Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009728.1 Kokia drynarioides strain JFW-HI SEQ_124447, 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: 47014
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Warning! 6 characters in sequence are not A, C, G, or T
Found at i:89 original size:13 final size:13
Alignment explanation
Indices: 70--122 Score: 65
Period size: 13 Copynumber: 4.2 Consensus size: 13
60 AAACACATTA
*
70 CCTTTCTTTC-CT
1 CCTTTCTTTCTTT
82 CTCTTTC-TTCTTT
1 C-CTTTCTTTCTTT
*
95 TCTTTCTTTCTTT
1 CCTTTCTTTCTTT
108 CCTTTCTTTCTTT
1 CCTTTCTTTCTTT
121 CC
1 CC
123 CGTTTATTTG
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
12 9 0.26
13 26 0.74
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (13 bp):
CCTTTCTTTCTTT
Found at i:90 original size:4 final size:4
Alignment explanation
Indices: 71--121 Score: 59
Period size: 4 Copynumber: 12.2 Consensus size: 4
61 AACACATTAC
*
71 CTTT CTTT CCTCT CTTT C-TT CTTTT CTTT CTTT CTTT CCTTT CTTT CTTT
1 CTTT CTTT -CTTT CTTT CTTT C-TTT CTTT CTTT CTTT -CTTT CTTT CTTT
121 C
1 C
122 CCGTTTATTT
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
3 3 0.07
4 28 0.68
5 10 0.24
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (4 bp):
CTTT
Found at i:101 original size:9 final size:9
Alignment explanation
Indices: 71--120 Score: 52
Period size: 9 Copynumber: 5.9 Consensus size: 9
61 AACACATTAC
*
71 CTTTCTTTC
1 CTTTCTTTT
*
80 CTCTC-TTT
1 CTTTCTTTT
88 C-TTCTTTT
1 CTTTCTTTT
96 CTTTC-TTT
1 CTTTCTTTT
*
104 CTTTCCTTT
1 CTTTCTTTT
113 CTTTCTTT
1 CTTTCTTT
121 CCCGTTTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
7 2 0.06
8 15 0.44
9 17 0.50
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (9 bp):
CTTTCTTTT
Found at i:11438 original size:28 final size:29
Alignment explanation
Indices: 11405--11460 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
11395 CCAAAAAATT
*
11405 ATTAACCGAC-CTCAACCGAATTAATTTG
1 ATTAACCGACGATCAACCGAATTAATTTG
*
11433 ATTAACCGACTGATTAACCGAATTAATT
1 ATTAACCGAC-GATCAACCGAATTAATT
11461 CGGTTTTACC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 10 0.42
30 14 0.58
ACGTcount: A:0.38, C:0.21, G:0.11, T:0.30
Consensus pattern (29 bp):
ATTAACCGACGATCAACCGAATTAATTTG
Found at i:14006 original size:23 final size:24
Alignment explanation
Indices: 13972--14018 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
13962 AAATAATTAA
13972 ACAATTCATTTCATA-ATTCAATT
1 ACAATTCATTTCATATATTCAATT
13995 ACAA-TCATTTTCATATTATTCAAT
1 ACAATTCA-TTTCATA-TATTCAAT
14019 CATATCTGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
22 3 0.14
23 11 0.52
25 7 0.33
ACGTcount: A:0.38, C:0.17, G:0.00, T:0.45
Consensus pattern (24 bp):
ACAATTCATTTCATATATTCAATT
Found at i:25085 original size:34 final size:34
Alignment explanation
Indices: 25047--25121 Score: 89
Period size: 33 Copynumber: 2.2 Consensus size: 34
25037 TTAACTTTTT
* *
25047 ATCTTAATTTGAAATTCAAATTAATCATTTTAAA
1 ATCTTAATGTAAAATTCAAATTAATCATTTTAAA
* * *
25081 ATCTTAA-GTAAAATTCAAATTACTCTTTTTTAA
1 ATCTTAATGTAAAATTCAAATTAATCATTTTAAA
*
25114 ATCCTAAT
1 ATCTTAAT
25122 AGAATTTATC
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
33 27 0.79
34 7 0.21
ACGTcount: A:0.41, C:0.12, G:0.03, T:0.44
Consensus pattern (34 bp):
ATCTTAATGTAAAATTCAAATTAATCATTTTAAA
Found at i:27267 original size:45 final size:45
Alignment explanation
Indices: 27203--27294 Score: 166
Period size: 45 Copynumber: 2.0 Consensus size: 45
27193 AAAGATGAAA
27203 ATATCATCTTTTTCATTATGTTAACCGTCCATGCCCTTTTCTTCC
1 ATATCATCTTTTTCATTATGTTAACCGTCCATGCCCTTTTCTTCC
**
27248 ATATCATCTTTTTCATTATGTTAGTCGTCCATGCCCTTTTCTTCC
1 ATATCATCTTTTTCATTATGTTAACCGTCCATGCCCTTTTCTTCC
27293 AT
1 AT
27295 TTCCAACTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.17, C:0.27, G:0.08, T:0.48
Consensus pattern (45 bp):
ATATCATCTTTTTCATTATGTTAACCGTCCATGCCCTTTTCTTCC
Found at i:28600 original size:23 final size:23
Alignment explanation
Indices: 28562--28628 Score: 73
Period size: 23 Copynumber: 2.9 Consensus size: 23
28552 CCTCAGTTAG
*
28562 TAGCACTGTGTGTGCTCTCTGAT
1 TAGCATTGTGTGTGCTCTCTGAT
* * * *
28585 TAGTACTT-TGTGTGCTTTTTTAT
1 TAGCA-TTGTGTGTGCTCTCTGAT
28608 TAGCATTGTGTGTGCTCTCTG
1 TAGCATTGTGTGTGCTCTCTG
28629 TTGCCCAGCA
Statistics
Matches: 33, Mismatches: 9, Indels: 4
0.72 0.20 0.09
Matches are distributed among these distances:
22 2 0.06
23 30 0.91
24 1 0.03
ACGTcount: A:0.12, C:0.16, G:0.24, T:0.48
Consensus pattern (23 bp):
TAGCATTGTGTGTGCTCTCTGAT
Found at i:36673 original size:17 final size:17
Alignment explanation
Indices: 36647--36682 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
36637 AAAAAAATAA
36647 TAAAAATATAAATATTT
1 TAAAAATATAAATATTT
*
36664 TAAAACTATAAATATTT
1 TAAAAATATAAATATTT
36681 TA
1 TA
36683 CTAAAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.42
Consensus pattern (17 bp):
TAAAAATATAAATATTT
Found at i:41012 original size:12 final size:12
Alignment explanation
Indices: 40978--41038 Score: 68
Period size: 12 Copynumber: 5.1 Consensus size: 12
40968 TTAACAACAA
*
40978 AACAACAAAAAT
1 AACAACAAAAAC
* *
40990 AGCAATAAAAAC
1 AACAACAAAAAC
*
41002 AACAACTAAAAC
1 AACAACAAAAAC
*
41014 AACAACAAAAAA
1 AACAACAAAAAC
*
41026 AACATCAAAAAC
1 AACAACAAAAAC
41038 A
1 A
41039 GCAATATAAT
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
12 39 1.00
ACGTcount: A:0.72, C:0.20, G:0.02, T:0.07
Consensus pattern (12 bp):
AACAACAAAAAC
Found at i:41012 original size:24 final size:24
Alignment explanation
Indices: 40976--41044 Score: 84
Period size: 24 Copynumber: 2.9 Consensus size: 24
40966 AATTAACAAC
*
40976 AAAACAACAAAAATAGCAATAAAA
1 AAAACAACAAAAACAGCAATAAAA
* * * *
41000 ACAACAACTAAAACAACAACAAAA
1 AAAACAACAAAAACAGCAATAAAA
*
41024 AAAACATCAAAAACAGCAATA
1 AAAACAACAAAAACAGCAATA
41045 TAATTTTTTA
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.71, C:0.19, G:0.03, T:0.07
Consensus pattern (24 bp):
AAAACAACAAAAACAGCAATAAAA
Found at i:42701 original size:24 final size:24
Alignment explanation
Indices: 42674--42724 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
42664 AAAAGGACGA
42674 AAAGTATAAATGGTATAAATAATG
1 AAAGTATAAATGGTATAAATAATG
42698 AAAGTATAAATGGTATAAATAATG
1 AAAGTATAAATGGTATAAATAATG
42722 AAA
1 AAA
42725 AATAAATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.57, C:0.00, G:0.16, T:0.27
Consensus pattern (24 bp):
AAAGTATAAATGGTATAAATAATG
Found at i:43917 original size:109 final size:109
Alignment explanation
Indices: 43715--43919 Score: 243
Period size: 109 Copynumber: 1.9 Consensus size: 109
43705 AGAATCAAGG
* * * * * * *
43715 CAATGTTCTTTTATTTTAGGGAATTCGAGAATTTGTACCCTAACGTGTTGGGTATAGCTTTTCTT
1 CAATGTTCTGTTATTTTAGGGAACTCGAAAAATTGTACCCTAACATGTTGGATATAGCTTTTCCT
* *
43780 TGAACCTAAATAATTGAGGATCCTATTTAAAACCGATAAATGTT
66 TGAACCTAAATAATAGAAGATCCTATTTAAAACCGATAAATGTT
* ** *
43824 CAATGTTCTGTTATTTTAGGGGACTCGAAAAATTGTGTCCTAACATGTTGGATAT-GATTTTTCC
1 CAATGTTCTGTTATTTTAGGGAACTCGAAAAATTGTACCCTAACATGTTGGATATAG-CTTTTCC
* *
43888 TTGAACCTAAGTAATAGAATAT-CTCATTTAAA
65 TTGAACCTAAATAATAGAAGATCCT-ATTTAAA
43920 CATCTCATTC
Statistics
Matches: 79, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
108 3 0.04
109 76 0.96
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.39
Consensus pattern (109 bp):
CAATGTTCTGTTATTTTAGGGAACTCGAAAAATTGTACCCTAACATGTTGGATATAGCTTTTCCT
TGAACCTAAATAATAGAAGATCCTATTTAAAACCGATAAATGTT
Done.