Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006279.1 Kokia drynarioides strain JFW-HI SEQ_120850, 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: 5533
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Found at i:537 original size:22 final size:23
Alignment explanation
Indices: 481--539 Score: 59
Period size: 22 Copynumber: 2.6 Consensus size: 23
471 ATTTTCAATG
481 TTAATAAATTATAAAAAATACTAT
1 TTAAT-AATTATAAAAAATACTAT
* **
505 TTTATTTTTATAATAAAA-A-TAT
1 TTAATAATTATAA-AAAATACTAT
527 TTAATAATTATAA
1 TTAATAATTATAA
540 CTATTCTAAT
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
22 13 0.46
23 7 0.25
24 8 0.29
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46
Consensus pattern (23 bp):
TTAATAATTATAAAAAATACTAT
Found at i:1026 original size:20 final size:19
Alignment explanation
Indices: 984--1031 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
974 AAATTAGTGC
984 TTTTAAAA-AATTACAAAA
1 TTTTAAAATAATTACAAAA
* *
1002 ATTTAAAATAATCTTCAAAA
1 TTTTAAAATAAT-TACAAAA
1022 TTTTAAAATA
1 TTTTAAAATA
1032 TTTATAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 7 0.28
19 3 0.12
20 15 0.60
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (19 bp):
TTTTAAAATAATTACAAAA
Found at i:1041 original size:20 final size:20
Alignment explanation
Indices: 984--1041 Score: 50
Period size: 20 Copynumber: 3.0 Consensus size: 20
974 AAATTAGTGC
* *
984 TTTTAAAA-AATTACAAAAA
1 TTTTAAAATATTTATAAAAA
* *
1003 -TTTAAAATAATCT-TCAAAA
1 TTTTAAAAT-ATTTATAAAAA
1022 TTTTAAAATATTTATAAAAA
1 TTTTAAAATATTTATAAAAA
1042 AAATTTTCCA
Statistics
Matches: 29, Mismatches: 6, Indels: 7
0.69 0.14 0.17
Matches are distributed among these distances:
18 7 0.24
19 7 0.24
20 15 0.52
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (20 bp):
TTTTAAAATATTTATAAAAA
Found at i:2716 original size:23 final size:23
Alignment explanation
Indices: 2688--2755 Score: 60
Period size: 23 Copynumber: 3.2 Consensus size: 23
2678 CCGTGAAGAA
2688 AAAGTTAAAAGCCATTTCTAAAG
1 AAAGTTAAAAGCCATTTCTAAAG
**
2711 AAAGTT----GCC-TTTC-AATCT
1 AAAGTTAAAAGCCATTTCTAA-AG
2729 AAA-TTAAAAGCCATTTCTAAAG
1 AAAGTTAAAAGCCATTTCTAAAG
2751 AAAGT
1 AAAGT
2756 CGCTTTTCAA
Statistics
Matches: 33, Mismatches: 4, Indels: 16
0.62 0.08 0.30
Matches are distributed among these distances:
17 4 0.12
18 7 0.21
19 3 0.09
21 3 0.09
22 7 0.21
23 9 0.27
ACGTcount: A:0.44, C:0.15, G:0.12, T:0.29
Consensus pattern (23 bp):
AAAGTTAAAAGCCATTTCTAAAG
Found at i:2736 original size:40 final size:40
Alignment explanation
Indices: 2692--2775 Score: 150
Period size: 40 Copynumber: 2.1 Consensus size: 40
2682 GAAGAAAAAG
*
2692 TTAAAAGCCATTTCTAAAGAAAGTTGCCTTTCAATCTAAA
1 TTAAAAGCCATTTCTAAAGAAAGTCGCCTTTCAATCTAAA
*
2732 TTAAAAGCCATTTCTAAAGAAAGTCGCTTTTCAATCTAAA
1 TTAAAAGCCATTTCTAAAGAAAGTCGCCTTTCAATCTAAA
2772 TTAA
1 TTAA
2776 CTGAAGAAAG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.40, C:0.17, G:0.10, T:0.33
Consensus pattern (40 bp):
TTAAAAGCCATTTCTAAAGAAAGTCGCCTTTCAATCTAAA
Found at i:2927 original size:23 final size:23
Alignment explanation
Indices: 2901--2944 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
2891 CTCAAAATAC
*
2901 AAACAGATCCAAACCTAAACCCT
1 AAACAGATCCAAACCCAAACCCT
*
2924 AAACAGATCTAAACCCAAACC
1 AAACAGATCCAAACCCAAACC
2945 AAGTCGGCCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.50, C:0.34, G:0.05, T:0.11
Consensus pattern (23 bp):
AAACAGATCCAAACCCAAACCCT
Found at i:3120 original size:30 final size:30
Alignment explanation
Indices: 3065--3121 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
3055 CGCTCAGCCC
*
3065 TTCCCCAGGCCATCAATGCGCCCTTTCAAA
1 TTCCCCAGGCCATCAATGCACCCTTTCAAA
* *
3095 TTCCCGAGGCCATCAATGCATCCTTTC
1 TTCCCCAGGCCATCAATGCACCCTTTC
3122 GGCTACCACC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.21, C:0.39, G:0.14, T:0.26
Consensus pattern (30 bp):
TTCCCCAGGCCATCAATGCACCCTTTCAAA
Found at i:4314 original size:19 final size:20
Alignment explanation
Indices: 4290--4329 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
4280 AAATTTATTT
4290 ACAT-AATGTCCAATTACAA
1 ACATAAATGTCCAATTACAA
*
4309 ACATAAATGTCCAGTTACAA
1 ACATAAATGTCCAATTACAA
4329 A
1 A
4330 TCAAGTTCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.47, C:0.20, G:0.07, T:0.25
Consensus pattern (20 bp):
ACATAAATGTCCAATTACAA
Found at i:5294 original size:20 final size:20
Alignment explanation
Indices: 5266--5306 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
5256 GTTTTCAAAA
*
5266 CATTTTAGATCTGGATCTTT
1 CATTCTAGATCTGGATCTTT
*
5286 CATTCTAGATCTGGATTTTT
1 CATTCTAGATCTGGATCTTT
5306 C
1 C
5307 GGAAAGGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.20, C:0.17, G:0.15, T:0.49
Consensus pattern (20 bp):
CATTCTAGATCTGGATCTTT
Done.