Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019834.1 Corchorus olitorius cultivar O-4 contig19867, 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: 25228
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.35
Found at i:2677 original size:22 final size:23
Alignment explanation
Indices: 2638--2683 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
2628 AATTTACTAT
2638 TTTTATATTTATGATTAACTGTG
1 TTTTATATTTATGATTAACTGTG
*
2661 TTTTA-ATTATAT-ATTAATTGTG
1 TTTTATATT-TATGATTAACTGTG
2683 T
1 T
2684 GTGGATATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.28, C:0.02, G:0.11, T:0.59
Consensus pattern (23 bp):
TTTTATATTTATGATTAACTGTG
Found at i:8393 original size:3 final size:3
Alignment explanation
Indices: 8387--8449 Score: 126
Period size: 3 Copynumber: 21.0 Consensus size: 3
8377 ATAACCTAAA
8387 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
8435 TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT
8450 GAACCTTAAA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:9007 original size:169 final size:169
Alignment explanation
Indices: 8753--9070 Score: 550
Period size: 169 Copynumber: 1.9 Consensus size: 169
8743 GGAGTTTAGA
*
8753 AGACTACACAAGCGGGTCTTAAAGGGTGACATGTGTCCCTTAGGGACTAGATTGAAATATATAAA
1 AGACTACACAAGCGGGTCTTAAAGGGTGACATGCGTCCCTTAGGGACTAGATTGAAATATATAAA
* *
8818 ACTTAATTAATTAAAAAATTGGACATGTGTCAACTCCACAATCCGCTTGTGGAGTTCAAAATTTA
66 ACTAAATTAATTAAAAAATTGGACATGTGTCAACTCCACAATCCGCTTGTGGAGTCCAAAATTTA
8883 CACCGCCGGTGTATCAAATTATACAATACACTGTCAAGC
131 CACCGCCGGTGTATCAAATTATACAATACACTGTCAAGC
* * *
8922 AGACTACACAAGCGGGT-TCTGAAGGGTGACATGCGT-CATCTAGGGACTAGATTGAAATATTTA
1 AGACTACACAAGCGGGTCT-TAAAGGGTGACATGCGTCCCT-TAGGGACTAGATTGAAATATATA
8985 AAACTAAATTAATTAAAAAATTGGACATGTGTCAACTCCACAATCCGCTTGTGGAGTCCAAAATT
64 AAACTAAATTAATTAAAAAATTGGACATGTGTCAACTCCACAATCCGCTTGTGGAGTCCAAAATT
9050 TACACCGCCGGTGTATCAAAT
129 TACACCGCCGGTGTATCAAAT
9071 AATTACCCTA
Statistics
Matches: 141, Mismatches: 6, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
168 3 0.02
169 138 0.98
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (169 bp):
AGACTACACAAGCGGGTCTTAAAGGGTGACATGCGTCCCTTAGGGACTAGATTGAAATATATAAA
ACTAAATTAATTAAAAAATTGGACATGTGTCAACTCCACAATCCGCTTGTGGAGTCCAAAATTTA
CACCGCCGGTGTATCAAATTATACAATACACTGTCAAGC
Found at i:10309 original size:4 final size:4
Alignment explanation
Indices: 10300--10361 Score: 54
Period size: 4 Copynumber: 14.2 Consensus size: 4
10290 AGATCCTACT
*
10300 TTTA TTTA TTTAAA TTTA -ATA TTTA TTTA TTTA TATTA TATATA TTATA
1 TTTA TTTA TTT--A TTTA TTTA TTTA TTTA TTTA T-TTA T-T-TA TT-TA
10349 TTTA TTTA TTTA T
1 TTTA TTTA TTTA T
10362 ATTTGTTAGT
Statistics
Matches: 51, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
3 2 0.04
4 30 0.59
5 12 0.24
6 7 0.14
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (4 bp):
TTTA
Found at i:10326 original size:21 final size:23
Alignment explanation
Indices: 10300--10356 Score: 82
Period size: 21 Copynumber: 2.5 Consensus size: 23
10290 AGATCCTACT
10300 TTTATTTATTTAAATT-TA-ATA
1 TTTATTTATTTAAATTATATATA
*
10321 TTTATTTATTTATATTATATATA
1 TTTATTTATTTAAATTATATATA
10344 TTATATTTATTTA
1 TT-TATTTATTTA
10357 TTTATATTTG
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
21 15 0.47
22 2 0.06
23 5 0.16
24 10 0.31
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (23 bp):
TTTATTTATTTAAATTATATATA
Found at i:10362 original size:21 final size:20
Alignment explanation
Indices: 10300--10363 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 20
10290 AGATCCTACT
10300 TTTATTTATTTAAATTTA-ATA
1 TTTATTTATTT--ATTTATATA
10321 TTTATTTATTTATATTATATATA
1 TTTATTTA-TT-TATT-TATATA
10344 TTATATTTATTTATTTATAT
1 TT-TATTTATTTATTTATAT
10364 TTGTTAGTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
21 16 0.42
22 8 0.21
23 8 0.21
24 6 0.16
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (20 bp):
TTTATTTATTTATTTATATA
Found at i:11957 original size:7 final size:7
Alignment explanation
Indices: 11939--12012 Score: 67
Period size: 7 Copynumber: 9.7 Consensus size: 7
11929 TTTTTCCCTG
11939 CTTCCAAT
1 CTTCC-AT
11947 CTTCCAT
1 CTTCCAT
11954 CTTCCAT
1 CTTCCAT
*
11961 CTTCCGT
1 CTTCCAT
*
11968 CCTTCCTT
1 -CTTCCAT
11976 ACTTCTCGATT
1 -CTTC-C-A-T
*
11987 TTTCCAT
1 CTTCCAT
11994 CTTCCAT
1 CTTCCAT
12001 CTTCCAT
1 CTTCCAT
12008 CTTCC
1 CTTCC
12013 TTCCTTCCTT
Statistics
Matches: 56, Mismatches: 6, Indels: 9
0.79 0.08 0.13
Matches are distributed among these distances:
7 34 0.61
8 16 0.29
9 2 0.04
10 3 0.05
11 1 0.02
ACGTcount: A:0.12, C:0.41, G:0.03, T:0.45
Consensus pattern (7 bp):
CTTCCAT
Found at i:16919 original size:19 final size:18
Alignment explanation
Indices: 16886--16921 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
16876 TGGAAATAAT
16886 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
16904 TCTTCAAATTGTCTTCAA
1 TCTTC-AATGGTCTTCAA
16922 TAAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (18 bp):
TCTTCAATGGTCTTCAAA
Found at i:21175 original size:60 final size:60
Alignment explanation
Indices: 21082--21201 Score: 240
Period size: 60 Copynumber: 2.0 Consensus size: 60
21072 GAGAGTATCT
21082 ACCATCAAGAGAAATCGCATCTCTAGTTCCCAATCAGGACAACAATCTGAACACCAATCC
1 ACCATCAAGAGAAATCGCATCTCTAGTTCCCAATCAGGACAACAATCTGAACACCAATCC
21142 ACCATCAAGAGAAATCGCATCTCTAGTTCCCAATCAGGACAACAATCTGAACACCAATCC
1 ACCATCAAGAGAAATCGCATCTCTAGTTCCCAATCAGGACAACAATCTGAACACCAATCC
21202 GAACAACAAT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.38, C:0.32, G:0.12, T:0.18
Consensus pattern (60 bp):
ACCATCAAGAGAAATCGCATCTCTAGTTCCCAATCAGGACAACAATCTGAACACCAATCC
Found at i:21198 original size:24 final size:24
Alignment explanation
Indices: 21172--21248 Score: 82
Period size: 24 Copynumber: 3.2 Consensus size: 24
21162 CTCTAGTTCC
* * *
21172 CAATCAGGACAACAATCTGAACAC
1 CAATCAGAACAACAATCAGAACAA
* *
21196 CAATCCGAACAACAATCAGGACAA
1 CAATCAGAACAACAATCAGAACAA
* * *
21220 CAATCTGAACACCAATCCGAACAA
1 CAATCAGAACAACAATCAGAACAA
21244 CAATC
1 CAATC
21249 TGTGCCTTCA
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 44 1.00
ACGTcount: A:0.47, C:0.31, G:0.10, T:0.12
Consensus pattern (24 bp):
CAATCAGAACAACAATCAGAACAA
Found at i:21199 original size:12 final size:12
Alignment explanation
Indices: 21180--21250 Score: 88
Period size: 12 Copynumber: 5.9 Consensus size: 12
21170 CCCAATCAGG
21180 ACAACAATCTGA
1 ACAACAATCTGA
* *
21192 ACACCAATCCGA
1 ACAACAATCTGA
* *
21204 ACAACAATCAGG
1 ACAACAATCTGA
21216 ACAACAATCTGA
1 ACAACAATCTGA
* *
21228 ACACCAATCCGA
1 ACAACAATCTGA
21240 ACAACAATCTG
1 ACAACAATCTG
21251 TGCCTTCACA
Statistics
Matches: 48, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 48 1.00
ACGTcount: A:0.46, C:0.31, G:0.10, T:0.13
Consensus pattern (12 bp):
ACAACAATCTGA
Found at i:21219 original size:36 final size:36
Alignment explanation
Indices: 21172--21248 Score: 154
Period size: 36 Copynumber: 2.1 Consensus size: 36
21162 CTCTAGTTCC
21172 CAATCAGGACAACAATCTGAACACCAATCCGAACAA
1 CAATCAGGACAACAATCTGAACACCAATCCGAACAA
21208 CAATCAGGACAACAATCTGAACACCAATCCGAACAA
1 CAATCAGGACAACAATCTGAACACCAATCCGAACAA
21244 CAATC
1 CAATC
21249 TGTGCCTTCA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.47, C:0.31, G:0.10, T:0.12
Consensus pattern (36 bp):
CAATCAGGACAACAATCTGAACACCAATCCGAACAA
Done.