Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010861.1 Kokia drynarioides strain JFW-HI SEQ_125829, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 5932
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:2018 original size:45 final size:45
Alignment explanation
Indices: 1954--2090 Score: 193
Period size: 45 Copynumber: 3.0 Consensus size: 45
1944 GCATAGCTTA
1954 TCAAGCCAAGGATATCAGCCTCAATTTGACGAGCCACCGCAATAC
1 TCAAGCCAAGGATATCAGCCTCAATTTGACGAGCCACCGCAATAC
* * *
1999 TCAAGCCAATGATATCAGCCTCAATTTGACGAGTCACCGTAATAC
1 TCAAGCCAAGGATATCAGCCTCAATTTGACGAGCCACCGCAATAC
* * * * * *
2044 TCAAGCCAAGGATATCAGGCTGAGTTTGACGAACCATCGCGATAC
1 TCAAGCCAAGGATATCAGCCTCAATTTGACGAGCCACCGCAATAC
2089 TC
1 TC
2091 TATTCCTCCT
Statistics
Matches: 80, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 80 1.00
ACGTcount: A:0.32, C:0.28, G:0.19, T:0.21
Consensus pattern (45 bp):
TCAAGCCAAGGATATCAGCCTCAATTTGACGAGCCACCGCAATAC
Found at i:2111 original size:21 final size:21
Alignment explanation
Indices: 2085--2127 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
2075 AACCATCGCG
* *
2085 ATACTCTATTCCTCCTGGGCA
1 ATACTCTACTCCTCCGGGGCA
2106 ATACTCTACTCCTCCGGGGCA
1 ATACTCTACTCCTCCGGGGCA
2127 A
1 A
2128 ATGGACCCTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.21, C:0.35, G:0.16, T:0.28
Consensus pattern (21 bp):
ATACTCTACTCCTCCGGGGCA
Found at i:5178 original size:746 final size:736
Alignment explanation
Indices: 3913--5394 Score: 2874
Period size: 746 Copynumber: 2.0 Consensus size: 736
3903 CTTGTATAGT
3913 CACGTTCCATCTACCTGGACAAATGGCTTGCAGTGAGGAAATGCTCGAACGCAGGGATCAAACGT
1 CACGTTCCATCTACCTGGACAAATGGCTTGCAGTGAGGAAATGCTCGAACGCAGGGATCAAACGT
3978 CCAAAATATATACTGAAAAATTCTTCTTCCCGGTTGCATGTTGTTATCTGAGCCATAATAAGGTC
66 CCAAAATATATACTGAAAAATTCTTCTTCCCGGTTGCATGTTGTTATCTGAGCCATAATAAGGTC
4043 GTGTCACCAACTCAATCGCAGTCCCCGGCACGTATTGTCGCATTGCGGCTATCCATCCTTGCAGC
131 GTGTCACCAACTCAATCGCAGTCCCCGGCACGTATTGTCGCATTGCGGCTATCCATCCTTGCAGC
4108 TCATTGTATGATGCATCCCAATCACTGAACAATTGTTCCATTGCCATCTGTTTCACAATCCATGC
196 TCATTGTATGATGCATCCCAATCACTGAACAATTGTTCCATTGCCATCTGTTTCACAATCCATGC
4173 TTTTCGATATGAAACACGATAATGGAATCGTGATTGCATGTCCACAATCAATGTAAAAACCTTGA
261 TTTTCGATATGAAACACGATAATGGAATCGTGATTGCATGTCCACAATCAATGTAAAAACCTTGA
4238 TGGTCGGGTCGTCCTTAACCATTAGCATGATATGTGTGCAGATGATTCTGGAATCAAGTTTCCGG
326 TGGTCGGGTCGTCCTTAACCATTAGCATGATATGTGTGCAGATGATTCTGGAATCAAGTTTCCGG
4303 TGATCTTCTAACAAACGTGTTGAACTGCATGTGTGAGCTTATCTCCCACATCTGCGACTTCTGGA
391 TGATCTTCTAACAAACGTGTTGAACTGCATGTGTGAGCTTATCTCCCACATCTGCGACTTCTGGA
4368 TAAATGCAGCTCGCACCCGCCACTTGCAACCTTCCGTCGACTTCCAGCACTCTCCAATATACAAT
456 TAAATGCAGCTCGCACCCGCCACTTGCAACCTTCCGTCGACTTCCAGCACTCTCCAATATACAAT
4433 GTCGGTTTAGACACTGCGACTTTGTAGTCTATCGACACATTCATGCTATATTGCTTAATAGCAAA
521 GTCGGTTTAGACACTGCGACTTTGTAGTCTATCGACACATTCATGCTATATTGCTTAATAGCAAA
4498 TATGCACTCTTCCTTGGATTCAAATTTTTGGCCCACAAACAACTCTTCACAATCTGCTGCTACGG
586 TATGCACTCTTCCTTGGATTCAAATTTTTGGCCCACAAACAACTCTTCACAATCTGCTGCTACGG
4563 TCAATCGGTGAGCAAGTACTATTTCAGGGTATTCCGCGAACTCGGCATGTGTCGCATCGGGGTTT
651 TCAATCGGTGAGCAAGTACTATTTCAGGGTATTCCGCGAACTCGGCATGTGTCGCATCGGGGTTT
4628 ATAAGCGACATGTGTGCTCCA
716 ATAAGCGACATGTGTGCTCCA
4649 NNNNNNNNNNCACGTTCCATCTACCTGGACAAATGGCTTGCAGTGAGGAAATGCTCGAACGCAGG
1 ----------CACGTTCCATCTACCTGGACAAATGGCTTGCAGTGAGGAAATGCTCGAACGCAGG
4714 GATCAAACGTCCAAAATATATACTGAAAAATTCTTCTTCCCGGTTGCATGTTGTTATCTGAGCCA
56 GATCAAACGTCCAAAATATATACTGAAAAATTCTTCTTCCCGGTTGCATGTTGTTATCTGAGCCA
4779 TAATAAGGTCGTGTCACCAACTCAATCGCAGTCCCCGGCACGTATTGTCGCATTGCGGCTATCCA
121 TAATAAGGTCGTGTCACCAACTCAATCGCAGTCCCCGGCACGTATTGTCGCATTGCGGCTATCCA
4844 TCCTTGCAGCTCATTGTATGATGCATCCCAATCACTGAACAATTGTTCCATTGCCATCTGTTTCA
186 TCCTTGCAGCTCATTGTATGATGCATCCCAATCACTGAACAATTGTTCCATTGCCATCTGTTTCA
4909 CAATCCATGCTTTTCGATATGAAACACGATAATGGAATCGTGATTGCATGTCCACAATCAATGTA
251 CAATCCATGCTTTTCGATATGAAACACGATAATGGAATCGTGATTGCATGTCCACAATCAATGTA
4974 AAAACCTTGATGGTCGGGTCGTCCTTAACCATTAGCATGATATGTGTGCAGATGATTCTGGAATC
316 AAAACCTTGATGGTCGGGTCGTCCTTAACCATTAGCATGATATGTGTGCAGATGATTCTGGAATC
5039 AAGTTTCCGGTGATCTTCTAACAAACGTGTTGAACTGCATGTGTGAGCTTATCTCCCACATCTGC
381 AAGTTTCCGGTGATCTTCTAACAAACGTGTTGAACTGCATGTGTGAGCTTATCTCCCACATCTGC
5104 GACTTCTGGATAAATGCAGCTCGCACCCGCCACTTGCAACCTTCCGTCGACTTCCAGCACTCTCC
446 GACTTCTGGATAAATGCAGCTCGCACCCGCCACTTGCAACCTTCCGTCGACTTCCAGCACTCTCC
5169 AATATACAATGTCGGTTTAGACACTGCGACTTTGTAGTCTATCGACACATTCATGCTATATTGCT
511 AATATACAATGTCGGTTTAGACACTGCGACTTTGTAGTCTATCGACACATTCATGCTATATTGCT
5234 TAATAGCAAATATGCACTCTTCCTTGGATTCAAATTTTTGGCCCACAAACAACTCTTCACAATCT
576 TAATAGCAAATATGCACTCTTCCTTGGATTCAAATTTTTGGCCCACAAACAACTCTTCACAATCT
5299 GCTGCTACGGTCAATCGGTGAGCAAGTACTATTTCAGGGTATTCCGCGAACTCGGCATGTGTCGC
641 GCTGCTACGGTCAATCGGTGAGCAAGTACTATTTCAGGGTATTCCGCGAACTCGGCATGTGTCGC
5364 ATCGGGGTTTATAAGCGACATGTGTGCTCCA
706 ATCGGGGTTTATAAGCGACATGTGTGCTCCA
5395 GGAGGATTAT
Statistics
Matches: 736, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
746 736 1.00
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.29
Consensus pattern (736 bp):
CACGTTCCATCTACCTGGACAAATGGCTTGCAGTGAGGAAATGCTCGAACGCAGGGATCAAACGT
CCAAAATATATACTGAAAAATTCTTCTTCCCGGTTGCATGTTGTTATCTGAGCCATAATAAGGTC
GTGTCACCAACTCAATCGCAGTCCCCGGCACGTATTGTCGCATTGCGGCTATCCATCCTTGCAGC
TCATTGTATGATGCATCCCAATCACTGAACAATTGTTCCATTGCCATCTGTTTCACAATCCATGC
TTTTCGATATGAAACACGATAATGGAATCGTGATTGCATGTCCACAATCAATGTAAAAACCTTGA
TGGTCGGGTCGTCCTTAACCATTAGCATGATATGTGTGCAGATGATTCTGGAATCAAGTTTCCGG
TGATCTTCTAACAAACGTGTTGAACTGCATGTGTGAGCTTATCTCCCACATCTGCGACTTCTGGA
TAAATGCAGCTCGCACCCGCCACTTGCAACCTTCCGTCGACTTCCAGCACTCTCCAATATACAAT
GTCGGTTTAGACACTGCGACTTTGTAGTCTATCGACACATTCATGCTATATTGCTTAATAGCAAA
TATGCACTCTTCCTTGGATTCAAATTTTTGGCCCACAAACAACTCTTCACAATCTGCTGCTACGG
TCAATCGGTGAGCAAGTACTATTTCAGGGTATTCCGCGAACTCGGCATGTGTCGCATCGGGGTTT
ATAAGCGACATGTGTGCTCCA
Done.