Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013723.1 Corchorus olitorius cultivar O-4 contig13756, 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: 58852
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:39412 original size:15 final size:15
Alignment explanation
Indices: 39394--39424 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
39384 CCGCCACCGC
39394 CATCTTTCTTTCCAT
1 CATCTTTCTTTCCAT
*
39409 CATCTTTCTTTTCAT
1 CATCTTTCTTTCCAT
39424 C
1 C
39425 TTTCTTCTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.32, G:0.00, T:0.55
Consensus pattern (15 bp):
CATCTTTCTTTCCAT
Found at i:41579 original size:22 final size:22
Alignment explanation
Indices: 41551--41592 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
41541 TTACATTAGC
*
41551 GAAACGATAATTTATGAACCGT
1 GAAACGATAATCTATGAACCGT
41573 GAAACGATAATCTATGAACC
1 GAAACGATAATCTATGAACC
41593 AACAAACCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.43, C:0.17, G:0.17, T:0.24
Consensus pattern (22 bp):
GAAACGATAATCTATGAACCGT
Found at i:41599 original size:22 final size:22
Alignment explanation
Indices: 41552--41599 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
41542 TACATTAGCG
* ***
41552 AAACGATAATTTATGAACCGTG
1 AAACGATAATCTATGAACCAAC
41574 AAACGATAATCTATGAACCAAC
1 AAACGATAATCTATGAACCAAC
41596 AAAC
1 AAAC
41600 CCTTTTCCCA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.48, C:0.19, G:0.12, T:0.21
Consensus pattern (22 bp):
AAACGATAATCTATGAACCAAC
Found at i:42973 original size:1 final size:1
Alignment explanation
Indices: 42967--43007 Score: 82
Period size: 1 Copynumber: 41.0 Consensus size: 1
42957 AGCTTAAATT
42967 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
43008 CCATATGATC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 40 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:51762 original size:31 final size:31
Alignment explanation
Indices: 51727--51785 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 31
51717 TTGGTCTGAC
*
51727 GTGGCCTTACCACGTGACATTTTGGTCCAAT
1 GTGGCATTACCACGTGACATTTTGGTCCAAT
** * *
51758 GTGGCATTGTCATGTGGCATTTTGGTCC
1 GTGGCATTACCACGTGACATTTTGGTCC
51786 GGCATATCGT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 23 1.00
ACGTcount: A:0.15, C:0.22, G:0.27, T:0.36
Consensus pattern (31 bp):
GTGGCATTACCACGTGACATTTTGGTCCAAT
Found at i:56576 original size:21 final size:21
Alignment explanation
Indices: 56531--56589 Score: 77
Period size: 21 Copynumber: 2.9 Consensus size: 21
56521 CTGTTTGACA
* *
56531 ACTGTACAAATGAGATTA--C
1 ACTGTACATATGAGATTATGT
*
56550 ACTGTACATATTAGATTATGT
1 ACTGTACATATGAGATTATGT
56571 ACTGTACATATGAGATTAT
1 ACTGTACATATGAGATTAT
56590 TAGAGCAGTG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 16 0.47
21 18 0.53
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.36
Consensus pattern (21 bp):
ACTGTACATATGAGATTATGT
Found at i:56667 original size:19 final size:19
Alignment explanation
Indices: 56639--56675 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
56629 TTTGGTCCCA
*
56639 AAACGGTGGTGAAACGGTC
1 AAACGATGGTGAAACGGTC
56658 AAACGATGGTGAAACGGT
1 AAACGATGGTGAAACGGT
56676 TACAGATAAG
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:0.35, C:0.14, G:0.35, T:0.16
Consensus pattern (19 bp):
AAACGATGGTGAAACGGTC
Found at i:57504 original size:21 final size:21
Alignment explanation
Indices: 57478--57525 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
57468 ATTTAAGTGG
57478 GATAATTTCTTTTGTTTATTT
1 GATAATTTCTTTTGTTTATTT
57499 GATAATTTCTTTTGTTTATTT
1 GATAATTTCTTTTGTTTATTT
57520 GATAAT
1 GATAAT
57526 ATATATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.23, C:0.04, G:0.10, T:0.62
Consensus pattern (21 bp):
GATAATTTCTTTTGTTTATTT
Found at i:57547 original size:8 final size:8
Alignment explanation
Indices: 57536--57561 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
57526 ATATATATAT
57536 ATATATGA
1 ATATATGA
57544 ATATATGA
1 ATATATGA
57552 ATATATGA
1 ATATATGA
57560 AT
1 AT
57562 GGACAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (8 bp):
ATATATGA
Found at i:58791 original size:20 final size:20
Alignment explanation
Indices: 58762--58801 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
58752 AAGCTAAGTA
*
58762 TAATAGTAATAATAATCAAT
1 TAATAATAATAATAATCAAT
58782 TAATAATAATAATAATCAAT
1 TAATAATAATAATAATCAAT
58802 CCCACTTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.57, C:0.05, G:0.03, T:0.35
Consensus pattern (20 bp):
TAATAATAATAATAATCAAT
Done.