Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014073.1 Corchorus olitorius cultivar O-4 contig14106, 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: 45878
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Found at i:6811 original size:50 final size:50
Alignment explanation
Indices: 6753--7078 Score: 537
Period size: 50 Copynumber: 6.5 Consensus size: 50
6743 CAGATATCAG
*
6753 GATTGAATTGGAAGACAGTTCAAAGGATAAGCAGAAGACGGTCCTTTTAA
1 GATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTAA
*
6803 GATTGAATTGGAAGACAGTTCGAAGGATAAGCGGAAGACGGT-CTTCTTAA
1 GATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTT-TTAA
*
6853 GATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGATGGTCCTTTTAA
1 GATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTAA
*
6903 GATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTTCTTTTTAA
1 GATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGG-TCCTTTTAA
*
6954 GATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGATCCTTTTAA
1 GATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTAA
* *
7004 GATTGAATTAGAAGACAGTTCAAAGGATAAGCGAAAGACGGTCCTTTTAA
1 GATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTAA
* * *
7054 TATTGGATTGGAAGACAATTCAAAG
1 GATTGAATTGGAAGACAGTTCAAAG
7079 AAGTTGATCG
Statistics
Matches: 258, Mismatches: 15, Indels: 6
0.92 0.05 0.02
Matches are distributed among these distances:
49 3 0.01
50 204 0.79
51 51 0.20
ACGTcount: A:0.37, C:0.11, G:0.27, T:0.25
Consensus pattern (50 bp):
GATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTAA
Found at i:7026 original size:151 final size:150
Alignment explanation
Indices: 6753--7078 Score: 537
Period size: 151 Copynumber: 2.2 Consensus size: 150
6743 CAGATATCAG
6753 GATTGAATTGGAAGACAGTTCAAAGGATAAGCAGAAGACGGTCCTTTTAAGATTGAATTGGAAGA
1 GATTGAATTGGAAGACAGTTCAAAGGATAAGCAGAAGACGGTCCTTTTAAGATTGAATTGGAAGA
* * *
6818 CAGTTCGAAGGATAAGCGGAAGACGGTCTTCTTAAGATTGAATTGGAAGACAGTTCAAAGGATAA
66 CAGTTCAAAGGATAAGCGGAAGACGATCTTCTTAAGATTGAATTAGAAGACAGTTCAAAGGATAA
* *
6883 GCGGAAGATGGTCCTTTTAA
131 GCGAAAGACGGTCCTTTTAA
* *
6903 GATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTTCTTTTTAAGATTGAATTGGAAG
1 GATTGAATTGGAAGACAGTTCAAAGGATAAGCAGAAGACGG-TCCTTTTAAGATTGAATTGGAAG
6968 ACAGTTCAAAGGATAAGCGGAAGACGATCCTT-TTAAGATTGAATTAGAAGACAGTTCAAAGGAT
65 ACAGTTCAAAGGATAAGCGGAAGACGAT-CTTCTTAAGATTGAATTAGAAGACAGTTCAAAGGAT
7032 AAGCGAAAGACGGTCCTTTTAA
129 AAGCGAAAGACGGTCCTTTTAA
* * *
7054 TATTGGATTGGAAGACAATTCAAAG
1 GATTGAATTGGAAGACAGTTCAAAG
7079 AAGTTGATCG
Statistics
Matches: 164, Mismatches: 10, Indels: 3
0.93 0.06 0.02
Matches are distributed among these distances:
150 40 0.24
151 121 0.74
152 3 0.02
ACGTcount: A:0.37, C:0.11, G:0.27, T:0.25
Consensus pattern (150 bp):
GATTGAATTGGAAGACAGTTCAAAGGATAAGCAGAAGACGGTCCTTTTAAGATTGAATTGGAAGA
CAGTTCAAAGGATAAGCGGAAGACGATCTTCTTAAGATTGAATTAGAAGACAGTTCAAAGGATAA
GCGAAAGACGGTCCTTTTAA
Found at i:7350 original size:27 final size:27
Alignment explanation
Indices: 7320--7392 Score: 119
Period size: 27 Copynumber: 2.7 Consensus size: 27
7310 TAGGGTTATT
7320 TAGGGGCATTTTGGTCATTTGCACGTC
1 TAGGGGCATTTTGGTCATTTGCACGTC
*
7347 TAGGGGCATTTTGGTCATTTGCATGTC
1 TAGGGGCATTTTGGTCATTTGCACGTC
* *
7374 CAGGGGCATTTTAGTCATT
1 TAGGGGCATTTTGGTCATT
7393 CTAAGGACAT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.16, C:0.16, G:0.29, T:0.38
Consensus pattern (27 bp):
TAGGGGCATTTTGGTCATTTGCACGTC
Found at i:12408 original size:2 final size:2
Alignment explanation
Indices: 12401--12437 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
12391 CAATTATTAC
12401 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
12438 CCCCCCCACT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:18958 original size:21 final size:21
Alignment explanation
Indices: 18932--18972 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
18922 ATATGATATA
18932 ATAACTTCGCCAAACTTAAAT
1 ATAACTTCGCCAAACTTAAAT
18953 ATAACTTCGCCAAACTTAAA
1 ATAACTTCGCCAAACTTAAA
18973 AATTTTAAAT
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:0.44, C:0.24, G:0.05, T:0.27
Consensus pattern (21 bp):
ATAACTTCGCCAAACTTAAAT
Found at i:19157 original size:42 final size:42
Alignment explanation
Indices: 19110--19192 Score: 123
Period size: 42 Copynumber: 2.0 Consensus size: 42
19100 TCGATATTAA
* *
19110 TTTTGAATATTAAATACGTTA-TTAATTATCAGGTGGAGTATG
1 TTTTGAATACTAAATAC-ATACTTAATTATCAGGTGGAGTATG
*
19152 TTTTGAATACTAAATACATACTTAATTATCAGGTGGGGTAT
1 TTTTGAATACTAAATACATACTTAATTATCAGGTGGAGTAT
19193 TTATCTACAT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
41 2 0.05
42 35 0.95
ACGTcount: A:0.34, C:0.07, G:0.18, T:0.41
Consensus pattern (42 bp):
TTTTGAATACTAAATACATACTTAATTATCAGGTGGAGTATG
Found at i:20552 original size:14 final size:13
Alignment explanation
Indices: 20525--20566 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
20515 CGACCTGGGC
20525 TTTTT-TTTTAAT
1 TTTTTATTTTAAT
20537 TTTTTATTTTAGAT
1 TTTTTATTTTA-AT
*
20551 TTATTATTATTAAT
1 TTTTTATT-TTAAT
20565 TT
1 TT
20567 AAATTTTGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
12 5 0.19
13 5 0.19
14 13 0.50
15 3 0.12
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (13 bp):
TTTTTATTTTAAT
Found at i:20614 original size:10 final size:10
Alignment explanation
Indices: 20601--20642 Score: 52
Period size: 10 Copynumber: 4.4 Consensus size: 10
20591 ATTAAGGTTT
20601 ATTATTGTTA
1 ATTATTGTTA
20611 ATTA--GTTA
1 ATTATTGTTA
20619 ATTATTGTTA
1 ATTATTGTTA
* *
20629 ATTACTATTA
1 ATTATTGTTA
20639 ATTA
1 ATTA
20643 ACTAATTTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
8 8 0.29
10 20 0.71
ACGTcount: A:0.36, C:0.02, G:0.07, T:0.55
Consensus pattern (10 bp):
ATTATTGTTA
Found at i:20942 original size:18 final size:18
Alignment explanation
Indices: 20919--20953 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
20909 AGAGGAGAGG
*
20919 AGGACAGGTGAGTAGCTT
1 AGGACAGGGGAGTAGCTT
20937 AGGACAGGGGAGTAGCT
1 AGGACAGGGGAGTAGCT
20954 CGGGACAGCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.11, G:0.43, T:0.17
Consensus pattern (18 bp):
AGGACAGGGGAGTAGCTT
Found at i:20959 original size:18 final size:18
Alignment explanation
Indices: 20919--20961 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
20909 AGAGGAGAGG
* *
20919 AGGACAGGTGAGTAGCTT
1 AGGACAGGGGAGTAGCTC
20937 AGGACAGGGGAGTAGCTC
1 AGGACAGGGGAGTAGCTC
*
20955 GGGACAG
1 AGGACAG
20962 CGGCTGTCGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.28, C:0.14, G:0.44, T:0.14
Consensus pattern (18 bp):
AGGACAGGGGAGTAGCTC
Found at i:22821 original size:41 final size:41
Alignment explanation
Indices: 22774--22869 Score: 138
Period size: 41 Copynumber: 2.3 Consensus size: 41
22764 AAAATAAAAT
***
22774 CCTAAATCAGGGGTGAAATTGAATCAATAAATAAACATTAC
1 CCTAAATCAGGGACAAAATTGAATCAATAAATAAACATTAC
* *
22815 CCTAAATCAGGGACAAAATTGAATCAATTAATAAGCATTAC
1 CCTAAATCAGGGACAAAATTGAATCAATAAATAAACATTAC
*
22856 TCTAAATCAGGGAC
1 CCTAAATCAGGGAC
22870 TAAGGTGAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.45, C:0.17, G:0.15, T:0.24
Consensus pattern (41 bp):
CCTAAATCAGGGACAAAATTGAATCAATAAATAAACATTAC
Found at i:25008 original size:21 final size:21
Alignment explanation
Indices: 24984--25028 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
24974 GGTGCCCACA
*
24984 TGGTTTCCTTGAGCACCCATG
1 TGGTTTCCTTGAGCACCCAGG
* *
25005 TGGTTTGCTTGAGGACCCAGG
1 TGGTTTCCTTGAGCACCCAGG
25026 TGG
1 TGG
25029 GCGGTGTCAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.13, C:0.22, G:0.33, T:0.31
Consensus pattern (21 bp):
TGGTTTCCTTGAGCACCCAGG
Found at i:26083 original size:26 final size:27
Alignment explanation
Indices: 26041--26092 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
26031 ATGATTTAGG
*
26041 GGTTACTAACTCCCTTT-TTCTTTTGA
1 GGTTACTAACACCCTTTCTTCTTTTGA
* *
26067 GGTTACTAACACTCTTTCTTTTTTTG
1 GGTTACTAACACCCTTTCTTCTTTTG
26093 TTTTCAGAGG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 15 0.68
27 7 0.32
ACGTcount: A:0.15, C:0.21, G:0.12, T:0.52
Consensus pattern (27 bp):
GGTTACTAACACCCTTTCTTCTTTTGA
Found at i:28517 original size:22 final size:20
Alignment explanation
Indices: 28488--28537 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
28478 GTAAGTGATG
*
28488 AAGTAGTGAAATTGATGATTA
1 AAGTAGTGAAATTG-TGAATA
*
28509 AAGTGAGTGAATTTGTGAATA
1 AAGT-AGTGAAATTGTGAATA
28530 AAGGTAGT
1 AA-GTAGT
28538 AGAAGAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 14 0.56
22 11 0.44
ACGTcount: A:0.40, C:0.00, G:0.28, T:0.32
Consensus pattern (20 bp):
AAGTAGTGAAATTGTGAATA
Found at i:30870 original size:21 final size:21
Alignment explanation
Indices: 30837--30885 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
30827 AAGAATTGTA
**
30837 GCTT-CTTGGAAATGGCTCTT
1 GCTTCCTTGGAAATCCCTCTT
*
30857 GCTTCCTTTGAAATCCCTCTT
1 GCTTCCTTGGAAATCCCTCTT
30878 GCATTCCT
1 GC-TTCCT
30886 AAAGCATTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 4 0.17
21 15 0.62
22 5 0.21
ACGTcount: A:0.14, C:0.29, G:0.16, T:0.41
Consensus pattern (21 bp):
GCTTCCTTGGAAATCCCTCTT
Found at i:31997 original size:27 final size:27
Alignment explanation
Indices: 31967--32019 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
31957 AAAAGTAACT
31967 AAGAAAAATAAAC-AAAAATAAAAAGAA
1 AAGAAAAAT-AACGAAAAATAAAAAGAA
*
31994 AAGAAAAATAACGAACAATAAAAAGA
1 AAGAAAAATAACGAAAAATAAAAAGA
32020 TAAGGTAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 3 0.12
27 21 0.88
ACGTcount: A:0.77, C:0.06, G:0.09, T:0.08
Consensus pattern (27 bp):
AAGAAAAATAACGAAAAATAAAAAGAA
Found at i:33727 original size:76 final size:76
Alignment explanation
Indices: 33590--33733 Score: 170
Period size: 76 Copynumber: 1.9 Consensus size: 76
33580 ACAAGGACCC
* * *
33590 CGACTCCACCTGGGCTCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCTTGAGGACCCAGGT
1 CGACTCCACCTGGGCTCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGCACCCAGAT
33655 GGGGGGTGTCA
66 GGGGGGTGTCA
* * *
33666 CGACTCCAGCTGGG-TGCCCACATGGTTTGTC-TGAAG-ACCCATGT-GTTTCGCCTGATCACCC
1 CGACTCCACCTGGGCT-CCCACATGG-TTGCCTTG-AGCACCCATGTGGTTT-GCCTGAGCACCC
33727 AGATGGG
62 AGATGGG
33734 CTGTGTCATA
Statistics
Matches: 58, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
75 5 0.09
76 47 0.81
77 6 0.10
ACGTcount: A:0.16, C:0.29, G:0.31, T:0.24
Consensus pattern (76 bp):
CGACTCCACCTGGGCTCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGCACCCAGAT
GGGGGGTGTCA
Found at i:45672 original size:7 final size:7
Alignment explanation
Indices: 45660--45684 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
45650 ACAATTGAGT
45660 TTTTCCC
1 TTTTCCC
45667 TTTTCCC
1 TTTTCCC
45674 TTTTCCC
1 TTTTCCC
45681 TTTT
1 TTTT
45685 AATTTCTTTA
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:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (7 bp):
TTTTCCC
Done.