Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold53
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: 4419549
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.31
Warning! 41486 characters in sequence are not A, C, G, or T
File 23 of 28
Found at i:3498188 original size:17 final size:15
Alignment explanation
Indices: 3498147--3498182 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
3498137 CTAGTTCGAC
*
3498147 AATTTTCTTTTCAAG
1 AATTTTATTTTCAAG
3498162 AATTTTATTTTCAAG
1 AATTTTATTTTCAAG
3498177 AATTTT
1 AATTTT
3498183 TTATTTATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.31, C:0.08, G:0.06, T:0.56
Consensus pattern (15 bp):
AATTTTATTTTCAAG
Found at i:3505908 original size:155 final size:156
Alignment explanation
Indices: 3505714--3506048 Score: 459
Period size: 155 Copynumber: 2.2 Consensus size: 156
3505704 AATTTACAAA
* * *
3505714 TTAATCTCTAAACTTTCTAAAATTTACAGAAAGGTCCCTAACATGTT-AAAAAGCCTAAAATATG
1 TTAATCCCTAAACTTTCTAAAATTTACAGAAAAGTCCCTAACATGTTGAAAAA-CCCAAAATATG
* * *
3505778 TTTAATAAGGCATGAAATAGT-TCTCATAT-AGTACTAGGGACTCTT-AGCCAAGCAAGGATACT
65 TTTAATAAGGCATGAAACAATCT-TCATATGA-CACTAGGGACT-TTCAGCCAAGCAAGGATACT
*
3505840 CAAAGAAAAAATTTTTAA-ACTTTTTGCAA-
127 CAAAGAAAAAAATTTTAACA-TTTTTGCAAT
* *
3505869 TTAAGTCCGTAAACTTTCTAAAATTTAGA-AAAAGTCCCTAACATGTTGAAAAACCCAAAATATG
1 TTAA-TCCCTAAACTTTCTAAAATTTACAGAAAAGTCCCTAACATGTTGAAAAACCCAAAATATG
* *
3505933 TTTAATAATGCATGAAACAATCTTCTTATGACACTAGGGACTTTCAGCCAAGCAAGGATACTCAA
65 TTTAATAAGGCATGAAACAATCTTCATATGACACTAGGGACTTTCAGCCAAGCAAGGATACTCAA
*
3505998 AGAAAAAAATTTTAACATTTTTGTAAT
130 AGAAAAAAATTTTAACATTTTTGCAAT
3506025 TTAATCCCTAAACTTTCTAAAATT
1 TTAATCCCTAAACTTTCTAAAATT
3506049 GCAAAATAGA
Statistics
Matches: 160, Mismatches: 13, Indels: 14
0.86 0.07 0.07
Matches are distributed among these distances:
154 2 0.01
155 125 0.78
156 33 0.21
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.31
Consensus pattern (156 bp):
TTAATCCCTAAACTTTCTAAAATTTACAGAAAAGTCCCTAACATGTTGAAAAACCCAAAATATGT
TTAATAAGGCATGAAACAATCTTCATATGACACTAGGGACTTTCAGCCAAGCAAGGATACTCAAA
GAAAAAAATTTTAACATTTTTGCAAT
Found at i:3508079 original size:32 final size:32
Alignment explanation
Indices: 3508038--3508102 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
3508028 TCCTATCCCT
* *
3508038 AGATTTTGGTGGAACCTGAAGGACCTTTTACA
1 AGATTTTGGTGGAACCTAAAAGACCTTTTACA
*
3508070 AGATTTTGGTGGAACCTAAAAGACTTTTTACA
1 AGATTTTGGTGGAACCTAAAAGACCTTTTACA
3508102 A
1 A
3508103 TTAACTTTGC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.32, C:0.14, G:0.22, T:0.32
Consensus pattern (32 bp):
AGATTTTGGTGGAACCTAAAAGACCTTTTACA
Found at i:3508928 original size:20 final size:19
Alignment explanation
Indices: 3508856--3508929 Score: 96
Period size: 20 Copynumber: 3.8 Consensus size: 19
3508846 TATATCCAGA
* *
3508856 TGTATCGATACATAATGCTT
1 TGTATCGATACATGAT-CAT
3508876 TGTATCGATACATGATCAT
1 TGTATCGATACATGATCAT
3508895 TGTATCGATACATGCA-CAAT
1 TGTATCGATACATG-ATC-AT
3508915 TGTATCGATACATGA
1 TGTATCGATACATGA
3508930 AACTAGCAAT
Statistics
Matches: 50, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
19 18 0.36
20 32 0.64
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.35
Consensus pattern (19 bp):
TGTATCGATACATGATCAT
Found at i:3508982 original size:20 final size:20
Alignment explanation
Indices: 3508957--3509010 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
3508947 CTACCAGTGT
*
3508957 TTGTATCGATACATGGAA-CA
1 TTGTATCGATACAT-GAAGAA
*
3508977 TTGTATCAATACATGAAGAA
1 TTGTATCGATACATGAAGAA
3508997 TTGTATCGATACAT
1 TTGTATCGATACAT
3509011 TGCCTCAAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
19 3 0.10
20 27 0.90
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (20 bp):
TTGTATCGATACATGAAGAA
Found at i:3510624 original size:15 final size:15
Alignment explanation
Indices: 3510604--3510638 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
3510594 AACCATCAAA
3510604 GATGATGAAGATAAT
1 GATGATGAAGATAAT
*
3510619 GATGATGATGATAAT
1 GATGATGAAGATAAT
3510634 GATGA
1 GATGA
3510639 AATTAACTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.29, T:0.29
Consensus pattern (15 bp):
GATGATGAAGATAAT
Found at i:3517774 original size:18 final size:21
Alignment explanation
Indices: 3517748--3517801 Score: 71
Period size: 18 Copynumber: 2.8 Consensus size: 21
3517738 ACATAAAGCT
*
3517748 TTGTATCGATACATGA-TC-A
1 TTGTATCGATACATGACACAA
3517767 TT-TATCGATACAT-ACACAA
1 TTGTATCGATACATGACACAA
3517786 TTGTATCGATACATGA
1 TTGTATCGATACATGA
3517802 AACTGGCAGT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
17 1 0.03
18 12 0.40
19 5 0.17
20 11 0.37
21 1 0.03
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (21 bp):
TTGTATCGATACATGACACAA
Found at i:3517794 original size:20 final size:19
Alignment explanation
Indices: 3517729--3517802 Score: 71
Period size: 20 Copynumber: 3.8 Consensus size: 19
3517719 CATATCTAGG
* * *
3517729 TGTATTGATACATAAAGCTT
1 TGTATCGATACATGAA-CAT
*
3517749 TGTATCGATACATGATCAT
1 TGTATCGATACATGAACAT
3517768 T-TATCGATACAT-ACACAAT
1 TGTATCGATACATGA-AC-AT
3517787 TGTATCGATACATGAA
1 TGTATCGATACATGAA
3517803 ACTGGCAGTA
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
17 1 0.02
18 12 0.27
19 6 0.13
20 25 0.56
21 1 0.02
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35
Consensus pattern (19 bp):
TGTATCGATACATGAACAT
Found at i:3517854 original size:20 final size:19
Alignment explanation
Indices: 3517829--3517882 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 19
3517819 CTACCACTGT
3517829 TTGTATCGATACATG-GCACA
1 TTGTATCGATACATGAG-A-A
3517849 TTGTATCGATACATGAAGAA
1 TTGTATCGATACATG-AGAA
3517869 TTGTATCGATACAT
1 TTGTATCGATACAT
3517883 TATCTCAAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 30 0.94
21 1 0.03
22 1 0.03
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Consensus pattern (19 bp):
TTGTATCGATACATGAGAA
Found at i:3519018 original size:148 final size:147
Alignment explanation
Indices: 3518667--3519240 Score: 606
Period size: 148 Copynumber: 3.9 Consensus size: 147
3518657 AACGAGTTGG
* * * *
3518667 TAGGGCTAGGTTTGGGAGAAAATGCTAGAAGGTCCTTAAGGTCTACCATCGACTTAGAAATGCTA
1 TAGGGCTAGGTTTGAGA-AAAATGCTAAAAGGTCCCTAAGGTCTACCATCGACTTAGAAATGCCA
** ** * * *
3518732 G-TGATTATAAAGGACTCAAAAAAGTAAAAGTGAACCTACGCCTAATATATACCC-TCGACAT-G
65 GATGATCCTAAAGGACTTGAAAAAGTAAAAGCGAACCTACGCCTAATATGTACCCTTAG-CATAG
*
3518794 AAGCAATCTGGTAATTTCA
129 AAGCAACCTGGTAATTTCA
* * * * *
3518813 TAAGGCTAGGTTTCCAGAAAAATGCTAAAAGGTCTCTAAGGTCTACCATTGACTTAGAAGTGCCC
1 TAGGGCTAGGTTT-GAGAAAAATGCTAAAAGGTCCCTAAGGTCTACCATCGACTTAGAAATG-CC
* * * * *
3518878 AG-TGATCCTAAAGGACATGAAAAAGTAAAAGCAAACCTACACCTAATACGTACCCTTAGCATAA
64 AGATGATCCTAAAGGACTTGAAAAAGTAAAAGCGAACCTACGCCTAATATGTACCCTTAGCATAG
** *
3518942 AAGCAACCCAGTAGTTTCA
129 AAGCAACCTGGTAATTTCA
* * *
3518961 TAGGGATAGGTTATGAGGGAAAAAAGCT-AAA-GTCCCTAAGGTCTACCATCGACTTAGAAACGC
1 TAGGGCTAGGTT-TGA--GAAAAATGCTAAAAGGTCCCTAAGGTCTACCATCGACTTAGAAATGC
* ** *
3519024 CTGATGATTTTAAAGGACTTGAAAAAGTAAAAACGAACCTACGCCTAATATGTACCCTTAGCATA
63 CAGATGATCCTAAAGGACTTGAAAAAGTAAAAGCGAACCTACGCCTAATATGTACCCTTAGCATA
3519089 GAAGCAACCTGGTAATTTCA
128 GAAGCAACCTGGTAATTTCA
* * *
3519109 TAGGGCTAGGTTTTTGA-AAAAATGCTAAAAGGTCCTTAAAGTCTACTATCGACTTA-AAAGTGC
1 TAGGGCTAGG--TTTGAGAAAAATGCTAAAAGGTCCCTAAGGTCTACCATCGACTTAGAAA-TGC
* * ** * * * * *
3519172 CCGATGAGCCTTGAGGACTTGAAAAAGTAAAAGTGAACCTATGCTTAATATGTACCTTTGGCATA
63 CAGATGATCCTAAAGGACTTGAAAAAGTAAAAGCGAACCTACGCCTAATATGTACCCTTAGCATA
3519237 GAAG
128 GAAG
3519241 TGACCCGGTG
Statistics
Matches: 352, Mismatches: 63, Indels: 24
0.80 0.14 0.05
Matches are distributed among these distances:
146 59 0.17
147 60 0.17
148 215 0.61
149 7 0.02
150 11 0.03
ACGTcount: A:0.37, C:0.18, G:0.20, T:0.25
Consensus pattern (147 bp):
TAGGGCTAGGTTTGAGAAAAATGCTAAAAGGTCCCTAAGGTCTACCATCGACTTAGAAATGCCAG
ATGATCCTAAAGGACTTGAAAAAGTAAAAGCGAACCTACGCCTAATATGTACCCTTAGCATAGAA
GCAACCTGGTAATTTCA
Found at i:3521370 original size:23 final size:22
Alignment explanation
Indices: 3521313--3521371 Score: 57
Period size: 23 Copynumber: 2.6 Consensus size: 22
3521303 TTATGACATC
*
3521313 AAATATAT-TTTATAATATATAT
1 AAATATATGTATA-AATATATAT
**
3521335 AAGATCCATGTATAAATATATAT
1 AA-ATATATGTATAAATATATAT
3521358 AAATATATAGTATA
1 AAATATAT-GTATA
3521372 TATTTTTTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
22 6 0.21
23 20 0.69
24 3 0.10
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.41
Consensus pattern (22 bp):
AAATATATGTATAAATATATAT
Found at i:3526986 original size:20 final size:20
Alignment explanation
Indices: 3526963--3527014 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
3526953 CACACCCAGA
*
3526963 TGTATCGATACATTATGCTT
1 TGTATCGATACATTATGCAT
* *
3526983 TGTATTGATACA-TATTCAT
1 TGTATCGATACATTATGCAT
3527002 TGTATCGATACAT
1 TGTATCGATACAT
3527015 GGACAATTGT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 16 0.59
20 11 0.41
ACGTcount: A:0.29, C:0.13, G:0.13, T:0.44
Consensus pattern (20 bp):
TGTATCGATACATTATGCAT
Found at i:3527006 original size:19 final size:19
Alignment explanation
Indices: 3526963--3527034 Score: 74
Period size: 20 Copynumber: 3.7 Consensus size: 19
3526953 CACACCCAGA
*
3526963 TGTATCGATACATTATGCTT
1 TGTATCGATACA-TATGCAT
* *
3526983 TGTATTGATACATATTCAT
1 TGTATCGATACATATGCAT
*
3527002 TGTATCGATACAT-GGACAAT
1 TGTATCGATACATATG-C-AT
3527022 TGTATCGATACAT
1 TGTATCGATACAT
3527035 GAAACTGGCA
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
19 18 0.41
20 26 0.59
ACGTcount: A:0.31, C:0.14, G:0.15, T:0.40
Consensus pattern (19 bp):
TGTATCGATACATATGCAT
Found at i:3527098 original size:13 final size:13
Alignment explanation
Indices: 3527080--3527109 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
3527070 GATACATGGC
3527080 ACATTGTATCGAT
1 ACATTGTATCGAT
3527093 ACATTGTATCGAT
1 ACATTGTATCGAT
3527106 ACAT
1 ACAT
3527110 GATGAATTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (13 bp):
ACATTGTATCGAT
Found at i:3527119 original size:33 final size:33
Alignment explanation
Indices: 3527066--3527129 Score: 87
Period size: 33 Copynumber: 1.9 Consensus size: 33
3527056 ACACTGTTTA
*
3527066 TATCGATACATGGCACATTGTATCGATACATTG
1 TATCGATACATGGCACATTGTAACGATACATTG
3527099 TATCGATACATGATG-A-ATTGTAACGATACAT
1 TATCGATACATG--GCACATTGTAACGATACAT
3527130 GATGAATTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 26 0.93
34 1 0.04
35 1 0.04
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Consensus pattern (33 bp):
TATCGATACATGGCACATTGTAACGATACATTG
Found at i:3527120 original size:20 final size:20
Alignment explanation
Indices: 3527095--3527149 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
3527085 GTATCGATAC
3527095 ATTGTATCGATACATGATGA
1 ATTGTATCGATACATGATGA
*
3527115 ATTGTAACGATACATGATGA
1 ATTGTATCGATACATGATGA
3527135 ATTGTATCGATACAT
1 ATTGTATCGATACAT
3527150 TGCTTCAAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.36, C:0.11, G:0.18, T:0.35
Consensus pattern (20 bp):
ATTGTATCGATACATGATGA
Found at i:3534599 original size:21 final size:22
Alignment explanation
Indices: 3534575--3534625 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 22
3534565 ATCAAGTCTT
* *
3534575 CTTCAAATTTCTT-ATTTTTCA
1 CTTCAAAATACTTCATTTTTCA
3534596 CTTCAAAATACTTCATTTTTCA
1 CTTCAAAATACTTCATTTTTCA
3534618 --TCAAAATA
1 CTTCAAAATA
3534626 ATCAACAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 8 0.30
21 11 0.41
22 8 0.30
ACGTcount: A:0.33, C:0.20, G:0.00, T:0.47
Consensus pattern (22 bp):
CTTCAAAATACTTCATTTTTCA
Found at i:3536337 original size:22 final size:23
Alignment explanation
Indices: 3536309--3536356 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
3536299 AAGGGAGAAA
* *
3536309 TTTTTATC-AAGGGAGAGAAATT
1 TTTTTATCAAAGGGAAAAAAATT
3536331 TTTTTATCAAAGGGAAAAAAATT
1 TTTTTATCAAAGGGAAAAAAATT
3536354 TTT
1 TTT
3536357 AACGAGAGCC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 8 0.35
23 15 0.65
ACGTcount: A:0.40, C:0.04, G:0.17, T:0.40
Consensus pattern (23 bp):
TTTTTATCAAAGGGAAAAAAATT
Found at i:3536942 original size:19 final size:19
Alignment explanation
Indices: 3536899--3536971 Score: 76
Period size: 20 Copynumber: 3.7 Consensus size: 19
3536889 CACACCTAGA
*
3536899 TGTATCGATACAT-TATGCTT
1 TGTATCGATACATGT-T-CAT
3536919 TGTATCGATACATGTTCAT
1 TGTATCGATACATGTTCAT
**
3536938 TGTATCGATACATGGACAAT
1 TGTATCGATACATGTTC-AT
*
3536958 TGTATCAATACATG
1 TGTATCGATACATG
3536972 AAACTGGCAG
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
19 17 0.36
20 29 0.62
21 1 0.02
ACGTcount: A:0.30, C:0.15, G:0.16, T:0.38
Consensus pattern (19 bp):
TGTATCGATACATGTTCAT
Found at i:3537015 original size:13 final size:13
Alignment explanation
Indices: 3536997--3537048 Score: 62
Period size: 13 Copynumber: 4.5 Consensus size: 13
3536987 ACCCTACCAC
3536997 ACATTGTATCGAT
1 ACATTGTATCGAT
3537010 ACATTGTATCGAT
1 ACATTGTATCGAT
3537023 ACA-TG-AT-G--
1 ACATTGTATCGAT
3537031 A-ATTGTATCGAT
1 ACATTGTATCGAT
3537043 ACATTG
1 ACATTG
3537049 CTTCAAACAG
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
7 1 0.03
8 3 0.09
9 2 0.06
10 2 0.06
11 2 0.06
12 3 0.09
13 20 0.61
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (13 bp):
ACATTGTATCGAT
Found at i:3538068 original size:21 final size:21
Alignment explanation
Indices: 3538056--3538108 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
3538046 AAGTTGCATT
3538056 TTTCATCCAAAAAATGCATGA
1 TTTCATCCAAAAAATGCATGA
** *
3538077 TTTCATCCAACCAATGCATCA
1 TTTCATCCAAAAAATGCATGA
*
3538098 TTTCATTCAAA
1 TTTCATCCAAA
3538109 GATACCTTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.38, C:0.25, G:0.06, T:0.32
Consensus pattern (21 bp):
TTTCATCCAAAAAATGCATGA
Found at i:3540259 original size:13 final size:13
Alignment explanation
Indices: 3540241--3540266 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3540231 CATTTTGGGA
3540241 TGTATCGATACAT
1 TGTATCGATACAT
3540254 TGTATCGATACAT
1 TGTATCGATACAT
3540267 CTTGTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3540263 original size:33 final size:32
Alignment explanation
Indices: 3540221--3540284 Score: 92
Period size: 33 Copynumber: 2.0 Consensus size: 32
3540211 TACAAGCCAA
* *
3540221 TGTATCGATACATTTTGGGATGTATCGATACAT
1 TGTATCGATACATCTTGGG-TGTATCAATACAT
*
3540254 TGTATCGATACATCTTGTGTGTATCAATACA
1 TGTATCGATACATCTTGGGTGTATCAATACA
3540285 AATAGTTAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 11 0.39
33 17 0.61
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.39
Consensus pattern (32 bp):
TGTATCGATACATCTTGGGTGTATCAATACAT
Found at i:3540373 original size:20 final size:21
Alignment explanation
Indices: 3540326--3540380 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
3540316 ACCAATGACC
*
3540326 TGTATCGATACATTCTTTACA
1 TGTATCGATACATTCTGTACA
*
3540347 AGTATCGATACATT-TGGT-CA
1 TGTATCGATACATTCT-GTACA
3540367 TGTATCGATACATT
1 TGTATCGATACATT
3540381 GTATCGATAC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
20 16 0.53
21 14 0.47
ACGTcount: A:0.29, C:0.16, G:0.15, T:0.40
Consensus pattern (21 bp):
TGTATCGATACATTCTGTACA
Found at i:3540423 original size:20 final size:20
Alignment explanation
Indices: 3540400--3540440 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
3540390 CTGTGCAATA
*
3540400 TGTATCGATACATTTGAAGG
1 TGTATCGATACATTTCAAGG
*
3540420 TGTATCGATATATTTCAAGG
1 TGTATCGATACATTTCAAGG
3540440 T
1 T
3540441 TTTGACCTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.29, C:0.10, G:0.22, T:0.39
Consensus pattern (20 bp):
TGTATCGATACATTTCAAGG
Found at i:3548122 original size:19 final size:20
Alignment explanation
Indices: 3548077--3548128 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
3548067 TTACAAGCCA
*
3548077 ATGTATCGATACATTTTGGG
1 ATGTATCGATACATCTTGGG
*
3548097 ATGTATCGATACATCTTGTG
1 ATGTATCGATACATCTTGGG
3548117 -TGTATCGATACA
1 ATGTATCGATACA
3548129 AACAGTTAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.40
20 18 0.60
ACGTcount: A:0.27, C:0.13, G:0.21, T:0.38
Consensus pattern (20 bp):
ATGTATCGATACATCTTGGG
Found at i:3548217 original size:20 final size:21
Alignment explanation
Indices: 3548170--3548224 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
3548160 GCCAATGACC
*
3548170 TGTATCGATACATTCTTTACA
1 TGTATCGATACATTCTGTACA
*
3548191 AGTATCGATACATT-TGGT-CA
1 TGTATCGATACATTCT-GTACA
3548211 TGTATCGATACATT
1 TGTATCGATACATT
3548225 GTATCGATAC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
20 16 0.53
21 14 0.47
ACGTcount: A:0.29, C:0.16, G:0.15, T:0.40
Consensus pattern (21 bp):
TGTATCGATACATTCTGTACA
Found at i:3550379 original size:21 final size:21
Alignment explanation
Indices: 3550368--3550415 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
3550358 AGTTGCATTT
3550368 TTTCATCCAAAAAATGCATGA
1 TTTCATCCAAAAAATGCATGA
* *
3550389 TTTCATCCAACAAATGCATCA
1 TTTCATCCAAAAAATGCATGA
3550410 TTTCAT
1 TTTCAT
3550416 TCATAGATAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.38, C:0.23, G:0.06, T:0.33
Consensus pattern (21 bp):
TTTCATCCAAAAAATGCATGA
Found at i:3554886 original size:73 final size:73
Alignment explanation
Indices: 3554793--3554938 Score: 238
Period size: 73 Copynumber: 2.0 Consensus size: 73
3554783 TGGCCACTTT
* *
3554793 TTTGGCATTTATCATCGATAGACCATAAATTGGATAATATACATGTTTAAGACGCTTTTCTTGTT
1 TTTGGCATTTATCATCGATAGACCATAAATTGGATAATATACATGTTTAAGACGCTATGCTTGTT
*
3554858 ATTATATG
66 ATCATATG
* * *
3554866 TTTGGCATTTATCATTGATAGACCATAAATTGGATAATATACATGTTTTAGATGCTATGCTTGTT
1 TTTGGCATTTATCATCGATAGACCATAAATTGGATAATATACATGTTTAAGACGCTATGCTTGTT
3554931 ATCATATG
66 ATCATATG
3554939 CAGTTTTTTA
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
73 67 1.00
ACGTcount: A:0.30, C:0.12, G:0.16, T:0.42
Consensus pattern (73 bp):
TTTGGCATTTATCATCGATAGACCATAAATTGGATAATATACATGTTTAAGACGCTATGCTTGTT
ATCATATG
Found at i:3558043 original size:25 final size:25
Alignment explanation
Indices: 3558015--3558065 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
3558005 AAATATGAAC
3558015 TCTTAAACTTGCTAGCTATCAAAGA
1 TCTTAAACTTGCTAGCTATCAAAGA
3558040 TCTTAAACTTGCTAGCTATCAAAGA
1 TCTTAAACTTGCTAGCTATCAAAGA
3558065 T
1 T
3558066 ACCCACCACC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.35, C:0.20, G:0.12, T:0.33
Consensus pattern (25 bp):
TCTTAAACTTGCTAGCTATCAAAGA
Found at i:3560153 original size:19 final size:18
Alignment explanation
Indices: 3560131--3560174 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
3560121 TTTAAAAAAT
*
3560131 ATAAATAATTTTATTTTTA
1 ATAAATAATATTA-TTTTA
3560150 ATAAAATAATATTATTTTA
1 AT-AAATAATATTATTTTA
3560169 ATAAAT
1 ATAAAT
3560175 TTATACATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 4 0.17
19 9 0.39
20 10 0.43
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
ATAAATAATATTATTTTA
Found at i:3560156 original size:20 final size:19
Alignment explanation
Indices: 3560128--3560173 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 19
3560118 TTTTTTAAAA
*
3560128 AATATAAATAATTTTATTTTT
1 AATA-AAATAATATTA-TTTT
3560149 AATAAAATAATATTATTTT
1 AATAAAATAATATTATTTT
3560168 AATAAA
1 AATAAA
3560174 TTTATACATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 10 0.42
20 10 0.42
21 4 0.17
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
AATAAAATAATATTATTTT
Found at i:3562670 original size:19 final size:20
Alignment explanation
Indices: 3562625--3562678 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 20
3562615 TTGCCAGTTT
**
3562625 CATGTATCGATACAATTGTG
1 CATGTATCGATACAATTGAA
3562645 CATGTATCGATACAA-TGAA
1 CATGTATCGATACAATTGAA
* *
3562664 TATGTATCAATACAA
1 CATGTATCGATACAA
3562679 AGCATAATGC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.31
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:3565145 original size:13 final size:13
Alignment explanation
Indices: 3565126--3565165 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
3565116 ATAGTAGCCC
3565126 ATGTATCGATACA
1 ATGTATCGATACA
* *
3565139 TTGTATCAATACA
1 ATGTATCGATACA
3565152 ATGTATCGATACA
1 ATGTATCGATACA
3565165 A
1 A
3565166 AGAACATTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3569190 original size:13 final size:13
Alignment explanation
Indices: 3569172--3569196 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3569162 CATTTCATAG
3569172 TGTATCGATACAA
1 TGTATCGATACAA
3569185 TGTATCGATACA
1 TGTATCGATACA
3569197 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3569261 original size:19 final size:19
Alignment explanation
Indices: 3569237--3569303 Score: 83
Period size: 19 Copynumber: 3.8 Consensus size: 19
3569227 CAGTAGCTAA
3569237 TTATGTATCGATACAACAC
1 TTATGTATCGATACAACAC
3569256 TTATGTATCGAT---ACA-
1 TTATGTATCGATACAACAC
3569271 -T-TGTATCGATACAACAC
1 TTATGTATCGATACAACAC
*
3569288 TTATGTATCAATACAA
1 TTATGTATCGATACAA
3569304 ATCGTTGAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
13 9 0.22
14 1 0.02
16 6 0.15
18 1 0.02
19 24 0.59
ACGTcount: A:0.37, C:0.18, G:0.10, T:0.34
Consensus pattern (19 bp):
TTATGTATCGATACAACAC
Found at i:3569277 original size:13 final size:13
Alignment explanation
Indices: 3569259--3569283 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3569249 ACAACACTTA
3569259 TGTATCGATACAT
1 TGTATCGATACAT
3569272 TGTATCGATACA
1 TGTATCGATACA
3569284 ACACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3569278 original size:32 final size:32
Alignment explanation
Indices: 3569240--3569302 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
3569230 TAGCTAATTA
*
3569240 TGTATCGATACAACACTTATGTATCGATACAT
1 TGTATCGATACAACACTTATGTATCAATACAT
3569272 TGTATCGATACAACACTTATGTATCAATACA
1 TGTATCGATACAACACTTATGTATCAATACA
3569303 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (32 bp):
TGTATCGATACAACACTTATGTATCAATACAT
Found at i:3570110 original size:120 final size:121
Alignment explanation
Indices: 3569893--3570180 Score: 345
Period size: 121 Copynumber: 2.4 Consensus size: 121
3569883 CAGTGTAATG
* * ** * * *
3569893 TGCCACTATGCAGATTCAAGGCTTGCAACACTGGACTTAAAGATGATGAGGATGAAGAGTGATAA
1 TGCCAATATGCTGATTCAAGGCCAGCAACATTGGACTTAAAGATGAAGAGGATGAAAAGTGATAA
*
3569958 AAGGATCAATACGTTGATTCACGGCCAACGATATTAGGTTTTAAAGATGATG-AA-GA
66 AAGGATCAATACGTTGATTCACGGCCAACGATATT-GGGTTTAAAGATGA-GAAAGGA
*
3570014 TGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAG-GTGA-GAAAAGTGAT-
1 TGCCAATATGCTGATTCAAGGCCAGCAACATTGGACTTAAAGATGAAGAG-GATGAAAAGTGATA
*
3570076 AAA-GATGCCAATATGTTGATTCACGGCCAACGATATTGGGTTTAAAGATGAGAAAAAGGA
65 AAAGGAT--CAATACGTTGATTCACGGCCAACGATATTGGGTTTAAAGATGAG--AAAGGA
* * * *
3570136 TGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATG
1 TGCCAATATGCTGATTCAAGGCCAGCAACATTGGACTTAAAGATG
3570181 GAATAGGTGC
Statistics
Matches: 145, Mismatches: 15, Indels: 13
0.84 0.09 0.08
Matches are distributed among these distances:
118 4 0.03
119 16 0.11
120 38 0.26
121 45 0.31
122 42 0.29
ACGTcount: A:0.36, C:0.14, G:0.25, T:0.25
Consensus pattern (121 bp):
TGCCAATATGCTGATTCAAGGCCAGCAACATTGGACTTAAAGATGAAGAGGATGAAAAGTGATAA
AAGGATCAATACGTTGATTCACGGCCAACGATATTGGGTTTAAAGATGAGAAAGGA
Found at i:3570121 original size:67 final size:68
Alignment explanation
Indices: 3570000--3570126 Score: 184
Period size: 67 Copynumber: 1.9 Consensus size: 68
3569990 ATTAGGTTTT
* *
3570000 AAAGATGATGAAGATGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGGTG
1 AAAGATGATAAAGATGCCAATATGCTGATTCAAGGCCAACAATATTGGACTTAAAGATGAAGGTG
3570065 AGA
66 AGA
* * * **
3570068 AAAG-TGATAAAGATGCCAATATGTTGATTCACGGCCAACGATATTGGGTTTAAAGATGA
1 AAAGATGATAAAGATGCCAATATGCTGATTCAAGGCCAACAATATTGGACTTAAAGATGA
3570127 GAAAAAGGAT
Statistics
Matches: 52, Mismatches: 7, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
67 48 0.92
68 4 0.08
ACGTcount: A:0.39, C:0.12, G:0.25, T:0.24
Consensus pattern (68 bp):
AAAGATGATAAAGATGCCAATATGCTGATTCAAGGCCAACAATATTGGACTTAAAGATGAAGGTG
AGA
Found at i:3570230 original size:22 final size:22
Alignment explanation
Indices: 3570205--3570272 Score: 54
Period size: 22 Copynumber: 3.1 Consensus size: 22
3570195 ATGCTGATTC
3570205 AAGGCCAGCTATATTGGACTTA
1 AAGGCCAGCTATATTGGACTTA
**
3570227 AAGGTGCCAG-TATGCT-GA-TTCA
1 AA-G-GCCAGCTATATTGGACTT-A
*
3570249 AA-GCCAGCTACATTGGACTTA
1 AAGGCCAGCTATATTGGACTTA
3570270 AAG
1 AAG
3570273 AAGAAGATGC
Statistics
Matches: 34, Mismatches: 5, Indels: 14
0.64 0.09 0.26
Matches are distributed among these distances:
19 5 0.15
20 3 0.09
21 7 0.21
22 9 0.26
23 5 0.15
24 5 0.15
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.25
Consensus pattern (22 bp):
AAGGCCAGCTATATTGGACTTA
Found at i:3570304 original size:49 final size:49
Alignment explanation
Indices: 3570139--3571296 Score: 1215
Period size: 49 Copynumber: 24.5 Consensus size: 49
3570129 AAAAGGATGT
* * *
3570139 CAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAATAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA-AG-A-AGGTGC
*
3570191 CAATATGCTGATTCAAGGCCAGCTATATTGGACTT-----A-AAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGC
* * *
3570234 CAGTATGCTGATTCAAAGCCAGCTACATTGGACTTAAAGAAGAAGATGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGC
* * *
3570283 CAATATGCTGATTCAAGGCCAGCGATACTGGACTT-----A-AAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGC
* *
3570326 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGC
* * * * *
3570375 CAATATGCTGATTCAAGGCCAGCGATATTAGACTT----TA-AAGGTGT
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGC
* **
3570419 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGGTG-AGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGC
* *
3570467 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAG-ACAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGC
* **
3570515 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTG-AGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGC
* * *
3570563 CAATGTGCTGATTCAAAGCCAGCTACATTGGACTTAAAGATGAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGC
* * * **
3570612 CAATATGCTGATTCAAGGCCAGCGATATTGGGCTTAAAGGTG-AGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGC
* *
3570660 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGATGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGC
* *
3570709 CAATATGCTGATTCAAGGCCAGCGATATTGGACTT----AA-AA-GTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGC
* * * * *
3570752 CAATGTGTTGATTCAAGACCAGCTACATTGGACTTAAAGATGAAGGTAC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGC
* * * *
3570801 CAATATGTTGATTCAAGGCCAGCGATATTGGACTT----TA-AAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGC
* * **
3570845 GAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGGTG-AGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGC
* * *
3570893 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGC
* * **
3570942 CAATATGTTGATTCAAGGCCAGCTATATTGGACTTAAAGGTG-AGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGC
* * *
3570990 CAATGTGCTGATTCAAGGCCAGCTACATTGGACCTAAAG-ACAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGC
* *
3571038 CAATATGCTGATTCAAGGCCAGCGATATTGGACTT-----A-AAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGC
* * * * *
3571081 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTGAAGAAAAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGC
* *
3571130 CAATATGCTGATTCAAGGCCAGCGATATTGGACTT-----AG-AGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGC
** * * * *
3571173 CAACGTGCTGATTCAAGGCTAGCGACATTGGTCTTAAAGAAAAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGC
* * *
3571222 CAATATGCTAATTCAAGGCCAGCGATATTGGACTTAGAGATGACA-AAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTA-A-A-GA-AGAAGGTGC
3571274 CAATATGCTGATTCAAGGCCAGC
1 CAATATGCTGATTCAAGGCCAGC
3571297 GATATTGGGC
Statistics
Matches: 937, Mismatches: 119, Indels: 100
0.81 0.10 0.09
Matches are distributed among these distances:
43 183 0.20
44 79 0.08
45 2 0.00
47 1 0.00
48 301 0.32
49 305 0.33
50 1 0.00
51 1 0.00
52 63 0.07
53 1 0.00
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (49 bp):
CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGC
Found at i:3570317 original size:92 final size:93
Alignment explanation
Indices: 3570129--3571257 Score: 1234
Period size: 92 Copynumber: 12.0 Consensus size: 93
3570119 AAAGATGAGA
* * *
3570129 AAAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAATAGGTGCCAA
1 AAAAGG-TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA-AG-A-AGGTGCCAA
3570194 TATGCTGATTCAAGGCCAGCTATATTGGACTT
62 TATGCTGATTCAAGGCCAGCTATATTGGACTT
* * * *
3570226 -AAAGGTGCCAGTATGCTGATTCAAAGCCAGCTACATTGGACTTAAAGAAGAAGATGCCAATATG
1 AAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATG
* *
3570290 CTGATTCAAGGCCAGCGATACTGGACTT
66 CTGATTCAAGGCCAGCTATATTGGACTT
*
3570318 -AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATG
1 AAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATG
* *
3570382 CTGATTCAAGGCCAGCGATATTAGACTT
66 CTGATTCAAGGCCAGCTATATTGGACTT
* * ** *
3570410 TAAAGGTGTCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGGTG-AGGTGCCAATGTG
1 AAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATG
*
3570474 CTGATTCAAGGCCAGCTACATTGGACTT
66 CTGATTCAAGGCCAGCTATATTGGACTT
* * **
3570502 AAAGACAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTG-AGGTGCCAA
1 --A-A-AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAA
* * *
3570566 TGTGCTGATTCAAAGCCAGCTACATTGGACTT
62 TATGCTGATTCAAGGCCAGCTATATTGGACTT
* * * * **
3570598 AAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTAAAGGTG-AGGTGCCA
1 --A-A--AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCA
* *
3570662 ATGTGCTGATTCAAGGCCAGCTACATTGGACTT
61 ATATGCTGATTCAAGGCCAGCTATATTGGACTT
* * *
3570695 AAAGAAGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT----AA-AA-GTGCCA
1 -AA-AAG--G-TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCA
* * * *
3570754 ATGTGTTGATTCAAGACCAGCTACATTGGACTT
61 ATATGCTGATTCAAGGCCAGCTATATTGGACTT
* * * * * * *
3570787 AAAGATGAAGGTACCAATATGTTGATTCAAGGCCAGCGATATTGGACTT----TA-AAGGTGCGA
1 --A-A--AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCA
* *
3570847 ATGTGCTGATTCAAGGCCAGCTACATTGGACTT
61 ATATGCTGATTCAAGGCCAGCTATATTGGACTT
* *
3570880 AAAGGTGAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAA
1 AAA----AGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAA
*
3570945 TATGTTGATTCAAGGCCAGCTATATTGGACTT
62 TATGCTGATTCAAGGCCAGCTATATTGGACTT
* *
3570977 AAAGGTGAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACCTAAAG-ACAAGGTGCCAA
1 AAA----AGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAA
*
3571041 TATGCTGATTCAAGGCCAGCGATATTGGACTT
62 TATGCTGATTCAAGGCCAGCTATATTGGACTT
* * * *
3571073 -AAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTGAAGAAAAAGGTGCCAATATG
1 AAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATG
*
3571137 CTGATTCAAGGCCAGCGATATTGGACTT
66 CTGATTCAAGGCCAGCTATATTGGACTT
* * * * * *
3571165 -AGAGGTGCCAACGTGCTGATTCAAGGCTAGCGACATTGGTCTTAAAGAAAAAGGTGCCAATATG
1 AAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATG
* *
3571229 CTAATTCAAGGCCAGCGATATTGGACTT
66 CTGATTCAAGGCCAGCTATATTGGACTT
3571257 A
1 A
3571258 GAGATGACAA
Statistics
Matches: 937, Mismatches: 70, Indels: 54
0.88 0.07 0.05
Matches are distributed among these distances:
88 1 0.00
90 1 0.00
91 42 0.04
92 402 0.43
93 89 0.09
94 6 0.01
95 46 0.05
96 138 0.15
97 212 0.23
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (93 bp):
AAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATG
CTGATTCAAGGCCAGCTATATTGGACTT
Found at i:3570710 original size:426 final size:422
Alignment explanation
Indices: 3570139--3571256 Score: 1846
Period size: 426 Copynumber: 2.6 Consensus size: 422
3570129 AAAAGGATGT
*
3570139 CAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAATAGGTGCCAATATGCTGATT
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G-A-AGGTGCCAATATGCTGATT
* * * *
3570204 CAAGGCCAGCTATATTGGACTTAAAGGTGCCAGTATGCTGATTCAAAGCCAGCTACATTGGACTT
63 CAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
*
3570269 AAAGAAGAAGATGCCAATATGCTGATTCAAGGCCAGCGATACTGGACTTAAAGGTGCCAATGTGC
128 AAAGAAGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGC
3570334 TGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCG
193 TGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCG
*
3570399 ATATTAGACTTTAAAGGTGTC-AATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGGTGAG
258 ATATTGGACTTTAAAGGTG-CGAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGGTGAG
*
3570463 GTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA-CAAGGTGCCAATATGCTGAT
322 GTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATCAAGATGCCAATATGCTGAT
3570527 TCAAGGCCAGCTATATTGGACTTAAAGGTGAGGTGC
387 TCAAGGCCAGCTATATTGGACTTAAAGGTGAGGTGC
*
3570563 CAATGTGCTGATTCAAAGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAA
*
3570628 GGCCAGCGATATTGGGCTTAAAGGTGAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGAC
66 GGCCAGCGATATTGGACTT-AA----AGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGAC
*
3570693 TTAAAGAAGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAAGTGCCAATGT
126 TTAAAGAAGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGT
* * * *
3570758 GTTGATTCAAGACCAGCTACATTGGACTTAAAGATGAAGGTACCAATATGTTGATTCAAGGCCAG
191 GCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAG
3570823 CGATATTGGACTTTAAAGGTGCGAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGGTGA
256 CGATATTGGACTTTAAAGGTGCGAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGGTGA
* *
3570888 GGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGTTGA
321 GGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATCAAGATGCCAATATGCTGA
3570953 TTCAAGGCCAGCTATATTGGACTTAAAGGTGAGGTGC
386 TTCAAGGCCAGCTATATTGGACTTAAAGGTGAGGTGC
* *
3570990 CAATGTGCTGATTCAAGGCCAGCTACATTGGACCTAAAGA-CAAGGTGCCAATATGCTGATTCAA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAA
* * *
3571054 GGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTGAA
66 GGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAA
* * * *
3571119 GAAAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAGAGGTGCCAACGTGCTGA
131 GAAGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGA
* * * ** *
3571184 TTCAAGGCTAGCGACATTGGTCTTAAAGAAAAAGGTGCCAATATGCTAATTCAAGGCCAGCGATA
196 TTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATA
3571249 TTGGACTT
261 TTGGACTT
3571257 AGAGATGACA
Statistics
Matches: 648, Mismatches: 39, Indels: 17
0.92 0.06 0.02
Matches are distributed among these distances:
421 203 0.31
422 3 0.00
423 1 0.00
424 39 0.06
425 3 0.00
426 308 0.48
427 91 0.14
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (422 bp):
CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAA
GGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAA
GAAGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGA
TTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATA
TTGGACTTTAAAGGTGCGAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGGTGAGGTGC
CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATCAAGATGCCAATATGCTGATTCAA
GGCCAGCTATATTGGACTTAAAGGTGAGGTGC
Found at i:3571297 original size:52 final size:50
Alignment explanation
Indices: 3571167--3571313 Score: 197
Period size: 52 Copynumber: 2.9 Consensus size: 50
3571157 TTGGACTTAG
** * * *
3571167 AGGTGCCAACGTGCTGATTCAAGGCTAGCGACATTGGTCTTA-AAGAAAA
1 AGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAGAAGAAAA
* *
3571216 AGGTGCCAATATGCTAATTCAAGGCCAGCGATATTGGACTTAGAGATGACAA
1 AGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAGA-A-GAAAA
*
3571268 AGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTAGAAG
1 AGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAGAAG
3571314 GGTTGCCACC
Statistics
Matches: 86, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
49 36 0.42
50 2 0.02
51 2 0.02
52 46 0.53
ACGTcount: A:0.32, C:0.18, G:0.27, T:0.23
Consensus pattern (50 bp):
AGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAGAAGAAAA
Found at i:3571351 original size:33 final size:33
Alignment explanation
Indices: 3571309--3571438 Score: 197
Period size: 33 Copynumber: 3.9 Consensus size: 33
3571299 TATTGGGCTT
* *
3571309 AGAAGGGTTGCCACCAACTTGTGTGGACTTTAG
1 AGAAAGGTTGCCACCAACTTGTGTGGGCTTTAG
*
3571342 AGAAAGGTTGCCACCGACTTGTGTGGGCTTTAG
1 AGAAAGGTTGCCACCAACTTGTGTGGGCTTTAG
*
3571375 AGAAGGGTTGCCACCAACTTGTGTGGGCTTTAG
1 AGAAAGGTTGCCACCAACTTGTGTGGGCTTTAG
* **
3571408 AAAAAGGTTGCCACTGACTTGTGTGGGCTTT
1 AGAAAGGTTGCCACCAACTTGTGTGGGCTTT
3571439 GAAAAGAAAA
Statistics
Matches: 88, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 88 1.00
ACGTcount: A:0.22, C:0.18, G:0.32, T:0.28
Consensus pattern (33 bp):
AGAAAGGTTGCCACCAACTTGTGTGGGCTTTAG
Found at i:3571406 original size:66 final size:66
Alignment explanation
Indices: 3571309--3571438 Score: 233
Period size: 66 Copynumber: 2.0 Consensus size: 66
3571299 TATTGGGCTT
*
3571309 AGAAGGGTTGCCACCAACTTGTGTGGACTTTAGAGAAAGGTTGCCACCGACTTGTGTGGGCTTTA
1 AGAAGGGTTGCCACCAACTTGTGTGGACTTTAGAAAAAGGTTGCCACCGACTTGTGTGGGCTTTA
3571374 G
66 G
* *
3571375 AGAAGGGTTGCCACCAACTTGTGTGGGCTTTAGAAAAAGGTTGCCACTGACTTGTGTGGGCTTT
1 AGAAGGGTTGCCACCAACTTGTGTGGACTTTAGAAAAAGGTTGCCACCGACTTGTGTGGGCTTT
3571439 GAAAAGAAAA
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 61 1.00
ACGTcount: A:0.22, C:0.18, G:0.32, T:0.28
Consensus pattern (66 bp):
AGAAGGGTTGCCACCAACTTGTGTGGACTTTAGAAAAAGGTTGCCACCGACTTGTGTGGGCTTTA
G
Found at i:3571489 original size:34 final size:34
Alignment explanation
Indices: 3571444--3571725 Score: 221
Period size: 34 Copynumber: 8.4 Consensus size: 34
3571434 GCTTTGAAAA
3571444 GAAAAAG-GTGCCACGGAGTTGTGGACTTAGAAG
1 GAAAAAGAGTGCCACGGAGTTGTGGACTTAGAAG
3571477 GAAAAAGAGTGCCACGGAGTTGTGGACTTAGAAG
1 GAAAAAGAGTGCCACGGAGTTGTGGACTTAGAAG
* *
3571511 GAAAAAGAGTGCCACGGAGTTGTGGGCTTAAAAG
1 GAAAAAGAGTGCCACGGAGTTGTGGACTTAGAAG
* ** * *
3571545 GTAAAAAGAATGCCACAAAGTTGTGGGCTTTA-AAA
1 G-AAAAAGAGTGCCACGGAGTTGTGGAC-TTAGAAG
* * * *
3571580 AAAAAAG-GTGCCACGGATTTGTGGGCTCTGGAGAAAA
1 GAAAAAGAGTGCCACGGAGTTGTGGACT-T--AG-AAG
* * * *
3571617 GAAAAAG-GTGCCACGGAGTAGTGGGCTTTGAAAA
1 GAAAAAGAGTGCCACGGAGTTGTGGACTTAG-AAG
*
3571651 GAAAAAG-GTGCCACGGA-TTGGTGGACTT---TG
1 GAAAAAGAGTGCCACGGAGTT-GTGGACTTAGAAG
* * * *
3571681 GAAAGAGA-TGCCACTGAATTGTGGACTTTGAA-
1 GAAAAAGAGTGCCACGGAGTTGTGGACTTAGAAG
3571713 G-AAAAGA-TGCCAC
1 GAAAAAGAGTGCCAC
3571726 TGAGGCGTTG
Statistics
Matches: 212, Mismatches: 23, Indels: 30
0.80 0.09 0.11
Matches are distributed among these distances:
30 22 0.10
31 13 0.06
32 2 0.01
33 24 0.11
34 94 0.44
35 26 0.12
36 4 0.02
37 27 0.13
ACGTcount: A:0.35, C:0.13, G:0.32, T:0.20
Consensus pattern (34 bp):
GAAAAAGAGTGCCACGGAGTTGTGGACTTAGAAG
Found at i:3571559 original size:35 final size:34
Alignment explanation
Indices: 3571429--3571667 Score: 240
Period size: 34 Copynumber: 6.9 Consensus size: 34
3571419 CACTGACTTG
3571429 TGTGGGCTTTGAAAA-GAAAAAG-GTGCCACGGAGT
1 TGTGGGC-TT-AAAAGGAAAAAGAGTGCCACGGAGT
* *
3571463 TGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGT
1 TGTGGGCTTAAAAGGAAAAAGAGTGCCACGGAGT
* *
3571497 TGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGT
1 TGTGGGCTTAAAAGGAAAAAGAGTGCCACGGAGT
* **
3571531 TGTGGGCTTAAAAGGTAAAAAGAATGCCACAAAGT
1 TGTGGGCTTAAAAGG-AAAAAGAGTGCCACGGAGT
* *
3571566 TGTGGGCTTTAAAA-AAAAAAG-GTGCCACGGATT
1 TGTGGGC-TTAAAAGGAAAAAGAGTGCCACGGAGT
*
3571599 TGTGGGCTCTGGAGAAAAGAAAAAG-GTGCCACGGAGT
1 TGTGGGCT-T--A-AAAGGAAAAAGAGTGCCACGGAGT
*
3571636 AGTGGGCTTTGAAAA-GAAAAAG-GTGCCACGGA
1 TGTGGGC-TT-AAAAGGAAAAAGAGTGCCACGGA
3571668 TTGGTGGACT
Statistics
Matches: 180, Mismatches: 15, Indels: 20
0.84 0.07 0.09
Matches are distributed among these distances:
32 4 0.02
33 25 0.14
34 88 0.49
35 27 0.15
36 11 0.06
37 24 0.13
38 1 0.01
ACGTcount: A:0.36, C:0.12, G:0.33, T:0.19
Consensus pattern (34 bp):
TGTGGGCTTAAAAGGAAAAAGAGTGCCACGGAGT
Found at i:3571724 original size:31 final size:31
Alignment explanation
Indices: 3571653--3571776 Score: 128
Period size: 31 Copynumber: 4.1 Consensus size: 31
3571643 TTTGAAAAGA
* * * *
3571653 AAAAGGTGCCACGGATTGGTGGACTTTG--G
1 AAAAGATGCCACTGAATCGTGGACTTTGAAG
*
3571682 AAAGAGATGCCACTGAATTGTGGACTTTGAAG
1 AAA-AGATGCCACTGAATCGTGGACTTTGAAG
** *
3571714 AAAAGATGCCACTGAGGCGTTGACTTTGAAG
1 AAAAGATGCCACTGAATCGTGGACTTTGAAG
* *
3571745 AAAAGATGCCATTGAGTCGTGGACTTT-AAG
1 AAAAGATGCCACTGAATCGTGGACTTTGAAG
3571775 AA
1 AA
3571777 GGTATTTGAA
Statistics
Matches: 81, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
29 3 0.04
30 26 0.32
31 48 0.59
32 4 0.05
ACGTcount: A:0.32, C:0.14, G:0.30, T:0.24
Consensus pattern (31 bp):
AAAAGATGCCACTGAATCGTGGACTTTGAAG
Found at i:3571907 original size:16 final size:17
Alignment explanation
Indices: 3571876--3571913 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
3571866 GATGCAAATA
* *
3571876 ATGATGTTATTGATGTT
1 ATGATGTCATTGATGTC
3571893 ATGATGTCA-TGATGTC
1 ATGATGTCATTGATGTC
3571909 ATGAT
1 ATGAT
3571914 TACAGCATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.26, C:0.05, G:0.24, T:0.45
Consensus pattern (17 bp):
ATGATGTCATTGATGTC
Found at i:3573084 original size:19 final size:18
Alignment explanation
Indices: 3573062--3573107 Score: 62
Period size: 19 Copynumber: 2.7 Consensus size: 18
3573052 GCCTTTGCAC
3573062 TTTTTTTTGTGTGTTGTTG
1 TTTTTTTTGTGTGTT-TTG
3573081 TTTTTTTT-T-TGTTTTG
1 TTTTTTTTGTGTGTTTTG
3573097 -TTTTTTTGTGT
1 TTTTTTTTGTGT
3573108 TTACTTTTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
15 7 0.28
16 4 0.16
17 5 0.20
18 1 0.04
19 8 0.32
ACGTcount: A:0.00, C:0.00, G:0.20, T:0.80
Consensus pattern (18 bp):
TTTTTTTTGTGTGTTTTG
Found at i:3584912 original size:33 final size:33
Alignment explanation
Indices: 3584848--3584913 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 33
3584838 AAATTTCCAG
* *
3584848 ATGTATCGATACAAAGATCAATGTATTGATACA
1 ATGTATCGATACAAAGATCAATATATCGATACA
**
3584881 ATGTATCGATACATTGAAT-AATATATCGATACA
1 ATGTATCGATACAAAG-ATCAATATATCGATACA
3584914 TTTCCTTGGC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
33 26 0.93
34 2 0.07
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.32
Consensus pattern (33 bp):
ATGTATCGATACAAAGATCAATATATCGATACA
Found at i:3586482 original size:13 final size:13
Alignment explanation
Indices: 3586464--3586488 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3586454 AGATTGCACA
3586464 GTATCGATACATT
1 GTATCGATACATT
3586477 GTATCGATACAT
1 GTATCGATACAT
3586489 GACCAAATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:3586501 original size:20 final size:21
Alignment explanation
Indices: 3586476--3586528 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
3586466 ATCGATACAT
**
3586476 TGTATCGATACATGACCA-AA
1 TGTATCGATACATGAAAAGAA
*
3586496 TGTATCGATACTTGAAAAGAA
1 TGTATCGATACATGAAAAGAA
3586517 TGTATCGATACA
1 TGTATCGATACA
3586529 GGTCATTGGC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 15 0.54
21 13 0.46
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (21 bp):
TGTATCGATACATGAAAAGAA
Found at i:3586599 original size:13 final size:13
Alignment explanation
Indices: 3586581--3586606 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3586571 ACACACAATA
3586581 TGTATCGATACAT
1 TGTATCGATACAT
3586594 TGTATCGATACAT
1 TGTATCGATACAT
3586607 CCCAAAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3586619 original size:20 final size:20
Alignment explanation
Indices: 3586594--3586646 Score: 106
Period size: 20 Copynumber: 2.6 Consensus size: 20
3586584 ATCGATACAT
3586594 TGTATCGATACATCCCAAAA
1 TGTATCGATACATCCCAAAA
3586614 TGTATCGATACATCCCAAAA
1 TGTATCGATACATCCCAAAA
3586634 TGTATCGATACAT
1 TGTATCGATACAT
3586647 TGGCTTGTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.38, C:0.23, G:0.11, T:0.28
Consensus pattern (20 bp):
TGTATCGATACATCCCAAAA
Found at i:3586622 original size:33 final size:32
Alignment explanation
Indices: 3586561--3586626 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 32
3586551 GTAGCCAAAT
*
3586561 TTGTATCGATACACACAATATGTATCGATACA
1 TTGTATCGATACACACAAAATGTATCGATACA
*
3586593 TTGTATCGATACATCCCAAAATGTATCGATACA
1 TTGTATCGATACA-CACAAAATGTATCGATACA
3586626 T
1 T
3586627 CCCAAAATGT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 13 0.42
33 18 0.58
ACGTcount: A:0.36, C:0.20, G:0.12, T:0.32
Consensus pattern (32 bp):
TTGTATCGATACACACAAAATGTATCGATACA
Found at i:3592971 original size:20 final size:20
Alignment explanation
Indices: 3592936--3592976 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 20
3592926 CAAATTTCTT
3592936 GTTTTTCACTTCAAAATACATC
1 GTTTTTCAC-TCAAAAT-CATC
3592958 GTTTTTCA-TCAAAATCATC
1 GTTTTTCACTCAAAATCATC
3592977 AACAAAAGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 7 0.37
22 8 0.42
ACGTcount: A:0.32, C:0.22, G:0.05, T:0.41
Consensus pattern (20 bp):
GTTTTTCACTCAAAATCATC
Found at i:3595264 original size:13 final size:13
Alignment explanation
Indices: 3595246--3595270 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3595236 AGATTGCACA
3595246 GTATCGATACATT
1 GTATCGATACATT
3595259 GTATCGATACAT
1 GTATCGATACAT
3595271 GACCAAATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:3595283 original size:20 final size:21
Alignment explanation
Indices: 3595258--3595310 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
3595248 ATCGATACAT
**
3595258 TGTATCGATACATGACCA-AA
1 TGTATCGATACATGAAAAGAA
*
3595278 TGTATCGATACTTGAAAAGAA
1 TGTATCGATACATGAAAAGAA
3595299 TGTATCGATACA
1 TGTATCGATACA
3595311 AGTCATTGGC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 15 0.54
21 13 0.46
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (21 bp):
TGTATCGATACATGAAAAGAA
Found at i:3595381 original size:13 final size:13
Alignment explanation
Indices: 3595363--3595388 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3595353 ACACACAATA
3595363 TGTATCGATACAT
1 TGTATCGATACAT
3595376 TGTATCGATACAT
1 TGTATCGATACAT
3595389 CCCAAAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3595404 original size:33 final size:32
Alignment explanation
Indices: 3595343--3595410 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 32
3595333 GTAGCCAAAT
*
3595343 TTGTATCGATACACACAATATGTATCGATACA
1 TTGTATCGATACACACAAAATGTATCGATACA
*
3595375 TTGTATCGATACATCCCAAAATGTATCGATACA
1 TTGTATCGATACA-CACAAAATGTATCGATACA
3595408 TTG
1 TTG
3595411 GTTTGTAACG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
32 13 0.39
33 20 0.61
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.32
Consensus pattern (32 bp):
TTGTATCGATACACACAAAATGTATCGATACA
Found at i:3597623 original size:3 final size:3
Alignment explanation
Indices: 3597615--3597645 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
3597605 TCCAAGTCAA
*
3597615 CAT CAT CAT CAT CAT CAT CAT CTT CAT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT C
3597646 TTTGATAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.29, C:0.35, G:0.00, T:0.35
Consensus pattern (3 bp):
CAT
Found at i:3599275 original size:33 final size:33
Alignment explanation
Indices: 3599233--3599297 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
3599223 TTTGAAGCAA
3599233 TGTATCGATACAAT-T-CATCATGTATCGATACAT
1 TGTATCGATACAATGTGC--CATGTATCGATACAT
*
3599266 TGTATCGATATAATGTGCCATGTATCGATACA
1 TGTATCGATACAATGTGCCATGTATCGATACA
3599298 AATAGTGGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 27 0.93
34 1 0.03
35 1 0.03
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.35
Consensus pattern (33 bp):
TGTATCGATACAATGTGCCATGTATCGATACAT
Found at i:3599371 original size:19 final size:19
Alignment explanation
Indices: 3599327--3599382 Score: 85
Period size: 19 Copynumber: 2.9 Consensus size: 19
3599317 CTGCCAGTTT
**
3599327 CATGTATCGATACAATTGTG
1 CATGTATCGATACAA-TGAA
3599347 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
3599366 CATGTATCGATACAATG
1 CATGTATCGATACAATG
3599383 TATCAATACA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
19 19 0.56
20 15 0.44
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.30
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:3601207 original size:2 final size:2
Alignment explanation
Indices: 3601202--3601238 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
3601192 ATTTTTTAGA
3601202 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3601239 CAATGCCTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3602638 original size:30 final size:31
Alignment explanation
Indices: 3602601--3602673 Score: 89
Period size: 29 Copynumber: 2.4 Consensus size: 31
3602591 TAAATTTATT
*
3602601 TTTAATATTTTTAATATATTTATAA-ATTAAA
1 TTTAATATTTTTAATA-ATTCATAATATTAAA
*
3602632 -TTAATA-TTTTATTAATTCATAATATTAAA
1 TTTAATATTTTTAATAATTCATAATATTAAA
3602661 TTTAATCATTTTT
1 TTTAAT-ATTTTT
3602674 TTTAATAATG
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
28 7 0.19
29 13 0.36
30 11 0.31
31 1 0.03
32 4 0.11
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (31 bp):
TTTAATATTTTTAATAATTCATAATATTAAA
Found at i:3604917 original size:2 final size:2
Alignment explanation
Indices: 3604910--3604957 Score: 69
Period size: 2 Copynumber: 24.0 Consensus size: 2
3604900 GTAAGTTGAA
* *
3604910 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT AT CT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
3604952 TT AT AT
1 AT AT AT
3604958 TGTTTAAGAA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:3608437 original size:21 final size:21
Alignment explanation
Indices: 3608426--3608478 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
3608416 AGTTGCTTTT
3608426 TTTCATCCAAAAAATGCATTC
1 TTTCATCCAAAAAATGCATTC
**
3608447 TTTCATCCAACCAATGCA-TC
1 TTTCATCCAAAAAATGCATTC
3608467 ATTTCATCCAAA
1 -TTTCATCCAAA
3608479 TATATCTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 2 0.07
21 26 0.93
ACGTcount: A:0.36, C:0.28, G:0.04, T:0.32
Consensus pattern (21 bp):
TTTCATCCAAAAAATGCATTC
Found at i:3616913 original size:21 final size:20
Alignment explanation
Indices: 3616867--3616916 Score: 61
Period size: 18 Copynumber: 2.6 Consensus size: 20
3616857 ACTTGTTTAT
*
3616867 ATTTAATA-ATTTTTAAAAT
1 ATTTAATATATTTTTAAAAA
3616886 A-TT-ATATATTTTTATAAAA
1 ATTTAATATATTTTTA-AAAA
3616905 ATTTAATATATT
1 ATTTAATATATT
3616917 AATAATTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 3 0.12
18 9 0.35
19 5 0.19
20 2 0.08
21 7 0.27
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
ATTTAATATATTTTTAAAAA
Found at i:3616939 original size:28 final size:28
Alignment explanation
Indices: 3616878--3616939 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
3616868 TTTAATAATT
* *
3616878 TTTAAAATATTATATATTTTTATAAAAA
1 TTTAATATATTATATAATTTTATAAAAA
*
3616906 TTTAATATATTA-ATAATTTTATTTAAAA
1 TTTAATATATTATATAATTTTA-TAAAAA
3616934 TTTAAT
1 TTTAAT
3616940 TTTTTTTCAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
27 8 0.27
28 22 0.73
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (28 bp):
TTTAATATATTATATAATTTTATAAAAA
Found at i:3616974 original size:23 final size:24
Alignment explanation
Indices: 3616936--3616980 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
3616926 ATTTAAAATT
* *
3616936 TAATTTTTTTTCATATTATATTTA
1 TAATTATTTTTCATATCATATTTA
3616960 TAATTATTTTT-ATATCATATT
1 TAATTATTTTTCATATCATATT
3616981 ATATTTTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 9 0.47
24 10 0.53
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.64
Consensus pattern (24 bp):
TAATTATTTTTCATATCATATTTA
Found at i:3616979 original size:28 final size:26
Alignment explanation
Indices: 3616938--3617033 Score: 110
Period size: 27 Copynumber: 3.7 Consensus size: 26
3616928 TTAAAATTTA
*
3616938 ATTTTTTTTCATATTATATTTATAATT
1 ATTTTTTATCATATTATATTT-TAATT
3616965 ATTTTTATATCATATTATATTTTAATT
1 ATTTTT-TATCATATTATATTTTAATT
*
3616992 ATTTTTTAT-GTATTATA--TTAA-T
1 ATTTTTTATCATATTATATTTTAATT
*
3617014 ATTTTATAATCATATTATAT
1 ATTTT-TTATCATATTATAT
3617034 CTAAAATTTA
Statistics
Matches: 61, Mismatches: 4, Indels: 10
0.81 0.05 0.13
Matches are distributed among these distances:
22 6 0.10
23 7 0.11
24 7 0.11
25 7 0.11
26 3 0.05
27 17 0.28
28 14 0.23
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.62
Consensus pattern (26 bp):
ATTTTTTATCATATTATATTTTAATT
Found at i:3619484 original size:79 final size:78
Alignment explanation
Indices: 3619399--3619836 Score: 275
Period size: 79 Copynumber: 5.6 Consensus size: 78
3619389 ACAACGAGGC
*
3619399 TGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATTATAGAAAATCGATGTTTTGAA
1 TGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATTGTAGAAAATCGATGTTTTGAA
3619464 AATAAAATCAGGAT
66 AATAAAATCAGG-T
* * * *
3619478 TGGAGTATCCCCGC-GAAAATAACGGGGTTAGAGTATCCCCGATTGT-GAGAAATCAATATTTT-
1 TGGAGTATCCCCTCAG-AAATAACGGGGTTGGAGTATCCCCGATTGTAGA-AAATCGATGTTTTG
* **
3619540 AGAAATAAAGTTGGGGT
64 A-AAATAAA-ATCAGGT
* * * * * *
3619557 TGGAGTATCCTCTCAGAAATAATGGGGTTGGAGTATTCCCGA-TG-A-AATAA-CG-GGGTTGGA
1 TGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATTGTAGAA-AATCGATGTTTTGA
** *** * * *
3619617 GTATCCTCGATTATGA
65 AAAT--AAAATCAGGT
*** * **** * * *
3619633 AAAATTGATGTTTTGA-AAATAAGATCGGAGTTGGAGTATCCCCGATTGTAGAAAATTGATGTTT
1 TGGAGT-ATCCCCTCAGAAAT-A-A-CGGGGTTGGAGTATCCCCGATTGTAGAAAATCGATGTTT
*
3619697 T-AGAAATAAAACCGAGGT
62 TGA-AAATAAAATC-AGGT
** ** * * * *
3619715 TGGAGTATCCTTTTGGAAATAACGGGGTTAGAGTATCCCTGATGGTGGAAAATCGATGTTTTGAA
1 TGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATTGTAGAAAATCGATGTTTTGAA
3619780 AATAAAATCGAGGT
66 AATAAAATC-AGGT
* *
3619794 TGGAGTATCCCCTCAGAAATAACAGGATTGGAGTATCCCCGAT
1 TGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGAT
3619837 GACGTAACGG
Statistics
Matches: 261, Mismatches: 75, Indels: 46
0.68 0.20 0.12
Matches are distributed among these distances:
75 4 0.02
76 11 0.04
77 9 0.03
78 7 0.03
79 195 0.75
80 8 0.03
81 10 0.04
82 12 0.05
83 5 0.02
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (78 bp):
TGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATTGTAGAAAATCGATGTTTTGAA
AATAAAATCAGGT
Found at i:3619627 original size:28 final size:28
Alignment explanation
Indices: 3619552--3619627 Score: 102
Period size: 28 Copynumber: 2.7 Consensus size: 28
3619542 AAATAAAGTT
* *
3619552 GGGGTTGGAGTATCCTCTCA-GAAATAAT
1 GGGGTTGGAGTATCCTC-GATGAAATAAC
3619580 GGGGTTGGAGTATTCC-CGATGAAATAAC
1 GGGGTTGGAGTA-TCCTCGATGAAATAAC
3619608 GGGGTTGGAGTATCCTCGAT
1 GGGGTTGGAGTATCCTCGAT
3619628 TATGAAAAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
27 4 0.09
28 36 0.84
29 3 0.07
ACGTcount: A:0.25, C:0.14, G:0.33, T:0.28
Consensus pattern (28 bp):
GGGGTTGGAGTATCCTCGATGAAATAAC
Found at i:3619666 original size:107 final size:107
Alignment explanation
Indices: 3619477--3619673 Score: 247
Period size: 107 Copynumber: 1.8 Consensus size: 107
3619467 AAAATCAGGA
* *
3619477 TTGGAGTATCCCCGCGAAAATAACGGGGTTAGAGTATCCCCGATTGTGAGAAATCAATATTTTAG
1 TTGGAGTATCCCCGCGAAAATAACGGGGTTAGAGTATCCCCGATTATGAAAAATCAATATTTTAG
* *
3619542 AAATAAAGTTGGGGTTGGAGTATCCTCTCAGAAATAATGGGG
66 AAATAAAGTCGGAGTTGGAGTATCCTCTCAGAAATAATGGGG
* * * * ** *
3619584 TTGGAGTATTCCCGATG-AAATAACGGGGTTGGAGTATCCTCGATTATGAAAAATTGATGTTTT-
1 TTGGAGTATCCCCG-CGAAAATAACGGGGTTAGAGTATCCCCGATTATGAAAAATCAATATTTTA
3619647 GAAA-ATAAGATCGGAGTTGGAGTATCC
65 GAAATA-AAG-TCGGAGTTGGAGTATCC
3619674 CCGATTGTAG
Statistics
Matches: 76, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
105 1 0.01
106 7 0.09
107 67 0.88
108 1 0.01
ACGTcount: A:0.31, C:0.13, G:0.27, T:0.29
Consensus pattern (107 bp):
TTGGAGTATCCCCGCGAAAATAACGGGGTTAGAGTATCCCCGATTATGAAAAATCAATATTTTAG
AAATAAAGTCGGAGTTGGAGTATCCTCTCAGAAATAATGGGG
Found at i:3619679 original size:51 final size:51
Alignment explanation
Indices: 3619610--3619724 Score: 146
Period size: 51 Copynumber: 2.3 Consensus size: 51
3619600 GAAATAACGG
* * *
3619610 GGTTGGAGTATCCTCGATTAT-GAAAAATTGATGTTTT-GAAAATAAGATCG-
1 GGTTGGAGTATCCCCGATTATAG-AAAATTGATGTTTTAG-AAATAAAACCGA
*
3619660 GAGTTGGAGTATCCCCGATTGTAGAAAATTGATGTTTTAGAAATAAAACCGA
1 G-GTTGGAGTATCCCCGATTATAGAAAATTGATGTTTTAGAAATAAAACCGA
3619712 GGTTGGAGTATCC
1 GGTTGGAGTATCC
3619725 TTTTGGAAAT
Statistics
Matches: 57, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
50 1 0.02
51 53 0.93
52 3 0.05
ACGTcount: A:0.33, C:0.10, G:0.25, T:0.31
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATAGAAAATTGATGTTTTAGAAATAAAACCGA
Found at i:3619847 original size:237 final size:237
Alignment explanation
Indices: 3619425--3619873 Score: 618
Period size: 237 Copynumber: 1.9 Consensus size: 237
3619415 AAATAACGGG
*
3619425 GTTGGAGTATCCCCGATTATAGAAAATCGATGTTTTGAAAATAAAATCAGGATTGGAGTATCCCC
1 GTTGGAGTATCCCCGATTATAGAAAATCGATGTTTTGAAAATAAAACCAGGATTGGAGTATCCCC
* * * *
3619490 GCGAAAATAACGGGGTTAGAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAAAGTTGGG
66 GCGAAAATAACGGGGTTAGAGTATCCCCGATGGTGAGAAATCAATATTTTAGAAATAAAATCGAG
* ** * *
3619555 GTTGGAGTATCCTCTCAGAAATAATGGGGTTGGAGTATTCCCGATGAAATAACGGGGTTGGAGTA
131 GTTGGAGTATCCCCTCAGAAATAACAGGATTGGAGTATCCCCGATGAAATAACGGGGTTGGAGTA
* *
3619620 TCCTCGATTATGAAAAATTGATGTTTTGAAAATAAGATCGGA
196 CCCCCGATTATGAAAAATTGATGTTTTGAAAATAAGATCGGA
* *
3619662 GTTGGAGTATCCCCGATTGTAGAAAATTGATGTTTT-AGAAATAAAACCGAGG-TTGGAGTATCC
1 GTTGGAGTATCCCCGATTATAGAAAATCGATGTTTTGA-AAATAAAACC-AGGATTGGAGTATCC
**** * * * *
3619725 TTTTGGAAATAACGGGGTTAGAGTATCCCTGATGGTG-GAAAATCGATGTTTT-GAAAATAAAAT
64 CCGCGAAAATAACGGGGTTAGAGTATCCCCGATGGTGAG-AAATCAATATTTTAG-AAATAAAAT
**
3619788 CGAGGTTGGAGTATCCCCTCAGAAATAACAGGATTGGAGTATCCCCGATGACGTAACGGGGTTGG
127 CGAGGTTGGAGTATCCCCTCAGAAATAACAGGATTGGAGTATCCCCGATGAAATAACGGGGTTGG
3619853 AGTACCCCCGATTATGAAAAA
192 AGTACCCCCGATTATGAAAAA
3619874 AATCAATATT
Statistics
Matches: 184, Mismatches: 24, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
236 3 0.02
237 178 0.97
238 3 0.02
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (237 bp):
GTTGGAGTATCCCCGATTATAGAAAATCGATGTTTTGAAAATAAAACCAGGATTGGAGTATCCCC
GCGAAAATAACGGGGTTAGAGTATCCCCGATGGTGAGAAATCAATATTTTAGAAATAAAATCGAG
GTTGGAGTATCCCCTCAGAAATAACAGGATTGGAGTATCCCCGATGAAATAACGGGGTTGGAGTA
CCCCCGATTATGAAAAATTGATGTTTTGAAAATAAGATCGGA
Found at i:3619936 original size:28 final size:29
Alignment explanation
Indices: 3619904--3619969 Score: 73
Period size: 28 Copynumber: 2.3 Consensus size: 29
3619894 AGCCGGGTTG
3619904 GAGTATCCCCT-TGGAAATAACGGGATTA
1 GAGTATCCCCTGTGGAAATAACGGGATTA
** * * *
3619932 GAGTAT-TTCTGTTGAAATAATGGGGTTA
1 GAGTATCCCCTGTGGAAATAACGGGATTA
3619960 GAGTATCCCC
1 GAGTATCCCC
3619970 AATTGTGAAA
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
27 2 0.07
28 26 0.90
29 1 0.03
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.30
Consensus pattern (29 bp):
GAGTATCCCCTGTGGAAATAACGGGATTA
Found at i:3620099 original size:51 final size:51
Alignment explanation
Indices: 3619977--3620099 Score: 147
Period size: 51 Copynumber: 2.4 Consensus size: 51
3619967 CCCAATTGTG
* **
3619977 AAAAATTGGTGTTTTAGAAATAAAATCAGAGTTGGAGTATCCCCGATTGCA
1 AAAAATTGATGTTTTAGAAATAAAATCAGAGTTGGAGTATCCCCGATTAAA
** * ** * *
3620028 GTAAATCGATCATTTAGAAATAAAATCGGAGTTGGAGTATCCTCGATTAAA
1 AAAAATTGATGTTTTAGAAATAAAATCAGAGTTGGAGTATCCCCGATTAAA
*
3620079 AAAAATTGATGTTTTGGAAAT
1 AAAAATTGATGTTTTAGAAAT
3620100 GGAACCGGGA
Statistics
Matches: 56, Mismatches: 16, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
51 56 1.00
ACGTcount: A:0.39, C:0.10, G:0.20, T:0.31
Consensus pattern (51 bp):
AAAAATTGATGTTTTAGAAATAAAATCAGAGTTGGAGTATCCCCGATTAAA
Found at i:3622494 original size:20 final size:20
Alignment explanation
Indices: 3622469--3622523 Score: 110
Period size: 20 Copynumber: 2.8 Consensus size: 20
3622459 GTAAACCCAG
3622469 AATGTATCGATACAATGAAC
1 AATGTATCGATACAATGAAC
3622489 AATGTATCGATACAATGAAC
1 AATGTATCGATACAATGAAC
3622509 AATGTATCGATACAA
1 AATGTATCGATACAA
3622524 ATTGTGAAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.45, C:0.15, G:0.15, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAATGAAC
Found at i:3630192 original size:79 final size:79
Alignment explanation
Indices: 3630107--3630693 Score: 719
Period size: 79 Copynumber: 7.4 Consensus size: 79
3630097 ATTCATATTT
* * *
3630107 TTATTTCTGAGGGGATACTCCAACCCTGGTTTTATTTTCAAAACACCAATTTTTCACAATCGGAG
1 TTATTTCTGAGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTTCACAATCGGGG
3630172 ATACTCCAACCCCG
66 ATACTCCAACCCCG
* * * * *
3630186 TTATTTCTGAAGGGATACTCCAATCCCAATTTTATTTTCAAAACACTAATTTTTCACAATCGAGG
1 TTATTTCTGAGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTTCACAATCGGGG
*
3630251 ATACTCCAACCCTG
66 ATACTCCAACCCCG
* * *
3630265 TTATTT-TCGAGGGGATACTCCAACCCCGATTTTATTTCCAAAATACCAAATTTTCACAATCGGG
1 TTATTTCT-GAGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTTCACAATCGGG
**
3630329 GATACTCCAACCCTA
65 GATACTCCAACCCCG
* * * *
3630344 TTATTTTTGAGGGGATATTCCAACCTCGATTTTATTTTCAAAACACCAATTTTTCACAATCAGGG
1 TTATTTCTGAGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTTCACAATCGGGG
***
3630409 ATACTCCAACATTG
66 ATACTCCAACCCCG
** * * * * *
3630423 TTATTTCCAAGGAGATACTCCAACCCCGATTTTATCTCCAAAACACTAATTTTTCACAATTGGGG
1 TTATTTCTGAGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTTCACAATCGGGG
3630488 ATACTCCAACCCCG
66 ATACTCCAACCCCG
** * * * *
3630502 TTATTTCCAAAGGGATACTCCAACCCTGGTTTTATTTTCAAAACACTAATTTTTCACAATCGGGG
1 TTATTTCTGAGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTTCACAATCGGGG
*
3630567 ATACTCTAACCCCG
66 ATACTCCAACCCCG
* * * * * * * * *
3630581 TTATTTC-GAGGGGATGCTCTAACCCCAATTTTATTTCCAAAACATCGATTTTTTACCATTGGGG
1 TTATTTCTGAGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTTCACAATCGGGG
3630645 ATACTCCAACCCCG
66 ATACTCCAACCCCG
* * * *
3630659 TTATTTCTGAAGGGATACTCCGACCTCGTTTTTAT
1 TTATTTCTGAGGGGATACTCCAACCCCGATTTTAT
3630694 CTCCAAAATA
Statistics
Matches: 434, Mismatches: 71, Indels: 6
0.85 0.14 0.01
Matches are distributed among these distances:
78 64 0.15
79 369 0.85
80 1 0.00
ACGTcount: A:0.29, C:0.25, G:0.13, T:0.33
Consensus pattern (79 bp):
TTATTTCTGAGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTTCACAATCGGGG
ATACTCCAACCCCG
Found at i:3643093 original size:27 final size:24
Alignment explanation
Indices: 3643049--3643115 Score: 80
Period size: 26 Copynumber: 2.7 Consensus size: 24
3643039 CTTTTTTTCC
*
3643049 AAAAAAAAAAAAACAAAATGAAACA
1 AAAAAAAAAAAAAAAAAATGAAA-A
3643074 AAAAAAAAACAACAAAAAAATGAAAA
1 AAAAAAAAA-AA-AAAAAAATGAAAA
* *
3643100 AAGAAAAAAGAAAAAA
1 AAAAAAAAAAAAAAAA
3643116 GAGAAAAGAA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
24 5 0.14
25 10 0.27
26 11 0.30
27 11 0.30
ACGTcount: A:0.85, C:0.06, G:0.06, T:0.03
Consensus pattern (24 bp):
AAAAAAAAAAAAAAAAAATGAAAA
Found at i:3643100 original size:24 final size:21
Alignment explanation
Indices: 3643049--3643115 Score: 62
Period size: 23 Copynumber: 3.0 Consensus size: 21
3643039 CTTTTTTTCC
3643049 AAAAAAAAAAAAACAAAATGAAA
1 AAAAAAAAAAAAACAAAA--AAA
*
3643072 CAAAAAAAAAACAACAAAAAAA
1 -AAAAAAAAAAAAACAAAAAAA
* *
3643094 TGAAAAAAGAAAAAAGAAAAAA
1 --AAAAAAAAAAAAACAAAAAA
3643116 GAGAAAAGAA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
22 3 0.08
23 17 0.46
24 17 0.46
ACGTcount: A:0.85, C:0.06, G:0.06, T:0.03
Consensus pattern (21 bp):
AAAAAAAAAAAAACAAAAAAA
Found at i:3643116 original size:7 final size:7
Alignment explanation
Indices: 3643088--3643127 Score: 62
Period size: 7 Copynumber: 5.6 Consensus size: 7
3643078 AAAAACAACA
3643088 AAAAAATG
1 AAAAAA-G
3643096 AAAAAAG
1 AAAAAAG
3643103 AAAAAAG
1 AAAAAAG
3643110 AAAAAAG
1 AAAAAAG
*
3643117 AGAAAAG
1 AAAAAAG
3643124 AAAA
1 AAAA
3643128 GAACCTACTT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
7 24 0.80
8 6 0.20
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (7 bp):
AAAAAAG
Found at i:3643122 original size:23 final size:23
Alignment explanation
Indices: 3643049--3643115 Score: 66
Period size: 24 Copynumber: 2.9 Consensus size: 23
3643039 CTTTTTTTCC
* *
3643049 AAAAAAAAAAAAACAAAATGAAA-C
1 AAAAAAAAAACAACAAAA--AAATG
3643073 AAAAAAAAAACAACAAAAAAATG
1 AAAAAAAAAACAACAAAAAAATG
*
3643096 AAAAAAGAAAA-AAGAAAAAA
1 AAAAAA-AAAACAACAAAAAA
3643116 GAGAAAAGAA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
22 3 0.08
23 14 0.37
24 21 0.55
ACGTcount: A:0.85, C:0.06, G:0.06, T:0.03
Consensus pattern (23 bp):
AAAAAAAAAACAACAAAAAAATG
Found at i:3644199 original size:61 final size:61
Alignment explanation
Indices: 3644119--3644838 Score: 888
Period size: 61 Copynumber: 11.9 Consensus size: 61
3644109 AAGACACTTT
* * *
3644119 CTTTTCAAAGCCCACACAAGTTGGTAGCATCTTCTAGTCCTTAAAGAGCAGGACGCCTTTTC
1 CTTTT-AAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGCAGGACGCCTTTTC
*
3644181 CTTTTAAAGCCCACACAAGTTGGTGGCACTTTGC-AGTCCTCAAAGAGCAGGACGCCTTTTC
1 CTTTTAAAGCCCACACAAGTTGGTGGCACCTT-CTAGTCCTCAAAGAGCAGGACGCCTTTTC
* * * *
3644242 CTTTTAAAGCCCACACAAGTTGGTGACACCTT-TCAATCCCCAAAGAGCAGGAC-AC-TTTC
1 CTTTTAAAGCCCACACAAGTTGGTGGCACCTTCT-AGTCCTCAAAGAGCAGGACGCCTTTTC
* * *
3644301 CTTTCAAAGTCCATACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGCAGGACAG-CTTTTC
1 CTTTTAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGCAGGAC-GCCTTTTC
* * * *
3644362 CTTTTAAAGCCCACATAAGTTGGTGACA-CTTTTCAGTCCTCAAAGAGTAGGACGCCTTTTC
1 CTTTTAAAGCCCACACAAGTTGGTGGCACCTTCT-AGTCCTCAAAGAGCAGGACGCCTTTTC
* * * *
3644423 CTTTTAAAGCCCACACAAGTTGGTGGCACTTTCCAGTCCTCAAAGAGCATGATGCCTTTTC
1 CTTTTAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGCAGGACGCCTTTTC
* *
3644484 CTTTTAAAG-CCACACAAGTTGGTGGCACCTT-TCAGTCCCCAAAGAGCAGGAC-AC-TTTC
1 CTTTTAAAGCCCACACAAGTTGGTGGCACCTTCT-AGTCCTCAAAGAGCAGGACGCCTTTTC
* * * * *
3644542 CTTTTAAAGCTCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAAGATGTCTTTTC
1 CTTTTAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGCAGGACGCCTTTTC
* * * *
3644603 CTTTTAAAGCCCACACAAGTTGGTGGCACATTCTAGTCCTCAAAAAGCAAGATGCCTTTTC
1 CTTTTAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGCAGGACGCCTTTTC
* * * * * *
3644664 CTTTTAAAGCCCACACAAGTTGGTGGCACTTTCCAGTCCTCGAAGAGCAAGATGCCTGTTC
1 CTTTTAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGCAGGACGCCTTTTC
* * **
3644725 CTTTTAAAGCCCACAAAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGA-TAC-TTTC
1 CTTTTAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGCAGGACGCCTTTTC
* * * *
3644784 TCTTTGCAAAGCCCATACAAGTTGATGGCACCTTCTAGTCCCCAAAGAGCAGGAC
1 -CTTT-TAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGCAGGAC
3644839 ACATTTAATT
Statistics
Matches: 576, Mismatches: 64, Indels: 36
0.85 0.09 0.05
Matches are distributed among these distances:
58 13 0.02
59 90 0.16
60 52 0.09
61 413 0.72
62 8 0.01
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.27
Consensus pattern (61 bp):
CTTTTAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGCAGGACGCCTTTTC
Found at i:3644401 original size:181 final size:183
Alignment explanation
Indices: 3644089--3644840 Score: 910
Period size: 181 Copynumber: 4.1 Consensus size: 183
3644079 AACCTTTTAT
* * * *
3644089 CCTTTCAGTCCCTAAAGAGCAAGACAC-TTTCTTTTCAAAGCCCACACAAGTTGGTAGCATCTTC
1 CCTTTCAGTCCCCAAAGAGCAAGACACTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTC
* *
3644153 TAGTCCTTAAAGAGCAGGAC-GCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTGCAG
66 TAGTCCTCAAAGAGCAGGACAGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCAG
*
3644217 TCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGACA
131 TCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * * *
3644270 CCTTTCAATCCCCAAAGAGCAGGACAC-TTTCCTTTCAAAGTCCATACAAGTTGGTGGCACCTTC
1 CCTTTCAGTCCCCAAAGAGCAAGACACTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTC
* *
3644334 TAGTCCTCAAAGAGCAGGACAG-CTTTTCCTTTTAAAGCCCACATAAGTTGGTGACACTTTTCAG
66 TAGTCCTCAAAGAGCAGGACAGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCAG
*
3644398 TCCTCAAAGAGTAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
131 TCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * *
3644451 -CTTTCCAGTCCTCAAAGAGCATGATGC-CTTTTCCTTTTAAAG-CCACACAAGTTGGTGGCACC
1 CCTTT-CAGTCCCCAAAGAGCAAGA--CACTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCACC
* *
3644513 TT-TCAGTCCCCAAAGAGCAGGACA--C-TTTCCTTTTAAAGCTCACACAAGTTGGTGGCACCTT
63 TTCT-AGTCCTCAAAGAGCAGGACAGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA-CTT
* * *
3644574 TT-AGTCCTCAAAGAGCAAGATGTCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
126 TTCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * * * *
3644631 -CATTCTAGTCCTCAAAAAGCAAGATGC-CTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACT
1 CCTTTC-AGTCCCCAAAGAGCAAGA--CACTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCACC
* * * * * * * *
3644694 TTCCAGTCCTCGAAGAGCAAGA-TGCCTGTTCCTTTTAAAGCCCACAAAAGTTGGTGGCACCTTC
63 TTCTAGTCCTCAAAGAGCAGGACAGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTT
** * * *
3644758 CAGTCCTCAAAGAGCAGGA-TAC-TTTCTCTTTGCAAAGCCCATACAAGTTGATGGCA
128 CAGTCCTCAAAGAGCAGGACGCCTTTTC-CTTT-TAAAGCCCACACAAGTTGGTGGCA
*
3644814 CC-TTCTAGTCCCCAAAGAGCAGGACAC
1 CCTTTC-AGTCCCCAAAGAGCAAGACAC
3644841 ATTTAATTTC
Statistics
Matches: 503, Mismatches: 50, Indels: 35
0.86 0.09 0.06
Matches are distributed among these distances:
179 1 0.00
180 121 0.24
181 229 0.46
182 52 0.10
183 99 0.20
184 1 0.00
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.27
Consensus pattern (183 bp):
CCTTTCAGTCCCCAAAGAGCAAGACACTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTC
TAGTCCTCAAAGAGCAGGACAGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCAG
TCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
Found at i:3644609 original size:241 final size:243
Alignment explanation
Indices: 3644102--3644839 Score: 1082
Period size: 241 Copynumber: 3.1 Consensus size: 243
3644092 TTCAGTCCCT
* *
3644102 AAAGAGCAAGACA-C-TTT-CTTTTCAAAGCCCACACAAGTTGGT-AGCA-TCTTCTAGTCCTTA
1 AAAGAGCAAGACAGCTTTTCCTTTT-AAAGCCCACACAAGTTGGTGA-CACTATTCTAGTCCTCA
*
3644162 AAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTGCAGTCCTCAAAGA
64 AAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCCAGTCCTCAAAGA
* * * *
3644227 GCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGACACCTTTCAATCCCCAAAGAGCAG
129 GCAAGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGCAG
3644292 GACACTTTCCTTTCAAAG-TCCATACAAGTTGGTGGCACCTTCTAGTCCTC
194 GACACTTTCCTTTCAAAGCT-CATACAAGTTGGTGGCACCTTCTAGTCCTC
* * *
3644342 AAAGAGCAGGACAGCTTTTCCTTTTAAAGCCCACATAAGTTGGTGACACTTTTC-AGTCCTCAAA
1 AAAGAGCAAGACAGCTTTTCCTTTTAAAGCCCACACAAGTTGGTGACACTATTCTAGTCCTCAAA
*
3644406 GAGTAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCCAGTCCTCAAAGAGC
66 GAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCCAGTCCTCAAAGAGC
*
3644471 ATGATGCCTTTTCCTTTTAAAG-CCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGA
131 AAGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGA
* * *
3644535 CACTTTCCTTTTAAAGCTCACACAAGTTGGTGGCACCTTTTAGTCCTC
196 CACTTTCCTTTCAAAGCTCATACAAGTTGGTGGCACCTTCTAGTCCTC
* *
3644583 AAAGAGCAAGA-TGTCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCAC-ATTCTAGTCCTCAA
1 AAAGAGCAAGACAG-CTTTTCCTTTTAAAGCCCACACAAGTTGGTGACACTATTCTAGTCCTCAA
* * * *
3644646 AAAGCAAGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCCAGTCCTCGAAGAG
65 AGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCCAGTCCTCAAAGAG
* * * *
3644711 CAAGATGCCTGTTCCTTTTAAAGCCCACAAAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGG
130 CAAGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGCAGG
* * * *
3644776 ATACTTTCTCTTTGCAAAGCCCATACAAGTTGATGGCACCTTCTAGTCCCC
195 ACACTTTC-CTTT-CAAAGCTCATACAAGTTGGTGGCACCTTCTAGTCCTC
*
3644827 AAAGAGCAGGACA
1 AAAGAGCAAGACA
3644840 CATTTAATTT
Statistics
Matches: 449, Mismatches: 37, Indels: 19
0.89 0.07 0.04
Matches are distributed among these distances:
240 16 0.04
241 217 0.48
242 161 0.36
243 14 0.03
244 41 0.09
ACGTcount: A:0.28, C:0.27, G:0.19, T:0.27
Consensus pattern (243 bp):
AAAGAGCAAGACAGCTTTTCCTTTTAAAGCCCACACAAGTTGGTGACACTATTCTAGTCCTCAAA
GAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCCAGTCCTCAAAGAGC
AAGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGA
CACTTTCCTTTCAAAGCTCATACAAGTTGGTGGCACCTTCTAGTCCTC
Found at i:3644883 original size:41 final size:42
Alignment explanation
Indices: 3644821--3644921 Score: 141
Period size: 41 Copynumber: 2.4 Consensus size: 42
3644811 GCACCTTCTA
*
3644821 GTCCCCAAAGAGCAGGACACATTTAATTTCC-TTTTTCCTTT
1 GTCCTCAAAGAGCAGGACACATTTAATTTCCTTTTTTCCTTT
* *
3644862 GTCCTCAAAGAGCATGACACATTTTATTTCCTTTTTTTCCTTT
1 GTCCTCAAAGAGCAGGACACATTTAATTTCC-TTTTTTCCTTT
* *
3644905 GTCCTCGAAGAACAGGA
1 GTCCTCAAAGAGCAGGA
3644922 TGTATTCCTT
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
41 28 0.54
43 24 0.46
ACGTcount: A:0.25, C:0.25, G:0.14, T:0.37
Consensus pattern (42 bp):
GTCCTCAAAGAGCAGGACACATTTAATTTCCTTTTTTCCTTT
Found at i:3645638 original size:13 final size:13
Alignment explanation
Indices: 3645620--3645671 Score: 81
Period size: 13 Copynumber: 4.2 Consensus size: 13
3645610 ACATTGTTCT
3645620 TTGTATCGATACA
1 TTGTATCGATACA
*
3645633 TTGTATCGAT-GA
1 TTGTATCGATACA
3645645 -TGTATCGATACA
1 TTGTATCGATACA
3645657 TTGTATCGATACA
1 TTGTATCGATACA
3645670 TT
1 TT
3645672 TCTTAATGTA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
11 9 0.26
12 2 0.06
13 24 0.69
ACGTcount: A:0.29, C:0.13, G:0.17, T:0.40
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:3645653 original size:24 final size:24
Alignment explanation
Indices: 3645621--3645666 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
3645611 CATTGTTCTT
3645621 TGTATCGATACATTGTATCGATGA
1 TGTATCGATACATTGTATCGATGA
3645645 TGTATCGATACATTGTATCGAT
1 TGTATCGATACATTGTATCGAT
3645667 ACATTTCTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.28, C:0.13, G:0.20, T:0.39
Consensus pattern (24 bp):
TGTATCGATACATTGTATCGATGA
Found at i:3647587 original size:22 final size:22
Alignment explanation
Indices: 3647559--3647603 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 22
3647549 AATTTTTTGA
3647559 TAACAATTGAGT-TCGAGGTGAT
1 TAACAATTGAGTCT-GAGGTGAT
3647581 TAACAATTGAGTCTGAGGTGAT
1 TAACAATTGAGTCTGAGGTGAT
3647603 T
1 T
3647604 TTTCAAAGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 21 0.95
23 1 0.05
ACGTcount: A:0.31, C:0.09, G:0.27, T:0.33
Consensus pattern (22 bp):
TAACAATTGAGTCTGAGGTGAT
Found at i:3648101 original size:79 final size:78
Alignment explanation
Indices: 3648012--3648619 Score: 678
Period size: 79 Copynumber: 7.7 Consensus size: 78
3648002 ATTCATATTT
* * * *
3648012 TTATTTCCGAGGGGATACTCCAACTCCGGTTTTATTTCCAAAACACCAATTTTTCATAATTGGGG
1 TTATTTCCGAGGGGATACTCCAAC-CCGATTTTATTTCCAAAACACTAATTTTTCACAATCGGGG
**
3648077 ATACTCCAACCTTG
65 ATACTCCAACCCCG
* * * * *
3648091 TTATATCCGAGGAGATACTCCAACCCTGGTTTTATTTCCAAGACACCAATTTTTCACAATCGGGG
1 TTATTTCCGAGGGGATACTCCAACCC-GATTTTATTTCCAAAACACTAATTTTTCACAATCGGGG
* *
3648156 ATGCTCCAACTCCG
65 ATACTCCAACCCCG
* * * *
3648170 TTATTTTCGAGAGGATACTTCAACCCCGATTTTATTTCCAAAACACTAATTTTTCACAATCGAGG
1 TTATTTCCGAGGGGATACTCCAA-CCCGATTTTATTTCCAAAACACTAATTTTTCACAATCGGGG
3648235 ATACTCCAACCCCG
65 ATACTCCAACCCCG
* * * * *
3648249 TT-TTTTCGAGGGGATACTCCGACCCCGATTTTATTTTCAAAACATTAATTTTTCACAATCGAGG
1 TTATTTCCGAGGGGATACTCC-AACCCGATTTTATTTCCAAAACACTAATTTTTCACAATCGGGG
*
3648313 ATACTCTAACCCCG
65 ATACTCCAACCCCG
** * *
3648327 TTATTTTTGAGGGGATACTTCAACCCTGATTTTATTTCCAAAACACTAATTTTCCACAATCGGGG
1 TTATTTCCGAGGGGATACTCCAACCC-GATTTTATTTCCAAAACACTAATTTTTCACAATCGGGG
3648392 ATACTCCAACCCCG
65 ATACTCCAACCCCG
* *** *
3648406 TTATTTCTGAGGGGATACTCCAACTCCGATTTTATTTTTGAAACACCAATTTTTCACAATCGGGG
1 TTATTTCCGAGGGGATACTCCAAC-CCGATTTTATTTCCAAAACACTAATTTTTCACAATCGGGG
* *
3648471 ATACTCTAATCCCG
65 ATACTCCAACCCCG
** * * * * * * * *
3648485 TTATTTTTGAGGGGATACTCGAACCCAATTTTATTTCTAAAACATTGATTTTCCACCATTGGGGA
1 TTATTTCCGAGGGGATACTCCAACCCGATTTTATTTCCAAAACACTAATTTTTCACAATCGGGGA
3648550 TACTCCAACCCCG
66 TACTCCAACCCCG
** * * * * *
3648563 TTATTTCTTAGGGGGTACTCCAACCCCGTTTTTATCTCCAAAATATTAAATTTTTCA
1 TTATTTCCGAGGGGATACTCCAA-CCCGATTTTATTTCCAAAACACT-AATTTTTCA
3648620 TCGGGAGATG
Statistics
Matches: 454, Mismatches: 67, Indels: 15
0.85 0.12 0.03
Matches are distributed among these distances:
78 138 0.30
79 304 0.67
80 12 0.03
ACGTcount: A:0.27, C:0.25, G:0.14, T:0.34
Consensus pattern (78 bp):
TTATTTCCGAGGGGATACTCCAACCCGATTTTATTTCCAAAACACTAATTTTTCACAATCGGGGA
TACTCCAACCCCG
Found at i:3648333 original size:157 final size:158
Alignment explanation
Indices: 3648012--3648605 Score: 744
Period size: 157 Copynumber: 3.8 Consensus size: 158
3648002 ATTCATATTT
* * * * * * * *
3648012 TTATTTCCGAGGGGATACTCCAACTCCGGTTTTATTTCCAAAACACCAATTTTTCATAATTGGGG
1 TTATTTTCGAGGGGATACTTCAACCCCGATTTTATTTCCAAAACACTAATTTTCCACAATCGGGG
** * * * * * *
3648077 ATACTCCAACCTTGTTATATCCGAGGAGATACTCCAACCCTGGTTTTATTTCCAAGACACCAATT
66 ATACTCCAACCCCGTTATTTCTGAGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATT
* * *
3648142 TTTCACAATCGGGGATGCTCCAACTCCG
131 TTTCACAATCGGGGATACTCTAACCCCG
* * *
3648170 TTATTTTCGAGAGGATACTTCAACCCCGATTTTATTTCCAAAACACTAATTTTTCACAATCGAGG
1 TTATTTTCGAGGGGATACTTCAACCCCGATTTTATTTCCAAAACACTAATTTTCCACAATCGGGG
* * * **
3648235 ATACTCCAACCCCGTTTTTTC-GAGGGGATACTCCGACCCCGATTTTATTTTCAAAACATTAATT
66 ATACTCCAACCCCGTTATTTCTGAGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATT
*
3648299 TTTCACAATCGAGGATACTCTAACCCCG
131 TTTCACAATCGGGGATACTCTAACCCCG
* *
3648327 TTATTTTTGAGGGGATACTTCAACCCTGATTTTATTTCCAAAACACTAATTTTCCACAATCGGGG
1 TTATTTTCGAGGGGATACTTCAACCCCGATTTTATTTCCAAAACACTAATTTTCCACAATCGGGG
* ***
3648392 ATACTCCAACCCCGTTATTTCTGAGGGGATACTCCAACTCCGATTTTATTTTTGAAACACCAATT
66 ATACTCCAACCCCGTTATTTCTGAGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATT
*
3648457 TTTCACAATCGGGGATACTCTAATCCCG
131 TTTCACAATCGGGGATACTCTAACCCCG
* * * * * * *
3648485 TTATTTTTGAGGGGATAC-TCGAA-CCCAATTTTATTTCTAAAACATTGATTTTCCACCATTGGG
1 TTATTTTCGAGGGGATACTTC-AACCCCGATTTTATTTCCAAAACACTAATTTTCCACAATCGGG
* * * *
3648548 GATACTCCAACCCCGTTATTTCTTAGGGGGTACTCCAACCCCGTTTTTATCTCCAAAA
65 GATACTCCAACCCCGTTATTTCTGAGGGGATACTCCAACCCCGATTTTATTTCCAAAA
3648606 TATTAAATTT
Statistics
Matches: 380, Mismatches: 54, Indels: 5
0.87 0.12 0.01
Matches are distributed among these distances:
157 224 0.59
158 156 0.41
ACGTcount: A:0.27, C:0.25, G:0.14, T:0.34
Consensus pattern (158 bp):
TTATTTTCGAGGGGATACTTCAACCCCGATTTTATTTCCAAAACACTAATTTTCCACAATCGGGG
ATACTCCAACCCCGTTATTTCTGAGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATT
TTTCACAATCGGGGATACTCTAACCCCG
Found at i:3648437 original size:236 final size:237
Alignment explanation
Indices: 3648012--3648605 Score: 730
Period size: 236 Copynumber: 2.5 Consensus size: 237
3648002 ATTCATATTT
* * * * * ** *
3648012 TTATTTCCGAGGGGATACTCCAACTCCGGTTTTATTTCCAAAACACCAATTTTTCATAATTGGGG
1 TTATTTTCGAGGGGATACTCCGACCCCGATTTTATTTTCAAAACATTAATTTTTCACAATTGGGG
** * ** * * *
3648077 ATACTCCAACCTTGTTATATCCGAGGAGATACTCCAACCCTGGTTTTATTTCCAAGACACCAATT
66 ATACTCCAACCCCGTTATTTTTGAGGGGATACTCCAACCCTGATTTTATTTCCAAAACACCAATT
* * * *
3648142 TTTCACAATCGGGGATGCTCCAACTCCGTTATTTTCGAGAGGATACTTCAACCCCGATTTTATTT
131 TTCCACAATCGGGGATACTCCAACCCCGTTATTTTCGAGAGGATACTCCAACCCCGATTTTATTT
*
3648207 CCAAAACACTAATTTTTCACAATCGAGGATACTCCAACCCCG
196 CCAAAACACCAATTTTTCACAATCGAGGATACTCCAACCCCG
* *
3648249 TT-TTTTCGAGGGGATACTCCGACCCCGATTTTATTTTCAAAACATTAATTTTTCACAATCGAGG
1 TTATTTTCGAGGGGATACTCCGACCCCGATTTTATTTTCAAAACATTAATTTTTCACAATTGGGG
* * *
3648313 ATACTCTAACCCCGTTATTTTTGAGGGGATACTTCAACCCTGATTTTATTTCCAAAACACTAATT
66 ATACTCCAACCCCGTTATTTTTGAGGGGATACTCCAACCCTGATTTTATTTCCAAAACACCAATT
* *
3648378 TTCCACAATCGGGGATACTCCAACCCCGTTA-TTTCTGAGGGGATACTCCAACTCCGATTTTATT
131 TTCCACAATCGGGGATACTCCAACCCCGTTATTTTC-GAGAGGATACTCCAACCCCGATTTTATT
*** * * *
3648442 TTTGAAACACCAATTTTTCACAATCGGGGATACTCTAATCCCG
195 TCCAAAACACCAATTTTTCACAATCGAGGATACTCCAACCCCG
* * * * * *
3648485 TTATTTTTGAGGGGATACT-CGAACCCAATTTTA-TTTCTAAAACATTGATTTTCCACCATTGGG
1 TTATTTTCGAGGGGATACTCCGACCCCGATTTTATTTTC-AAAACATTAATTTTTCACAATTGGG
* * * *
3648548 GATACTCCAACCCCGTTATTTCTT-AGGGGGTACTCCAACCCCGTTTTTATCTCCAAAA
65 GATACTCCAACCCCGTTATTT-TTGAGGGGATACTCCAACCCTGATTTTATTTCCAAAA
3648606 TATTAAATTT
Statistics
Matches: 305, Mismatches: 48, Indels: 9
0.84 0.13 0.02
Matches are distributed among these distances:
235 8 0.03
236 278 0.91
237 19 0.06
ACGTcount: A:0.27, C:0.25, G:0.14, T:0.34
Consensus pattern (237 bp):
TTATTTTCGAGGGGATACTCCGACCCCGATTTTATTTTCAAAACATTAATTTTTCACAATTGGGG
ATACTCCAACCCCGTTATTTTTGAGGGGATACTCCAACCCTGATTTTATTTCCAAAACACCAATT
TTCCACAATCGGGGATACTCCAACCCCGTTATTTTCGAGAGGATACTCCAACCCCGATTTTATTT
CCAAAACACCAATTTTTCACAATCGAGGATACTCCAACCCCG
Found at i:3653191 original size:14 final size:15
Alignment explanation
Indices: 3653167--3653202 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
3653157 TCTACAATCT
3653167 CTCCTAAATAAACAC
1 CTCCTAAATAAACAC
3653182 CTCC-AAATAAACAC
1 CTCCTAAATAAACAC
3653196 CT-CTAAA
1 CTCCTAAA
3653203 CACTTCTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 1 0.05
14 15 0.75
15 4 0.20
ACGTcount: A:0.47, C:0.33, G:0.00, T:0.19
Consensus pattern (15 bp):
CTCCTAAATAAACAC
Found at i:3653815 original size:22 final size:21
Alignment explanation
Indices: 3653790--3653837 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
3653780 ATAGCCAACA
3653790 TTTTCATGAATG-TCATTCATTG
1 TTTTCATGAATGTTCA-TCA-TG
* *
3653812 TTTTCTTGCATGTTCATCATG
1 TTTTCATGAATGTTCATCATG
3653833 TTTTC
1 TTTTC
3653838 CATGTCAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 7 0.30
22 13 0.57
23 3 0.13
ACGTcount: A:0.17, C:0.17, G:0.12, T:0.54
Consensus pattern (21 bp):
TTTTCATGAATGTTCATCATG
Found at i:3663382 original size:33 final size:33
Alignment explanation
Indices: 3663315--3663383 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
3663305 CCGTTACAAG
* **
3663315 CAATGTATCGATACAATTCATCATGTATTGATA
1 CAATGTATCGATACAATTCACCATGTATCAATA
*
3663348 CAATGTATCGATAC-ATTGTACCATGTATCAATA
1 CAATGTATCGATACAATT-CACCATGTATCAATA
3663381 CAA
1 CAA
3663384 ATAGTGGTAG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 3 0.10
33 28 0.90
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (33 bp):
CAATGTATCGATACAATTCACCATGTATCAATA
Found at i:3663449 original size:13 final size:13
Alignment explanation
Indices: 3663431--3663457 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3663421 TACAATGAAC
3663431 ATGTATCGATACA
1 ATGTATCGATACA
3663444 ATGTATCGATACA
1 ATGTATCGATACA
3663457 A
1 A
3663458 AGCATAATAT
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:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3669968 original size:21 final size:21
Alignment explanation
Indices: 3669926--3669968 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
3669916 CTTGTTTTTC
* *
3669926 TTAGCTAATTCATTATTTTCA
1 TTAGCTAATTCATTAATATCA
**
3669947 TTAGCTAATTTTTTAATATCA
1 TTAGCTAATTCATTAATATCA
3669968 T
1 T
3669969 CTTGCAATTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.12, G:0.05, T:0.53
Consensus pattern (21 bp):
TTAGCTAATTCATTAATATCA
Found at i:3670124 original size:15 final size:15
Alignment explanation
Indices: 3670086--3670124 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
3670076 TTTCAATTTT
*
3670086 AATAATTTTTTCTTC
1 AATAATTTTGTCTTC
* *
3670101 AAGATTTTTGTCTTC
1 AATAATTTTGTCTTC
3670116 AATAATTTT
1 AATAATTTT
3670125 TAACTTATTT
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.28, C:0.10, G:0.05, T:0.56
Consensus pattern (15 bp):
AATAATTTTGTCTTC
Found at i:3672248 original size:20 final size:20
Alignment explanation
Indices: 3672223--3672282 Score: 77
Period size: 19 Copynumber: 3.0 Consensus size: 20
3672213 CTACCAATTT
3672223 CATGTATCGATACAATTATC
1 CATGTATCGATACAATTATC
* **
3672243 CATGTATCAATACAA-TAAA
1 CATGTATCGATACAATTATC
3672262 CATGTATCGATACAATGTATC
1 CATGTATCGATACAAT-TATC
3672283 GATACAAAGC
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
19 16 0.50
20 14 0.44
21 2 0.06
ACGTcount: A:0.40, C:0.18, G:0.10, T:0.32
Consensus pattern (20 bp):
CATGTATCGATACAATTATC
Found at i:3672281 original size:13 final size:13
Alignment explanation
Indices: 3672263--3672289 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3672253 TACAATAAAC
3672263 ATGTATCGATACA
1 ATGTATCGATACA
3672276 ATGTATCGATACA
1 ATGTATCGATACA
3672289 A
1 A
3672290 AGCATAATGT
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:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3677303 original size:20 final size:20
Alignment explanation
Indices: 3677278--3677339 Score: 81
Period size: 20 Copynumber: 3.0 Consensus size: 20
3677268 AAATTTAACT
3677278 AGATGTATCGATACATTGAA
1 AGATGTATCGATACATTGAA
**
3677298 AGATGTATCGATACATCTAGGT
1 AGATGTATCGATACAT-T-GAA
3677320 A-ATGTATCGATACATTGAA
1 AGATGTATCGATACATTGAA
3677339 A
1 A
3677340 AAATATATCA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
19 2 0.06
20 17 0.47
21 15 0.42
22 2 0.06
ACGTcount: A:0.39, C:0.11, G:0.19, T:0.31
Consensus pattern (20 bp):
AGATGTATCGATACATTGAA
Found at i:3677337 original size:41 final size:42
Alignment explanation
Indices: 3677280--3677363 Score: 125
Period size: 42 Copynumber: 2.0 Consensus size: 42
3677270 ATTTAACTAG
* * *
3677280 ATGTATCGATACATTG-AAAGATGTATCGATACATCTAGGTA
1 ATGTATCGATACATTGAAAAAATATATCAATACATCTAGGTA
*
3677321 ATGTATCGATACATTGAAAAAATATATCAATACATCTGGGTA
1 ATGTATCGATACATTGAAAAAATATATCAATACATCTAGGTA
3677363 A
1 A
3677364 AAATGTGACT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
41 16 0.42
42 22 0.58
ACGTcount: A:0.40, C:0.12, G:0.17, T:0.31
Consensus pattern (42 bp):
ATGTATCGATACATTGAAAAAATATATCAATACATCTAGGTA
Found at i:3677348 original size:21 final size:21
Alignment explanation
Indices: 3677280--3677355 Score: 75
Period size: 21 Copynumber: 3.7 Consensus size: 21
3677270 ATTTAACTAG
*
3677280 ATGTATCGATACATTG-AAAG
1 ATGTATCGATACATTGAAAAA
***
3677300 ATGTATCGATACATCT-AGGTA
1 ATGTATCGATACAT-TGAAAAA
3677321 ATGTATCGATACATTGAAAAA
1 ATGTATCGATACATTGAAAAA
* *
3677342 ATATATCAATACAT
1 ATGTATCGATACAT
3677356 CTGGGTAAAA
Statistics
Matches: 44, Mismatches: 9, Indels: 5
0.76 0.16 0.09
Matches are distributed among these distances:
20 15 0.34
21 29 0.66
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.32
Consensus pattern (21 bp):
ATGTATCGATACATTGAAAAA
Found at i:3681067 original size:13 final size:13
Alignment explanation
Indices: 3681049--3681074 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3681039 TACACACAGT
3681049 ATGTATCGATACA
1 ATGTATCGATACA
3681062 ATGTATCGATACA
1 ATGTATCGATACA
3681075 CCATAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3681091 original size:33 final size:32
Alignment explanation
Indices: 3681031--3681094 Score: 92
Period size: 33 Copynumber: 2.0 Consensus size: 32
3681021 TAGCCAAACT
**
3681031 TGTATCGATACACACAGTATGTATCGATACAA
1 TGTATCGATACACACAAAATGTATCGATACAA
*
3681063 TGTATCGATACACCATAAAATGTATCGATACA
1 TGTATCGATACA-CACAAAATGTATCGATACA
3681095 TTGGCTTATA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 12 0.43
33 16 0.57
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (32 bp):
TGTATCGATACACACAAAATGTATCGATACAA
Found at i:3682705 original size:3 final size:3
Alignment explanation
Indices: 3682684--3682723 Score: 62
Period size: 3 Copynumber: 13.3 Consensus size: 3
3682674 CATCAAGGAC
* *
3682684 GAT GAA GAT GAT GAA GAT GAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT G
3682724 GTGACTCAGA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.38, C:0.00, G:0.35, T:0.28
Consensus pattern (3 bp):
GAT
Found at i:3685187 original size:16 final size:16
Alignment explanation
Indices: 3685151--3685187 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
3685141 GATAAAAATG
*
3685151 TCCAAATTGAAGAAGC
1 TCCAAAATGAAGAAGC
3685167 T-CAAAATGAAGAAGC
1 TCCAAAATGAAGAAGC
3685182 TCCAAA
1 TCCAAA
3685188 TAAAATTGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 14 0.74
16 5 0.26
ACGTcount: A:0.49, C:0.19, G:0.16, T:0.16
Consensus pattern (16 bp):
TCCAAAATGAAGAAGC
Found at i:3687050 original size:8 final size:8
Alignment explanation
Indices: 3687037--3687076 Score: 80
Period size: 8 Copynumber: 5.0 Consensus size: 8
3687027 ATTTGATTAA
3687037 ATTTTGTG
1 ATTTTGTG
3687045 ATTTTGTG
1 ATTTTGTG
3687053 ATTTTGTG
1 ATTTTGTG
3687061 ATTTTGTG
1 ATTTTGTG
3687069 ATTTTGTG
1 ATTTTGTG
3687077 TTGAATGATG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 32 1.00
ACGTcount: A:0.12, C:0.00, G:0.25, T:0.62
Consensus pattern (8 bp):
ATTTTGTG
Found at i:3687298 original size:13 final size:13
Alignment explanation
Indices: 3687280--3687317 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
3687270 CAGCATTCTT
3687280 TGTATCGATACAA
1 TGTATCGATACAA
* *
3687293 TGTATCAATACAC
1 TGTATCGATACAA
3687306 TGTATCGATACA
1 TGTATCGATACA
3687318 GGAAGATTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3689156 original size:31 final size:31
Alignment explanation
Indices: 3689118--3689226 Score: 148
Period size: 31 Copynumber: 3.5 Consensus size: 31
3689108 ATAAATTTTT
3689118 TGATTAAGGGGGAGAAAGAGATAAGTGCTTA
1 TGATTAAGGGGGAGAAAGAGATAAGTGCTTA
* * * * * *
3689149 TGATTAAGAGGGAGAATGCGAATAAAT-TTTT
1 TGATTAAGGGGGAGAAAGAG-ATAAGTGCTTA
3689180 TGATTAAGGGGGAGAAAGAGATAAGTGCTTA
1 TGATTAAGGGGGAGAAAGAGATAAGTGCTTA
3689211 TGATTAAGGGGGAGAA
1 TGATTAAGGGGGAGAA
3689227 TGCGAATTTA
Statistics
Matches: 64, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
30 5 0.08
31 54 0.84
32 5 0.08
ACGTcount: A:0.39, C:0.03, G:0.34, T:0.25
Consensus pattern (31 bp):
TGATTAAGGGGGAGAAAGAGATAAGTGCTTA
Found at i:3689204 original size:62 final size:62
Alignment explanation
Indices: 3689107--3689233 Score: 245
Period size: 62 Copynumber: 2.0 Consensus size: 62
3689097 AATATGTGCA
3689107 AATAAATTTTTTGATTAAGGGGGAGAAAGAGATAAGTGCTTATGATTAAGAGGGAGAATGCG
1 AATAAATTTTTTGATTAAGGGGGAGAAAGAGATAAGTGCTTATGATTAAGAGGGAGAATGCG
*
3689169 AATAAATTTTTTGATTAAGGGGGAGAAAGAGATAAGTGCTTATGATTAAGGGGGAGAATGCG
1 AATAAATTTTTTGATTAAGGGGGAGAAAGAGATAAGTGCTTATGATTAAGAGGGAGAATGCG
3689231 AAT
1 AAT
3689234 TTATTAAAAT
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 64 1.00
ACGTcount: A:0.39, C:0.03, G:0.31, T:0.28
Consensus pattern (62 bp):
AATAAATTTTTTGATTAAGGGGGAGAAAGAGATAAGTGCTTATGATTAAGAGGGAGAATGCG
Found at i:3689940 original size:13 final size:13
Alignment explanation
Indices: 3689922--3689946 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3689912 ACACACAATA
3689922 TGTATCGATACAT
1 TGTATCGATACAT
3689935 TGTATCGATACA
1 TGTATCGATACA
3689947 CCATAAAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3689943 original size:32 final size:33
Alignment explanation
Indices: 3689902--3689969 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 33
3689892 GTAGCCAAAC
*
3689902 TTGTATCGATACA-CACAATATGTATCGATACA
1 TTGTATCGATACACCACAAAATGTATCGATACA
*
3689934 TTGTATCGATACACCATAAAATGTATCGATACA
1 TTGTATCGATACACCACAAAATGTATCGATACA
3689967 TTG
1 TTG
3689970 GCTTGTAACG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
32 13 0.39
33 20 0.61
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.32
Consensus pattern (33 bp):
TTGTATCGATACACCACAAAATGTATCGATACA
Found at i:3689987 original size:10 final size:10
Alignment explanation
Indices: 3689969--3690003 Score: 61
Period size: 10 Copynumber: 3.5 Consensus size: 10
3689959 TCGATACATT
*
3689969 GGCTTGTAAC
1 GGCTAGTAAC
3689979 GGCTAGTAAC
1 GGCTAGTAAC
3689989 GGCTAGTAAC
1 GGCTAGTAAC
3689999 GGCTA
1 GGCTA
3690004 TATTTTCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.26, C:0.20, G:0.31, T:0.23
Consensus pattern (10 bp):
GGCTAGTAAC
Found at i:3704216 original size:17 final size:17
Alignment explanation
Indices: 3704196--3704231 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
3704186 TTTGATGGTT
3704196 TTTTTTTTTGCTTTTTA
1 TTTTTTTTTGCTTTTTA
*
3704213 TTTTTTTTTGTTTTTTA
1 TTTTTTTTTGCTTTTTA
3704230 TT
1 TT
3704232 CTTATGATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.06, C:0.03, G:0.06, T:0.86
Consensus pattern (17 bp):
TTTTTTTTTGCTTTTTA
Done.