Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013367.1 Corchorus capsularis cultivar CVL-1 contig13388, 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: 12150
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:166 original size:21 final size:19
Alignment explanation
Indices: 141--203 Score: 74
Period size: 19 Copynumber: 3.2 Consensus size: 19
131 GAGTGATTTT
141 TCATTACACTCAAA-ATTGA
1 TCATTACAC-CAAACATTGA
* *
160 TACCATTACACCAAATAATGA
1 T--CATTACACCAAACATTGA
181 TCATTACACCAAACATTGA
1 TCATTACACCAAACATTGA
200 TCAT
1 TCAT
204 ATTTTCCTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
19 21 0.55
20 4 0.11
21 13 0.34
ACGTcount: A:0.43, C:0.24, G:0.05, T:0.29
Consensus pattern (19 bp):
TCATTACACCAAACATTGA
Found at i:945 original size:2 final size:2
Alignment explanation
Indices: 940--972 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
930 AAGGGAAACA
*
940 AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
973 ATTATACGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1196 original size:2 final size:2
Alignment explanation
Indices: 1189--1232 Score: 65
Period size: 2 Copynumber: 23.0 Consensus size: 2
1179 CCACATCGAC
*
1189 TA TA TA TA TA TA TA TA -A TA TA TA TG TA TA T- TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1229 TA TA
1 TA TA
1233 ATAATATCTT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
1 2 0.05
2 36 0.95
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1210 original size:13 final size:13
Alignment explanation
Indices: 1192--1239 Score: 62
Period size: 13 Copynumber: 3.6 Consensus size: 13
1182 CATCGACTAT
1192 ATATATATATATA
1 ATATATATATATA
*
1205 ATATATATGTATATT
1 ATATATA--TATATA
1220 ATATATATATATA
1 ATATATATATATA
1233 ATA-ATAT
1 ATATATAT
1240 CTTCTTAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
12 4 0.13
13 15 0.48
15 12 0.39
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (13 bp):
ATATATATATATA
Found at i:1210 original size:15 final size:15
Alignment explanation
Indices: 1190--1239 Score: 73
Period size: 15 Copynumber: 3.3 Consensus size: 15
1180 CACATCGACT
1190 ATATATATATATATA
1 ATATATATATATATA
* *
1205 ATATATATGTATATT
1 ATATATATATATATA
1220 ATATATATATATAATA
1 ATATATATATAT-ATA
1236 ATAT
1 ATAT
1240 CTTCTTAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
15 24 0.80
16 6 0.20
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (15 bp):
ATATATATATATATA
Found at i:4179 original size:15 final size:16
Alignment explanation
Indices: 4150--4184 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
4140 ACTGAAAAAC
4150 ACCCAAACCAAAAATG
1 ACCCAAACCAAAAATG
*
4166 ACCCAAACC-TAAATG
1 ACCCAAACCAAAAATG
4181 ACCC
1 ACCC
4185 GACATTTGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.49, C:0.37, G:0.06, T:0.09
Consensus pattern (16 bp):
ACCCAAACCAAAAATG
Found at i:5126 original size:2 final size:2
Alignment explanation
Indices: 5119--5154 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
5109 TTCTGCTATG
5119 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5155 TTTATAGGTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5919 original size:11 final size:11
Alignment explanation
Indices: 5896--5925 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
5886 TTTTCTTTAT
5896 TAAATAT-ATA
1 TAAATATAATA
5906 TAAATATAATA
1 TAAATATAATA
5917 TAAATATAA
1 TAAATATAA
5926 CAAACTACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 7 0.37
11 12 0.63
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (11 bp):
TAAATATAATA
Found at i:7874 original size:2 final size:2
Alignment explanation
Indices: 7867--7894 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
7857 TGTATGCTAG
7867 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
7895 CACACACACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:10332 original size:26 final size:27
Alignment explanation
Indices: 10296--10349 Score: 101
Period size: 26 Copynumber: 2.0 Consensus size: 27
10286 CAAGCACATG
10296 TAACGAATTTCTTTCATTTTTTT-TTT
1 TAACGAATTTCTTTCATTTTTTTATTT
10322 TAACGAATTTCTTTCATTTTTTTATTT
1 TAACGAATTTCTTTCATTTTTTTATTT
10349 T
1 T
10350 TTGAAATGCT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 23 0.85
27 4 0.15
ACGTcount: A:0.20, C:0.11, G:0.04, T:0.65
Consensus pattern (27 bp):
TAACGAATTTCTTTCATTTTTTTATTT
Found at i:12125 original size:9 final size:9
Alignment explanation
Indices: 12099--12131 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
12089 ACTTTGATTT
12099 TTTTTTTTCC
1 TTTTTTTT-C
12109 TTTTTTTTC
1 TTTTTTTTC
12118 TTTTTTTT-
1 TTTTTTTTC
12126 TTTTTT
1 TTTTTT
12132 GGGGTTGCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 6 0.26
9 9 0.39
10 8 0.35
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (9 bp):
TTTTTTTTC
Done.