Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2303
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: 30060
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.34
Found at i:323 original size:2 final size:2
Alignment explanation
Indices: 316--340 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
306 AGTCAGCTTC
316 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
341 ATAAACTTTA
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:663 original size:13 final size:14
Alignment explanation
Indices: 634--665 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
624 AAAAATTAAA
634 AAATTAAAATATTT
1 AAATTAAAATATTT
648 AAATTAAAAT-TTT
1 AAATTAAAATATTT
661 AAATT
1 AAATT
666 TATTAAACAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 8 0.44
14 10 0.56
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
AAATTAAAATATTT
Found at i:4251 original size:171 final size:171
Alignment explanation
Indices: 3966--4309 Score: 670
Period size: 171 Copynumber: 2.0 Consensus size: 171
3956 AGCAATAGTG
3966 GAAGAAACCCCTGATGAACCAGCATATGTATCATCATGCTCGCGAATCTCTGGGAGATCCCTTGC
1 GAAGAAACCCCTGATGAACCAGCATATGTATCATCATGCTCGCGAATCTCTGGGAGATCCCTTGC
*
4031 CCTCGGTTCATTTTCAGGTAAATCTGAGTAGGCCGCATACATTTCTTGAAAACTAGAAGTACCCT
66 CCTCGGTTCATTTTCAGGTAAATCTGAGTAGGCCGCATACATTTCTTGAAAACCAGAAGTACCCT
4096 GCTTGGTTGTTTCACCATGCCCTTCAGGTTCCTTCTCATTA
131 GCTTGGTTGTTTCACCATGCCCTTCAGGTTCCTTCTCATTA
*
4137 GAAGAAAGCCCTGATGAACCAGCATATGTATCATCATGCTCGCGAATCTCTGGGAGATCCCTTGC
1 GAAGAAACCCCTGATGAACCAGCATATGTATCATCATGCTCGCGAATCTCTGGGAGATCCCTTGC
4202 CCTCGGTTCATTTTCAGGTAAATCTGAGTAGGCCGCATACATTTCTTGAAAACCAGAAGTACCCT
66 CCTCGGTTCATTTTCAGGTAAATCTGAGTAGGCCGCATACATTTCTTGAAAACCAGAAGTACCCT
4267 GCTTGGTTGTTTCACCATGCCCTTCAGGTTCCTTCTCATTA
131 GCTTGGTTGTTTCACCATGCCCTTCAGGTTCCTTCTCATTA
4308 GA
1 GA
4310 CTCAACCAAC
Statistics
Matches: 171, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
171 171 1.00
ACGTcount: A:0.24, C:0.26, G:0.20, T:0.30
Consensus pattern (171 bp):
GAAGAAACCCCTGATGAACCAGCATATGTATCATCATGCTCGCGAATCTCTGGGAGATCCCTTGC
CCTCGGTTCATTTTCAGGTAAATCTGAGTAGGCCGCATACATTTCTTGAAAACCAGAAGTACCCT
GCTTGGTTGTTTCACCATGCCCTTCAGGTTCCTTCTCATTA
Found at i:4955 original size:15 final size:15
Alignment explanation
Indices: 4935--4964 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
4925 CTCAGCTTGT
4935 TCAACATCCACAGAC
1 TCAACATCCACAGAC
*
4950 TCAACATCCCCAGAC
1 TCAACATCCACAGAC
4965 GATAGGCTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.43, G:0.07, T:0.13
Consensus pattern (15 bp):
TCAACATCCACAGAC
Found at i:6047 original size:60 final size:60
Alignment explanation
Indices: 5979--6096 Score: 200
Period size: 60 Copynumber: 2.0 Consensus size: 60
5969 GTCAACGCCA
* * *
5979 TCACCATCATCCTCATCATTTGCAGCGTGTTTCCAAGAGGACACCAGAGAAGAATCCAAT
1 TCACCATCATCCTCATCATCTGCAGCATGTTTCCAAGAGGAAACCAGAGAAGAATCCAAT
*
6039 TCACCATCATCCTCATCATCTGCAGCATGTTTCCAAGAGGAAACCAGAGAGGAATCCA
1 TCACCATCATCCTCATCATCTGCAGCATGTTTCCAAGAGGAAACCAGAGAAGAATCCA
6097 GCTCATCACC
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
60 54 1.00
ACGTcount: A:0.32, C:0.29, G:0.17, T:0.22
Consensus pattern (60 bp):
TCACCATCATCCTCATCATCTGCAGCATGTTTCCAAGAGGAAACCAGAGAAGAATCCAAT
Found at i:7021 original size:15 final size:15
Alignment explanation
Indices: 7001--7030 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
6991 TTAAATGAAA
*
7001 GAAGATCAATCAAAT
1 GAAGATCAACCAAAT
7016 GAAGATCAACCAAAT
1 GAAGATCAACCAAAT
7031 AGCTGGAAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.53, C:0.17, G:0.13, T:0.17
Consensus pattern (15 bp):
GAAGATCAACCAAAT
Found at i:7980 original size:3 final size:3
Alignment explanation
Indices: 7974--8012 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
7964 GTTTTTTTTC
7974 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
8013 ATGTTATTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:8932 original size:3 final size:3
Alignment explanation
Indices: 8926--8953 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
8916 AATTTTTTTC
8926 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
8954 GCTTTCTTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:9103 original size:29 final size:28
Alignment explanation
Indices: 9059--9123 Score: 89
Period size: 29 Copynumber: 2.3 Consensus size: 28
9049 CTCACTAATT
9059 TAAAATA-ATTTAATTT-AATTTAAATAA
1 TAAAATATATTTAATTTAAATTT-AATAA
*
9086 TAAAATATATTTATATTTAAATTTAATTA
1 TAAAATATATTTA-ATTTAAATTTAATAA
9115 TAAAATATA
1 TAAAATATA
9124 AAAATATTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
27 7 0.21
28 5 0.15
29 17 0.50
30 5 0.15
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (28 bp):
TAAAATATATTTAATTTAAATTTAATAA
Found at i:9128 original size:37 final size:35
Alignment explanation
Indices: 9066--9143 Score: 106
Period size: 37 Copynumber: 2.2 Consensus size: 35
9056 ATTTAAAATA
9066 ATTT-AATTTAATTTAAATAATAAAATATATTTAT
1 ATTTAAATTTAATTTAAATAATAAAATATATTTAT
*
9100 ATTTAAATTTAATTATAAA-ATATAAAAATATTTTTAT
1 ATTTAAATTTAATT-TAAATA-AT-AAAATATATTTAT
9137 ATTTAAA
1 ATTTAAA
9144 AAATAAAATA
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
34 4 0.10
35 10 0.26
36 6 0.15
37 19 0.49
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (35 bp):
ATTTAAATTTAATTTAAATAATAAAATATATTTAT
Found at i:9130 original size:29 final size:29
Alignment explanation
Indices: 9071--9153 Score: 78
Period size: 29 Copynumber: 2.8 Consensus size: 29
9061 AAATAATTTA
***
9071 ATTTAATTTAAATAATAAAATATATTTAT
1 ATTTAATTTAAATAATAAAATATAAAAAT
*
9100 ATTTAAATTT-AATTATAAAATATAAAAAT
1 ATTT-AATTTAAATAATAAAATATAAAAAT
*
9129 ATTTTTATATTTAAAAAATAAAATA
1 A--TTTA-ATTTAAATAATAAAATA
9154 AAATATTAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
29 20 0.47
30 6 0.14
31 7 0.16
32 10 0.23
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (29 bp):
ATTTAATTTAAATAATAAAATATAAAAAT
Found at i:9155 original size:37 final size:37
Alignment explanation
Indices: 9087--9169 Score: 96
Period size: 37 Copynumber: 2.2 Consensus size: 37
9077 TTTAAATAAT
** *
9087 AAAATATATTTATATTTAAATTTAATTATAAAATATA
1 AAAATATATTTATATTTAAAAATAATAATAAAATATA
* *
9124 AAAATATTTTTATATTTAAAAAATAA-AATAAAATATT
1 AAAATATATTTATATTT-AAAAATAATAATAAAATATA
*
9161 AAATTATAT
1 AAAATATAT
9170 CCGATTCGAT
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
37 32 0.84
38 6 0.16
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (37 bp):
AAAATATATTTATATTTAAAAATAATAATAAAATATA
Found at i:9883 original size:27 final size:26
Alignment explanation
Indices: 9803--9883 Score: 60
Period size: 27 Copynumber: 3.1 Consensus size: 26
9793 AAATTAAGTT
*
9803 AAAAAATATT-TTTAT-TTCATCTTTA
1 AAAAAATATTATTTATATT-ATCATTA
* * * *
9828 AAAATATTTTATTTATTAATT-TAAATA
1 AAAAAATATTATTTA-T-ATTATCATTA
9855 AAAAAATATTATTTACTATTATCATTA
1 AAAAAATATTATTTA-TATTATCATTA
9882 AA
1 AA
9884 TTTGATAATA
Statistics
Matches: 41, Mismatches: 10, Indels: 8
0.69 0.17 0.14
Matches are distributed among these distances:
25 8 0.20
26 7 0.17
27 24 0.59
29 2 0.05
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.48
Consensus pattern (26 bp):
AAAAAATATTATTTATATTATCATTA
Found at i:11773 original size:22 final size:21
Alignment explanation
Indices: 11740--11786 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
11730 AATAATTAAA
* *
11740 AAAATTATTAAAATTTTATTAT
1 AAAATTATT-AAATATTATCAT
11762 AAAA-TATGTAAATATTATCAT
1 AAAATTAT-TAAATATTATCAT
11783 AAAA
1 AAAA
11787 ATATATTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (21 bp):
AAAATTATTAAATATTATCAT
Found at i:12748 original size:20 final size:18
Alignment explanation
Indices: 12720--12768 Score: 53
Period size: 20 Copynumber: 2.6 Consensus size: 18
12710 AATTAGTTTG
* *
12720 ATTTGAAAATTTTAATTATT
1 ATTTAAAAATTTTAA--AAT
*
12740 ATTTAAAAATATTAAAAT
1 ATTTAAAAATTTTAAAAT
12758 ATTTAAAAATT
1 ATTTAAAAATT
12769 AATTTTTTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
18 12 0.48
20 13 0.52
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (18 bp):
ATTTAAAAATTTTAAAAT
Found at i:13277 original size:18 final size:18
Alignment explanation
Indices: 13241--13276 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
13231 TTTTATTTTT
13241 ATTTTATATTCAAATAAA
1 ATTTTATATTCAAATAAA
*
13259 ATTTTAT-TTTAAATAAA
1 ATTTTATATTCAAATAAA
13276 A
1 A
13277 AATTGCTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (18 bp):
ATTTTATATTCAAATAAA
Found at i:13351 original size:21 final size:21
Alignment explanation
Indices: 13314--13363 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
13304 AATATAAATT
13314 AAAATAAAAATTTATTT-AAA
1 AAAATAAAAATTTATTTCAAA
* * *
13334 AAAATTAAATTTTAATTTCAAT
1 AAAATAAAAATTT-ATTTCAAA
13356 AAAATAAA
1 AAAATAAA
13364 CATATATTGA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 11 0.46
21 4 0.17
22 9 0.38
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (21 bp):
AAAATAAAAATTTATTTCAAA
Found at i:15564 original size:67 final size:67
Alignment explanation
Indices: 15456--15589 Score: 268
Period size: 67 Copynumber: 2.0 Consensus size: 67
15446 ATTTGGTGGC
15456 ATCATCTAAATTACATTCTAAAATTGTAGCAGGTGTTCCATTTAGAAGGTTGTTTATGTGATTGC
1 ATCATCTAAATTACATTCTAAAATTGTAGCAGGTGTTCCATTTAGAAGGTTGTTTATGTGATTGC
15521 CT
66 CT
15523 ATCATCTAAATTACATTCTAAAATTGTAGCAGGTGTTCCATTTAGAAGGTTGTTTATGTGATTGC
1 ATCATCTAAATTACATTCTAAAATTGTAGCAGGTGTTCCATTTAGAAGGTTGTTTATGTGATTGC
15588 CT
66 CT
15590 TTCTATTCCA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 67 1.00
ACGTcount: A:0.28, C:0.13, G:0.18, T:0.40
Consensus pattern (67 bp):
ATCATCTAAATTACATTCTAAAATTGTAGCAGGTGTTCCATTTAGAAGGTTGTTTATGTGATTGC
CT
Found at i:20211 original size:17 final size:18
Alignment explanation
Indices: 20167--20212 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 18
20157 TTGATTTGAT
*
20167 ATTTATATAAATTTTTAAA
1 ATTTATA-AAATATTTAAA
*
20186 AATTA-AAAATATTT-AA
1 ATTTATAAAATATTTAAA
20202 ATTTATAAAAT
1 ATTTATAAAAT
20213 GCCCCCACGA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
16 6 0.26
17 12 0.52
18 1 0.04
19 4 0.17
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
ATTTATAAAATATTTAAA
Found at i:21901 original size:18 final size:19
Alignment explanation
Indices: 21866--21901 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
21856 ATTTTATCTT
*
21866 ATTTTTTAAATAATATTAA
1 ATTTTTTAAATAAAATTAA
21885 ATTTTTTAAA-AAAATTA
1 ATTTTTTAAATAAAATTA
21902 TAATAATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
ATTTTTTAAATAAAATTAA
Found at i:28784 original size:2 final size:2
Alignment explanation
Indices: 28777--28881 Score: 126
Period size: 2 Copynumber: 53.5 Consensus size: 2
28767 ACATAGCAAA
28777 AG AG AG AG AG AG AG AG AG AG AG AG -G AG AG AG AG -G AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
* * *
28817 ATG AG AG AG AG AG AC AG AG AG AG AG AC AG AG AG AC AG AG -G AG
1 A-G AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
* * *
28859 AT AG AC AG AG AG AG AG AC AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG A
28882 CAGGAAATCT
Statistics
Matches: 87, Mismatches: 12, Indels: 8
0.81 0.11 0.07
Matches are distributed among these distances:
1 3 0.03
2 82 0.94
3 2 0.02
ACGTcount: A:0.49, C:0.05, G:0.45, T:0.02
Consensus pattern (2 bp):
AG
Done.