Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023118.1 Corchorus olitorius cultivar O-4 contig23151, 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: 20802
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.32
Found at i:3199 original size:49 final size:49
Alignment explanation
Indices: 3133--3227 Score: 154
Period size: 49 Copynumber: 1.9 Consensus size: 49
3123 TTAGCGGAAA
* *
3133 ATGATTTAAGTTAAATCCTTTAAATGGTAGGATCAATATGGCTAATGAT
1 ATGATTTAAGTGAAATCCTTTAAACGGTAGGATCAATATGGCTAATGAT
* *
3182 ATGATTTAAGTGAAATCCTTTTAACGGTGGGATCAATATGGCTAAT
1 ATGATTTAAGTGAAATCCTTTAAACGGTAGGATCAATATGGCTAAT
3228 TGTTTCTTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
49 42 1.00
ACGTcount: A:0.35, C:0.09, G:0.20, T:0.36
Consensus pattern (49 bp):
ATGATTTAAGTGAAATCCTTTAAACGGTAGGATCAATATGGCTAATGAT
Found at i:5225 original size:43 final size:42
Alignment explanation
Indices: 5178--5507 Score: 409
Period size: 43 Copynumber: 7.8 Consensus size: 42
5168 ATAACGAGAA
* *
5178 ATGCCTCTGTGTTATATATGTGTTTGAGGATTTTGTAATAGAG
1 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTG-AATAAAG
* * *
5221 ATGCCCCTGTGTTATATATGTGTTTGGGGACTTTG-ATATAG
1 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGAATAAAG
*
5262 ATGCCTCTGTGTTATATATGTATTTGAGGACTTTGTAATAAAG
1 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTG-AATAAAG
* * *
5305 GTGCC-CATGTGTTATATATGTGTTTGGGGAC-TTGAATATAG
1 ATGCCTC-TGTGTTATATATGTGTTTGAGGACTTTGAATAAAG
*
5346 ATGTCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAAAG
1 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTG-AATAAAG
* * * *
5389 GTGCCCCTGTGTTATATATGTGTCTGGGGACTTTG-ATATAA-
1 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGAATA-AAG
*
5430 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTTGGAATAGAG
1 ATGCCTCTGTGTTATATATGTGTTTGAGGAC-TTT-GAATAAAG
* *
5474 ATGCCCCTGTGTTATATATGTGTTTGGGGACTTT
1 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTT
5508 TGGTTATTGG
Statistics
Matches: 248, Mismatches: 28, Indels: 22
0.83 0.09 0.07
Matches are distributed among these distances:
41 99 0.40
42 13 0.05
43 104 0.42
44 32 0.13
ACGTcount: A:0.22, C:0.10, G:0.26, T:0.42
Consensus pattern (42 bp):
ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGAATAAAG
Found at i:5290 original size:84 final size:84
Alignment explanation
Indices: 5178--5507 Score: 536
Period size: 84 Copynumber: 3.9 Consensus size: 84
5168 ATAACGAGAA
* *
5178 ATGCCTCTGTGTTATATATGTGTTTGAGGATTTTGTAATAGAGATGCCCCTGTGTTATATATGTG
1 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAAAGATGCCCCTGTGTTATATATGTG
5243 TTTGGGGACTTTGATATAG
66 TTTGGGGACTTTGATATAG
* * *
5262 ATGCCTCTGTGTTATATATGTATTTGAGGACTTTGTAATAAAGGTGCCCATGTGTTATATATGTG
1 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAAAGATGCCCCTGTGTTATATATGTG
5327 TTTGGGGAC-TTGAATATAG
66 TTTGGGGACTTTG-ATATAG
* *
5346 ATGTCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAAAGGTGCCCCTGTGTTATATATGTG
1 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAAAGATGCCCCTGTGTTATATATGTG
* *
5411 TCTGGGGACTTTGATATAA
66 TTTGGGGACTTTGATATAG
* *
5430 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTTGGAATAGAGATGCCCCTGTGTTATATATGT
1 ATGCCTCTGTGTTATATATGTGTTTGAGGAC-TTTGTAATAAAGATGCCCCTGTGTTATATATGT
5495 GTTTGGGGACTTT
65 GTTTGGGGACTTT
5508 TGGTTATTGG
Statistics
Matches: 228, Mismatches: 15, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
83 3 0.01
84 180 0.79
85 45 0.20
ACGTcount: A:0.22, C:0.10, G:0.26, T:0.42
Consensus pattern (84 bp):
ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAAAGATGCCCCTGTGTTATATATGTG
TTTGGGGACTTTGATATAG
Found at i:9180 original size:95 final size:95
Alignment explanation
Indices: 9017--9206 Score: 380
Period size: 95 Copynumber: 2.0 Consensus size: 95
9007 CTCCCTTAGA
9017 CTCCATTCATAAGCGAGATGGGTGTCCAAGGCTTCAGAAATTTCGACTCGCCCGTTTCTCCTTTT
1 CTCCATTCATAAGCGAGATGGGTGTCCAAGGCTTCAGAAATTTCGACTCGCCCGTTTCTCCTTTT
9082 CGCCAATTTGCAGATAGAAAGATGAAAGGG
66 CGCCAATTTGCAGATAGAAAGATGAAAGGG
9112 CTCCATTCATAAGCGAGATGGGTGTCCAAGGCTTCAGAAATTTCGACTCGCCCGTTTCTCCTTTT
1 CTCCATTCATAAGCGAGATGGGTGTCCAAGGCTTCAGAAATTTCGACTCGCCCGTTTCTCCTTTT
9177 CGCCAATTTGCAGATAGAAAGATGAAAGGG
66 CGCCAATTTGCAGATAGAAAGATGAAAGGG
9207 AAAGTGGTAG
Statistics
Matches: 95, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
95 95 1.00
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.27
Consensus pattern (95 bp):
CTCCATTCATAAGCGAGATGGGTGTCCAAGGCTTCAGAAATTTCGACTCGCCCGTTTCTCCTTTT
CGCCAATTTGCAGATAGAAAGATGAAAGGG
Found at i:11506 original size:19 final size:18
Alignment explanation
Indices: 11473--11508 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
11463 TGGAAATAAT
11473 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
11491 TCTTCAAATTGTCTTCAA
1 TCTTC-AATGGTCTTCAA
11509 TAAGTCTTCA
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:13400 original size:27 final size:27
Alignment explanation
Indices: 13362--13418 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
13352 AAGCCTTTGG
13362 TTCAATAGGGGGTGATAATCGATCTTC
1 TTCAATAGGGGGTGATAATCGATCTTC
13389 TTCAATAGGGGGTGATAATCGATCTTC
1 TTCAATAGGGGGTGATAATCGATCTTC
13416 TTC
1 TTC
13419 CTCTTCAAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.35
Consensus pattern (27 bp):
TTCAATAGGGGGTGATAATCGATCTTC
Found at i:14131 original size:22 final size:22
Alignment explanation
Indices: 14106--14149 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
14096 TAAGTCGATT
*
14106 ATTTGGCTCCTTTAAA-CGACAA
1 ATTT-GCTCCTTGAAATCGACAA
*
14128 ATTTTCTCCTTGAAATCGACAA
1 ATTTGCTCCTTGAAATCGACAA
14150 GTCCTTTGTC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.32, C:0.23, G:0.11, T:0.34
Consensus pattern (22 bp):
ATTTGCTCCTTGAAATCGACAA
Done.