Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001732.1 Kokia drynarioides strain JFW-HI SEQ_113437, 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: 24717
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Found at i:8486 original size:16 final size:16
Alignment explanation
Indices: 8465--8498 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
8455 AAAAAATTAT
*
8465 TAAAAATTCATAAAAA
1 TAAAAATACATAAAAA
*
8481 TAAAAATACTTAAAAA
1 TAAAAATACATAAAAA
8497 TA
1 TA
8499 GAGTTGAACT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (16 bp):
TAAAAATACATAAAAA
Found at i:9738 original size:22 final size:23
Alignment explanation
Indices: 9698--9765 Score: 57
Period size: 24 Copynumber: 2.9 Consensus size: 23
9688 TCGAGCCTCA
* *
9698 ATAATTTTTATGATATTAAAA-AT
1 ATAA-TTTTATAATTTTAAAATAT
* *
9721 ATAATTTTATTATTTTAATAATCT
1 ATAATTTTATAATTTTAA-AATAT
*
9745 ATATTTTTATAATATTTAAAA
1 ATAATTTTATAAT-TTTAAAA
9766 GATTAAATCA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
22 12 0.32
23 6 0.16
24 14 0.38
25 5 0.14
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.53
Consensus pattern (23 bp):
ATAATTTTATAATTTTAAAATAT
Found at i:9968 original size:3 final size:3
Alignment explanation
Indices: 9962--10021 Score: 95
Period size: 3 Copynumber: 20.0 Consensus size: 3
9952 TGCATTAACT
9962 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA GA-A ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA
*
10007 ATA ATA GTA ATA ATA
1 ATA ATA ATA ATA ATA
10022 GCAATAATGT
Statistics
Matches: 53, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
2 1 0.02
3 51 0.96
4 1 0.02
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:17398 original size:161 final size:160
Alignment explanation
Indices: 17099--17399 Score: 428
Period size: 161 Copynumber: 1.9 Consensus size: 160
17089 TGTTTTTGTT
* * * * *
17099 TATTATATATTTTGTAGATTTTTTTTAATTTTTACATAATTATAATTTTAAAATATATTTTATAA
1 TATTATATATTTTATAGAATTTCTTAAATTTTTACATAATTATAATTTAAAAATATATTTTATAA
* * *
17164 TTAAAAAAAAAATGAACAATGAATTTTAGAATTATTGTTAAAAAAGTTGTGAAAGTACCAAATTG
66 TT-AAAAAAAAATAAACAATGAATTTTAGAATTATTATTAAAAAAGTTGTAAAAGTACCAAATTG
17229 AATGTTGTAAAATTACATAATAAATAATATG
130 AATGTTGTAAAATTACATAATAAATAATATG
17260 TATTATATA-TTTATAGAATTTCTTAAATTTTTACATAATTATAAATTTAAAAAATATATTTTAT
1 TATTATATATTTTATAGAATTTCTTAAATTTTTACATAATTAT-AATTT-AAAAATATATTTTAT
** * *
17324 AATT-TCAAAAAATAAACAATGAATTTTCGGAATTATTATTAAAAATA-TTGTAAAAGTATCAAA
64 AATTAAAAAAAAATAAACAATGAATTTT-AGAATTATTATTAAAAA-AGTTGTAAAAGTACCAAA
17387 TTGAATGTTGTAA
127 TTGAATGTTGTAA
17400 CGATAGTTCA
Statistics
Matches: 124, Mismatches: 12, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
160 49 0.40
161 56 0.45
162 19 0.15
ACGTcount: A:0.46, C:0.04, G:0.08, T:0.43
Consensus pattern (160 bp):
TATTATATATTTTATAGAATTTCTTAAATTTTTACATAATTATAATTTAAAAATATATTTTATAA
TTAAAAAAAAATAAACAATGAATTTTAGAATTATTATTAAAAAAGTTGTAAAAGTACCAAATTGA
ATGTTGTAAAATTACATAATAAATAATATG
Found at i:18148 original size:19 final size:18
Alignment explanation
Indices: 18121--18176 Score: 60
Period size: 19 Copynumber: 3.0 Consensus size: 18
18111 CCACGTCAGC
*
18121 AAATGATTTTAAAATATT
1 AAATTATTTTAAAATATT
18139 AAAATTATTTTTTAAAATA-T
1 -AAATTA--TTTTAAAATATT
*
18159 AAATTATTTTAAATTATT
1 AAATTATTTTAAAATATT
18177 TTTTAAAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
17 9 0.28
18 1 0.03
19 11 0.34
20 1 0.03
21 10 0.31
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (18 bp):
AAATTATTTTAAAATATT
Found at i:18180 original size:30 final size:30
Alignment explanation
Indices: 18130--18227 Score: 141
Period size: 29 Copynumber: 3.3 Consensus size: 30
18120 CAAATGATTT
18130 TAAAA-TA-TTAAAATTATTTTTTAAAATA
1 TAAAATTATTTAAAATTATTTTTTAAAATA
*
18158 T-AAATTATTTTAAATTATTTTTTAAAATA
1 TAAAATTATTTAAAATTATTTTTTAAAATA
18187 TAAAATTA-TTAAAATTATTTTTTTAAAATAA
1 TAAAATTATTTAAAATTA-TTTTTTAAAAT-A
18218 TAAAATTATT
1 TAAAATTATT
18228 AAATAATTTT
Statistics
Matches: 62, Mismatches: 2, Indels: 8
0.86 0.03 0.11
Matches are distributed among these distances:
27 3 0.05
28 3 0.05
29 29 0.47
30 17 0.27
31 9 0.15
32 1 0.02
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (30 bp):
TAAAATTATTTAAAATTATTTTTTAAAATA
Found at i:18237 original size:30 final size:29
Alignment explanation
Indices: 18130--18237 Score: 116
Period size: 30 Copynumber: 3.7 Consensus size: 29
18120 CAAATGATTT
*
18130 TAAAA-TATTAAA-ATTATTTTTTAAAATA
1 TAAAATTATTAAATAAT-TTTTTTAAAATA
*
18158 T-AAATTATTTTAAATTA-TTTTTTAAAATA
1 TAAAATTA--TTAAATAATTTTTTTAAAATA
*
18187 TAAAATTATTAAAATTATTTTTTTAAAATAA
1 TAAAATTATT-AAATAATTTTTTTAAAAT-A
18218 TAAAATTATTAAATAATTTT
1 TAAAATTATTAAATAATTTT
18238 AATTTTCAAT
Statistics
Matches: 69, Mismatches: 3, Indels: 14
0.80 0.03 0.16
Matches are distributed among these distances:
27 3 0.04
28 5 0.07
29 19 0.28
30 31 0.45
31 11 0.16
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (29 bp):
TAAAATTATTAAATAATTTTTTTAAAATA
Found at i:20923 original size:45 final size:45
Alignment explanation
Indices: 20873--20960 Score: 149
Period size: 45 Copynumber: 2.0 Consensus size: 45
20863 TCAATAAGCG
* *
20873 CAGACCTTTCTTCTTCTCATTCTTTCTCATTTCTTGTTTTTGTTA
1 CAGACCTTTCTTCTTCTCATTCTTTCCCATTTCTTGTTCTTGTTA
*
20918 CAGACCTTTCTTCTTCTTATTCTTTCCCATTTCTTGTTCTTGT
1 CAGACCTTTCTTCTTCTCATTCTTTCCCATTTCTTGTTCTTGT
20961 CTCGATTTAG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.10, C:0.26, G:0.07, T:0.57
Consensus pattern (45 bp):
CAGACCTTTCTTCTTCTCATTCTTTCCCATTTCTTGTTCTTGTTA
Done.