Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016434.1 Corchorus capsularis cultivar CVL-1 contig16455, 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: 30510
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Found at i:11834 original size:12 final size:12
Alignment explanation
Indices: 11817--11900 Score: 51
Period size: 12 Copynumber: 6.5 Consensus size: 12
11807 GTTGTGGCCG
*
11817 GATGGCCTGTGC
1 GATGGCCCGTGC
11829 GATGGCCCGTGC
1 GATGGCCCGTGC
* *
11841 GTTGGCCGGTTGTGGTC
1 GATGGCC---CGT-G-C
*
11858 GGATGGCTCGTGC
1 -GATGGCCCGTGC
11871 GATGGCCCGTGC
1 GATGGCCCGTGC
* *
11883 GATGTCCCATGC
1 GATGGCCCGTGC
*
11895 GTTGGC
1 GATGGC
11901 TGGTCATGGC
Statistics
Matches: 55, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
12 42 0.76
13 1 0.02
14 1 0.02
15 4 0.07
16 1 0.02
17 1 0.02
18 5 0.09
ACGTcount: A:0.07, C:0.26, G:0.42, T:0.25
Consensus pattern (12 bp):
GATGGCCCGTGC
Found at i:11861 original size:42 final size:42
Alignment explanation
Indices: 11801--11883 Score: 141
Period size: 42 Copynumber: 2.0 Consensus size: 42
11791 AAGGGTCTAG
11801 TGGCCGGTTGTGGCCGGATGGC-CTGTGCGATGGCCCGTGCGT
1 TGGCCGGTTGTGGCCGGATGGCTC-GTGCGATGGCCCGTGCGT
*
11843 TGGCCGGTTGTGGTCGGATGGCTCGTGCGATGGCCCGTGCG
1 TGGCCGGTTGTGGCCGGATGGCTCGTGCGATGGCCCGTGCG
11884 ATGTCCCATG
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
42 38 0.97
43 1 0.03
ACGTcount: A:0.05, C:0.25, G:0.46, T:0.24
Consensus pattern (42 bp):
TGGCCGGTTGTGGCCGGATGGCTCGTGCGATGGCCCGTGCGT
Found at i:11926 original size:54 final size:54
Alignment explanation
Indices: 11817--11927 Score: 125
Period size: 54 Copynumber: 2.1 Consensus size: 54
11807 GTTGTGGCCG
* * ** * *
11817 GATGGCCTGTGCGATGGCCCGTGCGTTGGCCGGTTGTGGTCGGATGGCTCGTGC
1 GATGGCCCGTGCGATGGCCCATGCGTTGGCCGGTCATGGCCGGATGGCTCATGC
* * *
11871 GATGGCCCGTGCGATGTCCCATGCGTTGGCTGGTCATGGCCGG-TTGCTCCATGC
1 GATGGCCCGTGCGATGGCCCATGCGTTGGCCGGTCATGGCCGGATGGCT-CATGC
11925 GAT
1 GAT
11928 CATGGCCGGT
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
53 4 0.09
54 43 0.91
ACGTcount: A:0.08, C:0.26, G:0.40, T:0.26
Consensus pattern (54 bp):
GATGGCCCGTGCGATGGCCCATGCGTTGGCCGGTCATGGCCGGATGGCTCATGC
Found at i:17161 original size:33 final size:33
Alignment explanation
Indices: 17087--17233 Score: 174
Period size: 33 Copynumber: 4.5 Consensus size: 33
17077 TCTGTTTCTC
* * * *
17087 ATCACCCAAAACAGATTTATTTTCAATGC---C
1 ATCAACCAAAACAGAATTATTTGCAATGCTATG
*
17117 ATCAACCAAAACAGAATTATTTGCAATGTTATG
1 ATCAACCAAAACAGAATTATTTGCAATGCTATG
* *
17150 ATCAACAAAAACAGGATTATTTGCAATGCTATG
1 ATCAACCAAAACAGAATTATTTGCAATGCTATG
* **
17183 ATCAACCAAAACAAAATTATTTTTAATGCTATG
1 ATCAACCAAAACAGAATTATTTGCAATGCTATG
*
17216 TTCAACCAAAACAGAATT
1 ATCAACCAAAACAGAATT
17234 GTTTTCATCA
Statistics
Matches: 99, Mismatches: 15, Indels: 3
0.85 0.13 0.03
Matches are distributed among these distances:
30 25 0.25
33 74 0.75
ACGTcount: A:0.43, C:0.18, G:0.10, T:0.29
Consensus pattern (33 bp):
ATCAACCAAAACAGAATTATTTGCAATGCTATG
Found at i:17293 original size:33 final size:32
Alignment explanation
Indices: 17256--17360 Score: 104
Period size: 33 Copynumber: 3.2 Consensus size: 32
17246 ATTAGCATCC
*
17256 AAAACAGATTTAGTTTCATCTCAAACAACACCT
1 AAAACAGATTTAGTATCATCTCAAACAACA-CT
* *
17289 AAAACAAATTTAGTGTCAT-TGCAAACAACACT
1 AAAACAGATTTAGTATCATCT-CAAACAACACT
** * *
17321 CAAATTAGGTTTAGTATCATCCCAAACAACATCT
1 -AAAACAGATTTAGTATCATCTCAAACAACA-CT
17355 AAAACA
1 AAAACA
17361 CTCTTTTCAA
Statistics
Matches: 58, Mismatches: 10, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
32 3 0.05
33 53 0.91
34 2 0.03
ACGTcount: A:0.45, C:0.22, G:0.08, T:0.26
Consensus pattern (32 bp):
AAAACAGATTTAGTATCATCTCAAACAACACT
Found at i:20303 original size:33 final size:32
Alignment explanation
Indices: 20237--20365 Score: 187
Period size: 33 Copynumber: 4.1 Consensus size: 32
20227 AAAGGGTCAA
*
20237 ATGGCCGGTTGT-GCCTGGATG-GCT-CATGCG
1 ATGGCCGGTTGTGGCC-GGTTGTGCTCCATGCG
20267 ATGGCCGGTTGTGGCCGGTTGGTGCTCCATGCG
1 ATGGCCGGTTGTGGCCGGTT-GTGCTCCATGCG
20300 ATGGCCGGTTGTGGCCGGTTGGTGCTCCATGCG
1 ATGGCCGGTTGTGGCCGGTT-GTGCTCCATGCG
20333 ATGGCCGGTTGTGGCCGG-T-TGCTCCATGCG
1 ATGGCCGGTTGTGGCCGGTTGTGCTCCATGCG
20363 ATG
1 ATG
20366 TCACATGCGA
Statistics
Matches: 94, Mismatches: 1, Indels: 8
0.91 0.01 0.08
Matches are distributed among these distances:
30 29 0.31
31 4 0.04
32 4 0.04
33 57 0.61
ACGTcount: A:0.08, C:0.24, G:0.41, T:0.27
Consensus pattern (32 bp):
ATGGCCGGTTGTGGCCGGTTGTGCTCCATGCG
Found at i:20359 original size:63 final size:62
Alignment explanation
Indices: 20237--20365 Score: 183
Period size: 63 Copynumber: 2.0 Consensus size: 62
20227 AAAGGGTCAA
20237 ATGGCCGGTTGTGCCTGGATGGCTCATGCGATGGCCGGTTGTGGCCGGTTGGTGCTCCATGCG
1 ATGGCCGGTTGTGCCTGGATGGCTCATGCGATGGCCGGTTGTGGCCGGTT-GTGCTCCATGCG
*
20300 ATGGCCGGTTGTGGCC-GGTTGGTGCTCCATGCGATGGCCGGTTGTGGCCGG-T-TGCTCCATGC
1 ATGGCCGGTTGT-GCCTGGAT-G-GCT-CATGCGATGGCCGGTTGTGGCCGGTTGTGCTCCATGC
20362 G
62 G
20363 ATG
1 ATG
20366 TCACATGCGA
Statistics
Matches: 61, Mismatches: 1, Indels: 8
0.87 0.01 0.11
Matches are distributed among these distances:
63 29 0.48
64 4 0.07
65 4 0.07
66 24 0.39
ACGTcount: A:0.08, C:0.24, G:0.41, T:0.27
Consensus pattern (62 bp):
ATGGCCGGTTGTGCCTGGATGGCTCATGCGATGGCCGGTTGTGGCCGGTTGTGCTCCATGCG
Found at i:24803 original size:11 final size:10
Alignment explanation
Indices: 24786--24819 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
24776 TGGTCGAAAA
24786 TTTTTTTATT
1 TTTTTTTATT
24796 TATTTTTTATT
1 T-TTTTTTATT
*
24807 TTTTTATATT
1 TTTTTTTATT
24817 TTT
1 TTT
24820 CGATATAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 12 0.55
11 10 0.45
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (10 bp):
TTTTTTTATT
Found at i:25731 original size:30 final size:31
Alignment explanation
Indices: 25695--25790 Score: 103
Period size: 30 Copynumber: 3.1 Consensus size: 31
25685 AAAGGGTCAA
25695 ATGGCCGGTTGTG-C-TTGGATGGC-CCATGCG
1 ATGGCCGGTTGTGCCGTTGG-T-GCTCCATGCG
25725 ATGGCCGGTTGTGGCCGGTTGGTGCTCCATGCG
1 ATGGCCGGTTGT-GCC-GTTGGTGCTCCATGCG
*
25758 ATGGCCGGTTGTGGCCG--GTTGCTCCATGCG
1 ATGGCCGGTTGT-GCCGTTGGTGCTCCATGCG
25788 ATG
1 ATG
25791 TCACATGCGA
Statistics
Matches: 60, Mismatches: 1, Indels: 10
0.85 0.01 0.14
Matches are distributed among these distances:
30 27 0.45
31 1 0.02
32 4 0.07
33 24 0.40
34 4 0.07
ACGTcount: A:0.08, C:0.24, G:0.41, T:0.27
Consensus pattern (31 bp):
ATGGCCGGTTGTGCCGTTGGTGCTCCATGCG
Found at i:25760 original size:33 final size:30
Alignment explanation
Indices: 25718--25790 Score: 119
Period size: 33 Copynumber: 2.3 Consensus size: 30
25708 CTTGGATGGC
25718 CCATGCGATGGCCGGTTGTGGCCGGTTGGTGCT
1 CCATGCGATGGCCGGTTGTGGCCGG-T--TGCT
25751 CCATGCGATGGCCGGTTGTGGCCGGTTGCT
1 CCATGCGATGGCCGGTTGTGGCCGGTTGCT
25781 CCATGCGATG
1 CCATGCGATG
25791 TCACATGCGA
Statistics
Matches: 40, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
30 14 0.35
32 1 0.03
33 25 0.62
ACGTcount: A:0.08, C:0.26, G:0.40, T:0.26
Consensus pattern (30 bp):
CCATGCGATGGCCGGTTGTGGCCGGTTGCT
Found at i:28718 original size:21 final size:21
Alignment explanation
Indices: 28694--28747 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
28684 ACGGGTCAGG
*
28694 TGGCCGGGCATGCGATGGTGA
1 TGGCCGGGCATGCGATGGTAA
28715 TGGCCGGGCATGCGATGGTAA
1 TGGCCGGGCATGCGATGGTAA
*
28736 TGGCCGGCCATG
1 TGGCCGGGCATG
28748 TGGCCAGTCA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.15, C:0.22, G:0.44, T:0.19
Consensus pattern (21 bp):
TGGCCGGGCATGCGATGGTAA
Done.