Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012970.1 Corchorus capsularis cultivar CVL-1 contig12991, 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: 30130
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.33
Found at i:188 original size:32 final size:32
Alignment explanation
Indices: 151--234 Score: 114
Period size: 32 Copynumber: 2.6 Consensus size: 32
141 AACCTGAACT
151 CGAAAAAACCCGAACCCGAAAAAGCTCAAACC
1 CGAAAAAACCCGAACCCGAAAAAGCTCAAACC
* * * * *
183 TGAAAAAATCAGAACCCGAAAAATCTGAAACC
1 CGAAAAAACCCGAACCCGAAAAAGCTCAAACC
*
215 CGAAAAAACCCAAACCCGAA
1 CGAAAAAACCCGAACCCGAA
235 CCTGAAAAAA
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 43 1.00
ACGTcount: A:0.52, C:0.30, G:0.12, T:0.06
Consensus pattern (32 bp):
CGAAAAAACCCGAACCCGAAAAAGCTCAAACC
Found at i:246 original size:16 final size:16
Alignment explanation
Indices: 141--234 Score: 73
Period size: 16 Copynumber: 5.9 Consensus size: 16
131 AACCTGCCCG
* *
141 AACCTGAACTCGAAAA
1 AACCCGAACCCGAAAA
157 AACCCGAACCCGAAAA
1 AACCCGAACCCGAAAA
* * * *
173 AGCTCAAACCTGAAAA
1 AACCCGAACCCGAAAA
* *
189 AATCAGAACCCG-AAA
1 AACCCGAACCCGAAAA
* *
204 AATCTGAAACCCGAAAA
1 AACCCG-AACCCGAAAA
*
221 AACCCAAACCCGAA
1 AACCCGAACCCGAA
235 CCTGAAAAAA
Statistics
Matches: 60, Mismatches: 16, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
15 8 0.13
16 46 0.77
17 6 0.10
ACGTcount: A:0.51, C:0.30, G:0.12, T:0.07
Consensus pattern (16 bp):
AACCCGAACCCGAAAA
Found at i:6310 original size:1 final size:1
Alignment explanation
Indices: 6304--6333 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
6294 GGGAAATATC
6304 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
6334 CAAATATGGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:15098 original size:14 final size:14
Alignment explanation
Indices: 15079--15105 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
15069 AATGATTATA
15079 AAAGCAATAATAAG
1 AAAGCAATAATAAG
15093 AAAGCAATAATAA
1 AAAGCAATAATAA
15106 AGACAATACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.67, C:0.07, G:0.11, T:0.15
Consensus pattern (14 bp):
AAAGCAATAATAAG
Found at i:22504 original size:17 final size:17
Alignment explanation
Indices: 22474--22507 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
22464 TCTGGTCGAA
**
22474 ATTTTTTTTTTATTTTT
1 ATTTTTTTGATATTTTT
22491 ATTTTTTTGATATTTTT
1 ATTTTTTTGATATTTTT
22508 CGATATGACT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.00, G:0.03, T:0.82
Consensus pattern (17 bp):
ATTTTTTTGATATTTTT
Found at i:28369 original size:33 final size:30
Alignment explanation
Indices: 28321--28420 Score: 121
Period size: 33 Copynumber: 3.2 Consensus size: 30
28311 CCGGTCTTGT
* *
28321 CCGGATGGCCCAATCGATGGCCGGTTGTGG
1 CCGGTTGGTCCAATCGATGGCCGGTTGTGG
28351 CCGGTTGGTGCACCAATCGATGGCCGGTTGTGG
1 CCGGTTGGT---CCAATCGATGGCCGGTTGTGG
28384 CCGGTTGGTCC-ATGCGATGGCCGGTCATGTGG
1 CCGGTTGGTCCAAT-CGATGGCCGGT--TGTGG
28416 CCGGT
1 CCGGT
28421 GTTGCGCGGC
Statistics
Matches: 62, Mismatches: 2, Indels: 10
0.84 0.03 0.14
Matches are distributed among these distances:
29 2 0.03
30 20 0.32
32 10 0.16
33 30 0.48
ACGTcount: A:0.11, C:0.26, G:0.40, T:0.23
Consensus pattern (30 bp):
CCGGTTGGTCCAATCGATGGCCGGTTGTGG
Done.