Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012761.1 Kokia drynarioides strain JFW-HI SEQ_127773, 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: 38078
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:1401 original size:43 final size:43
Alignment explanation
Indices: 1315--1402 Score: 131
Period size: 43 Copynumber: 2.0 Consensus size: 43
1305 TCATTCACAC
* * * *
1315 GTAAACCTTTCAAAATTTGTTAAATCAAATTATAATAACGAAA
1 GTAAACCTTCCAAAAATTGTTAAATCAAATTACAACAACGAAA
*
1358 GTAAACCTTCCAAAAATTGTTAAATCAAATTACAACAATGAAA
1 GTAAACCTTCCAAAAATTGTTAAATCAAATTACAACAACGAAA
1401 GT
1 GT
1403 CATTTCTTAT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.49, C:0.14, G:0.08, T:0.30
Consensus pattern (43 bp):
GTAAACCTTCCAAAAATTGTTAAATCAAATTACAACAACGAAA
Found at i:6146 original size:21 final size:21
Alignment explanation
Indices: 6113--6156 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
6103 TTCTAAATTA
* *
6113 ATTTATATTTTATATTAG-ATT
1 ATTTAAATATTAT-TTAGCATT
6134 ATTTAAATATTATTTAGCATT
1 ATTTAAATATTATTTAGCATT
6155 AT
1 AT
6157 ATTTAAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.57
Consensus pattern (21 bp):
ATTTAAATATTATTTAGCATT
Found at i:6573 original size:38 final size:38
Alignment explanation
Indices: 6522--6604 Score: 166
Period size: 38 Copynumber: 2.2 Consensus size: 38
6512 GGGTGAATAC
6522 TTGAATTAATTAACAGTTTCACATGTCAAAATCAAATG
1 TTGAATTAATTAACAGTTTCACATGTCAAAATCAAATG
6560 TTGAATTAATTAACAGTTTCACATGTCAAAATCAAATG
1 TTGAATTAATTAACAGTTTCACATGTCAAAATCAAATG
6598 TTGAATT
1 TTGAATT
6605 CACGTGTTAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 45 1.00
ACGTcount: A:0.41, C:0.12, G:0.11, T:0.36
Consensus pattern (38 bp):
TTGAATTAATTAACAGTTTCACATGTCAAAATCAAATG
Found at i:6950 original size:13 final size:13
Alignment explanation
Indices: 6932--6956 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6922 TTTAAAATAG
6932 AAATTTTTTTATT
1 AAATTTTTTTATT
6945 AAATTTTTTTAT
1 AAATTTTTTTAT
6957 AATTTATAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
AAATTTTTTTATT
Found at i:11873 original size:21 final size:22
Alignment explanation
Indices: 11833--11873 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
11823 TTCAACTGTT
*
11833 GGTTCAATCAAATTTTTATCTC
1 GGTTCAATCAAATTTGTATCTC
*
11855 GGTTCAA-CCAATTTGTATC
1 GGTTCAATCAAATTTGTATC
11874 AATTCGCGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.27, C:0.20, G:0.12, T:0.41
Consensus pattern (22 bp):
GGTTCAATCAAATTTGTATCTC
Found at i:16072 original size:16 final size:16
Alignment explanation
Indices: 16053--16083 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
16043 TACGGATTCA
*
16053 AATCATTTCAAATTTT
1 AATCATATCAAATTTT
16069 AATCATATCAAATTT
1 AATCATATCAAATTT
16084 AAAACTACTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.13, G:0.00, T:0.45
Consensus pattern (16 bp):
AATCATATCAAATTTT
Found at i:22806 original size:89 final size:89
Alignment explanation
Indices: 22566--22819 Score: 246
Period size: 89 Copynumber: 2.8 Consensus size: 89
22556 GATGGGGTTG
* * * *
22566 TTTTCCCTATGATGATGCGGATAGTGTTTTTTTTTCATCGGCATCTTCTTTCATGTTTGTTTTAC
1 TTTTTCCTACGATGAT-CTGATAATGTTTTTTTTT-ATCGGCA---TCTTTCATGTTTGTTTTAC
* *
22631 TGCTTATATTCGAATTGTTTTGGTTTGTT
61 TGTTTATGTTCGAATTGTTTTGGTTTGTT
** * * * *
22660 TTTTTCCCTGTGATGATGCTGATAA--TATTTTTTTATCGGTATCTTTCATATTTGTTTTACTAT
1 TTTTT-CCTACGATGAT-CTGATAATGTTTTTTTTTATCGGCATCTTTCATGTTTGTTTTACTGT
**
22723 TTATGTTCGGGTTGTTTTGGTTTGTT
64 TTATGTTCGAATTGTTTTGGTTTGTT
** *
22749 TTTTT-CTACGATGCCAT-TGATAATGTTTTTTTTTATCGGCATCTTTCATGTCGGTTTTATTGT
1 TTTTTCCTACGATG--ATCTGATAATGTTTTTTTTTATCGGCATCTTTCATGTTTGTTTTACTGT
22812 TTATGTTC
64 TTATGTTC
22820 AGAGTGTTTT
Statistics
Matches: 134, Mismatches: 21, Indels: 15
0.79 0.12 0.09
Matches are distributed among these distances:
87 12 0.09
89 88 0.66
92 6 0.04
93 8 0.06
94 4 0.03
95 16 0.12
ACGTcount: A:0.15, C:0.13, G:0.17, T:0.56
Consensus pattern (89 bp):
TTTTTCCTACGATGATCTGATAATGTTTTTTTTTATCGGCATCTTTCATGTTTGTTTTACTGTTT
ATGTTCGAATTGTTTTGGTTTGTT
Found at i:29691 original size:23 final size:23
Alignment explanation
Indices: 29665--29718 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
29655 ACACTAGCGC
* * *
29665 GCTTACTGTTTCGCACTTCGTGT
1 GCTTACTGTTTCACACGTCATGT
*
29688 GCTTATTGTTTCACACGTCATGT
1 GCTTACTGTTTCACACGTCATGT
*
29711 GCCTACTG
1 GCTTACTG
29719 ATTTACGCTA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.13, C:0.26, G:0.20, T:0.41
Consensus pattern (23 bp):
GCTTACTGTTTCACACGTCATGT
Found at i:29762 original size:22 final size:22
Alignment explanation
Indices: 29737--29785 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
29727 TATGTGCGCA
*
29737 TATTGATTGCATTGTGTGTGCC
1 TATTGATTGCACTGTGTGTGCC
* *
29759 TATTGGTTGCACTGTGTGTGCT
1 TATTGATTGCACTGTGTGTGCC
29781 TATTG
1 TATTG
29786 TTTCCCTAGC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.12, C:0.12, G:0.29, T:0.47
Consensus pattern (22 bp):
TATTGATTGCACTGTGTGTGCC
Found at i:32693 original size:2 final size:2
Alignment explanation
Indices: 32686--32715 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
32676 TTCTCTTTAA
*
32686 AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
32716 GCATAAAATG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Done.