGATGTTA 59.627 34.615 0.00 0.0 0.00 2.41
2098 15920 1.747355 GTAGTAGCACGGAGGCACTTA 59.253 52.381 0.00 0.0 41.55 2.24
2147 15969 5.161943 AGGAGTTACTAACAATGGTGGTC 57.838 43.478 0.00 0.0 0.00 4.02
2300 16144 0.539986 TTAGTTTAGGGGCAGCGAGG 59.460 55.000 0.00 0.0 0.00 4.63
2332 16179 7.275888 AGTTCTTAGTTGATTGACATTTGCA 57.724 32.000 0.00 0.0 0.00 4.08
2384 16231 2.508526 AGATTGGTTCAAGCACTGGAC 58.491 47.619 0.00 0.0 31.66 4.02
2391 16238 9.561270 GTAAGAATAGAAAAGATTGGTTCAAGC 57.439 33.333 0.00 0.0 0.00 4.01
2408 16255 6.432783 TGTGTGGTGAAATTGGGTAAGAATAG 59.567 38.462 0.00 0.0 0.00 1.73
2443 16291 7.805163 AGGTCATGTATCAGGTGAAAATGATA 58.195 34.615 0.00 0.0 37.36 2.15


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

AutoCloner maintained by Alex Coulton.