Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018373.1 Corchorus olitorius cultivar O-4 contig18406, 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: 33570
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Found at i:620 original size:3 final size:3
Alignment explanation
Indices: 612--639 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
602 AGGAAAAATA
612 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
640 TAAATATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:3177 original size:145 final size:145
Alignment explanation
Indices: 3011--3301 Score: 505
Period size: 145 Copynumber: 2.0 Consensus size: 145
3001 GTTTTCTGTT
* * *
3011 GTCAAATTTTTATTTTTTGGAAATAAAACGGTGAAAACATGTTTGACAGGCTGTTTCCATTTTCA
1 GTCAAATTTTTATTTTTTGGAAACAAAACAGTGAAAACATGTTTGACAGACTGTTTCCATTTT-A
3076 AAAA-TTTTTGAAACAGAAGCAATGTTTTGGAAAAAAAGTAGAAGTAAGAATTTTGTGTATTTAT
65 AAAACTTTTTGAAACAGAAGCAATGTTTTGGAAAAAAA-TAGAAGTAAGAATTTTGTGTATTTAT
3140 GTTTTTTCCAAAACACA
129 GTTTTTTCCAAAACACA
* *
3157 GTCAATTTTTTA-TTTTTGGAAACAAAACAGTGAAAACATGTTTGGCAGACTGTTTCCATTTTAA
1 GTCAAATTTTTATTTTTTGGAAACAAAACAGTGAAAACATGTTTGACAGACTGTTTCCATTTTAA
3221 AAACTTTTTGAAACAGAAGCAATGTTTTGGAAAAAAATAGAAGTAAGAATTTTGTGTATTTATGT
66 AAACTTTTTGAAACAGAAGCAATGTTTTGGAAAAAAATAGAAGTAAGAATTTTGTGTATTTATGT
3286 TTTTTCCAAAACACA
131 TTTTTCCAAAACACA
3301 G
1 G
3302 AAACACATTG
Statistics
Matches: 139, Mismatches: 5, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
144 49 0.35
145 79 0.57
146 11 0.08
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.37
Consensus pattern (145 bp):
GTCAAATTTTTATTTTTTGGAAACAAAACAGTGAAAACATGTTTGACAGACTGTTTCCATTTTAA
AAACTTTTTGAAACAGAAGCAATGTTTTGGAAAAAAATAGAAGTAAGAATTTTGTGTATTTATGT
TTTTTCCAAAACACA
Found at i:3440 original size:16 final size:15
Alignment explanation
Indices: 3421--3471 Score: 57
Period size: 17 Copynumber: 3.1 Consensus size: 15
3411 CAACGCAACA
3421 AAAATAAAACGAAAAC
1 AAAA-AAAACGAAAAC
3437 AAAACAAAAACGAGAAAC
1 -AAA-AAAAACGA-AAAC
*
3455 AGAAAAAACGAAAAC
1 AAAAAAAACGAAAAC
3470 AA
1 AA
3472 TACCAAACGG
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
15 5 0.17
16 8 0.27
17 12 0.40
18 5 0.17
ACGTcount: A:0.75, C:0.14, G:0.10, T:0.02
Consensus pattern (15 bp):
AAAAAAAACGAAAAC
Found at i:5396 original size:2 final size:2
Alignment explanation
Indices: 5389--5422 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
5379 GTAATATTGA
5389 AT 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
5423 TATCCATCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25604 original size:6 final size:6
Alignment explanation
Indices: 25593--25617 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
25583 AACAATGGCC
25593 GTGTGG GTGTGG GTGTGG GTGTGG G
1 GTGTGG GTGTGG GTGTGG GTGTGG G
25618 CAGTGGGCAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.00, G:0.68, T:0.32
Consensus pattern (6 bp):
GTGTGG
Found at i:28138 original size:5 final size:5
Alignment explanation
Indices: 28128--28152 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
28118 TTTACTTGTA
28128 TTTTC TTTTC TTTTC TTTTC TTTTC
1 TTTTC TTTTC TTTTC TTTTC TTTTC
28153 ATTATTTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTC
Found at i:30266 original size:2 final size:2
Alignment explanation
Indices: 30261--30292 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
30251 TAGTATTAAA
30261 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
30293 GTGTGTGTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33178 original size:30 final size:30
Alignment explanation
Indices: 33142--33201 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
33132 TTTTCTTTTT
33142 CTTTTCCAGGTAACACACATCATGAGTTGA
1 CTTTTCCAGGTAACACACATCATGAGTTGA
33172 CTTTTCCAGGTAACACACATCATGAGTTGA
1 CTTTTCCAGGTAACACACATCATGAGTTGA
33202 TGGTATATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (30 bp):
CTTTTCCAGGTAACACACATCATGAGTTGA
Done.