Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012441.1 Corchorus olitorius cultivar O-4 contig12474, 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: 29147
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:932 original size:139 final size:139
Alignment explanation
Indices: 682--959 Score: 511
Period size: 139 Copynumber: 2.0 Consensus size: 139
672 GAAAAATTCT
682 GGTAAATGTAACTAATCATAATGAATATGACTTAAGCAGTAGCTGTATCAACTCACAATCTAAAA
1 GGTAAATGTAACTAATCATAATGAATATGACTTAAGCAGTAGCTGTATCAACTCACAATCTAAAA
*
747 ATACATCAACCATATTGCTAATGTTGGCAAATTCCTAGAAAGATTTGTCAATTCATCTTTTAAAA
66 ATACATCAACCATATTGCTAATGCTGGCAAATTCCTAGAAAGATTTGTCAATTCATCTTTTAAAA
812 CATTCACTC
131 CATTCACTC
* * * *
821 GGTAAATGTAACTAATCATGATGAATATGACTTAAGTAGTAGCTGTATCAACTCACAATCTAGAC
1 GGTAAATGTAACTAATCATAATGAATATGACTTAAGCAGTAGCTGTATCAACTCACAATCTAAAA
886 ATACATCAACCATATTGCTAATGCTGGCAAATTCCTAGAAAGATTTGTCAATTCATCTTTTAAAA
66 ATACATCAACCATATTGCTAATGCTGGCAAATTCCTAGAAAGATTTGTCAATTCATCTTTTAAAA
951 CATTCACTC
131 CATTCACTC
960 AACAAAGAGT
Statistics
Matches: 134, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
139 134 1.00
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.32
Consensus pattern (139 bp):
GGTAAATGTAACTAATCATAATGAATATGACTTAAGCAGTAGCTGTATCAACTCACAATCTAAAA
ATACATCAACCATATTGCTAATGCTGGCAAATTCCTAGAAAGATTTGTCAATTCATCTTTTAAAA
CATTCACTC
Found at i:1209 original size:147 final size:147
Alignment explanation
Indices: 942--1238 Score: 594
Period size: 147 Copynumber: 2.0 Consensus size: 147
932 GTCAATTCAT
942 CTTTTAAAACATTCACTCAACAAAGAGTCAAGGTATCCCCTAACTGATAATCCCATCATTTGAGC
1 CTTTTAAAACATTCACTCAACAAAGAGTCAAGGTATCCCCTAACTGATAATCCCATCATTTGAGC
1007 TATTCATGACTTTTATTTCTTTAAACAGGCATCGTTGATATAGATTCCAACTTTGTAGCTGGTTA
66 TATTCATGACTTTTATTTCTTTAAACAGGCATCGTTGATATAGATTCCAACTTTGTAGCTGGTTA
1072 GGATTCGAACTCGGTGC
131 GGATTCGAACTCGGTGC
1089 CTTTTAAAACATTCACTCAACAAAGAGTCAAGGTATCCCCTAACTGATAATCCCATCATTTGAGC
1 CTTTTAAAACATTCACTCAACAAAGAGTCAAGGTATCCCCTAACTGATAATCCCATCATTTGAGC
1154 TATTCATGACTTTTATTTCTTTAAACAGGCATCGTTGATATAGATTCCAACTTTGTAGCTGGTTA
66 TATTCATGACTTTTATTTCTTTAAACAGGCATCGTTGATATAGATTCCAACTTTGTAGCTGGTTA
1219 GGATTCGAACTCGGTGC
131 GGATTCGAACTCGGTGC
1236 CTT
1 CTT
1239 CCACAAAAAG
Statistics
Matches: 150, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
147 150 1.00
ACGTcount: A:0.29, C:0.21, G:0.15, T:0.34
Consensus pattern (147 bp):
CTTTTAAAACATTCACTCAACAAAGAGTCAAGGTATCCCCTAACTGATAATCCCATCATTTGAGC
TATTCATGACTTTTATTTCTTTAAACAGGCATCGTTGATATAGATTCCAACTTTGTAGCTGGTTA
GGATTCGAACTCGGTGC
Found at i:14776 original size:44 final size:46
Alignment explanation
Indices: 14726--14816 Score: 168
Period size: 44 Copynumber: 2.0 Consensus size: 46
14716 ATGCTTTGTA
14726 AGAATGTTCCAATCATATTGATAT-A-ATAATCATGCTAGATATAT
1 AGAATGTTCCAATCATATTGATATAATATAATCATGCTAGATATAT
14770 AGAATGTTCCAATCATATTGATATAATATAATCATGCTAGATATAT
1 AGAATGTTCCAATCATATTGATATAATATAATCATGCTAGATATAT
14816 A
1 A
14817 TAATAATCAT
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
44 24 0.53
45 1 0.02
46 20 0.44
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.36
Consensus pattern (46 bp):
AGAATGTTCCAATCATATTGATATAATATAATCATGCTAGATATAT
Found at i:14822 original size:22 final size:22
Alignment explanation
Indices: 14746--14826 Score: 69
Period size: 22 Copynumber: 3.6 Consensus size: 22
14736 AATCATATTG
14746 ATATAATAATCATGCTAGATAT
1 ATATAATAATCATGCTAGATAT
* * *
14768 ATAGAATGTTCCAATCAT-ATTGATAT
1 ATATAA---T--AATCATGCTAGATAT
14794 A-AT-ATAATCATGCTAGATAT
1 ATATAATAATCATGCTAGATAT
14814 ATATAATAATCAT
1 ATATAATAATCAT
14827 TCTGTATTCT
Statistics
Matches: 45, Mismatches: 6, Indels: 16
0.67 0.09 0.24
Matches are distributed among these distances:
19 6 0.13
20 7 0.16
21 3 0.07
22 13 0.29
24 1 0.02
25 2 0.04
26 7 0.16
27 6 0.13
ACGTcount: A:0.44, C:0.10, G:0.09, T:0.37
Consensus pattern (22 bp):
ATATAATAATCATGCTAGATAT
Found at i:19350 original size:4 final size:4
Alignment explanation
Indices: 19341--19374 Score: 54
Period size: 4 Copynumber: 9.0 Consensus size: 4
19331 AATATAGCAT
19341 TAAA TAAA TAAA TAAA T--A TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
19375 AATTCTACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
4 26 0.93
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
TAAA
Found at i:19363 original size:14 final size:14
Alignment explanation
Indices: 19344--19377 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
19334 ATAGCATTAA
19344 ATAAATAAATAAAT
1 ATAAATAAATAAAT
19358 ATAAATAAATAAAT
1 ATAAATAAATAAAT
*
19372 AAAAAT
1 ATAAAT
19378 TCTACTTATG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (14 bp):
ATAAATAAATAAAT
Found at i:22179 original size:13 final size:13
Alignment explanation
Indices: 22161--22186 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
22151 TATTTTTATA
22161 AATATTTTAATTT
1 AATATTTTAATTT
22174 AATATTTTAATTT
1 AATATTTTAATTT
22187 TAAAAATTGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
AATATTTTAATTT
Found at i:27092 original size:2 final size:2
Alignment explanation
Indices: 27085--27138 Score: 64
Period size: 2 Copynumber: 29.5 Consensus size: 2
27075 TAGTCTATCC
*
27085 AT AT AT AT AT AT AT AT AT TT AT -T AT A- AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
27124 -T AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT A
27139 ATAATAATAA
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
1 5 0.11
2 40 0.89
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:27102 original size:12 final size:12
Alignment explanation
Indices: 27085--27138 Score: 64
Period size: 11 Copynumber: 4.9 Consensus size: 12
27075 TAGTCTATCC
27085 ATATATATATAT
1 ATATATATATAT
*
27097 ATATATTTAT-T
1 ATATATATATAT
27108 ATA-ATATATAT
1 ATATATATATAT
27119 -TATAT-TATAT
1 ATATATATATAT
27129 ATATA-ATATA
1 ATATATATATA
27139 ATAATAATAA
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
10 12 0.33
11 15 0.42
12 9 0.25
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
ATATATATATAT
Found at i:27148 original size:14 final size:15
Alignment explanation
Indices: 27085--27150 Score: 53
Period size: 16 Copynumber: 4.2 Consensus size: 15
27075 TAGTCTATCC
27085 ATATATATATATATATA
1 ATATA-ATA-ATATATA
* *
27102 TTTATTATAATATATA
1 -ATATAATAATATATA
* *
27118 TTATATTATATATATA
1 ATATAATA-ATATATA
27134 ATATAATAATA-ATA
1 ATATAATAATATATA
27148 ATA
1 ATA
27151 ACAAATCTAT
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
14 6 0.15
15 9 0.22
16 20 0.49
17 3 0.07
18 3 0.07
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATATAATAATATATA
Done.