Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3343
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: 17910
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Found at i:1874 original size:3 final size:3
Alignment explanation
Indices: 1859--1930 Score: 67
Period size: 3 Copynumber: 24.3 Consensus size: 3
1849 AATACTAACG
* ** * *
1859 ATA ATA GTA ATA ATA ATA ACC ATA ATA ATA ATA GTA A-A CTA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
1906 ATA TTTA A-A ATA ATA ATA ATA ATA A
1 ATA -ATA ATA ATA ATA ATA ATA ATA A
1931 CATAAAATTG
Statistics
Matches: 54, Mismatches: 12, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
2 3 0.06
3 49 0.91
4 2 0.04
ACGTcount: A:0.61, C:0.04, G:0.03, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1987 original size:29 final size:29
Alignment explanation
Indices: 1942--2029 Score: 90
Period size: 29 Copynumber: 3.0 Consensus size: 29
1932 ATAAAATTGC
1942 TAAAATAT-GGGCTAAATCGAAATAAAACA
1 TAAAATATAGGGCTAAATCGAAATAAAA-A
* * *
1971 -AAAATATAGGGCGAAATTGAAAGAAAAA
1 TAAAATATAGGGCTAAATCGAAATAAAAA
* *
1999 TAAAATAAAAGGGACTAAATCAAAATAAAAA
1 TAAAAT-ATAGGG-CTAAATCGAAATAAAAA
2030 AAGAAACTGG
Statistics
Matches: 47, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
28 8 0.17
29 21 0.45
30 5 0.11
31 13 0.28
ACGTcount: A:0.61, C:0.07, G:0.15, T:0.17
Consensus pattern (29 bp):
TAAAATATAGGGCTAAATCGAAATAAAAA
Found at i:3543 original size:44 final size:43
Alignment explanation
Indices: 3452--3986 Score: 357
Period size: 44 Copynumber: 12.6 Consensus size: 43
3442 GGTCTATTCC
* * * *
3452 ACTGTAATCTCAGGGAAATAAGACCTGACA---CGATCTACTCT
1 ACTGTAATCTCAGGGAGATAAGATCT-ACATTTCAATCTGCTCT
* * * * * *
3493 GCTGTAA-CTTCAGAGAGATAAGATCCTTCATTTTAATCCGCTCC
1 ACTGTAATC-TCAGGGAGATAAGAT-CTACATTTCAATCTGCTCT
* *
3537 ACTGTAATCTCAGGGAGATAGGAT-TACTAGCTTCAATCTGCTCT
1 ACTGTAATCTCAGGGAGATAAGATCTAC-A-TTTCAATCTGCTCT
* *
3581 TCTGTAATCTCAGGGAGATAAGATCTGACA---CAATCTACTCT
1 ACTGTAATCTCAGGGAGATAAGATCT-ACATTTCAATCTGCTCT
* * * * * *
3622 ACTGTAA-CTTCAGAGAGATAAGATCCTTCGTTTTAATCCGCTCC
1 ACTGTAATC-TCAGGGAGATAAGAT-CTACATTTCAATCTGCTCT
* *
3666 ACTGTAATCTCAGGGAGATAGGAT-TACTAGCTTCAATCTGCTCT
1 ACTGTAATCTCAGGGAGATAAGATCTAC-A-TTTCAATCTGCTCT
* *
3710 TCTGTAATCTCAGGGAGATAAGATCTGACA---CAATCTACTCT
1 ACTGTAATCTCAGGGAGATAAGATCT-ACATTTCAATCTGCTCT
* * * * * *
3751 ACTGTAA-CTTCAGAGAGATAAGATCCTTCGTTTTAATCCGCTCC
1 ACTGTAATC-TCAGGGAGATAAGAT-CTACATTTCAATCTGCTCT
* *
3795 ACTGTAATCTCAGGGAGATAGGAT-TACTAGCTTCAATCTGCTCT
1 ACTGTAATCTCAGGGAGATAAGATCTAC-A-TTTCAATCTGCTCT
* * *
3839 TCTGTAATCTCAGGGAGATAAGATCTGACA---CGATCTACTCT
1 ACTGTAATCTCAGGGAGATAAGATCT-ACATTTCAATCTGCTCT
* *
3880 ACTGTAA-CTTCAGAGAGATAAGATC--C-TTT-AATC-GCTCC
1 ACTGTAATC-TCAGGGAGATAAGATCTACATTTCAATCTGCTCT
* *
3918 ACTGTAATCTCAGGGAGATAGGAT-TACTATCTTC-ATCTGCTCC
1 ACTGTAATCTCAGGGAGATAAGATCTAC-AT-TTCAATCTGCTCT
*
3961 GCTGTAATCTCAGGGAGATAAGATCT
1 ACTGTAATCTCAGGGAGATAAGATCT
3987 GAAATTCTTT
Statistics
Matches: 382, Mismatches: 69, Indels: 83
0.72 0.13 0.16
Matches are distributed among these distances:
38 24 0.06
39 5 0.01
40 4 0.01
41 113 0.30
42 17 0.04
43 28 0.07
44 176 0.46
45 9 0.02
46 6 0.02
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.30
Consensus pattern (43 bp):
ACTGTAATCTCAGGGAGATAAGATCTACATTTCAATCTGCTCT
Found at i:3617 original size:129 final size:129
Alignment explanation
Indices: 3453--3988 Score: 942
Period size: 129 Copynumber: 4.2 Consensus size: 129
3443 GTCTATTCCA
* * * *
3453 CTGTAATCTCAGGGAAATAAGACCTGACACGATCTACTCTGCTGTAACTTCAGAGAGATAAGATC
1 CTGTAATCTCAGGGAGATAAGATCTGACACAATCTACTCTACTGTAACTTCAGAGAGATAAGATC
*
3518 CTTCATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCTT
66 CTTCGTTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCTT
3582 CTGTAATCTCAGGGAGATAAGATCTGACACAATCTACTCTACTGTAACTTCAGAGAGATAAGATC
1 CTGTAATCTCAGGGAGATAAGATCTGACACAATCTACTCTACTGTAACTTCAGAGAGATAAGATC
3647 CTTCGTTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCTT
66 CTTCGTTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCTT
3711 CTGTAATCTCAGGGAGATAAGATCTGACACAATCTACTCTACTGTAACTTCAGAGAGATAAGATC
1 CTGTAATCTCAGGGAGATAAGATCTGACACAATCTACTCTACTGTAACTTCAGAGAGATAAGATC
3776 CTTCGTTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCTT
66 CTTCGTTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCTT
*
3840 CTGTAATCTCAGGGAGATAAGATCTGACACGATCTACTCTACTGTAACTTCAGAGAGATAAGAT-
1 CTGTAATCTCAGGGAGATAAGATCTGACACAATCTACTCTACTGTAACTTCAGAGAGATAAGATC
* **
3904 C--C--TTTAAT-CGCTCCACTGTAATCTCAGGGAGATAGGATTACTATCTTC-ATCTGCTCCG
66 CTTCGTTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCTT
3962 CTGTAATCTCAGGGAGATAAGATCTGA
1 CTGTAATCTCAGGGAGATAAGATCTGA
3989 AATTCTTTGG
Statistics
Matches: 398, Mismatches: 9, Indels: 7
0.96 0.02 0.02
Matches are distributed among these distances:
122 35 0.09
123 39 0.10
124 6 0.02
126 1 0.00
128 1 0.00
129 316 0.79
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.30
Consensus pattern (129 bp):
CTGTAATCTCAGGGAGATAAGATCTGACACAATCTACTCTACTGTAACTTCAGAGAGATAAGATC
CTTCGTTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCTT
Found at i:16291 original size:17 final size:18
Alignment explanation
Indices: 16269--16305 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
16259 TATAAAAAAA
16269 AAAATATG-CATATATAT
1 AAAATATGACATATATAT
16286 AAAATATGTACATATATAT
1 AAAATATG-ACATATATAT
16305 A
1 A
16306 GGTGTATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 8 0.44
19 10 0.56
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.35
Consensus pattern (18 bp):
AAAATATGACATATATAT
Found at i:16565 original size:36 final size:36
Alignment explanation
Indices: 16525--16604 Score: 92
Period size: 36 Copynumber: 2.2 Consensus size: 36
16515 ATACATATAA
* *
16525 ATATATATACT-TATAAAAATAAAAAT-ATGTATATGT
1 ATATATATA-TATATAAAAAGAAAAATGA-GTATACGT
* *
16561 ATATAGATATATATAAAAAGAAATATGAGTATACGT
1 ATATATATATATATAAAAAGAAAAATGAGTATACGT
16597 ATATATAT
1 ATATATAT
16605 TAAACAAATT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
35 1 0.03
36 35 0.95
37 1 0.03
ACGTcount: A:0.53, C:0.03, G:0.09, T:0.36
Consensus pattern (36 bp):
ATATATATATATATAAAAAGAAAAATGAGTATACGT
Found at i:16745 original size:3 final size:3
Alignment explanation
Indices: 16734--16796 Score: 78
Period size: 3 Copynumber: 21.3 Consensus size: 3
16724 CAATAATACC
*
16734 AAT ACT AAT AAT -AT AA- AGAT GAAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT A-AT -AAT AAT AAT AAT AAT AAT AAT AAT
16779 AAT AAT AAT AAT AA- AAT A
1 AAT AAT AAT AAT AAT AAT A
16797 CAAAGTACTA
Statistics
Matches: 53, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
2 5 0.09
3 45 0.85
4 2 0.04
5 1 0.02
ACGTcount: A:0.65, C:0.02, G:0.03, T:0.30
Consensus pattern (3 bp):
AAT
Done.