Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016775.1 Corchorus olitorius cultivar O-4 contig16808, 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: 6393
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Found at i:29 original size:4 final size:4
Alignment explanation
Indices: 15--118 Score: 62
Period size: 4 Copynumber: 27.8 Consensus size: 4
5 TTTTTAACTA
* * * * * *
15 TTAT CTAT TTAT TTA- TT-T TTAA CTAT TCAT ATAT TTAT TTA- CTAT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT
* * *
60 TTAT CTT-T TTAT TTAT TAAT TTAG TTA- TTAT CTAT TTAT TTAT TTA-
1 TTAT -TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT
106 TTA- TTAT TT-T TTA
1 TTAT TTAT TTAT TTA
119 GCTTACCTAT
Statistics
Matches: 75, Mismatches: 17, Indels: 16
0.69 0.16 0.15
Matches are distributed among these distances:
3 20 0.27
4 53 0.71
5 2 0.03
ACGTcount: A:0.27, C:0.06, G:0.01, T:0.66
Consensus pattern (4 bp):
TTAT
Found at i:49 original size:26 final size:25
Alignment explanation
Indices: 1--104 Score: 92
Period size: 25 Copynumber: 4.3 Consensus size: 25
*
1 TTTATTTTTAACTATTATCTATTTA
1 TTTATTTTTAACTATTATATATTTA
26 TTTATTTTTAACTATTCATATATTTA
1 TTTATTTTTAACTATT-ATATATTTA
* *
52 TTTACTATTTATCT-TT-T-TATTTA
1 TTTA-TTTTTAACTATTATATATTTA
* ** *
75 -TTA-ATTTAGTTATTATCTATTTA
1 TTTATTTTTAACTATTATATATTTA
98 TTTATTT
1 TTTATTT
105 ATTATTATTT
Statistics
Matches: 66, Mismatches: 6, Indels: 14
0.77 0.07 0.16
Matches are distributed among these distances:
20 6 0.09
21 2 0.03
22 4 0.06
23 12 0.18
24 4 0.06
25 17 0.26
26 14 0.21
27 7 0.11
ACGTcount: A:0.27, C:0.07, G:0.01, T:0.65
Consensus pattern (25 bp):
TTTATTTTTAACTATTATATATTTA
Found at i:60 original size:19 final size:19
Alignment explanation
Indices: 36--74 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
26 TTTATTTTTA
36 ACTATTCATATATTTATTT
1 ACTATTCATATATTTATTT
* * *
55 ACTATTTATCTTTTTATTT
1 ACTATTCATATATTTATTT
74 A
1 A
75 TTAATTTAGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.28, C:0.10, G:0.00, T:0.62
Consensus pattern (19 bp):
ACTATTCATATATTTATTT
Found at i:76 original size:27 final size:25
Alignment explanation
Indices: 1--107 Score: 90
Period size: 27 Copynumber: 4.1 Consensus size: 25
* *
1 TTTATTTTTAACTA-TTATCTATTTA
1 TTTA-TTTTATCTATTTATTTATTTA
* * *
26 TTTATTTTTAACTATTCATATATTTA
1 TTTA-TTTTATCTATTTATTTATTTA
* *
52 TTTACTATTTATCTTTTTATTTATTAA
1 TTTA-T-TTTATCTATTTATTTATTTA
79 TTTAGTTATTATCTATTTATTTATTTA
1 TTTA-TT-TTATCTATTTATTTATTTA
106 TT
1 TT
108 ATTATTTTTT
Statistics
Matches: 68, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
25 14 0.21
26 15 0.22
27 39 0.57
ACGTcount: A:0.27, C:0.07, G:0.01, T:0.65
Consensus pattern (25 bp):
TTTATTTTATCTATTTATTTATTTA
Found at i:90 original size:19 final size:19
Alignment explanation
Indices: 68--110 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
58 ATTTATCTTT
68 TTATTTATTAATTTAGTTA
1 TTATTTATTAATTTAGTTA
* * *
87 TTATCTATTTATTTATTTA
1 TTATTTATTAATTTAGTTA
106 TTATT
1 TTATT
111 ATTTTTTAGC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.67
Consensus pattern (19 bp):
TTATTTATTAATTTAGTTA
Found at i:3277 original size:14 final size:15
Alignment explanation
Indices: 3258--3304 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
3248 ATTTCCTTAA
3258 TTTCCTTCTTTTT-T
1 TTTCCTTCTTTTTCT
3272 TTTCCTTCCTTTTTCT
1 TTTCCTT-CTTTTTCT
* *
3288 TTTCTTTCTTTTCCT
1 TTTCCTTCTTTTTCT
3303 TT
1 TT
3305 CTATTTTTCT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 7 0.24
15 15 0.52
16 7 0.24
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTCCTTCTTTTTCT
Found at i:3318 original size:13 final size:13
Alignment explanation
Indices: 3281--3337 Score: 71
Period size: 13 Copynumber: 4.4 Consensus size: 13
3271 TTTTCCTTCC
*
3281 TTTTTCTTTTCTT
1 TTTTTCTTTTCTA
*
3294 TCTTTTCCTTTCTA
1 T-TTTTCTTTTCTA
3308 TTTTTCTTTTCTA
1 TTTTTCTTTTCTA
*
3321 TTTTTCTCTTCT-
1 TTTTTCTTTTCTA
3333 TTTTT
1 TTTTT
3338 TTTCTCCCTT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
12 5 0.13
13 23 0.59
14 11 0.28
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTTTCTTTTCTA
Found at i:3338 original size:13 final size:13
Alignment explanation
Indices: 3258--3338 Score: 60
Period size: 13 Copynumber: 6.2 Consensus size: 13
3248 ATTTCCTTAA
3258 TTTC-CTTCTTTT
1 TTTCTCTTCTTTT
* *
3270 TTTTTCCTTC-CTT
1 TTTCT-CTTCTTTT
*
3283 TTTCTTTTCTTTCT
1 TTTCTCTTCTTT-T
*
3297 TTTC-CTTTCTATT
1 TTTCTC-TTCTTTT
* *
3310 TTTCTTTTCTATT
1 TTTCTCTTCTTTT
3323 TTTCTCTTCTTTT
1 TTTCTCTTCTTTT
3336 TTT
1 TTT
3339 TTCTCCCTTT
Statistics
Matches: 53, Mismatches: 10, Indels: 11
0.72 0.14 0.15
Matches are distributed among these distances:
12 6 0.11
13 33 0.62
14 14 0.26
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.75
Consensus pattern (13 bp):
TTTCTCTTCTTTT
Found at i:3349 original size:25 final size:25
Alignment explanation
Indices: 3270--3350 Score: 69
Period size: 25 Copynumber: 3.2 Consensus size: 25
3260 TCCTTCTTTT
*
3270 TTTTTC-CTTCCTTTTTCTTTTCTTTC
1 TTTTTCTCTT-CTTTTT-TTTTCTCTC
* *
3296 TTTTCCT-TTCTATTTTTCTTT-TCTA
1 TTTTTCTCTTCT-TTTTT-TTTCTCTC
*
3321 TTTTTCTCTTCTTTTTTTTTCTCCC
1 TTTTTCTCTTCTTTTTTTTTCTCTC
3346 TTTTT
1 TTTTT
3351 GGGCTAGGCC
Statistics
Matches: 44, Mismatches: 6, Indels: 11
0.72 0.10 0.18
Matches are distributed among these distances:
24 3 0.07
25 23 0.52
26 18 0.41
ACGTcount: A:0.02, C:0.23, G:0.00, T:0.74
Consensus pattern (25 bp):
TTTTTCTCTTCTTTTTTTTTCTCTC
Done.