Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold8059.1
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: 5625
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:114 original size:64 final size:64
Alignment explanation
Indices: 13--141 Score: 249
Period size: 64 Copynumber: 2.0 Consensus size: 64
3 TCAAGGTTAG
13 ATTACATAATTTATTCACTATTTAATTCCATTCCTACTATTTTTAGTGATTTTTTAAAATCCAC
1 ATTACATAATTTATTCACTATTTAATTCCATTCCTACTATTTTTAGTGATTTTTTAAAATCCAC
*
77 ATTACATAATTTATTCACTATTTAATTCCATTCCTACTGTTTTTAGTGATTTTTTAAAATCCAC
1 ATTACATAATTTATTCACTATTTAATTCCATTCCTACTATTTTTAGTGATTTTTTAAAATCCAC
141 A
1 A
142 CCACTGCTGC
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 64 1.00
ACGTcount: A:0.31, C:0.17, G:0.04, T:0.48
Consensus pattern (64 bp):
ATTACATAATTTATTCACTATTTAATTCCATTCCTACTATTTTTAGTGATTTTTTAAAATCCAC
Found at i:859 original size:120 final size:121
Alignment explanation
Indices: 646--885 Score: 446
Period size: 120 Copynumber: 2.0 Consensus size: 121
636 TCATATACAC
*
646 ACATTCTCAAAATCATACCTACTTTACATTACCAACCCTTATATTCATACATAAGAGATCAACTT
1 ACATTCTCAAAATCATACCTACTTCACATTACCAACCCTTATATTCATACATAAGAGATCAACTT
*
711 AACCAAAAGTCGGAAGCTCATTAATCGACTGAGCGAATACTATT-TAAAAGGAATT
66 AACCAAAAGTCGGAAGCTCATTAATCGACTGAGCGAATACTATTCAAAAAGGAATT
*
766 ACATTCTCAAAATCATACCTACTTCACATTACCAACCCTTATATTCGTACATAAGAGATCAACTT
1 ACATTCTCAAAATCATACCTACTTCACATTACCAACCCTTATATTCATACATAAGAGATCAACTT
831 AACCAAAAGTCGGAAGCTCATTAATCGACTGAGCGAATACTATTCAAAAAGGAAT
66 AACCAAAAGTCGGAAGCTCATTAATCGACTGAGCGAATACTATTCAAAAAGGAAT
886 CGTATTAATT
Statistics
Matches: 116, Mismatches: 3, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
120 107 0.92
121 9 0.08
ACGTcount: A:0.40, C:0.23, G:0.10, T:0.27
Consensus pattern (121 bp):
ACATTCTCAAAATCATACCTACTTCACATTACCAACCCTTATATTCATACATAAGAGATCAACTT
AACCAAAAGTCGGAAGCTCATTAATCGACTGAGCGAATACTATTCAAAAAGGAATT
Found at i:1018 original size:40 final size:40
Alignment explanation
Indices: 972--1241 Score: 294
Period size: 40 Copynumber: 6.5 Consensus size: 40
962 CTCGCACAAG
* * * *
972 GCCTTCGGGTCTTAACCCGGATATGGTCACTAGCATAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAAT
* *
1012 GCCTTCGGGACTTAGCCCGGATATAGT-AGTTCGCACAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCA-CTAGCACAAAT
* * *
1052 GTCTTCGGGACTTAGCCCGAATATAGTAACTAGCACAAATGCCTTCGGT
1 GCCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAA---------T
* * *
1101 GCCTTCGGGACTTAGCCCGGATATAGTAACTCGCGCAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAAT
1141 GCCTTCGGGACTTAGCCCGGA-ATTAGTCACTAGCACAAAT
1 GCCTTCGGGACTTAGCCCGGATA-TAGTCACTAGCACAAAT
*
1181 GCCTTCGGGACTTAGCCCAGA-ATTAGTCACTAGCACAAAT
1 GCCTTCGGGACTTAGCCCGGATA-TAGTCACTAGCACAAAT
1221 GCCTTCGGGACTTAGCCCGGA
1 GCCTTCGGGACTTAGCCCGGA
1242 ATTATCATCC
Statistics
Matches: 199, Mismatches: 19, Indels: 24
0.82 0.08 0.10
Matches are distributed among these distances:
39 2 0.01
40 160 0.80
41 1 0.01
49 36 0.18
ACGTcount: A:0.26, C:0.27, G:0.24, T:0.24
Consensus pattern (40 bp):
GCCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAAT
Found at i:1126 original size:49 final size:49
Alignment explanation
Indices: 1054--1148 Score: 163
Period size: 49 Copynumber: 1.9 Consensus size: 49
1044 GCACAAATGT
1054 CTTCGGGACTTAGCCCGAATATAGTAACTAGCACAAATGCCTTCGGTGC
1 CTTCGGGACTTAGCCCGAATATAGTAACTAGCACAAATGCCTTCGGTGC
* * *
1103 CTTCGGGACTTAGCCCGGATATAGTAACTCGCGCAAATGCCTTCGG
1 CTTCGGGACTTAGCCCGAATATAGTAACTAGCACAAATGCCTTCGG
1149 GACTTAGCCC
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
49 43 1.00
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.24
Consensus pattern (49 bp):
CTTCGGGACTTAGCCCGAATATAGTAACTAGCACAAATGCCTTCGGTGC
Found at i:1173 original size:89 final size:89
Alignment explanation
Indices: 1011--1188 Score: 295
Period size: 89 Copynumber: 2.0 Consensus size: 89
1001 CTAGCATAAA
** *
1011 TGCCTTCGGGACTTAGCCCGGATATAGTAGTTCGCACAAATGTCTTCGGGACTTAGCCCGAATAT
1 TGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGAATAT
1076 AGTAACTAGCACAAATGCCTTCGG
66 AGTAACTAGCACAAATGCCTTCGG
*
1100 TGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCGCAAATGCCTTCGGGACTTAGCCCGGAAT-
1 TGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCC-GAATA
*
1164 TAGTCACTAGCACAAATGCCTTCGG
65 TAGTAACTAGCACAAATGCCTTCGG
1189 GACTTAGCCC
Statistics
Matches: 83, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
89 79 0.95
90 4 0.05
ACGTcount: A:0.25, C:0.26, G:0.24, T:0.25
Consensus pattern (89 bp):
TGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGAATAT
AGTAACTAGCACAAATGCCTTCGG
Found at i:1213 original size:129 final size:129
Alignment explanation
Indices: 972--1228 Score: 367
Period size: 129 Copynumber: 2.0 Consensus size: 129
962 CTCGCACAAG
* * * *
972 GCCTTCGGGTCTTAACCCGGATATGGTCACTAGCATAAATGCCTTCGGGACTTAGCCCGGATATA
1 GCCTTCGGGACTTAACCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATA
* * *
1037 GTAGTTCGCACAAATGTCTTCGGGACTTAGCCCGAATATAGTAACTAGCACAAATGCCTTCGGT
66 GTAGCTAGCACAAATGCCTTCGGGACTTAGCCCGAATATAGTAACTAGCACAAATGCCTTCGGT
* * *
1101 GCCTTCGGGACTTAGCCCGGATATAGTAACTCGCGCAAATGCCTTCGGGACTTAGCCCGGA-ATT
1 GCCTTCGGGACTTAACCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATA-T
*
1165 AGTCA-CTAGCACAAATGCCTTCGGGACTTAGCCCAGAAT-TAGTCACTAGCACAAATGCCTTCG
65 AGT-AGCTAGCACAAATGCCTTCGGGACTTAGCCC-GAATATAGTAACTAGCACAAATGCCTTCG
1228 G
128 G
1229 GACTTAGCCC
Statistics
Matches: 114, Mismatches: 11, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
128 1 0.01
129 108 0.95
130 5 0.04
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.25
Consensus pattern (129 bp):
GCCTTCGGGACTTAACCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATA
GTAGCTAGCACAAATGCCTTCGGGACTTAGCCCGAATATAGTAACTAGCACAAATGCCTTCGGT
Found at i:3918 original size:47 final size:47
Alignment explanation
Indices: 3845--3938 Score: 179
Period size: 47 Copynumber: 2.0 Consensus size: 47
3835 GTTCCGGGCT
*
3845 AAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCC
1 AAGTCCCGAAGGCATTTGTGCAAGTTACTATATCCGGGCTAAGTCCC
3892 AAGTCCCGAAGGCATTTGTGCAAGTTACTATATCCGGGCTAAGTCCC
1 AAGTCCCGAAGGCATTTGTGCAAGTTACTATATCCGGGCTAAGTCCC
3939 GAAGGCATTG
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.26
Consensus pattern (47 bp):
AAGTCCCGAAGGCATTTGTGCAAGTTACTATATCCGGGCTAAGTCCC
Found at i:3944 original size:87 final size:88
Alignment explanation
Indices: 3804--3978 Score: 264
Period size: 87 Copynumber: 2.0 Consensus size: 88
3794 TAACCGGGCT
* * *
3804 AAGTCCCAAAGGCATTTTGCGCTAGTGACTAGTTCCGGGCTAAGTCCCGAAGGCATTTGTGCGAG
1 AAGTCCCAAAGGCATTTTGCGCAAGTGACTAGTTCCGGGCTAAGTCCCGAAGGCATTGGTACGAG
3869 TTACTATATCCGGGCTAAGTCCC
66 TTACTATATCCGGGCTAAGTCCC
* * *
3892 AAGTCCCGAAGGCA-TTTGTGCAAGTTACTA-TATCCGGGCTAAGTCCCGAAGGCATTGGTACGA
1 AAGTCCCAAAGGCATTTTGCGCAAGTGACTAGT-TCCGGGCTAAGTCCCGAAGGCATTGGTACGA
*
3955 GTTACTATATCCGGGCTATGTCCC
65 GTTACTATATCCGGGCTAAGTCCC
3979 GAAGGCATTG
Statistics
Matches: 79, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
86 1 0.01
87 65 0.82
88 13 0.16
ACGTcount: A:0.23, C:0.25, G:0.26, T:0.26
Consensus pattern (88 bp):
AAGTCCCAAAGGCATTTTGCGCAAGTGACTAGTTCCGGGCTAAGTCCCGAAGGCATTGGTACGAG
TTACTATATCCGGGCTAAGTCCC
Found at i:3947 original size:40 final size:40
Alignment explanation
Indices: 3892--4021 Score: 167
Period size: 40 Copynumber: 3.3 Consensus size: 40
3882 GCTAAGTCCC
*
3892 AAGTCCCGAAGGCATTTGTGCAAGTTACTATATCCGGGCT
1 AAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCT
* *
3932 AAGTCCCGAAGGCATTGGTACGAGTTACTATATCCGGGCT
1 AAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCT
* * *
3972 ATGTCCCGAAGGCA-TTGAGCGAG-TAGCTATATCC-GGTT
1 AAGTCCCGAAGGCATTTGTGCGAGTTA-CTATATCCGGGCT
*
4010 AAATCCCGAAGG
1 AAGTCCCGAAGG
4022 TACTTGGCTT
Statistics
Matches: 79, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
38 15 0.19
39 14 0.18
40 50 0.63
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
AAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCT
Done.