Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006103.1 Kokia drynarioides strain JFW-HI SEQ_120608, 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: 17211
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 65 characters in sequence are not A, C, G, or T
Found at i:57 original size:10 final size:11
Alignment explanation
Indices: 35--65 Score: 55
Period size: 10 Copynumber: 2.9 Consensus size: 11
25 TTCTGACTTT
35 GAAAAATTATA
1 GAAAAATTATA
46 GAAAAATT-TA
1 GAAAAATTATA
56 GAAAAATTAT
1 GAAAAATTAT
66 TAGAGACTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.53
11 9 0.47
ACGTcount: A:0.61, C:0.00, G:0.10, T:0.29
Consensus pattern (11 bp):
GAAAAATTATA
Found at i:700 original size:23 final size:23
Alignment explanation
Indices: 668--721 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
658 ACGCTAGCGC
*
668 GCTTATTGTTTCGCACTTCATGT
1 GCTTACTGTTTCGCACTTCATGT
*
691 GCTTACTGTTTCGCACTTCGTGT
1 GCTTACTGTTTCGCACTTCATGT
*
714 GCCTACTG
1 GCTTACTG
722 ATTTGCGTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.11, C:0.26, G:0.20, T:0.43
Consensus pattern (23 bp):
GCTTACTGTTTCGCACTTCATGT
Found at i:757 original size:22 final size:22
Alignment explanation
Indices: 688--789 Score: 89
Period size: 23 Copynumber: 4.5 Consensus size: 22
678 TCGCACTTCA
* *
688 TGTGCTTACTGTTTCGCACT-TCG
1 TGTGCCTACTGATT-GCACTGT-G
** *
711 TGTGCCTACTGATTTGCGTTATG
1 TGTGCCTACTGA-TTGCACTGTG
*
734 TGCGCCTACTGATTGCACTGTG
1 TGTGCCTACTGATTGCACTGTG
*
756 TGTGCCTATTGGATTGCACTGTG
1 TGTGCCTACT-GATTGCACTGTG
*
779 TGTGCTTACTG
1 TGTGCCTACTG
790 TTTCCCCAAC
Statistics
Matches: 64, Mismatches: 12, Indels: 7
0.77 0.14 0.08
Matches are distributed among these distances:
22 16 0.25
23 45 0.70
24 3 0.05
ACGTcount: A:0.12, C:0.22, G:0.26, T:0.40
Consensus pattern (22 bp):
TGTGCCTACTGATTGCACTGTG
Found at i:789 original size:45 final size:46
Alignment explanation
Indices: 688--789 Score: 102
Period size: 45 Copynumber: 2.2 Consensus size: 46
678 TCGCACTTCA
* **
688 TGTGCTTACTGTTTCGCACTTCGTGTGCCTACTGATTTGCGTTATG
1 TGTGCTTACTGATTCGCACTTCGTGTGCCTACTGATTTGCACTATG
* * * *
734 TGCGCCTACTGATT-GCACTGT-GTGTGCCTATTGGA-TTGCACTGTG
1 TGTGCTTACTGATTCGCACT-TCGTGTGCCTACT-GATTTGCACTATG
779 TGTGCTTACTG
1 TGTGCTTACTG
790 TTTCCCCAAC
Statistics
Matches: 45, Mismatches: 9, Indels: 5
0.76 0.15 0.08
Matches are distributed among these distances:
45 31 0.69
46 14 0.31
ACGTcount: A:0.12, C:0.22, G:0.26, T:0.40
Consensus pattern (46 bp):
TGTGCTTACTGATTCGCACTTCGTGTGCCTACTGATTTGCACTATG
Found at i:1622 original size:19 final size:20
Alignment explanation
Indices: 1581--1622 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
1571 ATATTTAAAA
* * *
1581 TTAAAATATATTAGAATTCT
1 TTAAAATATATTAAAAATAT
1601 TTAAAA-ATATTAAAAATAT
1 TTAAAATATATTAAAAATAT
1620 TTA
1 TTA
1623 CAATTTGATC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (20 bp):
TTAAAATATATTAAAAATAT
Found at i:3972 original size:19 final size:18
Alignment explanation
Indices: 3948--3986 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
3938 CGTCCAGTTC
3948 AATTAAATAAAACATTAAA
1 AATTAAA-AAAACATTAAA
* *
3967 AATTAAAAATATATTAAA
1 AATTAAAAAAACATTAAA
3985 AA
1 AA
3987 CATTGATTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (18 bp):
AATTAAAAAAACATTAAA
Found at i:4086 original size:17 final size:19
Alignment explanation
Indices: 4059--4093 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
4049 CTTGTTGATT
4059 TCGATCTAAT-CGGTCCAA
1 TCGATCTAATCCGGTCCAA
4077 TCGA-CTAATCCGGTCCA
1 TCGATCTAATCCGGTCCA
4094 GTTTAAGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.26, C:0.31, G:0.17, T:0.26
Consensus pattern (19 bp):
TCGATCTAATCCGGTCCAA
Found at i:4220 original size:18 final size:18
Alignment explanation
Indices: 4178--4250 Score: 83
Period size: 18 Copynumber: 3.9 Consensus size: 18
4168 TTTAATAAGG
*
4178 TTTTATAAGATTTTAAATATG
1 TTTTATAA-ATTTT--ATATC
*
4199 TTTTATTAATTTTATATC
1 TTTTATAAATTTTATATC
* *
4217 TTTTATAAAATTTATATT
1 TTTTATAAATTTTATATC
4235 TTTTATAAATTTTATA
1 TTTTATAAATTTTATA
4251 AAGTTTATAT
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
18 34 0.74
20 5 0.11
21 7 0.15
ACGTcount: A:0.36, C:0.01, G:0.03, T:0.60
Consensus pattern (18 bp):
TTTTATAAATTTTATATC
Found at i:4230 original size:9 final size:9
Alignment explanation
Indices: 4199--4259 Score: 59
Period size: 9 Copynumber: 6.8 Consensus size: 9
4189 TTTAAATATG
*
4199 TTTTATTAA
1 TTTTATAAA
**
4208 TTTTATATC
1 TTTTATAAA
4217 TTTTATAAA
1 TTTTATAAA
* **
4226 ATTTATATT
1 TTTTATAAA
4235 TTTTATAAA
1 TTTTATAAA
4244 TTTTATAAA
1 TTTTATAAA
*
4253 GTTTATA
1 TTTTATA
4260 TTTTTAATAG
Statistics
Matches: 40, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
9 40 1.00
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (9 bp):
TTTTATAAA
Found at i:4238 original size:27 final size:27
Alignment explanation
Indices: 4208--4264 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
4198 GTTTTATTAA
**
4208 TTTTATATCTTTTATAAAATTTATATT
1 TTTTATAAATTTTATAAAATTTATATT
*
4235 TTTTATAAATTTTATAAAGTTTATATT
1 TTTTATAAATTTTATAAAATTTATATT
4262 TTT
1 TTT
4265 AATAGTTAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (27 bp):
TTTTATAAATTTTATAAAATTTATATT
Found at i:7741 original size:17 final size:17
Alignment explanation
Indices: 7719--7756 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
7709 TTTTATAAAA
7719 ATATTT-AATAATAAATG
1 ATATTTAAATAA-AAATG
*
7736 ATATTTAAATAAAAATT
1 ATATTTAAATAAAAATG
7753 ATAT
1 ATAT
7757 AGTTAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (17 bp):
ATATTTAAATAAAAATG
Found at i:8023 original size:20 final size:20
Alignment explanation
Indices: 7994--8031 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
7984 TTTGGGCTAA
7994 TTTTAAAATTT-ATTTGGAT
1 TTTTAAAATTTAATTTGGAT
8013 TTTTGAAAATTTAATTTGG
1 TTTT-AAAATTTAATTTGG
8032 CTATAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 4 0.24
20 7 0.41
21 6 0.35
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (20 bp):
TTTTAAAATTTAATTTGGAT
Found at i:8864 original size:2 final size:2
Alignment explanation
Indices: 8857--8886 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
8847 CTTAAAAATA
8857 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
8887 TATTTTTAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:14448 original size:16 final size:16
Alignment explanation
Indices: 14409--14455 Score: 64
Period size: 16 Copynumber: 3.1 Consensus size: 16
14399 AGTTAGTTTC
14409 AACTTAATTTTTTAAT
1 AACTTAATTTTTTAAT
14425 AA-TT-ATTTTTTCAA-
1 AACTTAATTTTTT-AAT
14439 AACTTAATTTTTTAAT
1 AACTTAATTTTTTAAT
14455 A
1 A
14456 CATATGGCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
14 9 0.33
15 8 0.30
16 10 0.37
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.55
Consensus pattern (16 bp):
AACTTAATTTTTTAAT
Found at i:14449 original size:15 final size:16
Alignment explanation
Indices: 14409--14455 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 16
14399 AGTTAGTTTC
*
14409 AACTTAATTTTTTAAT
1 AACTTAATTTTTCAAT
*
14425 AA-TTATTTTTTCAA-
1 AACTTAATTTTTCAAT
*
14439 AACTTAATTTTTTAAT
1 AACTTAATTTTTCAAT
14455 A
1 A
14456 CATATGGCTT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 2 0.08
15 20 0.80
16 3 0.12
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.55
Consensus pattern (16 bp):
AACTTAATTTTTCAAT
Found at i:14468 original size:30 final size:30
Alignment explanation
Indices: 14409--14468 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
14399 AGTTAGTTTC
***
14409 AACTTAATTTTTTAATAATTATTTTTTCAA
1 AACTTAATTTTTTAATAATTATGGCTTCAA
14439 AACTTAATTTTTTAATACA-TATGGCTTCAA
1 AACTTAATTTTTTAATA-ATTATGGCTTCAA
14469 CTTATATTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 25 0.96
31 1 0.04
ACGTcount: A:0.37, C:0.10, G:0.03, T:0.50
Consensus pattern (30 bp):
AACTTAATTTTTTAATAATTATGGCTTCAA
Done.