Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1287
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: 25313
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.36
Found at i:89 original size:17 final size:15
Alignment explanation
Indices: 39--85 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
29 CTATATCATT
*
39 ATATATTTTATCT-AA
1 ATAT-TTTTATTTAAA
54 ATATTTTTATTTAAA
1 ATATTTTTATTTAAA
*
69 ATATTATTTTTTTAAA
1 ATATT-TTTATTTAAA
85 A
1 A
86 ATATGTATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 7 0.25
15 11 0.39
16 10 0.36
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (15 bp):
ATATTTTTATTTAAA
Found at i:255 original size:18 final size:21
Alignment explanation
Indices: 193--255 Score: 60
Period size: 22 Copynumber: 3.1 Consensus size: 21
183 CATAACATAT
* * *
193 AAATATATTTTATAAATAATAT
1 AAATATATATTAT-ATTAATAA
*
215 AAATATATATTATATTAAAAA
1 AAATATATATTATATTAATAA
236 AAAT-TA-ATTA-ATTAATAA
1 AAATATATATTATATTAATAA
254 AA
1 AA
256 TTAGTGGTTG
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
18 9 0.25
19 4 0.11
20 2 0.06
21 9 0.25
22 12 0.33
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
AAATATATATTATATTAATAA
Found at i:960 original size:12 final size:12
Alignment explanation
Indices: 939--983 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
929 ATTTTGCTCA
939 ATTA-TTTAATT
1 ATTATTTTAATT
950 ATTATTTTAATT
1 ATTATTTTAATT
* *
962 TTTATATTTAAAT
1 ATTAT-TTTAATT
975 ATTATTTTA
1 ATTATTTTA
984 TTAAAATTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
11 4 0.14
12 15 0.52
13 10 0.34
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
ATTATTTTAATT
Found at i:993 original size:28 final size:29
Alignment explanation
Indices: 962--1038 Score: 76
Period size: 26 Copynumber: 2.8 Consensus size: 29
952 TATTTTAATT
*
962 TTTATATTTAAATATTATTTTATTA-AAA
1 TTTATATTTAAATATTATTTAATTATAAA
*
990 TTTA-A-TAAAATA-TATTTAATTATAAA
1 TTTATATTTAAATATTATTTAATTATAAA
1016 TTT-T-TTATAAAATATTATTTAAT
1 TTTATATT-T-AAATATTATTTAAT
1039 AAATACCACT
Statistics
Matches: 40, Mismatches: 3, Indels: 11
0.74 0.06 0.20
Matches are distributed among these distances:
25 9 0.22
26 13 0.32
27 1 0.03
28 9 0.22
29 8 0.20
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (29 bp):
TTTATATTTAAATATTATTTAATTATAAA
Found at i:1008 original size:14 final size:14
Alignment explanation
Indices: 989--1041 Score: 56
Period size: 14 Copynumber: 3.7 Consensus size: 14
979 TTTTATTAAA
989 ATTTAATAAAATAT
1 ATTTAATAAAATAT
1003 ATTTAATTATAAAT-T
1 ATTTAA-TA-AAATAT
*
1018 -TTTTATAAAATATT
1 ATTTAATAAAATA-T
1032 ATTTAATAAA
1 ATTTAATAAA
1042 TACCACTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
12 4 0.12
13 2 0.06
14 11 0.34
15 11 0.34
16 4 0.12
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
ATTTAATAAAATAT
Found at i:1016 original size:26 final size:27
Alignment explanation
Indices: 971--1038 Score: 86
Period size: 28 Copynumber: 2.5 Consensus size: 27
961 TTTTATATTT
*
971 AAATATTATTTTATTAAAA-TTTAATA
1 AAATATTATTTAATTAAAATTTTAATA
*
997 AAATA-TATTTAATTATAAATTTTTTATA
1 AAATATTATTTAATTA-AAA-TTTTAATA
1025 AAATATTATTTAAT
1 AAATATTATTTAAT
1039 AAATACCACT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
25 9 0.25
26 8 0.22
28 11 0.31
29 8 0.22
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (27 bp):
AAATATTATTTAATTAAAATTTTAATA
Found at i:1225 original size:13 final size:13
Alignment explanation
Indices: 1194--1233 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
1184 ATATATATAT
1194 AAAAAT-AATT-A
1 AAAAATAAATTAA
*
1205 AAATATAAATTAA
1 AAAAATAAATTAA
1218 AAAAATAAATTAA
1 AAAAATAAATTAA
1231 AAA
1 AAA
1234 TATATAGCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 5 0.20
12 4 0.16
13 16 0.64
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (13 bp):
AAAAATAAATTAA
Found at i:2844 original size:2 final size:2
Alignment explanation
Indices: 2837--2878 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
2827 ACTTAAGCTA
2837 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
2879 TCTTACAGAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4633 original size:34 final size:34
Alignment explanation
Indices: 4590--4659 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
4580 TACTTGGACA
4590 ATATTAAGGAGAATCATCAGCAAATTATTTATTT
1 ATATTAAGGAGAATCATCAGCAAATTATTTATTT
4624 ATATTAAGGAGAATCATCAGCAAATTATTTATTT
1 ATATTAAGGAGAATCATCAGCAAATTATTTATTT
4658 AT
1 AT
4660 TTATTTATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.41, C:0.09, G:0.11, T:0.39
Consensus pattern (34 bp):
ATATTAAGGAGAATCATCAGCAAATTATTTATTT
Found at i:11296 original size:15 final size:15
Alignment explanation
Indices: 11278--11366 Score: 81
Period size: 15 Copynumber: 5.8 Consensus size: 15
11268 TTTCATCTTG
*
11278 AATTTTTTTAATTTA
1 AATTTTTTAAATTTA
*
11293 AATTTTTAAAATTTAA
1 AATTTTTTAAATTT-A
*
11309 AATATTTTAAATTTA
1 AATTTTTTAAATTTA
*
11324 AATTATTTT-AATTTG
1 AATT-TTTTAAATTTA
*
11339 AATTTTATCAAATTTA
1 AATTTT-TTAAATTTA
* *
11355 TATTTTATAAAT
1 AATTTTTTAAAT
11367 GTTTTAATCA
Statistics
Matches: 59, Mismatches: 11, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
14 2 0.03
15 30 0.51
16 27 0.46
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (15 bp):
AATTTTTTAAATTTA
Found at i:11311 original size:16 final size:16
Alignment explanation
Indices: 11282--11334 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
11272 ATCTTGAATT
*
11282 TTTTTAATTT-AAAT-
1 TTTTAAATTTAAAATA
11296 TTTTAAAATTTAAAATA
1 TTTT-AAATTTAAAATA
*
11313 TTTTAAATTTAAATTA
1 TTTTAAATTTAAAATA
11329 TTTTAA
1 TTTTAA
11335 TTTGAATTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
14 4 0.12
15 5 0.15
16 21 0.62
17 4 0.12
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TTTTAAATTTAAAATA
Found at i:12351 original size:72 final size:72
Alignment explanation
Indices: 12262--12396 Score: 191
Period size: 72 Copynumber: 1.9 Consensus size: 72
12252 CTTCTGCAAC
* * *
12262 AAAGTTATTTTTCATTAAACATAAAAATTTTGATGATAATAATA-TTCTATAAACCAAAGATAAA
1 AAAGATATTTTTCATTAAACACAAAAATTTTGATAATAATAATACTT-TATAAACCAAAGATAAA
12326 CTTCAAAA
65 CTTCAAAA
* * * *
12334 AAAGATATTTTTCATTAAATACATAAATTTTGGTAATAATTATACTTTATAAACCAAAGATAA
1 AAAGATATTTTTCATTAAACACAAAAATTTTGATAATAATAATACTTTATAAACCAAAGATAA
12397 CCATATAAAA
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
72 53 0.96
73 2 0.04
ACGTcount: A:0.49, C:0.09, G:0.06, T:0.36
Consensus pattern (72 bp):
AAAGATATTTTTCATTAAACACAAAAATTTTGATAATAATAATACTTTATAAACCAAAGATAAAC
TTCAAAA
Found at i:14143 original size:2 final size:2
Alignment explanation
Indices: 14138--14177 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
14128 TTTGTTAACA
14138 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
14178 TTGTTTACAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16872 original size:3 final size:3
Alignment explanation
Indices: 16864--16900 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
16854 AACCAATCAT
16864 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
16901 GATGTGATTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:18968 original size:16 final size:16
Alignment explanation
Indices: 18944--18974 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
18934 TGCATATTTT
18944 TATTAATTATTTATTA
1 TATTAATTATTTATTA
*
18960 TATTTATTATTTATT
1 TATTAATTATTTATT
18975 TAAAATTATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TATTAATTATTTATTA
Found at i:22654 original size:13 final size:13
Alignment explanation
Indices: 22636--22660 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
22626 AGCCCAAACG
22636 GAAAAAGAAAAAT
1 GAAAAAGAAAAAT
22649 GAAAAAGAAAAA
1 GAAAAAGAAAAA
22661 AAAAAGGAGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.04
Consensus pattern (13 bp):
GAAAAAGAAAAAT
Done.