Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014773.1 Corchorus capsularis cultivar CVL-1 contig14794, 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: 24472
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:3335 original size:13 final size:13
Alignment explanation
Indices: 3314--3343 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
3304 TACATCAATG
3314 TTTTCTTCTTTTT
1 TTTTCTTCTTTTT
*
3327 TTTTTTTCTTTTT
1 TTTTCTTCTTTTT
3340 TTTT
1 TTTT
3344 GGGGGGAGGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (13 bp):
TTTTCTTCTTTTT
Found at i:3335 original size:16 final size:15
Alignment explanation
Indices: 3314--3343 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
3304 TACATCAATG
3314 TTTTCTTCTTTTTTTT
1 TTTTCTT-TTTTTTTT
3330 TTTTCTTTTTTTTT
1 TTTTCTTTTTTTTT
3344 GGGGGGAGGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (15 bp):
TTTTCTTTTTTTTTT
Found at i:8245 original size:21 final size:21
Alignment explanation
Indices: 8172--8245 Score: 53
Period size: 21 Copynumber: 3.5 Consensus size: 21
8162 GGGAACCCAT
* * *
8172 CATTAATACCATTTGGAGCAC
1 CATTATTACCATTTGCACCAC
* *
8193 CATTAATTCCCTTTTTGC-CC-C
1 CATT-ATTACC-ATTTGCACCAC
**
8214 CATTACCACCATTTGCACCAC
1 CATTATTACCATTTGCACCAC
8235 CATTATTACCA
1 CATTATTACCA
8246 CCATTCTTGT
Statistics
Matches: 38, Mismatches: 11, Indels: 8
0.67 0.19 0.14
Matches are distributed among these distances:
19 5 0.13
20 5 0.13
21 19 0.50
22 5 0.13
23 4 0.11
ACGTcount: A:0.27, C:0.34, G:0.07, T:0.32
Consensus pattern (21 bp):
CATTATTACCATTTGCACCAC
Found at i:8679 original size:12 final size:12
Alignment explanation
Indices: 8662--8723 Score: 67
Period size: 12 Copynumber: 5.4 Consensus size: 12
8652 GATGCTGAGG
*
8662 ATCATCCAACTC
1 ATCATCCAAGTC
*
8674 ATCATCAAAGTC
1 ATCATCCAAGTC
*
8686 ATCATCTAAGTC
1 ATCATCCAAGTC
8698 ATCAT--AA-TC
1 ATCATCCAAGTC
*
8707 ATCATCCAAATC
1 ATCATCCAAGTC
8719 ATCAT
1 ATCAT
8724 AATCATCATC
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
9 7 0.16
10 2 0.05
11 2 0.05
12 33 0.75
ACGTcount: A:0.39, C:0.29, G:0.03, T:0.29
Consensus pattern (12 bp):
ATCATCCAAGTC
Found at i:8699 original size:9 final size:9
Alignment explanation
Indices: 8686--8732 Score: 51
Period size: 9 Copynumber: 4.9 Consensus size: 9
8676 CATCAAAGTC
8686 ATCATC-TA
1 ATCATCATA
8694 AGTCATCATA
1 A-TCATCATA
8704 ATCATCATCCAA
1 ATCATCAT---A
8716 ATCATCATA
1 ATCATCATA
8725 ATCATCAT
1 ATCATCAT
8733 CACTGAAGTC
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
8 1 0.03
9 21 0.62
10 3 0.09
12 9 0.26
ACGTcount: A:0.40, C:0.26, G:0.02, T:0.32
Consensus pattern (9 bp):
ATCATCATA
Found at i:8699 original size:21 final size:21
Alignment explanation
Indices: 8662--8733 Score: 90
Period size: 21 Copynumber: 3.3 Consensus size: 21
8652 GATGCTGAGG
*
8662 ATCATCCAACTCATCATCAAAGTC
1 ATCATCCAAATCATCAT--AA-TC
* *
8686 ATCATCTAAGTCATCATAATC
1 ATCATCCAAATCATCATAATC
8707 ATCATCCAAATCATCATAATC
1 ATCATCCAAATCATCATAATC
8728 ATCATC
1 ATCATC
8734 ACTGAAGTCA
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
21 27 0.61
22 2 0.05
24 15 0.34
ACGTcount: A:0.39, C:0.29, G:0.03, T:0.29
Consensus pattern (21 bp):
ATCATCCAAATCATCATAATC
Found at i:8731 original size:12 final size:12
Alignment explanation
Indices: 8672--8734 Score: 50
Period size: 12 Copynumber: 5.8 Consensus size: 12
8662 ATCATCCAAC
8672 TCATCATCA-AA
1 TCATCATCATAA
8683 GTCATCATC-TAA
1 -TCATCATCATAA
*
8695 --GTCATCATAA
1 TCATCATCATAA
*
8705 TCATCATC-CAA
1 TCATCATCATAA
8716 --ATCATCATAA
1 TCATCATCATAA
8726 TCATCATCA
1 TCATCATCA
8735 CTGAAGTCAT
Statistics
Matches: 40, Mismatches: 4, Indels: 14
0.69 0.07 0.24
Matches are distributed among these distances:
9 11 0.28
10 5 0.12
11 2 0.05
12 22 0.55
ACGTcount: A:0.40, C:0.27, G:0.03, T:0.30
Consensus pattern (12 bp):
TCATCATCATAA
Found at i:13008 original size:15 final size:15
Alignment explanation
Indices: 12988--13019 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
12978 AGATACTATA
12988 TTAAGTAGTTTTCAT
1 TTAAGTAGTTTTCAT
13003 TTAAGTAGTTTTCAT
1 TTAAGTAGTTTTCAT
13018 TT
1 TT
13020 GATCATAACG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.25, C:0.06, G:0.12, T:0.56
Consensus pattern (15 bp):
TTAAGTAGTTTTCAT
Found at i:14479 original size:1 final size:1
Alignment explanation
Indices: 14473--14503 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
14463 TCAAGCAATC
14473 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
14504 ACTGCTGCCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:20222 original size:64 final size:64
Alignment explanation
Indices: 20121--20247 Score: 254
Period size: 64 Copynumber: 2.0 Consensus size: 64
20111 CTTTTTTTTT
20121 TTTATTTCTCCTAAATAGTTTTAAATTTAGAGTGATTTGATTACTATTGGATACTATAGTGTAC
1 TTTATTTCTCCTAAATAGTTTTAAATTTAGAGTGATTTGATTACTATTGGATACTATAGTGTAC
20185 TTTATTTCTCCTAAATAGTTTTAAATTTAGAGTGATTTGATTACTATTGGATACTATAGTGTA
1 TTTATTTCTCCTAAATAGTTTTAAATTTAGAGTGATTTGATTACTATTGGATACTATAGTGTA
20248 AATCTTGGAT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 63 1.00
ACGTcount: A:0.30, C:0.09, G:0.14, T:0.47
Consensus pattern (64 bp):
TTTATTTCTCCTAAATAGTTTTAAATTTAGAGTGATTTGATTACTATTGGATACTATAGTGTAC
Found at i:20956 original size:14 final size:14
Alignment explanation
Indices: 20937--20965 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
20927 AGATCTAGCA
20937 GCCATGTAATAACC
1 GCCATGTAATAACC
20951 GCCATGTAATAACC
1 GCCATGTAATAACC
20965 G
1 G
20966 ATTTAGTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.28, G:0.17, T:0.21
Consensus pattern (14 bp):
GCCATGTAATAACC
Done.