Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014133.1 Corchorus olitorius cultivar O-4 contig14166, 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: 37316
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:2608 original size:2 final size:2
Alignment explanation
Indices: 2601--2631 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2591 TTAATATACC
2601 TA TA TA TA TA TA TA TA -A TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2632 GAGAGAGAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2622 original size:13 final size:13
Alignment explanation
Indices: 2604--2629 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2594 ATATACCTAT
2604 ATATATATATATA
1 ATATATATATATA
2617 ATATATATATATA
1 ATATATATATATA
2630 TAGAGAGAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
ATATATATATATA
Found at i:2622 original size:15 final size:15
Alignment explanation
Indices: 2602--2631 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2592 TAATATACCT
2602 ATATATATATATATA
1 ATATATATATATATA
2617 ATATATATATATATA
1 ATATATATATATATA
2632 GAGAGAGAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
ATATATATATATATA
Found at i:2636 original size:2 final size:2
Alignment explanation
Indices: 2631--2659 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2621 ATATATATAT
2631 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2660 TTAATCTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:6390 original size:3 final size:3
Alignment explanation
Indices: 6384--6411 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
6374 TTCTTCTTCT
6384 TTG TTG TTG TTG TTG TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG T
6412 CTCTCTCTCT
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:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:18009 original size:24 final size:25
Alignment explanation
Indices: 17982--18043 Score: 76
Period size: 26 Copynumber: 2.5 Consensus size: 25
17972 ATATAAAATT
17982 TGAAGTTTTTTA-TTCTTC-AAAAAA
1 TGAAGTTTTTTATTTC-TCAAAAAAA
18006 TGAAG-TTTTTATTTCTCAAAAAAAAA
1 TGAAGTTTTTTATTTCTC--AAAAAAA
18032 TGAAGTTTTTTA
1 TGAAGTTTTTTA
18044 AGTTCAAATC
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
23 8 0.24
24 8 0.24
26 11 0.33
27 6 0.18
ACGTcount: A:0.39, C:0.06, G:0.10, T:0.45
Consensus pattern (25 bp):
TGAAGTTTTTTATTTCTCAAAAAAA
Found at i:18050 original size:26 final size:26
Alignment explanation
Indices: 18000--18051 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
17990 TTTATTCTTC
**
18000 AAAAAATGAAGTTTTTATTTCTCAAA
1 AAAAAATGAAGTTTTTAAGTCTCAAA
18026 AAAAAATGAAGTTTTTTAAGT-TCAAA
1 AAAAAATGAAG-TTTTTAAGTCTCAAA
18052 TCTCACAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 16 0.70
27 7 0.30
ACGTcount: A:0.48, C:0.06, G:0.10, T:0.37
Consensus pattern (26 bp):
AAAAAATGAAGTTTTTAAGTCTCAAA
Found at i:19135 original size:21 final size:19
Alignment explanation
Indices: 19110--19165 Score: 67
Period size: 21 Copynumber: 2.8 Consensus size: 19
19100 GCTGCTCTAA
19110 TAATCTCATCTGTACAATACC
1 TAATCTCATCTGTACAAT--C
* * *
19131 TAATCTAATCTGTACAGTG
1 TAATCTCATCTGTACAATC
19150 TAATCTCATCTGTACA
1 TAATCTCATCTGTACA
19166 GTTGCTAAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 15 0.48
21 16 0.52
ACGTcount: A:0.32, C:0.23, G:0.09, T:0.36
Consensus pattern (19 bp):
TAATCTCATCTGTACAATC
Found at i:19155 original size:19 final size:19
Alignment explanation
Indices: 19131--19167 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
19121 GTACAATACC
19131 TAATCTAATCTGTACAGTG
1 TAATCTAATCTGTACAGTG
*
19150 TAATCTCATCTGTACAGT
1 TAATCTAATCTGTACAGT
19168 TGCTAAACAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.38
Consensus pattern (19 bp):
TAATCTAATCTGTACAGTG
Found at i:26344 original size:23 final size:24
Alignment explanation
Indices: 26292--26347 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
26282 TATAGTACTT
*
26292 AATCTTAATTTGTTTGCACAAAAA
1 AATCTTAATTTGTTGGCACAAAAA
26316 AATCTTAATTTG-TGGC-CAAAAA
1 AATCTTAATTTGTTGGCACAAAAA
26338 AATTCTTAAT
1 AA-TCTTAAT
26348 CTTAATTCTT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 8 0.27
23 10 0.33
24 12 0.40
ACGTcount: A:0.41, C:0.12, G:0.09, T:0.38
Consensus pattern (24 bp):
AATCTTAATTTGTTGGCACAAAAA
Found at i:34526 original size:17 final size:16
Alignment explanation
Indices: 34504--34535 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
34494 AAACAAAAGA
34504 AAATTTTATTGGATATT
1 AAATTTTATT-GATATT
34521 AAATTTTATTGATAT
1 AAATTTTATTGATAT
34536 CTACTCAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (16 bp):
AAATTTTATTGATATT
Done.