Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012237.1 Corchorus olitorius cultivar O-4 contig12270, 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: 28259
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:106 original size:25 final size:24
Alignment explanation
Indices: 70--116 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
60 TCCTTCTATT
70 CATCTATCATC-AAGTTTTTCATC
1 CATCTATCATCAAAGTTTTTCATC
93 CATCTCATCCATCAAAGTTTTTCA
1 CATCT-AT-CATCAAAGTTTTTCA
117 AATTTTCTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.24
24 2 0.10
25 4 0.19
26 10 0.48
ACGTcount: A:0.28, C:0.28, G:0.04, T:0.40
Consensus pattern (24 bp):
CATCTATCATCAAAGTTTTTCATC
Found at i:1071 original size:15 final size:15
Alignment explanation
Indices: 1051--1082 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1041 CCTTGGGGGT
1051 TCAAAATCAACAAGC
1 TCAAAATCAACAAGC
*
1066 TCAAAATCGACAAGC
1 TCAAAATCAACAAGC
1081 TC
1 TC
1083 CACTTAGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.28, G:0.09, T:0.16
Consensus pattern (15 bp):
TCAAAATCAACAAGC
Found at i:1746 original size:66 final size:66
Alignment explanation
Indices: 1668--1794 Score: 184
Period size: 66 Copynumber: 1.9 Consensus size: 66
1658 AGTAATTCTG
*
1668 AACCTGATTTAAGTGTTGTTTGCAATGACA-TGAAATCTGTTTTAGATGTTGTTAGTGATGATAC
1 AACCTAATTTAAGTGTTGTTTGCAATGACACT-AAATCTGTTTTAGATGTTGTTAGTGATGATAC
1732 TA
65 TA
** * * *
1734 AACCTAATTTAAGTGTTGTTTGTGATGACACTAAATTTGTTTTAGGTGTTGTTTGTGATGA
1 AACCTAATTTAAGTGTTGTTTGCAATGACACTAAATCTGTTTTAGATGTTGTTAGTGATGA
1795 AACAAATTCT
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
66 53 0.98
67 1 0.02
ACGTcount: A:0.27, C:0.08, G:0.22, T:0.43
Consensus pattern (66 bp):
AACCTAATTTAAGTGTTGTTTGCAATGACACTAAATCTGTTTTAGATGTTGTTAGTGATGATACT
A
Found at i:1783 original size:33 final size:33
Alignment explanation
Indices: 1675--1809 Score: 132
Period size: 33 Copynumber: 4.1 Consensus size: 33
1665 CTGAACCTGA
**
1675 TTTAAGTGTTGTTTGCAATGACA-TGAAATCTGT
1 TTTAAGTGTTGTTTGTGATGACACT-AAATCTGT
* * * **
1708 TTT-AGATGTTGTTAGTGATGATACTAAACCTAA
1 TTTAAG-TGTTGTTTGTGATGACACTAAATCTGT
*
1741 TTTAAGTGTTGTTTGTGATGACACTAAATTTGT
1 TTTAAGTGTTGTTTGTGATGACACTAAATCTGT
* *
1774 TTTAGGTGTTGTTTGTGATGAAAC-AAATTCTGT
1 TTTAAGTGTTGTTTGTGATGACACTAAA-TCTGT
1807 TTT
1 TTT
1810 GGATGCTAAT
Statistics
Matches: 82, Mismatches: 16, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
32 5 0.06
33 74 0.90
34 3 0.04
ACGTcount: A:0.27, C:0.07, G:0.21, T:0.45
Consensus pattern (33 bp):
TTTAAGTGTTGTTTGTGATGACACTAAATCTGT
Found at i:5800 original size:21 final size:21
Alignment explanation
Indices: 5776--5821 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
5766 AGCTTGACTT
5776 GGCAGGTGGCGCGGATGGCCG
1 GGCAGGTGGCGCGGATGGCCG
*
5797 GGCAGGTGGCTCGGATGGCCG
1 GGCAGGTGGCGCGGATGGCCG
5818 GGCA
1 GGCA
5822 AGTGACTTGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.11, C:0.24, G:0.54, T:0.11
Consensus pattern (21 bp):
GGCAGGTGGCGCGGATGGCCG
Found at i:9898 original size:21 final size:20
Alignment explanation
Indices: 9859--9903 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
9849 GATTAAGAAT
* *
9859 TAAAAAGAAAGCAATTAAAC
1 TAAAAACAAAGCAAGTAAAC
*
9879 TAAAAACAAAGCAAAGTAAAT
1 TAAAAACAAAGC-AAGTAAAC
9900 TAAA
1 TAAA
9904 TCTAAATCTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.67, C:0.09, G:0.09, T:0.16
Consensus pattern (20 bp):
TAAAAACAAAGCAAGTAAAC
Found at i:10771 original size:31 final size:31
Alignment explanation
Indices: 10733--10795 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
10723 CATAGGGTGG
10733 CTATTTATAATGGAAATAACCCTAGAAAATC
1 CTATTTATAATGGAAATAACCCTAGAAAATC
10764 CTATTTATAATGGAAATAACCCTAGAAAATC
1 CTATTTATAATGGAAATAACCCTAGAAAATC
10795 C
1 C
10796 AATTCTAAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.44, C:0.17, G:0.10, T:0.29
Consensus pattern (31 bp):
CTATTTATAATGGAAATAACCCTAGAAAATC
Found at i:14882 original size:15 final size:15
Alignment explanation
Indices: 14862--14890 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
14852 CCTTGGAGGT
14862 TCAAAATCAACAAGC
1 TCAAAATCAACAAGC
14877 TCAAAATCAACAAG
1 TCAAAATCAACAAG
14891 ATCCACCACC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.24, G:0.07, T:0.14
Consensus pattern (15 bp):
TCAAAATCAACAAGC
Found at i:17247 original size:33 final size:33
Alignment explanation
Indices: 17177--17314 Score: 129
Period size: 33 Copynumber: 4.2 Consensus size: 33
17167 ATGATCAACC
** *
17177 AAAACAGATTT-GTTTTCATCACAATTAGCATCC-
1 AAAACAGATTTAG-TTTCATCACAAACAACA-CCT
17210 AAAACAGAATTT-GTTTCATCACAAACAACACCT
1 AAAACAG-ATTTAGTTTCATCACAAACAACACCT
* *
17243 AAAACAGATTTAGTGTCATCACAAACAACACTT
1 AAAACAGATTTAGTTTCATCACAAACAACACCT
** * * * *
17276 AAATTAGGTTTAGTATCATCACTAACAACATCT
1 AAAACAGATTTAGTTTCATCACAAACAACACCT
17309 AAAACA
1 AAAACA
17315 CTCCTTGCAA
Statistics
Matches: 88, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
32 6 0.07
33 77 0.88
34 5 0.06
ACGTcount: A:0.43, C:0.21, G:0.08, T:0.28
Consensus pattern (33 bp):
AAAACAGATTTAGTTTCATCACAAACAACACCT
Found at i:19589 original size:21 final size:21
Alignment explanation
Indices: 19565--19606 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
19555 TCCTTTGCAT
*
19565 ATGATCTCTAATGCCCTTCAA
1 ATGAACTCTAATGCCCTTCAA
* *
19586 ATGAACTCTTATGGCCTTCAA
1 ATGAACTCTAATGCCCTTCAA
19607 CTCTTCAAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (21 bp):
ATGAACTCTAATGCCCTTCAA
Found at i:20961 original size:25 final size:24
Alignment explanation
Indices: 20925--20971 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
20915 TCATTCTACT
20925 CATCTATCATC-AAGTTTTTCATC
1 CATCTATCATCAAAGTTTTTCATC
20948 CATCTTATCCATCAAAGTTTTTCA
1 CATC-TAT-CATCAAAGTTTTTCA
20972 AATTTTCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 4 0.19
24 3 0.14
25 4 0.19
26 10 0.48
ACGTcount: A:0.28, C:0.26, G:0.04, T:0.43
Consensus pattern (24 bp):
CATCTATCATCAAAGTTTTTCATC
Done.