Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018044.1 Corchorus olitorius cultivar O-4 contig18077, 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: 20898
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:633 original size:23 final size:23
Alignment explanation
Indices: 588--632 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
578 AAAATTGCAA
* *
588 ATTAAAAGTTTGAGGGGAAAAAT
1 ATTAAAAGTTAGAAGGGAAAAAT
611 ATTAAAAGTATAGAAGGGAAAA
1 ATTAAAAGT-TAGAAGGGAAAA
633 TGGTCATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 9 0.47
24 10 0.53
ACGTcount: A:0.53, C:0.00, G:0.24, T:0.22
Consensus pattern (23 bp):
ATTAAAAGTTAGAAGGGAAAAAT
Found at i:2091 original size:2 final size:2
Alignment explanation
Indices: 2084--2123 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
2074 GTTATCCTTT
2084 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2124 ATGTGGAGTC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4111 original size:38 final size:38
Alignment explanation
Indices: 4051--4125 Score: 132
Period size: 38 Copynumber: 2.0 Consensus size: 38
4041 ATTTCATTCT
* *
4051 TGTAATTCTTGTTTGTGTAATAAAAGTCACAAACAATG
1 TGTAATTCTTGTTAGTGCAATAAAAGTCACAAACAATG
4089 TGTAATTCTTGTTAGTGCAATAAAAGTCACAAACAAT
1 TGTAATTCTTGTTAGTGCAATAAAAGTCACAAACAAT
4126 CTTTTGGAGT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.35
Consensus pattern (38 bp):
TGTAATTCTTGTTAGTGCAATAAAAGTCACAAACAATG
Found at i:5857 original size:124 final size:125
Alignment explanation
Indices: 5691--6017 Score: 453
Period size: 124 Copynumber: 2.6 Consensus size: 125
5681 TTCTAAATAC
* *
5691 AATAGCGGCGTTTCTCACAAAAGACGCCGCTAAATAGTGGCGTTTCTGGAGTAAACGCCGCTATA
1 AATAGCGGCGTTTCTCATAAAAGACGCCGCTAAATAGTGGCGTTTCTGAAGTAAACGCCGCTATA
** *
5756 TATAATCTTATCCAAAGAATAGAAATTCGGTG-AA-ACTAAAAACATTATTTCTTGTTGGG
66 TATAATCTTATCCAAAGAATAGAAATTCGGTGCAATA-TAAAAACACCATTTCTTGATGGG
* ** *
5815 AATAGCGGCGTTTCTCATAAAAGACACAACTAAATAGTGGCGTTTCTCAAGTAAACGCCGCTATA
1 AATAGCGGCGTTTCTCATAAAAGACGCCGCTAAATAGTGGCGTTTCTGAAGTAAACGCCGCTATA
* * *
5880 TATAATCTTATCCAAAGAATAGAGATTTGGTGCAATTGATAAAAATACCATTTCTTGATGGG
66 TATAATCTTATCCAAAGAATAGAAATTCGGTGCAA-T-ATAAAAACACCATTTCTTGATGGG
* * * *
5942 AATAGCGGCGTTTCTCCTATGAA-ACGCCGCTAAATAGTGGTGTTTCTGTAGTAAACGCCGCTAT
1 AATAGCGGCGTTTCTCATA-AAAGACGCCGCTAAATAGTGGCGTTTCTGAAGTAAACGCCGCTAT
6006 ATATAATCTTAT
65 ATATAATCTTAT
6018 TTGAAATAGC
Statistics
Matches: 178, Mismatches: 20, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
124 89 0.50
125 2 0.01
127 84 0.47
128 3 0.02
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Consensus pattern (125 bp):
AATAGCGGCGTTTCTCATAAAAGACGCCGCTAAATAGTGGCGTTTCTGAAGTAAACGCCGCTATA
TATAATCTTATCCAAAGAATAGAAATTCGGTGCAATATAAAAACACCATTTCTTGATGGG
Found at i:5987 original size:32 final size:31
Alignment explanation
Indices: 5942--6004 Score: 74
Period size: 32 Copynumber: 2.0 Consensus size: 31
5932 TCTTGATGGG
5942 AATAGCGGCGTTTCTCCTA-TGAAACGCCGCTA
1 AATAGCGGCGTTTCT-CTAGT-AAACGCCGCTA
* * *
5974 AATAGTGGTGTTTCTGTAGTAAACGCCGCTA
1 AATAGCGGCGTTTCTCTAGTAAACGCCGCTA
6005 TATATAATCT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
31 13 0.48
32 14 0.52
ACGTcount: A:0.25, C:0.22, G:0.24, T:0.29
Consensus pattern (31 bp):
AATAGCGGCGTTTCTCTAGTAAACGCCGCTA
Found at i:7055 original size:19 final size:19
Alignment explanation
Indices: 7031--7067 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
7021 AGAGGGTTTG
7031 AAGGTTGAAA-AAGATGAAC
1 AAGGTT-AAAGAAGATGAAC
7050 AAGGTTAAAGAAGATGAA
1 AAGGTTAAAGAAGATGAA
7068 ATTTCTGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 3 0.18
19 14 0.82
ACGTcount: A:0.54, C:0.03, G:0.27, T:0.16
Consensus pattern (19 bp):
AAGGTTAAAGAAGATGAAC
Found at i:13365 original size:10 final size:10
Alignment explanation
Indices: 13352--13399 Score: 60
Period size: 10 Copynumber: 4.8 Consensus size: 10
13342 TACTATAGTG
13352 TATATATACA
1 TATATATACA
*
13362 TATACATACA
1 TATATATACA
*
13372 TATATATATA
1 TATATATACA
**
13382 TATATATGTA
1 TATATATACA
13392 TATATATA
1 TATATATA
13400 TAATTATGGT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
10 33 1.00
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (10 bp):
TATATATACA
Found at i:13378 original size:4 final size:4
Alignment explanation
Indices: 13352--13401 Score: 64
Period size: 4 Copynumber: 12.5 Consensus size: 4
13342 TACTATAGTG
* * * *
13352 TATA TATA CATA TACA TACA TATA TATA TATA TATA TGTA TATA TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
13400 TA
1 TA
13402 ATTATGGTGA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 40 1.00
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (4 bp):
TATA
Found at i:13388 original size:6 final size:6
Alignment explanation
Indices: 13352--13401 Score: 64
Period size: 6 Copynumber: 8.3 Consensus size: 6
13342 TACTATAGTG
* * * *
13352 TATATA TACATA TACATA CATATA TATATA TATATA TGTATA TATATA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
13400 TA
1 TA
13402 ATTATGGTGA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (6 bp):
TATATA
Found at i:20864 original size:2 final size:2
Alignment explanation
Indices: 20857--20897 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
20847 TCTCACCTGC
20857 AT AT AT AT AT AT 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 AT AT AT AT AT AT A
20898 C
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.