Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009272.1 Kokia drynarioides strain JFW-HI SEQ_123977, 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: 25624
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.31
Warning! 4 characters in sequence are not A, C, G, or T
Found at i:4042 original size:35 final size:35
Alignment explanation
Indices: 3994--4074 Score: 92
Period size: 35 Copynumber: 2.3 Consensus size: 35
3984 TTCCATTAAA
* *
3994 AAATATTTGTATTA-AACAAATTACCATAAATATAAT
1 AAATATTT-TATTATAACAAA-AAACATAAATATAAT
**
4030 AAATATTTTATTATATTAAAAAACATAAATATAAT
1 AAATATTTTATTATAACAAAAAACATAAATATAAT
*
4065 AAATGTTTTA
1 AAATATTTTA
4075 CTGTACTAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
35 27 0.69
36 12 0.31
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (35 bp):
AAATATTTTATTATAACAAAAAACATAAATATAAT
Found at i:16601 original size:32 final size:32
Alignment explanation
Indices: 16544--16660 Score: 99
Period size: 32 Copynumber: 3.8 Consensus size: 32
16534 AATTAGGTAC
*
16544 CAAATTAAG--AAAAATGATAAATTCAAGTAT
1 CAAATTAAGAAAAAAATGATAAATTCAAATAT
*
16574 CAAATTAAGAAAAAAATG-TCAAGTTCAAATAT
1 CAAATTAAGAAAAAAATGAT-AAATTCAAATAT
* *
16606 CAAATTAA-ATAAAAA--A-AAACT-AAATA-
1 CAAATTAAGAAAAAAATGATAAATTCAAATAT
*
16632 CTAAATTAAGAAAAAAATTATCAAATTCA
1 C-AAATTAAGAAAAAAATGAT-AAATTCA
16661 GATAATAAAT
Statistics
Matches: 69, Mismatches: 7, Indels: 19
0.73 0.07 0.20
Matches are distributed among these distances:
26 1 0.01
27 12 0.17
28 9 0.13
30 10 0.14
31 7 0.10
32 29 0.42
33 1 0.01
ACGTcount: A:0.61, C:0.09, G:0.06, T:0.25
Consensus pattern (32 bp):
CAAATTAAGAAAAAAATGATAAATTCAAATAT
Found at i:18281 original size:27 final size:26
Alignment explanation
Indices: 18240--18306 Score: 82
Period size: 27 Copynumber: 2.5 Consensus size: 26
18230 TTAATGATTC
* *
18240 AATATA-AATAGATATAATTATTATTT
1 AATATATAATATATATAATTA-AATTT
18266 AATATATAATATATATAATTAAATTT
1 AATATATAATATATATAATTAAATTT
*
18292 TATAATATAATATAT
1 AAT-ATATAATATAT
18307 TTAGGTTGGA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
26 12 0.33
27 24 0.67
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.46
Consensus pattern (26 bp):
AATATATAATATATATAATTAAATTT
Found at i:19813 original size:22 final size:20
Alignment explanation
Indices: 19788--19893 Score: 87
Period size: 22 Copynumber: 5.2 Consensus size: 20
19778 AATATATTGT
19788 TGTTTTGGTTGCTATTTTTTAC
1 TGTTTTGGTTG-T-TTTTTTAC
*
19810 TGTTTTAGTGTTGTGTTTTTAC
1 TGTTTT-G-GTTGTTTTTTTAC
19832 TGTTTT-G--GTTTTTTTAC
1 TGTTTTGGTTGTTTTTTTAC
19849 TGTTTTGG-TGCTATTTTTTAC
1 TGTTTTGGTTG-T-TTTTTTAC
* *
19870 TATTTTGG-TGTTGTTTTTAT
1 TGTTTTGGTTGTT-TTTTTAC
19890 TGTT
1 TGTT
19894 ATTTTTGTTG
Statistics
Matches: 72, Mismatches: 5, Indels: 16
0.77 0.05 0.17
Matches are distributed among these distances:
17 15 0.21
18 1 0.01
19 3 0.04
20 11 0.15
21 17 0.24
22 19 0.26
23 2 0.03
24 4 0.06
ACGTcount: A:0.08, C:0.06, G:0.20, T:0.66
Consensus pattern (20 bp):
TGTTTTGGTTGTTTTTTTAC
Found at i:19846 original size:39 final size:38
Alignment explanation
Indices: 19802--19878 Score: 109
Period size: 39 Copynumber: 2.0 Consensus size: 38
19792 TTGGTTGCTA
* * *
19802 TTTTTTACTGTTTTAGTGTTGTGTTTTTACTGTTTTGGT
1 TTTTTTACTGTTTTAGTGCTAT-TTTTTACTATTTTGGT
*
19841 TTTTTTACTGTTTTGGTGCTATTTTTTACTATTTTGGT
1 TTTTTTACTGTTTTAGTGCTATTTTTTACTATTTTGGT
19879 GTTGTTTTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
38 15 0.44
39 19 0.56
ACGTcount: A:0.09, C:0.06, G:0.18, T:0.66
Consensus pattern (38 bp):
TTTTTTACTGTTTTAGTGCTATTTTTTACTATTTTGGT
Found at i:19847 original size:17 final size:18
Alignment explanation
Indices: 19802--19886 Score: 82
Period size: 21 Copynumber: 4.3 Consensus size: 18
19792 TTGGTTGCTA
19802 TTTTTTACTGTTTTAGTGTTG
1 TTTTTTACTGTTTT-G-G-TG
19823 TGTTTTTACTGTTTTGGT-
1 T-TTTTTACTGTTTTGGTG
19841 TTTTTTACTGTTTTGGTG
1 TTTTTTACTGTTTTGGTG
*
19859 CTATTTTTTACTATTTTGGTG
1 ---TTTTTTACTGTTTTGGTG
19880 TTGTTTT
1 TT-TTTT
19887 TATTGTTATT
Statistics
Matches: 57, Mismatches: 1, Indels: 14
0.79 0.01 0.19
Matches are distributed among these distances:
17 16 0.28
18 3 0.05
19 5 0.09
20 1 0.02
21 19 0.33
22 13 0.23
ACGTcount: A:0.08, C:0.06, G:0.19, T:0.67
Consensus pattern (18 bp):
TTTTTTACTGTTTTGGTG
Done.