Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008856.1 Corchorus capsularis cultivar CVL-1 contig08877, 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: 14397
ACGTcount: A:0.26, C:0.23, G:0.17, T:0.33
Found at i:909 original size:25 final size:25
Alignment explanation
Indices: 875--927 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
865 ATCAATTAAG
*
875 AAACCCAAAGATTAAAAGTGAAAGA
1 AAACCAAAAGATTAAAAGTGAAAGA
*
900 AAACCAAAAGATTAAAAGTGAAATA
1 AAACCAAAAGATTAAAAGTGAAAGA
925 AAA
1 AAA
928 GGCCACATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.64, C:0.09, G:0.13, T:0.13
Consensus pattern (25 bp):
AAACCAAAAGATTAAAAGTGAAAGA
Found at i:1019 original size:22 final size:23
Alignment explanation
Indices: 973--1019 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
963 GAAGGGACCT
973 AAGAATTATTCTAAAAAGGAGGA
1 AAGAATTATTCTAAAAAGGAGGA
* *
996 AAGAATTATTGTAAAGA-GAGGA
1 AAGAATTATTCTAAAAAGGAGGA
1018 AA
1 AA
1020 TGATTCGGCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 7 0.32
23 15 0.68
ACGTcount: A:0.53, C:0.02, G:0.23, T:0.21
Consensus pattern (23 bp):
AAGAATTATTCTAAAAAGGAGGA
Found at i:9742 original size:16 final size:15
Alignment explanation
Indices: 9713--9755 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 15
9703 TCAAAAGTTG
9713 TTATTATCACTTATTA
1 TTATTATCA-TTATTA
9729 TTATTTATCATTATTA
1 TTA-TTATCATTATTA
9745 TTATTATCATT
1 TTATTATCATT
9756 TTTTTTAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
15 8 0.31
16 12 0.46
17 6 0.23
ACGTcount: A:0.30, C:0.09, G:0.00, T:0.60
Consensus pattern (15 bp):
TTATTATCATTATTA
Found at i:13669 original size:13 final size:13
Alignment explanation
Indices: 13624--13670 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
13614 ATCATTTTTA
13624 CTCTTTTCTTACT
1 CTCTTTTCTTACT
* *
13637 CT-TTTTACTAATT
1 CTCTTTT-CTTACT
13650 ACTCTTTTCTTACT
1 -CTCTTTTCTTACT
13664 CTCTTTT
1 CTCTTTT
13671 ATTTATTTCC
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
12 4 0.15
13 13 0.48
14 6 0.22
15 4 0.15
ACGTcount: A:0.13, C:0.26, G:0.00, T:0.62
Consensus pattern (13 bp):
CTCTTTTCTTACT
Found at i:13755 original size:21 final size:21
Alignment explanation
Indices: 13731--14180 Score: 232
Period size: 21 Copynumber: 21.1 Consensus size: 21
13721 ACTCTTTGAA
*
13731 TTACTGATCACCTTTTACTCT
1 TTACTGATTACCTTTTACTCT
*
13752 TTACTGATTACTATTTTACTC-
1 TTACTGATTAC-CTTTTACTCT
* * *
13773 TTACTAATTACCACTTTGCTC-
1 TTACTGATTACC-TTTTACTCT
**
13794 TTACTGATTACCTTTTACTGA
1 TTACTGATTACCTTTTACTCT
*
13815 TTACT-ATTTTACTCTTTACTGATTACCT
1 TTACTGA--TTAC-CTTT--T-ACT--CT
*
13843 TCTACTGATTACTATTTTACTC-
1 T-TACTGATTAC-CTTTTACTCT
* **
13865 TTACTGATTACCTTTTGCTGA
1 TTACTGATTACCTTTTACTCT
*
13886 TTAC----TA--TTTTACTTT
1 TTACTGATTACCTTTTACTCT
* *
13901 TTACTGATTACCTTCTTAATTT
1 TTACTGATTACCTT-TTACTCT
*
13923 TTACTGATTACTATTTTACTCT
1 TTACTGATTAC-CTTTTACTCT
*
13945 TTACTGATTACCATTTTACTTT
1 TTACTGATTACC-TTTTACTCT
* * * *
13967 TTAATGATTAGC-ATTGCT-T
1 TTACTGATTACCTTTTACTCT
* *
13986 CTTACTGATTA-CTATTACTTTT
1 -TTACTGATTACCTTTTAC-TCT
*
14008 TTACTGATTACTGTTTTACTC-
1 TTACTGATTAC-CTTTTACTCT
* *
14029 TTACTGATTACATTTTTCTTCT
1 TTACTGATTACCTTTTAC-TCT
* *
14051 TTACTAATTACTCTCTTACTCT
1 TTACTGATTAC-CTTTTACTCT
** *
14073 TT-CTGGCTACCTTTTACTTT
1 TTACTGATTACCTTTTACTCT
* *
14093 TTACTTATTACTATTTTACTC-
1 TTACTGATTAC-CTTTTACTCT
* *
14114 TTACTTATTCCCTTTTACTTCT
1 TTACTGATTACCTTTTAC-TCT
* *
14136 TTACTAATTACTCTCTTACTC-
1 TTACTGATTAC-CTTTTACTCT
14157 TTACTGATTACCTTTTACTTCT
1 TTACTGATTACCTTTTAC-TCT
14179 TT
1 TT
14181 TCCTTAATTA
Statistics
Matches: 331, Mismatches: 59, Indels: 77
0.71 0.13 0.16
Matches are distributed among these distances:
15 10 0.03
17 2 0.01
19 4 0.01
20 56 0.17
21 116 0.35
22 101 0.31
23 22 0.07
25 3 0.01
26 3 0.01
28 9 0.03
29 4 0.01
30 1 0.00
ACGTcount: A:0.21, C:0.21, G:0.05, T:0.53
Consensus pattern (21 bp):
TTACTGATTACCTTTTACTCT
Found at i:13826 original size:71 final size:71
Alignment explanation
Indices: 13774--13916 Score: 214
Period size: 71 Copynumber: 2.0 Consensus size: 71
13764 ATTTTACTCT
* *
13774 TACTAATTACCACTTTGCTCTTACTGATTACCTTTTACTGATTACTATTTTACTCTTTACTGATT
1 TACTAATTACCACTTTACTCTTACTGATTACCTTTTACTGATTACTATTTTACTCATTACTGATT
13839 ACCTTC
66 ACCTTC
* * * * **
13845 TACTGATTACTATTTTACTCTTACTGATTACCTTTTGCTGATTACTATTTTACTTTTTACTGATT
1 TACTAATTACCACTTTACTCTTACTGATTACCTTTTACTGATTACTATTTTACTCATTACTGATT
13910 ACCTTC
66 ACCTTC
13916 T
1 T
13917 TAATTTTTAC
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
71 66 1.00
ACGTcount: A:0.22, C:0.22, G:0.06, T:0.50
Consensus pattern (71 bp):
TACTAATTACCACTTTACTCTTACTGATTACCTTTTACTGATTACTATTTTACTCATTACTGATT
ACCTTC
Found at i:13841 original size:36 final size:36
Alignment explanation
Indices: 13794--13964 Score: 227
Period size: 36 Copynumber: 4.5 Consensus size: 36
13784 CACTTTGCTC
13794 TTACTGATTACCTTTTACTGATTACTATTTTACTCT
1 TTACTGATTACCTTTTACTGATTACTATTTTACTCT
*
13830 TTACTGATTACCTTCTACTGATTACTATTTTACTC-
1 TTACTGATTACCTTTTACTGATTACTATTTTACTCT
* *
13865 TTACTGATTACCTTTTGCTGATTACTATTTTACTTT
1 TTACTGATTACCTTTTACTGATTACTATTTTACTCT
13901 TTACTGATTACCTTCTTAATTTTTACTGATTACTATTTTACTCT
1 TTACTGATTA-C--C-----TTTTACTGATTACTATTTTACTCT
13945 TTACTGATTACCATTTTACT
1 TTACTGATTACC-TTTTACT
13965 TTTTAATGAT
Statistics
Matches: 119, Mismatches: 7, Indels: 17
0.83 0.05 0.12
Matches are distributed among these distances:
35 32 0.27
36 44 0.37
37 8 0.07
39 1 0.01
41 1 0.01
43 1 0.01
44 32 0.27
ACGTcount: A:0.22, C:0.19, G:0.06, T:0.53
Consensus pattern (36 bp):
TTACTGATTACCTTTTACTGATTACTATTTTACTCT
Found at i:14019 original size:15 final size:14
Alignment explanation
Indices: 13994--14034 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 14
13984 TTCTTACTGA
*
13994 TTACTATTACTTTT
1 TTACTATTACTGTT
14008 TTACTGATTACTGTT
1 TTACT-ATTACTGTT
*
14023 TTACTCTTACTG
1 TTACTATTACTG
14035 ATTACATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 11 0.46
15 13 0.54
ACGTcount: A:0.20, C:0.17, G:0.07, T:0.56
Consensus pattern (14 bp):
TTACTATTACTGTT
Found at i:14061 original size:128 final size:127
Alignment explanation
Indices: 13877--14180 Score: 328
Period size: 128 Copynumber: 2.4 Consensus size: 127
13867 ACTGATTACC
* * * * *
13877 TTTTGCTGATTACTATTTTACTTTTTACTGATTACCTTCTTAATT-TTTACTGATTACTATTTTA
1 TTTTACTGATTACTATTTTAC-TCTTACTGATTACCTT-TTACTTCTTTACTAATTACTATCTTA
*
13941 CTCTTTACTGATTACCATTTTACTTTTTAATGATTAGC-ATTGCT-TCTTACTGATT-ACTATTA
64 CTCTTT-CTGACTACC-TTTTACTTTTTAATGATTA-CTATT-CTATCTTACTGATTCACTATTA
14003 CTT
125 CTT
* * * *
14006 TTTTACTGATTACTGTTTTACTCTTACTGATTACATTTTTCTTCTTTACTAATTACTCTCTTACT
1 TTTTACTGATTACTATTTTACTCTTACTGATTACCTTTTACTTCTTTACTAATTACTATCTTACT
* * * * * * *
14071 CTTTCTGGCTACCTTTTACTTTTTACTTATTACTATTTTACTCTTACTTATTCCCTTTTACTT
66 CTTTCTGACTACCTTTTACTTTTTAATGATTACTATTCTA-TCTTACTGATTCACTATTACTT
* * * *
14134 CTTTACTAATTACTCTCTTACTCTTACTGATTACCTTTTACTTCTTT
1 TTTTACTGATTACTATTTTACTCTTACTGATTACCTTTTACTTCTTT
14181 TCCTTAATTA
Statistics
Matches: 147, Mismatches: 23, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
125 2 0.01
126 20 0.14
127 21 0.14
128 85 0.58
129 19 0.13
ACGTcount: A:0.20, C:0.20, G:0.05, T:0.55
Consensus pattern (127 bp):
TTTTACTGATTACTATTTTACTCTTACTGATTACCTTTTACTTCTTTACTAATTACTATCTTACT
CTTTCTGACTACCTTTTACTTTTTAATGATTACTATTCTATCTTACTGATTCACTATTACTT
Found at i:14094 original size:85 final size:85
Alignment explanation
Indices: 13901--14176 Score: 335
Period size: 85 Copynumber: 3.2 Consensus size: 85
13891 ATTTTACTTT
*
13901 TTACTGATTACCTTCTTAATTTTTACTGATTACTATTTTACTCTTTACTGATTACCATTTTACTT
1 TTACTGATTACCTT-TTACTTTTTACTGATTACTATTTTACTC-TTACTGATTA-CATTTTACTT
* * * * *
13966 -TTTAATGATTA-GC-ATTGCTTC
63 CTTTACTAATTACTCTCTTAC-TC
* * *
13987 TTACTGATTA-CTATTACTTTTTTACTGATTACTGTTTTACTCTTACTGATTACATTTTTCTTCT
1 TTACTGATTACCTTTTAC-TTTTTACTGATTACTATTTTACTCTTACTGATTACATTTTACTTCT
14051 TTACTAATTACTCTCTTACTC
65 TTACTAATTACTCTCTTACTC
* ** * * * *
14072 TTTCTGGCTACCTTTTACTTTTTACTTATTACTATTTTACTCTTACTTATTCCCTTTTACTTCTT
1 TTACTGATTACCTTTTACTTTTTACTGATTACTATTTTACTCTTACTGATTACATTTTACTTCTT
14137 TACTAATTACTCTCTTACTC
66 TACTAATTACTCTCTTACTC
14157 TTACTGATTACCTTTTACTT
1 TTACTGATTACCTTTTACTT
14177 CTTTTCCTTA
Statistics
Matches: 163, Mismatches: 22, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
83 9 0.06
84 22 0.13
85 113 0.69
86 19 0.12
ACGTcount: A:0.21, C:0.21, G:0.05, T:0.54
Consensus pattern (85 bp):
TTACTGATTACCTTTTACTTTTTACTGATTACTATTTTACTCTTACTGATTACATTTTACTTCTT
TACTAATTACTCTCTTACTC
Found at i:14335 original size:38 final size:38
Alignment explanation
Indices: 14278--14397 Score: 213
Period size: 38 Copynumber: 3.2 Consensus size: 38
14268 ATTACTATTT
*
14278 TTACCTTGACTCTTAATTATCAATTTTACTGGTTACTA
1 TTACTTTGACTCTTAATTATCAATTTTACTGGTTACTA
*
14316 TTACTTTGACTCTTGATTATCAATTTTACTGGTTACTA
1 TTACTTTGACTCTTAATTATCAATTTTACTGGTTACTA
*
14354 TTACTTTGACTCTTAATTATCAATTTTACTGATTACTA
1 TTACTTTGACTCTTAATTATCAATTTTACTGGTTACTA
14392 TTACTT
1 TTACTT
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 78 1.00
ACGTcount: A:0.26, C:0.17, G:0.07, T:0.50
Consensus pattern (38 bp):
TTACTTTGACTCTTAATTATCAATTTTACTGGTTACTA
Done.