Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010269.1 Corchorus capsularis cultivar CVL-1 contig10290, 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: 1860
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Found at i:727 original size:13 final size:12
Alignment explanation
Indices: 709--757 Score: 53
Period size: 13 Copynumber: 3.8 Consensus size: 12
699 TTCGGTTTGA
709 ATATATTATACAT
1 ATATATTATA-AT
*
722 ATATATATATATT
1 ATATAT-TATAAT
*
735 ACATATTAATAAT
1 ATATATT-ATAAT
748 ATATATTATA
1 ATATATTATA
758 TATTAAAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
12 4 0.13
13 22 0.73
14 4 0.13
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (12 bp):
ATATATTATAAT
Found at i:742 original size:7 final size:7
Alignment explanation
Indices: 709--762 Score: 60
Period size: 7 Copynumber: 8.1 Consensus size: 7
699 TTCGGTTTGA
709 ATATATT
1 ATATATT
*
716 ATACA-T
1 ATATATT
722 ATATA-T
1 ATATATT
728 ATATATT
1 ATATATT
*
735 ACATATT
1 ATATATT
*
742 A-ATAAT
1 ATATATT
748 ATATATT
1 ATATATT
755 ATATATT
1 ATATATT
762 A
1 A
763 AAATAAAATT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
6 16 0.40
7 24 0.60
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (7 bp):
ATATATT
Found at i:768 original size:22 final size:20
Alignment explanation
Indices: 726--767 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
716 ATACATATAT
726 ATATATATTACATATTAATA
1 ATATATATTACATATTAATA
*
746 ATATATATTATATATTAA-A
1 ATATATATTACATATTAATA
765 ATA
1 ATA
768 AAATTCTTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (20 bp):
ATATATATTACATATTAATA
Found at i:805 original size:20 final size:20
Alignment explanation
Indices: 780--818 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
770 ATTCTTACAT
780 ATATATATATTCTTATTTAC
1 ATATATATATTCTTATTTAC
800 ATATATATATTCTTATTTA
1 ATATATATATTCTTATTTA
819 ATAAAATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (20 bp):
ATATATATATTCTTATTTAC
Found at i:827 original size:20 final size:20
Alignment explanation
Indices: 774--828 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
764 AATAAAATTC
774 TTACATATATATATATTCTTAT
1 TTACATA-A-ATATATTCTTAT
*
796 TTACATATATATATTCTTAT
1 TTACATAAATATATTCTTAT
816 TTA-ATAAA-ATATT
1 TTACATAAATATATT
829 TTACATATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
18 5 0.16
19 4 0.13
20 15 0.48
22 7 0.23
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (20 bp):
TTACATAAATATATTCTTAT
Found at i:1038 original size:18 final size:18
Alignment explanation
Indices: 1015--1049 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1005 CCAACTTCAC
*
1015 AAACCGAATCACCCGACA
1 AAACCGAATCAACCGACA
*
1033 AAACCGACTCAACCGAC
1 AAACCGAATCAACCGAC
1050 CCATTTCACC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.40, G:0.11, T:0.06
Consensus pattern (18 bp):
AAACCGAATCAACCGACA
Found at i:1757 original size:66 final size:69
Alignment explanation
Indices: 1629--1764 Score: 170
Period size: 72 Copynumber: 2.0 Consensus size: 69
1619 CTAGTCGCGT
* * *
1629 GCGGCTCGCGATCGAACAATGGCTCTGTCGCGAGCAACCACGGCTCGTGACCAAGTCGTGGCTTG
1 GCGGCTCGCGATCGAACAATGGCTCCGTCGCGAG--ACCACGGC-CGTGACCAAGCCATGGCTTG
1694 GTCGCTC
63 GTCGCTC
* * *
1701 GCGGCTCGCGATCGAACCATGGCTCCGTCGTGAG-CCAC-G-CGTGACCGAGCCATGGCTTGGTC
1 GCGGCTCGCGATCGAACAATGGCTCCGTCGCGAGACCACGGCCGTGACCAAGCCATGGCTTGGTC
1763 GC
66 GC
1765 AACGCGGTCG
Statistics
Matches: 58, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
66 22 0.38
68 1 0.02
69 4 0.07
72 31 0.53
ACGTcount: A:0.15, C:0.33, G:0.33, T:0.18
Consensus pattern (69 bp):
GCGGCTCGCGATCGAACAATGGCTCCGTCGCGAGACCACGGCCGTGACCAAGCCATGGCTTGGTC
GCTC
Found at i:1854 original size:23 final size:20
Alignment explanation
Indices: 1802--1840 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1792 CTTTTTTTAA
*
1802 TTAATAATTAGTTATTATTT
1 TTAAAAATTAGTTATTATTT
1822 TTAAAAATTAGTTATTATT
1 TTAAAAATTAGTTATTATT
1841 ATTTTATATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (20 bp):
TTAAAAATTAGTTATTATTT
Done.