Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022850.1 Corchorus olitorius cultivar O-4 contig22883, 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: 8904
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Found at i:1858 original size:27 final size:27
Alignment explanation
Indices: 1828--1928 Score: 130
Period size: 27 Copynumber: 3.7 Consensus size: 27
1818 AAGTGAACTT
* *
1828 AAAATGACCAAAATCCCCCTGAATGTA
1 AAAATGACCGAAATGCCCCTGAATGTA
1855 AAAATGACCGAAATGCCCCTGAATGTA
1 AAAATGACCGAAATGCCCCTGAATGTA
* *
1882 AAAATGATCGAAATGCCCATGAATGTGCA
1 AAAATGACCGAAATGCCCCTGAATGT--A
**
1911 AAAATGACCCTAATGCCC
1 AAAATGACCGAAATGCCC
1929 TTGGTCATGC
Statistics
Matches: 65, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
27 49 0.75
29 16 0.25
ACGTcount: A:0.42, C:0.24, G:0.16, T:0.19
Consensus pattern (27 bp):
AAAATGACCGAAATGCCCCTGAATGTA
Found at i:2276 original size:69 final size:69
Alignment explanation
Indices: 2179--2383 Score: 229
Period size: 69 Copynumber: 3.0 Consensus size: 69
2169 AATCAATTTG
* * * *
2179 ATCTATTTGAAGATTTGCTGCACCGAGCCCACTGAGTCCATATTGATGATTCTACACCGAGTCAT
1 ATCTATTTGAAGATTGGATGCACCGAGCCCACTGAGTCCATATTGAAGATGCTACACCGAGTCAT
2244 CCTA
66 CCTA
*
2248 ATCTATTTGAAGATTGGATGCACCGAGCCTACTGAGTCCATATTGAAGATGCTACACCGAGTCAT
1 ATCTATTTGAAGATTGGATGCACCGAGCCCACTGAGTCCATATTGAAGATGCTACACCGAGTCAT
2313 -CTGA
66 CCT-A
* * * * * * *
2317 ATTCATCTTTGAAGA-T-GTTACACCGAG-TCATCTGAGTTCGTCTTTGAAGATGCTACACCGAG
1 A-TC-TATTTGAAGATTGGATGCACCGAGCCCA-CTGAGTCCAT-ATTGAAGATGCTACACCGAG
2379 TCATC
62 TCATC
2384 TGAATTCATC
Statistics
Matches: 117, Mismatches: 13, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
68 3 0.03
69 79 0.68
70 26 0.22
71 9 0.08
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (69 bp):
ATCTATTTGAAGATTGGATGCACCGAGCCCACTGAGTCCATATTGAAGATGCTACACCGAGTCAT
CCTA
Found at i:2296 original size:36 final size:35
Alignment explanation
Indices: 2185--2308 Score: 112
Period size: 34 Copynumber: 3.6 Consensus size: 35
2175 TTTGATCTAT
*
2185 TTGAAGATTTGCTGCACCGAGCCCACTGAGTCCATA
1 TTGAAGA-TTGCTGCACCGAGCCTACTGAGTCCATA
* * * * * *
2221 TTGATGATT-CTACACCGAGTCATCCT-AATCTAT-
1 TTGAAGATTGCTGCACCGAG-CCTACTGAGTCCATA
*
2254 TTGAAGATTGGATGCACCGAGCCTACTGAGTCCATA
1 TTGAAGATT-GCTGCACCGAGCCTACTGAGTCCATA
*
2290 TTGAAGA-TGCTACACCGAG
1 TTGAAGATTGCTGCACCGAG
2309 TCATCTGAAT
Statistics
Matches: 67, Mismatches: 16, Indels: 12
0.71 0.17 0.13
Matches are distributed among these distances:
33 8 0.12
34 27 0.40
35 19 0.28
36 13 0.19
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.27
Consensus pattern (35 bp):
TTGAAGATTGCTGCACCGAGCCTACTGAGTCCATA
Found at i:2332 original size:35 final size:35
Alignment explanation
Indices: 2290--2648 Score: 535
Period size: 35 Copynumber: 10.3 Consensus size: 35
2280 TGAGTCCATA
*
2290 TTGAAGATGCTACACCGAGTCATCTGAATTCATCT
1 TTGAAGATGCTACACCGAGTCATCTGAATTCAACT
* * **
2325 TTGAAGATGTTACACCGAGTCATCTGAGTTCGTCT
1 TTGAAGATGCTACACCGAGTCATCTGAATTCAACT
*
2360 TTGAAGATGCTACACCGAGTCATCTGAATTCATCT
1 TTGAAGATGCTACACCGAGTCATCTGAATTCAACT
2395 TTGAAGATGCTACACCGAGTCATCTGAA-T-AACT
1 TTGAAGATGCTACACCGAGTCATCTGAATTCAACT
* * *
2428 TTGAAGATGCTGCACCGAGTCATCTGAGTTCATCT
1 TTGAAGATGCTACACCGAGTCATCTGAATTCAACT
* *
2463 TTGAAGATGCTACACCGAGTCGTCTGGATTCAACT
1 TTGAAGATGCTACACCGAGTCATCTGAATTCAACT
**
2498 TTGAAGATGCTACACCGAGTCATCTGGGTTCAACT
1 TTGAAGATGCTACACCGAGTCATCTGAATTCAACT
*
2533 TTGAAGATGCTACACCGAGTCATCTGGATTCAACT
1 TTGAAGATGCTACACCGAGTCATCTGAATTCAACT
**
2568 TTGAAGATGCTACACCGAGTCATCTGGGTTCAACT
1 TTGAAGATGCTACACCGAGTCATCTGAATTCAACT
*
2603 TTGAAAATGCTACACCGAGTCATCTGAATAT-AACT
1 TTGAAGATGCTACACCGAGTCATCTGAAT-TCAACT
2638 TTGAAGATGCT
1 TTGAAGATGCT
2649 TTGGAAAATA
Statistics
Matches: 298, Mismatches: 23, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
33 29 0.10
34 2 0.01
35 266 0.89
36 1 0.00
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (35 bp):
TTGAAGATGCTACACCGAGTCATCTGAATTCAACT
Found at i:3068 original size:35 final size:35
Alignment explanation
Indices: 3026--3384 Score: 526
Period size: 35 Copynumber: 10.3 Consensus size: 35
3016 TGAGTCCATA
*
3026 TTGAAGATGCTACACCGAGTCATCTGAATTCATCT
1 TTGAAGATGCTACACCGAGTCATCTGAATTCAACT
* * **
3061 TTGAAGATGTTACACCGAGTCATCTGAGTTCGTCT
1 TTGAAGATGCTACACCGAGTCATCTGAATTCAACT
*
3096 TTGAAGATGCTACACCGAGTCATCTGAATTCATCT
1 TTGAAGATGCTACACCGAGTCATCTGAATTCAACT
*
3131 TTGAAGATGCTTCACCGAGTCATCTGAA-T-AACT
1 TTGAAGATGCTACACCGAGTCATCTGAATTCAACT
* * *
3164 TTGAAGATGCTGCACCGAGTCATCTGAGTTCATCT
1 TTGAAGATGCTACACCGAGTCATCTGAATTCAACT
* *
3199 TTGAAGATGCTACACCGAGTCGTCTGGATTCAACT
1 TTGAAGATGCTACACCGAGTCATCTGAATTCAACT
**
3234 TTGAAGATGCTACACCGAGTCATCTGGGTTCAACT
1 TTGAAGATGCTACACCGAGTCATCTGAATTCAACT
*
3269 TTGAAGATGCTACACCGAGTCATCTGGATTCAACT
1 TTGAAGATGCTACACCGAGTCATCTGAATTCAACT
**
3304 TTGAAGATGCTACACCGAGTCATCTGGGTTCAACT
1 TTGAAGATGCTACACCGAGTCATCTGAATTCAACT
*
3339 TTGAAAATGCTACACCGAGTCATCTGAATAT-AACT
1 TTGAAGATGCTACACCGAGTCATCTGAAT-TCAACT
3374 TTGAAGATGCT
1 TTGAAGATGCT
3385 TTGGAAAATA
Statistics
Matches: 297, Mismatches: 24, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
33 29 0.10
34 2 0.01
35 265 0.89
36 1 0.00
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (35 bp):
TTGAAGATGCTACACCGAGTCATCTGAATTCAACT
Found at i:3931 original size:50 final size:50
Alignment explanation
Indices: 3872--4018 Score: 186
Period size: 50 Copynumber: 2.9 Consensus size: 50
3862 TAAAGGCCCT
* * * * *
3872 TTGAAAAGCGAATTTTGACCTTGGACTCACAACTGGAATGCAATCTTACC
1 TTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGAAATCTTACC
* **
3922 TTGAAAAGCGAATTTTGATCTTGAACTCATAAATGGAAAGAAATCTTATT
1 TTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGAAATCTTACC
* * * *
3972 TTGAAAAGTGAATTTTGATCTTGAATTCATAAATGGAAAGGAATCTT
1 TTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGAAATCTT
4019 GTTATAAAAC
Statistics
Matches: 86, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 86 1.00
ACGTcount: A:0.37, C:0.13, G:0.18, T:0.33
Consensus pattern (50 bp):
TTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGAAATCTTACC
Found at i:4626 original size:13 final size:14
Alignment explanation
Indices: 4603--4637 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
4593 TCTCTTTTGA
4603 TTTGA-TTTGA-TT
1 TTTGATTTTGATTT
4615 TTTGATTTTGATTT
1 TTTGATTTTGATTT
4629 TTTGATTTT
1 TTTGATTTT
4638 TTTTGAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 5 0.24
13 5 0.24
14 11 0.52
ACGTcount: A:0.14, C:0.00, G:0.14, T:0.71
Consensus pattern (14 bp):
TTTGATTTTGATTT
Found at i:4641 original size:18 final size:19
Alignment explanation
Indices: 4597--4653 Score: 53
Period size: 19 Copynumber: 2.8 Consensus size: 19
4587 ATCAATTCTC
4597 TTTTGATTTGATTTGATTTTTGA
1 TTTTGATTT--TTTGA-TTTT-A
4620 TTTTGATTTTTTGATTTT-
1 TTTTGATTTTTTGATTTTA
*
4638 TTTTGAATTTCTTGAT
1 TTTTG-ATTTTTTGAT
4654 GGAGGGGACT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
18 5 0.16
19 9 0.28
20 4 0.12
21 5 0.16
23 9 0.28
ACGTcount: A:0.16, C:0.02, G:0.14, T:0.68
Consensus pattern (19 bp):
TTTTGATTTTTTGATTTTA
Found at i:8867 original size:41 final size:42
Alignment explanation
Indices: 8822--8904 Score: 123
Period size: 42 Copynumber: 2.0 Consensus size: 42
8812 AATAAGGATC
*
8822 AAATTGAAACAAATAGTAAAT-AGAATCCTAAATCAGGGACT
1 AAATTGAAACAAATAGTAAATAAGAATCCTAAAGCAGGGACT
***
8863 AAATTGTGTCAAATAGTAAATAAGAATCCTAAAGCAGGGACT
1 AAATTGAAACAAATAGTAAATAAGAATCCTAAAGCAGGGACT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
41 18 0.49
42 19 0.51
ACGTcount: A:0.48, C:0.12, G:0.17, T:0.23
Consensus pattern (42 bp):
AAATTGAAACAAATAGTAAATAAGAATCCTAAAGCAGGGACT
Done.