Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1348
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: 40496
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Found at i:8003 original size:27 final size:27
Alignment explanation
Indices: 7973--8177 Score: 205
Period size: 27 Copynumber: 7.6 Consensus size: 27
7963 ATATTAAGTC
* *
7973 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
*
8000 CGCACACTTAGTGCCACATAATCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
*
8028 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAATCAACT
** ** *
8055 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
** **
8082 CGCACACTTAGTGC-ATCATTTTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* ** *
8109 CGCACACTTAGTGCAACATGGTCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
** *
8136 CGCACACTTAGTGCTACATAGCCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
8163 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
8178 GTACAATTTA
Statistics
Matches: 155, Mismatches: 20, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
27 129 0.83
28 26 0.17
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:8112 original size:54 final size:54
Alignment explanation
Indices: 7973--8176 Score: 257
Period size: 54 Copynumber: 3.8 Consensus size: 54
7963 ATATTAAGTC
* * * **
7973 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCCACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCCACATGGTCAAA-T
* *
8028 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCCACATGGTCAAAT
** ** *
8082 CGCACACTTAGTGC-ATCATTTTCATTTCGCACACTTAGTGCAACATGGTCAAAT
1 CGCACACTTAGTGCTA-CATAGTCAACTCGCACACTTAGTGCCACATGGTCAAAT
* *
8136 CGCACACTTAGTGCTACATAGCCAAATCGCACACTTAGTGC
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGC
8177 TGTACAATTT
Statistics
Matches: 128, Mismatches: 19, Indels: 5
0.84 0.12 0.03
Matches are distributed among these distances:
53 1 0.01
54 80 0.62
55 47 0.37
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.26
Consensus pattern (54 bp):
CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCCACATGGTCAAAT
Found at i:8142 original size:81 final size:81
Alignment explanation
Indices: 8027--8176 Score: 228
Period size: 81 Copynumber: 1.9 Consensus size: 81
8017 ATAATCAAAC
* * * * * *
8027 TCGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCCGCATGGTCAATTCGCACACTTA
1 TCGCACACTTAGTGCAACATAGTCAAATCGCACACTTAGTGCCACATAGCCAAATCGCACACTTA
8092 GTGCATCATTTTCATT
66 GTGCATCATTTTCATT
* *
8108 TCGCACACTTAGTGCAACATGGTCAAATCGCACACTTAGTGCTACATAGCCAAATCGCACACTTA
1 TCGCACACTTAGTGCAACATAGTCAAATCGCACACTTAGTGCCACATAGCCAAATCGCACACTTA
8173 GTGC
66 GTGC
8177 TGTACAATTT
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
81 61 1.00
ACGTcount: A:0.27, C:0.29, G:0.17, T:0.27
Consensus pattern (81 bp):
TCGCACACTTAGTGCAACATAGTCAAATCGCACACTTAGTGCCACATAGCCAAATCGCACACTTA
GTGCATCATTTTCATT
Found at i:12367 original size:93 final size:93
Alignment explanation
Indices: 12241--12412 Score: 274
Period size: 93 Copynumber: 1.8 Consensus size: 93
12231 GCCCATAAGA
* * *
12241 GAACTCGGACTCAACTCAATGAGCTTGGGCGTTCACATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTTGGACGTTCACATCCATAAGTGAACTCAGACTCAACTCAA
12306 CGAGCTCGAATGCCTAGTTACATCTCAT
66 CGAGCTCGAATGCCTAGTTACATCTCAT
* *
12334 GAACTCGGACTCAACTCAACGAG-TTCGGACGTTCGCATTCATAAGTGAACTCAGACTCAACTCA
1 GAACTCGGACTCAACTCAACGAGCTT-GGACGTTCACATCCATAAGTGAACTCAGACTCAACTCA
*
12398 ACGAGCTCGGATGCC
65 ACGAGCTCGAATGCC
12413 CAAATATCCT
Statistics
Matches: 72, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
92 2 0.03
93 70 0.97
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTTGGACGTTCACATCCATAAGTGAACTCAGACTCAACTCAA
CGAGCTCGAATGCCTAGTTACATCTCAT
Found at i:12408 original size:46 final size:45
Alignment explanation
Indices: 12234--12408 Score: 176
Period size: 46 Copynumber: 3.8 Consensus size: 45
12224 GTAACCCGCC
* * * * *
12234 CATAAGAGAACTCGGACTCAACTCAATGAGCTTGGGCGTTCACATC
1 CATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACGTTC-CATT
* *
12280 CATAAGTGAACTCGGACTCAACTCAACGAGCTC-GA-ATGCCTAGTT
1 CATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACGTTCC-A-TT
* *
12325 ACATCTCA-TGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCATT
1 -CA--TAAGTGAACTCGGACTCAACTCAACGAGCTCGGACGTTC-CATT
*
12373 CATAAGTGAACTCAGACTCAACTCAACGAGCTCGGA
1 CATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
12409 TGCCCAAATA
Statistics
Matches: 106, Mismatches: 14, Indels: 18
0.77 0.10 0.13
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 4 0.04
46 60 0.57
47 28 0.26
48 6 0.06
49 3 0.03
50 1 0.01
ACGTcount: A:0.31, C:0.27, G:0.20, T:0.22
Consensus pattern (45 bp):
CATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACGTTCCATT
Found at i:23397 original size:34 final size:34
Alignment explanation
Indices: 23353--23432 Score: 106
Period size: 34 Copynumber: 2.4 Consensus size: 34
23343 ATATGTTAAC
*
23353 GGGCTTAGGCCCAGACTACTACTATTACTGAAAT
1 GGGCTAAGGCCCAGACTACTACTATTACTGAAAT
* * * * *
23387 GGGCTCAGGCCTAGATTGCTACTATTATTGAAAT
1 GGGCTAAGGCCCAGACTACTACTATTACTGAAAT
23421 GGGCTAAGGCCC
1 GGGCTAAGGCCC
23433 TAACTGTTAC
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.26, C:0.23, G:0.25, T:0.26
Consensus pattern (34 bp):
GGGCTAAGGCCCAGACTACTACTATTACTGAAAT
Found at i:35919 original size:39 final size:40
Alignment explanation
Indices: 35876--36137 Score: 291
Period size: 40 Copynumber: 6.6 Consensus size: 40
35866 TCCTCGTTCA
* * * * *
35876 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
35915 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
35955 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
35995 AATGCCTTCGGGACTTAACCCGGATTTAATATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * *
36035 AAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGG-ATTTAATAACTCGCACG
** * * *
36075 AATGCCTTC-GGATCTTAGTCCGGATAT-ATCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
36114 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
36138 CAGCATTCAA
Statistics
Matches: 197, Mismatches: 21, Indels: 10
0.86 0.09 0.04
Matches are distributed among these distances:
39 59 0.30
40 134 0.68
41 4 0.02
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:36079 original size:120 final size:118
Alignment explanation
Indices: 35876--36137 Score: 305
Period size: 119 Copynumber: 2.2 Consensus size: 118
35866 TCCTCGTTCA
* * * *
35876 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACTTAACCCGGATT
1 AATGCCTTCGGGACTTAGCCCGGATTTAATAACTCACACAAGGCCTTCGGGACTTAACCCGGATT
* * *
35941 TAATAACTCGCACGAATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCAC
66 TAATAACTCGCACAAATGCCTTC-GGATCTTAACCCGGATAT-ATAACTTAGCAC
* * * *
35994 GAATGCCTTCGGGACTTAACCCGGATTTAATATCTCGCACAAAGGCCTTCGGGGCTTAACCCGGA
1 -AATGCCTTCGGGACTTAGCCCGGATTTAATAACTCACAC-AAGGCCTTCGGGACTTAACCCGG-
* * ** *
36059 ATTT-GTATCTCGCACAAATGCCTTCGGATCTTAGTCCGGATATATCACTTAGCAC
63 ATTTAATAACTCGCACAAATGCCTTCGGATCTTAACCCGGATATATAACTTAGCAC
*
36114 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
36138 CAGCATTCAA
Statistics
Matches: 121, Mismatches: 18, Indels: 8
0.82 0.12 0.05
Matches are distributed among these distances:
119 62 0.51
120 55 0.45
121 4 0.03
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (118 bp):
AATGCCTTCGGGACTTAGCCCGGATTTAATAACTCACACAAGGCCTTCGGGACTTAACCCGGATT
TAATAACTCGCACAAATGCCTTCGGATCTTAACCCGGATATATAACTTAGCAC
Found at i:38380 original size:13 final size:13
Alignment explanation
Indices: 38362--38388 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
38352 AAGGTAAATA
38362 CGTTCCCATGAAC
1 CGTTCCCATGAAC
38375 CGTTCCCATGAAC
1 CGTTCCCATGAAC
38388 C
1 C
38389 ACTGAACTCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.41, G:0.15, T:0.22
Consensus pattern (13 bp):
CGTTCCCATGAAC
Done.