Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A07
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: 93829987
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4250000 characters in sequence are not A, C, G, or T
File 141 of 295
Found at i:43523492 original size:31 final size:31
Alignment explanation
Indices: 43523457--43523525 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
43523447 ATTCACATTT
* * *
43523457 TGATTCTGGTTCTGTTACCCGATACTAATTC
1 TGATTCTGATTCTATCACCCGATACTAATTC
* * *
43523488 TGATTCTGATTCTATCACCTGATTCTGATTC
1 TGATTCTGATTCTATCACCCGATACTAATTC
43523519 TGATTCT
1 TGATTCT
43523526 CATTTTGATT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.19, C:0.22, G:0.14, T:0.45
Consensus pattern (31 bp):
TGATTCTGATTCTATCACCCGATACTAATTC
Found at i:43523495 original size:6 final size:6
Alignment explanation
Indices: 43523484--43523546 Score: 58
Period size: 6 Copynumber: 10.3 Consensus size: 6
43523474 CCCGATACTA
* * *
43523484 ATTCTG ATTCTG ATTCT- ATCACCTG ATTCTG ATTCTG ATTCTC ATTTTG
1 ATTCTG ATTCTG ATTCTG AT--TCTG ATTCTG ATTCTG ATTCTG ATTCTG
43523533 ATTCT- AGTTCTG AT
1 ATTCTG A-TTCTG AT
43523547 AATGTTTCTT
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
5 3 0.07
6 38 0.83
7 3 0.07
8 2 0.04
ACGTcount: A:0.19, C:0.19, G:0.13, T:0.49
Consensus pattern (6 bp):
ATTCTG
Found at i:43529339 original size:43 final size:42
Alignment explanation
Indices: 43529211--43529352 Score: 126
Period size: 43 Copynumber: 3.3 Consensus size: 42
43529201 ATATGTGTTA
* * **
43529211 TCGTGTAAGACCACGTTTGGGATGTTGGCATCGAT-TTGTGATT
1 TCGTGTAAGACCATGTCTGGGA-CATGGCATCGATATT-TGATT
* ** *
43529254 TACGTGTAAGACCATGTCTGTGACATCCTCATCG-TATATGATT
1 T-CGTGTAAGACCATGTCTGGGACAT-GGCATCGATATTTGATT
*
43529297 TCGTGTAAGACCCTGTCTGGGACAATGGCATCGATATTTGATT
1 TCGTGTAAGACCATGTCTGGGAC-ATGGCATCGATATTTGATT
* *
43529340 ACATGTAAGACCA
1 TCGTGTAAGACCA
43529353 CATCTAGGAT
Statistics
Matches: 78, Mismatches: 16, Indels: 10
0.75 0.15 0.10
Matches are distributed among these distances:
42 25 0.32
43 29 0.37
44 24 0.31
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (42 bp):
TCGTGTAAGACCATGTCTGGGACATGGCATCGATATTTGATT
Found at i:43533975 original size:27 final size:27
Alignment explanation
Indices: 43533945--43534122 Score: 171
Period size: 27 Copynumber: 6.6 Consensus size: 27
43533935 ATATTGAGCC
* *
43533945 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* * *
43533972 CGCACACTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
43533999 CGCACACTTAGTGCTACATAGTCAGACT
1 CGCACACTTAGTGCTACATAATCA-ACT
** ** *
43534027 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
43534054 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* *
43534081 CGCACACTTAGTGCAACATAGTCGAA-T
1 CGCACACTTAGTGCTACATAATC-AACT
43534108 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
43534123 GTACAATTTA
Statistics
Matches: 127, Mismatches: 20, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
27 102 0.80
28 25 0.20
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:43534084 original size:82 final size:81
Alignment explanation
Indices: 43533966--43534121 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 81
43533956 TGCTATATAA
* * *
43533966 TCAACTCGCACACTTAGTGCCACGTAATCAAATCGCACACTTAGTGCTACATAGTCAGACTCGCA
1 TCAACTCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCAACATAGTC-GAATCGCA
43534031 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
43534048 TCAATTCGCACACTTAGTG-CATCATATTCATTTCGCACACTTAGTGCAACATAGTCGAATCGCA
1 TCAACTCGCACACTTAGTGCCA-CATAATCAAATCGCACACTTAGTGCAACATAGTCGAATCGCA
43534112 CACTTAGTGC
65 CACTTAGTGC
43534122 TGTACAATTT
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 19 0.29
82 47 0.71
ACGTcount: A:0.28, C:0.29, G:0.17, T:0.26
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCAACATAGTCGAATCGCAC
ACTTAGTGCCGCATGG
Found at i:43538502 original size:16 final size:16
Alignment explanation
Indices: 43538464--43538505 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
43538454 TATTAAGGAC
* *
43538464 TAAATTAAGAAATTTG
1 TAAATTGAGGAATTTG
43538480 TAAATTGAGGAATTTG
1 TAAATTGAGGAATTTG
43538496 TAAATTGAGG
1 TAAATTGAGG
43538506 GGTCAAAATG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.00, G:0.21, T:0.36
Consensus pattern (16 bp):
TAAATTGAGGAATTTG
Found at i:43539188 original size:42 final size:43
Alignment explanation
Indices: 43539112--43539220 Score: 125
Period size: 42 Copynumber: 2.6 Consensus size: 43
43539102 GATTTGTGAT
*
43539112 TTACGTGTAAGACCATGTCTGGGACATCGACATC-GTATATGA
1 TTACGTGTAAGACCCTGTCTGGGACATCGACATCGGTATATGA
** * *
43539154 TTTTGTGTAAGACCCTGTCTGGGACAGT-GGCATCGGTATTTGA
1 TTACGTGTAAGACCCTGTCTGGGACA-TCGACATCGGTATATGA
*
43539197 TTACATGTAAGACCAC-GTCTGGGA
1 TTACGTGTAAGACC-CTGTCTGGGA
43539221 TGCTGACATT
Statistics
Matches: 56, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
42 28 0.50
43 27 0.48
44 1 0.02
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (43 bp):
TTACGTGTAAGACCCTGTCTGGGACATCGACATCGGTATATGA
Found at i:43540901 original size:98 final size:98
Alignment explanation
Indices: 43540710--43540919 Score: 307
Period size: 98 Copynumber: 2.2 Consensus size: 98
43540700 CATGTGTGGC
** * * *
43540710 CCACAGCCTTGGCACAC-GGCGTGTGTGGCTAATTTGAATGGTACACGGGCTAGACATACAGGCG
1 CCACAGCCAAGGCATACGGGCGAGTGTGGCTAATTTGAATGGTACACGGGCTAGACACACAGGCG
43540774 TGTAGTTAGCTGTGTGACCCAAGTCAGTTTCGA
66 TGTAGTTAGCTGTGTGACCCAAGTCAGTTTCGA
* *
43540807 CCACGGCCAAGGCATACGGGCGAGTGTGGCT-ATTTCGAATGGTACACGGGCTAGACACACGGGC
1 CCACAGCCAAGGCATACGGGCGAGTGTGGCTAATTT-GAATGGTACACGGGCTAGACACACAGGC
* * *
43540871 GTGTGGTTAGTTGTGTGACCTAAGTCAGTTTCGA
65 GTGTAGTTAGCTGTGTGACCCAAGTCAGTTTCGA
43540905 CCACAGCCAAGGCAT
1 CCACAGCCAAGGCAT
43540920 TATGCCCTGT
Statistics
Matches: 100, Mismatches: 11, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
97 17 0.17
98 83 0.83
ACGTcount: A:0.23, C:0.23, G:0.31, T:0.23
Consensus pattern (98 bp):
CCACAGCCAAGGCATACGGGCGAGTGTGGCTAATTTGAATGGTACACGGGCTAGACACACAGGCG
TGTAGTTAGCTGTGTGACCCAAGTCAGTTTCGA
Found at i:43548825 original size:80 final size:80
Alignment explanation
Indices: 43548692--43548852 Score: 304
Period size: 80 Copynumber: 2.0 Consensus size: 80
43548682 TTTGAGACAG
*
43548692 TTGAAAATGCAACTAGGATTTTTGGTAATCAAACTGAAAATATAGCTACTAATGAAATTAAAACC
1 TTGAAAATACAACTAGGATTTTTGGTAATCAAACTGAAAATATAGCTACTAATGAAATTAAAACC
43548757 GAATATACAAGAGAA
66 GAATATACAAGAGAA
43548772 TTGAAAATACAACTAGGATTTTTGGTAATCAAACTGAAAATATAGCTACTAATGAAATTAAAACC
1 TTGAAAATACAACTAGGATTTTTGGTAATCAAACTGAAAATATAGCTACTAATGAAATTAAAACC
*
43548837 GAATATACAGGAGAA
66 GAATATACAAGAGAA
43548852 T
1 T
43548853 CTTCTAATCA
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
80 79 1.00
ACGTcount: A:0.47, C:0.11, G:0.15, T:0.27
Consensus pattern (80 bp):
TTGAAAATACAACTAGGATTTTTGGTAATCAAACTGAAAATATAGCTACTAATGAAATTAAAACC
GAATATACAAGAGAA
Found at i:43553997 original size:28 final size:28
Alignment explanation
Indices: 43553957--43554035 Score: 104
Period size: 28 Copynumber: 2.8 Consensus size: 28
43553947 GCAATCAAAG
* * *
43553957 ATGGTACTCAGTGTACGAAATATTGAGA
1 ATGGCACTTAGTGTGCGAAATATTGAGA
*
43553985 ATGGCACTTAGTGTGCGAGATATTGAGA
1 ATGGCACTTAGTGTGCGAAATATTGAGA
* *
43554013 ATGACACTTAGTGTGCAAAATAT
1 ATGGCACTTAGTGTGCGAAATAT
43554036 CGAATGATTC
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.34, C:0.11, G:0.25, T:0.29
Consensus pattern (28 bp):
ATGGCACTTAGTGTGCGAAATATTGAGA
Found at i:43558889 original size:56 final size:56
Alignment explanation
Indices: 43558759--43558892 Score: 214
Period size: 56 Copynumber: 2.4 Consensus size: 56
43558749 CAAACAAGGC
* * *
43558759 CTTACTCGCACACATATACCGGAATCACATATCGATGCCAACGTATTAAACGTGGT
1 CTTACTCGCACACATATATCGAAATCACATATCGATGCCAACATATTAAACGTGGT
*
43558815 CTTACTTGCACACATATATCGAAATCACATATCGATGCCAACATATTAAACGTGGT
1 CTTACTCGCACACATATATCGAAATCACATATCGATGCCAACATATTAAACGTGGT
**
43558871 CTTACTCAAACACATATATCGA
1 CTTACTCGCACACATATATCGA
43558893 TGCCATGGTC
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
56 71 1.00
ACGTcount: A:0.35, C:0.25, G:0.13, T:0.27
Consensus pattern (56 bp):
CTTACTCGCACACATATATCGAAATCACATATCGATGCCAACATATTAAACGTGGT
Found at i:43563604 original size:15 final size:16
Alignment explanation
Indices: 43563584--43563617 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
43563574 AGATTTATAC
*
43563584 ATTATCACTGA-TTTG
1 ATTATCACCGATTTTG
43563599 ATTATCACCGATTTTG
1 ATTATCACCGATTTTG
43563615 ATT
1 ATT
43563618 CAATTTTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.26, C:0.15, G:0.12, T:0.47
Consensus pattern (16 bp):
ATTATCACCGATTTTG
Found at i:43565965 original size:38 final size:38
Alignment explanation
Indices: 43565882--43565980 Score: 117
Period size: 38 Copynumber: 2.6 Consensus size: 38
43565872 TGAATATAAT
* * * **
43565882 AATTATAATTACCATAATTATAATAATTTTTTACCAAA
1 AATTACAATTACAATAATTATAATAATATTCGACCAAA
* * **
43565920 AAATACAATTACAATAATTATAATAATATTCGATCGCA
1 AATTACAATTACAATAATTATAATAATATTCGACCAAA
43565958 AATTACAATTACAATAATTATAA
1 AATTACAATTACAATAATTATAA
43565981 CAAGGATTTC
Statistics
Matches: 51, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
38 51 1.00
ACGTcount: A:0.51, C:0.11, G:0.02, T:0.36
Consensus pattern (38 bp):
AATTACAATTACAATAATTATAATAATATTCGACCAAA
Found at i:43575409 original size:9 final size:9
Alignment explanation
Indices: 43575382--43575417 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
43575372 TTATTAAATT
43575382 ATATATTTA
1 ATATATTTA
43575391 AT-TA--TA
1 ATATATTTA
43575397 ATATATTTA
1 ATATATTTA
43575406 ATATATTTA
1 ATATATTTA
43575415 ATA
1 ATA
43575418 ATAATTATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
6 4 0.17
7 2 0.08
8 2 0.08
9 16 0.67
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (9 bp):
ATATATTTA
Found at i:43575409 original size:24 final size:26
Alignment explanation
Indices: 43575382--43575446 Score: 80
Period size: 24 Copynumber: 2.5 Consensus size: 26
43575372 TTATTAAATT
43575382 ATATATTTAATTATAA-TATATTT-A
1 ATATATTTAATTATAATTATATTTAA
* *
43575406 ATATATTTAATAATAATTATGTTTAA
1 ATATATTTAATTATAATTATATTTAA
*
43575432 ATATGATTAAATTAT
1 ATAT-ATTTAATTAT
43575447 TTATTTTTGA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
24 15 0.44
25 6 0.18
26 5 0.15
27 8 0.24
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (26 bp):
ATATATTTAATTATAATTATATTTAA
Found at i:43575622 original size:44 final size:45
Alignment explanation
Indices: 43575573--43575667 Score: 131
Period size: 45 Copynumber: 2.1 Consensus size: 45
43575563 TTACACCTCT
*
43575573 ATTACATTCAACCAAACA-CAGTTTTACTATTACGA-CTCTATTCC
1 ATTACATTCAACCAAACAGCAGATTTACTATTAC-ACCTCTATTCC
** *
43575617 ATTACATTCAACCAAACAGTTGATTTGCTATTACACCTCTATTCC
1 ATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCC
43575662 ATTACA
1 ATTACA
43575668 CCTCTAATCC
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
44 19 0.42
45 26 0.58
ACGTcount: A:0.34, C:0.26, G:0.05, T:0.35
Consensus pattern (45 bp):
ATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCC
Found at i:43575667 original size:16 final size:16
Alignment explanation
Indices: 43575648--43575699 Score: 86
Period size: 16 Copynumber: 3.2 Consensus size: 16
43575638 GATTTGCTAT
* *
43575648 TACACCTCTATTCCAT
1 TACACCTCTAATCCAA
43575664 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
43575680 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
43575696 TACA
1 TACA
43575700 GCGAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.35, C:0.37, G:0.00, T:0.29
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:43575981 original size:11 final size:12
Alignment explanation
Indices: 43575958--43575992 Score: 54
Period size: 11 Copynumber: 3.0 Consensus size: 12
43575948 ATTATAAAAT
43575958 CATAAAATATTA
1 CATAAAATATTA
*
43575970 CA-AAAATCTTA
1 CATAAAATATTA
43575981 CATAAAATATTA
1 CATAAAATATTA
43575993 AAAATTATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.31
Consensus pattern (12 bp):
CATAAAATATTA
Found at i:43576047 original size:19 final size:20
Alignment explanation
Indices: 43575982--43576073 Score: 98
Period size: 20 Copynumber: 4.7 Consensus size: 20
43575972 AAAATCTTAC
* *
43575982 ATAAAATATTAAAAATTAT-
1 ATAAATTATAAAAAATTATA
* *
43576001 TTAAACTTATAAAAAATTATT
1 ATAAA-TTATAAAAAATTATA
*
43576022 ATAAATTCTAAAAAATTATA
1 ATAAATTATAAAAAATTATA
43576042 AT-AATTATAAAAAATTATA
1 ATAAATTATAAAAAATTATA
* *
43576061 AAAAAATATAAAA
1 ATAAATTATAAAA
43576074 TTTCTTAAAA
Statistics
Matches: 61, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
19 21 0.34
20 36 0.59
21 4 0.07
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (20 bp):
ATAAATTATAAAAAATTATA
Found at i:43576049 original size:9 final size:9
Alignment explanation
Indices: 43575931--43576133 Score: 79
Period size: 10 Copynumber: 20.8 Consensus size: 9
43575921 CATTTGTCTA
43575931 ATAAAAATAT
1 ATAAAAAT-T
43575941 ATAAAAGATT
1 ATAAAA-ATT
*
43575951 AT-AAAATC
1 ATAAAAATT
43575959 ATAAAATATT
1 ATAAAA-ATT
*
43575969 ACAAAAATCT
1 ATAAAAAT-T
*
43575979 -TACATAAAAT
1 ATA-A-AAATT
43575989 ATTAAAAATT
1 A-TAAAAATT
* *
43575999 ATTTAAACTT
1 A-TAAAAATT
43576009 ATAAAAAATT
1 AT-AAAAATT
*
43576019 ATTATAAATT
1 A-TAAAAATT
*
43576029 CTAAAAAATT
1 AT-AAAAATT
*
43576039 ATAATAATT
1 ATAAAAATT
43576048 ATAAAAAATT
1 AT-AAAAATT
*
43576058 ATAAAAAAAT
1 AT-AAAAATT
*
43576068 ATAAAATTT
1 ATAAAAATT
* **
43576077 CTTAAAAGCCT
1 -ATAAAA-ATT
43576088 ATAAAAATT
1 ATAAAAATT
*
43576097 ATAATTTAATT
1 ATAA--AAATT
43576108 A-AAAATATAT
1 ATAAAA-AT-T
*
43576118 ATATAAATT
1 ATAAAAATT
43576127 ATAAAAA
1 ATAAAAA
43576134 AATTTAGGGG
Statistics
Matches: 145, Mismatches: 29, Indels: 39
0.68 0.14 0.18
Matches are distributed among these distances:
8 5 0.03
9 38 0.26
10 84 0.58
11 16 0.11
12 2 0.01
ACGTcount: A:0.60, C:0.04, G:0.01, T:0.34
Consensus pattern (9 bp):
ATAAAAATT
Found at i:43576057 original size:29 final size:28
Alignment explanation
Indices: 43576013--43576075 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 28
43576003 AAACTTATAA
* * * *
43576013 AAAATTATTATAAATTCTAAAAAATTAT
1 AAAATTATAAAAAATTATAAAAAAATAT
43576041 AATAATTATAAAAAATTATAAAAAAATAT
1 AA-AATTATAAAAAATTATAAAAAAATAT
43576070 AAAATT
1 AAAATT
43576076 TCTTAAAAGC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 6 0.20
29 24 0.80
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (28 bp):
AAAATTATAAAAAATTATAAAAAAATAT
Found at i:43576197 original size:9 final size:9
Alignment explanation
Indices: 43576169--43576408 Score: 92
Period size: 10 Copynumber: 24.8 Consensus size: 9
43576159 AATACATGAC
43576169 TTTTTATAA
1 TTTTTATAA
* *
43576178 CTATTAT-A
1 TTTTTATAA
43576186 TTTTTATAA
1 TTTTTATAA
*
43576195 TTTTTATAG
1 TTTTTATAA
* ** *
43576204 CTAATACAA
1 TTTTTATAA
*
43576213 GTTTGTATAAA
1 -TTTTTAT-AA
*
43576224 TTTTTAAATA
1 TTTTTATA-A
43576234 TTTTTA-ATA
1 TTTTTATA-A
*
43576243 TGTTTTATATT
1 T-TTTTATA-A
*
43576254 TTTTTATTA
1 TTTTTATAA
*
43576263 TTCTTATAA
1 TTTTTATAA
43576272 TTTTTTTATAA
1 --TTTTTATAA
*
43576283 TTTAT-TAA
1 TTTTTATAA
43576291 TTTTT-TAA
1 TTTTTATAA
43576299 TTTTATATAA
1 TTTT-TATAA
43576309 GTTTTTATAA
1 -TTTTTATAA
*
43576319 TATTTATAA
1 TTTTTATAA
*
43576328 TATTTTATGAT
1 T-TTTTAT-AA
43576339 TTTCCTTATAA
1 TTT--TTATAA
*
43576350 GTTTTATAA
1 TTTTTATAA
43576359 GTTTTTTGTATAA
1 ---TTTT-TATAA
**
43576372 AATTTATAA
1 TTTTTATAA
*
43576381 CTTTATATAAA
1 -TTTTTAT-AA
43576392 TTTTTAATAA
1 TTTTT-ATAA
43576402 TTTTTAT
1 TTTTTAT
43576409 TAGAAAATTG
Statistics
Matches: 173, Mismatches: 36, Indels: 44
0.68 0.14 0.17
Matches are distributed among these distances:
8 20 0.12
9 57 0.33
10 58 0.34
11 26 0.15
12 7 0.04
13 5 0.03
ACGTcount: A:0.33, C:0.03, G:0.04, T:0.60
Consensus pattern (9 bp):
TTTTTATAA
Found at i:43576297 original size:18 final size:19
Alignment explanation
Indices: 43576248--43576340 Score: 77
Period size: 19 Copynumber: 4.9 Consensus size: 19
43576238 TAATATGTTT
* *
43576248 TATATTTTTTTATTATTCT-
1 TATAATTTTTTATAATT-TA
43576267 TATAATTTTTTTATAATTTA
1 TATAA-TTTTTTATAATTTA
*
43576287 T-TAATTTTTTA-ATTTTA
1 TATAATTTTTTATAATTTA
*
43576304 TATAAGTTTTTATAATATT-
1 TATAATTTTTTATAAT-TTA
* *
43576323 TATAATATTTTATGATTT
1 TATAATTTTTTATAATTT
43576341 TCCTTATAAG
Statistics
Matches: 61, Mismatches: 8, Indels: 11
0.76 0.10 0.14
Matches are distributed among these distances:
17 6 0.10
18 18 0.30
19 23 0.38
20 14 0.23
ACGTcount: A:0.31, C:0.01, G:0.02, T:0.66
Consensus pattern (19 bp):
TATAATTTTTTATAATTTA
Found at i:43576313 original size:19 final size:18
Alignment explanation
Indices: 43576267--43576326 Score: 59
Period size: 18 Copynumber: 3.1 Consensus size: 18
43576257 TTATTATTCT
*
43576267 TATAATTTTTTTATAATTTA
1 TATAA-TTTTTTA-ATTTTA
43576287 T-TAATTTTTTAATTTTA
1 TATAATTTTTTAATTTTA
43576304 TATAAGTTTTTATAATATTTA
1 TATAA-TTTTT-TAAT-TTTA
43576325 TA
1 TA
43576327 ATATTTTATG
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
17 6 0.17
18 10 0.29
19 8 0.23
20 5 0.14
21 6 0.17
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (18 bp):
TATAATTTTTTAATTTTA
Found at i:43580435 original size:27 final size:27
Alignment explanation
Indices: 43580405--43580705 Score: 355
Period size: 27 Copynumber: 11.2 Consensus size: 27
43580395 TAATAAAGAG
*
43580405 AAATTACTAAAATACCCTTGATTTGTA
1 AAATTACTAAAATACCCTCGATTTGTA
*
43580432 AAATTA-TCAAAATACCCCCGATTTGTA
1 AAATTACT-AAAATACCCTCGATTTGTA
* *
43580459 AAATTACTGAAATACCCTCGA-TTGTG
1 AAATTACTAAAATACCCTCGATTTGTA
* *
43580485 AAATTACTGAAATACCCTCGA-TTGTG
1 AAATTACTAAAATACCCTCGATTTGTA
* *
43580511 AAATTACCAAAATACCCCCGATTTGTA
1 AAATTACTAAAATACCCTCGATTTGTA
* *
43580538 AAATTACTGAAACACCCTCGATTTGTA
1 AAATTACTAAAATACCCTCGATTTGTA
* * *
43580565 AAATTACCT-AAACACCCTCAATTTGTG
1 AAATTA-CTAAAATACCCTCGATTTGTA
* *
43580592 AAATTACGAAAACACCCTCGATTTGTA
1 AAATTACTAAAATACCCTCGATTTGTA
*
43580619 AAATTACTGAAATACCCTCGATTTGTA
1 AAATTACTAAAATACCCTCGATTTGTA
*
43580646 AAATTAAC-GAAATACCCTCGATTTGTA
1 AAATT-ACTAAAATACCCTCGATTTGTA
43580673 AAATTACTGAAACAT-CCC-CGATTTGTA
1 AAATTACT-AAA-ATACCCTCGATTTGTA
43580700 AAATTA
1 AAATTA
43580706 TCGAAATAAC
Statistics
Matches: 243, Mismatches: 22, Indels: 18
0.86 0.08 0.06
Matches are distributed among these distances:
26 52 0.21
27 179 0.74
28 10 0.04
29 2 0.01
ACGTcount: A:0.39, C:0.21, G:0.10, T:0.30
Consensus pattern (27 bp):
AAATTACTAAAATACCCTCGATTTGTA
Found at i:43580628 original size:81 final size:80
Alignment explanation
Indices: 43580405--43580713 Score: 403
Period size: 81 Copynumber: 3.8 Consensus size: 80
43580395 TAATAAAGAG
* *
43580405 AAATTACTAAAATACCCTTGATTTGTAAAATTATC-AAAATACCCCCGATTTGTAAAATTACTGA
1 AAATTACT-AAATACCCTCGATTTGTAAAATTA-CGAAAACACCCCCGATTTGTAAAATTACTGA
*
43580469 AATACCCTCGA-TTGTG
64 AATACCCTCGATTTGTA
* * *
43580485 AAATTACTGAAATACCCTCGA-TTGTGAAATTACCAAAATACCCCCGATTTGTAAAATTACTGAA
1 AAATTACT-AAATACCCTCGATTTGTAAAATTACGAAAACACCCCCGATTTGTAAAATTACTGAA
*
43580549 ACACCCTCGATTTGTA
65 ATACCCTCGATTTGTA
* * * *
43580565 AAATTACCTAAACACCCTCAATTTGTGAAATTACGAAAACACCCTCGATTTGTAAAATTACTGAA
1 AAATTA-CTAAATACCCTCGATTTGTAAAATTACGAAAACACCCCCGATTTGTAAAATTACTGAA
43580630 ATACCCTCGATTTGTA
65 ATACCCTCGATTTGTA
* *
43580646 AAATTAACGAAATACCCTCGATTTGTAAAATTACTG-AAACATCCCCGATTTGTAAAATTA-TCG
1 AAATT-ACTAAATACCCTCGATTTGTAAAATTAC-GAAAACACCCCCGATTTGTAAAATTACT-G
43580709 AAATA
63 AAATA
43580714 ACCTTGTAGT
Statistics
Matches: 205, Mismatches: 17, Indels: 13
0.87 0.07 0.06
Matches are distributed among these distances:
78 1 0.00
79 49 0.24
80 40 0.20
81 113 0.55
82 2 0.01
ACGTcount: A:0.39, C:0.20, G:0.10, T:0.30
Consensus pattern (80 bp):
AAATTACTAAATACCCTCGATTTGTAAAATTACGAAAACACCCCCGATTTGTAAAATTACTGAAA
TACCCTCGATTTGTA
Found at i:43581234 original size:11 final size:11
Alignment explanation
Indices: 43581218--43581245 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
43581208 ATTGCATGTA
43581218 TGATATTATTG
1 TGATATTATTG
43581229 TGATATTATTG
1 TGATATTATTG
43581240 TGATAT
1 TGATAT
43581246 GGGCTTTGGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.18, T:0.54
Consensus pattern (11 bp):
TGATATTATTG
Found at i:43581865 original size:17 final size:18
Alignment explanation
Indices: 43581815--43581865 Score: 95
Period size: 18 Copynumber: 2.9 Consensus size: 18
43581805 AGTAAGAAGG
43581815 GTTTTCAATGAAAACATA
1 GTTTTCAATGAAAACATA
43581833 GTTTTCAATGAAAACATA
1 GTTTTCAATGAAAACATA
43581851 GTTTTCAAT-AAAACA
1 GTTTTCAATGAAAACA
43581866 CTTCAATGTG
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
17 6 0.18
18 27 0.82
ACGTcount: A:0.45, C:0.12, G:0.10, T:0.33
Consensus pattern (18 bp):
GTTTTCAATGAAAACATA
Found at i:43583594 original size:49 final size:50
Alignment explanation
Indices: 43583522--43583755 Score: 276
Period size: 49 Copynumber: 4.7 Consensus size: 50
43583512 TGGGGTCACG
43583522 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT-GGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTAGGTCGCA
* * * * * * * *
43583571 TGTGTAGTACTAAGTGCAAGCTACTATGCGTACCCGATAACTTCGATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAA-TTAGGTCGCA
* * ** *
43583622 TGTGTAGTACTAAGTGTAGGCTACTACGTGTATCAGATGGTTAGGTC-AA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTAGGTCGCA
*
43583671 GTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT-GGTCGCA
1 -TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTAGGTCGCA
* * *
43583721 TGTGTAGTACTAAGTGTAGGCTACTATGCGTACCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCA
43583756 CATAGCTTTG
Statistics
Matches: 152, Mismatches: 29, Indels: 8
0.80 0.15 0.04
Matches are distributed among these distances:
49 71 0.47
50 45 0.30
51 36 0.24
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.29
Consensus pattern (50 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTAGGTCGCA
Found at i:43586349 original size:28 final size:27
Alignment explanation
Indices: 43586290--43586352 Score: 81
Period size: 28 Copynumber: 2.3 Consensus size: 27
43586280 TGGGAAGTAG
* *
43586290 TTGGGCCTGAGGGCCATATGAATGTGA
1 TTGGGCCTGAGGGCCATATGAACGAGA
* *
43586317 ATGGGCCTGATGGGCCATGTGAACGAGA
1 TTGGGCCTGA-GGGCCATATGAACGAGA
43586345 TTGGGCCT
1 TTGGGCCT
43586353 AAAGGGGCCA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 9 0.30
28 21 0.70
ACGTcount: A:0.21, C:0.17, G:0.38, T:0.24
Consensus pattern (27 bp):
TTGGGCCTGAGGGCCATATGAACGAGA
Found at i:43586801 original size:80 final size:81
Alignment explanation
Indices: 43586668--43587051 Score: 506
Period size: 80 Copynumber: 4.8 Consensus size: 81
43586658 ATAATAAAGA
* * *
43586668 GAAATTACTAAAATACCCTCGATTTGTAAAATTACTGAAATGCCCTCGATTTGTAAAATTACTGA
1 GAAATTACTGAAATACCCTCGATTTGTAAAATTACCGAAATACCCTCGATTTGTAAAATTACTGA
43586733 AATACCCTCGA-TTGT
66 AATACCCTCGATTTGT
* * **
43586748 GAAATTACTGAAATACCCTCGATTTGTAAAATTACCAAAATACCCCCGATTTGTAAAATTACCAA
1 GAAATTACTGAAATACCCTCGATTTGTAAAATTACCGAAATACCCTCGATTTGTAAAATTACTGA
43586813 AATACCCTCGA-TTGT
66 AATACCCTCGATTTGT
** * * *
43586828 GAAATTACTGAAATACCCTCGATTTGTAAAATTATTGAAATACCCTTGATTTATGAAATTA-TCG
1 GAAATTACTGAAATACCCTCGATTTGTAAAATTACCGAAATACCCTCGATTTGTAAAATTACT-G
*
43586892 AAACACCCTCGATTTGT
65 AAATACCCTCGATTTGT
* * * * * ** * *
43586909 GAAATTACCGAAACACCTTCGATTTGTAAAATTACCTAAACACCCTTAATTTGTAAATTTATTGA
1 GAAATTACTGAAATACCCTCGATTTGTAAAATTACCGAAATACCCTCGATTTGTAAAATTACTGA
*
43586974 AATAGCCTCGATTTGT
66 AATACCCTCGATTTGT
*
43586990 AAAATTA-TCGAAATACCCTCGATTTGTAAAATTACCGAAATACCCTCGATTTGTAAAATTAC
1 GAAATTACT-GAAATACCCTCGATTTGTAAAATTACCGAAATACCCTCGATTTGTAAAATTAC
43587052 CAAAACACTC
Statistics
Matches: 260, Mismatches: 40, Indels: 7
0.85 0.13 0.02
Matches are distributed among these distances:
80 138 0.53
81 121 0.47
82 1 0.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.32
Consensus pattern (81 bp):
GAAATTACTGAAATACCCTCGATTTGTAAAATTACCGAAATACCCTCGATTTGTAAAATTACTGA
AATACCCTCGATTTGT
Found at i:43587052 original size:27 final size:27
Alignment explanation
Indices: 43586669--43587116 Score: 481
Period size: 27 Copynumber: 16.7 Consensus size: 27
43586659 TAATAAAGAG
**
43586669 AAATTACTAAAATACCCTCGATTTGTA
1 AAATTACCGAAATACCCTCGATTTGTA
* *
43586696 AAATTACTGAAATGCCCTCGATTTGTA
1 AAATTACCGAAATACCCTCGATTTGTA
* *
43586723 AAATTACTGAAATACCCTCGA-TTGTG
1 AAATTACCGAAATACCCTCGATTTGTA
*
43586749 AAATTACTGAAATACCCTCGATTTGTA
1 AAATTACCGAAATACCCTCGATTTGTA
* *
43586776 AAATTACCAAAATACCCCCGATTTGTA
1 AAATTACCGAAATACCCTCGATTTGTA
* *
43586803 AAATTACCAAAATACCCTCGA-TTGTG
1 AAATTACCGAAATACCCTCGATTTGTA
*
43586829 AAATTACTGAAATACCCTCGATTTGTA
1 AAATTACCGAAATACCCTCGATTTGTA
** * * *
43586856 AAATTATTGAAATACCCTTGATTTATG
1 AAATTACCGAAATACCCTCGATTTGTA
* * *
43586883 AAATTATCGAAACACCCTCGATTTGTG
1 AAATTACCGAAATACCCTCGATTTGTA
* *
43586910 AAATTACCGAAACACCTTCGATTTGTA
1 AAATTACCGAAATACCCTCGATTTGTA
* * **
43586937 AAATTACCTAAACACCCTTAATTTGTA
1 AAATTACCGAAATACCCTCGATTTGTA
* ** *
43586964 AATTTATTGAAATAGCCTCGATTTGTA
1 AAATTACCGAAATACCCTCGATTTGTA
*
43586991 AAATTATCGAAATACCCTCGATTTGTA
1 AAATTACCGAAATACCCTCGATTTGTA
43587018 AAATTACCGAAATACCCTCGATTTGTA
1 AAATTACCGAAATACCCTCGATTTGTA
* * * **
43587045 AAATTACCAAAACACTCCT-AATTTAAA
1 AAATTACCGAAATAC-CCTCGATTTGTA
* * * *
43587072 AAATTATCAAAATACCCTTG-TAGTGTA
1 AAATTACCGAAATACCCTCGAT-TTGTA
*
43587099 AAATTGCCGAAATACCCT
1 AAATTACCGAAATACCCT
43587117 TGTAGTGTAA
Statistics
Matches: 362, Mismatches: 54, Indels: 10
0.85 0.13 0.02
Matches are distributed among these distances:
26 52 0.14
27 307 0.85
28 3 0.01
ACGTcount: A:0.38, C:0.20, G:0.10, T:0.32
Consensus pattern (27 bp):
AAATTACCGAAATACCCTCGATTTGTA
Found at i:43587157 original size:27 final size:27
Alignment explanation
Indices: 43587081--43587158 Score: 104
Period size: 27 Copynumber: 2.9 Consensus size: 27
43587071 AAAATTATCA
43587081 AAATACCCTTGTAGTGTAAAATTG-CCG
1 AAATACCCTTGTAGTGTAAAA-TGACCG
*
43587108 AAATACCCTTGTAGTGTAAAATGACTG
1 AAATACCCTTGTAGTGTAAAATGACCG
* * *
43587135 ACATACCCCTGTAGGGTAAAATGA
1 AAATACCCTTGTAGTGTAAAATGA
43587159 TTGTTTTGCC
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
26 2 0.04
27 44 0.96
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.27
Consensus pattern (27 bp):
AAATACCCTTGTAGTGTAAAATGACCG
Found at i:43587528 original size:31 final size:31
Alignment explanation
Indices: 43587493--43587556 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
43587483 CCTTTTCATA
**
43587493 TTTCATATTTCATAACACTGGGTTGAAGCCT
1 TTTCATATTTCATAACACTGGGCCGAAGCCT
* **
43587524 TTTCATGTTTCATATTACTGGGCCGAAGCCT
1 TTTCATATTTCATAACACTGGGCCGAAGCCT
43587555 TT
1 TT
43587557 CGTTTAATGG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.22, C:0.20, G:0.17, T:0.41
Consensus pattern (31 bp):
TTTCATATTTCATAACACTGGGCCGAAGCCT
Found at i:43587849 original size:26 final size:26
Alignment explanation
Indices: 43587779--43587900 Score: 205
Period size: 26 Copynumber: 4.8 Consensus size: 26
43587769 CCTCTTTAAT
*
43587779 AACTGGGGCA-AAGCCCTTTT-GATA
1 AACTGGGGCATAAGCCCTTTTCAATA
43587803 AACTGGGGCA-AAGCCCTTTTCAATA
1 AACTGGGGCATAAGCCCTTTTCAATA
43587828 AACTGGGGCATAAGCCCTTTTCAATA
1 AACTGGGGCATAAGCCCTTTTCAATA
43587854 AACTGGGGCATAAGCCCTTTTCAATA
1 AACTGGGGCATAAGCCCTTTTCAATA
*
43587880 AACTAGGGCATAAGCCCTTTT
1 AACTGGGGCATAAGCCCTTTT
43587901 GCACTTCCTC
Statistics
Matches: 94, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
24 20 0.21
25 13 0.14
26 61 0.65
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.26
Consensus pattern (26 bp):
AACTGGGGCATAAGCCCTTTTCAATA
Found at i:43587975 original size:20 final size:20
Alignment explanation
Indices: 43587950--43588044 Score: 133
Period size: 20 Copynumber: 4.8 Consensus size: 20
43587940 TTATGATTAC
*
43587950 ATCATGTGCATTTCATACAT
1 ATCATGTGCATATCATACAT
43587970 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
* *
43587990 ATCATGTGCATTTTATACAT
1 ATCATGTGCATATCATACAT
43588010 ATCATGTGCATATCATATCA-
1 ATCATGTGCATATCATA-CAT
43588030 ATCATGT--ATATCATA
1 ATCATGTGCATATCATA
43588045 TCCCACGTAT
Statistics
Matches: 69, Mismatches: 5, Indels: 4
0.88 0.06 0.05
Matches are distributed among these distances:
18 8 0.12
20 59 0.86
21 2 0.03
ACGTcount: A:0.34, C:0.18, G:0.09, T:0.39
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:43587981 original size:11 final size:11
Alignment explanation
Indices: 43587950--43588025 Score: 56
Period size: 11 Copynumber: 7.5 Consensus size: 11
43587940 TTATGATTAC
43587950 ATCATGTGCAT
1 ATCATGTGCAT
* *
43587961 TTCA--TACAT
1 ATCATGTGCAT
43587970 ATCATGTGCAT
1 ATCATGTGCAT
*
43587981 ATCA--TACAT
1 ATCATGTGCAT
43587990 ATCATGTGCAT
1 ATCATGTGCAT
* * *
43588001 -T-TTATACAT
1 ATCATGTGCAT
43588010 ATCATGTGCAT
1 ATCATGTGCAT
43588021 ATCAT
1 ATCAT
43588026 ATCAATCATG
Statistics
Matches: 47, Mismatches: 12, Indels: 12
0.66 0.17 0.17
Matches are distributed among these distances:
9 20 0.43
10 2 0.04
11 25 0.53
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.39
Consensus pattern (11 bp):
ATCATGTGCAT
Found at i:43587994 original size:40 final size:40
Alignment explanation
Indices: 43587950--43588036 Score: 149
Period size: 40 Copynumber: 2.2 Consensus size: 40
43587940 TTATGATTAC
43587950 ATCATGTGCATTTCATACATATCATGTGCATATCATA-CA
1 ATCATGTGCATTTCATACATATCATGTGCATATCATATCA
*
43587989 TATCATGTGCATTTTATACATATCATGTGCATATCATATCA
1 -ATCATGTGCATTTCATACATATCATGTGCATATCATATCA
43588030 ATCATGT
1 ATCATGT
43588037 ATATCATATC
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
40 43 0.96
41 2 0.04
ACGTcount: A:0.32, C:0.18, G:0.10, T:0.39
Consensus pattern (40 bp):
ATCATGTGCATTTCATACATATCATGTGCATATCATATCA
Found at i:43588042 original size:9 final size:10
Alignment explanation
Indices: 43587967--43588043 Score: 54
Period size: 9 Copynumber: 7.8 Consensus size: 10
43587957 GCATTTCATA
43587967 CATATCATGT
1 CATATCATGT
*
43587977 GCATATCAT-A
1 -CATATCATGT
43587987 CATATCATGT
1 CATATCATGT
* * *
43587997 GCATTTTAT-A
1 -CATATCATGT
43588007 CATATCATGT
1 CATATCATGT
*
43588017 GCATATCATAT
1 -CATATCATGT
43588028 CA-ATCATGT
1 CATATCATGT
43588037 -ATATCAT
1 CATATCAT
43588044 ATCCCACGTA
Statistics
Matches: 51, Mismatches: 10, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
8 1 0.02
9 25 0.49
10 2 0.04
11 23 0.45
ACGTcount: A:0.34, C:0.18, G:0.09, T:0.39
Consensus pattern (10 bp):
CATATCATGT
Found at i:43594535 original size:41 final size:41
Alignment explanation
Indices: 43594480--43594569 Score: 166
Period size: 41 Copynumber: 2.2 Consensus size: 41
43594470 TGGAAATATA
43594480 ACAG-TTCA-ATGATTGTTTTCGCATTGTCGTAGCCTAACT
1 ACAGTTTCATATGATTGTTTTCGCATTGTCGTAGCCTAACT
43594519 ACAGTTTCATATGATTGTTTTCGCATTGTCGTAGCCTAACT
1 ACAGTTTCATATGATTGTTTTCGCATTGTCGTAGCCTAACT
43594560 ACAGTTTCAT
1 ACAGTTTCAT
43594570 TCCTACTATT
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
39 4 0.08
40 4 0.08
41 41 0.84
ACGTcount: A:0.23, C:0.20, G:0.17, T:0.40
Consensus pattern (41 bp):
ACAGTTTCATATGATTGTTTTCGCATTGTCGTAGCCTAACT
Found at i:43596011 original size:23 final size:25
Alignment explanation
Indices: 43595974--43596122 Score: 85
Period size: 26 Copynumber: 5.9 Consensus size: 25
43595964 CTAGAGGCCT
43595974 AGCCTCTTTTAAT-AACTGGGGCGA
1 AGCCTCTTTTAATAAACTGGGGCGA
* *
43595998 AGCC-CTTTTGATAAACTGGGGCAA
1 AGCCTCTTTTAATAAACTGGGGCGA
* * * *
43596022 AACACT-TTTCAATAAACTAGGGCATA
1 AGC-CTCTTTTAATAAACTGGGGC-GA
* * *
43596048 AACC-CTTTTCAATAAACTTGGGCATA
1 AGCCTCTTTT-AATAAACTGGGGC-GA
* *
43596074 AGCC-CTTTGCAATAAACTGGGGCATA
1 AGCCTCTTT-TAATAAACTGGGGC-GA
*
43596100 AGCC-CTTTTCAATAAACTAGGGC
1 AGCCTCTTTT-AATAAACTGGGGC
43596123 ATAAGCCCTT
Statistics
Matches: 103, Mismatches: 14, Indels: 14
0.79 0.11 0.11
Matches are distributed among these distances:
23 7 0.07
24 16 0.16
25 19 0.18
26 61 0.59
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.27
Consensus pattern (25 bp):
AGCCTCTTTTAATAAACTGGGGCGA
Found at i:43596057 original size:26 final size:26
Alignment explanation
Indices: 43595997--43596134 Score: 190
Period size: 26 Copynumber: 5.4 Consensus size: 26
43595987 AACTGGGGCG
* *
43595997 AAGCCCTTTT-GATAAACTGGGGCA-
1 AAGCCCTTTTCAATAAACTAGGGCAT
* *
43596021 AAACACTTTTCAATAAACTAGGGCAT
1 AAGCCCTTTTCAATAAACTAGGGCAT
* *
43596047 AAACCCTTTTCAATAAACTTGGGCAT
1 AAGCCCTTTTCAATAAACTAGGGCAT
* *
43596073 AAGCCCTTTGCAATAAACTGGGGCAT
1 AAGCCCTTTTCAATAAACTAGGGCAT
43596099 AAGCCCTTTTCAATAAACTAGGGCAT
1 AAGCCCTTTTCAATAAACTAGGGCAT
43596125 AAGCCCTTTT
1 AAGCCCTTTT
43596135 GCACTTCCTC
Statistics
Matches: 101, Mismatches: 11, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
24 8 0.08
25 12 0.12
26 81 0.80
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (26 bp):
AAGCCCTTTTCAATAAACTAGGGCAT
Found at i:43596209 original size:20 final size:20
Alignment explanation
Indices: 43596184--43596250 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
43596174 TTATGATTAC
43596184 ATCATGTGCATTTCATACAT
1 ATCATGTGCATTTCATACAT
*
43596204 ATCATGTGCATATCATACAT
1 ATCATGTGCATTTCATACAT
*
43596224 ATCATGTGCATTTTATACAT
1 ATCATGTGCATTTCATACAT
43596244 ATCATGT
1 ATCATGT
43596251 ATATCATATC
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.31, C:0.18, G:0.10, T:0.40
Consensus pattern (20 bp):
ATCATGTGCATTTCATACAT
Found at i:43596228 original size:40 final size:38
Alignment explanation
Indices: 43596184--43596258 Score: 123
Period size: 40 Copynumber: 1.9 Consensus size: 38
43596174 TTATGATTAC
43596184 ATCATGTGCATTTCATACATATCATGTGCATATCATACAT
1 ATCATGTGCATTTCATACATATCATGT--ATATCATACAT
*
43596224 ATCATGTGCATTTTATACATATCATGTATATCATA
1 ATCATGTGCATTTCATACATATCATGTATATCATA
43596259 TCCCACGTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
38 8 0.24
40 26 0.76
ACGTcount: A:0.33, C:0.17, G:0.09, T:0.40
Consensus pattern (38 bp):
ATCATGTGCATTTCATACATATCATGTATATCATACAT
Found at i:43599483 original size:34 final size:34
Alignment explanation
Indices: 43599445--43599512 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
43599435 AATTAAAATG
43599445 AAAAATGAAAAATAAACCCTAATCTAATTTCAGT
1 AAAAATGAAAAATAAACCCTAATCTAATTTCAGT
43599479 AAAAATGAAAAATAAACCCTAATCTAATTTCAGT
1 AAAAATGAAAAATAAACCCTAATCTAATTTCAGT
43599513 GTTAGTCTCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.53, C:0.15, G:0.06, T:0.26
Consensus pattern (34 bp):
AAAAATGAAAAATAAACCCTAATCTAATTTCAGT
Found at i:43604535 original size:85 final size:84
Alignment explanation
Indices: 43604405--43604568 Score: 229
Period size: 85 Copynumber: 1.9 Consensus size: 84
43604395 TACCGTACCA
* **
43604405 ATGCCATATCCCAGATATGGTCTTACATGTAATCTCGTATCGATGCCAATAGCCCAGCTATGGTC
1 ATGCCATATCCCAGATATGGTCTTACACGTAATCTCGTATCGATGCC-ATAGCCCAAATATGGTC
43604470 TTACACAAAGTCTCATATCG
65 TTACACAAAGTCTCATATCG
* * * * * *
43604490 ATGCCATATCCCATATATGGTCTTAGACGTAGTCTTGTATTGATGCCATATCCCAAATATGGTCT
1 ATGCCATATCCCAGATATGGTCTTACACGTAATCTCGTATCGATGCCATAGCCCAAATATGGTCT
*
43604555 TACACATAGTCTCA
66 TACACAAAGTCTCA
43604569 GTAACCCTAA
Statistics
Matches: 69, Mismatches: 10, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
84 28 0.41
85 41 0.59
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.32
Consensus pattern (84 bp):
ATGCCATATCCCAGATATGGTCTTACACGTAATCTCGTATCGATGCCATAGCCCAAATATGGTCT
TACACAAAGTCTCATATCG
Found at i:43604565 original size:42 final size:42
Alignment explanation
Indices: 43604405--43604567 Score: 200
Period size: 42 Copynumber: 3.9 Consensus size: 42
43604395 TACCGTACCA
** *
43604405 ATGCCATATCCCAGATATGGTCTTACATGTAATCTCGTATCG
1 ATGCCATATCCCAGATATGGTCTTACACATAGTCTCGTATCG
* * * *
43604447 ATGCCAATAGCCCAGCTATGGTCTTACACAAAGTCTCATATCG
1 ATGCC-ATATCCCAGATATGGTCTTACACATAGTCTCGTATCG
* * * * *
43604490 ATGCCATATCCCATATATGGTCTTAGACGTAGTCTTGTATTG
1 ATGCCATATCCCAGATATGGTCTTACACATAGTCTCGTATCG
*
43604532 ATGCCATATCCCAAATATGGTCTTACACATAGTCTC
1 ATGCCATATCCCAGATATGGTCTTACACATAGTCTC
43604568 AGTAACCCTA
Statistics
Matches: 100, Mismatches: 20, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
42 65 0.65
43 35 0.35
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.32
Consensus pattern (42 bp):
ATGCCATATCCCAGATATGGTCTTACACATAGTCTCGTATCG
Found at i:43605108 original size:3 final size:3
Alignment explanation
Indices: 43605100--43605128 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
43605090 AAATAAACTC
43605100 TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
43605129 ACATCAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:43606232 original size:28 final size:29
Alignment explanation
Indices: 43606177--43606234 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
43606167 TGTTTAGAAA
* * **
43606177 TTTTAAAGAAAATTATTTTTTTTGAAAAT
1 TTTTAAAGAAAATCATGTTTTTAAAAAAT
43606206 TTTTAAAGAAAATCA-GTTTTTAAAAAAT
1 TTTTAAAGAAAATCATGTTTTTAAAAAAT
43606234 T
1 T
43606235 AACTCGAACA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
28 11 0.44
29 14 0.56
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.47
Consensus pattern (29 bp):
TTTTAAAGAAAATCATGTTTTTAAAAAAT
Found at i:43613211 original size:13 final size:13
Alignment explanation
Indices: 43613193--43613221 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
43613183 TATAGCTTGT
43613193 CCCATTGACTATG
1 CCCATTGACTATG
43613206 CCCATTGACTATG
1 CCCATTGACTATG
43613219 CCC
1 CCC
43613222 TAGATATGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.21, C:0.38, G:0.14, T:0.28
Consensus pattern (13 bp):
CCCATTGACTATG
Found at i:43613331 original size:43 final size:43
Alignment explanation
Indices: 43613253--43613376 Score: 142
Period size: 43 Copynumber: 2.9 Consensus size: 43
43613243 TCACATATCG
* * * * * *
43613253 ATGCCACTGTCCCAGACAGGGTCCTACGCGAAATCA-AATAACA
1 ATGCCAATGTCCCAAACATGGTCTTACACGTAATCACAAT-ACA
*
43613296 ATGCCAATGTTCCAAACATGGTCTTACACGTAATCACAATACA
1 ATGCCAATGTCCCAAACATGGTCTTACACGTAATCACAATACA
** *
43613339 ATTTCAATGTCCCAAACATGGTCTTACATGTAATCACA
1 ATGCCAATGTCCCAAACATGGTCTTACACGTAATCACA
43613377 TCTCAGTAAC
Statistics
Matches: 69, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
43 66 0.96
44 3 0.04
ACGTcount: A:0.35, C:0.27, G:0.14, T:0.24
Consensus pattern (43 bp):
ATGCCAATGTCCCAAACATGGTCTTACACGTAATCACAATACA
Found at i:43614530 original size:12 final size:12
Alignment explanation
Indices: 43614500--43614530 Score: 55
Period size: 11 Copynumber: 2.7 Consensus size: 12
43614490 TATCATGCTG
43614500 TAAATATTAAAA
1 TAAATATTAAAA
43614512 T-AATATTAAAA
1 TAAATATTAAAA
43614523 TAAATATT
1 TAAATATT
43614531 TTGACTTTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 11 0.61
12 7 0.39
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (12 bp):
TAAATATTAAAA
Found at i:43615073 original size:24 final size:24
Alignment explanation
Indices: 43615041--43615111 Score: 124
Period size: 24 Copynumber: 3.0 Consensus size: 24
43615031 CTGTCAGGAG
43615041 AGGATTTAGGAGTTGATAAGGGAT
1 AGGATTTAGGAGTTGATAAGGGAT
43615065 AGGATTTAGGAGTTGATAAGGGAT
1 AGGATTTAGGAGTTGATAAGGGAT
**
43615089 AGGATTTAGGAGCAGATAAGGGA
1 AGGATTTAGGAGTTGATAAGGGA
43615112 GGAAATCTAG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.35, C:0.01, G:0.38, T:0.25
Consensus pattern (24 bp):
AGGATTTAGGAGTTGATAAGGGAT
Found at i:43615123 original size:48 final size:48
Alignment explanation
Indices: 43615041--43615134 Score: 111
Period size: 48 Copynumber: 1.9 Consensus size: 48
43615031 CTGTCAGGAG
** * *
43615041 AGGATTTAGGAGTTGATAAGGGATAGGATTTAGGAGTTGAT-AAGGGAT
1 AGGATTTAGGAGCAGATAAGGGA-AGGATCTAGGAGCTGATCAAGGGAT
43615089 AGGATTTAGGAGCAGATAAGGG-AGGAAATCTAGGAGCTGATCAAGG
1 AGGATTTAGGAGCAGATAAGGGAAGG--ATCTAGGAGCTGATCAAGG
43615135 AAACAAGAGG
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
46 3 0.08
48 32 0.82
49 4 0.10
ACGTcount: A:0.35, C:0.04, G:0.37, T:0.23
Consensus pattern (48 bp):
AGGATTTAGGAGCAGATAAGGGAAGGATCTAGGAGCTGATCAAGGGAT
Found at i:43616571 original size:29 final size:29
Alignment explanation
Indices: 43616529--43616615 Score: 87
Period size: 29 Copynumber: 3.1 Consensus size: 29
43616519 AGGAAGCGTC
*
43616529 CTGGTGGCTATGCCACATATATATCTGTT
1 CTGGTGGCTCTGCCACATATATATCTGTT
43616558 CTGGTGGCTCTGCCACGAT-TATA--TGTAT
1 CTGGTGGCTCTGCCAC-ATATATATCTGT-T
* *
43616586 CTGGTGACTCTGTCAC--AT-TATCTGTT
1 CTGGTGGCTCTGCCACATATATATCTGTT
43616612 CTGG
1 CTGG
43616616 CAGCCATGCT
Statistics
Matches: 50, Mismatches: 3, Indels: 13
0.76 0.05 0.20
Matches are distributed among these distances:
25 2 0.04
26 6 0.12
27 6 0.12
28 15 0.30
29 19 0.38
30 2 0.04
ACGTcount: A:0.17, C:0.22, G:0.23, T:0.38
Consensus pattern (29 bp):
CTGGTGGCTCTGCCACATATATATCTGTT
Found at i:43619175 original size:37 final size:38
Alignment explanation
Indices: 43619134--43619220 Score: 97
Period size: 40 Copynumber: 2.3 Consensus size: 38
43619124 CGATGGGGCG
43619134 TTGGTCGCCAC-TTTGCTTCG-ACTTAGCCGATGAGACA
1 TTGGTCGCCACTTTTGCTTCGAAC-TAGCCGATGAGACA
* * * *
43619171 TTGGTCGTCACTTATTTGCTTCGAACTATCCGATGAGGCG
1 TTGGTCGCCAC-T-TTTGCTTCGAACTAGCCGATGAGACA
43619211 TTGGTCGCCA
1 TTGGTCGCCA
43619221 TTCTGGTGTG
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
37 10 0.24
40 29 0.71
41 2 0.05
ACGTcount: A:0.17, C:0.25, G:0.25, T:0.32
Consensus pattern (38 bp):
TTGGTCGCCACTTTTGCTTCGAACTAGCCGATGAGACA
Found at i:43621538 original size:47 final size:47
Alignment explanation
Indices: 43621468--43621673 Score: 277
Period size: 47 Copynumber: 4.4 Consensus size: 47
43621458 GATGTACAAG
* * * *
43621468 GTGTGTATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
1 GTGTATATATGAGATAAGACCTAATGGCCAATGTGATGAATGTGAAA
* *
43621515 GTGTATACATGAGATAAGACCTAATGGCCAACGTGATGAATGTGAAA
1 GTGTATATATGAGATAAGACCTAATGGCCAATGTGATGAATGTGAAA
* * *
43621562 GTGTATATATGAGATAAGACCTAATGGCCGATGTGATGGATGTGAAG
1 GTGTATATATGAGATAAGACCTAATGGCCAATGTGATGAATGTGAAA
* * * *
43621609 GTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGGATGTGAAA
1 GTGTATATATGAGATAAGACCTAATGGCCAATGTGATGAATGTGAAA
* *
43621656 GTGTATAAATGTGATAAG
1 GTGTATATATGAGATAAG
43621674 TCCCGAAGGG
Statistics
Matches: 142, Mismatches: 17, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
47 142 1.00
ACGTcount: A:0.33, C:0.09, G:0.30, T:0.28
Consensus pattern (47 bp):
GTGTATATATGAGATAAGACCTAATGGCCAATGTGATGAATGTGAAA
Found at i:43623020 original size:20 final size:20
Alignment explanation
Indices: 43622995--43623032 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
43622985 TTGTCCACGA
43622995 CAGGCCACACGGGCATGTTC
1 CAGGCCACACGGGCATGTTC
43623015 CAGGCCACACGGGCATGT
1 CAGGCCACACGGGCATGT
43623033 CTCGGCCAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.21, C:0.34, G:0.32, T:0.13
Consensus pattern (20 bp):
CAGGCCACACGGGCATGTTC
Found at i:43626890 original size:40 final size:40
Alignment explanation
Indices: 43626652--43626876 Score: 287
Period size: 40 Copynumber: 5.7 Consensus size: 40
43626642 TCGAATGATG
* * * * *
43626652 TCCGGGCTAAGTCCCGAAGGC-TTTATGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
43626692 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
43626732 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
43626771 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
43626811 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
43626852 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
43626877 AACGAGTAGC
Statistics
Matches: 164, Mismatches: 16, Indels: 10
0.86 0.08 0.05
Matches are distributed among these distances:
39 34 0.21
40 121 0.74
41 9 0.05
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:43634967 original size:40 final size:40
Alignment explanation
Indices: 43634729--43634953 Score: 278
Period size: 40 Copynumber: 5.7 Consensus size: 40
43634719 TCGAATGATG
* * * * *
43634729 TCCGGGCTAAGTCCCGAAGGC-TTTATGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * * *
43634769 TCCGGACTAAGAT-CCGAAGGAATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
43634809 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
43634848 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
43634888 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
43634929 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
43634954 AACGAGTAGC
Statistics
Matches: 162, Mismatches: 18, Indels: 10
0.85 0.09 0.05
Matches are distributed among these distances:
39 33 0.20
40 120 0.74
41 9 0.06
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:43639798 original size:3 final size:3
Alignment explanation
Indices: 43639790--43639833 Score: 65
Period size: 3 Copynumber: 15.0 Consensus size: 3
43639780 AGGTATTTAC
43639790 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TT- TTA TCTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA
43639834 ATTGAGATAA
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
2 4 0.11
3 31 0.82
4 3 0.08
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:43649153 original size:41 final size:41
Alignment explanation
Indices: 43649096--43649177 Score: 155
Period size: 41 Copynumber: 2.0 Consensus size: 41
43649086 TCTTACCGAA
43649096 GCCTTATTGTTTCATAATCTCAGTAACTATAAGCTTGGCGT
1 GCCTTATTGTTTCATAATCTCAGTAACTATAAGCTTGGCGT
*
43649137 GCCTTATTTTTTCATAATCTCAGTAACTATAAGCTTGGCGT
1 GCCTTATTGTTTCATAATCTCAGTAACTATAAGCTTGGCGT
43649178 ACATCCCTAT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.40
Consensus pattern (41 bp):
GCCTTATTGTTTCATAATCTCAGTAACTATAAGCTTGGCGT
Found at i:43649377 original size:42 final size:42
Alignment explanation
Indices: 43649299--43649497 Score: 114
Period size: 42 Copynumber: 4.6 Consensus size: 42
43649289 TAAGATGCCA
* * * * *
43649299 ATGCCATGTCCCATACATGGTCTTACATGGGA-TCTCACATCG
1 ATGCCATATCCCAGATATGGTCTTACA-CGAATTCTCACATCG
* **
43649341 ATGCCATATCCCAGATATGGTCTTATACGAATTCTCATTTCG
1 ATGCCATATCCCAGATATGGTCTTACACGAATTCTCACATCG
* * ** * *** *
43649383 ATGCCATGTTCCAGACGTGGTCTTACACGAAATCTTGTATCA
1 ATGCCATATCCCAGATATGGTCTTACACGAATTCTCACATCG
** * * *
43649425 ATGCTGTATCCCAGATATGGTCTCACATG-ATAACTCATACTGATGCTG
1 ATGCCATATCCCAGATATGGTCTTACACGAAT-TCTC--AC--AT-C-G
43649473 ATGCCATATCCCAGATATGGTCTTA
1 ATGCCATATCCCAGATATGGTCTTA
43649498 TACGGTATCT
Statistics
Matches: 114, Mismatches: 35, Indels: 10
0.72 0.22 0.06
Matches are distributed among these distances:
41 3 0.03
42 86 0.75
46 2 0.02
47 1 0.01
48 22 0.19
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.32
Consensus pattern (42 bp):
ATGCCATATCCCAGATATGGTCTTACACGAATTCTCACATCG
Found at i:43653157 original size:52 final size:51
Alignment explanation
Indices: 43652920--43653183 Score: 167
Period size: 52 Copynumber: 5.1 Consensus size: 51
43652910 GTAAATGTGA
* * *** *
43652920 AAGTCCATTAGGACAATCTAATTGGAAAGTCCGTCGGGACAATCTAATGTGG
1 AAGTCCGTCAGGACAATCTAATTGGAAAGTCTACCAGGACAATCTAATG-GG
* * * * * **
43652972 AAGCCCATTAGGACAATCTAATTAGG-AAGTCTGCTAGGATGATCTAATGTGG
1 AAGTCCGTCAGGACAATCTAATT-GGAAAGTCTACCAGGACAATCTAATG-GG
* * * * * * ** *
43653024 -ACTCTTGTCAAGACAATCCAATT-GAGAAGTCTACAAAGATTATATAATGTGG
1 AAGTC-CGTCAGGACAATCTAATTGGA-AAGTCTACCAGGACAATCTAATG-GG
* *
43653076 -AGTCTGTCAGGACAATCTAATTGGAAAGTCTGCCAGGACAATCTAATGAGG
1 AAGTCCGTCAGGACAATCTAATTGGAAAGTCTACCAGGACAATCTAATG-GG
* * * **
43653127 AAGTCCGTCCGGACAATCTATTTGGGAAGTCTATTAGGACAATCTAATTGGG
1 AAGTCCGTCAGGACAATCTAATTGGAAAGTCTACCAGGACAATCTAA-TGGG
43653179 AAGTC
1 AAGTC
43653184 TATAAGGTTG
Statistics
Matches: 169, Mismatches: 36, Indels: 14
0.77 0.16 0.06
Matches are distributed among these distances:
50 1 0.01
51 37 0.22
52 127 0.75
53 4 0.02
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (51 bp):
AAGTCCGTCAGGACAATCTAATTGGAAAGTCTACCAGGACAATCTAATGGG
Found at i:43653185 original size:26 final size:26
Alignment explanation
Indices: 43652920--43653186 Score: 125
Period size: 26 Copynumber: 10.3 Consensus size: 26
43652910 GTAAATGTGA
* *
43652920 AAGTCCATTAGGACAATCTAATTGGA
1 AAGTCTATTAGGACAATCTAATTGGG
** **
43652946 AAGTCCGTCGGGACAATCTAA-TGTGG
1 AAGTCTATTAGGACAATCTAATTG-GG
* * *
43652972 AAGCCCATTAGGACAATCTAATTAGG
1 AAGTCTATTAGGACAATCTAATTGGG
** **
43652998 AAGTCTGCTAGGATGATCTAA-TGTGG
1 AAGTCTATTAGGACAATCTAATTG-GG
* * * *
43653024 -ACTCT-TGTCAAGACAATCCAATTGAG
1 AAGTCTAT-T-AGGACAATCTAATTGGG
** * ** *
43653050 AAGTCTACAAAGATTATATAA-TGTGG
1 AAGTCTATTAGGACAATCTAATTG-GG
* * *
43653076 -AGTCTGTCAGGACAATCTAATTGGA
1 AAGTCTATTAGGACAATCTAATTGGG
***
43653101 AAGTCTGCCAGGACAATCTAA-TGAGG
1 AAGTCTATTAGGACAATCTAATTG-GG
** ** *
43653127 AAGTCCGTCCGGACAATCTATTTGGG
1 AAGTCTATTAGGACAATCTAATTGGG
43653153 AAGTCTATTAGGACAATCTAATTGGG
1 AAGTCTATTAGGACAATCTAATTGGG
43653179 AAGTCTAT
1 AAGTCTAT
43653187 AAGGTTGATT
Statistics
Matches: 178, Mismatches: 50, Indels: 26
0.70 0.20 0.10
Matches are distributed among these distances:
25 26 0.15
26 143 0.80
27 9 0.05
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.27
Consensus pattern (26 bp):
AAGTCTATTAGGACAATCTAATTGGG
Found at i:43666879 original size:35 final size:35
Alignment explanation
Indices: 43666833--43666902 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 35
43666823 CTTACTTGTA
43666833 AACACATATCAGAATCATATAACGATGCCATGGTC
1 AACACATATCAGAATCATATAACGATGCCATGGTC
* *
43666868 AACACATATCAGAATTATATCACGATGCCATGGTC
1 AACACATATCAGAATCATATAACGATGCCATGGTC
43666903 TTACTCGCAC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.39, C:0.23, G:0.14, T:0.24
Consensus pattern (35 bp):
AACACATATCAGAATCATATAACGATGCCATGGTC
Found at i:43671274 original size:35 final size:35
Alignment explanation
Indices: 43671234--43671437 Score: 219
Period size: 35 Copynumber: 5.8 Consensus size: 35
43671224 AGGTAAGTAT
* *
43671234 ATGTGAGGTTATATTGAACTTGTATATTCGGCTGC
1 ATGTGAGGTTATATTGAACTTGTATATTCGGTTAC
* *
43671269 ATGTGAGGTTATATTGAACTTGTTTATTCGATTAC
1 ATGTGAGGTTATATTGAACTTGTATATTCGGTTAC
*
43671304 ATGTGAGCTTATATTGAACTTGTATATTCGGTTAC
1 ATGTGAGGTTATATTGAACTTGTATATTCGGTTAC
** * * * * *
43671339 ACATGAGATTATATTGAATTTGTATATTTGGTCAT
1 ATGTGAGGTTATATTGAACTTGTATATTCGGTTAC
* * * * * *
43671374 ATGAGATGTTTTATTGAACTTGAACATTAGGTTAC
1 ATGTGAGGTTATATTGAACTTGTATATTCGGTTAC
* * *
43671409 ATGTGATGATATATTGAACTTATATATTC
1 ATGTGAGGTTATATTGAACTTGTATATTC
43671438 AGCCATATGA
Statistics
Matches: 136, Mismatches: 33, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
35 136 1.00
ACGTcount: A:0.28, C:0.09, G:0.20, T:0.43
Consensus pattern (35 bp):
ATGTGAGGTTATATTGAACTTGTATATTCGGTTAC
Found at i:43671424 original size:105 final size:105
Alignment explanation
Indices: 43671237--43671437 Score: 246
Period size: 105 Copynumber: 1.9 Consensus size: 105
43671227 TAAGTATATG
* * *** *
43671237 TGAGGTTATATTGAACTTGTATATTCGGCTGCATGTGAGGTTATATTGAACTTGTTTATTCGATT
1 TGAGATTATATTGAACTTGTATATTCGGCTGCATATGAGGTTATATTGAACTTGAACATTAGATT
* *
43671302 ACATGTGAGCTTATATTGAACTTGTATATTCGGTTACACA
66 ACATGTGAGCATATATTGAACTTATATATTCGGTTACACA
* * * *
43671342 TGAGATTATATTGAATTTGTATATTTGG-T-CATATGAGATGTTTTATTGAACTTGAACATTAGG
1 TGAGATTATATTGAACTTGTATATTCGGCTGCATATGAG--GTTATATTGAACTTGAACATTAGA
43671405 TTACATGTGATG-ATATATTGAACTTATATATTC
64 TTACATGTGA-GCATATATTGAACTTATATATTC
43671438 AGCCATATGA
Statistics
Matches: 81, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
103 7 0.09
104 1 0.01
105 72 0.89
106 1 0.01
ACGTcount: A:0.28, C:0.09, G:0.19, T:0.43
Consensus pattern (105 bp):
TGAGATTATATTGAACTTGTATATTCGGCTGCATATGAGGTTATATTGAACTTGAACATTAGATT
ACATGTGAGCATATATTGAACTTATATATTCGGTTACACA
Found at i:43676690 original size:51 final size:51
Alignment explanation
Indices: 43676626--43676761 Score: 155
Period size: 51 Copynumber: 2.7 Consensus size: 51
43676616 TGGAAACATG
*
43676626 ATCTTAAAAGATATGATATTATAATCTTAGAGATCTTAGATATGATATGGA
1 ATCTTAAAAGATATGATATTATAATCTTAGAGATCTTAGATAAGATATGGA
* * * ** * * ** *
43676677 ATCTTATAAGATATTATTTTATAAGATTACATATCTTATCTAAGATATGTA
1 ATCTTAAAAGATATGATATTATAATCTTAGAGATCTTAGATAAGATATGGA
* *
43676728 ATCTTAGAAGATATGATATTATATTCTTAGAGAT
1 ATCTTAAAAGATATGATATTATAATCTTAGAGAT
43676762 TTGATGGTAG
Statistics
Matches: 66, Mismatches: 19, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
51 66 1.00
ACGTcount: A:0.40, C:0.07, G:0.12, T:0.41
Consensus pattern (51 bp):
ATCTTAAAAGATATGATATTATAATCTTAGAGATCTTAGATAAGATATGGA
Found at i:43684207 original size:27 final size:27
Alignment explanation
Indices: 43684177--43684354 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
43684167 ATATTGAGCC
* * * *
43684177 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
43684204 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
43684231 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
43684259 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
43684286 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
43684313 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
43684340 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
43684355 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:43684316 original size:82 final size:81
Alignment explanation
Indices: 43684198--43684353 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
43684188 TGCTATATAA
* *
43684198 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
43684263 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
43684280 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
43684344 CACTTAGTGC
65 CACTTAGTGC
43684354 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:43692320 original size:27 final size:27
Alignment explanation
Indices: 43692290--43692384 Score: 136
Period size: 27 Copynumber: 3.5 Consensus size: 27
43692280 GATATTGAGC
* *
43692290 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* *
43692317 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
43692344 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
43692372 CGCACACTTAGTG
1 CGCACACTTAGTG
43692385 GCATCAATTC
Statistics
Matches: 60, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
27 44 0.73
28 16 0.27
ACGTcount: A:0.32, C:0.28, G:0.15, T:0.25
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:43700437 original size:27 final size:27
Alignment explanation
Indices: 43700407--43700584 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
43700397 ATATTGAGTC
* * * *
43700407 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
43700434 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
43700461 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
43700489 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
43700516 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
43700543 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
43700570 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
43700585 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:43700546 original size:82 final size:81
Alignment explanation
Indices: 43700428--43700583 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
43700418 TGCTATATAA
* *
43700428 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
43700493 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
43700510 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
43700574 CACTTAGTGC
65 CACTTAGTGC
43700584 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:43707586 original size:26 final size:27
Alignment explanation
Indices: 43707504--43707593 Score: 146
Period size: 27 Copynumber: 3.4 Consensus size: 27
43707494 TGGATAAGTT
*
43707504 GTAGAATTACCAAAATACCCCTGTAAG
1 GTAGAATTACCGAAATACCCCTGTAAG
*
43707531 GTAGAATTACCGAAATACCCCTGTAGG
1 GTAGAATTACCGAAATACCCCTGTAAG
*
43707558 GTAGAATTACCGAAATACCCTTGT-AG
1 GTAGAATTACCGAAATACCCCTGTAAG
43707584 GTAGAATTAC
1 GTAGAATTAC
43707594 TCATATACCC
Statistics
Matches: 59, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
26 11 0.19
27 48 0.81
ACGTcount: A:0.37, C:0.20, G:0.19, T:0.24
Consensus pattern (27 bp):
GTAGAATTACCGAAATACCCCTGTAAG
Found at i:43707613 original size:53 final size:54
Alignment explanation
Indices: 43707504--43707621 Score: 159
Period size: 53 Copynumber: 2.2 Consensus size: 54
43707494 TGGATAAGTT
43707504 GTAGAATTACCAAAATACCCCTGTAAGGTAGAATTACCGAAATACCCCTGTAGG
1 GTAGAATTACCAAAATACCCCTGTAAGGTAGAATTACCGAAATACCCCTGTAGG
* * * * *
43707558 GTAGAATTACCGAAATACCCTTGT-AGGTAGAATTACTC-ATATACCCTTGTGGG
1 GTAGAATTACCAAAATACCCCTGTAAGGTAGAATTAC-CGAAATACCCCTGTAGG
*
43707611 GTAAAATTACC
1 GTAGAATTACC
43707622 TTTTTGCCCC
Statistics
Matches: 57, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
53 34 0.60
54 23 0.40
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.26
Consensus pattern (54 bp):
GTAGAATTACCAAAATACCCCTGTAAGGTAGAATTACCGAAATACCCCTGTAGG
Found at i:43707620 original size:27 final size:26
Alignment explanation
Indices: 43707504--43707621 Score: 130
Period size: 27 Copynumber: 4.4 Consensus size: 26
43707494 TGGATAAGTT
* * *
43707504 GTAGAATTACCAAAATACCCCTGTAAG
1 GTAGAATTACCGAAATACCCTTGT-GG
*
43707531 GTAGAATTACCGAAATACCCCTGTAGG
1 GTAGAATTACCGAAATACCCTTGT-GG
*
43707558 GTAGAATTACCGAAATACCCTTGTAG
1 GTAGAATTACCGAAATACCCTTGTGG
*
43707584 GTAGAATTACTC-ATATACCCTTGTGGG
1 GTAGAATTAC-CGAAATACCCTTGT-GG
*
43707611 GTAAAATTACC
1 GTAGAATTACC
43707622 TTTTTGCCCC
Statistics
Matches: 82, Mismatches: 7, Indels: 5
0.87 0.07 0.05
Matches are distributed among these distances:
26 23 0.28
27 59 0.72
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.26
Consensus pattern (26 bp):
GTAGAATTACCGAAATACCCTTGTGG
Found at i:43708359 original size:67 final size:68
Alignment explanation
Indices: 43708250--43708389 Score: 201
Period size: 67 Copynumber: 2.1 Consensus size: 68
43708240 GAGGAAGCGT
* * * *
43708250 TCTGGCAGCCTCGCTGCAATCTGGTGGCCTCGCCGC-ACATATATGTTCTGGTGACTTCGTCACA
1 TCTGGCAGCCTCGCTGCAATCTGGTGGCCTCGCCACAACATATATGTTCTGGTGACCTAGCCACA
43708314 ATA
66 ATA
* * *
43708317 TCTGGCAGCCTCGCTGCAATCTGGTGGCTTCGCCACATATATATATGTTCTGGTGGCCTAGCCAC
1 TCTGGCAGCCTCGCTGCAATCTGGTGGCCTCGCCACA-ACATATATGTTCTGGTGACCTAGCCAC
43708382 AATA
65 AATA
43708386 TCTG
1 TCTG
43708390 TATCTGGTGA
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
67 34 0.53
69 30 0.47
ACGTcount: A:0.19, C:0.29, G:0.24, T:0.29
Consensus pattern (68 bp):
TCTGGCAGCCTCGCTGCAATCTGGTGGCCTCGCCACAACATATATGTTCTGGTGACCTAGCCACA
ATA
Found at i:43724680 original size:78 final size:79
Alignment explanation
Indices: 43724597--43724796 Score: 294
Period size: 85 Copynumber: 2.5 Consensus size: 79
43724587 TTAACATGTA
*
43724597 TAACCGTGGCATATCCACTTAGCACCATGTTACATGT-TGGTATATCCACTTACCACTACGTTAA
1 TAACCGTGGCATATCCACTTAGCACCATGTTACATGTCTGGTATATCCACTTACCACAACGTTAA
43724661 TGAATCAATATATG
66 TGAATCAATATATG
* **
43724675 TAACCGTGGCATATCCACTTAGCACCATGTTATATGTTTAGCCGTGGTATATCCACTTAGTACAA
1 TAACCGTGGCATATCCACTTAGCACCATGTTACATG--T---C-TGGTATATCCACTTACCACAA
43724740 CGTTAATGAATCAATATATG
60 CGTTAATGAATCAATATATG
*
43724760 TAACCGTGGCATATCCACTTAGCACCACGTTACATGT
1 TAACCGTGGCATATCCACTTAGCACCATGTTACATGT
43724797 ATCAATATGT
Statistics
Matches: 109, Mismatches: 6, Indels: 9
0.88 0.05 0.07
Matches are distributed among these distances:
78 35 0.32
80 1 0.01
83 1 0.01
85 72 0.66
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.32
Consensus pattern (79 bp):
TAACCGTGGCATATCCACTTAGCACCATGTTACATGTCTGGTATATCCACTTACCACAACGTTAA
TGAATCAATATATG
Found at i:43724816 original size:48 final size:48
Alignment explanation
Indices: 43724716--43724846 Score: 183
Period size: 48 Copynumber: 2.8 Consensus size: 48
43724706 ATATGTTTAG
* * *
43724716 CCGTGGTATATCCACTTAGTACAACGTTA-ATGAATCAATATATGTAA
1 CCGTGGTATATCCACTTAGCACCACGTTACATGTATCAATATATGTAA
* *
43724763 CCGTGGCATATCCACTTAGCACCACGTTACATGTATCAATATGTGTAA
1 CCGTGGTATATCCACTTAGCACCACGTTACATGTATCAATATATGTAA
* * *
43724811 TCGTGGTATATCCACTTAGCACCACATTACACGTAT
1 CCGTGGTATATCCACTTAGCACCACGTTACATGTAT
43724847 AACCGTGGTA
Statistics
Matches: 74, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
47 26 0.35
48 48 0.65
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (48 bp):
CCGTGGTATATCCACTTAGCACCACGTTACATGTATCAATATATGTAA
Found at i:43731799 original size:35 final size:35
Alignment explanation
Indices: 43731759--43731964 Score: 200
Period size: 35 Copynumber: 5.9 Consensus size: 35
43731749 AGGTAAGTAT
* * *
43731759 ATGTGAGGTTATATTGAACTTGTGTATTCGGCTGC
1 ATGTGAGGTTATATTGAACTTGTATATTCGGTTAC
* *
43731794 ATGTGAGGTTATATTGAACTTGTGTATTCGATTAC
1 ATGTGAGGTTATATTGAACTTGTATATTCGGTTAC
* *
43731829 ATGTGAGCTTATATTGAACTTGTATATTCTGTTAC
1 ATGTGAGGTTATATTGAACTTGTATATTCGGTTAC
* * *
43731864 ATGTGAGATTATATTGAATTTGTATATTCAG--AC
1 ATGTGAGGTTATATTGAACTTGTATATTCGGTTAC
* * * * * **
43731897 ATATGAGATGTTTTATTGAACTTGAACATTAGACTAC
1 ATGTGAG--GTTATATTGAACTTGTATATTCGGTTAC
* * *
43731934 ATGTGATGATATATTGAACTTATATATTCGG
1 ATGTGAGGTTATATTGAACTTGTATATTCGG
43731965 CCATATGAAA
Statistics
Matches: 139, Mismatches: 28, Indels: 8
0.79 0.16 0.05
Matches are distributed among these distances:
33 8 0.06
35 124 0.89
37 7 0.05
ACGTcount: A:0.29, C:0.09, G:0.20, T:0.42
Consensus pattern (35 bp):
ATGTGAGGTTATATTGAACTTGTATATTCGGTTAC
Found at i:43738302 original size:46 final size:46
Alignment explanation
Indices: 43738176--43738303 Score: 193
Period size: 46 Copynumber: 2.8 Consensus size: 46
43738166 ATTTGGGCAT
* * * *
43738176 CTGAGCTCGTTGAGTTGAGTCTGAGTTCACTTATAGATGGGAATGT
1 CTGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGGGAACGC
*
43738222 CTGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAACGC
1 CTGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGGGAACGC
* *
43738268 CTGAGCTCATTGAGTTGAGTCCGAGTTCGCTTATGG
1 CTGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
43738304 GCAGGTTACA
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 75 1.00
ACGTcount: A:0.20, C:0.17, G:0.30, T:0.33
Consensus pattern (46 bp):
CTGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGGGAACGC
Found at i:43743435 original size:37 final size:37
Alignment explanation
Indices: 43743385--43743459 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
43743375 ACAGATTGAC
43743385 TAAATCAGGCCATTTTATTCCGGTACGCACTGATTAT
1 TAAATCAGGCCATTTTATTCCGGTACGCACTGATTAT
* *
43743422 TAAATCAGTCCATTTTATTCTGGTACGCACTGATTAT
1 TAAATCAGGCCATTTTATTCCGGTACGCACTGATTAT
43743459 T
1 T
43743460 CTCTTGATAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.27, C:0.20, G:0.15, T:0.39
Consensus pattern (37 bp):
TAAATCAGGCCATTTTATTCCGGTACGCACTGATTAT
Found at i:43749773 original size:25 final size:25
Alignment explanation
Indices: 43749738--43749787 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
43749728 AGTTGTCAAG
43749738 AAAAAATTTTCTAAAGAAATTATTTC
1 AAAAAATTTTCTAAAGAAATT-TTTC
*
43749764 AAAAAA-TTTCTAAAGATATTTTTC
1 AAAAAATTTTCTAAAGAAATTTTTC
43749788 TTATTTATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 4 0.17
25 13 0.57
26 6 0.26
ACGTcount: A:0.48, C:0.08, G:0.04, T:0.40
Consensus pattern (25 bp):
AAAAAATTTTCTAAAGAAATTTTTC
Found at i:43765127 original size:46 final size:46
Alignment explanation
Indices: 43765075--43765247 Score: 199
Period size: 46 Copynumber: 3.7 Consensus size: 46
43765065 TGGTTGAGCA
*
43765075 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * * *
43765121 TTCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CG
* *
43765168 TCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* *
43765214 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
43765248 GGGGCGGGTT
Statistics
Matches: 105, Mismatches: 15, Indels: 14
0.78 0.11 0.10
Matches are distributed among these distances:
43 6 0.06
45 3 0.03
46 60 0.57
47 28 0.27
48 3 0.03
50 5 0.05
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:43765231 original size:93 final size:93
Alignment explanation
Indices: 43765072--43765242 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
43765062 GGATGGTTGA
* **
43765072 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTTCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
43765137 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * *
43765165 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
43765230 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
43765243 ACTTAGGGGC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:43786334 original size:22 final size:22
Alignment explanation
Indices: 43786309--43786364 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
43786299 AATTGTTTGG
*
43786309 TGACATCACAATGTAGAAGAGA
1 TGACATCACAACGTAGAAGAGA
***
43786331 TGACATCATGGCGTAGAAGAGA
1 TGACATCACAACGTAGAAGAGA
*
43786353 TGACACCACAAC
1 TGACATCACAAC
43786365 TTCAGACCTA
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.41, C:0.20, G:0.23, T:0.16
Consensus pattern (22 bp):
TGACATCACAACGTAGAAGAGA
Found at i:43788684 original size:13 final size:13
Alignment explanation
Indices: 43788650--43788684 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
43788640 GTTATTCGTT
*
43788650 ATTCTCATAAATA
1 ATTCTCAAAAATA
43788663 ATGTCTCAAAAATA
1 AT-TCTCAAAAATA
43788677 ATTCTCAA
1 ATTCTCAA
43788685 GCAATCATGC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.46, C:0.17, G:0.03, T:0.34
Consensus pattern (13 bp):
ATTCTCAAAAATA
Found at i:43790371 original size:25 final size:26
Alignment explanation
Indices: 43790341--43790394 Score: 83
Period size: 25 Copynumber: 2.1 Consensus size: 26
43790331 AGCCCACTAA
43790341 AAACCCAAACACCCCAAA-ACAACCC
1 AAACCCAAACACCCCAAATACAACCC
* *
43790366 AAACCCACACAGCCCAAATACAACCC
1 AAACCCAAACACCCCAAATACAACCC
43790392 AAA
1 AAA
43790395 ATCAAAAAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
25 16 0.62
26 10 0.38
ACGTcount: A:0.52, C:0.44, G:0.02, T:0.02
Consensus pattern (26 bp):
AAACCCAAACACCCCAAATACAACCC
Found at i:43791540 original size:7 final size:7
Alignment explanation
Indices: 43791512--43791550 Score: 57
Period size: 7 Copynumber: 6.0 Consensus size: 7
43791502 ACTACTATAG
43791512 TTTATTA
1 TTTATTA
43791519 -TTATTA
1 TTTATTA
43791525 -TTA-TA
1 TTTATTA
43791530 TTTATTA
1 TTTATTA
43791537 TTTATTA
1 TTTATTA
43791544 TTTATTA
1 TTTATTA
43791551 GCATTGGTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 2 0.07
6 12 0.40
7 16 0.53
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (7 bp):
TTTATTA
Found at i:43791752 original size:29 final size:28
Alignment explanation
Indices: 43791698--43791762 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 28
43791688 ATGCATATAC
43791698 ATATTA-ACATTATTATGTATGTTTTTAA
1 ATATTATACATTATTATGTA-GTTTTTAA
*
43791726 ATATTATACATATATATATGTA-TTTTTAT
1 ATATTATACAT-TAT-TATGTAGTTTTTAA
43791755 ATATTATA
1 ATATTATA
43791763 TCGTGTACAT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
28 6 0.18
29 18 0.55
30 3 0.09
31 6 0.18
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.54
Consensus pattern (28 bp):
ATATTATACATTATTATGTAGTTTTTAA
Found at i:43792377 original size:3 final size:3
Alignment explanation
Indices: 43792369--43792405 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
43792359 ATCTCACTTT
* *
43792369 TTA TTA TTA TTA CTA TTA TTA TTA TTA TCA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
43792406 CGTTCGCGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:43794803 original size:16 final size:13
Alignment explanation
Indices: 43794787--43794820 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
43794777 ACTAAGTAAT
43794787 AATAATATAA-GAA
1 AATAATA-AATGAA
43794800 AATAATAAATGAA
1 AATAATAAATGAA
43794813 AATAATAA
1 AATAATAA
43794821 CAATAACTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 2 0.10
13 18 0.90
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.24
Consensus pattern (13 bp):
AATAATAAATGAA
Found at i:43794901 original size:14 final size:14
Alignment explanation
Indices: 43794882--43794913 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
43794872 ACTAAAACTA
43794882 AAAATAATAACAAT
1 AAAATAATAACAAT
*
43794896 AAAATAATAATAAT
1 AAAATAATAACAAT
43794910 AAAA
1 AAAA
43794914 CTAAGAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.22
Consensus pattern (14 bp):
AAAATAATAACAAT
Found at i:43794973 original size:25 final size:24
Alignment explanation
Indices: 43794931--43794984 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 24
43794921 ATATAGGAAA
43794931 AATAAAACAAATAATAAT-AAATAT
1 AATAAAACAAATAATAATGAAA-AT
*
43794955 AATAACAATAAATAATAATGAAAAT
1 AATAA-AACAAATAATAATGAAAAT
43794980 AATAA
1 AATAA
43794985 TAAATAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 5 0.19
25 19 0.70
26 3 0.11
ACGTcount: A:0.70, C:0.04, G:0.02, T:0.24
Consensus pattern (24 bp):
AATAAAACAAATAATAATGAAAAT
Found at i:43794993 original size:15 final size:15
Alignment explanation
Indices: 43794882--43794993 Score: 58
Period size: 15 Copynumber: 7.3 Consensus size: 15
43794872 ACTAAAACTA
*
43794882 AAAATAATAA-CAAT
1 AAAATAATAATAAAT
43794896 AAAATAATAAT-AAT
1 AAAATAATAATAAAT
* *
43794910 AAAACTAAGAA-ATAT
1 AAAA-TAATAATAAAT
43794925 AGGAAA-AATAA-AACA-
1 A--AAATAATAATAA-AT
43794940 AATAATAATAAATATAAT
1 AA-AATAAT-AATA-AAT
43794958 AACAATAAATAAT-AAT
1 AA-AAT-AATAATAAAT
43794974 GAAAATAATAATAAAT
1 -AAAATAATAATAAAT
43794990 AAAA
1 AAAA
43794994 AGAAACAAAG
Statistics
Matches: 78, Mismatches: 5, Indels: 29
0.70 0.04 0.26
Matches are distributed among these distances:
13 1 0.01
14 19 0.24
15 27 0.35
16 12 0.15
17 7 0.09
18 9 0.12
19 3 0.04
ACGTcount: A:0.71, C:0.04, G:0.04, T:0.22
Consensus pattern (15 bp):
AAAATAATAATAAAT
Found at i:43798849 original size:23 final size:24
Alignment explanation
Indices: 43798794--43798851 Score: 64
Period size: 23 Copynumber: 2.4 Consensus size: 24
43798784 AACAAAAGAC
* * *
43798794 AAATTAAAATGTAAAAATTTAATTA
1 AAATAAAAATATAAAAA-TTAAATA
*
43798819 AAACAAAAATATAAAAA-TAAATA
1 AAATAAAAATATAAAAATTAAATA
43798842 AAATAAAAAT
1 AAATAAAAAT
43798852 GGCTAAATTA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
23 14 0.50
25 14 0.50
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.26
Consensus pattern (24 bp):
AAATAAAAATATAAAAATTAAATA
Found at i:43804114 original size:28 final size:29
Alignment explanation
Indices: 43804083--43804141 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 29
43804073 AAAGTGATTT
*
43804083 TTGACAAAAATGTCAATT-A-GGGATTAAA
1 TTGACAAAAATGTAAATTGAGGGGA-TAAA
* *
43804111 TTGAGAAAAGTGTAAATTGAGGGGATAAA
1 TTGACAAAAATGTAAATTGAGGGGATAAA
43804140 TT
1 TT
43804142 TTAAAATAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
28 15 0.58
29 7 0.27
30 4 0.15
ACGTcount: A:0.44, C:0.03, G:0.24, T:0.29
Consensus pattern (29 bp):
TTGACAAAAATGTAAATTGAGGGGATAAA
Found at i:43804683 original size:43 final size:44
Alignment explanation
Indices: 43804635--43804800 Score: 164
Period size: 43 Copynumber: 3.9 Consensus size: 44
43804625 CATGATGAGA
*
43804635 TTACATGTAAGACCATGTCTAGGACATTGGCATTGTAT-TGTGT
1 TTACATGTAAGACCATATCTAGGACATTGGCATTGTATATGTGT
* * *
43804678 TTACATGTAAGACCATGTCTAGGACATTAGCATCAT-TATATG-AT
1 TTACATGTAAGACCATATCTAGGACATTGGCAT--TGTATATGTGT
* * * * *
43804722 TT-CGTGTAAGACCATATCTGGGACATTGGCATCG-ATATATGA
1 TTACATGTAAGACCATATCTAGGACATTGGCATTGTATATGTGT
* * *
43804764 TAACATGTAAGACCATATCTGGGATA-TGGCATTGTAT
1 TTACATGTAAGACCATATCTAGGACATTGGCATTGTAT
43804801 GAGCCCTACG
Statistics
Matches: 102, Mismatches: 14, Indels: 14
0.78 0.11 0.11
Matches are distributed among these distances:
41 4 0.04
42 8 0.08
43 81 0.79
44 6 0.06
45 3 0.03
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.34
Consensus pattern (44 bp):
TTACATGTAAGACCATATCTAGGACATTGGCATTGTATATGTGT
Found at i:43812191 original size:43 final size:42
Alignment explanation
Indices: 43812143--43812248 Score: 126
Period size: 43 Copynumber: 2.5 Consensus size: 42
43812133 TGAGATTACA
*
43812143 TGTAAGACCATGTCTGGGACAATGGCAT-TGTAT-TGTGTTTATG
1 TGTAAGACCATGTCTGGGACAATGGCATAT-TATATG-ATTT-TG
* *
43812186 TGTAAGACCATGTCTAGGACATTGGCATCATTATATGATTTTG
1 TGTAAGACCATGTCTGGGACAATGGCAT-ATTATATGATTTTG
*
43812229 TGTAAGACCACGTCTGGGAC
1 TGTAAGACCATGTCTGGGAC
43812249 GTTAGCATCA
Statistics
Matches: 55, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
43 46 0.84
44 6 0.11
45 3 0.05
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.34
Consensus pattern (42 bp):
TGTAAGACCATGTCTGGGACAATGGCATATTATATGATTTTG
Found at i:43812257 original size:43 final size:43
Alignment explanation
Indices: 43812184--43812267 Score: 123
Period size: 43 Copynumber: 2.0 Consensus size: 43
43812174 ATTGTGTTTA
* * *
43812184 TGTGTAAGACCATGTCTAGGACATTGGCATCATTATATGATTT
1 TGTGTAAGACCACGTCTAGGACATTAGCATCAATATATGATTT
* *
43812227 TGTGTAAGACCACGTCTGGGACGTTAGCATCAATATATGAT
1 TGTGTAAGACCACGTCTAGGACATTAGCATCAATATATGAT
43812268 AACATGTAAG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.29, C:0.15, G:0.23, T:0.33
Consensus pattern (43 bp):
TGTGTAAGACCACGTCTAGGACATTAGCATCAATATATGATTT
Found at i:43812276 original size:43 final size:43
Alignment explanation
Indices: 43812186--43812281 Score: 111
Period size: 43 Copynumber: 2.2 Consensus size: 43
43812176 TGTGTTTATG
* * * ****
43812186 TGTAAGACCATGTCTAGGACATTGGCATCATTATATGATTTTG
1 TGTAAGACCACGTCTAGGACATTAGCATCAATATATGATAACA
* *
43812229 TGTAAGACCACGTCTGGGACGTTAGCATCAATATATGATAACA
1 TGTAAGACCACGTCTAGGACATTAGCATCAATATATGATAACA
43812272 TGTAAGACCA
1 TGTAAGACCA
43812282 TATTTGGGAT
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (43 bp):
TGTAAGACCACGTCTAGGACATTAGCATCAATATATGATAACA
Found at i:43813638 original size:46 final size:46
Alignment explanation
Indices: 43813492--43813662 Score: 200
Period size: 46 Copynumber: 3.7 Consensus size: 46
43813482 TTTTTGTGCT
* * * * *
43813492 AGTGTAAGGCATGTCTGGGACATGCATCGGCCACATTATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGTGACGAGAGCC
* * * * *
43813538 AGTGTAAGACCATGTCTGGGACATGGCATCGACATTGAGACGAGAGCT
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTCGTGACGAGAGCC
**
43813586 AGTGTAAGACATGTCTAAGACATGCATCGGCCTCGTGACGTA-AGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGTGACG-AGAGCC
43813632 AGTGTAAGACATGTCTGGGACATGCATCGGC
1 AGTGTAAGACATGTCTGGGACATGCATCGGC
43813663 TACGAGATGT
Statistics
Matches: 103, Mismatches: 19, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
46 53 0.51
47 27 0.26
48 23 0.22
ACGTcount: A:0.27, C:0.21, G:0.30, T:0.22
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGTGACGAGAGCC
Found at i:43813719 original size:46 final size:44
Alignment explanation
Indices: 43813586--43813708 Score: 113
Period size: 46 Copynumber: 2.7 Consensus size: 44
43813576 GACGAGAGCT
** * * * *
43813586 AGTGTAAGACATGTCTAAGACATGCATCGGCCT-CGTGACGTAAGCC
1 AGTGTAAGACATGTCTGGGACATGAATCGG-CTACGAGATGT--GTC
*
43813632 AGTGTAAGACATGTCTGGGACATGCATCGGCTACGAGATGTGTC
1 AGTGTAAGACATGTCTGGGACATGAATCGGCTACGAGATGTGTC
* *
43813676 AGTGTAAGACTCTGTCTGGGACGTGGAATCGGC
1 AGTGTAAGAC-ATGTCTGGGACAT-GAATCGGC
43813709 ATGAATATGT
Statistics
Matches: 66, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
44 12 0.18
45 13 0.20
46 41 0.62
ACGTcount: A:0.25, C:0.20, G:0.31, T:0.24
Consensus pattern (44 bp):
AGTGTAAGACATGTCTGGGACATGAATCGGCTACGAGATGTGTC
Found at i:43816033 original size:37 final size:37
Alignment explanation
Indices: 43815974--43816082 Score: 182
Period size: 37 Copynumber: 2.9 Consensus size: 37
43815964 AGCTCAGACG
* *
43815974 AAATCTCCACACGAAGTTATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
*
43816011 AAATCTCCACATGTAGTCATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
*
43816048 TAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
43816083 ATATATTTCC
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 67 1.00
ACGTcount: A:0.27, C:0.30, G:0.19, T:0.24
Consensus pattern (37 bp):
AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
Found at i:43816283 original size:48 final size:48
Alignment explanation
Indices: 43816229--43816363 Score: 234
Period size: 48 Copynumber: 2.8 Consensus size: 48
43816219 GCACATCGCC
*
43816229 TACATATTTCACACTAGCCCTTCGGCTTTACCACATATACATATCTCA
1 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCA
* *
43816277 TACATATTTCACACTAGCCATTCGGCTTTACCACATATGCATGTCTCA
1 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCA
*
43816325 TACATATTTCACATTAGCCATTCGGCTTTACCACATATA
1 TACATATTTCACACTAGCCATTCGGCTTTACCACATATA
43816364 TGCATGTTCA
Statistics
Matches: 82, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 82 1.00
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.34
Consensus pattern (48 bp):
TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCA
Found at i:43816405 original size:22 final size:22
Alignment explanation
Indices: 43816379--43816454 Score: 59
Period size: 22 Copynumber: 3.3 Consensus size: 22
43816369 GTTCATATTC
43816379 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
* *
43816401 ATCACACATAT-G-CATGCTC-ACATT
1 AT--CACAT-TGGCCAT--TCGGCCTT
43816425 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
43816448 ATCACAT
1 ATCACAT
43816455 ACATGCATGT
Statistics
Matches: 41, Mismatches: 4, Indels: 18
0.65 0.06 0.29
Matches are distributed among these distances:
22 12 0.29
23 12 0.29
24 12 0.29
25 5 0.12
ACGTcount: A:0.25, C:0.32, G:0.13, T:0.30
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:43816412 original size:47 final size:47
Alignment explanation
Indices: 43816333--43816620 Score: 441
Period size: 47 Copynumber: 6.1 Consensus size: 47
43816323 CATACATATT
* * * *
43816333 TCACATTAGCCATTCGGCTTTACCACATATATGCATGTTCATATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
* *
43816380 TCACATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
* *
43816427 TCACATTGGCCATTCGGCCTTATCACATACATGCATGTTCATATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
* *
43816474 TCACATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
*
43816521 TCACATTGGCCATTCGGCCTTATCACATACATGCATGTTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
* * **
43816568 TCACATTGGCCATTCGGCCTTATCTCATATATACACATTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
43816615 TCACAT
1 TCACAT
43816621 AAAATCATAA
Statistics
Matches: 219, Mismatches: 22, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 219 1.00
ACGTcount: A:0.26, C:0.30, G:0.11, T:0.33
Consensus pattern (47 bp):
TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
Found at i:43816454 original size:94 final size:94
Alignment explanation
Indices: 43816293--43816620 Score: 482
Period size: 94 Copynumber: 3.5 Consensus size: 94
43816283 TTTCACACTA
* * * *
43816293 GCCATTCGGCTTTA-C-CACATATGCATGTCTCATACATAT-TTCACATTAGCCATTCGGCTTTA
1 GCCATTCGGCCTTATCACACATATGCATG-CTC--ACAT-TCATCACATTGGCCATTCGGCCTTA
* *
43816355 CCACATATATGCATGTTCATATTCATCACATTG
62 TCACATACATGCATGTTCATATTCATCACATTG
43816388 GCCATTCGGCCTTATCACACATATGCATGCTCACATTCATCACATTGGCCATTCGGCCTTATCAC
1 GCCATTCGGCCTTATCACACATATGCATGCTCACATTCATCACATTGGCCATTCGGCCTTATCAC
43816453 ATACATGCATGTTCATATTCATCACATTG
66 ATACATGCATGTTCATATTCATCACATTG
43816482 GCCATTCGGCCTTATCACACATATGCATGCTCACATTCATCACATTGGCCATTCGGCCTTATCAC
1 GCCATTCGGCCTTATCACACATATGCATGCTCACATTCATCACATTGGCCATTCGGCCTTATCAC
*
43816547 ATACATGCATGTTCACATTCATCACATTG
66 ATACATGCATGTTCATATTCATCACATTG
* * * ***
43816576 GCCATTCGGCCTTATCTCATATATACACATTCACATTCATCACAT
1 GCCATTCGGCCTTATCACACATATGCATGCTCACATTCATCACAT
43816621 AAAATCATAA
Statistics
Matches: 217, Mismatches: 13, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
93 1 0.00
94 187 0.86
95 13 0.06
96 4 0.02
97 12 0.06
ACGTcount: A:0.26, C:0.29, G:0.12, T:0.33
Consensus pattern (94 bp):
GCCATTCGGCCTTATCACACATATGCATGCTCACATTCATCACATTGGCCATTCGGCCTTATCAC
ATACATGCATGTTCATATTCATCACATTG
Found at i:43816548 original size:22 final size:22
Alignment explanation
Indices: 43816473--43816548 Score: 59
Period size: 22 Copynumber: 3.3 Consensus size: 22
43816463 GTTCATATTC
43816473 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
* *
43816495 ATCACACATAT-G-CATGCTC-ACATT
1 AT--CACAT-TGGCCAT--TCGGCCTT
43816519 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
43816542 ATCACAT
1 ATCACAT
43816549 ACATGCATGT
Statistics
Matches: 41, Mismatches: 4, Indels: 18
0.65 0.06 0.29
Matches are distributed among these distances:
22 12 0.29
23 12 0.29
24 12 0.29
25 5 0.12
ACGTcount: A:0.25, C:0.32, G:0.13, T:0.30
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:43822541 original size:19 final size:19
Alignment explanation
Indices: 43822517--43822555 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
43822507 ATACCACTTA
43822517 AATGAATGGAGGCGTGACT
1 AATGAATGGAGGCGTGACT
43822536 AATGAATGGAGGCGTGACT
1 AATGAATGGAGGCGTGACT
43822555 A
1 A
43822556 TCAACCTACC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.33, C:0.10, G:0.36, T:0.21
Consensus pattern (19 bp):
AATGAATGGAGGCGTGACT
Found at i:43829329 original size:19 final size:18
Alignment explanation
Indices: 43829307--43829346 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
43829297 TGAATAAAAC
*
43829307 TTATCTACCTAAATAAGAT
1 TTATCTAACTAAATAA-AT
43829326 TTATCTAACTAAATAAAT
1 TTATCTAACTAAATAAAT
43829344 TTA
1 TTA
43829347 AAATATATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.45, C:0.12, G:0.03, T:0.40
Consensus pattern (18 bp):
TTATCTAACTAAATAAAT
Found at i:43831362 original size:42 final size:42
Alignment explanation
Indices: 43831273--43831363 Score: 128
Period size: 42 Copynumber: 2.2 Consensus size: 42
43831263 TACTAATTAG
* **
43831273 GAAAATAATTTCCTTATTCTAATAAACTACTAAAACATGAGG
1 GAAAATAATTTCCTTATTCTAATAAACTACTAAAACATAAAA
* *
43831315 GAAAATAGTTTCCTTATTCTAATAAACTACTAAAAGATAAAA
1 GAAAATAATTTCCTTATTCTAATAAACTACTAAAACATAAAA
*
43831357 TAAAATA
1 GAAAATA
43831364 TGAATAAAAC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.49, C:0.12, G:0.08, T:0.31
Consensus pattern (42 bp):
GAAAATAATTTCCTTATTCTAATAAACTACTAAAACATAAAA
Found at i:43831396 original size:19 final size:18
Alignment explanation
Indices: 43831374--43831413 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
43831364 TGAATAAAAC
* *
43831374 TTATCTACCTTAATAAGAT
1 TTATCTAACTAAATAA-AT
43831393 TTATCTAACTAAATAAAT
1 TTATCTAACTAAATAAAT
43831411 TTA
1 TTA
43831414 AAATATATAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.42, C:0.12, G:0.03, T:0.42
Consensus pattern (18 bp):
TTATCTAACTAAATAAAT
Found at i:43840179 original size:22 final size:22
Alignment explanation
Indices: 43840154--43840198 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
43840144 TTTAATAAAA
43840154 AAAATATCTACAAAATATTCCT
1 AAAATATCTACAAAATATTCCT
* *
43840176 AAAATATTTACAGAATATTCCT
1 AAAATATCTACAAAATATTCCT
43840198 A
1 A
43840199 CACTCCCCCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.49, C:0.16, G:0.02, T:0.33
Consensus pattern (22 bp):
AAAATATCTACAAAATATTCCT
Found at i:43844769 original size:22 final size:22
Alignment explanation
Indices: 43844744--43844788 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
43844734 TTTAATAAAA
43844744 AAAATATCTACAAAATATTCCT
1 AAAATATCTACAAAATATTCCT
* * *
43844766 AAAATATTTATAGAATATTCCT
1 AAAATATCTACAAAATATTCCT
43844788 A
1 A
43844789 CACAAAATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.49, C:0.13, G:0.02, T:0.36
Consensus pattern (22 bp):
AAAATATCTACAAAATATTCCT
Found at i:43845431 original size:44 final size:45
Alignment explanation
Indices: 43845364--43845448 Score: 138
Period size: 44 Copynumber: 1.9 Consensus size: 45
43845354 TGAACATTAA
*
43845364 ATTTTATTTTTAATGATTTTTAAAGTGCTT-ATAACATTCTATAAT
1 ATTTTATTTATAATGATTTTTAAAGTG-TTCATAACATTCTATAAT
43845409 ATTTTATTTAT-ATGATTTTTAAAGTGTTCATAACATTCTA
1 ATTTTATTTATAATGATTTTTAAAGTGTTCATAACATTCTA
43845449 ATTCATAAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
43 2 0.05
44 26 0.68
45 10 0.26
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.53
Consensus pattern (45 bp):
ATTTTATTTATAATGATTTTTAAAGTGTTCATAACATTCTATAAT
Found at i:43864832 original size:28 final size:26
Alignment explanation
Indices: 43864763--43864880 Score: 140
Period size: 23 Copynumber: 4.6 Consensus size: 26
43864753 AAATGTCCAA
43864763 CCAAAACACACCAG---TATAATCCT
1 CCAAAACACACCAGATATATAATCCT
43864786 CCAAAACACACCAG---TATAATCCT
1 CCAAAACACACCAGATATATAATCCT
43864809 CCAAAACACACCAGTATCATATAATCCT
1 CCAAAACACACCAG-AT-ATATAATCCT
*
43864837 CCCAAACACACCAGAATAATATAATCCAT
1 CCAAAACACACCAG-AT-ATATAATCC-T
43864866 CCAAAACACACCAGA
1 CCAAAACACACCAGA
43864881 ATAGCACAAA
Statistics
Matches: 85, Mismatches: 4, Indels: 7
0.89 0.04 0.07
Matches are distributed among these distances:
23 37 0.44
28 34 0.40
29 14 0.16
ACGTcount: A:0.46, C:0.34, G:0.04, T:0.16
Consensus pattern (26 bp):
CCAAAACACACCAGATATATAATCCT
Found at i:43864845 original size:51 final size:53
Alignment explanation
Indices: 43864777--43864879 Score: 147
Period size: 51 Copynumber: 1.9 Consensus size: 53
43864767 AACACACCAG
43864777 TATAATCCTCCAAAACACACCAG-TATAATCC-TCCAAAACACACCAGTATCA
1 TATAATCCTCCAAAACACACCAGATATAATCCATCCAAAACACACCAGTATCA
*
43864828 TATAATCCTCCCAAACACACCAGAATAATATAATCCATCCAAAACACACCAG
1 TATAATCCTCCAAAACACACCAG----ATATAATCCATCCAAAACACACCAG
43864880 AATAGCACAA
Statistics
Matches: 45, Mismatches: 1, Indels: 6
0.87 0.02 0.12
Matches are distributed among these distances:
51 22 0.49
56 8 0.18
57 15 0.33
ACGTcount: A:0.45, C:0.33, G:0.04, T:0.18
Consensus pattern (53 bp):
TATAATCCTCCAAAACACACCAGATATAATCCATCCAAAACACACCAGTATCA
Found at i:43867498 original size:13 final size:13
Alignment explanation
Indices: 43867480--43867504 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
43867470 ACGAAACTTT
43867480 AATACTAACTTAA
1 AATACTAACTTAA
43867493 AATACTAACTTA
1 AATACTAACTTA
43867505 TTAACAATCC
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:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (13 bp):
AATACTAACTTAA
Done.