Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024563.1 Corchorus olitorius cultivar O-4 contig24596, 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: 16698
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:483 original size:21 final size:22
Alignment explanation
Indices: 457--498 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
447 TTAAAAGAAT
457 AATAAACG-AAAAAAAGAAAAC
1 AATAAACGAAAAAAAAGAAAAC
478 AATAAACGAAAAAAAAGAAAA
1 AATAAACGAAAAAAAAGAAAA
499 AAAGAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.79, C:0.07, G:0.10, T:0.05
Consensus pattern (22 bp):
AATAAACGAAAAAAAAGAAAAC
Found at i:1735 original size:9 final size:9
Alignment explanation
Indices: 1716--1769 Score: 74
Period size: 9 Copynumber: 6.0 Consensus size: 9
1706 TATGAAAATC
1716 CTTTCTTTTT
1 CTTT-TTTTT
1726 CTTTTTTTT
1 CTTTTTTTT
*
1735 C-TTATTTT
1 CTTTTTTTT
*
1743 CTTTTTCTT
1 CTTTTTTTT
1752 CTTTTTTTT
1 CTTTTTTTT
1761 CTTTTTTTT
1 CTTTTTTTT
1770 GGACCCACAT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
8 7 0.18
9 28 0.72
10 4 0.10
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (9 bp):
CTTTTTTTT
Found at i:1749 original size:14 final size:13
Alignment explanation
Indices: 1727--1769 Score: 54
Period size: 12 Copynumber: 3.4 Consensus size: 13
1717 TTTCTTTTTC
1727 TTTTTTTTCTTAT
1 TTTTTTTTCTTAT
*
1740 TTTCTTTTTCTT-C
1 TTT-TTTTTCTTAT
1753 TTTTTTTTCTT-T
1 TTTTTTTTCTTAT
1765 TTTTT
1 TTTTT
1770 GGACCCACAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
12 13 0.48
13 6 0.22
14 8 0.30
ACGTcount: A:0.02, C:0.12, G:0.00, T:0.86
Consensus pattern (13 bp):
TTTTTTTTCTTAT
Found at i:3773 original size:131 final size:124
Alignment explanation
Indices: 3526--3781 Score: 361
Period size: 123 Copynumber: 2.0 Consensus size: 124
3516 CATTGTTTAA
* *
3526 ACTTTTATAGTTTTACTCAACTAAAAACTCTAATTTTGTTTAATTAAATATAATATCTTTATAAT
1 ACTTTTACAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATATAATATCTTTATAAT
3591 TTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAA-ATTTTTAAATAT
66 TTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATATTTTTAAATAT
** * *
3649 ACTTTTACAGTTTTACTCAACTAAAAGTTCTATTTTTATTTAATTAAATCTAATATCCTTATACC
1 ACTTTTACAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATATAATAT-CTT-TA--
* *
3714 TATTTTATTTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGTATTTTTTTAAAT
62 TA----ATTTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATATTTTTAAAT
3779 AT
123 AT
3781 A
1 A
3782 TTTCTTAAAT
Statistics
Matches: 116, Mismatches: 8, Indels: 9
0.87 0.06 0.07
Matches are distributed among these distances:
123 50 0.43
124 3 0.03
125 2 0.02
127 2 0.02
131 47 0.41
132 12 0.10
ACGTcount: A:0.38, C:0.10, G:0.02, T:0.50
Consensus pattern (124 bp):
ACTTTTACAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATATAATATCTTTATAAT
TTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATATTTTTAAATAT
Found at i:4652 original size:17 final size:16
Alignment explanation
Indices: 4630--4680 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 16
4620 GGGTATACTC
4630 TTTTTCCTTCTTGAGG
1 TTTTTCCTTCTTGAGG
*
4646 ATTTTTCCTAC-TG-GG
1 -TTTTTCCTTCTTGAGG
4661 TTTTTCC-TCTTGAAGG
1 TTTTTCCTTCTTG-AGG
4677 TTTT
1 TTTT
4681 AACGAGACAC
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
13 1 0.03
14 9 0.31
15 2 0.07
16 8 0.28
17 9 0.31
ACGTcount: A:0.10, C:0.18, G:0.18, T:0.55
Consensus pattern (16 bp):
TTTTTCCTTCTTGAGG
Found at i:12503 original size:41 final size:41
Alignment explanation
Indices: 12455--12634 Score: 180
Period size: 41 Copynumber: 4.3 Consensus size: 41
12445 GGGTCGAATG
* * * *
12455 ACTTGGTCCTGAATTGACAATCTAATTCAAGGATCTTGATA
1 ACTTGGTCTTGAATTGATAATTTAATTCAAGGATCTCGATA
* * *
12496 ACTTGGTCTTGAATTGATAATAATTCGATTCAAGGGTCTCGATG
1 ACTTGGTCTTGAATTGATAAT--TT-AATTCAAGGATCTCGATA
* * *
12540 ACTTGTTCTTGAATTGATAATTTAATTCAAGGGTCTCGATG
1 ACTTGGTCTTGAATTGATAATTTAATTCAAGGATCTCGATA
*** * * *
12581 ACTCAATCTTGAATTGATAATTTAATTAAAGGGTCTCGATG
1 ACTTGGTCTTGAATTGATAATTTAATTCAAGGATCTCGATA
*
12622 ACTTGATCTTGAA
1 ACTTGGTCTTGAA
12635 CAAACAAAAA
Statistics
Matches: 121, Mismatches: 15, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
41 84 0.69
42 2 0.02
43 1 0.01
44 34 0.28
ACGTcount: A:0.30, C:0.14, G:0.19, T:0.37
Consensus pattern (41 bp):
ACTTGGTCTTGAATTGATAATTTAATTCAAGGATCTCGATA
Found at i:12553 original size:85 final size:82
Alignment explanation
Indices: 12434--12634 Score: 226
Period size: 85 Copynumber: 2.4 Consensus size: 82
12424 GTTCGATTTG
* * * *
12434 ATTTTATTCAAGGG--TCGAATGACTTGGTCCTGAATTGACAATCTAATTCAAGGATCTTGATAA
1 ATTTAATTCAAGGGTCTCG-ATGACTTGATCTTGAATTGACAATCTAATTCAAGGATCTCGATAA
***
12497 CTTGGTCTTGAATTGATA
65 CTCAATCTTGAATTGATA
* * * * *
12515 ATAATTCGATTCAAGGGTCTCGATGACTTGTTCTTGAATTGATAATTTAATTCAAGGGTCTCGAT
1 AT--TT-AATTCAAGGGTCTCGATGACTTGATCTTGAATTGACAATCTAATTCAAGGATCTCGAT
*
12580 GACTCAATCTTGAATTGATA
63 AACTCAATCTTGAATTGATA
*
12600 ATTTAATTAAAGGGTCTCGATGACTTGATCTTGAA
1 ATTTAATTCAAGGGTCTCGATGACTTGATCTTGAA
12635 CAAACAAAAA
Statistics
Matches: 101, Mismatches: 14, Indels: 9
0.81 0.11 0.07
Matches are distributed among these distances:
81 2 0.02
82 28 0.28
83 4 0.04
84 9 0.09
85 55 0.54
86 3 0.03
ACGTcount: A:0.30, C:0.13, G:0.19, T:0.37
Consensus pattern (82 bp):
ATTTAATTCAAGGGTCTCGATGACTTGATCTTGAATTGACAATCTAATTCAAGGATCTCGATAAC
TCAATCTTGAATTGATA
Found at i:12751 original size:16 final size:16
Alignment explanation
Indices: 12730--12760 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
12720 TCTGAAAATA
12730 CTTCAGAGCTTTTCTG
1 CTTCAGAGCTTTTCTG
12746 CTTCAGAGCTTTTCT
1 CTTCAGAGCTTTTCT
12761 ACTTTCTGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.13, C:0.26, G:0.16, T:0.45
Consensus pattern (16 bp):
CTTCAGAGCTTTTCTG
Found at i:15920 original size:13 final size:13
Alignment explanation
Indices: 15878--15922 Score: 56
Period size: 12 Copynumber: 3.5 Consensus size: 13
15868 TCATGCACCC
*
15878 AAAACAATTTATTT
1 AAAACAATTTA-AT
*
15892 AAAACCATTT-AT
1 AAAACAATTTAAT
15904 AAAACAATTTAAT
1 AAAACAATTTAAT
15917 AAAACA
1 AAAACA
15923 GTAATAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
12 10 0.37
13 8 0.30
14 9 0.33
ACGTcount: A:0.58, C:0.11, G:0.00, T:0.31
Consensus pattern (13 bp):
AAAACAATTTAAT
Done.