Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1590
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: 28657
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.25
Found at i:5999 original size:42 final size:43
Alignment explanation
Indices: 5946--6051 Score: 151
Period size: 42 Copynumber: 2.5 Consensus size: 43
5936 GGTGGCTCGA
* *
5946 ATGTGCGGGAGCCTCGAGCACCATCCGCACCTAGGAG-GTCGG
1 ATGTGCGGGAGCCTCGAGCACCATCCGCACCTAGGAGCCTCAG
* * * *
5988 ATGTGCCGGAGCCTCGAGCACCATCTGCACCTTGGTGCCTCAG
1 ATGTGCGGGAGCCTCGAGCACCATCCGCACCTAGGAGCCTCAG
6031 ATGTGCGGGAGCCTCGAGCAC
1 ATGTGCGGGAGCCTCGAGCAC
6052 TATCGATAAC
Statistics
Matches: 56, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
42 33 0.59
43 23 0.41
ACGTcount: A:0.18, C:0.32, G:0.33, T:0.17
Consensus pattern (43 bp):
ATGTGCGGGAGCCTCGAGCACCATCCGCACCTAGGAGCCTCAG
Found at i:6048 original size:43 final size:41
Alignment explanation
Indices: 5929--6051 Score: 147
Period size: 42 Copynumber: 2.9 Consensus size: 41
5919 AGCAGCACCG
*
5929 GCACCCTGGTGGCTCGAATGTGCGGGAGCCTCGAGCACCATCC
1 GCACCTTGGT-GCTCG-ATGTGCGGGAGCCTCGAGCACCATCC
* * * * *
5972 GCACCTAGGAGGTCGGATGTGCCGGAGCCTCGAGCACCATCT
1 GCACCTTGGTGCTC-GATGTGCGGGAGCCTCGAGCACCATCC
6014 GCACCTTGGTGCCTCAGATGTGCGGGAGCCTCGAGCAC
1 GCACCTTGGTG-CTC-GATGTGCGGGAGCCTCGAGCAC
6052 TATCGATAAC
Statistics
Matches: 67, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
42 36 0.54
43 31 0.46
ACGTcount: A:0.17, C:0.33, G:0.33, T:0.17
Consensus pattern (41 bp):
GCACCTTGGTGCTCGATGTGCGGGAGCCTCGAGCACCATCC
Found at i:6618 original size:43 final size:42
Alignment explanation
Indices: 6524--6692 Score: 196
Period size: 42 Copynumber: 4.0 Consensus size: 42
6514 CAAGAGTCTC
* * * *
6524 CGGCACCTTGGTGGCTCCGATATACGGGAGCCTTGAGCACCAT
1 CGGCACCTTGGT-GCTCGGATGTGCGGGAGCCTCGAGCACCAT
*
6567 CGGTACCTTGGTGCTCGGATGTGCGGGAGCCTCG-GCCACCAT
1 CGGCACCTTGGTGCTCGGATGTGCGGGAGCCTCGAG-CACCAT
* * * *
6609 CGGCAACCTTGGTGCTTGGATGTGCGAGAGGCTCGAGCACCAC
1 CGGC-ACCTTGGTGCTCGGATGTGCGGGAGCCTCGAGCACCAT
* * *
6652 CGACACCTTGGTGCTAGGATGTGCGGAAGCCTCGAGCACCA
1 CGGCACCTTGGTGCTCGGATGTGCGGGAGCCTCGAGCACCA
6693 AAGCTAAAGT
Statistics
Matches: 108, Mismatches: 15, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
41 1 0.01
42 60 0.56
43 46 0.43
44 1 0.01
ACGTcount: A:0.18, C:0.30, G:0.33, T:0.20
Consensus pattern (42 bp):
CGGCACCTTGGTGCTCGGATGTGCGGGAGCCTCGAGCACCAT
Found at i:6803 original size:34 final size:33
Alignment explanation
Indices: 6763--6842 Score: 96
Period size: 30 Copynumber: 2.5 Consensus size: 33
6753 TCAGACACAT
6763 GAATGTCAG-CTGGTAGCGTTTCAAAAAAAAAAAA
1 GAATGTC-GCCTGGTAGC-TTTCAAAAAAAAAAAA
**
6797 GAATGTCGCCTGGTAGCTTTC--ATCAAAAAAA
1 GAATGTCGCCTGGTAGCTTTCAAAAAAAAAAAA
6828 -AATGTCGCCTGGTAG
1 GAATGTCGCCTGGTAG
6843 TGTAGCGTAG
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
30 15 0.35
31 8 0.19
33 5 0.12
34 15 0.35
ACGTcount: A:0.38, C:0.16, G:0.23, T:0.24
Consensus pattern (33 bp):
GAATGTCGCCTGGTAGCTTTCAAAAAAAAAAAA
Found at i:12206 original size:24 final size:24
Alignment explanation
Indices: 12178--12251 Score: 78
Period size: 24 Copynumber: 3.1 Consensus size: 24
12168 CCGGTTAGGT
* **
12178 TCCCGGTGGTGCTCCGGTGATCCA
1 TCCCGGCGGTGCTCCGACGATCCA
12202 TCCCGGCGGTGCTCCGACGATCCA
1 TCCCGGCGGTGCTCCGACGATCCA
* * * *
12226 T-CTGGCGGCGCACCGGCGATCCA
1 TCCCGGCGGTGCTCCGACGATCCA
12249 TCC
1 TCC
12252 TGGCATATAG
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
23 19 0.45
24 23 0.55
ACGTcount: A:0.11, C:0.39, G:0.31, T:0.19
Consensus pattern (24 bp):
TCCCGGCGGTGCTCCGACGATCCA
Found at i:12245 original size:23 final size:24
Alignment explanation
Indices: 12191--12255 Score: 78
Period size: 23 Copynumber: 2.8 Consensus size: 24
12181 CGGTGGTGCT
* * * *
12191 CCGGTGATCCATCCCGGCGGTGCT
1 CCGGCGATCCATCCTGGCGGCGCA
*
12215 CCGACGATCCAT-CTGGCGGCGCA
1 CCGGCGATCCATCCTGGCGGCGCA
12238 CCGGCGATCCATCCTGGC
1 CCGGCGATCCATCCTGGC
12256 ATATAGAAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
23 19 0.56
24 15 0.44
ACGTcount: A:0.12, C:0.40, G:0.31, T:0.17
Consensus pattern (24 bp):
CCGGCGATCCATCCTGGCGGCGCA
Found at i:12402 original size:42 final size:42
Alignment explanation
Indices: 12354--13100 Score: 878
Period size: 42 Copynumber: 17.6 Consensus size: 42
12344 CACATGGCAG
*
12354 CATCGGCACCTTGGTGGCTCGGATGTGTGGG-GCCTCGAGCAC
1 CATCGGCACCTTGGT-GCTCGGATGTGCGGGAGCCTCGAGCAC
* *
12396 CATCGGCACCTTGGTGCTTGGATGTGCGAGAGCCTCGAGCAC
1 CATCGGCACCTTGGTGCTCGGATGTGCGGGAGCCTCGAGCAC
* *
12438 CATCGGCACCTTGGTGGCTCGGATGTGCAGGAGCCTCGAGCAG
1 CATCGGCACCTTGGT-GCTCGGATGTGCGGGAGCCTCGAGCAC
* * *
12481 CATCGGCACCTTGGTGCTTGGATGTGCGGGAGCCTCGAGGAG
1 CATCGGCACCTTGGTGCTCGGATGTGCGGGAGCCTCGAGCAC
* ** *
12523 CATCGGCACCTTGGTGCTGGGATGTGTAGGAGCCCCGAGC-C
1 CATCGGCACCTTGGTGCTCGGATGTGCGGGAGCCTCGAGCAC
**
12564 GCATCGGCACCTTGGTGGCTCGGAT-TGCGGGAGCCTCGAGCGG
1 -CATCGGCACCTTGGT-GCTCGGATGTGCGGGAGCCTCGAGCAC
* * * *
12607 CATCGGCACCTTTGTGCTTGGATGTGCGAGAGCCTCGACCAC
1 CATCGGCACCTTGGTGCTCGGATGTGCGGGAGCCTCGAGCAC
* *
12649 CGTCGGCACCTTGGTGGCTCGGATGTGCGGGAGGCTCGAGCAC
1 CATCGGCACCTTGGT-GCTCGGATGTGCGGGAGCCTCGAGCAC
* *
12692 CATCGGCACCTTGGTGCTTGGATGTGCGGGAGCC-CTGACCAC
1 CATCGGCACCTTGGTGCTCGGATGTGCGGGAGCCTC-GAGCAC
* *
12734 CATCGGCACCTTGGTGCTGGGATGTGCGGGAGCCTCGAGCAG
1 CATCGGCACCTTGGTGCTCGGATGTGCGGGAGCCTCGAGCAC
* *
12776 CATCGGCACCTTGGTGCT-GAGATGTGCGGGAGCCTCGACCAG
1 CATCGGCACCTTGGTGCTCG-GATGTGCGGGAGCCTCGAGCAC
** * *
12818 CATCTACACCTTGGTGCCTCGGATGTGCGGGAGCCTTGAGCAG
1 CATCGGCACCTTGGTG-CTCGGATGTGCGGGAGCCTCGAGCAC
* * * * ** *
12861 CATCTGCACATTGGTGCTTGCATGTAAGAGAGCCTC-ATGCAC
1 CATCGGCACCTTGGTGCTCGGATGTGCGGGAGCCTCGA-GCAC
* * *
12903 CATCGACACCTTGGTGCCTCGGATGTGCGAGAGCCTCGAGCAG
1 CATCGGCACCTTGGTG-CTCGGATGTGCGGGAGCCTCGAGCAC
* * *
12946 CATCGGCACCTTGGTGCTGGGATGTGCGGGAGCCTCGACCAG
1 CATCGGCACCTTGGTGCTCGGATGTGCGGGAGCCTCGAGCAC
* * *
12988 CATCGGCACCTTGGGGGCTCGGATGTGCAGGAGCGTCG-GACAC
1 CATCGGCACCTT-GGTGCTCGGATGTGCGGGAGCCTCGAG-CAC
**
13031 CATCGGCAACCTTGGTGCTTAGATGTGCGGGAGCCTCGAGCAC
1 CATCGGC-ACCTTGGTGCTCGGATGTGCGGGAGCCTCGAGCAC
*
13074 CATCGGCACCTTGGTGCCTGGGATGTG
1 CATCGGCACCTTGGTG-CTCGGATGTG
13101 TGGGCTAAAG
Statistics
Matches: 606, Mismatches: 79, Indels: 39
0.84 0.11 0.05
Matches are distributed among these distances:
41 22 0.04
42 355 0.59
43 221 0.36
44 8 0.01
ACGTcount: A:0.16, C:0.28, G:0.36, T:0.21
Consensus pattern (42 bp):
CATCGGCACCTTGGTGCTCGGATGTGCGGGAGCCTCGAGCAC
Found at i:12502 original size:85 final size:84
Alignment explanation
Indices: 12350--13100 Score: 922
Period size: 85 Copynumber: 8.9 Consensus size: 84
12340 AGAGCACATG
* *
12350 GCAGCATCGGCACCTTGGTGGCTCGGATGTGTGGG-GCCTCGAGCACCATCGGCACCTTGGTGCT
1 GCAGCATCGGCACCTTGGT-GCTTGGATGTGCGGGAGCCTCGAGCACCATCGGCACCTTGGTGCT
* *
12414 TGGATGTGCGAGAGCCTCGA
65 CGGATGTGCGGGAGCCTCGA
* * * *
12434 GCACCATCGGCACCTTGGTGGCTCGGATGTGCAGGAGCCTCGAGCAGCATCGGCACCTTGGTGCT
1 GCAGCATCGGCACCTTGGT-GCTTGGATGTGCGGGAGCCTCGAGCACCATCGGCACCTTGGTGCT
*
12499 TGGATGTGCGGGAGCCTCGA
65 CGGATGTGCGGGAGCCTCGA
* * ** *
12519 GGAGCATCGGCACCTTGGTGCTGGGATGTGTAGGAGCCCCGAGC-CGCATCGGCACCTTGGTGGC
1 GCAGCATCGGCACCTTGGTGCTTGGATGTGCGGGAGCCTCGAGCAC-CATCGGCACCTTGGT-GC
12583 TCGGAT-TGCGGGAGCCTCGA
64 TCGGATGTGCGGGAGCCTCGA
* * * * *
12603 GCGGCATCGGCACCTTTGTGCTTGGATGTGCGAGAGCCTCGACCACCGTCGGCACCTTGGTGGCT
1 GCAGCATCGGCACCTTGGTGCTTGGATGTGCGGGAGCCTCGAGCACCATCGGCACCTTGGT-GCT
*
12668 CGGATGTGCGGGAGGCTCGA
65 CGGATGTGCGGGAGCCTCGA
* *
12688 GCACCATCGGCACCTTGGTGCTTGGATGTGCGGGAGCC-CTGACCACCATCGGCACCTTGGTGCT
1 GCAGCATCGGCACCTTGGTGCTTGGATGTGCGGGAGCCTC-GAGCACCATCGGCACCTTGGTGCT
*
12752 GGGATGTGCGGGAGCCTCGA
65 CGGATGTGCGGGAGCCTCGA
* * **
12772 GCAGCATCGGCACCTTGGTGC-TGAGATGTGCGGGAGCCTCGACCAGCATCTACACCTTGGTGCC
1 GCAGCATCGGCACCTTGGTGCTTG-GATGTGCGGGAGCCTCGAGCACCATCGGCACCTTGGTG-C
*
12836 TCGGATGTGCGGGAGCCTTGA
64 TCGGATGTGCGGGAGCCTCGA
* * * ** * *
12857 GCAGCATCTGCACATTGGTGCTTGCATGTAAGAGAGCCTC-ATGCACCATCGACACCTTGGTGCC
1 GCAGCATCGGCACCTTGGTGCTTGGATGTGCGGGAGCCTCGA-GCACCATCGGCACCTTGGTG-C
*
12921 TCGGATGTGCGAGAGCCTCGA
64 TCGGATGTGCGGGAGCCTCGA
* * * *
12942 GCAGCATCGGCACCTTGGTGCTGGGATGTGCGGGAGCCTCGACCAGCATCGGCACCTTGGGGGCT
1 GCAGCATCGGCACCTTGGTGCTTGGATGTGCGGGAGCCTCGAGCACCATCGGCACCTT-GGTGCT
* *
13007 CGGATGTGCAGGAGCGTCG-
65 CGGATGTGCGGGAGCCTCGA
* *
13026 GACACCATCGGCAACCTTGGTGCTTAGATGTGCGGGAGCCTCGAGCACCATCGGCACCTTGGTGC
1 G-CAGCATCGGC-ACCTTGGTGCTTGGATGTGCGGGAGCCTCGAGCACCATCGGCACCTTGGTG-
*
13091 CTGGGATGTG
63 CTCGGATGTG
13101 TGGGCTAAAG
Statistics
Matches: 583, Mismatches: 68, Indels: 30
0.86 0.10 0.04
Matches are distributed among these distances:
83 2 0.00
84 218 0.37
85 305 0.52
86 58 0.10
ACGTcount: A:0.16, C:0.28, G:0.36, T:0.21
Consensus pattern (84 bp):
GCAGCATCGGCACCTTGGTGCTTGGATGTGCGGGAGCCTCGAGCACCATCGGCACCTTGGTGCTC
GGATGTGCGGGAGCCTCGA
Found at i:12717 original size:211 final size:212
Alignment explanation
Indices: 12353--13100 Score: 992
Period size: 211 Copynumber: 3.5 Consensus size: 212
12343 GCACATGGCA
*
12353 GCATCGGCACCTTGGTGGCTCGGATGTGTGGG-GCCTCGAGCACCATCGGCACCTTGGTGCTTGG
1 GCATCGGCACCTTGGTGGCTCGGATGTGCGGGAGCCTCGAGCACCATCGGCACCTTGGTGCTTGG
* *
12417 ATGTGCGAGAGCCTCGAGCACCATCGGCACCTTGGTGGCTCGGATGTGCAGGAGCCTCGAGCAGC
66 ATGTGCGAGAGCCTCGAGCACCATCGGCACCTTGGTGGCTCGGATGTGCGGGAGCCTCGAGCACC
*
12482 ATCGGCACCTTGGTGCTTGGATGTGCGGGAGCCTCGAGGAGCATCGGCACCTTGGTGCTGGGATG
131 ATCGGCACCTTGGTGCTTGGATGTGCGGGAGCCTCGAGCAGCATCGGCACCTTGGTGCTGGGATG
** *
12547 TGTAGGAGCCCCGAGCC
196 TGCGGGAGCCTCGAGCC
** *
12564 GCATCGGCACCTTGGTGGCTCGGAT-TGCGGGAGCCTCGAGCGGCATCGGCACCTTTGTGCTTGG
1 GCATCGGCACCTTGGTGGCTCGGATGTGCGGGAGCCTCGAGCACCATCGGCACCTTGGTGCTTGG
* * *
12628 ATGTGCGAGAGCCTCGACCACCGTCGGCACCTTGGTGGCTCGGATGTGCGGGAGGCTCGAGCACC
66 ATGTGCGAGAGCCTCGAGCACCATCGGCACCTTGGTGGCTCGGATGTGCGGGAGCCTCGAGCACC
* *
12693 ATCGGCACCTTGGTGCTTGGATGTGCGGGAGCC-CTGACCACCATCGGCACCTTGGTGCTGGGAT
131 ATCGGCACCTTGGTGCTTGGATGTGCGGGAGCCTC-GAGCAGCATCGGCACCTTGGTGCTGGGAT
*
12757 GTGCGGGAGCCTCGAGCA
195 GTGCGGGAGCCTCGAGCC
* * ** *
12775 GCATCGGCACCTTGGT-GCT-GAGATGTGCGGGAGCCTCGACCAGCATCTACACCTTGGTGCCTC
1 GCATCGGCACCTTGGTGGCTCG-GATGTGCGGGAGCCTCGAGCACCATCGGCACCTTGGTG-CTT
* * * * * * * ** *
12838 GGATGTGCGGGAGCCTTGAGCAGCATCTGCACATTGGT-GCTTGCATGTAAGAGAGCCTC-ATGC
64 GGATGTGCGAGAGCCTCGAGCACCATCGGCACCTTGGTGGCTCGGATGTGCGGGAGCCTCGA-GC
* * *
12901 ACCATCGACACCTTGGTGCCTCGGATGTGCGAGAGCCTCGAGCAGCATCGGCACCTTGGTGCTGG
128 ACCATCGGCACCTTGGTG-CTTGGATGTGCGGGAGCCTCGAGCAGCATCGGCACCTTGGTGCTGG
12966 GATGTGCGGGAGCCTCGA-CC
192 GATGTGCGGGAGCCTCGAGCC
* * *
12986 AGCATCGGCACCTTGGGGGCTCGGATGTGCAGGAGCGTCG-GACACCATCGGCAACCTTGGTGCT
1 -GCATCGGCACCTTGGTGGCTCGGATGTGCGGGAGCCTCGAG-CACCATCGGC-ACCTTGGTGCT
* * * *
13050 TAGATGTGCGGGAGCCTCGAGCACCATCGGCACCTTGGTGCCTGGGATGTG
63 TGGATGTGCGAGAGCCTCGAGCACCATCGGCACCTTGGTGGCTCGGATGTG
13101 TGGGCTAAAG
Statistics
Matches: 465, Mismatches: 58, Indels: 25
0.85 0.11 0.05
Matches are distributed among these distances:
209 1 0.00
210 13 0.03
211 267 0.57
212 106 0.23
213 61 0.13
214 17 0.04
ACGTcount: A:0.16, C:0.28, G:0.36, T:0.21
Consensus pattern (212 bp):
GCATCGGCACCTTGGTGGCTCGGATGTGCGGGAGCCTCGAGCACCATCGGCACCTTGGTGCTTGG
ATGTGCGAGAGCCTCGAGCACCATCGGCACCTTGGTGGCTCGGATGTGCGGGAGCCTCGAGCACC
ATCGGCACCTTGGTGCTTGGATGTGCGGGAGCCTCGAGCAGCATCGGCACCTTGGTGCTGGGATG
TGCGGGAGCCTCGAGCC
Found at i:21243 original size:42 final size:42
Alignment explanation
Indices: 21197--21341 Score: 200
Period size: 42 Copynumber: 3.4 Consensus size: 42
21187 TGAATGTGTG
* * *
21197 GGAGCCTCGAGCACCATCTGCATCTAGGCGGTCGGATGTGCC
1 GGAGCCTCGAGCACCATCCGCACCTAGGAGGTCGGATGTGCC
*
21239 GGAGCCTCGAGCACCATCCGCACCTAGGAGGTCGAATGTGCC
1 GGAGCCTCGAGCACCATCCGCACCTAGGAGGTCGGATGTGCC
* * * **
21281 GGAGCCTCGAGCACCATCCGCACCTTGGTGCCTCGGATGTGTG
1 GGAGCCTCGAGCACCATCCGCACCTAGGAG-GTCGGATGTGCC
21324 GGAGCCTCGAGCACCATC
1 GGAGCCTCGAGCACCATC
21342 GGCAACTTTG
Statistics
Matches: 92, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
42 66 0.72
43 26 0.28
ACGTcount: A:0.18, C:0.33, G:0.32, T:0.17
Consensus pattern (42 bp):
GGAGCCTCGAGCACCATCCGCACCTAGGAGGTCGGATGTGCC
Found at i:21894 original size:42 final size:42
Alignment explanation
Indices: 21814--21979 Score: 199
Period size: 42 Copynumber: 3.9 Consensus size: 42
21804 GAGTCTCCGG
* ** *
21814 CACCTTGGTGGCTCGGATATGTAGGAGCCTCGAGCACCATCGG
1 CACCTTGGT-GCTCGGATGTGCGGGAGCCTCGAGCACCATCGA
*
21857 CACCTTGGTGCTTGGATGTGCGGGAGCCTCG-GCCACCATCGA
1 CACCTTGGTGCTCGGATGTGCGGGAGCCTCGAG-CACCATCGA
* * * *
21899 CAACCTTGGCGCTCGGATGTGCGAGAGGCTCGAGCACCACCGA
1 C-ACCTTGGTGCTCGGATGTGCGGGAGCCTCGAGCACCATCGA
* *
21942 CACCTTGGTGCTAGGATGTGCGGAAGCCTCGAGCACCA
1 CACCTTGGTGCTCGGATGTGCGGGAGCCTCGAGCACCA
21980 AAGCTAAAGT
Statistics
Matches: 105, Mismatches: 15, Indels: 7
0.83 0.12 0.06
Matches are distributed among these distances:
41 1 0.01
42 59 0.56
43 44 0.42
44 1 0.01
ACGTcount: A:0.19, C:0.30, G:0.33, T:0.19
Consensus pattern (42 bp):
CACCTTGGTGCTCGGATGTGCGGGAGCCTCGAGCACCATCGA
Found at i:27154 original size:43 final size:43
Alignment explanation
Indices: 27088--27756 Score: 843
Period size: 43 Copynumber: 15.7 Consensus size: 43
27078 CTTTAGCCCA
* *
27088 CACATCCAAG-CACCAAGGTTGCCGATGGTG-TCCGAGGCTCCCG
1 CACATCCGAGCCACCAAGG-TGCCGATGCTGCT-CGAGGCTCCCG
* * **
27131 CACATCTGAGCCCCCAAGGTGCCGATGCTGGACGAGGCTCCCG
1 CACATCCGAGCCACCAAGGTGCCGATGCTGCTCGAGGCTCCCG
*
27174 CACATCCGAGCCACCAAGGTGCCGATGCTGGTCGAGGCTCCCG
1 CACATCCGAGCCACCAAGGTGCCGATGCTGCTCGAGGCTCCCG
* *
27217 CATATCCCAG-CACCAAGGTGCCGATGCTGCTCGAGGCTCCCG
1 CACATCCGAGCCACCAAGGTGCCGATGCTGCTCGAGGCTCCCG
* * * *
27259 CACATCCGAGCCAACAAGGTGCCGATGGTGCACGAGGCTCCCC
1 CACATCCGAGCCACCAAGGTGCCGATGCTGCTCGAGGCTCCCG
* * *
27302 CACATGCAAG-CACCAAGGTGCAGATGCTGCTCGAGGCTCCCG
1 CACATCCGAGCCACCAAGGTGCCGATGCTGCTCGAGGCTCCCG
* * ** *
27344 TACATCCGAGGCACCAAGGTGTGGATGCTGCTCAAGGCTCCCG
1 CACATCCGAGCCACCAAGGTGCCGATGCTGCTCGAGGCTCCCG
* * *
27387 CACATCCCAG-CACCAAGGTGCCGATGGTGCTCGAGGCTCCTG
1 CACATCCGAGCCACCAAGGTGCCGATGCTGCTCGAGGCTCCCG
* *
27429 CACATCCGAGCCACCAAGGTGCCGATGGTGGTCGAGGCTCCCG
1 CACATCCGAGCCACCAAGGTGCCGATGCTGCTCGAGGCTCCCG
* * * * *
27472 CACATCC-AACCACCAAGGTGCCTATGCCGCTTGAGGCTCCCA
1 CACATCCGAGCCACCAAGGTGCCGATGCTGCTCGAGGCTCCCG
* * *
27514 CACATCTGAGCCACCAAGGTGCCGATGCGGCTCGGGGCTCCCG
1 CACATCCGAGCCACCAAGGTGCCGATGCTGCTCGAGGCTCCCG
* * *
27557 CACATCCCAG-CACCAAGGTACCGATGCTCCTCGAGGCTCCCG
1 CACATCCGAGCCACCAAGGTGCCGATGCTGCTCGAGGCTCCCG
* *
27599 CACATCCAAG-CACCAAGGTGCCAATGCTGCTCGAGGCTCCCG
1 CACATCCGAGCCACCAAGGTGCCGATGCTGCTCGAGGCTCCCG
* * *
27641 CACATCCGAGCCACCAAGGTTCCGATGGTGGTCGAGGCTCCCG
1 CACATCCGAGCCACCAAGGTGCCGATGCTGCTCGAGGCTCCCG
* * *
27684 CACATCCAAG-CACCAAGGTGCCGATGGTGCTCGAGGCCCCCG
1 CACATCCGAGCCACCAAGGTGCCGATGCTGCTCGAGGCTCCCG
*
27726 CACATCCGAGCCACCAAGGTGCCGATACTGC
1 CACATCCGAGCCACCAAGGTGCCGATGCTGC
27757 CATGTGCTCC
Statistics
Matches: 542, Mismatches: 76, Indels: 16
0.85 0.12 0.03
Matches are distributed among these distances:
42 256 0.47
43 279 0.51
44 7 0.01
ACGTcount: A:0.21, C:0.37, G:0.28, T:0.15
Consensus pattern (43 bp):
CACATCCGAGCCACCAAGGTGCCGATGCTGCTCGAGGCTCCCG
Found at i:27258 original size:85 final size:85
Alignment explanation
Indices: 27088--27756 Score: 842
Period size: 85 Copynumber: 7.9 Consensus size: 85
27078 CTTTAGCCCA
* * ** *
27088 CACATCCAAG-CACCAAGGTTGCCGATGGTG-TCCGAGGCTCCCGCACATCTGAGCCCCCAAGGT
1 CACATCCGAGCCACCAAGG-TGCCGATGCTGCT-CGAGGCTCCCGCACATCCCAG-CACCAAGGT
**
27151 GCCGATGCTGGACGAGGCTCCCG
63 GCCGATGCTGCTCGAGGCTCCCG
* *
27174 CACATCCGAGCCACCAAGGTGCCGATGCTGGTCGAGGCTCCCGCATATCCCAGCACCAAGGTGCC
1 CACATCCGAGCCACCAAGGTGCCGATGCTGCTCGAGGCTCCCGCACATCCCAGCACCAAGGTGCC
27239 GATGCTGCTCGAGGCTCCCG
66 GATGCTGCTCGAGGCTCCCG
* * * * * * *
27259 CACATCCGAGCCAACAAGGTGCCGATGGTGCACGAGGCTCCCCCACATGCAAGCACCAAGGTGCA
1 CACATCCGAGCCACCAAGGTGCCGATGCTGCTCGAGGCTCCCGCACATCCCAGCACCAAGGTGCC
27324 GATGCTGCTCGAGGCTCCCG
66 GATGCTGCTCGAGGCTCCCG
* * ** *
27344 TACATCCGAGGCACCAAGGTGTGGATGCTGCTCAAGGCTCCCGCACATCCCAGCACCAAGGTGCC
1 CACATCCGAGCCACCAAGGTGCCGATGCTGCTCGAGGCTCCCGCACATCCCAGCACCAAGGTGCC
* *
27409 GATGGTGCTCGAGGCTCCTG
66 GATGCTGCTCGAGGCTCCCG
* * * *
27429 CACATCCGAGCCACCAAGGTGCCGATGGTGGTCGAGGCTCCCGCACATCCAACCACCAAGGTGCC
1 CACATCCGAGCCACCAAGGTGCCGATGCTGCTCGAGGCTCCCGCACATCCCAGCACCAAGGTGCC
* * * *
27494 TATGCCGCTTGAGGCTCCCA
66 GATGCTGCTCGAGGCTCCCG
* * * *
27514 CACATCTGAGCCACCAAGGTGCCGATGCGGCTCGGGGCTCCCGCACATCCCAGCACCAAGGTACC
1 CACATCCGAGCCACCAAGGTGCCGATGCTGCTCGAGGCTCCCGCACATCCCAGCACCAAGGTGCC
*
27579 GATGCTCCTCGAGGCTCCCG
66 GATGCTGCTCGAGGCTCCCG
* * * *
27599 CACATCCAAG-CACCAAGGTGCCAATGCTGCTCGAGGCTCCCGCACATCCGAGCCACCAAGGTTC
1 CACATCCGAGCCACCAAGGTGCCGATGCTGCTCGAGGCTCCCGCACATCCCAG-CACCAAGGTGC
* *
27663 CGATGGTGGTCGAGGCTCCCG
65 CGATGCTGCTCGAGGCTCCCG
* * * *
27684 CACATCCAAG-CACCAAGGTGCCGATGGTGCTCGAGGCCCCCGCACATCCGAGCCACCAAGGTGC
1 CACATCCGAGCCACCAAGGTGCCGATGCTGCTCGAGGCTCCCGCACATCCCAG-CACCAAGGTGC
*
27748 CGATACTGC
65 CGATGCTGC
27757 CATGTGCTCC
Statistics
Matches: 504, Mismatches: 76, Indels: 7
0.86 0.13 0.01
Matches are distributed among these distances:
84 38 0.08
85 420 0.83
86 37 0.07
87 9 0.02
ACGTcount: A:0.21, C:0.37, G:0.28, T:0.15
Consensus pattern (85 bp):
CACATCCGAGCCACCAAGGTGCCGATGCTGCTCGAGGCTCCCGCACATCCCAGCACCAAGGTGCC
GATGCTGCTCGAGGCTCCCG
Found at i:27422 original size:127 final size:127
Alignment explanation
Indices: 27088--27756 Score: 876
Period size: 127 Copynumber: 5.2 Consensus size: 127
27078 CTTTAGCCCA
* * *
27088 CACATCCAAGCACCAAGGTTGCCGATGGTG-TCCGAGGCTCCCGCACATCTGAGCCCCCAAGGTG
1 CACATCCAAGCACCAAGG-TGCCGATGCTGCT-CGAGGCTCCCGCACATCCGAGCCACCAAGGTG
* ** * *
27152 CCGATGCTGGACGAGGCTCCCGCACATCCGAGCCACCAAGGTGCCGATGCTGGTCGAGGCTCCCG
64 CCGATGGTGCTCGAGGCTCCCGCACATCCAAG-CACCAAGGTGCCGATGCTGCTCGAGGCTCCCG
* * *
27217 CATATCCCAGCACCAAGGTGCCGATGCTGCTCGAGGCTCCCGCACATCCGAGCCAACAAGGTGCC
1 CACATCCAAGCACCAAGGTGCCGATGCTGCTCGAGGCTCCCGCACATCCGAGCCACCAAGGTGCC
* * * *
27282 GATGGTGCACGAGGCTCCCCCACATGCAAGCACCAAGGTGCAGATGCTGCTCGAGGCTCCCG
66 GATGGTGCTCGAGGCTCCCGCACATCCAAGCACCAAGGTGCCGATGCTGCTCGAGGCTCCCG
* * ** * *
27344 TACATCCGAGGCACCAAGGTGTGGATGCTGCTCAAGGCTCCCGCACATCCCAG-CACCAAGGTGC
1 CACATCC-AAGCACCAAGGTGCCGATGCTGCTCGAGGCTCCCGCACATCCGAGCCACCAAGGTGC
* * * *
27408 CGATGGTGCTCGAGGCTCCTGCACATCCGAGCCACCAAGGTGCCGATGGTGGTCGAGGCTCCCG
65 CGATGGTGCTCGAGGCTCCCGCACATCCAAG-CACCAAGGTGCCGATGCTGCTCGAGGCTCCCG
* * * * * *
27472 CACATCCAACCACCAAGGTGCCTATGCCGCTTGAGGCTCCCACACATCTGAGCCACCAAGGTGCC
1 CACATCCAAGCACCAAGGTGCCGATGCTGCTCGAGGCTCCCGCACATCCGAGCCACCAAGGTGCC
* * * *
27537 GATGCG-GCTCGGGGCTCCCGCACATCCCAGCACCAAGGTACCGATGCTCCTCGAGGCTCCCG
66 GATG-GTGCTCGAGGCTCCCGCACATCCAAGCACCAAGGTGCCGATGCTGCTCGAGGCTCCCG
* *
27599 CACATCCAAGCACCAAGGTGCCAATGCTGCTCGAGGCTCCCGCACATCCGAGCCACCAAGGTTCC
1 CACATCCAAGCACCAAGGTGCCGATGCTGCTCGAGGCTCCCGCACATCCGAGCCACCAAGGTGCC
* * *
27664 GATGGTGGTCGAGGCTCCCGCACATCCAAGCACCAAGGTGCCGATGGTGCTCGAGGCCCCCG
66 GATGGTGCTCGAGGCTCCCGCACATCCAAGCACCAAGGTGCCGATGCTGCTCGAGGCTCCCG
* *
27726 CACATCCGAGCCACCAAGGTGCCGATACTGC
1 CACATCCAAG-CACCAAGGTGCCGATGCTGC
27757 CATGTGCTCC
Statistics
Matches: 467, Mismatches: 66, Indels: 15
0.85 0.12 0.03
Matches are distributed among these distances:
126 1 0.00
127 253 0.54
128 195 0.42
129 18 0.04
ACGTcount: A:0.21, C:0.37, G:0.28, T:0.15
Consensus pattern (127 bp):
CACATCCAAGCACCAAGGTGCCGATGCTGCTCGAGGCTCCCGCACATCCGAGCCACCAAGGTGCC
GATGGTGCTCGAGGCTCCCGCACATCCAAGCACCAAGGTGCCGATGCTGCTCGAGGCTCCCG
Found at i:27909 original size:24 final size:24
Alignment explanation
Indices: 27851--27927 Score: 86
Period size: 24 Copynumber: 3.3 Consensus size: 24
27841 TTTTCTATAT
* **
27851 GCCGGGA-GGATCGCCAGAGTGCC
1 GCCGGGATGGATCGCCGGAGCACC
* *
27874 GCC-AGATGGATCGCCGGAGCACT
1 GCCGGGATGGATCGCCGGAGCACC
*
27897 GCCGGGATGGATCGCTGGAGCACC
1 GCCGGGATGGATCGCCGGAGCACC
27921 GCCGGGA
1 GCCGGGA
27928 ACCTAACTGG
Statistics
Matches: 44, Mismatches: 8, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
22 2 0.05
23 18 0.41
24 24 0.55
ACGTcount: A:0.18, C:0.30, G:0.42, T:0.10
Consensus pattern (24 bp):
GCCGGGATGGATCGCCGGAGCACC
Found at i:28191 original size:43 final size:42
Alignment explanation
Indices: 28138--28243 Score: 124
Period size: 43 Copynumber: 2.5 Consensus size: 42
28128 TTTAGATTTA
* *
28138 GTGCTCGAGGCTTCCGCATATCTTAGCAACAAGTTTGCCGATG
1 GTGCTCGAGGCTTCCGCATATCTGAGCAACAAG-GTGCCGATG
* * * *
28181 GTGGC-CGAGGCTTCCGTACATCTGAGCACCAAGGTGCTGATG
1 GT-GCTCGAGGCTTCCGCATATCTGAGCAACAAGGTGCCGATG
*
28223 GTGCTCGAGGCTCCCGCATAT
1 GTGCTCGAGGCTTCCGCATAT
28244 TCGAGCCTCC
Statistics
Matches: 52, Mismatches: 9, Indels: 5
0.79 0.14 0.08
Matches are distributed among these distances:
41 2 0.04
42 22 0.42
43 26 0.50
44 2 0.04
ACGTcount: A:0.19, C:0.27, G:0.29, T:0.25
Consensus pattern (42 bp):
GTGCTCGAGGCTTCCGCATATCTGAGCAACAAGGTGCCGATG
Done.