Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009561.1 Kokia drynarioides strain JFW-HI SEQ_124273, 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: 8237
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Found at i:465 original size:22 final size:24
Alignment explanation
Indices: 424--467 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
414 TCCAAATACA
*
424 AATTGAGGCCCACTTTACAAACTC
1 AATTGAGGCCCACATTACAAACTC
448 AATTG-GGCCCA-ATTACAAAC
1 AATTGAGGCCCACATTACAAAC
468 GACCCAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 8 0.42
23 6 0.32
24 5 0.26
ACGTcount: A:0.36, C:0.27, G:0.14, T:0.23
Consensus pattern (24 bp):
AATTGAGGCCCACATTACAAACTC
Found at i:1065 original size:3 final size:3
Alignment explanation
Indices: 1057--1135 Score: 113
Period size: 3 Copynumber: 26.0 Consensus size: 3
1047 CTACTGATAT
* ** *
1057 TAA TAA TAA CAA TAA TTAA TGT TAA CAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1103 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1136 AAAAGGAAAT
Statistics
Matches: 67, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
3 64 0.96
4 3 0.04
ACGTcount: A:0.63, C:0.03, G:0.01, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1859 original size:29 final size:28
Alignment explanation
Indices: 1825--1899 Score: 71
Period size: 28 Copynumber: 2.6 Consensus size: 28
1815 TTTTAGACCC
*
1825 TCAAATTTAAATTTTACCCTCTAACTTTT
1 TCAAAATTAAATTTTACCC-CTAACTTTT
** * *
1854 T-AAAATTCCATTTTAACCCTAATTTTT
1 TCAAAATTAAATTTTACCCCTAACTTTT
1881 TCAAAAATTATAATTTTAC
1 TC-AAAATTA-AATTTTAC
1900 ATCTAAACTT
Statistics
Matches: 35, Mismatches: 8, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
27 9 0.26
28 13 0.37
29 7 0.20
30 6 0.17
ACGTcount: A:0.36, C:0.17, G:0.00, T:0.47
Consensus pattern (28 bp):
TCAAAATTAAATTTTACCCCTAACTTTT
Found at i:1954 original size:30 final size:29
Alignment explanation
Indices: 1908--2241 Score: 159
Period size: 29 Copynumber: 11.3 Consensus size: 29
1898 ACATCTAAAC
* **
1908 TTTCC-AAAATTCCATTTTTGACCTTGATT
1 TTTCCAAAAATTACATTTTT-ACCCCGATT
**
1937 TTTCCAAAAATTACATTTTTACCCACGAAC
1 TTTCCAAAAATTACATTTTTACCC-CGATT
**
1967 TTT-CAAAAATT-CTATTTTTTACCCTAATT
1 TTTCCAAAAATTAC-A-TTTTTACCCCGATT
* * * **
1996 TTTCAAAAAAAATTATATTTTTACCCCTAAAC
1 TTTC--CAAAAATTACATTTTTACCCC-GATT
* * *
2028 TTT-CTAAAATTCCATTTTTACCAC-ATTTT
1 TTTCCAAAAATTACATTTTTACCCCGA--TT
* * * **
2057 TTTCCAAAAATCACATTTTTGCCCTCAAAC
1 TTTCCAAAAATTACATTTTTACCC-CGATT
*
2087 TTTCC-AAAATTCCATTTTTAACCCCGATT
1 TTTCCAAAAATTACATTTTT-ACCCCGATT
* * *
2116 TTTCCATAAATTACCA-TTCTACCCCCGA-A
1 TTTCCAAAAATTA-CATTTTTA-CCCCGATT
* *
2145 TTTCCAAAAATTTCATTTTTGACCTCGATT
1 TTTCCAAAAATTACATTTTT-ACCCCGATT
*
2175 TTTCCAAAAATTACCA-TTTTACCCTCGA-A
1 TTTCCAAAAATTA-CATTTTTACCC-CGATT
* * *
2204 CTTCC-AAAATTTCATTTTTTACCTCGATT
1 TTTCCAAAAATTACA-TTTTTACCCCGATT
*
2233 CTTCCAAAA
1 TTTCCAAAA
2242 GTAGCATTTT
Statistics
Matches: 228, Mismatches: 50, Indels: 53
0.69 0.15 0.16
Matches are distributed among these distances:
27 3 0.01
28 12 0.05
29 98 0.43
30 87 0.38
31 14 0.06
32 14 0.06
ACGTcount: A:0.31, C:0.25, G:0.03, T:0.41
Consensus pattern (29 bp):
TTTCCAAAAATTACATTTTTACCCCGATT
Found at i:1968 original size:59 final size:59
Alignment explanation
Indices: 1836--2257 Score: 335
Period size: 59 Copynumber: 7.2 Consensus size: 59
1826 CAAATTTAAA
* ** * * * * *
1836 TTTTACCCTCTAACTTTTTAAAATTCCA-TTTTAACCCTAATTTTTTCAAAAATTATAA
1 TTTTACCCTCAAACTTTCCAAAATTCCATTTTTAACCTTGATTTTTCCAAAAATTACAT
* *
1894 TTTTA-CATCTAAACTTTCCAAAATTCCATTTTTGACCTTGATTTTTCCAAAAATTACAT
1 TTTTACCCTC-AAACTTTCCAAAATTCCATTTTTAACCTTGATTTTTCCAAAAATTACAT
* * * * * * * * *
1953 TTTTACCCACGAACTTTCAAAAATTCTATTTTTTACCCTAATTTTTCAAAAAAAATTATAT
1 TTTTACCCTCAAACTTTCCAAAATTCCATTTTTAACCTTGATTTTTC--CAAAAATTACAT
* * *
2014 TTTTACCC-CTAAACTTTCTAAAATTCCATTTTTACCACATT--TTTTTCCAAAAATCACAT
1 TTTTACCCTC-AAACTTTCCAAAATTCCATTTTTA--ACCTTGATTTTTCCAAAAATTACAT
* ** *
2073 TTTTGCCCTCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTTTCCATAAATTACCA-
1 TTTTACCCTCAAACTTTCCAAAATTCCATTTTTAACCTTGATTTTTCCAAAAATTA-CAT
* * * * * *
2132 TTCTACCCCCGAA-TTTCCAAAAATTTCATTTTTGACCTCGATTTTTCCAAAAATTACCA-
1 TTTTACCCTCAAACTTTCC-AAAATTCCATTTTTAACCTTGATTTTTCCAAAAATTA-CAT
* * * * * *
2191 TTTTACCCTCGAAC-TTCCAAAATTTCATTTTTTACCTCGATTCTTCC-AAAAGTAGCA-
1 TTTTACCCTCAAACTTTCCAAAATTCCATTTTTAACCTTGATTTTTCCAAAAATTA-CAT
2248 TTTTACCCTC
1 TTTTACCCTC
2258 GAATGTCTAG
Statistics
Matches: 300, Mismatches: 50, Indels: 29
0.79 0.13 0.08
Matches are distributed among these distances:
57 23 0.08
58 52 0.17
59 172 0.57
60 6 0.02
61 44 0.15
63 3 0.01
ACGTcount: A:0.32, C:0.24, G:0.03, T:0.42
Consensus pattern (59 bp):
TTTTACCCTCAAACTTTCCAAAATTCCATTTTTAACCTTGATTTTTCCAAAAATTACAT
Found at i:2223 original size:29 final size:29
Alignment explanation
Indices: 2135--2310 Score: 89
Period size: 29 Copynumber: 6.0 Consensus size: 29
2125 ATTACCATTC
* *
2135 TACCCCCGAATTTCCAAAAATTTCATTTTT
1 TACCCTCGAACTTCC-AAAATTTCATTTTT
* ** *
2165 GA-CCTCGATTTTTCCAAAAATTACCA--TTT
1 TACCCTCGA-ACTTCC-AAAATT-TCATTTTT
2194 TACCCTCGAACTTCCAAAATTTCATTTTT
1 TACCCTCGAACTTCCAAAATTTCATTTTT
* **
2223 TA-CCTCGATTCTTCCAAAAGTAGCA--TTT
1 TACCCTCGA-ACTTCCAAAA-TTTCATTTTT
* *
2251 TACCCTCGAA-TGTCTAGAAATCTCATTTTT
1 TACCCTCGAACT-TCCA-AAATTTCATTTTT
*
2281 GACCCTCG-ACTTTCCCAAAATTATCATTTT
1 TACCCTCGAAC-TT-CCAAAATT-TCATTTT
2311 GCCTCTCGAG
Statistics
Matches: 112, Mismatches: 18, Indels: 31
0.70 0.11 0.19
Matches are distributed among these distances:
27 3 0.03
28 23 0.21
29 37 0.33
30 37 0.33
31 12 0.11
ACGTcount: A:0.28, C:0.26, G:0.07, T:0.39
Consensus pattern (29 bp):
TACCCTCGAACTTCCAAAATTTCATTTTT
Found at i:6262 original size:20 final size:20
Alignment explanation
Indices: 6237--6278 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
6227 TACAATGTTC
*
6237 AAAAAAAGA-AATAGAAATA
1 AAAAAAAAATAATAGAAATA
*
6256 AAAAAAAAATAATAGTAATA
1 AAAAAAAAATAATAGAAATA
6276 AAA
1 AAA
6279 TAGCAATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.79, C:0.00, G:0.07, T:0.14
Consensus pattern (20 bp):
AAAAAAAAATAATAGAAATA
Found at i:6455 original size:11 final size:10
Alignment explanation
Indices: 6435--6477 Score: 52
Period size: 11 Copynumber: 4.2 Consensus size: 10
6425 GAAATGTCAT
*
6435 AAAATGAATA
1 AAAATAAATA
6445 ACAAATAAATA
1 A-AAATAAATA
6456 AAAATAAGATA
1 AAAATAA-ATA
6467 AAAAT-AATA
1 AAAATAAATA
6476 AA
1 AA
6478 TACACATTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
9 5 0.17
10 8 0.27
11 17 0.57
ACGTcount: A:0.74, C:0.02, G:0.05, T:0.19
Consensus pattern (10 bp):
AAAATAAATA
Found at i:8092 original size:12 final size:13
Alignment explanation
Indices: 8071--8103 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
8061 TTTAATTGAC
*
8071 TTTATATTTTT-T
1 TTTATTTTTTTAT
8083 TTTATTTTTTTAT
1 TTTATTTTTTTAT
8096 TTTATTTT
1 TTTATTTT
8104 GAGCCAGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 10 0.53
13 9 0.47
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (13 bp):
TTTATTTTTTTAT
Done.