Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014386.1 Corchorus capsularis cultivar CVL-1 contig14407, 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: 22478
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.32
Found at i:10 original size:2 final size:2
Alignment explanation
Indices: 4--37 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1 ATA
4 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
38 GCAATTTGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1998 original size:31 final size:31
Alignment explanation
Indices: 1963--2021 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
1953 ATACCGCGTG
1963 TCACTTTTTGGTACACGTGACGTGCCACGTA
1 TCACTTTTTGGTACACGTGACGTGCCACGTA
*
1994 TCACTTTTTGGTACATGTGACGTGCCAC
1 TCACTTTTTGGTACACGTGACGTGCCAC
2022 TTTTTTGGCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.19, C:0.25, G:0.22, T:0.34
Consensus pattern (31 bp):
TCACTTTTTGGTACACGTGACGTGCCACGTA
Found at i:2068 original size:30 final size:31
Alignment explanation
Indices: 2032--2107 Score: 84
Period size: 30 Copynumber: 2.5 Consensus size: 31
2022 TTTTTTGGCA
* *
2032 CACGTGGCATGTCACATGTCACTTTTTGAT-
1 CACGTGGCATGCCACATGTCACTTTTTAATC
** *
2062 CACGTGGTC-TGCCATGTGTTACTTTTTAATC
1 CACGTGG-CATGCCACATGTCACTTTTTAATC
2093 CACGTGGCATGCCAC
1 CACGTGGCATGCCAC
2108 GTCAGATATC
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
30 24 0.65
31 13 0.35
ACGTcount: A:0.18, C:0.26, G:0.21, T:0.34
Consensus pattern (31 bp):
CACGTGGCATGCCACATGTCACTTTTTAATC
Found at i:3462 original size:3 final size:3
Alignment explanation
Indices: 3454--3484 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
3444 ATAGATCTAG
3454 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
3485 CTATACTAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:6852 original size:25 final size:24
Alignment explanation
Indices: 6799--6851 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 24
6789 TACATCAACT
* *
6799 AAACTACTAAACATATTATTGCCAA
1 AAACTACTAAACATATTACTACC-A
6824 AAACTACTAAACATATTAAACTACCA
1 AAACTACTAAACATATT--ACTACCA
6850 AA
1 AA
6852 CAAACATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 17 0.71
26 3 0.12
27 4 0.17
ACGTcount: A:0.53, C:0.21, G:0.02, T:0.25
Consensus pattern (24 bp):
AAACTACTAAACATATTACTACCA
Found at i:6932 original size:7 final size:7
Alignment explanation
Indices: 6922--6946 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
6912 CAACTTTCAA
6922 CCTCAGG
1 CCTCAGG
6929 CCTCAGG
1 CCTCAGG
6936 CCTCAGG
1 CCTCAGG
6943 CCTC
1 CCTC
6947 TCCTTCCTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.48, G:0.24, T:0.16
Consensus pattern (7 bp):
CCTCAGG
Found at i:10648 original size:178 final size:178
Alignment explanation
Indices: 10344--10673 Score: 502
Period size: 178 Copynumber: 1.9 Consensus size: 178
10334 TAAGCACAAA
* * * *
10344 TTATGTAATATTAAGTAGACCGTCTATTTCCGTTAATCGAAACAACTAATTCTTTGGAAGCATTT
1 TTATATAATATTAAGTAGACCGTCTATTCCCGTTAACCGAAACAACAAATTCTTTGGAAGCATTT
* *
10409 TTTATACCTTGAACGTTAAATTTAATTTTCGAGTCCTTCATGAAAGTTGTAGATCATGGAACAAC
66 TTGATACCTTGAACATTAAATTTAATTTTCGAGTCCTTCATGAAAGTTGTAGATCATGGAACAAC
*
10474 CTTTCAAGAGACACTTGAATCATCTCAATCAGACATCTAGAGTAAAAG
131 CTTTCAAGAGACACTTAAATCATCTCAATCAGACATCTAGAGTAAAAG
* *
10522 TTATATAATATTAAGTGGACTGTCTATTCCCGTTAACCGAAACAACAAATT-TTTCGGAAGCATT
1 TTATATAATATTAAGTAGACCGTCTATTCCCGTTAACCGAAACAACAAATTCTTT-GGAAGCATT
*
10586 TTTGATA-CTTGAAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATCATGGAACA
65 TTTGATACCTTG-AACATTAAATTTAATTTTCGAGTCCTTCATGAAAGTTGTAGATCATGGAACA
* * * *
10650 ATCTTTTAATAGACATTTAAATCA
129 ACCTTTCAAGAGACACTTAAATCA
10674 CCTTAATCGG
Statistics
Matches: 136, Mismatches: 14, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
177 7 0.05
178 129 0.95
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (178 bp):
TTATATAATATTAAGTAGACCGTCTATTCCCGTTAACCGAAACAACAAATTCTTTGGAAGCATTT
TTGATACCTTGAACATTAAATTTAATTTTCGAGTCCTTCATGAAAGTTGTAGATCATGGAACAAC
CTTTCAAGAGACACTTAAATCATCTCAATCAGACATCTAGAGTAAAAG
Found at i:20600 original size:22 final size:21
Alignment explanation
Indices: 20557--20600 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
20547 TATATACTTA
*
20557 TTGCTAAACATCGTCCCCTTT
1 TTGCTAAACACCGTCCCCTTT
*
20578 TTGCTAAATACCG-CTCCCTTT
1 TTGCTAAACACCGTC-CCCTTT
20599 TT
1 TT
20601 ACACTTTTGC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 19 0.95
ACGTcount: A:0.18, C:0.32, G:0.09, T:0.41
Consensus pattern (21 bp):
TTGCTAAACACCGTCCCCTTT
Found at i:20774 original size:26 final size:26
Alignment explanation
Indices: 20745--20812 Score: 109
Period size: 26 Copynumber: 2.6 Consensus size: 26
20735 TTCCTTCATT
20745 TTAATCATAAACTAATTAAATACTAA
1 TTAATCATAAACTAATTAAATACTAA
* *
20771 TTAATAATAAACTAATTAGATACTAA
1 TTAATCATAAACTAATTAAATACTAA
*
20797 TTAAACATAAACTAAT
1 TTAATCATAAACTAAT
20813 AAACTAAGTA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.54, C:0.10, G:0.01, T:0.34
Consensus pattern (26 bp):
TTAATCATAAACTAATTAAATACTAA
Found at i:20836 original size:52 final size:51
Alignment explanation
Indices: 20745--20862 Score: 122
Period size: 52 Copynumber: 2.4 Consensus size: 51
20735 TTCCTTCATT
* *
20745 TTAATCATAAACTAATTAAATACTAATTAATAATAAACTAATTAGATACTAA
1 TTAAACATAAACTAATTAAATACTAATTAATAATAAACTAATTA-AAACTAA
* * *
20797 TTAAACATAAACTAA-TAAACTAAGTAATT-TTAATTAACTAATTAAAACTAA
1 TTAAACATAAACTAATTAAA-T-ACTAATTAATAATAAACTAATTAAAACTAA
20848 -T---CATAAACTAATTAA
1 TTAAACATAAACTAATTAA
20863 TATTAAAAAA
Statistics
Matches: 58, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
47 10 0.17
48 3 0.05
50 1 0.02
51 10 0.17
52 28 0.48
53 6 0.10
ACGTcount: A:0.54, C:0.10, G:0.02, T:0.34
Consensus pattern (51 bp):
TTAAACATAAACTAATTAAATACTAATTAATAATAAACTAATTAAAACTAA
Found at i:20894 original size:11 final size:10
Alignment explanation
Indices: 20867--20893 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
20857 AATTAATATT
20867 AAAAAAATTA
1 AAAAAAATTA
20877 AAAAAAATTA
1 AAAAAAATTA
20887 AAAAAAA
1 AAAAAAA
20894 AAAAAAGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (10 bp):
AAAAAAATTA
Done.