Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003665.1 Kokia drynarioides strain JFW-HI SEQ_116578, 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: 11370
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Found at i:1165 original size:23 final size:23
Alignment explanation
Indices: 1139--1259 Score: 181
Period size: 23 Copynumber: 5.2 Consensus size: 23
1129 ACACTAGCGC
1139 GCTCTCTGATTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
1162 GCTCTCTGATTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
* *
1185 GCTCTCTGTTTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
1208 GCTCTCTGTTATTAGCACT-TCGTGT
1 GCTCTCTG--ATTAGCACTGT-GTGT
*
1233 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
1256 GCTC
1 GCTC
1260 AGTACTTTGT
Statistics
Matches: 91, Mismatches: 3, Indels: 8
0.89 0.03 0.08
Matches are distributed among these distances:
23 69 0.76
24 2 0.02
25 20 0.22
ACGTcount: A:0.12, C:0.23, G:0.23, T:0.42
Consensus pattern (23 bp):
GCTCTCTGATTAGCACTGTGTGT
Found at i:1226 original size:48 final size:45
Alignment explanation
Indices: 1139--1302 Score: 196
Period size: 48 Copynumber: 3.7 Consensus size: 45
1129 ACACTAGCGC
*
1139 GCTCTCTGATTAGCACTGTGTGTGCTCTCTGATTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTTTGTGTGCTCTCTGATTAGCACT-TGTGT
*
1185 GCTCTCTGTTTAGCACTTTGTGTGCTCTCTGTTATTAGCACTTCGTGT
1 GCTCTCTGATTAGCACTTTGTGTGCTCTCTG--ATTAGCACTT-GTGT
* *
1233 GCTCTCTGATTAGCACTTTGTGTG--CTC--AGTA-C-TTTGTGT
1 GCTCTCTGATTAGCACTTTGTGTGCTCTCTGATTAGCACTTGTGT
* *
1272 ACTCTCTGTTTAGCACTTTGTGTGCTCTCTG
1 GCTCTCTGATTAGCACTTTGTGTGCTCTCTG
1303 TTGCCCAGCA
Statistics
Matches: 104, Mismatches: 7, Indels: 17
0.81 0.05 0.13
Matches are distributed among these distances:
39 26 0.25
40 2 0.02
41 4 0.04
42 3 0.03
46 32 0.31
47 1 0.01
48 36 0.35
ACGTcount: A:0.12, C:0.23, G:0.23, T:0.43
Consensus pattern (45 bp):
GCTCTCTGATTAGCACTTTGTGTGCTCTCTGATTAGCACTTGTGT
Found at i:1288 original size:39 final size:39
Alignment explanation
Indices: 1224--1298 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 39
1214 TGTTATTAGC
*
1224 ACTTCGTGTGCTCTCTGATTAGCACTTTGTGTGCTCAGT
1 ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTCAGT
* *
1263 ACTTTGTGTACTCTCTGTTTAGCACTTTGTGTGCTC
1 ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTC
1299 TCTGTTGCCC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.44
Consensus pattern (39 bp):
ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTCAGT
Found at i:3857 original size:29 final size:30
Alignment explanation
Indices: 3794--3858 Score: 75
Period size: 29 Copynumber: 2.2 Consensus size: 30
3784 TCTTTTTTTT
3794 TTTACAAAATACCCATTAACCCAATACACCA
1 TTTACAAAATACCCA-TAACCCAATACACCA
*
3825 --TACAAACTACCCA-AACCCAATGAC-CCA
1 TTTACAAAATACCCATAACCCAAT-ACACCA
3852 TTTACAA
1 TTTACAA
3859 CCTTAGCCGA
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
27 11 0.37
28 2 0.07
29 17 0.57
ACGTcount: A:0.45, C:0.34, G:0.02, T:0.20
Consensus pattern (30 bp):
TTTACAAAATACCCATAACCCAATACACCA
Found at i:5204 original size:30 final size:29
Alignment explanation
Indices: 5144--5325 Score: 163
Period size: 29 Copynumber: 6.2 Consensus size: 29
5134 TCGAACTTCT
* *
5144 CAAAAATCATATTTTGACCCCTCGAACTTTC
1 CAAAAATCACATTTTGA--CCTCAAACTTTC
*
5175 CAAAAATTACATTTTGACCATCAAACTTTC
1 CAAAAATCACATTTTGACC-TCAAACTTTC
* *
5205 CAAAAATCACATTTTGAGTCTAAAACTTTC
1 CAAAAATCACATTTTGA-CCTCAAACTTTC
* *
5235 C-AAAATCTCATTTTGACCCCAAAC-TTC
1 CAAAAATCACATTTTGACCTCAAACTTTC
* *
5262 ACAAAAATCACATTTTAACC-CTAAACTTTT
1 -CAAAAATCACATTTTGACCTC-AAACTTTC
* * * * *
5292 TAAAAATCACAATTTAACCCCAAACTCTC
1 CAAAAATCACATTTTGACCTCAAACTTTC
5321 CAAAA
1 CAAAA
5326 CTTCATTTTT
Statistics
Matches: 126, Mismatches: 18, Indels: 16
0.79 0.11 0.10
Matches are distributed among these distances:
27 3 0.02
28 7 0.06
29 62 0.49
30 38 0.30
31 16 0.13
ACGTcount: A:0.40, C:0.26, G:0.03, T:0.30
Consensus pattern (29 bp):
CAAAAATCACATTTTGACCTCAAACTTTC
Found at i:6474 original size:123 final size:123
Alignment explanation
Indices: 6255--6619 Score: 565
Period size: 123 Copynumber: 2.9 Consensus size: 123
6245 AATTTCGTTA
* *
6255 AATATTAAAAACATGAAAGTTAATATCCTTTTGGAAAGGATATAATGTTTTAATAAACCTTCCAT
1 AATATTAAAAACATGGAAGTTAATATCCTTTTGGAAAAGATATAATGTTTTAATAAACCTTCCAT
6320 ATATTTCTTTAAA-GAAATATTTCCATTTTAATATGAGATATTATATAAAAGAAAATTG
66 ATATTTCTTTAAATG-AATATTTCCATTTTAATATGAGATATTATATAAAAGAAAATTG
*
6378 AATATTAAAAACACGGAAGTTAATATCCTTTTGGAAAAGATATAATGTTTTAATAAACCTTCCAT
1 AATATTAAAAACATGGAAGTTAATATCCTTTTGGAAAAGATATAATGTTTTAATAAACCTTCCAT
*
6443 ATATTTCTTTAAATGAATATTTCCATTTTAATATGAGATATTATATAAAAGGAAATTG
66 ATATTTCTTTAAATGAATATTTCCATTTTAATATGAGATATTATATAAAAGAAAATTG
*
6501 AATATTAAAAACATGGAAGTTAATATCCTTTT-GAAAAGGGTATAATGTTTTAATAAACCTTCCA
1 AATATTAAAAACATGGAAGTTAATATCCTTTTGGAAAA-GATATAATGTTTTAATAAACCTTCCA
* * * * *
6565 TATATTGCTCTAAAGATGTATATTTTCATTTTAATACT-AGATATTAAAATAAAAG
65 TATATTTCT-TTAA-ATGAATATTTCCATTTTAATA-TGAGATATT-ATATAAAAG
6620 GAAAGATAGC
Statistics
Matches: 225, Mismatches: 11, Indels: 9
0.92 0.04 0.04
Matches are distributed among these distances:
122 5 0.02
123 181 0.80
124 4 0.02
125 26 0.12
126 9 0.04
ACGTcount: A:0.43, C:0.09, G:0.10, T:0.38
Consensus pattern (123 bp):
AATATTAAAAACATGGAAGTTAATATCCTTTTGGAAAAGATATAATGTTTTAATAAACCTTCCAT
ATATTTCTTTAAATGAATATTTCCATTTTAATATGAGATATTATATAAAAGAAAATTG
Done.