Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013791.1 Corchorus olitorius cultivar O-4 contig13824, 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: 2249
ACGTcount: A:0.40, C:0.13, G:0.14, T:0.33
Found at i:988 original size:102 final size:104
Alignment explanation
Indices: 852--1060 Score: 291
Period size: 105 Copynumber: 2.0 Consensus size: 104
842 TAATATATCT
* *
852 AAGTTTTTTAATAAAATTAGTAAAATGATAAAAATAAAATAG-GC-AT-AATGATATTAGATTTA
1 AAGTATTTTAATAAAATTAGTAAAATGATAAAAATAAAATAGTGCTATAAAT-ATATTACATTTA
* *
914 ATTAAATAAAAATAGAGGTTTTAGTTGAGTAAAACTATAA
65 ATCAAATAAAAATAGAGGTTTTAGTTGAATAAAACTATAA
* * *
954 AAGTATTTTAATTTAAA-TAGTAAAATGGTAAAAATAAAATAGTTCTTATAAATATATTACATTT
1 AAGTATTTTAA-TAAAATTAGTAAAATGATAAAAATAAAATAGTGC-TATAAATATATTACATTT
*
1018 AATCAAATAAAAATAGAGTTTTTAGTTGAATAAAACTATAA
64 AATCAAATAAAAATAGAGGTTTTAGTTGAATAAAACTATAA
1059 AA
1 AA
1061 ATTTAAGCAA
Statistics
Matches: 94, Mismatches: 8, Indels: 7
0.86 0.07 0.06
Matches are distributed among these distances:
102 34 0.36
103 5 0.05
105 52 0.55
106 3 0.03
ACGTcount: A:0.51, C:0.03, G:0.11, T:0.35
Consensus pattern (104 bp):
AAGTATTTTAATAAAATTAGTAAAATGATAAAAATAAAATAGTGCTATAAATATATTACATTTAA
TCAAATAAAAATAGAGGTTTTAGTTGAATAAAACTATAA
Found at i:1691 original size:3 final size:3
Alignment explanation
Indices: 1679--1714 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
1669 TATAGTAGAG
1679 ATA A-A ATA ATA ATA ATA ATA ATA AT- ATA AT- ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1715 TAGTATAGGT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
2 6 0.20
3 24 0.80
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1728 original size:6 final size:6
Alignment explanation
Indices: 1702--1755 Score: 57
Period size: 6 Copynumber: 10.0 Consensus size: 6
1692 AATAATAATA
*
1702 ATATA- ATATA- ATATAG -TATAG GTATAG ATATAG ATATAG ATAT--
1 ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG
1745 -TATAG ATATAG
1 ATATAG ATATAG
1756 GTAGTATAGA
Statistics
Matches: 43, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
3 3 0.07
5 15 0.35
6 25 0.58
ACGTcount: A:0.48, C:0.00, G:0.15, T:0.37
Consensus pattern (6 bp):
ATATAG
Found at i:1748 original size:27 final size:26
Alignment explanation
Indices: 1702--1755 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 26
1692 AATAATAATA
*
1702 ATATAATATAATATAGTATAGGTATAG
1 ATATAATATAATATA-TATAGATATAG
1729 ATATAGATATAGATAT-TATAGATATAG
1 ATATA-ATATA-ATATATATAGATATAG
1756 GTAGTATAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 15 0.62
28 5 0.21
29 4 0.17
ACGTcount: A:0.48, C:0.00, G:0.15, T:0.37
Consensus pattern (26 bp):
ATATAATATAATATATATAGATATAG
Found at i:1763 original size:15 final size:15
Alignment explanation
Indices: 1714--1767 Score: 60
Period size: 15 Copynumber: 3.8 Consensus size: 15
1704 ATAATATAAT
*
1714 ATAGTATAGGTATAG
1 ATAGTATAGATATAG
1729 --A-TATAGATATAG
1 ATAGTATAGATATAG
*
1741 ATATTATAGATATAG
1 ATAGTATAGATATAG
*
1756 GTAGTATAGATA
1 ATAGTATAGATA
1768 ATATAGAAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
12 10 0.30
13 1 0.03
14 1 0.03
15 21 0.64
ACGTcount: A:0.44, C:0.00, G:0.20, T:0.35
Consensus pattern (15 bp):
ATAGTATAGATATAG
Found at i:1772 original size:33 final size:32
Alignment explanation
Indices: 1699--1774 Score: 84
Period size: 33 Copynumber: 2.3 Consensus size: 32
1689 AATAATAATA
*
1699 ATAATATA-ATATAATATAGTATAGGTATAGAT
1 ATAATATAGATAT-ATATAGTATAGGTATAGAG
*
1731 ATAGATATAGATAT-TATAGATATAGGTAGTATAG
1 ATA-ATATAGATATATATAG-TATAGGTA-TAGAG
1765 ATAATATAGA
1 ATAATATAGA
1775 AGATAGAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
32 8 0.21
33 20 0.53
34 10 0.26
ACGTcount: A:0.49, C:0.00, G:0.16, T:0.36
Consensus pattern (32 bp):
ATAATATAGATATATATAGTATAGGTATAGAG
Found at i:2222 original size:2 final size:2
Alignment explanation
Indices: 2215--2249 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2205 TAGTTTTGAG
2215 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 A
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.