Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007681.1 Kokia drynarioides strain JFW-HI SEQ_122312, 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: 2411
ACGTcount: A:0.34, C:0.19, G:0.12, T:0.35
Found at i:2083 original size:86 final size:86
Alignment explanation
Indices: 1923--2121 Score: 198
Period size: 86 Copynumber: 2.3 Consensus size: 86
1913 CTGAATCGTC
1923 CAAAAATCACATTTTGACCCCTAAACTTCCTAAAATTACAATTTTGACCCTAAATATTCCAAAAT
1 CAAAAATCACATTTTGACCCCTAAACTTCCTAAAATTACAATTTTGACCCTAAATATTCCAAAAT
1988 TACCATTTT-ACCCCAAACTCA
66 TA-CATTTTAACCCCAAACTCA
* * * *
2009 CAAAAAT-ACAATTTTCGA-CCCTGAACTTTCTAAAAATTACCATTTT-ACCCTTAAAT-TTCTA
1 CAAAAATCAC-ATTTT-GACCCCTAAACTTCCT-AAAATTACAATTTTGACCC-TAAATATTCCA
*
2070 AAATTTA-ATTTTTAACCCCAAATTTTC-
62 AAA-TTACA-TTTTAACCCCAAA--CTCA
*
2097 CAAAAATTACCATTTT-ACCCCTAAA
1 CAAAAATCA-CATTTTGACCCCTAAA
2122 TGTCTAAAAA
Statistics
Matches: 95, Mismatches: 6, Indels: 22
0.77 0.05 0.18
Matches are distributed among these distances:
85 3 0.03
86 38 0.40
87 32 0.34
88 13 0.14
89 8 0.08
90 1 0.01
ACGTcount: A:0.39, C:0.25, G:0.02, T:0.34
Consensus pattern (86 bp):
CAAAAATCACATTTTGACCCCTAAACTTCCTAAAATTACAATTTTGACCCTAAATATTCCAAAAT
TACATTTTAACCCCAAACTCA
Found at i:2116 original size:29 final size:28
Alignment explanation
Indices: 1921--2191 Score: 151
Period size: 29 Copynumber: 9.2 Consensus size: 28
1911 CCCTGAATCG
* *
1921 TCCAAAAATCA-CATTTTGACCCCTAAACT
1 TCCAAAAATTACCATTTT-ACCCC-AAATT
* * *
1950 TCCTAAAATTACAATTTTGACCCTAAATAT
1 TCCAAAAATTACCATTTT-ACCCCAAAT-T
*
1980 TCC-AAAATTACCATTTTACCCCAAA-C
1 TCCAAAAATTACCATTTTACCCCAAATT
* * *
2006 TCACAAAAA-TACAATTTTCGACCCTGAACTT
1 TC-CAAAAATTACCATTTT--ACCC-CAAATT
* *
2037 TCTAAAAATTACCATTTTACCCTTAAATT
1 TCCAAAAATTACCATTTTACCC-CAAATT
* *
2066 TCTAAAATTTA--ATTTTTAACCCCAAATTT
1 TCCAAAAATTACCA-TTTT-ACCCCAAA-TT
*
2095 TCCAAAAATTACCATTTTACCCCTAAATG
1 TCCAAAAATTACCATTTTACCCC-AAATT
* *
2124 TCTAAAAATT-CCATTTTTTTATCCCAAATTT
1 TCCAAAAATTACCA---TTTTACCCCAAA-TT
* * *
2155 TTCAAAAATTACCATTGTACCTCGAAACTT
1 TCCAAAAATTACCATTTTACC-CCAAA-TT
2185 TCCAAAA
1 TCCAAAA
2192 CTTATGTTTT
Statistics
Matches: 190, Mismatches: 31, Indels: 41
0.73 0.12 0.16
Matches are distributed among these distances:
26 2 0.01
27 10 0.05
28 21 0.11
29 83 0.44
30 43 0.23
31 28 0.15
32 3 0.02
ACGTcount: A:0.38, C:0.24, G:0.03, T:0.35
Consensus pattern (28 bp):
TCCAAAAATTACCATTTTACCCCAAATT
Found at i:2122 original size:58 final size:59
Alignment explanation
Indices: 1921--2339 Score: 259
Period size: 58 Copynumber: 7.1 Consensus size: 59
1911 CCCTGAATCG
* * * *
1921 TCCAAAAATCA-CATTTTGACCCCTAAACTTCCTAAAATTACAA-TTTTGACCCTAAATAT
1 TCCAAAAATTACCATTTT-ACCCCTAAACTTTCTAAAATT-CAATTTTTGACCCCAAATTT
** * * * ** *
1980 TCC-AAAATTACCATTTTACCCC-AAACTCACAAAAATACAATTTTCGACCCTGAACTT
1 TCCAAAAATTACCATTTTACCCCTAAACTTTCTAAAATTCAATTTTTGACCCCAAATTT
* * * *
2037 TCTAAAAATTACCATTTTACCCTTAAA-TTTCTAAAATTTAATTTTTAACCCCAAATTT
1 TCCAAAAATTACCATTTTACCCCTAAACTTTCTAAAATTCAATTTTTGACCCCAAATTT
* * * *
2095 TCCAAAAATTACCATTTTACCCCTAAA-TGTCTAAAAATTCCATTTTTTTATCCCAAATTT
1 TCCAAAAATTACCATTTTACCCCTAAACTTTCT-AAAATT-CAATTTTTGACCCCAAATTT
* * * * * * ** * **
2155 TTCAAAAATTACCATTGTACCTCGAAACTTTCCAAAACTT-ATGTTTTTTCCCCCCGAA-CA
1 TCCAAAAATTACCATTTTACCCCTAAACTTTCTAAAA-TTCA--ATTTTTGACCCCAAATTT
* * * ** * * * *
2215 TCCAATAATTACCATTTTACTCGTGGA-TGTT-TGAAAATTCCATTTTTGATCTCGAATTT
1 TCCAAAAATTACCATTTTACCCCTAAACT-TTCT-AAAATTCAATTTTTGACCCCAAATTT
* * * *
2274 TCCAAAAATTACAATGTTACTCCCT-AACTTCCTAAAATTGC-ATTTTTGACCCCAAACTT
1 TCCAAAAATTACCATTTTAC-CCCTAAACTTTCTAAAATT-CAATTTTTGACCCCAAATTT
2333 TCCAAAA
1 TCCAAAA
2340 CTTATCGTTT
Statistics
Matches: 273, Mismatches: 69, Indels: 36
0.72 0.18 0.10
Matches are distributed among these distances:
56 3 0.01
57 25 0.09
58 89 0.33
59 68 0.25
60 72 0.26
61 16 0.06
ACGTcount: A:0.35, C:0.24, G:0.05, T:0.36
Consensus pattern (59 bp):
TCCAAAAATTACCATTTTACCCCTAAACTTTCTAAAATTCAATTTTTGACCCCAAATTT
Found at i:2202 original size:60 final size:57
Alignment explanation
Indices: 2035--2208 Score: 177
Period size: 60 Copynumber: 2.9 Consensus size: 57
2025 GACCCTGAAC
* * *
2035 TTTCTAAAAATTACCATTTTACCCTTAAATTTCTAAAATTTAATTTTTAACCCCAAATT
1 TTTC-AAAAATTACCATTTTACCC-TAAATTTCTAAAAATTATTTTTTTACCCCAAATT
* * *
2094 TTCCAAAAATTACCATTTTACCCCTAAATGTCTAAAAATTCCATTTTTTTATCCCAAATT
1 TTTCAAAAATTACCATTTTA-CCCTAAATTTCTAAAAATT--ATTTTTTTACCCCAAATT
* * * * *
2154 TTTCAAAAATTACCATTGTACCTCGAAACTTTCCAAAACTTATGTTTTTTCCCCC
1 TTTCAAAAATTACCATTTTACC-CTAAA-TTTCTAAAAATTAT-TTTTTTACCCC
2209 CGAACATCCA
Statistics
Matches: 95, Mismatches: 14, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
58 30 0.32
59 10 0.11
60 46 0.48
61 9 0.09
ACGTcount: A:0.34, C:0.23, G:0.02, T:0.41
Consensus pattern (57 bp):
TTTCAAAAATTACCATTTTACCCTAAATTTCTAAAAATTATTTTTTTACCCCAAATT
Done.