Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024379.1 Corchorus olitorius cultivar O-4 contig24412, 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: 5867
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:2884 original size:42 final size:42
Alignment explanation
Indices: 2799--2887 Score: 110
Period size: 42 Copynumber: 2.1 Consensus size: 42
2789 ATCTCTGTTG
* * *
2799 ATATTTGTTATACATCCTTCATGCATGGTCCATGTCTTTGTAT
1 ATATATGTTATACATCCATCATGCA-GATCCATGTCTTTGTAT
2842 ATATATGTTCATACATCCATCATGC-GATCCAT-TCCTTTGTAT
1 ATATATGTT-ATACATCCATCATGCAGATCCATGT-CTTTGTAT
2884 ATAT
1 ATAT
2888 GTTCATGCAT
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
41 1 0.02
42 18 0.44
43 8 0.20
44 14 0.34
ACGTcount: A:0.25, C:0.20, G:0.11, T:0.44
Consensus pattern (42 bp):
ATATATGTTATACATCCATCATGCAGATCCATGTCTTTGTAT
Found at i:3516 original size:20 final size:21
Alignment explanation
Indices: 3491--3542 Score: 56
Period size: 19 Copynumber: 2.6 Consensus size: 21
3481 TTTGAGAAAA
3491 AACAAAACAAGAT-TCTTTTG
1 AACAAAACAAGATGTCTTTTG
* *
3511 AAC-AAACAA-TTGTGTTTTG
1 AACAAAACAAGATGTCTTTTG
*
3530 AACAAAAAAAGAT
1 AACAAAACAAGAT
3543 AAGATGAGAT
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
18 1 0.04
19 15 0.60
20 8 0.32
21 1 0.04
ACGTcount: A:0.50, C:0.12, G:0.12, T:0.27
Consensus pattern (21 bp):
AACAAAACAAGATGTCTTTTG
Found at i:4061 original size:15 final size:14
Alignment explanation
Indices: 4038--4101 Score: 60
Period size: 14 Copynumber: 4.5 Consensus size: 14
4028 CAAGACATGT
* *
4038 TTTTAAAGAAAATTG
1 TTTTCAAGAAAA-GG
4053 TTTTCAAGAAAAGG
1 TTTTCAAGAAAAGG
4067 TTTTCAA-AAATAGG
1 TTTTCAAGAAA-AGG
*
4081 TTTTCAA-AAATGAG
1 TTTTCAAGAAAAG-G
4095 TTTTCAA
1 TTTTCAA
4102 AAGGTTTTGG
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
13 4 0.09
14 29 0.66
15 11 0.25
ACGTcount: A:0.42, C:0.06, G:0.14, T:0.38
Consensus pattern (14 bp):
TTTTCAAGAAAAGG
Found at i:4071 original size:14 final size:13
Alignment explanation
Indices: 4052--4103 Score: 68
Period size: 14 Copynumber: 3.8 Consensus size: 13
4042 AAAGAAAATT
4052 GTTTTCAAGAAAAG
1 GTTTTCAA-AAAAG
4066 GTTTTCAAAAATAG
1 GTTTTCAAAAA-AG
*
4080 GTTTTCAAAAATG
1 GTTTTCAAAAAAG
4093 AGTTTTCAAAA
1 -GTTTTCAAAA
4104 GGTTTTGGGT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
13 4 0.11
14 31 0.89
ACGTcount: A:0.42, C:0.08, G:0.15, T:0.35
Consensus pattern (13 bp):
GTTTTCAAAAAAG
Found at i:4409 original size:12 final size:12
Alignment explanation
Indices: 4392--4429 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
4382 CACTTCATCG
4392 AATTCAAATCAA
1 AATTCAAATCAA
*
4404 AATTCAAATTAA
1 AATTCAAATCAA
*
4416 AGTTCAAATCAA
1 AATTCAAATCAA
4428 AA
1 AA
4430 GTGAATCAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.58, C:0.13, G:0.03, T:0.26
Consensus pattern (12 bp):
AATTCAAATCAA
Found at i:4792 original size:12 final size:12
Alignment explanation
Indices: 4777--4819 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
4767 AAAAAACAAA
4777 AAAAAAGAAATG
1 AAAAAAGAAATG
*
4789 AAAAATGAAATG
1 AAAAAAGAAATG
4801 AAAAAATG--ATG
1 AAAAAA-GAAATG
4812 AAAAAAGA
1 AAAAAAGA
4820 GAAATAAGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
10 1 0.04
11 9 0.33
12 16 0.59
13 1 0.04
ACGTcount: A:0.72, C:0.00, G:0.16, T:0.12
Consensus pattern (12 bp):
AAAAAAGAAATG
Found at i:5811 original size:50 final size:50
Alignment explanation
Indices: 5731--5867 Score: 238
Period size: 50 Copynumber: 2.7 Consensus size: 50
5721 CCATCCGAAT
* * * *
5731 ACATAGGCTTTTCAACAAGCCAAGCTCGTTTCCATACGGGTCAATTATCA
1 ACATGGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCA
5781 ACATGGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCA
1 ACATGGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCA
5831 ACATGGGCTTTTCCACAAGCCAAACTCGTTTCCATAC
1 ACATGGGCTTTTCCACAAGCCAAACTCGTTTCCATAC
Statistics
Matches: 83, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
50 83 1.00
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.28
Consensus pattern (50 bp):
ACATGGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCA
Done.