Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003861.1 Kokia drynarioides strain JFW-HI SEQ_116890, 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: 18418
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1064 original size:22 final size:19
Alignment explanation
Indices: 1035--1078 Score: 61
Period size: 22 Copynumber: 2.2 Consensus size: 19
1025 ACTTTCATGA
1035 TTAACTTAATTAATCACCTAT
1 TTAACTTAATTAAT--CCTAT
1056 TTAATCTTAATTAATCCTAT
1 TTAA-CTTAATTAATCCTAT
1076 TTA
1 TTA
1079 TTATCAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 8 0.36
21 4 0.18
22 10 0.45
ACGTcount: A:0.36, C:0.16, G:0.00, T:0.48
Consensus pattern (19 bp):
TTAACTTAATTAATCCTAT
Found at i:3229 original size:30 final size:30
Alignment explanation
Indices: 3193--3249 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
3183 AGAAGCCAAG
* *
3193 TTGAACGACCAATGATTTCAGGTGATCAAC
1 TTGAACGACCAATGATTGCAAGTGATCAAC
3223 TTGAACGACCAATGATTGCAAGTGATC
1 TTGAACGACCAATGATTGCAAGTGATC
3250 GGCTACTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.26
Consensus pattern (30 bp):
TTGAACGACCAATGATTGCAAGTGATCAAC
Found at i:8156 original size:19 final size:19
Alignment explanation
Indices: 8115--8156 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
8105 ACAAAAGATT
8115 AAAAGGATTGAATTTAAAA
1 AAAAGGATTGAATTTAAAA
*
8134 AAAA-GATTTAATTTAAAA
1 AAAAGGATTGAATTTAAAA
8152 GAAAA
1 -AAAA
8157 CAGAATAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 13 0.62
19 8 0.38
ACGTcount: A:0.62, C:0.00, G:0.12, T:0.26
Consensus pattern (19 bp):
AAAAGGATTGAATTTAAAA
Found at i:16769 original size:23 final size:23
Alignment explanation
Indices: 16734--17224 Score: 696
Period size: 23 Copynumber: 21.3 Consensus size: 23
16724 ATCTTAATTC
16734 TTTAAGCACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* * *
16757 TTTAATCATAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
16780 TTTAAGCACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* * *
16803 TTTAATCATAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
16826 TTTAAGCACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
16849 TTTATGCATAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
16872 TTTAAGCACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
16895 TTTAAGCACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
*
16918 TTTGAA-CACAAATCATATTAATA
1 TTT-AAGCACAAATCACATTAATA
16941 TTTAAGCACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
*
16964 TTTCAGCACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
*
16987 TTTAAGCATAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
** * *
17010 TTTAAGCATGAATTATATTAATA
1 TTTAAGCACAAATCACATTAATA
* * * *
17033 TTTGAGCATAAATTATATTAATA
1 TTTAAGCACAAATCACATTAATA
17056 TTTAAGCACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* * * *
17079 TTTGAGTATAAACCACATTAATA
1 TTTAAGCACAAATCACATTAATA
*
17102 CTTAAGCACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
**
17125 CATAAGCACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* * *
17148 TTTAATCATAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
*
17171 TTTAAGCACAAATTACATTAATA
1 TTTAAGCACAAATCACATTAATA
17194 TTTAAGCACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
17217 TTTAAGCA
1 TTTAAGCA
17225 TAGATATAAG
Statistics
Matches: 416, Mismatches: 50, Indels: 4
0.89 0.11 0.01
Matches are distributed among these distances:
22 2 0.00
23 412 0.99
24 2 0.00
ACGTcount: A:0.47, C:0.14, G:0.04, T:0.34
Consensus pattern (23 bp):
TTTAAGCACAAATCACATTAATA
Found at i:17598 original size:18 final size:18
Alignment explanation
Indices: 17575--17612 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
17565 ATTATTGGCT
17575 GGTGCCTACCTGACAAGC
1 GGTGCCTACCTGACAAGC
* *
17593 GGTGCCTATCTGACAGGC
1 GGTGCCTACCTGACAAGC
17611 GG
1 GG
17613 CACCTAATGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.18, C:0.29, G:0.34, T:0.18
Consensus pattern (18 bp):
GGTGCCTACCTGACAAGC
Found at i:18311 original size:2 final size:2
Alignment explanation
Indices: 18306--18334 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
18296 TATTAAAACA
18306 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
18335 ACTCAATTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.