Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019414.1 Corchorus olitorius cultivar O-4 contig19447, 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: 55015
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:2592 original size:12 final size:13
Alignment explanation
Indices: 2571--2600 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
2561 TTTCCTTTCT
2571 TTTTTGCTACATA
1 TTTTTGCTACATA
2584 TTTTT-CTACATA
1 TTTTTGCTACATA
2596 TTTTT
1 TTTTT
2601 TTCAGAGATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.20, C:0.13, G:0.03, T:0.63
Consensus pattern (13 bp):
TTTTTGCTACATA
Found at i:3720 original size:2 final size:2
Alignment explanation
Indices: 3713--3737 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3703 CCATGTCTTT
3713 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
3738 GTAAGCATCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3857 original size:5 final size:5
Alignment explanation
Indices: 3843--3875 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
3833 TTTTGGATTA
3843 ATAT- ATATG ATATG ATATG ATATG ATATG ATAT
1 ATATG ATATG ATATG ATATG ATATG ATATG ATAT
3876 ATACACTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 4 0.14
5 24 0.86
ACGTcount: A:0.42, C:0.00, G:0.15, T:0.42
Consensus pattern (5 bp):
ATATG
Found at i:11165 original size:18 final size:18
Alignment explanation
Indices: 11142--11177 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
11132 CTTTGTTAGT
11142 AAAGAAACAGAAAGCAAA
1 AAAGAAACAGAAAGCAAA
11160 AAAGAAACAGAAAGCAAA
1 AAAGAAACAGAAAGCAAA
11178 CTATATACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.72, C:0.11, G:0.17, T:0.00
Consensus pattern (18 bp):
AAAGAAACAGAAAGCAAA
Found at i:13274 original size:170 final size:170
Alignment explanation
Indices: 12992--13330 Score: 617
Period size: 170 Copynumber: 2.0 Consensus size: 170
12982 TCCAGTTCTA
12992 AATTCCCATTTCAAATACCAAACTAACATATCGTTCAGGAACAACAATGCTTCAAAGGTTTCCCA
1 AATTCCCATTTCAAATACCAAACTAACATATCGTTCAGGAACAACAATGCTTCAAAGGTTTCCCA
*
13057 AGTTAATTTAACAAACAAATAACCGTCAAACACTCCAGCCACACAACAAGTATACTATTTTCAGT
66 AGTTAATTTAACAAACAAATAACCATCAAACACTCCAGCCACACAACAAGTATACTATTTTCAGT
13122 AATTGTAAACTGGGTATTAAGCTATTAACTAAGAAAAAGC
131 AATTGTAAACTGGGTATTAAGCTATTAACTAAGAAAAAGC
* *
13162 AATTCCCGTTTCAAATACCAAATTAACATATCGTTCAGGAACAACAATGCTTCAAAGGTTTCCCA
1 AATTCCCATTTCAAATACCAAACTAACATATCGTTCAGGAACAACAATGCTTCAAAGGTTTCCCA
* *
13227 AGTTAATTTAACAAACAGATTACCATCATAA-ACTCCAGCCACACAACAAGTATACTATTTTCAG
66 AGTTAATTTAACAAACAAATAACCATCA-AACACTCCAGCCACACAACAAGTATACTATTTTCAG
13291 TAATTGTAAACTGGGTATTAAGCTATTAACTAAGAAAAAG
130 TAATTGTAAACTGGGTATTAAGCTATTAACTAAGAAAAAG
13331 AGAAAAAAAT
Statistics
Matches: 163, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
170 161 0.99
171 2 0.01
ACGTcount: A:0.41, C:0.21, G:0.11, T:0.27
Consensus pattern (170 bp):
AATTCCCATTTCAAATACCAAACTAACATATCGTTCAGGAACAACAATGCTTCAAAGGTTTCCCA
AGTTAATTTAACAAACAAATAACCATCAAACACTCCAGCCACACAACAAGTATACTATTTTCAGT
AATTGTAAACTGGGTATTAAGCTATTAACTAAGAAAAAGC
Found at i:22654 original size:8 final size:8
Alignment explanation
Indices: 22641--22678 Score: 58
Period size: 8 Copynumber: 4.8 Consensus size: 8
22631 AAAACCTCTG
*
22641 TTTATTCT
1 TTTAATCT
*
22649 TTTATTCT
1 TTTAATCT
22657 TTTAATCT
1 TTTAATCT
22665 TTTAATCT
1 TTTAATCT
22673 TTTAAT
1 TTTAAT
22679 AGATTCTTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
8 29 1.00
ACGTcount: A:0.21, C:0.11, G:0.00, T:0.68
Consensus pattern (8 bp):
TTTAATCT
Found at i:23970 original size:18 final size:19
Alignment explanation
Indices: 23932--23971 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
23922 CATATTCTCA
*
23932 TTACAATCAGAATCATCTT
1 TTACAATCAAAATCATCTT
23951 TTACAATCAAAATC-TCTT
1 TTACAATCAAAATCATCTT
23969 TTA
1 TTA
23972 TATGGCAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.38, C:0.20, G:0.03, T:0.40
Consensus pattern (19 bp):
TTACAATCAAAATCATCTT
Found at i:24687 original size:5 final size:5
Alignment explanation
Indices: 24677--24710 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
24667 GGATCAAATG
24677 ACATT ACATT ACATT ACATT ACATT ACATT ACAT
1 ACATT ACATT ACATT ACATT ACATT ACATT ACAT
24711 ATAATAAACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.41, C:0.21, G:0.00, T:0.38
Consensus pattern (5 bp):
ACATT
Found at i:48231 original size:6 final size:6
Alignment explanation
Indices: 48222--48249 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
48212 CACGGCCCCG
48222 GCCTCA GCCTCA GCCTCA GCCTCA GCCT
1 GCCTCA GCCTCA GCCTCA GCCTCA GCCT
48250 TTCGCGTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.14, C:0.50, G:0.18, T:0.18
Consensus pattern (6 bp):
GCCTCA
Found at i:51144 original size:6 final size:6
Alignment explanation
Indices: 51127--51160 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
51117 GCCGCAGACT
* *
51127 CAGCCC CGGCCC CAGCCC AAGCCC CAGCCC CAGC
1 CAGCCC CAGCCC CAGCCC CAGCCC CAGCCC CAGC
51161 ATATTTTTTC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.18, C:0.62, G:0.21, T:0.00
Consensus pattern (6 bp):
CAGCCC
Found at i:54260 original size:15 final size:15
Alignment explanation
Indices: 54240--54270 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
54230 AAGATTAATC
54240 TCTTTCAACCAGGAA
1 TCTTTCAACCAGGAA
54255 TCTTTCAACCAGGAA
1 TCTTTCAACCAGGAA
54270 T
1 T
54271 GTAACAGGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.26, G:0.13, T:0.29
Consensus pattern (15 bp):
TCTTTCAACCAGGAA
Done.