Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3109
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: 21981
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:3095 original size:13 final size:12
Alignment explanation
Indices: 3064--3118 Score: 51
Period size: 12 Copynumber: 4.6 Consensus size: 12
3054 TGTGAAACAG
*
3064 AAAAGAAATTGA
1 AAAAGAAGTTGA
3076 AAAAGAAGTTGA
1 AAAAGAAGTTGA
*
3088 AGAAAGAAG-AGA
1 A-AAAGAAGTTGA
*
3100 AAATG-AGTTAGA
1 AAAAGAAGTT-GA
3112 AAAAGAA
1 AAAAGAA
3119 ACAAAAGAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
10 2 0.06
11 3 0.09
12 21 0.62
13 8 0.24
ACGTcount: A:0.64, C:0.00, G:0.24, T:0.13
Consensus pattern (12 bp):
AAAAGAAGTTGA
Found at i:19124 original size:33 final size:33
Alignment explanation
Indices: 19086--19148 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
19076 GATTACTCAC
19086 TTCACTCG-TTTCTTTT-ACAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTTT
*
19119 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
19149 AATTTCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.13, C:0.27, G:0.06, T:0.54
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAAGCTCTCTTTCTTT
Found at i:19161 original size:13 final size:13
Alignment explanation
Indices: 19145--19202 Score: 55
Period size: 13 Copynumber: 4.3 Consensus size: 13
19135 TCAAGCTCTC
19145 TTTCAATTTCTTT
1 TTTCAATTTCTTT
**
19158 TTTCGCTTT-TTCT
1 TTTCAATTTCTT-T
19171 TTTCAATTTTCTTT
1 TTTCAA-TTTCTTT
*
19185 TCTTCATTTTCTTT
1 T-TTCAATTTCTTT
19199 TTTC
1 TTTC
19203 TCACTTTTTC
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
12 2 0.06
13 15 0.42
14 13 0.36
15 6 0.17
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.71
Consensus pattern (13 bp):
TTTCAATTTCTTT
Found at i:19280 original size:6 final size:6
Alignment explanation
Indices: 19215--19267 Score: 56
Period size: 6 Copynumber: 9.2 Consensus size: 6
19205 ACTTTTTCGA
* ** *
19215 TTTCTT TTTCTT TTGCAA TTTCTT TTTCTT TTTC-T TTTCTT TTT-GT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT
19261 TTTCTT T
1 TTTCTT T
19268 CAATTTCTTT
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
5 9 0.24
6 28 0.76
ACGTcount: A:0.04, C:0.15, G:0.04, T:0.77
Consensus pattern (6 bp):
TTTCTT
Found at i:19280 original size:16 final size:15
Alignment explanation
Indices: 19215--19278 Score: 56
Period size: 15 Copynumber: 3.9 Consensus size: 15
19205 ACTTTTTCGA
19215 TTTCTTTTTCTTTTGC
1 TTTCTTTTTCTTTT-C
19231 AATTTCTTTTTCTTTTTC
1 --TTTCTTTTTC-TTTTC
*
19249 TTTTCTTTTTGTTTTC
1 -TTTCTTTTTCTTTTC
**
19265 TTTCAATTTCTTTT
1 TTTCTTTTTCTTTT
19279 TCAATCTCTT
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
15 11 0.28
16 5 0.12
17 9 0.22
18 11 0.28
19 4 0.10
ACGTcount: A:0.06, C:0.16, G:0.03, T:0.75
Consensus pattern (15 bp):
TTTCTTTTTCTTTTC
Found at i:19289 original size:38 final size:40
Alignment explanation
Indices: 19220--19296 Score: 104
Period size: 38 Copynumber: 2.0 Consensus size: 40
19210 TTCGATTTCT
** * *
19220 TTTTCTTTTGCAATTTCTTTTTCTTTTTCTTTTCTTTTTG
1 TTTTCTTTTGCAATTTCTTTTTCAATCTCTTTTCCTTTTG
19260 TTTTC-TTT-CAATTTCTTTTTCAATCTCTTTTCCTTTT
1 TTTTCTTTTGCAATTTCTTTTTCAATCTCTTTTCCTTTT
19297 CTCGCTCAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
38 25 0.76
39 3 0.09
40 5 0.15
ACGTcount: A:0.08, C:0.18, G:0.03, T:0.71
Consensus pattern (40 bp):
TTTTCTTTTGCAATTTCTTTTTCAATCTCTTTTCCTTTTG
Found at i:20304 original size:28 final size:28
Alignment explanation
Indices: 20273--20329 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
20263 GCAAGACTTT
20273 TCACTTTTTTTAACTTGATTTTTTTTGC
1 TCACTTTTTTTAACTTGATTTTTTTTGC
** **
20301 TCACTTTTTTTTTCTTTCTTTTTTTTGC
1 TCACTTTTTTTAACTTGATTTTTTTTGC
20329 T
1 T
20330 TTTTTTTTCA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.09, C:0.16, G:0.05, T:0.70
Consensus pattern (28 bp):
TCACTTTTTTTAACTTGATTTTTTTTGC
Found at i:20322 original size:13 final size:12
Alignment explanation
Indices: 20305--20350 Score: 56
Period size: 13 Copynumber: 3.7 Consensus size: 12
20295 TTTTGCTCAC
20305 TTTTTTTTTCTT
1 TTTTTTTTTCTT
20317 TCTTTTTTTTGCTT
1 T-TTTTTTTT-CTT
**
20331 TTTTTTTCACTT
1 TTTTTTTTTCTT
20343 TTTTTTTT
1 TTTTTTTT
20351 GAATTTCAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
12 11 0.38
13 14 0.48
14 4 0.14
ACGTcount: A:0.02, C:0.11, G:0.02, T:0.85
Consensus pattern (12 bp):
TTTTTTTTTCTT
Found at i:20331 original size:14 final size:14
Alignment explanation
Indices: 20291--20337 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
20281 TTTAACTTGA
**
20291 TTTTTTTTGCTCAC
1 TTTTTTTTGCTTTC
*
20305 TTTTTTTTTCTTTC
1 TTTTTTTTGCTTTC
20319 TTTTTTTTGCTTT-
1 TTTTTTTTGCTTTC
20332 TTTTTT
1 TTTTTT
20338 CACTTTTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
13 6 0.21
14 23 0.79
ACGTcount: A:0.02, C:0.13, G:0.04, T:0.81
Consensus pattern (14 bp):
TTTTTTTTGCTTTC
Found at i:20331 original size:24 final size:24
Alignment explanation
Indices: 20304--20351 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
20294 TTTTTGCTCA
*
20304 CTTTTTTTTTC-TTTCTTTTTTTTG
1 CTTTTTTTTTCACTT-TTTTTTTTG
20328 CTTTTTTTTTCACTTTTTTTTTTG
1 CTTTTTTTTTCACTTTTTTTTTTG
20352 AATTTCAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 20 0.91
25 2 0.09
ACGTcount: A:0.02, C:0.12, G:0.04, T:0.81
Consensus pattern (24 bp):
CTTTTTTTTTCACTTTTTTTTTTG
Done.