Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013432.1 Corchorus capsularis cultivar CVL-1 contig13453, 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: 31023
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Found at i:263 original size:29 final size:29
Alignment explanation
Indices: 227--295 Score: 93
Period size: 29 Copynumber: 2.4 Consensus size: 29
217 CTTGGCAACA
****
227 GGGCTTATTTGGCCTTTTTAAGAGTTCAG
1 GGGCTTATTTGGCCGAAATAAGAGTTCAG
*
256 GGGCTTATTTGGCCGAAATAATAGTTCAG
1 GGGCTTATTTGGCCGAAATAAGAGTTCAG
285 GGGCTTATTTG
1 GGGCTTATTTG
296 ACGATTCAGT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.20, C:0.13, G:0.29, T:0.38
Consensus pattern (29 bp):
GGGCTTATTTGGCCGAAATAAGAGTTCAG
Found at i:8782 original size:6 final size:6
Alignment explanation
Indices: 8771--8807 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
8761 CTGCATGATG
8771 TTGTTC TTGTTC TTGTTC TTGTTC TTGTTC TTGTTC T
1 TTGTTC TTGTTC TTGTTC TTGTTC TTGTTC TTGTTC T
8808 GCTCTATTAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.00, C:0.16, G:0.16, T:0.68
Consensus pattern (6 bp):
TTGTTC
Found at i:12887 original size:2 final size:2
Alignment explanation
Indices: 12880--12922 Score: 58
Period size: 2 Copynumber: 23.5 Consensus size: 2
12870 ATGATATAGC
12880 AT AT AT AT AT -T AT -T AT AT AT AT AT A- AT AT AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12918 AT AT A
1 AT AT A
12923 AGGCAACATT
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
1 4 0.11
2 33 0.89
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:12903 original size:18 final size:18
Alignment explanation
Indices: 12880--12923 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
12870 ATGATATAGC
12880 ATATATAT-AT-TATTAT
1 ATATATATAATATATTAT
12896 ATATATATAATATATTAT
1 ATATATATAATATATTAT
12914 ATATATATAA
1 ATATATATAA
12924 GGCAACATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
16 8 0.31
17 2 0.08
18 16 0.62
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
ATATATATAATATATTAT
Found at i:19141 original size:2 final size:2
Alignment explanation
Indices: 19128--19167 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
19118 TTGAATAACC
*
19128 AT AT AT AA AT AT AT 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 AT AT AT AT
19168 TTTAGTGTAC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:19728 original size:101 final size:103
Alignment explanation
Indices: 19536--19735 Score: 262
Period size: 101 Copynumber: 2.0 Consensus size: 103
19526 GTATGCTTAT
* * *
19536 GACCTCCCATCCTGTCAAAGGTATTTTCAAGTACCAAAAACTTTTACTTTCGTTGCATTTCCACA
1 GACCTCCCATCCTGTCAAAGGAATTTTCAAATACCAAAAACTGTTACTTTCGTTGCATTTCCACA
* * * *
19601 ATTATGTGATGTGTTGATTTAGGGAAGTAATTTTGTGA
66 ATTATATAATATGTTGATATAGGGAAGTAATTTTGTGA
* * * *
19639 GACCT-CCATCCTGTCAAAGGAATTTTCAAATACC-TAAACTGTTATTTTTGTTGCATTTCTACA
1 GACCTCCCATCCTGTCAAAGGAATTTTCAAATACCAAAAACTGTTACTTTCGTTGCATTTCCACA
*
19702 ATTATATAAATATGTTGA-ATATGGAAGTAATTTT
66 ATTATAT-AATATGTTGATATAGGGAAGTAATTTT
19736 CTGATGAGTT
Statistics
Matches: 84, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
101 44 0.52
102 35 0.42
103 5 0.06
ACGTcount: A:0.30, C:0.16, G:0.15, T:0.39
Consensus pattern (103 bp):
GACCTCCCATCCTGTCAAAGGAATTTTCAAATACCAAAAACTGTTACTTTCGTTGCATTTCCACA
ATTATATAATATGTTGATATAGGGAAGTAATTTTGTGA
Found at i:30453 original size:12 final size:12
Alignment explanation
Indices: 30421--30459 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
30411 ATGGAATTAA
30421 ATATCCGTCG--
1 ATATCCGTCGAT
30431 ATA-CC-TCGAT
1 ATATCCGTCGAT
30441 ATATCCGTCGAT
1 ATATCCGTCGAT
30453 ATATCCG
1 ATATCCG
30460 ATATCTGTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
8 3 0.12
9 2 0.08
10 6 0.24
11 2 0.08
12 12 0.48
ACGTcount: A:0.26, C:0.28, G:0.15, T:0.31
Consensus pattern (12 bp):
ATATCCGTCGAT
Found at i:30583 original size:10 final size:10
Alignment explanation
Indices: 30570--30595 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
30560 AAATCTCGAT
30570 ATATCCGTAA
1 ATATCCGTAA
30580 ATATCCGTAA
1 ATATCCGTAA
30590 ATATCC
1 ATATCC
30596 ATATTAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.38, C:0.23, G:0.08, T:0.31
Consensus pattern (10 bp):
ATATCCGTAA
Done.