Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003525.1 Kokia drynarioides strain JFW-HI SEQ_116368, 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: 92752
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:434 original size:5 final size:5
Alignment explanation
Indices: 424--449 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
414 AGGATAATGT
424 ATTAA ATTAA ATTAA ATTAA ATTAA A
1 ATTAA ATTAA ATTAA ATTAA ATTAA A
450 AGGATCGAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
ATTAA
Found at i:1656 original size:7 final size:7
Alignment explanation
Indices: 1646--1671 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
1636 TGCAAGTTGC
1646 AATGGCA
1 AATGGCA
1653 AATGGCA
1 AATGGCA
1660 AATGGCA
1 AATGGCA
1667 AATGG
1 AATGG
1672 TTTGGCGGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.42, C:0.12, G:0.31, T:0.15
Consensus pattern (7 bp):
AATGGCA
Found at i:2166 original size:14 final size:15
Alignment explanation
Indices: 2147--2181 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
2137 CAAACTTCAT
2147 TTATTTA-TTAAATA
1 TTATTTATTTAAATA
2161 TTATTTATTTTAAATA
1 TTATTTA-TTTAAATA
2177 TTATT
1 TTATT
2182 AAATTAACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 7 0.37
16 12 0.63
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TTATTTATTTAAATA
Found at i:2932 original size:18 final size:18
Alignment explanation
Indices: 2876--2938 Score: 63
Period size: 18 Copynumber: 3.4 Consensus size: 18
2866 TATCATGAAT
* *
2876 TATTATTATAATTGTTGTA
1 TATTATTTTAAGT-TTGTA
** *
2895 TATTATTTTATTTTTTTA
1 TATTATTTTAAGTTTGTA
*
2913 TATAATTTTAAGTTTGTA
1 TATTATTTTAAGTTTGTA
2931 TATTATTT
1 TATTATTT
2939 AAAAATAATA
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
18 25 0.69
19 11 0.31
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
TATTATTTTAAGTTTGTA
Found at i:3620 original size:14 final size:14
Alignment explanation
Indices: 3601--3631 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
3591 TTAATTGATT
3601 TTTAATTAAATAAA
1 TTTAATTAAATAAA
*
3615 TTTAATTAATTAAA
1 TTTAATTAAATAAA
3629 TTT
1 TTT
3632 TCTAAATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TTTAATTAAATAAA
Found at i:4878 original size:38 final size:39
Alignment explanation
Indices: 4802--4880 Score: 133
Period size: 40 Copynumber: 2.0 Consensus size: 39
4792 CACGTTTGCC
4802 TTATCCTTGGCTAGTTGACAACCATACTACTTCTAATCTG
1 TTATCCTTGGCTAGTTGACAACCA-ACTACTTCTAATCTG
*
4842 TTATCCTTGGCTAGTTGACAACC-ACTACTTTTAATCTG
1 TTATCCTTGGCTAGTTGACAACCAACTACTTCTAATCTG
4880 T
1 T
4881 CATGAAAATG
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
38 15 0.39
40 23 0.61
ACGTcount: A:0.24, C:0.24, G:0.13, T:0.39
Consensus pattern (39 bp):
TTATCCTTGGCTAGTTGACAACCAACTACTTCTAATCTG
Found at i:23517 original size:26 final size:26
Alignment explanation
Indices: 23481--23530 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
23471 AAATTTTTTC
* * *
23481 TCTGTTCTCTTTGTACCATTATTACT
1 TCTGTTATCTTGGTACCACTATTACT
23507 TCTGTTATCTTGGTACCACTATTA
1 TCTGTTATCTTGGTACCACTATTA
23531 TATCTTCTGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.18, C:0.22, G:0.10, T:0.50
Consensus pattern (26 bp):
TCTGTTATCTTGGTACCACTATTACT
Found at i:42082 original size:18 final size:18
Alignment explanation
Indices: 42042--42084 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
42032 TTTTCAGTTG
42042 TAATTAATGTAAAATTTT
1 TAATTAATGTAAAATTTT
* *
42060 CAATTAAT-TAAATTTATT
1 TAATTAATGTAAAATT-TT
42078 TAATTAA
1 TAATTAA
42085 AAAATTATTC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (18 bp):
TAATTAATGTAAAATTTT
Found at i:57778 original size:27 final size:28
Alignment explanation
Indices: 57725--57783 Score: 91
Period size: 28 Copynumber: 2.1 Consensus size: 28
57715 CCATGCCACC
*
57725 TTTCTATCTGATAAAAAAATTTAAATTT
1 TTTCCATCTGATAAAAAAATTTAAATTT
* *
57753 TTTCCATCTGATAAAAAAATTCAATTTT
1 TTTCCATCTGATAAAAAAATTTAAATTT
57781 TTT
1 TTT
57784 TTGTGTTGGC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.39, C:0.10, G:0.03, T:0.47
Consensus pattern (28 bp):
TTTCCATCTGATAAAAAAATTTAAATTT
Found at i:57832 original size:77 final size:77
Alignment explanation
Indices: 57681--57833 Score: 234
Period size: 78 Copynumber: 2.0 Consensus size: 77
57671 CCACCTATTT
*
57681 ATCTGATAAAAAAAATCAAATTTTTTTGTGTCGGCCATGCCACCTTTCTATCTGATAAAAAAATT
1 ATCTGATAAAAAAAATCAAATTTTTTTGTGTCGGCCATGCCACCTTTCTATCTGATAAAAAAAAT
*
57746 TAAATTTTTTCC
66 CAAATTTTTTCC
* * * * *
57758 ATCTGATAAAAAAATTCAATTTTTTTTTGTGTTGGCCATGCCACCTTTTTATTTGATAAAAAAAA
1 ATCTGATAAAAAAAATCAA-ATTTTTTTGTGTCGGCCATGCCACCTTTCTATCTGATAAAAAAAA
57823 TCAAATTTTTT
65 TCAAATTTTTT
57834 GGTGTTGGTC
Statistics
Matches: 68, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
77 18 0.26
78 50 0.74
ACGTcount: A:0.35, C:0.14, G:0.09, T:0.42
Consensus pattern (77 bp):
ATCTGATAAAAAAAATCAAATTTTTTTGTGTCGGCCATGCCACCTTTCTATCTGATAAAAAAAAT
CAAATTTTTTCC
Found at i:57904 original size:62 final size:59
Alignment explanation
Indices: 57816--57954 Score: 172
Period size: 62 Copynumber: 2.3 Consensus size: 59
57806 TTATTTGATA
* * * * *
57816 AAAAAAATCAAATTTTTTGGTGTTGGTCATTGTA-TGGTTGACACCACCTTTTTTATCTAGT
1 AAAAAAATCAAATTTTTTGGTATTGGTCA-TGCATTGATCGACACCACCTATTTTATC-A-T
57877 AAAAAAATCAAATTTTGTTGGTATTGGTCATGCATTGATCGACACCACCTATTTTATCAT
1 AAAAAAATCAAATTTT-TTGGTATTGGTCATGCATTGATCGACACCACCTATTTTATCAT
* *
57937 ATAAAAATCAATTTTTTT
1 AAAAAAATCAAATTTTTT
57955 TTTGTTTTGG
Statistics
Matches: 69, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
59 2 0.03
60 15 0.22
61 20 0.29
62 32 0.46
ACGTcount: A:0.32, C:0.14, G:0.13, T:0.41
Consensus pattern (59 bp):
AAAAAAATCAAATTTTTTGGTATTGGTCATGCATTGATCGACACCACCTATTTTATCAT
Found at i:58853 original size:18 final size:17
Alignment explanation
Indices: 58832--58895 Score: 59
Period size: 17 Copynumber: 3.9 Consensus size: 17
58822 AATTAGAAAT
58832 GAAATTTAAAATATAAAC
1 GAAA-TTAAAATATAAAC
58850 GAAATTACAAAT-T--A-
1 GAAATTA-AAATATAAAC
58864 -AAATTAAAATATAAAC
1 GAAATTAAAATATAAAC
58880 GAAATTACAAAT-TAAA
1 GAAATTA-AAATATAAA
58896 TTAAAAAAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 15
0.72 0.00 0.28
Matches are distributed among these distances:
12 4 0.10
13 7 0.18
15 2 0.05
17 14 0.36
18 12 0.31
ACGTcount: A:0.62, C:0.06, G:0.05, T:0.27
Consensus pattern (17 bp):
GAAATTAAAATATAAAC
Found at i:58871 original size:30 final size:30
Alignment explanation
Indices: 58822--58913 Score: 132
Period size: 30 Copynumber: 3.1 Consensus size: 30
58812 AAAAAATAAT
* * *
58822 AATTAGAAATGAAATTTAAAATATAAACGA
1 AATTACAAATTAAAATTAAAATATAAACGA
58852 AATTACAAATTAAAATTAAAATATAAACGA
1 AATTACAAATTAAAATTAAAATATAAACGA
*
58882 AATTACAAATT-AAATTAAAAAAATAAACGA
1 AATTACAAATTAAAATT-AAAATATAAACGA
58912 AA
1 AA
58914 AAAATCAAAA
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
29 5 0.09
30 52 0.91
ACGTcount: A:0.64, C:0.05, G:0.05, T:0.25
Consensus pattern (30 bp):
AATTACAAATTAAAATTAAAATATAAACGA
Found at i:80238 original size:23 final size:25
Alignment explanation
Indices: 80208--80263 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
80198 CAAGAGGACT
80208 ACGGCTAGAG-T-CTTTTTTGACAG
1 ACGGCTAGAGTTGCTTTTTTGACAG
* *
80231 ACGGCTAGGGTTGTTTTTTTGACAG
1 ACGGCTAGAGTTGCTTTTTTGACAG
*
80256 ACGACTAG
1 ACGGCTAG
80264 GGTTTTTGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 9 0.32
24 1 0.04
25 18 0.64
ACGTcount: A:0.21, C:0.16, G:0.29, T:0.34
Consensus pattern (25 bp):
ACGGCTAGAGTTGCTTTTTTGACAG
Found at i:80254 original size:25 final size:25
Alignment explanation
Indices: 80220--80267 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
80210 GGCTAGAGTC
*
80220 TTTTTTGACAGACGGCTAGGGTTGT
1 TTTTTTGACAGACGACTAGGGTTGT
80245 TTTTTTGACAGACGACTAGGGTT
1 TTTTTTGACAGACGACTAGGGTT
80268 TTTGAAATCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.19, C:0.12, G:0.29, T:0.40
Consensus pattern (25 bp):
TTTTTTGACAGACGACTAGGGTTGT
Found at i:83635 original size:43 final size:43
Alignment explanation
Indices: 83574--83661 Score: 176
Period size: 43 Copynumber: 2.0 Consensus size: 43
83564 ACCTTAGTTG
83574 TTTTCTGTTTTCCAATGTAGGGGATATAACATAACAGAAGTCT
1 TTTTCTGTTTTCCAATGTAGGGGATATAACATAACAGAAGTCT
83617 TTTTCTGTTTTCCAATGTAGGGGATATAACATAACAGAAGTCT
1 TTTTCTGTTTTCCAATGTAGGGGATATAACATAACAGAAGTCT
83660 TT
1 TT
83662 CTCTAAATTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.39
Consensus pattern (43 bp):
TTTTCTGTTTTCCAATGTAGGGGATATAACATAACAGAAGTCT
Found at i:85331 original size:6 final size:6
Alignment explanation
Indices: 85322--85350 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
85312 TGCTCCTCCA
85322 AACCCT AACCCT AACCCT AACCCT AACCC
1 AACCCT AACCCT AACCCT AACCCT AACCC
85351 CACGCCTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.52, G:0.00, T:0.14
Consensus pattern (6 bp):
AACCCT
Done.