Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015058.1 Corchorus olitorius cultivar O-4 contig15091, 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: 13356
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:1722 original size:83 final size:83
Alignment explanation
Indices: 1632--1800 Score: 311
Period size: 83 Copynumber: 2.0 Consensus size: 83
1622 AATTATAATC
*
1632 TTCTTGCATTAGAGATCGATAACCTTCTTAATTGATTAATGTTTAACTTCGTTCTTAATAGCCCT
1 TTCTTGCATCAGAGATCGATAACCTTCTTAATTGATTAATGTTTAACTTCGTTCTTAATAGCCCT
*
1697 GTAGATTTTTTTAGTAAA
66 GTAGATTTTTTTAATAAA
1715 TTCTTGCATCAGAGATCGATAACCTTCTTAATTGATTAATGTTTAACTTCGTTCTTAATAGCCCT
1 TTCTTGCATCAGAGATCGATAACCTTCTTAATTGATTAATGTTTAACTTCGTTCTTAATAGCCCT
*
1780 GTAGTTTTTTTTAATAAA
66 GTAGATTTTTTTAATAAA
1798 TTC
1 TTC
1801 AAATAAGAAA
Statistics
Matches: 83, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
83 83 1.00
ACGTcount: A:0.27, C:0.15, G:0.12, T:0.45
Consensus pattern (83 bp):
TTCTTGCATCAGAGATCGATAACCTTCTTAATTGATTAATGTTTAACTTCGTTCTTAATAGCCCT
GTAGATTTTTTTAATAAA
Found at i:7490 original size:49 final size:49
Alignment explanation
Indices: 7433--7551 Score: 238
Period size: 49 Copynumber: 2.4 Consensus size: 49
7423 TTGGTGATAC
7433 TTTAAGCCTTAATCGGGTAATTGATTTGTTAAGTTAACAATAGGGGTAA
1 TTTAAGCCTTAATCGGGTAATTGATTTGTTAAGTTAACAATAGGGGTAA
7482 TTTAAGCCTTAATCGGGTAATTGATTTGTTAAGTTAACAATAGGGGTAA
1 TTTAAGCCTTAATCGGGTAATTGATTTGTTAAGTTAACAATAGGGGTAA
7531 TTTAAGCCTTAATCGGGTAAT
1 TTTAAGCCTTAATCGGGTAAT
7552 CTTATCTAAA
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 70 1.00
ACGTcount: A:0.32, C:0.09, G:0.22, T:0.37
Consensus pattern (49 bp):
TTTAAGCCTTAATCGGGTAATTGATTTGTTAAGTTAACAATAGGGGTAA
Found at i:7779 original size:15 final size:15
Alignment explanation
Indices: 7750--7779 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
7740 TTTGTTCCTA
*
7750 GTTTAATTGTTTTCT
1 GTTTAATTGCTTTCT
7765 GTTTAATTGCTTTCT
1 GTTTAATTGCTTTCT
7780 TTCAACCTCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.10, G:0.13, T:0.63
Consensus pattern (15 bp):
GTTTAATTGCTTTCT
Found at i:8279 original size:23 final size:23
Alignment explanation
Indices: 8243--8298 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
8233 TGCGTTTTTG
* * *
8243 AAAAAAAAAAGTTTTTGCGTCAT
1 AAAAAAAATAGTTTCTGCATCAT
* **
8266 AAAAAAAATTGTTTCTGCATTTT
1 AAAAAAAATAGTTTCTGCATCAT
8289 AAAAAAAATA
1 AAAAAAAATA
8299 TTTTTCTTTA
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.52, C:0.07, G:0.09, T:0.32
Consensus pattern (23 bp):
AAAAAAAATAGTTTCTGCATCAT
Found at i:8381 original size:14 final size:14
Alignment explanation
Indices: 8358--8389 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
8348 CTACTAACAA
8358 TTTTTCTTTTGAGT
1 TTTTTCTTTTGAGT
*
8372 TTTTTTTTTTGAGT
1 TTTTTCTTTTGAGT
8386 TTTT
1 TTTT
8390 CTAGGAAGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.06, C:0.03, G:0.12, T:0.78
Consensus pattern (14 bp):
TTTTTCTTTTGAGT
Found at i:11458 original size:32 final size:33
Alignment explanation
Indices: 11421--11486 Score: 80
Period size: 32 Copynumber: 2.0 Consensus size: 33
11411 TCTCAAGCTT
* *
11421 CTACCAGGCCCCAACCGGCCATTC-CCGCGCCA
1 CTACCAAGCCACAACCGGCCATTCACCGCGCCA
** *
11453 CTACCAAGCCATTACCGGCCATTCACCGTGCCA
1 CTACCAAGCCACAACCGGCCATTCACCGCGCCA
11486 C
1 C
11487 CACCGGTTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
32 20 0.71
33 8 0.29
ACGTcount: A:0.21, C:0.48, G:0.17, T:0.14
Consensus pattern (33 bp):
CTACCAAGCCACAACCGGCCATTCACCGCGCCA
Found at i:11504 original size:21 final size:21
Alignment explanation
Indices: 11478--11532 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
11468 CGGCCATTCA
**
11478 CCGTGCCACCACCGGTTAAGC
1 CCGTGCCACCACCGGCCAAGC
*
11499 CCGTGCCACCACCGGCCATGC
1 CCGTGCCACCACCGGCCAAGC
*
11520 CCGTGCCATCACC
1 CCGTGCCACCACC
11533 ATTCCAAGCC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.16, C:0.49, G:0.22, T:0.13
Consensus pattern (21 bp):
CCGTGCCACCACCGGCCAAGC
Done.