Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002647.1 Kokia drynarioides strain JFW-HI SEQ_114883, 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: 26818
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Found at i:2803 original size:5 final size:5
Alignment explanation
Indices: 2790--2828 Score: 53
Period size: 5 Copynumber: 7.8 Consensus size: 5
2780 TTTATGAACT
*
2790 TTTTT TTTTC TTTTC TTTTC TTTTC TTCTTC -TTTC TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TT-TTC TTTTC TTTT
2829 ATGCGATTGA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
4 3 0.10
5 25 0.81
6 3 0.10
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTC
Found at i:11013 original size:25 final size:24
Alignment explanation
Indices: 10985--11125 Score: 86
Period size: 24 Copynumber: 5.9 Consensus size: 24
10975 TTTCAGAAAT
10985 TTAGCTCATACGAGCCTAGACAAAA
1 TTAGCTCATACGAGCCTAGA-AAAA
* * * **
11010 TTAGCTCATACAAGCCCAGATAGG
1 TTAGCTCATACGAGCCTAGAAAAA
* **
11034 TTAGCTCTTACGAGCCTAG-AATG
1 TTAGCTCATACGAGCCTAGAAAAA
* * * ***
11057 TTAGCTCTTACAAGCCCAGAATGG
1 TTAGCTCATACGAGCCTAGAAAAA
* * ***
11081 TTAGCTCTTACGAGCCCAGAATGG
1 TTAGCTCATACGAGCCTAGAAAAA
*
11105 TTAGCTCTTACGAGCCTAGAA
1 TTAGCTCATACGAGCCTAGAA
11126 TGCTTAGCTC
Statistics
Matches: 99, Mismatches: 16, Indels: 3
0.84 0.14 0.03
Matches are distributed among these distances:
23 19 0.19
24 62 0.63
25 18 0.18
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.25
Consensus pattern (24 bp):
TTAGCTCATACGAGCCTAGAAAAA
Found at i:11087 original size:71 final size:72
Alignment explanation
Indices: 11010--11170 Score: 254
Period size: 71 Copynumber: 2.2 Consensus size: 72
11000 CTAGACAAAA
* *
11010 TTAGCTCATACAAGCCCAG-ATAGGTTAGCTCTTACGAGCCTAGAATG-TTAGCTCTTACAAGCC
1 TTAGCTCTTACGAGCCCAGAAT-GGTTAGCTCTTACGAGCCTAGAATGCTTAGCTCTTACAAGCC
*
11073 CAGAATGG
65 CAAAATGG
**
11081 TTAGCTCTTACGAGCCCAGAATGGTTAGCTCTTACGAGCCTAGAATGCTTAGCTCTTATTAGCCC
1 TTAGCTCTTACGAGCCCAGAATGGTTAGCTCTTACGAGCCTAGAATGCTTAGCTCTTACAAGCCC
11146 AAAATGG
66 AAAATGG
11153 TTAGCTCTTACGAGCCCA
1 TTAGCTCTTACGAGCCCA
11171 AAATCATATT
Statistics
Matches: 83, Mismatches: 5, Indels: 3
0.91 0.05 0.03
Matches are distributed among these distances:
71 42 0.51
72 41 0.49
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.27
Consensus pattern (72 bp):
TTAGCTCTTACGAGCCCAGAATGGTTAGCTCTTACGAGCCTAGAATGCTTAGCTCTTACAAGCCC
AAAATGG
Found at i:11174 original size:24 final size:24
Alignment explanation
Indices: 11010--11170 Score: 218
Period size: 24 Copynumber: 6.8 Consensus size: 24
11000 CTAGACAAAA
* *
11010 TTAGCTCATACAAGCCCAG-ATAGG
1 TTAGCTCTTACGAGCCCAGAAT-GG
*
11034 TTAGCTCTTACGAGCCTAGAAT-G
1 TTAGCTCTTACGAGCCCAGAATGG
*
11057 TTAGCTCTTACAAGCCCAGAATGG
1 TTAGCTCTTACGAGCCCAGAATGG
11081 TTAGCTCTTACGAGCCCAGAATGG
1 TTAGCTCTTACGAGCCCAGAATGG
* *
11105 TTAGCTCTTACGAGCCTAGAATGC
1 TTAGCTCTTACGAGCCCAGAATGG
** *
11129 TTAGCTCTTATTAGCCCAAAATGG
1 TTAGCTCTTACGAGCCCAGAATGG
11153 TTAGCTCTTACGAGCCCA
1 TTAGCTCTTACGAGCCCA
11171 AAATCATATT
Statistics
Matches: 120, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
23 21 0.17
24 97 0.81
25 2 0.02
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.27
Consensus pattern (24 bp):
TTAGCTCTTACGAGCCCAGAATGG
Found at i:15792 original size:22 final size:22
Alignment explanation
Indices: 15766--15817 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
15756 AGCATGTACA
* *
15766 GTGCTCTCCGTATAGCACGTTT
1 GTGCTCTCCGTATAGCACCTTG
*
15788 GTGCTCTCCGTTTAGCACCTTG
1 GTGCTCTCCGTATAGCACCTTG
15810 GTGCTCTC
1 GTGCTCTC
15818 TGTTCATTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.10, C:0.31, G:0.23, T:0.37
Consensus pattern (22 bp):
GTGCTCTCCGTATAGCACCTTG
Found at i:19146 original size:14 final size:15
Alignment explanation
Indices: 19127--19159 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
19117 ATTACGTTGG
19127 AAAACA-ACAAAATA
1 AAAACATACAAAATA
*
19141 AAAACATCCAAAATA
1 AAAACATACAAAATA
19156 AAAA
1 AAAA
19160 TTGGGCTAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.76, C:0.15, G:0.00, T:0.09
Consensus pattern (15 bp):
AAAACATACAAAATA
Found at i:21900 original size:21 final size:21
Alignment explanation
Indices: 21862--21901 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
21852 TACCCTACAC
* * *
21862 TTCTATCGATACATGTATGAG
1 TTCTACCGAAACAAGTATGAG
21883 TTCTACCGAAACAAGTATG
1 TTCTACCGAAACAAGTATG
21902 CAGAATCTCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (21 bp):
TTCTACCGAAACAAGTATGAG
Found at i:22487 original size:52 final size:52
Alignment explanation
Indices: 22424--22610 Score: 329
Period size: 52 Copynumber: 3.6 Consensus size: 52
22414 AAAGAATCAC
* * *
22424 ATACTCACGATGACACCTAGTCATCGAACCTCATAATCTGTAAAGGATTCAT
1 ATACTCACGATGACACGTAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
*
22476 ATACTCACGATGACACGTAGTCATCGGACCTCATAATCCATAAAGGATTCAT
1 ATACTCACGATGACACGTAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
22528 ATACTCACGATGACACGTAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACGTAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
*
22580 ATACTCACCATGACACGTAGTCATCGGACCT
1 ATACTCACGATGACACGTAGTCATCGGACCT
22611 TTTTCATTTA
Statistics
Matches: 129, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 129 1.00
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.25
Consensus pattern (52 bp):
ATACTCACGATGACACGTAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
Done.