Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01000949.1 Corchorus capsularis cultivar CVL-1 contig00949, 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: 20686
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.29
Found at i:108 original size:22 final size:22
Alignment explanation
Indices: 60--108 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
50 AATTCATAAA
*
60 AAATAAATATCAAGGTTAAAAT
1 AAATAAATATCAAGGTCAAAAT
* *
82 AAATAAATAT-AATGTCAATAT
1 AAATAAATATCAAGGTCAAAAT
103 ATAATA
1 A-AATA
109 TATGAATATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 9 0.39
22 14 0.61
ACGTcount: A:0.59, C:0.04, G:0.06, T:0.31
Consensus pattern (22 bp):
AAATAAATATCAAGGTCAAAAT
Found at i:7471 original size:18 final size:18
Alignment explanation
Indices: 7448--7487 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
7438 CCTCGCGTTT
7448 ACTTTTTTGCAAATCTTG
1 ACTTTTTTGCAAATCTTG
7466 ACTTTTTTGCAAATCTTG
1 ACTTTTTTGCAAATCTTG
7484 ACTT
1 ACTT
7488 GTGGTTTATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.23, C:0.17, G:0.10, T:0.50
Consensus pattern (18 bp):
ACTTTTTTGCAAATCTTG
Found at i:17723 original size:16 final size:16
Alignment explanation
Indices: 17704--17781 Score: 61
Period size: 16 Copynumber: 4.9 Consensus size: 16
17694 GTGCTTTCTA
17704 GGGAGAGTGATTCCAT
1 GGGAGAGTGATTCCAT
* * *
17720 GGGAGAATCACTCCA-
1 GGGAGAGTGATTCCAT
* **
17735 AGGAGAGTGATTAAAT
1 GGGAGAGTGATTCCAT
* *
17751 GGTAGAGTTCATTCCAT
1 GGGAGAG-TGATTCCAT
17768 -GGAGAGTGATTCCA
1 GGGAGAGTGATTCCA
17782 AGGAAAGTGC
Statistics
Matches: 44, Mismatches: 16, Indels: 5
0.68 0.25 0.08
Matches are distributed among these distances:
15 16 0.36
16 22 0.50
17 6 0.14
ACGTcount: A:0.31, C:0.14, G:0.31, T:0.24
Consensus pattern (16 bp):
GGGAGAGTGATTCCAT
Found at i:17740 original size:31 final size:32
Alignment explanation
Indices: 17705--17781 Score: 93
Period size: 32 Copynumber: 2.4 Consensus size: 32
17695 TGCTTTCTAG
17705 GGAGAGTGATTCCATGGGAGA-ATCACTCCAA
1 GGAGAGTGATTCCATGGGAGAGATCACTCCAA
** * * * *
17736 GGAGAGTGATTAAATGGTAGAGTTCATTCCAT
1 GGAGAGTGATTCCATGGGAGAGATCACTCCAA
17768 GGAGAGTGATTCCA
1 GGAGAGTGATTCCA
17782 AGGAAAGTGC
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
31 18 0.49
32 19 0.51
ACGTcount: A:0.31, C:0.14, G:0.30, T:0.25
Consensus pattern (32 bp):
GGAGAGTGATTCCATGGGAGAGATCACTCCAA
Found at i:17800 original size:31 final size:31
Alignment explanation
Indices: 17683--17801 Score: 91
Period size: 31 Copynumber: 3.8 Consensus size: 31
17673 GTTTGTTACT
* * *
17683 TTCCAAGGAAAGTGCTTTCTAGGGAGAGTGA
1 TTCCAAGGAAAGTGCATTCCATGGAGAGTGA
* * *
17714 TTCCATGGGAGAA-T-CACTCCAAGGAGAGTGA
1 TTCCA-AGGA-AAGTGCATTCCATGGAGAGTGA
* * *
17745 TT-AAATGGTAGAGTTCATTCCATGGAGAGTGA
1 TTCCAA-GG-AAAGTGCATTCCATGGAGAGTGA
*
17777 TTCCAAGGAAAGTGCTTTCCATGGA
1 TTCCAAGGAAAGTGCATTCCATGGA
17802 AAGTCTCTCC
Statistics
Matches: 67, Mismatches: 14, Indels: 14
0.71 0.15 0.15
Matches are distributed among these distances:
30 4 0.06
31 36 0.54
32 23 0.34
33 4 0.06
ACGTcount: A:0.30, C:0.15, G:0.29, T:0.26
Consensus pattern (31 bp):
TTCCAAGGAAAGTGCATTCCATGGAGAGTGA
Found at i:17802 original size:16 final size:15
Alignment explanation
Indices: 17761--17805 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
17751 GGTAGAGTTC
*
17761 ATTCCATGGAGAGTG
1 ATTCCATGGAAAGTG
*
17776 ATTCCAAGGAAAGTG
1 ATTCCATGGAAAGTG
*
17791 CTTTCCATGGAAAGT
1 -ATTCCATGGAAAGT
17806 CTCTCCATAC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
15 13 0.52
16 12 0.48
ACGTcount: A:0.31, C:0.16, G:0.27, T:0.27
Consensus pattern (15 bp):
ATTCCATGGAAAGTG
Found at i:17953 original size:53 final size:53
Alignment explanation
Indices: 17888--18041 Score: 200
Period size: 53 Copynumber: 2.9 Consensus size: 53
17878 TCCTACCTTT
* *
17888 TTTTAGTTTAACCAAACCATGGAAAGTGTTTCCATCTTTTACTTTCCCACATG
1 TTTTAATTTAACCAAACTATGGAAAGTGTTTCCATCTTTTACTTTCCCACATG
* * * *
17941 TTTTATTTTAACCAAACTATAGAAAGTGTTTCCATCATTTACTTTCCCGCATG
1 TTTTAATTTAACCAAACTATGGAAAGTGTTTCCATCTTTTACTTTCCCACATG
* * * * *
17994 TTTTAATTCAACCAAACTATGGACAGTCTTTCCACCCTATTACTTTCC
1 TTTTAATTTAACCAAACTATGGAAAGTGTTTCCA-TCTTTTACTTTCC
18042 ATGTAAAATA
Statistics
Matches: 87, Mismatches: 13, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
53 77 0.89
54 10 0.11
ACGTcount: A:0.27, C:0.24, G:0.09, T:0.40
Consensus pattern (53 bp):
TTTTAATTTAACCAAACTATGGAAAGTGTTTCCATCTTTTACTTTCCCACATG
Found at i:18497 original size:220 final size:222
Alignment explanation
Indices: 18114--18555 Score: 816
Period size: 220 Copynumber: 2.0 Consensus size: 222
18104 CAAATTACAG
*
18114 AGAGAAACCCTATCAACTGCTGTTTAATATGTTATGTTGAACCAAAAAATATTACTATTTTTACA
1 AGAGAAACCCTATCAACTGCAGTTTAATATGTTATGTTGAACCAAAAAATATTACTATTTTTACA
18179 GAAAATAAATAAAGCCTTAGTAATTAGTTCATCTATAGGTCTCTGTCAATGCAACAAAAAGACCT
66 GAAAATAAATAAAGCCTTAGTAATTAGTTCATCTATAGGTCTCTGTCAATGCAACAAAAAGACCT
* *
18244 GAAATTCTGTCATAAGAATCCATATGTGCAACGGATGTTCTCAACAAGGAACAGAAAATGAGATA
131 GAAATTCTGTCATAAGAATACATATGTGCAACGGAGGTTCTCAACAAGGAACAGAAAATGAGATA
18309 TAAACAAT-GTGTATTTTTTACATTCT
196 TAAACAATGGTGTATTTTTTACATTCT
18335 AGAGAAACCCTATCAACTGCAGTTTAATATGTTATGTTGAACC-AAAAATATTACTATTTTTACA
1 AGAGAAACCCTATCAACTGCAGTTTAATATGTTATGTTGAACCAAAAAATATTACTATTTTTACA
* *
18399 GAAAATAAATGAAGCCTTAGTAATTAGTTCATCTATAGGTCTCTGTCAATGCAGCAAAAAGACCT
66 GAAAATAAATAAAGCCTTAGTAATTAGTTCATCTATAGGTCTCTGTCAATGCAACAAAAAGACCT
*
18464 GAAATTCTGTCATAAGAATACATGTGTGCAACGGAGGTTCTCAACAAGGAACAGAAAATGAGATA
131 GAAATTCTGTCATAAGAATACATATGTGCAACGGAGGTTCTCAACAAGGAACAGAAAATGAGATA
18529 TAAACAATGGTGTATTTTTTACATTCT
196 TAAACAATGGTGTATTTTTTACATTCT
18556 CAATCATATA
Statistics
Matches: 214, Mismatches: 6, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
220 154 0.72
221 60 0.28
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.31
Consensus pattern (222 bp):
AGAGAAACCCTATCAACTGCAGTTTAATATGTTATGTTGAACCAAAAAATATTACTATTTTTACA
GAAAATAAATAAAGCCTTAGTAATTAGTTCATCTATAGGTCTCTGTCAATGCAACAAAAAGACCT
GAAATTCTGTCATAAGAATACATATGTGCAACGGAGGTTCTCAACAAGGAACAGAAAATGAGATA
TAAACAATGGTGTATTTTTTACATTCT
Done.