Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014703.1 Corchorus capsularis cultivar CVL-1 contig14724, 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: 29938
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:6957 original size:12 final size:13
Alignment explanation
Indices: 6913--6957 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
6903 AATTATTGTT
6913 TGCTTTATTAATC
1 TGCTTTATTAATC
*
6926 TGCTTTATTAATT
1 TGCTTTATTAATC
6939 TGCTTTA-TAATC
1 TGCTTTATTAATC
*
6951 TGATTTA
1 TGCTTTA
6958 GATTTAGATT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
12 10 0.34
13 19 0.66
ACGTcount: A:0.24, C:0.11, G:0.09, T:0.56
Consensus pattern (13 bp):
TGCTTTATTAATC
Found at i:6963 original size:6 final size:6
Alignment explanation
Indices: 6952--6986 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
6942 TTTATAATCT
6952 GATTTA GATTTA GATTTA GATTTA GATTTA GATTT
1 GATTTA GATTTA GATTTA GATTTA GATTTA GATTT
6987 GCTTTGCTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.17, T:0.51
Consensus pattern (6 bp):
GATTTA
Found at i:18773 original size:16 final size:16
Alignment explanation
Indices: 18752--18784 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
18742 GCAAAGAGGT
18752 TTCAAAAATCCAAGAA
1 TTCAAAAATCCAAGAA
*
18768 TTCAAAAATTCAAGAA
1 TTCAAAAATCCAAGAA
18784 T
1 T
18785 CAGGAATCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.55, C:0.15, G:0.06, T:0.24
Consensus pattern (16 bp):
TTCAAAAATCCAAGAA
Found at i:18841 original size:38 final size:39
Alignment explanation
Indices: 18799--18903 Score: 135
Period size: 38 Copynumber: 2.7 Consensus size: 39
18789 AATCAAATTC
18799 TCAAAGTTTTCAATTTAGGGAAAGATCC-AACCAAG-TTT
1 TCAAAGTTTTCAATTTAGGGAAAGATCCTAACC-AGTTTT
*
18837 TCAAAGTTTT-AGATTTAGGGAAAGATCCTATCCAGTTTT
1 TCAAAGTTTTCA-ATTTAGGGAAAGATCCTAACCAGTTTT
* *
18876 TAAAAGATTTTCAAATTAGGGAAAGATC
1 TCAAAG-TTTTCAATTTAGGGAAAGATC
18904 TCGTCAAAAG
Statistics
Matches: 59, Mismatches: 3, Indels: 8
0.84 0.04 0.11
Matches are distributed among these distances:
37 1 0.02
38 28 0.47
39 11 0.19
40 18 0.31
41 1 0.02
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.33
Consensus pattern (39 bp):
TCAAAGTTTTCAATTTAGGGAAAGATCCTAACCAGTTTT
Found at i:20011 original size:33 final size:33
Alignment explanation
Indices: 19941--20078 Score: 120
Period size: 33 Copynumber: 4.2 Consensus size: 33
19931 ATGATCAACC
** *
19941 AAAACAGATTT-GTTTTCATCACAATTAGCATCC-
1 AAAACAGATTTAG-TTTCATCACAAACAACA-CCT
19974 AAAACAGATTTAGTTTCATCACAAACAACACCT
1 AAAACAGATTTAGTTTCATCACAAACAACACCT
* **
20007 AAAACAGATTTAGTGTCATTGCAAACAACA-CT
1 AAAACAGATTTAGTTTCATCACAAACAACACCT
** * * * *
20039 CAAATTAGGTTTAGTATCATCGCAAACAACATCT
1 -AAAACAGATTTAGTTTCATCACAAACAACACCT
20073 AAAACA
1 AAAACA
20079 CTCTTTGCAA
Statistics
Matches: 88, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
32 4 0.05
33 81 0.92
34 3 0.03
ACGTcount: A:0.43, C:0.21, G:0.09, T:0.27
Consensus pattern (33 bp):
AAAACAGATTTAGTTTCATCACAAACAACACCT
Found at i:24724 original size:19 final size:18
Alignment explanation
Indices: 24700--24736 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
24690 TTGAAGATTT
24700 CTTGAAGATAATTTGAAGA
1 CTTGAAGATAA-TTGAAGA
*
24719 CTTGAAGATTATTGAAGA
1 CTTGAAGATAATTGAAGA
24737 ATTATTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.41, C:0.05, G:0.22, T:0.32
Consensus pattern (18 bp):
CTTGAAGATAATTGAAGA
Done.