Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021120.1 Corchorus olitorius cultivar O-4 contig21153, 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: 59496
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:1914 original size:19 final size:18
Alignment explanation
Indices: 1881--1916 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
1871 TTGAAATTAT
1881 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
1899 TCTTCAAATTGTCTTCAA
1 TCTTC-AATGGTCTTCAA
1917 TAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (18 bp):
TCTTCAATGGTCTTCAAA
Found at i:2512 original size:125 final size:124
Alignment explanation
Indices: 2295--2530 Score: 325
Period size: 125 Copynumber: 1.9 Consensus size: 124
2285 TACCACAGTA
* *
2295 GCCATGCTACTGACCTCCTTTGTTGATAAAGAACAGAACTTCGGTTGAAGTGCCCATCAGCATTT
1 GCCATGCTACTGACCTCCTTTGTTGATAAAGAACAGAACTTCGGTTAAAGTGCCCAGCAGCATTT
* * *
2360 CTCGGCAGCGGAACCTCCTCCTTGGCAGAGTGACATGTCAGCAAGGTTGCACCAGTTTT
66 CTCAGCAGCGGAACCTCCTCCTCGGCAGAGTGACACGTCAGCAAGGTTGCACCAGTTTT
** * * *
2419 GCCATGCTGTTGACCTTCTTTGTTGATGAAGGATA-AG-ACTTTGGTTAAAGTTGCCCAGCAGCA
1 GCCATGCTACTGACCTCCTTTGTTGAT-AAAGA-ACAGAACTTCGGTTAAAG-TGCCCAGCAGCA
2482 GTTTC-CAGCAGCGGAACCTCCTCCTCGGCAGAGTGACACGTCAGCAAGG
63 -TTTCTCAGCAGCGGAACCTCCTCCTCGGCAGAGTGACACGTCAGCAAGG
2531 CAGTCCCACG
Statistics
Matches: 98, Mismatches: 10, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
124 35 0.36
125 58 0.59
126 5 0.05
ACGTcount: A:0.23, C:0.26, G:0.25, T:0.26
Consensus pattern (124 bp):
GCCATGCTACTGACCTCCTTTGTTGATAAAGAACAGAACTTCGGTTAAAGTGCCCAGCAGCATTT
CTCAGCAGCGGAACCTCCTCCTCGGCAGAGTGACACGTCAGCAAGGTTGCACCAGTTTT
Found at i:3370 original size:2 final size:2
Alignment explanation
Indices: 3363--3387 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3353 TTCAAGTTCC
3363 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 T
3388 GTCCACATAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4145 original size:79 final size:79
Alignment explanation
Indices: 4014--4168 Score: 301
Period size: 79 Copynumber: 2.0 Consensus size: 79
4004 TGAGTTGATA
4014 TATTAATTAAAATATATATGGGCATGTTTCATATATCTGGTTAACAAGTCCTATCCAAAATAAAT
1 TATTAATTAAAATATATATGGGCATGTTTCATATATCTGGTTAACAAGTCCTATCCAAAATAAAT
4079 TGCAGGTATAGCAT
66 TGCAGGTATAGCAT
*
4093 TATTAATTAAAATATATATGGGCATGTTTCATATATCTGGTTAACAAGTCCTATCCTAAATAAAT
1 TATTAATTAAAATATATATGGGCATGTTTCATATATCTGGTTAACAAGTCCTATCCAAAATAAAT
4158 TGCAGGTATAG
66 TGCAGGTATAG
4169 GCGTATAGCA
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
79 75 1.00
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.36
Consensus pattern (79 bp):
TATTAATTAAAATATATATGGGCATGTTTCATATATCTGGTTAACAAGTCCTATCCAAAATAAAT
TGCAGGTATAGCAT
Found at i:5934 original size:24 final size:24
Alignment explanation
Indices: 5907--5959 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
5897 AAATAATATA
* *
5907 ATATAATTAAA-TAATTATATTTAT
1 ATATAATAAAATTAAATA-ATTTAT
5931 ATATAATAAAATTAAATAATTTAT
1 ATATAATAAAATTAAATAATTTAT
5955 ATATA
1 ATATA
5960 TACATTAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 21 0.81
25 5 0.19
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (24 bp):
ATATAATAAAATTAAATAATTTAT
Found at i:5937 original size:29 final size:28
Alignment explanation
Indices: 5902--5961 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 28
5892 TATATAAATA
* *
5902 ATATAATATAATTAAATAATTATATTTAT
1 ATATAATAAAATTAAATAATT-TATATAT
5931 ATATAATAAAATTAAATAATTTATATAT
1 ATATAATAAAATTAAATAATTTATATAT
5959 ATA
1 ATA
5962 CATTAATTAG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 9 0.31
29 20 0.69
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (28 bp):
ATATAATAAAATTAAATAATTTATATAT
Found at i:15033 original size:6 final size:6
Alignment explanation
Indices: 15022--15050 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
15012 GTGAAGGATC
15022 ATCATG ATCATG ATCATG ATCATG ATCAT
1 ATCATG ATCATG ATCATG ATCATG ATCAT
15051 CACAACATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.34
Consensus pattern (6 bp):
ATCATG
Found at i:17723 original size:20 final size:21
Alignment explanation
Indices: 17695--17737 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
17685 CAAAACTGTC
*
17695 AAAAGGGGGCGGTAAGTAGCA
1 AAAAGGGGGCGGTAAATAGCA
17716 AAAAGGGGGCGGTAAATAGCA
1 AAAAGGGGGCGGTAAATAGCA
17737 A
1 A
17738 CTCCCTTATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.42, C:0.09, G:0.40, T:0.09
Consensus pattern (21 bp):
AAAAGGGGGCGGTAAATAGCA
Found at i:24306 original size:20 final size:22
Alignment explanation
Indices: 24267--24306 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
24257 ATGAAAGATA
24267 AATTTGACCTATGAAACAGACT
1 AATTTGACCTATGAAACAGACT
24289 AATTTGACC-ATG-AACAGA
1 AATTTGACCTATGAAACAGA
24307 GAAGATAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.33
21 3 0.17
22 9 0.50
ACGTcount: A:0.42, C:0.17, G:0.15, T:0.25
Consensus pattern (22 bp):
AATTTGACCTATGAAACAGACT
Found at i:31255 original size:24 final size:27
Alignment explanation
Indices: 31227--31287 Score: 83
Period size: 29 Copynumber: 2.3 Consensus size: 27
31217 TCTAGCTTAT
31227 ATTATAAAC-TATAG-ATAT-TATAGA
1 ATTATAAACATATAGAATATATATAGA
31251 ATTATAAACTATATAGAAATATATATAGA
1 ATTATAAAC-ATATAG-AATATATATAGA
31280 ATTATAAA
1 ATTATAAA
31288 TACTAAGTAC
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
24 9 0.28
26 5 0.16
28 4 0.12
29 14 0.44
ACGTcount: A:0.54, C:0.03, G:0.07, T:0.36
Consensus pattern (27 bp):
ATTATAAACATATAGAATATATATAGA
Found at i:31265 original size:17 final size:16
Alignment explanation
Indices: 31245--31289 Score: 53
Period size: 12 Copynumber: 3.0 Consensus size: 16
31235 CTATAGATAT
31245 TATAGAATTATAAACTA
1 TATAGAATTATAAA-TA
31262 TATAGAA--AT--ATA
1 TATAGAATTATAAATA
31274 TATAGAATTATAAATA
1 TATAGAATTATAAATA
31290 CTAAGTACCG
Statistics
Matches: 24, Mismatches: 0, Indels: 9
0.73 0.00 0.27
Matches are distributed among these distances:
12 9 0.38
13 1 0.04
14 2 0.08
15 2 0.08
16 3 0.12
17 7 0.29
ACGTcount: A:0.56, C:0.02, G:0.07, T:0.36
Consensus pattern (16 bp):
TATAGAATTATAAATA
Found at i:31482 original size:12 final size:12
Alignment explanation
Indices: 31467--31492 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
31457 AATTGCTTAT
31467 AAAAAAACAAAA
1 AAAAAAACAAAA
31479 AAAAAAACAAAA
1 AAAAAAACAAAA
31491 AA
1 AA
31493 TATAGTGAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAAAAACAAAA
Found at i:43315 original size:2 final size:2
Alignment explanation
Indices: 43308--43353 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
43298 GTGATTTGTA
43308 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
43350 CT CT
1 CT CT
43354 ATTTGTATCC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Done.