Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024760.1 Corchorus olitorius cultivar O-4 contig24793, 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: 93540
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:970 original size:102 final size:102
Alignment explanation
Indices: 794--996 Score: 379
Period size: 102 Copynumber: 2.0 Consensus size: 102
784 TACATGATTA
*
794 GCTAGCTTACCAAAACGCTAATCTATGAGCCAACAAACCTAGTGAAATCTCATTACAATTCAAAT
1 GCTAGCTTACCAAAACGCTAATCTATGAACCAACAAACCTAGTGAAATCTCATTACAATTCAAAT
859 AAATCTCTATGCCCAAACATCTAAATGAGAATTCACG
66 AAATCTCTATGCCCAAACATCTAAATGAGAATTCACG
*
896 GCTAGCTTACCGAAACGCTAATCTATGAACCAACAAACCTAGTGAAATCTCATTACAATTCAAAT
1 GCTAGCTTACCAAAACGCTAATCTATGAACCAACAAACCTAGTGAAATCTCATTACAATTCAAAT
*
961 AAATCTCTATGCCTAAACATCTAAATGAGAATTCAC
66 AAATCTCTATGCCCAAACATCTAAATGAGAATTCAC
997 ATTCCGTGAG
Statistics
Matches: 98, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
102 98 1.00
ACGTcount: A:0.40, C:0.24, G:0.10, T:0.25
Consensus pattern (102 bp):
GCTAGCTTACCAAAACGCTAATCTATGAACCAACAAACCTAGTGAAATCTCATTACAATTCAAAT
AAATCTCTATGCCCAAACATCTAAATGAGAATTCACG
Found at i:4615 original size:7 final size:7
Alignment explanation
Indices: 4603--4627 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
4593 AATTTCAATA
4603 TCAATTC
1 TCAATTC
4610 TCAATTC
1 TCAATTC
4617 TCAATTC
1 TCAATTC
4624 TCAA
1 TCAA
4628 GTGAAGTGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.32, C:0.28, G:0.00, T:0.40
Consensus pattern (7 bp):
TCAATTC
Found at i:5230 original size:7 final size:6
Alignment explanation
Indices: 5211--5240 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
5201 AACCAAAGAC
*
5211 AAGAAA AAGAAA AAGTAA AAGAAA AAGAAA
1 AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA
5241 TCATCTTTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (6 bp):
AAGAAA
Found at i:13144 original size:19 final size:20
Alignment explanation
Indices: 13120--13177 Score: 73
Period size: 19 Copynumber: 2.9 Consensus size: 20
13110 CTGTTTGATA
13120 ACTGTACAGATGAGATTA-C
1 ACTGTACAGATGAGATTAGC
* *
13139 ACTGTACAGATTAGATTATGT
1 ACTGTACAGATGAGATTA-GC
*
13160 AATGTACAGATGAGATTA
1 ACTGTACAGATGAGATTA
13178 TTAGAGCAAC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 17 0.52
21 16 0.48
ACGTcount: A:0.38, C:0.10, G:0.21, T:0.31
Consensus pattern (20 bp):
ACTGTACAGATGAGATTAGC
Found at i:14424 original size:5 final size:5
Alignment explanation
Indices: 14414--14439 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
14404 CATGAAGATC
14414 GTATT GTATT GTATT GTATT GTATT G
1 GTATT GTATT GTATT GTATT GTATT G
14440 CACCCACAAA
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:0.19, C:0.00, G:0.23, T:0.58
Consensus pattern (5 bp):
GTATT
Found at i:17665 original size:9 final size:9
Alignment explanation
Indices: 17651--17675 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
17641 GGCTGCGGCT
17651 GCGGCTGAG
1 GCGGCTGAG
17660 GCGGCTGAG
1 GCGGCTGAG
17669 GCGGCTG
1 GCGGCTG
17676 CGGCTCTTGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.08, C:0.24, G:0.56, T:0.12
Consensus pattern (9 bp):
GCGGCTGAG
Found at i:19005 original size:7 final size:7
Alignment explanation
Indices: 18993--19023 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
18983 AGCTAGCTGT
18993 AGGGTGA
1 AGGGTGA
19000 AGGGTGA
1 AGGGTGA
19007 AGGGTGA
1 AGGGTGA
19014 AGGGTGA
1 AGGGTGA
19021 AGG
1 AGG
19024 TTGTGGGATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.29, C:0.00, G:0.58, T:0.13
Consensus pattern (7 bp):
AGGGTGA
Found at i:22877 original size:24 final size:24
Alignment explanation
Indices: 22811--22869 Score: 100
Period size: 24 Copynumber: 2.5 Consensus size: 24
22801 CTTGGCTGTC
*
22811 GTTGCAATCCTGGATTTGATTGAG
1 GTTGCAATCCTGGATTTGACTGAG
*
22835 GTTGCAATCTTGGATTTGACTGAG
1 GTTGCAATCCTGGATTTGACTGAG
22859 GTTGCAATCCT
1 GTTGCAATCCT
22870 CTACTTGATT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.20, C:0.15, G:0.27, T:0.37
Consensus pattern (24 bp):
GTTGCAATCCTGGATTTGACTGAG
Found at i:24818 original size:2 final size:2
Alignment explanation
Indices: 24811--24843 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
24801 CCAAAAAGAA
24811 AT 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 AT A
24844 AATTCAAAGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:25523 original size:27 final size:27
Alignment explanation
Indices: 25485--25569 Score: 98
Period size: 32 Copynumber: 3.0 Consensus size: 27
25475 CCTCATAAGC
*
25485 CAAACCACAGATATTAAGCCCTTAACT
1 CAAACCACAGATCTTAAGCCCTTAACT
*
25512 CAAACCACAGATCTTAAACCCTTAATTTTACT
1 CAAACCACAGATCTTAAGCCCTT-A----ACT
*
25544 CAAAACACAGATCTTAAGCCCTTAAC
1 CAAACCACAGATCTTAAGCCCTTAAC
25570 ACAACACTTG
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
27 23 0.47
28 1 0.02
31 1 0.02
32 24 0.49
ACGTcount: A:0.40, C:0.29, G:0.06, T:0.25
Consensus pattern (27 bp):
CAAACCACAGATCTTAAGCCCTTAACT
Found at i:26032 original size:20 final size:20
Alignment explanation
Indices: 26009--26048 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
25999 GAGAGAAAAG
26009 CGACGGAAAGAAGAGAGATT
1 CGACGGAAAGAAGAGAGATT
*
26029 CGACGGAGAGAAGAGAGATT
1 CGACGGAAAGAAGAGAGATT
26049 TGTCAAATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.42, C:0.10, G:0.38, T:0.10
Consensus pattern (20 bp):
CGACGGAAAGAAGAGAGATT
Found at i:26484 original size:14 final size:14
Alignment explanation
Indices: 26445--26484 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
26435 GAAAATTAGC
**
26445 AATAATTATTGGAA
1 AATAATTATTATAA
*
26459 AATAATAATTATAA
1 AATAATTATTATAA
26473 AATAATTATTAT
1 AATAATTATTAT
26485 TGTTTCAATA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (14 bp):
AATAATTATTATAA
Found at i:29001 original size:64 final size:64
Alignment explanation
Indices: 28901--29024 Score: 187
Period size: 64 Copynumber: 1.9 Consensus size: 64
28891 CACAAAACGG
* * *
28901 AAAAAAAGAGCTCGCTAAGTTGAAAATCCTGTAAAGGACG-ACTTAGGCAAAAGTTAGAGCGGAA
1 AAAAAAAAAGCTCGCTAAGTTGAAAATCCTGCAAAGGA-GAACTTAGGCAAAACTTAGAGCGGAA
* *
28965 AAAAAAAAAGCTCGTTAAGTTGAAAATTCTGCAAAGGAGAACTTAGGCAAAACTTAGAGC
1 AAAAAAAAAGCTCGCTAAGTTGAAAATCCTGCAAAGGAGAACTTAGGCAAAACTTAGAGC
29025 ACAAAAATAA
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
63 1 0.02
64 53 0.98
ACGTcount: A:0.45, C:0.14, G:0.23, T:0.19
Consensus pattern (64 bp):
AAAAAAAAAGCTCGCTAAGTTGAAAATCCTGCAAAGGAGAACTTAGGCAAAACTTAGAGCGGAA
Found at i:29741 original size:16 final size:16
Alignment explanation
Indices: 29720--29752 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
29710 ATTAGAAAGT
29720 AGAAAAGCTCTGAAGC
1 AGAAAAGCTCTGAAGC
29736 AGAAAAGCTCTGAAGC
1 AGAAAAGCTCTGAAGC
29752 A
1 A
29753 TTTTCAGATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.45, C:0.18, G:0.24, T:0.12
Consensus pattern (16 bp):
AGAAAAGCTCTGAAGC
Found at i:29903 original size:41 final size:41
Alignment explanation
Indices: 29846--30069 Score: 277
Period size: 41 Copynumber: 5.4 Consensus size: 41
29836 TTTTCGTTTG
*
29846 TTCAAGATCAAGTCATTGAGACCCTTGAATTAAATTATCAA
1 TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATCAA
** *
29887 TTCAAGATTGAGTCATTGAGACCCTTGAATTAAATTATCAA
1 TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATCAA
** *
29928 TTCAAGATTGAGTCATCGAGACCCTTGAATTAAATTATAAA
1 TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATCAA
* **
29969 TTCAAGAACAAGTCATCGAGACCCTTGAAGCGAATTATTATCAA
1 TTCAAGATCAAGTCATCGAGACCCTTGAA-TTAA--ATTATCAA
* * * * *
30013 TTCAAGACCAAGTCGTCAAGACCCTTGAATTAGATTGTCAA
1 TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATCAA
*
30054 TTCAAGACCAAGTCAT
1 TTCAAGATCAAGTCAT
30070 TCGACTCTTG
Statistics
Matches: 162, Mismatches: 18, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
41 126 0.78
42 2 0.01
43 1 0.01
44 33 0.20
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.29
Consensus pattern (41 bp):
TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATCAA
Found at i:43867 original size:33 final size:31
Alignment explanation
Indices: 43829--43974 Score: 139
Period size: 33 Copynumber: 4.5 Consensus size: 31
43819 GCTATGATCA
** *
43829 ACCAAAACAGATTTGTTTTCATCACAATTAGC
1 ACCAAAACAGATTTG-TTTCATCACAAACAAC
43861 ATCCAAAACAGAATTTGTTTCATCACAAACAAC
1 A-CCAAAACAG-ATTTGTTTCATCACAAACAAC
*
43894 ACCTAAAACAGATTTGGTGTCATCACAAACAAC
1 ACC-AAAACAGATTT-GTTTCATCACAAACAAC
** * * *
43927 ACTCAAATTAGGTTTAGTATCATCGCAAACAAC
1 AC-CAAAACAGATTT-GTTTCATCACAAACAAC
43960 ATCCAAAACAGATTT
1 A-CCAAAACAGATTT
43975 AGAATTACTC
Statistics
Matches: 95, Mismatches: 13, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
32 7 0.07
33 81 0.85
34 7 0.07
ACGTcount: A:0.42, C:0.23, G:0.10, T:0.26
Consensus pattern (31 bp):
ACCAAAACAGATTTGTTTCATCACAAACAAC
Found at i:52567 original size:30 final size:30
Alignment explanation
Indices: 52533--52592 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
52523 TTTCCTATAT
*
52533 TTGGGCCGAAAATTAGCAATAATTATTGGA
1 TTGGGCCGAAAATTAGAAATAATTATTGGA
52563 TTGGGCCGAAAATTAGAAATAATTATTGGA
1 TTGGGCCGAAAATTAGAAATAATTATTGGA
52593 AAATAATTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.38, C:0.08, G:0.23, T:0.30
Consensus pattern (30 bp):
TTGGGCCGAAAATTAGAAATAATTATTGGA
Found at i:57425 original size:11 final size:11
Alignment explanation
Indices: 57405--57436 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
57395 ACAGCGCAAT
57405 AAAAATAAAAC
1 AAAAATAAAAC
*
57416 AAAAACAAAAC
1 AAAAATAAAAC
57427 AAAAATAAAA
1 AAAAATAAAA
57437 AAACAGAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.84, C:0.09, G:0.00, T:0.06
Consensus pattern (11 bp):
AAAAATAAAAC
Found at i:61005 original size:31 final size:31
Alignment explanation
Indices: 60948--61025 Score: 99
Period size: 31 Copynumber: 2.5 Consensus size: 31
60938 ATTTTTAGCC
*
60948 ACCAATTTGAG-CTAAACCTTTTAAAAGTTG
1 ACCAATTTGAGCCTAAACATTTTAAAAGTTG
60978 -CTCAATTTGAGCCTAAA-ATTTTCAAAAGTTG
1 AC-CAATTTGAGCCTAAACATTTT-AAAAGTTG
*
61009 ACAAATTTGAGCCTAAA
1 ACCAATTTGAGCCTAAA
61026 GACAGAAACG
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
29 1 0.02
30 13 0.31
31 27 0.64
32 1 0.02
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.32
Consensus pattern (31 bp):
ACCAATTTGAGCCTAAACATTTTAAAAGTTG
Found at i:64143 original size:20 final size:21
Alignment explanation
Indices: 64105--64144 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
64095 GTTTTAGGGT
* *
64105 GTTGCATATTTTGATTTTATG
1 GTTGCATATTTTAAATTTATG
64126 GTTG-ATATTTTAAATTTAT
1 GTTGCATATTTTAAATTTAT
64145 TAATAACTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.25, C:0.03, G:0.15, T:0.57
Consensus pattern (21 bp):
GTTGCATATTTTAAATTTATG
Found at i:82343 original size:27 final size:26
Alignment explanation
Indices: 82305--82406 Score: 159
Period size: 28 Copynumber: 3.7 Consensus size: 26
82295 GGTCATTTAG
82305 GGGGCATTTTGGTCATTTTTGCATTCA
1 GGGGCATTTTGGTCA-TTTTGCATTCA
82332 GGGGCATTTTGGTCATTTTGCATGTTCA
1 GGGGCATTTTGGTCATTTTGCA--TTCA
82360 GGGGCATTTTGGTCATTTTGCACATTCA
1 GGGGCATTTTGGTCATTTTG--CATTCA
82388 GGGGCATTTTGGTCATTTT
1 GGGGCATTTTGGTCATTTT
82407 AAGTTCACAT
Statistics
Matches: 71, Mismatches: 0, Indels: 7
0.91 0.00 0.09
Matches are distributed among these distances:
26 7 0.10
27 15 0.21
28 47 0.66
30 2 0.03
ACGTcount: A:0.15, C:0.15, G:0.27, T:0.43
Consensus pattern (26 bp):
GGGGCATTTTGGTCATTTTGCATTCA
Found at i:88790 original size:14 final size:14
Alignment explanation
Indices: 88766--88798 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
88756 TGTGCCTATC
*
88766 TAATG-AAAATGTT
1 TAATGCAAAATGTA
88779 TAATGCAAAATGTA
1 TAATGCAAAATGTA
88793 TAATGC
1 TAATGC
88799 CTGAACTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.45, C:0.06, G:0.15, T:0.33
Consensus pattern (14 bp):
TAATGCAAAATGTA
Found at i:92031 original size:36 final size:36
Alignment explanation
Indices: 91991--92062 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
91981 CATTCTCAAC
91991 ACCACCATTTGAACCAGTTTTTCCTACCCATCCAAT
1 ACCACCATTTGAACCAGTTTTTCCTACCCATCCAAT
*
92027 ACCACCATTTGAACCAGTTTTTCCTACCCCTCCAAT
1 ACCACCATTTGAACCAGTTTTTCCTACCCATCCAAT
92063 GAAACCATCA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.26, C:0.38, G:0.06, T:0.31
Consensus pattern (36 bp):
ACCACCATTTGAACCAGTTTTTCCTACCCATCCAAT
Found at i:92070 original size:36 final size:36
Alignment explanation
Indices: 91994--92070 Score: 120
Period size: 36 Copynumber: 2.1 Consensus size: 36
91984 TCTCAACACC
*
91994 ACCATTTGAACCAGTTTTTCCTACCCATCCAATACC
1 ACCATTTGAACCAGTTTTTCCTACCCATCCAATACA
*
92030 ACCATTTGAACCAGTTTTTCCTACCCCTCCAATGA-A
1 ACCATTTGAACCAGTTTTTCCTACCCATCCAAT-ACA
92066 ACCAT
1 ACCAT
92071 CACCAACTGT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
36 37 0.97
37 1 0.03
ACGTcount: A:0.29, C:0.35, G:0.06, T:0.30
Consensus pattern (36 bp):
ACCATTTGAACCAGTTTTTCCTACCCATCCAATACA
Done.