Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A02
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: 100057689
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3589301 characters in sequence are not A, C, G, or T
File 119 of 295
Found at i:40904927 original size:22 final size:21
Alignment explanation
Indices: 40904886--40904928 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
40904876 TAATTTTAGG
*
40904886 TTTAGTTTTCTCTAAGCTTTT
1 TTTAGTTTTCTCTAAACTTTT
40904907 TTTAGTTTT-TCTATACACTTTT
1 TTTAGTTTTCTCTA-A-ACTTTT
40904929 CTAGGGTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 4 0.21
21 10 0.53
22 5 0.26
ACGTcount: A:0.16, C:0.14, G:0.07, T:0.63
Consensus pattern (21 bp):
TTTAGTTTTCTCTAAACTTTT
Found at i:40912950 original size:47 final size:47
Alignment explanation
Indices: 40912880--40913135 Score: 187
Period size: 46 Copynumber: 5.5 Consensus size: 47
40912870 ATGCCGATAC
* *
40912880 CATGTCCCAAACATGGTCTTACACTGGCTCATCCATCAA-GTCAATG
1 CATGTCCCAGACATGGTCTTACACTGGCTCATCCATCAAGGTCGATG
* * * *
40912926 CTATGTCCTAGACATGGTCTTACACTGACACATCTCAT-AA-CT-GATG
1 C-ATGTCCCAGACATGGTCTTACACTGGCTCATC-CATCAAGGTCGATG
*
40912972 CATGTCCCAGACAT-GTCTTACACTGGCTGACAT-C-TCAAGGCCGATG
1 CATGTCCCAGACATGGTCTTACACTGGCT--CATCCATCAAGGTCGATG
* * * *
40913018 CATGTCCCAGACAT-GTCTTACACTAGCTC-TCCTCTCAATGTCGTTG
1 CATGTCCCAGACATGGTCTTACACTGGCTCATCC-ATCAAGGTCGATG
** * * *
40913064 CTATGTCTTAGACATGATCTTACACTGGCTC--CCAT-AATGTGGCCTATG
1 C-ATGTCCCAGACATGGTCTTACACTGGCTCATCCATCAA---GGTCGATG
*
40913112 CATGTCTCAGACAT-GTCTTACACT
1 CATGTCCCAGACATGGTCTTACACT
40913136 AGCGCACAAA
Statistics
Matches: 169, Mismatches: 26, Indels: 30
0.75 0.12 0.13
Matches are distributed among these distances:
43 2 0.01
44 17 0.10
45 14 0.08
46 59 0.35
47 56 0.33
48 21 0.12
ACGTcount: A:0.25, C:0.29, G:0.17, T:0.30
Consensus pattern (47 bp):
CATGTCCCAGACATGGTCTTACACTGGCTCATCCATCAAGGTCGATG
Found at i:40914921 original size:16 final size:16
Alignment explanation
Indices: 40914902--40914933 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
40914892 GCAAGGACAT
40914902 ATCGATGCATATTTTA
1 ATCGATGCATATTTTA
40914918 ATCGATGCATATTTTA
1 ATCGATGCATATTTTA
40914934 TAAAGTTCCT
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:0.31, C:0.12, G:0.12, T:0.44
Consensus pattern (16 bp):
ATCGATGCATATTTTA
Found at i:40915233 original size:18 final size:18
Alignment explanation
Indices: 40915199--40915233 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
40915189 ACATGCCCTC
*
40915199 ATAATCACTTATCACATA
1 ATAATCACTTATAACATA
*
40915217 ATAATCACTTTTAACAT
1 ATAATCACTTATAACAT
40915234 GTTTAACATG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.20, G:0.00, T:0.37
Consensus pattern (18 bp):
ATAATCACTTATAACATA
Found at i:40919010 original size:21 final size:21
Alignment explanation
Indices: 40918986--40919034 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
40918976 TTCTACTTAG
* * *
40918986 GTCCAGTCTAATATCTTGTTA
1 GTCCAATCCAATATCCTGTTA
*
40919007 GTCCAATCCAATGTCCTGTTA
1 GTCCAATCCAATATCCTGTTA
40919028 GTCCAAT
1 GTCCAAT
40919035 TAGTTACATC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.24, C:0.24, G:0.14, T:0.37
Consensus pattern (21 bp):
GTCCAATCCAATATCCTGTTA
Found at i:40920259 original size:35 final size:38
Alignment explanation
Indices: 40920220--40920289 Score: 94
Period size: 35 Copynumber: 1.9 Consensus size: 38
40920210 TATCCCATAA
40920220 AATCCTAATC-AATC-CCTAAAA-ATA-AGGTTTGTAAG
1 AATCC-AATCTAATCTCCTAAAAGATAGAGGTTTGTAAG
*
40920255 AATCCAATCTTATCTCCTAAAAGATAGAGGTTTGT
1 AATCCAATCTAATCTCCTAAAAGATAGAGGTTTGT
40920290 TGAAAACTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
34 4 0.13
35 8 0.27
36 7 0.23
37 3 0.10
38 8 0.27
ACGTcount: A:0.39, C:0.17, G:0.13, T:0.31
Consensus pattern (38 bp):
AATCCAATCTAATCTCCTAAAAGATAGAGGTTTGTAAG
Found at i:40923713 original size:9 final size:9
Alignment explanation
Indices: 40923662--40923717 Score: 51
Period size: 9 Copynumber: 6.2 Consensus size: 9
40923652 TTCTTTCTTA
40923662 TTTATTTAT
1 TTTATTTAT
*
40923671 TTAATTT-T
1 TTTATTTAT
**
40923679 TTTAAGTAT
1 TTTATTTAT
*
40923688 TTTATTTGT
1 TTTATTTAT
*
40923697 CCTTATTTAT
1 -TTTATTTAT
40923707 TTTATTTAT
1 TTTATTTAT
40923716 TT
1 TT
40923718 GTTTATTATT
Statistics
Matches: 35, Mismatches: 10, Indels: 4
0.71 0.20 0.08
Matches are distributed among these distances:
8 5 0.14
9 23 0.66
10 7 0.20
ACGTcount: A:0.21, C:0.04, G:0.04, T:0.71
Consensus pattern (9 bp):
TTTATTTAT
Found at i:40923811 original size:12 final size:12
Alignment explanation
Indices: 40923783--40923818 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 12
40923773 TTTTTTAAAA
40923783 TTTTAAATATATAT
1 TTTTAAA-AT-TAT
40923797 TTTTAAAATTAT
1 TTTTAAAATTAT
40923809 TTTTAAAATT
1 TTTTAAAATT
40923819 TTAAATATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 13 0.59
13 2 0.09
14 7 0.32
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
TTTTAAAATTAT
Found at i:40923839 original size:20 final size:20
Alignment explanation
Indices: 40923797--40923856 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
40923787 AAATATATAT
*
40923797 TTTTAAA-ATTATTTTTAAAA
1 TTTTAAATATTATTTTT-TAA
*
40923817 TTTTAAATATTATTTTTTTA
1 TTTTAAATATTATTTTTTAA
40923837 TTTTAAATA-TATTTTTTAA
1 TTTTAAATATTATTTTTTAA
40923856 T
1 T
40923857 AATATAAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
19 10 0.28
20 17 0.47
21 9 0.25
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
TTTTAAATATTATTTTTTAA
Found at i:40923940 original size:156 final size:155
Alignment explanation
Indices: 40923775--40924095 Score: 368
Period size: 156 Copynumber: 2.1 Consensus size: 155
40923765 TATAATATTT
**
40923775 TTTTAAAATTTTAAATA-TAT-A-TT-TTTAAAATTATTTTTAAAATTTTAAATATTATTT-TTT
1 TTTT-AAATTTTAAATAGTATAATTTGTTTAAAA-TATTTTTAAAATTTTAAATATT-TTTATAA
* *
40923835 TATTTTAAATATATTTTTTAATAATATAAAA-AT-TTAAATATTTTAAATATATGACCTTTCAAT
63 TATTTT-AA-AT-TTTTTTAATAATATAAAATATATT--AT-TTTTAAAGATATGACCTTTCAAA
40923898 TTTATTATTAGTTTTATAATATTTTAAATGTATA
122 TTTATTATTAGTTTTATAATATTTTAAATGTATA
* * * * * *
40923932 TTTTAAATTTTAAATATGTTTAATTTGTTTTAAATATTTTTAATATTTTTAGTGTTTTTATAATA
1 TTTTAAATTTTAAATA-GTATAATTTGTTTAAAATATTTTTAAAATTTTAAATATTTTTATAATA
* ** *
40923997 TTTTTAATTTTTTTAATTTTTTAAAATATATTATTTTTAAAGATATGACCTTTCAAATTTATTAT
65 TTTTAAATTTTTTTAATAATATAAAATATATTATTTTTAAAGATATGACCTTTCAAATTTATTAT
*
40924062 TTGTTTTATAATATTTTAAATGTATA
130 TAGTTTTATAATATTTTAAATGTATA
40924088 TTTTAAAT
1 TTTTAAAT
40924096 ATTTTTTAAA
Statistics
Matches: 141, Mismatches: 15, Indels: 17
0.82 0.09 0.10
Matches are distributed among these distances:
156 74 0.52
157 21 0.15
158 6 0.04
159 7 0.05
160 27 0.19
161 6 0.04
ACGTcount: A:0.37, C:0.02, G:0.03, T:0.58
Consensus pattern (155 bp):
TTTTAAATTTTAAATAGTATAATTTGTTTAAAATATTTTTAAAATTTTAAATATTTTTATAATAT
TTTAAATTTTTTTAATAATATAAAATATATTATTTTTAAAGATATGACCTTTCAAATTTATTATT
AGTTTTATAATATTTTAAATGTATA
Found at i:40923970 original size:29 final size:28
Alignment explanation
Indices: 40923938--40924025 Score: 104
Period size: 29 Copynumber: 3.1 Consensus size: 28
40923928 TATATTTTAA
* *
40923938 ATTTTAAATATGTTTAATTTGTTTTAAAT
1 ATTTTTAATATTTTTAATTT-TTTTAAAT
* *
40923967 ATTTTTAATATTTTTAGTGTTTTTATAAT
1 ATTTTTAATATTTTTAATTTTTTTA-AAT
* *
40923996 ATTTTTAATTTTTTTAATTTTTTAAAAT
1 ATTTTTAATATTTTTAATTTTTTTAAAT
40924024 AT
1 AT
40924026 ATTATTTTTA
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
28 10 0.20
29 40 0.80
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.64
Consensus pattern (28 bp):
ATTTTTAATATTTTTAATTTTTTTAAAT
Found at i:40923997 original size:20 final size:18
Alignment explanation
Indices: 40923932--40924020 Score: 74
Period size: 20 Copynumber: 4.8 Consensus size: 18
40923922 TAAATGTATA
* *
40923932 TTTTAA-ATTTTAAATAT
1 TTTTAATATTTTTAATTT
* * *
40923949 GTTTAATTTGTTTTAAATAT
1 TTTTAATAT-TTTT-AATTT
*
40923969 TTTTAATATTTTTAGTGTT
1 TTTTAATATTTTTAAT-TT
40923988 TTTATAATATTTTTAATTT
1 TTT-TAATATTTTTAATTT
40924007 TTTTAAT-TTTTTAA
1 TTTTAATATTTTTAA
40924021 AATATATTAT
Statistics
Matches: 59, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
17 12 0.20
18 7 0.12
19 16 0.27
20 24 0.41
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.65
Consensus pattern (18 bp):
TTTTAATATTTTTAATTT
Found at i:40924007 original size:17 final size:17
Alignment explanation
Indices: 40923986--40924020 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
40923976 ATTTTTAGTG
40923986 TTTTTATAATATTTTTAA
1 TTTTTATAAT-TTTTTAA
*
40924004 TTTTTTTAATTTTTTAA
1 TTTTTATAATTTTTTAA
40924021 AATATATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTTTATAATTTTTTAA
Found at i:40924111 original size:19 final size:21
Alignment explanation
Indices: 40924087--40924136 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 21
40924077 TTAAATGTAT
40924087 ATTTTAA-AT-ATTTTTTAAA
1 ATTTTAATATAATTTTTTAAA
40924106 ATTTTAAATATAATTTTTTAAA
1 ATTTT-AATATAATTTTTTAAA
40924128 ATTATTAAT
1 ATT-TTAAT
40924137 TTTAAAATTG
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
19 5 0.19
20 2 0.07
21 2 0.07
22 16 0.59
23 2 0.07
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
ATTTTAATATAATTTTTTAAA
Found at i:40926227 original size:2 final size:2
Alignment explanation
Indices: 40926216--40926251 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
40926206 ATATAGCCAA
40926216 AC AC -C AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
40926252 TATATATGTG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:40927138 original size:41 final size:42
Alignment explanation
Indices: 40927078--40927199 Score: 129
Period size: 41 Copynumber: 2.9 Consensus size: 42
40927068 ATGCTATCTC
* * * *
40927078 ATATTGATGCCACTGTCCTAGACAAGGTCTTACACGAATCAA
1 ATATCGATGCCAATGTCCTAGACATGGTCTTACACGAACCAA
* * *
40927120 ATA-CGATGCCAATGTCCTATACATGGTCTTATACGTAACCAC
1 ATATCGATGCCAATGTCCTAGACATGGTCTTACACG-AACCAA
* * * *
40927162 ATATCGATGCCAACGTCCCAGACGTGGTTTTACACGAA
1 ATATCGATGCCAATGTCCTAGACATGGTCTTACACGAA
40927200 AACACATATC
Statistics
Matches: 65, Mismatches: 13, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
41 27 0.42
42 12 0.18
43 26 0.40
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.26
Consensus pattern (42 bp):
ATATCGATGCCAATGTCCTAGACATGGTCTTACACGAACCAA
Found at i:40927206 original size:43 final size:42
Alignment explanation
Indices: 40927077--40927210 Score: 119
Period size: 43 Copynumber: 3.2 Consensus size: 42
40927067 GATGCTATCT
* * * *
40927077 CATATTGATGCC-ACTGTCCTAGACAAGGTCTTACACGAATCA
1 CATATCGATGCCAAC-GTCCCAGACATGGTCTTACACGAAACA
* * * * * *
40927119 AATA-CGATGCCAATGTCCTATACATGGTCTTATACGTAACCA
1 CATATCGATGCCAACGTCCCAGACATGGTCTTACACG-AAACA
* *
40927161 CATATCGATGCCAACGTCCCAGACGTGGTTTTACACGAAAACA
1 CATATCGATGCCAACGTCCCAGACATGGTCTTACACG-AAACA
40927204 CATATCG
1 CATATCG
40927211 GATCCTATGT
Statistics
Matches: 73, Mismatches: 16, Indels: 5
0.78 0.17 0.05
Matches are distributed among these distances:
41 25 0.34
42 11 0.15
43 37 0.51
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.25
Consensus pattern (42 bp):
CATATCGATGCCAACGTCCCAGACATGGTCTTACACGAAACA
Found at i:40927813 original size:15 final size:15
Alignment explanation
Indices: 40927790--40927819 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
40927780 TCAAAAATTC
40927790 CAATACAAAACATAT
1 CAATACAAAACATAT
*
40927805 CAATCCAAAACATAT
1 CAATACAAAACATAT
40927820 TTTTTGTATT
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:0.57, C:0.23, G:0.00, T:0.20
Consensus pattern (15 bp):
CAATACAAAACATAT
Found at i:40933599 original size:20 final size:19
Alignment explanation
Indices: 40933574--40933617 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
40933564 TATATATATT
*
40933574 AAATAAAGTTATTTTTTAAC
1 AAATAAA-TCATTTTTTAAC
*
40933594 AAATAAATCCTTTTTTAAC
1 AAATAAATCATTTTTTAAC
40933613 AAATA
1 AAATA
40933618 TTTTTCTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.48, C:0.09, G:0.02, T:0.41
Consensus pattern (19 bp):
AAATAAATCATTTTTTAAC
Found at i:40933696 original size:19 final size:18
Alignment explanation
Indices: 40933672--40933717 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 18
40933662 AATATTATTT
*
40933672 TTTAAAATTTTAAATAGAA
1 TTTAAAAATTTAAATA-AA
* *
40933691 TTTAAAAATTTGAATATA
1 TTTAAAAATTTAAATAAA
40933709 TTTAAAAAT
1 TTTAAAAAT
40933718 AATTAAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 10 0.42
19 14 0.58
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.43
Consensus pattern (18 bp):
TTTAAAAATTTAAATAAA
Found at i:40933870 original size:21 final size:20
Alignment explanation
Indices: 40933846--40933910 Score: 55
Period size: 20 Copynumber: 3.1 Consensus size: 20
40933836 ATTTAAATGT
40933846 TTTATATTATTAAAAAATATA
1 TTTA-ATTATTAAAAAATATA
*
40933867 TTTAA-AATTAAAAAAATAATA
1 TTTAATTATT-AAAAAAT-ATA
40933888 TTTAGAATT-TTAAAAAATA-A
1 TTT--AATTATTAAAAAATATA
40933908 TTT
1 TTT
40933911 CAAAAATATA
Statistics
Matches: 37, Mismatches: 2, Indels: 11
0.74 0.04 0.22
Matches are distributed among these distances:
19 3 0.08
20 12 0.32
21 11 0.30
22 7 0.19
23 4 0.11
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (20 bp):
TTTAATTATTAAAAAATATA
Found at i:40933876 original size:22 final size:22
Alignment explanation
Indices: 40933851--40933915 Score: 75
Period size: 21 Copynumber: 3.0 Consensus size: 22
40933841 AATGTTTTAT
40933851 ATTATTAAAAAATATATTTAAA
1 ATTATTAAAAAATATATTTAAA
*
40933873 ATTA--AAAAAATAATATTTAGA
1 ATTATTAAAAAAT-ATATTTAAA
40933894 ATT-TTAAAAAATA-ATTTCAAA
1 ATTATTAAAAAATATATTT-AAA
40933915 A
1 A
40933916 ATATATATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
20 11 0.30
21 15 0.41
22 11 0.30
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (22 bp):
ATTATTAAAAAATATATTTAAA
Found at i:40933900 original size:23 final size:20
Alignment explanation
Indices: 40933854--40933908 Score: 67
Period size: 22 Copynumber: 2.6 Consensus size: 20
40933844 GTTTTATATT
40933854 ATTAAAAAAT-ATATTTAAA
1 ATTAAAAAATAATATTTAAA
40933873 ATTAAAAAAATAATATTTAGAA
1 ATT-AAAAAATAATATTTA-AA
*
40933895 TTTTAAAAAATAAT
1 -ATTAAAAAATAAT
40933909 TTCAAAAATA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
19 3 0.10
20 7 0.23
21 7 0.23
22 12 0.39
23 2 0.06
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (20 bp):
ATTAAAAAATAATATTTAAA
Found at i:40933953 original size:21 final size:22
Alignment explanation
Indices: 40933906--40933953 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
40933896 TTTAAAAAAT
* *
40933906 AATTTCAAAAATATATATTTAA
1 AATTTAAAAAATATATATTAAA
40933928 AATTTAAAAAATAT-TA-TAAA
1 AATTTAAAAAATATATATTAAA
40933948 ACATTT
1 A-ATTT
40933954 TAAATATACA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 4 0.17
21 6 0.26
22 13 0.57
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (22 bp):
AATTTAAAAAATATATATTAAA
Found at i:40933954 original size:56 final size:55
Alignment explanation
Indices: 40933857--40933970 Score: 142
Period size: 56 Copynumber: 2.1 Consensus size: 55
40933847 TTATATTATT
* *
40933857 AAAAAATATATTTAAAATTAAAAAAATAATATTTAGAATTTTAAAAAATA-ATTTC
1 AAAAAATATATTTAAAATTAAAAAAATAATATTAAAAATTTT-AAAAATACATTTC
* * *
40933912 AAAAATATATATTTAAAATTTAAAAAATATTA-TAAAACATTTTAAATATACATTTC
1 AAAAA-ATATATTTAAAATTAAAAAAATAATATTAAAA-ATTTTAAAAATACATTTC
40933968 AAA
1 AAA
40933971 TTTTTTAAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
55 14 0.27
56 37 0.73
ACGTcount: A:0.59, C:0.04, G:0.01, T:0.37
Consensus pattern (55 bp):
AAAAAATATATTTAAAATTAAAAAAATAATATTAAAAATTTTAAAAATACATTTC
Found at i:40934002 original size:4 final size:4
Alignment explanation
Indices: 40933986--40934056 Score: 54
Period size: 4 Copynumber: 16.5 Consensus size: 4
40933976 TAAAATCAAT
* * *
40933986 AATA AACA AATA AATAA AATA AATA AGGACA AATA AA-A AACTTA AAGA
1 AATA AATA AATA AAT-A AATA AATA A--ATA AATA AATA AA--TA AATA
40934034 AAGTA AATA AATA AATA AATA AA
1 AA-TA AATA AATA AATA AATA AA
40934057 GAAGAAAAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
3 3 0.06
4 38 0.70
5 7 0.13
6 6 0.11
ACGTcount: A:0.72, C:0.04, G:0.06, T:0.18
Consensus pattern (4 bp):
AATA
Found at i:40934021 original size:23 final size:23
Alignment explanation
Indices: 40933976--40934058 Score: 73
Period size: 23 Copynumber: 3.7 Consensus size: 23
40933966 TCAAATTTTT
* *
40933976 TAAAATCAATAATAAACAAATAAA
1 TAAAATAAATAA-AGACAAATAAA
*
40934000 TAAAATAAATAAGGACAAATAAA
1 TAAAATAAATAAAGACAAATAAA
* * *
40934023 -AAACTTAAAGAAAG-TAAATAAA
1 TAAA-ATAAATAAAGACAAATAAA
40934045 T-AAATAAATAAAGA
1 TAAAATAAATAAAGA
40934059 AGAAAAAAGC
Statistics
Matches: 47, Mismatches: 9, Indels: 8
0.73 0.14 0.12
Matches are distributed among these distances:
21 8 0.17
22 12 0.26
23 16 0.34
24 11 0.23
ACGTcount: A:0.70, C:0.05, G:0.06, T:0.19
Consensus pattern (23 bp):
TAAAATAAATAAAGACAAATAAA
Found at i:40934796 original size:24 final size:24
Alignment explanation
Indices: 40934769--40934814 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
40934759 TAATACATTT
40934769 AATA-TTAATTTTTTTAATTTTTAG
1 AATATTTAA-TTTTTTAATTTTTAG
40934793 AATATTTAATTTTTTAATTTTT
1 AATATTTAATTTTTTAATTTTT
40934815 GAAAATAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (24 bp):
AATATTTAATTTTTTAATTTTTAG
Found at i:40934821 original size:25 final size:24
Alignment explanation
Indices: 40934769--40934821 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
40934759 TAATACATTT
*
40934769 AATATTAATTTTTTTAATTTTTAG
1 AATATTAATTTTTTTAATTTTTAA
40934793 AATATTTAA-TTTTTTAATTTTTGAA
1 AATA-TTAATTTTTTTAATTTTT-AA
40934818 AATA
1 AATA
40934822 ATTTCCACGT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 17 0.65
25 9 0.35
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (24 bp):
AATATTAATTTTTTTAATTTTTAA
Found at i:40936268 original size:24 final size:24
Alignment explanation
Indices: 40936241--40936292 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
40936231 TTAGTAAGTC
*
40936241 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
40936265 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
40936289 AAAT
1 AAAT
40936293 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:40938237 original size:24 final size:24
Alignment explanation
Indices: 40938210--40938261 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
40938200 TTAGTAAGTC
*
40938210 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
40938234 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
40938258 AAAT
1 AAAT
40938262 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:40942457 original size:15 final size:15
Alignment explanation
Indices: 40942437--40942468 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
40942427 CTATTAAGAA
40942437 GAAGACGAGGTTGTG
1 GAAGACGAGGTTGTG
40942452 GAAGACGAGGTTGTG
1 GAAGACGAGGTTGTG
40942467 GA
1 GA
40942469 CCATAAAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.28, C:0.06, G:0.47, T:0.19
Consensus pattern (15 bp):
GAAGACGAGGTTGTG
Found at i:40944747 original size:48 final size:47
Alignment explanation
Indices: 40944676--40944845 Score: 187
Period size: 48 Copynumber: 3.6 Consensus size: 47
40944666 ACGAAATCTC
* * * *
40944676 GTGTAAGACCATGTCTGGGACATGGCATCAGTGTTGATATGTGAACTA
1 GTGTAAGACCATATCTGGGACATGGCATC-GCGTTGATATGTGAGCCA
* * * *
40944724 GTGTAAGACCATGTCTGGGACATGACATCGGCATTAATATGTGAGCCA
1 GTGTAAGACCATATCTGGGACATGGCATC-GCGTTGATATGTGAGCCA
* * * *
40944772 GTATAAGACCATATCTAGGACATGGCATCGACGTTGATATATGTGCCA
1 GTGTAAGACCATATCTGGGACATGGCATCG-CGTTGATATGTGAGCCA
* *
40944820 GTGTAAGACCATATATGGGATATGGC
1 GTGTAAGACCATATCTGGGACATGGC
40944846 GTTGATATGA
Statistics
Matches: 102, Mismatches: 19, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
47 1 0.01
48 101 0.99
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.27
Consensus pattern (47 bp):
GTGTAAGACCATATCTGGGACATGGCATCGCGTTGATATGTGAGCCA
Found at i:40944887 original size:42 final size:42
Alignment explanation
Indices: 40944850--40944930 Score: 117
Period size: 42 Copynumber: 1.9 Consensus size: 42
40944840 TATGGCGTTG
** *
40944850 ATATGAGATTTCATGTAAGACCATGTCTGCGACATGGCACCA
1 ATATGAGATCCCATGTAAGACCATGTCTGGGACATGGCACCA
* *
40944892 ATATGAGGTCCCGTGTAAGACCATGTCTGGGACATGGCA
1 ATATGAGATCCCATGTAAGACCATGTCTGGGACATGGCA
40944931 TCGGCATCGA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.25
Consensus pattern (42 bp):
ATATGAGATCCCATGTAAGACCATGTCTGGGACATGGCACCA
Found at i:40949756 original size:39 final size:40
Alignment explanation
Indices: 40949686--40949762 Score: 95
Period size: 39 Copynumber: 1.9 Consensus size: 40
40949676 TTGTCATTAC
*
40949686 TAATTTCAAAAAACACAAAATAAATTGTAAT-AGAAAAAG
1 TAATTTAAAAAAACACAAAATAAATTGTAATAAGAAAAAG
** *
40949725 TAATTTAAAAAAAC-CTTAATACAATTTTAATAAGAAAA
1 TAATTTAAAAAAACACAAAATA-AATTGTAATAAGAAAA
40949763 GAGAGTTGAG
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
38 5 0.16
39 21 0.66
40 6 0.19
ACGTcount: A:0.60, C:0.08, G:0.05, T:0.27
Consensus pattern (40 bp):
TAATTTAAAAAAACACAAAATAAATTGTAATAAGAAAAAG
Found at i:40949834 original size:22 final size:21
Alignment explanation
Indices: 40949792--40949834 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
40949782 AAAATTGAGT
*
40949792 GAGAAATTAAGAGGGAATTGA
1 GAGAAATTAAGAGAGAATTGA
* *
40949813 GAGAAATTTGAGAGAGATTTGA
1 GAGAAA-TTAAGAGAGAATTGA
40949835 TAATGTGAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.44, C:0.00, G:0.33, T:0.23
Consensus pattern (21 bp):
GAGAAATTAAGAGAGAATTGA
Found at i:40949917 original size:17 final size:15
Alignment explanation
Indices: 40949886--40949915 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
40949876 AGAATTAGGG
40949886 TTATATAGAAAAAAA
1 TTATATAGAAAAAAA
40949901 TTATATAGAAAAAAA
1 TTATATAGAAAAAAA
40949916 AAGGCGTTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.27
Consensus pattern (15 bp):
TTATATAGAAAAAAA
Found at i:40954947 original size:32 final size:32
Alignment explanation
Indices: 40954911--40954989 Score: 113
Period size: 32 Copynumber: 2.5 Consensus size: 32
40954901 TGAAATTAGT
* *
40954911 TTGTTGGATTTTGAACATATTATGTTTTAAAC
1 TTGTTAGATATTGAACATATTATGTTTTAAAC
** *
40954943 TTGTTAGATATTGAATTTATTATGTTTTAAGC
1 TTGTTAGATATTGAACATATTATGTTTTAAAC
40954975 TTGTTAGATATTGAA
1 TTGTTAGATATTGAA
40954990 ATGATTGACG
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.29, C:0.04, G:0.16, T:0.51
Consensus pattern (32 bp):
TTGTTAGATATTGAACATATTATGTTTTAAAC
Found at i:40956033 original size:21 final size:22
Alignment explanation
Indices: 40956009--40956059 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 22
40955999 TATTTATGCT
*
40956009 TAATGCTATATATT-ATAAAAA
1 TAATGATATATATTCATAAAAA
*
40956030 TAAT-ATATTTATTCATAAAAA
1 TAATGATATATATTCATAAAAA
*
40956051 -AATGTTATA
1 TAATGATATA
40956060 ATTTTTTATC
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
20 10 0.42
21 14 0.58
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.41
Consensus pattern (22 bp):
TAATGATATATATTCATAAAAA
Found at i:40971825 original size:17 final size:18
Alignment explanation
Indices: 40971793--40971828 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
40971783 TAAATAAACG
*
40971793 AAAATATTCATTAAAAAT
1 AAAATATTCATCAAAAAT
40971811 AAAATATTCA-CAAAAAT
1 AAAATATTCATCAAAAAT
40971828 A
1 A
40971829 GTCAAACAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (18 bp):
AAAATATTCATCAAAAAT
Found at i:40976929 original size:3 final size:3
Alignment explanation
Indices: 40976921--40976950 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
40976911 TGAATAAATA
*
40976921 AAT AAT AAT AAT AGT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
40976951 TCATTTAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:40981761 original size:62 final size:62
Alignment explanation
Indices: 40981665--40981797 Score: 239
Period size: 62 Copynumber: 2.1 Consensus size: 62
40981655 ATAGAAAAAG
* * *
40981665 AAGAAATAGGATAAGGCTCCAAGACGTGTATCAAGCCACTATCTTTAAGGTTATATTGACCA
1 AAGAAGTAAGATAAGGCTCCAAGACGTGTATCAAGCCACTATCTTTAAGGTTATATTGACAA
40981727 AAGAAGTAAGATAAGGCTCCAAGACGTGTATCAAGCCACTATCTTTAAGGTTATATTGACAA
1 AAGAAGTAAGATAAGGCTCCAAGACGTGTATCAAGCCACTATCTTTAAGGTTATATTGACAA
40981789 AAGAAGTAA
1 AAGAAGTAA
40981798 ACGTTAAAAA
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
62 68 1.00
ACGTcount: A:0.40, C:0.16, G:0.20, T:0.25
Consensus pattern (62 bp):
AAGAAGTAAGATAAGGCTCCAAGACGTGTATCAAGCCACTATCTTTAAGGTTATATTGACAA
Found at i:40982126 original size:58 final size:58
Alignment explanation
Indices: 40982062--40982178 Score: 234
Period size: 58 Copynumber: 2.0 Consensus size: 58
40982052 TAACAAACAC
40982062 ATATTATTTTGCATTAATTACTAGAATTAAAAATAAAATATTTAAGTGAAAAAGTATA
1 ATATTATTTTGCATTAATTACTAGAATTAAAAATAAAATATTTAAGTGAAAAAGTATA
40982120 ATATTATTTTGCATTAATTACTAGAATTAAAAATAAAATATTTAAGTGAAAAAGTATA
1 ATATTATTTTGCATTAATTACTAGAATTAAAAATAAAATATTTAAGTGAAAAAGTATA
40982178 A
1 A
40982179 CGCCCCATAT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 59 1.00
ACGTcount: A:0.50, C:0.03, G:0.09, T:0.38
Consensus pattern (58 bp):
ATATTATTTTGCATTAATTACTAGAATTAAAAATAAAATATTTAAGTGAAAAAGTATA
Found at i:40989887 original size:25 final size:25
Alignment explanation
Indices: 40989857--40989906 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
40989847 CATAATGTCA
40989857 TTTATTCTTCCATCATACATTTCAT
1 TTTATTCTTCCATCATACATTTCAT
40989882 TTTATTCTTCCATCATACATTTCAT
1 TTTATTCTTCCATCATACATTTCAT
40989907 ACTTTCATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.52
Consensus pattern (25 bp):
TTTATTCTTCCATCATACATTTCAT
Found at i:40996351 original size:17 final size:18
Alignment explanation
Indices: 40996329--40996362 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
40996319 CACATTGAAG
40996329 TGTTTT-ATCGAAAACCT
1 TGTTTTCATCGAAAACCT
*
40996346 TGTTTTCATTGAAAACC
1 TGTTTTCATCGAAAACC
40996363 CTTCTTTGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.41
Consensus pattern (18 bp):
TGTTTTCATCGAAAACCT
Found at i:41005011 original size:28 final size:28
Alignment explanation
Indices: 41004941--41005016 Score: 127
Period size: 27 Copynumber: 2.8 Consensus size: 28
41004931 TTTAGCCCCT
*
41004941 TTAGGCCCAATCTCATTCATATGGCCCA
1 TTAGGCCCAATCACATTCATATGGCCCA
*
41004969 -TCGGCCCAATCACATTCATATGGCCCA
1 TTAGGCCCAATCACATTCATATGGCCCA
41004996 TTAGGCCCAATCACATTCATA
1 TTAGGCCCAATCACATTCATA
41005017 GTCATGCAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
27 25 0.57
28 19 0.43
ACGTcount: A:0.28, C:0.33, G:0.13, T:0.26
Consensus pattern (28 bp):
TTAGGCCCAATCACATTCATATGGCCCA
Found at i:41005078 original size:17 final size:18
Alignment explanation
Indices: 41005056--41005089 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
41005046 TGCCTATTAT
41005056 GGGCCC-TATAGCCCATC
1 GGGCCCATATAGCCCATC
*
41005073 GGGCCCATTTAGCCCAT
1 GGGCCCATATAGCCCAT
41005090 TCTGGTCCGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.18, C:0.38, G:0.24, T:0.21
Consensus pattern (18 bp):
GGGCCCATATAGCCCATC
Found at i:41005531 original size:21 final size:21
Alignment explanation
Indices: 41005502--41005541 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
41005492 ACTAAACAAA
*
41005502 AAGTGACTCGCAAATCATCTT
1 AAGTCACTCGCAAATCATCTT
**
41005523 AAGTCACTCTTAAATCATC
1 AAGTCACTCGCAAATCATC
41005542 CATGACTATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.35, C:0.25, G:0.10, T:0.30
Consensus pattern (21 bp):
AAGTCACTCGCAAATCATCTT
Found at i:41019791 original size:16 final size:16
Alignment explanation
Indices: 41019772--41019803 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
41019762 AATTGTTTTA
41019772 TTACAAAATTTCACTT
1 TTACAAAATTTCACTT
*
41019788 TTACATAATTTCACTT
1 TTACAAAATTTCACTT
41019804 ACTCCATTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.19, G:0.00, T:0.47
Consensus pattern (16 bp):
TTACAAAATTTCACTT
Found at i:41020089 original size:50 final size:49
Alignment explanation
Indices: 41020012--41020340 Score: 238
Period size: 50 Copynumber: 6.6 Consensus size: 49
41020002 CCCTGGTATG
* *
41020012 CATAGTAGCCTGCACTTAGTATTACACATGCAGCCTATCAATCTAGTACA
1 CATAGTAGCCTGCACTTAGTACTACACATGCAGCCTATCAA-CTGGTACA
* * * *
41020062 CGTAGTAGCCTGCACTTAGTACTACACACTTG-AG-TTAACCAACTGATACA
1 CATAGTAGCCTGCACTTAGTACTACACA--TGCAGCCT-ATCAACTGGTACA
* * * ** * * *
41020112 CGTAGTAGCTTGCACTTAGTACTACACACATG-ATCGAAGTTAACGGGTACG
1 CATAGTAGCCTGCACTTAGTACT--ACACATGCAGCCTA-TCAACTGGTACA
* *
41020163 CATAGTAGCTTGCACTTAGTACTACACATGC-GACCTATCAATCTAGTACA
1 CATAGTAGCCTGCACTTAGTACTACACATGCAG-CCTATCAA-CTGGTACA
* * * * ** * * *
41020213 CGTACTAGCCTGCACTTAGTACTACACATGTGATCGAAGTTAACGGGTACG
1 CATAGTAGCCTGCACTTAGTACTACACATG-CAGCCTA-TCAACTGGTACA
*
41020264 CATAGTA-CTTGCACTTAGTACTACACATGC-GACCTATCAATCTGGTACA
1 CATAGTAGCCTGCACTTAGTACTACACATGCAG-CCTATCAA-CTGGTACA
* * *
41020313 CATAGTAACCCGCAATTAGTACTACACA
1 CATAGTAGCCTGCACTTAGTACTACACA
41020341 CGTGACTTAC
Statistics
Matches: 216, Mismatches: 47, Indels: 32
0.73 0.16 0.11
Matches are distributed among these distances:
48 3 0.01
49 25 0.12
50 131 0.61
51 47 0.22
52 10 0.05
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.26
Consensus pattern (49 bp):
CATAGTAGCCTGCACTTAGTACTACACATGCAGCCTATCAACTGGTACA
Found at i:41020189 original size:101 final size:101
Alignment explanation
Indices: 41020064--41020341 Score: 357
Period size: 101 Copynumber: 2.8 Consensus size: 101
41020054 CTAGTACACG
* * ** * *
41020064 TAGTAGCCTGCACTTAGTACTACACACT-TGAGTTAACCAA-CT-GATACACGTAGTAGCTTGCA
1 TAGTAGCTTGCACTTAGTACTACACA-TGCGACCT-ACCAATCTAG-TACACGTACTAGCCTGCA
41020126 CTTAGTACTACACACATGATCGAAGTTAACGGGTACGCA
63 CTTAGTACTACACACATGATCGAAGTTAACGGGTACGCA
*
41020165 TAGTAGCTTGCACTTAGTACTACACATGCGACCTATCAATCTAGTACACGTACTAGCCTGCACTT
1 TAGTAGCTTGCACTTAGTACTACACATGCGACCTACCAATCTAGTACACGTACTAGCCTGCACTT
**
41020230 AGTACTACACATGTGATCGAAGTTAACGGGTACGCA
66 AGTACTACACACATGATCGAAGTTAACGGGTACGCA
* * * * * * *
41020266 TAGTA-CTTGCACTTAGTACTACACATGCGACCTATCAATCTGGTACACATAGTAACCCGCAATT
1 TAGTAGCTTGCACTTAGTACTACACATGCGACCTACCAATCTAGTACACGTACTAGCCTGCACTT
41020330 AGTACTACACAC
66 AGTACTACACAC
41020342 GTGACTTACA
Statistics
Matches: 158, Mismatches: 16, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
100 69 0.44
101 88 0.56
102 1 0.01
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.26
Consensus pattern (101 bp):
TAGTAGCTTGCACTTAGTACTACACATGCGACCTACCAATCTAGTACACGTACTAGCCTGCACTT
AGTACTACACACATGATCGAAGTTAACGGGTACGCA
Found at i:41020275 original size:151 final size:151
Alignment explanation
Indices: 41020006--41020290 Score: 407
Period size: 151 Copynumber: 1.9 Consensus size: 151
41019996 GAAGCTCCCT
* * *
41020006 GGTATGCATAGTAGCCTGCACTTAGTATTACACATGCAGCCTATCAATCTAGTACACGTAGTAGC
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCAGCCTATCAATCTAGTACACGTACTAGC
* * *
41020071 CTGCACTTAGTACTACACACTTGAGTTAACCAACTGATACACGTAGTAGCTTGCACTTAGTACTA
66 CTGCACTTAGTACTACACACTTGAGTGAACCAACGGATACACATAGTAGCTTGCACTTAGTACTA
41020136 CACACATGATCGAAGTTAACG
131 CACACATGATCGAAGTTAACG
*
41020157 GGTACGCATAGTAGCTTGCACTTAGTACTACACATGC-GACCTATCAATCTAGTACACGTACTAG
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCAG-CCTATCAATCTAGTACACGTACTAG
** * *
41020221 CCTGCACTTAGTACTACACA-TGTGA-TCGAAGTTAACGGGTACGCATAGTA-CTTGCACTTAGT
65 CCTGCACTTAGTACTACACACT-TGAGT-GAA-CCAACGGATACACATAGTAGCTTGCACTTAGT
41020283 ACTACACA
127 ACTACACA
41020291 TGCGACCTAT
Statistics
Matches: 119, Mismatches: 11, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
150 3 0.03
151 103 0.87
152 13 0.11
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (151 bp):
GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCAGCCTATCAATCTAGTACACGTACTAGC
CTGCACTTAGTACTACACACTTGAGTGAACCAACGGATACACATAGTAGCTTGCACTTAGTACTA
CACACATGATCGAAGTTAACG
Found at i:41020332 original size:100 final size:101
Alignment explanation
Indices: 41020127--41020345 Score: 359
Period size: 100 Copynumber: 2.2 Consensus size: 101
41020117 TAGCTTGCAC
*
41020127 TTAGTACTACACACATGATCGAAGTTAACGGGTACGCATAGTAGCTTGCACTTAGTACTACACAT
1 TTAGTACTACACACGTGATCGAAGTTAACGGGTACGCATAGTAGCTTGCACTTAGTACTACACAT
* * * *
41020192 GCGACCTATCAATCTAGTACACGTACTAGCCTGCAC
66 GCGACCTATCAATCTAGTACACATACTAACCCGCAA
*
41020228 TTAGTACTACACATGTGATCGAAGTTAACGGGTACGCATAGTA-CTTGCACTTAGTACTACACAT
1 TTAGTACTACACACGTGATCGAAGTTAACGGGTACGCATAGTAGCTTGCACTTAGTACTACACAT
* *
41020292 GCGACCTATCAATCTGGTACACATAGTAACCCGCAA
66 GCGACCTATCAATCTAGTACACATACTAACCCGCAA
41020328 TTAGTACTACACACGTGA
1 TTAGTACTACACACGTGA
41020346 CTTACAATGG
Statistics
Matches: 109, Mismatches: 9, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
100 68 0.62
101 41 0.38
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.26
Consensus pattern (101 bp):
TTAGTACTACACACGTGATCGAAGTTAACGGGTACGCATAGTAGCTTGCACTTAGTACTACACAT
GCGACCTATCAATCTAGTACACATACTAACCCGCAA
Found at i:41021018 original size:30 final size:30
Alignment explanation
Indices: 41020961--41021019 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 30
41020951 TAAAAATCAT
* * *
41020961 ACTTTTACAAATTTTCATTTTGACCCCTAA
1 ACTTTCACAAATTTGCACTTTGACCCCTAA
* *
41020991 ACTTTCACATATTTGCACTTTGGCCCCTA
1 ACTTTCACAAATTTGCACTTTGACCCCTA
41021020 GGCTCGTAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.25, C:0.27, G:0.07, T:0.41
Consensus pattern (30 bp):
ACTTTCACAAATTTGCACTTTGACCCCTAA
Found at i:41026464 original size:18 final size:18
Alignment explanation
Indices: 41026437--41026479 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
41026427 CAGGGGGTTT
*
41026437 TGAA-AATGTTTTGAAAG
1 TGAATAATGTTTAGAAAG
41026454 TGAATAATGTTTAGAAAG
1 TGAATAATGTTTAGAAAG
41026472 TGAATAAT
1 TGAATAAT
41026480 CAAATCAGCG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 4 0.17
18 20 0.83
ACGTcount: A:0.44, C:0.00, G:0.21, T:0.35
Consensus pattern (18 bp):
TGAATAATGTTTAGAAAG
Found at i:41032507 original size:250 final size:250
Alignment explanation
Indices: 41032090--41032558 Score: 613
Period size: 250 Copynumber: 1.9 Consensus size: 250
41032080 CTTGAACGGT
* * *
41032090 GTTCCTCCTACTAGATAGATTATACATAAAGGCTGTTGTTCATCTGGTGCCGCTGCGAGTTGACA
1 GTTCCTCCCACTAAATAGATTATACATAAAGGCTGTTGTTCATCTAGTGCCGCTGCGAGTTGACA
* * * * * *
41032155 TATTTTCTCTTCGACCATCTCGTTTGGTTCATCGAATGAGAAAATTTATTTGGTGTAAGATATGG
66 TATGTTCTCTTCAACCATCTCGTTCGGTTCATCAAATGAGAAAATTTACTCGGTGTAAGATATGG
** * * * *
41032220 TTTTGAATCTAGGATTTGGTCATTTACGGCATCAAATGGCTGCTTTTCATAGTTTTTGGGCCAAT
131 TTTCAAATCTAGGATTTGGTCATTTACCGCATCAAATGGATGCTTTTCACAGTTTTTAGGCCAAT
*
41032285 TTCTCAATTTCTGGTTCAAACTCTAAAGTTCAAACCCGATTTTAACTCAAACAAC
196 TTCTCAATTTCTAGTTCAAACTCTAAAGTTCAAACCCGATTTTAACTCAAACAAC
* * * * *
41032340 GTTCCTCCCACTAAATAGGTTATACATAAGGGTTTTTGTTCATCTAGTGCCGCTGCGAGTTGGCA
1 GTTCCTCCCACTAAATAGATTATACATAAAGGCTGTTGTTCATCTAGTGCCGCTGCGAGTTGACA
* ** *
41032405 TATAGTT-TGTTCAACCATCTC-TGTCGGTTTGTCAAACTG-GAAAATTTCCTCGGTGTAAGATA
66 TAT-GTTCTCTTCAACCATCTCGT-TCGGTTCATCAAA-TGAGAAAATTTACTCGGTGTAAGATA
* * * *
41032467 TGGTTTCAAATCCTA-GATTTGGTCGTTTACCGCGTCAAATGGATTCTTTTCGCAGTTTTTAGGC
128 TGGTTTCAAAT-CTAGGATTTGGTCATTTACCGCATCAAATGGATGCTTTTCACAGTTTTTAGGC
41032531 CAATTTCTCAATTTCTAGTTCAAACTCT
192 CAATTTCTCAATTTCTAGTTCAAACTCT
41032559 GGAGTTCTTC
Statistics
Matches: 186, Mismatches: 29, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
249 1 0.01
250 178 0.96
251 7 0.04
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.38
Consensus pattern (250 bp):
GTTCCTCCCACTAAATAGATTATACATAAAGGCTGTTGTTCATCTAGTGCCGCTGCGAGTTGACA
TATGTTCTCTTCAACCATCTCGTTCGGTTCATCAAATGAGAAAATTTACTCGGTGTAAGATATGG
TTTCAAATCTAGGATTTGGTCATTTACCGCATCAAATGGATGCTTTTCACAGTTTTTAGGCCAAT
TTCTCAATTTCTAGTTCAAACTCTAAAGTTCAAACCCGATTTTAACTCAAACAAC
Found at i:41032945 original size:17 final size:19
Alignment explanation
Indices: 41032920--41032955 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
41032910 AAACAATTAA
41032920 TTAATATT-GGAAATAAAT
1 TTAATATTGGGAAATAAAT
41032938 TTAA-ATTGGGAAATAAAT
1 TTAATATTGGGAAATAAAT
41032956 ATAGATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.18
18 14 0.82
ACGTcount: A:0.50, C:0.00, G:0.14, T:0.36
Consensus pattern (19 bp):
TTAATATTGGGAAATAAAT
Found at i:41035717 original size:31 final size:31
Alignment explanation
Indices: 41035679--41035819 Score: 194
Period size: 31 Copynumber: 4.5 Consensus size: 31
41035669 TTTAACGGTT
* *
41035679 ACTGGGCCGAAGCCTTTTCATTAAT-ATAACC
1 ACTGGGCCGAAGCCTTTTCATAAATCAT-ATC
41035710 ACTGGGCCGAAGCCTTTTCATAAATCATATC
1 ACTGGGCCGAAGCCTTTTCATAAATCATATC
* *
41035741 ACTAGGCTGAAGCCTTTTCATAAATCATATC
1 ACTGGGCCGAAGCCTTTTCATAAATCATATC
* * *
41035772 ACTGGGTCGAAGCCTTTTCATTATTCATATC
1 ACTGGGCCGAAGCCTTTTCATAAATCATATC
*
41035803 ACTAGGCCGAAGCCTTT
1 ACTGGGCCGAAGCCTTT
41035820 ACTGTAAACG
Statistics
Matches: 98, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
31 96 0.98
32 2 0.02
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (31 bp):
ACTGGGCCGAAGCCTTTTCATAAATCATATC
Found at i:41036050 original size:25 final size:25
Alignment explanation
Indices: 41036022--41036091 Score: 113
Period size: 25 Copynumber: 2.8 Consensus size: 25
41036012 CTCTTTAAAT
41036022 AACTGGGGCAAAGCCCTTTTCGATA
1 AACTGGGGCAAAGCCCTTTTCGATA
* * *
41036047 AACTGAGGCAAAGCCCTTTTTGGTA
1 AACTGGGGCAAAGCCCTTTTCGATA
41036072 AACTGGGGCAAAGCCCTTTT
1 AACTGGGGCAAAGCCCTTTT
41036092 ACACTTCCTC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 41 1.00
ACGTcount: A:0.27, C:0.23, G:0.24, T:0.26
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTCGATA
Found at i:41036155 original size:11 final size:11
Alignment explanation
Indices: 41036139--41036207 Score: 76
Period size: 11 Copynumber: 6.7 Consensus size: 11
41036129 TATATGAGTT
41036139 TATCATGTGCA
1 TATCATGTGCA
*
41036150 TATCA--TACA
1 TATCATGTGCA
41036159 TATCATGTGCA
1 TATCATGTGCA
*
41036170 TATCA--TACA
1 TATCATGTGCA
41036179 TATCATGTGCA
1 TATCATGTGCA
41036190 TATCATGT-CA
1 TATCATGTGCA
*
41036200 AATCATGT
1 TATCATGT
41036208 ATATCAAAAT
Statistics
Matches: 49, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
9 16 0.33
10 9 0.18
11 24 0.49
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.36
Consensus pattern (11 bp):
TATCATGTGCA
Found at i:41036164 original size:20 final size:20
Alignment explanation
Indices: 41036139--41036195 Score: 114
Period size: 20 Copynumber: 2.9 Consensus size: 20
41036129 TATATGAGTT
41036139 TATCATGTGCATATCATACA
1 TATCATGTGCATATCATACA
41036159 TATCATGTGCATATCATACA
1 TATCATGTGCATATCATACA
41036179 TATCATGTGCATATCAT
1 TATCATGTGCATATCAT
41036196 GTCAAATCAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.33, C:0.19, G:0.11, T:0.37
Consensus pattern (20 bp):
TATCATGTGCATATCATACA
Found at i:41042812 original size:79 final size:81
Alignment explanation
Indices: 41042710--41042894 Score: 218
Period size: 79 Copynumber: 2.3 Consensus size: 81
41042700 GCTACTCGTT
* * * *
41042710 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAATTGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTC-GAATCTTAACCC
* *
41042773 GGATTTAGT-AATTCGCA
64 GGATATAGTCAATTAGCA
* **
41042790 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGAATCTTAGTCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGAATCTTAACCCGG
* *
41042854 ATATGGTCACTTAGCA
66 ATATAGTCAATTAGCA
41042870 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
41042895 CATCATTCAA
Statistics
Matches: 90, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
78 2 0.02
79 52 0.58
80 36 0.40
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.25
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGAATCTTAACCCGG
ATATAGTCAATTAGCA
Found at i:41042894 original size:40 final size:40
Alignment explanation
Indices: 41042691--41042894 Score: 197
Period size: 40 Copynumber: 5.1 Consensus size: 40
41042681 CGGAATTTAA
** *
41042691 CCGGATATAGCTAC-TCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TACTTCGCACAAATGCCTTCGGGACTTAGC
* * *
41042731 CCGGTTATAGTAAC-TCGCACAATTGCCTTCGGGACTTAAC
1 CCGGATATAGT-ACTTCGCACAAATGCCTTCGGGACTTAGC
* *
41042771 CCGGATTTAGTAATTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTACTTCGCACAAATGCCTTCGGGACTTAGC
* *
41042810 CCGGA-ATTAGTA-TCTCGCACAAATGCCTTC-GAATCTTAGT
1 CCGGATA-TAGTACT-TCGCACAAATGCCTTCGGGA-CTTAGC
* *
41042850 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGT-ACTTCGCACAAATGCCTTCGGGACTTAGC
41042890 CCGGA
1 CCGGA
41042895 CATCATTCAA
Statistics
Matches: 136, Mismatches: 18, Indels: 20
0.78 0.10 0.11
Matches are distributed among these distances:
38 2 0.01
39 33 0.24
40 88 0.65
41 12 0.09
42 1 0.01
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAGTACTTCGCACAAATGCCTTCGGGACTTAGC
Found at i:41048903 original size:27 final size:26
Alignment explanation
Indices: 41048855--41048906 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
41048845 GCGAGGCTTC
*
41048855 CAGATATTGTGACGAAGTCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
* *
41048881 CAGATATATGTGGCGAGGCCACCAGA
1 CAGATAT-TGTGACGAAGCCACCAGA
41048907 TTGTAGCGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.35, C:0.21, G:0.27, T:0.17
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:41050648 original size:22 final size:22
Alignment explanation
Indices: 41050620--41050663 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
41050610 TTTTGAACCA
41050620 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
41050642 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
41050664 AAATACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:41051310 original size:27 final size:27
Alignment explanation
Indices: 41051280--41051421 Score: 162
Period size: 27 Copynumber: 5.3 Consensus size: 27
41051270 GGGGCAAAAT
* *
41051280 GGTAATTTTACCCCACAAGGGTATCTC
1 GGTAATTTTACCCTACAAGGGTATTTC
*
41051307 GGTAATTTTACCCTACAGGGGTATTTC
1 GGTAATTTTACCCTACAAGGGTATTTC
*
41051334 GAT-ATTTCTACCCTACAAGGGTATTTC
1 GGTAATTT-TACCCTACAAGGGTATTTC
* * * *
41051361 GATAATTCTATCCTACAGGGGTATTTC
1 GGTAATTTTACCCTACAAGGGTATTTC
*
41051388 GGT-ATTTCTACTCTACAAGGGTATTTC
1 GGTAATTT-TACCCTACAAGGGTATTTC
*
41051415 TGTAATT
1 GGTAATT
41051422 CTACAACTTA
Statistics
Matches: 97, Mismatches: 14, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
26 7 0.07
27 84 0.87
28 6 0.06
ACGTcount: A:0.25, C:0.20, G:0.18, T:0.37
Consensus pattern (27 bp):
GGTAATTTTACCCTACAAGGGTATTTC
Found at i:41051346 original size:54 final size:54
Alignment explanation
Indices: 41051284--41051425 Score: 205
Period size: 54 Copynumber: 2.6 Consensus size: 54
41051274 CAAAATGGTA
* * *
41051284 ATTT-TACCCCACAAGGGTATCTCGGTAATTTTACCCTACAGGGGTATTTCGAT
1 ATTTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCGAT
* * *
41051337 ATTTCTACCCTACAAGGGTATTTCGATAATTCTATCCTACAGGGGTATTTCGGT
1 ATTTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCGAT
* *
41051391 ATTTCTACTCTACAAGGGTATTTCTGTAATTCTAC
1 ATTTCTACCCTACAAGGGTATTTCGGTAATTCTAC
41051426 AACTTATCCA
Statistics
Matches: 78, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
53 4 0.05
54 74 0.95
ACGTcount: A:0.25, C:0.21, G:0.17, T:0.37
Consensus pattern (54 bp):
ATTTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCGAT
Found at i:41053181 original size:18 final size:18
Alignment explanation
Indices: 41053153--41053195 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
41053143 TAGGGGGTTT
41053153 TGAAT-ATGTTTAAAAAG
1 TGAATAATGTTTAAAAAG
*
41053170 TGAATAATGTTTAGAAAG
1 TGAATAATGTTTAAAAAG
41053188 TGAATAAT
1 TGAATAAT
41053196 CGAATCAGCG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 5 0.21
18 19 0.79
ACGTcount: A:0.47, C:0.00, G:0.19, T:0.35
Consensus pattern (18 bp):
TGAATAATGTTTAAAAAG
Found at i:41059279 original size:39 final size:39
Alignment explanation
Indices: 41059225--41059301 Score: 127
Period size: 39 Copynumber: 2.0 Consensus size: 39
41059215 GTCTATACAA
* *
41059225 AATCTCATCGAACTATATTTATTTTTCACGAATAGTACT
1 AATCTCATCAAACTATATTTATTTTTCACAAATAGTACT
*
41059264 AATCTCATCAAACTATATTTCTTTTTCACAAATAGTAC
1 AATCTCATCAAACTATATTTATTTTTCACAAATAGTAC
41059302 GGGGGCACCT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.35, C:0.19, G:0.05, T:0.40
Consensus pattern (39 bp):
AATCTCATCAAACTATATTTATTTTTCACAAATAGTACT
Found at i:41070961 original size:16 final size:16
Alignment explanation
Indices: 41070940--41070970 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
41070930 CTGCAATGCC
41070940 CCAAAAATCTCGAAAT
1 CCAAAAATCTCGAAAT
41070956 CCAAAAATCTCGAAA
1 CCAAAAATCTCGAAA
41070971 CCTTGAATTT
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:0.52, C:0.26, G:0.06, T:0.16
Consensus pattern (16 bp):
CCAAAAATCTCGAAAT
Found at i:41072490 original size:29 final size:28
Alignment explanation
Indices: 41072458--41072517 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
41072448 GGGCTTAACA
**
41072458 GGCCACATAAATGTGATTTGGGCCTAATG
1 GGCCACATAAATACGA-TTGGGCCTAATG
* * *
41072487 GGCCATATGAATACGATTGGGCTTAATG
1 GGCCACATAAATACGATTGGGCCTAATG
41072515 GGC
1 GGC
41072518 TAGATACAGG
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
28 14 0.54
29 12 0.46
ACGTcount: A:0.27, C:0.17, G:0.30, T:0.27
Consensus pattern (28 bp):
GGCCACATAAATACGATTGGGCCTAATG
Found at i:41075906 original size:25 final size:25
Alignment explanation
Indices: 41075878--41075930 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
41075868 CTGAATTTAG
*
41075878 AAAACACTGTAGTTAGAACTTTCTA
1 AAAACACTGTAGTTAGAACTTCCTA
*
41075903 AAAACACTGTAGTTAGTACTTCCTA
1 AAAACACTGTAGTTAGAACTTCCTA
41075928 AAA
1 AAA
41075931 CTGTACTGAG
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:0.17, G:0.11, T:0.30
Consensus pattern (25 bp):
AAAACACTGTAGTTAGAACTTCCTA
Found at i:41082411 original size:53 final size:54
Alignment explanation
Indices: 41082331--41082548 Score: 215
Period size: 54 Copynumber: 4.0 Consensus size: 54
41082321 TCGGGAACCT
* * * * * **
41082331 TTTCCTTTTTGAACTTACCATTTCCATGTCTTGACATGGTCTTATGTGGTATCC
1 TTTCCTTATAGAACTCACCAATGCCATGTCTTGACATGGTCTTACATGGTATCC
* * * *
41082385 TTGCCTTAT-GAACTCACCAATGCCATGACTTGAAATGGTCTTACATGGGA-CC
1 TTTCCTTATAGAACTCACCAATGCCATGTCTTGACATGGTCTTACATGGTATCC
* * * *
41082437 TTTTCCTTATAGTAACTCATCAATGCCATGTCTTGATATGGTCTTACATGATTTCC
1 -TTTCCTTATAG-AACTCACCAATGCCATGTCTTGACATGGTCTTACATGGTATCC
* * * * * *
41082493 TTTCCTTATAGAACTTATCAATGCCATGCCTTGCCATGGTTTTACATGATATCC
1 TTTCCTTATAGAACTCACCAATGCCATGTCTTGACATGGTCTTACATGGTATCC
41082547 TT
1 TT
41082549 ATCGTACCAA
Statistics
Matches: 137, Mismatches: 23, Indels: 8
0.82 0.14 0.05
Matches are distributed among these distances:
52 2 0.01
53 41 0.30
54 47 0.34
55 45 0.33
56 2 0.01
ACGTcount: A:0.22, C:0.23, G:0.15, T:0.40
Consensus pattern (54 bp):
TTTCCTTATAGAACTCACCAATGCCATGTCTTGACATGGTCTTACATGGTATCC
Found at i:41082538 original size:54 final size:55
Alignment explanation
Indices: 41082354--41082548 Score: 209
Period size: 55 Copynumber: 3.6 Consensus size: 55
41082344 CTTACCATTT
* ** * * *
41082354 CCATGTCTTGACATGGTCTTATGTGGTATCCTTGCCTTAT-G-AACTCACCAATG
1 CCATGCCTTGACATGGTCTTACATGATATCCTTTCCTTATAGTAACTCATCAATG
* * **
41082407 CCATGACTTGAAATGGTCTTACATGGGA-CCTTTTCCTTATAGTAACTCATCAATG
1 CCATGCCTTGACATGGTCTTACATGATATCC-TTTCCTTATAGTAACTCATCAATG
* * * *
41082462 CCATGTCTTGATATGGTCTTACATGATTTCCTTTCCTTATAG-AACTTATCAATG
1 CCATGCCTTGACATGGTCTTACATGATATCCTTTCCTTATAGTAACTCATCAATG
* *
41082516 CCATGCCTTGCCATGGTTTTACATGATATCCTT
1 CCATGCCTTGACATGGTCTTACATGATATCCTT
41082549 ATCGTACCAA
Statistics
Matches: 120, Mismatches: 18, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
52 2 0.02
53 31 0.26
54 40 0.33
55 45 0.38
56 2 0.02
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.38
Consensus pattern (55 bp):
CCATGCCTTGACATGGTCTTACATGATATCCTTTCCTTATAGTAACTCATCAATG
Found at i:41082643 original size:47 final size:47
Alignment explanation
Indices: 41082527--41082648 Score: 181
Period size: 47 Copynumber: 2.6 Consensus size: 47
41082517 CATGCCTTGC
* * * *
41082527 CATGGTTTTACATGATATCCTTATCGTACCAAATGCCATGTTCCAAA
1 CATGGTCTTACATGGTATCCTTGTCTTACCAAATGCCATGTTCCAAA
* * *
41082574 CAAGGTCTTACATGGTATCCTTGTCTTACCAAATGTCATTTTCCAAA
1 CATGGTCTTACATGGTATCCTTGTCTTACCAAATGCCATGTTCCAAA
41082621 CATGGTCTTACATGGTATCCTTGTCTTA
1 CATGGTCTTACATGGTATCCTTGTCTTA
41082649 GTGCCAATGC
Statistics
Matches: 67, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
47 67 1.00
ACGTcount: A:0.26, C:0.23, G:0.14, T:0.37
Consensus pattern (47 bp):
CATGGTCTTACATGGTATCCTTGTCTTACCAAATGCCATGTTCCAAA
Found at i:41088786 original size:51 final size:51
Alignment explanation
Indices: 41088731--41088928 Score: 324
Period size: 51 Copynumber: 3.9 Consensus size: 51
41088721 TGAACCTTAG
* *
41088731 GAATAAAATAGCTTTAGACACAAGTGTGGTACTATGTGAAGACCACTTTGT
1 GAATAAAATAGCTTTGGACACAAGTGTGGTACTATGTGAAGGCCACTTTGT
* * *
41088782 GAATATAATAGCTTTGGACACAAGTTTGGTATTATGTGAAGGCCACTTTGT
1 GAATAAAATAGCTTTGGACACAAGTGTGGTACTATGTGAAGGCCACTTTGT
* *
41088833 GAATAAAATAGCTTTGGACACAAGTGTGGTACTATGTGAAGGCTAGTTTGT
1 GAATAAAATAGCTTTGGACACAAGTGTGGTACTATGTGAAGGCCACTTTGT
*
41088884 GAATAAAATAGCTTTGGACATAAGTGTGGTACTATGTGAAGGCCA
1 GAATAAAATAGCTTTGGACACAAGTGTGGTACTATGTGAAGGCCA
41088929 TTGTGTATCC
Statistics
Matches: 135, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 135 1.00
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.31
Consensus pattern (51 bp):
GAATAAAATAGCTTTGGACACAAGTGTGGTACTATGTGAAGGCCACTTTGT
Found at i:41095047 original size:28 final size:27
Alignment explanation
Indices: 41094979--41095122 Score: 156
Period size: 28 Copynumber: 5.4 Consensus size: 27
41094969 GATATGACAT
* *
41094979 TGTGCTAAGTGAAATAAGGCCATGGCA
1 TGTGCTAAGTGAAATAAGTCCATGGAA
41095006 --T-CTAAGTGAAATAAGTCCATGGTAA
1 TGTGCTAAGTGAAATAAGTCCATGG-AA
41095031 TGTGCTAAGTGAAATAAGTCCATGGCAA
1 TGTGCTAAGTGAAATAAGTCCATGG-AA
*
41095059 TGTGCTAAGTGAAATAAGTCCATGGCA
1 TGTGCTAAGTGAAATAAGTCCATGGAA
* * *
41095086 --T-CTAAGTGAAATAGGTCTATGGCAT
1 TGTGCTAAGTGAAATAAGTCCATGG-AA
*
41095111 TGTGCTCAGTGA
1 TGTGCTAAGTGA
41095123 GAAACTTCCC
Statistics
Matches: 100, Mismatches: 9, Indels: 15
0.81 0.07 0.12
Matches are distributed among these distances:
24 39 0.39
25 3 0.03
27 3 0.03
28 55 0.55
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.27
Consensus pattern (27 bp):
TGTGCTAAGTGAAATAAGTCCATGGAA
Found at i:41095091 original size:52 final size:55
Alignment explanation
Indices: 41094980--41095122 Score: 174
Period size: 52 Copynumber: 2.7 Consensus size: 55
41094970 ATATGACATT
*
41094980 GTGCTAAGTGAAATAAGGCCATGGC-A--T-CTAAGTGAAATAAGTCCATGGTAA
1 GTGCTAAGTGAAATAAGTCCATGGCAATGTGCTAAGTGAAATAAGTCCATGGTAA
*
41095031 TGTGCTAAGTGAAATAAGTCCATGGCAATGTGCTAAGTGAAATAAGTCCATGG-CA
1 -GTGCTAAGTGAAATAAGTCCATGGCAATGTGCTAAGTGAAATAAGTCCATGGTAA
* * * *
41095086 -T-CTAAGTGAAATAGGTCTATGGCATTGTGCTCAGTGA
1 GTGCTAAGTGAAATAAGTCCATGGCAATGTGCTAAGTGA
41095123 GAAACTTCCC
Statistics
Matches: 81, Mismatches: 6, Indels: 8
0.85 0.06 0.08
Matches are distributed among these distances:
52 56 0.69
53 2 0.02
55 2 0.02
56 21 0.26
ACGTcount: A:0.34, C:0.14, G:0.26, T:0.27
Consensus pattern (55 bp):
GTGCTAAGTGAAATAAGTCCATGGCAATGTGCTAAGTGAAATAAGTCCATGGTAA
Found at i:41095222 original size:51 final size:51
Alignment explanation
Indices: 41095146--41095343 Score: 281
Period size: 51 Copynumber: 3.9 Consensus size: 51
41095136 TGAACCTTAG
* *
41095146 GAATAAAATAGCTTTGGACATAAGTGTGGTACTATGTGAAGGCCAGTTTGT
1 GAATAAAATAGCTTTGGACACAAGTGTGGTACTATGTGAAGGCCAATTTGT
* * * * *
41095197 GAATATAATAGCTTTAGACACAAGTGTGATACTATGTGAAGGTCACTTTGT
1 GAATAAAATAGCTTTGGACACAAGTGTGGTACTATGTGAAGGCCAATTTGT
**
41095248 GAATAAAATATTTTTGGACACAAGTGTGGTACTATGTGAAGGCCAATTTGT
1 GAATAAAATAGCTTTGGACACAAGTGTGGTACTATGTGAAGGCCAATTTGT
* *
41095299 GAATAAAATAGTTTTGG-CTACAAGGGTGGTACTATGTGAAGGCCA
1 GAATAAAATAGCTTTGGAC-ACAAGTGTGGTACTATGTGAAGGCCA
41095344 CCATGTATCT
Statistics
Matches: 131, Mismatches: 15, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
50 1 0.01
51 130 0.99
ACGTcount: A:0.33, C:0.11, G:0.25, T:0.31
Consensus pattern (51 bp):
GAATAAAATAGCTTTGGACACAAGTGTGGTACTATGTGAAGGCCAATTTGT
Found at i:41098214 original size:46 final size:44
Alignment explanation
Indices: 41098113--41098235 Score: 140
Period size: 46 Copynumber: 2.7 Consensus size: 44
41098103 TGATATGTGT
* *
41098113 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCTACATTATGA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCTACATCAAGA
* * * *
41098157 GTGTCATTGTAAGACATGTCTGGGACATGCATTGGCATTGAGA-CAAGA
1 G-CT-AGTGTAAGACATGTCTGGGACATGCATCGGC--T-ACATCAAGA
41098205 GCTAGTGTAAGACATGTCTGGGACATGCATC
1 GCTAGTGTAAGACATGTCTGGGACATGCATC
41098236 TACCTCGAGA
Statistics
Matches: 65, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
44 1 0.02
45 1 0.02
46 55 0.85
47 1 0.02
48 5 0.08
49 2 0.03
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.27
Consensus pattern (44 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCGGCTACATCAAGA
Found at i:41098427 original size:49 final size:49
Alignment explanation
Indices: 41098208--41098429 Score: 199
Period size: 49 Copynumber: 4.7 Consensus size: 49
41098198 GACAAGAGCT
* * *
41098208 AGTGTAAGACATGTCTGGGACAT-GCATCTACCTCGAGATAT-ACAAG-C
1 AGTGTAAGACCTGTCTGGGACATGGCATCGACCTCGATATATGA-AAGTC
* * * * * * *
41098255 TAGTGTAAGACCTGTCTGGTACATGGCGTC-AGCT---TGT-TGTATGTT
1 -AGTGTAAGACCTGTCTGGGACATGGCATCGACCTCGATATATGAAAGTC
* * * * * * *
41098300 AGTTTAAGACCTATCTGGGACATGGCATCAACATCGATAGATGAGAGCC
1 AGTGTAAGACCTGTCTGGGACATGGCATCGACCTCGATATATGAAAGTC
*
41098349 AGTGTAAGACCTATCTGGGACATGGCATCGACCTCGATATATGAAAGTC
1 AGTGTAAGACCTGTCTGGGACATGGCATCGACCTCGATATATGAAAGTC
*
41098398 AGTGTAAGACCTGTCTAGGACATGGCATCGAC
1 AGTGTAAGACCTGTCTGGGACATGGCATCGAC
41098430 TGTGATGTGC
Statistics
Matches: 136, Mismatches: 30, Indels: 15
0.75 0.17 0.08
Matches are distributed among these distances:
44 28 0.21
45 3 0.02
48 25 0.18
49 80 0.59
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26
Consensus pattern (49 bp):
AGTGTAAGACCTGTCTGGGACATGGCATCGACCTCGATATATGAAAGTC
Found at i:41106497 original size:27 final size:28
Alignment explanation
Indices: 41106458--41106526 Score: 104
Period size: 27 Copynumber: 2.5 Consensus size: 28
41106448 TTTTAAGCCT
*
41106458 AATCTCATTCATATGGCCCATC-GGCCC
1 AATCACATTCATATGGCCCATCAGGCCC
* *
41106485 AATCACATCCATATGGCCCATCAGGTCC
1 AATCACATTCATATGGCCCATCAGGCCC
41106513 AATCACATTCATAT
1 AATCACATTCATAT
41106527 TCATGCAATC
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
27 20 0.54
28 17 0.46
ACGTcount: A:0.29, C:0.33, G:0.12, T:0.26
Consensus pattern (28 bp):
AATCACATTCATATGGCCCATCAGGCCC
Found at i:41112025 original size:13 final size:13
Alignment explanation
Indices: 41112007--41112077 Score: 52
Period size: 13 Copynumber: 5.4 Consensus size: 13
41111997 ATGTGTAAAT
41112007 GAAATGGTTATAC
1 GAAATGGTTATAC
* *
41112020 GAAATGTTTATATA
1 GAAATGGTTATA-C
* * *
41112034 GAAATAGATATAT
1 GAAATGGTTATAC
* *
41112047 GAAACGGTTATAT
1 GAAATGGTTATAC
* *
41112060 GAAGTGTTTATAC
1 GAAATGGTTATAC
41112073 GAAAT
1 GAAAT
41112078 ATTTTTAGGA
Statistics
Matches: 43, Mismatches: 14, Indels: 2
0.73 0.24 0.03
Matches are distributed among these distances:
13 34 0.79
14 9 0.21
ACGTcount: A:0.42, C:0.04, G:0.20, T:0.34
Consensus pattern (13 bp):
GAAATGGTTATAC
Found at i:41112038 original size:27 final size:26
Alignment explanation
Indices: 41112005--41112077 Score: 74
Period size: 27 Copynumber: 2.8 Consensus size: 26
41111995 ATATGTGTAA
*
41112005 ATGAAATGGTTATACGAAATGTTTAT
1 ATGAAATGGTTATACGAAATGGTTAT
* * * *
41112031 ATAGAAATAGATATATGAAACGGTTAT
1 AT-GAAATGGTTATACGAAATGGTTAT
* *
41112058 ATGAAGTGTTTATACGAAAT
1 ATGAAATGGTTATACGAAAT
41112078 ATTTTTAGGA
Statistics
Matches: 35, Mismatches: 11, Indels: 2
0.73 0.23 0.04
Matches are distributed among these distances:
26 14 0.40
27 21 0.60
ACGTcount: A:0.42, C:0.04, G:0.19, T:0.34
Consensus pattern (26 bp):
ATGAAATGGTTATACGAAATGGTTAT
Found at i:41113642 original size:134 final size:134
Alignment explanation
Indices: 41113418--41113702 Score: 351
Period size: 134 Copynumber: 2.1 Consensus size: 134
41113408 TGTCGTAGCT
* * *
41113418 GAGCTATGGTCTTACACAACATACCCTGTGTTTACTGTGCTAACAAACTCTGTATACTGCCATAA
1 GAGCTTTGGTCTTACACAACATACCCTGTGTTTACTGTCCCAACAAACTCTGTATACTGCCATAA
** * * *
41113483 TCGAGTTATGGTCTTACACAACATACAACATGTTTACTATCCTAGCAGACTCTCTATGCTATCAT
66 TCGAACTATGATCATACACAACATACAACATGTTTACTATCCTAGCAGACTCTCTATGCTACCAT
41113548 AGTC
131 AGTC
* * **
41113552 GAGCTTTGGTCTTACACAACATA-CCTCGTGTTTACTGTCCCGACAGAA-TCTTTATGTTGCCAT
1 GAGCTTTGGTCTTACACAACATACCCT-GTGTTTACTGTCCCAACA-AACTCTGTATACTGCCAT
* ** ** * *
41113615 AGTCGAACTATGATCATACACAACATACCTCATGTTTACTATCCTAGTGGACTCTTTATGCTGCC
64 AATCGAACTATGATCATACACAACATACAACATGTTTACTATCCTAGCAGACTCTCTATGCTACC
41113680 ATAGTC
129 ATAGTC
41113686 GAG-TTATGGTCTTACAC
1 GAGCTT-TGGTCTTACAC
41113703 CTTATACCTT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
133 5 0.04
134 122 0.95
135 2 0.02
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.33
Consensus pattern (134 bp):
GAGCTTTGGTCTTACACAACATACCCTGTGTTTACTGTCCCAACAAACTCTGTATACTGCCATAA
TCGAACTATGATCATACACAACATACAACATGTTTACTATCCTAGCAGACTCTCTATGCTACCAT
AGTC
Found at i:41113711 original size:67 final size:67
Alignment explanation
Indices: 41113422--41113702 Score: 298
Period size: 67 Copynumber: 4.2 Consensus size: 67
41113412 GTAGCTGAGC
* * * * * * * *
41113422 TATGGTCTTACACAACATACC-CTGTGTTTACTGTGCTAACAAACTCTGTATACTGCCATAATCG
1 TATGGTCTTACACAACATACCTC-ATGTTTACTATCCTAGCAGACTCTTTATGCTGCCATAGTCG
41113486 AGT
65 AGT
** * **
41113489 TATGGTCTTACACAACATACAACATGTTTACTATCCTAGCAGACTCTCTATGCTATCATAGTCGA
1 TATGGTCTTACACAACATACCTCATGTTTACTATCCTAGCAGACTCTTTATGCTGCCATAGTCGA
41113554 GCT
66 G-T
* * * * *
41113557 T-TGGTCTTACACAACATACCTCGTGTTTACTGTCC-CGACAGAATCTTTATGTTGCCATAGTCG
1 TATGGTCTTACACAACATACCTCATGTTTACTATCCTAG-CAGACTCTTTATGCTGCCATAGTCG
**
41113620 AAC
65 AGT
* * **
41113623 TATGATCATACACAACATACCTCATGTTTACTATCCTAGTGGACTCTTTATGCTGCCATAGTCGA
1 TATGGTCTTACACAACATACCTCATGTTTACTATCCTAGCAGACTCTTTATGCTGCCATAGTCGA
41113688 GT
66 GT
41113690 TATGGTCTTACAC
1 TATGGTCTTACAC
41113703 CTTATACCTT
Statistics
Matches: 173, Mismatches: 36, Indels: 10
0.79 0.16 0.05
Matches are distributed among these distances:
66 2 0.01
67 167 0.97
68 4 0.02
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.33
Consensus pattern (67 bp):
TATGGTCTTACACAACATACCTCATGTTTACTATCCTAGCAGACTCTTTATGCTGCCATAGTCGA
GT
Found at i:41123404 original size:30 final size:29
Alignment explanation
Indices: 41123359--41123432 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 29
41123349 TAAAGCCATC
* * *
41123359 CATAAATAT-TATATATGTATAA-TCACT
1 CATATATATGTATATATATATAACCCACT
41123386 CATGTATATATGTATATATATATAACCCCACT
1 CA--TATATATGTATATATATATAA-CCCACT
41123418 CATATATATGTATAT
1 CATATATATGTATAT
41123433 TGCCAATTCC
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
27 2 0.05
29 6 0.15
30 25 0.64
32 6 0.15
ACGTcount: A:0.41, C:0.14, G:0.05, T:0.41
Consensus pattern (29 bp):
CATATATATGTATATATATATAACCCACT
Found at i:41123886 original size:66 final size:66
Alignment explanation
Indices: 41123774--41123910 Score: 175
Period size: 66 Copynumber: 2.1 Consensus size: 66
41123764 CACATGCCCA
* * * * *
41123774 TGTGAAAAATGATGAGCATAGTGACTTGTGACACACGGCCACGCCACATGCCCGTGTGCTAGGCC
1 TGTGAAAAATGATGAGCATACTGACTTCTGACACACAGCCAAGCCACACGCCCGTGTGCTAGGCC
*
41123839 T
66 G
* * * * *
41123840 TGTGAAAAATGGTGAGTATTCTGGCTTCTGACACACAGCCAAGCCACACGCCTGTGTGCTAGGCC
1 TGTGAAAAATGATGAGCATACTGACTTCTGACACACAGCCAAGCCACACGCCCGTGTGCTAGGCC
41123905 G
66 G
41123906 TGTGA
1 TGTGA
41123911 GCCTACTGAC
Statistics
Matches: 60, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
66 60 1.00
ACGTcount: A:0.25, C:0.25, G:0.28, T:0.23
Consensus pattern (66 bp):
TGTGAAAAATGATGAGCATACTGACTTCTGACACACAGCCAAGCCACACGCCCGTGTGCTAGGCC
G
Found at i:41127120 original size:15 final size:15
Alignment explanation
Indices: 41127100--41127131 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
41127090 AAAGATAGCT
41127100 TTAGAACCATGGATC
1 TTAGAACCATGGATC
41127115 TTAGAACCATGGATC
1 TTAGAACCATGGATC
41127130 TT
1 TT
41127132 TAATTTTCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (15 bp):
TTAGAACCATGGATC
Found at i:41127619 original size:3 final size:3
Alignment explanation
Indices: 41127611--41127662 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
41127601 ATTTAGTCTC
41127611 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
41127659 TAT T
1 TAT T
41127663 TTACTAATGC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:41133814 original size:53 final size:53
Alignment explanation
Indices: 41133630--41133838 Score: 215
Period size: 55 Copynumber: 3.9 Consensus size: 53
41133620 CATTAGGGTT
* * *
41133630 TAAGGATACCATGTAAGACCATGCTAAGGCATGGAAATTGGTAAGGTTTC-TAAGG
1 TAAGGATACCATGTAAGACCATGCCAAGACATGG-CATTGGTAA-G-TTCATAAGG
* * * * *
41133685 CAAGGAAATCATGTAAGACCATGTCAAGACATGGCATTGATAAGTTACTATAAGG
1 TAAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTT-C-ATAAGG
* * * *
41133740 CAAAGG-TCCCATGTAAGACCATGCCAAGGCATGGCATTGGTGAGTTCATAAGG
1 -TAAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTCATAAGG
* * *
41133793 TAAGGATACCATGTAAGACCATGTCGAGACATGGCAATGGTAAGTT
1 TAAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTT
41133839 TCAAAAGGGT
Statistics
Matches: 126, Mismatches: 23, Indels: 12
0.78 0.14 0.07
Matches are distributed among these distances:
52 6 0.05
53 42 0.33
54 8 0.06
55 66 0.52
56 4 0.03
ACGTcount: A:0.35, C:0.16, G:0.26, T:0.23
Consensus pattern (53 bp):
TAAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTCATAAGG
Found at i:41133837 original size:108 final size:110
Alignment explanation
Indices: 41133638--41133838 Score: 291
Period size: 108 Copynumber: 1.8 Consensus size: 110
41133628 TTTAAGGATA
* *
41133638 CCATGTAAGACCATGCTAAGGCATGGAAATTGGTAAGGTTTCTAAGGCAAGGAAATCATGTAAGA
1 CCATGTAAGACCATGCCAAGGCATGGAAATTGGTAAGGTTTCTAAGGCAAGGAAACCATGTAAGA
*
41133703 CCATGTCAAGACATGGCATTGATAAGTTACTATAAGGCAAAGGTC
66 CCATGTCAAGACATGGCAATGATAAGTTACTATAAGGCAAAGGTC
* * * *
41133748 CCATGTAAGACCATGCCAAGGCATGG-CATTGGTGA-G-TTCATAAGGTAAGGATACCATGTAAG
1 CCATGTAAGACCATGCCAAGGCATGGAAATTGGTAAGGTTTC-TAAGGCAAGGAAACCATGTAAG
* *
41133810 ACCATGTCGAGACATGGCAATGGTAAGTT
65 ACCATGTCAAGACATGGCAATGATAAGTT
41133839 TCAAAAGGGT
Statistics
Matches: 81, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
107 3 0.04
108 46 0.57
109 7 0.09
110 25 0.31
ACGTcount: A:0.34, C:0.16, G:0.26, T:0.23
Consensus pattern (110 bp):
CCATGTAAGACCATGCCAAGGCATGGAAATTGGTAAGGTTTCTAAGGCAAGGAAACCATGTAAGA
CCATGTCAAGACATGGCAATGATAAGTTACTATAAGGCAAAGGTC
Found at i:41138859 original size:126 final size:126
Alignment explanation
Indices: 41138631--41138885 Score: 483
Period size: 126 Copynumber: 2.0 Consensus size: 126
41138621 CAGAGTTTCT
*
41138631 GATCAGTCCTGACGGTTGTTTGATGTTCAGAGATAGGGTATGCGTACCGAAGAATGATGAGCTTA
1 GATCAGTCCTGACGGTTGTTTGATGTTCAGAGATAGGGTATGCATACCGAAGAATGATGAGCTTA
41138696 TTCGAAAGATCTTACAGGAAGCACATAGTAGTACTTTGTCTATTCATCCAGGTAGTACAAA
66 TTCGAAAGATCTTACAGGAAGCACATAGTAGTACTTTGTCTATTCATCCAGGTAGTACAAA
*
41138757 GATCAGTTCTGACGGTTGTTTGATGTTCAGAGATAGGGTATGCATACCGAAGAATGATGAGCTTA
1 GATCAGTCCTGACGGTTGTTTGATGTTCAGAGATAGGGTATGCATACCGAAGAATGATGAGCTTA
*
41138822 TTCGAAAGATCTTACAGGAAGCACATAGTAGTTCTTTGTCTATTCATCCAGGTAGTACAAA
66 TTCGAAAGATCTTACAGGAAGCACATAGTAGTACTTTGTCTATTCATCCAGGTAGTACAAA
41138883 GAT
1 GAT
41138886 GTATAATGAT
Statistics
Matches: 126, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
126 126 1.00
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.30
Consensus pattern (126 bp):
GATCAGTCCTGACGGTTGTTTGATGTTCAGAGATAGGGTATGCATACCGAAGAATGATGAGCTTA
TTCGAAAGATCTTACAGGAAGCACATAGTAGTACTTTGTCTATTCATCCAGGTAGTACAAA
Found at i:41140965 original size:55 final size:54
Alignment explanation
Indices: 41140878--41141093 Score: 242
Period size: 55 Copynumber: 4.0 Consensus size: 54
41140868 ATTAGGGTTT
* *
41140878 AAGGATATCATGTAAGACCATG-CTAAGGCATGGCAATTGGTAAGGTTTC-TAAGGC
1 AAGGATACCATGTAAGACCATGTC-AAGACATGGC-ATTGGTAA-GTTTCATAAGGC
* * * *
41140933 AAGGAAATCATGTAAGACCATGTCAAGACATGGCATTGATAAGTTACCATAAGGC
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGGTAAGTT-TCATAAGGC
* * * *
41140988 AAAGG-TCCCATGTAAGACCATGCCAAGGCATGGCATTGGTGAG-TTCATAAGGC
1 -AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGGTAAGTTTCATAAGGC
* * *
41141041 AAGGATACCATGTAAGACCATGTCGAGACATGGCAATGGTAAGTTTCAAAAGG
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGGTAAGTTTCATAAGG
41141094 ATACCACATA
Statistics
Matches: 136, Mismatches: 19, Indels: 13
0.81 0.11 0.08
Matches are distributed among these distances:
52 4 0.03
53 43 0.32
54 17 0.12
55 67 0.49
56 5 0.04
ACGTcount: A:0.35, C:0.17, G:0.26, T:0.22
Consensus pattern (54 bp):
AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGGTAAGTTTCATAAGGC
Found at i:41141084 original size:108 final size:110
Alignment explanation
Indices: 41140886--41141085 Score: 307
Period size: 108 Copynumber: 1.8 Consensus size: 110
41140876 TTAAGGATAT
* *
41140886 CATGTAAGACCATGCTAAGGCATGGCAATTGGTAAGGTTTCTAAGGCAAGGAAATCATGTAAGAC
1 CATGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGCAAGGAAACCATGTAAGAC
*
41140951 CATGTCAAGACATGGCATTGATAAGTTACCATAAGGCAAAGGTCC
66 CATGTCAAGACATGGCAATGATAAGTTACCATAAGGCAAAGGTCC
* *
41140996 CATGTAAGACCATGCCAAGGCATGGC-ATTGGTGA-G-TTCATAAGGCAAGGATACCATGTAAGA
1 CATGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTC-TAAGGCAAGGAAACCATGTAAGA
* *
41141058 CCATGTCGAGACATGGCAATGGTAAGTT
65 CCATGTCAAGACATGGCAATGATAAGTT
41141086 TCAAAAGGAT
Statistics
Matches: 82, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
107 3 0.04
108 47 0.57
109 7 0.09
110 25 0.30
ACGTcount: A:0.34, C:0.17, G:0.26, T:0.23
Consensus pattern (110 bp):
CATGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGCAAGGAAACCATGTAAGAC
CATGTCAAGACATGGCAATGATAAGTTACCATAAGGCAAAGGTCC
Found at i:41147528 original size:25 final size:25
Alignment explanation
Indices: 41147499--41147559 Score: 95
Period size: 25 Copynumber: 2.4 Consensus size: 25
41147489 ACAAGCTGTA
*
41147499 AACGGTAAGCTCCTCTGAGCTGAAT
1 AACGGCAAGCTCCTCTGAGCTGAAT
*
41147524 AACGGCAAGCTCCTCTGAGTTGAAT
1 AACGGCAAGCTCCTCTGAGCTGAAT
*
41147549 AATGGCAAGCT
1 AACGGCAAGCT
41147560 TATGCAAGCT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.30, C:0.23, G:0.25, T:0.23
Consensus pattern (25 bp):
AACGGCAAGCTCCTCTGAGCTGAAT
Found at i:41151297 original size:40 final size:41
Alignment explanation
Indices: 41151253--41151346 Score: 122
Period size: 40 Copynumber: 2.3 Consensus size: 41
41151243 TGATTATGCT
* *
41151253 TGGCACTAAGTGTGCG-GTTTAATATAGCTTCGGCTATA-AA
1 TGGCACTAAGTGTGCGAG-TTAAGATAGCTCCGGCTATATAA
**
41151293 TGGCACTAAGTGTGCGAGTTGGGATAGCTCCGGCTATATAA
1 TGGCACTAAGTGTGCGAGTTAAGATAGCTCCGGCTATATAA
41151334 -GGCACTAAGTGTG
1 TGGCACTAAGTGTG
41151347 TGATATCGAC
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
40 45 0.94
41 3 0.06
ACGTcount: A:0.26, C:0.16, G:0.30, T:0.29
Consensus pattern (41 bp):
TGGCACTAAGTGTGCGAGTTAAGATAGCTCCGGCTATATAA
Found at i:41159893 original size:19 final size:19
Alignment explanation
Indices: 41159869--41159916 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
41159859 CAAATACATC
*
41159869 AACAGAAGCTCGAAAGCTA
1 AACAGAAGCTCGAAAGCAA
41159888 AACAGAAGCTCGAAAGCAA
1 AACAGAAGCTCGAAAGCAA
*
41159907 AATAGAAGCT
1 AACAGAAGCT
41159917 TGTAAGAGCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.50, C:0.19, G:0.21, T:0.10
Consensus pattern (19 bp):
AACAGAAGCTCGAAAGCAA
Found at i:41159936 original size:21 final size:21
Alignment explanation
Indices: 41159906--41159949 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
41159896 CTCGAAAGCA
* *
41159906 AAATAGAAGCTTGTAAGAGCT
1 AAATAAAAGCTTCTAAGAGCT
41159927 AAATAAAAGCTTCTAAGAGCT
1 AAATAAAAGCTTCTAAGAGCT
41159948 AA
1 AA
41159950 TTCACCCAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.48, C:0.11, G:0.18, T:0.23
Consensus pattern (21 bp):
AAATAAAAGCTTCTAAGAGCT
Found at i:41160870 original size:70 final size:70
Alignment explanation
Indices: 41160784--41160923 Score: 253
Period size: 70 Copynumber: 2.0 Consensus size: 70
41160774 CAAAAATATG
*
41160784 AAAAACCAGCTTAAGCTCTCTCTCCTATGGCGTTTTAGGCCGAAATTGAAGAACAAATACCTAAA
1 AAAAACCAGCTTAAGCTCTCTCTCCTATGGCGTTTTAGGCCGAAATTGAAAAACAAATACCTAAA
41160849 AAACT
66 AAACT
* *
41160854 AAAAACCAGCTTAAGCTCTCTCTCCTATGGCGTTTTAGGCCGAAATTGAAAAAGAAATGCCTAAA
1 AAAAACCAGCTTAAGCTCTCTCTCCTATGGCGTTTTAGGCCGAAATTGAAAAACAAATACCTAAA
41160919 AAACT
66 AAACT
41160924 TTCCAATTCC
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
70 67 1.00
ACGTcount: A:0.39, C:0.22, G:0.15, T:0.24
Consensus pattern (70 bp):
AAAAACCAGCTTAAGCTCTCTCTCCTATGGCGTTTTAGGCCGAAATTGAAAAACAAATACCTAAA
AAACT
Found at i:41163054 original size:4 final size:4
Alignment explanation
Indices: 41163045--41163156 Score: 152
Period size: 4 Copynumber: 28.0 Consensus size: 4
41163035 GTCGTCAAGA
* *
41163045 AGAG AGAG AGGG AGAG AGAG AGAG AGAG AGAG AGAG AGAG TGAG AGAG
1 AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG
* * * * * *
41163093 AGTG AGTG AGTG AGTG AGTG AGTG AGAG AGAG AGAG AGAG AGAG AGAG
1 AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG
41163141 AGAG AGAG AGAG AGAG
1 AGAG AGAG AGAG AGAG
41163157 TGTGTGTGTG
Statistics
Matches: 102, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 102 1.00
ACGTcount: A:0.43, C:0.00, G:0.51, T:0.06
Consensus pattern (4 bp):
AGAG
Found at i:41163059 original size:6 final size:6
Alignment explanation
Indices: 41163045--41163156 Score: 152
Period size: 6 Copynumber: 18.7 Consensus size: 6
41163035 GTCGTCAAGA
* *
41163045 AGAGAG AGAGGG AGAGAG AGAGAG AGAGAG AGAGAG AGAGTG AGAGAG
1 AGAGAG AGAGAG AGAGAG AGAGAG AGAGAG AGAGAG AGAGAG AGAGAG
* * * * * *
41163093 AGTGAG TGAGTG AGTGAG TGAGTG AGAGAG AGAGAG AGAGAG AGAGAG
1 AGAGAG AGAGAG AGAGAG AGAGAG AGAGAG AGAGAG AGAGAG AGAGAG
41163141 AGAGAG AGAGAG AGAG
1 AGAGAG AGAGAG AGAG
41163157 TGTGTGTGTG
Statistics
Matches: 90, Mismatches: 16, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 90 1.00
ACGTcount: A:0.43, C:0.00, G:0.51, T:0.06
Consensus pattern (6 bp):
AGAGAG
Found at i:41163161 original size:2 final size:2
Alignment explanation
Indices: 41163156--41163186 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
41163146 GAGAGAGAGA
41163156 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
41163187 CACGTTTGTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.52, T:0.48
Consensus pattern (2 bp):
GT
Found at i:41165882 original size:47 final size:48
Alignment explanation
Indices: 41165812--41166122 Score: 220
Period size: 47 Copynumber: 6.6 Consensus size: 48
41165802 GTATAATGCT
*
41165812 GATGCCATGTCCCAGACACGGTCTTACACTGGCTCTCACGT-TAAGTC
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCACGTCTAAGTC
* * * * ** *
41165859 GATGCCATGTCTCAGACATGGTCTTACACTGACTCTCATGTATCCGTGAT
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCACGTCTAAGT--C
* * * * *
41165909 GATGCCATGTCCCAAAAATGGTCTTACACTGACACATCA--TGT-AGTC
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTC-TCACGTCTAAGTC
* * *
41165955 GATG-CATGTCCCAGACAT-GTCTTACACTGGCT-TACATC-TCGAGGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCT-CA-CGTCTAAGTC
* * *
41166001 GATG-TATGTCCCAGACAT-GTCTTACACTAGCTCT--CGTCTCAATGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCACGTCT-AA-GTC
* ** * * *
41166047 AATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGT-GGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCA-CGTCTAAGTC
41166095 GATG-CATGTCCCAGACAT-GTCTTACACT
1 GATGCCATGTCCCAGACATGGTCTTACACT
41166123 AGCACACAAA
Statistics
Matches: 213, Mismatches: 34, Indels: 35
0.76 0.12 0.12
Matches are distributed among these distances:
42 1 0.00
43 3 0.01
44 14 0.07
45 14 0.07
46 52 0.24
47 65 0.31
48 26 0.12
49 2 0.01
50 31 0.15
51 5 0.02
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.28
Consensus pattern (48 bp):
GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCACGTCTAAGTC
Found at i:41166004 original size:46 final size:46
Alignment explanation
Indices: 41165954--41166122 Score: 216
Period size: 46 Copynumber: 3.6 Consensus size: 46
41165944 ATCATGTAGT
41165954 CGATGCATGTCCCAGACATGTCTTACACTGGCT-TACATCTCGAGGC
1 CGATGCATGTCCCAGACATGTCTTACACTGGCTCT-CATCTCGAGGC
* * * * *
41166000 CGATGTATGTCCCAGACATGTCTTACACTAGCTCTCGTCTCAATGC
1 CGATGCATGTCCCAGACATGTCTTACACTGGCTCTCATCTCGAGGC
* * *
41166046 CAATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAAT-GTGGC
1 CGATG-CATGTCCCAGACAT-GTCTTACACTGGCTCTCAT-CTCGAGGC
41166094 CGATGCATGTCCCAGACATGTCTTACACT
1 CGATGCATGTCCCAGACATGTCTTACACT
41166123 AGCACACAAA
Statistics
Matches: 105, Mismatches: 14, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
46 53 0.50
47 28 0.27
48 23 0.22
49 1 0.01
ACGTcount: A:0.22, C:0.30, G:0.20, T:0.28
Consensus pattern (46 bp):
CGATGCATGTCCCAGACATGTCTTACACTGGCTCTCATCTCGAGGC
Found at i:41169169 original size:28 final size:28
Alignment explanation
Indices: 41169104--41169202 Score: 119
Period size: 28 Copynumber: 3.5 Consensus size: 28
41169094 CATGAGATTG
* * *
41169104 GCACTAAGTGTGCGGGTTCAAATTGTATA
1 GCACTAAGTGTGCGAGTT-AGATTATATA
*
41169133 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTAGATTATATA
* *
41169161 GCACTAAGTGTGCGAGTTCGACTAT-TAA
1 GCACTAAGTGTGCGAGTTAGATTATAT-A
41169189 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
41169203 GGCTTATTAT
Statistics
Matches: 63, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
27 1 0.02
28 45 0.71
29 17 0.27
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.30
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTAGATTATATA
Found at i:41176397 original size:16 final size:16
Alignment explanation
Indices: 41176376--41176407 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
41176366 ACATGAACCA
41176376 ACTAAACTAAACCCGG
1 ACTAAACTAAACCCGG
41176392 ACTAAACTAAACCCGG
1 ACTAAACTAAACCCGG
41176408 TTGTAATGAA
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:0.31, G:0.12, T:0.12
Consensus pattern (16 bp):
ACTAAACTAAACCCGG
Found at i:41177422 original size:55 final size:55
Alignment explanation
Indices: 41177337--41177447 Score: 195
Period size: 55 Copynumber: 2.0 Consensus size: 55
41177327 TTTTGTAAAT
*
41177337 TTTGTGGTATTGGCCACCAATTTTCTATTTGAGCCGACTCATTTGCCCATGAGAA
1 TTTGTGGTATTGGCCACCAATTTTCAATTTGAGCCGACTCATTTGCCCATGAGAA
* *
41177392 TTTGTGGTTTTGGCCACTAATTTTCAATTTGAGCCGACTCATTTGCCCATGAGAA
1 TTTGTGGTATTGGCCACCAATTTTCAATTTGAGCCGACTCATTTGCCCATGAGAA
41177447 T
1 T
41177448 AGATATATAA
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 53 1.00
ACGTcount: A:0.22, C:0.21, G:0.20, T:0.38
Consensus pattern (55 bp):
TTTGTGGTATTGGCCACCAATTTTCAATTTGAGCCGACTCATTTGCCCATGAGAA
Found at i:41179560 original size:19 final size:17
Alignment explanation
Indices: 41179526--41179562 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
41179516 ACTTCTAAAA
41179526 AAAATAAAATTAACAAT
1 AAAATAAAATTAACAAT
41179543 AAAATAAGAATTATACAAT
1 AAAATAA-AATTA-ACAAT
41179562 A
1 A
41179563 TTCAAATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 7 0.39
18 5 0.28
19 6 0.33
ACGTcount: A:0.68, C:0.05, G:0.03, T:0.24
Consensus pattern (17 bp):
AAAATAAAATTAACAAT
Found at i:41179598 original size:14 final size:14
Alignment explanation
Indices: 41179566--41179599 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
41179556 TACAATATTC
*
41179566 AAATAATAACAGTA
1 AAATAATAACAATA
41179580 AAATAATAACAATA
1 AAATAATAACAATA
*
41179594 TAATAA
1 AAATAA
41179600 CAAAACGATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.68, C:0.06, G:0.03, T:0.24
Consensus pattern (14 bp):
AAATAATAACAATA
Found at i:41183014 original size:12 final size:11
Alignment explanation
Indices: 41182986--41183015 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
41182976 ATTTTTTTTA
41182986 TTTTTAAGAAT
1 TTTTTAAGAAT
41182997 TTTTTAAGAAT
1 TTTTTAAGAAT
41183008 TTATTTAA
1 TT-TTTAA
41183016 ATAAAAATAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.72
12 5 0.28
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.57
Consensus pattern (11 bp):
TTTTTAAGAAT
Found at i:41185734 original size:21 final size:22
Alignment explanation
Indices: 41185683--41185725 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
41185673 GCTTGGTGTA
*
41185683 AAAATAAAAAAACAGTAATTGG
1 AAAATAACAAAACAGTAATTGG
*
41185705 AAAATAACAAAACATTAATTG
1 AAAATAACAAAACAGTAATTG
41185726 AAACAAACAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.63, C:0.07, G:0.09, T:0.21
Consensus pattern (22 bp):
AAAATAACAAAACAGTAATTGG
Found at i:41193421 original size:25 final size:26
Alignment explanation
Indices: 41193378--41193426 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
41193368 ATTTTTTTTA
*
41193378 AAAATATAATATAAGAAT-ATAAAGT
1 AAAATATAATAAAAGAATAATAAAGT
41193403 AAAATA-AATAAAAGAAATAATAAA
1 AAAATATAATAAAAG-AATAATAAA
41193427 AAGAATAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 7 0.33
25 9 0.43
26 5 0.24
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.22
Consensus pattern (26 bp):
AAAATATAATAAAAGAATAATAAAGT
Found at i:41193506 original size:16 final size:17
Alignment explanation
Indices: 41193485--41193521 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
41193475 TTGAGGGAAA
41193485 GAAAGAAAGAA-AAA-GG
1 GAAAGAAA-AAGAAATGG
41193501 GAAAGAAAAAGAAATGG
1 GAAAGAAAAAGAAATGG
41193518 GAAA
1 GAAA
41193522 ATTAGGGCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 2 0.11
16 11 0.58
17 6 0.32
ACGTcount: A:0.68, C:0.00, G:0.30, T:0.03
Consensus pattern (17 bp):
GAAAGAAAAAGAAATGG
Found at i:41195914 original size:46 final size:46
Alignment explanation
Indices: 41195864--41196085 Score: 299
Period size: 46 Copynumber: 4.8 Consensus size: 46
41195854 TGGTTGAGCA
41195864 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
41195910 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
41195956 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
**
41196001 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACA
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
41196049 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
41196086 GCGGGTTACA
Statistics
Matches: 156, Mismatches: 11, Indels: 18
0.84 0.06 0.10
Matches are distributed among these distances:
42 2 0.01
43 5 0.03
45 3 0.02
46 109 0.70
47 29 0.19
48 2 0.01
50 4 0.03
51 2 0.01
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:41196033 original size:93 final size:93
Alignment explanation
Indices: 41195910--41196078 Score: 302
Period size: 93 Copynumber: 1.8 Consensus size: 93
41195900 GATGCGAATG
***
41195910 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGTTGA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACACCCGAACTCGTTGAGTTGA
41195975 GTCCGAGTTCGTGAGATGTAACTAGGCA
66 GTCCGAGTTCGTGAGATGTAACTAGGCA
*
41196003 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACACCCGAGCTCGTTGAGTTGA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACACCCGAACTCGTTGAGTTGA
41196068 GTCCGAGTTCG
66 GTCCGAGTTCG
41196079 CTTATGGGCG
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.28
Consensus pattern (93 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACACCCGAACTCGTTGAGTTGA
GTCCGAGTTCGTGAGATGTAACTAGGCA
Found at i:41203529 original size:46 final size:46
Alignment explanation
Indices: 41203479--41203653 Score: 207
Period size: 45 Copynumber: 3.8 Consensus size: 46
41203469 TGGTTGAGCA
41203479 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
41203525 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
41203570 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-C
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
41203617 ACCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
41203654 GCGGGTTACA
Statistics
Matches: 110, Mismatches: 10, Indels: 19
0.79 0.07 0.14
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 37 0.34
46 29 0.26
47 29 0.26
48 2 0.02
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:41203594 original size:47 final size:47
Alignment explanation
Indices: 41203476--41203645 Score: 194
Period size: 46 Copynumber: 3.7 Consensus size: 47
41203466 GGATGGTTGA
*
41203476 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGA-GGATGCGAAT
* *
41203524 G--TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA-GATG-TAACT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGAGGATGCGAA-T
*
41203567 AGGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-
1 --GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGA-GGATGCGAAT
*
41203616 -CA-CCGAGCTCGTTGAGTTGAGTCCGAGTTC
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTC
41203646 GCTTATGGGC
Statistics
Matches: 106, Mismatches: 7, Indels: 21
0.79 0.05 0.16
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 30 0.28
46 31 0.29
47 29 0.27
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.28
Consensus pattern (47 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGAGGATGCGAAT
Found at i:41205574 original size:17 final size:17
Alignment explanation
Indices: 41205549--41205582 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
41205539 TTTTGAGTCC
41205549 ACACAGCCTGGCACATG
1 ACACAGCCTGGCACATG
*
41205566 ACACGGCCTGGCACATG
1 ACACAGCCTGGCACATG
41205583 GGCGTGTGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.35, G:0.26, T:0.12
Consensus pattern (17 bp):
ACACAGCCTGGCACATG
Found at i:41211310 original size:21 final size:20
Alignment explanation
Indices: 41211281--41211328 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
41211271 ATGTATTTGC
* *
41211281 TTATTATTTAATAAATAATAA
1 TTATAATTTAAAAAAT-ATAA
41211302 TTATAATTTTAAAAAATATAA
1 TTATAA-TTTAAAAAATATAA
41211323 -TATAAT
1 TTATAAT
41211329 AATATAAAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 1 0.04
20 5 0.21
21 9 0.38
22 9 0.38
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
TTATAATTTAAAAAATATAA
Done.