Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_2193
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: 24856
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Found at i:326 original size:29 final size:29
Alignment explanation
Indices: 284--383 Score: 148
Period size: 29 Copynumber: 3.5 Consensus size: 29
274 CATGAAATTG
284 GCACTAAGTGTGCGGGTTCAAATTGTATA
1 GCACTAAGTGTGCGGGTTCAAATTGTATA
*
313 GCACTAAGTGTGCGGGTTCAAGTTGTATA
1 GCACTAAGTGTGCGGGTTCAAATTGTATA
* * *
342 GCACTAAGTGTGCGAGTTC-GATTATATA
1 GCACTAAGTGTGCGGGTTCAAATTGTATA
*
370 ACACTAAGTGTGCG
1 GCACTAAGTGTGCG
384 ACTTACTATA
Statistics
Matches: 65, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
28 19 0.29
29 46 0.71
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (29 bp):
GCACTAAGTGTGCGGGTTCAAATTGTATA
Found at i:7822 original size:29 final size:28
Alignment explanation
Indices: 7780--7880 Score: 148
Period size: 29 Copynumber: 3.5 Consensus size: 28
7770 CATGAAATTG
7780 GCACTAAGTGTGCGGGTTCAATTTGTATA
1 GCACTAAGTGTGCGGGTTCAA-TTGTATA
7809 GCACTAAGTGTGCGGGTTCAAGTTGTATA
1 GCACTAAGTGTGCGGGTTCAA-TTGTATA
* * *
7838 GCACTAAGTGTGCGAGTTCGATTATATA
1 GCACTAAGTGTGCGGGTTCAATTGTATA
*
7866 ACACTAAGTGTGCGG
1 GCACTAAGTGTGCGG
7881 ACTTACTATA
Statistics
Matches: 66, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
28 19 0.29
29 47 0.71
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.31
Consensus pattern (28 bp):
GCACTAAGTGTGCGGGTTCAATTGTATA
Found at i:15897 original size:15 final size:15
Alignment explanation
Indices: 15857--15897 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 15
15847 TTTTACTTAT
15857 AATGTACATATATGAG
1 AATGT-CATATATGAG
*
15873 AATATCATAT-T-AG
1 AATGTCATATATGAG
15886 AATGTCATATAT
1 AATGTCATATAT
15898 CAAGAAACAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 11 0.50
14 2 0.09
15 5 0.23
16 4 0.18
ACGTcount: A:0.44, C:0.07, G:0.12, T:0.37
Consensus pattern (15 bp):
AATGTCATATATGAG
Found at i:18521 original size:25 final size:25
Alignment explanation
Indices: 18487--18538 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
18477 CAACCAGATT
18487 GGAACTCCCAAATATTTATTAAAAG
1 GGAACTCCCAAATATTTATTAAAAG
18512 GGAACTCCCAAATATTTATTAAAAG
1 GGAACTCCCAAATATTTATTAAAAG
18537 GG
1 GG
18539 TTAATTTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.27
Consensus pattern (25 bp):
GGAACTCCCAAATATTTATTAAAAG
Found at i:19035 original size:25 final size:25
Alignment explanation
Indices: 19001--19052 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
18991 CAACCAGATT
19001 GGAACTCCCAAATATTTATTAAAAG
1 GGAACTCCCAAATATTTATTAAAAG
19026 GGAACTCCCAAATATTTATTAAAAG
1 GGAACTCCCAAATATTTATTAAAAG
19051 GG
1 GG
19053 TTAATTTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.27
Consensus pattern (25 bp):
GGAACTCCCAAATATTTATTAAAAG
Found at i:24081 original size:27 final size:26
Alignment explanation
Indices: 24044--24158 Score: 149
Period size: 27 Copynumber: 4.3 Consensus size: 26
24034 AGCATGGCTG
* *
24044 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
24070 CCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
24098 CCAGAACAGATATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* * *
24125 CCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
24152 CCAGAAC
1 CCAGAAC
24159 GCTTCCTCCA
Statistics
Matches: 80, Mismatches: 6, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
26 5 0.06
27 58 0.73
28 17 0.21
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:24108 original size:54 final size:54
Alignment explanation
Indices: 24044--24158 Score: 169
Period size: 54 Copynumber: 2.1 Consensus size: 54
24034 AGCATGGCTG
*
24044 CCAGAACAGATA-ATGTGACAGAGTCACCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGAT-CAGATAATCGTGGCAGAGCCA
* * * *
24098 CCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
24152 CCAGAAC
1 CCAGAAC
24159 GCTTCCTCCA
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
54 37 0.67
55 18 0.33
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (54 bp):
CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
Found at i:24587 original size:16 final size:15
Alignment explanation
Indices: 24566--24595 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
24556 AAAATACCGA
24566 CTTTTCGGCATTTTGG
1 CTTTTCGGC-TTTTGG
24582 CTTTTCGGCTTTTG
1 CTTTTCGGCTTTTG
24596 CCAATCTAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.03, C:0.20, G:0.23, T:0.53
Consensus pattern (15 bp):
CTTTTCGGCTTTTGG
Done.