Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015170.1 Kokia drynarioides strain JFW-HI SEQ_130214, 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: 40965
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.35
Found at i:264 original size:10 final size:10
Alignment explanation
Indices: 230--266 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
220 TTTTTTTCCT
230 CTCCTTCTTC
1 CTCCTTCTTC
240 C-CCTTC-TC
1 CTCCTTCTTC
248 CTCCTTCTTC
1 CTCCTTCTTC
*
258 CTTCTTCTT
1 CTCCTTCTT
267 TCTTTCTTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
8 3 0.12
9 10 0.42
10 11 0.46
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (10 bp):
CTCCTTCTTC
Found at i:277 original size:22 final size:24
Alignment explanation
Indices: 243--306 Score: 62
Period size: 22 Copynumber: 2.8 Consensus size: 24
233 CTTCTTCCCC
* *
243 TTCTCCTCCTTCTTCCTTCT-TCT
1 TTCTTCTCTTTCTTCCTTCTCTCT
*
266 TTCTT-TCTTTCTTTCTT-TCTCT
1 TTCTTCTCTTTCTTCCTTCTCTCT
* *
288 TTTTTCTCTTTTTTCCTTC
1 TTCTTCTCTTTCTTCCTTC
307 ATTTTTCGTT
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
21 1 0.03
22 17 0.53
23 14 0.44
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (24 bp):
TTCTTCTCTTTCTTCCTTCTCTCT
Found at i:299 original size:8 final size:9
Alignment explanation
Indices: 260--306 Score: 55
Period size: 8 Copynumber: 5.6 Consensus size: 9
250 CCTTCTTCCT
260 TCTTCTTTC
1 TCTTCTTTC
269 T-TTCTTTC
1 TCTTCTTTC
277 T-TTCTTTC
1 TCTTCTTTC
*
285 TCTTTTTTC
1 TCTTCTTTC
*
294 TCTTTTTTC
1 TCTTCTTTC
303 -CTTC
1 TCTTC
307 ATTTTTCGTT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
8 19 0.54
9 16 0.46
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (9 bp):
TCTTCTTTC
Found at i:667 original size:8 final size:9
Alignment explanation
Indices: 647--677 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
637 TTTTATTTTT
647 AAATATATAA
1 AAATA-ATAA
657 AAATAATAA
1 AAATAATAA
666 AAATAATAA
1 AAATAATAA
675 AAA
1 AAA
678 AAAACACGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 16 0.76
10 5 0.24
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (9 bp):
AAATAATAA
Found at i:1959 original size:18 final size:19
Alignment explanation
Indices: 1925--1960 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1915 TCAAAATTTT
*
1925 TTATATGTATCAATTGAAG
1 TTATATGTATAAATTGAAG
1944 TTATAT-TATAAATTGAA
1 TTATATGTATAAATTGAA
1961 TTAAAGTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.42, C:0.03, G:0.11, T:0.44
Consensus pattern (19 bp):
TTATATGTATAAATTGAAG
Found at i:23857 original size:17 final size:17
Alignment explanation
Indices: 23832--23874 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
23822 TTCTCTATTG
* * *
23832 TTTTATTTATTTTTTTA
1 TTTTTTTTACTTTTCTA
*
23849 TTTTTTTTACTTTTCTC
1 TTTTTTTTACTTTTCTA
23866 TTTTTTTTA
1 TTTTTTTTA
23875 AAGGCAAAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.12, C:0.07, G:0.00, T:0.81
Consensus pattern (17 bp):
TTTTTTTTACTTTTCTA
Found at i:24294 original size:31 final size:29
Alignment explanation
Indices: 24210--24298 Score: 81
Period size: 31 Copynumber: 2.9 Consensus size: 29
24200 TTTAATTTTT
* * *
24210 AATATTTAACCATTTTGTTAATTTAATCCC
1 AATATTTAA-AATTTTATAAATTTAATCCC
*
24240 GATA-TTAAAATTTTCAATAAATTTAATCCTC
1 AATATTTAAAATTTT--ATAAATTTAATCC-C
*
24271 AATATTTAAATATTTTATCAATTTAATC
1 AATATTTAAA-ATTTTATAAATTTAATC
24299 TTAATTCTGA
Statistics
Matches: 48, Mismatches: 6, Indels: 9
0.76 0.10 0.14
Matches are distributed among these distances:
28 5 0.10
29 4 0.08
30 14 0.29
31 15 0.31
32 5 0.10
33 5 0.10
ACGTcount: A:0.39, C:0.12, G:0.02, T:0.46
Consensus pattern (29 bp):
AATATTTAAAATTTTATAAATTTAATCCC
Found at i:26057 original size:29 final size:30
Alignment explanation
Indices: 25999--26057 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
25989 AAAATTATTC
* *
25999 AAATTAAAATTTTATATATAAAATTGCACA
1 AAATTAAAAGTTTATATATAAAATTACACA
26029 AAATT-AAAGTTTATATATGAAAA-TACACA
1 AAATTAAAAGTTTATATAT-AAAATTACACA
26058 TTAAAACAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 17 0.65
30 9 0.35
ACGTcount: A:0.54, C:0.07, G:0.05, T:0.34
Consensus pattern (30 bp):
AAATTAAAAGTTTATATATAAAATTACACA
Found at i:26073 original size:31 final size:29
Alignment explanation
Indices: 26005--26080 Score: 73
Period size: 29 Copynumber: 2.6 Consensus size: 29
25995 ATTCAAATTA
* **
26005 AAATTTTATATATAAAATTGCACAAAATT
1 AAATTTTATATATAAAATTACACAAAAAC
*
26034 AAAGTTTATATATGAAAA-TACACATTAAAAC
1 AAATTTTATATAT-AAAATTACACA--AAAAC
*
26065 AAATTTTATGTATAAA
1 AAATTTTATATATAAA
26081 TTTAATATTC
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
29 17 0.45
30 7 0.18
31 14 0.37
ACGTcount: A:0.53, C:0.07, G:0.05, T:0.36
Consensus pattern (29 bp):
AAATTTTATATATAAAATTACACAAAAAC
Found at i:26827 original size:26 final size:24
Alignment explanation
Indices: 26791--26838 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
26781 TTGATATAGG
*
26791 TTTTTATTTTTTTATATAATTTAT
1 TTTTTATTTTTTTATACAATTTAT
26815 TTTTTAATATTTTTTATACAATTT
1 TTTTT-AT-TTTTTTATACAATTT
26839 CTAATTTATC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 5 0.24
25 2 0.10
26 14 0.67
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (24 bp):
TTTTTATTTTTTTATACAATTTAT
Found at i:26830 original size:17 final size:17
Alignment explanation
Indices: 26791--26831 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
26781 TTGATATAGG
*
26791 TTTTTATTTTTTTATAT
1 TTTTTATTTTTTAATAT
**
26808 AATTTATTTTTTAATAT
1 TTTTTATTTTTTAATAT
26825 TTTTTAT
1 TTTTTAT
26832 ACAATTTCTA
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTTATTTTTTAATAT
Found at i:28760 original size:2 final size:2
Alignment explanation
Indices: 28753--28777 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
28743 AATAAAATTG
28753 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 A
28778 CAAAACAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.