Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1892
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: 18304
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Found at i:205 original size:6 final size:6
Alignment explanation
Indices: 194--235 Score: 50
Period size: 6 Copynumber: 6.8 Consensus size: 6
184 CGGACCCCCT
*
194 TTTTTG TTTTTG TTTGTTT TTTATTG TTTTTG TTTTT- TTTTT
1 TTTTTG TTTTTG TTT-TTG TTT-TTG TTTTTG TTTTTG TTTTT
236 TTGGTTTTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
5 5 0.16
6 17 0.53
7 10 0.31
ACGTcount: A:0.02, C:0.00, G:0.12, T:0.86
Consensus pattern (6 bp):
TTTTTG
Found at i:211 original size:10 final size:10
Alignment explanation
Indices: 196--244 Score: 57
Period size: 10 Copynumber: 4.9 Consensus size: 10
186 GACCCCCTTT
196 TTTGTTTTTG
1 TTTGTTTTTG
206 TTTGTTTTT-
1 TTTGTTTTTG
215 TATTGTTTTTG
1 T-TTGTTTTTG
*
226 TTT-TTTTTT
1 TTTGTTTTTG
235 TTTGGTTTTT
1 TTT-GTTTTT
245 CATTTTTTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
9 9 0.26
10 19 0.56
11 6 0.18
ACGTcount: A:0.02, C:0.00, G:0.14, T:0.84
Consensus pattern (10 bp):
TTTGTTTTTG
Found at i:222 original size:20 final size:18
Alignment explanation
Indices: 193--293 Score: 78
Period size: 20 Copynumber: 5.3 Consensus size: 18
183 CCGGACCCCC
193 TTTTTTGTTTTTGTTTGTT
1 TTTTTTGTTTTTGTTT-TT
212 TTTTATTGTTTTTGTTTTTT
1 TTTT-TTGTTTTTG-TTTTT
*
232 TTTTTTGGTTTTTCATTTTT
1 TTTTTT-GTTTTT-GTTTTT
* *
252 TTCGTTTTTTTTTTGGTTTT
1 TT--TTTTGTTTTTGTTTTT
** *
272 TCATTT-TTTTCGTTTTT
1 TTTTTTGTTTTTGTTTTT
289 TTTTT
1 TTTTT
294 GGAGGACGCC
Statistics
Matches: 66, Mismatches: 10, Indels: 14
0.73 0.11 0.16
Matches are distributed among these distances:
17 12 0.18
18 3 0.05
19 6 0.09
20 33 0.50
21 8 0.12
22 4 0.06
ACGTcount: A:0.03, C:0.04, G:0.11, T:0.82
Consensus pattern (18 bp):
TTTTTTGTTTTTGTTTTT
Found at i:225 original size:16 final size:15
Alignment explanation
Indices: 201--293 Score: 79
Period size: 16 Copynumber: 6.3 Consensus size: 15
191 CCTTTTTTGT
201 TTTTGTTTGTTTTTTA
1 TTTT-TTTGTTTTTTA
217 TTGTTTTTGTTTTTT-
1 TT-TTTTTGTTTTTTA
* *
232 TTTTTTGGTTTTTCA
1 TTTTTTTGTTTTTTA
247 TTTTTTTCG--TTTT-
1 TTTTTTT-GTTTTTTA
* *
260 TTTTTTGGTTTTTCA
1 TTTTTTTGTTTTTTA
275 TTTTTTTCGTTTTTT-
1 TTTTTTT-GTTTTTTA
290 TTTT
1 TTTT
294 GGAGGACGCC
Statistics
Matches: 62, Mismatches: 8, Indels: 15
0.73 0.09 0.18
Matches are distributed among these distances:
12 1 0.02
13 6 0.10
14 16 0.26
15 18 0.29
16 19 0.31
17 2 0.03
ACGTcount: A:0.03, C:0.04, G:0.11, T:0.82
Consensus pattern (15 bp):
TTTTTTTGTTTTTTA
Found at i:243 original size:28 final size:30
Alignment explanation
Indices: 194--293 Score: 134
Period size: 28 Copynumber: 3.3 Consensus size: 30
184 CGGACCCCCT
* *
194 TTTTTGTTTTTGTTTGTTTTTTATTGTTTTT-G
1 TTTTT-TTTTT-TTGGTTTTTCATT-TTTTTCG
226 TTTTTTTTTTTTGGTTTTTCATTTTTTTCG
1 TTTTTTTTTTTTGGTTTTTCATTTTTTTCG
256 --TTTTTTTTTTGGTTTTTCATTTTTTTCG
1 TTTTTTTTTTTTGGTTTTTCATTTTTTTCG
284 TTTTTTTTTT
1 TTTTTTTTTT
294 GGAGGACGCC
Statistics
Matches: 63, Mismatches: 2, Indels: 8
0.86 0.03 0.11
Matches are distributed among these distances:
28 28 0.44
29 5 0.08
30 20 0.32
31 5 0.08
32 5 0.08
ACGTcount: A:0.03, C:0.04, G:0.11, T:0.82
Consensus pattern (30 bp):
TTTTTTTTTTTTGGTTTTTCATTTTTTTCG
Found at i:294 original size:28 final size:28
Alignment explanation
Indices: 228--295 Score: 136
Period size: 28 Copynumber: 2.4 Consensus size: 28
218 TGTTTTTGTT
228 TTTTTTTTTTGGTTTTTCATTTTTTTCG
1 TTTTTTTTTTGGTTTTTCATTTTTTTCG
256 TTTTTTTTTTGGTTTTTCATTTTTTTCG
1 TTTTTTTTTTGGTTTTTCATTTTTTTCG
284 TTTTTTTTTTGG
1 TTTTTTTTTTGG
296 AGGACGCCGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.03, C:0.06, G:0.12, T:0.79
Consensus pattern (28 bp):
TTTTTTTTTTGGTTTTTCATTTTTTTCG
Found at i:6471 original size:10 final size:10
Alignment explanation
Indices: 6456--6482 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
6446 TGCTAACTAA
6456 GTTTTTGTTT
1 GTTTTTGTTT
6466 GTTTTTGTTT
1 GTTTTTGTTT
6476 GTTTTTG
1 GTTTTTG
6483 CTTGATACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.00, C:0.00, G:0.22, T:0.78
Consensus pattern (10 bp):
GTTTTTGTTT
Found at i:14003 original size:52 final size:52
Alignment explanation
Indices: 13918--14042 Score: 214
Period size: 52 Copynumber: 2.4 Consensus size: 52
13908 ATATGAAAAG
* * *
13918 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAACT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
*
13970 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
14022 TTGCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
14043 AAGATCAGTG
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 69 1.00
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.36
Consensus pattern (52 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
Found at i:14055 original size:52 final size:51
Alignment explanation
Indices: 13918--14062 Score: 202
Period size: 52 Copynumber: 2.8 Consensus size: 51
13908 ATATGAAAAG
* *
13918 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAACT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
* *
13970 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
*
14022 TTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 TTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
14063 ATGTATCGAT
Statistics
Matches: 84, Mismatches: 7, Indels: 4
0.88 0.07 0.04
Matches are distributed among these distances:
51 2 0.02
52 82 0.98
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAAT
Found at i:14069 original size:13 final size:13
Alignment explanation
Indices: 14051--14075 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
14041 CAAAGATCAG
14051 TGTATCGATACAA
1 TGTATCGATACAA
14064 TGTATCGATACA
1 TGTATCGATACA
14076 TGTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:14158 original size:13 final size:13
Alignment explanation
Indices: 14140--14164 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
14130 CAAAAAAATA
14140 TGTATCGATACAT
1 TGTATCGATACAT
14153 TGTATCGATACA
1 TGTATCGATACA
14165 ACATTTTATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:14158 original size:33 final size:33
Alignment explanation
Indices: 14118--14184 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
14108 AGTAGCTTAA
14118 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
14151 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
14184 A
1 A
14185 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Done.