Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_4704
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: 13801
ACGTcount: A:0.22, C:0.25, G:0.29, T:0.24
Found at i:3404 original size:70 final size:68
Alignment explanation
Indices: 3318--3522 Score: 241
Period size: 70 Copynumber: 3.0 Consensus size: 68
3308 TGGTGGTCGC
*
3318 GGGAGCCTCGG-ACCATCG-GCCT-GCTTGGTCTCGGAGCCTCGGCACCTCGCAACCTAGGCCCT
1 GGGAGCCTCGGCACCATCGCACCTGGCTT-GTCTCGGAGCCTCGGCACCTCGC-ACCTAGG-CCT
3380 GGTCGTG
63 GGT-GTG
* *
3387 GGGAGCCTCGGCACCATCGCACCTGGCTTGT-TCGGAGCCTCGGCACCAC-C-CCTA-GCCTTGT
1 GGGAGCCTCGGCACCATCGCACCTGGCTTGTCTCGGAGCCTCGGCACCTCGCACCTAGGCCTGGT
3448 GT-
66 GTG
3450 GGGAGCC-C-GCACCATCGCACCTGGCCTTGTCGTCGGAGCCTCGGCACCATCGGCACCTAGGCC
1 GGGAGCCTCGGCACCATCGCACCTGG-CTTGTC-TCGGAGCCTCGGCACC-TC-GCACCTAGGCC
3513 TGGTGTG
62 TGGTGTG
3520 GGG
1 GGG
3523 CTGCACCTGG
Statistics
Matches: 119, Mismatches: 5, Indels: 23
0.81 0.03 0.16
Matches are distributed among these distances:
61 16 0.13
62 6 0.05
63 7 0.06
64 18 0.15
65 6 0.05
66 1 0.01
67 5 0.04
68 4 0.03
69 20 0.17
70 27 0.23
71 5 0.04
72 4 0.03
ACGTcount: A:0.12, C:0.37, G:0.33, T:0.19
Consensus pattern (68 bp):
GGGAGCCTCGGCACCATCGCACCTGGCTTGTCTCGGAGCCTCGGCACCTCGCACCTAGGCCTGGT
GTG
Found at i:3575 original size:37 final size:35
Alignment explanation
Indices: 3350--3594 Score: 197
Period size: 32 Copynumber: 7.3 Consensus size: 35
3340 GCTTGGTCTC
*
3350 GGAGCCTCGGCACC-TCGCAACCTAGGCCCTGGTCGTGG
1 GGAG-CTCGGCACCATCGC-ACCTAGG-CCTTGTCGT-G
*
3388 GGAGCCTCGGCACCATCGCACCT-GG-CTTGT--TC
1 GGAG-CTCGGCACCATCGCACCTAGGCCTTGTCGTG
3420 GGAGCCTCGGCACCA-C-C-CCTA-GCCTTGT-GTG
1 GGAG-CTCGGCACCATCGCACCTAGGCCTTGTCGTG
* *
3451 GGAGC-CCGCACCATCGCACCT-GGCCTTGTCGTC
1 GGAGCTCGGCACCATCGCACCTAGGCCTTGTCGTG
*
3484 GGAGCCTCGGCACCATCGGCACCTAGGCCTGGT-GTG
1 GGAG-CTCGGCACCATC-GCACCTAGGCCTTGTCGTG
*
3520 GG-GCT--GCACC-T-GGA-CTAGGCCTTGTCGTG
1 GGAGCTCGGCACCATCGCACCTAGGCCTTGTCGTG
3549 GGAGCTCGGGCACCATCGGCACCTAGGCC-TGTCGTG
1 GGAGCTC-GGCACCATC-GCACCTAGGCCTTGTCGTG
3585 GAGAGCTCGG
1 G-GAGCTCGG
3595 GTCCTCGGCA
Statistics
Matches: 173, Mismatches: 11, Indels: 48
0.75 0.05 0.21
Matches are distributed among these distances:
28 10 0.06
29 18 0.10
30 11 0.06
31 8 0.05
32 30 0.17
33 12 0.07
34 4 0.02
35 14 0.08
36 22 0.13
37 22 0.13
38 18 0.10
39 4 0.02
ACGTcount: A:0.13, C:0.35, G:0.33, T:0.18
Consensus pattern (35 bp):
GGAGCTCGGCACCATCGCACCTAGGCCTTGTCGTG
Found at i:12663 original size:38 final size:40
Alignment explanation
Indices: 12533--12784 Score: 424
Period size: 38 Copynumber: 6.3 Consensus size: 40
12523 CGGATGTCGA
12533 GAGCCTCGGCACCATCGGCAACCTAGGCCTTGGTCGT-CG
1 GAGCCTCGGCACCATCGGCAACCTAGGCCTTGGTCGTGCG
12572 GAGCCTCGGCACCATCGGCAACCTAGGCCTTGGTCGTAGCGG
1 GAGCCTCGGCACCATCGGCAACCTAGGCCTTGGTCGT-GC-G
12614 GAGCCTCGGCACCATCGGCAACCTAGGCCTTGGT-GTG-G
1 GAGCCTCGGCACCATCGGCAACCTAGGCCTTGGTCGTGCG
12652 GAGCCTCGGCACCATCGGCAACCTAGGCCCTTGGTCGTGCG
1 GAGCCTCGGCACCATCGGCAACCTAGG-CCTTGGTCGTGCG
12693 GAGCCTCGGCACCATC-G-AACCTAGGCCTTGGTCGTGCG
1 GAGCCTCGGCACCATCGGCAACCTAGGCCTTGGTCGTGCG
*
12731 GAGCCTCGGCACCATCGGCAACCTAGGCCCCTGGTCGTGCG
1 GAGCCTCGGCACCATCGGCAACCTAGG-CCTTGGTCGTGCG
12772 GAGCCTCGGCACC
1 GAGCCTCGGCACC
12785 GACCTGCCCC
Statistics
Matches: 203, Mismatches: 1, Indels: 16
0.92 0.00 0.07
Matches are distributed among these distances:
38 57 0.28
39 53 0.26
40 13 0.06
41 45 0.22
42 35 0.17
ACGTcount: A:0.15, C:0.36, G:0.32, T:0.17
Consensus pattern (40 bp):
GAGCCTCGGCACCATCGGCAACCTAGGCCTTGGTCGTGCG
Found at i:12664 original size:119 final size:120
Alignment explanation
Indices: 12533--12784 Score: 424
Period size: 119 Copynumber: 2.1 Consensus size: 120
12523 CGGATGTCGA
12533 GAGCCTCGGCACCATCGGCAACCTAGG-CCTTGGTCGT-CGGAGCCTCGGCACCATCGGCAACCT
1 GAGCCTCGGCACCATCGGCAACCTAGGCCCTTGGTCGTGCGGAGCCTCGGCACCATC-G-AACCT
*
12596 AGGCCTTGGTCGTAGCGGGAGCCTCGGCACCATCGGCAACCTAGG-CCTTGGT-GTG-G
64 AGGCCTTGGTCGT-GC-GGAGCCTCGGCACCATCGGCAACCTAGGCCCCTGGTCGTGCG
12652 GAGCCTCGGCACCATCGGCAACCTAGGCCCTTGGTCGTGCGGAGCCTCGGCACCATCGAACCTAG
1 GAGCCTCGGCACCATCGGCAACCTAGGCCCTTGGTCGTGCGGAGCCTCGGCACCATCGAACCTAG
12717 GCCTTGGTCGTGCGGAGCCTCGGCACCATCGGCAACCTAGGCCCCTGGTCGTGCG
66 GCCTTGGTCGTGCGGAGCCTCGGCACCATCGGCAACCTAGGCCCCTGGTCGTGCG
12772 GAGCCTCGGCACC
1 GAGCCTCGGCACC
12785 GACCTGCCCC
Statistics
Matches: 127, Mismatches: 1, Indels: 9
0.93 0.01 0.07
Matches are distributed among these distances:
117 28 0.22
118 8 0.06
119 48 0.38
120 25 0.20
121 18 0.14
ACGTcount: A:0.15, C:0.36, G:0.32, T:0.17
Consensus pattern (120 bp):
GAGCCTCGGCACCATCGGCAACCTAGGCCCTTGGTCGTGCGGAGCCTCGGCACCATCGAACCTAG
GCCTTGGTCGTGCGGAGCCTCGGCACCATCGGCAACCTAGGCCCCTGGTCGTGCG
Found at i:12741 original size:79 final size:80
Alignment explanation
Indices: 12533--12784 Score: 431
Period size: 79 Copynumber: 3.2 Consensus size: 80
12523 CGGATGTCGA
12533 GAGCCTCGGCACCATCGGCAACCTAGGCCTTGGTCGTCGGAGCCTCGGCACCATCGGCAACCTAG
1 GAGCCTCGGCACCATCGGCAACCTAGGCCTTGGTCGTCGGAGCCTCGGCACCATCGGCAACCTAG
12598 G-CCTTGGTCGTAGCGG
66 GCCCTTGGTCGT-GC-G
*
12614 GAGCCTCGGCACCATCGGCAACCTAGGCCTTGGT-GTGGGAGCCTCGGCACCATCGGCAACCTAG
1 GAGCCTCGGCACCATCGGCAACCTAGGCCTTGGTCGTCGGAGCCTCGGCACCATCGGCAACCTAG
12678 GCCCTTGGTCGTGCG
66 GCCCTTGGTCGTGCG
12693 GAGCCTCGGCACCATC-G-AACCTAGGCCTTGGTCGTGCGGAGCCTCGGCACCATCGGCAACCTA
1 GAGCCTCGGCACCATCGGCAACCTAGGCCTTGGTCGT-CGGAGCCTCGGCACCATCGGCAACCTA
*
12756 GGCCCCTGGTCGTGCG
65 GGCCCTTGGTCGTGCG
12772 GAGCCTCGGCACC
1 GAGCCTCGGCACC
12785 GACCTGCCCC
Statistics
Matches: 165, Mismatches: 3, Indels: 8
0.94 0.02 0.05
Matches are distributed among these distances:
77 15 0.09
78 3 0.02
79 71 0.43
80 32 0.19
81 44 0.27
ACGTcount: A:0.15, C:0.36, G:0.32, T:0.17
Consensus pattern (80 bp):
GAGCCTCGGCACCATCGGCAACCTAGGCCTTGGTCGTCGGAGCCTCGGCACCATCGGCAACCTAG
GCCCTTGGTCGTGCG
Found at i:12992 original size:41 final size:41
Alignment explanation
Indices: 12939--13036 Score: 162
Period size: 41 Copynumber: 2.4 Consensus size: 41
12929 CTTGGATGAC
*
12939 AGCC-CGGACACCATCGCAACCTAGGCCCTTGGTCGTGCGGG
1 AGCCTCGG-CACCATCGCAACCTAGGCCCTTGGTCATGCGGG
*
12980 AGCCTCGGCACCATCGTAACCTAGGCCCTTGGTCATGCGGG
1 AGCCTCGGCACCATCGCAACCTAGGCCCTTGGTCATGCGGG
13021 AGCCTCGGCACCATCG
1 AGCCTCGGCACCATCG
13037 GCCCTGCTCG
Statistics
Matches: 54, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
41 51 0.94
42 3 0.06
ACGTcount: A:0.17, C:0.37, G:0.30, T:0.16
Consensus pattern (41 bp):
AGCCTCGGCACCATCGCAACCTAGGCCCTTGGTCATGCGGG
Done.