Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012767.1 Corchorus olitorius cultivar O-4 contig12800, 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: 38498
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:924 original size:46 final size:46
Alignment explanation
Indices: 866--970 Score: 201
Period size: 46 Copynumber: 2.3 Consensus size: 46
856 AATTGTCAAT
866 AAATTACTAATTAATTATTATTATTTATTCATTATGTAAAAAGAAC
1 AAATTACTAATTAATTATTATTATTTATTCATTATGTAAAAAGAAC
*
912 AAATTACTAATTAATTATTATTATTTATTCATTATGTAAAAGGAAC
1 AAATTACTAATTAATTATTATTATTTATTCATTATGTAAAAAGAAC
958 AAATTACTAATTA
1 AAATTACTAATTA
971 TAAATTTATC
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 58 1.00
ACGTcount: A:0.46, C:0.07, G:0.05, T:0.43
Consensus pattern (46 bp):
AAATTACTAATTAATTATTATTATTTATTCATTATGTAAAAAGAAC
Found at i:1676 original size:41 final size:42
Alignment explanation
Indices: 1597--1676 Score: 119
Period size: 41 Copynumber: 1.9 Consensus size: 42
1587 ATCTGTCCAT
*
1597 GTCATCTGTCCACGTGGCTCAAAAAGCCACGTGGCCAAACCAC
1 GTCATCTGTCCACGTGGC-CAAAAAGCCACGTGACCAAACCAC
1640 GTCATCT-TCCCACGTGG-CAAAAAGCCACGTGACCAAA
1 GTCATCTGT-CCACGTGGCCAAAAAGCCACGTGACCAAA
1677 AATATTGTGG
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
41 19 0.54
42 1 0.03
43 15 0.43
ACGTcount: A:0.30, C:0.34, G:0.20, T:0.16
Consensus pattern (42 bp):
GTCATCTGTCCACGTGGCCAAAAAGCCACGTGACCAAACCAC
Found at i:4629 original size:12 final size:12
Alignment explanation
Indices: 4612--4641 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
4602 TGTGCGTGGG
4612 TTTCATGTGCAT
1 TTTCATGTGCAT
*
4624 TTTCATGTGCCT
1 TTTCATGTGCAT
4636 TTTCAT
1 TTTCAT
4642 TGTAGGGTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.13, C:0.20, G:0.13, T:0.53
Consensus pattern (12 bp):
TTTCATGTGCAT
Found at i:14606 original size:31 final size:31
Alignment explanation
Indices: 14579--14677 Score: 164
Period size: 31 Copynumber: 3.2 Consensus size: 31
14569 GATTGCATCA
*
14579 TTGGGGACAGATTTGAGCCGATTTTGCAACG
1 TTGGGGACTGATTTGAGCCGATTTTGCAACG
14610 TT-GGGACTGATTTGAGCCGATTTTGCAACG
1 TTGGGGACTGATTTGAGCCGATTTTGCAACG
*
14640 TTGGGGACTGGTTTGAGCCGATTTTGCAACG
1 TTGGGGACTGATTTGAGCCGATTTTGCAACG
*
14671 TTAGGGA
1 TTGGGGA
14678 TTTAATTAAC
Statistics
Matches: 64, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
30 29 0.45
31 35 0.55
ACGTcount: A:0.20, C:0.15, G:0.33, T:0.31
Consensus pattern (31 bp):
TTGGGGACTGATTTGAGCCGATTTTGCAACG
Found at i:18414 original size:2 final size:2
Alignment explanation
Indices: 18402--18432 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
18392 CGACCCCGAA
18402 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18433 TGGGTTTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:18579 original size:29 final size:29
Alignment explanation
Indices: 18537--18592 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
18527 CCTTGTACGG
* *
18537 TGTTGAAAGCTTGTAATTGTGGTGTTGAT
1 TGTTGAAAACTTGTAATTGTGGCGTTGAT
18566 TGTTGAAAACTTGTAATTGTGGCGTTG
1 TGTTGAAAACTTGTAATTGTGGCGTTG
18593 TAAACTTGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.21, C:0.05, G:0.30, T:0.43
Consensus pattern (29 bp):
TGTTGAAAACTTGTAATTGTGGCGTTGAT
Found at i:18758 original size:6 final size:6
Alignment explanation
Indices: 18747--18776 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
18737 CATTCCCCGC
*
18747 CGGGGA CGGGGA CGGGGA CGGGGA CAGGGA
1 CGGGGA CGGGGA CGGGGA CGGGGA CGGGGA
18777 TAAGGTCTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.20, C:0.17, G:0.63, T:0.00
Consensus pattern (6 bp):
CGGGGA
Found at i:25808 original size:31 final size:32
Alignment explanation
Indices: 25750--25809 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
25740 GTCATCTATA
**
25750 TATAAAGGTGAAAGATGGCAAAAAAAAAAATC
1 TATAAAGGTGAAAGACAGCAAAAAAAAAAATC
*
25782 TATAAAGGTGAAA-ACAGCCAAAAAAAAA
1 TATAAAGGTGAAAGACAGCAAAAAAAAAA
25810 TAATAATTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 12 0.48
32 13 0.52
ACGTcount: A:0.62, C:0.08, G:0.17, T:0.13
Consensus pattern (32 bp):
TATAAAGGTGAAAGACAGCAAAAAAAAAAATC
Found at i:26636 original size:20 final size:21
Alignment explanation
Indices: 26611--26660 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 21
26601 AGTTTGTGGC
26611 AGTTTTTTTTTTAA-ATGGAT
1 AGTTTTTTTTTTAAGATGGAT
*
26631 AG--TTTTATTTAAGATGGAT
1 AGTTTTTTTTTTAAGATGGAT
*
26650 AGTTTTATTTT
1 AGTTTTTTTTT
26661 GTTTTGAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
18 9 0.38
19 8 0.33
20 2 0.08
21 5 0.21
ACGTcount: A:0.26, C:0.00, G:0.16, T:0.58
Consensus pattern (21 bp):
AGTTTTTTTTTTAAGATGGAT
Found at i:26641 original size:18 final size:19
Alignment explanation
Indices: 26615--26659 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
26605 TGTGGCAGTT
*
26615 TTTTTTTTAA-ATGGATAG
1 TTTTATTTAAGATGGATAG
26633 TTTTATTTAAGATGGATAG
1 TTTTATTTAAGATGGATAG
26652 TTTTATTT
1 TTTTATTT
26660 TGTTTTGAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 9 0.36
19 16 0.64
ACGTcount: A:0.27, C:0.00, G:0.16, T:0.58
Consensus pattern (19 bp):
TTTTATTTAAGATGGATAG
Found at i:33308 original size:17 final size:17
Alignment explanation
Indices: 33286--33320 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
33276 GAGGAGATTC
*
33286 TGAGATCTTCAGAATTT
1 TGAGATATTCAGAATTT
33303 TGAGATATTCAGAATTT
1 TGAGATATTCAGAATTT
33320 T
1 T
33321 TTTAATAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.31, C:0.09, G:0.17, T:0.43
Consensus pattern (17 bp):
TGAGATATTCAGAATTT
Done.