Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002843.1 Kokia drynarioides strain JFW-HI SEQ_115231, 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: 25425
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.34
Found at i:2056 original size:82 final size:81
Alignment explanation
Indices: 1929--2201 Score: 291
Period size: 82 Copynumber: 3.4 Consensus size: 81
1919 GGGATTTTAT
* * * * * * * * *
1929 CATAAACGCCGCTATTGTTCTGACCTTTAGCGGCGCTTGACCATAAACGCCGCTATTGCTCTAAC
1 CATAAGCGCCGCTATTGCTATGACCTTTAGCGGCGCTT-TCCATAAGCGTCACTATTGCTATGAC
* *
1994 CTTTAGCGACGCTTGCC
65 ATTTAGCGGCGCTTGCC
* * *
2011 CATAAGCACCGCTATTGCTATGACCTTTAGCGGCACTTTCTCATAAGCGTTACTATT-CTATGAC
1 CATAAGCGCCGCTATTGCTATGACCTTTAGCGGCGCTTTC-CATAAGCGTCACTATTGCTATGAC
* * *
2075 TTTTAGCGGCGCTTTCT
65 ATTTAGCGGCGCTTGCC
* * *
2092 CATAAGCGCCGCTATTACTATGACTTTTAACGGCGCTTTCACATAAGCGTCACTATTGCTATGAC
1 CATAAGCGCCGCTATTGCTATGACCTTTAGCGGCGCTTTC-CATAAGCGTCACTATTGCTATGAC
*
2157 ATTTAGTGGCGC-TGTCC
65 ATTTAGCGGCGCTTG-CC
*
2174 CATAAGCGCCGCTATTGCTCT-ACCTTTA
1 CATAAGCGCCGCTATTGCTATGACCTTTA
2202 CCTTTTGCGT
Statistics
Matches: 158, Mismatches: 30, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
81 76 0.48
82 82 0.52
ACGTcount: A:0.22, C:0.28, G:0.18, T:0.32
Consensus pattern (81 bp):
CATAAGCGCCGCTATTGCTATGACCTTTAGCGGCGCTTTCCATAAGCGTCACTATTGCTATGACA
TTTAGCGGCGCTTGCC
Found at i:2083 original size:40 final size:41
Alignment explanation
Indices: 1940--2192 Score: 213
Period size: 41 Copynumber: 6.2 Consensus size: 41
1930 ATAAACGCCG
* * * * * * *
1940 CTATTGTTCTGACCTTTAGCGGCGCTTGAC-CATAAACGCCG
1 CTATTGCTATGACTTTTAGCGGCGCTT-TCTCATAAGCGTCA
* * * * * * ** *
1981 CTATTGCTCTAACCTTTAGCGACGCTTGCCCATAAGCACCG
1 CTATTGCTATGACTTTTAGCGGCGCTTTCTCATAAGCGTCA
* * *
2022 CTATTGCTATGACCTTTAGCGGCACTTTCTCATAAGCGTTA
1 CTATTGCTATGACTTTTAGCGGCGCTTTCTCATAAGCGTCA
* *
2063 CTATT-CTATGACTTTTAGCGGCGCTTTCTCATAAGCGCCG
1 CTATTGCTATGACTTTTAGCGGCGCTTTCTCATAAGCGTCA
* * *
2103 CTATTACTATGACTTTTAACGGCGCTTTCACATAAGCGTCA
1 CTATTGCTATGACTTTTAGCGGCGCTTTCTCATAAGCGTCA
* * * * * *
2144 CTATTGCTATGACATTTAGTGGCGCTGTCCCATAAGCGCCG
1 CTATTGCTATGACTTTTAGCGGCGCTTTCTCATAAGCGTCA
2185 CTATTGCT
1 CTATTGCT
2193 CTACCTTTAC
Statistics
Matches: 177, Mismatches: 33, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
40 36 0.20
41 141 0.80
ACGTcount: A:0.21, C:0.28, G:0.19, T:0.32
Consensus pattern (41 bp):
CTATTGCTATGACTTTTAGCGGCGCTTTCTCATAAGCGTCA
Found at i:2113 original size:81 final size:82
Alignment explanation
Indices: 1981--2189 Score: 267
Period size: 81 Copynumber: 2.6 Consensus size: 82
1971 ATAAACGCCG
* * * * * * * *
1981 CTATTGCTCTAACCTTTAGCGACGCTTGCCCATAAGCACCGCTATTGCTATGACCTTTAGCGGCA
1 CTATTGCTATGACATTTAGCGGCGCTTTCCCATAAGCGCCGCTATTACTATGACCTTTAACGGCA
* *
2046 CTTTCTCATAAGCGTTA
66 CTTTCACATAAGCGTCA
* * * *
2063 CTATT-CTATGACTTTTAGCGGCGCTTTCTCATAAGCGCCGCTATTACTATGACTTTTAACGGCG
1 CTATTGCTATGACATTTAGCGGCGCTTTCCCATAAGCGCCGCTATTACTATGACCTTTAACGGCA
2127 CTTTCACATAAGCGTCA
66 CTTTCACATAAGCGTCA
* *
2144 CTATTGCTATGACATTTAGTGGCGCTGTCCCATAAGCGCCGCTATT
1 CTATTGCTATGACATTTAGCGGCGCTTTCCCATAAGCGCCGCTATT
2190 GCTCTACCTT
Statistics
Matches: 109, Mismatches: 17, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
81 68 0.62
82 41 0.38
ACGTcount: A:0.22, C:0.27, G:0.18, T:0.33
Consensus pattern (82 bp):
CTATTGCTATGACATTTAGCGGCGCTTTCCCATAAGCGCCGCTATTACTATGACCTTTAACGGCA
CTTTCACATAAGCGTCA
Found at i:2189 original size:122 final size:123
Alignment explanation
Indices: 1929--2201 Score: 282
Period size: 122 Copynumber: 2.2 Consensus size: 123
1919 GGGATTTTAT
* * * * *
1929 CATAAACGCCGCTATTGTTCTGACCTTTAGCGGCGCTTGACCATAAACGCCGCTATTGCTCTAAC
1 CATAAGCGCCGCTATTGCTATGACCTTTAGCGGCGCTTGACCATAAACGCCGCTATTACTATAAC
* * * * * *
1994 CTTTAGCGACGCTTGCCCATAAGCACCGCTATTGCTATGACCTTTAGCGGCACTTTCT
66 CTTTAACGACGCTTGCACATAAGCACCACTATTGCTATGACATTTAGCGGCACTGTCC
*** * * * *
2052 CATAAGCGTTACTATT-CTATGACTTTTAGCGGCGCTT-TCTCATAAGCGCCGCTATTACTATGA
1 CATAAGCGCCGCTATTGCTATGACCTTTAGCGGCGCTTGAC-CATAAACGCCGCTATTACTATAA
* * * ** * *
2115 CTTTTAACGGCGCTTTCACATAAGCGTCACTATTGCTATGACATTTAGTGGCGCTGTCC
65 CCTTTAACGACGCTTGCACATAAGCACCACTATTGCTATGACATTTAGCGGCACTGTCC
*
2174 CATAAGCGCCGCTATTGCTCT-ACCTTTA
1 CATAAGCGCCGCTATTGCTATGACCTTTA
2202 CCTTTTGCGT
Statistics
Matches: 118, Mismatches: 30, Indels: 5
0.77 0.20 0.03
Matches are distributed among these distances:
121 1 0.01
122 102 0.86
123 15 0.13
ACGTcount: A:0.22, C:0.28, G:0.18, T:0.32
Consensus pattern (123 bp):
CATAAGCGCCGCTATTGCTATGACCTTTAGCGGCGCTTGACCATAAACGCCGCTATTACTATAAC
CTTTAACGACGCTTGCACATAAGCACCACTATTGCTATGACATTTAGCGGCACTGTCC
Found at i:6178 original size:21 final size:21
Alignment explanation
Indices: 6152--6282 Score: 86
Period size: 21 Copynumber: 6.2 Consensus size: 21
6142 TGTGAGGATG
*
6152 ATTTAGGGTTTATGGTTTATA
1 ATTTAGGGTTTATGGTTTATC
**
6173 ATTTAGTATTTATGGTTTAGT-
1 ATTTAGGGTTTATGGTTTA-TC
* *
6194 GTTTAGGGTTT-GGTGTTTATC
1 ATTTAGGGTTTATG-GTTTATC
* *** **
6215 ATTTATGGTTTATCACTTAGG
1 ATTTAGGGTTTATGGTTTATC
* * *
6236 GTTTAGGGTTTATAGCTTATC
1 ATTTAGGGTTTATGGTTTATC
* *
6257 ACTTAGGGTTTAGGGTTTATC
1 ATTTAGGGTTTATGGTTTATC
6278 ATTTA
1 ATTTA
6283 AATATTAGTG
Statistics
Matches: 80, Mismatches: 26, Indels: 8
0.70 0.23 0.07
Matches are distributed among these distances:
20 2 0.03
21 77 0.96
22 1 0.01
ACGTcount: A:0.21, C:0.05, G:0.24, T:0.50
Consensus pattern (21 bp):
ATTTAGGGTTTATGGTTTATC
Found at i:6209 original size:14 final size:14
Alignment explanation
Indices: 6174--6212 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
6164 TGGTTTATAA
* *
6174 TTTAGTATTTATGG
1 TTTAGTGTTTAGGG
6188 TTTAGTGTTTAGGG
1 TTTAGTGTTTAGGG
*
6202 TTTGGTGTTTA
1 TTTAGTGTTTA
6213 TCATTTATGG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.15, C:0.00, G:0.28, T:0.56
Consensus pattern (14 bp):
TTTAGTGTTTAGGG
Found at i:6239 original size:28 final size:28
Alignment explanation
Indices: 6208--6269 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
6198 AGGGTTTGGT
* * *
6208 GTTTATCATTTATGGTTTATCACTTAGG
1 GTTTAGCATTTATAGCTTATCACTTAGG
**
6236 GTTTAGGGTTTATAGCTTATCACTTAGG
1 GTTTAGCATTTATAGCTTATCACTTAGG
6264 GTTTAG
1 GTTTAG
6270 GGTTTATCAT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.21, C:0.10, G:0.23, T:0.47
Consensus pattern (28 bp):
GTTTAGCATTTATAGCTTATCACTTAGG
Found at i:6290 original size:28 final size:28
Alignment explanation
Indices: 6259--6339 Score: 92
Period size: 28 Copynumber: 2.9 Consensus size: 28
6249 AGCTTATCAC
*
6259 TTAGGGTTTAGGGTTTATCATTTA-AAT
1 TTAGGGTTTAAGGTTTATCATTTAGAAT
* * **
6286 ATTAGTGTTTAAGGTTTTTCATTTAGGGT
1 -TTAGGGTTTAAGGTTTATCATTTAGAAT
*
6315 TTAAGGTTTAAGGTTTATCATTTAG
1 TTAGGGTTTAAGGTTTATCATTTAG
6340 GGTTTAAAAA
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
28 43 0.98
29 1 0.02
ACGTcount: A:0.25, C:0.04, G:0.22, T:0.49
Consensus pattern (28 bp):
TTAGGGTTTAAGGTTTATCATTTAGAAT
Found at i:6310 original size:14 final size:14
Alignment explanation
Indices: 6293--6345 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 14
6283 AATATTAGTG
*
6293 TTTAAGGTTTTTCA
1 TTTAAGGTTTATCA
* ***
6307 TTTAGGGTTTAAGG
1 TTTAAGGTTTATCA
6321 TTTAAGGTTTATCA
1 TTTAAGGTTTATCA
*
6335 TTTAGGGTTTA
1 TTTAAGGTTTA
6346 AAAATACTTT
Statistics
Matches: 29, Mismatches: 10, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.23, C:0.04, G:0.23, T:0.51
Consensus pattern (14 bp):
TTTAAGGTTTATCA
Found at i:6340 original size:28 final size:28
Alignment explanation
Indices: 6292--6346 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
6282 AAATATTAGT
*
6292 GTTTAAGGTTTTTCATTTAGGGTTTAAG
1 GTTTAAGGTTTATCATTTAGGGTTTAAG
6320 GTTTAAGGTTTATCATTTAGGGTTTAA
1 GTTTAAGGTTTATCATTTAGGGTTTAA
6347 AAATACTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.24, C:0.04, G:0.24, T:0.49
Consensus pattern (28 bp):
GTTTAAGGTTTATCATTTAGGGTTTAAG
Found at i:14025 original size:28 final size:28
Alignment explanation
Indices: 13971--14026 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
13961 GATAAGATTG
*
13971 TATAAAATAAATTTAATTTTGACTTTAT
1 TATAAAATAAATTTAATTTTGAATTTAT
*
13999 TATAAAATAAATTTAATTTTTAATTTAT
1 TATAAAATAAATTTAATTTTGAATTTAT
14027 AGATAAGATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (28 bp):
TATAAAATAAATTTAATTTTGAATTTAT
Found at i:15855 original size:22 final size:22
Alignment explanation
Indices: 15799--15860 Score: 63
Period size: 25 Copynumber: 2.7 Consensus size: 22
15789 TTTAAAAATT
15799 ATAAAAATATA-AATTATTAAA
1 ATAAAAATATATAATTATTAAA
** *
15820 ATAACGAAATTATATTTTTATTATA
1 ATAA--AAA-TATATAATTATTAAA
15845 ATAAAAATATATAATT
1 ATAAAAATATATAATT
15861 TAATTCCGTC
Statistics
Matches: 32, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
21 4 0.12
22 7 0.22
23 6 0.19
24 4 0.12
25 11 0.34
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (22 bp):
ATAAAAATATATAATTATTAAA
Found at i:19211 original size:43 final size:43
Alignment explanation
Indices: 19102--19350 Score: 193
Period size: 43 Copynumber: 5.8 Consensus size: 43
19092 GTTTATGAGG
* * * **
19102 AAAAACGTCGCT--AGAACATGATTTTTAGCGGCG-TTTTCCC
1 AAAAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTACCCC
* * * *
19142 ATAAACGCCGCTAAAAAACATTGTCTTTAGCGACGCTTACCCC
1 AAAAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTACCCC
* * *
19185 AAAAACACCGCTAAAGGACATGGTCTTTAGCGGCGCTTCTACCAC
1 AAAAACGCCGCTAAAGAACATGGTCTTTAGCGGCGC-T-TACCCC
** * * * *
19230 AAACCCTGCCGCTAAAGAACATGATCTTTAGCGGTG-TTTCTCC
1 AAAAAC-GCCGCTAAAGAACATGGTCTTTAGCGGCGCTTACCCC
* * *
19273 AACAAACTCCGCTAAAGAATATGGTCTTTAGCGGTGCTT-CTCCC
1 AA-AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTAC-CCC
* * **
19317 ACAAACGCCGCTGAAGAACATAATCTTTAGCGGC
1 AAAAACGCCGCTAAAGAACATGGTCTTTAGCGGC
19351 ACTTTTCTCA
Statistics
Matches: 162, Mismatches: 38, Indels: 15
0.75 0.18 0.07
Matches are distributed among these distances:
40 10 0.06
42 16 0.10
43 93 0.57
44 9 0.06
45 9 0.06
46 25 0.15
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.24
Consensus pattern (43 bp):
AAAAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTACCCC
Found at i:19285 original size:132 final size:131
Alignment explanation
Indices: 19114--19350 Score: 305
Period size: 132 Copynumber: 1.8 Consensus size: 131
19104 AAACGTCGCT
* * * *
19114 AGAACATGATTTTTAGCGGCGTTTTCCCATAAACGCCGCTAAAAAACATTGTCTTTAGCGACGCT
1 AGAACATGATCTTTAGCGGCGTTTTCCAACAAACGCCGCTAAAAAACATGGTCTTTAGCGACGCT
* **
19179 TAC-CCCAAAAACACCGCTAAAGGACATGGTCTTTAGCGGCGCTTCTACCACAAACCCTGCCGCT
66 T-CTCCCAAAAACACCGCTAAAGAACATAATCTTTAGCGGCGCTTCTACCACAAACCCTGCCGCT
19243 AA
130 AA
* * * * **
19245 AGAACATGATCTTTAGCGGTGTTTCTCCAACAAACTCCGCTAAAGAATATGGTCTTTAGCGGTGC
1 AGAACATGATCTTTAGCGGCGTTT-TCCAACAAACGCCGCTAAAAAACATGGTCTTTAGCGACGC
* * *
19310 TTCTCCCACAAACGCCGCTGAAGAACATAATCTTTAGCGGC
65 TTCTCCCAAAAACACCGCTAAAGAACATAATCTTTAGCGGC
19351 ACTTTTCTCA
Statistics
Matches: 88, Mismatches: 16, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
131 23 0.26
132 65 0.74
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.25
Consensus pattern (131 bp):
AGAACATGATCTTTAGCGGCGTTTTCCAACAAACGCCGCTAAAAAACATGGTCTTTAGCGACGCT
TCTCCCAAAAACACCGCTAAAGAACATAATCTTTAGCGGCGCTTCTACCACAAACCCTGCCGCTA
A
Found at i:19374 original size:86 final size:88
Alignment explanation
Indices: 19114--19349 Score: 241
Period size: 89 Copynumber: 2.7 Consensus size: 88
19104 AAACGTCGCT
* * * * * * ** **
19114 AGAACATGATTTTTAGCGGCG-TTTTCCCATAAA-C-GCCGCTAAAAAACATTGTCTTTAGCGAC
1 AGAACATGGTCTTTAGCGGCGCTTCTACCACAAACCTGCCGCTAAAGAACATAATCTTTAGCGGT
* * *
19176 GCTTACCCCAA-AAACACCGCTAA
66 G-TTTCTCCAACAAACTCCGCTAA
* *
19199 AGGACATGGTCTTTAGCGGCGCTTCTACCACAAACCCTGCCGCTAAAGAACATGATCTTTAGCGG
1 AGAACATGGTCTTTAGCGGCGCTTCTACCACAAA-CCTGCCGCTAAAGAACATAATCTTTAGCGG
19264 TGTTTCTCCAACAAACTCCGCTAA
65 TGTTTCTCCAACAAACTCCGCTAA
* * * *
19288 AGAATATGGTCTTTAGCGGTGCTTCTCCCACAAA-C-GCCGCTGAAGAACATAATCTTTAGCGG
1 AGAACATGGTCTTTAGCGGCGCTTCTACCACAAACCTGCCGCTAAAGAACATAATCTTTAGCGG
19350 CACTTTTCTC
Statistics
Matches: 126, Mismatches: 20, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
85 18 0.14
86 34 0.27
87 1 0.01
88 8 0.06
89 65 0.52
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.25
Consensus pattern (88 bp):
AGAACATGGTCTTTAGCGGCGCTTCTACCACAAACCTGCCGCTAAAGAACATAATCTTTAGCGGT
GTTTCTCCAACAAACTCCGCTAA
Done.