Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017127.1 Corchorus olitorius cultivar O-4 contig17160, 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: 20313
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Found at i:1808 original size:2 final size:2
Alignment explanation
Indices: 1803--1831 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1793 TATGTGTGTG
1803 TA TA 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 TA TA T
1832 GTCTGCAAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5695 original size:38 final size:38
Alignment explanation
Indices: 5604--5722 Score: 132
Period size: 38 Copynumber: 3.1 Consensus size: 38
5594 TCAGGGCTGT
* *
5604 TGAAAATCTACTTAAATATCA-AAAATGCCTGCTCGGGGCAC
1 TGAAACTCTACTTGAATA-CAGAAAA-GCCTGCTCGGGG--C
* * *
5645 TGGAACTCTACTTGAATACAGAAAGGCATGCTCGGGGC
1 TGAAACTCTACTTGAATACAGAAAAGCCTGCTCGGGGC
* *
5683 TGAAACTCTACTTGAATACTGAAAAGCCCGCTCGGGGC
1 TGAAACTCTACTTGAATACAGAAAAGCCTGCTCGGGGC
5721 TG
1 TG
5723 TTGGAAATTT
Statistics
Matches: 67, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
38 36 0.54
40 13 0.19
41 18 0.27
ACGTcount: A:0.31, C:0.23, G:0.24, T:0.23
Consensus pattern (38 bp):
TGAAACTCTACTTGAATACAGAAAAGCCTGCTCGGGGC
Found at i:5965 original size:38 final size:38
Alignment explanation
Indices: 5895--6362 Score: 411
Period size: 38 Copynumber: 12.7 Consensus size: 38
5885 AATTGAAAAC
* * *
5895 TGCTGGAAGATTACCTGTTTCCAGTTAACTTTGAT-AT
1 TGCTGAAAGATGACCTGTTTCCAGTCAACTTTGATAAT
* * * *
5932 CTGTTGAAAGACGACCTGTTTCCAGTCACCTTTGATAAC
1 -TGCTGAAAGATGACCTGTTTCCAGTCAACTTTGATAAT
* *
5971 TGCTGAATGATGACCTGTTTCCAGTCAACTTTGATAACC
1 TGCTGAAAGATGACCTGTTTCCAGTCAACTTTGATAA-T
*
6010 T-CTGAAAGATGACCTGTTTCCAGTCAACTTCGATAAT
1 TGCTGAAAGATGACCTGTTTCCAGTCAACTTTGATAAT
* * * *
6047 TTCTAAAAGATGACATGTTTCCAGTCAACTTTGATGAT
1 TGCTGAAAGATGACCTGTTTCCAGTCAACTTTGATAAT
* * *
6085 TGCTGAAAGATGACATGTTTCTAGTCAACTTTGATGAT
1 TGCTGAAAGATGACCTGTTTCCAGTCAACTTTGATAAT
* *
6123 TGCTAAAAGA--ACCTGTTTCCAGTCGA-TCTTGATAA-
1 TGCTGAAAGATGACCTGTTTCCAGTCAACT-TTGATAAT
* *
6158 --C-------CGA--TGTTTCCAGTCAACTTTGATGAT
1 TGCTGAAAGATGACCTGTTTCCAGTCAACTTTGATAAT
*
6185 TGCTGAAA-AGTGACCTGTTTCCAGTCAACTTTGATGAT
1 TGCTGAAAGA-TGACCTGTTTCCAGTCAACTTTGATAAT
*
6223 AT-CTGAAAGATGACATGTTTCCAGTCAACTTTGATAAT
1 -TGCTGAAAGATGACCTGTTTCCAGTCAACTTTGATAAT
* * * *
6261 TGTTGAAAGATTACCTGTTCCCAGTCAA-TCTTAATAAT
1 TGCTGAAAGATGACCTGTTTCCAGTCAACT-TTGATAAT
* * * * *
6299 TGTTGAAAGATGACCTGTTTCTAGTCGACCTTAATAACT
1 TGCTGAAAGATGACCTGTTTCCAGTCAACTTTGATAA-T
* * *
6338 T-TTGAAAGATGACTTGTTACCAGTC
1 TGCTGAAAGATGACCTGTTTCCAGTC
6363 TTGATGCCAC
Statistics
Matches: 361, Mismatches: 44, Indels: 50
0.79 0.10 0.11
Matches are distributed among these distances:
26 18 0.05
27 1 0.00
28 1 0.00
29 1 0.00
33 1 0.00
35 1 0.00
36 21 0.06
37 3 0.01
38 307 0.85
39 7 0.02
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (38 bp):
TGCTGAAAGATGACCTGTTTCCAGTCAACTTTGATAAT
Found at i:6178 original size:100 final size:101
Alignment explanation
Indices: 6061--6248 Score: 292
Period size: 100 Copynumber: 1.9 Consensus size: 101
6051 AAAAGATGAC
*
6061 ATGTTTCCAGTCAACTTTGATGATTGCTG-AAAGATGACATGTTTCTAGTCAACTTTGATGAT-T
1 ATGTTTCCAGTCAACTTTGATGATTGCTGAAAAG-TGACATGTTTCCAGTCAACTTTGATGATAT
*
6124 GCTAAAAGA-ACCTGTTTCCAGTCGATCTTGATAACCG
65 -CTAAAAGAGACATGTTTCCAGTCGATCTTGATAACCG
*
6161 ATGTTTCCAGTCAACTTTGATGATTGCTGAAAAGTGACCTGTTTCCAGTCAACTTTGATGATATC
1 ATGTTTCCAGTCAACTTTGATGATTGCTGAAAAGTGACATGTTTCCAGTCAACTTTGATGATATC
*
6226 TGAAAGATGACATGTTTCCAGTC
66 TAAAAGA-GACATGTTTCCAGTC
6249 AACTTTGATA
Statistics
Matches: 80, Mismatches: 4, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
100 62 0.77
101 5 0.06
102 13 0.16
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (101 bp):
ATGTTTCCAGTCAACTTTGATGATTGCTGAAAAGTGACATGTTTCCAGTCAACTTTGATGATATC
TAAAAGAGACATGTTTCCAGTCGATCTTGATAACCG
Found at i:6229 original size:138 final size:139
Alignment explanation
Indices: 6024--6297 Score: 401
Period size: 138 Copynumber: 2.0 Consensus size: 139
6014 AAAGATGACC
*
6024 TGTTTCCAGTCAACTTCGATAATTTCTAAAAGATGACATGTTTCCAGTCAACTTTGATGATTGCT
1 TGTTTCCAGTCAACTTCGATAATTGCTAAAAGATGACATGTTTCCAGTCAACTTTGATGATTGCT
* * * *
6089 GAAAGATGACATGTTTCTAGTCAACTTTGATGATTGCTAAAAGA-ACCTGTTTCCAGTCGATCTT
66 GAAAGATGACATGTTTCCAGTCAACTTTGATAATTGCTAAAAGATACCTGTTCCCAGTCAATCTT
*
6153 GATAACCGA
131 AATAACCGA
* * *
6162 TGTTTCCAGTCAACTTTGATGATTGCTGAAAAG-TGACCTGTTTCCAGTCAACTTTGATGATAT-
1 TGTTTCCAGTCAACTTCGATAATTGCT-AAAAGATGACATGTTTCCAGTCAACTTTGATGAT-TG
* *
6225 CTGAAAGATGACATGTTTCCAGTCAACTTTGATAATTGTTGAAAGATTACCTGTTCCCAGTCAAT
64 CTGAAAGATGACATGTTTCCAGTCAACTTTGATAATTGCTAAAAGA-TACCTGTTCCCAGTCAAT
6290 CTTAATAA
128 CTTAATAA
6298 TTGTTGAAAG
Statistics
Matches: 121, Mismatches: 11, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
138 93 0.77
139 6 0.05
140 22 0.18
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (139 bp):
TGTTTCCAGTCAACTTCGATAATTGCTAAAAGATGACATGTTTCCAGTCAACTTTGATGATTGCT
GAAAGATGACATGTTTCCAGTCAACTTTGATAATTGCTAAAAGATACCTGTTCCCAGTCAATCTT
AATAACCGA
Found at i:7130 original size:17 final size:17
Alignment explanation
Indices: 7108--7142 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
7098 GAAATAGTGC
7108 ATTCTTGTTGGTACATT
1 ATTCTTGTTGGTACATT
*
7125 ATTCTTGTTGGTATATT
1 ATTCTTGTTGGTACATT
7142 A
1 A
7143 ACATTATGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.20, C:0.09, G:0.17, T:0.54
Consensus pattern (17 bp):
ATTCTTGTTGGTACATT
Found at i:8779 original size:32 final size:32
Alignment explanation
Indices: 8711--8809 Score: 101
Period size: 32 Copynumber: 3.1 Consensus size: 32
8701 AAAATGCCTT
* * * *
8711 TATTTAGCAGCGTTTATAGAAGC-AAACACCCT
1 TATTTAGCGGCGTCTATAGAA-CAAAACGCCCC
* *
8743 TATTTAGCGGCGTCTATAGAATAAAATGCCCC
1 TATTTAGCGGCGTCTATAGAACAAAACGCCCC
* * *
8775 TATTTAGCGGTGTCTACAGAACAAAACGCCGC
1 TATTTAGCGGCGTCTATAGAACAAAACGCCCC
8807 TAT
1 TAT
8810 ATTTAACTGA
Statistics
Matches: 55, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
32 55 1.00
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.27
Consensus pattern (32 bp):
TATTTAGCGGCGTCTATAGAACAAAACGCCCC
Found at i:15891 original size:16 final size:16
Alignment explanation
Indices: 15872--15909 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
15862 CAAGTCTAGG
15872 TTATTTTAAGTTT-ATA
1 TTATTTTAAGTTTCA-A
*
15888 TTATTTTGAGTTTCAA
1 TTATTTTAAGTTTCAA
15904 TTATTT
1 TTATTT
15910 CAATCTCTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 19 0.95
17 1 0.05
ACGTcount: A:0.26, C:0.03, G:0.08, T:0.63
Consensus pattern (16 bp):
TTATTTTAAGTTTCAA
Found at i:20054 original size:16 final size:17
Alignment explanation
Indices: 20033--20140 Score: 74
Period size: 17 Copynumber: 6.2 Consensus size: 17
20023 TAGATACCAA
*
20033 AAAAAG-AATTGATACC
1 AAAAAGCAATTCATACC
20049 AAAAAGCAATTCATACC
1 AAAAAGCAATTCATACC
** *
20066 AAAAAAAATAATTCATACA
1 --AAAAAGCAATTCATACC
* * **
20085 AGAAAAACAGTAGATACC
1 A-AAAAGCAATTCATACC
*
20103 AAAAAACAATTCATACC
1 AAAAAGCAATTCATACC
* **
20120 AAAAGGCAGCTCATACC
1 AAAAAGCAATTCATACC
20137 AAAA
1 AAAA
20141 GAAAAAAACA
Statistics
Matches: 72, Mismatches: 16, Indels: 7
0.76 0.17 0.07
Matches are distributed among these distances:
16 6 0.08
17 40 0.56
18 12 0.17
19 14 0.19
ACGTcount: A:0.57, C:0.19, G:0.08, T:0.16
Consensus pattern (17 bp):
AAAAAGCAATTCATACC
Found at i:20118 original size:17 final size:17
Alignment explanation
Indices: 20026--20123 Score: 88
Period size: 17 Copynumber: 5.5 Consensus size: 17
20016 CTAACAGTAG
* *
20026 ATACCAAAAAAAGAATTG
1 ATACC-AAAAAACAATTC
*
20044 ATACCAAAAAGCAATTC
1 ATACCAAAAAACAATTC
*
20061 ATACCAAAAAAAATAATTC
1 ATACC--AAAAAACAATTC
* * **
20080 ATACAAGAAAAACAGTAG
1 ATACCA-AAAAACAATTC
20098 ATACCAAAAAACAATTC
1 ATACCAAAAAACAATTC
20115 ATACCAAAA
1 ATACCAAAA
20124 GGCAGCTCAT
Statistics
Matches: 63, Mismatches: 14, Indels: 7
0.75 0.17 0.08
Matches are distributed among these distances:
17 32 0.51
18 17 0.27
19 14 0.22
ACGTcount: A:0.60, C:0.17, G:0.06, T:0.16
Consensus pattern (17 bp):
ATACCAAAAAACAATTC
Found at i:20170 original size:15 final size:16
Alignment explanation
Indices: 20152--20182 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
20142 AAAAAAACAG
20152 TTCATA-CAAAAAGAA
1 TTCATACCAAAAAGAA
20167 TTCATACCAAAAAGAA
1 TTCATACCAAAAAGAA
20183 CAGAGTCATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.58, C:0.16, G:0.06, T:0.19
Consensus pattern (16 bp):
TTCATACCAAAAAGAA
Done.