Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017542.1 Corchorus olitorius cultivar O-4 contig17575, 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: 86727
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:2242 original size:2 final size:2
Alignment explanation
Indices: 2235--2259 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2225 GTGTTGAATA
2235 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
2260 CCATTTTCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:29300 original size:37 final size:37
Alignment explanation
Indices: 29250--29327 Score: 131
Period size: 37 Copynumber: 2.1 Consensus size: 37
29240 TTTTTACAGG
* *
29250 ATAATAATTGGGTAAAGAGGTAATTATCAAATTAAAT
1 ATAATAATTGGGTAAAGAGCTAATTAGCAAATTAAAT
29287 ATAATAATTGGGTAAAGAGCTAATTAGCAAATTAAAT
1 ATAATAATTGGGTAAAGAGCTAATTAGCAAATTAAAT
29324 -TAAT
1 ATAAT
29328 CAGTGATTAG
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
36 4 0.10
37 35 0.90
ACGTcount: A:0.49, C:0.04, G:0.15, T:0.32
Consensus pattern (37 bp):
ATAATAATTGGGTAAAGAGCTAATTAGCAAATTAAAT
Found at i:35435 original size:6 final size:6
Alignment explanation
Indices: 35424--35452 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
35414 CCTTTTGAAT
35424 GGAAAA GGAAAA GGAAAA GGAAAA -GAAAA
1 GGAAAA GGAAAA GGAAAA GGAAAA GGAAAA
35453 TAAGAAAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.22
6 18 0.78
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (6 bp):
GGAAAA
Found at i:39953 original size:17 final size:17
Alignment explanation
Indices: 39926--39958 Score: 50
Period size: 16 Copynumber: 1.9 Consensus size: 17
39916 AGCATACCAA
39926 CTTTTTTTTT-CTTTTT
1 CTTTTTTTTTCCTTTTT
39942 CTTTTTTCTTTCCTTTT
1 CTTTTTT-TTTCCTTTT
39959 ACCTTGAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 3 0.20
18 5 0.33
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (17 bp):
CTTTTTTTTTCCTTTTT
Found at i:41038 original size:7 final size:7
Alignment explanation
Indices: 41026--41065 Score: 71
Period size: 7 Copynumber: 5.7 Consensus size: 7
41016 ATCAACCCCA
41026 TGCAAAT
1 TGCAAAT
41033 TGCAAAT
1 TGCAAAT
41040 TGCAAAT
1 TGCAAAT
41047 TGCAAAT
1 TGCAAAT
41054 TGCAAAT
1 TGCAAAT
*
41061 CGCAA
1 TGCAA
41066 TCCCCTTTCC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.42, C:0.17, G:0.15, T:0.25
Consensus pattern (7 bp):
TGCAAAT
Found at i:43489 original size:11 final size:11
Alignment explanation
Indices: 43473--43497 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
43463 TTCATAGTAG
43473 TTACTAATTAA
1 TTACTAATTAA
43484 TTACTAATTAA
1 TTACTAATTAA
43495 TTA
1 TTA
43498 TAGTAAGTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (11 bp):
TTACTAATTAA
Found at i:59296 original size:7 final size:7
Alignment explanation
Indices: 59261--59295 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
59251 TCTTGGATTC
59261 TCCC-CT
1 TCCCTCT
59267 TCCCTCT
1 TCCCTCT
59274 TCCCTCT
1 TCCCTCT
59281 TCCCTCT
1 TCCCTCT
*
59288 TTCCTCT
1 TCCCTCT
59295 T
1 T
59296 TTCTCAGTGA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
6 4 0.15
7 23 0.85
ACGTcount: A:0.00, C:0.54, G:0.00, T:0.46
Consensus pattern (7 bp):
TCCCTCT
Found at i:70478 original size:21 final size:19
Alignment explanation
Indices: 70423--70480 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
70413 CTGTTTAGCA
70423 ACTGTACAGATGAGATTAC
1 ACTGTACAGATGAGATTAC
* * * *
70442 ACTGTATAAATTAGATTAGGT
1 ACTGTACAGATGAGATTA--C
70463 ACTGTACAGATGAGATTA
1 ACTGTACAGATGAGATTA
70481 TTAGAGCAGC
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
19 15 0.50
21 15 0.50
ACGTcount: A:0.38, C:0.10, G:0.21, T:0.31
Consensus pattern (19 bp):
ACTGTACAGATGAGATTAC
Found at i:71410 original size:6 final size:6
Alignment explanation
Indices: 71399--71433 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
71389 TCCTTTTGGA
71399 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT -TTTTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT
71434 CTGGTGAATC
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.17
6 24 0.83
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (6 bp):
ATTTTT
Found at i:86046 original size:3 final size:3
Alignment explanation
Indices: 86038--86090 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
86028 AATGTTTGTT
86038 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
86086 TTA TT
1 TTA TT
86091 TGTGTGTCCC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Done.