Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001517.1 Kokia drynarioides strain JFW-HI SEQ_113078, 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: 3202
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Found at i:2059 original size:29 final size:29
Alignment explanation
Indices: 2035--2177 Score: 103
Period size: 30 Copynumber: 4.8 Consensus size: 29
2025 CTAAAATTTT
* **
2035 ATTTTTAACCTCGATTTTCCAAAAAAATAT
1 ATTTTTAACCTCGATTTTCC-AAAAATTCC
*
2065 ATTTTT-ACCTCCAAACTTTT-C-AAAATTCC
1 ATTTTTAACCT-C-GA-TTTTCCAAAAATTCC
* * * *
2094 ATTTTTGACCTCAATTTTTCTAAAATTACC
1 ATTTTTAACCTCGATTTTCCAAAAATT-CC
* * *
2124 ATTTTTACCCCCGAATTTCCAAAAATTCC
1 ATTTTTAACCTCGATTTTCCAAAAATTCC
*
2153 ATTTTTGACCTCGATTTTTCCAAAA
1 ATTTTTAACCTCGA-TTTTCCAAAA
2178 TAATCATTTT
Statistics
Matches: 90, Mismatches: 15, Indels: 16
0.74 0.12 0.13
Matches are distributed among these distances:
27 4 0.04
28 3 0.03
29 35 0.39
30 42 0.47
31 2 0.02
32 4 0.04
ACGTcount: A:0.32, C:0.23, G:0.03, T:0.41
Consensus pattern (29 bp):
ATTTTTAACCTCGATTTTCCAAAAATTCC
Found at i:2067 original size:59 final size:58
Alignment explanation
Indices: 1995--2279 Score: 194
Period size: 59 Copynumber: 4.8 Consensus size: 58
1985 GGTTTTATTA
** *
1995 AAAAAAATTATATTTTTACCCCTAAACTTTCTAAAATTTTATTTTTAACCTCGATTTTCC
1 AAAAAAA-TATATTTTTACCCC-AAACTTTCTAAAATTCCATTTTTGACCTCGATTTTCC
* *
2055 AAAAAAATATATTTTTACCTCCAAACTTT-TCAAAATTCCATTTTTGACCTCAATTTTTC
1 AAAAAAATATATTTTTACC-CCAAACTTTCT-AAAATTCCATTTTTGACCTCGATTTTCC
* * * * *
2114 -TAAAATTACCATTTTTACCCCCGAA-TTTCCAAAAATTCCATTTTTGACCTCGATTTTTCC
1 AAAAAAATA-TATTTTTA-CCCCAAACTTT-CTAAAATTCCATTTTTGACCTCGA-TTTTCC
* * ** * *
2174 AAAATAAT-CA-TTTTACTCCCGGA-TGTCATAAAATTCCATTTTTGACC-CTGAACTTTCC
1 AAAAAAATATATTTTTAC-CCCAAACTTTC-TAAAATTCCATTTTTGACCTC-G-ATTTTCC
* * *
2232 -AAAAATTATCA-TTTTACCCTCGAA-TATCTAAAAATTCCATTTTTGACC
1 AAAAAAATAT-ATTTTTACCC-CAAACTTTCT-AAAATTCCATTTTTGACC
2280 CCAAACTTTC
Statistics
Matches: 185, Mismatches: 24, Indels: 33
0.76 0.10 0.14
Matches are distributed among these distances:
57 8 0.04
58 49 0.26
59 108 0.58
60 16 0.09
61 4 0.02
ACGTcount: A:0.33, C:0.22, G:0.04, T:0.40
Consensus pattern (58 bp):
AAAAAAATATATTTTTACCCCAAACTTTCTAAAATTCCATTTTTGACCTCGATTTTCC
Found at i:2178 original size:29 final size:29
Alignment explanation
Indices: 2081--2178 Score: 112
Period size: 29 Copynumber: 3.4 Consensus size: 29
2071 ACCTCCAAAC
*
2081 TTTT-CAAAATTCCATTTTTGACCTCAAT
1 TTTTCCAAAATTCCATTTTTGACCTCGAT
* *
2109 TTTTCTAAAATTACCATTTTT-ACCCCCGA-
1 TTTTCCAAAATT-CCATTTTTGA-CCTCGAT
*
2138 ATTTCCAAAAATTCCATTTTTGACCTCGAT
1 TTTTCC-AAAATTCCATTTTTGACCTCGAT
2168 TTTTCCAAAAT
1 TTTTCCAAAAT
2179 AATCATTTTA
Statistics
Matches: 57, Mismatches: 7, Indels: 11
0.76 0.09 0.15
Matches are distributed among these distances:
28 4 0.07
29 29 0.51
30 24 0.42
ACGTcount: A:0.30, C:0.23, G:0.04, T:0.43
Consensus pattern (29 bp):
TTTTCCAAAATTCCATTTTTGACCTCGAT
Found at i:2186 original size:30 final size:29
Alignment explanation
Indices: 2035--2187 Score: 84
Period size: 29 Copynumber: 5.2 Consensus size: 29
2025 CTAAAATTTT
* *
2035 ATTTTTAACCTCGATTTTCCAAAAAAAT-
1 ATTTTTGACCTCGATTTTCCAAAATAATC
* *
2063 ATATTTTTACCTCCAAACTTTT-CAAAAT--TCC
1 AT-TTTTGACCT-C-GA-TTTTCCAAAATAAT-C
* * * *
2094 ATTTTTGACCTCAATTTTTCTAAAATTACC
1 ATTTTTGACCTCGA-TTTTCCAAAATAATC
* * *
2124 ATTTTT-ACCCCCGAATTTCCAAAA-ATTCC
1 ATTTTTGA-CCTCGATTTTCCAAAATAAT-C
2153 ATTTTTGACCTCGATTTTTCCAAAATAATC
1 ATTTTTGACCTCGA-TTTTCCAAAATAATC
2183 ATTTT
1 ATTTT
2188 ACTCCCGGAT
Statistics
Matches: 94, Mismatches: 17, Indels: 26
0.69 0.12 0.19
Matches are distributed among these distances:
28 8 0.09
29 36 0.38
30 36 0.38
31 10 0.11
32 4 0.04
ACGTcount: A:0.32, C:0.22, G:0.03, T:0.42
Consensus pattern (29 bp):
ATTTTTGACCTCGATTTTCCAAAATAATC
Found at i:2216 original size:58 final size:57
Alignment explanation
Indices: 2086--2279 Score: 214
Period size: 59 Copynumber: 3.3 Consensus size: 57
2076 CAAACTTTTC
* * * *
2086 AAAATTCCATTTTTGACCTCAATTTTTCTAAAATTACCATTTTTACCCCCGAATTTCCA-
1 AAAATTCCATTTTTGACCTCGATTTTTCCAAAATTATCA-TTTTA-CCCCGAATAT-CAT
* * *
2145 AAAATTCCATTTTTGACCTCGATTTTTCCAAAATAATCATTTTACTCCCGGATGTCAT
1 AAAATTCCATTTTTGACCTCGATTTTTCCAAAATTATCATTTTAC-CCCGAATATCAT
**
2203 AAAATTCCATTTTTGACC-CTGAACTTTCCAAAAATTATCATTTTACCCTCGAATATC-T
1 AAAATTCCATTTTTGACCTC-GATTTTTCC-AAAATTATCATTTTACCC-CGAATATCAT
2261 AAAAATTCCATTTTTGACC
1 -AAAATTCCATTTTTGACC
2280 CCAAACTTTC
Statistics
Matches: 118, Mismatches: 11, Indels: 12
0.84 0.08 0.09
Matches are distributed among these distances:
57 4 0.03
58 40 0.34
59 74 0.63
ACGTcount: A:0.31, C:0.24, G:0.06, T:0.39
Consensus pattern (57 bp):
AAAATTCCATTTTTGACCTCGATTTTTCCAAAATTATCATTTTACCCCGAATATCAT
Found at i:2297 original size:30 final size:29
Alignment explanation
Indices: 2086--2369 Score: 144
Period size: 30 Copynumber: 9.8 Consensus size: 29
2076 CAAACTTTTC
* * *
2086 AAAATTCCATTTTTGACCTC-AATTTTTCT
1 AAAATTCCATTTTTGACCCCGAA-TTTCCA
2115 AAAATTACCATTTTT-ACCCCCGAATTTCCA
1 AAAATT-CCATTTTTGA-CCCCGAATTTCCA
* *
2145 AAAATTCCATTTTTGACCTCGATTTTTCCA
1 AAAATTCCATTTTTGACCCCGA-ATTTCCA
* * *
2175 AAATAAT-CA-TTTT-ACTCCCGGATGT-CA
1 AAA-ATTCCATTTTTGAC-CCCGAATTTCCA
*
2202 TAAAATTCCATTTTTGACCCTGAACTTTCCA
1 -AAAATTCCATTTTTGACCCCGAA-TTTCCA
* * *
2233 AAAATTATCA-TTTT-ACCCTCGAATATCTA
1 AAAATT-CCATTTTTGACCC-CGAATTTCCA
* *
2262 AAAATTCCATTTTTGACCCCAAACTTTCCC
1 AAAATTCCATTTTTGACCCCGAA-TTTCCA
* * * * **
2292 AAAATTACAATTTTG-CCCTGAGTGACC-
1 AAAATTCCATTTTTGACCCCGAATTTCCA
* *
2319 AAAATTACCA-TTTTG-CCCCCAAGTATCCA
1 AAAATT-CCATTTTTGACCCCGAA-TTTCCA
*
2348 AAAA-TCTCATTTTTGACTCCGA
1 AAAATTC-CATTTTTGACCCCGA
2370 TTGTTTTATT
Statistics
Matches: 193, Mismatches: 38, Indels: 47
0.69 0.14 0.17
Matches are distributed among these distances:
27 20 0.10
28 22 0.11
29 69 0.36
30 74 0.38
31 8 0.04
ACGTcount: A:0.32, C:0.25, G:0.07, T:0.36
Consensus pattern (29 bp):
AAAATTCCATTTTTGACCCCGAATTTCCA
Found at i:2332 original size:117 final size:117
Alignment explanation
Indices: 2085--2296 Score: 273
Period size: 117 Copynumber: 1.8 Consensus size: 117
2075 CCAAACTTTT
* * * *
2085 CAAAATTCCATTTTTGACCTCAATTTTTCTAAAATTACCATTTTTACCCCCGAATTTCCAAAAAT
1 CAAAATTCCATTTTTGACCTCAACTTTCCAAAAATTACCATTTTTACCCCCGAATATCCAAAAAT
* * * * *
2150 TCCATTTTTGACCTCGATTTTTCCAAAATAATCATTTTACTCCCGGATGTCA
66 TCCATTTTTGACCCCAACTTTCCCAAAATAATCATTTTACTCCCGGATGACA
* * * * *
2202 TAAAATTCCATTTTTGACCCTGAACTTTCCAAAAATTATCA-TTTTACCCTCGAATATCTAAAAA
1 CAAAATTCCATTTTTGA-CCTCAACTTTCCAAAAATTACCATTTTTACCCCCGAATATCCAAAAA
2266 TTCCATTTTTGACCCCAAACTTTCCCAAAAT
65 TTCCATTTTTGACCCC-AACTTTCCCAAAAT
2297 TACAATTTTG
Statistics
Matches: 80, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
117 51 0.64
118 29 0.36
ACGTcount: A:0.32, C:0.25, G:0.05, T:0.38
Consensus pattern (117 bp):
CAAAATTCCATTTTTGACCTCAACTTTCCAAAAATTACCATTTTTACCCCCGAATATCCAAAAAT
TCCATTTTTGACCCCAACTTTCCCAAAATAATCATTTTACTCCCGGATGACA
Done.