Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020606.1 Corchorus olitorius cultivar O-4 contig20639, 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: 31278
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:454 original size:16 final size:16
Alignment explanation
Indices: 435--477 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
425 TGTCTCCGTC
435 TCTGTATGTCTATGTA
1 TCTGTATGTCTATGTA
* * *
451 TCTGTCTGTTTATGTG
1 TCTGTATGTCTATGTA
*
467 TCTGTGTGTCT
1 TCTGTATGTCT
478 GTGTCTTCCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.09, C:0.14, G:0.23, T:0.53
Consensus pattern (16 bp):
TCTGTATGTCTATGTA
Found at i:1560 original size:42 final size:42
Alignment explanation
Indices: 1513--1595 Score: 148
Period size: 42 Copynumber: 2.0 Consensus size: 42
1503 TAAATTCTAG
* *
1513 TACTCCATCTCTAGGTAATTCATCAAAATAAAGTTAATATTC
1 TACTCCATCTCTAGATAATTCATCAAAATAAAGCTAATATTC
1555 TACTCCATCTCTAGATAATTCATCAAAATAAAGCTAATATT
1 TACTCCATCTCTAGATAATTCATCAAAATAAAGCTAATATT
1596 AATTGTTGCT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.40, C:0.19, G:0.06, T:0.35
Consensus pattern (42 bp):
TACTCCATCTCTAGATAATTCATCAAAATAAAGCTAATATTC
Found at i:6568 original size:22 final size:22
Alignment explanation
Indices: 6519--6569 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
6509 AAATATTACC
* **
6519 ATAATTATTTTTGGCAGCCATA
1 ATAATTATTTTTGCCAGAAATA
6541 ATAATTATTTTTGCCAAGAAATA
1 ATAATTATTTTTGCC-AGAAATA
6564 A-AATTA
1 ATAATTA
6570 GGCAATAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 19 0.76
23 6 0.24
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.39
Consensus pattern (22 bp):
ATAATTATTTTTGCCAGAAATA
Found at i:9480 original size:18 final size:18
Alignment explanation
Indices: 9457--9546 Score: 110
Period size: 18 Copynumber: 5.0 Consensus size: 18
9447 GTAAATCCTA
9457 GGGAACTAACTTTGAATG
1 GGGAACTAACTTTGAATG
*
9475 GGGAACTGACTTTGAATG
1 GGGAACTAACTTTGAATG
* *
9493 AGGAACTAGCTTTGAATG
1 GGGAACTAACTTTGAATG
*
9511 GAGAACTAACTTTGAAT-
1 GGGAACTAACTTTGAATG
* *
9528 GAGAGACTGACTTTGAATG
1 GGGA-ACTAACTTTGAATG
9547 ATCCTTAACA
Statistics
Matches: 62, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
17 4 0.06
18 58 0.94
ACGTcount: A:0.33, C:0.11, G:0.28, T:0.28
Consensus pattern (18 bp):
GGGAACTAACTTTGAATG
Found at i:12805 original size:18 final size:17
Alignment explanation
Indices: 12781--12833 Score: 70
Period size: 18 Copynumber: 3.0 Consensus size: 17
12771 GTCAATCCTA
12781 GGGAACTAACTTTGAAT
1 GGGAACTAACTTTGAAT
*
12798 GAGGAACTAGCTTTGAAT
1 G-GGAACTAACTTTGAAT
*
12816 GGAGAACTGACTTTGAAT
1 GG-GAACTAACTTTGAAT
12834 AAGAGACTGA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
17 2 0.06
18 29 0.94
ACGTcount: A:0.34, C:0.11, G:0.26, T:0.28
Consensus pattern (17 bp):
GGGAACTAACTTTGAAT
Found at i:12842 original size:18 final size:18
Alignment explanation
Indices: 12783--12851 Score: 63
Period size: 18 Copynumber: 3.8 Consensus size: 18
12773 CAATCCTAGG
*
12783 GAACTAACTTTGAAT-GA
1 GAACTGACTTTGAATAGA
*
12800 GGAACT-AGCTTTGAATGGA
1 -GAACTGA-CTTTGAATAGA
12819 GAACTGACTTTGAATA-A
1 GAACTGACTTTGAATAGA
*
12836 GAGACTGATTTTGAAT
1 GA-ACTGACTTTGAAT
12852 GATCCTTAAC
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
17 4 0.09
18 38 0.84
19 3 0.07
ACGTcount: A:0.36, C:0.10, G:0.23, T:0.30
Consensus pattern (18 bp):
GAACTGACTTTGAATAGA
Found at i:17250 original size:35 final size:35
Alignment explanation
Indices: 17211--17284 Score: 121
Period size: 35 Copynumber: 2.1 Consensus size: 35
17201 ACTTTTGTAA
* * *
17211 GCTTTGTTGTTGTTTTGTTGATGGAGACGAACTTT
1 GCTTTGTTGTTGCTTTGTTGATAGAGAAGAACTTT
17246 GCTTTGTTGTTGCTTTGTTGATAGAGAAGAACTTT
1 GCTTTGTTGTTGCTTTGTTGATAGAGAAGAACTTT
17281 GCTT
1 GCTT
17285 CAGATTTGGT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.16, C:0.09, G:0.27, T:0.47
Consensus pattern (35 bp):
GCTTTGTTGTTGCTTTGTTGATAGAGAAGAACTTT
Found at i:19865 original size:34 final size:34
Alignment explanation
Indices: 19827--19897 Score: 142
Period size: 34 Copynumber: 2.1 Consensus size: 34
19817 CAATCGTTTG
19827 CAAGGATTTGTGGCAGCCATCAATTGAAGGAGGA
1 CAAGGATTTGTGGCAGCCATCAATTGAAGGAGGA
19861 CAAGGATTTGTGGCAGCCATCAATTGAAGGAGGA
1 CAAGGATTTGTGGCAGCCATCAATTGAAGGAGGA
19895 CAA
1 CAA
19898 TTGATTTGCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.34, C:0.15, G:0.31, T:0.20
Consensus pattern (34 bp):
CAAGGATTTGTGGCAGCCATCAATTGAAGGAGGA
Found at i:25764 original size:35 final size:35
Alignment explanation
Indices: 25725--25828 Score: 126
Period size: 35 Copynumber: 3.1 Consensus size: 35
25715 ACTTTTGTAA
* * *
25725 GCTTTGTTGTTGGTTTGTTGATGGAGACGAACTTT
1 GCTTTGTTATTGCTTTGTTGATGGAGAAGAACTTT
25760 GCTTTGTTATTGCTTTGTTGATGGAGAAGAACTTT
1 GCTTTGTTATTGCTTTGTTGATGGAGAAGAACTTT
**
25795 GC-TTCATATCTGC--T-TTGATGGAGAAGAACTTT
1 GCTTTGTTAT-TGCTTTGTTGATGGAGAAGAACTTT
25827 GC
1 GC
25829 CTTGAATTTG
Statistics
Matches: 63, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
32 20 0.32
33 1 0.02
34 5 0.08
35 37 0.59
ACGTcount: A:0.19, C:0.12, G:0.27, T:0.42
Consensus pattern (35 bp):
GCTTTGTTATTGCTTTGTTGATGGAGAAGAACTTT
Found at i:25849 original size:53 final size:53
Alignment explanation
Indices: 25787--25895 Score: 209
Period size: 53 Copynumber: 2.1 Consensus size: 53
25777 TTGATGGAGA
*
25787 AGAACTTTGCTTCATATCTGCTTTGATGGAGAAGAACTTTGCCTTGAATTTGG
1 AGAACTTTGCTTCAGATCTGCTTTGATGGAGAAGAACTTTGCCTTGAATTTGG
25840 AGAACTTTGCTTCAGATCTGCTTTGATGGAGAAGAACTTTGCCTTGAATTTGG
1 AGAACTTTGCTTCAGATCTGCTTTGATGGAGAAGAACTTTGCCTTGAATTTGG
25893 AGA
1 AGA
25896 GATTGTTGGT
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 55 1.00
ACGTcount: A:0.26, C:0.15, G:0.24, T:0.36
Consensus pattern (53 bp):
AGAACTTTGCTTCAGATCTGCTTTGATGGAGAAGAACTTTGCCTTGAATTTGG
Found at i:30335 original size:16 final size:15
Alignment explanation
Indices: 30297--30338 Score: 75
Period size: 15 Copynumber: 2.7 Consensus size: 15
30287 ACAGAGGTTG
30297 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
30312 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
30327 ACTAGAAAACAA
1 AC-AGAAAACAA
30339 AGCAAAGTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 17 0.65
16 9 0.35
ACGTcount: A:0.67, C:0.14, G:0.07, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Done.