Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-JGI_221_v2.0
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: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 133 of 206
Found at i:40427802 original size:50 final size:49
Alignment explanation
Indices: 40427730--40427851 Score: 147
Period size: 49 Copynumber: 2.5 Consensus size: 49
40427720 TACCCCAGAT
* **
40427730 ATGGTCTTACATGGGAGTTCTCATATCGGTGCC-CATGCCATGTCCCAGGC
1 ATGGTCTTACGTGGGACCTCTCATATCGGTGCCACA--CCATGTCCCAGGC
* * * * *
40427780 ATGGTCTTACGGGGGACCTCTCATCTTGGTGCCACACCATGTCCCTGTC
1 ATGGTCTTACGTGGGACCTCTCATATCGGTGCCACACCATGTCCCAGGC
40427829 ATGGTCTTACGTGGGACCTCTCA
1 ATGGTCTTACGTGGGACCTCTCA
40427852 AAATCTCAAT
Statistics
Matches: 62, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
49 33 0.53
50 27 0.44
51 2 0.03
ACGTcount: A:0.16, C:0.30, G:0.25, T:0.29
Consensus pattern (49 bp):
ATGGTCTTACGTGGGACCTCTCATATCGGTGCCACACCATGTCCCAGGC
Found at i:40432017 original size:16 final size:16
Alignment explanation
Indices: 40431996--40432026 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
40431986 GGCACTAATA
*
40431996 TTACTTTCTCCAACTG
1 TTACTTGCTCCAACTG
40432012 TTACTTGCTCCAACT
1 TTACTTGCTCCAACT
40432027 CCCAGATTCC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.32, G:0.06, T:0.42
Consensus pattern (16 bp):
TTACTTGCTCCAACTG
Found at i:40439361 original size:14 final size:14
Alignment explanation
Indices: 40439337--40439370 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
40439327 GGTAGCTTGT
40439337 TTGTGTCACTTTAGG
1 TTGT-TCACTTTAGG
40439352 TTGTTCACTTTAGG
1 TTGTTCACTTTAGG
40439366 TTGTT
1 TTGTT
40439371 TGTGTTATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 15 0.79
15 4 0.21
ACGTcount: A:0.12, C:0.12, G:0.24, T:0.53
Consensus pattern (14 bp):
TTGTTCACTTTAGG
Found at i:40447843 original size:51 final size:52
Alignment explanation
Indices: 40447754--40447852 Score: 150
Period size: 51 Copynumber: 1.9 Consensus size: 52
40447744 TACATGACTA
*
40447754 AATTTAATGATGTAAACTTTAACTAACATAGGAGTTACATAAATGCATGTCAT
1 AATTTAATGATGCAAACTTTAACTAACATAGGAGTTACAT-AATGCATGTCAT
40447807 AATTT-ATGATGCAAAC-TTAACTAACAT-GAGAGTTACATAATGCATG
1 AATTTAATGATGCAAACTTTAACTAACATAG-GAGTTACATAATGCATG
40447853 ACTTTATTAA
Statistics
Matches: 44, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
50 9 0.20
51 20 0.45
52 10 0.23
53 5 0.11
ACGTcount: A:0.41, C:0.12, G:0.14, T:0.32
Consensus pattern (52 bp):
AATTTAATGATGCAAACTTTAACTAACATAGGAGTTACATAATGCATGTCAT
Found at i:40452531 original size:20 final size:22
Alignment explanation
Indices: 40452506--40452553 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
40452496 TGAATCTGTC
40452506 AAAAATAA-T-AAAAATTCACT
1 AAAAATAATTGAAAAATTCACT
* *
40452526 AAAAATAATTGTAAAATTGACT
1 AAAAATAATTGAAAAATTCACT
40452548 AAAAAT
1 AAAAAT
40452554 TAACATGTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 8 0.33
21 1 0.04
22 15 0.62
ACGTcount: A:0.62, C:0.06, G:0.04, T:0.27
Consensus pattern (22 bp):
AAAAATAATTGAAAAATTCACT
Found at i:40452591 original size:19 final size:19
Alignment explanation
Indices: 40452567--40452646 Score: 69
Period size: 18 Copynumber: 4.3 Consensus size: 19
40452557 CATGTTCAAA
* *
40452567 ATTTTAATATAATTTAATT
1 ATTTTAATAAAAATTAATT
*
40452586 ATTTT-ATAAAAATTAA-A
1 ATTTTAATAAAAATTAATT
*
40452603 ATTTTTAA-AATAATTTAATT
1 A-TTTTAATAA-AAATTAATT
*
40452623 ATTTT-ATAAAAATTATTT
1 ATTTTAATAAAAATTAATT
40452641 ATTTTA
1 ATTTTA
40452647 TGACAAAAAT
Statistics
Matches: 48, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
17 1 0.02
18 28 0.58
19 18 0.38
20 1 0.02
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
ATTTTAATAAAAATTAATT
Found at i:40452646 original size:37 final size:36
Alignment explanation
Indices: 40452564--40452637 Score: 130
Period size: 37 Copynumber: 2.0 Consensus size: 36
40452554 TAACATGTTC
*
40452564 AAAATTTTAATATAATTTAATTATTTTATAAAAATT
1 AAAATTTTAAAATAATTTAATTATTTTATAAAAATT
40452600 AAAATTTTTAAAATAATTTAATTATTTTATAAAAATT
1 AAAA-TTTTAAAATAATTTAATTATTTTATAAAAATT
40452637 A
1 A
40452638 TTTATTTTAT
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
36 4 0.11
37 32 0.89
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (36 bp):
AAAATTTTAAAATAATTTAATTATTTTATAAAAATT
Found at i:40452792 original size:24 final size:25
Alignment explanation
Indices: 40452751--40452797 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
40452741 AAATTCCAGA
*
40452751 AAGAATTTCTCAGAAAC-ACTTTTG
1 AAGAATTCCTCAGAAACAACTTTTG
40452775 AAGAATTCCTTCAG-AACAACTTT
1 AAGAATTCC-TCAGAAACAACTTT
40452798 CTTCTCAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 11 0.55
25 9 0.45
ACGTcount: A:0.38, C:0.19, G:0.11, T:0.32
Consensus pattern (25 bp):
AAGAATTCCTCAGAAACAACTTTTG
Found at i:40462934 original size:22 final size:21
Alignment explanation
Indices: 40462909--40462952 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
40462899 TGATAAACTT
40462909 TAATATATA-ATTATATTATTTA
1 TAATATATATATTA-ATT-TTTA
*
40462931 TAATTTATATATTAATTTTTA
1 TAATATATATATTAATTTTTA
40462952 T
1 T
40462953 CAACTCAGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 5 0.25
22 11 0.55
23 4 0.20
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TAATATATATATTAATTTTTA
Found at i:40466335 original size:42 final size:41
Alignment explanation
Indices: 40466279--40466494 Score: 185
Period size: 33 Copynumber: 5.5 Consensus size: 41
40466269 ATTCCCACAA
40466279 GGGGTTGCTAAGTGCTGATTCCACCGTATTTTAAATGTGAAG
1 GGGGTTGCTAAGTGCTGATTCCACCGTA-TTTAAATGTGAAG
* * *
40466321 GGGGTTGCTAAGTGCTGATTCC-TCG-A-AT-CAT-T---G
1 GGGGTTGCTAAGTGCTGATTCCACCGTATTTAAATGTGAAG
* *
40466354 GTGGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTGAAA
1 GGGGTTGCTAAGTGCTGATTCCACCGTAT-TTAAATGTGAAG
* *
40466396 GGGGTTGCTAAGTGCTGATTCC-CAG-A-TT-CAT-T---G
1 GGGGTTGCTAAGTGCTGATTCCACCGTATTTAAATGTGAAG
* * *
40466429 GTGGTTGCTAAGTGCTGATTCCACCATATTTTTAAATGTGGAAA
1 GGGGTTGCTAAGTGCTGATTCCACCGTA--TTTAAATGT-GAAG
40466473 GGGGTTGCTAAGTGCTGATTCC
1 GGGGTTGCTAAGTGCTGATTCC
40466495 CCGAATCATT
Statistics
Matches: 136, Mismatches: 18, Indels: 38
0.71 0.09 0.20
Matches are distributed among these distances:
33 43 0.32
34 3 0.02
35 2 0.01
36 2 0.01
37 5 0.04
38 7 0.05
39 3 0.02
40 3 0.02
41 4 0.03
42 43 0.32
44 21 0.15
ACGTcount: A:0.22, C:0.16, G:0.28, T:0.34
Consensus pattern (41 bp):
GGGGTTGCTAAGTGCTGATTCCACCGTATTTAAATGTGAAG
Found at i:40466380 original size:75 final size:74
Alignment explanation
Indices: 40466252--40466531 Score: 417
Period size: 75 Copynumber: 3.8 Consensus size: 74
40466242 GAAAATAAAG
*
40466252 GGGGTTGCTAAGTGCTGATTCCC--A-CA-AGG-GGTTGCTAAGTGCTGATTCCACCGTATTTTA
1 GGGGTTGCTAAGTGCTGATTCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATTTTA
*
40466312 AATGTGAAG
66 AATGTGAAA
*
40466321 GGGGTTGCTAAGTGCTGATTCCTCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATCTT
1 GGGGTTGCTAAGTGCTGATTCC-CGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATTTT
40466386 AAATGTGAAA
65 AAATGTGAAA
* *
40466396 GGGGTTGCTAAGTGCTGATTCCCAGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCATATTTT
1 GGGGTTGCTAAGTGCTGATTCCC-GAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTA-TTT
40466461 TAAATGTGGAAA
64 TAAATGT-GAAA
* *
40466473 GGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTACTGAATCCACCG
1 GGGGTTGCTAAGTGCTGATT-CCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCG
40466532 GTAACGGATA
Statistics
Matches: 191, Mismatches: 10, Indels: 12
0.90 0.05 0.06
Matches are distributed among these distances:
69 22 0.12
70 1 0.01
72 1 0.01
73 2 0.01
74 3 0.02
75 95 0.50
76 9 0.05
77 55 0.29
78 3 0.02
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.32
Consensus pattern (74 bp):
GGGGTTGCTAAGTGCTGATTCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATTTTA
AATGTGAAA
Found at i:40466515 original size:152 final size:144
Alignment explanation
Indices: 40466252--40466531 Score: 434
Period size: 152 Copynumber: 1.9 Consensus size: 144
40466242 GAAAATAAAG
*
40466252 GGGGTTGCTAAGTGCTGATTCCCACAAGGGGTTGCTAAGTGCTGATTCCACCGTATTTTAAATGT
1 GGGGTTGCTAAGTGCTGATTCCCACAAGGGGTTGCTAAGTGCTGATTCCACCATATTTTAAATGT
* * * *
40466317 GAAGGGGGTTGCTAAGTGCTGATTCCTCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTA
66 GAAAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTACTGAATCCACCGTA
40466382 TCTTAAATGTGAAA
131 TCTTAAATGTGAAA
*
40466396 GGGGTTGCTAAGTGCTGATTCCCAGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCATATTTT
1 GGGGTTGCTAAGTGCTGATTCCC--A--CA-AGG-GGTTGCTAAGTGCTGATTCCACCATA-TTT
40466461 TAAATGTGGAAAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTACTGAAT
59 TAAATGT-GAAAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTACTGAAT
40466526 CCACCG
123 CCACCG
40466532 GTAACGGATA
Statistics
Matches: 122, Mismatches: 6, Indels: 8
0.90 0.04 0.06
Matches are distributed among these distances:
144 23 0.19
146 1 0.01
148 2 0.02
149 2 0.02
150 25 0.20
151 10 0.08
152 59 0.48
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.32
Consensus pattern (144 bp):
GGGGTTGCTAAGTGCTGATTCCCACAAGGGGTTGCTAAGTGCTGATTCCACCATATTTTAAATGT
GAAAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTACTGAATCCACCGTA
TCTTAAATGTGAAA
Found at i:40468706 original size:12 final size:13
Alignment explanation
Indices: 40468691--40468723 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
40468681 TTATTTTTAT
40468691 TTTTTAA-CTTAG
1 TTTTTAACCTTAG
40468703 TTTTTAACCCTTAG
1 TTTTTAA-CCTTAG
40468717 TTTTTAA
1 TTTTTAA
40468724 TCATCTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.37
14 12 0.63
ACGTcount: A:0.24, C:0.12, G:0.06, T:0.58
Consensus pattern (13 bp):
TTTTTAACCTTAG
Found at i:40474682 original size:50 final size:50
Alignment explanation
Indices: 40474609--40474799 Score: 235
Period size: 51 Copynumber: 3.8 Consensus size: 50
40474599 TATTATCATT
*
40474609 CGATACACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTA
1 CGATACACATAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTA
* * *
40474659 CGATCCACATAGTAGCCTCCACATAGAACTACACACGTGATCAAAGGTTTT-
1 CGATACACATAGTAGCCTTCACATAGTACTACACACGTGATC-AA-GTTTTA
* * * *
40474710 C-AGTACACATAGTAGCCTTCACTTAGTACTACACATGTGA-CCATTATTTA
1 CGA-TACACATAGTAGCCTTCACATAGTACTACACACGTGATCAAGT-TTTA
*
40474760 TCGATACACGTAGTAGCCTTCACATAGTACTACACACGTG
1 -CGATACACATAGTAGCCTTCACATAGTACTACACACGTG
40474800 TTCATCGATA
Statistics
Matches: 120, Mismatches: 14, Indels: 13
0.82 0.10 0.09
Matches are distributed among these distances:
48 1 0.01
49 4 0.03
50 40 0.33
51 69 0.57
52 6 0.05
ACGTcount: A:0.32, C:0.26, G:0.15, T:0.27
Consensus pattern (50 bp):
CGATACACATAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTA
Found at i:40474744 original size:26 final size:26
Alignment explanation
Indices: 40474713--40474795 Score: 68
Period size: 26 Copynumber: 3.2 Consensus size: 26
40474703 AGGTTTTCAG
40474713 TACACATAGTAGCCTTCACTTAGTAC
1 TACACATAGTAGCCTTCACTTAGTAC
*
40474739 TACACAT-GT-GACCATT-ATTTA-T-C
1 TACACATAGTAG-CC-TTCACTTAGTAC
* *
40474762 GATACACGTAGTAGCCTTCACATAGTAC
1 --TACACATAGTAGCCTTCACTTAGTAC
40474790 TACACA
1 TACACA
40474796 CGTGTTCATC
Statistics
Matches: 43, Mismatches: 5, Indels: 18
0.65 0.08 0.27
Matches are distributed among these distances:
23 1 0.02
24 2 0.05
25 16 0.37
26 21 0.49
27 2 0.05
28 1 0.02
ACGTcount: A:0.33, C:0.25, G:0.12, T:0.30
Consensus pattern (26 bp):
TACACATAGTAGCCTTCACTTAGTAC
Found at i:40476163 original size:20 final size:22
Alignment explanation
Indices: 40476140--40476187 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
40476130 GAGCTGTTAC
40476140 AAAAATAA-T-CAAAATTCACT
1 AAAAATAATTGCAAAATTCACT
* *
40476160 AAAAATAATTGTAAAATTGACT
1 AAAAATAATTGCAAAATTCACT
40476182 AAAAAT
1 AAAAAT
40476188 TAACATGTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 8 0.33
21 1 0.04
22 15 0.62
ACGTcount: A:0.60, C:0.08, G:0.04, T:0.27
Consensus pattern (22 bp):
AAAAATAATTGCAAAATTCACT
Found at i:40478695 original size:24 final size:22
Alignment explanation
Indices: 40478654--40478697 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 22
40478644 CATTATTCAA
*
40478654 ATTTCATATACATGTATCATAC
1 ATTTCATATACATATATCATAC
40478676 ATTTCATATATCAATATATCAT
1 ATTTCATATA-C-ATATATCAT
40478698 GTAACATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 10 0.53
23 1 0.05
24 8 0.42
ACGTcount: A:0.39, C:0.16, G:0.02, T:0.43
Consensus pattern (22 bp):
ATTTCATATACATATATCATAC
Found at i:40486075 original size:24 final size:22
Alignment explanation
Indices: 40486034--40486077 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 22
40486024 CATTATTCAA
*
40486034 ATTTCATATACATGTATCATAC
1 ATTTCATATACATATATCATAC
40486056 ATTTCATATATCAATATATCAT
1 ATTTCATATA-C-ATATATCAT
40486078 GTAACATCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 10 0.53
23 1 0.05
24 8 0.42
ACGTcount: A:0.39, C:0.16, G:0.02, T:0.43
Consensus pattern (22 bp):
ATTTCATATACATATATCATAC
Found at i:40488933 original size:25 final size:25
Alignment explanation
Indices: 40488868--40488933 Score: 59
Period size: 25 Copynumber: 2.6 Consensus size: 25
40488858 CGTTACATCA
40488868 TAAGCTC-CTCCGAGCTGAATAATAG
1 TAAGCTCTCT-CGAGCTGAATAATAG
*
40488893 TAAGCTCATGCT--AGCTGAAT-ATCGG
1 TAAGCTC-T-CTCGAGCTGAATAAT-AG
40488918 TAAGCTCTCTCGAGCT
1 TAAGCTCTCTCGAGCT
40488934 AAGAATCGAT
Statistics
Matches: 34, Mismatches: 1, Indels: 12
0.72 0.02 0.26
Matches are distributed among these distances:
23 2 0.06
24 3 0.09
25 27 0.79
28 2 0.06
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.27
Consensus pattern (25 bp):
TAAGCTCTCTCGAGCTGAATAATAG
Found at i:40489093 original size:20 final size:20
Alignment explanation
Indices: 40489054--40489090 Score: 67
Period size: 19 Copynumber: 1.9 Consensus size: 20
40489044 GGAAATTACA
40489054 CAATTCACAAACATATAATT
1 CAATTCACAAACATATAATT
40489074 CAATTCA-AAACATATAA
1 CAATTCACAAACATATAA
40489091 ATTTACAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.54, C:0.19, G:0.00, T:0.27
Consensus pattern (20 bp):
CAATTCACAAACATATAATT
Found at i:40492446 original size:22 final size:22
Alignment explanation
Indices: 40492421--40492467 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
40492411 ACAAGATATA
*
40492421 TGGCAGTTTATATGCAATTATG
1 TGGCAGTTTATATACAATTATG
*
40492443 TGGCAGTTTATCTACAATTATG
1 TGGCAGTTTATATACAATTATG
40492465 TGG
1 TGG
40492468 TGGCTTGTCC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.26, C:0.11, G:0.23, T:0.40
Consensus pattern (22 bp):
TGGCAGTTTATATACAATTATG
Found at i:40499958 original size:50 final size:50
Alignment explanation
Indices: 40499903--40500155 Score: 296
Period size: 50 Copynumber: 5.1 Consensus size: 50
40499893 TATTCCAGAT
** * * **
40499903 ATGGTCTTACATGAGATTTCTCATATCGGTGCCCATTCCATGTCCAAGAC
1 ATGGTCTTACATGAGACCTCTCATCTCGGTGCCAACGCCATGTCCAAGAC
* * *
40499953 ATGGTCTTAC-GGGGAACCTCTCATCTCGGTGCCAATGCCATGTCCCAA-AC
1 ATGGTCTTACATGAG-ACCTCTCATCTCGGTGCCAACGCCATGT-CCAAGAC
* *
40500003 ATGGTCTTACATGAGACCTCTTATCTCGGTGCCAACGCCATGTCCCAGAC
1 ATGGTCTTACATGAGACCTCTCATCTCGGTGCCAACGCCATGTCCAAGAC
* * * *
40500053 AAGGTCTTACATGGGACCCCTTATCTCGGTGCCAACAG-CATGTCCAAGAC
1 ATGGTCTTACATGAGACCTCTCATCTCGGTGCCAAC-GCCATGTCCAAGAC
* * *
40500103 ATGGTCTTACATGGGACCTCTTATCTCGGTGCCAACGCCATGTCCCAGAC
1 ATGGTCTTACATGAGACCTCTCATCTCGGTGCCAACGCCATGTCCAAGAC
40500153 ATG
1 ATG
40500156 CCAACGCCAT
Statistics
Matches: 178, Mismatches: 19, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
49 6 0.03
50 165 0.93
51 7 0.04
ACGTcount: A:0.23, C:0.30, G:0.21, T:0.26
Consensus pattern (50 bp):
ATGGTCTTACATGAGACCTCTCATCTCGGTGCCAACGCCATGTCCAAGAC
Found at i:40500160 original size:22 final size:22
Alignment explanation
Indices: 40500132--40500177 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
40500122 CTTATCTCGG
40500132 TGCCAACGCCATGTCCCAGACA
1 TGCCAACGCCATGTCCCAGACA
40500154 TGCCAACGCCATGTCCCAGACA
1 TGCCAACGCCATGTCCCAGACA
40500176 TG
1 TG
40500178 GTCTTACATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.26, C:0.39, G:0.20, T:0.15
Consensus pattern (22 bp):
TGCCAACGCCATGTCCCAGACA
Found at i:40517241 original size:88 final size:88
Alignment explanation
Indices: 40517087--40517262 Score: 262
Period size: 88 Copynumber: 2.0 Consensus size: 88
40517077 GATATTTTGG
* * *
40517087 CCTTGTGATCTTACGAGACTATTGGATATAGTTGCCATACCAAAGGATTGTGAGTACTTACCTTT
1 CCTTATGATCTTACGAGACCATTGGACATAGTTGCCATACCAAAGGATTGTGAGTACTTACCTTT
* *
40517152 GTGATGTGATTTTTAGGCGTTGA
66 GTAATATGATTTTTAGGCGTTGA
* * * *
40517175 CCTTATGATCTTATGAGACCATTGGACATAGTTGGCATACCATAGGATTGTGATTACTTACCTTT
1 CCTTATGATCTTACGAGACCATTGGACATAGTTGCCATACCAAAGGATTGTGAGTACTTACCTTT
*
40517240 GTAATATGATTTTTGGGCGTTGA
66 GTAATATGATTTTTAGGCGTTGA
40517263 GGCCCAGGGA
Statistics
Matches: 78, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
88 78 1.00
ACGTcount: A:0.24, C:0.15, G:0.23, T:0.38
Consensus pattern (88 bp):
CCTTATGATCTTACGAGACCATTGGACATAGTTGCCATACCAAAGGATTGTGAGTACTTACCTTT
GTAATATGATTTTTAGGCGTTGA
Found at i:40554799 original size:38 final size:38
Alignment explanation
Indices: 40554725--40554824 Score: 159
Period size: 38 Copynumber: 2.7 Consensus size: 38
40554715 TGCTCTCTTG
*
40554725 TTTCTTTTCTGTCAATTTGCT-CC-CAGTTTATTTTCT
1 TTTCTTTTCTGTCGATTTGCTCCCTCAGTTTATTTTCT
*
40554761 TTTCTTTTCTGTTGATTTGCTCCCTCAGTTTATTTTCT
1 TTTCTTTTCTGTCGATTTGCTCCCTCAGTTTATTTTCT
*
40554799 TTTCTTTTCTGCCGATTTGCTCCCTC
1 TTTCTTTTCTGTCGATTTGCTCCCTC
40554825 TGTCCCTCTG
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
36 19 0.33
37 2 0.03
38 37 0.64
ACGTcount: A:0.08, C:0.25, G:0.10, T:0.57
Consensus pattern (38 bp):
TTTCTTTTCTGTCGATTTGCTCCCTCAGTTTATTTTCT
Found at i:40558397 original size:26 final size:26
Alignment explanation
Indices: 40558363--40558424 Score: 115
Period size: 26 Copynumber: 2.4 Consensus size: 26
40558353 TATATTTTTA
*
40558363 TTAAATTATATTTAATAATAATTATT
1 TTAAATTATATGTAATAATAATTATT
40558389 TTAAATTATATGTAATAATAATTATT
1 TTAAATTATATGTAATAATAATTATT
40558415 TTAAATTATA
1 TTAAATTATA
40558425 CAAATTCATA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (26 bp):
TTAAATTATATGTAATAATAATTATT
Found at i:40558631 original size:25 final size:26
Alignment explanation
Indices: 40558599--40558653 Score: 71
Period size: 24 Copynumber: 2.2 Consensus size: 26
40558589 TTATTAAATT
*
40558599 ATATATTTTAATTATAA-TATATTTA
1 ATATATTTTAATAATAATTATATTTA
*
40558624 ATATA-TTTAATAATAATTATGTTTA
1 ATATATTTTAATAATAATTATATTTA
40558649 A-ATAT
1 ATATAT
40558654 GATTAAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
24 13 0.50
25 13 0.50
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (26 bp):
ATATATTTTAATAATAATTATATTTA
Found at i:40558820 original size:39 final size:40
Alignment explanation
Indices: 40558777--40558881 Score: 113
Period size: 44 Copynumber: 2.5 Consensus size: 40
40558767 TTCCATTATG
40558777 CTATTACACCTCTATTCCATTCAACCAAACACAAGA-TTA
1 CTATTACACCTCTATTCCATTCAACCAAACACAAGATTTA
* *** *
40558816 CTATTACGCCTCTATTCCATTACATTCAACCAAACAGTTGATTTG
1 CTATTACACCTCTATT-C----CATTCAACCAAACACAAGATTTA
40558861 CTATTACACCTCTATTCCATT
1 CTATTACACCTCTATTCCATT
40558882 ACACCTCTAA
Statistics
Matches: 54, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
39 15 0.28
40 5 0.09
44 17 0.31
45 17 0.31
ACGTcount: A:0.31, C:0.30, G:0.05, T:0.34
Consensus pattern (40 bp):
CTATTACACCTCTATTCCATTCAACCAAACACAAGATTTA
Found at i:40558875 original size:45 final size:44
Alignment explanation
Indices: 40558775--40558884 Score: 131
Period size: 45 Copynumber: 2.6 Consensus size: 44
40558765 TTTTCCATTA
40558775 TGCTATTACACCTCTATT-C----CATTCAACCAAACACAAGAT
1 TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGAT
* * ***
40558814 TACTATTACGCCTCTATTCCATTACATTCAACCAAACAGTTGATT
1 TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGA-T
40558859 TGCTATTACACCTCTATTCCATTACA
1 TGCTATTACACCTCTATTCCATTACA
40558885 CCTCTAATCC
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
39 16 0.28
40 1 0.02
44 16 0.28
45 25 0.43
ACGTcount: A:0.32, C:0.29, G:0.05, T:0.34
Consensus pattern (44 bp):
TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGAT
Found at i:40558884 original size:16 final size:16
Alignment explanation
Indices: 40558865--40558916 Score: 86
Period size: 16 Copynumber: 3.2 Consensus size: 16
40558855 GATTTGCTAT
* *
40558865 TACACCTCTATTCCAT
1 TACACCTCTAATCCAA
40558881 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
40558897 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
40558913 TACA
1 TACA
40558917 GCGAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.35, C:0.37, G:0.00, T:0.29
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:40563859 original size:19 final size:19
Alignment explanation
Indices: 40563835--40563871 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
40563825 TAGACATAAT
40563835 TTTCTTTAAAAACTTGGCG
1 TTTCTTTAAAAACTTGGCG
40563854 TTTCTTTAAAAACTTGGC
1 TTTCTTTAAAAACTTGGC
40563872 TTACTTAGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.43
Consensus pattern (19 bp):
TTTCTTTAAAAACTTGGCG
Found at i:40568342 original size:31 final size:32
Alignment explanation
Indices: 40568283--40568346 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
40568273 GGCAAATTAC
40568283 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
40568315 AAGAGTAATTGAATCCTAAT-AAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
40568346 A
1 A
40568347 NNNNNNNNNN
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 12 0.38
32 20 0.62
ACGTcount: A:0.47, C:0.12, G:0.09, T:0.31
Consensus pattern (32 bp):
AAGAGTAATTGAATCCTAATAAAAACTCTTTA
Found at i:40574062 original size:13 final size:13
Alignment explanation
Indices: 40574044--40574070 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
40574034 CACAAACTTC
40574044 AAAGAAAAAAAGA
1 AAAGAAAAAAAGA
40574057 AAAGAAAAAAAGA
1 AAAGAAAAAAAGA
40574070 A
1 A
40574071 TCGACGAAAC
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:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (13 bp):
AAAGAAAAAAAGA
Found at i:40574239 original size:3 final size:3
Alignment explanation
Indices: 40574231--40574262 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
40574221 AACGAGAATA
40574231 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
40574263 AAGGATAGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:40574622 original size:31 final size:32
Alignment explanation
Indices: 40574563--40574627 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
40574553 GGCAAATTAC
40574563 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
40574595 AAGAGTAATTGAATCCTAAT-AAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
40574626 AA
1 AA
40574628 ATTATCTAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 13 0.39
32 20 0.61
ACGTcount: A:0.48, C:0.12, G:0.09, T:0.31
Consensus pattern (32 bp):
AAGAGTAATTGAATCCTAATAAAAACTCTTTA
Found at i:40576091 original size:20 final size:20
Alignment explanation
Indices: 40576045--40576103 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 20
40576035 GTATAAACTG
* *
40576045 TAATTCATTCATATAACCAG
1 TAATTCATTCATATAAACAA
* * *
40576065 TAGTTCATTCGTATAAATAA
1 TAATTCATTCATATAAACAA
*
40576085 TAATTCATCCATATAAACA
1 TAATTCATTCATATAAACA
40576104 CATATCTTAT
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.42, C:0.17, G:0.05, T:0.36
Consensus pattern (20 bp):
TAATTCATTCATATAAACAA
Found at i:40576315 original size:23 final size:23
Alignment explanation
Indices: 40576287--40576406 Score: 102
Period size: 23 Copynumber: 5.1 Consensus size: 23
40576277 AGGCTCTATT
40576287 GAGCTGAAATGGTAAGCT-TTGAC
1 GAGCTGAAATGGTAAGCTCTT-AC
*
40576310 GAGCTGAACA--GTAAGCTCATAC
1 GAGCTGAA-ATGGTAAGCTCTTAC
* * *
40576332 GAGCTGAAACGGTAAGCTCTAAT
1 GAGCTGAAATGGTAAGCTCTTAC
* *
40576355 GAGCTGAAAATAGTAGGCTCTTAC
1 GAGCTG-AAATGGTAAGCTCTTAC
*
40576379 GAGCTGAAATATCGGTAAGCTCATAC
1 GAGCTG-AA-AT-GGTAAGCTCTTAC
40576405 GA
1 GA
40576407 ACTGTGGTGA
Statistics
Matches: 78, Mismatches: 12, Indels: 11
0.77 0.12 0.11
Matches are distributed among these distances:
21 1 0.01
22 17 0.22
23 24 0.31
24 22 0.28
25 2 0.03
26 12 0.15
ACGTcount: A:0.34, C:0.17, G:0.26, T:0.23
Consensus pattern (23 bp):
GAGCTGAAATGGTAAGCTCTTAC
Found at i:40576326 original size:22 final size:23
Alignment explanation
Indices: 40576308--40576406 Score: 85
Period size: 24 Copynumber: 4.2 Consensus size: 23
40576298 GTAAGCTTTG
40576308 ACGAGCTG-AACAGTAAGCTCAT
1 ACGAGCTGAAACAGTAAGCTCAT
*
40576330 ACGAGCTGAAACGGTAAGCTC-T
1 ACGAGCTGAAACAGTAAGCTCAT
* * * *
40576352 AATGAGCTGAAAATAGTAGGCTCTT
1 -ACGAGCTG-AAACAGTAAGCTCAT
*
40576377 ACGAGCTGAAATATCGGTAAGCTCAT
1 ACGAGCTG-AA-A-CAGTAAGCTCAT
40576403 ACGA
1 ACGA
40576407 ACTGTGGTGA
Statistics
Matches: 61, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
22 9 0.15
23 18 0.30
24 20 0.33
25 2 0.03
26 12 0.20
ACGTcount: A:0.35, C:0.19, G:0.24, T:0.21
Consensus pattern (23 bp):
ACGAGCTGAAACAGTAAGCTCAT
Found at i:40576336 original size:45 final size:46
Alignment explanation
Indices: 40576270--40576388 Score: 125
Period size: 45 Copynumber: 2.6 Consensus size: 46
40576260 CTAAGCTGAT
* * * *
40576270 AAACAGTAGGCTC-TATTGAGCTGAAATGGTAAGCTTTGACGAGCTG
1 AAACAGTAAGCTCATA-CGAGCTGAAATGGTAAGCTCTAACGAGCTG
* *
40576316 -AACAGTAAGCTCATACGAGCTGAAACGGTAAGCTCTAATGAGCTG
1 AAACAGTAAGCTCATACGAGCTGAAATGGTAAGCTCTAACGAGCTG
* * *
40576361 AAAATAGTAGGCTCTTACGAGCTGAAAT
1 -AAACAGTAAGCTCATACGAGCTGAAAT
40576389 ATCGGTAAGC
Statistics
Matches: 60, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
45 36 0.60
46 2 0.03
47 22 0.37
ACGTcount: A:0.34, C:0.17, G:0.25, T:0.24
Consensus pattern (46 bp):
AAACAGTAAGCTCATACGAGCTGAAATGGTAAGCTCTAACGAGCTG
Found at i:40576811 original size:66 final size:67
Alignment explanation
Indices: 40576557--40576942 Score: 564
Period size: 67 Copynumber: 5.8 Consensus size: 67
40576547 AATAATTCAA
* * *
40576557 TTTCTCAAATCACATATATATAATCTATTCAATTAAATACATACATTTAAATACTCAATTTGCAT
1 TTTCTCAAATCACATACATATAATCAATTCAATTAAATACATACATTTAAATACTCAATTCGCAT
40576622 AC
66 AC
* * * * *
40576624 CTTCCCAAATCACATATATATAATCGATTTAATTAAATACATACATTTAAATACTCAATTCGCAT
1 TTTCTCAAATCACATACATATAATCAATTCAATTAAATACATACATTTAAATACTCAATTCGCAT
40576689 AC
66 AC
* * *
40576691 TTTCTCAAAT--CATATATATTATCAATTCAATTAAATACATACATTTAATTACTCAATTCGCAT
1 TTTCTCAAATCACATACATATAATCAATTCAATTAAATACATACATTTAAATACTCAATTCGCAT
40576754 AC
66 AC
* * *
40576756 TTTCTC-AATCACATACATATAATCGATTTAATTAAATACATACATTTCAATACTCAATTCGCAT
1 TTTCTCAAATCACATACATATAATCAATTCAATTAAATACATACATTTAAATACTCAATTCGCAT
40576820 AC
66 AC
* * * *
40576822 TTTCTCAAATCATATACATATAATCAATTAAATTAAATACATACATTTAATTACTCAATTC-CCT
1 TTTCTCAAATCACATACATATAATCAATTCAATTAAATACATACATTTAAATACTCAATTCGCAT
40576886 AC
66 AC
* *
40576888 TTTCTCAAATCACATGCATATAATCAATTGAATTAAATACATACATTTAAATACT
1 TTTCTCAAATCACATACATATAATCAATTCAATTAAATACATACATTTAAATACT
40576943 ATTGCAATTT
Statistics
Matches: 289, Mismatches: 27, Indels: 7
0.89 0.08 0.02
Matches are distributed among these distances:
64 3 0.01
65 57 0.20
66 110 0.38
67 119 0.41
ACGTcount: A:0.41, C:0.19, G:0.02, T:0.37
Consensus pattern (67 bp):
TTTCTCAAATCACATACATATAATCAATTCAATTAAATACATACATTTAAATACTCAATTCGCAT
AC
Found at i:40579818 original size:27 final size:27
Alignment explanation
Indices: 40579779--40579911 Score: 147
Period size: 27 Copynumber: 5.1 Consensus size: 27
40579769 CTATTCAGTA
*
40579779 ACAGTACAGTGTGGGCCTTAGCCCAAT
1 ACAGTACAATGTGGGCCTTAGCCCAAT
40579806 ACAGTACAATGT-GGCCTTAGCCCAAT
1 ACAGTACAATGTGGGCCTTAGCCCAAT
40579832 ACAGTAACAATGT-GG-----GCCCAAT
1 ACAGT-ACAATGTGGGCCTTAGCCCAAT
* *
40579854 GCAGTA-ATATGTGGGTCTTAGCCCAAT
1 ACAGTACA-ATGTGGGCCTTAGCCCAAT
*
40579881 ACAGTAACAATGTGGGCCTTCGCCCAAT
1 ACAGT-ACAATGTGGGCCTTAGCCCAAT
40579909 ACA
1 ACA
40579912 ATATCGGTAC
Statistics
Matches: 91, Mismatches: 5, Indels: 19
0.79 0.04 0.17
Matches are distributed among these distances:
20 1 0.01
21 5 0.05
22 13 0.14
26 19 0.21
27 31 0.34
28 21 0.23
29 1 0.01
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.23
Consensus pattern (27 bp):
ACAGTACAATGTGGGCCTTAGCCCAAT
Found at i:40579859 original size:48 final size:49
Alignment explanation
Indices: 40579799--40579898 Score: 159
Period size: 49 Copynumber: 2.1 Consensus size: 49
40579789 GTGGGCCTTA
40579799 GCCCAATACAGTACA-ATGT-GGCCTTAGCCCAATACAGTAACAATGTGG
1 GCCCAATACAGTA-ATATGTGGGCCTTAGCCCAATACAGTAACAATGTGG
* *
40579847 GCCCAATGCAGTAATATGTGGGTCTTAGCCCAATACAGTAACAATGTGG
1 GCCCAATACAGTAATATGTGGGCCTTAGCCCAATACAGTAACAATGTGG
40579896 GCC
1 GCC
40579899 TTCGCCCAAT
Statistics
Matches: 48, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
47 1 0.02
48 16 0.33
49 31 0.65
ACGTcount: A:0.31, C:0.24, G:0.23, T:0.22
Consensus pattern (49 bp):
GCCCAATACAGTAATATGTGGGCCTTAGCCCAATACAGTAACAATGTGG
Found at i:40580052 original size:26 final size:26
Alignment explanation
Indices: 40580022--40580122 Score: 130
Period size: 26 Copynumber: 3.9 Consensus size: 26
40580012 AACACACCAA
* * * *
40580022 TATCGCAGAAAAGCTGCCAATAATAT
1 TATCGCAGCAAAGCTGCCAGTAACAG
* *
40580048 TATCGCAGCGAAGCTGCTAGTAACAG
1 TATCGCAGCAAAGCTGCCAGTAACAG
* *
40580074 TATCTCAGCGAAGCTGCCAGTAACAG
1 TATCGCAGCAAAGCTGCCAGTAACAG
40580100 TATCGCAGCAAAGCTGCCAGTAA
1 TATCGCAGCAAAGCTGCCAGTAA
40580123 TAGTGTACTT
Statistics
Matches: 65, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 65 1.00
ACGTcount: A:0.35, C:0.24, G:0.22, T:0.20
Consensus pattern (26 bp):
TATCGCAGCAAAGCTGCCAGTAACAG
Found at i:40580353 original size:27 final size:27
Alignment explanation
Indices: 40580292--40580577 Score: 266
Period size: 27 Copynumber: 10.3 Consensus size: 27
40580282 AGGTATAACA
*
40580292 GTCATATTACCCTATAGGGGGTATTTCG
1 GTCATTTTACCCTAT-GGGGGTATTTCG
* * *
40580320 GTTATTTTACCCTATGGGAGTAATTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
*
40580347 GTCATTTTACCCTATGGGGGTATTGCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* *
40580374 GTCATTTTACCTTATGGGTGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* * * * *
40580401 ATTATTTTACTCTACGGGGGTATTTCA
1 GTCATTTTACCCTATGGGGGTATTTCG
* * *
40580428 GTCATTTTACCCTACGAGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTCG
*** *
40580455 GTCATTTTACCCTAAACCCTACAAAGGTATTTCA
1 GTCATTTTACCCT--A---T--GGGGGTATTTCG
* *
40580489 GTCATTTTACCCTATAGGGGTATTTCA
1 GTCATTTTACCCTATGGGGGTATTTCG
* * *
40580516 GTCATATTACCCTATAGGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTCG
*
40580543 GTCATTTTACCCTATGGAGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
*
40580570 GTTATTTT
1 GTCATTTT
40580578 TTTCTACAGG
Statistics
Matches: 212, Mismatches: 39, Indels: 15
0.80 0.15 0.06
Matches are distributed among these distances:
27 175 0.83
28 13 0.06
29 2 0.01
32 1 0.00
34 21 0.10
ACGTcount: A:0.21, C:0.17, G:0.21, T:0.41
Consensus pattern (27 bp):
GTCATTTTACCCTATGGGGGTATTTCG
Found at i:40580484 original size:34 final size:34
Alignment explanation
Indices: 40580436--40580502 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 34
40580426 CAGTCATTTT
* * **
40580436 ACCCTACGAGGGTATTTTGGTCATTTTACCCTAA
1 ACCCTACAAAGGTATTTCAGTCATTTTACCCTAA
40580470 ACCCTACAAAGGTATTTCAGTCATTTTACCCTA
1 ACCCTACAAAGGTATTTCAGTCATTTTACCCTA
40580503 TAGGGGTATT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.27, C:0.25, G:0.13, T:0.34
Consensus pattern (34 bp):
ACCCTACAAAGGTATTTCAGTCATTTTACCCTAA
Found at i:40581303 original size:24 final size:22
Alignment explanation
Indices: 40581278--40581324 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 22
40581268 CCCAAATCCC
40581278 AATATTCCCTCCTCGAATCTCTCCA
1 AATA-TCCCTCCTC-AAT-TCTCCA
*
40581303 AATATCTCTCCTCAATTCTCCA
1 AATATCCCTCCTCAATTCTCCA
40581325 GTGTAAACTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 3 0.14
24 8 0.38
25 4 0.19
ACGTcount: A:0.26, C:0.38, G:0.02, T:0.34
Consensus pattern (22 bp):
AATATCCCTCCTCAATTCTCCA
Found at i:40583155 original size:40 final size:40
Alignment explanation
Indices: 40583094--40583330 Score: 291
Period size: 40 Copynumber: 5.9 Consensus size: 40
40583084 CGATTGAAAT
* * * *
40583094 TACCAAAGTATAAACTA-GGGCACGTATGTGCAATCAAGAG
1 TACCGAAGTACAAAC-AGGGGCACATATGTGCAATCAAGGG
*
40583134 TACCGAAGTACAAACAGGGGCACATATGTACAATC-AGGG
1 TACCGAAGTACAAACAGGGGCACATATGTGCAATCAAGGG
* *
40583173 ATA-CGAAAGTACAAACAAGGGCACATATGTGCAATCAGGGG
1 -TACCG-AAGTACAAACAGGGGCACATATGTGCAATCAAGGG
* * * *
40583214 TACCGAAGTACAAATAGAGGCACGTATGTGCAATTAAGGG
1 TACCGAAGTACAAACAGGGGCACATATGTGCAATCAAGGG
* * *
40583254 TACCAAAGTACAAACAGGAGCACATATGTGCAATCAGGGG
1 TACCGAAGTACAAACAGGGGCACATATGTGCAATCAAGGG
*
40583294 TACCGAAGTACAAACAGGGGCACGTATGTGCAATCAA
1 TACCGAAGTACAAACAGGGGCACATATGTGCAATCAA
40583331 TATAATTAAC
Statistics
Matches: 167, Mismatches: 25, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
39 6 0.04
40 156 0.93
41 5 0.03
ACGTcount: A:0.39, C:0.19, G:0.25, T:0.17
Consensus pattern (40 bp):
TACCGAAGTACAAACAGGGGCACATATGTGCAATCAAGGG
Found at i:40583166 original size:20 final size:20
Alignment explanation
Indices: 40583141--40583322 Score: 80
Period size: 20 Copynumber: 9.1 Consensus size: 20
40583131 GAGTACCGAA
40583141 GTACAAACAGGGGCACATAT
1 GTACAAACAGGGGCACATAT
* ** *
40583161 GTACAATCAGGGATACGA-AA
1 GTACAAACAGGGGCAC-ATAT
*
40583181 GTACAAACAAGGGCACATAT
1 GTACAAACAGGGGCACATAT
* * * ** *
40583201 GTGCAATCAGGGGTACCGAA
1 GTACAAACAGGGGCACATAT
* * *
40583221 GTACAAATAGAGGCACGTAT
1 GTACAAACAGGGGCACATAT
* ** * * *
40583241 GTGCAATTAAGGGTACCA-AA
1 GTACAAACAGGGGCA-CATAT
*
40583261 GTACAAACAGGAGCACATAT
1 GTACAAACAGGGGCACATAT
* * * ** *
40583281 GTGCAATCAGGGGTACCGAA
1 GTACAAACAGGGGCACATAT
*
40583301 GTACAAACAGGGGCACGTAT
1 GTACAAACAGGGGCACATAT
40583321 GT
1 GT
40583323 GCAATCAATA
Statistics
Matches: 107, Mismatches: 51, Indels: 8
0.64 0.31 0.05
Matches are distributed among these distances:
19 3 0.03
20 102 0.95
21 2 0.02
ACGTcount: A:0.38, C:0.18, G:0.27, T:0.16
Consensus pattern (20 bp):
GTACAAACAGGGGCACATAT
Found at i:40583236 original size:80 final size:78
Alignment explanation
Indices: 40583094--40583329 Score: 337
Period size: 80 Copynumber: 3.0 Consensus size: 78
40583084 CGATTGAAAT
* * * * *
40583094 TACCAAAGTATAAACTAGGGCACGTATGTGCAATCAAGAGTACCGAAGTACAAACAGGGGCACAT
1 TACCAAAGTACAAAC-AGGGCACATATGTGCAATCAGGGGTACCGAAGTACAAACAGGGGCACGT
*
40583159 ATGTACAATCAGGG
65 ATGTGCAATCAGGG
* * *
40583173 ATACGAAAGTACAAACAAGGGCACATATGTGCAATCAGGGGTACCGAAGTACAAATAGAGGCACG
1 -TACCAAAGTACAAAC-AGGGCACATATGTGCAATCAGGGGTACCGAAGTACAAACAGGGGCACG
*
40583238 TATGTGCAATTAAGGG
64 TATGTGCAA-TCAGGG
40583254 TACCAAAGTACAAACAGGAGCACATATGTGCAATCAGGGGTACCGAAGTACAAACAGGGGCACGT
1 TACCAAAGTACAAACAGG-GCACATATGTGCAATCAGGGGTACCGAAGTACAAACAGGGGCACGT
40583319 ATGTGCAATCA
65 ATGTGCAATCA
40583330 ATATAATTAA
Statistics
Matches: 139, Mismatches: 15, Indels: 5
0.87 0.09 0.03
Matches are distributed among these distances:
79 5 0.04
80 129 0.93
81 5 0.04
ACGTcount: A:0.39, C:0.19, G:0.25, T:0.17
Consensus pattern (78 bp):
TACCAAAGTACAAACAGGGCACATATGTGCAATCAGGGGTACCGAAGTACAAACAGGGGCACGTA
TGTGCAATCAGGG
Found at i:40583315 original size:120 final size:120
Alignment explanation
Indices: 40583094--40583329 Score: 350
Period size: 120 Copynumber: 2.0 Consensus size: 120
40583084 CGATTGAAAT
* * *
40583094 TACCAAAGTATAAACTAGGGCACGTATGTGCAATCAAGAGTACCGAAGTACAAACAGGGGCACAT
1 TACCAAAGTACAAACTAGGGCACGTATGTGCAATCAAGAGTACCAAAGTACAAACAGGAGCACAT
40583159 ATGTACAATCAGGGATACGAAAGTACAAACAAGGGCACATATGTGCAATCAGGGG
66 ATGTACAATCAGGGATACGAAAGTACAAACAAGGGCACATATGTGCAATCAGGGG
* * *
40583214 TACCGAAGTACAAA-TAGAGGCACGTATGTGCAATTAAGGGTACCAAAGTACAAACAGGAGCACA
1 TACCAAAGTACAAACTAG-GGCACGTATGTGCAATCAAGAGTACCAAAGTACAAACAGGAGCACA
* * * *
40583278 TATGTGCAATCAGGGGTACCG-AAGTACAAACAGGGGCACGTATGTGCAATCA
65 TATGTACAATCAGGGATA-CGAAAGTACAAACAAGGGCACATATGTGCAATCA
40583330 ATATAATTAA
Statistics
Matches: 104, Mismatches: 10, Indels: 4
0.88 0.08 0.03
Matches are distributed among these distances:
119 3 0.03
120 99 0.95
121 2 0.02
ACGTcount: A:0.39, C:0.19, G:0.25, T:0.17
Consensus pattern (120 bp):
TACCAAAGTACAAACTAGGGCACGTATGTGCAATCAAGAGTACCAAAGTACAAACAGGAGCACAT
ATGTACAATCAGGGATACGAAAGTACAAACAAGGGCACATATGTGCAATCAGGGG
Found at i:40586487 original size:15 final size:15
Alignment explanation
Indices: 40586467--40586496 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
40586457 ATTATCGTTG
*
40586467 AGACCATGATCATTC
1 AGACCAGGATCATTC
40586482 AGACCAGGATCATTC
1 AGACCAGGATCATTC
40586497 TGTTCTTTAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (15 bp):
AGACCAGGATCATTC
Found at i:40596161 original size:2 final size:2
Alignment explanation
Indices: 40596156--40596186 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
40596146 TAAATTAATC
*
40596156 AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
40596187 GCTATCAGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:40602852 original size:26 final size:27
Alignment explanation
Indices: 40602803--40602853 Score: 79
Period size: 26 Copynumber: 1.9 Consensus size: 27
40602793 TTCTTCTCTC
40602803 TTTTCTGTTATTTGCTTGCTAGTTTCA
1 TTTTCTGTTATTTGCTTGCTAGTTTCA
40602830 TTTTCTGTT-TTTGCTT-CTGAGTTT
1 TTTTCTGTTATTTGCTTGCT-AGTTT
40602854 GTTTCTTCAC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 2 0.09
26 12 0.52
27 9 0.39
ACGTcount: A:0.08, C:0.14, G:0.16, T:0.63
Consensus pattern (27 bp):
TTTTCTGTTATTTGCTTGCTAGTTTCA
Found at i:40607768 original size:26 final size:27
Alignment explanation
Indices: 40607719--40607769 Score: 79
Period size: 26 Copynumber: 1.9 Consensus size: 27
40607709 TTCTTCTCTC
40607719 TTTTCTGTTATTTGCTTGCTAGTTTCA
1 TTTTCTGTTATTTGCTTGCTAGTTTCA
40607746 TTTTCTGTT-TTTGCTT-CTGAGTTT
1 TTTTCTGTTATTTGCTTGCT-AGTTT
40607770 GTTTCTTCAC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 2 0.09
26 12 0.52
27 9 0.39
ACGTcount: A:0.08, C:0.14, G:0.16, T:0.63
Consensus pattern (27 bp):
TTTTCTGTTATTTGCTTGCTAGTTTCA
Found at i:40615082 original size:15 final size:15
Alignment explanation
Indices: 40615062--40615097 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
40615052 ATTAATTAAT
40615062 GTTTGATATGAATAA
1 GTTTGATATGAATAA
40615077 GTTTGATATGAATAA
1 GTTTGATATGAATAA
40615092 GTTTGA
1 GTTTGA
40615098 CATTAAATAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.22, T:0.42
Consensus pattern (15 bp):
GTTTGATATGAATAA
Found at i:40628299 original size:25 final size:25
Alignment explanation
Indices: 40628266--40628318 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
40628256 TGAAAGCCGA
* *
40628266 AAAACATCAAGGATCTGCTTATCTG
1 AAAACATCAAGGATCTACTTATCCG
40628291 AAAACATCAAGGATCTACTTATCCG
1 AAAACATCAAGGATCTACTTATCCG
40628316 AAA
1 AAA
40628319 GCACAAGTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.42, C:0.21, G:0.13, T:0.25
Consensus pattern (25 bp):
AAAACATCAAGGATCTACTTATCCG
Found at i:40630910 original size:156 final size:157
Alignment explanation
Indices: 40630630--40630943 Score: 540
Period size: 156 Copynumber: 2.0 Consensus size: 157
40630620 CAAGAAACAT
* *
40630630 AATCATAGTGAGTTAGTCCAGTATGTTGTTCTCTAACACATACTCATGCATCAATTTTGACATCC
1 AATCATAGTGAGTTAGTCCAGTATGTTGTTCTCTAACACATACTCATGAATCAATCTTGACATCC
*
40630695 CTGTGTCAATGAAAACACTTTGCCATCAATCAACTACACATTAGCCTCAATGCATTATCATTGTT
66 CTATGTCAATGAAAACACTTTGCCATCAATCAACTACACATTAGCCTCAATGCATTATCATTGTT
*
40630760 CAAGCCCACAATAATACTTAACTAAGG
131 CAAACCCACAATAATACTTAACTAAGG
* *
40630787 AATCATAGTGAGTTAGTCCAGTATGTTGTTCTCTAATACATACTCATGAATCGATCTTGACATCC
1 AATCATAGTGAGTTAGTCCAGTATGTTGTTCTCTAACACATACTCATGAATCAATCTTGACATCC
**
40630852 CTATG-CAATGAAAACACTTTGTTATCAATCAACTACACATTAGCCTCAATGCATTATCATTGTT
66 CTATGTCAATGAAAACACTTTGCCATCAATCAACTACACATTAGCCTCAATGCATTATCATTGTT
*
40630916 CAAACCCACAATAATACTTGACTAAGG
131 CAAACCCACAATAATACTTAACTAAGG
40630943 A
1 A
40630944 CATTTTAAGA
Statistics
Matches: 148, Mismatches: 9, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
156 83 0.56
157 65 0.44
ACGTcount: A:0.34, C:0.23, G:0.12, T:0.32
Consensus pattern (157 bp):
AATCATAGTGAGTTAGTCCAGTATGTTGTTCTCTAACACATACTCATGAATCAATCTTGACATCC
CTATGTCAATGAAAACACTTTGCCATCAATCAACTACACATTAGCCTCAATGCATTATCATTGTT
CAAACCCACAATAATACTTAACTAAGG
Found at i:40631802 original size:19 final size:20
Alignment explanation
Indices: 40631774--40631817 Score: 72
Period size: 19 Copynumber: 2.2 Consensus size: 20
40631764 AATAAAATAA
40631774 TTTCTGGAAAATAATTTACT
1 TTTCTGGAAAATAATTTACT
*
40631794 TTTCT-GAAAATGATTTACT
1 TTTCTGGAAAATAATTTACT
40631813 TTTCT
1 TTTCT
40631818 AGTGTTTGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 18 0.78
20 5 0.22
ACGTcount: A:0.30, C:0.11, G:0.09, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATAATTTACT
Found at i:40635073 original size:16 final size:16
Alignment explanation
Indices: 40635052--40635089 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
40635042 TTTTTTATGC
*
40635052 TTAAAACTGATTGTTA
1 TTAAAACTAATTGTTA
*
40635068 TTAAAATTAATTGTTA
1 TTAAAACTAATTGTTA
40635084 TTAAAA
1 TTAAAA
40635090 TTATATCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.45
Consensus pattern (16 bp):
TTAAAACTAATTGTTA
Found at i:40635090 original size:16 final size:16
Alignment explanation
Indices: 40635061--40635092 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
40635051 CTTAAAACTG
40635061 ATTGTTATTAAAATTA
1 ATTGTTATTAAAATTA
40635077 ATTGTTATTAAAATTA
1 ATTGTTATTAAAATTA
40635093 TATCAAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (16 bp):
ATTGTTATTAAAATTA
Found at i:40636601 original size:25 final size:26
Alignment explanation
Indices: 40636573--40636632 Score: 88
Period size: 25 Copynumber: 2.4 Consensus size: 26
40636563 AACTAAGCAG
40636573 AATACAGATTGAACATACAACCCA-A
1 AATACAGATTGAACATACAACCCAGA
* *
40636598 AATACAAATTGAACATACAATCCAGA
1 AATACAGATTGAACATACAACCCAGA
40636624 AA-ACAGATT
1 AATACAGATT
40636633 CCAAAATTCC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
25 28 0.90
26 3 0.10
ACGTcount: A:0.53, C:0.20, G:0.08, T:0.18
Consensus pattern (26 bp):
AATACAGATTGAACATACAACCCAGA
Found at i:40646745 original size:3 final size:3
Alignment explanation
Indices: 40646737--40646780 Score: 61
Period size: 3 Copynumber: 14.7 Consensus size: 3
40646727 AATCATTAAA
* * *
40646737 AAT AAT AAT AAT AAT TAT ATT AAC AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
40646781 AATTCTTATT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:40646939 original size:18 final size:18
Alignment explanation
Indices: 40646918--40646959 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
40646908 GCATTTTTCA
40646918 CTAATTTCGAATTTTCCT
1 CTAATTTCGAATTTTCCT
40646936 CTAATTTCGAATTTTCCT
1 CTAATTTCGAATTTTCCT
40646954 C-AATTT
1 CTAATTT
40646960 AATCCCTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 5 0.21
18 19 0.79
ACGTcount: A:0.24, C:0.21, G:0.05, T:0.50
Consensus pattern (18 bp):
CTAATTTCGAATTTTCCT
Found at i:40647502 original size:17 final size:18
Alignment explanation
Indices: 40647482--40647521 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
40647472 CATCTTTTTT
40647482 TTTATATTTTA-TTTTAC
1 TTTATATTTTATTTTTAC
40647499 TTTAT-TTTTATTTTTAC
1 TTTATATTTTATTTTTAC
40647516 -TTATAT
1 TTTATAT
40647522 AATATAATAC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
16 9 0.43
17 12 0.57
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTATATTTTATTTTTAC
Found at i:40647526 original size:5 final size:5
Alignment explanation
Indices: 40647518--40647568 Score: 84
Period size: 5 Copynumber: 10.2 Consensus size: 5
40647508 ATTTTTACTT
* *
40647518 ATATA ATATA ATACA ATACA ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
40647568 A
1 A
40647569 AACATAAAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 44 1.00
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (5 bp):
ATATA
Found at i:40650030 original size:16 final size:17
Alignment explanation
Indices: 40649997--40650031 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
40649987 TGGCATTTCT
*
40649997 AAATTTAGTTTATTAAC
1 AAATTTAGCTTATTAAC
40650014 AAATTTAGCTT-TTAAC
1 AAATTTAGCTTATTAAC
40650030 AA
1 AA
40650032 TTATTCAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.43, C:0.09, G:0.06, T:0.43
Consensus pattern (17 bp):
AAATTTAGCTTATTAAC
Found at i:40664549 original size:103 final size:104
Alignment explanation
Indices: 40664209--40664579 Score: 611
Period size: 105 Copynumber: 3.6 Consensus size: 104
40664199 TGTATATAAA
** * * *
40664209 AGGGGTTGCTGTGTGCTGATTCCCCGATTTATGGGTGGTGCTATGTGCG-TGATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGAT-ATCCACCATATCT
**
40664273 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
65 TTGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
40664313 AGGGGTTGCTAAGTGCTGATTCCCCGATTTCATTGGTGGTGCTAAGTGCGATATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGA-TTCATTGGTGGTGCTAAGTGCGATATCCACCATATCT
*
40664378 TTGAAATGAAAAGGGGGGTTGCTATGTGCTGATTCCCCCG
65 TTGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
40664418 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
40664483 TGAAAT-AAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
66 TGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
* **
40664521 AGGGGTTGCTAAGTGCTGATTCCCCGATTCAGTGGTGGTGCTAAGTGCGGGATCCACCA
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCA
40664580 ATAACGGCTA
Statistics
Matches: 253, Mismatches: 12, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
103 87 0.34
104 69 0.27
105 96 0.38
106 1 0.00
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (104 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
TGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
Found at i:40673900 original size:28 final size:28
Alignment explanation
Indices: 40673863--40673957 Score: 127
Period size: 28 Copynumber: 3.4 Consensus size: 28
40673853 ATACAACATG
* * * *
40673863 CAGTAGCAGTCTGGGCCTAAGCCCTATA
1 CAGTAACAGTATGGGCCTTAGCCCAATA
*
40673891 CAGCAACAGTATGGGCCTTAGCCCAATA
1 CAGTAACAGTATGGGCCTTAGCCCAATA
* *
40673919 TAGTAACAGTGTGGGCCTTAGCCCAATA
1 CAGTAACAGTATGGGCCTTAGCCCAATA
40673947 CAGTAACAGTA
1 CAGTAACAGTA
40673958 CAATGCTGTA
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 57 1.00
ACGTcount: A:0.31, C:0.25, G:0.23, T:0.21
Consensus pattern (28 bp):
CAGTAACAGTATGGGCCTTAGCCCAATA
Found at i:40674119 original size:26 final size:26
Alignment explanation
Indices: 40674062--40674138 Score: 91
Period size: 26 Copynumber: 3.0 Consensus size: 26
40674052 ACACCAATAT
* * *
40674062 CACAGCAAGGCTGCCAGTAATAGTGA
1 CACAGCAAAGCTGCCAGTAACAGTAA
**
40674088 TGCAGCAAAGCTGCCAGTAACAGTAA
1 CACAGCAAAGCTGCCAGTAACAGTAA
* *
40674114 CACAGCAAAGTTACCAGTAACAGTA
1 CACAGCAAAGCTGCCAGTAACAGTA
40674139 TATGTGGCAA
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 42 1.00
ACGTcount: A:0.39, C:0.23, G:0.22, T:0.16
Consensus pattern (26 bp):
CACAGCAAAGCTGCCAGTAACAGTAA
Found at i:40674389 original size:27 final size:27
Alignment explanation
Indices: 40674316--40674392 Score: 109
Period size: 27 Copynumber: 2.9 Consensus size: 27
40674306 GGTATAACAA
* * *
40674316 TCATTTTACTCTTCAGGGGCATTTCGG
1 TCATTTTACCCTTCGGGGGTATTTCGG
* *
40674343 TCATTTTACCCTTCGAGGGTATTTTGG
1 TCATTTTACCCTTCGGGGGTATTTCGG
40674370 TCATTTTACCCTTCGGGGGTATT
1 TCATTTTACCCTTCGGGGGTATT
40674393 GAGATGAATA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 44 1.00
ACGTcount: A:0.14, C:0.21, G:0.22, T:0.43
Consensus pattern (27 bp):
TCATTTTACCCTTCGGGGGTATTTCGG
Found at i:40674438 original size:23 final size:23
Alignment explanation
Indices: 40674404--40674454 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
40674394 AGATGAATAT
*
40674404 TGTAATATCCCGAAAATTACTAC
1 TGTAATACCCCGAAAATTACTAC
40674427 TGTAATACCCCGAAAATTACTAC
1 TGTAATACCCCGAAAATTACTAC
*
40674450 AGTAA
1 TGTAA
40674455 GAAAGTTGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.41, C:0.22, G:0.10, T:0.27
Consensus pattern (23 bp):
TGTAATACCCCGAAAATTACTAC
Found at i:40677526 original size:50 final size:50
Alignment explanation
Indices: 40677424--40678061 Score: 886
Period size: 50 Copynumber: 12.6 Consensus size: 50
40677414 TGTGAGCCAG
* * *
40677424 TGTAAGACAATGTTTGGGACATGGCATTGGCATCATTGAGATTACGAGAGGTCCCA
1 TGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGAGA-T--GAGAGGTCCCA
* * *
40677480 TATAAGACCATGTTTGGGACATGGCATTGGCATCGAGATGAGAGGTCCCA
1 TGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCA
* *
40677530 TGTAAGACCATGTCTGAGACATGGCATTGGCACTGAGATGAGAGGTCCCA
1 TGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCA
40677580 TGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCA
1 TGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCA
* *
40677630 TGTATGACCATGTTTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCA
1 TGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCA
* *
40677680 TGTAAGACCATGTCTAGGACATGGCCTTGGCACCGAGATGAGAGGTCCCA
1 TGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCA
* * *
40677730 TGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATTAGAGGTCTCA
1 TGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCA
* *
40677780 TGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATTAGAGGTCCCA
1 TGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCA
* *
40677830 TGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGCGGTCCCA
1 TGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCA
*
40677880 TGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCA
1 TGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCA
* * *
40677930 TGTAAGACCATGTCTAGGACATGCCGTTGGCACC-AGGATGAGAGGCCTCCC-
1 TGTAAGACCATGTCTGGGACATGGCATTGGCACCGA-GATGAGAGG--TCCCA
* * * **
40677981 -GTAAGACCATGTTTGGGACATGGCATGGGCACCGATATGAGAACTCCCA
1 TGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCA
* * * *
40678030 TGTAAGACCATATCTAGGATATGACATTGGCA
1 TGTAAGACCATGTCTGGGACATGGCATTGGCA
40678062 GTACAGGAAA
Statistics
Matches: 535, Mismatches: 41, Indels: 18
0.90 0.07 0.03
Matches are distributed among these distances:
48 4 0.01
49 1 0.00
50 490 0.92
51 1 0.00
52 5 0.01
53 4 0.01
56 30 0.06
ACGTcount: A:0.26, C:0.21, G:0.31, T:0.22
Consensus pattern (50 bp):
TGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCA
Found at i:40679625 original size:23 final size:23
Alignment explanation
Indices: 40679589--40679632 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
40679579 GGGATAAATG
*
40679589 TAATATCCCAAAAATTACTACTA
1 TAATACCCCAAAAATTACTACTA
*
40679612 TAATACCCCGAAAATTACTAC
1 TAATACCCCAAAAATTACTAC
40679633 AGTAAGAAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.45, C:0.25, G:0.02, T:0.27
Consensus pattern (23 bp):
TAATACCCCAAAAATTACTACTA
Found at i:40685153 original size:16 final size:17
Alignment explanation
Indices: 40685126--40685160 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
40685116 ATACCCCTTT
40685126 CACCTATTCATTCAACA
1 CACCTATTCATTCAACA
*
40685143 CACCT-TTCATTCCACA
1 CACCTATTCATTCAACA
40685159 CA
1 CA
40685161 TTTCTCTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.31, C:0.40, G:0.00, T:0.29
Consensus pattern (17 bp):
CACCTATTCATTCAACA
Found at i:40696260 original size:18 final size:18
Alignment explanation
Indices: 40696237--40696272 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
40696227 CCAACTTAAC
40696237 TTACTATAAGCTAATAAG
1 TTACTATAAGCTAATAAG
40696255 TTACTATAAGCTAATAAG
1 TTACTATAAGCTAATAAG
40696273 AGCAAGAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.33
Consensus pattern (18 bp):
TTACTATAAGCTAATAAG
Found at i:40699388 original size:16 final size:15
Alignment explanation
Indices: 40699354--40699394 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 15
40699344 GGTGATAATA
40699354 ATTAATATATAATTAT
1 ATTAAT-TATAATTAT
*
40699370 ATTTATTATAATGTAT
1 ATTAATTATAAT-TAT
40699386 ATTAATTAT
1 ATTAATTAT
40699395 TATCAACTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 6 0.27
16 16 0.73
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
ATTAATTATAATTAT
Found at i:40722901 original size:50 final size:51
Alignment explanation
Indices: 40722812--40722995 Score: 156
Period size: 50 Copynumber: 3.5 Consensus size: 51
40722802 TTGTACTACT
* * * * * **
40722812 AATGACATATCCCAGATATGGTCTTAAATGGGAGTTCTCATATCGGTGTCC
1 AATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATATCGGTGTCC
* * *
40722863 -ATTCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGGTG-CC
1 AATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATATCGGTGTCC
* * * * * **
40722912 AACGCCATGTCTCGGACATTGTCTTACATGGGACCTCTCATAATCTCAATGATGCC
1 AATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCAT-A--TCGGTG-T-CC
40722968 AATGCCATGTCCCAGACATGGTCTTACA
1 AATGCCATGTCCCAGACATGGTCTTACA
40722996 TGAGATCTCT
Statistics
Matches: 102, Mismatches: 24, Indels: 9
0.76 0.18 0.07
Matches are distributed among these distances:
49 2 0.02
50 70 0.69
53 4 0.04
56 26 0.25
ACGTcount: A:0.24, C:0.27, G:0.21, T:0.28
Consensus pattern (51 bp):
AATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATATCGGTGTCC
Found at i:40735579 original size:20 final size:20
Alignment explanation
Indices: 40735554--40735604 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
40735544 CATTTTTGGT
*
40735554 TCATTCGAGCTCAAGTTAGC
1 TCATTCGAGCTCAAGTCAGC
40735574 TCATTCGAGCTCAAGTCAGC
1 TCATTCGAGCTCAAGTCAGC
*
40735594 ACATT-GAGCTC
1 TCATTCGAGCTC
40735605 GTTATTAGCT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 6 0.21
20 23 0.79
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.27
Consensus pattern (20 bp):
TCATTCGAGCTCAAGTCAGC
Found at i:40735828 original size:41 final size:41
Alignment explanation
Indices: 40735783--40735913 Score: 226
Period size: 41 Copynumber: 3.2 Consensus size: 41
40735773 CCTATTTTCA
*
40735783 TACATGTTATAAATATGTCTGGACGAATTTAATGCTGCCAC
1 TACATGTTATAAATATGCCTGGACGAATTTAATGCTGCCAC
*
40735824 TACATGTTATAAATATGCCTGGGCGAATTTAATGCTGCCAC
1 TACATGTTATAAATATGCCTGGACGAATTTAATGCTGCCAC
*
40735865 TACATGTTATAAATATGCCTGGACGAATTTAATGCTGCTAC
1 TACATGTTATAAATATGCCTGGACGAATTTAATGCTGCCAC
*
40735906 CACATGTT
1 TACATGTT
40735914 TGGCCGAATT
Statistics
Matches: 85, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 85 1.00
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.34
Consensus pattern (41 bp):
TACATGTTATAAATATGCCTGGACGAATTTAATGCTGCCAC
Found at i:40747547 original size:50 final size:49
Alignment explanation
Indices: 40747489--40747682 Score: 183
Period size: 50 Copynumber: 3.9 Consensus size: 49
40747479 CATTGAGGTT
* *
40747489 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAG
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CGAC
** * * * * *
40747539 ATGAGAGGTCCCCCGTAAGACCGTGTTTGGGACATGGCATGGGCACAAAT
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAC-GAC
** * * *
40747589 ATGAGAACTCCCATATAAGACCATATCTGGGATATGGCATTGGCA-GTAC
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACG-AC
* * ** *
40747638 AAGAAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
40747683 TGTTATTATC
Statistics
Matches: 114, Mismatches: 28, Indels: 5
0.78 0.19 0.03
Matches are distributed among these distances:
49 39 0.34
50 75 0.66
ACGTcount: A:0.28, C:0.22, G:0.28, T:0.22
Consensus pattern (49 bp):
ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACGAC
Found at i:40754671 original size:50 final size:50
Alignment explanation
Indices: 40754565--40754806 Score: 209
Period size: 50 Copynumber: 4.7 Consensus size: 50
40754555 GGTGATGAGA
* * * *
40754565 TCCCATGTAAGACCATGTTTGGAACATGGCATTGGCATCATTGAGGTTATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGA---CATGAGAGG
* * *
40754621 TCCCATGTAAGACCATGTCCGGGACATGGCGTTGGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGACATGAGAGG
** * * * **
40754671 TCCCCCGTAAGACCGTGTCTGGGACATGGCATGGGCACCGATATGAGAAA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGACATGAGAGG
* * * * * *
40754721 TCCCATGTAAGACCATATTTGGGATATGGCATTGGCA--GTACAAGAAACG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-ACATGAGAGG
* *
40754770 TCCCATGTAAGACCATGTCTGAGACATGGCTTTGGCA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
40754807 TGTTATTATT
Statistics
Matches: 153, Mismatches: 32, Indels: 9
0.79 0.16 0.05
Matches are distributed among these distances:
48 1 0.01
49 37 0.24
50 79 0.52
53 2 0.01
55 1 0.01
56 33 0.22
ACGTcount: A:0.27, C:0.21, G:0.29, T:0.23
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGACATGAGAGG
Found at i:40756344 original size:32 final size:31
Alignment explanation
Indices: 40756303--40756419 Score: 153
Period size: 32 Copynumber: 3.6 Consensus size: 31
40756293 GCGATGCTAA
*
40756303 TGATGGCTTTGTGCCAGTCATAGTACCGTTAC
1 TGATGGCTTTGTGCGA-TCATAGTACCGTTAC
*
40756335 TGATGGCTTTGTTTCGATCATAGTACCGTTAC
1 TGATGGCTTTG-TGCGATCATAGTACCGTTAC
*
40756367 TGATGGCTTTGTGCTGATCATATTACCGTTAC
1 TGATGGCTTTGTGC-GATCATAGTACCGTTAC
* *
40756399 CGATGGCTGTGTGTCGATCAT
1 TGATGGCTTTGTG-CGATCAT
40756420 TTCACTATTA
Statistics
Matches: 76, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
31 2 0.03
32 70 0.92
33 4 0.05
ACGTcount: A:0.18, C:0.20, G:0.25, T:0.38
Consensus pattern (31 bp):
TGATGGCTTTGTGCGATCATAGTACCGTTAC
Found at i:40756481 original size:32 final size:31
Alignment explanation
Indices: 40756303--40756483 Score: 141
Period size: 32 Copynumber: 5.7 Consensus size: 31
40756293 GCGATGCTAA
40756303 TGATGGCTTTGTGCC-AGTCATAGTACCGTTAC
1 TGATGGCTTTGTGCCGA-TCATA-TACCGTTAC
**
40756335 TGATGGCTTTGTTTCGATCATAGTACCGTTAC
1 TGATGGCTTTGTGCCGATCATA-TACCGTTAC
*
40756367 TGATGGCTTTGTGCTGATCATATTACCGTTAC
1 TGATGGCTTTGTGCCGATCATA-TACCGTTAC
* * * * **
40756399 CGATGGCTGTGTGTCGATCATTTCACTATTAC
1 TGATGGCTTTGTGCCGATCATAT-ACCGTTAC
* * * * * *
40756431 AGATTG-TTGTGTGTCGGTCATATCACTGCTAC
1 TGATGGCTT-TGTGCCGATCATAT-ACCGTTAC
*
40756463 TGATGGCTTTGTGCCGGTCAT
1 TGATGGCTTTGTGCCGATCAT
40756484 GATGCCTATG
Statistics
Matches: 122, Mismatches: 23, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
31 2 0.02
32 117 0.96
33 3 0.02
ACGTcount: A:0.18, C:0.20, G:0.24, T:0.38
Consensus pattern (31 bp):
TGATGGCTTTGTGCCGATCATATACCGTTAC
Found at i:40768537 original size:29 final size:29
Alignment explanation
Indices: 40768502--40768571 Score: 104
Period size: 29 Copynumber: 2.4 Consensus size: 29
40768492 TGATCGACCA
* *
40768502 ATGAAAAGGGATAGCTTTGGTTATCGATT
1 ATGAAAAGGGATAGCTTCGATTATCGATT
**
40768531 ATGAAAATAGATAGCTTCGATTATCGATT
1 ATGAAAAGGGATAGCTTCGATTATCGATT
40768560 ATGAAAAGGGAT
1 ATGAAAAGGGAT
40768572 GGTGACGACC
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.37, C:0.07, G:0.24, T:0.31
Consensus pattern (29 bp):
ATGAAAAGGGATAGCTTCGATTATCGATT
Found at i:40768591 original size:29 final size:29
Alignment explanation
Indices: 40768559--40768729 Score: 200
Period size: 29 Copynumber: 5.9 Consensus size: 29
40768549 GATTATCGAT
40768559 TATGAAAAGGGATGGTGACGACCATCAAC
1 TATGAAAAGGGATGGTGACGACCATCAAC
* * * *
40768588 TATGAAAAGGGATGGTAATGACCATGAAA
1 TATGAAAAGGGATGGTGACGACCATCAAC
*
40768617 TATGAAAAGGGATAGTGACGACCATCAAC
1 TATGAAAAGGGATGGTGACGACCATCAAC
* * *
40768646 TATGAAAAGGGATGGTGACAACCATCGAT
1 TATGAAAAGGGATGGTGACGACCATCAAC
**
40768675 TAATGAAAAGGGATGGTTTCGACCATCGAA-
1 T-ATGAAAAGGGATGGTGACGACCATC-AAC
* **
40768705 TATGAAAATGGATGGTTTCGACCAT
1 TATGAAAAGGGATGGTGACGACCAT
40768730 TGAATATGAA
Statistics
Matches: 122, Mismatches: 18, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
29 98 0.80
30 23 0.19
31 1 0.01
ACGTcount: A:0.39, C:0.13, G:0.26, T:0.22
Consensus pattern (29 bp):
TATGAAAAGGGATGGTGACGACCATCAAC
Found at i:40768660 original size:58 final size:56
Alignment explanation
Indices: 40768559--40768760 Score: 208
Period size: 58 Copynumber: 3.5 Consensus size: 56
40768549 GATTATCGAT
*
40768559 TATGAAAAGGGATGGTGACGACCATCAACTATGAAAAGGGATGGTAATGACCATGAAA
1 TATGAAAAGGGATAGTGACGACCATCAACTATGAAAAGGGATGGT-ATGACCATG-AA
** *
40768617 TATGAAAAGGGATAGTGACGACCATCAACTATGAAAAGGGATGGTGACAACCATCGAT
1 TATGAAAAGGGATAGTGACGACCATCAACTATGAAAAGGGATGGT-ATGACCAT-GAA
* ** * *
40768675 TAATGAAAAGGGATGGTTTCGACCATCGAA-TATGAAAATGGATGGTTTCGACCATTGAA
1 T-ATGAAAAGGGATAGTGACGACCATC-AACTATGAAAAGGGATGGTAT-GACCA-TGAA
* * * *
40768734 TATGAAAATGGACAGTTACTACCATCA
1 TATGAAAAGGGATAGTGACGACCATCA
40768761 TTTAGAACAC
Statistics
Matches: 121, Mismatches: 18, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
57 1 0.01
58 72 0.60
59 45 0.37
60 3 0.02
ACGTcount: A:0.39, C:0.14, G:0.25, T:0.22
Consensus pattern (56 bp):
TATGAAAAGGGATAGTGACGACCATCAACTATGAAAAGGGATGGTATGACCATGAA
Found at i:40768757 original size:29 final size:29
Alignment explanation
Indices: 40768553--40768759 Score: 105
Period size: 29 Copynumber: 7.1 Consensus size: 29
40768543 AGCTTCGATT
* * ** *
40768553 ATCGATTATGAAAAGGGATGGTGACGACC
1 ATCGAATATGAAAATGGACAGTTACGACC
* ** * *
40768582 ATC-AACTATGAAAAGGGATGGTAATGACC
1 ATCGAA-TATGAAAATGGACAGTTACGACC
* * *
40768611 AT-GAAATATGAAAAGGGATAGTGACGACC
1 ATCG-AATATGAAAATGGACAGTTACGACC
* ** * *
40768640 ATC-AACTATGAAAAGGGATGGTGACAACC
1 ATCGAA-TATGAAAATGGACAGTTACGACC
* * ** *
40768669 ATCGATTAATGAAAAGGGATGGTTTCGACC
1 ATCGAAT-ATGAAAATGGACAGTTACGACC
** *
40768699 ATCGAATATGAAAATGGATGGTTTCGACC
1 ATCGAATATGAAAATGGACAGTTACGACC
* *
40768728 ATTGAATATGAAAATGGACAGTTACTACC
1 ATCGAATATGAAAATGGACAGTTACGACC
40768757 ATC
1 ATC
40768760 ATTTAGAACA
Statistics
Matches: 151, Mismatches: 20, Indels: 14
0.82 0.11 0.08
Matches are distributed among these distances:
28 3 0.02
29 120 0.79
30 28 0.19
ACGTcount: A:0.39, C:0.14, G:0.25, T:0.23
Consensus pattern (29 bp):
ATCGAATATGAAAATGGACAGTTACGACC
Found at i:40768758 original size:88 final size:88
Alignment explanation
Indices: 40768559--40768759 Score: 203
Period size: 88 Copynumber: 2.3 Consensus size: 88
40768549 GATTATCGAT
** * * *
40768559 TATGAAAAGGGATGGTGACGACCATCAACT-ATGAAAAGGGATGGTAATGACCATGAAATATGAA
1 TATGAAAAGGGACAGTGACAACCATCGATTAATGAAAAGGGATGGTAATGACCATGAAATATGAA
40768623 AAGGGATAGTGACGACCATCAAC
66 AAGGGATAGTGACGACCATCAAC
** *
40768646 TATGAAAAGGGATGGTGACAACCATCGATTAATGAAAAGGGATGGT-TTCGACCATCG-AATATG
1 TATGAAAAGGGACAGTGACAACCATCGATTAATGAAAAGGGATGGTAAT-GACCAT-GAAATATG
* * ** *
40768709 AAAATGGATGGTTTCGACCATTGAA-
64 AAAAGGGATAGTGACGACCA-TCAAC
* * *
40768734 TATGAAAATGGACAGTTACTACCATC
1 TATGAAAAGGGACAGTGACAACCATC
40768760 ATTTAGAACA
Statistics
Matches: 96, Mismatches: 14, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
87 28 0.29
88 64 0.67
89 4 0.04
ACGTcount: A:0.39, C:0.14, G:0.25, T:0.22
Consensus pattern (88 bp):
TATGAAAAGGGACAGTGACAACCATCGATTAATGAAAAGGGATGGTAATGACCATGAAATATGAA
AAGGGATAGTGACGACCATCAAC
Found at i:40777576 original size:50 final size:50
Alignment explanation
Indices: 40777467--40777650 Score: 158
Period size: 51 Copynumber: 3.7 Consensus size: 50
40777457 AGTTGCTAGG
* * *
40777467 TCACGTGTGTAGTACTATGTGTAGGCTACTATGTGTACCGGAATGATAGG
1 TCACGTGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGAATGATAGA
* * * * *
40777517 TCGCATGTGTAGCACTATGTGCA-GCTACTATGCGTACCGG-ATAGCTTCGA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGAAT-G-ATAGA
* * * * * * *
40777567 TCACGTGTGTAGTACTTTATGCAGGCTACTACGTGTATCGG-ATGAAAATGG
1 TCACGTGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGAATG-ATA-GA
* *
40777618 TCACATGTGTAGTACTATGTGTAGGCTACTATG
1 TCACGTGTGTAGTACTATGTGCAGGCTACTATG
40777651 TGAACCGGGT
Statistics
Matches: 104, Mismatches: 26, Indels: 7
0.76 0.19 0.05
Matches are distributed among these distances:
48 2 0.02
49 17 0.16
50 40 0.38
51 45 0.43
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.32
Consensus pattern (50 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGAATGATAGA
Found at i:40782260 original size:20 final size:20
Alignment explanation
Indices: 40782235--40782457 Score: 123
Period size: 20 Copynumber: 11.2 Consensus size: 20
40782225 AAATGAAGAA
40782235 GTGCCCCTGAATGCACATCT
1 GTGCCCCTGAATGCACATCT
** * *
40782255 GTGCCCCTGTTTGCACTTCG
1 GTGCCCCTGAATGCACATCT
*
40782275 GTGCCTCTGAATGCACATCT
1 GTGCCCCTGAATGCACATCT
* * * * * *
40782295 ATGCCTCT-ATTTACACTTCA
1 GTGCCCCTGA-ATGCACATCT
* *
40782315 GTG-CCCTAAATGCACATTT
1 GTGCCCCTGAATGCACATCT
** *
40782334 GTGCCCCTGTTTGCACTTC-
1 GTGCCCCTGAATGCACATCT
40782353 GATGCCCCTGAATGCACATCT
1 G-TGCCCCTGAATGCACATCT
* * ** * *
40782374 ATG-CCTTGTTTGCACTTCA
1 GTGCCCCTGAATGCACATCT
* *
40782393 GTGCCCCTAAATGCACATTT
1 GTGCCCCTGAATGCACATCT
** * *
40782413 GTGCCCCTGTTTTCACTTC-
1 GTGCCCCTGAATGCACATCT
40782432 GCTGCCCCTGAATGCACATCT
1 G-TGCCCCTGAATGCACATCT
*
40782453 ATGCC
1 GTGCC
40782458 TTATTTGCAC
Statistics
Matches: 141, Mismatches: 54, Indels: 16
0.67 0.26 0.08
Matches are distributed among these distances:
19 27 0.19
20 114 0.81
ACGTcount: A:0.17, C:0.33, G:0.17, T:0.32
Consensus pattern (20 bp):
GTGCCCCTGAATGCACATCT
Found at i:40782279 original size:40 final size:40
Alignment explanation
Indices: 40782235--40782520 Score: 312
Period size: 40 Copynumber: 7.2 Consensus size: 40
40782225 AAATGAAGAA
*
40782235 GTGCCCCTGAATGCACATCTGTGCCCCTGTTTGCACTTCG
1 GTGCCCCTGAATGCACATCTATGCCCCTGTTTGCACTTCG
* * * * *
40782275 GTGCCTCTGAATGCACATCTATGCCTCTATTTACACTTCA
1 GTGCCCCTGAATGCACATCTATGCCCCTGTTTGCACTTCG
* * *
40782315 GTG-CCCTAAATGCACATTTGTGCCCCTGTTTGCACTTCG
1 GTGCCCCTGAATGCACATCTATGCCCCTGTTTGCACTTCG
* * *
40782354 ATGCCCCTGAATGCACATCTATG-CCTTGTTTGCACTTCA
1 GTGCCCCTGAATGCACATCTATGCCCCTGTTTGCACTTCG
* * * *
40782393 GTGCCCCTAAATGCACATTTGTGCCCCTGTTTTCACTTCG
1 GTGCCCCTGAATGCACATCTATGCCCCTGTTTGCACTTCG
* * *
40782433 CTGCCCCTGAATGCACATCTATG-CCTTATTTGCACTTCG
1 GTGCCCCTGAATGCACATCTATGCCCCTGTTTGCACTTCG
* * * *
40782472 GTGCCCCT-AATCGCACAT-TCATGCTCCTGATTGCAATTTG
1 GTGCCCCTGAAT-GCACATCT-ATGCCCCTGTTTGCACTTCG
40782512 GTGCCCCTG
1 GTGCCCCTG
40782521 TTAAGCATCT
Statistics
Matches: 199, Mismatches: 41, Indels: 11
0.79 0.16 0.04
Matches are distributed among these distances:
38 4 0.02
39 92 0.46
40 103 0.52
ACGTcount: A:0.17, C:0.32, G:0.18, T:0.33
Consensus pattern (40 bp):
GTGCCCCTGAATGCACATCTATGCCCCTGTTTGCACTTCG
Found at i:40782339 original size:79 final size:79
Alignment explanation
Indices: 40782234--40782490 Score: 401
Period size: 79 Copynumber: 3.3 Consensus size: 79
40782224 AAAATGAAGA
* * * *
40782234 AGTGCCCCTGAATGCACATCTGTGCCCCTGTTTGCACTTCGGTGCCTCTGAATGCACATCTATGC
1 AGTGCCCCTAAATGCACATTTGTGCCCCTGTTTGCACTTCGATGCCCCTGAATGCACATCTATGC
*
40782299 CTCTATTTACACTTC
66 CT-TATTTGCACTTC
40782314 AGTG-CCCTAAATGCACATTTGTGCCCCTGTTTGCACTTCGATGCCCCTGAATGCACATCTATGC
1 AGTGCCCCTAAATGCACATTTGTGCCCCTGTTTGCACTTCGATGCCCCTGAATGCACATCTATGC
*
40782378 CTTGTTTGCACTTC
66 CTTATTTGCACTTC
* *
40782392 AGTGCCCCTAAATGCACATTTGTGCCCCTGTTTTCACTTCGCTGCCCCTGAATGCACATCTATGC
1 AGTGCCCCTAAATGCACATTTGTGCCCCTGTTTGCACTTCGATGCCCCTGAATGCACATCTATGC
40782457 CTTATTTGCACTTC
66 CTTATTTGCACTTC
*
40782471 GGTGCCCCT-AATCGCACATT
1 AGTGCCCCTAAAT-GCACATT
40782491 CATGCTCCTG
Statistics
Matches: 165, Mismatches: 10, Indels: 5
0.92 0.06 0.03
Matches are distributed among these distances:
78 17 0.10
79 144 0.87
80 4 0.02
ACGTcount: A:0.18, C:0.32, G:0.17, T:0.33
Consensus pattern (79 bp):
AGTGCCCCTAAATGCACATTTGTGCCCCTGTTTGCACTTCGATGCCCCTGAATGCACATCTATGC
CTTATTTGCACTTC
Found at i:40782517 original size:79 final size:79
Alignment explanation
Indices: 40782234--40782520 Score: 391
Period size: 79 Copynumber: 3.6 Consensus size: 79
40782224 AAAATGAAGA
* *
40782234 AGTGCCCCTGAATGCACA-TCTGTGCCCCTGTTTGCACTTCGGTGCCTCTGAATGCACATCTATG
1 AGTGCCCCTAAATGCACATTC-GTGCCCCTGTTTGCACTTCGGTGCCCCTGAATGCACATCTATG
*
40782298 CCTCTATTTACACTTC
65 CCT-TATTTGCACTTC
* *
40782314 AGTG-CCCTAAATGCACATTTGTGCCCCTGTTTGCACTTCGATGCCCCTGAATGCACATCTATGC
1 AGTGCCCCTAAATGCACATTCGTGCCCCTGTTTGCACTTCGGTGCCCCTGAATGCACATCTATGC
*
40782378 CTTGTTTGCACTTC
66 CTTATTTGCACTTC
* * *
40782392 AGTGCCCCTAAATGCACATTTGTGCCCCTGTTTTCACTTCGCTGCCCCTGAATGCACATCTATGC
1 AGTGCCCCTAAATGCACATTCGTGCCCCTGTTTGCACTTCGGTGCCCCTGAATGCACATCTATGC
40782457 CTTATTTGCACTTC
66 CTTATTTGCACTTC
* * * * * *
40782471 GGTGCCCCT-AATCGCACATTCATGCTCCTGATTGCAATTTGGTGCCCCTG
1 AGTGCCCCTAAAT-GCACATTCGTGCCCCTGTTTGCACTTCGGTGCCCCTG
40782521 TTAAGCATCT
Statistics
Matches: 186, Mismatches: 18, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
78 17 0.09
79 164 0.88
80 5 0.03
ACGTcount: A:0.17, C:0.32, G:0.18, T:0.33
Consensus pattern (79 bp):
AGTGCCCCTAAATGCACATTCGTGCCCCTGTTTGCACTTCGGTGCCCCTGAATGCACATCTATGC
CTTATTTGCACTTC
Found at i:40791374 original size:24 final size:25
Alignment explanation
Indices: 40791347--40791396 Score: 61
Period size: 23 Copynumber: 2.1 Consensus size: 25
40791337 AAATTGGAAA
40791347 AAAAAT-GAGAAAGAA-AAAGAAAAG
1 AAAAATAGA-AAAGAAGAAAGAAAAG
*
40791371 -AAAATAGAAAAGAAGAAAGGAAAG
1 AAAAATAGAAAAGAAGAAAGAAAAG
40791395 AA
1 AA
40791397 TGAGGTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
23 11 0.50
24 10 0.45
25 1 0.05
ACGTcount: A:0.74, C:0.00, G:0.22, T:0.04
Consensus pattern (25 bp):
AAAAATAGAAAAGAAGAAAGAAAAG
Found at i:40791394 original size:12 final size:11
Alignment explanation
Indices: 40791343--40791396 Score: 56
Period size: 12 Copynumber: 4.7 Consensus size: 11
40791333 AGGAAAATTG
*
40791343 GAAAA-AAAAT
1 GAAAAGAAAAA
40791353 GAGAAAGAAAAA
1 GA-AAAGAAAAA
40791365 GAAAAGAAAATA
1 GAAAAGAAAA-A
40791377 GAAAAGAAGAAA
1 GAAAAGAA-AAA
*
40791389 GGAAAGAA
1 GAAAAGAA
40791397 TGAGGTAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
10 2 0.05
11 11 0.29
12 23 0.61
13 2 0.05
ACGTcount: A:0.74, C:0.00, G:0.22, T:0.04
Consensus pattern (11 bp):
GAAAAGAAAAA
Found at i:40794064 original size:13 final size:13
Alignment explanation
Indices: 40794048--40794095 Score: 64
Period size: 13 Copynumber: 3.7 Consensus size: 13
40794038 ATGAAATATT
40794048 TTAAAATAAATTG
1 TTAAAATAAATTG
40794061 TT-AAATATAATT-
1 TTAAAATA-AATTG
40794073 TTAAAATAAATTG
1 TTAAAATAAATTG
40794086 TTAAATATAA
1 TTAAA-ATAA
40794096 TTTTACATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
12 11 0.35
13 16 0.52
14 4 0.13
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (13 bp):
TTAAAATAAATTG
Found at i:40794076 original size:12 final size:12
Alignment explanation
Indices: 40794045--40794100 Score: 62
Period size: 12 Copynumber: 4.5 Consensus size: 12
40794035 TTAATGAAAT
40794045 ATTTTAAAATAA
1 ATTTTAAAATAA
40794057 ATTGTT-AAATATA
1 ATT-TTAAAATA-A
40794070 ATTTTAAAATAA
1 ATTTTAAAATAA
40794082 ATTGTT-AAATATA
1 ATT-TTAAAATA-A
40794095 ATTTTA
1 ATTTTA
40794101 CATTTTATTA
Statistics
Matches: 38, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
12 21 0.55
13 17 0.45
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (12 bp):
ATTTTAAAATAA
Found at i:40794078 original size:25 final size:25
Alignment explanation
Indices: 40794045--40794100 Score: 112
Period size: 25 Copynumber: 2.2 Consensus size: 25
40794035 TTAATGAAAT
40794045 ATTTTAAAATAAATTGTTAAATATA
1 ATTTTAAAATAAATTGTTAAATATA
40794070 ATTTTAAAATAAATTGTTAAATATA
1 ATTTTAAAATAAATTGTTAAATATA
40794095 ATTTTA
1 ATTTTA
40794101 CATTTTATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (25 bp):
ATTTTAAAATAAATTGTTAAATATA
Found at i:40794097 original size:13 final size:13
Alignment explanation
Indices: 40794051--40794097 Score: 64
Period size: 12 Copynumber: 3.8 Consensus size: 13
40794041 AAATATTTTA
40794051 AAATA-AATTGTT
1 AAATATAATTGTT
40794063 AAATATAATT-TT
1 AAATATAATTGTT
40794075 AAA-ATAAATTGTT
1 AAATAT-AATTGTT
40794088 AAATATAATT
1 AAATATAATT
40794098 TTACATTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
11 2 0.06
12 14 0.45
13 13 0.42
14 2 0.06
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (13 bp):
AAATATAATTGTT
Found at i:40805231 original size:53 final size:50
Alignment explanation
Indices: 40805068--40805242 Score: 233
Period size: 50 Copynumber: 3.4 Consensus size: 50
40805058 GGGAATGAGA
40805068 TCCCATGTAAGACCATGTCTGGGACATGGCGTAGGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCGTAGGCACCGAGATGAGAGG
*
40805118 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCGTAGGCACCGAGATGAGAGG
** * * * **
40805168 TCCCCCGTAAGACCAAGTCTGGGACATGGTGGCATAGGCACCGATATGAGAAC
1 TCCCATGTAAGACCATGTCTGGGACA---TGGCGTAGGCACCGAGATGAGAGG
* *
40805221 TCTCATGTAAGACCATATCTGG
1 TCCCATGTAAGACCATGTCTGG
40805243 AATATGACAT
Statistics
Matches: 108, Mismatches: 14, Indels: 3
0.86 0.11 0.02
Matches are distributed among these distances:
50 72 0.67
53 36 0.33
ACGTcount: A:0.26, C:0.23, G:0.30, T:0.20
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCGTAGGCACCGAGATGAGAGG
Found at i:40805256 original size:103 final size:100
Alignment explanation
Indices: 40805074--40805257 Score: 242
Period size: 103 Copynumber: 1.8 Consensus size: 100
40805064 GAGATCCCAT
* * ** *
40805074 GTAAGACCATGTCTGGGACATGGCGTAGGCACCGAGATGAGAGGTCCCATGTAAGACCATGTCTG
1 GTAAGACCAAGTCTGGGACATGGCATAGGCACCGAGATGAGAACTCCCATGTAAGACCATATCTG
* * *
40805139 GGACATGGCGTTGGCACCGAGATGAGAGGTCCCCC
66 GAACATGACATTGGCACCGAGATGAGAGGTCCCCC
* *
40805174 GTAAGACCAAGTCTGGGACATGGTGGCATAGGCACCGATATGAGAACTCTCATGTAAGACCATAT
1 GTAAGACCAAGTCTGGGACA---TGGCATAGGCACCGAGATGAGAACTCCCATGTAAGACCATAT
*
40805239 CTGGAATATGACATTGGCA
63 CTGGAACATGACATTGGCA
40805258 GTAAAGAAAA
Statistics
Matches: 70, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
100 19 0.27
103 51 0.73
ACGTcount: A:0.28, C:0.22, G:0.30, T:0.20
Consensus pattern (100 bp):
GTAAGACCAAGTCTGGGACATGGCATAGGCACCGAGATGAGAACTCCCATGTAAGACCATATCTG
GAACATGACATTGGCACCGAGATGAGAGGTCCCCC
Found at i:40807218 original size:50 final size:50
Alignment explanation
Indices: 40807141--40807436 Score: 403
Period size: 50 Copynumber: 5.9 Consensus size: 50
40807131 TTTTCTGTAT
* * * * * ** *
40807141 TGCCAATGCCATATCCCAAATATGGTCTTACATAGGATTTCTCATATCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * * * * **
40807191 TGCCCATGCCATCTCCTAGACAAGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
40807241 TGCCAACGCCATGTCCCAGACATGGTCTTACATAGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
40807291 CGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGA
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * *
40807341 TGCGAACGCCATGTCCCATACATGGTCTTACATGGGACCTCTCATCTCAG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
40807391 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATC
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATC
40807437 ATGGCTCACA
Statistics
Matches: 216, Mismatches: 30, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 216 1.00
ACGTcount: A:0.22, C:0.32, G:0.20, T:0.25
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:40807267 original size:100 final size:100
Alignment explanation
Indices: 40807093--40807436 Score: 433
Period size: 100 Copynumber: 3.5 Consensus size: 100
40807083 ATAATAAAAA
* * ** * *
40807093 GCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA--TGTTTTCT-GTATTGCCAATGCCATAT
1 GCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCG-A-TGCCAACGCCATGT
* ** *
40807155 CCCAAATATGGTCTTACATAGGATTTCTCATATCGGT
64 CCCAAACATGGTCTTACATAGGACCTCTCATCTCGGT
* * * * * ** *
40807192 GCCCATGCCATCTCCTAGACAAGGTCTTACGGGGGACCTCTCATCTCGGTGCCAACGCCATGTCC
1 GCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGATGCCAACGCCATGTCC
* *
40807257 CAGACATGGTCTTACATAGGACCTCTCATCTCGGC
66 CAAACATGGTCTTACATAGGACCTCTCATCTCGGT
*
40807292 GCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGATGCGAACGCCATGTCC
1 GCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGATGCCAACGCCATGTCC
* * *
40807357 CATACATGGTCTTACATGGGACCTCTCATCTCAGT
66 CAAACATGGTCTTACATAGGACCTCTCATCTCGGT
40807392 GCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATC
1 GCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATC
40807437 ATGGCTCACA
Statistics
Matches: 210, Mismatches: 32, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
99 29 0.14
100 175 0.83
101 5 0.02
102 1 0.00
ACGTcount: A:0.22, C:0.31, G:0.20, T:0.26
Consensus pattern (100 bp):
GCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGATGCCAACGCCATGTCC
CAAACATGGTCTTACATAGGACCTCTCATCTCGGT
Found at i:40811837 original size:50 final size:50
Alignment explanation
Indices: 40811748--40812319 Score: 779
Period size: 50 Copynumber: 11.7 Consensus size: 50
40811738 CAATGTCATA
* ** * * * *
40811748 TCCCAGATATGGTCTTACAT-GGAGTTCTCATATCAGTGCCCATGCCATG
1 TCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATG
** ** **
40811797 TCAAAGACATGGTCTTACGGGGGACCTCTCATCTCGGTGCCAACGCCACA
1 TCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATG
* * *
40811847 TCCCAGACCTAGTCTTACATGAGACCTCTCATCTCGGTGCCAACGCCATG
1 TCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATG
40811897 TCCC--A-A-------ACATGGGACCTCTCATCTCGGTGCCAACGCCATG
1 TCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATG
* *
40811937 TCCCAGACATGGTCTTACATGGGACCTCTCATCTCAGTGCCAACGTCATG
1 TCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATG
* * *
40811987 TCCCAGACATGCTCTTACATGGGACCTCTCATCTCGGTGGCAATGCCATG
1 TCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATG
* *
40812037 TCCCAGACATGCTCTTACATAGGACCTCTCATCTCGGTGCCAACGCCATG
1 TCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATG
40812087 TCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATG
1 TCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATG
* * *
40812137 TCCCAGACATGGTCTTACATGGGACCTCTCATCTTGGTTCCAACGCTATG
1 TCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATG
* * *
40812187 TCCCCGACATGATCTTACATGGGACCTCTCATCTCGGTGCCAACGCCAAG
1 TCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATG
* *
40812237 TCCTAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATA
1 TCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATG
*
40812287 TCCCAGACATGGTCTTTCATGGGACCTCTCATC
1 TCCCAGACATGGTCTTACATGGGACCTCTCATC
40812320 ATGGCTCACA
Statistics
Matches: 460, Mismatches: 52, Indels: 21
0.86 0.10 0.04
Matches are distributed among these distances:
40 37 0.08
42 1 0.00
43 1 0.00
48 1 0.00
49 15 0.03
50 405 0.88
ACGTcount: A:0.22, C:0.33, G:0.20, T:0.25
Consensus pattern (50 bp):
TCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATG
Found at i:40811918 original size:40 final size:40
Alignment explanation
Indices: 40811863--40811948 Score: 154
Period size: 40 Copynumber: 2.1 Consensus size: 40
40811853 ACCTAGTCTT
*
40811863 ACATGAGACCTCTCATCTCGGTGCCAACGCCATGTCCCAA
1 ACATGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAA
*
40811903 ACATGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAG
1 ACATGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAA
40811943 ACATGG
1 ACATGG
40811949 TCTTACATGG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.23, C:0.36, G:0.21, T:0.20
Consensus pattern (40 bp):
ACATGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAA
Found at i:40821447 original size:50 final size:49
Alignment explanation
Indices: 40821393--40821587 Score: 239
Period size: 50 Copynumber: 3.9 Consensus size: 49
40821383 TATTGAGATT
* * * *
40821393 ATGAGAGGTCCCATGCAAGACCATGTCTAGGATATGGTGTTGGCACCGAG
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGG-ATTGGCACCGAG
40821443 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAG
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGG-ATTGGCACCGAG
* * *
40821493 ATGAGAGGTCCCCTGTAAGACCATGTATGGGACATGGCA-TGAGCACCGAT
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGG-ATTG-GCACCGAG
** * *
40821543 ATGAGAACTCCCATGTAAGACCATATCTGGGATATGGCATTGGCA
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGG-ATTGGCA
40821588 GTACAGAAAA
Statistics
Matches: 129, Mismatches: 14, Indels: 4
0.88 0.10 0.03
Matches are distributed among these distances:
49 2 0.02
50 125 0.97
51 2 0.02
ACGTcount: A:0.28, C:0.21, G:0.30, T:0.22
Consensus pattern (49 bp):
ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGATTGGCACCGAG
Found at i:40821448 original size:58 final size:58
Alignment explanation
Indices: 40821339--40821487 Score: 145
Period size: 50 Copynumber: 2.7 Consensus size: 58
40821329 TTAAGGGAAT
* * * *
40821339 GAGGTCCCATGTAAGACCATGTCTGGGACATGGATTGGCATCACTATTGAGATTATGA
1 GAGGTCCCATGCAAGACCATGTCTAGGACATGGATTGGCATCACGAATGAGATTATGA
* *
40821397 GAGGTCCCATGCAAGACCATGTCTAGGATATGGTGTTGGCA-C-C----GAG---ATGA
1 GAGGTCCCATGCAAGACCATGTCTAGGACATGG-ATTGGCATCACGAATGAGATTATGA
* *
40821447 GAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
1 GAGGTCCCATGCAAGACCATGTCTAGGACATGG-ATTGGCA
40821488 CCGAGATGAG
Statistics
Matches: 81, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
50 40 0.49
53 3 0.04
57 1 0.01
58 31 0.38
59 6 0.07
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.24
Consensus pattern (58 bp):
GAGGTCCCATGCAAGACCATGTCTAGGACATGGATTGGCATCACGAATGAGATTATGA
Found at i:40821513 original size:100 final size:100
Alignment explanation
Indices: 40821393--40821587 Score: 266
Period size: 100 Copynumber: 1.9 Consensus size: 100
40821383 TATTGAGATT
* * ** **
40821393 ATGAGAGGTCCCATGCAAGACCATGTCTAGGATATGGTGTTG-GCACCGAGATGAGAGGTCCCAT
1 ATGAGAGGTCCCATGCAAGACCATGTATAGGACATGG-CATGAGCACCGAGATGAGAACTCCCAT
*
40821457 GTAAGACCATGTCTGGGACATGGCATTGGCACCGAG
65 GTAAGACCATATCTGGGACATGGCATTGGCACCGAG
* * * *
40821493 ATGAGAGGTCCCCTGTAAGACCATGTATGGGACATGGCATGAGCACCGATATGAGAACTCCCATG
1 ATGAGAGGTCCCATGCAAGACCATGTATAGGACATGGCATGAGCACCGAGATGAGAACTCCCATG
*
40821558 TAAGACCATATCTGGGATATGGCATTGGCA
66 TAAGACCATATCTGGGACATGGCATTGGCA
40821588 GTACAGAAAA
Statistics
Matches: 82, Mismatches: 12, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
99 2 0.02
100 80 0.98
ACGTcount: A:0.28, C:0.21, G:0.30, T:0.22
Consensus pattern (100 bp):
ATGAGAGGTCCCATGCAAGACCATGTATAGGACATGGCATGAGCACCGAGATGAGAACTCCCATG
TAAGACCATATCTGGGACATGGCATTGGCACCGAG
Found at i:40821853 original size:12 final size:12
Alignment explanation
Indices: 40821836--40821874 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
40821826 ATGAGTTATT
40821836 TAAGTAAGCAAG
1 TAAGTAAGCAAG
*
40821848 TAAGTAAACAAG
1 TAAGTAAGCAAG
* *
40821860 TAAGTGAGTAAG
1 TAAGTAAGCAAG
40821872 TAA
1 TAA
40821875 AGAAGCGAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.51, C:0.05, G:0.23, T:0.21
Consensus pattern (12 bp):
TAAGTAAGCAAG
Found at i:40823360 original size:11 final size:11
Alignment explanation
Indices: 40823340--40823398 Score: 50
Period size: 11 Copynumber: 5.5 Consensus size: 11
40823330 ATGATGACTG
40823340 ATGA-GAATGA
1 ATGAGGAATGA
40823350 ATGAGGAATGA
1 ATGAGGAATGA
* * *
40823361 TTGAGGGATGC
1 ATGAGGAATGA
*
40823372 GTGAGGAATG-
1 ATGAGGAATGA
*
40823382 ATGAATGAATGA
1 ATG-AGGAATGA
40823394 ATGAG
1 ATGAG
40823399 AGGGTCTTAT
Statistics
Matches: 38, Mismatches: 8, Indels: 5
0.75 0.16 0.10
Matches are distributed among these distances:
10 6 0.16
11 29 0.76
12 3 0.08
ACGTcount: A:0.39, C:0.02, G:0.37, T:0.22
Consensus pattern (11 bp):
ATGAGGAATGA
Found at i:40832877 original size:16 final size:16
Alignment explanation
Indices: 40832856--40832886 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
40832846 TGAAGAAATA
40832856 TTTAAAATTATTATTT
1 TTTAAAATTATTATTT
40832872 TTTAAAATTATTATT
1 TTTAAAATTATTATT
40832887 AAAATAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTAAAATTATTATTT
Found at i:40832952 original size:68 final size:66
Alignment explanation
Indices: 40832880--40833007 Score: 159
Period size: 68 Copynumber: 1.9 Consensus size: 66
40832870 TTTTTAAAAT
* *
40832880 TATTATTAAAATAA-AATTGAAATATTAAATACTTTATTAAAATAATAAATTATATTAAATATAT
1 TATTAATAAAATAATAATT-AAATAATAAATA-TTTATTAAAATAATAAA-TATATTAAATATAT
40832944 TAAA
63 TAAA
** * * *
40832948 TATTAATAATTTAATAATTTAATAATAAATATTTATTAAAATTATAAATATATTCAATAT
1 TATTAATAAAATAATAATTAAATAATAAATATTTATTAAAATAATAAATATATTAAATAT
40833008 CAGAAATTTG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
66 11 0.21
67 16 0.31
68 21 0.40
69 4 0.08
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.44
Consensus pattern (66 bp):
TATTAATAAAATAATAATTAAATAATAAATATTTATTAAAATAATAAATATATTAAATATATTAA
A
Found at i:40836450 original size:60 final size:60
Alignment explanation
Indices: 40836230--40836459 Score: 219
Period size: 60 Copynumber: 3.9 Consensus size: 60
40836220 AGTCAGGGAC
* * * ** * *
40836230 ACCAAAGTGCGAACAGGGGCACGA-CGTGCAAACAGGGATACTGAAGTTTATATAGGTGT
1 ACCAAAGTGCGAACAAGGGCACAATCGTGCAAACAGGGACACCAAAGTGTATATAGGGGT
* * * * * * * * *
40836289 GCCGAAGTGTGAACAAAGGCACAATCCTGCAAACAGGGACACTAAGGTGTACATAGGGGC
1 ACCAAAGTGCGAACAAGGGCACAATCGTGCAAACAGGGACACCAAAGTGTATATAGGGGT
* * * *
40836349 ACCAAAGTGCAAACAAGGGCAAAATCATGCAAATAGGGACACCAAAGTGTATATAGGGGT
1 ACCAAAGTGCGAACAAGGGCACAATCGTGCAAACAGGGACACCAAAGTGTATATAGGGGT
* * * ** *
40836409 ACCAGAGTGCGAACAGGGGCACAGTCGTGCAAACAATGACACCGAAGTGTA
1 ACCAAAGTGCGAACAAGGGCACAATCGTGCAAACAGGGACACCAAAGTGTA
40836460 GAGAGGGGCA
Statistics
Matches: 134, Mismatches: 36, Indels: 1
0.78 0.21 0.01
Matches are distributed among these distances:
59 18 0.13
60 116 0.87
ACGTcount: A:0.37, C:0.20, G:0.29, T:0.15
Consensus pattern (60 bp):
ACCAAAGTGCGAACAAGGGCACAATCGTGCAAACAGGGACACCAAAGTGTATATAGGGGT
Found at i:40836473 original size:20 final size:20
Alignment explanation
Indices: 40836448--40836490 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
40836438 CAAACAATGA
* * *
40836448 CACCGAAGTGTAGAGAGGGG
1 CACCGAAGAGTAAACAGGGG
40836468 CACCGAAGAGTAAACAGGGG
1 CACCGAAGAGTAAACAGGGG
40836488 CAC
1 CAC
40836491 TTCTTCATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.21, G:0.37, T:0.07
Consensus pattern (20 bp):
CACCGAAGAGTAAACAGGGG
Found at i:40840445 original size:15 final size:16
Alignment explanation
Indices: 40840416--40840445 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
40840406 CAAACATGCT
40840416 TTAACACATTATCAAA
1 TTAACACATTATCAAA
40840432 TTAACACA-TATCAA
1 TTAACACATTATCAA
40840446 CAAGGCACCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.50, C:0.20, G:0.00, T:0.30
Consensus pattern (16 bp):
TTAACACATTATCAAA
Found at i:40841661 original size:25 final size:24
Alignment explanation
Indices: 40841619--40841676 Score: 64
Period size: 25 Copynumber: 2.4 Consensus size: 24
40841609 AGCTATAAAC
*
40841619 CGGTAAGCTCGTATGAGCTGAGAAT
1 CGGTAAGCTCGTACGAGCTG-GAAT
*
40841644 CGGTAAGCTC-TCACGAGCTGTAAT
1 CGGTAAGCTCGT-ACGAGCTGGAAT
*
40841668 CGATAAGCT
1 CGGTAAGCT
40841677 AATACAAGCT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
24 12 0.41
25 17 0.59
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.24
Consensus pattern (24 bp):
CGGTAAGCTCGTACGAGCTGGAAT
Found at i:40845074 original size:27 final size:27
Alignment explanation
Indices: 40844702--40845070 Score: 353
Period size: 27 Copynumber: 13.7 Consensus size: 27
40844692 TACCCTCGAT
* * * **
40844702 GGGTAAAATGATCGAAATGCCCCCATA
1 GGGTAAAATGACCGTAATACCCCTGTA
* *
40844729 GGGTAAAATGACTGTAATACCCCTATA
1 GGGTAAAATGACCGTAATACCCCTGTA
* *
40844756 GGGTAAAATAACCGTAATACCCCTATA
1 GGGTAAAATGACCGTAATACCCCTGTA
* * *
40844783 GGGTAAAATAACCGTAATGCCCCTATA
1 GGGTAAAATGACCGTAATACCCCTGTA
* *
40844810 GGGTAAAATGACCGTATTACCCCAGTA
1 GGGTAAAATGACCGTAATACCCCTGTA
*
40844837 GGGTAAAATGACTC-TAATACCCCTATA
1 GGGTAAAATGAC-CGTAATACCCCTGTA
* * *
40844864 GGGTAAAATAACCATAATGCCCCTGTA
1 GGGTAAAATGACCGTAATACCCCTGTA
* *
40844891 GGGTAAAATAACCGTAATACCCTTGTA
1 GGGTAAAATGACCGTAATACCCCTGTA
* * * * **
40844918 AGGTGAAATAACCATAATACCTTTGTA
1 GGGTAAAATGACCGTAATACCCCTGTA
* * *
40844945 GGGTAAAATGACCATAATGCCCCAGTA
1 GGGTAAAATGACCGTAATACCCCTGTA
* * **
40844972 TGGTAAAATGACCATAATGGCCCTGTA
1 GGGTAAAATGACCGTAATACCCCTGTA
* * *
40844999 AGGTAAAATGACCATAATACCCGTGTA
1 GGGTAAAATGACCGTAATACCCCTGTA
** * * *
40845026 CTGTAAAATTACCGTAATGCCCCTGTC
1 GGGTAAAATGACCGTAATACCCCTGTA
40845053 GGGTAAAATGACCGTAAT
1 GGGTAAAATGACCGTAAT
40845071 GCCCTGGTGG
Statistics
Matches: 290, Mismatches: 50, Indels: 4
0.84 0.15 0.01
Matches are distributed among these distances:
26 1 0.00
27 288 0.99
28 1 0.00
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.24
Consensus pattern (27 bp):
GGGTAAAATGACCGTAATACCCCTGTA
Found at i:40845170 original size:24 final size:23
Alignment explanation
Indices: 40845111--40845192 Score: 92
Period size: 24 Copynumber: 3.5 Consensus size: 23
40845101 TTCGAGGTCA
* * * *
40845111 AATGATTGTTTTGTCTGTGGTTA
1 AATGACTGATTTGTCTGTGTTTG
40845134 AATGACTGATTTGTCTGTGTTTG
1 AATGACTGATTTGTCTGTGTTTG
* *
40845157 ATATGACTGGTTTGTCTATGATTTG
1 A-ATGACTGATTTGTCTGTG-TTTG
40845182 AATGACTGATT
1 AATGACTGATT
40845193 CTAAGCATGG
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
23 20 0.40
24 25 0.50
25 5 0.10
ACGTcount: A:0.21, C:0.07, G:0.24, T:0.48
Consensus pattern (23 bp):
AATGACTGATTTGTCTGTGTTTG
Found at i:40845322 original size:26 final size:26
Alignment explanation
Indices: 40845293--40845366 Score: 121
Period size: 26 Copynumber: 2.8 Consensus size: 26
40845283 TATACTACTA
*
40845293 CTGGCAGCTTTGCTGCGATACTGTTG
1 CTGGCAGCTTTGCTGCGATACTGTTC
*
40845319 CTGGCAGCTTTGCTGCGATATTGTTC
1 CTGGCAGCTTTGCTGCGATACTGTTC
*
40845345 CTGGCAGCTTTGCTACGATACT
1 CTGGCAGCTTTGCTGCGATACT
40845367 ACTGATGGCT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 44 1.00
ACGTcount: A:0.14, C:0.24, G:0.27, T:0.35
Consensus pattern (26 bp):
CTGGCAGCTTTGCTGCGATACTGTTC
Found at i:40845375 original size:26 final size:26
Alignment explanation
Indices: 40845284--40845375 Score: 87
Period size: 26 Copynumber: 3.5 Consensus size: 26
40845274 TTGGCCACAT
40845284 ATACTACT-ACTGGCAGCTTTGCTGCG
1 ATACTACTGA-TGGCAGCTTTGCTGCG
** *
40845310 ATACTGTTGCTGGCAGCTTTGCTGCG
1 ATACTACTGATGGCAGCTTTGCTGCG
* ** ** *
40845336 ATATTGTTCCTGGCAGCTTTGCTACG
1 ATACTACTGATGGCAGCTTTGCTGCG
40845362 ATACTACTGATGGC
1 ATACTACTGATGGC
40845376 TTTGTACCGA
Statistics
Matches: 54, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
26 54 1.00
ACGTcount: A:0.17, C:0.24, G:0.25, T:0.34
Consensus pattern (26 bp):
ATACTACTGATGGCAGCTTTGCTGCG
Done.