Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2133
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: 45315
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Found at i:3895 original size:17 final size:18
Alignment explanation
Indices: 3863--3896 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3853 AGGCAGCCAA
3863 CATAATTTCTTTATGTGT
1 CATAATTTCTTTATGTGT
3881 CATAATTTC-TTATGTG
1 CATAATTTCTTTATGTG
3897 CTTAAAGGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.24, C:0.12, G:0.12, T:0.53
Consensus pattern (18 bp):
CATAATTTCTTTATGTGT
Found at i:4935 original size:2 final size:2
Alignment explanation
Indices: 4930--4973 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
4920 GTGTGTGTGT
4930 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
4972 GA
1 GA
4974 CCTTGTATGA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:9375 original size:17 final size:16
Alignment explanation
Indices: 9346--9384 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
9336 TTTTAACAAA
* *
9346 TAAAAAATTAAAATTT
1 TAAAAAATAAAAATCT
9362 TAAATAAATAAAAATCT
1 TAAA-AAATAAAAATCT
9379 TAAAAA
1 TAAAAA
9385 TATTATAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (16 bp):
TAAAAAATAAAAATCT
Found at i:16708 original size:20 final size:20
Alignment explanation
Indices: 16683--16724 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
16673 AAAAAAATAT
16683 ATTAAAGATTATATT-ATTAA
1 ATTAAA-ATTATATTGATTAA
*
16703 ATTAAAATTATTTTGATTAA
1 ATTAAAATTATATTGATTAA
16723 AT
1 AT
16725 ATTCAACTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (20 bp):
ATTAAAATTATATTGATTAA
Found at i:18971 original size:35 final size:30
Alignment explanation
Indices: 18907--18970 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 30
18897 TTCCATTGTG
*
18907 TTATTTTTTTAATAAATAATAATATATTAA
1 TTATTTTTTTAATAAAAAATAATATATTAA
18937 TTATTATTTTTAATACAAAAATAATAT-TTAA
1 TTATT-TTTTTAATA-AAAAATAATATATTAA
18968 TTA
1 TTA
18971 ACTTTAAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
30 5 0.16
31 16 0.52
32 10 0.32
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (30 bp):
TTATTTTTTTAATAAAAAATAATATATTAA
Found at i:19206 original size:129 final size:132
Alignment explanation
Indices: 19022--19280 Score: 386
Period size: 131 Copynumber: 2.0 Consensus size: 132
19012 AAAATTAAAT
*
19022 TAAAAAAAGTTTATTATTATTATTATTTAATAAAATTAAAAATAATATTTAATTAAGTTAAAAA-
1 TAAAAAAAGTTTATTATTATAATTATTTAATAAAATTAAAAATAATATTTAATTAAGTTAAAAAC
*
19086 A-TTACATTAACAAATTAAAATATTAATTATATAT-TTTTATAAAAATAAAAAGTATTAAAATAA
66 ATTTACATTAACAAATTAAAATATTAATTAT-TATGTTTT-TAAAAATAAAAAATATTAAAATAA
19149 AAAA
129 AAAA
* *
19153 TAAAAAAGGTTTTTTATTATAATT-TTTAATAAAA-T-AAAATAAATATTTAATTAAGTTAAAAA
1 TAAAAAAAGTTTATTATTATAATTATTTAATAAAATTAAAAAT-AATATTTAATTAAGTTAAAAA
* * *
19215 CATTTACATTAACAAATTAAAATATTAATTATTATGTTTTTTAAAATAAAAAATTTTAAATTAAA
65 CATTTACATTAACAAATTAAAATATTAATTATTATGTTTTTAAAAATAAAAAATATTAAAATAAA
19280 A
130 A
19281 TTTTATTAAT
Statistics
Matches: 117, Mismatches: 7, Indels: 9
0.88 0.05 0.07
Matches are distributed among these distances:
128 5 0.04
129 22 0.19
130 36 0.31
131 54 0.46
ACGTcount: A:0.55, C:0.02, G:0.03, T:0.41
Consensus pattern (132 bp):
TAAAAAAAGTTTATTATTATAATTATTTAATAAAATTAAAAATAATATTTAATTAAGTTAAAAAC
ATTTACATTAACAAATTAAAATATTAATTATTATGTTTTTAAAAATAAAAAATATTAAAATAAAA
AA
Found at i:23050 original size:26 final size:26
Alignment explanation
Indices: 23021--23093 Score: 66
Period size: 24 Copynumber: 2.9 Consensus size: 26
23011 ATTAATATTT
*
23021 TAAATTT-ATATATAATAAAATAAAAA
1 TAAATTTCATA-AAAATAAAATAAAAA
*
23047 TAAATTTCATAAAAAT-AAAT-TAAA
1 TAAATTTCATAAAAATAAAATAAAAA
*
23071 TTAATTT--TAAAAATAAAAATAAA
1 TAAATTTCATAAAAAT-AAAATAAA
23094 TTAGATTTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
22 7 0.18
24 13 0.33
25 5 0.13
26 11 0.28
27 3 0.08
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.34
Consensus pattern (26 bp):
TAAATTTCATAAAAATAAAATAAAAA
Found at i:23076 original size:24 final size:23
Alignment explanation
Indices: 23056--23101 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
23046 ATAAATTTCA
*
23056 TAAAAAT-AAATTAAATTAATTT
1 TAAAAATAAAAATAAATTAATTT
23078 TAAAAATAAAAATAAATTAGATTT
1 TAAAAATAAAAATAAATTA-ATTT
23102 AAATTTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 7 0.33
23 10 0.48
24 4 0.19
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (23 bp):
TAAAAATAAAAATAAATTAATTT
Found at i:23566 original size:39 final size:43
Alignment explanation
Indices: 23508--23593 Score: 108
Period size: 41 Copynumber: 2.1 Consensus size: 43
23498 TAAACCCTTT
*
23508 TTAATTTAATTTTTATTTAAAAATAATT-AATATT-TATTTTA
1 TTAATATAATTTTTATTTAAAAATAATTAAATATTATATTTTA
** *
23549 TTAATATAA-TTTT-TTTAAAGTTAATTAAATATTATTTTTTA
1 TTAATATAATTTTTATTTAAAAATAATTAAATATTATATTTTA
23590 TTAA
1 TTAA
23594 AAATAATAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
39 11 0.28
40 10 0.26
41 18 0.46
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (43 bp):
TTAATATAATTTTTATTTAAAAATAATTAAATATTATATTTTA
Found at i:25286 original size:2 final size:2
Alignment explanation
Indices: 25228--25277 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
25218 AAACATATTG
25228 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
25270 AT AT AT AT
1 AT AT AT AT
25278 GAGATATATG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:27178 original size:21 final size:21
Alignment explanation
Indices: 27153--27198 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
27143 TTTGTTTGTA
27153 TATTTATTT-T-TATCATGATTT
1 TATTTATTTATCTATC-T-ATTT
27174 TATTTATTTATCTATCTATTT
1 TATTTATTTATCTATCTATTT
27195 TATT
1 TATT
27199 GTGTTTGTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 17 0.74
22 2 0.09
23 4 0.17
ACGTcount: A:0.24, C:0.07, G:0.02, T:0.67
Consensus pattern (21 bp):
TATTTATTTATCTATCTATTT
Found at i:29868 original size:2 final size:2
Alignment explanation
Indices: 29861--29896 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
29851 ACTTACATTT
29861 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
29897 AAGATAAGGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:32429 original size:2 final size:2
Alignment explanation
Indices: 32424--32454 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
32414 TTTTTTCATG
32424 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
32455 GGATGAGCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:33686 original size:2 final size:2
Alignment explanation
Indices: 33679--33726 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
33669 CATTTCGTAC
33679 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
33721 AC AT AT
1 AT AT AT
33727 GTGGAACTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:36750 original size:2 final size:2
Alignment explanation
Indices: 36745--36769 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
36735 ATATATATAT
36745 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
36770 AATAGAATCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:36892 original size:22 final size:22
Alignment explanation
Indices: 36861--36902 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
36851 ACAATATCAT
* *
36861 TTTAATATTAATATTTAATAAA
1 TTTAAAATTAAAATTTAATAAA
36883 TTTAAAATTAAAATTTAATA
1 TTTAAAATTAAAATTTAATA
36903 TTTATAACCC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
TTTAAAATTAAAATTTAATAAA
Found at i:37107 original size:3 final size:3
Alignment explanation
Indices: 37099--37153 Score: 103
Period size: 3 Copynumber: 18.7 Consensus size: 3
37089 ACCAAAAGAC
37099 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
37146 AAT AAT AA
1 AAT AAT AA
37154 AATTAAAAAG
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 49 0.96
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:37302 original size:2 final size:2
Alignment explanation
Indices: 37295--37344 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
37285 TTCTTCATGA
37295 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
37337 AT AT AT AT
1 AT AT AT AT
37345 TAAGATTACT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:37638 original size:4 final size:4
Alignment explanation
Indices: 37631--37659 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
37621 AGCTAGTTCT
37631 TTTA TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA T
37660 ACATGGCTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:38967 original size:2 final size:2
Alignment explanation
Indices: 38960--38989 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
38950 TTTCTTACCC
38960 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
38990 TAACTAACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:41616 original size:18 final size:18
Alignment explanation
Indices: 41586--41634 Score: 55
Period size: 20 Copynumber: 2.6 Consensus size: 18
41576 CGTAATTATG
41586 AAAAAATAAAAA-TAATT
1 AAAAAATAAAAATTAATT
*
41603 AAAAAATTAGAAATTAATTT
1 AAAAAA-TAAAAATTAA-TT
41623 AAACAAATAAAA
1 AAA-AAATAAAA
41635 TAAGTGAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 6 0.23
18 5 0.19
19 3 0.12
20 9 0.35
21 3 0.12
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.24
Consensus pattern (18 bp):
AAAAAATAAAAATTAATT
Found at i:41635 original size:19 final size:17
Alignment explanation
Indices: 41586--41635 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 17
41576 CGTAATTATG
*
41586 AAAAAATAAAAATAATT
1 AAAAAATAAAATTAATT
41603 AAAAAATTAGAAATTAATTT
1 AAAAAA-TA-AAATTAA-TT
41623 AAACAAATAAAAT
1 AAA-AAATAAAAT
41636 AAGTGAAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
17 6 0.21
18 2 0.07
19 10 0.36
20 7 0.25
21 3 0.11
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (17 bp):
AAAAAATAAAATTAATT
Found at i:44117 original size:11 final size:10
Alignment explanation
Indices: 44086--44122 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
44076 AAAATTAATT
44086 TAAAAACAAA
1 TAAAAACAAA
44096 TAAAAACAAA
1 TAAAAACAAA
*
44106 TAAAATCTAAA
1 TAAAAAC-AAA
44117 TAAAAA
1 TAAAAA
44123 TATTTAAGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
10 16 0.67
11 8 0.33
ACGTcount: A:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (10 bp):
TAAAAACAAA
Done.