Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011119.1 Corchorus capsularis cultivar CVL-1 contig11140, 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: 25873
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:1109 original size:2 final size:2
Alignment explanation
Indices: 1102--1141 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
1092 TATTTTGTTT
*
1102 AG AG AG AG AG AG AG AG -G AG GG AG -G AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1142 TATTTAATAG
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 2 0.06
2 32 0.94
ACGTcount: A:0.45, C:0.00, G:0.55, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2813 original size:23 final size:23
Alignment explanation
Indices: 2787--2832 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
2777 AACCTATAAT
2787 TTATAGGCCCAAAAGTATAGATA
1 TTATAGGCCCAAAAGTATAGATA
2810 TTATAGGCCCAAAAGTATAGATA
1 TTATAGGCCCAAAAGTATAGATA
2833 AACTCTGGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.26
Consensus pattern (23 bp):
TTATAGGCCCAAAAGTATAGATA
Found at i:6922 original size:2 final size:2
Alignment explanation
Indices: 6915--6943 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
6905 CTATTTAAAG
6915 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 A
6944 CACTATTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:13141 original size:17 final size:17
Alignment explanation
Indices: 13116--13149 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
13106 AAGGGTTTTC
*
13116 ATATCATATATATAATA
1 ATATAATATATATAATA
13133 ATATAATATATATAATA
1 ATATAATATATATAATA
13150 TATGTTGTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (17 bp):
ATATAATATATATAATA
Found at i:13145 original size:9 final size:9
Alignment explanation
Indices: 13116--13152 Score: 58
Period size: 9 Copynumber: 4.2 Consensus size: 9
13106 AAGGGTTTTC
*
13116 ATATCATAT
1 ATATAATAT
13125 ATATAATA-
1 ATATAATAT
13133 ATATAATAT
1 ATATAATAT
13142 ATATAATAT
1 ATATAATAT
13151 AT
1 AT
13153 GTTGTCAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
8 8 0.31
9 18 0.69
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (9 bp):
ATATAATAT
Found at i:19495 original size:21 final size:21
Alignment explanation
Indices: 19469--19519 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 21
19459 AAATATTATA
*
19469 TTTATCTTATCATGGGTAGTT
1 TTTATCTTATAATGGGTAGTT
*
19490 TTTATC-TAAAATGGGTAGTT
1 TTTATCTTATAATGGGTAGTT
*
19510 TTTATTTTAT
1 TTTATCTTAT
19520 TTAGAATTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 17 0.68
21 8 0.32
ACGTcount: A:0.24, C:0.06, G:0.16, T:0.55
Consensus pattern (21 bp):
TTTATCTTATAATGGGTAGTT
Found at i:19758 original size:13 final size:13
Alignment explanation
Indices: 19742--19768 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
19732 GGAAAAAGGA
19742 AAAAAGAAAAAAG
1 AAAAAGAAAAAAG
19755 AAAAAGAAAAAAG
1 AAAAAGAAAAAAG
19768 A
1 A
19769 GTTGCATTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (13 bp):
AAAAAGAAAAAAG
Found at i:19768 original size:7 final size:7
Alignment explanation
Indices: 19733--19768 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
19723 CTTCATTTGG
*
19733 GAAAAAG
1 GAAAAAA
19740 GAAAAAA
1 GAAAAAA
19747 GAAAAAA
1 GAAAAAA
19754 G-AAAAA
1 GAAAAAA
19760 GAAAAAA
1 GAAAAAA
19767 GA
1 GA
19769 GTTGCATTGA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
6 6 0.22
7 21 0.78
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (7 bp):
GAAAAAA
Found at i:25832 original size:31 final size:31
Alignment explanation
Indices: 25790--25861 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 31
25780 ATTGTCATAG
*
25790 TATTATATTTTTTAACATTTTCTTGTCTTCAA
1 TATTAT-TTTTTTAACATATTCTTGTCTTCAA
* * **
25822 TATTTTTTTTTTGAGGTATTCTTGTCTTCAA
1 TATTATTTTTTTAACATATTCTTGTCTTCAA
25853 TATTATTTT
1 TATTATTTT
25862 ACTTTATTTG
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
31 29 0.85
32 5 0.15
ACGTcount: A:0.21, C:0.10, G:0.07, T:0.62
Consensus pattern (31 bp):
TATTATTTTTTTAACATATTCTTGTCTTCAA
Done.