Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010104.1 Kokia drynarioides strain JFW-HI SEQ_124890, 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: 3935
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.35
Warning! 100 characters in sequence are not A, C, G, or T
Found at i:1229 original size:15 final size:14
Alignment explanation
Indices: 1204--1256 Score: 70
Period size: 15 Copynumber: 3.6 Consensus size: 14
1194 CATTTGTATT
1204 TGGGCCATTGTAAC
1 TGGGCCATTGTAAC
**
1218 TGGGCCACTTGTATT
1 TGGGCCA-TTGTAAC
1233 TGGGCCATCTGTAAC
1 TGGGCCAT-TGTAAC
1248 TGGGCCATT
1 TGGGCCATT
1257 TGTTTTGGAT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
14 9 0.27
15 24 0.73
ACGTcount: A:0.17, C:0.23, G:0.28, T:0.32
Consensus pattern (14 bp):
TGGGCCATTGTAAC
Found at i:1239 original size:29 final size:30
Alignment explanation
Indices: 1197--1264 Score: 113
Period size: 29 Copynumber: 2.3 Consensus size: 30
1187 ATTAGACCAT
1197 TTGTATTTGGGCCAT-TGTAACTGGGCCAC
1 TTGTATTTGGGCCATCTGTAACTGGGCCAC
*
1226 TTGTATTTGGGCCATCTGTAACTGGGCCAT
1 TTGTATTTGGGCCATCTGTAACTGGGCCAC
1256 TTGT-TTTGG
1 TTGTATTTGG
1265 ATTTTTTTGT
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
29 20 0.54
30 17 0.46
ACGTcount: A:0.15, C:0.18, G:0.28, T:0.40
Consensus pattern (30 bp):
TTGTATTTGGGCCATCTGTAACTGGGCCAC
Found at i:1348 original size:17 final size:17
Alignment explanation
Indices: 1288--1350 Score: 90
Period size: 17 Copynumber: 3.7 Consensus size: 17
1278 CGGACTTTTC
* *
1288 TAAATTTAATTTTATAA
1 TAAATTTAAATTTAAAA
*
1305 TAAATTTAAATTTCAAA
1 TAAATTTAAATTTAAAA
1322 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
*
1339 TAAACTTAAATT
1 TAAATTTAAATT
1351 CAATTTCCAA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 41 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:2104 original size:139 final size:138
Alignment explanation
Indices: 1816--2373 Score: 811
Period size: 139 Copynumber: 4.1 Consensus size: 138
1806 ATTCGCTTAT
* * * * * * * * *
1816 GAATTTGGTTCACTTCTCAGTACCTCATCTGGAAGATCTGCTTGCTTCAAGCCTCGTTTGGGTCT
1 GAATCTGGTTCACTTCTCCGTATCTCATCAGGAAGATTTGCTCGTTTCGAGCCTCGTTTGGGTTT
* * * *
1881 CCTTCTCAGCGTCTCATCGGGAAGATG----ATCACTGTTTCAATCCGTTTCTCTGTATCTCATT
66 TCTTCTCAGTGTCTCATCAGGAAGATGATCCATCACTGTTTCAATCCGTTTCTCTGTATCTCATC
1942 AGGAAGAC
131 AGGAAGAC
*
1950 GAATCTGATTCACTTCTCCGTATCTCATCAGGAAGATTTGCTC-TCTTCGAGCCTCGTTTGGGTT
1 GAATCTGGTTCACTTCTCCGTATCTCATCAGGAAGATTTGCTCGT-TTCGAGCCTCGTTTGGGTT
*
2014 TTCTTCTCAGTGTCTCATCAGGAAGATGATCTCATCACTGTTTCGATCCGTTTCTCTGTATCTCA
65 TTCTTCTCAGTGTCTCATCAGGAAGATGATC-CATCACTGTTTCAATCCGTTTCTCTGTATCTCA
*
2079 TCAGGAATAC
129 TCAGGAAGAC
*
2089 GAATCTGGTTCACTTCTCCGTATCTCATCAGGAAGATTTGCTCGTTTCGAGCCTTGTTTGGGTTT
1 GAATCTGGTTCACTTCTCCGTATCTCATCAGGAAGATTTGCTCGTTTCGAGCCTCGTTTGGGTTT
* * *
2154 TCTTCTTAGTGTCTCATGAGGAAGATGATCACATCACTGTTTCGATCCGTTTCTCTGTATCTCAT
66 TCTTCTCAGTGTCTCATCAGGAAGATGATC-CATCACTGTTTCAATCCGTTTCTCTGTATCTCAT
*
2219 CAGGAATAC
130 CAGGAAGAC
* * * *
2228 GAATCTGGTTCATTTCTTCGTATCTCATCAGGAAGATTTGCTCGTTTAGAGCCTTGTTTGGGTTT
1 GAATCTGGTTCACTTCTCCGTATCTCATCAGGAAGATTTGCTCGTTTCGAGCCTCGTTTGGGTTT
*
2293 TCTTCTAAGTGTCTCATCAGGAAGATGATCCCATCACTGTTTCAATCCGTTTCTCTGTATCTCAT
66 TCTTCTCAGTGTCTCATCAGGAAGATGAT-CCATCACTGTTTCAATCCGTTTCTCTGTATCTCAT
2358 CAGGAAGAC
130 CAGGAAGAC
2367 GAATCTG
1 GAATCTG
2374 CTTTGTGGAT
Statistics
Matches: 388, Mismatches: 28, Indels: 11
0.91 0.07 0.03
Matches are distributed among these distances:
134 78 0.20
139 308 0.79
140 2 0.01
ACGTcount: A:0.20, C:0.23, G:0.20, T:0.37
Consensus pattern (138 bp):
GAATCTGGTTCACTTCTCCGTATCTCATCAGGAAGATTTGCTCGTTTCGAGCCTCGTTTGGGTTT
TCTTCTCAGTGTCTCATCAGGAAGATGATCCATCACTGTTTCAATCCGTTTCTCTGTATCTCATC
AGGAAGAC
Found at i:3133 original size:48 final size:48
Alignment explanation
Indices: 3065--3239 Score: 136
Period size: 48 Copynumber: 3.5 Consensus size: 48
3055 TTGTTTGGGT
*
3065 TTTCTTCTGTGTCTCATCAGGAAGATGATCCCATCACTGTTTCGATCCG
1 TTTC-TCTGTATCTCATCAGGAAGATGATCCCATCACTGTTTCGATCCG
* * *** * * **
3114 TTTCTCTGTATCTCATCAGGAATATTTGCTCGTTTCGAGCCTCGTTTGGGT-TT
1 TTTCTCTGTATCTCATCAGGAAGA--TGATCCCATC-A--CT-GTTTCGATCCG
* * * * *
3167 TCTTCTCAGTGTCTCATCATGAAGATAATCCCATCACTATTTCGATCCG
1 T-TTCTCTGTATCTCATCAGGAAGATGATCCCATCACTGTTTCGATCCG
3216 TTTCTCTGTATCTCATCAGGAAGA
1 TTTCTCTGTATCTCATCAGGAAGA
3240 CGAATCTGCT
Statistics
Matches: 91, Mismatches: 27, Indels: 17
0.67 0.20 0.13
Matches are distributed among these distances:
48 43 0.47
49 7 0.08
50 6 0.07
51 2 0.02
52 5 0.05
53 3 0.03
54 25 0.27
ACGTcount: A:0.19, C:0.25, G:0.17, T:0.39
Consensus pattern (48 bp):
TTTCTCTGTATCTCATCAGGAAGATGATCCCATCACTGTTTCGATCCG
Found at i:3226 original size:102 final size:100
Alignment explanation
Indices: 3021--3239 Score: 366
Period size: 102 Copynumber: 2.2 Consensus size: 100
3011 TCACTTCTTC
* *
3021 GTATCTCATCAGGAAGATTTGCTCGTTTTGAGCCTTGTTTGGGTTTTCTTCTGTGTCTCATCAGG
1 GTATCTCATCAGGAAGATTTGCTCGTTTCGAGCCTCGTTTGGGTTTTCTTCTGTGTCTCATCAGG
* *
3086 AAGATGATCCCATCACTGTTTCGATCCGTTTCTCT
66 AAGATAATCCCATCACTATTTCGATCCGTTTCTCT
*
3121 GTATCTCATCAGGAATATTTGCTCGTTTCGAGCCTCGTTTGGGTTTTCTTCTCAGTGTCTCATCA
1 GTATCTCATCAGGAAGATTTGCTCGTTTCGAGCCTCGTTTGGGTTTTCTTCT--GTGTCTCATCA
*
3186 TGAAGATAATCCCATCACTATTTCGATCCGTTTCTCT
64 GGAAGATAATCCCATCACTATTTCGATCCGTTTCTCT
3223 GTATCTCATCAGGAAGA
1 GTATCTCATCAGGAAGA
3240 CGAATCTGCT
Statistics
Matches: 110, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
100 49 0.45
102 61 0.55
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.39
Consensus pattern (100 bp):
GTATCTCATCAGGAAGATTTGCTCGTTTCGAGCCTCGTTTGGGTTTTCTTCTGTGTCTCATCAGG
AAGATAATCCCATCACTATTTCGATCCGTTTCTCT
Done.