Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019005.1 Corchorus olitorius cultivar O-4 contig19038, 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: 25444
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:1247 original size:25 final size:24
Alignment explanation
Indices: 1189--1245 Score: 96
Period size: 25 Copynumber: 2.3 Consensus size: 24
1179 TCCAATTAGT
1189 TGATTAAATTAGATTTGAGCTACA
1 TGATTAAATTAGATTTGAGCTACA
*
1213 TGAATGAAATTAGATTTGAGCTACA
1 TG-ATTAAATTAGATTTGAGCTACA
1238 TGATTAAA
1 TGATTAAA
1246 ATGCAACAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 7 0.23
25 23 0.77
ACGTcount: A:0.40, C:0.07, G:0.18, T:0.35
Consensus pattern (24 bp):
TGATTAAATTAGATTTGAGCTACA
Found at i:10421 original size:50 final size:50
Alignment explanation
Indices: 10361--10465 Score: 165
Period size: 50 Copynumber: 2.1 Consensus size: 50
10351 TAAAACTTAT
**
10361 GTTTAAAATTAGTAGGGGTATTTTACATATTTCACATCAAGGTTTTTGAA
1 GTTTAAAATTAGTAAAGGTATTTTACATATTTCACATCAAGGTTTTTGAA
* * *
10411 GTTTAGAATTAGTAAAGGTATTTTAGATATTTCAGATCAAGGTTTTTGAA
1 GTTTAAAATTAGTAAAGGTATTTTACATATTTCACATCAAGGTTTTTGAA
10461 GTTTA
1 GTTTA
10466 TAAAATTAAT
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.32, C:0.06, G:0.19, T:0.43
Consensus pattern (50 bp):
GTTTAAAATTAGTAAAGGTATTTTACATATTTCACATCAAGGTTTTTGAA
Found at i:11035 original size:2 final size:2
Alignment explanation
Indices: 11028--11092 Score: 56
Period size: 2 Copynumber: 36.5 Consensus size: 2
11018 TTATAATTAA
* *
11028 AT AT AT AT -T AT AT AT AT AT AT A- AA AT A- AT AT -T AG AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11066 AT AT A- AT -T AT AT AT AT A- AT A- AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
11093 ATTATTAATC
Statistics
Matches: 52, Mismatches: 3, Indels: 16
0.73 0.04 0.23
Matches are distributed among these distances:
1 8 0.15
2 44 0.85
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.45
Consensus pattern (2 bp):
AT
Found at i:11089 original size:31 final size:34
Alignment explanation
Indices: 11023--11088 Score: 98
Period size: 34 Copynumber: 1.9 Consensus size: 34
11013 AATATTTATA
11023 ATTAAATATATATTATATATATATATAAAATAAT
1 ATTAAATATATATTATATATATATATAAAATAAT
* *
11057 ATTAGATATATATAAT-TATATATATAATAATA
1 ATTAAATATATATTATATATATATATAA-AATA
11089 TATAATTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 11 0.38
34 18 0.62
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (34 bp):
ATTAAATATATATTATATATATATATAAAATAAT
Found at i:11101 original size:14 final size:12
Alignment explanation
Indices: 11012--11096 Score: 72
Period size: 12 Copynumber: 7.2 Consensus size: 12
11002 GACCGTTTAG
*
11012 TAATATTTATAAT
1 TAATATATAT-AT
11025 TAA-ATATATAT
1 TAATATATATAT
11036 T-ATATATATAT
1 TAATATATATAT
*
11047 ATAAAATA-ATAT
1 -TAATATATATAT
11059 TAGATATATATAAT
1 TA-ATATATAT-AT
*
11073 T-ATATATATAA
1 TAATATATATAT
11084 TAATATATA-AT
1 TAATATATATAT
11095 TA
1 TA
11097 TTAATCGGTT
Statistics
Matches: 60, Mismatches: 5, Indels: 16
0.74 0.06 0.20
Matches are distributed among these distances:
10 1 0.02
11 18 0.30
12 29 0.48
13 9 0.15
14 3 0.05
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (12 bp):
TAATATATATAT
Found at i:20205 original size:3 final size:3
Alignment explanation
Indices: 20197--20252 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
20187 CTTTGGTAAA
20197 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
20245 AAT AAT AA
1 AAT AAT AA
20253 GCTCTCCATT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:20598 original size:6 final size:6
Alignment explanation
Indices: 20582--20611 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
20572 CAGCCTCTAC
20582 ATATCTT ATATTT ATATTT ATATTT ATATT
1 ATAT-TT ATATTT ATATTT ATATTT ATATT
20612 ATGAAAAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 19 0.83
7 4 0.17
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (6 bp):
ATATTT
Found at i:23763 original size:2 final size:2
Alignment explanation
Indices: 23751--23788 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
23741 ATTGGATTTT
23751 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
23789 TGGAGCCAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:24853 original size:16 final size:15
Alignment explanation
Indices: 24828--24857 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
24818 CAAGATTAAG
24828 TATAATTATTTTCAT
1 TATAATTATTTTCAT
24843 TATATATTATTTTCA
1 TATA-ATTATTTTCA
24858 AAAGAGACTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (15 bp):
TATAATTATTTTCAT
Found at i:25293 original size:16 final size:16
Alignment explanation
Indices: 25229--25296 Score: 75
Period size: 16 Copynumber: 4.2 Consensus size: 16
25219 AAATTTGGGT
*
25229 ACCCAAACCCGAAATT
1 ACCCAAACCCGAAATG
* * *
25245 ACCCGAATCC-AAACG
1 ACCCAAACCCGAAATG
*
25260 ACCTAAACCCGAAAATG
1 ACCCAAACCCG-AAATG
25277 ACCCAAACCCGAAATG
1 ACCCAAACCCGAAATG
25293 ACCC
1 ACCC
25297 GACAGATTAA
Statistics
Matches: 41, Mismatches: 9, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
15 10 0.24
16 17 0.41
17 14 0.34
ACGTcount: A:0.43, C:0.38, G:0.10, T:0.09
Consensus pattern (16 bp):
ACCCAAACCCGAAATG
Done.