Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020519.1 Corchorus olitorius cultivar O-4 contig20552, 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: 31315
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:1791 original size:20 final size:21
Alignment explanation
Indices: 1753--1801 Score: 73
Period size: 20 Copynumber: 2.4 Consensus size: 21
1743 GGTTTAACGT
*
1753 GGTTTGACAATTAAAATTTGG
1 GGTTTGACAATTAAAATTTAG
*
1774 GGTTTGACCATT-AAATTTAG
1 GGTTTGACAATTAAAATTTAG
1794 GGTTTGAC
1 GGTTTGAC
1802 TGTTGATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 15 0.58
21 11 0.42
ACGTcount: A:0.29, C:0.08, G:0.24, T:0.39
Consensus pattern (21 bp):
GGTTTGACAATTAAAATTTAG
Found at i:2211 original size:21 final size:21
Alignment explanation
Indices: 2185--2234 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
2175 GTATATTCTG
2185 GTCAAACTCC-AAATTTCAATA
1 GTCAAACTCCAAAATTT-AATA
*
2206 GTCAAACCCCAAAATTTAATA
1 GTCAAACTCCAAAATTTAATA
*
2227 GTTAAACT
1 GTCAAACT
2235 TTATTAAACC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 19 0.76
22 6 0.24
ACGTcount: A:0.44, C:0.22, G:0.06, T:0.28
Consensus pattern (21 bp):
GTCAAACTCCAAAATTTAATA
Found at i:3465 original size:45 final size:45
Alignment explanation
Indices: 3414--3539 Score: 218
Period size: 45 Copynumber: 2.8 Consensus size: 45
3404 AGCAACAATT
* *
3414 AATATTAGGTTTATTTTAATGAATTACCTAGAGATGGAGGAGTAG
1 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGGAGTAG
3459 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGGAGT-G
1 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGGAGTAG
3503 TAATATTAGCTTTATTTTGATGAATTACCTAGAGATG
1 -AATATTAGCTTTATTTTGATGAATTACCTAGAGATG
3540 AAGTAGAATT
Statistics
Matches: 78, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
44 1 0.01
45 77 0.99
ACGTcount: A:0.33, C:0.06, G:0.22, T:0.38
Consensus pattern (45 bp):
AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGGAGTAG
Found at i:3843 original size:2 final size:2
Alignment explanation
Indices: 3836--3865 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3826 TAGATTTGAA
3836 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
3866 CGAAAGGGAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9005 original size:15 final size:15
Alignment explanation
Indices: 8985--9015 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
8975 AGTACTATGT
8985 AGTATAACTAATTAA
1 AGTATAACTAATTAA
*
9000 AGTATAATTAATTAA
1 AGTATAACTAATTAA
9015 A
1 A
9016 TACATGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.03, G:0.06, T:0.35
Consensus pattern (15 bp):
AGTATAACTAATTAA
Found at i:10492 original size:21 final size:24
Alignment explanation
Indices: 10463--10513 Score: 63
Period size: 22 Copynumber: 2.2 Consensus size: 24
10453 TTTTGAACTC
10463 ATTATT-TATCATTTAA-AATATAT
1 ATTATTAT-TCATTTAATAATATAT
*
10486 -TTATTATTTATTTAATAATATAT
1 ATTATTATTCATTTAATAATATAT
10509 ATTAT
1 ATTAT
10514 ATCTAAGATA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
22 12 0.50
23 8 0.33
24 4 0.17
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (24 bp):
ATTATTATTCATTTAATAATATAT
Found at i:14946 original size:16 final size:16
Alignment explanation
Indices: 14895--14947 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
14885 CTGACCCGAG
* **
14895 ACCCGAATAACTTGGA
1 ACCCGAATGACTCAGA
*
14911 ACCCGAATGA-TCCGA
1 ACCCGAATGACTCAGA
14926 GACCCGAATGACTCAGA
1 -ACCCGAATGACTCAGA
14943 ACCCG
1 ACCCG
14948 GTCGAATTAC
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
15 3 0.10
16 24 0.77
17 4 0.13
ACGTcount: A:0.34, C:0.32, G:0.21, T:0.13
Consensus pattern (16 bp):
ACCCGAATGACTCAGA
Found at i:15200 original size:7 final size:7
Alignment explanation
Indices: 15190--15231 Score: 70
Period size: 7 Copynumber: 6.3 Consensus size: 7
15180 ATTTAAAATG
15190 GACTAGT
1 GACTAGT
15197 GACTAGT
1 GACTAGT
15204 -ACTAGT
1 GACTAGT
15210 GACTAGT
1 GACTAGT
15217 -ACTAGT
1 GACTAGT
15223 GACTAGT
1 GACTAGT
15230 GA
1 GA
15232 GCTCTATATA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
6 12 0.36
7 21 0.64
ACGTcount: A:0.31, C:0.14, G:0.26, T:0.29
Consensus pattern (7 bp):
GACTAGT
Found at i:15209 original size:13 final size:13
Alignment explanation
Indices: 15191--15229 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
15181 TTTAAAATGG
15191 ACTAGTGACTAGT
1 ACTAGTGACTAGT
15204 ACTAGTGACTAGT
1 ACTAGTGACTAGT
15217 ACTAGTGACTAGT
1 ACTAGTGACTAGT
15230 GAGCTCTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (13 bp):
ACTAGTGACTAGT
Found at i:15215 original size:20 final size:20
Alignment explanation
Indices: 15190--15231 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
15180 ATTTAAAATG
15190 GACTAGTGACTAGTACTAGT
1 GACTAGTGACTAGTACTAGT
15210 GACTAGT-ACTAGTGACTAGT
1 GACTAGTGACTAGT-ACTAGT
15230 GA
1 GA
15232 GCTCTATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.31, C:0.14, G:0.26, T:0.29
Consensus pattern (20 bp):
GACTAGTGACTAGTACTAGT
Found at i:18731 original size:128 final size:119
Alignment explanation
Indices: 18460--18775 Score: 345
Period size: 128 Copynumber: 2.6 Consensus size: 119
18450 ATGTAGCTAG
* *
18460 TGCCTCGTTAAAAACCTTAAG-CTGGAAAACCCAATGGGACAAAACC-AGTCATAAGGAAAAAAG
1 TGCCTCATTAAAAACCTTAAGTC-GGAAAACCCAATGGGACAAAACCGA-TCATAAGGGAAAAAG
** * *
18523 AGTGCAGCATATCAAGTCCATTTGTCTTCTGGACAAATATTACAAGTGCTCTTTAT
64 AGTGCAGCATATCAAGTCCATTTGTCTTCAAGACAAACATTACAAGTGCTCATTAT
** * *
18579 TGCCTCATTAAAAACCTTGTGTCGGAAAACCCAATGGGACAAAACCGAACAGAAGGGAAAAAGAG
1 TGCCTCATTAAAAACCTTAAGTCGGAAAACCCAATGGGACAAAACCGATCATAAGGGAAAAAGAG
* *
18644 TGCTAGACCA-ATTTAAGTCCATGTAAATGTCTTCAAGACAATTACATCTA-AATGTGCT-ATTG
66 TGC-AG--CATA-TCAAGTCCAT-T---TGTCTTCAAGACAA--ACAT-TACAA-GTGCTCATTA
18706 T
119 T
**
18707 TGCCTCATTAAAAACCTTAAGTCGGAAAACCCTGTGGGACAAAACCGATCATAAGGGAAAAAGAG
1 TGCCTCATTAAAAACCTTAAGTCGGAAAACCCAATGGGACAAAACCGATCATAAGGGAAAAAGAG
18772 TGCA
66 TGCA
18776 ACGCACTTTA
Statistics
Matches: 165, Mismatches: 18, Indels: 20
0.81 0.09 0.10
Matches are distributed among these distances:
119 58 0.35
120 4 0.02
121 1 0.01
122 11 0.07
123 1 0.01
126 12 0.07
127 1 0.01
128 70 0.42
129 7 0.04
ACGTcount: A:0.38, C:0.20, G:0.19, T:0.23
Consensus pattern (119 bp):
TGCCTCATTAAAAACCTTAAGTCGGAAAACCCAATGGGACAAAACCGATCATAAGGGAAAAAGAG
TGCAGCATATCAAGTCCATTTGTCTTCAAGACAAACATTACAAGTGCTCATTAT
Found at i:22729 original size:60 final size:60
Alignment explanation
Indices: 22536--22924 Score: 481
Period size: 60 Copynumber: 6.4 Consensus size: 60
22526 GAAAGGTAAA
* * * *** * * *
22536 ATCATGACAACTTCTGGTGTCAATTGAATAAAATTATGACATCTTCAAATGTCTATTGGAAATTT
1 ATCATGACAACTTCTGGTGTCAATTG--CAAAATCATGACAACTTCTGGTGTCAATT-GCAA--G
* * * ** *
22601 ATCATGACAACTTCTGGTGTCAATTGAATAAAATTATGACATCTTCAAGTATCAATTGCAAG
1 ATCATGACAACTTCTGGTGTCAATTG--CAAAATCATGACAACTTCTGGTGTCAATTGCAAG
* *
22663 ATCATGACAACTTCTGGTGTCAATTGCAAGATCATGACAACTTCTGGTGTCAATTGCAAT
1 ATCATGACAACTTCTGGTGTCAATTGCAAAATCATGACAACTTCTGGTGTCAATTGCAAG
* *
22723 ATCATGACAACTTCTGGTGTCAATTGCAACATCATGACAACTTCTGGTGTCAATTGCAAA
1 ATCATGACAACTTCTGGTGTCAATTGCAAAATCATGACAACTTCTGGTGTCAATTGCAAG
22783 ATCATGACAACTTCTGGTGTCAATTGCAAAATCATGACAACTTCTGGTGTCAATTGCAAG
1 ATCATGACAACTTCTGGTGTCAATTGCAAAATCATGACAACTTCTGGTGTCAATTGCAAG
* * * * * *
22843 AGCATGACAACTTCTGGTGTCATTTGTAAGACCATGACAACTTCTGGTGTCAATTGTAAG
1 ATCATGACAACTTCTGGTGTCAATTGCAAAATCATGACAACTTCTGGTGTCAATTGCAAG
*
22903 ACCATGACAACTTCTGGTGTCA
1 ATCATGACAACTTCTGGTGTCA
22925 TTTGTAAGTA
Statistics
Matches: 300, Mismatches: 24, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
60 217 0.72
62 26 0.09
64 3 0.01
65 54 0.18
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (60 bp):
ATCATGACAACTTCTGGTGTCAATTGCAAAATCATGACAACTTCTGGTGTCAATTGCAAG
Found at i:22932 original size:30 final size:30
Alignment explanation
Indices: 22601--22924 Score: 477
Period size: 30 Copynumber: 10.7 Consensus size: 30
22591 TTGGAAATTT
* *
22601 ATCATGACAACTTCTGGTGTCAATTGAATAAA
1 ATCATGACAACTTCTGGTGTCAATTG--CAAG
* * ** *
22633 ATTATGACATCTTCAAGTATCAATTGCAAG
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
22663 ATCATGACAACTTCTGGTGTCAATTGCAAG
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
*
22693 ATCATGACAACTTCTGGTGTCAATTGCAAT
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
*
22723 ATCATGACAACTTCTGGTGTCAATTGCAAC
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
*
22753 ATCATGACAACTTCTGGTGTCAATTGCAAA
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
*
22783 ATCATGACAACTTCTGGTGTCAATTGCAAA
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
22813 ATCATGACAACTTCTGGTGTCAATTGCAAG
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
* * *
22843 AGCATGACAACTTCTGGTGTCATTTGTAAG
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
* *
22873 ACCATGACAACTTCTGGTGTCAATTGTAAG
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
*
22903 ACCATGACAACTTCTGGTGTCA
1 ATCATGACAACTTCTGGTGTCA
22925 TTTGTAAGTA
Statistics
Matches: 271, Mismatches: 21, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
30 250 0.92
32 21 0.08
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (30 bp):
ATCATGACAACTTCTGGTGTCAATTGCAAG
Found at i:24732 original size:14 final size:14
Alignment explanation
Indices: 24713--24760 Score: 71
Period size: 14 Copynumber: 3.5 Consensus size: 14
24703 ATCTAACTTT
24713 ATTAATCAACAATA
1 ATTAATCAACAATA
* *
24727 ATTAATCAAC-TTT
1 ATTAATCAACAATA
24740 ATTAATCAACAATA
1 ATTAATCAACAATA
24754 ATTAATC
1 ATTAATC
24761 GTAAATTAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
13 11 0.38
14 18 0.62
ACGTcount: A:0.50, C:0.15, G:0.00, T:0.35
Consensus pattern (14 bp):
ATTAATCAACAATA
Found at i:24737 original size:27 final size:27
Alignment explanation
Indices: 24707--24760 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
24697 ACTTACATCT
24707 AACTTTATTAATCAACAATAATTAATC
1 AACTTTATTAATCAACAATAATTAATC
24734 AACTTTATTAATCAACAATAATTAATC
1 AACTTTATTAATCAACAATAATTAATC
24761 GTAAATTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.48, C:0.15, G:0.00, T:0.37
Consensus pattern (27 bp):
AACTTTATTAATCAACAATAATTAATC
Found at i:24745 original size:13 final size:13
Alignment explanation
Indices: 24707--24749 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
24697 ACTTACATCT
24707 AACTTTATTAATC
1 AACTTTATTAATC
* *
24720 AACAATAATTAATC
1 AAC-TTTATTAATC
24734 AACTTTATTAATC
1 AACTTTATTAATC
24747 AAC
1 AAC
24750 AATAATTAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
13 14 0.56
14 11 0.44
ACGTcount: A:0.47, C:0.16, G:0.00, T:0.37
Consensus pattern (13 bp):
AACTTTATTAATC
Found at i:26300 original size:27 final size:28
Alignment explanation
Indices: 26150--26299 Score: 185
Period size: 28 Copynumber: 5.4 Consensus size: 28
26140 TACTCCTTAC
* *
26150 TTTGGTCATTTTTCATGTCTAGGGGCAT
1 TTTGGTCATTTTGCATGTCCAGGGGCAT
* *
26178 TTTGGTCATTTTTCATGTTCAGGGGCAT
1 TTTGGTCATTTTGCATGTCCAGGGGCAT
* * *
26206 TTTGGTCATTTTACATGCCCAGAGGCAT
1 TTTGGTCATTTTGCATGTCCAGGGGCAT
* *
26234 TTTGGTCATTTTGCAAGTCCAAGGGCAT
1 TTTGGTCATTTTGCATGTCCAGGGGCAT
* * *
26262 TTTGGTCA-TTTGCACGTTCAGGGGCGT
1 TTTGGTCATTTTGCATGTCCAGGGGCAT
26289 TTTGGTCATTT
1 TTTGGTCATTT
26300 GAAGTCTACT
Statistics
Matches: 106, Mismatches: 15, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
27 23 0.22
28 83 0.78
ACGTcount: A:0.16, C:0.17, G:0.25, T:0.42
Consensus pattern (28 bp):
TTTGGTCATTTTGCATGTCCAGGGGCAT
Found at i:28145 original size:53 final size:53
Alignment explanation
Indices: 28055--28156 Score: 159
Period size: 53 Copynumber: 1.9 Consensus size: 53
28045 TCAGCAAGTC
* *
28055 ACAAGTTCAGCATTATATGAGCATAACAGAACACATCAACATAGCATGGCCTG
1 ACAAATTCAGCATTATATGAGCATAACAGAACACATCAACATAACATGGCCTG
* * *
28108 ACAAATTCATCATTATATGAGCATAATAGGACACATCAACATAACATGG
1 ACAAATTCAGCATTATATGAGCATAACAGAACACATCAACATAACATGG
28157 TTTGGTATTT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
53 44 1.00
ACGTcount: A:0.42, C:0.21, G:0.15, T:0.23
Consensus pattern (53 bp):
ACAAATTCAGCATTATATGAGCATAACAGAACACATCAACATAACATGGCCTG
Found at i:29607 original size:15 final size:16
Alignment explanation
Indices: 29583--29622 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
29573 AGAGGTTGAA
*
29583 AGAAAGCAATTAAAC-
1 AGAAAACAATTAAACT
*
29598 AGAAAACAATTATACT
1 AGAAAACAATTAAACT
29614 AGAAAACAA
1 AGAAAACAA
29623 AGCAAAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.62, C:0.12, G:0.10, T:0.15
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Done.