Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009824.1 Kokia drynarioides strain JFW-HI SEQ_124545, 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: 44460
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1279 original size:15 final size:14
Alignment explanation
Indices: 1259--1324 Score: 82
Period size: 15 Copynumber: 4.6 Consensus size: 14
1249 GTATTGAGGC
1259 AAAAGAAGAAGAAA
1 AAAAGAAGAAGAAA
1273 GAAAAGAAGAAGAAA
1 -AAAAGAAGAAGAAA
*
1288 AACAAGAAG-A-AAC
1 AA-AAGAAGAAGAAA
1301 AAAAGAAGAAGAAA
1 AAAAGAAGAAGAAA
1315 AAGAAGAAGA
1 AA-AAGAAGA
1325 TGTTGCCTCG
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
12 6 0.13
13 5 0.11
14 7 0.16
15 27 0.60
ACGTcount: A:0.74, C:0.03, G:0.23, T:0.00
Consensus pattern (14 bp):
AAAAGAAGAAGAAA
Found at i:1296 original size:27 final size:27
Alignment explanation
Indices: 1259--1324 Score: 114
Period size: 27 Copynumber: 2.4 Consensus size: 27
1249 GTATTGAGGC
*
1259 AAAAGAAGAAGAAAGAAAAGAAGAAGA
1 AAAAGAAGAAGAAACAAAAGAAGAAGA
*
1286 AAAACAAGAAGAAACAAAAGAAGAAGA
1 AAAAGAAGAAGAAACAAAAGAAGAAGA
1313 AAAAGAAGAAGA
1 AAAAGAAGAAGA
1325 TGTTGCCTCG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.74, C:0.03, G:0.23, T:0.00
Consensus pattern (27 bp):
AAAAGAAGAAGAAACAAAAGAAGAAGA
Found at i:1323 original size:12 final size:13
Alignment explanation
Indices: 1258--1324 Score: 66
Period size: 12 Copynumber: 5.0 Consensus size: 13
1248 GGTATTGAGG
1258 CAAAAGAAGAAGAAA
1 CAAAAGAAGAAG--A
*
1273 GAAAAGAAGAAGA
1 CAAAAGAAGAAGA
*
1286 -AAAACAAGAAGAAA
1 CAAAAGAAGAAG--A
1300 CAAAAGAAGAAGA
1 CAAAAGAAGAAGA
1313 -AAAAGAAGAAGA
1 CAAAAGAAGAAGA
1325 TGTTGCCTCG
Statistics
Matches: 46, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
12 22 0.48
13 2 0.04
14 1 0.02
15 21 0.46
ACGTcount: A:0.73, C:0.04, G:0.22, T:0.00
Consensus pattern (13 bp):
CAAAAGAAGAAGA
Found at i:4071 original size:90 final size:90
Alignment explanation
Indices: 3966--4148 Score: 276
Period size: 90 Copynumber: 2.0 Consensus size: 90
3956 TTCTGGACGT
* ** *
3966 AATTCTAGATCCTCTTATGCAACGACAACTTCGGACACATTCATGCATCGATACTTCTGGACAGG
1 AATTCTAGATCCTCTTATGCAACGACAACTCCGGACACATTCATGCATCGATACTTCTAAACAAG
*
4031 TTCCTACAGTGACATCTTTGGGCGC
66 TTCCTACAGTGACATCTTTGGGCAC
* ** *
4056 AATTCTAGATCCTCTTTTGCAGTGACAACTCCGGACACATTCATGCATTGATACTTCTAAACAAG
1 AATTCTAGATCCTCTTATGCAACGACAACTCCGGACACATTCATGCATCGATACTTCTAAACAAG
*
4121 TTCCTATAGTGACATCTTTGGGCAC
66 TTCCTACAGTGACATCTTTGGGCAC
4146 AAT
1 AAT
4149 GCTAAACAGA
Statistics
Matches: 83, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
90 83 1.00
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.31
Consensus pattern (90 bp):
AATTCTAGATCCTCTTATGCAACGACAACTCCGGACACATTCATGCATCGATACTTCTAAACAAG
TTCCTACAGTGACATCTTTGGGCAC
Found at i:4167 original size:90 final size:90
Alignment explanation
Indices: 3982--4172 Score: 231
Period size: 90 Copynumber: 2.1 Consensus size: 90
3972 AGATCCTCTT
* * ** *
3982 ATGCAACGACAACTTCGGACACATTCATGCATCGATACTTCTGGACAGGTTCCTACAGTGACATC
1 ATGCAGCGACAACTCCGGACACATTCATGCATCGATACTTCTAAACAAGTTCCTACAGTGACATC
* * * * *
4047 TTTGGGCGCAATTCTAGATCCTCTT
66 TTTGGGCACAATGCTAGAACCACTA
* * * *
4072 TTGCAGTGACAACTCCGGACACATTCATGCATTGATACTTCTAAACAAGTTCCTATAGTGACATC
1 ATGCAGCGACAACTCCGGACACATTCATGCATCGATACTTCTAAACAAGTTCCTACAGTGACATC
*
4137 TTTGGGCACAATGCTA-AACAGACTA
66 TTTGGGCACAATGCTAGAAC-CACTA
4162 ATGCAGCGACA
1 ATGCAGCGACA
4173 TAATAGTAAA
Statistics
Matches: 83, Mismatches: 17, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
89 2 0.02
90 81 0.98
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.27
Consensus pattern (90 bp):
ATGCAGCGACAACTCCGGACACATTCATGCATCGATACTTCTAAACAAGTTCCTACAGTGACATC
TTTGGGCACAATGCTAGAACCACTA
Found at i:11061 original size:16 final size:16
Alignment explanation
Indices: 11040--11081 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 16
11030 TGGTAAAACA
11040 AATAAAATGCAGA-GAC
1 AATAAAATGCA-ATGAC
11056 AATAAAAATGCAATGAC
1 AAT-AAAATGCAATGAC
11073 AATTAAAAT
1 AA-TAAAAT
11082 AAATACATGC
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
16 4 0.17
17 18 0.78
18 1 0.04
ACGTcount: A:0.60, C:0.10, G:0.12, T:0.19
Consensus pattern (16 bp):
AATAAAATGCAATGAC
Found at i:27011 original size:72 final size:72
Alignment explanation
Indices: 26896--27114 Score: 240
Period size: 72 Copynumber: 3.0 Consensus size: 72
26886 AGTTGAATTA
* * * * * * * * *
26896 CATAAACCTATATAAGCTGACGAGTGTAAATGTGTGCAAGCTGACGAGCATAAACGTATATAAGC
1 CATAAACATATACAAGATGACGAGCGTAAACGTATACAAGCTGACGAGCGTAAACGTATATAAGT
26961 TGACGAG
66 TGACGAG
* * * * * **
26968 CATAAACATGTGCAAGATGATGAGCGTAAACGTATATAAGCTGACGAGCGTAAACGTGTGCAAGT
1 CATAAACATATACAAGATGACGAGCGTAAACGTATACAAGCTGACGAGCGTAAACGTATATAAGT
27033 TGACGAG
66 TGACGAG
* * * * *
27040 CATAAACATATATAAGCTGACGAGCGTAAACGTGTGCAAGCTGACAAGCGTAAACGTATATAAGT
1 CATAAACATATACAAGATGACGAGCGTAAACGTATACAAGCTGACGAGCGTAAACGTATATAAGT
*
27105 TGACAAG
66 TGACGAG
27112 CAT
1 CAT
27115 CAACGTGTAT
Statistics
Matches: 118, Mismatches: 29, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
72 118 1.00
ACGTcount: A:0.38, C:0.16, G:0.24, T:0.21
Consensus pattern (72 bp):
CATAAACATATACAAGATGACGAGCGTAAACGTATACAAGCTGACGAGCGTAAACGTATATAAGT
TGACGAG
Found at i:27120 original size:48 final size:48
Alignment explanation
Indices: 26896--27122 Score: 301
Period size: 48 Copynumber: 4.7 Consensus size: 48
26886 AGTTGAATTA
* ** *
26896 CATAAACCTATATAAGCTGACGAGTGTAAATGTGTGCAAGCTGACGAG
1 CATAAACGTATATAAGCTGACGAGCATAAACGTGTGCAAGCTGACGAG
* * *
26944 CATAAACGTATATAAGCTGACGAGCATAAACATGTGCAAGATGATGAG
1 CATAAACGTATATAAGCTGACGAGCATAAACGTGTGCAAGCTGACGAG
* * *
26992 CGTAAACGTATATAAGCTGACGAGCGTAAACGTGTGCAAGTTGACGAG
1 CATAAACGTATATAAGCTGACGAGCATAAACGTGTGCAAGCTGACGAG
* * *
27040 CATAAACATATATAAGCTGACGAGCGTAAACGTGTGCAAGCTGACAAG
1 CATAAACGTATATAAGCTGACGAGCATAAACGTGTGCAAGCTGACGAG
* * * *
27088 CGTAAACGTATATAAGTTGACAAGCATCAACGTGT
1 CATAAACGTATATAAGCTGACGAGCATAAACGTGT
27123 ATAAGTAGAA
Statistics
Matches: 157, Mismatches: 22, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
48 157 1.00
ACGTcount: A:0.37, C:0.17, G:0.24, T:0.22
Consensus pattern (48 bp):
CATAAACGTATATAAGCTGACGAGCATAAACGTGTGCAAGCTGACGAG
Found at i:27128 original size:24 final size:24
Alignment explanation
Indices: 26898--27127 Score: 199
Period size: 24 Copynumber: 9.6 Consensus size: 24
26888 TTGAATTACA
* *
26898 TAAACCTATATAAGCTGACGAGTG
1 TAAACGTATATAAGCTGACGAGCG
* * ** *
26922 TAAATGTGTGCAAGCTGACGAGCA
1 TAAACGTATATAAGCTGACGAGCG
*
26946 TAAACGTATATAAGCTGACGAGCA
1 TAAACGTATATAAGCTGACGAGCG
* * ** * *
26970 TAAACATGTGCAAGATGATGAGCG
1 TAAACGTATATAAGCTGACGAGCG
26994 TAAACGTATATAAGCTGACGAGCG
1 TAAACGTATATAAGCTGACGAGCG
* ** * *
27018 TAAACGTGTGCAAGTTGACGAGCA
1 TAAACGTATATAAGCTGACGAGCG
*
27042 TAAACATATATAAGCTGACGAGCG
1 TAAACGTATATAAGCTGACGAGCG
* ** *
27066 TAAACGTGTGCAAGCTGACAAGCG
1 TAAACGTATATAAGCTGACGAGCG
* * *
27090 TAAACGTATATAAGTTGACAAGCA
1 TAAACGTATATAAGCTGACGAGCG
* *
27114 TCAACGTGTATAAG
1 TAAACGTATATAAG
27128 TAGAAGTGCA
Statistics
Matches: 159, Mismatches: 47, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
24 159 1.00
ACGTcount: A:0.38, C:0.16, G:0.24, T:0.22
Consensus pattern (24 bp):
TAAACGTATATAAGCTGACGAGCG
Found at i:27142 original size:72 final size:72
Alignment explanation
Indices: 26921--27142 Score: 232
Period size: 72 Copynumber: 3.1 Consensus size: 72
26911 GCTGACGAGT
* * * **
26921 GTAAATGTGTGCAAGCTGACGAGCATAAACGTATATAAGCTGACGAGCATAAACATGTGCAAG-A
1 GTAAACGTGTGCAAGCTGACGAGCGTAAACGTATATAAGTTGACGAGCATAAACATGTATAAGTA
*
26985 TGATGAGC
66 -GAAGAGC
* ** * ** *
26993 GTAAACGTATATAAGCTGACGAGCGTAAACGTGTGCAAGTTGACGAGCATAAACATATATAAGCT
1 GTAAACGTGTGCAAGCTGACGAGCGTAAACGTATATAAGTTGACGAGCATAAACATGTATAAG-T
*
27058 -GACGAGC
65 AGAAGAGC
* * * *
27065 GTAAACGTGTGCAAGCTGACAAGCGTAAACGTATATAAGTTGACAAGCATCAACGTGTATAAGTA
1 GTAAACGTGTGCAAGCTGACGAGCGTAAACGTATATAAGTTGACGAGCATAAACATGTATAAGTA
*
27130 GAAGTGC
66 GAAGAGC
*
27137 ATAAAC
1 GTAAAC
27143 TAAATGAAAT
Statistics
Matches: 120, Mismatches: 27, Indels: 6
0.78 0.18 0.04
Matches are distributed among these distances:
71 1 0.01
72 119 0.99
ACGTcount: A:0.38, C:0.16, G:0.25, T:0.21
Consensus pattern (72 bp):
GTAAACGTGTGCAAGCTGACGAGCGTAAACGTATATAAGTTGACGAGCATAAACATGTATAAGTA
GAAGAGC
Found at i:28211 original size:20 final size:20
Alignment explanation
Indices: 28186--28223 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
28176 GGAACAAAAT
*
28186 TTACAATAAAACAAATTAAC
1 TTACAAGAAAACAAATTAAC
28206 TTACAAGAAAACAAATTA
1 TTACAAGAAAACAAATTA
28224 TCTTGGCTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.61, C:0.13, G:0.03, T:0.24
Consensus pattern (20 bp):
TTACAAGAAAACAAATTAAC
Done.