Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015689.1 Corchorus olitorius cultivar O-4 contig15722, 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: 10243
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Found at i:1755 original size:23 final size:27
Alignment explanation
Indices: 1729--1779 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
1719 TGTCCACATT
1729 ATTTTT-A-AAAT-ATAA-TATATATA
1 ATTTTTAAGAAATCATAACTATATATA
1752 ATTTTTAAGAAATCATAACTATATATA
1 ATTTTTAAGAAATCATAACTATATATA
1779 A
1 A
1780 AAATTTATCA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
23 6 0.25
24 1 0.04
25 4 0.17
26 4 0.17
27 9 0.38
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (27 bp):
ATTTTTAAGAAATCATAACTATATATA
Found at i:1997 original size:21 final size:21
Alignment explanation
Indices: 1928--2113 Score: 128
Period size: 22 Copynumber: 8.6 Consensus size: 21
1918 TGAATATTTT
1928 TATGAAATTTTGATAACTACCC
1 TATGAAATTTTGATAACTA-CC
* *
1950 TATTAAATTTTGATAACCACGC
1 TATGAAATTTTGATAACTAC-C
*
1972 TATGAAATTTTGATAATTACC
1 TATGAAATTTTGATAACTACC
* *
1993 TATGAAATTGTGATAAAC-CCC
1 TATGAAATTTTGAT-AACTACC
* **
2014 ATATGAAACTTTGATAACCTAAA
1 -TATGAAATTTTGATAA-CTACC
*
2037 TATGAAATTTT-ATTAAACCTTCC
1 TATGAAATTTTGA-T-AA-CTACC
* *
2060 TATGAAATTTTG-TAACCTTCT
1 TATGAAATTTTGATAA-CTACC
* *
2081 TATG-ATTTTTGATAACCTCCC
1 TATGAAATTTTGATAA-CTACC
*
2102 TATGAGATTTTG
1 TATGAAATTTTG
2114 TTAATCTCCC
Statistics
Matches: 131, Mismatches: 23, Indels: 20
0.75 0.13 0.11
Matches are distributed among these distances:
20 6 0.05
21 42 0.32
22 67 0.51
23 16 0.12
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.39
Consensus pattern (21 bp):
TATGAAATTTTGATAACTACC
Found at i:2008 original size:43 final size:44
Alignment explanation
Indices: 1928--2031 Score: 133
Period size: 43 Copynumber: 2.4 Consensus size: 44
1918 TGAATATTTT
* *
1928 TATGAAATTTTGATAACTACCCTATTAAATTTTGAT-AACCACGC-
1 TATGAAATTTTGATAACTACCCTATGAAATTGTGATAAACC-C-CA
*
1972 TATGAAATTTTGATAATTA-CCTATGAAATTGTGATAAACCCCA
1 TATGAAATTTTGATAACTACCCTATGAAATTGTGATAAACCCCA
*
2015 TATGAAACTTTGATAAC
1 TATGAAATTTTGATAAC
2032 CTAAATATGA
Statistics
Matches: 53, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
42 1 0.02
43 30 0.57
44 22 0.42
ACGTcount: A:0.38, C:0.15, G:0.11, T:0.36
Consensus pattern (44 bp):
TATGAAATTTTGATAACTACCCTATGAAATTGTGATAAACCCCA
Found at i:2122 original size:22 final size:22
Alignment explanation
Indices: 1928--2138 Score: 110
Period size: 22 Copynumber: 9.7 Consensus size: 22
1918 TGAATATTTT
*
1928 TATGAAATTTTGATAA-CTACCC
1 TATGAGATTTTGATAACCT-CCC
* * * *
1950 TATTAAATTTTGATAACCACGC
1 TATGAGATTTTGATAACCTCCC
* * *
1972 TATGAAATTTTGATAA-TTACC
1 TATGAGATTTTGATAACCTCCC
* * *
1993 TATGAAATTGTGATAAACC-CCA
1 TATGAGATTTTGAT-AACCTCCC
* * ***
2015 TATGAAACTTTGATAACCTAAA
1 TATGAGATTTTGATAACCTCCC
* *
2037 TATGAAATTTT-ATTAAACCTTCC
1 TATGAGATTTTGA-T-AACCTCCC
* * *
2060 TATGAAATTTTG-TAACCTTCT
1 TATGAGATTTTGATAACCTCCC
*
2081 TATGA-TTTTTGATAACCTCCC
1 TATGAGATTTTGATAACCTCCC
* *
2102 TATGAGATTTTGTTAATCTCCC
1 TATGAGATTTTGATAACCTCCC
* *
2124 TATTAGTTTTTGATA
1 TATGAGATTTTGATA
2139 TTATAGTATG
Statistics
Matches: 150, Mismatches: 30, Indels: 18
0.76 0.15 0.09
Matches are distributed among these distances:
20 5 0.03
21 43 0.29
22 85 0.57
23 17 0.11
ACGTcount: A:0.34, C:0.16, G:0.10, T:0.41
Consensus pattern (22 bp):
TATGAGATTTTGATAACCTCCC
Found at i:6876 original size:12 final size:13
Alignment explanation
Indices: 6859--6892 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
6849 ATAATTTATT
*
6859 TAAAACCATTT-A
1 TAAAACAATTTAA
6871 TAAAACAATTTAA
1 TAAAACAATTTAA
6884 TAAAACAAT
1 TAAAACAAT
6893 AATAAAATAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 10 0.50
13 10 0.50
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (13 bp):
TAAAACAATTTAA
Found at i:7459 original size:28 final size:28
Alignment explanation
Indices: 7423--7496 Score: 148
Period size: 28 Copynumber: 2.6 Consensus size: 28
7413 TAACCTTCTA
7423 AGGGTAAAACGGTAATTTAGTCACTCTT
1 AGGGTAAAACGGTAATTTAGTCACTCTT
7451 AGGGTAAAACGGTAATTTAGTCACTCTT
1 AGGGTAAAACGGTAATTTAGTCACTCTT
7479 AGGGTAAAACGGTAATTT
1 AGGGTAAAACGGTAATTT
7497 TATGCCCATA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 46 1.00
ACGTcount: A:0.34, C:0.12, G:0.23, T:0.31
Consensus pattern (28 bp):
AGGGTAAAACGGTAATTTAGTCACTCTT
Done.