Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014386.1 Corchorus olitorius cultivar O-4 contig14419, 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: 9490
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Found at i:1176 original size:16 final size:16
Alignment explanation
Indices: 1155--1186 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1145 TCATATAAAA
1155 TCTTGTTAATAAGAAT
1 TCTTGTTAATAAGAAT
*
1171 TCTTGTTAATGAGAAT
1 TCTTGTTAATAAGAAT
1187 ATTGATGAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.06, G:0.16, T:0.44
Consensus pattern (16 bp):
TCTTGTTAATAAGAAT
Found at i:2810 original size:31 final size:30
Alignment explanation
Indices: 2774--2846 Score: 94
Period size: 29 Copynumber: 2.4 Consensus size: 30
2764 ATACCCCACA
*
2774 AGTCCCTCTACTTACACAAAAGAATCAATTT
1 AGTCCCTCTACTTACA-AAAACAATCAATTT
* **
2805 GGTCCCTCTAC-TACAAAAACTGTCAATTT
1 AGTCCCTCTACTTACAAAAACAATCAATTT
2834 AGTCCCTCTACTT
1 AGTCCCTCTACTT
2847 GCAACTTTGT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
29 21 0.58
30 5 0.14
31 10 0.28
ACGTcount: A:0.32, C:0.29, G:0.08, T:0.32
Consensus pattern (30 bp):
AGTCCCTCTACTTACAAAAACAATCAATTT
Found at i:7811 original size:16 final size:16
Alignment explanation
Indices: 7790--7821 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
7780 ATGAGTCGAA
7790 ACATATTTTGGTATAC
1 ACATATTTTGGTATAC
*
7806 ACATATTTTGTTATAC
1 ACATATTTTGGTATAC
7822 GGTAAAGGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.31, C:0.12, G:0.09, T:0.47
Consensus pattern (16 bp):
ACATATTTTGGTATAC
Found at i:8737 original size:40 final size:40
Alignment explanation
Indices: 8692--8770 Score: 115
Period size: 40 Copynumber: 2.0 Consensus size: 40
8682 GATAATGATG
*
8692 TGAAAATTTGATAA-CATCATTATGAAATTTCGAAAATCTA
1 TGAAAATTTGATAACCAT-ACTATGAAATTTCGAAAATCTA
* *
8732 TGAAAATTTGATAACCATACTATGAAATTTTGATAATCT
1 TGAAAATTTGATAACCATACTATGAAATTTCGAAAATCT
8771 CCCTATGAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
40 32 0.91
41 3 0.09
ACGTcount: A:0.43, C:0.10, G:0.10, T:0.37
Consensus pattern (40 bp):
TGAAAATTTGATAACCATACTATGAAATTTCGAAAATCTA
Found at i:8756 original size:22 final size:22
Alignment explanation
Indices: 8692--8835 Score: 81
Period size: 22 Copynumber: 6.8 Consensus size: 22
8682 GATAATGATG
*
8692 TGAAAATTTGATAA-CATCATTA
1 TGAAAATTTGATAACCAT-ACTA
8714 TG-AAATTTCGA-AA--AT-CTA
1 TGAAAATTT-GATAACCATACTA
8732 TGAAAATTTGATAACCATACTA
1 TGAAAATTTGATAACCATACTA
* * *
8754 TGAAATTTTGATAATC-TCCCTA
1 TGAAAATTTGATAACCAT-ACTA
* * *
8776 TGAAATTTTGATAATCACACTA
1 TGAAAATTTGATAACCATACTA
* * ***
8798 T-AAAA-TTGGTAGCTGCACTA
1 TGAAAATTTGATAACCATACTA
8818 TGAAAATTTTGATAACCA
1 TGAAAA-TTTGATAACCA
8836 CACCATTAAG
Statistics
Matches: 95, Mismatches: 16, Indels: 21
0.72 0.12 0.16
Matches are distributed among these distances:
18 6 0.06
19 8 0.08
20 13 0.14
21 18 0.19
22 44 0.46
23 6 0.06
ACGTcount: A:0.41, C:0.13, G:0.11, T:0.35
Consensus pattern (22 bp):
TGAAAATTTGATAACCATACTA
Found at i:8788 original size:44 final size:43
Alignment explanation
Indices: 8729--8865 Score: 125
Period size: 44 Copynumber: 3.1 Consensus size: 43
8719 TTTCGAAAAT
* * *
8729 CTATGAAAATTTGATAACCATACTATGAAATTTTGATAATCTCC
1 CTATGAAATTTTGATAACCACACTAT-AAATTTTGATAAACTCC
* * * * *
8773 CTATGAAATTTTGATAATCACACTATAAA-ATTGGT-AGCTGCA
1 CTATGAAATTTTGATAACCACACTATAAATTTTGATAAACT-CC
* * *
8815 CTATGAAAATTTTGATAACCACACCATTAAGTTTCGATAAACTCC
1 CTATG-AAATTTTGATAACCACACTA-TAAATTTTGATAAACTCC
8860 CTATGA
1 CTATGA
8866 GAATGAAACA
Statistics
Matches: 73, Mismatches: 15, Indels: 10
0.74 0.15 0.10
Matches are distributed among these distances:
41 3 0.04
42 10 0.14
43 21 0.29
44 27 0.37
45 9 0.12
46 3 0.04
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.34
Consensus pattern (43 bp):
CTATGAAATTTTGATAACCACACTATAAATTTTGATAAACTCC
Found at i:8987 original size:26 final size:26
Alignment explanation
Indices: 8949--8998 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
8939 ATTTTGTTAG
8949 CCTCCCTAGGAAACTTTGATAACCTC
1 CCTCCCTAGGAAACTTTGATAACCTC
* *
8975 CCTCCCTATGAAATTTTGATAACC
1 CCTCCCTAGGAAACTTTGATAACC
8999 ACACAATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.28, C:0.32, G:0.10, T:0.30
Consensus pattern (26 bp):
CCTCCCTAGGAAACTTTGATAACCTC
Found at i:9064 original size:22 final size:22
Alignment explanation
Indices: 9028--9174 Score: 84
Period size: 22 Copynumber: 6.7 Consensus size: 22
9018 CCTTCGTACA
* *
9028 CTCTAAGAAAATTTGATAACCT
1 CTCTATGAAATTTTGATAACCT
* * * *
9050 TTTTATGAAATTTTGGTAACGT
1 CTCTATGAAATTTTGATAACCT
* * *
9072 CTGTATGGAATTTTGTTAA-CT
1 CTCTATGAAATTTTGATAACCT
* **
9093 ACACTATGACGTTTTGATAACCT
1 -CTCTATGAAATTTTGATAACCT
* * *
9116 TTATATGAAATTTT-AGTAACCA
1 CTCTATGAAATTTTGA-TAACCT
* *
9138 CACTATGAAAATTTGATAACCT
1 CTCTATGAAATTTTGATAACCT
*
9160 -TCCTATGTAATTTTG
1 CT-CTATGAAATTTTG
9175 GTTTGATTGA
Statistics
Matches: 89, Mismatches: 31, Indels: 10
0.68 0.24 0.08
Matches are distributed among these distances:
21 2 0.02
22 84 0.94
23 3 0.03
ACGTcount: A:0.33, C:0.14, G:0.13, T:0.41
Consensus pattern (22 bp):
CTCTATGAAATTTTGATAACCT
Found at i:9108 original size:44 final size:44
Alignment explanation
Indices: 9060--9159 Score: 103
Period size: 44 Copynumber: 2.3 Consensus size: 44
9050 TTTTATGAAA
* * * * *
9060 TTTTGGTAACGTCTGTATGGAATTTT-GTTAACTACACTATGACG
1 TTTTGATAACCTCTATATGAAATTTTAG-TAACCACACTATGACG
* **
9104 TTTTGATAACCTTTATATGAAATTTTAGTAACCACACTATGAAA
1 TTTTGATAACCTCTATATGAAATTTTAGTAACCACACTATGACG
*
9148 ATTTGATAACCT
1 TTTTGATAACCT
9160 TCCTATGTAA
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
44 45 0.98
45 1 0.02
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.40
Consensus pattern (44 bp):
TTTTGATAACCTCTATATGAAATTTTAGTAACCACACTATGACG
Done.