Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007632.1 Kokia drynarioides strain JFW-HI SEQ_122263, 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: 14176
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Found at i:1542 original size:60 final size:59
Alignment explanation
Indices: 1455--1625 Score: 150
Period size: 59 Copynumber: 2.9 Consensus size: 59
1445 TTGAATTTTG
* ** *
1455 AAAAAAAA-CTTAGGTACCAAATTAGGAAGAAAATG-CAAAGTTCAGGTACCAAATTGGGT
1 AAAAAAAAGTTTAGGTACCAAACAAGGAA-AAAATGTC-AAGTTCAGGTACCAAATTAGGT
** * * * *
1514 CCAAAAAAGTTTAGGTACCAAACAAGGAATAAGTGTCTAGTTCAGGTATCAAATTAGGT
1 AAAAAAAAGTTTAGGTACCAAACAAGGAAAAAATGTCAAGTTCAGGTACCAAATTAGGT
* *** * * *
1573 AAAAAAAAGTTTAGGTATCAAATTTGG-AAAAATATCAAGTTAAGATACCAAAT
1 AAAAAAAAGTTTAGGTACCAAACAAGGAAAAAATGTCAAGTTCAGGTACCAAAT
1626 GTTATATTAA
Statistics
Matches: 87, Mismatches: 23, Indels: 5
0.76 0.20 0.04
Matches are distributed among these distances:
58 19 0.22
59 50 0.57
60 18 0.21
ACGTcount: A:0.47, C:0.11, G:0.18, T:0.24
Consensus pattern (59 bp):
AAAAAAAAGTTTAGGTACCAAACAAGGAAAAAATGTCAAGTTCAGGTACCAAATTAGGT
Found at i:1588 original size:28 final size:27
Alignment explanation
Indices: 1552--1604 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
1542 ATAAGTGTCT
1552 AGTTCAGGTATCAAATTAGGTAAAAAAA
1 AGTTCAGGTATCAAATTAGG-AAAAAAA
* *
1580 AGTTTAGGTATCAAATTTGGAAAAA
1 AGTTCAGGTATCAAATTAGGAAAAA
1605 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:9040 original size:23 final size:23
Alignment explanation
Indices: 9014--9254 Score: 254
Period size: 23 Copynumber: 10.5 Consensus size: 23
9004 GTTATGATTC
*
9014 ATGTG-TTATATGCTTAAACATTA
1 ATGTGATT-TATGCTTAAATATTA
**
9037 ATGTGATTTGGGCTTAAATATTA
1 ATGTGATTTATGCTTAAATATTA
** ** * *
9060 ACATGATTTGGGCTGAAATATAA
1 ATGTGATTTATGCTTAAATATTA
*
9083 AAGTGATTTATGCTTAAATATTA
1 ATGTGATTTATGCTTAAATATTA
* *
9106 ATGTAATTTGTGCTTAAATATTA
1 ATGTGATTTATGCTTAAATATTA
* **
9129 GTACGATTTATGCTTAAA-AGTTA
1 ATGTGATTTATGCTTAAATA-TTA
*
9152 ATGTGATTTATAG-TTAAAGATTA
1 ATGTGATTTAT-GCTTAAATATTA
* *
9175 ATGTGATTTGTGCTTAAATGTTA
1 ATGTGATTTATGCTTAAATATTA
*
9198 ATATGATTTATGCTTAAATATTA
1 ATGTGATTTATGCTTAAATATTA
*
9221 ATGTGATGTATGCTTAAATATTA
1 ATGTGATTTATGCTTAAATATTA
9244 ATGTGATTTAT
1 ATGTGATTTAT
9255 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:9137 original size:69 final size:69
Alignment explanation
Indices: 9014--9252 Score: 304
Period size: 69 Copynumber: 3.5 Consensus size: 69
9004 GTTATGATTC
* * * ** *
9014 ATGTG-TTATATGCTTAAACATTAATGTGATTTGGGCTTAAATATTAACATGATTTGGGCTGAAA
1 ATGTGATT-TATGCTTAAATATTAATGTGATTTGTGCTTAAATATTAATATGATTTATGCTTAAA
*
9078 TATAA
65 TATTA
* * * *
9083 AAGTGATTTATGCTTAAATATTAATGTAATTTGTGCTTAAATATTAGTACGATTTATGCTTAAA-
1 ATGTGATTTATGCTTAAATATTAATGTGATTTGTGCTTAAATATTAATATGATTTATGCTTAAAT
9147 AGTTA
66 A-TTA
* *
9152 ATGTGATTTATAG-TTAAAGATTAATGTGATTTGTGCTTAAATGTTAATATGATTTATGCTTAAA
1 ATGTGATTTAT-GCTTAAATATTAATGTGATTTGTGCTTAAATATTAATATGATTTATGCTTAAA
9216 TATTA
65 TATTA
*
9221 ATGTGATGTATGCTTAAATATTAATGTGATTT
1 ATGTGATTTATGCTTAAATATTAATGTGATTT
9253 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:10001 original size:19 final size:18
Alignment explanation
Indices: 9962--10003 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
9952 ACTGAGCCTA
*
9962 AATTAAAATATATAAATT
1 AATTAAAAAATATAAATT
9980 AATTAATAAAATATACAA-T
1 AATTAA-AAAATATA-AATT
9999 AATTA
1 AATTA
10004 TTAAGAATGA
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:10210 original size:16 final size:17
Alignment explanation
Indices: 10169--10251 Score: 62
Period size: 18 Copynumber: 4.7 Consensus size: 17
10159 TATTATATGC
10169 TTTTTATATATTGTTAA
1 TTTTTATATATTGTTAA
* *
10186 -TTGTATATATTTTTAAA
1 TTTTTATATATTGTT-AA
*
10203 TTTTTATAAATT-TATACA
1 TTTTTATATATTGT-TA-A
* *
10221 CTTTTATATATTGATATA
1 TTTTTATATATTGTTA-A
10239 TATTTTATATATT
1 T-TTTTATATATT
10252 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:10253 original size:8 final size:8
Alignment explanation
Indices: 10191--10276 Score: 57
Period size: 8 Copynumber: 10.1 Consensus size: 8
10181 GTTAATTGTA
*
10191 TATATTTT
1 TATATATT
* *
10199 TAAATTTT
1 TATATATT
*
10207 TATAAATT
1 TATATATT
*
10215 TATACACTTT
1 TATATA--TT
10225 TATATATT
1 TATATATT
10233 GATATATATTT
1 --TATATA-TT
10244 TATATATT
1 TATATATT
*
10252 TATATAAAT
1 TATAT-ATT
10261 T-TATATT
1 TATATATT
10268 TATATATT
1 TATATATT
10276 T
1 T
10277 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:10279 original size:10 final size:10
Alignment explanation
Indices: 10139--10262 Score: 52
Period size: 10 Copynumber: 13.3 Consensus size: 10
10129 TATTGTAACT
10139 TTTTTATATA
1 TTTTTATATA
*
10149 TTTTTA-AAA
1 TTTTTATATA
* * *
10158 ATATTATATGC
1 TTTTTATAT-A
10169 TTTTTATATA
1 TTTTTATATA
*
10179 -TTGT-TA-A
1 TTTTTATATA
*
10186 -TTGTATATA
1 TTTTTATATA
10195 TTTTTA-A-A
1 TTTTTATATA
10203 TTTTTATA-A
1 TTTTTATATA
* *
10212 -ATTTATACA
1 TTTTTATATA
*
10221 CTTTTATATA
1 TTTTTATATA
**
10231 TTGATATATA
1 TTTTTATATA
10241 -TTTTATATA
1 TTTTTATATA
* *
10250 TTTATATAAA
1 TTTTTATATA
10260 TTT
1 TTT
10263 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
Found at i:12539 original size:22 final size:24
Alignment explanation
Indices: 12509--12552 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
12499 TAAAGTGGGC
12509 CATGCAAATTA-AATTATTTAAAA
1 CATGCAAATTATAATTATTTAAAA
*
12532 CATG-AAATTATATTTATTTAA
1 CATGCAAATTATAATTATTTAA
12553 TGGACATGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.48, C:0.07, G:0.05, T:0.41
Consensus pattern (24 bp):
CATGCAAATTATAATTATTTAAAA
Done.