Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012416.1 Kokia drynarioides strain JFW-HI SEQ_127420, 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: 14544
ACGTcount: A:0.33, C:0.20, G:0.14, T:0.33
Found at i:3285 original size:19 final size:22
Alignment explanation
Indices: 3215--3295 Score: 78
Period size: 23 Copynumber: 3.7 Consensus size: 22
3205 ATTATTGTAA
* * **
3215 ACATAACATACATAATTATATAT
1 ACATAACATACATAA-CAGATGG
3238 ACATAACATACATAACAGTATGG
1 ACATAACATACATAACAG-ATGG
3261 ACCATAACATACATAACAG-T-G
1 A-CATAACATACATAACAGATGG
3282 -CATAACATACATAA
1 ACATAACATACATAA
3296 TTATACATAC
Statistics
Matches: 52, Mismatches: 4, Indels: 8
0.81 0.06 0.12
Matches are distributed among these distances:
19 14 0.27
21 1 0.02
22 2 0.04
23 18 0.35
24 17 0.33
ACGTcount: A:0.51, C:0.19, G:0.06, T:0.25
Consensus pattern (22 bp):
ACATAACATACATAACAGATGG
Found at i:3287 original size:10 final size:9
Alignment explanation
Indices: 3263--3310 Score: 53
Period size: 9 Copynumber: 5.2 Consensus size: 9
3253 CAGTATGGAC
3263 CATAACATA
1 CATAACATA
*
3272 CATAACAGTG
1 CATAACA-TA
3282 CATAACATA
1 CATAACATA
*
3291 CATAATTATA
1 CATAA-CATA
3301 CAT-ACATA
1 CATAACATA
3309 CA
1 CA
3311 CAAACAATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
8 5 0.15
9 14 0.42
10 14 0.42
ACGTcount: A:0.50, C:0.21, G:0.04, T:0.25
Consensus pattern (9 bp):
CATAACATA
Found at i:3304 original size:19 final size:21
Alignment explanation
Indices: 3215--3310 Score: 67
Period size: 19 Copynumber: 4.6 Consensus size: 21
3205 ATTATTGTAA
3215 ACATAACATACATAATTATATAT
1 ACATAACATACATAA-TAT-TAT
* *
3238 ACATAACATACATAACAGTAT
1 ACATAACATACATAATATTAT
* *
3259 GGACCATAACATACATAACA--GT
1 --A-CATAACATACATAATATTAT
*
3281 GCATAACATACAT-A-ATTAT
1 ACATAACATACATAATATTAT
3300 ACAT-ACATACA
1 ACATAACATACA
3311 CAAACAATAA
Statistics
Matches: 62, Mismatches: 6, Indels: 15
0.75 0.07 0.18
Matches are distributed among these distances:
17 1 0.02
18 8 0.13
19 16 0.26
21 3 0.05
22 2 0.03
23 16 0.26
24 16 0.26
ACGTcount: A:0.50, C:0.19, G:0.05, T:0.26
Consensus pattern (21 bp):
ACATAACATACATAATATTAT
Found at i:3986 original size:18 final size:19
Alignment explanation
Indices: 3963--4000 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
3953 GGTGTTAAAA
3963 AGTTTTT-AATTCTTTTTT
1 AGTTTTTCAATTCTTTTTT
*
3981 AGTTTTTCAATTTTTTTTT
1 AGTTTTTCAATTCTTTTTT
4000 A
1 A
4001 ATGTTTCATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.18, C:0.05, G:0.05, T:0.71
Consensus pattern (19 bp):
AGTTTTTCAATTCTTTTTT
Found at i:4007 original size:19 final size:19
Alignment explanation
Indices: 3970--4008 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
3960 AAAAGTTTTT
* *
3970 AATTCTTTTTTAGTTTTTC
1 AATTCTTTTTTAATGTTTC
*
3989 AATTTTTTTTTAATGTTTC
1 AATTCTTTTTTAATGTTTC
4008 A
1 A
4009 TTAATTTTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.21, C:0.08, G:0.05, T:0.67
Consensus pattern (19 bp):
AATTCTTTTTTAATGTTTC
Found at i:10116 original size:17 final size:18
Alignment explanation
Indices: 10082--10117 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
10072 TGAATTTCTA
10082 TCCAATTTATACCCTAAT
1 TCCAATTTATACCCTAAT
*
10100 TCCAATTTA-ATCCTAAT
1 TCCAATTTATACCCTAAT
10117 T
1 T
10118 AACTCATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.33, C:0.25, G:0.00, T:0.42
Consensus pattern (18 bp):
TCCAATTTATACCCTAAT
Found at i:14490 original size:84 final size:84
Alignment explanation
Indices: 14349--14517 Score: 320
Period size: 84 Copynumber: 2.0 Consensus size: 84
14339 AGAGAAAAGT
*
14349 AAACTTTTAATAGTAATTGATTAATGTGATTTAAATTTAAATTACACTTGAAATGATGAAATATT
1 AAACTTTTAATAGTAATTGATTAATGTGATTTAAATTTAAATTACACTTGAAATGATGAAATACT
*
14414 TTAACTATCAGATTAATAA
66 TTAACTATCAGATCAATAA
14433 AAACTTTTAATAGTAATTGATTAATGTGATTTAAATTTAAATTACACTTGAAATGATGAAATACT
1 AAACTTTTAATAGTAATTGATTAATGTGATTTAAATTTAAATTACACTTGAAATGATGAAATACT
14498 TTAACTATCAGATCAATAA
66 TTAACTATCAGATCAATAA
14517 A
1 A
14518 TAGAATTCGT
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
84 83 1.00
ACGTcount: A:0.44, C:0.07, G:0.09, T:0.39
Consensus pattern (84 bp):
AAACTTTTAATAGTAATTGATTAATGTGATTTAAATTTAAATTACACTTGAAATGATGAAATACT
TTAACTATCAGATCAATAA
Done.