Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013349.1 Kokia drynarioides strain JFW-HI SEQ_128372, 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: 11650
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Found at i:680 original size:17 final size:17
Alignment explanation
Indices: 655--734 Score: 74
Period size: 17 Copynumber: 4.7 Consensus size: 17
645 TAAATAGATT
*
655 TAAACTTAAATTTATAA
1 TAAATTTAAATTTATAA
672 TAAATTTAAATTT-TAA
1 TAAATTTAAATTTATAA
*
688 GTAAATTTAAACTTA-AA
1 -TAAATTTAAATTTATAA
* * * *
705 AAAACCTTAATTTTAAAA
1 TAAA-TTTAAATTTATAA
723 TAAATTTAAATT
1 TAAATTTAAATT
735 CTGTTGGGCC
Statistics
Matches: 50, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
16 6 0.12
17 39 0.78
18 5 0.10
ACGTcount: A:0.53, C:0.05, G:0.01, T:0.41
Consensus pattern (17 bp):
TAAATTTAAATTTATAA
Found at i:996 original size:21 final size:22
Alignment explanation
Indices: 970--1019 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
960 GTTATTCACC
970 AAAAAAAA-GTTAATTTATGGA
1 AAAAAAAATGTTAATTTATGGA
*
991 AAAAAAAATGTTAGTTTATGGA
1 AAAAAAAATGTTAATTTATGGA
*
1013 ATAAAAA
1 AAAAAAA
1020 CACTGATGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
21 8 0.31
22 18 0.69
ACGTcount: A:0.58, C:0.00, G:0.14, T:0.28
Consensus pattern (22 bp):
AAAAAAAATGTTAATTTATGGA
Found at i:1234 original size:21 final size:22
Alignment explanation
Indices: 1189--1248 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
1179 GATCTAAGGG
1189 AAAATAAAAGAAACA-A-AATTA
1 AAAATAAAAGAAA-ATAGAATTA
1210 AAAATAAAAGAAAATAGAATTA
1 AAAATAAAAGAAAATAGAATTA
*
1232 AAAGA-AATAGAAAATAG
1 AAA-ATAAAAGAAAATAG
1249 GGAAGTCGAA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
20 1 0.03
21 14 0.40
22 19 0.54
23 1 0.03
ACGTcount: A:0.73, C:0.02, G:0.10, T:0.15
Consensus pattern (22 bp):
AAAATAAAAGAAAATAGAATTA
Found at i:1241 original size:15 final size:16
Alignment explanation
Indices: 1214--1243 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1204 AAATTAAAAA
1214 TAAAAGAAAATAGAAT
1 TAAAAGAAAATAGAAT
1230 TAAAAG-AAATAGAA
1 TAAAAGAAAATAGAA
1244 AATAGGGAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.70, C:0.00, G:0.13, T:0.17
Consensus pattern (16 bp):
TAAAAGAAAATAGAAT
Found at i:2022 original size:172 final size:172
Alignment explanation
Indices: 1736--2081 Score: 649
Period size: 172 Copynumber: 2.0 Consensus size: 172
1726 GGATTCTAAG
1736 CCTCATGAACCTTGGAGGAATATTTGATAACCTTCGGCTAGAAGATTTTTTAGTTACTTATGATT
1 CCTCATGAACCTTGGAGGAATATTTGATAACCTTCGGCTAGAAGATTTTTTAGTTACTTATGATT
*
1801 TTGGGAAAGAACACAAGATAATAAAATAAAGCTTTTATTGAACTAGGGATTTAGAGAGATGTAGG
66 TTGGGAAAGAACACAAGATAATAAAATAAAGCTTTTATTGAACTAGGGATTTAGAGAGATGGAGG
*
1866 ATTTTTCATTGAATAGGG-AATGAATAATTCAATCACTCCACC
131 ATTTTTCAATGAAT-GGGAAATGAATAATTCAATCACTCCACC
1908 CCTCATGAACCTTGGAGGAATATTTGATAACCTTCGGCTAGAAGATTTTTTAGTTACTTATGATT
1 CCTCATGAACCTTGGAGGAATATTTGATAACCTTCGGCTAGAAGATTTTTTAGTTACTTATGATT
*
1973 TTGGGGAAGAACACAAGATAATAAAATAAAGCTTTTATTGAACTAGGGATTTAGAGAGATGGAGG
66 TTGGGAAAGAACACAAGATAATAAAATAAAGCTTTTATTGAACTAGGGATTTAGAGAGATGGAGG
2038 ATTTTTCAATGAATGGGAAATGAATAATTCAATCACTCCACC
131 ATTTTTCAATGAATGGGAAATGAATAATTCAATCACTCCACC
2080 CC
1 CC
2082 CTATTTATAG
Statistics
Matches: 170, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
171 3 0.02
172 167 0.98
ACGTcount: A:0.35, C:0.13, G:0.20, T:0.32
Consensus pattern (172 bp):
CCTCATGAACCTTGGAGGAATATTTGATAACCTTCGGCTAGAAGATTTTTTAGTTACTTATGATT
TTGGGAAAGAACACAAGATAATAAAATAAAGCTTTTATTGAACTAGGGATTTAGAGAGATGGAGG
ATTTTTCAATGAATGGGAAATGAATAATTCAATCACTCCACC
Found at i:2244 original size:19 final size:19
Alignment explanation
Indices: 2220--2262 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
2210 AAACATAAAT
2220 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
2239 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
2258 TAAAT
1 TAAAT
2263 CCTAATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:8007 original size:18 final size:17
Alignment explanation
Indices: 7965--8014 Score: 59
Period size: 18 Copynumber: 3.0 Consensus size: 17
7955 ATATATTATT
7965 TAAAATT-AATTATTAA
1 TAAAATTAAATTATTAA
* *
7981 TACAATTAAATTATTTGA
1 TAAAATTAAATTA-TTAA
7999 TAAAATTAAATT-TTAA
1 TAAAATTAAATTATTAA
8015 ATTCGATTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
16 9 0.32
17 5 0.18
18 14 0.50
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (17 bp):
TAAAATTAAATTATTAA
Found at i:8726 original size:29 final size:29
Alignment explanation
Indices: 8694--8752 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
8684 ACTTGAAGCG
8694 TCAAAATGTCCAATGTGGTACCTAAAGTT
1 TCAAAATGTCCAATGTGGTACCTAAAGTT
* *
8723 TCAAAATGTCCAATGTGGTATCTGAAGTT
1 TCAAAATGTCCAATGTGGTACCTAAAGTT
8752 T
1 T
8753 AATTTCGTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.34
Consensus pattern (29 bp):
TCAAAATGTCCAATGTGGTACCTAAAGTT
Done.