Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011355.1 Corchorus olitorius cultivar O-4 contig11388, 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: 4619
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Found at i:2333 original size:10 final size:10
Alignment explanation
Indices: 2312--2342 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
2302 AAATAAGGAA
2312 AACAAG-AAG
1 AACAAGTAAG
2321 AACAAGTAAG
1 AACAAGTAAG
2331 AACAAGTAAG
1 AACAAGTAAG
2341 AA
1 AA
2343 TTTGATGAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 6 0.29
10 15 0.71
ACGTcount: A:0.65, C:0.10, G:0.19, T:0.06
Consensus pattern (10 bp):
AACAAGTAAG
Found at i:3330 original size:20 final size:22
Alignment explanation
Indices: 3305--3348 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 22
3295 GCTTTTTAAA
3305 TTACTGACTACCAT-TT-CTTT
1 TTACTGACTACCATATTACTTT
*
3325 TTACTGATTACCATATTACTTT
1 TTACTGACTACCATATTACTTT
3347 TT
1 TT
3349 GAGTTTGATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 13 0.62
21 2 0.10
22 6 0.29
ACGTcount: A:0.23, C:0.20, G:0.05, T:0.52
Consensus pattern (22 bp):
TTACTGACTACCATATTACTTT
Found at i:3410 original size:22 final size:22
Alignment explanation
Indices: 3385--3576 Score: 183
Period size: 22 Copynumber: 9.0 Consensus size: 22
3375 AATTTAATTT
*
3385 CTGATTACCGTTTTATTCTTTA
1 CTGATTACCATTTTATTCTTTA
** *
3407 CTGATTACCATTACATTTTTTA
1 CTGATTACCATTTTATTCTTTA
*
3429 TTGATTACCATTTTACTTCTTTA
1 CTGATTACCATTTTA-TTCTTTA
3452 CTGATTACCATTTTACTT-TTTA
1 CTGATTACCATTTTA-TTCTTTA
*
3474 CTGATTACCAGTTTATTCTTTA
1 CTGATTACCATTTTATTCTTTA
3496 -TAGATTACCATTTTA--C---A
1 CT-GATTACCATTTTATTCTTTA
3513 --GATTACCATTTTACTT-TTTA
1 CTGATTACCATTTTA-TTCTTTA
*
3533 --GTTTAACCATTTTATTCTTTA
1 CTGATT-ACCATTTTATTCTTTA
*
3554 CTGATTACCATTTTATTCATTA
1 CTGATTACCATTTTATTCTTTA
3576 C
1 C
3577 CATTACTTTT
Statistics
Matches: 143, Mismatches: 14, Indels: 26
0.78 0.08 0.14
Matches are distributed among these distances:
15 13 0.09
17 1 0.01
20 7 0.05
21 16 0.11
22 80 0.56
23 26 0.18
ACGTcount: A:0.24, C:0.18, G:0.06, T:0.52
Consensus pattern (22 bp):
CTGATTACCATTTTATTCTTTA
Found at i:3457 original size:45 final size:44
Alignment explanation
Indices: 3385--3507 Score: 167
Period size: 45 Copynumber: 2.8 Consensus size: 44
3375 AATTTAATTT
* *
3385 CTGATTACCGTTTTATTCTTTACTGATTACCATTACATTTTTTA
1 CTGATTACCATTTTATTCTTTACTGATTACCATTACACTTTTTA
* **
3429 TTGATTACCATTTTACTTCTTTACTGATTACCATTTTACTTTTTA
1 CTGATTACCATTTTA-TTCTTTACTGATTACCATTACACTTTTTA
*
3474 CTGATTACCAGTTTATTCTTTA-TAGATTACCATT
1 CTGATTACCATTTTATTCTTTACT-GATTACCATT
3508 TTACAGATTA
Statistics
Matches: 70, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
43 1 0.01
44 30 0.43
45 39 0.56
ACGTcount: A:0.24, C:0.18, G:0.07, T:0.52
Consensus pattern (44 bp):
CTGATTACCATTTTATTCTTTACTGATTACCATTACACTTTTTA
Found at i:3466 original size:67 final size:67
Alignment explanation
Indices: 3385--3511 Score: 186
Period size: 67 Copynumber: 1.9 Consensus size: 67
3375 AATTTAATTT
* * *
3385 CTGATTACCGTTTTA-TTCTTTACTGATTACCA-TTACATTTTTTATTGATTACCATTTTACTTC
1 CTGATTACCATTTTACTT-TTTACTGATTACCAGTT-CATTCTTTATAGATTACCATTTTACTTC
3448 TTTA
64 TTTA
*
3452 CTGATTACCATTTTACTTTTTACTGATTACCAGTTTATTCTTTATAGATTACCATTTTAC
1 CTGATTACCATTTTACTTTTTACTGATTACCAGTTCATTCTTTATAGATTACCATTTTAC
3512 AGATTACCAT
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
67 50 0.93
68 4 0.07
ACGTcount: A:0.24, C:0.18, G:0.06, T:0.52
Consensus pattern (67 bp):
CTGATTACCATTTTACTTTTTACTGATTACCAGTTCATTCTTTATAGATTACCATTTTACTTCTT
TA
Found at i:3515 original size:15 final size:15
Alignment explanation
Indices: 3492--3526 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
3482 CAGTTTATTC
*
3492 TTTATAGATTACCAT
1 TTTACAGATTACCAT
3507 TTTACAGATTACCAT
1 TTTACAGATTACCAT
3522 TTTAC
1 TTTAC
3527 TTTTTAGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.31, C:0.17, G:0.06, T:0.46
Consensus pattern (15 bp):
TTTACAGATTACCAT
Found at i:3519 original size:37 final size:36
Alignment explanation
Indices: 3469--3546 Score: 95
Period size: 37 Copynumber: 2.1 Consensus size: 36
3459 CCATTTTACT
* *
3469 TTTTACTGATTACCAGTTTATTCTTTATAGATT-ACCA
1 TTTTACAGATTACCA-TTT-TACTTTATAGATTAACCA
* *
3506 TTTTACAGATTACCATTTTACTTTTTAGTTTAACCA
1 TTTTACAGATTACCATTTTACTTTATAGATTAACCA
3542 TTTTA
1 TTTTA
3547 TTCTTTACTG
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
35 10 0.28
36 12 0.33
37 14 0.39
ACGTcount: A:0.27, C:0.15, G:0.06, T:0.51
Consensus pattern (36 bp):
TTTTACAGATTACCATTTTACTTTATAGATTAACCA
Found at i:3530 original size:21 final size:21
Alignment explanation
Indices: 3506--3568 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
3496 TAGATTACCA
3506 TTTTACAGATTACCATTTTAC
1 TTTTACAGATTACCATTTTAC
* * *
3527 TTTT-TAGTTTAACCATTTTAT
1 TTTTACAGATT-ACCATTTTAC
*
3548 TCTTTACTGATTACCATTTTA
1 T-TTTACAGATTACCATTTTA
3569 TTCATTACCA
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
20 4 0.12
21 14 0.42
22 12 0.36
23 3 0.09
ACGTcount: A:0.25, C:0.16, G:0.05, T:0.54
Consensus pattern (21 bp):
TTTTACAGATTACCATTTTAC
Found at i:3576 original size:58 final size:58
Alignment explanation
Indices: 3455--3596 Score: 175
Period size: 58 Copynumber: 2.4 Consensus size: 58
3445 TTCTTTACTG
*
3455 ATTACCATTTTACTTTTTACTGATTACCAGTTTATTCTTTATAGATTACCATTTTACAG
1 ATTACCATTTTACTTTTTAC-GATTACCAGTTTATTCTTTATAGATTACCATTTTACAC
* * **
3514 ATTACCATTTTACTTTTTA-GTTTAACCATTTTATTCTTTACT-GATTACCATTTTATTC
1 ATTACCATTTTACTTTTTACGATT-ACCAGTTTATTCTTTA-TAGATTACCATTTTACAC
3572 ATTACCA--TTACTTTTTACTGATTAC
1 ATTACCATTTTACTTTTTAC-GATTAC
3597 TATTTTACTT
Statistics
Matches: 73, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
56 10 0.14
57 5 0.07
58 38 0.52
59 20 0.27
ACGTcount: A:0.26, C:0.18, G:0.05, T:0.51
Consensus pattern (58 bp):
ATTACCATTTTACTTTTTACGATTACCAGTTTATTCTTTATAGATTACCATTTTACAC
Found at i:3643 original size:15 final size:15
Alignment explanation
Indices: 3623--3667 Score: 58
Period size: 14 Copynumber: 3.1 Consensus size: 15
3613 GATTACCATA
*
3623 ACCATTTTACTTTTT
1 ACCATTTTACTCTTT
*
3638 ACCA-TTTAC-CATT
1 ACCATTTTACTCTTT
3651 ACCATTTTACTCTTT
1 ACCATTTTACTCTTT
3666 AC
1 AC
3668 TGATTACCGT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
13 6 0.24
14 10 0.40
15 9 0.36
ACGTcount: A:0.24, C:0.27, G:0.00, T:0.49
Consensus pattern (15 bp):
ACCATTTTACTCTTT
Found at i:3680 original size:28 final size:27
Alignment explanation
Indices: 3592--3695 Score: 104
Period size: 28 Copynumber: 3.7 Consensus size: 27
3582 CTTTTTACTG
*
3592 ATTACTATTTTACTTTTCACTGATTACC
1 ATTACCATTTTACTTTT-ACTGATTACC
* *
3620 ATAACCATTTTACTTTTTAC-CATTTACC
1 ATTACCATTTTAC-TTTTACTGA-TTACC
3648 ATTACCATTTTACTCTTTACTGATTACC
1 ATTACCATTTTACT-TTTACTGATTACC
* *
3676 GTTA-CTTTTTACTTATTACT
1 ATTACCATTTTACTT-TTACT
3696 ATTTCACTCT
Statistics
Matches: 64, Mismatches: 7, Indels: 11
0.78 0.09 0.13
Matches are distributed among these distances:
26 1 0.02
27 15 0.23
28 43 0.67
29 5 0.08
ACGTcount: A:0.25, C:0.22, G:0.03, T:0.50
Consensus pattern (27 bp):
ATTACCATTTTACTTTTACTGATTACC
Found at i:3710 original size:35 final size:35
Alignment explanation
Indices: 3671--3777 Score: 162
Period size: 35 Copynumber: 3.1 Consensus size: 35
3661 TCTTTACTGA
* *
3671 TTACCGTTACTTTTTACTTATTACTATTTCACTCT
1 TTACCATTACTTTTTACTTATTACTATTTTACTCT
*
3706 TTACCATTACTTTTCA-TTGATTACTATTTTACTCT
1 TTACCATTACTTTTTACTT-ATTACTATTTTACTCT
*
3741 TTACCATTACTTTTTACTGATTACTATTTTACTCT
1 TTACCATTACTTTTTACTTATTACTATTTTACTCT
3776 TT
1 TT
3778 GAACTAATTA
Statistics
Matches: 65, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
34 2 0.03
35 62 0.95
36 1 0.02
ACGTcount: A:0.21, C:0.21, G:0.03, T:0.55
Consensus pattern (35 bp):
TTACCATTACTTTTTACTTATTACTATTTTACTCT
Found at i:3833 original size:168 final size:166
Alignment explanation
Indices: 3555--3868 Score: 393
Period size: 168 Copynumber: 1.9 Consensus size: 166
3545 TATTCTTTAC
* * *
3555 TGATTACCATTTTATTCATTACCATTACTTTTTACTGATTACTATTTTACTTTTCACTGATTACC
1 TGATTACCATTTTACTCATTACCATTACTTTTTACTGATTACTATTTTACTCTT--CTGA-TACA
* *
3620 ATAACCATTTTACTTTTTACCATTTACCATTACCATTTTACTCTTTACTGATTACCGTTAC-TTT
63 ATAACCATTTTACTTTTTACAATTTACCATTACCATTTTACTCTTTACTGATTACCATTACTTTT
* *
3684 TTACTTATTACTATTTCACTCTTTACCATTACTTTTCAT
128 TTACTGATTACCATTTCACTCTTTACCATTACTTTTCAT
* *
3723 TGATTACTATTTTACTCTTTACCATTACTTTTTACTGATTACTATTTTACTCTT-TGA-ACTAAT
1 TGATTACCATTTTACTCATTACCATTACTTTTTACTGATTACTATTTTACTCTTCTGATAC-AAT
* * ** *
3786 TACCATTTTACTTTTTGA-AATTTATTTCTGATTACTGTTTTACTCTTTACTGATTATCATTACT
65 AACCATTTTACTTTTT-ACAATTTA---C-CATTACCATTTTACTCTTTACTGATTACCATTACT
3850 TTTTTACTGATTACCATTT
125 TTTTTACTGATTACCATTT
3869 TACTTTTGAA
Statistics
Matches: 125, Mismatches: 14, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
163 2 0.02
164 22 0.18
165 4 0.03
167 1 0.01
168 79 0.63
169 17 0.14
ACGTcount: A:0.24, C:0.19, G:0.04, T:0.52
Consensus pattern (166 bp):
TGATTACCATTTTACTCATTACCATTACTTTTTACTGATTACTATTTTACTCTTCTGATACAATA
ACCATTTTACTTTTTACAATTTACCATTACCATTTTACTCTTTACTGATTACCATTACTTTTTTA
CTGATTACCATTTCACTCTTTACCATTACTTTTCAT
Found at i:3875 original size:21 final size:21
Alignment explanation
Indices: 3813--3875 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 21
3803 AAATTTATTT
**
3813 CTGATTACTGTTTTACTCTTTA
1 CTGATTACCATTTTACT-TTTA
*
3835 CTGATTATCA--TTACTTTTTTA
1 CTGATTACCATTTTAC--TTTTA
3856 CTGATTACCATTTTACTTTT
1 CTGATTACCATTTTACTTTT
3876 GAATTTAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 9
0.72 0.09 0.20
Matches are distributed among these distances:
20 4 0.12
21 17 0.52
22 8 0.24
23 4 0.12
ACGTcount: A:0.21, C:0.17, G:0.06, T:0.56
Consensus pattern (21 bp):
CTGATTACCATTTTACTTTTA
Found at i:3939 original size:3 final size:3
Alignment explanation
Indices: 3931--3994 Score: 112
Period size: 3 Copynumber: 21.7 Consensus size: 3
3921 TGACACCATT
3931 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
*
3979 TTC TTC -TC TTT TTC TT
1 TTC TTC TTC TTC TTC TT
3995 GATTTTCCTT
Statistics
Matches: 58, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
2 2 0.03
3 56 0.97
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Done.