Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015053.1 Corchorus olitorius cultivar O-4 contig15086, 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: 5446
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.32
Found at i:2523 original size:54 final size:54
Alignment explanation
Indices: 2393--2993 Score: 582
Period size: 54 Copynumber: 11.1 Consensus size: 54
2383 ACCTCGATCA
* ** *
2393 CGAAAACCTTTCTTGGAGTGACCGTACTGGATCAAAT-TGGAGATCAACTCTGATCAT
1 CGAAAA-C-TTCTTGGAATGACCACACTGGATC--ATCTGGAGATCAACTCTGATCTT
* * *
2450 CGAAAACTTCTT-GAACGACCACACTGGATCATCTGGAGATCAACTCTAATTTT
1 CGAAAACTTCTTGGAATGACCACACTGGATCATCTGGAGATCAACTCTGATCTT
* * * * *
2503 CGAAAACTTCTTGAAACGACCACACCGGATCATCTGAAGATCAAATCTGATCTT
1 CGAAAACTTCTTGGAATGACCACACTGGATCATCTGGAGATCAACTCTGATCTT
* * *
2557 CGAGAACTTCTTGAAACGACCACACTGGATCATCTGGAGATCAACTCTGATCTT
1 CGAAAACTTCTTGGAATGACCACACTGGATCATCTGGAGATCAACTCTGATCTT
* * * * *
2611 AGAAAACTTCTCGGAA-GAACCGCACTGGAACATCTGGACATCAACTCTGAT-TAT
1 CGAAAACTTCTTGGAATG-ACCACACTGGATCATCTGGAGATCAACTCTGATCT-T
* * * *
2665 CAAAAACTTCTTGGAATGACCACACCGGATCATCT-AAGGATCAACTCTGACCGTT
1 CGAAAACTTCTTGGAATGACCACACTGGATCATCTGGA-GATCAACTCTGATC-TT
* * * *
2720 -AAAAACTTCTTAGAATGACCGCACTGGATCATCT-GAGGATCAACTCTGACCATT
1 CGAAAACTTCTTGGAATGACCACACTGGATCATCTGGA-GATCAACTCTGATC-TT
* * *
2774 -GAAAACTTCTTGAAATGACCGCACTAGATCATCT-GAGGATCAACTCTGATCATT
1 CGAAAACTTCTTGGAATGACCACACTGGATCATCTGGA-GATCAACTCTGATC-TT
* * * * *
2828 -TAAAACTTCTTGGAATGACCACACTAGATCAATCTAG-GATCAACTCTAATCAT
1 CGAAAACTTCTTGGAATGACCACACTGGATC-ATCTGGAGATCAACTCTGATCTT
* * * * *
2881 CGAAAACTTCTTGGAATGACCGCACCGGACCATTTGG-GATCAACTCTGGTCATT
1 CGAAAACTTCTTGGAATGACCACACTGGATCATCTGGAGATCAACTCTGATC-TT
* *
2935 -GAAAACTTCTTGGAATGACCATACTGGATCAATCT-GAGATCAACTCTGATCAT
1 CGAAAACTTCTTGGAATGACCACACTGGATC-ATCTGGAGATCAACTCTGATCTT
2988 CGAAAA
1 CGAAAA
2994 ACCGGACCAT
Statistics
Matches: 464, Mismatches: 65, Indels: 33
0.83 0.12 0.06
Matches are distributed among these distances:
52 2 0.00
53 77 0.17
54 365 0.79
55 11 0.02
56 3 0.01
57 6 0.01
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (54 bp):
CGAAAACTTCTTGGAATGACCACACTGGATCATCTGGAGATCAACTCTGATCTT
Found at i:3057 original size:90 final size:90
Alignment explanation
Indices: 2904--3083 Score: 351
Period size: 90 Copynumber: 2.0 Consensus size: 90
2894 GAATGACCGC
*
2904 ACCGGACCATTTGGGATCAACTCTGGTCATTGAAAACTTCTTGGAATGACCATACTGGATCAATC
1 ACCGGACCATTTGGGATCAACTCTGGTCATTGAAAACTTCTTGGAATGACCACACTGGATCAATC
2969 TGAGATCAACTCTGATCATCGAAAA
66 TGAGATCAACTCTGATCATCGAAAA
2994 ACCGGACCATTTGGGATCAACTCTGGTCATTGAAAACTTCTTGGAATGACCACACTGGATCAATC
1 ACCGGACCATTTGGGATCAACTCTGGTCATTGAAAACTTCTTGGAATGACCACACTGGATCAATC
3059 TGAGATCAACTCTGATCATCGAAAA
66 TGAGATCAACTCTGATCATCGAAAA
3084 CTTCTTGGAA
Statistics
Matches: 89, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
90 89 1.00
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (90 bp):
ACCGGACCATTTGGGATCAACTCTGGTCATTGAAAACTTCTTGGAATGACCACACTGGATCAATC
TGAGATCAACTCTGATCATCGAAAA
Found at i:3090 original size:54 final size:54
Alignment explanation
Indices: 3008--3258 Score: 310
Period size: 54 Copynumber: 4.6 Consensus size: 54
2998 GACCATTTGG
* *
3008 GATCAACTCTGGTCATTGAAAACTTCTTGGAATGACCACACTGGATCAATCT-GA
1 GATCAACTCTGATCATCGAAAACTTCTTGGAATGACCACACTGGATC-ATCTGGA
* * *
3062 GATCAACTCTGATCATCGAAAACTTCTTGGAACT-TCCGCACTGGATCATCTAGA
1 GATCAACTCTGATCATCGAAAACTTCTTGGAA-TGACCACACTGGATCATCTGGA
* * *
3116 GATCAACTTTGTTCATCGAAAATTTCTTGGAATGACCACACTGGATCAAT-TGGA
1 GATCAACTCTGATCATCGAAAACTTCTTGGAATGACCACACTGGATC-ATCTGGA
* * * * * *
3170 TATCAACTCTGATCATCTAAAACTTCTTGGAATGACCGCACTGGATCTTTTGGG
1 GATCAACTCTGATCATCGAAAACTTCTTGGAATGACCACACTGGATCATCTGGA
* *
3224 GATCAACTCTGACCATAGAAAACTTCTTGGAATGA
1 GATCAACTCTGATCATCGAAAACTTCTTGGAATGA
3259 GATCAACTGT
Statistics
Matches: 170, Mismatches: 22, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
53 6 0.04
54 161 0.95
55 3 0.02
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (54 bp):
GATCAACTCTGATCATCGAAAACTTCTTGGAATGACCACACTGGATCATCTGGA
Found at i:3123 original size:144 final size:143
Alignment explanation
Indices: 2864--3137 Score: 372
Period size: 144 Copynumber: 1.9 Consensus size: 143
2854 GATCAATCTA
* * * *
2864 GGATCAACTCTAATCATCGAAAACTTCTTGGAATGACCGCACCGGACCATTTGGGATCAACTCTG
1 GGATCAACTCTAATCATCGAAAACTTCTTGGAATGACCACACCGGACAATCTGAGATCAACTCTG
* * *
2929 GTCATTGAAAACTTCTTGGAATGACCATACTGGATCAATCTGAGATCAACTCTGATCATCGAAAA
66 ATCATCGAAAACTTCTTGGAATGACCACACTGGATCAATCTGAGATCAACTCTGATCATCGAAAA
2994 ACCGGACCATTTG
131 ACCGGACCATTTG
** * *
3007 GGATCAACTCTGGTCATTGAAAACTTCTTGGAATGACCACACTGGATCAATCTGAGATCAACTCT
1 GGATCAACTCTAATCATCGAAAACTTCTTGGAATGACCACACCGGA-CAATCTGAGATCAACTCT
* * * *
3072 GATCATCGAAAACTTCTTGGAACT-TCCGCACTGGATC-ATCTAGAGATCAACTTTGTTCATCGA
65 GATCATCGAAAACTTCTTGGAA-TGACCACACTGGATCAATCT-GAGATCAACTCTGATCATCGA
3135 AAA
128 AAA
3138 TTTCTTGGAA
Statistics
Matches: 113, Mismatches: 15, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
143 45 0.40
144 67 0.59
145 1 0.01
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.27
Consensus pattern (143 bp):
GGATCAACTCTAATCATCGAAAACTTCTTGGAATGACCACACCGGACAATCTGAGATCAACTCTG
ATCATCGAAAACTTCTTGGAATGACCACACTGGATCAATCTGAGATCAACTCTGATCATCGAAAA
ACCGGACCATTTG
Found at i:3197 original size:108 final size:108
Alignment explanation
Indices: 3008--3258 Score: 344
Period size: 108 Copynumber: 2.3 Consensus size: 108
2998 GACCATTTGG
* *
3008 GATCAACTCTGGTCATTGAAAACTTCTTGGAATGACCACACTGGATCAATCTGAGATCAACTCTG
1 GATCAACTCTGATCATAGAAAACTTCTTGGAATGACCACACTGGATCAATCTGAGATCAACTCTG
*
3073 ATCATCGAAAACTTCTTGGAACT-TCCGCACTGGATCATCTAGA
66 ATCATCGAAAACTTCTTGGAA-TGACCGCACTGGATCATCTAGA
* * * * *
3116 GATCAACTTTGTTCATCGAAAATTTCTTGGAATGACCACACTGGATCAAT-TGGATATCAACTCT
1 GATCAACTCTGATCATAGAAAACTTCTTGGAATGACCACACTGGATCAATCT-GAGATCAACTCT
* * * * *
3180 GATCATCTAAAACTTCTTGGAATGACCGCACTGGATCTTTTGGG
65 GATCATCGAAAACTTCTTGGAATGACCGCACTGGATCATCTAGA
*
3224 GATCAACTCTGACCATAGAAAACTTCTTGGAATGA
1 GATCAACTCTGATCATAGAAAACTTCTTGGAATGA
3259 GATCAACTGT
Statistics
Matches: 125, Mismatches: 16, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
107 2 0.02
108 123 0.98
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (108 bp):
GATCAACTCTGATCATAGAAAACTTCTTGGAATGACCACACTGGATCAATCTGAGATCAACTCTG
ATCATCGAAAACTTCTTGGAATGACCGCACTGGATCATCTAGA
Found at i:3263 original size:35 final size:35
Alignment explanation
Indices: 3224--3493 Score: 364
Period size: 35 Copynumber: 7.7 Consensus size: 35
3214 ATCTTTTGGG
* *
3224 GATCAACTCTGACCAT-AGAAAACTTCTTGGAATGA
1 GATCAACTCTGATCATCA-AAAACTTCTTGAAATGA
* * * *
3259 GATCAACTGTGATCAACGAAAACTTCTTGAAAGGA
1 GATCAACTCTGATCATCAAAAACTTCTTGAAATGA
3294 GATCAACTCTGATCATCAAAAACTTCTTGAAATGA
1 GATCAACTCTGATCATCAAAAACTTCTTGAAATGA
* *
3329 GATCAACTCTGATCATAAAAAAACTTCTTGAAAGGA
1 GATCAACTCTGATCAT-CAAAAACTTCTTGAAATGA
* * *
3365 GATCAACTTTGATCATAAAAAACTTC-TGAAAGGA
1 GATCAACTCTGATCATCAAAAACTTCTTGAAATGA
*
3399 GATCAACTCTGATCATCAAAAACTTCTTGAGATGA
1 GATCAACTCTGATCATCAAAAACTTCTTGAAATGA
*
3434 GATCAACTCTGATAATCAAAAACTTCTTGAAATGA
1 GATCAACTCTGATCATCAAAAACTTCTTGAAATGA
* * *
3469 GATCAACTATGATCAACGAAAACTT
1 GATCAACTCTGATCATCAAAAACTT
3494 ATATGAAAGA
Statistics
Matches: 209, Mismatches: 23, Indels: 6
0.88 0.10 0.03
Matches are distributed among these distances:
34 32 0.15
35 145 0.69
36 32 0.15
ACGTcount: A:0.41, C:0.18, G:0.14, T:0.26
Consensus pattern (35 bp):
GATCAACTCTGATCATCAAAAACTTCTTGAAATGA
Found at i:3265 original size:251 final size:249
Alignment explanation
Indices: 2757--3290 Score: 625
Period size: 251 Copynumber: 2.1 Consensus size: 249
2747 ATCATCTGAG
* *
2757 GATCAACTCTGACCATTGAAAACTTCTTGAAATGACCGCACTAGATCATCTGAGGATCAACTCTG
1 GATCAACTCTGATCATTGAAAACTTCTTGAAATGACCACACTAGATCATCTGAGGATCAACTCTG
**
2822 ATCATTTAAAACTTCTTGGAATGACCACACTAGATCAATCTAGGATCAACTCTAATCATCGAAAA
66 ATCATCGAAAACTTCTTGGAATGACCACACTAGATCAATCTAGGATCAACTCTAATCATCGAAAA
* * *
2887 CTTCTTGGAATGACCGCACCGGACCATTTGGGATCAACTCTGGTCATTGAAAACTTCTTGGAATG
131 CTTCTTGGAATGACCACACCGGACCAATTGGGATCAACTCTGATCATTGAAAACTTCTTGGAATG
* * * *
2952 ACCATACTGGATCAATCTGAGATCAACTCTGATCATCGAAAAACCGGACCATTTGG
196 ACCACACTGGATCAATCTGAGATCAACTCTGACCATAGAAAAACCGGA-CA-TTGA
* * *
3008 GATCAACTCTGGTCATTGAAAACTTCTTGGAATGACCACACTGGATCAATCTGA-GATCAACTCT
1 GATCAACTCTGATCATTGAAAACTTCTTGAAATGACCACACTAGATC-ATCTGAGGATCAACTCT
* * * * **
3072 GATCATCGAAAACTTCTTGGAACT-TCCGCACTGGATC-ATCTAGAGATCAACTTTGTTCATCGA
65 GATCATCGAAAACTTCTTGGAA-TGACCACACTAGATCAATCTAG-GATCAACTCTAATCATCGA
* * * *
3135 AAATTTCTTGGAATGACCACACTGGATCAATTGGATATCAACTCTGATCATCT-AAAACTTCTTG
128 AAACTTCTTGGAATGACCACACCGGACCAATTGG-GATCAACTCTGATCAT-TGAAAACTTCTTG
* * * *
3199 GAATGACCGCACTGGATC-TTTTGGGGATCAACTCTGACCATAG-AAAACTTCTTGGA-A-TGA
191 GAATGACCACACTGGATCAATCT-GAGATCAACTCTGACCATAGAAAAAC--C--GGACATTGA
* **
3259 GATCAACTGTGATCAACGAAAACTTCTTGAAA
1 GATCAACTCTGATCATTGAAAACTTCTTGAAA
3291 GGAGATCAAC
Statistics
Matches: 240, Mismatches: 33, Indels: 20
0.82 0.11 0.07
Matches are distributed among these distances:
250 6 0.03
251 163 0.68
252 65 0.27
253 3 0.01
255 3 0.01
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.28
Consensus pattern (249 bp):
GATCAACTCTGATCATTGAAAACTTCTTGAAATGACCACACTAGATCATCTGAGGATCAACTCTG
ATCATCGAAAACTTCTTGGAATGACCACACTAGATCAATCTAGGATCAACTCTAATCATCGAAAA
CTTCTTGGAATGACCACACCGGACCAATTGGGATCAACTCTGATCATTGAAAACTTCTTGGAATG
ACCACACTGGATCAATCTGAGATCAACTCTGACCATAGAAAAACCGGACATTGA
Found at i:3414 original size:105 final size:105
Alignment explanation
Indices: 3224--3502 Score: 409
Period size: 105 Copynumber: 2.6 Consensus size: 105
3214 ATCTTTTGGG
* * * * *
3224 GATCAACTCTGACCATAGAAAACTTCTTGGAATGAGATCAACTGTGATCAACGAAAACTTCTTGA
1 GATCAACTCTGATCATAAAAAACTTCTTGAAATGAGATCAACTATGATCAACAAAAACTTCTTGA
3289 AAGGAGATCAACTCTGATCATCAAAAACTTCTTGAAATGA
66 AAGGAGATCAACTCTGATCATCAAAAACTTCTTGAAATGA
* *
3329 GATCAACTCTGATCATAAAAAAACTTCTTGAAAGGAGATCAACTTTGATCATA-AAAAACTTC-T
1 GATCAACTCTGATCAT-AAAAAACTTCTTGAAATGAGATCAACTATGATCA-ACAAAAACTTCTT
*
3392 GAAAGGAGATCAACTCTGATCATCAAAAACTTCTTGAGATGA
64 GAAAGGAGATCAACTCTGATCATCAAAAACTTCTTGAAATGA
* * * *
3434 GATCAACTCTGATAATCAAAAACTTCTTGAAATGAGATCAACTATGATCAACGAAAACTTATATG
1 GATCAACTCTGATCATAAAAAACTTCTTGAAATGAGATCAACTATGATCAACAAAAACTTCT-TG
3499 AAAG
65 AAAG
3503 ACCGCACAGG
Statistics
Matches: 156, Mismatches: 13, Indels: 9
0.88 0.07 0.05
Matches are distributed among these distances:
103 1 0.01
104 38 0.24
105 72 0.46
106 44 0.28
107 1 0.01
ACGTcount: A:0.42, C:0.18, G:0.15, T:0.26
Consensus pattern (105 bp):
GATCAACTCTGATCATAAAAAACTTCTTGAAATGAGATCAACTATGATCAACAAAAACTTCTTGA
AAGGAGATCAACTCTGATCATCAAAAACTTCTTGAAATGA
Found at i:3520 original size:140 final size:141
Alignment explanation
Indices: 3237--3524 Score: 357
Period size: 140 Copynumber: 2.0 Consensus size: 141
3227 CAACTCTGAC
* * * * *
3237 CATAGAAAACTTCTTGGAATGAGATCAACTGTGATCAACGAAAACTTCTTGAAAGGAGATCAACT
1 CATAAAAAACTTCTTGAAAGGAGATCAACTCTGATCAACAAAAACTTCTTGAAAGGAGATCAACT
* * * *
3302 CTGATCATCAAAAACTTCTTGAAATGAGATCAACTCTGATCATAAAAAAACTTCTTGAAAGGAGA
66 CTGATAATCAAAAACTTCTTGAAATGAGATCAACTATGATCATAAAAAAACTTATTGAAAGGACA
* ** *
3367 TCAACTTTGAT
131 GCAACGGTCAT
* * *
3378 CATAAAAAACTTC-TGAAAGGAGATCAACTCTGATCATCAAAAACTTCTTGAGATGAGATCAACT
1 CATAAAAAACTTCTTGAAAGGAGATCAACTCTGATCAACAAAAACTTCTTGAAAGGAGATCAACT
**
3442 CTGATAATCAAAAACTTCTTGAAATGAGATCAACTATGATCA-ACGAAAACTTATATGAAA-GAC
66 CTGATAATCAAAAACTTCTTGAAATGAGATCAACTATGATCATAAAAAAACTTAT-TGAAAGGAC
* *
3505 CGCACAGGGTCAT
130 AGCA-ACGGTCAT
3518 CATAAAA
1 CATAAAA
3525 TCAACTTAGA
Statistics
Matches: 125, Mismatches: 20, Indels: 5
0.83 0.13 0.03
Matches are distributed among these distances:
139 13 0.10
140 100 0.80
141 12 0.10
ACGTcount: A:0.42, C:0.18, G:0.15, T:0.25
Consensus pattern (141 bp):
CATAAAAAACTTCTTGAAAGGAGATCAACTCTGATCAACAAAAACTTCTTGAAAGGAGATCAACT
CTGATAATCAAAAACTTCTTGAAATGAGATCAACTATGATCATAAAAAAACTTATTGAAAGGACA
GCAACGGTCAT
Found at i:3553 original size:54 final size:54
Alignment explanation
Indices: 3486--3655 Score: 243
Period size: 54 Copynumber: 3.1 Consensus size: 54
3476 TATGATCAAC
* *
3486 GAAAACTTATATGAAAGACCGCACAGGGTCATCAT-AAAATCAACTTAGATCCCT
1 GAAAACTTCTATGAAAGACCGCACAGGGTCATC-TGAAAATCAACTTAGATCTCT
* * *
3540 GAAAACTTCTATGAAAGACCGCACAGGGTCATCTGAAGATCAACTTAAATCTTT
1 GAAAACTTCTATGAAAGACCGCACAGGGTCATCTGAAAATCAACTTAGATCTCT
* ** *
3594 TAAAACTTCTATGAAAGACCGCACAGGGTCATCTGAACCTCAACTTAGATATCT
1 GAAAACTTCTATGAAAGACCGCACAGGGTCATCTGAAAATCAACTTAGATCTCT
3648 GAAAACTT
1 GAAAACTT
3656 TAAAAAATCG
Statistics
Matches: 103, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
53 1 0.01
54 102 0.99
ACGTcount: A:0.38, C:0.22, G:0.15, T:0.25
Consensus pattern (54 bp):
GAAAACTTCTATGAAAGACCGCACAGGGTCATCTGAAAATCAACTTAGATCTCT
Found at i:4855 original size:39 final size:39
Alignment explanation
Indices: 4777--4857 Score: 101
Period size: 39 Copynumber: 2.1 Consensus size: 39
4767 ATATTTTTGA
** * *
4777 AAAACATTTTTTCTCTTTTAAAAAGATTGCACTTTGAGG
1 AAAACATTTTTTCTCTTTTAAAAAGATCACACCTAGAGG
*
4816 AAAACATTTTTT-TCTTTTGAAAAAGATCACGCCTAGAGG
1 AAAACATTTTTTCTCTTTT-AAAAAGATCACACCTAGAGG
4855 AAA
1 AAA
4858 GTTTCATTCC
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
38 6 0.17
39 30 0.83
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.36
Consensus pattern (39 bp):
AAAACATTTTTTCTCTTTTAAAAAGATCACACCTAGAGG
Found at i:5067 original size:20 final size:22
Alignment explanation
Indices: 5035--5080 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
5025 CTTTCCTCCG
5035 TCTTTTGCTTTTTCAACT-TTT
1 TCTTTTGCTTTTTCAACTCTTT
*
5056 TCTTTT-CTTTTTCAATTCTTT
1 TCTTTTGCTTTTTCAACTCTTT
5077 TCTT
1 TCTT
5081 CATTTTTCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 10 0.43
21 13 0.57
ACGTcount: A:0.09, C:0.20, G:0.02, T:0.70
Consensus pattern (22 bp):
TCTTTTGCTTTTTCAACTCTTT
Done.