Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021034.1 Corchorus olitorius cultivar O-4 contig21067, 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: 37079
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:132 original size:31 final size:29
Alignment explanation
Indices: 66--145 Score: 106
Period size: 29 Copynumber: 2.7 Consensus size: 29
56 CTCATTTTTG
* * *
66 AAACGTAAGGGATTAATTTGTCCCGAAAA
1 AAACATAAGGGATTATTTTGTCCCAAAAA
95 AAACATAAGGGATTATTTTGTCCCAAAAGCA
1 AAACATAAGGGATTATTTTGTCCCAAAA--A
*
126 AAACATAAGGGATTTTTTTG
1 AAACATAAGGGATTATTTTG
146 GGTATTTAGC
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
29 25 0.56
31 20 0.44
ACGTcount: A:0.40, C:0.12, G:0.19, T:0.29
Consensus pattern (29 bp):
AAACATAAGGGATTATTTTGTCCCAAAAA
Found at i:2898 original size:74 final size:72
Alignment explanation
Indices: 2809--2945 Score: 204
Period size: 74 Copynumber: 1.9 Consensus size: 72
2799 TATATTTGAG
* **
2809 GTGTGTATTGGTAGTTTAATTT-TTTGTGATTAAAATTTATTCTTTCCTTTTAATAAGAATTTAA
1 GTGTGTATTGATAGTTTAATTTATTT-TGATTAAAATTTA-TAATT-CTTTTAATAAGAATTTAA
2873 AGTGTTCGGA
63 AGTGTTCGGA
*
2883 GTGTGTATTGATAGTTTACTTTATTTTGATTAAAATTTATAATTCTTTTAATAAGAATTTAAA
1 GTGTGTATTGATAGTTTAATTTATTTTGATTAAAATTTATAATTCTTTTAATAAGAATTTAAA
2946 ATTTTTTAAA
Statistics
Matches: 58, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
72 19 0.33
73 3 0.05
74 33 0.57
75 3 0.05
ACGTcount: A:0.31, C:0.04, G:0.15, T:0.50
Consensus pattern (72 bp):
GTGTGTATTGATAGTTTAATTTATTTTGATTAAAATTTATAATTCTTTTAATAAGAATTTAAAGT
GTTCGGA
Found at i:3757 original size:21 final size:21
Alignment explanation
Indices: 3733--3800 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 21
3723 AAATTCTCTG
3733 TAAATTAAGAAATACTCAACT
1 TAAATTAAGAAATACTCAACT
* * **
3754 TAAATCATAGAAA-ATTC-TTT
1 TAAATTA-AGAAATACTCAACT
3774 GTAAATTAAGAAATACTCAACT
1 -TAAATTAAGAAATACTCAACT
*
3796 CAAAT
1 TAAAT
3801 CCTGATCCTT
Statistics
Matches: 34, Mismatches: 9, Indels: 8
0.67 0.18 0.16
Matches are distributed among these distances:
20 6 0.18
21 22 0.65
22 6 0.18
ACGTcount: A:0.50, C:0.13, G:0.06, T:0.31
Consensus pattern (21 bp):
TAAATTAAGAAATACTCAACT
Found at i:3780 original size:42 final size:42
Alignment explanation
Indices: 3721--3801 Score: 144
Period size: 42 Copynumber: 1.9 Consensus size: 42
3711 GCTAAGTCTT
*
3721 GAAAATTCTCTGTAAATTAAGAAATACTCAACTTAAATCATA
1 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA
*
3763 GAAAATTCTTTGTAAATTAAGAAATACTCAACTCAAATC
1 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATC
3802 CTGATCCTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.47, C:0.15, G:0.07, T:0.31
Consensus pattern (42 bp):
GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA
Found at i:3937 original size:55 final size:57
Alignment explanation
Indices: 3867--3982 Score: 200
Period size: 56 Copynumber: 2.1 Consensus size: 57
3857 TTTATTTTGT
*
3867 AGAATAATTAAGTAGAGATA-GGGGATAGGATTTATTATAACATTTATTGTGTGAA-
1 AGAATAATTAAGTAGAGATAGGGGGATAGGATTTATTACAACATTTATTGTGTGAAG
*
3922 AGAATAATTAAGTAGAGATAGGGGGATATGATTTATTACAACATTTATTGTGTGAAG
1 AGAATAATTAAGTAGAGATAGGGGGATAGGATTTATTACAACATTTATTGTGTGAAG
3979 AGAA
1 AGAA
3983 ACGATAATTA
Statistics
Matches: 57, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
55 20 0.35
56 33 0.58
57 4 0.07
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.33
Consensus pattern (57 bp):
AGAATAATTAAGTAGAGATAGGGGGATAGGATTTATTACAACATTTATTGTGTGAAG
Found at i:4452 original size:1 final size:1
Alignment explanation
Indices: 4446--4476 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
4436 GGCCCAACCG
4446 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
4477 CCAGCAGACT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:10093 original size:7 final size:7
Alignment explanation
Indices: 10081--10110 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
10071 CAGCCACCAC
10081 CCTCTCT
1 CCTCTCT
10088 CCTCTCT
1 CCTCTCT
10095 CCTCTCT
1 CCTCTCT
10102 CCTCTCT
1 CCTCTCT
10109 CC
1 CC
10111 AACGTGGCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.00, C:0.60, G:0.00, T:0.40
Consensus pattern (7 bp):
CCTCTCT
Found at i:16957 original size:2 final size:2
Alignment explanation
Indices: 16950--16977 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
16940 TTTTGATACT
16950 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
16978 GTAATATCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:18571 original size:9 final size:9
Alignment explanation
Indices: 18557--18581 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
18547 CATCTCGATT
18557 AAATTCTCA
1 AAATTCTCA
18566 AAATTCTCA
1 AAATTCTCA
18575 AAATTCT
1 AAATTCT
18582 AACGTTAGCC
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:0.44, C:0.20, G:0.00, T:0.36
Consensus pattern (9 bp):
AAATTCTCA
Found at i:20505 original size:37 final size:37
Alignment explanation
Indices: 20464--20534 Score: 115
Period size: 37 Copynumber: 1.9 Consensus size: 37
20454 ACATAATTAT
* *
20464 TCATAAAGTTATGTCTATCTGGAAAGACATGTATTGA
1 TCATAAAGTTATGTCTATATGAAAAGACATGTATTGA
*
20501 TCATAAAGTTGTGTCTATATGAAAAGACATGTAT
1 TCATAAAGTTATGTCTATATGAAAAGACATGTAT
20535 GTTGATCAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.37, C:0.10, G:0.18, T:0.35
Consensus pattern (37 bp):
TCATAAAGTTATGTCTATATGAAAAGACATGTATTGA
Found at i:23870 original size:14 final size:14
Alignment explanation
Indices: 23851--23884 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
23841 TTTAACCAAT
23851 TCATACCCAGTAAA
1 TCATACCCAGTAAA
23865 TCATACCCAGTAAA
1 TCATACCCAGTAAA
23879 TCATAC
1 TCATAC
23885 TTTTTAAACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.41, C:0.29, G:0.06, T:0.24
Consensus pattern (14 bp):
TCATACCCAGTAAA
Found at i:24203 original size:17 final size:17
Alignment explanation
Indices: 24167--24206 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
24157 ATCACCCCCC
24167 AGATCACTAGTGATCTA
1 AGATCACTAGTGATCTA
*
24184 AGATTACTAGTGATGC-A
1 AGATCACTAGTGAT-CTA
24201 AGATCA
1 AGATCA
24207 ATGGTAATCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
17 19 0.95
18 1 0.05
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.28
Consensus pattern (17 bp):
AGATCACTAGTGATCTA
Found at i:33375 original size:27 final size:27
Alignment explanation
Indices: 33336--33426 Score: 78
Period size: 27 Copynumber: 3.4 Consensus size: 27
33326 ATTCAAGGGT
* * *
33336 ATTTTTGTAATTTGCATGTACAGGGGC
1 ATTTTGGTCATTTGCATATACAGGGGC
* * *
33363 ATTTTGGTCATTT--TTACACTAAGGGC
1 ATTTTGGTCATTTGCATATAC-AGGGGC
*
33389 ATTTTGGTCATTTGCATATTCAGGGGC
1 ATTTTGGTCATTTGCATATACAGGGGC
**
33416 ACGTTGGTCAT
1 ATTTTGGTCAT
33427 CTTAAGTTCA
Statistics
Matches: 49, Mismatches: 12, Indels: 6
0.73 0.18 0.09
Matches are distributed among these distances:
25 3 0.06
26 18 0.37
27 25 0.51
28 3 0.06
ACGTcount: A:0.21, C:0.14, G:0.24, T:0.41
Consensus pattern (27 bp):
ATTTTGGTCATTTGCATATACAGGGGC
Found at i:33413 original size:26 final size:26
Alignment explanation
Indices: 33326--33413 Score: 68
Period size: 26 Copynumber: 3.3 Consensus size: 26
33316 CATTAGGCTC
* * *
33326 ATTCAAGGGTATTTTTGTAATTTGCAT
1 ATTC-AGGGCATTTTGGTCATTTGCAT
* * ** *
33353 GTACAGGGGCATTTTGGTCATTTTTAC
1 ATTCA-GGGCATTTTGGTCATTTGCAT
* *
33380 ACTAAGGGCATTTTGGTCATTTGCAT
1 ATTCAGGGCATTTTGGTCATTTGCAT
33406 ATTCAGGG
1 ATTCAGGG
33414 GCACGTTGGT
Statistics
Matches: 43, Mismatches: 17, Indels: 3
0.68 0.27 0.05
Matches are distributed among these distances:
26 25 0.58
27 18 0.42
ACGTcount: A:0.23, C:0.12, G:0.24, T:0.41
Consensus pattern (26 bp):
ATTCAGGGCATTTTGGTCATTTGCAT
Done.