Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3221
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: 41830
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:10760 original size:38 final size:38
Alignment explanation
Indices: 10686--10782 Score: 104
Period size: 38 Copynumber: 2.5 Consensus size: 38
10676 TAAATTAGTT
* ** *
10686 TGAGTCTTAATTATGTCATAATTTGAACACCATTAATA
1 TGAGTTTTAATTATGTCATAAGCTAAACACCATTAATA
* *
10724 TGAGTTTTAATTATGTCATAAGCTAAACATCTTTAATA
1 TGAGTTTTAATTATGTCATAAGCTAAACACCATTAATA
* * *
10762 AGGGATTTTAATTATGCCATA
1 TGAG-TTTTAATTATGTCATA
10783 GTTTAGGACA
Statistics
Matches: 49, Mismatches: 9, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
38 34 0.69
39 15 0.31
ACGTcount: A:0.36, C:0.11, G:0.12, T:0.40
Consensus pattern (38 bp):
TGAGTTTTAATTATGTCATAAGCTAAACACCATTAATA
Found at i:12333 original size:42 final size:42
Alignment explanation
Indices: 12274--12479 Score: 250
Period size: 42 Copynumber: 4.9 Consensus size: 42
12264 CTAGGGTTAC
* *
12274 TAAGATTACATGTAAGACCATATCTGGGATATGGCATCTATA
1 TAAGATTTCATGTAAGACCATATCTGGGATATGGCATCGATA
* *
12316 TAAGATTTCATGTAAGACCGTATCCGGGATATGGCATCGATA
1 TAAGATTTCATGTAAGACCATATCTGGGATATGGCATCGATA
* * * *
12358 TGAGATTTCGTGTAAGACCATATCTGGGATATGTCATCAATA
1 TAAGATTTCATGTAAGACCATATCTGGGATATGGCATCGATA
* * *
12400 TAAGATTTCGTGTAAGACCATAGCTGGGCTATTGGCATCGATA
1 TAAGATTTCATGTAAGACCATATCTGGGATA-TGGCATCGATA
** * * * *
12443 CGAGATTACATGTAAAACCAAATCTAGGATATGGCAT
1 TAAGATTTCATGTAAGACCATATCTGGGATATGGCAT
12480 TGGTACGGTA
Statistics
Matches: 139, Mismatches: 24, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
42 108 0.78
43 31 0.22
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.30
Consensus pattern (42 bp):
TAAGATTTCATGTAAGACCATATCTGGGATATGGCATCGATA
Found at i:12417 original size:84 final size:85
Alignment explanation
Indices: 12276--12479 Score: 284
Period size: 84 Copynumber: 2.4 Consensus size: 85
12266 AGGGTTACTA
* * *
12276 AGATTACATGTAAGACCATATCTGGGATATGGCATCTATATAAGATTTCATGTAAGACCGTATCC
1 AGATTACATGTAAGACCATATCTGGGATATGGCATCAATATAAGATTTCATGTAAGACCATAGCC
*
12341 GGGATA-TGGCATCGATATG
66 GGGATATTGGCATCGATACG
* * * * *
12360 AGATTTCGTGTAAGACCATATCTGGGATATGTCATCAATATAAGATTTCGTGTAAGACCATAGCT
1 AGATTACATGTAAGACCATATCTGGGATATGGCATCAATATAAGATTTCATGTAAGACCATAGCC
*
12425 GGGCTATTGGCATCGATACG
66 GGGATATTGGCATCGATACG
* * *
12445 AGATTACATGTAAAACCAAATCTAGGATATGGCAT
1 AGATTACATGTAAGACCATATCTGGGATATGGCAT
12480 TGGTACGGTA
Statistics
Matches: 103, Mismatches: 16, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
84 62 0.60
85 41 0.40
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (85 bp):
AGATTACATGTAAGACCATATCTGGGATATGGCATCAATATAAGATTTCATGTAAGACCATAGCC
GGGATATTGGCATCGATACG
Found at i:15503 original size:110 final size:110
Alignment explanation
Indices: 15306--15536 Score: 313
Period size: 110 Copynumber: 2.1 Consensus size: 110
15296 AGATCGCATC
*
15306 AGACCACGTGGTAGAGACCCATGGCATTATATGACAATGAGGATATTCATGGTGTAGCCTACAGT
1 AGACCACGTGGTAGAGACCCATGGCATTATATGACAATGAGGATACTCATGGTGTAGCCTACAGT
* * * * *
15371 AAGATGTAAATCAGACTAGTAGATCACCATATTAAGATATGTGTA
66 AAGATGTAAACCAGACTAGTAGATCACAACATGAAGATATGTATA
* * * *
15416 GGACCACGTGGTATAGACCCATGGCATTATATGACAATGAGGATACTCATGTTGTATCCT-CTAG
1 AGACCACGTGGTAGAGACCCATGGCATTATATGACAATGAGGATACTCATGGTGTAGCCTAC-AG
* *
15480 TGAGATGTAAACC-GAACTGGTAGATCACAACATGAAGATATGTATA
65 TAAGATGTAAACCAG-ACTAGTAGATCACAACATGAAGATATGTATA
*
15526 AGACCATGTGG
1 AGACCACGTGG
15537 GAGAAGCTCC
Statistics
Matches: 105, Mismatches: 14, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
109 2 0.02
110 103 0.98
ACGTcount: A:0.34, C:0.16, G:0.23, T:0.26
Consensus pattern (110 bp):
AGACCACGTGGTAGAGACCCATGGCATTATATGACAATGAGGATACTCATGGTGTAGCCTACAGT
AAGATGTAAACCAGACTAGTAGATCACAACATGAAGATATGTATA
Found at i:21761 original size:14 final size:16
Alignment explanation
Indices: 21737--21769 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
21727 ATTTTCAGTG
21737 TTTATTATGTGTGA-A
1 TTTATTATGTGTGACA
21752 TTTA-TATGTGTGACA
1 TTTATTATGTGTGACA
21767 TTT
1 TTT
21770 TCGTGACTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.24, C:0.03, G:0.18, T:0.55
Consensus pattern (16 bp):
TTTATTATGTGTGACA
Found at i:25376 original size:99 final size:96
Alignment explanation
Indices: 25204--25432 Score: 240
Period size: 96 Copynumber: 2.4 Consensus size: 96
25194 CCTCGTGACG
* * ** *
25204 TAAGCCAGTGTAAGA-CATGTCTGGGACAT-CCATCAG-CTACGA-GATG-T-GTCAGTATAAGA
1 TAAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCT-CGATTTTGATAGTCAGTATAAAA
* *
25263 CCATGTCTGGGACATGGCATCTGCACGGAT-ATGTGA
65 CCATGTCTAGGACATGGAATC-G-AC--ATGATG-GA
* * * * *
25299 -GAGCTAGTGTAAGACCATGTTTGGGACATGGCGTCGGCCTCGATTTTGATAGTCAGTGTAAAAC
1 TAAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGATTTTGATAGTCAGTATAAAAC
25363 CATGTCTAGGACATGGAATCGACATGATGGA
66 CATGTCTAGGACATGGAATCGACATGATGGA
25394 TAAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGC
1 TAAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGC
25433 AGTATACCCT
Statistics
Matches: 110, Mismatches: 16, Indels: 15
0.78 0.11 0.11
Matches are distributed among these distances:
94 12 0.11
95 17 0.15
96 44 0.40
97 6 0.05
98 2 0.02
99 29 0.26
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.24
Consensus pattern (96 bp):
TAAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGATTTTGATAGTCAGTATAAAAC
CATGTCTAGGACATGGAATCGACATGATGGA
Found at i:26470 original size:28 final size:28
Alignment explanation
Indices: 26425--26479 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
26415 GGGCTAGGAC
* *
26425 ACATGTCATGGCCGTGTGAGGGACACGG
1 ACATGTCATGCCCATGTGAGGGACACGG
26453 ACATGTCATGCCCATGTGAGGGACACG
1 ACATGTCATGCCCATGTGAGGGACACG
26480 AGCTATAGAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.24, C:0.24, G:0.35, T:0.18
Consensus pattern (28 bp):
ACATGTCATGCCCATGTGAGGGACACGG
Found at i:28610 original size:46 final size:46
Alignment explanation
Indices: 28543--28705 Score: 184
Period size: 46 Copynumber: 3.5 Consensus size: 46
28533 CGCCCCTAAG
*
28543 TGAACTCAGACTCAACTCAACGAGCTCAGACGTTCGCATCCATAAA
1 TGAACTCAGACTCAACTCAACGAGCTCAGACGTTAGCATCCATAAA
* * * * * **
28589 TGAACTCAGACTCAACTCAACGAGTTCAGATGCCTAG-TTACATCTCA
1 TGAACTCAGACTCAACTCAACGAGCTCAGACG-TTAGCATCCAT-AAA
* * * * *
28636 TGAACTCGGACTCAACTCAACGAGCTCGGACATTTGCATCCATAAG
1 TGAACTCAGACTCAACTCAACGAGCTCAGACGTTAGCATCCATAAA
28682 TGAACTCAGACTCAACTCAACGAG
1 TGAACTCAGACTCAACTCAACGAG
28706 TTTGGATGCT
Statistics
Matches: 93, Mismatches: 21, Indels: 6
0.77 0.17 0.05
Matches are distributed among these distances:
46 59 0.63
47 34 0.37
ACGTcount: A:0.33, C:0.29, G:0.17, T:0.21
Consensus pattern (46 bp):
TGAACTCAGACTCAACTCAACGAGCTCAGACGTTAGCATCCATAAA
Found at i:30204 original size:46 final size:46
Alignment explanation
Indices: 30137--30301 Score: 160
Period size: 46 Copynumber: 3.6 Consensus size: 46
30127 CGCCCCTAAG
30137 TGAACTCAGACTCAACTCAACGAGTTCAGG-CGTTCGCATCCATAAA
1 TGAACTCAGACTCAACTCAACGAGTTCAGGACGTT-GCATCCATAAA
* * * * *
30183 TGAACTCGGACCCAACTCAACGAGTTCAGATGCCTAGTTACAT-C-T-CA
1 TGAACTCAGACTCAACTCAACGAGTTCAG--GAC--GTTGCATCCATAAA
* * * *
30230 TGAACTCGGACTCAACTCAACGAGCTC-GGACATTTGCATCCATAAG
1 TGAACTCAGACTCAACTCAACGAGTTCAGGAC-GTTGCATCCATAAA
30276 TGAACTCAGACTCAACTCAACGAGTT
1 TGAACTCAGACTCAACTCAACGAGTT
30302 TGGATGCTCA
Statistics
Matches: 98, Mismatches: 13, Indels: 16
0.77 0.10 0.13
Matches are distributed among these distances:
43 6 0.06
44 3 0.03
45 1 0.01
46 52 0.53
47 26 0.27
48 2 0.02
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.32, C:0.28, G:0.18, T:0.22
Consensus pattern (46 bp):
TGAACTCAGACTCAACTCAACGAGTTCAGGACGTTGCATCCATAAA
Found at i:31826 original size:93 final size:93
Alignment explanation
Indices: 31716--31886 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
31706 GCCCCTAAGT
* *
31716 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAATGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
31781 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
* * *
31809 GAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
31874 CGAGTTCGGATGC
66 CGAGTTCGGATGC
31887 TCAACCATCC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:31883 original size:46 final size:46
Alignment explanation
Indices: 31711--31883 Score: 208
Period size: 46 Copynumber: 3.7 Consensus size: 46
31701 AACCCGCCCC
* * * *
31711 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
* * *
31757 TAAATGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-ATTTGCATCCA
* *
31805 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
31850 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
31884 TGCTCAACCA
Statistics
Matches: 107, Mismatches: 13, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
43 6 0.06
44 2 0.02
45 2 0.02
46 60 0.56
47 29 0.27
48 2 0.02
49 2 0.02
50 4 0.04
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
Done.