Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2157
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: 40417
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:6083 original size:40 final size:40
Alignment explanation
Indices: 6039--6224 Score: 225
Period size: 40 Copynumber: 4.7 Consensus size: 40
6029 GCTCCTCGTT
* *
6039 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCACA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCACA
* *
6079 CAAATGCCTTCGGGACTTAACCCGGATTTTGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCACA
*
6119 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCACA
* * * * *
6159 CAAATGCCTTC-GGATCTTAATCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAACTCA-CA
*
6200 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
6225 CATCATTCAA
Statistics
Matches: 129, Mismatches: 13, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
39 3 0.02
40 115 0.89
41 11 0.09
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCACA
Found at i:6153 original size:80 final size:82
Alignment explanation
Indices: 6039--6224 Score: 256
Period size: 80 Copynumber: 2.3 Consensus size: 82
6029 GCTCCTCGTT
*
6039 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCACACAAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGATTATAGTAACTCACACAAATGCCTTC-GGATCTTAACCC
* * *
6102 GGATTTTGTAAC-TCGCA
65 GGATATGGTAACTTAGCA
* * *
6119 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCACAAATGCCTTCGGATCTTAATCCG
1 CAAATGCCTTCGGGACTTAGCCCGGATTATAGTAACTCACACAAATGCCTTCGGATCTTAACCCG
*
6183 GATATGGTCACTTAGCA
66 GATATGGTAACTTAGCA
6200 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
6225 CATCATTCAA
Statistics
Matches: 94, Mismatches: 9, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
79 3 0.03
80 81 0.86
81 10 0.11
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTATAGTAACTCACACAAATGCCTTCGGATCTTAACCCG
GATATGGTAACTTAGCA
Found at i:15191 original size:46 final size:47
Alignment explanation
Indices: 15116--15289 Score: 171
Period size: 46 Copynumber: 3.7 Consensus size: 47
15106 TGTAACCCGC
* **
15116 CCATAAGCGAACTCAAACTCAACTCAACGAGCTCGAG-C-GTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGAGACAGTT-GCAT
* * * *
15162 CCATGAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTC-GA-GAC-AGTTGCAT
* * * *
15212 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTC-AGACAATTGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGAGACAGTTGCAT
15255 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCG
15290 GATGCTCAAC
Statistics
Matches: 105, Mismatches: 14, Indels: 17
0.77 0.10 0.12
Matches are distributed among these distances:
43 6 0.06
44 3 0.03
45 3 0.03
46 54 0.51
47 28 0.27
48 3 0.03
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.31, C:0.30, G:0.19, T:0.20
Consensus pattern (47 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGAGACAGTTGCAT
Found at i:15282 original size:93 final size:93
Alignment explanation
Indices: 15123--15294 Score: 258
Period size: 93 Copynumber: 1.8 Consensus size: 93
15113 CGCCCATAAG
* *
15123 CGAACTCAAACTCAACTCAACGAGCTCGAGCGTTCGCATCCATGAGTGAACTCGGACTCAACTCA
1 CGAACTCAAACTCAACTCAACGAGCTCGAGCATTCGCATCCATAAGTGAACTCGGACTCAACTCA
*
15188 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGCTCGGATGCCTAGTTACATCTCA
** *
15216 CGAACTCGGACTCAACTCAACGAGTTC-AGACAATT-GCATCCATAAGTGAACTCGGACTCAACT
1 CGAACTCAAACTCAACTCAACGAGCTCGAG-C-ATTCGCATCCATAAGTGAACTCGGACTCAACT
15279 CAACGAGCTCGGATGC
64 CAACGAGCTCGGATGC
15295 TCAACCATCC
Statistics
Matches: 71, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
92 2 0.03
93 67 0.94
94 2 0.03
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (93 bp):
CGAACTCAAACTCAACTCAACGAGCTCGAGCATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGCTCGGATGCCTAGTTACATCTCA
Found at i:15310 original size:46 final size:45
Alignment explanation
Indices: 15167--15310 Score: 120
Period size: 46 Copynumber: 3.1 Consensus size: 45
15157 CGCATCCATG
*
15167 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT-CTC
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCC-A---ACATCCTA
* *
15215 A-CGAACTCGGACTCAACTCAACGAGTTC--A-GACAATTGCATCCATA
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCAA---CATCC-TA
*
15260 AGTGAACTCGGACTCAACTCAACGAGCTCGGATGCTCAACCATCCT-
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGC-CAA-CATCCTA
15306 AGTGA
1 AGTGA
15311 CATGTCACTT
Statistics
Matches: 79, Mismatches: 7, Indels: 22
0.73 0.06 0.20
Matches are distributed among these distances:
40 1 0.01
43 4 0.05
44 3 0.04
45 3 0.04
46 30 0.38
47 27 0.34
48 7 0.09
49 1 0.01
50 3 0.04
ACGTcount: A:0.31, C:0.28, G:0.19, T:0.22
Consensus pattern (45 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCAACATCCTA
Found at i:18861 original size:40 final size:40
Alignment explanation
Indices: 18760--18979 Score: 248
Period size: 40 Copynumber: 5.5 Consensus size: 40
18750 TATTCGAATG
* * *
18760 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGTGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGC-GAGTGACT
* * *
18801 ATATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGACT
* * * *
18841 ATATCCGGGCCAAAACCCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGACT
* * * *
18881 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGACT
* **
18921 ATATCCGGGCTAAGACCCGAAGGC-CTTGTGCGAGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGACT
*
18960 ATATCC-GGCTAA-ATCCGAAG
1 ATATCCGGGCTAAGACCCGAAG
18980 ATACTTGGGT
Statistics
Matches: 152, Mismatches: 27, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
37 7 0.05
38 6 0.04
39 15 0.10
40 96 0.63
41 28 0.18
ACGTcount: A:0.25, C:0.24, G:0.26, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGACT
Found at i:27599 original size:15 final size:15
Alignment explanation
Indices: 27577--27637 Score: 79
Period size: 15 Copynumber: 4.1 Consensus size: 15
27567 AGGAAACCGA
27577 AAAGAAATCCAAGAT
1 AAAGAAATCCAAGAT
*
27592 AGAGAAATCC-AGAAT
1 AAAGAAATCCAAG-AT
*
27607 AAAGAAATCCAAAAT
1 AAAGAAATCCAAGAT
*
27622 AAAGAAACCCAAGAT
1 AAAGAAATCCAAGAT
27637 A
1 A
27638 CGATACTATG
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
14 2 0.05
15 36 0.92
16 1 0.03
ACGTcount: A:0.61, C:0.15, G:0.13, T:0.11
Consensus pattern (15 bp):
AAAGAAATCCAAGAT
Found at i:30398 original size:45 final size:45
Alignment explanation
Indices: 30234--30407 Score: 194
Period size: 45 Copynumber: 3.8 Consensus size: 45
30224 TGTAACCCGC
* * *
30234 CCATAAGCGAACTC-GACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATT-GCAT
* * *
30279 CCATGAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTGCAT
*
30329 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTGCAT
*
30371 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
30408 TGCTCAACCA
Statistics
Matches: 109, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
42 5 0.05
43 2 0.02
44 3 0.03
45 41 0.38
46 20 0.18
47 29 0.27
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (45 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTGCAT
Found at i:30398 original size:92 final size:92
Alignment explanation
Indices: 30241--30410 Score: 288
Period size: 92 Copynumber: 1.8 Consensus size: 92
30231 CGCCCATAAG
* * *
30241 CGAACTCGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATGAGTGAACTCGGACTCAACTCAA
1 CGAACTCGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
30306 CGAGTTCGGATGCCTAGTTACATCTCA
66 CGAGTTCGGATGCCTAGTTACATCTCA
*
30333 CGAACTCGGACTCAACTCAACGAGTTCGGACATT-GCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTC-GACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
30397 ACGAGTTCGGATGC
65 ACGAGTTCGGATGC
30411 TCAACCATCC
Statistics
Matches: 73, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
92 50 0.68
93 23 0.32
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (92 bp):
CGAACTCGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCA
Found at i:33175 original size:46 final size:46
Alignment explanation
Indices: 33012--33184 Score: 196
Period size: 46 Copynumber: 3.8 Consensus size: 46
33002 GGTTGAGCAT
*
33012 CCGAACTCGTTGAGTTGAGT-CGAGTTCACTTATGGATGCGAATG-
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
* * * * *
33056 TCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--AATG-TAACTAGGC
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC---GC
33101 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 --CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
*
33149 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
33185 GCGGGTTACA
Statistics
Matches: 106, Mismatches: 12, Indels: 20
0.77 0.09 0.14
Matches are distributed among these distances:
41 2 0.02
42 3 0.03
44 22 0.21
45 7 0.07
46 35 0.33
47 27 0.25
48 4 0.04
50 3 0.03
51 3 0.03
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (46 bp):
CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
Done.