Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022538.1 Corchorus olitorius cultivar O-4 contig22571, 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: 12576
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Found at i:56 original size:32 final size:32
Alignment explanation
Indices: 20--115 Score: 129
Period size: 33 Copynumber: 2.9 Consensus size: 32
10 CCACAATAGC
**
20 GGCGTTTATTAATCAAAACGCCACTATTTAGT
1 GGCGTTTAAAAATCAAAACGCCACTATTTAGT
**
52 GGCGTTTACAAAATCAAAACGCCACTAAATAGT
1 GGCGTTTA-AAAATCAAAACGCCACTATTTAGT
*
85 GGCGTTTACAACATCAAAACGCCACTATTTA
1 GGCGTTTA-AAAATCAAAACGCCACTATTTA
116 TAATTTGAGA
Statistics
Matches: 56, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
32 8 0.14
33 48 0.86
ACGTcount: A:0.36, C:0.22, G:0.15, T:0.27
Consensus pattern (32 bp):
GGCGTTTAAAAATCAAAACGCCACTATTTAGT
Found at i:70 original size:33 final size:33
Alignment explanation
Indices: 30--115 Score: 145
Period size: 33 Copynumber: 2.6 Consensus size: 33
20 GGCGTTTATT
30 AATCAAAACGCCACTATTTAGTGGCGTTTACAA
1 AATCAAAACGCCACTATTTAGTGGCGTTTACAA
**
63 AATCAAAACGCCACTAAATAGTGGCGTTTACAA
1 AATCAAAACGCCACTATTTAGTGGCGTTTACAA
*
96 CATCAAAACGCCACTATTTA
1 AATCAAAACGCCACTATTTA
116 TAATTTGAGA
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 48 1.00
ACGTcount: A:0.40, C:0.23, G:0.13, T:0.24
Consensus pattern (33 bp):
AATCAAAACGCCACTATTTAGTGGCGTTTACAA
Found at i:223 original size:63 final size:65
Alignment explanation
Indices: 101--250 Score: 187
Period size: 63 Copynumber: 2.3 Consensus size: 65
91 TACAACATCA
* *** * *
101 AAACGCCACTATTTATAATTTGAGATATATTTTTTTTTAAAAAAATCCTTAAATATAGCGGCGTT
1 AAACGCCACTATATATAATTTGAGATATA-TTTTTAAAAAAAAAACCCTTAAATATAGCGGCGTC
166 T
65 T
*
167 AAACGCCCCTATATATAATTTGAGATA-A-TTTTAAAAAAAAAACCCTTAAATATAGCGGCGTCT
1 AAACGCCACTATATATAATTTGAGATATATTTTTAAAAAAAAAACCCTTAAATATAGCGGCGTCT
* * *
230 AAGCGCCGCTATATACAATTT
1 AAACGCCACTATATATAATTT
251 AAAAAACTTG
Statistics
Matches: 74, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
63 48 0.65
65 1 0.01
66 25 0.34
ACGTcount: A:0.39, C:0.16, G:0.11, T:0.34
Consensus pattern (65 bp):
AAACGCCACTATATATAATTTGAGATATATTTTTAAAAAAAAAACCCTTAAATATAGCGGCGTCT
Found at i:319 original size:24 final size:24
Alignment explanation
Indices: 287--333 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
277 AATGTATAGC
*
287 GGCGTTTAAACGCCTCTAAATGAT
1 GGCGTTTAAACGCCGCTAAATGAT
*
311 GGCGTTTAAACGCCGCTATATGA
1 GGCGTTTAAACGCCGCTAAATGA
334 CGGCACCTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (24 bp):
GGCGTTTAAACGCCGCTAAATGAT
Found at i:387 original size:23 final size:22
Alignment explanation
Indices: 355--416 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
345 GCGGCGTAGT
*
355 AAAAAACGCCGCTATTTG-AAA
1 AAAAAACGCCGCTATATGTAAA
* *
376 TAGCAAAACGCCGCAATATGTAAA
1 -A-AAAAACGCCGCTATATGTAAA
400 AAAAAACGCCGCTATAT
1 AAAAAACGCCGCTATAT
417 TAATATTTTC
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
22 15 0.45
23 15 0.45
24 3 0.09
ACGTcount: A:0.47, C:0.21, G:0.15, T:0.18
Consensus pattern (22 bp):
AAAAAACGCCGCTATATGTAAA
Found at i:2301 original size:19 final size:17
Alignment explanation
Indices: 2261--2301 Score: 55
Period size: 19 Copynumber: 2.3 Consensus size: 17
2251 CGCCGTCTCG
2261 TTCTCTTTTCTTTTTGT
1 TTCTCTTTTCTTTTTGT
*
2278 GTCTCTGTTTCTTCTTTGT
1 TTCTCT-TTTCTT-TTTGT
2297 TTCTC
1 TTCTC
2302 CTCTGTGTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
17 5 0.25
18 6 0.30
19 9 0.45
ACGTcount: A:0.00, C:0.22, G:0.10, T:0.68
Consensus pattern (17 bp):
TTCTCTTTTCTTTTTGT
Found at i:11540 original size:29 final size:30
Alignment explanation
Indices: 11501--11561 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 30
11491 TATAAATAAT
* *
11501 ATAATATAATTAAATAA-TTATATTTATAC
1 ATAATAAAATTAAATAATTTATATGTATAC
*
11530 ATAATAAAATTGAATAATTTATATGTATAC
1 ATAATAAAATTAAATAATTTATATGTATAC
11560 AT
1 AT
11562 TAATTAGAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 15 0.54
30 13 0.46
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (30 bp):
ATAATAAAATTAAATAATTTATATGTATAC
Done.