Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008174.1 Kokia drynarioides strain JFW-HI SEQ_122833, 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: 18125
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.36
Found at i:37 original size:17 final size:17
Alignment explanation
Indices: 11--80 Score: 106
Period size: 17 Copynumber: 4.2 Consensus size: 17
1 ATTGGACATT
11 ATTT-AAATAAATTTAA
1 ATTTAAAATAAATTTAA
*
27 ATTTCAAATAAATTTAA
1 ATTTAAAATAAATTTAA
*
44 ATTTAAAATAAACTTAA
1 ATTTAAAATAAATTTAA
*
61 TTTTAAAATAAATTTAA
1 ATTTAAAATAAATTTAA
78 ATT
1 ATT
81 CTGTTGGACC
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
16 4 0.08
17 44 0.92
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (17 bp):
ATTTAAAATAAATTTAA
Found at i:52 original size:7 final size:6
Alignment explanation
Indices: 18--80 Score: 53
Period size: 6 Copynumber: 11.0 Consensus size: 6
8 ATTATTTAAA
* * *
18 TAAATT TAAATT TCAAA-- TAAATT TAAATT TAAA-A TAAACT TAATTT
1 TAAATT TAAATT T-AAATT TAAATT TAAATT TAAATT TAAATT TAAATT
*
64 TAAA-A TAAATT TAAATT
1 TAAATT TAAATT TAAATT
81 CTGTTGGACC
Statistics
Matches: 45, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
4 3 0.07
5 9 0.20
6 30 0.67
7 3 0.07
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (6 bp):
TAAATT
Found at i:2346 original size:22 final size:20
Alignment explanation
Indices: 2318--2408 Score: 50
Period size: 22 Copynumber: 4.5 Consensus size: 20
2308 TAAATTTTAT
2318 TAATTATAATTATTTAAGTGTA
1 TAATTATAATTATTTAA-T-TA
*
2340 TAATTATCACAATT-TTT-ATTT
1 TAATTAT---AATTATTTAATTA
*
2361 TAATATATAA--ATTTTA-T-
1 TAAT-TATAATTATTTAATTA
2378 TAATTATAATTATTTAAGTGTA
1 TAATTATAATTATTTAA-T-TA
2400 TAATTATAA
1 TAATTATAA
2409 ATATATAAAA
Statistics
Matches: 55, Mismatches: 2, Indels: 24
0.68 0.02 0.30
Matches are distributed among these distances:
16 5 0.09
17 4 0.07
18 9 0.16
19 3 0.05
21 6 0.11
22 20 0.36
23 1 0.02
24 3 0.05
25 4 0.07
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (20 bp):
TAATTATAATTATTTAATTA
Found at i:3527 original size:23 final size:23
Alignment explanation
Indices: 3484--3528 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
3474 AATAATTTTA
*
3484 ATGTATTTAATATTCTTAAAATG
1 ATGTATTTAATATTCTAAAAATG
*
3507 ATGTATTTACCTATT-TAAAAAT
1 ATGTATTTA-ATATTCTAAAAAT
3529 TTTTTTTACT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.47
Consensus pattern (23 bp):
ATGTATTTAATATTCTAAAAATG
Found at i:3989 original size:6 final size:6
Alignment explanation
Indices: 3978--4010 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
3968 CGTTAGTTCA
*
3978 ACAAAT ACAAAT ACAAAT ATAAAT ACAAAT ACA
1 ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACA
4011 TTGATTTGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.67, C:0.15, G:0.00, T:0.18
Consensus pattern (6 bp):
ACAAAT
Found at i:4672 original size:22 final size:22
Alignment explanation
Indices: 4647--4689 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
4637 TTAGTAATAA
* *
4647 TTTTATCTTTAAAGTGTTTTTT
1 TTTTATCTTAAAAGTGCTTTTT
4669 TTTTATCTTAAAAGTGCTTTT
1 TTTTATCTTAAAAGTGCTTTT
4690 AAAAAATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.21, C:0.07, G:0.09, T:0.63
Consensus pattern (22 bp):
TTTTATCTTAAAAGTGCTTTTT
Found at i:4856 original size:17 final size:18
Alignment explanation
Indices: 4830--4872 Score: 63
Period size: 17 Copynumber: 2.4 Consensus size: 18
4820 AATTGTAATT
4830 TTTATAATAGTTT-TATTA
1 TTTATAATAGTTTATA-TA
4848 TTT-TAATAGTTTATATA
1 TTTATAATAGTTTATATA
4865 TTTATAAT
1 TTTATAAT
4873 TTTTAGAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 14 0.61
18 9 0.39
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (18 bp):
TTTATAATAGTTTATATA
Found at i:4877 original size:17 final size:17
Alignment explanation
Indices: 4830--4877 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
4820 AATTGTAATT
4830 TTTATAATAGTTTTATTA
1 TTTATAATA-TTTTATTA
*
4848 TTT-TAATAGTTTATATA
1 TTTATAATATTTTAT-TA
4865 TTTATAAT-TTTTA
1 TTTATAATATTTTA
4878 GAATGTTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 5 0.19
17 14 0.54
18 7 0.27
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.62
Consensus pattern (17 bp):
TTTATAATATTTTATTA
Found at i:9285 original size:21 final size:22
Alignment explanation
Indices: 9250--9292 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
9240 AATATTATTT
9250 ATTAATTAATTTAATTAAATAA
1 ATTAATTAATTTAATTAAATAA
*
9272 ATTAATT-TTTTAATTAAATAA
1 ATTAATTAATTTAATTAAATAA
9293 TTTTTTCAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
ATTAATTAATTTAATTAAATAA
Found at i:9289 original size:17 final size:17
Alignment explanation
Indices: 9253--9308 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
9243 ATTATTTATT
* *
9253 AATTAATTTAATTAAATA
1 AATTAATTT-TTTAATTA
9271 AATTAATTTTTTAATTA
1 AATTAATTTTTTAATTA
*
9288 AA-TAATTTTTTCAATTC
1 AATTAATTTTTT-AATTA
9305 AATT
1 AATT
9309 CTTTTTTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
16 9 0.27
17 14 0.42
18 10 0.30
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.52
Consensus pattern (17 bp):
AATTAATTTTTTAATTA
Found at i:14305 original size:69 final size:68
Alignment explanation
Indices: 14100--14307 Score: 192
Period size: 69 Copynumber: 3.0 Consensus size: 68
14090 GCCTTATATA
* * **
14100 CTTCTTTCTCCATTAAATCAATAACCC-CTTTATCTGTGGCCACCACATCACAAAAGGT-TGTAT
1 CTTCTTGCTCCATTAAATCAAT-ACCCACTTTATCCGTGGCC-CCACATCACAAGTGGTGT-TAT
14163 CATGTT
63 CATGTT
* * * * * * *
14169 CTTTTTGC-CTCATTGATTCAATTCACACTTTATCCCTAGACCCCACATCACAAGT-G-GTTATG
1 CTTCTTGCTC-CATTAAATCAATACCCACTTTATCCGT-GGCCCCACATCACAAGTGGTGTTAT-
14231 ACATGTT
63 -CATGTT
* *
14238 CTTCTTGCTCCATTAAAACAATACCCACTTTATCCGTGGCCTTCACATCACAAGTGGTGTTATCA
1 CTTCTTGCTCCATTAAATCAATACCCACTTTATCCGTGGCC-CCACATCACAAGTGGTGTTATCA
14303 TGTT
65 TGTT
14307 C
1 C
14308 CATCATTGAC
Statistics
Matches: 109, Mismatches: 20, Indels: 20
0.73 0.13 0.13
Matches are distributed among these distances:
67 3 0.03
68 8 0.07
69 88 0.81
70 5 0.05
71 5 0.05
ACGTcount: A:0.25, C:0.28, G:0.12, T:0.35
Consensus pattern (68 bp):
CTTCTTGCTCCATTAAATCAATACCCACTTTATCCGTGGCCCCACATCACAAGTGGTGTTATCAT
GTT
Done.