Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2688
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: 23552
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.33
Found at i:172 original size:19 final size:19
Alignment explanation
Indices: 131--178 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
121 TATCGTACAT
* ** *
131 TGTAACGATACATGTTCAT
1 TGTATCGATACATGGACAA
150 TGTATCGATACATGGACAA
1 TGTATCGATACATGGACAA
169 TGTATCGATA
1 TGTATCGATA
179 GATGAAACTG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Consensus pattern (19 bp):
TGTATCGATACATGGACAA
Found at i:3262 original size:13 final size:13
Alignment explanation
Indices: 3244--3271 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
3234 ATACAAAGAT
3244 CAATGTATCGATA
1 CAATGTATCGATA
3257 CAATGTATCGATA
1 CAATGTATCGATA
3270 CA
1 CA
3272 TTGAATAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:3263 original size:33 final size:33
Alignment explanation
Indices: 3226--3291 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
3216 AAATTCCTAG
3226 ATGTATCAATACAAAG-ATCAATGTATCGATACA
1 ATGTATCAATACAAAGAAT-AATGTATCGATACA
* **
3259 ATGTATCGATACATTGAATAATGTATCGATACA
1 ATGTATCAATACAAAGAATAATGTATCGATACA
3292 TTTCCTTGGC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 27 0.93
34 2 0.07
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (33 bp):
ATGTATCAATACAAAGAATAATGTATCGATACA
Found at i:4412 original size:9 final size:9
Alignment explanation
Indices: 4398--4429 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
4388 GCTTTCATAC
4398 TTTTTTCTT
1 TTTTTTCTT
4407 TTTTTTCTT
1 TTTTTTCTT
*
4416 TTTTCTCTT
1 TTTTTTCTT
4425 TTTTT
1 TTTTT
4430 GTTCTCTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (9 bp):
TTTTTTCTT
Found at i:4418 original size:16 final size:17
Alignment explanation
Indices: 4397--4429 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
4387 AGCTTTCATA
4397 CTTTTTTCT-TTTTTTT
1 CTTTTTTCTCTTTTTTT
4413 CTTTTTTCTCTTTTTTT
1 CTTTTTTCTCTTTTTTT
4430 GTTCTCTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (17 bp):
CTTTTTTCTCTTTTTTT
Found at i:20188 original size:13 final size:13
Alignment explanation
Indices: 20172--20230 Score: 67
Period size: 13 Copynumber: 5.0 Consensus size: 13
20162 ACATTTCATC
20172 ATGTATCGATACA
1 ATGTATCGATACA
20185 ATGTATCGATAC-
1 ATGTATCGATACA
*
20197 AT-T-T---TACC
1 ATGTATCGATACA
20205 ATGTATCGATACA
1 ATGTATCGATACA
20218 ATGTATCGATACA
1 ATGTATCGATACA
20231 TTTTACCATG
Statistics
Matches: 39, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
7 3 0.08
8 2 0.05
9 1 0.03
10 2 0.05
11 1 0.03
12 2 0.05
13 28 0.72
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.34
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:20193 original size:33 final size:33
Alignment explanation
Indices: 20156--20251 Score: 174
Period size: 33 Copynumber: 2.9 Consensus size: 33
20146 CAAGCTATGC
* *
20156 ATCGATACATTTCATCATGTATCGATACAATGT
1 ATCGATACATTTTACCATGTATCGATACAATGT
20189 ATCGATACATTTTACCATGTATCGATACAATGT
1 ATCGATACATTTTACCATGTATCGATACAATGT
20222 ATCGATACATTTTACCATGTATCGATACAA
1 ATCGATACATTTTACCATGTATCGATACAA
20252 ATAGTGATAG
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 61 1.00
ACGTcount: A:0.34, C:0.19, G:0.11, T:0.35
Consensus pattern (33 bp):
ATCGATACATTTTACCATGTATCGATACAATGT
Found at i:20210 original size:20 final size:20
Alignment explanation
Indices: 20185--20250 Score: 83
Period size: 20 Copynumber: 3.6 Consensus size: 20
20175 TATCGATACA
20185 ATGTATCGATACATTTTACC
1 ATGTATCGATACATTTTACC
20205 ATGTATCGATAC-----A--
1 ATGTATCGATACATTTTACC
20218 ATGTATCGATACATTTTACC
1 ATGTATCGATACATTTTACC
20238 ATGTATCGATACA
1 ATGTATCGATACA
20251 AATAGTGATA
Statistics
Matches: 39, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
13 12 0.31
15 1 0.03
18 1 0.03
20 25 0.64
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTTTACC
Found at i:20324 original size:19 final size:19
Alignment explanation
Indices: 20280--20335 Score: 85
Period size: 19 Copynumber: 2.9 Consensus size: 19
20270 CTACTAGTTT
**
20280 CATGTATCGATACAATTGTC
1 CATGTATCGATACAA-TGAA
20300 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
20319 CATGTATCGATACAATG
1 CATGTATCGATACAATG
20336 TATCGATACA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
19 19 0.56
20 15 0.44
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:20338 original size:13 final size:13
Alignment explanation
Indices: 20320--20346 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
20310 TACAATGAAC
20320 ATGTATCGATACA
1 ATGTATCGATACA
20333 ATGTATCGATACA
1 ATGTATCGATACA
20346 A
1 A
20347 AGTAAGATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:20362 original size:33 final size:32
Alignment explanation
Indices: 20301--20365 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
20291 ACAATTGTCC
*
20301 ATGTATCGATACAATGAACATGTATCGATACA
1 ATGTATCGATACAAAGAACATGTATCGATACA
*
20333 ATGTATCGATACAAAGTAAGATGTATCGATACA
1 ATGTATCGATACAAAG-AACATGTATCGATACA
20366 TCTGGGTGTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 15 0.50
33 15 0.50
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.28
Consensus pattern (32 bp):
ATGTATCGATACAAAGAACATGTATCGATACA
Done.