Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007323.1 Kokia drynarioides strain JFW-HI SEQ_121939, 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: 12227
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.32
Found at i:879 original size:18 final size:18
Alignment explanation
Indices: 856--902 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
846 TTACTAAAAA
856 CTATTTTACAAAATAATC
1 CTATTTTACAAAATAATC
874 CTATTTTACAAAATAATC
1 CTATTTTACAAAATAATC
* *
892 GTATTTAACAA
1 CTATTTTACAA
903 CCAAACTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.45, C:0.15, G:0.02, T:0.38
Consensus pattern (18 bp):
CTATTTTACAAAATAATC
Found at i:1678 original size:20 final size:22
Alignment explanation
Indices: 1653--1696 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
1643 TAAAAATTGT
1653 ATAATT-T-CCAAATAATATTA
1 ATAATTATGCCAAATAATATTA
1673 ATAATTGATGCCAAATAATATTA
1 ATAATT-ATGCCAAATAATATTA
1696 A
1 A
1697 AAAAAGCAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 6 0.29
22 1 0.05
23 14 0.67
ACGTcount: A:0.50, C:0.09, G:0.05, T:0.36
Consensus pattern (22 bp):
ATAATTATGCCAAATAATATTA
Found at i:1764 original size:21 final size:22
Alignment explanation
Indices: 1728--1785 Score: 64
Period size: 22 Copynumber: 2.5 Consensus size: 22
1718 AACAACTGCG
*
1728 AAACATCAATAAAACAACACT-A
1 AAACATCCA-AAAACAACACTGA
*
1750 AAACATCCAAAAACAGCACTGA
1 AAACATCCAAAAACAACACTGA
1772 AAACAGTACCAAAA
1 AAACA-T-CCAAAA
1786 TGAACCAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
21 10 0.32
22 14 0.45
23 1 0.03
24 6 0.19
ACGTcount: A:0.60, C:0.24, G:0.05, T:0.10
Consensus pattern (22 bp):
AAACATCCAAAAACAACACTGA
Found at i:1797 original size:21 final size:21
Alignment explanation
Indices: 1771--1839 Score: 102
Period size: 21 Copynumber: 3.2 Consensus size: 21
1761 AACAGCACTG
*
1771 AAAACAGTACCAAAATGAACC
1 AAAACAGTACCAAAATGCACC
*
1792 AAAACAGTACCAAAATGCACTA
1 AAAACAGTACCAAAATGCAC-C
1814 AAAACAGTACCAAAACTGCACC
1 AAAACAGTACCAAAA-TGCACC
1836 AAAA
1 AAAA
1840 ACAACATCAA
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
21 19 0.44
22 19 0.44
23 5 0.12
ACGTcount: A:0.57, C:0.25, G:0.09, T:0.10
Consensus pattern (21 bp):
AAAACAGTACCAAAATGCACC
Found at i:1803 original size:11 final size:11
Alignment explanation
Indices: 1771--1839 Score: 54
Period size: 11 Copynumber: 6.4 Consensus size: 11
1761 AACAGCACTG
1771 AAAACAGTACC
1 AAAACAGTACC
* *
1782 AAAA-TGAACC
1 AAAACAGTACC
1792 AAAACAGTACC
1 AAAACAGTACC
*
1803 AAAATGCACTA--
1 AAAA--CAGTACC
1814 AAAACAGTACC
1 AAAACAGTACC
* *
1825 AAAACTGCACC
1 AAAACAGTACC
1836 AAAA
1 AAAA
1840 ACAACATCAA
Statistics
Matches: 45, Mismatches: 8, Indels: 10
0.71 0.13 0.16
Matches are distributed among these distances:
9 4 0.09
10 8 0.18
11 29 0.64
13 4 0.09
ACGTcount: A:0.57, C:0.25, G:0.09, T:0.10
Consensus pattern (11 bp):
AAAACAGTACC
Found at i:1839 original size:23 final size:23
Alignment explanation
Indices: 1771--1888 Score: 125
Period size: 23 Copynumber: 5.3 Consensus size: 23
1761 AACAGCACTG
*
1771 AAAACAGTACCAAAA-TGAACC-
1 AAAACAGTACCAAAACTGCACCA
*
1792 AAAACAGTACCAAAA-TGCACTA
1 AAAACAGTACCAAAACTGCACCA
1814 AAAACAGTACCAAAACTGCACCA
1 AAAACAGTACCAAAACTGCACCA
** * * * *
1837 AAAACAACATCAAATCAGCACGA
1 AAAACAGTACCAAAACTGCACCA
* *
1860 AAAATAGTACCAAATCTGCACCA
1 AAAACAGTACCAAAACTGCACCA
1883 AAAACA
1 AAAACA
1889 ACCTCCAAAA
Statistics
Matches: 79, Mismatches: 16, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
21 19 0.24
22 15 0.19
23 45 0.57
ACGTcount: A:0.55, C:0.25, G:0.08, T:0.11
Consensus pattern (23 bp):
AAAACAGTACCAAAACTGCACCA
Found at i:2064 original size:18 final size:18
Alignment explanation
Indices: 2018--2068 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
2008 ATCGAAGAAG
*
2018 CATCATTCTCATCATCCT
1 CATCATTCTCATCATCAT
*** *
2036 CATCGCCCTCATCGTCAT
1 CATCATTCTCATCATCAT
2054 CATCATTCTCATCAT
1 CATCATTCTCATCAT
2069 TCCTGCAATA
Statistics
Matches: 24, Mismatches: 9, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.22, C:0.39, G:0.04, T:0.35
Consensus pattern (18 bp):
CATCATTCTCATCATCAT
Found at i:5766 original size:28 final size:27
Alignment explanation
Indices: 5714--5766 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
5704 TATACTTTAC
* *
5714 ATATATTATTAATTAAAATTGAAAATA
1 ATATATTATTAATTAAAAATAAAAATA
5741 ATATATTTATTAATTAAAAATAAAAA
1 ATATA-TTATTAATTAAAAATAAAAA
5767 ATTTGAAACA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (27 bp):
ATATATTATTAATTAAAAATAAAAATA
Found at i:9515 original size:21 final size:21
Alignment explanation
Indices: 9491--9544 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
9481 TGTGATAGTT
*
9491 CTACCGATACAAGT-ATGACTA
1 CTACCGATACAA-TCATCACTA
* *
9512 CTACCGAAACAATCATCACTT
1 CTACCGATACAATCATCACTA
9533 CTACCGATACAA
1 CTACCGATACAA
9545 CAAACTCTAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 1 0.04
21 27 0.96
ACGTcount: A:0.39, C:0.30, G:0.09, T:0.22
Consensus pattern (21 bp):
CTACCGATACAATCATCACTA
Found at i:10762 original size:194 final size:195
Alignment explanation
Indices: 10322--10763 Score: 541
Period size: 195 Copynumber: 2.3 Consensus size: 195
10312 GTACTTGATA
** * * * * *
10322 CTGCTCACATGAGCTATCGAGGACTAGCAACATATGCGGTACCTCAGCCATCGATGCGATATCTG
1 CTGCTCACACAAGCTGTCGAGGACTCGCAACATATGCGGTACCTCAGCCATTGATACAATATCTG
* * *
10387 TGCATATAACTGTTCCCTAACGATGTTGCTCACACGAGTTGTCAAGAATATGCATTTATGCATAA
66 TGCATATAACTGTTCCCTAACGATGCTGCTCACACGAGTTGTCAAGAATATGCACTTATGAATAA
** * * *
10452 ATCCCAACCATTGTAAGACCTGTAATCCATTCTTGGATTCTTTTCTCGTTTCCTAACTCACGATG
131 ATCCCAACCATCATAAGACATATAATCCATTCTTGGATTCTTTTCTCATTTCCTAACTCACGATG
* *
10517 CTGCTGACACGAGCTGTCGAGGACTCGCAACATATGCGGTACCTCAGCCATTGATACAATATCTG
1 CTGCTCACACAAGCTGTCGAGGACTCGCAACATATGCGGTACCTCAGCCATTGATACAATATCTG
** ** ** * *
10582 TGCATATAACTGTTTTCTAACGATGCTGCTGGCACGAGTTGTTGATAATATTCACTTA-GAATAA
66 TGCATATAACTGTTCCCTAACGATGCTGCTCACACGAGTTGTCAAGAATATGCACTTATGAATAA
* * * *
10646 ATCTCAGCCATCATAGGACATATAATCCATTCTTGGATTCTTTTCTCATTT-CTCGACTCAC-AG
131 ATCCCAACCATCATAAGACATATAATCCATTCTTGGATTCTTTTCTCATTTCCT-AACTCACGA-
10709 TG
194 TG
* * *
10711 CT-CTTCACACAAGCTGTCGAGGACTCGTAACATATGTGGTACGTCAGCCATTG
1 CTGC-TCACACAAGCTGTCGAGGACTCGCAACATATGCGGTACCTCAGCCATTG
10764 CGTCAGTTTC
Statistics
Matches: 212, Mismatches: 32, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
193 4 0.02
194 102 0.48
195 106 0.50
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.31
Consensus pattern (195 bp):
CTGCTCACACAAGCTGTCGAGGACTCGCAACATATGCGGTACCTCAGCCATTGATACAATATCTG
TGCATATAACTGTTCCCTAACGATGCTGCTCACACGAGTTGTCAAGAATATGCACTTATGAATAA
ATCCCAACCATCATAAGACATATAATCCATTCTTGGATTCTTTTCTCATTTCCTAACTCACGATG
Found at i:11163 original size:45 final size:45
Alignment explanation
Indices: 11107--11205 Score: 180
Period size: 45 Copynumber: 2.2 Consensus size: 45
11097 ACTTTTCACT
*
11107 TTTATTAAATTTAGTCCTTTAGCTCAAAACTTGCAAATTAACCAG
1 TTTATTTAATTTAGTCCTTTAGCTCAAAACTTGCAAATTAACCAG
*
11152 TTTATTTAATTTAGTCCTTTAGCTCAAAACTTGCAAATTAACCAT
1 TTTATTTAATTTAGTCCTTTAGCTCAAAACTTGCAAATTAACCAG
11197 TTTATTTAA
1 TTTATTTAA
11206 ATTTCCAACT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 52 1.00
ACGTcount: A:0.34, C:0.16, G:0.07, T:0.42
Consensus pattern (45 bp):
TTTATTTAATTTAGTCCTTTAGCTCAAAACTTGCAAATTAACCAG
Done.