Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1003
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: 27943
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31
Found at i:8564 original size:40 final size:40
Alignment explanation
Indices: 8490--8669 Score: 190
Period size: 40 Copynumber: 4.5 Consensus size: 40
8480 CTCGTTCAAA
*
8490 TGCCTTCGGGACATAG-CCGG-TTATAGTAACTCGCACAAT
1 TGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCACAAT
* *
8529 TGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACAAA
1 TGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACAAT
* *
8569 TGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCACAAT
1 TGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACAAT
* * * * * *
8608 TGTCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCACAA-
1 TGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCACAAT
*
8648 AGCCTTCGGGACTTAGCCCGGA
1 TGCCTTCGGGACTTAGCCCGGA
8670 CATCATTCAA
Statistics
Matches: 117, Mismatches: 18, Indels: 11
0.80 0.12 0.08
Matches are distributed among these distances:
38 2 0.02
39 45 0.38
40 58 0.50
41 12 0.10
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.27
Consensus pattern (40 bp):
TGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACAAT
Found at i:8596 original size:79 final size:82
Alignment explanation
Indices: 8486--8669 Score: 220
Period size: 79 Copynumber: 2.3 Consensus size: 82
8476 GCTACTCGTT
* *
8486 CAAATGCCTTCGGGACATAG-CCGG-TTATAGTAACTCGCACAATTGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAATTGCCTTC-GGATCTTAACCC
* *
8548 GGATTTAGTAAC-TCGCA
65 GGATATAGTAACTTAGCA
* * **
8565 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAATTGTCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAATTGCCTTCGGATCTTAACCCG
* *
8628 GATATGGTCACTTAGCA
66 GATATAGTAACTTAGCA
8645 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
8670 CATCATTCAA
Statistics
Matches: 90, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
78 7 0.08
79 63 0.70
80 20 0.22
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAATTGCCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA
Found at i:16260 original size:53 final size:54
Alignment explanation
Indices: 16192--16395 Score: 221
Period size: 53 Copynumber: 3.8 Consensus size: 54
16182 TTCCTTTTTA
* * *
16192 AACTTACCATTGCCATGTCTTGACATGGTCTTACGTGGTATCCTTGCCTTAT-G
1 AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG
* * * * *
16245 AACTCACCATTGCCATGCCTTGGCATGGTCTTACATGGGATCTTTGCCTTATAG
1 AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG
* * * * * * * *
16299 AAGTTTATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCATTTTAA
1 AA-CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG
* * *
16354 AACTTACCAATGTCATGCCTTGGCATGGTCTTACTTGGTATC
1 AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATC
16396 TTTAAACCCT
Statistics
Matches: 122, Mismatches: 27, Indels: 3
0.80 0.18 0.02
Matches are distributed among these distances:
53 46 0.38
54 35 0.29
55 41 0.34
ACGTcount: A:0.22, C:0.23, G:0.18, T:0.37
Consensus pattern (54 bp):
AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG
Found at i:19230 original size:27 final size:28
Alignment explanation
Indices: 19146--19243 Score: 135
Period size: 27 Copynumber: 3.5 Consensus size: 28
19136 CATGAGATTG
* * * *
19146 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
19175 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
19203 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
19230 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
19244 GACTTAATAT
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 24 0.38
28 22 0.34
29 18 0.28
ACGTcount: A:0.27, C:0.13, G:0.29, T:0.32
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:19254 original size:27 final size:27
Alignment explanation
Indices: 19174--19256 Score: 96
Period size: 27 Copynumber: 3.0 Consensus size: 27
19164 TAAATTGTAC
* *
19174 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
19202 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTGAATATAT
*
19229 AGCACTGAGTGTGCGGACTT-AATATAT
1 AGCACTAAGTGTGC-GACTTGAATATAT
19256 A
1 A
19257 TTTTTGAATC
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
27 30 0.60
28 20 0.40
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTGAATATAT
Found at i:19257 original size:29 final size:27
Alignment explanation
Indices: 19146--19257 Score: 98
Period size: 28 Copynumber: 4.0 Consensus size: 27
19136 CATGAGATTG
** * *
19146 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGC-GACTT-AATTATATA
* *
19175 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGA-CTTAATTATATA
* *
19203 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGACTTAATTATATA
*
19230 GCACTGAGTGTGCGGACTTAATATATAT
1 GCACTAAGTGTGC-GACTTAAT-TATAT
19258 TTTTGAATCA
Statistics
Matches: 72, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
27 23 0.32
28 28 0.39
29 21 0.29
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (27 bp):
GCACTAAGTGTGCGACTTAATTATATA
Found at i:27287 original size:28 final size:30
Alignment explanation
Indices: 27219--27289 Score: 119
Period size: 30 Copynumber: 2.4 Consensus size: 30
27209 TAATGTTAGC
27219 AGCACTAAGTGTGCGAGTTTGATTTATAAT
1 AGCACTAAGTGTGCGAGTTTGATTTATAAT
27249 AGCACTAAGTGTGCGAGTTTGA-TTAT-AT
1 AGCACTAAGTGTGCGAGTTTGATTTATAAT
*
27277 AGCACTGAGTGTG
1 AGCACTAAGTGTG
27290 GGAATAACTA
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
28 14 0.35
29 4 0.10
30 22 0.55
ACGTcount: A:0.28, C:0.11, G:0.27, T:0.34
Consensus pattern (30 bp):
AGCACTAAGTGTGCGAGTTTGATTTATAAT
Done.