Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015212.1 Corchorus capsularis cultivar CVL-1 contig15233, 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: 14209
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:1230 original size:22 final size:22
Alignment explanation
Indices: 1196--1298 Score: 68
Period size: 22 Copynumber: 4.7 Consensus size: 22
1186 CTACTAAAAT
*
1196 TTATTAAAATTTCATAGTTAAG
1 TTATCAAAATTTCATAGTTAAG
* * **
1218 TTATCAAAGTTTCTTA-TGGAG
1 TTATCAAAATTTCATAGTTAAG
* * * *
1239 TTTATGACAATTTTATAGATAA-
1 -TTATCAAAATTTCATAGTTAAG
*
1261 TTATCAAAATTTCATATGGT-AG
1 TTATCAAAATTTCATA-GTTAAG
*
1283 TTATCAAAGTTTCATA
1 TTATCAAAATTTCATA
1299 AAAATTTTCA
Statistics
Matches: 59, Mismatches: 18, Indels: 8
0.69 0.21 0.09
Matches are distributed among these distances:
21 17 0.29
22 41 0.69
23 1 0.02
ACGTcount: A:0.37, C:0.08, G:0.12, T:0.44
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTTAAG
Found at i:2903 original size:14 final size:14
Alignment explanation
Indices: 2874--2930 Score: 68
Period size: 14 Copynumber: 4.3 Consensus size: 14
2864 AAAAAGACTC
2874 AAAACC-TTT-TTG
1 AAAACCATTTCTTG
2886 AAAACTCATTTC-TG
1 AAAAC-CATTTCTTG
2900 AAAACCATTTCTTG
1 AAAACCATTTCTTG
*
2914 AAAACAATTT-TTG
1 AAAACCATTTCTTG
2927 AAAA
1 AAAA
2931 ATGTCTCTTA
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
12 5 0.12
13 14 0.35
14 21 0.52
ACGTcount: A:0.42, C:0.16, G:0.07, T:0.35
Consensus pattern (14 bp):
AAAACCATTTCTTG
Found at i:7106 original size:13 final size:14
Alignment explanation
Indices: 7083--7111 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
7073 ACTTCTACTC
7083 AATGCATGAATGCA
1 AATGCATGAATGCA
7097 AATG-ATGAATGCA
1 AATGCATGAATGCA
7110 AA
1 AA
7112 GTCCAATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.48, C:0.10, G:0.21, T:0.21
Consensus pattern (14 bp):
AATGCATGAATGCA
Found at i:10213 original size:27 final size:27
Alignment explanation
Indices: 10183--10234 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
10173 CCCTAAATGC
*
10183 AAAATGACCAAAATGCCTCTGGATGTG
1 AAAATGACCAAAATGCCCCTGGATGTG
10210 AAAATGACCAAAATGCCCCTGGATG
1 AAAATGACCAAAATGCCCCTGGATG
10235 ACCCTAATGC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.19
Consensus pattern (27 bp):
AAAATGACCAAAATGCCCCTGGATGTG
Found at i:10289 original size:2 final size:2
Alignment explanation
Indices: 10282--10314 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
10272 GAGTGTTTAC
10282 AT AT AT AT AT AT AT AT AT AT AT AT -T AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
10315 AAAACAACGA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 27 0.93
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:11048 original size:35 final size:35
Alignment explanation
Indices: 11001--11072 Score: 92
Period size: 35 Copynumber: 2.1 Consensus size: 35
10991 GATCCTCTTT
*
11001 GATATTAGAGTTAGTAGGGTATTAAAGTGTTTGGA
1 GATATTAGAGTTAGTAGGGTATTAAAGTGTTTAGA
* * *
11036 GATATT-GAAGTTAGTGGGGTCTTAAGGTGTTTAGA
1 GATATTAG-AGTTAGTAGGGTATTAAAGTGTTTAGA
11071 GA
1 GA
11073 GCTTAAGATT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
34 1 0.03
35 31 0.97
ACGTcount: A:0.29, C:0.01, G:0.33, T:0.36
Consensus pattern (35 bp):
GATATTAGAGTTAGTAGGGTATTAAAGTGTTTAGA
Found at i:11139 original size:2 final size:2
Alignment explanation
Indices: 11127--11163 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
11117 ATGAAGTAGT
* *
11127 TC TC TC AC TC TC TC TG TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
11164 ATTATATATA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.03, C:0.46, G:0.03, T:0.49
Consensus pattern (2 bp):
TC
Found at i:11171 original size:2 final size:2
Alignment explanation
Indices: 11166--11205 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
11156 CTCTCTCTAT
* *
11166 TA TA TA TA TA TA TA TA TA TA TA TA TG TA TG 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
11206 ATAGTGTGGC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (2 bp):
TA
Found at i:13377 original size:30 final size:30
Alignment explanation
Indices: 13337--13395 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
13327 TGTCTTCAAG
13337 TCCATAATAAGTCCTT-GGCGCATAATTCCT
1 TCCATAATAAG-CCTTGGGCGCATAATTCCT
* *
13367 TCCATGATAAGCCTTGGGCGCATCATTCC
1 TCCATAATAAGCCTTGGGCGCATAATTCC
13396 CTCCCCCTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 4 0.15
30 22 0.85
ACGTcount: A:0.24, C:0.29, G:0.17, T:0.31
Consensus pattern (30 bp):
TCCATAATAAGCCTTGGGCGCATAATTCCT
Found at i:13843 original size:33 final size:33
Alignment explanation
Indices: 13806--13910 Score: 106
Period size: 33 Copynumber: 3.2 Consensus size: 33
13796 ATTAGCATCC
13806 AAAACAGATTTAGTATCATCACAAACAACACTT
1 AAAACAGATTTAGTATCATCACAAACAACACTT
* * *
13839 AAAACAGATTTAGTGTCATTGA-AAACAACACTC
1 AAAACAGATTTAGTATCA-TCACAAACAACACTT
** * * *
13872 AAATTAGGTTTAGAATCATCGCAAACAACA-TCT
1 AAAACAGATTTAGTATCATCACAAACAACACT-T
13905 AAAACA
1 AAAACA
13911 CTCTTTGCAA
Statistics
Matches: 56, Mismatches: 13, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
32 2 0.04
33 52 0.93
34 2 0.04
ACGTcount: A:0.48, C:0.19, G:0.10, T:0.24
Consensus pattern (33 bp):
AAAACAGATTTAGTATCATCACAAACAACACTT
Done.