Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2872
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: 34354
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Found at i:248 original size:78 final size:78
Alignment explanation
Indices: 39--270 Score: 340
Period size: 79 Copynumber: 2.9 Consensus size: 78
29 TTATATCTGA
* *
39 AAGTAAATTTGCCAAAAAGATGTTCTACAATAACTTGATATCAACGACAGAACCACTAATAGAGG
1 AAGT-AATTTGGCAAAAAGATGTTCTACAATAACTTGATATCAACAACAGAACCACTAATAGAGG
104 GGATTAT-GGGAAT
65 GGATTATGGGGAAT
*
117 AAGTATATATTGGCAAAAAGATGTTCTACAATAACTTGATATCAACTACAGAACCACTAATAGAG
1 AAGTA-AT-TTGGCAAAAAGATGTTCTACAATAACTTGATATCAACAACAGAACCACTAATAGAG
182 GGGATTATGGGGAAT
64 GGGATTATGGGGAAT
* ** * *
197 AAGTAATTTGGCAAAAAGATGTTCTAGAATAACTCAATATCAACAATAGAACCACTATTAGAGGG
1 AAGTAATTTGGCAAAAAGATGTTCTACAATAACTTGATATCAACAACAGAACCACTAATAGAGGG
*
262 AATTTATGG
66 GA-TTATGG
271 TCAATATTGG
Statistics
Matches: 141, Mismatches: 9, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
77 1 0.01
78 59 0.42
79 70 0.50
80 11 0.08
ACGTcount: A:0.42, C:0.13, G:0.19, T:0.26
Consensus pattern (78 bp):
AAGTAATTTGGCAAAAAGATGTTCTACAATAACTTGATATCAACAACAGAACCACTAATAGAGGG
GATTATGGGGAAT
Found at i:3332 original size:32 final size:31
Alignment explanation
Indices: 3282--3341 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 31
3272 TTTCTGGATC
* *
3282 AAATTGGTCATTAAGATTAGCATTCGTTACAT
1 AAATTGCTCATTAAGATTAACATT-GTTACAT
* *
3314 AAATTGCTCCTTATGATTAACATTGTTA
1 AAATTGCTCATTAAGATTAACATTGTTA
3342 GTTTTCTGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 4 0.17
32 20 0.83
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.40
Consensus pattern (31 bp):
AAATTGCTCATTAAGATTAACATTGTTACAT
Found at i:3624 original size:19 final size:18
Alignment explanation
Indices: 3551--3623 Score: 76
Period size: 18 Copynumber: 3.9 Consensus size: 18
3541 TAGCTTTATT
3551 TTTTTTAATTTTAAAATA
1 TTTTTTAATTTTAAAATA
* * *
3569 ATTTTAAATTTTTTAAA-A
1 TTTTTTAA-TTTTAAAATA
*
3587 TTTTTTAATTATTATAATTA
1 TTTTTTAATT-TTA-AAATA
3607 TTTTTTAATTTTAAAAT
1 TTTTTTAATTTTAAAAT
3624 TTGTTAGAGA
Statistics
Matches: 43, Mismatches: 8, Indels: 8
0.73 0.14 0.14
Matches are distributed among these distances:
17 2 0.05
18 18 0.42
19 12 0.28
20 11 0.26
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTTTTAATTTTAAAATA
Found at i:3624 original size:28 final size:26
Alignment explanation
Indices: 3551--3624 Score: 76
Period size: 28 Copynumber: 2.7 Consensus size: 26
3541 TAGCTTTATT
* *
3551 TTTTTTAATTTTAAAATAATTTTAAA
1 TTTTTTAATTTTAAAATTATTATAAA
**
3577 TTTTTTAAAATTTTTTAATTATTATAATTA
1 TTTTTT--AATTTTAAAATTATTATAA--A
3607 TTTTTTAATTTTAAAATT
1 TTTTTTAATTTTAAAATT
3625 TGTTAGAGAA
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
26 6 0.16
28 25 0.66
30 7 0.18
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (26 bp):
TTTTTTAATTTTAAAATTATTATAAA
Found at i:6675 original size:12 final size:14
Alignment explanation
Indices: 6655--6686 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
6645 TCTTTCAAAG
*
6655 CTTTTTTTTTTTCT
1 CTTTTTTTGTTTCT
6669 CTTTTTTTGTTTCT
1 CTTTTTTTGTTTCT
6683 CTTT
1 CTTT
6687 CTTGTGCTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.00, C:0.16, G:0.03, T:0.81
Consensus pattern (14 bp):
CTTTTTTTGTTTCT
Found at i:6938 original size:17 final size:16
Alignment explanation
Indices: 6918--6949 Score: 55
Period size: 16 Copynumber: 1.9 Consensus size: 16
6908 GGTACTATTG
6918 TATATTTGTTTATTTTT
1 TATATTT-TTTATTTTT
6935 TATATTTTTTATTTT
1 TATATTTTTTATTTT
6950 AAAAAATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.78
Consensus pattern (16 bp):
TATATTTTTTATTTTT
Found at i:10415 original size:16 final size:16
Alignment explanation
Indices: 10394--10427 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
10384 ATGTTTTCCC
*
10394 TTTTCTGGTCAAATTA
1 TTTTCTAGTCAAATTA
10410 TTTTCTAGTCAAATTA
1 TTTTCTAGTCAAATTA
10426 TT
1 TT
10428 AGTATTACTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.26, C:0.12, G:0.09, T:0.53
Consensus pattern (16 bp):
TTTTCTAGTCAAATTA
Found at i:30905 original size:19 final size:19
Alignment explanation
Indices: 30883--30920 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
30873 ATAATTATAC
30883 ATAAAAATTTAAATTTAAA
1 ATAAAAATTTAAATTTAAA
*
30902 ATAAAATTTTAAATTTAAA
1 ATAAAAATTTAAATTTAAA
30921 TTTTTTTCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
ATAAAAATTTAAATTTAAA
Found at i:30924 original size:13 final size:13
Alignment explanation
Indices: 30887--30924 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
30877 TTATACATAA
30887 AAATTTAAA-TTT
1 AAATTTAAATTTT
* *
30899 AAAATAAAATTTT
1 AAATTTAAATTTT
30912 AAATTTAAATTTT
1 AAATTTAAATTTT
30925 TTTCATATAT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
12 7 0.33
13 14 0.67
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
AAATTTAAATTTT
Found at i:34215 original size:2 final size:2
Alignment explanation
Indices: 34208--34236 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
34198 ATCAAATGGG
34208 GA GA GA GA GA GA GA -A GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
34237 AGAATCTACC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
GA
Found at i:34227 original size:13 final size:13
Alignment explanation
Indices: 34209--34234 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
34199 TCAAATGGGG
34209 AGAGAGAGAGAGA
1 AGAGAGAGAGAGA
34222 AGAGAGAGAGAGA
1 AGAGAGAGAGAGA
34235 GAAGAATCTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (13 bp):
AGAGAGAGAGAGA
Found at i:34228 original size:15 final size:15
Alignment explanation
Indices: 34208--34239 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
34198 ATCAAATGGG
34208 GAGAGAGAGAGAGAA
1 GAGAGAGAGAGAGAA
34223 GAGAGAGAGAGAGAA
1 GAGAGAGAGAGAGAA
34238 GA
1 GA
34240 ATCTACCCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (15 bp):
GAGAGAGAGAGAGAA
Done.