Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3079
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: 27141
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Found at i:6903 original size:39 final size:39
Alignment explanation
Indices: 6867--7057 Score: 215
Period size: 39 Copynumber: 4.8 Consensus size: 39
6857 GGATATAGCT
* *
6867 ACTCGCTCAAATGCCTTCGGACATAGCCCGGTTATAGTA
1 ACTCGCACAAATGCCTTCGGACTTAGCCCGGTTATAGTA
*
6906 ACTCGCACAAATGCCTTCGGGACTTAACCCGGATT-TAGTA
1 ACTCGCACAAATGCCTTC-GGACTTAGCCCGG-TTATAGTA
* * *
6946 ACTCGCACCAATGCCTTCGGGCTTAGCCCGG-AATTAGTA
1 ACTCGCACAAATGCCTTCGGACTTAGCCCGGTTA-TAGTA
* * *
6985 ACTCGCACAAATGCCTTCGGATCTTAGTCCGGATATAGTC
1 ACTCGCACAAATGCCTTCGGA-CTTAGCCCGGTTATAGTA
* *
7025 ACTTAGCACAAAAGCCTTCGGGACTTAGCCCGG
1 AC-TCGCACAAATGCCTTC-GGACTTAGCCCGG
7058 ATATCATTCG
Statistics
Matches: 129, Mismatches: 15, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
39 52 0.40
40 48 0.37
41 26 0.20
42 3 0.02
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (39 bp):
ACTCGCACAAATGCCTTCGGACTTAGCCCGGTTATAGTA
Found at i:6948 original size:40 final size:40
Alignment explanation
Indices: 6867--7059 Score: 241
Period size: 40 Copynumber: 4.8 Consensus size: 40
6857 GGATATAGCT
* *
6867 ACTCGCTCAAATGCCTTC-GGACATAGCCCGG-TTATAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATT-TAGTA
*
6906 ACTCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
* *
6946 ACTCGCACCAATGCCTTCGGG-CTTAGCCCGGAATTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
* * *
6985 ACTCGCACAAATGCCTTC-GGATCTTAGTCCGGATATAGTC
1 ACTCGCACAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTA
* *
7025 ACTTAGCACAAAAGCCTTCGGGACTTAGCCCGGAT
1 AC-TCGCACAAATGCCTTCGGGACTTAGCCCGGAT
7060 ATCATTCGAA
Statistics
Matches: 134, Mismatches: 14, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
38 2 0.01
39 50 0.37
40 52 0.39
41 27 0.20
42 3 0.02
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
Found at i:6973 original size:79 final size:77
Alignment explanation
Indices: 6841--7058 Score: 242
Period size: 79 Copynumber: 2.7 Consensus size: 77
6831 GAATCACATA
* * * * * *
6841 CCTTCGGAATTTAACCGGATATAGCTACTCGCTCAAATGCCTTCGGACATAGCCCGG-TTATAGT
1 CCTTCGGGACTTAACCGGATATAG-TACTCGCACAAATGCCTTCGGGCTTAGCCCGGAAT-TAGT
6905 AACTCGCACAAATG
64 AACTCGCACAAATG
* *
6919 CCTTCGGGACTTAACCCGGATTTAGTAACTCGCACCAATGCCTTCGGGCTTAGCCCGGAATTAGT
1 CCTTCGGGACTTAA-CCGGATATAGT-ACTCGCACAAATGCCTTCGGGCTTAGCCCGGAATTAGT
6984 AACTCGCACAAATG
64 AACTCGCACAAATG
* * *
6998 CCTTC-GGATCTTAGTCCGGATATAGTCACTTAGCACAAAAGCCTTCGGGACTTAGCCCGGA
1 CCTTCGGGA-CTTA-ACCGGATATAGT-AC-TCGCACAAATGCCTTCGGG-CTTAGCCCGGA
7059 TATCATTCGA
Statistics
Matches: 119, Mismatches: 14, Indels: 11
0.83 0.10 0.08
Matches are distributed among these distances:
78 16 0.13
79 75 0.63
80 17 0.14
81 11 0.09
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (77 bp):
CCTTCGGGACTTAACCGGATATAGTACTCGCACAAATGCCTTCGGGCTTAGCCCGGAATTAGTAA
CTCGCACAAATG
Found at i:12329 original size:68 final size:64
Alignment explanation
Indices: 12122--12338 Score: 172
Period size: 68 Copynumber: 3.3 Consensus size: 64
12112 TAGTACCACC
* * * * * *
12122 CATGTGACCTAGC--CAGTTTATCTCGTAGCTCTCTTGTCTACATGGTGTCCTTCACCTGGAACC
1 CATGTGACCTAGCTACA-TATATCCCGTAGCTCTCTTGTCTACATGATG---TACACATAGAACC
*
12185 ATG
62 ATA
* * * * **
12188 CATGTGACCTAGCTACATATATCCCGTAGCTCTCTTGTCTATATGGTGTACACATAGTATCACC
1 CATGTGACCTAGCTACATATATCCCGTAGCTCTCTTGTCTACATGATGTACACATAGAACCATA
* * *
12252 CATGCGACCTAGCTACATCATAATGTCTCGTAGCTCTCTTGTAC-ACATGATGTGCAC-TCAGAA
1 CATGTGACCTAGCTACAT-AT-A--TCCCGTAGCTCTCTTGT-CTACATGATGTACACAT-AGAA
12315 CCATA
60 CCATA
12320 CATGTGACCTAGCTACATA
1 CATGTGACCTAGCTACATA
12339 CCATCTGTAT
Statistics
Matches: 123, Mismatches: 20, Indels: 15
0.78 0.13 0.09
Matches are distributed among these distances:
64 26 0.21
65 2 0.02
66 14 0.11
67 30 0.24
68 50 0.41
69 1 0.01
ACGTcount: A:0.24, C:0.28, G:0.17, T:0.31
Consensus pattern (64 bp):
CATGTGACCTAGCTACATATATCCCGTAGCTCTCTTGTCTACATGATGTACACATAGAACCATA
Found at i:16373 original size:7 final size:7
Alignment explanation
Indices: 16361--16386 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
16351 TCAGTTTTAT
16361 TTATTTC
1 TTATTTC
16368 TTATTTC
1 TTATTTC
16375 TTATTTC
1 TTATTTC
16382 TTATT
1 TTATT
16387 CCATTTTAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.12, G:0.00, T:0.73
Consensus pattern (7 bp):
TTATTTC
Found at i:18606 original size:19 final size:19
Alignment explanation
Indices: 18569--18606 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
18559 TAGGTCGTTT
*
18569 TGGGCCTCAATGGGCCGTG
1 TGGGCCTCAATAGGCCGTG
18588 TGGGCC-CAATAGGCTCGTG
1 TGGGCCTCAATAGGC-CGTG
18607 GGCCCACACG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.13, C:0.26, G:0.39, T:0.21
Consensus pattern (19 bp):
TGGGCCTCAATAGGCCGTG
Found at i:18931 original size:27 final size:27
Alignment explanation
Indices: 18828--18933 Score: 115
Period size: 27 Copynumber: 3.9 Consensus size: 27
18818 AGACCCCAAT
** **
18828 TTGTAAAATTACTAAAATACCC-CCGA
1 TTGTAAAATTACCGAAATACCCTTAGA
*
18854 TTCGTAAAATTACCGAAATACCCCTAGA
1 TT-GTAAAATTACCGAAATACCCTTAGA
* *
18882 TTGTAAAATTATCGAAATACCCTTAGT
1 TTGTAAAATTACCGAAATACCCTTAGA
* *
18909 TTGTAAAATTACCAAAATGCCCTTA
1 TTGTAAAATTACCGAAATACCCTTA
18934 TAGTGTATGT
Statistics
Matches: 68, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
26 2 0.03
27 62 0.91
28 4 0.06
ACGTcount: A:0.40, C:0.21, G:0.09, T:0.30
Consensus pattern (27 bp):
TTGTAAAATTACCGAAATACCCTTAGA
Found at i:20203 original size:25 final size:25
Alignment explanation
Indices: 20174--20223 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
20164 ACCACCTGAA
*
20174 TCGGGGAATCAGCACTTAGCAACCC
1 TCGGGGAATCAGCACATAGCAACCC
20199 TCGGGGAATCAGCACATAGCAACCC
1 TCGGGGAATCAGCACATAGCAACCC
20224 CCTTTCATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.30, C:0.32, G:0.24, T:0.14
Consensus pattern (25 bp):
TCGGGGAATCAGCACATAGCAACCC
Found at i:20305 original size:26 final size:27
Alignment explanation
Indices: 20253--20321 Score: 97
Period size: 26 Copynumber: 2.6 Consensus size: 27
20243 GGTGGATATC
20253 GCACTTAGC-ACCACCAATCGGGGAATCA
1 GCACTTAGCAACC-CC-ATCGGGGAATCA
20281 GCACTTAGCAACCCC-TCGGGGAATCA
1 GCACTTAGCAACCCCATCGGGGAATCA
*
20307 GCACATAGCAACCCC
1 GCACTTAGCAACCCC
20322 CTTTCACATT
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
26 25 0.64
28 11 0.28
29 3 0.08
ACGTcount: A:0.30, C:0.36, G:0.20, T:0.13
Consensus pattern (27 bp):
GCACTTAGCAACCCCATCGGGGAATCA
Found at i:20403 original size:26 final size:26
Alignment explanation
Indices: 20373--20423 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
20363 CACCAATGAA
*
20373 CGGGGAATCAGCACTTAGCAACCCCT
1 CGGGGAATCAGCACATAGCAACCCCT
20399 CGGGGAATCAGCACATAGCAACCCC
1 CGGGGAATCAGCACATAGCAACCCC
20424 CTTTCACATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.29, C:0.35, G:0.24, T:0.12
Consensus pattern (26 bp):
CGGGGAATCAGCACATAGCAACCCCT
Found at i:20409 original size:102 final size:102
Alignment explanation
Indices: 20144--20500 Score: 588
Period size: 102 Copynumber: 3.6 Consensus size: 102
20134 TAACCGTTAT
*
20144 TGGTGGATCTCGCACTTAGCACCACC-TGAATCGGGGAATCAGCACTTAGCAA-CCCTCGGGGAA
1 TGGTGGATATCGCACTTAGCACCACCATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGAA
20207 TCAGCACATAGCAACCCCCTTT--CATTTCAAAGATA
66 TCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
20242 TGGTGGATATCGCACTTAGCACCACC---AATCGGGGAATCAGCACTTAGCAACCCCTCGGGGAA
1 TGGTGGATATCGCACTTAGCACCACCATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGAA
20304 TCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
66 TCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
20341 TGGTGGATATCGCACTTAGCACCACCAATGAA-CGGGGAATCAGCACTTAGCAACCCCTCGGGGA
1 TGGTGGATATCGCACTTAGCACCACC-ATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGA
20405 ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
65 ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
* * **
20443 TGGTGGATCA-CGCACATAGCACCACCATAAATCGGGGAATCAGCACACAGCAACCCCT
1 TGGTGGAT-ATCGCACTTAGCACCACCATGAATCGGGGAATCAGCACTTAGCAACCCCT
20501 TTATATACAA
Statistics
Matches: 245, Mismatches: 5, Indels: 14
0.93 0.02 0.05
Matches are distributed among these distances:
96 24 0.10
97 33 0.13
98 25 0.10
99 39 0.16
101 4 0.02
102 117 0.48
103 3 0.01
ACGTcount: A:0.31, C:0.30, G:0.20, T:0.19
Consensus pattern (102 bp):
TGGTGGATATCGCACTTAGCACCACCATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGAA
TCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
Found at i:20857 original size:29 final size:29
Alignment explanation
Indices: 20824--20887 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
20814 TAATCCACCA
20824 CCCAACTTTTTG-AAAATTACAATTTTGCC
1 CCCAAC-TTTTGCAAAATTACAATTTTGCC
* * *
20853 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGCAAAATTACAATTTTGCC
20883 CCCAA
1 CCCAA
20888 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (29 bp):
CCCAACTTTTGCAAAATTACAATTTTGCC
Found at i:20861 original size:30 final size:30
Alignment explanation
Indices: 20831--20887 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
20821 CCACCCAACT
20831 TTTTG-AAAATTACAATTTTGCCCCCAAAC
1 TTTTGCAAAATTACAATTTTGCCCCCAAAC
* * *
20860 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGCCCCCAA
20888 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTGCCCCCAAAC
Done.