Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold1692
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, 837
Length: 1395
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.28
Found at i:79 original size:16 final size:16
Alignment explanation
Indices: 23--94 Score: 56
Period size: 16 Copynumber: 4.4 Consensus size: 16
13 CAAGGGTAAG
23 TTACATAATACACAAC
1 TTACATAATACACAAC
* * *
39 TTATGCA-ACTTACATAAG
1 TTA--CATA-ATACACAAC
*
57 TTTCATAATACACAAC
1 TTACATAATACACAAC
* *
73 TTACATAAGACATAAC
1 TTACATAATACACAAC
89 TTACAT
1 TTACAT
95 GTGTAAATAA
Statistics
Matches: 42, Mismatches: 10, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
16 30 0.71
17 2 0.05
18 10 0.24
ACGTcount: A:0.44, C:0.21, G:0.04, T:0.31
Consensus pattern (16 bp):
TTACATAATACACAAC
Found at i:93 original size:25 final size:25
Alignment explanation
Indices: 23--93 Score: 65
Period size: 25 Copynumber: 2.8 Consensus size: 25
13 CAAGGGTAAG
* * **
23 TTACATAATACACAACTTATGCAAC
1 TTACATAAGACATAACTTACACAAC
*
48 TTACATAAGTTTCATAA--TACACAAC
1 TTACATAAG--ACATAACTTACACAAC
73 TTACATAAGACATAACTTACA
1 TTACATAAGACATAACTTACA
94 TGTGTAAATA
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
23 5 0.14
25 27 0.75
27 4 0.11
ACGTcount: A:0.45, C:0.21, G:0.04, T:0.30
Consensus pattern (25 bp):
TTACATAAGACATAACTTACACAAC
Found at i:215 original size:16 final size:16
Alignment explanation
Indices: 159--230 Score: 56
Period size: 16 Copynumber: 4.4 Consensus size: 16
149 CAAGGGTAAG
159 TTACATAATACACAAC
1 TTACATAATACACAAC
* * *
175 TTATGCA-ACTTACATAAG
1 TTA--CATA-ATACACAAC
*
193 TTTCATAATACACAAC
1 TTACATAATACACAAC
* *
209 TTACATAAGACATAAC
1 TTACATAATACACAAC
225 TTACAT
1 TTACAT
231 GTGTAAATAA
Statistics
Matches: 42, Mismatches: 10, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
16 30 0.71
17 2 0.05
18 10 0.24
ACGTcount: A:0.44, C:0.21, G:0.04, T:0.31
Consensus pattern (16 bp):
TTACATAATACACAAC
Found at i:229 original size:25 final size:25
Alignment explanation
Indices: 159--229 Score: 65
Period size: 25 Copynumber: 2.8 Consensus size: 25
149 CAAGGGTAAG
* * **
159 TTACATAATACACAACTTATGCAAC
1 TTACATAAGACATAACTTACACAAC
*
184 TTACATAAGTTTCATAA--TACACAAC
1 TTACATAAG--ACATAACTTACACAAC
209 TTACATAAGACATAACTTACA
1 TTACATAAGACATAACTTACA
230 TGTGTAAATA
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
23 5 0.14
25 27 0.75
27 4 0.11
ACGTcount: A:0.45, C:0.21, G:0.04, T:0.30
Consensus pattern (25 bp):
TTACATAAGACATAACTTACACAAC
Found at i:245 original size:136 final size:136
Alignment explanation
Indices: 1--540 Score: 1080
Period size: 136 Copynumber: 4.0 Consensus size: 136
1 GGATGAATTTGTCAAGGGTAAGTTACATAATACACAACTTATGCAACTTACATAAGTTTCATAAT
1 GGATGAATTTGTCAAGGGTAAGTTACATAATACACAACTTATGCAACTTACATAAGTTTCATAAT
66 ACACAACTTACATAAGACATAACTTACATGTGTAAATAATACAGAACTTACATAACTTACATACC
66 ACACAACTTACATAAGACATAACTTACATGTGTAAATAATACAGAACTTACATAACTTACATACC
131 GTTCTT
131 GTTCTT
137 GGATGAATTTGTCAAGGGTAAGTTACATAATACACAACTTATGCAACTTACATAAGTTTCATAAT
1 GGATGAATTTGTCAAGGGTAAGTTACATAATACACAACTTATGCAACTTACATAAGTTTCATAAT
202 ACACAACTTACATAAGACATAACTTACATGTGTAAATAATACAGAACTTACATAACTTACATACC
66 ACACAACTTACATAAGACATAACTTACATGTGTAAATAATACAGAACTTACATAACTTACATACC
267 GTTCTT
131 GTTCTT
273 GGATGAATTTGTCAAGGGTAAGTTACATAATACACAACTTATGCAACTTACATAAGTTTCATAAT
1 GGATGAATTTGTCAAGGGTAAGTTACATAATACACAACTTATGCAACTTACATAAGTTTCATAAT
338 ACACAACTTACATAAGACATAACTTACATGTGTAAATAATACAGAACTTACATAACTTACATACC
66 ACACAACTTACATAAGACATAACTTACATGTGTAAATAATACAGAACTTACATAACTTACATACC
403 GTTCTT
131 GTTCTT
409 GGATGAATTTGTCAAGGGTAAGTTACATAATACACAACTTATGCAACTTACATAAGTTTCATAAT
1 GGATGAATTTGTCAAGGGTAAGTTACATAATACACAACTTATGCAACTTACATAAGTTTCATAAT
474 ACACAACTTACATAAGACATAACTTACATGTGTAAATAATACAGAACTTACATAACTTACATACC
66 ACACAACTTACATAAGACATAACTTACATGTGTAAATAATACAGAACTTACATAACTTACATACC
539 GT
131 GT
541 AGAATGCCCG
Statistics
Matches: 404, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
136 404 1.00
ACGTcount: A:0.41, C:0.18, G:0.11, T:0.31
Consensus pattern (136 bp):
GGATGAATTTGTCAAGGGTAAGTTACATAATACACAACTTATGCAACTTACATAAGTTTCATAAT
ACACAACTTACATAAGACATAACTTACATGTGTAAATAATACAGAACTTACATAACTTACATACC
GTTCTT
Found at i:351 original size:16 final size:16
Alignment explanation
Indices: 295--366 Score: 56
Period size: 16 Copynumber: 4.4 Consensus size: 16
285 CAAGGGTAAG
295 TTACATAATACACAAC
1 TTACATAATACACAAC
* * *
311 TTATGCA-ACTTACATAAG
1 TTA--CATA-ATACACAAC
*
329 TTTCATAATACACAAC
1 TTACATAATACACAAC
* *
345 TTACATAAGACATAAC
1 TTACATAATACACAAC
361 TTACAT
1 TTACAT
367 GTGTAAATAA
Statistics
Matches: 42, Mismatches: 10, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
16 30 0.71
17 2 0.05
18 10 0.24
ACGTcount: A:0.44, C:0.21, G:0.04, T:0.31
Consensus pattern (16 bp):
TTACATAATACACAAC
Found at i:365 original size:25 final size:25
Alignment explanation
Indices: 295--365 Score: 65
Period size: 25 Copynumber: 2.8 Consensus size: 25
285 CAAGGGTAAG
* * **
295 TTACATAATACACAACTTATGCAAC
1 TTACATAAGACATAACTTACACAAC
*
320 TTACATAAGTTTCATAA--TACACAAC
1 TTACATAAG--ACATAACTTACACAAC
345 TTACATAAGACATAACTTACA
1 TTACATAAGACATAACTTACA
366 TGTGTAAATA
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
23 5 0.14
25 27 0.75
27 4 0.11
ACGTcount: A:0.45, C:0.21, G:0.04, T:0.30
Consensus pattern (25 bp):
TTACATAAGACATAACTTACACAAC
Found at i:487 original size:16 final size:16
Alignment explanation
Indices: 431--502 Score: 56
Period size: 16 Copynumber: 4.4 Consensus size: 16
421 CAAGGGTAAG
431 TTACATAATACACAAC
1 TTACATAATACACAAC
* * *
447 TTATGCA-ACTTACATAAG
1 TTA--CATA-ATACACAAC
*
465 TTTCATAATACACAAC
1 TTACATAATACACAAC
* *
481 TTACATAAGACATAAC
1 TTACATAATACACAAC
497 TTACAT
1 TTACAT
503 GTGTAAATAA
Statistics
Matches: 42, Mismatches: 10, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
16 30 0.71
17 2 0.05
18 10 0.24
ACGTcount: A:0.44, C:0.21, G:0.04, T:0.31
Consensus pattern (16 bp):
TTACATAATACACAAC
Found at i:501 original size:25 final size:25
Alignment explanation
Indices: 431--501 Score: 65
Period size: 25 Copynumber: 2.8 Consensus size: 25
421 CAAGGGTAAG
* * **
431 TTACATAATACACAACTTATGCAAC
1 TTACATAAGACATAACTTACACAAC
*
456 TTACATAAGTTTCATAA--TACACAAC
1 TTACATAAG--ACATAACTTACACAAC
481 TTACATAAGACATAACTTACA
1 TTACATAAGACATAACTTACA
502 TGTGTAAATA
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
23 5 0.14
25 27 0.75
27 4 0.11
ACGTcount: A:0.45, C:0.21, G:0.04, T:0.30
Consensus pattern (25 bp):
TTACATAAGACATAACTTACACAAC
Found at i:1246 original size:90 final size:90
Alignment explanation
Indices: 1093--1263 Score: 315
Period size: 90 Copynumber: 1.9 Consensus size: 90
1083 GTATGCGGCC
* *
1093 ACTCCCGTTGGATAAGTAAAAACGCAGAAGGTGGGAACGACGATGAAAATGATGCACAGTCAAGA
1 ACTCCCGTTGGATAAGTAAAAACACAGAAGGTGGGAACGACAATGAAAATGATGCACAGTCAAGA
*
1158 AAGAAGCCAGTTAAGATTTTACGGT
66 AAGAAGCCAGTCAAGATTTTACGGT
1183 ACTCCCGTTGGATAAGTAAAAACACAGAAGGTGGGAACGACAATGAAAATGATGCACAGTCAAGA
1 ACTCCCGTTGGATAAGTAAAAACACAGAAGGTGGGAACGACAATGAAAATGATGCACAGTCAAGA
1248 AAGAAGCCAGTCAAGA
66 AAGAAGCCAGTCAAGA
1264 AACAAGCTTT
Statistics
Matches: 78, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
90 78 1.00
ACGTcount: A:0.42, C:0.16, G:0.26, T:0.16
Consensus pattern (90 bp):
ACTCCCGTTGGATAAGTAAAAACACAGAAGGTGGGAACGACAATGAAAATGATGCACAGTCAAGA
AAGAAGCCAGTCAAGATTTTACGGT
Found at i:1260 original size:16 final size:16
Alignment explanation
Indices: 1239--1270 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1229 AAATGATGCA
*
1239 CAGTCAAGAAAGAAGC
1 CAGTCAAGAAACAAGC
1255 CAGTCAAGAAACAAGC
1 CAGTCAAGAAACAAGC
1271 TTTTCATGTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.50, C:0.22, G:0.22, T:0.06
Consensus pattern (16 bp):
CAGTCAAGAAACAAGC
Done.