Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005458.1 Corchorus capsularis cultivar CVL-1 contig05476, 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: 3317
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Found at i:1834 original size:13 final size:14
Alignment explanation
Indices: 1816--1860 Score: 58
Period size: 14 Copynumber: 3.2 Consensus size: 14
1806 CTAAATTGAC
1816 ATTATTAAAATTT-
1 ATTATTAAAATTTA
1829 ATTATTTAAAATTTA
1 ATTA-TTAAAATTTA
1844 ATTA-TAAAATTTCA
1 ATTATTAAAATTT-A
1858 ATT
1 ATT
1861 TAGACCGAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
13 12 0.41
14 13 0.45
15 4 0.14
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (14 bp):
ATTATTAAAATTTA
Found at i:2029 original size:167 final size:165
Alignment explanation
Indices: 1753--2081 Score: 459
Period size: 167 Copynumber: 2.0 Consensus size: 165
1743 ATAAAAGTTT
* *
1753 GAATAATGGAAAACTTTATGTTTTCTGATTGTACCATCTTTTCAAATATATTTCTAAATTGACAT
1 GAATAATGGAAAACTTTATGTTTTCCGATTGCACCATCTTTTCAAATATATTTCTAAATTGACAT
*
1818 TATTAAAATTTATTATTTAAAATTTAATTATAAAATTTCAATTTAGACCGAATTATAAGTTTTGT
66 TATTAAAATTTATAATTT-AAATTTAATTATAAAATTTCAATTTAGACCGAATTATAAG-TTTGT
1883 AAAATTGATTTTCA-TTGATGAACATGCAAATTTGTAC
129 AAAATTGATTTT-AGTTGATGAACATGCAAATTTGTAC
* * * **
1920 GAATAATGGGAAACTTTATGTTTTCCGATTGCACCCTTTTTTCCAAATATATTTCTAAATTTCCA
1 GAATAATGGAAAACTTTATGTTTTCCGATTGCACCATCTTTT-CAAATATATTTCTAAATTGACA
* *
1985 TTATTAAAATTCGGTATAATTT-GA-TTATTTA-AAAATTTCAATTTAGACCGAATTATAAGTTT
65 TTATTAAAATT---TATAATTTAAATTTAATTATAAAATTTCAATTTAGACCGAATTATAAGTTT
* *
2047 GTCAAATTGATTTTAGTTGATGAACATGTAAATTT
127 GTAAAATTGATTTTAGTTGATGAACATGCAAATTT
2082 CCTTTACTAT
Statistics
Matches: 145, Mismatches: 12, Indels: 11
0.86 0.07 0.07
Matches are distributed among these distances:
165 1 0.01
166 34 0.23
167 65 0.45
168 37 0.26
169 1 0.01
171 7 0.05
ACGTcount: A:0.36, C:0.10, G:0.11, T:0.43
Consensus pattern (165 bp):
GAATAATGGAAAACTTTATGTTTTCCGATTGCACCATCTTTTCAAATATATTTCTAAATTGACAT
TATTAAAATTTATAATTTAAATTTAATTATAAAATTTCAATTTAGACCGAATTATAAGTTTGTAA
AATTGATTTTAGTTGATGAACATGCAAATTTGTAC
Found at i:2123 original size:19 final size:20
Alignment explanation
Indices: 2096--2133 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
2086 TACTATCATT
2096 TTTTGAATTT-AATATTTTAC
1 TTTTGAATTTCAAT-TTTTAC
2116 TTTT-AATTTCAATTTTTA
1 TTTTGAATTTCAATTTTTA
2134 AATGTCAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTGAATTTCAATTTTTAC
Found at i:2330 original size:22 final size:21
Alignment explanation
Indices: 2302--2450 Score: 113
Period size: 22 Copynumber: 6.7 Consensus size: 21
2292 TGTCTCTATC
2302 TGGTTATCAAAATTTCATCAGA
1 TGGTTATCAAAATTTCAT-AGA
* *
2324 TGGTTATTATAATTTCATGAGGA
1 TGGTTATCAAAATTTCAT-A-GA
* *
2347 -GGTTATCAAAATTCCATAATA
1 TGGTTATCAAAATTTCAT-AGA
*
2368 TGGTTACCAAAATTTCATATGGA
1 TGGTTATCAAAATTTCATA--GA
* *
2391 -AGTTATCAAAATTTCATAGTG
1 TGGTTATCAAAATTTCATAG-A
*
2412 TGGTTACCAAAATTTCATAGGA
1 TGGTTATCAAAATTTCATA-GA
*
2434 TCAGGTTATTAAAATTT
1 T--GGTTATCAAAATTT
2451 TTTAGGTTTG
Statistics
Matches: 99, Mismatches: 19, Indels: 16
0.74 0.14 0.12
Matches are distributed among these distances:
20 1 0.01
21 2 0.02
22 80 0.81
23 4 0.04
24 12 0.12
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.38
Consensus pattern (21 bp):
TGGTTATCAAAATTTCATAGA
Found at i:2371 original size:44 final size:44
Alignment explanation
Indices: 2303--2430 Score: 159
Period size: 44 Copynumber: 2.9 Consensus size: 44
2293 GTCTCTATCT
* * ** *
2303 GGTTATCAAAATTTCATCAGATGGTTATTATAATTTCATGA-GGA
1 GGTTATCAAAATTTCATAATATGGTTACCAAAATTTCAT-ATGGA
*
2347 GGTTATCAAAATTCCATAATATGGTTACCAAAATTTCATATGGA
1 GGTTATCAAAATTTCATAATATGGTTACCAAAATTTCATATGGA
* * *
2391 AGTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATA
1 GGTTATCAAAATTTCATAATATGGTTACCAAAATTTCATA
2431 GGATCAGGTT
Statistics
Matches: 73, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
43 1 0.01
44 72 0.99
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.37
Consensus pattern (44 bp):
GGTTATCAAAATTTCATAATATGGTTACCAAAATTTCATATGGA
Found at i:2485 original size:22 final size:22
Alignment explanation
Indices: 2302--2485 Score: 102
Period size: 22 Copynumber: 8.3 Consensus size: 22
2292 TGTCTCTATC
* *
2302 TGGTTATCAAAATTTCATCA-GA
1 TGGTTATTAAAATTTCAT-AGGG
*
2324 TGGTTATTATAATTTCAT-GAGG
1 TGGTTATTAAAATTTCATAG-GG
* * * ***
2346 AGGTTATCAAAATTCCATAATA
1 TGGTTATTAAAATTTCATAGGG
** *
2368 TGGTTACCAAAATTTCATATGG
1 TGGTTATTAAAATTTCATAGGG
** * *
2390 AAGTTATCAAAATTTCATAGTG
1 TGGTTATTAAAATTTCATAGGG
** *
2412 TGGTTACCAAAATTTCATAGGA
1 TGGTTATTAAAATTTCATAGGG
** *
2434 TCAGGTTATTAAAATTTTTTAGGT
1 T--GGTTATTAAAATTTCATAGGG
* *
2458 TTGTTATTGAAATTTCATAGGG
1 TGGTTATTAAAATTTCATAGGG
2480 TGGTTA
1 TGGTTA
2486 ATTATCACAA
Statistics
Matches: 120, Mismatches: 37, Indels: 10
0.72 0.22 0.06
Matches are distributed among these distances:
22 103 0.86
24 17 0.14
ACGTcount: A:0.34, C:0.09, G:0.17, T:0.40
Consensus pattern (22 bp):
TGGTTATTAAAATTTCATAGGG
Done.