Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_1156
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: 35737
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.33
Found at i:229 original size:34 final size:34
Alignment explanation
Indices: 156--229 Score: 96
Period size: 34 Copynumber: 2.2 Consensus size: 34
146 TGCATATCTA
*
156 TTACTGTTACTGAATTGGGCTAAGACCCACACTG
1 TTACTGATACTGAATTGGGCTAAGACCCACACTG
* * *
190 ATACTGATACTGTATTGGGCTAAGGCCCTA-ACTG
1 TTACTGATACTGAATTGGGCTAAGACCC-ACACTG
224 TTACTG
1 TTACTG
230 GACTGTTACT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
34 33 0.97
35 1 0.03
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.31
Consensus pattern (34 bp):
TTACTGATACTGAATTGGGCTAAGACCCACACTG
Found at i:2306 original size:40 final size:40
Alignment explanation
Indices: 2262--2341 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
2252 GCACGGGGTG
2262 CCATTGTCTATTGTGTCAGATAGAGATCCAAGATTTACTT
1 CCATTGTCTATTGTGTCAGATAGAGATCCAAGATTTACTT
2302 CCATTGTCTATTGTGTCAGATAGAGATCCAAGATTTACTT
1 CCATTGTCTATTGTGTCAGATAGAGATCCAAGATTTACTT
2342 TGAGATTTTG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (40 bp):
CCATTGTCTATTGTGTCAGATAGAGATCCAAGATTTACTT
Found at i:6435 original size:40 final size:40
Alignment explanation
Indices: 6334--6443 Score: 112
Period size: 40 Copynumber: 2.7 Consensus size: 40
6324 TATTAAATCG
* * * *
6334 AAACTATCTCAATATTGCACACTTAGTGCCATATATAGCCG
1 AAACTATTTCAA-ATCGCACACTTAGTGCTATATATAGCCC
** * * * * *
6375 AAGGTATTCCAATTCACACACTTACTGCTATTTATAGCCC
1 AAACTATTTCAAATCGCACACTTAGTGCTATATATAGCCC
6415 AAACTATTTCAAATCGCACACTTAGTGCT
1 AAACTATTTCAAATCGCACACTTAGTGCT
6444 GAACATAGTC
Statistics
Matches: 52, Mismatches: 17, Indels: 1
0.74 0.24 0.01
Matches are distributed among these distances:
40 44 0.85
41 8 0.15
ACGTcount: A:0.33, C:0.25, G:0.11, T:0.31
Consensus pattern (40 bp):
AAACTATTTCAAATCGCACACTTAGTGCTATATATAGCCC
Found at i:9193 original size:93 final size:93
Alignment explanation
Indices: 9080--9251 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
9070 CGCCCATAAG
* *
9080 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
9145 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
9173 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
9238 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
9252 TCAACCATCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:9248 original size:46 final size:46
Alignment explanation
Indices: 9073--9248 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
9063 TGTAACCCGC
* * *
9073 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
9119 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
9169 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
9212 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
9249 TGCTCAACCA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 63 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:16686 original size:46 final size:46
Alignment explanation
Indices: 16619--16839 Score: 299
Period size: 46 Copynumber: 4.8 Consensus size: 46
16609 TGTAACCCGC
* * * * *
16619 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCACAT
16665 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCACAT
* *
16715 -C-TCA-TGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCACAT
16758 CCATAAGTGAACTCGGACTCAA-TCAACGAGTTCGGACATTCACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCACAT
16803 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
16840 TGCTCAACCA
Statistics
Matches: 156, Mismatches: 9, Indels: 20
0.84 0.05 0.11
Matches are distributed among these distances:
42 2 0.01
43 4 0.03
44 2 0.01
45 46 0.29
46 63 0.40
47 30 0.19
48 2 0.01
49 2 0.01
50 3 0.02
51 2 0.01
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCACAT
Found at i:16852 original size:93 final size:94
Alignment explanation
Indices: 16619--16839 Score: 321
Period size: 93 Copynumber: 2.4 Consensus size: 94
16609 TGTAACCCGC
* * *
16619 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCATCCATAAGTGAACTCGGACT
16684 CAACTCAACGAGTTCGGATGCCTAGTTACAT
66 CAACTCAACGAGTTCGGA--CCTAGTTACAT
* *
16715 -C-TCA-TGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCATCCATAAGTGAACTCGGACT
16777 CAA-TCAACGAGTTCGGA-C-A-TTCACAT
66 CAACTCAACGAGTTCGGACCTAGTT-ACAT
16803 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
16840 TGCTCAACCA
Statistics
Matches: 115, Mismatches: 6, Indels: 13
0.86 0.04 0.10
Matches are distributed among these distances:
87 2 0.02
88 5 0.04
89 2 0.02
90 2 0.02
91 30 0.26
92 14 0.12
93 57 0.50
94 2 0.02
95 1 0.01
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.21
Consensus pattern (94 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCATCCATAAGTGAACTCGGACT
CAACTCAACGAGTTCGGACCTAGTTACAT
Found at i:29066 original size:43 final size:43
Alignment explanation
Indices: 28911--29067 Score: 119
Period size: 43 Copynumber: 3.7 Consensus size: 43
28901 ATGTGTTTTT
* * * *
28911 GTGTAAGACCATGCCTGGGACGTTGGCATC-ACT-TATGATTTAT
1 GTGTAAGACCACGTCTGGGACGTTGGCATCGA-TATTTGA-TTAC
* * * * *
28954 GTGTAAGACCA-GATCTGTGATGATGGCATTG-TATTTGATTTC
1 GTGTAAGACCACG-TCTGGGACGTTGGCATCGATATTTGATTAC
*
28996 GTGTAAGACC-CTGTCTGGGATAG-TGGCATCGATATTTGATTAC
1 GTGTAAGACCAC-GTCTGGGA-CGTTGGCATCGATATTTGATTAC
* *
29039 ATGTAAGACCACGTCTGAGACGTTGGCAT
1 GTGTAAGACCACGTCTGGGACGTTGGCAT
29068 TGTACGAGCT
Statistics
Matches: 90, Mismatches: 15, Indels: 18
0.73 0.12 0.15
Matches are distributed among these distances:
42 28 0.31
43 61 0.68
44 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.32
Consensus pattern (43 bp):
GTGTAAGACCACGTCTGGGACGTTGGCATCGATATTTGATTAC
Done.