Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010023.1 Corchorus olitorius cultivar O-4 contig10055, 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: 16718
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Found at i:8291 original size:26 final size:25
Alignment explanation
Indices: 8270--8319 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
8260 TATAAAAACC
8270 AAACCAAAGTGAAAGTTTTAAAAGA
1 AAACCAAAGTGAAAGTTTTAAAAGA
* * *
8295 AATCCCAAGTGAAATTTTTAAAAGA
1 AAACCAAAGTGAAAGTTTTAAAAGA
8320 GAGGTTCTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.52, C:0.10, G:0.14, T:0.24
Consensus pattern (25 bp):
AAACCAAAGTGAAAGTTTTAAAAGA
Found at i:8292 original size:25 final size:25
Alignment explanation
Indices: 8264--8317 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
8254 TACACCTATA
8264 AAAACCAAA-CCAAAGTGAAAGTTTT
1 AAAA-CAAATCCAAAGTGAAAGTTTT
* * *
8289 AAAAGAAATCCCAAGTGAAATTTTT
1 AAAACAAATCCAAAGTGAAAGTTTT
8314 AAAA
1 AAAA
8318 GAGAGGTTCT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 3 0.12
25 22 0.88
ACGTcount: A:0.54, C:0.13, G:0.11, T:0.22
Consensus pattern (25 bp):
AAAACAAATCCAAAGTGAAAGTTTT
Found at i:14023 original size:13 final size:13
Alignment explanation
Indices: 14005--14030 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
13995 TGATGATGAG
14005 AGCAATCAACAAT
1 AGCAATCAACAAT
14018 AGCAATCAACAAT
1 AGCAATCAACAAT
14031 TGCTAGTGGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.23, G:0.08, T:0.15
Consensus pattern (13 bp):
AGCAATCAACAAT
Found at i:14849 original size:5 final size:5
Alignment explanation
Indices: 14841--14903 Score: 53
Period size: 5 Copynumber: 13.2 Consensus size: 5
14831 TATAAAACAA
* * *
14841 AAAAC AAAAC -AAAC AAAAA AAAAT AAAAC AAAGC AAAA- AAAA- AAAGA-
1 AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAA-AC
*
14888 AAATC AAAAC AAAAC A
1 AAAAC AAAAC AAAAC A
14904 TGTTAACCCT
Statistics
Matches: 48, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
4 11 0.23
5 37 0.77
ACGTcount: A:0.81, C:0.13, G:0.03, T:0.03
Consensus pattern (5 bp):
AAAAC
Found at i:14863 original size:19 final size:20
Alignment explanation
Indices: 14839--14883 Score: 74
Period size: 19 Copynumber: 2.3 Consensus size: 20
14829 AATATAAAAC
14839 AAAAAACAAAACAAA-CAAA
1 AAAAAACAAAACAAAGCAAA
*
14858 AAAAAATAAAACAAAGCAAA
1 AAAAAACAAAACAAAGCAAA
14878 AAAAAA
1 AAAAAA
14884 AAGAAAATCA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.84, C:0.11, G:0.02, T:0.02
Consensus pattern (20 bp):
AAAAAACAAAACAAAGCAAA
Found at i:14898 original size:28 final size:29
Alignment explanation
Indices: 14845--14900 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 29
14835 AAACAAAAAA
14845 CAAAACAAACAAAAAAAAATAAAACAAAG
1 CAAAACAAACAAAAAAAAATAAAACAAAG
*
14874 CAAAA-AAA-AAAAGAAAATCAAAACAAA
1 CAAAACAAACAAAAAAAAAT-AAAACAAA
14901 ACATGTTAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 9 0.36
28 11 0.44
29 5 0.20
ACGTcount: A:0.80, C:0.12, G:0.04, T:0.04
Consensus pattern (29 bp):
CAAAACAAACAAAAAAAAATAAAACAAAG
Found at i:14901 original size:19 final size:18
Alignment explanation
Indices: 14834--14901 Score: 55
Period size: 20 Copynumber: 3.5 Consensus size: 18
14824 TTTTGAATAT
14834 AAAACAAAAAACAAAACAAAC
1 AAAA-AAAAAA-AAAA-AAAC
*
14855 AAAAAAAAATAAAACAAAGC
1 AAAAAAAAA-AAAA-AAAAC
* *
14875 AAAAAAAAAAAGAAAATC
1 AAAAAAAAAAAAAAAAAC
*
14893 AAAACAAAA
1 AAAAAAAAA
14902 CATGTTAACC
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
18 12 0.29
19 3 0.07
20 20 0.49
21 6 0.15
ACGTcount: A:0.82, C:0.12, G:0.03, T:0.03
Consensus pattern (18 bp):
AAAAAAAAAAAAAAAAAC
Found at i:15837 original size:16 final size:16
Alignment explanation
Indices: 15818--15924 Score: 83
Period size: 16 Copynumber: 6.7 Consensus size: 16
15808 TTCGGGCGGG
*
15818 TTCGGGTTCGGGTTTT
1 TTCGGGTTCGGGTTAT
15834 TTCGGGTTCGGG-TATT
1 TTCGGGTTCGGGTTA-T
* *
15850 TTCGGGTTCGGATTAA
1 TTCGGGTTCGGGTTAT
* **
15866 GTCGAATTCGGGTTAT
1 TTCGGGTTCGGGTTAT
**
15882 TTCGGCCTCGGGTTAT
1 TTCGGGTTCGGGTTAT
* * *
15898 GTCGGATTC-GGATATT
1 TTCGGGTTCGGGTTA-T
15914 TTCGGGTTCGG
1 TTCGGGTTCGG
15925 TCTCGGGTAG
Statistics
Matches: 69, Mismatches: 18, Indels: 7
0.73 0.19 0.07
Matches are distributed among these distances:
15 5 0.07
16 61 0.88
17 3 0.04
ACGTcount: A:0.10, C:0.15, G:0.35, T:0.40
Consensus pattern (16 bp):
TTCGGGTTCGGGTTAT
Found at i:15854 original size:32 final size:32
Alignment explanation
Indices: 15818--15924 Score: 117
Period size: 32 Copynumber: 3.3 Consensus size: 32
15808 TTCGGGCGGG
* * *
15818 TTCGGGTTCGGGTTTTTTCGGGTTCGGGTATT
1 TTCGGGTTCGGGTTATGTCGGATTCGGGTATT
* * *
15850 TTCGGGTTCGGATTAAGTCGAATTCGGGT-TAT
1 TTCGGGTTCGGGTTATGTCGGATTCGGGTAT-T
** *
15882 TTCGGCCTCGGGTTATGTCGGATTCGGATATT
1 TTCGGGTTCGGGTTATGTCGGATTCGGGTATT
15914 TTCGGGTTCGG
1 TTCGGGTTCGG
15925 TCTCGGGTAG
Statistics
Matches: 59, Mismatches: 14, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
31 1 0.02
32 57 0.97
33 1 0.02
ACGTcount: A:0.10, C:0.15, G:0.35, T:0.40
Consensus pattern (32 bp):
TTCGGGTTCGGGTTATGTCGGATTCGGGTATT
Found at i:15923 original size:6 final size:6
Alignment explanation
Indices: 15914--15979 Score: 50
Period size: 6 Copynumber: 11.5 Consensus size: 6
15904 TTCGGATATT
* * *
15914 TTCGGG TTC-GG TCTCGGG -TAGGG TTCGGG TTCAGG CTCGGG -TCGGG
1 TTCGGG TTCGGG T-TCGGG TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG
* *
15960 TTCAGG CTCGGG -TCGGG TTC
1 TTCGGG TTCGGG TTCGGG TTC
15980 AGGCTCGAGT
Statistics
Matches: 47, Mismatches: 8, Indels: 10
0.72 0.12 0.15
Matches are distributed among these distances:
5 17 0.36
6 28 0.60
7 2 0.04
ACGTcount: A:0.05, C:0.21, G:0.45, T:0.29
Consensus pattern (6 bp):
TTCGGG
Found at i:15944 original size:23 final size:23
Alignment explanation
Indices: 15914--15962 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
15904 TTCGGATATT
15914 TTCGGGTTC-GGTCTCGGGTAGGG
1 TTCGGGTTCAGG-CTCGGGTAGGG
*
15937 TTCGGGTTCAGGCTCGGGTCGGG
1 TTCGGGTTCAGGCTCGGGTAGGG
15960 TTC
1 TTC
15963 AGGCTCGGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 22 0.92
24 2 0.08
ACGTcount: A:0.04, C:0.20, G:0.45, T:0.31
Consensus pattern (23 bp):
TTCGGGTTCAGGCTCGGGTAGGG
Found at i:15958 original size:17 final size:17
Alignment explanation
Indices: 15938--15986 Score: 98
Period size: 17 Copynumber: 2.9 Consensus size: 17
15928 CGGGTAGGGT
15938 TCGGGTTCAGGCTCGGG
1 TCGGGTTCAGGCTCGGG
15955 TCGGGTTCAGGCTCGGG
1 TCGGGTTCAGGCTCGGG
15972 TCGGGTTCAGGCTCG
1 TCGGGTTCAGGCTCG
15987 AGTTTGATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 32 1.00
ACGTcount: A:0.06, C:0.24, G:0.45, T:0.24
Consensus pattern (17 bp):
TCGGGTTCAGGCTCGGG
Found at i:16130 original size:5 final size:5
Alignment explanation
Indices: 16120--16153 Score: 54
Period size: 5 Copynumber: 7.2 Consensus size: 5
16110 TATTGATAAT
16120 ATATA ATATA ATATA ATAT- A-ATA ATATA ATATA A
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA A
16154 CATTATTATC
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
3 2 0.07
4 2 0.07
5 23 0.85
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
ATATA
Found at i:16145 original size:13 final size:13
Alignment explanation
Indices: 16115--16153 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
16105 AAGTTTATTG
16115 ATAATAT-ATA-A
1 ATAATATAATATA
16126 TATAATATAATATA
1 -ATAATATAATATA
16140 ATAATATAATATA
1 ATAATATAATATA
16153 A
1 A
16154 CATTATTATC
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 7 0.28
13 17 0.68
14 1 0.04
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
ATAATATAATATA
Found at i:16460 original size:31 final size:31
Alignment explanation
Indices: 16425--16496 Score: 78
Period size: 31 Copynumber: 2.3 Consensus size: 31
16415 TAAATTATTG
*
16425 CAAATTAAAACAAAT-TAAG-CATTAAATTAAA
1 CAAATTAAAA-AAATGAAAGTC-TTAAATTAAA
*
16456 CAAA-TAATTAAAATGAAAGTCTTAAATTAAA
1 CAAATTAA-AAAAATGAAAGTCTTAAATTAAA
16487 CAAATTAAAA
1 CAAATTAAAA
16497 GATGATAGAC
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
30 7 0.21
31 23 0.68
32 4 0.12
ACGTcount: A:0.61, C:0.08, G:0.04, T:0.26
Consensus pattern (31 bp):
CAAATTAAAAAAATGAAAGTCTTAAATTAAA
Done.