Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008829.1 Corchorus capsularis cultivar CVL-1 contig08850, 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: 8018
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.30
Found at i:808 original size:55 final size:55
Alignment explanation
Indices: 682--794 Score: 208
Period size: 55 Copynumber: 2.1 Consensus size: 55
672 AAAAAGGGGC
*
682 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTTAAGCTAATAGTAATCAGTA
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGCTAATAGTAATCAGTA
*
737 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTAATCAGTA
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGCTAATAGTAATCAGTA
792 AAT
1 AAT
795 TGAGTAATCA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
55 56 1.00
ACGTcount: A:0.50, C:0.07, G:0.17, T:0.27
Consensus pattern (55 bp):
AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGCTAATAGTAATCAGTA
Found at i:1174 original size:21 final size:22
Alignment explanation
Indices: 1066--1177 Score: 54
Period size: 21 Copynumber: 5.2 Consensus size: 22
1056 AAGGTATCTA
* *
1066 AAAGGGTAAAATG-GTAATTAGT
1 AAAGAGTAAAA-GAGTAATCAGT
* * *
1088 AAAGAGTGAAATAGTAATCAAT
1 AAAGAGTAAAAGAGTAATCAGT
* **
1110 -AAGAGTAAAAGAGCAAAGAGT
1 AAAGAGTAAAAGAGTAATCAGT
** * **
1131 AACCAGT-AAAGA-AAAAAATGT
1 AAAGAGTAAAAGAGTAATCA-GT
1152 AAAGAGT-AAAGAGTAATCAGT
1 AAAGAGTAAAAGAGTAATCAGT
1173 AAAGA
1 AAAGA
1178 AAACATAGTA
Statistics
Matches: 66, Mismatches: 20, Indels: 9
0.69 0.21 0.09
Matches are distributed among these distances:
20 4 0.06
21 39 0.59
22 23 0.35
ACGTcount: A:0.55, C:0.04, G:0.22, T:0.18
Consensus pattern (22 bp):
AAAGAGTAAAAGAGTAATCAGT
Found at i:4018 original size:14 final size:14
Alignment explanation
Indices: 3999--4050 Score: 54
Period size: 14 Copynumber: 3.7 Consensus size: 14
3989 CAAGAGATAT
*
3999 TTTTCAAAAAATTG
1 TTTTCAAAAAATAG
*
4013 TTTTCAAGAAAA-GG
1 TTTTCAA-AAAATAG
4027 TTTTC-AAAAATGAG
1 TTTTCAAAAAAT-AG
4041 TTTTCAAAAA
1 TTTTCAAAAA
4051 GGTTTAGAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
12 4 0.12
13 1 0.03
14 19 0.59
15 8 0.25
ACGTcount: A:0.44, C:0.08, G:0.12, T:0.37
Consensus pattern (14 bp):
TTTTCAAAAAATAG
Found at i:4043 original size:28 final size:26
Alignment explanation
Indices: 3999--4055 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 26
3989 CAAGAGATAT
*
3999 TTTTCAAAAAATTGTTTTCAAGAAAAGG
1 TTTTCAAAAAATAGTTTTC-A-AAAAGG
4027 TTTTC-AAAAATGAGTTTTCAAAAAGG
1 TTTTCAAAAAAT-AGTTTTCAAAAAGG
4053 TTT
1 TTT
4056 AGAGTTTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
26 9 0.33
27 7 0.26
28 11 0.41
ACGTcount: A:0.40, C:0.07, G:0.14, T:0.39
Consensus pattern (26 bp):
TTTTCAAAAAATAGTTTTCAAAAAGG
Found at i:7024 original size:68 final size:68
Alignment explanation
Indices: 6780--7063 Score: 328
Period size: 68 Copynumber: 4.2 Consensus size: 68
6770 AATGCTTCGA
* * **
6780 CTTTTCCATAAGTCAAACTCGTTTCCGTACGAGT-AAGTTCAAGCCTTGGTTCCATCCAAGCAGC
1 CTTTTCCACAAGCCAAACTCGTTTCCACACGAGTCAA--TCAAGCCTTGGTTCCATCCAAGCAGC
*
6844 AGGGG
64 AAGGG
* * *
6849 CTTTTCCACAAGTCAAACTCGTTTCCACACGAGCCAATCAAGCCTTGGTTCTATCCAAGCAGCAA
1 CTTTTCCACAAGCCAAACTCGTTTCCACACGAGTCAATCAAGCCTTGGTTCCATCCAAGCAGCAA
6914 GGG
66 GGG
* * **
6917 C--TTCCACCAGCCAAACTCGTTTCCACATGAGTCAATTTAGCCTTGGTTCCATCCAAGCAGCAA
1 CTTTTCCACAAGCCAAACTCGTTTCCACACGAGTCAATCAAGCCTTGGTTCCATCCAAGCAGCAA
6980 GGG
66 GGG
* * * * * **
6983 CTTTTCCACAAGCCAAACTCGTTTTCATATGAGTTATTTTAGCCTTGGTTCCATCCAAGCAG---
1 CTTTTCCACAAGCCAAACTCGTTTCCACACGAGTCAATCAAGCCTTGGTTCCATCCAAGCAGCAA
7045 GGG
66 GGG
*
7048 CTTTTCCATAAGCCAA
1 CTTTTCCACAAGCCAA
7064 GTTCATTTCC
Statistics
Matches: 193, Mismatches: 19, Indels: 10
0.87 0.09 0.05
Matches are distributed among these distances:
65 18 0.09
66 59 0.31
68 84 0.44
69 30 0.16
70 2 0.01
ACGTcount: A:0.26, C:0.29, G:0.18, T:0.27
Consensus pattern (68 bp):
CTTTTCCACAAGCCAAACTCGTTTCCACACGAGTCAATCAAGCCTTGGTTCCATCCAAGCAGCAA
GGG
Found at i:7084 original size:134 final size:132
Alignment explanation
Indices: 6821--7084 Score: 323
Period size: 134 Copynumber: 2.0 Consensus size: 132
6811 AGTAAGTTCA
* *
6821 AGCCTTGGTTCCATCCAAGCAGCAGGGGCTTTTCCACAAGTCAAACTCGTTTCCACACGAGCCAA
1 AGCCTTGGTTCCATCCAAGCAGCAAGGGCTTTTCCACAAGCCAAACTCGTTTCCACACGAGCCAA
* * *
6886 TCAAGCCTTGGTTCTATCCAAGCAGCAAGGGCTTCCACCAGCCAAACTCGTTTCCACATGAGTCA
66 TCAAGCCTTGGTTCCATCCAAGCAG--AGGGCTTCCACAAGCCAAACTCATTTCCACATGAGTCA
6951 ATTT
129 ATTT
* * * ** *
6955 AGCCTTGGTTCCATCCAAGCAGCAAGGGCTTTTCCACAAGCCAAACTCGTTTTCATATGAGTTAT
1 AGCCTTGGTTCCATCCAAGCAGCAAGGGCTTTTCCACAAGCCAAACTCGTTTCCACACGAGCCAA
** * ** *
7020 TTTAGCCTTGGTTCCATCCAAGCAG-GGGCTTTTCCATAAGCCAAGTTCATTTCCATATGAAGTC
66 TCAAGCCTTGGTTCCATCCAAGCAGAGGGC--TTCCACAAGCCAAACTCATTTCCACATG-AGTC
7084 A
128 A
7085 GTCTTCCAAG
Statistics
Matches: 110, Mismatches: 17, Indels: 6
0.83 0.13 0.05
Matches are distributed among these distances:
131 4 0.04
133 22 0.20
134 84 0.76
ACGTcount: A:0.26, C:0.28, G:0.19, T:0.27
Consensus pattern (132 bp):
AGCCTTGGTTCCATCCAAGCAGCAAGGGCTTTTCCACAAGCCAAACTCGTTTCCACACGAGCCAA
TCAAGCCTTGGTTCCATCCAAGCAGAGGGCTTCCACAAGCCAAACTCATTTCCACATGAGTCAAT
TT
Found at i:7847 original size:14 final size:14
Alignment explanation
Indices: 7828--7857 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
7818 TTGCATATTA
*
7828 AGTTTAGTCCATTT
1 AGTTTAATCCATTT
7842 AGTTTAATCCATTT
1 AGTTTAATCCATTT
7856 AG
1 AG
7858 ATTACTATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.27, C:0.13, G:0.13, T:0.47
Consensus pattern (14 bp):
AGTTTAATCCATTT
Done.