Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001818.1 Kokia drynarioides strain JFW-HI SEQ_113559, 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: 2070
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Found at i:376 original size:14 final size:14
Alignment explanation
Indices: 359--397 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
349 TTCAATTTTC
*
359 CTTTTTTATTAATA
1 CTTTATTATTAATA
373 CTTTATTATTAATA
1 CTTTATTATTAATA
387 --TTATTATTAAT
1 CTTTATTATTAAT
398 TATTATTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 11 0.46
14 13 0.54
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (14 bp):
CTTTATTATTAATA
Found at i:383 original size:3 final size:3
Alignment explanation
Indices: 375--413 Score: 51
Period size: 3 Copynumber: 12.3 Consensus size: 3
365 TATTAATACT
*
375 TTA TTA TTA ATA TTA TTA TTAA TTA TTA TTAA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TT-A TTA TTA TT-A TTA TTA T
414 ACTTACGATC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
3 26 0.81
4 6 0.19
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:401 original size:10 final size:10
Alignment explanation
Indices: 375--413 Score: 60
Period size: 10 Copynumber: 3.7 Consensus size: 10
365 TATTAATACT
375 TTATTATTAATA
1 TTATTATT-A-A
387 TTATTATTAA
1 TTATTATTAA
397 TTATTATTAA
1 TTATTATTAA
407 TTATTAT
1 TTATTAT
414 ACTTACGATC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 18 0.67
11 1 0.04
12 8 0.30
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (10 bp):
TTATTATTAA
Found at i:1160 original size:35 final size:34
Alignment explanation
Indices: 1119--1225 Score: 115
Period size: 35 Copynumber: 3.1 Consensus size: 34
1109 TATAGTAAGT
* *
1119 TTTAAATTTAAATATAAATCTAAATTTATATTAAA
1 TTTAAATTTAAA-ATAAATCTAAATTTAAAATAAA
* *
1154 TTTAAATTTTAAAATCAATTTAAATTTAAAATAAA
1 TTTAAA-TTTAAAATAAATCTAAATTTAAAATAAA
* * * **
1189 TTTATATTCAAAATAAATTTAACCTTAAAATAAA
1 TTTAAATTTAAAATAAATCTAAATTTAAAATAAA
1223 TTT
1 TTT
1226 TAGTATGAGT
Statistics
Matches: 62, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
34 27 0.44
35 29 0.47
36 6 0.10
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (34 bp):
TTTAAATTTAAAATAAATCTAAATTTAAAATAAA
Found at i:1166 original size:7 final size:6
Alignment explanation
Indices: 1119--1210 Score: 66
Period size: 6 Copynumber: 15.8 Consensus size: 6
1109 TATAGTAAGT
* * *
1119 TTTAAA TTTAAA TATAAA TCTAAA TTTATA -TTAAA TTTAAA TTTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA -TTTAAA
* * * * * *
1167 -ATCAA TTTAAA TTTAAA -ATAAA TTTATA TTCAAA -ATAAA TTTAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA
1211 CCTTAAAATA
Statistics
Matches: 64, Mismatches: 17, Indels: 10
0.70 0.19 0.11
Matches are distributed among these distances:
5 14 0.22
6 44 0.69
7 6 0.09
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (6 bp):
TTTAAA
Found at i:1201 original size:17 final size:17
Alignment explanation
Indices: 1119--1225 Score: 124
Period size: 17 Copynumber: 6.2 Consensus size: 17
1109 TATAGTAAGT
1119 TTTAAATTTAAATATAAA
1 TTTAAATTTAAA-ATAAA
* * *
1137 TCTAAATTTATATTAAA
1 TTTAAATTTAAAATAAA
*
1154 TTTAAATTTTAAAATCAA
1 TTTAAA-TTTAAAATAAA
1172 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
* *
1189 TTTATATTCAAAATAAA
1 TTTAAATTTAAAATAAA
**
1206 TTTAACCTTAAAATAAA
1 TTTAAATTTAAAATAAA
1223 TTT
1 TTT
1226 TAGTATGAGT
Statistics
Matches: 74, Mismatches: 14, Indels: 3
0.81 0.15 0.03
Matches are distributed among these distances:
17 50 0.68
18 24 0.32
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:2045 original size:2 final size:2
Alignment explanation
Indices: 2038--2070 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
2028 CATTTCAGAT
*
2038 AC AC AC AC AC AC AC AC AC AC AT AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.45, G:0.00, T:0.03
Consensus pattern (2 bp):
AC
Done.