Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024463.1 Corchorus olitorius cultivar O-4 contig24496, 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: 13984
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Found at i:1570 original size:12 final size:13
Alignment explanation
Indices: 1552--1581 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
1542 GTTTTCTTTA
1552 ATTTTCTTGATTG
1 ATTTTCTTGATTG
1565 -TTTTCTTGATTG
1 ATTTTCTTGATTG
1577 ATTTT
1 ATTTT
1582 AATTGCTAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.13, C:0.07, G:0.13, T:0.67
Consensus pattern (13 bp):
ATTTTCTTGATTG
Found at i:5035 original size:335 final size:335
Alignment explanation
Indices: 4425--5095 Score: 1315
Period size: 335 Copynumber: 2.0 Consensus size: 335
4415 GACTTAATCA
4425 TCATCAAAAAACAAAGTTCTTTTCGGAAGTTAAACATTACATATGGGATGATCCACTTTTATTCC
1 TCATCAAAAAACAAAGTTCTTTTCGGAAGTTAAACATTACATATGGGATGATCCACTTTTATTCC
4490 ATAAATGTACTGATGGTGTCATTCGAAGATGTGTTCCTGAGGAAGAGATGGTTTCTATCCTCACT
66 ATAAATGTACTGATGGTGTCATTCGAAGATGTGTTCCTGAGGAAGAGATGGTTTCTATCCTCACT
4555 CATTGTCATTCACTTCCTTGTGGAGGACATCATGGTGCTTCTAAAACAGCAGCTAAGGTACTTCA
131 CATTGTCATTCACTTCCTTGTGGAGGACATCATGGTGCTTCTAAAACAGCAGCTAAGGTACTTCA
4620 ATGTGGTTTCTTTTGGCCTACACTCTTTAAGGATGCAATAAGTTTTGTAATGTCATGTGACCGAT
196 ATGTGGTTTCTTTTGGCCTACACTCTTTAAGGATGCAATAAGTTTTGTAATGTCATGTGACCGAT
*
4685 GTCAAAGAACTGGTACTATAAGCAGAAGGCATGAGATGCCTCCATCAGGTATTCTAGAAGTTGAA
261 GTCAAAGAACTGGTACTATAAGCAGAAGGCATGAGATGCCTCAATCAGGTATTCTAGAAGTTGAA
4750 ATCTTTGATG
326 ATCTTTGATG
4760 TCATCAAAAAACAAAGTTCTTTTCGGAAGTTAAACATTACATATGGGATGATCCACTTTTATTCC
1 TCATCAAAAAACAAAGTTCTTTTCGGAAGTTAAACATTACATATGGGATGATCCACTTTTATTCC
*
4825 ATAGATGTACTGATGGTGTCATTCGAAGATGTGTTCCTGAGGAAGAGATGGTTTCTATCCTCACT
66 ATAAATGTACTGATGGTGTCATTCGAAGATGTGTTCCTGAGGAAGAGATGGTTTCTATCCTCACT
*
4890 CATTGTCATTCACTTCCTTGTGGAGGACATCATGGTGCTTCTAAAACAGCGGCTAAGGTACTTCA
131 CATTGTCATTCACTTCCTTGTGGAGGACATCATGGTGCTTCTAAAACAGCAGCTAAGGTACTTCA
4955 ATGTGGTTTCTTTTGGCCTACACTCTTTAAGGATGCAATAAGTTTTGTAATGTCATGTGACCGAT
196 ATGTGGTTTCTTTTGGCCTACACTCTTTAAGGATGCAATAAGTTTTGTAATGTCATGTGACCGAT
5020 GTCAAAGAACTGGTACTATAAGCAGAAGGCATGAGATGCCTCAATCAGGTATTCTAGAAGTTGAA
261 GTCAAAGAACTGGTACTATAAGCAGAAGGCATGAGATGCCTCAATCAGGTATTCTAGAAGTTGAA
5085 ATCTTTGATG
326 ATCTTTGATG
5095 T
1 T
5096 TTGGGGACTT
Statistics
Matches: 333, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
335 333 1.00
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (335 bp):
TCATCAAAAAACAAAGTTCTTTTCGGAAGTTAAACATTACATATGGGATGATCCACTTTTATTCC
ATAAATGTACTGATGGTGTCATTCGAAGATGTGTTCCTGAGGAAGAGATGGTTTCTATCCTCACT
CATTGTCATTCACTTCCTTGTGGAGGACATCATGGTGCTTCTAAAACAGCAGCTAAGGTACTTCA
ATGTGGTTTCTTTTGGCCTACACTCTTTAAGGATGCAATAAGTTTTGTAATGTCATGTGACCGAT
GTCAAAGAACTGGTACTATAAGCAGAAGGCATGAGATGCCTCAATCAGGTATTCTAGAAGTTGAA
ATCTTTGATG
Found at i:11766 original size:21 final size:21
Alignment explanation
Indices: 11723--11777 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
11713 GGCACTGAAT
* **
11723 GGTGATGGCACGGGCATGGCC
1 GGTGGTGGCACGGGCATAACC
*
11744 GGTGGTGGCACGGGCTTAACC
1 GGTGGTGGCACGGGCATAACC
*
11765 GGTGGTGTCACGG
1 GGTGGTGGCACGG
11778 TGAATGCCCG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.13, C:0.22, G:0.47, T:0.18
Consensus pattern (21 bp):
GGTGGTGGCACGGGCATAACC
Done.