Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022481.1 Corchorus olitorius cultivar O-4 contig22514, 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: 68249
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:17786 original size:4 final size:4
Alignment explanation
Indices: 17777--17806 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
17767 CAAGTTGTAT
17777 TTTC TTTC TTTC TTTC TTTC TTT- TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT
17807 TTCATTTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 22 0.88
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (4 bp):
TTTC
Found at i:22141 original size:2 final size:2
Alignment explanation
Indices: 22134--22164 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
22124 GTAACTTTCA
22134 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
22165 ATGTGGAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:22959 original size:10 final size:10
Alignment explanation
Indices: 22944--22980 Score: 58
Period size: 10 Copynumber: 3.8 Consensus size: 10
22934 AACATAAGAG
22944 TTTTTTCTCT
1 TTTTTTCTCT
22954 TTTTTTCTCT
1 TTTTTTCTCT
22964 TTTTTTCT-T
1 TTTTTTCTCT
*
22973 TTTGTTCT
1 TTTTTTCT
22981 TTTGGTTTTG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
9 8 0.31
10 18 0.69
ACGTcount: A:0.00, C:0.16, G:0.03, T:0.81
Consensus pattern (10 bp):
TTTTTTCTCT
Found at i:24709 original size:18 final size:18
Alignment explanation
Indices: 24676--24710 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
24666 ACGAGGTGGT
*
24676 GAACGAGAATACCGAGGC
1 GAACGAGAATAACGAGGC
*
24694 GAACGAGAGTAACGAGG
1 GAACGAGAATAACGAGG
24711 GGGTGACCTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.17, G:0.37, T:0.06
Consensus pattern (18 bp):
GAACGAGAATAACGAGGC
Found at i:26465 original size:19 final size:19
Alignment explanation
Indices: 26441--26481 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
26431 AAATTACATT
26441 ATCAAAGATAATAACAAGA
1 ATCAAAGATAATAACAAGA
26460 ATCAAAGATAATAACAAGA
1 ATCAAAGATAATAACAAGA
26479 ATC
1 ATC
26482 TTTCTCGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.61, C:0.12, G:0.10, T:0.17
Consensus pattern (19 bp):
ATCAAAGATAATAACAAGA
Found at i:27064 original size:5 final size:5
Alignment explanation
Indices: 27054--27079 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
27044 TAAAACTATT
27054 TTAAA TTAAA TTAAA TTAAA TTAAA T
1 TTAAA TTAAA TTAAA TTAAA TTAAA T
27080 ACTTCTCTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
TTAAA
Found at i:37687 original size:122 final size:127
Alignment explanation
Indices: 37488--37741 Score: 360
Period size: 122 Copynumber: 2.0 Consensus size: 127
37478 CATTGTTTAA
* *
37488 ACTTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCTTTATAAT
1 ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAAT
*
37553 TTTTACCATTTTACTATTTTA-A-TT-A-AAAAAAC-T-TATATATTAGAATTTTTTAAATAT
66 TTTTA-CATTTTACCATTTTACATTTAATAAAAAACTTATATATATTAGAATTTTTTAAATAT
*
37610 ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATATC
1 ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATA-A
*
37675 TATTTTA-TTTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAAT
65 T-TTTTACATTTTACCATTTTAC-A-TTTAA-TAAAAAACTTATATATATTAGAATTTTTTAAAT
37739 AT
126 AT
37741 A
1 A
37742 TTTCTTAAAT
Statistics
Matches: 116, Mismatches: 5, Indels: 13
0.87 0.04 0.10
Matches are distributed among these distances:
122 73 0.63
123 1 0.01
124 6 0.05
126 2 0.02
127 1 0.01
129 7 0.06
130 1 0.01
131 25 0.22
ACGTcount: A:0.38, C:0.11, G:0.02, T:0.50
Consensus pattern (127 bp):
ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAAT
TTTTACATTTTACCATTTTACATTTAATAAAAAACTTATATATATTAGAATTTTTTAAATAT
Found at i:37749 original size:13 final size:14
Alignment explanation
Indices: 37728--37765 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
37718 ATATATTAGA
37728 ATTTTTTAAAT-AT
1 ATTTTTTAAATGAT
*
37741 ATTTCTTAAATGAT
1 ATTTTTTAAATGAT
37755 ATTTTTTAAAT
1 ATTTTTTAAAT
37766 TTTACAATCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 10 0.45
14 12 0.55
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.58
Consensus pattern (14 bp):
ATTTTTTAAATGAT
Found at i:38730 original size:30 final size:30
Alignment explanation
Indices: 38684--38760 Score: 86
Period size: 30 Copynumber: 2.6 Consensus size: 30
38674 ATATTGTATA
* *
38684 GGTCCCTCGACTTACAAAAAAAGATCAATTT
1 GGTCTCTCTACTTACAAAAAAAG-TCAATTT
**
38715 GGTC-CTCCTAC-TACAAAAATTGTCAATTT
1 GGTCTCT-CTACTTACAAAAAAAGTCAATTT
38744 GGTCTCTCTACTTACAA
1 GGTCTCTCTACTTACAA
38761 TTTGGTGTCA
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
29 15 0.38
30 18 0.45
31 7 0.17
ACGTcount: A:0.32, C:0.25, G:0.12, T:0.31
Consensus pattern (30 bp):
GGTCTCTCTACTTACAAAAAAAGTCAATTT
Found at i:39042 original size:31 final size:31
Alignment explanation
Indices: 39009--39128 Score: 88
Period size: 31 Copynumber: 3.9 Consensus size: 31
38999 ATATATAATC
39009 AATTGACAGATTTTATTAAGTAGAGGGACTC-
1 AATTGACAGATTTTA-TAAGTAGAGGGACTCA
* ** *
39040 AATCGAC-GCCAAATTGTAAGTAGAGGGA-TCA
1 AATTGACAG--ATTTTATAAGTAGAGGGACTCA
*
39071 AATTGACAGTTTTTAT-AGTAGAGGGAC-CA
1 AATTGACAGATTTTATAAGTAGAGGGACTCA
*** *
39100 AATTGATCCTTTTTTGTAAGTAGAGGGAC
1 AATTGA-CAGATTTTATAAGTAGAGGGAC
39129 CTGTACGGTA
Statistics
Matches: 70, Mismatches: 12, Indels: 14
0.73 0.12 0.15
Matches are distributed among these distances:
29 18 0.26
30 13 0.19
31 35 0.50
32 4 0.06
ACGTcount: A:0.34, C:0.12, G:0.24, T:0.30
Consensus pattern (31 bp):
AATTGACAGATTTTATAAGTAGAGGGACTCA
Found at i:39129 original size:31 final size:30
Alignment explanation
Indices: 39053--39129 Score: 102
Period size: 29 Copynumber: 2.6 Consensus size: 30
39043 CGACGCCAAA
*
39053 TTGTAAGTAGAGGGATCAAATTGACAGTTT
1 TTGTAAGTAGAGGGACCAAATTGACAGTTT
* **
39083 TTAT-AGTAGAGGGACCAAATTGATCCTTTT
1 TTGTAAGTAGAGGGACCAAATTGA-CAGTTT
39113 TTGTAAGTAGAGGGACC
1 TTGTAAGTAGAGGGACC
39130 TGTACGGTAT
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
29 18 0.45
30 10 0.25
31 12 0.30
ACGTcount: A:0.31, C:0.10, G:0.26, T:0.32
Consensus pattern (30 bp):
TTGTAAGTAGAGGGACCAAATTGACAGTTT
Found at i:47221 original size:21 final size:21
Alignment explanation
Indices: 47195--47235 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
47185 TTGTTCATAT
47195 AAACACCGTTTTTTAATGTGA
1 AAACACCGTTTTTTAATGTGA
47216 AAACACCGTTTTTTAATGTG
1 AAACACCGTTTTTTAATGTG
47236 CAATCTCCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.39
Consensus pattern (21 bp):
AAACACCGTTTTTTAATGTGA
Found at i:48162 original size:28 final size:28
Alignment explanation
Indices: 48130--48185 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
48120 AGGTTTGTTT
48130 GTTGGCTCATAAATTAGCGTTTCGGTAA
1 GTTGGCTCATAAATTAGCGTTTCGGTAA
48158 GTTGGCTCATAAATTAGCGTTTCGGTAA
1 GTTGGCTCATAAATTAGCGTTTCGGTAA
48186 TGTAGCTAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.25, C:0.14, G:0.25, T:0.36
Consensus pattern (28 bp):
GTTGGCTCATAAATTAGCGTTTCGGTAA
Found at i:65391 original size:31 final size:33
Alignment explanation
Indices: 65321--65391 Score: 85
Period size: 31 Copynumber: 2.2 Consensus size: 33
65311 CTATTTGATT
*
65321 CAATCAATTTTGAGCTCCTAATTCCATTAATTA
1 CAATCAATTTTGAGCTCCTAATTCAATTAATTA
* *
65354 CTATCAA-TTTGAGC-CCTAA-TCAATTACTTCA
1 CAATCAATTTTGAGCTCCTAATTCAATTAATT-A
65385 CAATCAA
1 CAATCAA
65392 ATAAGCAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
30 8 0.24
31 12 0.36
32 7 0.21
33 6 0.18
ACGTcount: A:0.35, C:0.24, G:0.06, T:0.35
Consensus pattern (33 bp):
CAATCAATTTTGAGCTCCTAATTCAATTAATTA
Done.