Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016593.1 Corchorus olitorius cultivar O-4 contig16626, 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: 63767
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1975 original size:129 final size:134
Alignment explanation
Indices: 1826--2068 Score: 343
Period size: 129 Copynumber: 1.8 Consensus size: 134
1816 CATTGTTTAA
* * * *
1826 ACTTTTATAGTTTTATTCAACTAAAAACTCTAATTTTATTTATTTAAATCTAATAT-C-T-T-TA
1 ACTTTTACAGTTTTACTCAACTAAAAAATCTAATTTTATTTAATTAAATCTAATATCCTTATCTA
1887 -TGATTTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATATATATTAGAATTTTTTAA
66 TTGATTTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATATATATTAGAATTTTTTAA
1951 ATAT
131 ATAT
*
1955 ACTTTTACAGTTTTACTCAACTAAAAAATCTATTTTTATTTAATTAAATCTAATATCCTTATACC
1 ACTTTTACAGTTTTACTCAACTAAAAAATCTAATTTTATTTAATTAAATCTAATATCCTTAT--C
* * * *
2020 TATTTTATTTTTACCATTTTATTATTTTATTTCAAAAACTTATATATAT
64 TA-TTGATTTTTACCATTTTACTATTTTAATTAAAAAACTTATATATAT
2069 TAGAATTTTT
Statistics
Matches: 97, Mismatches: 9, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
129 51 0.53
130 1 0.01
131 1 0.01
132 1 0.01
135 2 0.02
137 41 0.42
ACGTcount: A:0.37, C:0.11, G:0.02, T:0.51
Consensus pattern (134 bp):
ACTTTTACAGTTTTACTCAACTAAAAAATCTAATTTTATTTAATTAAATCTAATATCCTTATCTA
TTGATTTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATATATATTAGAATTTTTTAA
ATAT
Found at i:10647 original size:2 final size:2
Alignment explanation
Indices: 10640--10673 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
10630 AGCAAAGCAA
10640 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10674 TTGCAACCTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:14107 original size:21 final size:20
Alignment explanation
Indices: 14059--14107 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 20
14049 TATTATATAG
*
14059 ATGAGATT-ATATTATACAA
1 ATGAGATTAATACTATACAA
* *
14078 ATCAAATTAATTACTATACAA
1 ATGAGATTAA-TACTATACAA
14099 ATGAGATTA
1 ATGAGATTA
14108 TTATAACAAC
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
19 6 0.26
20 1 0.04
21 16 0.70
ACGTcount: A:0.49, C:0.08, G:0.08, T:0.35
Consensus pattern (20 bp):
ATGAGATTAATACTATACAA
Found at i:22658 original size:19 final size:20
Alignment explanation
Indices: 22634--22691 Score: 64
Period size: 19 Copynumber: 2.9 Consensus size: 20
22624 TTGTTTAACA
22634 ACTGTACAGATGAGATTA-C
1 ACTGTACAGATGAGATTAGC
* * *
22653 ACTGTACAGATTAGAATAGGT
1 ACTGTACAGATGAGATTA-GC
*
22674 ACTGTACAAATGAGATTA
1 ACTGTACAGATGAGATTA
22692 TTAGAATAGC
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
19 16 0.52
21 15 0.48
ACGTcount: A:0.40, C:0.12, G:0.21, T:0.28
Consensus pattern (20 bp):
ACTGTACAGATGAGATTAGC
Found at i:29169 original size:6 final size:6
Alignment explanation
Indices: 29160--29201 Score: 66
Period size: 6 Copynumber: 7.0 Consensus size: 6
29150 TGGAGTTACT
* *
29160 GGTGCT GGTGCT GGTGCC GGTGCC GGTGCC GGTGCC GGTGCC
1 GGTGCC GGTGCC GGTGCC GGTGCC GGTGCC GGTGCC GGTGCC
29202 TCATGTTCGG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.00, C:0.29, G:0.50, T:0.21
Consensus pattern (6 bp):
GGTGCC
Found at i:34642 original size:39 final size:40
Alignment explanation
Indices: 34586--34666 Score: 128
Period size: 39 Copynumber: 2.0 Consensus size: 40
34576 TTTAATTCCT
34586 ATGTAATATATATAATAACTAAAATACTTACATCAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATCAATTAA
* * *
34626 ATGTAATA-CTATAATAACTGAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATCAATTAA
34665 AT
1 AT
34667 TCTTAGGTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
39 30 0.79
40 8 0.21
ACGTcount: A:0.51, C:0.10, G:0.04, T:0.36
Consensus pattern (40 bp):
ATGTAATATATATAATAACTAAAATACTTACATCAATTAA
Found at i:34696 original size:24 final size:23
Alignment explanation
Indices: 34657--34702 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 23
34647 AATACTTACA
34657 TTAATTAAATTCTTAGGTATTTT
1 TTAATTAAATTCTTAGGTATTTT
*
34680 TTAATTCAAATTTTTAGGTATTT
1 TTAATT-AAATTCTTAGGTATTT
34703 GTGCAAACAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 6 0.29
24 15 0.71
ACGTcount: A:0.30, C:0.04, G:0.09, T:0.57
Consensus pattern (23 bp):
TTAATTAAATTCTTAGGTATTTT
Found at i:35180 original size:202 final size:203
Alignment explanation
Indices: 34773--35182 Score: 680
Period size: 204 Copynumber: 2.0 Consensus size: 203
34763 TTCCTTAATA
* *
34773 ATAAATAAATCGGATCTTAATATCTTTTATGATTTTGAAATTTTGTTTGACATTGATCTAATTTA
1 ATAAATAAATCGGATCTTAATATCTTTTATAATTTTGAAATTTTATTTGACATTGATCTAATTTA
* *
34838 GTTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTTGGTATAGTTCTATACATATAATAGT
66 ATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTTGGTATAGTTCTATACATATAATAAT
* *
34903 AATGTGTTGTATCTTATTCACTACAAATTTGTTAGTAATCTTAGACTTGAAAAATTAATAACATT
131 AATGTGTTGCATCTTATTCACTACAAATTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATT
34968 CACCATTG
196 CACCATTG
* * * *
34976 ATAAATAATTTGGATCTTTAATTTCTTTTATAATTTTGAAATTTTATTTGACATTGATCTGATTT
1 ATAAATAAATCGGATC-TTAATATCTTTTATAATTTTGAAATTTTATTTGACATTGATCTAATTT
* *
35041 AATTTAATAAATCAACCACTAATGTTCAACTACTTTTTTTTGGTATAGTT-T-TATATATAATAA
65 AATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTTGGTATAGTTCTATACATATAATAA
*
35104 TAATGTGTTGCATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACAT
130 TAATGTGTTGCATCTTATTCACTACAAATTTGTTAGTAATCTTAGACTTAAAAAATTAATAACAT
35169 TCACCATTG
195 TCACCATTG
35178 ATAAA
1 ATAAA
35183 GTTATTAAGC
Statistics
Matches: 193, Mismatches: 13, Indels: 3
0.92 0.06 0.01
Matches are distributed among these distances:
202 86 0.45
203 15 0.08
204 92 0.48
ACGTcount: A:0.35, C:0.11, G:0.09, T:0.44
Consensus pattern (203 bp):
ATAAATAAATCGGATCTTAATATCTTTTATAATTTTGAAATTTTATTTGACATTGATCTAATTTA
ATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTTGGTATAGTTCTATACATATAATAAT
AATGTGTTGCATCTTATTCACTACAAATTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATT
CACCATTG
Found at i:35723 original size:36 final size:36
Alignment explanation
Indices: 35676--35745 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
35666 GAGATTTTGG
* *
35676 AGAAATATGATAATCAAAATTACAAAAAATGTAATA
1 AGAAATATGATAACCAAAATCACAAAAAATGTAATA
*
35712 AGAAATATGATAACCAAAATCACAAAAGATGTAA
1 AGAAATATGATAACCAAAATCACAAAAAATGTAA
35746 GGTTATTGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.60, C:0.09, G:0.10, T:0.21
Consensus pattern (36 bp):
AGAAATATGATAACCAAAATCACAAAAAATGTAATA
Found at i:37104 original size:58 final size:58
Alignment explanation
Indices: 37006--37115 Score: 161
Period size: 58 Copynumber: 1.9 Consensus size: 58
36996 ATCATGTCTC
*
37006 GGTCCTAAAACGTCTTTTTTAGCCATCTAATAAAAAAACATGTCACTCGATAAGCCTT
1 GGTCCGAAAACGTCTTTTTTAGCCATCTAATAAAAAAACATGTCACTCGATAAGCCTT
* *
37064 GGTCCGAAAACGTCTTTTTTTATG-CATCTAAT-AAAGAACATGTCACTTGATA
1 GGTCCGAAAACGTC-TTTTTTA-GCCATCTAATAAAAAAACATGTCACTCGATA
37116 TTTGATTAAT
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
58 31 0.66
59 15 0.32
60 1 0.02
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.33
Consensus pattern (58 bp):
GGTCCGAAAACGTCTTTTTTAGCCATCTAATAAAAAAACATGTCACTCGATAAGCCTT
Found at i:48458 original size:12 final size:13
Alignment explanation
Indices: 48441--48474 Score: 52
Period size: 12 Copynumber: 2.6 Consensus size: 13
48431 TCTCACTCCC
48441 ATGAAATATGAA-
1 ATGAAATATGAAG
48453 ATGAAATATGAATG
1 ATGAAATATGAA-G
48467 ATGAAATA
1 ATGAAATA
48475 ATACTGAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 12 0.60
14 8 0.40
ACGTcount: A:0.56, C:0.00, G:0.18, T:0.26
Consensus pattern (13 bp):
ATGAAATATGAAG
Found at i:48745 original size:7 final size:7
Alignment explanation
Indices: 48735--48763 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
48725 ACCCTTGGAA
48735 GAGGGAG
1 GAGGGAG
48742 GAGGGAG
1 GAGGGAG
48749 GAGGGAG
1 GAGGGAG
48756 GAGGGAG
1 GAGGGAG
48763 G
1 G
48764 CTTAAGCTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.28, C:0.00, G:0.72, T:0.00
Consensus pattern (7 bp):
GAGGGAG
Found at i:58413 original size:16 final size:16
Alignment explanation
Indices: 58385--58417 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
58375 ACAAAGAGAA
58385 TGAAGCTCTTTTCCTTT
1 TGAAGCTCTTTT-CTTT
58402 TGAAGC-CTTTTCTTT
1 TGAAGCTCTTTTCTTT
58417 T
1 T
58418 ATTTATTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 5 0.31
17 6 0.38
ACGTcount: A:0.12, C:0.21, G:0.12, T:0.55
Consensus pattern (16 bp):
TGAAGCTCTTTTCTTT
Done.