Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017241.1 Corchorus olitorius cultivar O-4 contig17274, 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: 32879
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.33
Found at i:876 original size:31 final size:33
Alignment explanation
Indices: 838--899 Score: 92
Period size: 32 Copynumber: 1.9 Consensus size: 33
828 ATTAATTCAT
*
838 CAAAT-AAAATGATTTCTATA-ATTTAAAGCAG
1 CAAATAAAAATGATTTATATAGATTTAAAGCAG
869 CAAATAAAAATGATTTATATAGTATTTAAAG
1 CAAATAAAAATGATTTATATAG-ATTTAAAG
900 TTTAAACCAC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
31 5 0.19
32 14 0.52
34 8 0.30
ACGTcount: A:0.50, C:0.06, G:0.10, T:0.34
Consensus pattern (33 bp):
CAAATAAAAATGATTTATATAGATTTAAAGCAG
Found at i:2900 original size:6 final size:6
Alignment explanation
Indices: 2889--2956 Score: 52
Period size: 6 Copynumber: 11.3 Consensus size: 6
2879 TTGACAGCGC
* * *
2889 AACAAA AAC-AA AACGAA AAC-GA AACAAA AACAAAA AACAGAAA AACGAA
1 AACAAA AACAAA AACAAA AACAAA AACAAA AAC-AAA AAC--AAA AACAAA
*
2938 AAC-GA AACAAA AACAAA AA
1 AACAAA AACAAA AACAAA AA
2957 ACAGAAAAAC
Statistics
Matches: 51, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
5 13 0.25
6 26 0.51
7 6 0.12
8 6 0.12
ACGTcount: A:0.76, C:0.16, G:0.07, T:0.00
Consensus pattern (6 bp):
AACAAA
Found at i:2913 original size:11 final size:11
Alignment explanation
Indices: 2889--2955 Score: 66
Period size: 11 Copynumber: 6.2 Consensus size: 11
2879 TTGACAGCGC
2889 AACAAAAACAA
1 AACAAAAACAA
* *
2900 AACGAAAACGA
1 AACAAAAACAA
2911 AACAAAAACAA
1 AACAAAAACAA
*
2922 AA-AACAGA-AA
1 AACAA-AAACAA
* *
2932 AACGAAAACGA
1 AACAAAAACAA
2943 AACAAAAACAA
1 AACAAAAACAA
2954 AA
1 AA
2956 AACAGAAAAA
Statistics
Matches: 43, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
10 8 0.19
11 35 0.81
ACGTcount: A:0.76, C:0.16, G:0.07, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:2937 original size:26 final size:26
Alignment explanation
Indices: 2889--2970 Score: 82
Period size: 32 Copynumber: 3.1 Consensus size: 26
2879 TTGACAGCGC
2889 AACAAAAAC--AAAAC-G-AAAACGA
1 AACAAAAACAAAAAACAGAAAAACGA
2911 AACAAAAACAAAAAACAGAAAAACGAAAACGA
1 AACAAAAACAAAAAACAG----A--AAAACGA
2943 AACAAAAACAAAAAACAGAAAAACGA
1 AACAAAAACAAAAAACAGAAAAACGA
2969 AA
1 AA
2971 ATGATACCAA
Statistics
Matches: 50, Mismatches: 0, Indels: 16
0.76 0.00 0.24
Matches are distributed among these distances:
22 9 0.18
24 5 0.10
25 1 0.02
26 9 0.18
28 1 0.02
32 25 0.50
ACGTcount: A:0.76, C:0.16, G:0.09, T:0.00
Consensus pattern (26 bp):
AACAAAAACAAAAAACAGAAAAACGA
Found at i:2937 original size:32 final size:32
Alignment explanation
Indices: 2898--2971 Score: 148
Period size: 32 Copynumber: 2.3 Consensus size: 32
2888 CAACAAAAAC
2898 AAAACGAAAACGAAACAAAAACAAAAAACAGA
1 AAAACGAAAACGAAACAAAAACAAAAAACAGA
2930 AAAACGAAAACGAAACAAAAACAAAAAACAGA
1 AAAACGAAAACGAAACAAAAACAAAAAACAGA
2962 AAAACGAAAA
1 AAAACGAAAA
2972 TGATACCAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.76, C:0.15, G:0.09, T:0.00
Consensus pattern (32 bp):
AAAACGAAAACGAAACAAAAACAAAAAACAGA
Found at i:6564 original size:31 final size:31
Alignment explanation
Indices: 6524--6685 Score: 200
Period size: 31 Copynumber: 5.3 Consensus size: 31
6514 GCATGAGGCA
*
6524 TGCCACGTGTCACTTTTTGGTACACATGGCG
1 TGCCACGTGTCACTTTTTGGTACACGTGGCG
* * * *
6555 TGACACGTGTCACTTTTTGGTATATGTGGTG
1 TGCCACGTGTCACTTTTTGGTACACGTGGCG
* * *
6586 TGTCACGTGTCACTTTTTGGTGCATGTGGCG
1 TGCCACGTGTCACTTTTTGGTACACGTGGCG
6617 TGCCACGTGTCACTTTTTGGTACACGTGGCG
1 TGCCACGTGTCACTTTTTGGTACACGTGGCG
** * * *
6648 TGCCACAAGTCGCTTTTTGGTACACATGGCA
1 TGCCACGTGTCACTTTTTGGTACACGTGGCG
6679 TG-CACGT
1 TGCCACGT
6686 CGGACACCAT
Statistics
Matches: 112, Mismatches: 19, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
30 3 0.03
31 109 0.97
ACGTcount: A:0.15, C:0.22, G:0.28, T:0.35
Consensus pattern (31 bp):
TGCCACGTGTCACTTTTTGGTACACGTGGCG
Found at i:7709 original size:51 final size:51
Alignment explanation
Indices: 7633--7736 Score: 199
Period size: 51 Copynumber: 2.0 Consensus size: 51
7623 CATTTTAGGA
7633 ATGTCGGTTTGAGCTTTTAGTAAATAAAAATATAAATTCAATTCAACTTTC
1 ATGTCGGTTTGAGCTTTTAGTAAATAAAAATATAAATTCAATTCAACTTTC
*
7684 ATGTCGGTTTGAGTTTTTAGTAAATAAAAATATAAATTCAATTCAACTTTC
1 ATGTCGGTTTGAGCTTTTAGTAAATAAAAATATAAATTCAATTCAACTTTC
7735 AT
1 AT
7737 TTGACCACAC
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.40
Consensus pattern (51 bp):
ATGTCGGTTTGAGCTTTTAGTAAATAAAAATATAAATTCAATTCAACTTTC
Found at i:8088 original size:46 final size:46
Alignment explanation
Indices: 8013--8102 Score: 137
Period size: 46 Copynumber: 2.0 Consensus size: 46
8003 TACCATGTTA
* *
8013 AACAGAACATACCTGAGCTTTTATACCATGTTAAGCATCCAACCGC
1 AACAGAACAGACCTAAGCTTTTATACCATGTTAAGCATCCAACCGC
*
8059 AACAGGACAGACCTAAG-TTTTGATACCATGTTAAGCATCCAACC
1 AACAGAACAGACCTAAGCTTTT-ATACCATGTTAAGCATCCAACC
8103 TAAAACCAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
45 4 0.10
46 36 0.90
ACGTcount: A:0.36, C:0.27, G:0.14, T:0.23
Consensus pattern (46 bp):
AACAGAACAGACCTAAGCTTTTATACCATGTTAAGCATCCAACCGC
Found at i:13060 original size:21 final size:21
Alignment explanation
Indices: 13016--13056 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
13006 TAGGTTTGAG
13016 ATTAAGGATAACAAATGGGTT
1 ATTAAGGATAACAAATGGGTT
13037 ATTAA-GATAA-AAATGTGGTT
1 ATTAAGGATAACAAATG-GGTT
13057 TATTGATCCT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.26
20 9 0.47
21 5 0.26
ACGTcount: A:0.44, C:0.02, G:0.22, T:0.32
Consensus pattern (21 bp):
ATTAAGGATAACAAATGGGTT
Found at i:23892 original size:4 final size:4
Alignment explanation
Indices: 23883--23916 Score: 68
Period size: 4 Copynumber: 8.5 Consensus size: 4
23873 GGACTTCGAC
23883 AATA AATA AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AATA AATA AA
23917 CAAAATAAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:30664 original size:31 final size:31
Alignment explanation
Indices: 30629--30691 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
30619 ATATGTTTTT
* * *
30629 CTTTTGGCTAAATGCTCAATTTGGTCCTAAA
1 CTTTTGACGAAATGCTCAATTTGGTCATAAA
*
30660 CTTTTGACGGAATGCTCAATTTGGTCATAAA
1 CTTTTGACGAAATGCTCAATTTGGTCATAAA
30691 C
1 C
30692 CTTTAGACTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.27, C:0.19, G:0.17, T:0.37
Consensus pattern (31 bp):
CTTTTGACGAAATGCTCAATTTGGTCATAAA
Found at i:30918 original size:23 final size:23
Alignment explanation
Indices: 30892--30937 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
30882 TCTTGTATTT
*
30892 TTCTCTTTCTTCAACGTCTTCTC
1 TTCTCTTTCCTCAACGTCTTCTC
* * *
30915 TTCTGTTTCCTCACCTTCTTCTC
1 TTCTCTTTCCTCAACGTCTTCTC
30938 CTTCGATTTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.07, C:0.37, G:0.04, T:0.52
Consensus pattern (23 bp):
TTCTCTTTCCTCAACGTCTTCTC
Found at i:32113 original size:30 final size:30
Alignment explanation
Indices: 32077--32136 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
32067 AAACTTGAGA
32077 TTTGGAGGATTATGCCCAACCAAATACACT
1 TTTGGAGGATTATGCCCAACCAAATACACT
32107 TTTGGAGGATTATGCCCAACCAAATACACT
1 TTTGGAGGATTATGCCCAACCAAATACACT
32137 GACATGGTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.27
Consensus pattern (30 bp):
TTTGGAGGATTATGCCCAACCAAATACACT
Found at i:32494 original size:79 final size:79
Alignment explanation
Indices: 32386--32540 Score: 231
Period size: 79 Copynumber: 2.0 Consensus size: 79
32376 AAAATCTTTC
* *
32386 ACCTCCAAGCATTTGAAAAAAAAAAGCTTTTACCCACTTTCCA-AAACCAAAAAAGGAAATTGCT
1 ACCTCCAAGCATTTGAAAAAAAAAAGC-TTTACCCACTTTCCAGAAACAAAAAAAGGAAATTGCA
32450 TCTATGACCGAATAA
65 TCTATGACCGAATAA
** * *
32465 ACCTCCAAGCATTTGAAAAAAAATTGCTTTGCCCACTTTCCAGAAACAAAAAAATGAAATTGCAT
1 ACCTCCAAGCATTTGAAAAAAAAAAGCTTTACCCACTTTCCAGAAACAAAAAAAGGAAATTGCAT
*
32530 CTTTGACCGAA
66 CTATGACCGAA
32541 AAAAAATTTC
Statistics
Matches: 68, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
78 14 0.21
79 54 0.79
ACGTcount: A:0.43, C:0.23, G:0.11, T:0.24
Consensus pattern (79 bp):
ACCTCCAAGCATTTGAAAAAAAAAAGCTTTACCCACTTTCCAGAAACAAAAAAAGGAAATTGCAT
CTATGACCGAATAA
Done.