Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012924.1 Corchorus olitorius cultivar O-4 contig12957, 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: 45381
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.30
Found at i:4025 original size:289 final size:289
Alignment explanation
Indices: 3506--4079 Score: 1148
Period size: 289 Copynumber: 2.0 Consensus size: 289
3496 CTAAAACATC
3506 TTCAACTAAACCCTCAGGTTTAATGTTAGTTCTATCAGCAAATTGTATAGTCAGATCAGTTTCAG
1 TTCAACTAAACCCTCAGGTTTAATGTTAGTTCTATCAGCAAATTGTATAGTCAGATCAGTTTCAG
3571 TCACAGGTTCAATTTTCAATTGTGAATAGACAGAATAAGGCATGATGTTAATTGGAGAACCAAAT
66 TCACAGGTTCAATTTTCAATTGTGAATAGACAGAATAAGGCATGATGTTAATTGGAGAACCAAAT
3636 TCACACATGGCCTTTTCTATCTGATTCTTTCCTATTTTACAAGGAATAGAAAAAGATCCTATATC
131 TCACACATGGCCTTTTCTATCTGATTCTTTCCTATTTTACAAGGAATAGAAAAAGATCCTATATC
3701 ATGACTTTTATGATGCAGTTTTCTCTGGTATGCAGCAGATACATTCTCATTCATGCAAGCATATT
196 ATGACTTTTATGATGCAGTTTTCTCTGGTATGCAGCAGATACATTCTCATTCATGCAAGCATATT
3766 TTTCAGAAAACTTACTCTTAGTCATATTT
261 TTTCAGAAAACTTACTCTTAGTCATATTT
3795 TTCAACTAAACCCTCAGGTTTAATGTTAGTTCTATCAGCAAATTGTATAGTCAGATCAGTTTCAG
1 TTCAACTAAACCCTCAGGTTTAATGTTAGTTCTATCAGCAAATTGTATAGTCAGATCAGTTTCAG
3860 TCACAGGTTCAATTTTCAATTGTGAATAGACAGAATAAGGCATGATGTTAATTGGAGAACCAAAT
66 TCACAGGTTCAATTTTCAATTGTGAATAGACAGAATAAGGCATGATGTTAATTGGAGAACCAAAT
3925 TCACACATGGCCTTTTCTATCTGATTCTTTCCTATTTTACAAGGAATAGAAAAAGATCCTATATC
131 TCACACATGGCCTTTTCTATCTGATTCTTTCCTATTTTACAAGGAATAGAAAAAGATCCTATATC
3990 ATGACTTTTATGATGCAGTTTTCTCTGGTATGCAGCAGATACATTCTCATTCATGCAAGCATATT
196 ATGACTTTTATGATGCAGTTTTCTCTGGTATGCAGCAGATACATTCTCATTCATGCAAGCATATT
4055 TTTCAGAAAACTTACTCTTAGTCAT
261 TTTCAGAAAACTTACTCTTAGTCAT
4080 GCATAATTCT
Statistics
Matches: 285, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
289 285 1.00
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.36
Consensus pattern (289 bp):
TTCAACTAAACCCTCAGGTTTAATGTTAGTTCTATCAGCAAATTGTATAGTCAGATCAGTTTCAG
TCACAGGTTCAATTTTCAATTGTGAATAGACAGAATAAGGCATGATGTTAATTGGAGAACCAAAT
TCACACATGGCCTTTTCTATCTGATTCTTTCCTATTTTACAAGGAATAGAAAAAGATCCTATATC
ATGACTTTTATGATGCAGTTTTCTCTGGTATGCAGCAGATACATTCTCATTCATGCAAGCATATT
TTTCAGAAAACTTACTCTTAGTCATATTT
Found at i:6890 original size:19 final size:18
Alignment explanation
Indices: 6857--6892 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
6847 TGGAAATAAT
6857 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
6875 TCTTCAAATTGTCTTCAA
1 TCTTC-AATGGTCTTCAA
6893 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:15814 original size:15 final size:17
Alignment explanation
Indices: 15784--15815 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
15774 AAATCATCTA
15784 TTCTCTATTGTGTCTTT
1 TTCTCTATTGTGTCTTT
15801 TTCT-TATT-TGTCTTT
1 TTCTCTATTGTGTCTTT
15816 CCAATCAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 4 0.27
17 4 0.27
ACGTcount: A:0.06, C:0.16, G:0.09, T:0.69
Consensus pattern (17 bp):
TTCTCTATTGTGTCTTT
Found at i:16086 original size:19 final size:19
Alignment explanation
Indices: 16064--16114 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
16054 GCGCTGAAAT
16064 TAATTAATTATTAATTAAA
1 TAATTAATTATTAATTAAA
* *
16083 TAA-TAATTATTTTATTGAA
1 TAATTAATTA-TTAATTAAA
16102 TAATT-ATTATTAA
1 TAATTAATTATTAA
16115 AAATCCCACA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
18 9 0.33
19 17 0.63
20 1 0.04
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (19 bp):
TAATTAATTATTAATTAAA
Found at i:28272 original size:13 final size:13
Alignment explanation
Indices: 28254--28279 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
28244 CTTGGCATGA
28254 GTGATGATTTTTG
1 GTGATGATTTTTG
28267 GTGATGATTTTTG
1 GTGATGATTTTTG
28280 TTGTTACCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.31, T:0.54
Consensus pattern (13 bp):
GTGATGATTTTTG
Found at i:28348 original size:46 final size:46
Alignment explanation
Indices: 28292--28383 Score: 148
Period size: 46 Copynumber: 2.0 Consensus size: 46
28282 GTTACCTTGA
* *
28292 TCTTTCGAAGCCATTGAAGCTTGAAAAGTTGTTGGAAAATTCGGCT
1 TCTTTCGAAGCCATTGAAGCTTGAAAAGTTGCTGGAAAATTAGGCT
* *
28338 TCTTTGGAAGCCATTGAAGCTTGAGAAGTTGCTGGAAAATTAGGCT
1 TCTTTCGAAGCCATTGAAGCTTGAAAAGTTGCTGGAAAATTAGGCT
28384 AAGTATGGTA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 42 1.00
ACGTcount: A:0.28, C:0.14, G:0.26, T:0.32
Consensus pattern (46 bp):
TCTTTCGAAGCCATTGAAGCTTGAAAAGTTGCTGGAAAATTAGGCT
Found at i:30181 original size:51 final size:50
Alignment explanation
Indices: 30080--30185 Score: 126
Period size: 51 Copynumber: 2.1 Consensus size: 50
30070 GTTCTTCATA
* **
30080 TTTTCCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTCTTTTAGTGT
1 TTTTCCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTCGTACAGTGT
* *
30130 TTTTCTCTTGTTTCA-ATCTTGTCTCCGGACATACAAACACT-GTACACGTGT
1 TTTTC-CTTGTTT-AGATCTTGTCTCAGGACAAACAAACACTCGTACA-GTGT
30181 TTTTC
1 TTTTC
30186 ATTCAGAAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
50 7 0.15
51 40 0.83
52 1 0.02
ACGTcount: A:0.22, C:0.23, G:0.13, T:0.42
Consensus pattern (50 bp):
TTTTCCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTCGTACAGTGT
Found at i:42986 original size:21 final size:21
Alignment explanation
Indices: 42947--42995 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
42937 TCAATGCTTT
**
42947 AGGAATGCAAGAGGGATTTCAA
1 AGGAA-GCAAGAGCCATTTCAA
*
42969 AGGAAGCAAGAGCCATTTCCA
1 AGGAAGCAAGAGCCATTTCAA
42990 A-GAAGC
1 AGGAAGC
42996 TACAATTCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 5 0.21
21 14 0.58
22 5 0.21
ACGTcount: A:0.41, C:0.16, G:0.29, T:0.14
Consensus pattern (21 bp):
AGGAAGCAAGAGCCATTTCAA
Done.