Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007651.1 Kokia drynarioides strain JFW-HI SEQ_122282, 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: 4137
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.37
Found at i:1279 original size:19 final size:19
Alignment explanation
Indices: 1234--1283 Score: 61
Period size: 17 Copynumber: 2.8 Consensus size: 19
1224 AAAAAAAATA
* *
1234 ATAATAAAA-AGAAAATTT
1 ATAATAAAATAAAAAAGTT
1252 AT-A-AAAATAAAAAAGTT
1 ATAATAAAATAAAAAAGTT
1269 ATAATAAAATAAAAA
1 ATAATAAAATAAAAA
1284 TATTAAATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 4 0.15
17 10 0.37
18 3 0.11
19 10 0.37
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.24
Consensus pattern (19 bp):
ATAATAAAATAAAAAAGTT
Found at i:1292 original size:18 final size:18
Alignment explanation
Indices: 1227--1292 Score: 52
Period size: 19 Copynumber: 3.8 Consensus size: 18
1217 AAATCATAAA
*
1227 AAAAATAAT-AATAAAA-
1 AAAAATATTAAATAAAAT
*
1243 AGAAAAT-TTATA-AAAAT
1 A-AAAATATTAAATAAAAT
1260 AAAAA-AGTTATAATAAAAT
1 AAAAATA-TTA-AATAAAAT
1279 AAAAATATTAAATA
1 AAAAATATTAAATA
1293 TTAAATTTGA
Statistics
Matches: 39, Mismatches: 3, Indels: 14
0.70 0.05 0.25
Matches are distributed among these distances:
16 10 0.26
17 10 0.26
18 5 0.13
19 13 0.33
20 1 0.03
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAAATATTAAATAAAAT
Found at i:1357 original size:17 final size:19
Alignment explanation
Indices: 1329--1367 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
1319 TTATAAAAAA
*
1329 AAAACTTATAAATATT-AT
1 AAAACTTATAAAAATTAAT
1347 AAAAC-TATAAAAATTAAT
1 AAAACTTATAAAAATTAAT
1365 AAA
1 AAA
1368 TTAATAAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (19 bp):
AAAACTTATAAAAATTAAT
Found at i:1874 original size:19 final size:19
Alignment explanation
Indices: 1850--1908 Score: 75
Period size: 19 Copynumber: 3.1 Consensus size: 19
1840 AGTCTCATTC
1850 AAGTTTTTATAATTTTTAT
1 AAGTTTTTATAATTTTTAT
* *
1869 AAGTTTATATCAATTTTAAT
1 AAGTTTTTAT-AATTTTTAT
*
1889 -ATTTTTTATAATTTTTAT
1 AAGTTTTTATAATTTTTAT
1907 AA
1 AA
1909 AATTTTAATA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
18 8 0.24
19 17 0.52
20 8 0.24
ACGTcount: A:0.36, C:0.02, G:0.03, T:0.59
Consensus pattern (19 bp):
AAGTTTTTATAATTTTTAT
Found at i:1895 original size:29 final size:28
Alignment explanation
Indices: 1848--1918 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 28
1838 CCAGTCTCAT
*
1848 TCAAGTTTTTATAATTTTTATAAGTTTATA
1 TCAA-TTTTAATAATTTTTATAA-TTTATA
* *
1878 TCAATTTTAATATTTTTTATAATTTTTA
1 TCAATTTTAATAATTTTTATAATTTATA
*
1906 TAAAATTTTAATA
1 T-CAATTTTAATA
1919 CGTTTTTTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
28 6 0.17
29 26 0.72
30 4 0.11
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.58
Consensus pattern (28 bp):
TCAATTTTAATAATTTTTATAATTTATA
Found at i:1994 original size:10 final size:9
Alignment explanation
Indices: 1853--1981 Score: 78
Period size: 9 Copynumber: 13.0 Consensus size: 9
1843 CTCATTCAAG
1853 TTTTTATAA
1 TTTTTATAA
1862 TTTTTATAA
1 TTTTTATAA
*
1871 GTTTATATCAA
1 -TTTTTAT-AA
* *
1882 TTTTAATAT
1 TTTTTATAA
1891 TTTTTATAA
1 TTTTTATAA
1900 TTTTTATAAAA
1 TTTTTAT--AA
* *
1911 TTTTAATACGT
1 TTTTTATA--A
*
1922 TTTTTTTAA
1 TTTTTATAA
*
1931 TGTTTTAAATA
1 T-TTTTATA-A
1942 TATTTTATTAA
1 T-TTTTA-TAA
*
1953 TTTTATTAGAA
1 -TTT-TTATAA
1964 TTTTTATAA
1 TTTTTATAA
1973 TTTTTATAA
1 TTTTTATAA
1982 ATTTATATCA
Statistics
Matches: 92, Mismatches: 17, Indels: 22
0.70 0.13 0.17
Matches are distributed among these distances:
9 40 0.43
10 19 0.21
11 28 0.30
12 5 0.05
ACGTcount: A:0.34, C:0.02, G:0.03, T:0.61
Consensus pattern (9 bp):
TTTTTATAA
Found at i:2820 original size:15 final size:14
Alignment explanation
Indices: 2787--2824 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
2777 ACGGTTAATC
2787 AATCG-ATTAATTG
1 AATCGAATTAATTG
*
2800 AATCGAATTAATATT
1 AATCGAATTAAT-TG
2815 AATCGAATTA
1 AATCGAATTA
2825 GATTAGTTCG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 5 0.23
14 6 0.27
15 11 0.50
ACGTcount: A:0.45, C:0.08, G:0.11, T:0.37
Consensus pattern (14 bp):
AATCGAATTAATTG
Found at i:3014 original size:22 final size:22
Alignment explanation
Indices: 2973--3031 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
2963 CCTCCTCAAA
* * *
2973 TTTTTTGAAATTTCTTATTATAT
1 TTTTTTAAAATTT-TAATTAAAT
2996 TTTTTTAAAATTTTAATTAAAT
1 TTTTTTAAAATTTTAATTAAAT
**
3018 TCATTTAAAATTTT
1 TTTTTTAAAATTTT
3032 TAAAAATTCT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
22 19 0.61
23 12 0.39
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.61
Consensus pattern (22 bp):
TTTTTTAAAATTTTAATTAAAT
Found at i:3038 original size:32 final size:31
Alignment explanation
Indices: 2996--3076 Score: 85
Period size: 30 Copynumber: 2.6 Consensus size: 31
2986 CTTATTATAT
*
2996 TTTTTTAAAATTTTAATTAAAT-TCATTTAAAA
1 TTTTTAAAAATTTTAATTAAATCTCA--TAAAA
* *
3028 TTTTTAAAAATTCTCATT-AATCTCATAAAA
1 TTTTTAAAAATTTTAATTAAATCTCATAAAA
* *
3058 ATTTTAAAAATCTTAATTA
1 TTTTTAAAAATTTTAATTA
3077 GACCCTTTTC
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
30 19 0.47
31 3 0.08
32 18 0.45
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.48
Consensus pattern (31 bp):
TTTTTAAAAATTTTAATTAAATCTCATAAAA
Found at i:3040 original size:21 final size:21
Alignment explanation
Indices: 2999--3040 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
2989 ATTATATTTT
2999 TTTAAAATTTTAATTAAATTCA
1 TTTAAAATTTTAA-TAAATTCA
3021 TTTAAAATTTTTAA-AAATTC
1 TTTAAAA-TTTTAATAAATTC
3041 TCATTAATCT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.32
22 7 0.37
23 6 0.32
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (21 bp):
TTTAAAATTTTAATAAATTCA
Done.