Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003964.1 Kokia drynarioides strain JFW-HI SEQ_117057, 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: 5955
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Found at i:4138 original size:26 final size:28
Alignment explanation
Indices: 4074--4141 Score: 77
Period size: 26 Copynumber: 2.4 Consensus size: 28
4064 TAGAATTTAT
*
4074 AATTTATAATAAATAAAATTTAAAAGTTGA
1 AATTTA-AATAAATAAAATTGAAAAG-TGA
* *
4104 AATTGAAATAAATGAAA-TGAAAA-TGA
1 AATTTAAATAAATAAAATTGAAAAGTGA
4130 AATTTAAATAAA
1 AATTTAAATAAA
4142 AGTTGAAATT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
26 14 0.41
28 5 0.15
29 10 0.29
30 5 0.15
ACGTcount: A:0.60, C:0.00, G:0.09, T:0.31
Consensus pattern (28 bp):
AATTTAAATAAATAAAATTGAAAAGTGA
Found at i:4160 original size:23 final size:22
Alignment explanation
Indices: 4134--4276 Score: 111
Period size: 23 Copynumber: 6.5 Consensus size: 22
4124 AAATGAAATT
4134 TAAATAAAAGTTGAAATTTATAA
1 TAAATAAAA-TTGAAATTTATAA
* *
4157 TAAATAGAATTTATAATTTATAA
1 TAAATAAAATTGA-AATTTATAA
*
4180 TAAATAAAATTTGAAATTGA-AA
1 TAAATAAAA-TTGAAATTTATAA
4202 TGAAATGAAAA-TGAAA-TT-TAA
1 T-AAAT-AAAATTGAAATTTATAA
*
4223 T---TAAAAGTTGAAATTTAAAA
1 TAAATAAAA-TTGAAATTTATAA
* *
4243 TAAATAGAATTTATAATTTATAA
1 TAAATAAAATTGA-AATTTATAA
4266 TAAAATAAAAT
1 T-AAATAAAAT
4277 AAAATTTTAA
Statistics
Matches: 95, Mismatches: 11, Indels: 27
0.71 0.08 0.20
Matches are distributed among these distances:
16 4 0.04
17 1 0.01
18 5 0.05
19 2 0.02
20 3 0.03
21 4 0.04
22 14 0.15
23 47 0.49
24 15 0.16
ACGTcount: A:0.57, C:0.00, G:0.08, T:0.36
Consensus pattern (22 bp):
TAAATAAAATTGAAATTTATAA
Found at i:4232 original size:86 final size:86
Alignment explanation
Indices: 4106--4402 Score: 352
Period size: 86 Copynumber: 3.6 Consensus size: 86
4096 AAAGTTGAAA
*
4106 TTGAAA-T-AAATGAAATGAAAATGAAATTTAAATAAAAGTTGAAATTTATAATAAATAGAATTT
1 TTGAAATTGAAATGAAATGAAAATGAAATTTAATTAAAAGTTGAAATTTATAATAAATAGAATTT
4169 ATAATTTATAATAAATAAAAT
66 ATAATTTATAATAAATAAAAT
*
4190 TTGAAATTGAAATGAAATGAAAATGAAATTTAATTAAAAGTTGAAATTTAAAATAAATAGAATTT
1 TTGAAATTGAAATGAAATGAAAATGAAATTTAATTAAAAGTTGAAATTTATAATAAATAGAATTT
4255 ATAATTTATAATAAAATAAAA-
66 ATAATTTATAAT-AAATAAAAT
* * * * * *
4276 -TAAAATTTTAAATTTTAAATTG-AAATGAAATTTAATTAAAAGTTTAAATTTATAAT--TTATA
1 TTGAAA-TTGAAA--TGAAA-TGAAAATGAAATTTAATTAAAAGTTGAAATTTATAATAAATAGA
** *
4337 A--TA-AA--TA-AAT-TTTGAAAT
62 ATTTATAATTTATAATAAATAAAAT
4355 TTGAAATTGAAATGAAATGAAAATGAAATTTAATTAAAAGTTGAAATT
1 TTGAAATTGAAATGAAATGAAAATGAAATTTAATTAAAAGTTGAAATT
4403 AAATGAAATT
Statistics
Matches: 187, Mismatches: 16, Indels: 27
0.81 0.07 0.12
Matches are distributed among these distances:
76 2 0.01
77 31 0.17
78 4 0.02
79 5 0.03
80 7 0.04
81 2 0.01
83 2 0.01
84 8 0.04
85 5 0.03
86 75 0.40
87 8 0.04
88 36 0.19
89 2 0.01
ACGTcount: A:0.55, C:0.00, G:0.09, T:0.37
Consensus pattern (86 bp):
TTGAAATTGAAATGAAATGAAAATGAAATTTAATTAAAAGTTGAAATTTATAATAAATAGAATTT
ATAATTTATAATAAATAAAAT
Found at i:4290 original size:36 final size:36
Alignment explanation
Indices: 4250--4345 Score: 108
Period size: 36 Copynumber: 2.7 Consensus size: 36
4240 AAATAAATAG
*
4250 AATTTATAATTTATAATAAAATAAAATAAAATTTTA
1 AATTTATAATTTATAATAAAATAAAATAAAAGTTTA
* * * *
4286 AATTT-TAAATTGA-AATGAAATTTAATTAAAAGTTTA
1 AATTTAT-AATTTATAAT-AAAATAAAATAAAAGTTTA
4322 AATTTATAATTTATAAT-AAATAAA
1 AATTTATAATTTATAATAAAATAAA
4346 TTTTGAAATT
Statistics
Matches: 48, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
35 9 0.19
36 35 0.73
37 4 0.08
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (36 bp):
AATTTATAATTTATAATAAAATAAAATAAAAGTTTA
Found at i:4324 original size:29 final size:30
Alignment explanation
Indices: 4204--4325 Score: 92
Period size: 29 Copynumber: 4.2 Consensus size: 30
4194 AATTGAAATG
* * *
4204 AAATGAAAATGAAATTTAA-TTAAAAGTTG
1 AAATTAAAATGAAATATAATTTAAAAGTTT
* *
4233 AAATTTAAAAT-AAATAGAATTTATAA-TTT
1 AAA-TTAAAATGAAATATAATTTAAAAGTTT
* * * *
4262 ATAA-TAAAATAAAATAAAATTTTAAATTTT
1 A-AATTAAAATGAAATATAATTTAAAAGTTT
* *
4292 AAATTGAAATGAAATTTAA-TTAAAAGTTT
1 AAATTAAAATGAAATATAATTTAAAAGTTT
4321 AAATT
1 AAATT
4326 TATAATTTAT
Statistics
Matches: 73, Mismatches: 14, Indels: 12
0.74 0.14 0.12
Matches are distributed among these distances:
28 6 0.08
29 39 0.53
30 28 0.38
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.38
Consensus pattern (30 bp):
AAATTAAAATGAAATATAATTTAAAAGTTT
Found at i:4366 original size:6 final size:6
Alignment explanation
Indices: 4348--4471 Score: 63
Period size: 6 Copynumber: 22.0 Consensus size: 6
4338 TAAATAAATT
* * *
4348 TTGAAA TTTGAAA TTGAAA -TGAAA -TGAAA ATGAAA TT-TAA TTAAAA
1 TTGAAA -TTGAAA TTGAAA TTGAAA TTGAAA TTGAAA TTGAAA TTGAAA
* *
4394 GTTGAAA TT-AAA -TGAAA TTTAAA -TGAAA -TGAAA ATGAAA -T-ATAA
1 -TTGAAA TTGAAA TTGAAA TTGAAA TTGAAA TTGAAA TTGAAA TTGA-AA
* * * *
4438 -TGAAA ATGAAA TTCAAA TTCAAA TTCAAA -TGAAA
1 TTGAAA TTGAAA TTGAAA TTGAAA TTGAAA TTGAAA
4472 AACATAAGAA
Statistics
Matches: 99, Mismatches: 9, Indels: 20
0.77 0.07 0.16
Matches are distributed among these distances:
4 2 0.02
5 39 0.39
6 47 0.47
7 11 0.11
ACGTcount: A:0.56, C:0.02, G:0.12, T:0.30
Consensus pattern (6 bp):
TTGAAA
Found at i:4372 original size:11 final size:11
Alignment explanation
Indices: 4356--4471 Score: 62
Period size: 11 Copynumber: 10.5 Consensus size: 11
4346 TTTTGAAATT
4356 TGAAATTGAAA
1 TGAAATTGAAA
4367 TGAAA-TGAAAA
1 TGAAATTG-AAA
* *
4378 TGAAATTTAAT
1 TGAAATTGAAA
*
4389 TAAAAGTTGAAA
1 TGAAA-TTGAAA
*
4401 TTAAA-TGAAA
1 TGAAATTGAAA
*
4411 TTTAAA-TGAAA
1 -TGAAATTGAAA
*
4422 TGAAAATGAAA
1 TGAAATTGAAA
4433 T-ATAA-TGAAAA
1 TGA-AATTG-AAA
*
4444 TGAAATTCAAA
1 TGAAATTGAAA
* *
4455 TTCAAATTCAAA
1 -TGAAATTGAAA
4467 TGAAA
1 TGAAA
4472 AACATAAGAA
Statistics
Matches: 85, Mismatches: 10, Indels: 20
0.74 0.09 0.17
Matches are distributed among these distances:
10 14 0.16
11 50 0.59
12 21 0.25
ACGTcount: A:0.57, C:0.03, G:0.12, T:0.28
Consensus pattern (11 bp):
TGAAATTGAAA
Found at i:4381 original size:16 final size:16
Alignment explanation
Indices: 4356--4449 Score: 91
Period size: 16 Copynumber: 5.8 Consensus size: 16
4346 TTTTGAAATT
*
4356 TGAAATTGAAATGAAA
1 TGAAAATGAAATGAAA
**
4372 TGAAAATGAAATTTAA
1 TGAAAATGAAATGAAA
* *
4388 TTAAAAGTTGAAATTAAA
1 TGAAAA--TGAAATGAAA
* *
4406 TGAAATTTAAATGAAA
1 TGAAAATGAAATGAAA
4422 TGAAAATGAAAT-ATAA
1 TGAAAATGAAATGA-AA
4438 TGAAAATGAAAT
1 TGAAAATGAAAT
4450 TCAAATTCAA
Statistics
Matches: 64, Mismatches: 11, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
15 1 0.02
16 50 0.78
18 13 0.20
ACGTcount: A:0.57, C:0.00, G:0.14, T:0.29
Consensus pattern (16 bp):
TGAAAATGAAATGAAA
Found at i:4418 original size:50 final size:50
Alignment explanation
Indices: 4355--4471 Score: 157
Period size: 50 Copynumber: 2.3 Consensus size: 50
4345 ATTTTGAAAT
* * *
4355 TTGAAATTGAAATGAAATGAAAATGAAATTTAATTAAAAGTTGAAATT-AAA
1 TTGAAATTCAAATGAAATGAAAATGAAATATAATGAAAA--TGAAATTCAAA
*
4406 -TGAAATTTAAATGAAATGAAAATGAAATATAATGAAAATGAAATTCAAA
1 TTGAAATTCAAATGAAATGAAAATGAAATATAATGAAAATGAAATTCAAA
*
4455 TTCAAATTCAAATGAAA
1 TTGAAATTCAAATGAAA
4472 AACATAAGAA
Statistics
Matches: 59, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
48 7 0.12
49 3 0.05
50 49 0.83
ACGTcount: A:0.56, C:0.03, G:0.12, T:0.29
Consensus pattern (50 bp):
TTGAAATTCAAATGAAATGAAAATGAAATATAATGAAAATGAAATTCAAA
Done.