Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023302.1 Corchorus olitorius cultivar O-4 contig23335, 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: 23682
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.33
Found at i:2207 original size:44 final size:46
Alignment explanation
Indices: 2144--2229 Score: 140
Period size: 44 Copynumber: 1.9 Consensus size: 46
2134 ATACGAGTGG
*
2144 TTAAACTAAAGTTAGAATAC-A-ATATGCATGATAAACTAATGTGC
1 TTAAACTAAACTTAGAATACAATATATGCATGATAAACTAATGTGC
*
2188 TTAAACTAAACTTAGAATACAATATATGTATGATAAACTAAT
1 TTAAACTAAACTTAGAATACAATATATGCATGATAAACTAAT
2230 ACGATATATG
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
44 19 0.50
45 1 0.03
46 18 0.47
ACGTcount: A:0.48, C:0.10, G:0.10, T:0.31
Consensus pattern (46 bp):
TTAAACTAAACTTAGAATACAATATATGCATGATAAACTAATGTGC
Found at i:2236 original size:24 final size:24
Alignment explanation
Indices: 2203--2248 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
2193 CTAAACTTAG
*
2203 AATACAATATATGTATGATAAACT
1 AATACAATATATGCATGATAAACT
* *
2227 AATACGATATATGCATTATAAA
1 AATACAATATATGCATGATAAA
2249 GTAACACATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.50, C:0.09, G:0.09, T:0.33
Consensus pattern (24 bp):
AATACAATATATGCATGATAAACT
Found at i:2535 original size:18 final size:18
Alignment explanation
Indices: 2512--2556 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
2502 AATCGTTGAA
2512 AATTATTAATTGAATAAT
1 AATTATTAATTGAATAAT
**
2530 AATTATTTTTTGAATAAT
1 AATTATTAATTGAATAAT
*
2548 TATTATTAA
1 AATTATTAA
2557 AAATCCTACA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.51
Consensus pattern (18 bp):
AATTATTAATTGAATAAT
Found at i:4002 original size:51 final size:50
Alignment explanation
Indices: 3901--4002 Score: 111
Period size: 51 Copynumber: 2.0 Consensus size: 50
3891 GTTCTTCATA
* **
3901 TTTTCCTTGTTTAGATCTTGTCTCAGGACAATCAAACACTCTTTTAGTGT
1 TTTTCCTTGTTTAGATCTTGTCTCAGGACAATCAAACACTCATACAGTGT
*
3951 TTTTCTCTTGTTTCA-ATCTTGTCTCCGGAC-ATACAAACACT-ATACACGTGT
1 TTTTC-CTTGTTT-AGATCTTGTCTCAGGACAAT-CAAACACTCATACA-GTGT
4002 T
1 T
4003 CTTCATTCAG
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
50 9 0.20
51 34 0.77
52 1 0.02
ACGTcount: A:0.23, C:0.23, G:0.13, T:0.42
Consensus pattern (50 bp):
TTTTCCTTGTTTAGATCTTGTCTCAGGACAATCAAACACTCATACAGTGT
Found at i:5026 original size:30 final size:29
Alignment explanation
Indices: 4987--5044 Score: 89
Period size: 30 Copynumber: 2.0 Consensus size: 29
4977 ACACTCTTAA
* *
4987 TCTTTGGAAGATTCTCAATTATATTTCTT
1 TCTTTGGAAGATTCTCAAATAAATTTCTT
5016 TCTTTAGGAAGATTCTCAAATAAATTTCT
1 TCTTT-GGAAGATTCTCAAATAAATTTCT
5045 GGCCTTTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 5 0.19
30 21 0.81
ACGTcount: A:0.29, C:0.14, G:0.10, T:0.47
Consensus pattern (29 bp):
TCTTTGGAAGATTCTCAAATAAATTTCTT
Found at i:10839 original size:27 final size:27
Alignment explanation
Indices: 10809--10864 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
10799 GCCTCTAGTG
10809 TTTGGAATAGTACAAGCCTTAGTTGGA
1 TTTGGAATAGTACAAGCCTTAGTTGGA
10836 TTTGGAATAGTACAAGCCTTAGTTGGA
1 TTTGGAATAGTACAAGCCTTAGTTGGA
10863 TT
1 TT
10865 AGTAACTTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.29, C:0.11, G:0.25, T:0.36
Consensus pattern (27 bp):
TTTGGAATAGTACAAGCCTTAGTTGGA
Found at i:11352 original size:48 final size:48
Alignment explanation
Indices: 11291--11400 Score: 150
Period size: 47 Copynumber: 2.3 Consensus size: 48
11281 AGATGTGATT
* * * * *
11291 TTGGGTTTTGCTGTTTTTTGCTATTAGATTCTTATGGCATGTGCTTTG
1 TTGGGTTCTGCTGTTTTTTGCAATCAGATTCTTATGACATATGCTTTG
*
11339 TTGGGTTCTGCTG-TTTTTGCAATCAGATTCTTATGATATATGCTTTG
1 TTGGGTTCTGCTGTTTTTTGCAATCAGATTCTTATGACATATGCTTTG
*
11386 TTGGGTTCTGATGTT
1 TTGGGTTCTGCTGTT
11401 CTTCAATTAG
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
47 41 0.76
48 13 0.24
ACGTcount: A:0.13, C:0.11, G:0.25, T:0.52
Consensus pattern (48 bp):
TTGGGTTCTGCTGTTTTTTGCAATCAGATTCTTATGACATATGCTTTG
Found at i:16778 original size:2 final size:2
Alignment explanation
Indices: 16771--16799 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
16761 AGTGAAGGAT
16771 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
16800 GTTATAGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.