Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007520.1 Corchorus capsularis cultivar CVL-1 contig07541, 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: 21755
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Found at i:1984 original size:16 final size:16
Alignment explanation
Indices: 1963--1993 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1953 AATTTTCAGA
1963 ATCAACAAAACATCAT
1 ATCAACAAAACATCAT
*
1979 ATCAACGAAACATCA
1 ATCAACAAAACATCA
1994 ACTTAAAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.26, G:0.03, T:0.16
Consensus pattern (16 bp):
ATCAACAAAACATCAT
Found at i:8665 original size:17 final size:17
Alignment explanation
Indices: 8643--8678 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
8633 GTCAAACATT
8643 TTCGGGGTTGTTCAATG
1 TTCGGGGTTGTTCAATG
8660 TTCGGGGTTGTTCAATG
1 TTCGGGGTTGTTCAATG
8677 TT
1 TT
8679 GGACTTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.11, C:0.11, G:0.33, T:0.44
Consensus pattern (17 bp):
TTCGGGGTTGTTCAATG
Found at i:8853 original size:7 final size:7
Alignment explanation
Indices: 8841--8866 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
8831 TTTTCAACTC
8841 TCTTCCT
1 TCTTCCT
8848 TCTTCCT
1 TCTTCCT
8855 TCTTCCT
1 TCTTCCT
8862 TCTTC
1 TCTTC
8867 AGGCCTCCTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.00, C:0.42, G:0.00, T:0.58
Consensus pattern (7 bp):
TCTTCCT
Found at i:9087 original size:18 final size:18
Alignment explanation
Indices: 9064--9123 Score: 75
Period size: 18 Copynumber: 3.2 Consensus size: 18
9054 ATAAATCACA
9064 AAATCACAAAATCTTGAC
1 AAATCACAAAATCTTGAC
*
9082 AAATCACAAAATCTTGGGAT
1 AAATCACAAAATCTT--GAC
*
9102 ATAATCACAAAAACTTGAC
1 A-AATCACAAAATCTTGAC
9121 AAA
1 AAA
9124 CCCAAATTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
18 17 0.47
19 3 0.08
20 3 0.08
21 13 0.36
ACGTcount: A:0.52, C:0.18, G:0.08, T:0.22
Consensus pattern (18 bp):
AAATCACAAAATCTTGAC
Found at i:13336 original size:22 final size:22
Alignment explanation
Indices: 13284--13336 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
13274 ACTAACATTA
* * *
13284 ATATAGTAGAAGTAGGTAGATAG
1 ATATA-TAGAAGTAGATACATAC
*
13307 ATAGATAGAAGTAGATACATAC
1 ATATATAGAAGTAGATACATAC
13329 ATATATAG
1 ATATATAG
13337 TCTTGTTAGA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
22 21 0.84
23 4 0.16
ACGTcount: A:0.47, C:0.04, G:0.23, T:0.26
Consensus pattern (22 bp):
ATATATAGAAGTAGATACATAC
Found at i:14138 original size:15 final size:16
Alignment explanation
Indices: 14113--14142 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
14103 AATTTGCTAA
14113 AATTCATTATATGAAC
1 AATTCATTATATGAAC
14129 AATT-ATTATATGAA
1 AATTCATTATATGAA
14143 TAAATACTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.40
Consensus pattern (16 bp):
AATTCATTATATGAAC
Found at i:14211 original size:3 final size:3
Alignment explanation
Indices: 14205--14243 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
14195 TTTTTTTTAC
14205 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
14244 CTTAGTAATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:16649 original size:23 final size:22
Alignment explanation
Indices: 16597--16649 Score: 52
Period size: 23 Copynumber: 2.4 Consensus size: 22
16587 CTAAGTTTTT
* *
16597 TAATTAAATTAGTAAAATGATA
1 TAATTAAAATAGTAAAAGGATA
* * *
16619 AAAATAAAATAGGTATAAGGATA
1 TAATTAAAATA-GTAAAAGGATA
16642 TAATTAAA
1 TAATTAAA
16650 TAAAAAATAA
Statistics
Matches: 23, Mismatches: 7, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
22 8 0.35
23 15 0.65
ACGTcount: A:0.58, C:0.00, G:0.11, T:0.30
Consensus pattern (22 bp):
TAATTAAAATAGTAAAAGGATA
Found at i:16946 original size:3 final size:3
Alignment explanation
Indices: 16940--16989 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
16930 TAGATTATTA
16940 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
16988 TT
1 TT
16990 ATACCGAGTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Done.