Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009915.1 Kokia drynarioides strain JFW-HI SEQ_124655, 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: 7245
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Found at i:162 original size:6 final size:6
Alignment explanation
Indices: 153--238 Score: 72
Period size: 6 Copynumber: 14.5 Consensus size: 6
143 ATTTGTTTAA
* *
153 AAATTT AAATTT -ATTTT AAATTT AAATTT -ACTTT AAAATTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT -AAATTT AAATTT
* * *
200 -AATTT AAGTTT AAAATT -ATTTT CAAATTT AAAGTTT AAA
1 AAATTT AAATTT AAATTT AAATTT -AAATTT AAA-TTT AAA
239 ATAAATAAAA
Statistics
Matches: 63, Mismatches: 10, Indels: 13
0.73 0.12 0.15
Matches are distributed among these distances:
5 16 0.25
6 33 0.52
7 14 0.22
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (6 bp):
AAATTT
Found at i:162 original size:18 final size:17
Alignment explanation
Indices: 121--236 Score: 119
Period size: 17 Copynumber: 6.6 Consensus size: 17
111 CCATACTCTC
121 TTTAAATTTATTTTAAAA
1 TTTAAATTTA-TTTAAAA
*
139 -TTAAATTTGTTTAAAAA
1 TTTAAATTTATTT-AAAA
*
156 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTAAAA
173 TTTAAATTTACTTTAAAA
1 TTTAAATTTA-TTTAAAA
*
191 TTTAAATTTAATTT-AAG
1 TTTAAATTT-ATTTAAAA
* *
208 TTTAAAATTATTTTCAAA
1 TTTAAATTTA-TTTAAAA
226 TTTAAAGTTTA
1 TTTAAA-TTTA
237 AAATAAATAA
Statistics
Matches: 83, Mismatches: 8, Indels: 13
0.80 0.08 0.12
Matches are distributed among these distances:
16 4 0.05
17 38 0.46
18 37 0.45
19 4 0.05
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.53
Consensus pattern (17 bp):
TTTAAATTTATTTAAAA
Found at i:167 original size:35 final size:35
Alignment explanation
Indices: 121--236 Score: 135
Period size: 35 Copynumber: 3.3 Consensus size: 35
111 CCATACTCTC
*
121 TTTAAATTTATTTTAAAATTAAATTT-GTTTAAAAA
1 TTTAAATTTATTTTAAAATTAAATTTACTTT-AAAA
*
156 TTTAAATTTATTTTAAATTTAAATTTACTTTAAAA
1 TTTAAATTTATTTTAAAATTAAATTTACTTTAAAA
* ** * * *
191 TTTAAATTTAATTTAAGTTTAAAATTATTTTCAAA
1 TTTAAATTTATTTTAAAATTAAATTTACTTTAAAA
226 TTTAAAGTTTA
1 TTTAAA-TTTA
237 AAATAAATAA
Statistics
Matches: 72, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
35 65 0.90
36 7 0.10
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.53
Consensus pattern (35 bp):
TTTAAATTTATTTTAAAATTAAATTTACTTTAAAA
Found at i:203 original size:11 final size:11
Alignment explanation
Indices: 154--212 Score: 57
Period size: 11 Copynumber: 5.2 Consensus size: 11
144 TTTGTTTAAA
154 AATTTAAATTT
1 AATTTAAATTT
*
165 ATTTTAAATTT
1 AATTTAAATTT
*
176 AAATTT-ACTTT
1 -AATTTAAATTT
187 AAAATTTAAATTT
1 --AATTTAAATTT
*
200 AATTTAAGTTT
1 AATTTAAATTT
211 AA
1 AA
213 AATTATTTTC
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
11 26 0.65
12 10 0.25
13 4 0.10
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (11 bp):
AATTTAAATTT
Found at i:1012 original size:15 final size:15
Alignment explanation
Indices: 992--1033 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
982 ATAAATGTTT
992 TGATATTAATAATAA
1 TGATATTAATAATAA
*
1007 TGATATTAATAATTA
1 TGATATTAATAATAA
*
1022 TTA-ATTAATAAT
1 TGATATTAATAAT
1034 TATTAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 9 0.36
15 16 0.64
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (15 bp):
TGATATTAATAATAA
Found at i:1030 original size:14 final size:14
Alignment explanation
Indices: 996--1039 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
986 ATGTTTTGAT
* *
996 ATTAATAATAATGA
1 ATTAATAATTATTA
1010 TATTAATAATTATTA
1 -ATTAATAATTATTA
1025 ATTAATAATTATTA
1 ATTAATAATTATTA
1039 A
1 A
1040 AAAAGGGGGA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
14 15 0.56
15 12 0.44
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (14 bp):
ATTAATAATTATTA
Found at i:2328 original size:30 final size:29
Alignment explanation
Indices: 2236--2643 Score: 235
Period size: 29 Copynumber: 13.6 Consensus size: 29
2226 TCCCTAAACT
* ** *
2236 TTCCAAAAATCCCATTTTAACCCTAAACT
1 TTCCAAAAATCCCATTTTTACCCCGAACC
* *
2265 TTCCAAAATTACCA-TTTTACCCTCGAA-C
1 TTCCAAAAATCCCATTTTTACCC-CGAACC
*
2293 TTCTAAAAATCCCATTTTTGACCCCGAACC
1 TTCCAAAAATCCCATTTTT-ACCCCGAACC
* **
2323 TTCTAAAAATTAC-TATTTTACCCTCGAA-C
1 TTCCAAAAATCCCAT-TTTTACCC-CGAACC
2352 TTCCAAAAATCCCATTTTTTACCATTTTACCCCCGAA-C
1 TTCCAAAAATCCCA-----T----TTTTA-CCCCGAACC
* *
2390 TTCCAAAAATCCCATTTTTGACCACGAAAC
1 TTCCAAAAATCCCATTTTT-ACCCCGAACC
* * * *
2420 TTCTAAAAATTACCATTTTT-CCCCTAAAC
1 TTCCAAAAA-TCCCATTTTTACCCCGAACC
2449 TTCCAAAAATCCCATTTTTGACCCCGAACC
1 TTCCAAAAATCCCATTTTT-ACCCCGAACC
* * * *
2479 TTCTAAAATTACCA-TTTGACCCCCGAACC
1 TTCCAAAAATCCCATTTTTA-CCCCGAACC
* * *
2508 TTCTAAAAATTACCA-TTTTACCCCCGAA-G
1 TTCCAAAAA-TCCCATTTTTA-CCCCGAACC
*
2537 TTCCAAAAATCCCATTTTTGACCTCGAACC
1 TTCCAAAAATCCCATTTTT-ACCCCGAACC
* * * *
2567 TTCTGAAAATTACCA-TTTTACCTTCGAA-C
1 TTC-CAAAAATCCCATTTTTACC-CCGAACC
**
2596 TTCCAAAAATCCCATTTTTTATTCCGAACC
1 TTCCAAAAATCCCA-TTTTTACCCCGAACC
* *
2626 TTCCAAAACTACCATTTT
1 TTCCAAAAATCCCATTTT
2644 GCCCCCGTGC
Statistics
Matches: 303, Mismatches: 45, Indels: 62
0.74 0.11 0.15
Matches are distributed among these distances:
28 40 0.13
29 116 0.38
30 100 0.33
31 17 0.06
33 1 0.00
35 1 0.00
38 25 0.08
39 3 0.01
ACGTcount: A:0.32, C:0.31, G:0.04, T:0.33
Consensus pattern (29 bp):
TTCCAAAAATCCCATTTTTACCCCGAACC
Found at i:2335 original size:59 final size:59
Alignment explanation
Indices: 2236--2643 Score: 309
Period size: 59 Copynumber: 6.8 Consensus size: 59
2226 TCCCTAAACT
* ** * *
2236 TTCCAAAAATCCCA-TTTTAACCCTAAACTTTC-CAAAATTACCATTTTACCCTCGAAC
1 TTCCAAAAATCCCATTTTTGACCCCGAACCTTCTAAAAATTACCATTTTACCCTCGAAC
* *
2293 TTCTAAAAATCCCATTTTTGACCCCGAACCTTCTAAAAATTACTATTTTACCCTCGAAC
1 TTCCAAAAATCCCATTTTTGACCCCGAACCTTCTAAAAATTACCATTTTACCCTCGAAC
* * * *
2352 TTCCAAAAATCCCATTTTTTACCATTTTACCCCCGAA-CTTCCAAAAA-TCCCATTTTTGA-CCA
1 TTCCAAAAATCCCA----TT----TTTGA-CCCCGAACCTTCTAAAAATTACCA-TTTT-ACCCT
2414 CGAAAC
55 CG-AAC
* * * * * *
2420 TTCTAAAAATTACCATTTTT--CCCCTAAACTTCCAAAAA-TCCCATTTTTGACCC-CGAACC
1 TTCCAAAAA-TCCCATTTTTGACCCCGAACCTTCTAAAAATTACCA-TTTT-ACCCTCGAA-C
* * * * *
2479 TTCTAAAATTACCA--TTTGACCCCCGAACCTTCTAAAAATTACCATTTTACCCCCGAAG
1 TTCCAAAAATCCCATTTTTGA-CCCCGAACCTTCTAAAAATTACCATTTTACCCTCGAAC
* * *
2537 TTCCAAAAATCCCATTTTTGACCTCGAACCTTCTGAAAATTACCATTTTACCTTCGAAC
1 TTCCAAAAATCCCATTTTTGACCCCGAACCTTCTAAAAATTACCATTTTACCCTCGAAC
* ** * *
2596 TTCCAAAAATCCCATTTTTTATTCCGAACCTTC-CAAAACTACCATTTT
1 TTCCAAAAATCCCATTTTTGACCCCGAACCTTCTAAAAATTACCATTTT
2644 GCCCCCGTGC
Statistics
Matches: 290, Mismatches: 36, Indels: 49
0.77 0.10 0.13
Matches are distributed among these distances:
56 3 0.01
57 13 0.04
58 55 0.19
59 154 0.53
60 11 0.04
61 3 0.01
63 2 0.01
65 2 0.01
66 3 0.01
67 21 0.07
68 19 0.07
69 4 0.01
ACGTcount: A:0.32, C:0.31, G:0.04, T:0.33
Consensus pattern (59 bp):
TTCCAAAAATCCCATTTTTGACCCCGAACCTTCTAAAAATTACCATTTTACCCTCGAAC
Found at i:2389 original size:38 final size:38
Alignment explanation
Indices: 2332--2413 Score: 137
Period size: 38 Copynumber: 2.2 Consensus size: 38
2322 CTTCTAAAAA
* *
2332 TTACTATTTTACCCTCGAACTTCCAAAAATCCCATTTT
1 TTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTT
2370 TTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTT
1 TTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTT
*
2408 TGACCA
1 TTACCA
2414 CGAAACTTCT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.29, C:0.32, G:0.04, T:0.35
Consensus pattern (38 bp):
TTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTT
Found at i:2398 original size:97 final size:96
Alignment explanation
Indices: 2273--2555 Score: 345
Period size: 97 Copynumber: 3.0 Consensus size: 96
2263 CTTTCCAAAA
* *
2273 TTACCATTTTACCCTCGAACTTCTAAAAATCCCATTTTTGACCCCGAACCTTCTAAAAATTACTA
1 TTACCATTTTACCCCCGAACTTCTAAAAATCCCATTTTTGACCCCGAACCTTCTAAAAATTACCA
2338 TTTTACCCTCGAACTTCCAAAAATCCCATTTT
66 TTTTACCC-CGAACTTCCAAAAATCCCATTTT
* * *
2370 TTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCACGAAACTTCTAAAAATTACCA
1 TTACCATTTTACCCCCGAACTTCTAAAAATCCCATTTTTGACCCCGAACCTTCTAAAAATTACCA
* *
2435 TTTTTCCCCTAAACTTCCAAAAATCCCA----
66 TTTTACCCC-GAACTTCCAAAAATCCCATTTT
* * *
2463 TT----TTTGA-CCCCGAACCTTCTAAAATTACCA--TTTGACCCCCGAACCTTCTAAAAATTAC
1 TTACCATTTTACCCCCGAA-CTTCTAAAAATCCCATTTTTGA-CCCCGAACCTTCTAAAAATTAC
*
2521 CATTTTACCCCCGAAGTTCCAAAAATCCCATTTT
64 CATTTTA-CCCCGAACTTCCAAAAATCCCATTTT
2555 T
1 T
2556 GACCTCGAAC
Statistics
Matches: 162, Mismatches: 16, Indels: 21
0.81 0.08 0.11
Matches are distributed among these distances:
87 5 0.03
88 49 0.30
89 20 0.12
92 1 0.01
93 2 0.01
96 1 0.01
97 84 0.52
ACGTcount: A:0.32, C:0.31, G:0.05, T:0.33
Consensus pattern (96 bp):
TTACCATTTTACCCCCGAACTTCTAAAAATCCCATTTTTGACCCCGAACCTTCTAAAAATTACCA
TTTTACCCCGAACTTCCAAAAATCCCATTTT
Found at i:2511 original size:88 final size:88
Alignment explanation
Indices: 2406--2614 Score: 280
Period size: 88 Copynumber: 2.4 Consensus size: 88
2396 AAATCCCATT
*
2406 TTTGA-CCACGAAACTTCTAAAAATTACCATTTTTCCCCTAAACTTCCAAAAATCCCATTTTTGA
1 TTTGACCCACG-AACTTCTAAAAATTACCATTTTTCCCCCAAACTTCCAAAAATCCCATTTTTGA
2470 CCCCGAACCTTCT-AAAATTACCA
65 CCCCGAACCTTCTGAAAATTACCA
* * * *
2493 TTTGACCCCCGAACCTTCTAAAAATTACCATTTTACCCCCGAAGTTCCAAAAATCCCATTTTTGA
1 TTTGACCCACGAA-CTTCTAAAAATTACCATTTTTCCCCCAAACTTCCAAAAATCCCATTTTTGA
*
2558 CCTCGAACCTTCTGAAAATTACCA
65 CCCCGAACCTTCTGAAAATTACCA
* ** * *
2582 TTTTACCTTCGAACTTCCAAAAA-TCCCATTTTT
1 TTTGACCCACGAACTTCTAAAAATTACCATTTTT
2615 TATTCCGAAC
Statistics
Matches: 107, Mismatches: 12, Indels: 6
0.86 0.10 0.05
Matches are distributed among these distances:
87 15 0.14
88 72 0.67
89 20 0.19
ACGTcount: A:0.32, C:0.30, G:0.06, T:0.32
Consensus pattern (88 bp):
TTTGACCCACGAACTTCTAAAAATTACCATTTTTCCCCCAAACTTCCAAAAATCCCATTTTTGAC
CCCGAACCTTCTGAAAATTACCA
Done.