Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024292.1 Corchorus olitorius cultivar O-4 contig24325, 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: 10181
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.33
Found at i:1845 original size:33 final size:34
Alignment explanation
Indices: 1775--1914 Score: 121
Period size: 33 Copynumber: 4.2 Consensus size: 34
1765 ATGATCAACC
** *
1775 AAAACAG-ATTT-GTTTTCATCACAATTAGCATCC-
1 AAAACAGAATTTAG-TTTCATCACAAACAACA-CCT
1808 AAAACAGAATTT-GTTTCATCACAAACAACACCT
1 AAAACAGAATTTAGTTTCATCACAAACAACACCT
* *
1841 AAAACA-AATTTAGTGTCATCACAAACAACACTT
1 AAAACAGAATTTAGTTTCATCACAAACAACACCT
** * * * *
1874 AAATTAG-GTTTAGTATCATCACTAACAACATCT
1 AAAACAGAATTTAGTTTCATCACAAACAACACCT
1907 AAAACAGA
1 AAAACAGA
1915 TTTCATGTCA
Statistics
Matches: 88, Mismatches: 14, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
32 7 0.08
33 76 0.86
34 5 0.06
ACGTcount: A:0.44, C:0.21, G:0.08, T:0.27
Consensus pattern (34 bp):
AAAACAGAATTTAGTTTCATCACAAACAACACCT
Found at i:1895 original size:66 final size:66
Alignment explanation
Indices: 1823--1949 Score: 184
Period size: 66 Copynumber: 1.9 Consensus size: 66
1813 AGAATTTGTT
*
1823 TCATCACAAACAACACCTAAAACAAATTT-AGTGTCATCACAAACAACACTTAAATTAGGTTTAG
1 TCATCACAAACAACACCTAAAACAAATTTCA-TGTCATCACAAACAACACTTAAATCAGGTTTAG
1887 TA
65 TA
* * * **
1889 TCATCACTAACAACATCTAAAACAGATTTCATGTCATTGCAAACAACACTTAAATCAGGTT
1 TCATCACAAACAACACCTAAAACAAATTTCATGTCATCACAAACAACACTTAAATCAGGTT
1950 CAGAATTACT
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
66 53 0.98
67 1 0.02
ACGTcount: A:0.43, C:0.22, G:0.08, T:0.27
Consensus pattern (66 bp):
TCATCACAAACAACACCTAAAACAAATTTCATGTCATCACAAACAACACTTAAATCAGGTTTAGT
A
Found at i:7866 original size:19 final size:18
Alignment explanation
Indices: 7837--7878 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
7827 GGAGTAATTT
* *
7837 TTAAGTAAAAATATTATA
1 TTAAATAAAAATATAATA
7855 TATAAATAAAAATATAATA
1 T-TAAATAAAAATATAATA
7874 TTAAA
1 TTAAA
7879 ATAATTAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (18 bp):
TTAAATAAAAATATAATA
Found at i:7882 original size:19 final size:19
Alignment explanation
Indices: 7842--7878 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
7832 AATTTTTAAG
*
7842 TAAAAATATTATATATAAA
1 TAAAAATATAATATATAAA
7861 TAAAAATATAATAT-TAAA
1 TAAAAATATAATATATAAA
7879 ATAATTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
TAAAAATATAATATATAAA
Found at i:9362 original size:21 final size:21
Alignment explanation
Indices: 9337--9394 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 21
9327 TCTTTTAGTG
9337 ATTTATTAAACTTTTTAATAA
1 ATTTATTAAACTTTTTAATAA
* **
9358 CTTTATTAAGTTTTTTAATAA
1 ATTTATTAAACTTTTTAATAA
**
9379 AAATATTAAACTTTTT
1 ATTTATTAAACTTTTT
9395 TTGTGATCTT
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.40, C:0.05, G:0.02, T:0.53
Consensus pattern (21 bp):
ATTTATTAAACTTTTTAATAA
Done.