Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2505
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: 27965
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32
Found at i:4733 original size:40 final size:40
Alignment explanation
Indices: 4678--4902 Score: 299
Period size: 40 Copynumber: 5.6 Consensus size: 40
4668 TATTCGGATG
4678 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
*
4718 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTAGTTGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGC-A--AGTTACT
* * *
4761 ATACCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
* * * *
4801 ATTTCCGGGCTAAGACCCGAAGGCATGTGTGCGAGTTACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
* * * *
4841 ATATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTGCG
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
*
4881 ATATCC-GGCTAAATCCCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGG
4903 TACTTGGTTT
Statistics
Matches: 163, Mismatches: 19, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
39 14 0.09
40 111 0.68
41 1 0.01
43 37 0.23
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
Found at i:4821 original size:83 final size:80
Alignment explanation
Indices: 4682--4902 Score: 286
Period size: 83 Copynumber: 2.7 Consensus size: 80
4672 CGGATGATAT
* * *
4682 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATATCCGGGCTAAGACCCGAAGGCATGTG
*
4747 TGCGAGTAGTTGCTATAC
66 TGC--G-AGTTACTATAC
* *
4765 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATTTCCGGGCTAAGACCCGAAGGCATGTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATATCCGGGCTAAGACCCGAAGGCATGTG
*
4830 TGCGAGTTACTATAT
66 TGCGAGTTACTATAC
* * *
4845 CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTG-CGATATCC-GGCTAA-ATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAG-TGACTATATCCGGGCTAAGA-CCCGAAGG
4903 TACTTGGTTT
Statistics
Matches: 125, Mismatches: 11, Indels: 8
0.87 0.08 0.06
Matches are distributed among these distances:
78 1 0.01
79 14 0.11
80 44 0.35
81 3 0.02
83 63 0.50
ACGTcount: A:0.23, C:0.23, G:0.29, T:0.25
Consensus pattern (80 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATATCCGGGCTAAGACCCGAAGGCATGTG
TGCGAGTTACTATAC
Found at i:13197 original size:81 final size:79
Alignment explanation
Indices: 13061--13278 Score: 289
Period size: 81 Copynumber: 2.7 Consensus size: 79
13051 CGGATGATAT
* *
13061 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTATATCCGGGCTAAGTCCCGAAGGCATGTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATATCCGGGCTAAGACCCGAAGGCATGTG
13126 CGAGTAGTTGCTATAC
66 CGAG-AGTT-CTATAC
* *
13142 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATTTCCGGGCTAAGACCCGAAGGCATGTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATATCCGGGCTAAGACCCGAAGGCATGTG
* * *
13207 TGCGAGTTCTATAT
66 CGAGAGTTCTATAC
* * *
13221 CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTG-CGATATCC-GGCTAA-ATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAG-TGACTATATCCGGGCTAAGA-CCCGAAGG
13279 TACTTGGTTT
Statistics
Matches: 124, Mismatches: 11, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
77 1 0.01
78 14 0.11
79 40 0.32
80 6 0.05
81 63 0.51
ACGTcount: A:0.22, C:0.23, G:0.29, T:0.25
Consensus pattern (79 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATATCCGGGCTAAGACCCGAAGGCATGTG
CGAGAGTTCTATAC
Found at i:13236 original size:39 final size:40
Alignment explanation
Indices: 13057--13278 Score: 288
Period size: 40 Copynumber: 5.6 Consensus size: 40
13047 TATTCGGATG
* *
13057 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTGCT
* * *
13097 ATATCCGGGCTAAGTCCCGAAGGCATGTGCGAGTAGTTGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCG-AGTTGCT
* *
13138 ATACCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTG-CT
* * *
13178 ATTTCCGGGCTAAGACCCGAAGGCATGTGTGCGAGTT-CT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTGCT
* *
13217 ATATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTGCG
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTGCT
*
13257 ATATCC-GGCTAAATCCCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGG
13279 TACTTGGTTT
Statistics
Matches: 156, Mismatches: 22, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
39 51 0.33
40 70 0.45
41 35 0.22
ACGTcount: A:0.23, C:0.23, G:0.29, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTGCT
Found at i:15921 original size:94 final size:92
Alignment explanation
Indices: 15677--15934 Score: 267
Period size: 94 Copynumber: 2.8 Consensus size: 92
15667 ATGCATGCTG
* * * *
15677 ATGCATGTCCCAGACATGTCTTACACTAGCA--CA-ACTCTTAGCC-AATGCATGTCCCAGACAT
1 ATGCATGTCACAGACATGTCTTACACTAGCACTCATAAT-ATGGCCGAA-GCATGTCCCAGACAT
*
15738 GTCTTACACTGGCTAACTCTGTCGAGGCCA
64 GTCTTACACTAGC-AACTCTGTCGAGGCCA
* * *
15768 ATGCATGTCACAGACATGTCTTACTCTAGCACTCATAATATGGCTGAAGCATGTCCCAGACCTGT
1 ATGCATGTCACAGACATGTCTTACACTAGCACTCATAATATGGCCGAAGCATGTCCCAGACATGT
* * *
15833 CTTACACTAGC-CCTC-GTCTGGATGCCG
66 CTTACACTAGCAACTCTGTC--GAGGCCA
* * * * *
15860 ATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTGGCCGAAGCATGTCCCAGATAT
1 ATG-CATGTCACAGACAT-GTCTTACACTAGCACTCATAATATGGCCGAAGCATGTCCCAGACAT
15925 GTCTTACACT
64 GTCTTACACT
15935 GGCGCACAAA
Statistics
Matches: 140, Mismatches: 19, Indels: 13
0.81 0.11 0.08
Matches are distributed among these distances:
90 3 0.02
91 32 0.23
92 8 0.06
93 44 0.31
94 53 0.38
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27
Consensus pattern (92 bp):
ATGCATGTCACAGACATGTCTTACACTAGCACTCATAATATGGCCGAAGCATGTCCCAGACATGT
CTTACACTAGCAACTCTGTCGAGGCCA
Found at i:15935 original size:46 final size:46
Alignment explanation
Indices: 15639--15937 Score: 204
Period size: 47 Copynumber: 6.4 Consensus size: 46
15629 GCCATATCCT
* *
15639 AGACATGGTCTTACACTGGCTCTCATATATGCAT-GCTGATGCATGTCCC
1 AGACAT-GTCTTACACTGGCTCTCATA-ATG--TGGCCGAAGCATGTCCC
* * * * *
15688 AGACATGTCTTACACTAG--CACA-ACTCTTAGCC-AATGCATGTCCC
1 AGACATGTCTTACACTGGCTCTCATAAT-GTGGCCGAA-GCATGTCCC
* * *
15732 AGACATGTCTTACACTGGCTAACTC-T-GTCGAGGCC-AATGCATGTCAC
1 AGACATGTCTTACACTGGCT--CTCATAAT-GTGGCCGAA-GCATGTCCC
* * * * *
15779 AGACATGTCTTACTCTAGCACTCATAATATGGCTGAAGCATGTCCC
1 AGACATGTCTTACACTGGCTCTCATAATGTGGCCGAAGCATGTCCC
* * * * * *
15825 AGACCTGTCTTACACTAGCCCTCGT-CTG-GATGCCGATGCCATGTCCC
1 AGACATGTCTTACACTGGCTCTCATAATGTG--GCCGAAG-CATGTCCC
15872 AGACATGGTCTTACACTGGCTCTCATAATGTGGCCGAAGCATGTCCC
1 AGACAT-GTCTTACACTGGCTCTCATAATGTGGCCGAAGCATGTCCC
*
15919 AGATATGTCTTACACTGGC
1 AGACATGTCTTACACTGGC
15938 GCACAAATAA
Statistics
Matches: 197, Mismatches: 36, Indels: 37
0.73 0.13 0.14
Matches are distributed among these distances:
43 2 0.01
44 30 0.15
45 5 0.03
46 54 0.27
47 62 0.31
48 35 0.18
49 8 0.04
50 1 0.01
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (46 bp):
AGACATGTCTTACACTGGCTCTCATAATGTGGCCGAAGCATGTCCC
Found at i:19734 original size:47 final size:47
Alignment explanation
Indices: 19621--19764 Score: 213
Period size: 46 Copynumber: 3.1 Consensus size: 47
19611 TTAGGATTTT
*
19621 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCC-AATGGCCA
1 ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCA
*
19667 ATGTGATGAATGTGAGCATGCATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCA
* * * *
19714 ATGTGGTGAATATGAACATGCATATGTG-G-TAAAGCCGAATGGTCA
1 ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCA
19759 ATGTGA
1 ATGTGA
19765 AATATATATA
Statistics
Matches: 89, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
45 19 0.21
46 37 0.42
47 33 0.37
ACGTcount: A:0.33, C:0.12, G:0.29, T:0.26
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCA
Found at i:19796 original size:50 final size:50
Alignment explanation
Indices: 19723--19869 Score: 235
Period size: 50 Copynumber: 3.0 Consensus size: 50
19713 AATGTGGTGA
*
19723 ATATGA-ACATGCATATGTGGTAAAGCCGAATGGTCAATGTGAAATATAT
1 ATATGAGATATGCATATGTGGTAAAGCCGAATGGTCAATGTGAAATATAT
*
19772 ATATGGGATATGCATATGTGGTAAAGCCGAATGGTCAATGTGAAATATAT
1 ATATGAGATATGCATATGTGGTAAAGCCGAATGGTCAATGTGAAATATAT
* *
19822 ATATGAGATATGTATATGTGGTAAAGCCGAATGG-CTAGTGTGAAATAT
1 ATATGAGATATGCATATGTGGTAAAGCCGAATGGTC-AATGTGAAATAT
19870 GTAGGCGATG
Statistics
Matches: 91, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
49 6 0.07
50 85 0.93
ACGTcount: A:0.37, C:0.08, G:0.25, T:0.30
Consensus pattern (50 bp):
ATATGAGATATGCATATGTGGTAAAGCCGAATGGTCAATGTGAAATATAT
Found at i:20127 original size:37 final size:37
Alignment explanation
Indices: 20019--20127 Score: 191
Period size: 37 Copynumber: 2.9 Consensus size: 37
20009 GGAAATATAT
*
20019 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
20056 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
* *
20093 TCCGGGTAAGACCCGATAACTTCGTGTGGAGATTT
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTT
20128 CGTCTGAGCT
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 69 1.00
ACGTcount: A:0.23, C:0.19, G:0.31, T:0.27
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
Found at i:21706 original size:40 final size:40
Alignment explanation
Indices: 21390--21694 Score: 507
Period size: 39 Copynumber: 7.8 Consensus size: 40
21380 TGAGAATTAG
21390 AGTGATATATCCGGGCTAAGT-CCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
21429 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
21469 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
21509 AGTG--ATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
*
21547 AGTGATGTATCC-GGCTAAGTCCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
*
21586 AGTGATGTATCCGGGCTAAGT-CCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
*
21625 AGTGATGTATCC-GGCTAAGT-CCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
* * *
21663 GGTGTTATATCCGGGCTAGGTCCCGAAGAGCA
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCA
21695 ATCATGCTGG
Statistics
Matches: 255, Mismatches: 5, Indels: 11
0.94 0.02 0.04
Matches are distributed among these distances:
38 73 0.29
39 97 0.38
40 85 0.33
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.25
Consensus pattern (40 bp):
AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
Done.