Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007631.1 Kokia drynarioides strain JFW-HI SEQ_122262, 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: 10759
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Found at i:1556 original size:28 final size:27
Alignment explanation
Indices: 1520--1572 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
1510 ATAAGTGTCT
1520 AGTTCAGGTATCAAATTAGGTAAAAAAA
1 AGTTCAGGTATCAAATTAGG-AAAAAAA
* *
1548 AGTTTAGGTATCAAATTTGGAAAAA
1 AGTTCAGGTATCAAATTAGGAAAAA
1573 TATCAAGTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.47, C:0.06, G:0.19, T:0.28
Consensus pattern (27 bp):
AGTTCAGGTATCAAATTAGGAAAAAAA
Found at i:9008 original size:23 final size:23
Alignment explanation
Indices: 8982--9222 Score: 254
Period size: 23 Copynumber: 10.5 Consensus size: 23
8972 GTTATGATTC
*
8982 ATGTG-TTATATGCTTAAACATTA
1 ATGTGATT-TATGCTTAAATATTA
**
9005 ATGTGATTTGGGCTTAAATATTA
1 ATGTGATTTATGCTTAAATATTA
** ** * *
9028 ACATGATTTGGGCTGAAATATAA
1 ATGTGATTTATGCTTAAATATTA
*
9051 AAGTGATTTATGCTTAAATATTA
1 ATGTGATTTATGCTTAAATATTA
* *
9074 ATGTAATTTGTGCTTAAATATTA
1 ATGTGATTTATGCTTAAATATTA
* **
9097 GTACGATTTATGCTTAAA-AGTTA
1 ATGTGATTTATGCTTAAATA-TTA
*
9120 ATGTGATTTATAG-TTAAAGATTA
1 ATGTGATTTAT-GCTTAAATATTA
* *
9143 ATGTGATTTGTGCTTAAATGTTA
1 ATGTGATTTATGCTTAAATATTA
*
9166 ATATGATTTATGCTTAAATATTA
1 ATGTGATTTATGCTTAAATATTA
*
9189 ATGTGATGTATGCTTAAATATTA
1 ATGTGATTTATGCTTAAATATTA
9212 ATGTGATTTAT
1 ATGTGATTTAT
9223 TTGTAGATAG
Statistics
Matches: 180, Mismatches: 33, Indels: 10
0.81 0.15 0.04
Matches are distributed among these distances:
22 2 0.01
23 174 0.97
24 4 0.02
ACGTcount: A:0.35, C:0.05, G:0.17, T:0.44
Consensus pattern (23 bp):
ATGTGATTTATGCTTAAATATTA
Found at i:9105 original size:69 final size:69
Alignment explanation
Indices: 8982--9220 Score: 304
Period size: 69 Copynumber: 3.5 Consensus size: 69
8972 GTTATGATTC
* * * ** *
8982 ATGTG-TTATATGCTTAAACATTAATGTGATTTGGGCTTAAATATTAACATGATTTGGGCTGAAA
1 ATGTGATT-TATGCTTAAATATTAATGTGATTTGTGCTTAAATATTAATATGATTTATGCTTAAA
*
9046 TATAA
65 TATTA
* * * *
9051 AAGTGATTTATGCTTAAATATTAATGTAATTTGTGCTTAAATATTAGTACGATTTATGCTTAAA-
1 ATGTGATTTATGCTTAAATATTAATGTGATTTGTGCTTAAATATTAATATGATTTATGCTTAAAT
9115 AGTTA
66 A-TTA
* *
9120 ATGTGATTTATAG-TTAAAGATTAATGTGATTTGTGCTTAAATGTTAATATGATTTATGCTTAAA
1 ATGTGATTTAT-GCTTAAATATTAATGTGATTTGTGCTTAAATATTAATATGATTTATGCTTAAA
9184 TATTA
65 TATTA
*
9189 ATGTGATGTATGCTTAAATATTAATGTGATTT
1 ATGTGATTTATGCTTAAATATTAATGTGATTT
9221 ATTTGTAGAT
Statistics
Matches: 146, Mismatches: 19, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
68 2 0.01
69 140 0.96
70 4 0.03
ACGTcount: A:0.35, C:0.05, G:0.17, T:0.44
Consensus pattern (69 bp):
ATGTGATTTATGCTTAAATATTAATGTGATTTGTGCTTAAATATTAATATGATTTATGCTTAAAT
ATTA
Found at i:9969 original size:19 final size:18
Alignment explanation
Indices: 9930--9971 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
9920 ACTGAGCCTA
*
9930 AATTAAAATATATAAATT
1 AATTAAAAAATATAAATT
9948 AATTAATAAAATATACAA-T
1 AATTAA-AAAATATA-AATT
9967 AATTA
1 AATTA
9972 TTAAGAACGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 6 0.29
19 13 0.62
20 2 0.10
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (18 bp):
AATTAAAAAATATAAATT
Found at i:10178 original size:16 final size:17
Alignment explanation
Indices: 10137--10219 Score: 62
Period size: 18 Copynumber: 4.7 Consensus size: 17
10127 TATTATATGC
10137 TTTTTATATATTGTTAA
1 TTTTTATATATTGTTAA
* *
10154 -TTGTATATATTTTTAAA
1 TTTTTATATATTGTT-AA
*
10171 TTTTTATAAATT-TATACA
1 TTTTTATATATTGT-TA-A
* *
10189 CTTTTATATATTGATATA
1 TTTTTATATATTGTTA-A
10207 TATTTTATATATT
1 T-TTTTATATATT
10220 TATATAAATT
Statistics
Matches: 51, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
16 12 0.24
17 4 0.08
18 24 0.47
19 11 0.22
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.60
Consensus pattern (17 bp):
TTTTTATATATTGTTAA
Found at i:10221 original size:8 final size:8
Alignment explanation
Indices: 10159--10244 Score: 57
Period size: 8 Copynumber: 10.1 Consensus size: 8
10149 GTTAATTGTA
*
10159 TATATTTT
1 TATATATT
* *
10167 TAAATTTT
1 TATATATT
*
10175 TATAAATT
1 TATATATT
*
10183 TATACACTTT
1 TATATA--TT
10193 TATATATT
1 TATATATT
10201 GATATATATTT
1 --TATATA-TT
10212 TATATATT
1 TATATATT
*
10220 TATATAAAT
1 TATAT-ATT
10229 T-TATATT
1 TATATATT
10236 TATATATT
1 TATATATT
10244 T
1 T
10245 TTAAACTAAT
Statistics
Matches: 63, Mismatches: 8, Indels: 14
0.74 0.09 0.16
Matches are distributed among these distances:
7 3 0.05
8 36 0.57
9 9 0.14
10 13 0.21
11 2 0.03
ACGTcount: A:0.37, C:0.02, G:0.01, T:0.59
Consensus pattern (8 bp):
TATATATT
Found at i:10247 original size:10 final size:10
Alignment explanation
Indices: 10107--10230 Score: 52
Period size: 10 Copynumber: 13.3 Consensus size: 10
10097 TATTGTAACT
10107 TTTTTATATA
1 TTTTTATATA
*
10117 TTTTTA-AAA
1 TTTTTATATA
* * *
10126 ATATTATATGC
1 TTTTTATAT-A
10137 TTTTTATATA
1 TTTTTATATA
*
10147 -TTGT-TA-A
1 TTTTTATATA
*
10154 -TTGTATATA
1 TTTTTATATA
10163 TTTTTA-A-A
1 TTTTTATATA
10171 TTTTTATA-A
1 TTTTTATATA
* *
10180 -ATTTATACA
1 TTTTTATATA
*
10189 CTTTTATATA
1 TTTTTATATA
**
10199 TTGATATATA
1 TTTTTATATA
10209 -TTTTATATA
1 TTTTTATATA
* *
10218 TTTATATAAA
1 TTTTTATATA
10228 TTT
1 TTT
10231 ATATTTATAT
Statistics
Matches: 85, Mismatches: 20, Indels: 18
0.69 0.16 0.15
Matches are distributed among these distances:
7 5 0.06
8 17 0.20
9 21 0.25
10 35 0.41
11 7 0.08
ACGTcount: A:0.35, C:0.02, G:0.03, T:0.59
Consensus pattern (10 bp):
TTTTTATATA
Done.