Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017348.1 Corchorus olitorius cultivar O-4 contig17381, 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: 16710
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Found at i:74 original size:18 final size:18
Alignment explanation
Indices: 51--85 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
41 TGAAGCTTAG
*
51 AGAGAGAGAGACAAATGT
1 AGAGAGAGAGAAAAATGT
69 AGAGAGAGAGAAAAATG
1 AGAGAGAGAGAAAAATG
86 GAGTAGAAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.03, G:0.34, T:0.09
Consensus pattern (18 bp):
AGAGAGAGAGAAAAATGT
Found at i:2867 original size:22 final size:22
Alignment explanation
Indices: 2841--2895 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
2831 GAAGAAAACA
2841 AAATTTCATAGAAAGGTTCTCG
1 AAATTTCATAGAAAGGTTCTCG
* * *
2863 AAATTTTATAGGAAGGTTTTCG
1 AAATTTCATAGAAAGGTTCTCG
*
2885 AAATTACATAG
1 AAATTTCATAG
2896 CATCATTATC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.38, C:0.09, G:0.18, T:0.35
Consensus pattern (22 bp):
AAATTTCATAGAAAGGTTCTCG
Found at i:2933 original size:44 final size:44
Alignment explanation
Indices: 2885--2983 Score: 112
Period size: 44 Copynumber: 2.2 Consensus size: 44
2875 AAGGTTTTCG
*
2885 AAATTACATAGCATCATTATCGA-AATTTCAT-AAGAAGACTATCA
1 AAATTTCATAGCATCATTATC-ATAATTTCATAAAG-AGACTATCA
** * **
2929 AAATTTCATAGTGTGATTATCATAATTTCATAAAGAGGTTATCA
1 AAATTTCATAGCATCATTATCATAATTTCATAAAGAGACTATCA
2973 AAATTTCATAG
1 AAATTTCATAG
2984 TGTAGTTACA
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
43 1 0.02
44 43 0.91
45 3 0.06
ACGTcount: A:0.42, C:0.12, G:0.11, T:0.34
Consensus pattern (44 bp):
AAATTTCATAGCATCATTATCATAATTTCATAAAGAGACTATCA
Found at i:2949 original size:22 final size:22
Alignment explanation
Indices: 2924--2986 Score: 81
Period size: 22 Copynumber: 2.9 Consensus size: 22
2914 ATAAGAAGAC
2924 TATCAAAATTTCATAGTGTGAT
1 TATCAAAATTTCATAGTGTGAT
* ** * *
2946 TATCATAATTTCATAAAGAGGT
1 TATCAAAATTTCATAGTGTGAT
2968 TATCAAAATTTCATAGTGT
1 TATCAAAATTTCATAGTGT
2987 AGTTACACCT
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.40
Consensus pattern (22 bp):
TATCAAAATTTCATAGTGTGAT
Found at i:3128 original size:29 final size:29
Alignment explanation
Indices: 3085--3146 Score: 115
Period size: 29 Copynumber: 2.1 Consensus size: 29
3075 AAAGAAAACT
3085 AGTACTAATACTATAAACGGACGAGTAAA
1 AGTACTAATACTATAAACGGACGAGTAAA
*
3114 AGTACTAATATTATAAACGGACGAGTAAA
1 AGTACTAATACTATAAACGGACGAGTAAA
3143 AGTA
1 AGTA
3147 TGTTGGAGTA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.48, C:0.11, G:0.18, T:0.23
Consensus pattern (29 bp):
AGTACTAATACTATAAACGGACGAGTAAA
Found at i:7042 original size:21 final size:21
Alignment explanation
Indices: 7017--7057 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
7007 TTACAATACT
7017 AAGTTATTGAAAA-AGTTATAA
1 AAGTTA-TGAAAATAGTTATAA
7038 AAGTTATGAAAATAGTTATA
1 AAGTTATGAAAATAGTTATA
7058 TATATCTACC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.51, C:0.00, G:0.15, T:0.34
Consensus pattern (21 bp):
AAGTTATGAAAATAGTTATAA
Found at i:9413 original size:13 final size:13
Alignment explanation
Indices: 9371--9415 Score: 56
Period size: 12 Copynumber: 3.5 Consensus size: 13
9361 TCATGCACCC
*
9371 AAAACAATTTATTT
1 AAAACAATTTA-AT
*
9385 AAAACCATTT-AT
1 AAAACAATTTAAT
9397 AAAACAATTTAAT
1 AAAACAATTTAAT
9410 AAAACA
1 AAAACA
9416 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
Found at i:10931 original size:22 final size:21
Alignment explanation
Indices: 10906--10953 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 21
10896 CCTTAAAATT
10906 AAATTGCAGCCCCTTTTT-AGCC
1 AAATTGCA-CCCCTTTTTCA-CC
* *
10928 AAATTTCATCCCTTTTTCACC
1 AAATTGCACCCCTTTTTCACC
10949 AAATT
1 AAATT
10954 TCATTAGTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 15 0.65
22 8 0.35
ACGTcount: A:0.27, C:0.29, G:0.06, T:0.38
Consensus pattern (21 bp):
AAATTGCACCCCTTTTTCACC
Found at i:10940 original size:21 final size:21
Alignment explanation
Indices: 10916--10957 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
10906 AAATTGCAGC
10916 CCCTTTTT-AGCCAAATTTCAT
1 CCCTTTTTCA-CCAAATTTCAT
10937 CCCTTTTTCACCAAATTTCAT
1 CCCTTTTTCACCAAATTTCAT
10958 TAGTCTCTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 19 0.95
22 1 0.05
ACGTcount: A:0.24, C:0.31, G:0.02, T:0.43
Consensus pattern (21 bp):
CCCTTTTTCACCAAATTTCAT
Found at i:11371 original size:2 final size:2
Alignment explanation
Indices: 11364--11397 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
11354 CATGTGTTTT
11364 AG AG AG AG AG AG AG AG AG 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
11398 CTCATTGGGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:15831 original size:13 final size:13
Alignment explanation
Indices: 15789--15833 Score: 56
Period size: 12 Copynumber: 3.5 Consensus size: 13
15779 TCATGCACCC
*
15789 AAAACAATTTATTT
1 AAAACAATTTA-AT
*
15803 AAAACCATTT-AT
1 AAAACAATTTAAT
15815 AAAACAATTTAAT
1 AAAACAATTTAAT
15828 AAAACA
1 AAAACA
15834 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
Found at i:16274 original size:27 final size:27
Alignment explanation
Indices: 16244--16317 Score: 80
Period size: 28 Copynumber: 2.7 Consensus size: 27
16234 TCCAGCATTT
16244 AAGGGCAAAACTGTAATTTAG-TCAACC
1 AAGGGCAAAACTGTAATTTAGCT-AACC
* *
16271 AAGGGTAAAA-TGGTAATTTTAGCTGACC
1 AAGGGCAAAACT-GTAA-TTTAGCTAACC
*
16299 AAGGGCAAAACAGTAATTT
1 AAGGGCAAAACTGTAATTT
16318 TGACATCTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
26 1 0.03
27 16 0.41
28 21 0.54
29 1 0.03
ACGTcount: A:0.41, C:0.14, G:0.22, T:0.24
Consensus pattern (27 bp):
AAGGGCAAAACTGTAATTTAGCTAACC
Done.