Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017355.1 Corchorus olitorius cultivar O-4 contig17388, 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: 14930
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.31
Found at i:2503 original size:12 final size:12
Alignment explanation
Indices: 2486--2511 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2476 TATAATTAAT
2486 ATAACATATTTA
1 ATAACATATTTA
2498 ATAACATATTTA
1 ATAACATATTTA
2510 AT
1 AT
2512 TATTTTTAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (12 bp):
ATAACATATTTA
Found at i:2545 original size:26 final size:26
Alignment explanation
Indices: 2498--2547 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
2488 AACATATTTA
*
2498 ATAACATATTTAATTATTTTTAGAAT
1 ATAACATATTTAATTATATTTAGAAT
2524 ATAACATATTTAATT-TAATTTAGA
1 ATAACATATTTAATTAT-ATTTAGA
2548 TTTACATCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 1 0.05
26 21 0.95
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.48
Consensus pattern (26 bp):
ATAACATATTTAATTATATTTAGAAT
Found at i:3934 original size:2 final size:2
Alignment explanation
Indices: 3927--3960 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
3917 GCTTTGTCAC
3927 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3961 GGAATTTGGT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:4122 original size:43 final size:42
Alignment explanation
Indices: 4068--4359 Score: 371
Period size: 43 Copynumber: 6.8 Consensus size: 42
4058 CATAAGGAAA
*
4068 AATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAG
1 AATGCCCCTGTGTTATATATGTGTTTGAGGACTTTGTAATAG
4110 AATTGCCCCTGTGTTATATATGTGTTTGAGGACTTTG-ATATAG
1 AA-TGCCCCTGTGTTATATATGTGTTTGAGGACTTTGTA-ATAG
* *
4153 -ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTTGGAATAG
1 AATGCCCCTGTGTTATATATGTGTTTGAGGAC-TTTGTAATAG
* *
4195 AAATGCCCCCGTGTTATATATGTGTTTGGGGACTTTGAATTAATAG
1 -AATGCCCCTGTGTTATATATGTGTTTGAGGACTTTG---TAATAG
*
4241 AATTGCCCCTGTGTTATATATGTGTTTGGGGAC-TTG-ATATAG
1 AA-TGCCCCTGTGTTATATATGTGTTTGAGGACTTTGTA-ATAG
*
4283 -ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATA-
1 AATGCCCCTGTGTTATATATGTGTTTGAGGACTTTGTAATAG
*
4323 AAGGTGCCCCTGTGTTATATATGTGTTTGGGGACTTT
1 AA--TGCCCCTGTGTTATATATGTGTTTGAGGACTTT
4360 TTGGTTATTG
Statistics
Matches: 223, Mismatches: 11, Indels: 31
0.84 0.04 0.12
Matches are distributed among these distances:
40 28 0.13
41 38 0.17
42 17 0.08
43 73 0.33
44 28 0.13
45 5 0.02
46 34 0.15
ACGTcount: A:0.22, C:0.11, G:0.25, T:0.41
Consensus pattern (42 bp):
AATGCCCCTGTGTTATATATGTGTTTGAGGACTTTGTAATAG
Found at i:4308 original size:130 final size:126
Alignment explanation
Indices: 4066--4359 Score: 473
Period size: 129 Copynumber: 2.3 Consensus size: 126
4056 GCCATAAGGA
* *
4066 AAAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAATTGCCCCTGTGTTATATAT
1 AAAATGCCCCTGTGTTATATATGTGTTTGGGGACTTTGTAATAGAATTGCCCCTGTGTTATATAT
4131 GTGTTTGAGGACTTTGATATAGATGCCTCTGTGTTATATATGTGTTTGAGGACTTTTGGAAT
66 GTGTTTGAGGACTTTGATATAGATGCCTCTGTGTTATATATGTGTTTGAGGAC-TTTGGAAT
*
4193 AGAAATGCCCCCGTGTTATATATGTGTTTGGGGACTTTGAATTAATAGAATTGCCCCTGTGTTAT
1 A-AAATGCCCCTGTGTTATATATGTGTTTGGGGACTTTG---TAATAGAATTGCCCCTGTGTTAT
* *
4258 ATATGTGTTTGGGGAC-TTGATATAGATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAAT
62 ATATGTGTTTGAGGACTTTGATATAGATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGGAAT
*
4322 AAAGGTGCCCCTGTGTTATATATGTGTTTGGGGACTTT
1 AAA-ATGCCCCTGTGTTATATATGTGTTTGGGGACTTT
4360 TTGGTTATTG
Statistics
Matches: 155, Mismatches: 7, Indels: 8
0.91 0.04 0.05
Matches are distributed among these distances:
127 1 0.01
128 36 0.23
129 40 0.26
130 40 0.26
131 38 0.25
ACGTcount: A:0.23, C:0.11, G:0.25, T:0.41
Consensus pattern (126 bp):
AAAATGCCCCTGTGTTATATATGTGTTTGGGGACTTTGTAATAGAATTGCCCCTGTGTTATATAT
GTGTTTGAGGACTTTGATATAGATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGGAAT
Found at i:9734 original size:19 final size:21
Alignment explanation
Indices: 9710--9754 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
9700 CCTTAACTTC
9710 TTCTCCT-TCC-CCT-TCATCT
1 TTCTCCTGTCCTCCTATC-TCT
9729 TTCTCCTGTCCTCCTATCTCT
1 TTCTCCTGTCCTCCTATCTCT
9750 TTCTC
1 TTCTC
9755 TTCTCCCAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 7 0.30
20 3 0.13
21 11 0.48
22 2 0.09
ACGTcount: A:0.04, C:0.44, G:0.02, T:0.49
Consensus pattern (21 bp):
TTCTCCTGTCCTCCTATCTCT
Found at i:10895 original size:29 final size:29
Alignment explanation
Indices: 10863--10941 Score: 106
Period size: 29 Copynumber: 2.7 Consensus size: 29
10853 ATGGATTAGA
10863 TAACGTTATATCCTGAATTAAC-TTTTTTG
1 TAACGTTATATCCTGAATT-ACGTTTTTTG
*
10892 TAACGTTATATCCTGAATTGCGTTTTTTG
1 TAACGTTATATCCTGAATTACGTTTTTTG
*
10921 TCAAACCTTATATCCTGAATT
1 T--AACGTTATATCCTGAATT
10942 GATTATTTAG
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
28 1 0.02
29 27 0.60
31 17 0.38
ACGTcount: A:0.27, C:0.16, G:0.11, T:0.46
Consensus pattern (29 bp):
TAACGTTATATCCTGAATTACGTTTTTTG
Done.