Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2327
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: 31303
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Found at i:563 original size:46 final size:46
Alignment explanation
Indices: 496--662 Score: 172
Period size: 46 Copynumber: 3.7 Consensus size: 46
486 AACCCGCCCC
*
496 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCATCCA
*
542 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG--G-C--GTTCGCATCCA
* * * *
590 TCA-CGAACTCGGACTCAACTCAAC--G-TC-GACATTCG-ATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCATCCA
630 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG
663 ATGCACAGTG
Statistics
Matches: 99, Mismatches: 9, Indels: 27
0.73 0.07 0.20
Matches are distributed among these distances:
38 4 0.04
39 1 0.01
40 3 0.03
41 20 0.20
43 2 0.02
44 4 0.04
45 2 0.02
46 32 0.32
47 20 0.20
48 3 0.03
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCATCCA
Found at i:630 original size:88 final size:92
Alignment explanation
Indices: 501--666 Score: 277
Period size: 88 Copynumber: 1.8 Consensus size: 92
491 GCCCCTAAGT
* *
501 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAAC-AGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
566 CGAGTTCGGATGCCTAGTTACATCTCAC
65 CGAGTTCGGATGCCTAGTTACATCTCAC
594 GAACTCGGACTCAACTCAAC-G-TC-GACATTCG-ATCCATAAGTGAACTCGGACTCAACTCAAC
1 GAACTCGGACTCAACTCAACAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
655 GAGTTCGGATGC
66 GAGTTCGGATGC
667 ACAGTGACTC
Statistics
Matches: 71, Mismatches: 2, Indels: 5
0.91 0.03 0.06
Matches are distributed among these distances:
88 42 0.59
89 6 0.08
90 2 0.03
91 1 0.01
93 20 0.28
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (92 bp):
GAACTCGGACTCAACTCAACAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
GAGTTCGGATGCCTAGTTACATCTCAC
Found at i:1169 original size:30 final size:30
Alignment explanation
Indices: 1135--1194 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
1125 ATTTAATACG
1135 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
1165 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
1195 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:7756 original size:46 final size:46
Alignment explanation
Indices: 7601--7768 Score: 156
Period size: 46 Copynumber: 3.7 Consensus size: 46
7591 AACCCGTCCC
* * *
7601 TAAGTGAACTCGGACTCAACTCAATGAGCTCGGGCATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
* *
7647 TAAGTGAACTC--A---GACTCAACGAGTTCGGATGCCTAGTT-ACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCATCCA
* * *
7690 TCA-CGAACTCAGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
7735 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
7769 TGCTCAACCA
Statistics
Matches: 96, Mismatches: 12, Indels: 28
0.71 0.09 0.21
Matches are distributed among these distances:
41 13 0.14
42 8 0.08
43 6 0.06
44 6 0.06
45 6 0.06
46 41 0.43
47 16 0.17
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
Found at i:7787 original size:46 final size:45
Alignment explanation
Indices: 7694--7779 Score: 120
Period size: 46 Copynumber: 1.9 Consensus size: 45
7684 TACATCTCAC
* *
7694 GAACTCAGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGT
1 GAACTCAGACTCAACTCAACGAGTTCGGA-ATGCGCAACCATAAGT
* *
7740 GAACTCGGACTCAACTCAACGAGTTCGG-ATGCTCAACCAT
1 GAACTCAGACTCAACTCAACGAGTTCGGAATGCGCAACCAT
7780 CCTAGTGACT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
44 9 0.25
46 27 0.75
ACGTcount: A:0.31, C:0.29, G:0.19, T:0.21
Consensus pattern (45 bp):
GAACTCAGACTCAACTCAACGAGTTCGGAATGCGCAACCATAAGT
Found at i:10952 original size:16 final size:17
Alignment explanation
Indices: 10931--10964 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
10921 AAATATTATG
10931 AAATAAA-ACCAAACAA
1 AAATAAACACCAAACAA
*
10947 AAATAAACATCAAACAA
1 AAATAAACACCAAACAA
10964 A
1 A
10965 TGCCATCCCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.74, C:0.18, G:0.00, T:0.09
Consensus pattern (17 bp):
AAATAAACACCAAACAA
Found at i:11710 original size:41 final size:42
Alignment explanation
Indices: 11665--11762 Score: 121
Period size: 41 Copynumber: 2.4 Consensus size: 42
11655 AAATAGGGAT
* * *
11665 TAAATTGATAAATGTGTAAAG-TTAGTGGTTAAAATGTAAAA
1 TAAATTGAAAAATATGGAAAGCTTAGTGGTTAAAATGTAAAA
***
11706 TAAA-TGAAAAATATGGGCTGCTTAGTGGTTAAAATGTAAAA
1 TAAATTGAAAAATATGGAAAGCTTAGTGGTTAAAATGTAAAA
11747 TAAA-TGAAAAATATGG
1 TAAATTGAAAAATATGG
11763 GCTGCTAGGG
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
40 10 0.20
41 40 0.80
ACGTcount: A:0.47, C:0.02, G:0.20, T:0.31
Consensus pattern (42 bp):
TAAATTGAAAAATATGGAAAGCTTAGTGGTTAAAATGTAAAA
Found at i:11763 original size:41 final size:41
Alignment explanation
Indices: 11686--11768 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
11676 ATGTGTAAAG
11686 TTAGTGGTTAAAATGTAAAATAAATGAAAAATATGGGCTGC
1 TTAGTGGTTAAAATGTAAAATAAATGAAAAATATGGGCTGC
11727 TTAGTGGTTAAAATGTAAAATAAATGAAAAATATGGGCTGC
1 TTAGTGGTTAAAATGTAAAATAAATGAAAAATATGGGCTGC
11768 T
1 T
11769 AGGGGCATTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.43, C:0.05, G:0.22, T:0.30
Consensus pattern (41 bp):
TTAGTGGTTAAAATGTAAAATAAATGAAAAATATGGGCTGC
Found at i:17056 original size:27 final size:27
Alignment explanation
Indices: 17021--17146 Score: 139
Period size: 27 Copynumber: 4.6 Consensus size: 27
17011 TTAGTTTACC
*
17021 AAATTACCAAAATACCCTCGATTAGCA
1 AAATTACCAAAATACCCTCGATTAGTA
17048 AAATTACCAAAATACCCTCGATTAGTA
1 AAATTACCAAAATACCCTCGATTAGTA
* * *
17075 AAATTACTAAAATACCC-CTGGTTTGTA
1 AAATTACCAAAATACCCTC-GATTAGTA
* *
17102 AAATTACCAAAAATACCCTTG-TAAGGTA
1 AAATTACC-AAAATACCCTCGATTA-GTA
* *
17130 GAATTACCTAAATACCC
1 AAATTACCAAAATACCC
17147 CTGTAGGGTA
Statistics
Matches: 85, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
26 1 0.01
27 64 0.75
28 20 0.24
ACGTcount: A:0.43, C:0.22, G:0.09, T:0.26
Consensus pattern (27 bp):
AAATTACCAAAATACCCTCGATTAGTA
Found at i:17151 original size:27 final size:27
Alignment explanation
Indices: 17103--17351 Score: 240
Period size: 27 Copynumber: 9.3 Consensus size: 27
17093 TGGTTTGTAA
* * *
17103 AATTACCAAAAATACCCTTGTAAGGTAG
1 AATTACC-TAAATACCCCTGTAGGGTAG
17131 AATTACCTAAATACCCCTGTAGGGTAG
1 AATTACCTAAATACCCCTGTAGGGTAG
* *
17158 -ATTA-CTAAAATACCCCTATAAGGTAG
1 AATTACCT-AAATACCCCTGTAGGGTAG
* *
17184 AATTACCGAAATACCCCTATAGGGTAG
1 AATTACCTAAATACCCCTGTAGGGTAG
* *
17211 AATTACCGAAATACCCTTGTAGGGTAG
1 AATTACCTAAATACCCCTGTAGGGTAG
*
17238 AATTA-CTGAAATACCCCTGTATGGTAG
1 AATTACCT-AAATACCCCTGTAGGGTAG
* *
17265 AATTACCGAAA-ACCCTTGTAGGGTAG
1 AATTACCTAAATACCCCTGTAGGGTAG
* * *
17291 AAATA-CTGAAATACCCTTGTAGGGTAA
1 AATTACCT-AAATACCCCTGTAGGGTAG
* * * *
17318 AATTATC-AAGATACCCTTGTGGGGTAA
1 AATTACCTAA-ATACCCCTGTAGGGTAG
17345 AATTACC
1 AATTACC
17352 ATTTTTCCCC
Statistics
Matches: 191, Mismatches: 21, Indels: 19
0.83 0.09 0.08
Matches are distributed among these distances:
25 3 0.02
26 44 0.23
27 134 0.70
28 10 0.05
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.26
Consensus pattern (27 bp):
AATTACCTAAATACCCCTGTAGGGTAG
Found at i:17183 original size:53 final size:54
Alignment explanation
Indices: 17049--17337 Score: 309
Period size: 53 Copynumber: 5.4 Consensus size: 54
17039 CGATTAGCAA
* * * * ** *
17049 AATTACCAAAATACCCTCGATTA-GTAAAATTACTAAAATACCCCTGGT-TTGTAA
1 AATTACCAAAATACCCTTG-TAAGGTAGAATTACTGAAATACCCCT-GTAGGGTAG
17103 AATTACCAAAAATACCCTTGTAAGGTAGAATTACCT-AAATACCCCTGTAGGGTAG
1 AATTACC-AAAATACCCTTGTAAGGTAGAATTA-CTGAAATACCCCTGTAGGGTAG
* * * * *
17158 -ATTACTAAAATACCCCTATAAGGTAGAATTACCGAAATACCCCTATAGGGTAG
1 AATTACCAAAATACCCTTGTAAGGTAGAATTACTGAAATACCCCTGTAGGGTAG
* * *
17211 AATTACCGAAATACCCTTGTAGGGTAGAATTACTGAAATACCCCTGTATGGTAG
1 AATTACCAAAATACCCTTGTAAGGTAGAATTACTGAAATACCCCTGTAGGGTAG
* * * * *
17265 AATTACCGAAA-ACCCTTGTAGGGTAGAAATACTGAAATACCCTTGTAGGGTAA
1 AATTACCAAAATACCCTTGTAAGGTAGAATTACTGAAATACCCCTGTAGGGTAG
* *
17318 AATTATCAAGATACCCTTGT
1 AATTACCAAAATACCCTTGT
17338 GGGGTAAAAT
Statistics
Matches: 202, Mismatches: 26, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
52 1 0.00
53 87 0.43
54 80 0.40
55 32 0.16
56 2 0.01
ACGTcount: A:0.38, C:0.19, G:0.16, T:0.27
Consensus pattern (54 bp):
AATTACCAAAATACCCTTGTAAGGTAGAATTACTGAAATACCCCTGTAGGGTAG
Found at i:17223 original size:80 final size:81
Alignment explanation
Indices: 17076--17322 Score: 329
Period size: 80 Copynumber: 3.1 Consensus size: 81
17066 CGATTAGTAA
* * * * *
17076 AATTACTAAAATACCCCTGGT-TTGTAAAATTACCAAAAATACCCTTGTAAGGTAGAATTACCTA
1 AATTACTAAAATACCCCT-GTATGGTAGAATTACC-GAAATACCCTTGTAGGGTAGAATTACCGA
*
17140 AATACCCCTGTAGGGTAG
64 AATACCCTTGTAGGGTAG
* * * *
17158 -ATTACTAAAATACCCCTATAAGGTAGAATTACCGAAATACCCCTATAGGGTAGAATTACCGAAA
1 AATTACTAAAATACCCCTGTATGGTAGAATTACCGAAATACCCTTGTAGGGTAGAATTACCGAAA
17222 TACCCTTGTAGGGTAG
66 TACCCTTGTAGGGTAG
* * *
17238 AATTACTGAAATACCCCTGTATGGTAGAATTACCGAAA-ACCCTTGTAGGGTAGAAATACTGAAA
1 AATTACTAAAATACCCCTGTATGGTAGAATTACCGAAATACCCTTGTAGGGTAGAATTACCGAAA
*
17302 TACCCTTGTAGGGTAA
66 TACCCTTGTAGGGTAG
17318 AATTA
1 AATTA
17323 TCAAGATACC
Statistics
Matches: 145, Mismatches: 18, Indels: 6
0.86 0.11 0.04
Matches are distributed among these distances:
80 84 0.58
81 61 0.42
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.27
Consensus pattern (81 bp):
AATTACTAAAATACCCCTGTATGGTAGAATTACCGAAATACCCTTGTAGGGTAGAATTACCGAAA
TACCCTTGTAGGGTAG
Found at i:17332 original size:80 final size:81
Alignment explanation
Indices: 17072--17351 Score: 318
Period size: 80 Copynumber: 3.5 Consensus size: 81
17062 CCCTCGATTA
* * *
17072 GTAAAATTACTAAAATACCCCTGGT-TTGTAAAATTACCAAAAATACCCTTGTAAGGTAGAATTA
1 GTAAAATTACTAAAATACCCCT-GTATGGTAAAATTACC-GAAATACCCTTGTAGGGTAGAATTA
*
17136 CCT-AAATACCCCTGTAGG
64 -CTGAAATACCCTTGTAGG
* * * * * * *
17154 GT-AGATTACTAAAATACCCCTATAAGGTAGAATTACCGAAATACCCCTATAGGGTAGAATTACC
1 GTAAAATTACTAAAATACCCCTGTATGGTAAAATTACCGAAATACCCTTGTAGGGTAGAATTACT
17218 GAAATACCCTTGTAGG
66 GAAATACCCTTGTAGG
* * * *
17234 GTAGAATTACTGAAATACCCCTGTATGGTAGAATTACCGAAA-ACCCTTGTAGGGTAGAAATACT
1 GTAAAATTACTAAAATACCCCTGTATGGTAAAATTACCGAAATACCCTTGTAGGGTAGAATTACT
17298 GAAATACCCTTGTAGG
66 GAAATACCCTTGTAGG
* * **
17314 GTAAAATTA-TCAAGATACCCTTGTGGGGTAAAATTACC
1 GTAAAATTACT-AAAATACCCCTGTATGGTAAAATTACC
17352 ATTTTTCCCC
Statistics
Matches: 167, Mismatches: 27, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
79 2 0.01
80 101 0.60
81 62 0.37
82 2 0.01
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (81 bp):
GTAAAATTACTAAAATACCCCTGTATGGTAAAATTACCGAAATACCCTTGTAGGGTAGAATTACT
GAAATACCCTTGTAGG
Found at i:18045 original size:27 final size:26
Alignment explanation
Indices: 18001--18051 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
17991 CTCGCTACAA
*
18001 TCTGGTGGCCTCGCCACATATATCTGT
1 TCTGGTGACCTCGCCACA-ATATCTGT
* *
18028 TCTGGTGACTTCGTCACAATATCT
1 TCTGGTGACCTCGCCACAATATCT
18052 AGTAGCCTCT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 6 0.29
27 15 0.71
ACGTcount: A:0.18, C:0.27, G:0.20, T:0.35
Consensus pattern (26 bp):
TCTGGTGACCTCGCCACAATATCTGT
Found at i:18120 original size:26 final size:27
Alignment explanation
Indices: 18091--18150 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
18081 CCACATATAT
*
18091 ATATCTGT-TCTGGTGGCCTAGCCACA
1 ATATCTGTATCTGGTGACCTAGCCACA
* * *
18117 ATATCTGTATCTGGTGACTTTGTCACA
1 ATATCTGTATCTGGTGACCTAGCCACA
18144 ATATCTG
1 ATATCTG
18151 GCAGCCTTGC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.37
Consensus pattern (27 bp):
ATATCTGTATCTGGTGACCTAGCCACA
Found at i:20239 original size:27 final size:27
Alignment explanation
Indices: 20203--20274 Score: 99
Period size: 27 Copynumber: 2.6 Consensus size: 27
20193 TTAGTTTACC
20203 AAATTACCAAAATACCCTCGATTAGCA
1 AAATTACCAAAATACCCTCGATTAGCA
* * * *
20230 AAATTACCAAAATACCCTTGGTTTGTA
1 AAATTACCAAAATACCCTCGATTAGCA
20257 AAATTACCAAAAATACCC
1 AAATTACC-AAAATACCC
20275 CTATAAGGTA
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
27 31 0.77
28 9 0.22
ACGTcount: A:0.44, C:0.24, G:0.07, T:0.25
Consensus pattern (27 bp):
AAATTACCAAAATACCCTCGATTAGCA
Found at i:20302 original size:27 final size:27
Alignment explanation
Indices: 20258--20508 Score: 322
Period size: 27 Copynumber: 9.3 Consensus size: 27
20248 TGGTTTGTAA
* * *
20258 AATTACCAAAAATACCCCTATAAGGTAG
1 AATTACC-GAAATACCCCTGTAGGGTAG
20286 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
20313 AATTACTGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* ** *
20340 AATTTCTTAAATACCCCTGTAAGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
20367 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
20394 AATTACTGAAATACCCCTATAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
20421 AATTACCGAAATACCCTTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * *
20448 AAATACTGAAATACCCCTGTAGGGTAA
1 AATTACCGAAATACCCCTGTAGGGTAG
* * * * *
20475 AATTACCGAGATACTCTTCTAGGGTAA
1 AATTACCGAAATACCCCTGTAGGGTAG
20502 AATTACC
1 AATTACC
20509 ATTTTTCCCC
Statistics
Matches: 197, Mismatches: 26, Indels: 1
0.88 0.12 0.00
Matches are distributed among these distances:
27 190 0.96
28 7 0.04
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.25
Consensus pattern (27 bp):
AATTACCGAAATACCCCTGTAGGGTAG
Found at i:21202 original size:27 final size:26
Alignment explanation
Indices: 21158--21208 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
21148 CTCGCTACAA
*
21158 TCTGGTGGCCTCGCCACATATATCTGT
1 TCTGGTGACCTCGCCACA-ATATCTGT
* *
21185 TCTGGTGACTTCGTCACAATATCT
1 TCTGGTGACCTCGCCACAATATCT
21209 AGTAGCCTCT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 6 0.29
27 15 0.71
ACGTcount: A:0.18, C:0.27, G:0.20, T:0.35
Consensus pattern (26 bp):
TCTGGTGACCTCGCCACAATATCTGT
Done.