Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012409.1 Corchorus olitorius cultivar O-4 contig12442, 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: 17163
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.34
Found at i:829 original size:20 final size:19
Alignment explanation
Indices: 798--879 Score: 71
Period size: 20 Copynumber: 4.2 Consensus size: 19
788 CAGGAGGAAG
798 AAAG-AAAGAAAAAAAGAA
1 AAAGAAAAGAAAAAAAGAA
**
816 AAAGAAAGAGAAAAAACTAA
1 AAAGAAA-AGAAAAAAAGAA
836 AAAGAAATA-AATAATAAAGAAA
1 AAAGAAA-AGAA-AA-AAAG-AA
858 AAAGAATAAG-AAAAAAGAA
1 AAAGAA-AAGAAAAAAAGAA
877 AAA
1 AAA
880 AAGACACGTT
Statistics
Matches: 52, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
18 4 0.08
19 9 0.17
20 24 0.46
21 4 0.08
22 10 0.19
23 1 0.02
ACGTcount: A:0.79, C:0.01, G:0.13, T:0.06
Consensus pattern (19 bp):
AAAGAAAAGAAAAAAAGAA
Found at i:861 original size:7 final size:7
Alignment explanation
Indices: 795--880 Score: 70
Period size: 7 Copynumber: 12.3 Consensus size: 7
785 GTGCAGGAGG
795 AAGAAAGA
1 AAGAAA-A
803 AAGAAAA
1 AAGAAAA
810 AA-AGAAA
1 AAGA-AAA
817 AAG-AAA
1 AAGAAAA
*
823 GAGAAAA
1 AAGAAAA
**
830 AACTAAA
1 AAGAAAA
837 AAGAAATA
1 AAGAAA-A
* *
845 AATAATA
1 AAGAAAA
852 AAGAAAA
1 AAGAAAA
*
859 AAG-AAT
1 AAGAAAA
865 AAGAAAA
1 AAGAAAA
872 AAGAAAA
1 AAGAAAA
879 AA
1 AA
881 AGACACGTTA
Statistics
Matches: 61, Mismatches: 12, Indels: 11
0.73 0.14 0.13
Matches are distributed among these distances:
6 11 0.18
7 39 0.64
8 11 0.18
ACGTcount: A:0.79, C:0.01, G:0.14, T:0.06
Consensus pattern (7 bp):
AAGAAAA
Found at i:880 original size:20 final size:20
Alignment explanation
Indices: 807--880 Score: 73
Period size: 20 Copynumber: 3.6 Consensus size: 20
797 GAAAGAAAGA
807 AAAAAAG-AAAAAGAA-AGAG
1 AAAAAAGAAAAAAGAATA-AG
**
826 AAAAAACTAAAAAGAAATAA-
1 AAAAAAGAAAAAAG-AATAAG
846 ATAATAAAGAAAAAAGAATAAG
1 A-AA-AAAGAAAAAAGAATAAG
868 AAAAAAGAAAAAA
1 AAAAAAGAAAAAA
881 AGACACGTTA
Statistics
Matches: 46, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
19 6 0.13
20 17 0.37
21 12 0.26
22 11 0.24
ACGTcount: A:0.80, C:0.01, G:0.12, T:0.07
Consensus pattern (20 bp):
AAAAAAGAAAAAAGAATAAG
Found at i:8444 original size:25 final size:25
Alignment explanation
Indices: 8415--8465 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
8405 AAAATTGGCA
8415 ACCTAAAATAACAATCACAAATTTG
1 ACCTAAAATAACAATCACAAATTTG
* * *
8440 ACCTAAAATACCAATTACATATTTG
1 ACCTAAAATAACAATCACAAATTTG
8465 A
1 A
8466 TCTCATTTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.49, C:0.20, G:0.04, T:0.27
Consensus pattern (25 bp):
ACCTAAAATAACAATCACAAATTTG
Found at i:11966 original size:36 final size:36
Alignment explanation
Indices: 11926--11999 Score: 121
Period size: 36 Copynumber: 2.1 Consensus size: 36
11916 CCCATTTTGA
* *
11926 AAAAAAAATTATTGTGCCAAAAAAGAAACTACCATT
1 AAAAAAAATTATCGTGCCAAAAAAGAAAATACCATT
*
11962 AAAAAAACTTATCGTGCCAAAAAAGAAAATACCATT
1 AAAAAAAATTATCGTGCCAAAAAAGAAAATACCATT
11998 AA
1 AA
12000 CTACCTATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.57, C:0.15, G:0.08, T:0.20
Consensus pattern (36 bp):
AAAAAAAATTATCGTGCCAAAAAAGAAAATACCATT
Found at i:12239 original size:11 final size:11
Alignment explanation
Indices: 12196--12233 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
12186 TTCCTATATA
12196 AAATTAATTAT
1 AAATTAATTAT
12207 CAAA-TAATTAT
1 -AAATTAATTAT
12218 AAATTAATTAT
1 AAATTAATTAT
12229 AAATT
1 AAATT
12234 TGTTATGAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 3 0.12
11 19 0.76
12 3 0.12
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (11 bp):
AAATTAATTAT
Done.