Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024367.1 Corchorus olitorius cultivar O-4 contig24400, 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: 22247
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:831 original size:21 final size:21
Alignment explanation
Indices: 802--868 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 21
792 GGCTTGGAAT
*
802 GGTGATGGCACGGGCATGGCC
1 GGTGGTGGCACGGGCATGGCC
* * **
823 GGTGGTGGCACGAGCTTAACC
1 GGTGGTGGCACGGGCATGGCC
* *
844 GGTGGTGGCATGGTGAATGGCC
1 GGTGGTGGCACGG-GCATGGCC
866 GGT
1 GGT
869 AATGGCTTGG
Statistics
Matches: 34, Mismatches: 11, Indels: 1
0.74 0.24 0.02
Matches are distributed among these distances:
21 27 0.79
22 7 0.21
ACGTcount: A:0.15, C:0.19, G:0.46, T:0.19
Consensus pattern (21 bp):
GGTGGTGGCACGGGCATGGCC
Found at i:14343 original size:27 final size:27
Alignment explanation
Indices: 14313--14378 Score: 123
Period size: 27 Copynumber: 2.4 Consensus size: 27
14303 TTTATTTTAG
*
14313 AAAACGCAAAAACACTTTTTTTTTTCA
1 AAAACGCAAAAACAATTTTTTTTTTCA
14340 AAAACGCAAAAACAATTTTTTTTTTCA
1 AAAACGCAAAAACAATTTTTTTTTTCA
14367 AAAACGCAAAAA
1 AAAACGCAAAAA
14379 AAAAATCTTG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.48, C:0.17, G:0.05, T:0.30
Consensus pattern (27 bp):
AAAACGCAAAAACAATTTTTTTTTTCA
Found at i:14738 original size:19 final size:19
Alignment explanation
Indices: 14714--14756 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
14704 TAAGGATGAC
14714 AATAATAA-AAAAATAAATA
1 AATAATAATAAAAATAAA-A
*
14733 AATAATAATAATAATAAAA
1 AATAATAATAAAAATAAAA
14752 AATAA
1 AATAA
14757 CAAATACAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (19 bp):
AATAATAATAAAAATAAAA
Found at i:14788 original size:16 final size:17
Alignment explanation
Indices: 14758--14790 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
14748 AAAAAATAAC
*
14758 AAATACAAATTAATTTA
1 AAATACAAATAAATTTA
14775 AAATA-AAATAAATTTA
1 AAATACAAATAAATTTA
14791 TACAAGAAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (17 bp):
AAATACAAATAAATTTA
Found at i:15722 original size:27 final size:26
Alignment explanation
Indices: 15692--15770 Score: 88
Period size: 27 Copynumber: 3.0 Consensus size: 26
15682 GCACTTAGGT
*
15692 CATTTAGGGGCATTTTGGTCTTTTTTG
1 CATTTAGGGGCATTTTGGTC-TTTTTC
* *
15719 CATTCAGGGGCATTTTGGTC-ATTTC
1 CATTTAGGGGCATTTTGGTCTTTTTC
*
15744 CATGTTCAGGGGCATTTTGGTCATTTT
1 CAT-TT-AGGGGCATTTTGGTCTTTTT
15771 AGGTTCATTT
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
25 6 0.14
26 1 0.02
27 34 0.77
28 3 0.07
ACGTcount: A:0.14, C:0.15, G:0.25, T:0.46
Consensus pattern (26 bp):
CATTTAGGGGCATTTTGGTCTTTTTC
Found at i:20212 original size:28 final size:28
Alignment explanation
Indices: 20158--20212 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
20148 TTAAAATCAC
*
20158 TCACTACAACTCGCCACCCATTGTAGAA
1 TCACTACAACTCGCCACCCATAGTAGAA
* *
20186 TCACTGCAATTCGCCA-CCATAGCTAGA
1 TCACTACAACTCGCCACCCATAG-TAGA
20213 TTTCCCCAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.31, C:0.35, G:0.13, T:0.22
Consensus pattern (28 bp):
TCACTACAACTCGCCACCCATAGTAGAA
Found at i:21831 original size:74 final size:72
Alignment explanation
Indices: 21746--21922 Score: 202
Period size: 73 Copynumber: 2.4 Consensus size: 72
21736 AAAAATGCTT
* *
21746 TTGATGGGAACTTTCCCACTTTGAAAAC-T-AAAACTGAAAATGACAGGAACTTTCCCTAAATTG
1 TTGATGGGAACTTTCCCAATTTAAAAACTTAAAAACTG--AATG---GGAACTTTCCC-AAATTG
21809 -AAAAC-TAAAAC
60 AAAAACTTAAAAC
*
21820 TTGATGGGAACTTTCCCAATTTAAAAACTTTGAAAAACTGAATGGGAACTTTCCCAATTTGAAAA
1 TTGATGGGAACTTTCCCAATTTAAAAAC-TT-AAAAACTGAATGGGAACTTTCCCAAATTGAAAA
21885 ACTTAAAAC
64 ACTTAAAAC
* *
21894 -TGGTGGGAACTTTCCCAATTAAAAAACTT
1 TTGATGGGAACTTTCCCAATTTAAAAACTT
21923 TGAACATGAT
Statistics
Matches: 92, Mismatches: 5, Indels: 14
0.83 0.05 0.13
Matches are distributed among these distances:
72 7 0.08
73 41 0.45
74 32 0.35
76 5 0.05
78 7 0.08
ACGTcount: A:0.40, C:0.18, G:0.14, T:0.28
Consensus pattern (72 bp):
TTGATGGGAACTTTCCCAATTTAAAAACTTAAAAACTGAATGGGAACTTTCCCAAATTGAAAAAC
TTAAAAC
Found at i:21910 original size:35 final size:35
Alignment explanation
Indices: 21747--21922 Score: 166
Period size: 38 Copynumber: 4.9 Consensus size: 35
21737 AAAATGCTTT
*
21747 TGATGGGAACTTTCCCACTTTG-AAAAC-TAAAAC
1 TGATGGGAACTTTCCCAATTTGAAAAACTTAAAAC
*
21780 TGAAAATGACAGGAACTTTCCCTAAATTG-AAAAC-TAAAAC
1 TG---ATG---GGAACTTTCCC-AATTTGAAAAACTTAAAAC
21820 TTGATGGGAACTTTCCCAATTT-AAAAACTTTGAAAAAC
1 -TGATGGGAACTTTCCCAATTTGAAAAAC-TT--AAAAC
21858 TGAATGGGAACTTTCCCAATTTGAAAAACTTAAAAC
1 TG-ATGGGAACTTTCCCAATTTGAAAAACTTAAAAC
* *
21894 TGGTGGGAACTTTCCCAA-TTAAAAAACTT
1 TGATGGGAACTTTCCCAATTTGAAAAACTT
21923 TGAACATGAT
Statistics
Matches: 123, Mismatches: 5, Indels: 29
0.78 0.03 0.18
Matches are distributed among these distances:
33 2 0.02
34 19 0.15
35 26 0.21
36 11 0.09
37 2 0.02
38 29 0.24
39 17 0.14
40 15 0.12
41 2 0.02
ACGTcount: A:0.40, C:0.18, G:0.14, T:0.28
Consensus pattern (35 bp):
TGATGGGAACTTTCCCAATTTGAAAAACTTAAAAC
Found at i:21910 original size:73 final size:73
Alignment explanation
Indices: 21791--21926 Score: 213
Period size: 73 Copynumber: 1.9 Consensus size: 73
21781 GAAAATGACA
*
21791 GGAACTTTCCCTAAATTGAAAACTAAAACTTGATGGGAACTTTCCCAATTTAAAAACTTTGAAAA
1 GGAACTTTCCCTAAATTGAAAACTAAAACTTGATGGGAACTTTCCCAATTAAAAAACTTTGAAAA
21856 ACTGAATG
66 ACTGAATG
* *
21864 GGAACTTTCCC-AATTTGAAAAACTTAAAAC-TGGTGGGAACTTTCCCAATTAAAAAACTTTGAA
1 GGAACTTTCCCTAAATTG-AAAAC-TAAAACTTGATGGGAACTTTCCCAATTAAAAAACTTTGAA
21927 CATGATGAAA
Statistics
Matches: 58, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
72 5 0.09
73 47 0.81
74 6 0.10
ACGTcount: A:0.40, C:0.17, G:0.14, T:0.29
Consensus pattern (73 bp):
GGAACTTTCCCTAAATTGAAAACTAAAACTTGATGGGAACTTTCCCAATTAAAAAACTTTGAAAA
ACTGAATG
Found at i:21966 original size:21 final size:20
Alignment explanation
Indices: 21940--21979 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
21930 GATGAAATTT
*
21940 TTTTTTATTTTTGAGTTTTTAA
1 TTTTTT-TTTTAGA-TTTTTAA
21962 TTTTTTTTTTAGATTTTT
1 TTTTTTTTTTAGATTTTT
21980 GAAAACCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 6 0.35
22 6 0.35
ACGTcount: A:0.15, C:0.00, G:0.07, T:0.78
Consensus pattern (20 bp):
TTTTTTTTTTAGATTTTTAA
Done.