Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023525.1 Corchorus olitorius cultivar O-4 contig23558, 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: 13364
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Found at i:2605 original size:5 final size:5
Alignment explanation
Indices: 2578--2644 Score: 61
Period size: 5 Copynumber: 13.6 Consensus size: 5
2568 AAATCTAAAC
*
2578 TTTGTT TTTGT TTT-T CTTT-T TTTGT TTTGT TTTGC TTTG- TTTGT TTTGT
1 TTTG-T TTTGT TTTGT -TTTGT TTTGT TTTGT TTTGT TTTGT TTTGT TTTGT
*
2627 TTTTT TTTGGT TTT-T TTT
1 TTTGT TTT-GT TTTGT TTT
2645 TAATTTTATA
Statistics
Matches: 54, Mismatches: 3, Indels: 10
0.81 0.04 0.15
Matches are distributed among these distances:
4 12 0.22
5 34 0.63
6 8 0.15
ACGTcount: A:0.00, C:0.03, G:0.15, T:0.82
Consensus pattern (5 bp):
TTTGT
Found at i:2607 original size:19 final size:19
Alignment explanation
Indices: 2578--2634 Score: 80
Period size: 19 Copynumber: 3.0 Consensus size: 19
2568 AAATCTAAAC
2578 TTTGTTTTTGTTTTTCTTTT
1 TTTG-TTTTGTTTTTCTTTT
* *
2598 TTTGTTTTGTTTTGCTTTG
1 TTTGTTTTGTTTTTCTTTT
2617 TTTGTTTTGTTTTT-TTTT
1 TTTGTTTTGTTTTTCTTTT
2635 GGTTTTTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
18 3 0.09
19 26 0.79
20 4 0.12
ACGTcount: A:0.00, C:0.04, G:0.14, T:0.82
Consensus pattern (19 bp):
TTTGTTTTGTTTTTCTTTT
Found at i:2620 original size:14 final size:15
Alignment explanation
Indices: 2598--2640 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
2588 TTTTTCTTTT
2598 TTTGTTTTGTTTTGC
1 TTTGTTTTGTTTTGC
*
2613 TTTG-TTTGTTTTGT
1 TTTGTTTTGTTTTGC
*
2627 TTTTTTTTGGTTTT
1 TTTGTTTT-GTTTT
2641 TTTTTAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 12 0.50
15 7 0.29
16 5 0.21
ACGTcount: A:0.00, C:0.02, G:0.19, T:0.79
Consensus pattern (15 bp):
TTTGTTTTGTTTTGC
Found at i:4937 original size:11 final size:11
Alignment explanation
Indices: 4921--4950 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
4911 CCTCATCACC
4921 TAATAATAATA
1 TAATAATAATA
4932 TAATAATAATA
1 TAATAATAATA
*
4943 AAATAATA
1 TAATAATA
4951 GTTATCAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
TAATAATAATA
Found at i:4940 original size:14 final size:14
Alignment explanation
Indices: 4921--4950 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
4911 CCTCATCACC
*
4921 TAATAATAATATAA
1 TAATAATAAAATAA
4935 TAATAATAAAATAA
1 TAATAATAAAATAA
4949 TA
1 TA
4951 GTTATCAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
TAATAATAAAATAA
Found at i:7126 original size:2 final size:2
Alignment explanation
Indices: 7119--7144 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
7109 ATTTCTTACA
7119 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
7145 TTTTGAAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11065 original size:6 final size:6
Alignment explanation
Indices: 11056--11085 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
11046 GAAAAAACAA
11056 AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC
1 AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC
11086 GCCTACAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.83, C:0.17, G:0.00, T:0.00
Consensus pattern (6 bp):
AAAAAC
Found at i:12778 original size:8 final size:8
Alignment explanation
Indices: 12765--12789 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
12755 AAATTCAAAT
12765 ATATATAA
1 ATATATAA
12773 ATATATAA
1 ATATATAA
12781 ATATATAA
1 ATATATAA
12789 A
1 A
12790 AAATAAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (8 bp):
ATATATAA
Done.