Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2908
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: 30285
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:145 original size:13 final size:13
Alignment explanation
Indices: 108--165 Score: 55
Period size: 13 Copynumber: 4.3 Consensus size: 13
98 GAAAAGTAGA
108 GAAAAAAGAAAA-T
1 GAAAAAA-AAAATT
121 GAAGAAAGAAAAATT
1 GAA-AAA-AAAAATT
**
136 GAAAAAAAAAAGC
1 GAAAAAAAAAATT
*
149 GAAAAAAGAAATT
1 GAAAAAAAAAATT
162 GAAA
1 GAAA
166 GAGAGCTTGA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
13 22 0.59
14 10 0.27
15 5 0.14
ACGTcount: A:0.72, C:0.02, G:0.17, T:0.09
Consensus pattern (13 bp):
GAAAAAAAAAATT
Found at i:199 original size:33 final size:32
Alignment explanation
Indices: 162--223 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 32
152 AAAAGAAATT
162 GAAAGAGAG-CT-TGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTGT-AAAAGAAA-C-AGTGAAAAA
195 GAAAGAGAGTCTGTAAAAGAAACAGTGAA
1 GAAAGAGAGTCTGTAAAAGAAACAGTGAA
224 GTGAGTAATC
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
32 6 0.22
33 10 0.37
34 10 0.37
35 1 0.04
ACGTcount: A:0.55, C:0.06, G:0.26, T:0.13
Consensus pattern (32 bp):
GAAAGAGAGTCTGTAAAAGAAACAGTGAAAAA
Found at i:1982 original size:20 final size:20
Alignment explanation
Indices: 1959--2012 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
1949 AGTTTTTCCC
*
1959 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
1979 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
1999 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
2013 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:1994 original size:30 final size:30
Alignment explanation
Indices: 1959--2032 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
1949 AGTTTTTCCC
1959 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
1989 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
2019 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
2033 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:2022 original size:20 final size:20
Alignment explanation
Indices: 1959--2023 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
1949 AGTTTTTCCC
* * * *
1959 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
1979 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
1998 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
2019 AGCTC
1 AGCTC
2024 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:7276 original size:13 final size:13
Alignment explanation
Indices: 7258--7286 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
7248 AATAGTTGTG
7258 TGTTATTTAATTA
1 TGTTATTTAATTA
7271 TGTTATTTAATTA
1 TGTTATTTAATTA
7284 TGT
1 TGT
7287 AGGTTAGCCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.28, C:0.00, G:0.10, T:0.62
Consensus pattern (13 bp):
TGTTATTTAATTA
Found at i:9315 original size:13 final size:13
Alignment explanation
Indices: 9297--9322 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
9287 ACCTGAAAGC
9297 AATTTAATTCATA
1 AATTTAATTCATA
9310 AATTTAATTCATA
1 AATTTAATTCATA
9323 TTAGGACACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (13 bp):
AATTTAATTCATA
Found at i:16395 original size:30 final size:31
Alignment explanation
Indices: 16361--16457 Score: 101
Period size: 30 Copynumber: 3.2 Consensus size: 31
16351 AGCTCACTCC
*
16361 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* * * * *
16391 TAGCTCAAC-TTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* *
16421 CAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
16451 TAGCTCA
1 TAGCTCA
16458 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
30 47 0.92
31 4 0.08
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (31 bp):
TAGCTCAACTTTCAGCTCACGAGCTAAACCT
Found at i:18194 original size:21 final size:20
Alignment explanation
Indices: 18158--18207 Score: 73
Period size: 21 Copynumber: 2.5 Consensus size: 20
18148 ATCAGCTCAC
*
18158 TTGAGCTCATTTTAGCTCGT
1 TTGAGCTCAATTTAGCTCGT
18178 TTGAGCTCGAATTTAGCTCGT
1 TTGAGCTC-AATTTAGCTCGT
*
18199 TTCAGCTCA
1 TTGAGCTCA
18208 TTCCTTTTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 9 0.33
21 18 0.67
ACGTcount: A:0.18, C:0.22, G:0.20, T:0.40
Consensus pattern (20 bp):
TTGAGCTCAATTTAGCTCGT
Found at i:18446 original size:13 final size:13
Alignment explanation
Indices: 18428--18456 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
18418 AATAGTTGTG
18428 TGTTATTTAATTA
1 TGTTATTTAATTA
18441 TGTTATTTAATTA
1 TGTTATTTAATTA
18454 TGT
1 TGT
18457 AGGTTAGTCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.28, C:0.00, G:0.10, T:0.62
Consensus pattern (13 bp):
TGTTATTTAATTA
Found at i:18518 original size:16 final size:17
Alignment explanation
Indices: 18499--18532 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
18489 CATTTAATGC
18499 AATGTGCA-TGAACGGG
1 AATGTGCATTGAACGGG
*
18515 AATGTTCATTGAACGGG
1 AATGTGCATTGAACGGG
18532 A
1 A
18533 GGATACATGC
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:0.32, C:0.12, G:0.32, T:0.24
Consensus pattern (17 bp):
AATGTGCATTGAACGGG
Found at i:20904 original size:68 final size:67
Alignment explanation
Indices: 20832--20981 Score: 171
Period size: 67 Copynumber: 2.2 Consensus size: 67
20822 CATCATGTGT
* * * *
20832 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACC
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACC
20894 ATGTAG
62 ATGTAG
** * *
20900 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
20965 AG
66 AG
20967 ACAAGAGAGCTACGA
1 ACAAGAGAGCTACGA
20982 GATAAACTGG
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
64 20 0.29
65 7 0.10
66 4 0.06
67 26 0.37
68 13 0.19
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (67 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
AG
Found at i:20937 original size:64 final size:64
Alignment explanation
Indices: 20856--21039 Score: 185
Period size: 67 Copynumber: 2.8 Consensus size: 64
20846 AGACATTATG
* *
20856 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * * *
20920 ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
20985 AA
63 AA
* * * * *
20987 ACTG--GCTAAGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGAGAGC
21040 CGAACTATAT
Statistics
Matches: 97, Mismatches: 18, Indels: 11
0.77 0.14 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.20
64 21 0.22
65 8 0.08
66 15 0.15
67 31 0.32
68 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.29, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:23694 original size:30 final size:30
Alignment explanation
Indices: 23660--23757 Score: 90
Period size: 30 Copynumber: 3.3 Consensus size: 30
23650 AGCTCACTCC
23660 TAGCTCATATTCAGCTCACGAGCTAAACCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
** * * * * *
23690 TAGCTCAGCTTCAGCTTAGGAGTTTAATCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
* * *
23720 CAGCTCA-ACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
23750 TAGCTCAT
1 TAGCTCAT
23758 TTTAGTTTAA
Statistics
Matches: 50, Mismatches: 16, Indels: 3
0.72 0.23 0.04
Matches are distributed among these distances:
30 50 1.00
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.30
Consensus pattern (30 bp):
TAGCTCATATTCAGCTCACGAGCTAAACCT
Found at i:25446 original size:42 final size:42
Alignment explanation
Indices: 25400--25481 Score: 101
Period size: 42 Copynumber: 2.0 Consensus size: 42
25390 CAATATAGTA
* * **
25400 CAAAAAAAAGTTATACAAGTCAAAAAAATTTGAAAAAAAATT
1 CAAAAAAAAGTTAGAAAAGAAAAAAAAATTTGAAAAAAAATT
* * *
25442 CAAAAAATATTTCGAAAAGAAAAAAAAATTTGAAAAAAAA
1 CAAAAAAAAGTTAGAAAAGAAAAAAAAATTTGAAAAAAAA
25482 GTGTTTAATG
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
42 33 1.00
ACGTcount: A:0.67, C:0.06, G:0.07, T:0.20
Consensus pattern (42 bp):
CAAAAAAAAGTTAGAAAAGAAAAAAAAATTTGAAAAAAAATT
Found at i:25476 original size:18 final size:18
Alignment explanation
Indices: 25443--25481 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
25433 AAAAAAATTC
*
25443 AAAAAATATTTCGAAAAGA
1 AAAAAAAATTTCGAAAA-A
25462 AAAAAAAATTT-GAAAAA
1 AAAAAAAATTTCGAAAAA
25479 AAA
1 AAA
25482 GTGTTTAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 4 0.21
18 5 0.26
19 10 0.53
ACGTcount: A:0.72, C:0.03, G:0.08, T:0.18
Consensus pattern (18 bp):
AAAAAAAATTTCGAAAAA
Found at i:27504 original size:46 final size:46
Alignment explanation
Indices: 27350--27511 Score: 181
Period size: 46 Copynumber: 3.5 Consensus size: 46
27340 GGGTTGTGCG
* * *
27350 CGGAC-CAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACT
1 CGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACT
* * * *
27395 CGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT--TTCA-CGAACT
1 CGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCATCCATAAGTGAACT
27442 CGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACT
1 CGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACT
27488 CGGACTCAACTCAACGAGTTCGGA
1 CGGACTCAACTCAACGAGTTCGGA
27512 TGCTCAACCA
Statistics
Matches: 96, Mismatches: 11, Indels: 19
0.76 0.09 0.15
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 1 0.01
45 7 0.07
46 45 0.47
47 29 0.30
48 2 0.02
49 1 0.01
50 3 0.03
51 2 0.02
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (46 bp):
CGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACT
Found at i:27967 original size:29 final size:30
Alignment explanation
Indices: 27935--27993 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
27925 ATTTAATACG
27935 AACTTTGGAAAAATTACACTTTT-CCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
27964 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
27994 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 20 0.77
30 6 0.23
ACGTcount: A:0.31, C:0.25, G:0.07, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Done.