Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_3692
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: 17552
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Found at i:1933 original size:3 final size:3
Alignment explanation
Indices: 1925--1977 Score: 61
Period size: 3 Copynumber: 17.7 Consensus size: 3
1915 AATAAATAGG
* * * * *
1925 TAA TAA TAA CAA TAG TAG TAG TAG TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1973 TAA TA
1 TAA TA
1978 GTAGGACTAA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.58, C:0.02, G:0.08, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:3006 original size:15 final size:15
Alignment explanation
Indices: 2986--3042 Score: 114
Period size: 15 Copynumber: 3.8 Consensus size: 15
2976 GGGCATGGTA
2986 ATTGGGTTTGTGGGT
1 ATTGGGTTTGTGGGT
3001 ATTGGGTTTGTGGGT
1 ATTGGGTTTGTGGGT
3016 ATTGGGTTTGTGGGT
1 ATTGGGTTTGTGGGT
3031 ATTGGGTTTGTG
1 ATTGGGTTTGTG
3043 TTAGTGGGCC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 42 1.00
ACGTcount: A:0.07, C:0.00, G:0.46, T:0.47
Consensus pattern (15 bp):
ATTGGGTTTGTGGGT
Found at i:3014 original size:8 final size:8
Alignment explanation
Indices: 2988--3042 Score: 62
Period size: 8 Copynumber: 7.2 Consensus size: 8
2978 GCATGGTAAT
2988 TGGGTTTG
1 TGGGTTTG
*
2996 TGGGTAT-
1 TGGGTTTG
3003 TGGGTTTG
1 TGGGTTTG
*
3011 TGGGTAT-
1 TGGGTTTG
3018 TGGGTTTG
1 TGGGTTTG
*
3026 TGGGTAT-
1 TGGGTTTG
3033 TGGGTTTG
1 TGGGTTTG
3041 TG
1 TG
3043 TTAGTGGGCC
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
7 18 0.47
8 20 0.53
ACGTcount: A:0.05, C:0.00, G:0.47, T:0.47
Consensus pattern (8 bp):
TGGGTTTG
Found at i:3287 original size:41 final size:41
Alignment explanation
Indices: 3230--3416 Score: 160
Period size: 44 Copynumber: 4.4 Consensus size: 41
3220 AATCCATTGT
* *
3230 ACTTCAGGGAAATAAGACTTGATGCGATCTGCTCTACTGCA
1 ACTTCAGAGAGATAAGACTTGATGCGATCTGCTCTACTGCA
*** *
3271 ACTTCAGAGAGATAAGATCTGTGATTTTAATCCGCTCTACTGCA
1 ACTTCAGAGAGATAAGA-CT-TGA-TGCGATCTGCTCTACTGCA
* * * * *
3315 ACTTCAGAGAGATAGGA-TTGGTTTCTTCTATCTGCTCCACTGCA
1 ACTTCAGAGAGATAAGACTT-G---ATGCGATCTGCTCTACTGCA
* * * *
3359 ACTTCAGGGAGATAAGACTTGATGCGATCTACTCTGCTGTA
1 ACTTCAGAGAGATAAGACTTGATGCGATCTGCTCTACTGCA
*
3400 ACCTCAGAGAGATAAGA
1 ACTTCAGAGAGATAAGA
3417 TCCTTTATTT
Statistics
Matches: 115, Mismatches: 23, Indels: 16
0.75 0.15 0.10
Matches are distributed among these distances:
41 44 0.38
42 4 0.03
43 3 0.03
44 62 0.54
45 2 0.02
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (41 bp):
ACTTCAGAGAGATAAGACTTGATGCGATCTGCTCTACTGCA
Found at i:3316 original size:44 final size:43
Alignment explanation
Indices: 3260--3457 Score: 168
Period size: 44 Copynumber: 4.6 Consensus size: 43
3250 GATGCGATCT
3260 GCTCTACTGCAACTTCAGAGAGATAAGATCTGTGATTTTAATCC
1 GCTCTACTGCAACTTCAGAGAGATAAGATCT-TGATTTTAATCC
* * * * *
3304 GCTCTACTGCAACTTCAGAGAGATAGGAT-TGGTTTCTTCTATCT
1 GCTCTACTGCAACTTCAGAGAGATAAGATCTTGATT-TT-AATCC
* * *** *
3348 GCTCCACTGCAACTTCAGGGAGATAAGA-CTTGA-TGCGATCT
1 GCTCTACTGCAACTTCAGAGAGATAAGATCTTGATTTTAATCC
* * * * *
3389 ACTCTGCTGTAACCTCAGAGAGATAAGATCCTTTATTTTAATCC
1 GCTCTACTGCAACTTCAGAGAGATAAGAT-CTTGATTTTAATCC
* * *
3433 GCTCCACTGTAACTTCAGGGAGATA
1 GCTCTACTGCAACTTCAGAGAGATA
3458 GGATAGTGTC
Statistics
Matches: 119, Mismatches: 29, Indels: 12
0.74 0.18 0.08
Matches are distributed among these distances:
41 26 0.22
42 3 0.03
43 8 0.07
44 82 0.69
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (43 bp):
GCTCTACTGCAACTTCAGAGAGATAAGATCTTGATTTTAATCC
Found at i:3460 original size:129 final size:128
Alignment explanation
Indices: 3230--3503 Score: 381
Period size: 129 Copynumber: 2.1 Consensus size: 128
3220 AATCCATTGT
* * *
3230 ACTTCAGGGAAATAAGACTTGATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGA
1 ACTTCAGGGAGATAAGACTTGATGCGATCTACTCTACTGCAACCTCAGAGAGATAAGATCTGTGA
* * * *
3295 TTTTAATCCGCTCTACTGCAACTTCAGAGAGATAGGATTGGTTTCTTCTATCTGCTCCACTGCA
66 TTTTAATCCGCTCCACTGCAACTTCAGAGAGATAGGA-TAGTGTCTTCGATCTGCTCCACTGCA
* * *
3359 ACTTCAGGGAGATAAGACTTGATGCGATCTACTCTGCTGTAACCTCAGAGAGATAAGATCCT-TT
1 ACTTCAGGGAGATAAGACTTGATGCGATCTACTCTACTGCAACCTCAGAGAGATAAGAT-CTGTG
* * * *
3423 ATTTTAATCCGCTCCACTGTAACTTCAGGGAGATAGGATAGTGTCTTCGATCTGCTCCGCTGTA
65 ATTTTAATCCGCTCCACTGCAACTTCAGAGAGATAGGATAGTGTCTTCGATCTGCTCCACTGCA
3487 A-TCTCAGGGAGATAAGA
1 ACT-TCAGGGAGATAAGA
3504 TCTCTGGCTT
Statistics
Matches: 129, Mismatches: 14, Indels: 5
0.87 0.09 0.03
Matches are distributed among these distances:
127 1 0.01
128 36 0.28
129 90 0.70
130 2 0.02
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.30
Consensus pattern (128 bp):
ACTTCAGGGAGATAAGACTTGATGCGATCTACTCTACTGCAACCTCAGAGAGATAAGATCTGTGA
TTTTAATCCGCTCCACTGCAACTTCAGAGAGATAGGATAGTGTCTTCGATCTGCTCCACTGCA
Found at i:3500 original size:87 final size:85
Alignment explanation
Indices: 3339--3545 Score: 220
Period size: 87 Copynumber: 2.4 Consensus size: 85
3329 GGATTGGTTT
* * * *
3339 CTTCTATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGATGCGATCTACTCTGCTGTAACCT
1 CTTCAATCCGCTCCACTGTAACTTCAGGGAGATAAGACTTGATGCGATCTACTCCGCTGTAACCT
*
3404 CAGAGAGATAAGATC-CTTTA
66 CAGAGAGATAAGATCTC-TGA
* * * * * *
3424 TTTTAATCCGCTCCACTGTAACTTCAGGGAGATAGGA-TAGTGTCTTCGATCTGCTCCGCTGTAA
1 CTTCAATCCGCTCCACTGTAACTTCAGGGAGATAAGACT--TG-ATGCGATCTACTCCGCTGTAA
* * *
3488 TCTCAGGGAGATAAGATCTCTGG
63 CCTCAGAGAGATAAGATCTCTGA
* *
3511 CTTCAATCTGCTCCACTGTAACCTCAGGGAGATAA
1 CTTCAATCCGCTCCACTGTAACTTCAGGGAGATAA
3546 TATCTGAAAT
Statistics
Matches: 99, Mismatches: 19, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
84 1 0.01
85 31 0.31
86 2 0.02
87 64 0.65
88 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (85 bp):
CTTCAATCCGCTCCACTGTAACTTCAGGGAGATAAGACTTGATGCGATCTACTCCGCTGTAACCT
CAGAGAGATAAGATCTCTGA
Found at i:3530 original size:44 final size:43
Alignment explanation
Indices: 3339--3550 Score: 146
Period size: 44 Copynumber: 4.9 Consensus size: 43
3329 GGATTGGTTT
* *
3339 CTTCTATCTGCTCCACTGCAACTTCAGGGAGATAAGA-CT-T-G
1 CTTCAATCTGCTCCACTGTAAC-TCAGGGAGATAAGATCTCTGG
* * * * ** * **
3380 ATGCGATCTACTCTGCTGTAACCTCAGAGAGATAAGATC-CTTTA
1 CTTCAATCTGCTCCACTGTAA-CTCAGGGAGATAAGATCTC-TGG
* * * * ** *
3424 TTTTAATCCGCTCCACTGTAACTTCAGGGAGATAGGAT-AGTGT
1 CTTCAATCTGCTCCACTGTAAC-TCAGGGAGATAAGATCTCTGG
* *
3467 CTTCGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGG
1 CTTCAATCTGCTCCACTGTAA-CTCAGGGAGATAAGATCTCTGG
*
3511 CTTCAATCTGCTCCACTGTAACCTCAGGGAGATAATATCT
1 CTTCAATCTGCTCCACTGTAA-CTCAGGGAGATAAGATCT
3551 GAAATTCTCC
Statistics
Matches: 127, Mismatches: 35, Indels: 15
0.72 0.20 0.08
Matches are distributed among these distances:
41 27 0.21
42 2 0.02
43 33 0.26
44 65 0.51
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.30
Consensus pattern (43 bp):
CTTCAATCTGCTCCACTGTAACTCAGGGAGATAAGATCTCTGG
Found at i:3702 original size:44 final size:46
Alignment explanation
Indices: 3647--3764 Score: 143
Period size: 46 Copynumber: 2.6 Consensus size: 46
3637 CTTTTAATCC
* * * *
3647 GCTCCATTGTAATCTCAAGGAGATAGGAT-T--ACTATCTTTGATCT
1 GCTCCACTGTAATCTCAGGGAGATAAGATCTGAAAT-TCTTTGATCT
* *
3691 GCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTTGGTCT
1 GCTCCACTGTAATCTCAGGGAGATAAGATCTGAAATTCTTTGATCT
*
3737 GTTCCACTGTAATCTCAGGGAGATAAGA
1 GCTCCACTGTAATCTCAGGGAGATAAGA
3765 CCTGTATAAT
Statistics
Matches: 63, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
44 25 0.40
45 1 0.02
46 35 0.56
47 2 0.03
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.32
Consensus pattern (46 bp):
GCTCCACTGTAATCTCAGGGAGATAAGATCTGAAATTCTTTGATCT
Found at i:16509 original size:3 final size:3
Alignment explanation
Indices: 16501--16551 Score: 66
Period size: 3 Copynumber: 16.7 Consensus size: 3
16491 AATAAATAGG
* * *
16501 TAA TAA TAA CAA TAG TAG TATA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
16547 TAA TA
1 TAA TA
16552 GTAGGACTAA
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
3 41 0.95
4 2 0.05
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:17536 original size:16 final size:17
Alignment explanation
Indices: 17515--17552 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
17505 GGCATTGGTA
17515 ATTGGG-TTT-GTGGGGT
1 ATTGGGTTTTGGT-GGGT
17531 ATTGGGTTTTGGTGGGT
1 ATTGGGTTTTGGTGGGT
17548 ATTGG
1 ATTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 6 0.30
17 12 0.60
18 2 0.10
ACGTcount: A:0.08, C:0.00, G:0.47, T:0.45
Consensus pattern (17 bp):
ATTGGGTTTTGGTGGGT
Done.