Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004157.1 Kokia drynarioides strain JFW-HI SEQ_117374, 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: 11879
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Found at i:428 original size:3 final size:3
Alignment explanation
Indices: 420--472 Score: 54
Period size: 3 Copynumber: 17.3 Consensus size: 3
410 TTCGGCTTTT
* * *
420 TTA TTA TTA TTA ATA TTTA TTA TTA TTA TTA -TA TTA TTA ATA ATA
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
465 TTAA TTA T
1 TT-A TTA T
473 AGTTGCCATT
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
2 2 0.05
3 36 0.84
4 5 0.12
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:1242 original size:6 final size:6
Alignment explanation
Indices: 1231--1297 Score: 57
Period size: 6 Copynumber: 11.3 Consensus size: 6
1221 TATAATAAGT
* * ** *
1231 TTTAAA TTTAAA TATAAA TCTAAA TTTAAA TTTTAAA -ACAAA TTTAAT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA -TTTAAA TTTAAA TTTAAA
*
1279 TTTAAA -ATAAA TTTAAA TT
1 TTTAAA TTTAAA TTTAAA TT
1298 CAAAATCAAT
Statistics
Matches: 47, Mismatches: 11, Indels: 6
0.73 0.17 0.09
Matches are distributed among these distances:
5 7 0.15
6 34 0.72
7 6 0.13
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (6 bp):
TTTAAA
Found at i:1254 original size:18 final size:17
Alignment explanation
Indices: 1233--1330 Score: 74
Period size: 17 Copynumber: 5.6 Consensus size: 17
1223 TAATAAGTTT
*
1233 TAAATTTAAATATAAATC
1 TAAATTTAAATTTAAA-C
1251 TAAATTTAAATTTTAAAAC
1 TAAATTTAAA-TTT-AAAC
* *
1270 -AAATTTAATTTTAAAA
1 TAAATTTAAATTTAAAC
* *
1286 TAAATTTAAATTCAAAA
1 TAAATTTAAATTTAAAC
* *
1303 TCAATTT-AATCTTAAAA
1 TAAATTTAAAT-TTAAAC
1320 TAAATCTTAAA
1 TAAAT-TTAAA
1331 ATAGGTTTAA
Statistics
Matches: 66, Mismatches: 8, Indels: 11
0.78 0.09 0.13
Matches are distributed among these distances:
16 6 0.09
17 32 0.48
18 20 0.30
19 5 0.08
20 3 0.05
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (17 bp):
TAAATTTAAATTTAAAC
Found at i:1281 original size:17 final size:17
Alignment explanation
Indices: 1252--1329 Score: 77
Period size: 17 Copynumber: 4.5 Consensus size: 17
1242 ATATAAATCT
1252 AAATTTAAATTTTAAAAC
1 AAATTT-AATTTTAAAAC
*
1270 AAATTTAATTTTAAAAT
1 AAATTTAATTTTAAAAC
* *
1287 AAATTTAAATTCAAAATC
1 AAATTTAATTTTAAAA-C
* *
1305 -AATTTAATCTTAAAAT
1 AAATTTAATTTTAAAAC
1321 AAATCTTAA
1 AAAT-TTAA
1330 AATAGGTTTA
Statistics
Matches: 49, Mismatches: 8, Indels: 6
0.78 0.13 0.10
Matches are distributed among these distances:
17 39 0.80
18 10 0.20
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (17 bp):
AAATTTAATTTTAAAAC
Found at i:1318 original size:34 final size:35
Alignment explanation
Indices: 1251--1330 Score: 110
Period size: 34 Copynumber: 2.3 Consensus size: 35
1241 AATATAAATC
* *
1251 TAAATTTAAATTTTAAAACAAATTTAATTTTAAAA
1 TAAATTTAAATTTCAAAACAAATTTAATCTTAAAA
1286 TAAATTTAAA-TTCAAAATC-AATTTAATCTTAAAA
1 TAAATTTAAATTTCAAAA-CAAATTTAATCTTAAAA
1320 TAAATCTTAAA
1 TAAAT-TTAAA
1331 ATAGGTTTAA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
34 25 0.61
35 16 0.39
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (35 bp):
TAAATTTAAATTTCAAAACAAATTTAATCTTAAAA
Found at i:7878 original size:18 final size:19
Alignment explanation
Indices: 7852--7896 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
7842 AATAGTCAAA
* *
7852 TAGTTGTTATTTGGTTT-G
1 TAGTAGTTATTTGATTTAG
7870 TAGTAGTTATTTGATTTAG
1 TAGTAGTTATTTGATTTAG
7889 TAGATAGT
1 TAG-TAGT
7897 GGTCCTACTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 15 0.65
19 4 0.17
20 4 0.17
ACGTcount: A:0.22, C:0.00, G:0.24, T:0.53
Consensus pattern (19 bp):
TAGTAGTTATTTGATTTAG
Found at i:11845 original size:2 final size:2
Alignment explanation
Indices: 11838--11869 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
11828 GTTGATAATC
11838 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11870 GAAATCGAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.