Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167827.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_10, whole genome shotgun sequence
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: 24162007
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 47000 characters in sequence are not A, C, G, or T
File 50 of 131
Found at i:10307069 original size:70 final size:70
Alignment explanation
Indices: 10306812--10307170 Score: 185
Period size: 70 Copynumber: 5.1 Consensus size: 70
10306802 GACTAAGTTG
* * ** *
10306812 CAAGTCAAAAAATGAAAATAA-TTGAGATTAAACCATGAGTCAAGAAATAAATATGA-TCAAGAC
1 CAAGTCAAAATATGAAAATAACTAG-GATTAAACCATGAGTCAAGAAATAAATATGACT-GGGAT
*
10306875 TAAGCCA
64 TGAGCCA
* * * * * * * * *
10306882 TAAGTTGAAAA-ATG-AAATAACCAAGATTAAACTATGAGT-AAAAAACAAAAGATGACTGGCAT
1 CAAG-TCAAAATATGAAAATAACTAGGATTAAACCATGAGTCAAGAAA-TAAATATGACTGGGAT
*
10306944 CGAGCCA
64 TGAGCCA
* * * * ** * ** * *
10306951 CAAGTAAAAATTTCAAAATGACTAGGATTGGACTACAAGTCGATAAATAAATATGACTGGGATTG
1 CAAGTCAAAATATGAAAATAACTAGGATTAAACCATGAGTCAAGAAATAAATATGACTGGGATTG
* *
10307016 TGCCG
66 AGCCA
* * * ** * *
10307021 CAAGTCAAAATATGAAAATGATTAGGATTAAACCATGAGTCAAGAAATAAATATGAATAAGACTA
1 CAAGTCAAAATATGAAAATAACTAGGATTAAACCATGAGTCAAGAAATAAATATGACTGGGATTG
10307086 AGCCA
66 AGCCA
* * * * *** * *
10307091 CAAGTTGAGAAACA--AAAATGATCTA-GATTGAACCGCAAGTCGAGAAATAAATATGACTGAGA
1 CAAG-TCA-AAATATGAAAAT-AACTAGGATTAAACCATGAGTCAAGAAATAAATATGACTGGGA
*
10307153 TTGAGCCG
63 TTGAGCCA
10307161 CAAGTCAAAA
1 CAAGTCAAAA
10307171 GATAGAGACG
Statistics
Matches: 211, Mismatches: 68, Indels: 22
0.70 0.23 0.07
Matches are distributed among these distances:
68 13 0.06
69 39 0.18
70 142 0.67
71 13 0.06
72 4 0.02
ACGTcount: A:0.48, C:0.13, G:0.18, T:0.21
Consensus pattern (70 bp):
CAAGTCAAAATATGAAAATAACTAGGATTAAACCATGAGTCAAGAAATAAATATGACTGGGATTG
AGCCA
Found at i:10307102 original size:35 final size:36
Alignment explanation
Indices: 10307058--10307146 Score: 85
Period size: 35 Copynumber: 2.5 Consensus size: 36
10307048 TTAAACCATG
*
10307058 AGTCAAGAAATAAATATGAAT-AAGACT-AAGCCACA
1 AGTCGAGAAATAAATATGAATCAAGACTGAA-CCACA
* * * * * *
10307093 AGTTGAGAAACAAAAATG-ATCTAGATTGAACCGCA
1 AGTCGAGAAATAAATATGAATCAAGACTGAACCACA
10307128 AGTCGAGAAATAAATATGA
1 AGTCGAGAAATAAATATGA
10307147 CTGAGATTGA
Statistics
Matches: 41, Mismatches: 10, Indels: 5
0.73 0.18 0.09
Matches are distributed among these distances:
34 2 0.05
35 37 0.90
36 2 0.05
ACGTcount: A:0.51, C:0.12, G:0.18, T:0.19
Consensus pattern (36 bp):
AGTCGAGAAATAAATATGAATCAAGACTGAACCACA
Found at i:10307154 original size:35 final size:34
Alignment explanation
Indices: 10307098--10307286 Score: 130
Period size: 35 Copynumber: 5.4 Consensus size: 34
10307088 CCACAAGTTG
* *
10307098 AGAAACAAAAATGATCT-AGATTGAACCGCAAGTC
1 AGAAATAAAGATGA-CTGAGATTGAACCGCAAGTC
* *
10307132 GAGAAATAAATATGACTGAGATTGAGCCGCAAGTC
1 -AGAAATAAAGATGACTGAGATTGAACCGCAAGTC
* * * * *
10307167 AAAAGATAGAGACGA-TAGAAATTGAACCGCAAGTTA
1 AGAA-ATAAAGATGACT-GAGATTGAACCGCAAG-TC
* * * * * *
10307203 AGTAATAACGATGACTGGGACTGAAGCACAAGTC
1 AGAAATAAAGATGACTGAGATTGAACCGCAAGTC
* * *
10307237 AGAAGATAGAGATAACTGAGATTGAACCGCAAGTT
1 AGAA-ATAAAGATGACTGAGATTGAACCGCAAGTC
*
10307272 AAAGAATAAAGATGA
1 AGA-AATAAAGATGA
10307287 TGATCATGAT
Statistics
Matches: 114, Mismatches: 33, Indels: 14
0.71 0.20 0.09
Matches are distributed among these distances:
34 10 0.09
35 99 0.87
36 5 0.04
ACGTcount: A:0.46, C:0.13, G:0.23, T:0.18
Consensus pattern (34 bp):
AGAAATAAAGATGACTGAGATTGAACCGCAAGTC
Found at i:10307191 original size:70 final size:70
Alignment explanation
Indices: 10307117--10307286 Score: 175
Period size: 70 Copynumber: 2.4 Consensus size: 70
10307107 AATGATCTAG
* * * * *
10307117 ATTGAACCGCAAGTCGAGAAATAAATATGACTGAGATTG-AGCCGCAAGTCAAAAGATAGAGACG
1 ATTGAACCGCAAGTCAAGAAATAAAGATGACTGAGACTGAAG-CACAAGTCAAAAGATAGAGACA
10307181 A-TAGAA
65 ACT-GAA
* * * * * *
10307187 ATTGAACCGCAAGTTAAGTAATAACGATGACTGGGACTGAAGCACAAGTCAGAAGATAGAGATAA
1 ATTGAACCGCAAGTCAAGAAATAAAGATGACTGAGACTGAAGCACAAGTCAAAAGATAGAGACAA
*
10307252 CTGAG
66 CTGAA
*
10307257 ATTGAACCGCAAGTTAA-AGAATAAAGATGA
1 ATTGAACCGCAAGTCAAGA-AATAAAGATGA
10307287 TGATCATGAT
Statistics
Matches: 83, Mismatches: 14, Indels: 6
0.81 0.14 0.06
Matches are distributed among these distances:
70 80 0.96
71 3 0.04
ACGTcount: A:0.44, C:0.14, G:0.24, T:0.18
Consensus pattern (70 bp):
ATTGAACCGCAAGTCAAGAAATAAAGATGACTGAGACTGAAGCACAAGTCAAAAGATAGAGACAA
CTGAA
Found at i:10307437 original size:35 final size:34
Alignment explanation
Indices: 10307398--10307509 Score: 116
Period size: 35 Copynumber: 3.2 Consensus size: 34
10307388 AACAACTGAA
* *
10307398 ATTAAATTGTGAGTTAGAAAATAAAAATGATCTAG
1 ATTAAATCGTGAGTCAGAAAATAAAAATGATC-AG
** * *
10307433 ATTAAATCGCAAGTCAGAGAATAATAATGATCAGG
1 ATTAAATCGTGAGTCAGAAAATAAAAATGATCA-G
** *
10307468 ATTAACCCATGAGTCAGAAAATAAAAATGATCGAG
1 ATTAAATCGTGAGTCAGAAAATAAAAATGATC-AG
10307503 ATTAAAT
1 ATTAAAT
10307510 TGCAAGCCAT
Statistics
Matches: 60, Mismatches: 15, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
34 1 0.02
35 58 0.97
36 1 0.02
ACGTcount: A:0.48, C:0.09, G:0.17, T:0.26
Consensus pattern (34 bp):
ATTAAATCGTGAGTCAGAAAATAAAAATGATCAG
Found at i:10320180 original size:17 final size:17
Alignment explanation
Indices: 10320150--10320205 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
10320140 ATAAATTTGC
*
10320150 AAAAAATAATTAAAAGAA
1 AAAAAAGAA-TAAAAGAA
*
10320168 AAAAAAGAATAAATGAA
1 AAAAAAGAATAAAAGAA
* *
10320185 AAAGAGGAATAATAA-AA
1 AAAAAAGAATAA-AAGAA
10320202 AAAA
1 AAAA
10320206 CCTAAATTGT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
17 22 0.71
18 9 0.29
ACGTcount: A:0.77, C:0.00, G:0.11, T:0.12
Consensus pattern (17 bp):
AAAAAAGAATAAAAGAA
Found at i:10323640 original size:3 final size:3
Alignment explanation
Indices: 10323632--10323680 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
10323622 TTTGCTATTG
10323632 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
10323680 T
1 T
10323681 TTTTTGATAG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:10324191 original size:19 final size:19
Alignment explanation
Indices: 10324167--10324205 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
10324157 AAATTGAGAC
10324167 ACTAGAGATTTGATTTTCT
1 ACTAGAGATTTGATTTTCT
10324186 ACTAGAGATTTGATTTTCT
1 ACTAGAGATTTGATTTTCT
10324205 A
1 A
10324206 TATTCTTTGC
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:0.28, C:0.10, G:0.15, T:0.46
Consensus pattern (19 bp):
ACTAGAGATTTGATTTTCT
Found at i:10325056 original size:134 final size:134
Alignment explanation
Indices: 10324818--10325075 Score: 360
Period size: 134 Copynumber: 1.9 Consensus size: 134
10324808 TTAAAGTTAC
* * *
10324818 TTCTAATAGACAACTTGGAATAAAATAATAAATTAGACAAAAATCTATAGAATGAAAATTTGTTC
1 TTCTAATAGACAACTTGAAACAAAACAATAAATTAGACAAAAATCTATAGAATGAAAATTTGTTC
* * * *
10324883 ATTATAATTAGTTAGGCCTCACTCATTCACTCTTAGCCTACTTAC-GTTTGTGTACAAAAATAAA
66 ACTATAATTAGCTAGGCCTCACTCATTCACTATTAGCCTACTT-CTGTTTATGTACAAAAATAAA
10324947 GTAGT
130 GTAGT
* *
10324952 TTCTAATAGACAACTTGAAACAAAACAATAAGTTAGACAAAGATCTATAGAATGAAAA-TTGTTT
1 TTCTAATAGACAACTTGAAACAAAACAATAAATTAGACAAAAATCTATAGAATGAAAATTTG-TT
* * *
10325016 TACTATAATTAGCTAGGCCTTACTCACTT-ACTATTGGCCTACTTCTGTTTATGTACAAAA
65 CACTATAATTAGCTAGGCCTCACTCA-TTCACTATTAGCCTACTTCTGTTTATGTACAAAA
10325076 TGAGATTACT
Statistics
Matches: 109, Mismatches: 12, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
133 4 0.04
134 103 0.94
135 2 0.02
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (134 bp):
TTCTAATAGACAACTTGAAACAAAACAATAAATTAGACAAAAATCTATAGAATGAAAATTTGTTC
ACTATAATTAGCTAGGCCTCACTCATTCACTATTAGCCTACTTCTGTTTATGTACAAAAATAAAG
TAGT
Found at i:10331094 original size:10 final size:10
Alignment explanation
Indices: 10331061--10331167 Score: 52
Period size: 10 Copynumber: 11.4 Consensus size: 10
10331051 TAATTAAAAG
10331061 AAAATTACTAA
1 AAAATT-CTAA
*
10331072 ATAATTC-ATA
1 AAAATTCTA-A
10331082 AAAATTCTAA
1 AAAATTCTAA
*
10331092 AAAATTAT-A
1 AAAATTCTAA
*
10331101 AAAATTTTAA
1 AAAATTCTAA
*
10331111 AAAA--CT-G
1 AAAATTCTAA
* *
10331118 AATATTTTAA
1 AAAATTCTAA
*
10331128 AAAATTGTAA
1 AAAATTCTAA
10331138 AAAA--CTAA
1 AAAATTCTAA
*
10331146 AAAA-GCTAA
1 AAAATTCTAA
*
10331155 AATATT-TAA
1 AAAATTCTAA
10331164 AAAA
1 AAAA
10331168 AATTTATGAA
Statistics
Matches: 73, Mismatches: 15, Indels: 18
0.69 0.14 0.17
Matches are distributed among these distances:
7 3 0.04
8 8 0.11
9 23 0.32
10 33 0.45
11 6 0.08
ACGTcount: A:0.62, C:0.06, G:0.03, T:0.30
Consensus pattern (10 bp):
AAAATTCTAA
Found at i:10331103 original size:19 final size:20
Alignment explanation
Indices: 10331061--10331114 Score: 74
Period size: 19 Copynumber: 2.7 Consensus size: 20
10331051 TAATTAAAAG
*
10331061 AAAATTACTAAATAATTCATA
1 AAAATT-CTAAAAAATTCATA
10331082 AAAATTCTAAAAAATT-ATA
1 AAAATTCTAAAAAATTCATA
*
10331101 AAAATTTTAAAAAA
1 AAAATTCTAAAAAA
10331115 CTGAATATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 16 0.52
20 9 0.29
21 6 0.19
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (20 bp):
AAAATTCTAAAAAATTCATA
Found at i:10331149 original size:36 final size:37
Alignment explanation
Indices: 10331080--10331168 Score: 92
Period size: 36 Copynumber: 2.5 Consensus size: 37
10331070 AAATAATTCA
* ** *
10331080 TAAAA-ATTCTAAAAAATTATAAAAATTTTAAAAAAC
1 TAAAATATTTTAAAAAATTATAAAAAACTAAAAAAAC
* * *
10331116 T-GAATATTTTAAAAAATTGTAAAAAACTAAAAAAGC
1 TAAAATATTTTAAAAAATTATAAAAAACTAAAAAAAC
*
10331152 TAAAATATTTAAAAAAA
1 TAAAATATTTTAAAAAA
10331169 ATTTATGAAA
Statistics
Matches: 42, Mismatches: 9, Indels: 3
0.78 0.17 0.06
Matches are distributed among these distances:
35 2 0.05
36 27 0.64
37 13 0.31
ACGTcount: A:0.63, C:0.04, G:0.03, T:0.29
Consensus pattern (37 bp):
TAAAATATTTTAAAAAATTATAAAAAACTAAAAAAAC
Found at i:10331334 original size:20 final size:21
Alignment explanation
Indices: 10331309--10331353 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
10331299 AATTAAAAAT
10331309 AAAAAATCT-AAAATTTTTTG
1 AAAAAATCTAAAAATTTTTTG
*
10331329 AAAAAATTTAAAAATTTTTTG
1 AAAAAATCTAAAAATTTTTTG
10331350 AAAA
1 AAAA
10331354 TTATAATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 8 0.35
21 15 0.65
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (21 bp):
AAAAAATCTAAAAATTTTTTG
Found at i:10331642 original size:33 final size:34
Alignment explanation
Indices: 10331580--10331654 Score: 100
Period size: 36 Copynumber: 2.2 Consensus size: 34
10331570 TTTCAGTTTG
*
10331580 TTTTAAAAAACTTTAGGTTTTTTTAATTTTCAAAAT
1 TTTTAAAAAACTTTA-GATTTTTTAATTTTC-AAAT
*
10331616 TTTTCAAAAACTTTA-ATTTTTT-ATTTTCAAAT
1 TTTTAAAAAACTTTAGATTTTTTAATTTTCAAAT
10331648 TTTTAAA
1 TTTTAAA
10331655 GTTTTTGTGA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
32 10 0.28
33 6 0.17
34 6 0.17
36 14 0.39
ACGTcount: A:0.36, C:0.07, G:0.03, T:0.55
Consensus pattern (34 bp):
TTTTAAAAAACTTTAGATTTTTTAATTTTCAAAT
Found at i:10331805 original size:11 final size:11
Alignment explanation
Indices: 10331791--10331857 Score: 50
Period size: 11 Copynumber: 6.2 Consensus size: 11
10331781 ATATTTTAGA
10331791 TTTTTTAAAAT
1 TTTTTTAAAAT
10331802 TTTTTTGAAAA-
1 TTTTTT-AAAAT
*
10331813 -TTTTTAGAAT
1 TTTTTTAAAAT
*
10331823 TTGTTTT-GAAT
1 TT-TTTTAAAAT
* *
10331834 TTTTTAAAAAG
1 TTTTTTAAAAT
*
10331845 TTTTTGAAAAT
1 TTTTTTAAAAT
10331856 TT
1 TT
10331858 CATTTAATGC
Statistics
Matches: 45, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
9 3 0.07
10 8 0.18
11 26 0.58
12 8 0.18
ACGTcount: A:0.33, C:0.00, G:0.09, T:0.58
Consensus pattern (11 bp):
TTTTTTAAAAT
Found at i:10331807 original size:20 final size:20
Alignment explanation
Indices: 10331772--10331842 Score: 63
Period size: 21 Copynumber: 3.5 Consensus size: 20
10331762 TTTATTATAA
* *
10331772 TTTTTAAAAATATTTTAGAT
1 TTTTTAAAATTTTTTTAGAT
* *
10331792 TTTTTAAAATTTTTTTGAAAA
1 TTTTTAAAATTTTTTT-AGAT
*
10331813 TTTTTAGAATTTGTTTT-GAAT
1 TTTTTAAAATTT-TTTTAG-AT
10331834 TTTTTAAAA
1 TTTTTAAAA
10331843 AGTTTTTGAA
Statistics
Matches: 40, Mismatches: 8, Indels: 5
0.75 0.15 0.09
Matches are distributed among these distances:
20 14 0.35
21 22 0.55
22 4 0.10
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.58
Consensus pattern (20 bp):
TTTTTAAAATTTTTTTAGAT
Found at i:10331807 original size:31 final size:31
Alignment explanation
Indices: 10331772--10331849 Score: 88
Period size: 31 Copynumber: 2.5 Consensus size: 31
10331762 TTTATTATAA
10331772 TTTTTAAAAATATTTTAG-ATTT-TTTAAAATT
1 TTTTTAAAAAT-TTTTAGAATTTGTTTAAAA-T
* **
10331803 TTTTTGAAAATTTTTAGAATTTGTTTTGAAT
1 TTTTTAAAAATTTTTAGAATTTGTTTAAAAT
10331834 TTTTTAAAAAGTTTTT
1 TTTTTAAAAA-TTTTT
10331850 GAAAATTTCA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
30 6 0.15
31 24 0.60
32 10 0.25
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.59
Consensus pattern (31 bp):
TTTTTAAAAATTTTTAGAATTTGTTTAAAAT
Found at i:10331849 original size:20 final size:21
Alignment explanation
Indices: 10331772--10331852 Score: 62
Period size: 20 Copynumber: 4.0 Consensus size: 21
10331762 TTTATTATAA
10331772 TTTTTAAAAA-TATTTT-AGAT
1 TTTTTAAAAATTATTTTGA-AT
* *
10331792 TTTTT-AAAATTTTTTTGAAAA
1 TTTTTAAAAATTATTTTG-AAT
* * *
10331813 TTTTTAGAATTTGTTTTGAAT
1 TTTTTAAAAATTATTTTGAAT
*
10331834 TTTTTAAAAAGT-TTTTGAA
1 TTTTTAAAAATTATTTTGAA
10331853 AATTTCATTT
Statistics
Matches: 48, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
19 4 0.08
20 17 0.35
21 17 0.35
22 10 0.21
ACGTcount: A:0.35, C:0.00, G:0.09, T:0.57
Consensus pattern (21 bp):
TTTTTAAAAATTATTTTGAAT
Found at i:10333228 original size:23 final size:22
Alignment explanation
Indices: 10333202--10333255 Score: 81
Period size: 23 Copynumber: 2.4 Consensus size: 22
10333192 TTAAGAATTT
*
10333202 ATAAATAATAATTAGTGCGTATA
1 ATAAATAATAA-TAGTGAGTATA
10333225 ATAAATAGATAATAGTGAGTATA
1 ATAAATA-ATAATAGTGAGTATA
10333248 ATAAATAA
1 ATAAATAA
10333256 AAAATAATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 1 0.03
23 24 0.83
24 4 0.14
ACGTcount: A:0.54, C:0.02, G:0.13, T:0.31
Consensus pattern (22 bp):
ATAAATAATAATAGTGAGTATA
Found at i:10334852 original size:10 final size:11
Alignment explanation
Indices: 10334820--10334857 Score: 51
Period size: 10 Copynumber: 3.4 Consensus size: 11
10334810 AATTAATATA
10334820 AAATAATTTTAAT
1 AAATAATTTT--T
10334833 AAATAATTTTT
1 AAATAATTTTT
10334844 AAA-AATTTTT
1 AAATAATTTTT
10334854 AAAT
1 AAAT
10334858 TTATTCTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 10 0.42
11 4 0.17
13 10 0.42
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
AAATAATTTTT
Found at i:10339116 original size:16 final size:15
Alignment explanation
Indices: 10339085--10339129 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 15
10339075 GGTTTAAAAT
10339085 AATAATAATAATTAAA
1 AATAATAATAA-TAAA
10339101 AATATATAATAATAAA
1 AATA-ATAATAATAAA
*
10339117 TATCAATAATAAT
1 AAT-AATAATAAT
10339130 GTTTTTTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
16 18 0.69
17 8 0.31
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (15 bp):
AATAATAATAATAAA
Found at i:10339787 original size:14 final size:13
Alignment explanation
Indices: 10339740--10339787 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
10339730 ACCTAAACCC
10339740 TAAAATCGAAACT
1 TAAAATCGAAACT
*
10339753 CTAAAATTGAAACCT
1 -TAAAATCGAAA-CT
*
10339768 TGAAATCGAAACGT
1 TAAAATCGAAAC-T
10339782 TAAAAT
1 TAAAAT
10339788 AAAATCTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
13 1 0.04
14 25 0.89
15 2 0.07
ACGTcount: A:0.50, C:0.15, G:0.10, T:0.25
Consensus pattern (13 bp):
TAAAATCGAAACT
Found at i:10339842 original size:26 final size:26
Alignment explanation
Indices: 10339807--10339866 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
10339797 AAACCCAATC
*
10339807 AAAACCCTAAACTTAAA-ACCTTAAAT
1 AAAACCCTAAAATTAAAGACC-TAAAT
* *
10339833 GAAACCCTAAAATTAAAGTCCTAAAT
1 AAAACCCTAAAATTAAAGACCTAAAT
10339859 AAAACCCT
1 AAAACCCT
10339867 GAATGAAACC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 27 0.93
27 2 0.07
ACGTcount: A:0.52, C:0.23, G:0.03, T:0.22
Consensus pattern (26 bp):
AAAACCCTAAAATTAAAGACCTAAAT
Found at i:10339843 original size:12 final size:12
Alignment explanation
Indices: 10339795--10339877 Score: 53
Period size: 12 Copynumber: 6.7 Consensus size: 12
10339785 AATAAAATCT
10339795 TAAAACCC--AA
1 TAAAACCCTAAA
10339805 TCAAAACCCTAAA
1 T-AAAACCCTAAA
*
10339818 CTTAAAACCTTAAA
1 --TAAAACCCTAAA
*
10339832 TGAAACCCTAAAA
1 TAAAACCCT-AAA
**
10339845 TTAAAGTCCTAAA
1 -TAAAACCCTAAA
*
10339858 TAAAACCCTGAA
1 TAAAACCCTAAA
*
10339870 TGAAACCC
1 TAAAACCC
10339878 GAAACCCTAA
Statistics
Matches: 56, Mismatches: 10, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
10 1 0.02
11 7 0.12
12 23 0.41
13 8 0.14
14 16 0.29
15 1 0.02
ACGTcount: A:0.51, C:0.25, G:0.05, T:0.19
Consensus pattern (12 bp):
TAAAACCCTAAA
Found at i:10341498 original size:22 final size:22
Alignment explanation
Indices: 10341473--10341559 Score: 61
Period size: 22 Copynumber: 3.7 Consensus size: 22
10341463 GTTAGGACAC
10341473 TGTATATATTTTGTTATTTTGT
1 TGTATATATTTTGTTATTTTGT
*
10341495 TGTATTATATGATTTTTTATTTTGTT
1 TGTA-TATAT--TTTGTTATTTTG-T
* *
10341521 TGGAT-TATTTAT-TTATTTTAT
1 TGTATATATTT-TGTTATTTTGT
*
10341542 TGATATTTAATTTTGTTA
1 TG-TATAT-ATTTTGTTA
10341560 CATACATCAT
Statistics
Matches: 52, Mismatches: 4, Indels: 16
0.72 0.06 0.22
Matches are distributed among these distances:
21 3 0.06
22 15 0.29
23 8 0.15
24 10 0.19
25 12 0.23
26 4 0.08
ACGTcount: A:0.22, C:0.00, G:0.11, T:0.67
Consensus pattern (22 bp):
TGTATATATTTTGTTATTTTGT
Found at i:10341527 original size:26 final size:25
Alignment explanation
Indices: 10341475--10341534 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
10341465 TAGGACACTG
*
10341475 TATATATTTTGTTATTTTGTTGTAT
1 TATATATTTTGTTATTTTGTTGGAT
10341500 TATATGATTTT-TTATTTTGTTTGGAT
1 TATAT-ATTTTGTTATTTTG-TTGGAT
*
10341526 TATTTATTT
1 TATATATTT
10341535 ATTTTATTGA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
25 17 0.55
26 14 0.45
ACGTcount: A:0.20, C:0.00, G:0.12, T:0.68
Consensus pattern (25 bp):
TATATATTTTGTTATTTTGTTGGAT
Found at i:10351011 original size:8 final size:8
Alignment explanation
Indices: 10350998--10351053 Score: 51
Period size: 8 Copynumber: 6.5 Consensus size: 8
10350988 TTGCTTGAAG
10350998 AAAAAAGA
1 AAAAAAGA
10351006 AAAAAAGA
1 AAAAAAGA
10351014 AAAAAATTGA
1 AAAAAA--GA
10351024 AAAATTAA-A
1 AAAA--AAGA
*
10351033 AAAAAATAA
1 AAAAAA-GA
10351042 AAAAAAGA
1 AAAAAAGA
10351050 AAAA
1 AAAA
10351054 CAATAAACCA
Statistics
Matches: 41, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
7 2 0.05
8 19 0.46
9 12 0.29
10 6 0.15
12 2 0.05
ACGTcount: A:0.84, C:0.00, G:0.07, T:0.09
Consensus pattern (8 bp):
AAAAAAGA
Found at i:10352207 original size:105 final size:105
Alignment explanation
Indices: 10352013--10352465 Score: 364
Period size: 105 Copynumber: 4.3 Consensus size: 105
10352003 TTCATCTTGA
* * * * * *
10352013 TCATT-TTTAATTTTTGACTTACGGTTTTAGTCTC-AGTCATTGTTGTTTCTCGATTTACGGCTC
1 TCATTCTTT-ATTCTTGACTTACGG-CTTAGTCTCGA-TCATCGTTGTTTCTCGATCTGCAGCTC
* *
10352076 AGT-CTTGATAGTATTTATTTTCTGACTTATGGTTCAATCCTAG
63 AATCCTAG-TAGTATTTATTTTCTGACTTATGGTTCAATCCTAG
* * *
10352119 TCATTCTTTATTTTTGACTTACGGCTTAGCCTCGATCATCATTGTTTCTCGATCTGCAGCTCAAT
1 TCATTCTTTATTCTTGACTTACGGCTTAGTCTCGATCATCGTTGTTTCTCGATCTGCAGCTCAAT
10352184 CCTAGTAGTATTTATCTTT-TGACTTACT-GTTCAATTCC-AG
66 CCTAGTAGTATTTAT-TTTCTGACTTA-TGGTTCAA-TCCTAG
* ** * * * * * * *
10352224 TCATTCTTTATTCTTGACTTGCTACTTAGTTTTGGTCATCGTTGTTTCTCAATCTGTAGCTTAGT
1 TCATTCTTTATTCTTGACTTACGGCTTAGTCTCGATCATCGTTGTTTCTCGATCTGCAGCTCAAT
* * *** * ** *
10352289 CTTGGTAACCTTTATTTTCTAACTTGCGGTTCAATCTTAG
66 CCTAGTAGTATTTATTTTCTGACTTATGGTTCAATCCTAG
* * * * *
10352329 TCATTCTTTATTCCTGGCTTGCAGCTTAGTCTCGATCATTGTTGTTTCTCGATCTGCAGCTCAAT
1 TCATTCTTTATTCTTGACTTACGGCTTAGTCTCGATCATCGTTGTTTCTCGATCTGCAGCTCAAT
* * * * * * *
10352394 CGC-AGTCA-TTTTTATTTTATGATTTGTGGTTTAATCCCAA
66 C-CTAGT-AGTATTTATTTTCTGACTTATGGTTCAATCCTAG
* * *
10352434 TCATTCTTTATTCTTAACTTGCGGTTTAGTCT
1 TCATTCTTTATTCTTGACTTACGGCTTAGTCT
10352466 TGCTCTTCAT
Statistics
Matches: 276, Mismatches: 60, Indels: 23
0.77 0.17 0.06
Matches are distributed among these distances:
104 5 0.02
105 236 0.86
106 32 0.12
107 3 0.01
ACGTcount: A:0.18, C:0.20, G:0.15, T:0.47
Consensus pattern (105 bp):
TCATTCTTTATTCTTGACTTACGGCTTAGTCTCGATCATCGTTGTTTCTCGATCTGCAGCTCAAT
CCTAGTAGTATTTATTTTCTGACTTATGGTTCAATCCTAG
Found at i:10352494 original size:210 final size:210
Alignment explanation
Indices: 10352089--10352480 Score: 486
Period size: 210 Copynumber: 1.9 Consensus size: 210
10352079 CTTGATAGTA
* * ** *
10352089 TTTATTTTCTGACTTATGGTTCAATCCTAGTCATTCTTTATTTTTGACTTACGGCTTAGCCTCGA
1 TTTATTTTCTAACTTACGGTTCAATCCTAGTCATTCTTTATTCCTGACTTACAGCTTAGCCTCGA
10352154 TCATCATTGTTTCTCGATCTGCAGCTCAATCCTAGTAGTATTTATCTTTTGACTTACTGTTCAAT
66 TCATCATTGTTTCTCGATCTGCAGCTCAATCCTAGTAGTATTTATCTTTTGACTTACTGTTCAAT
* * * * * * *
10352219 TCCAGTCATTCTTTATTCTTGACTTGCTACTTAGTTTTGGTCATCGTTGTTTCTCAATCTGTAGC
131 CCCAATCATTCTTTATTCTTAACTTGCGACTTAGTCTTGCTCATCATTGTTTCTCAATCTGTAGC
10352284 TTAGTCTTGGTAACC
196 TTAGTCTTGGTAACC
* * * * *
10352299 TTTATTTTCTAACTTGCGGTTCAATCTTAGTCATTCTTTATTCCTGGCTTGCAGCTTAGTCTCGA
1 TTTATTTTCTAACTTACGGTTCAATCCTAGTCATTCTTTATTCCTGACTTACAGCTTAGCCTCGA
** * **
10352364 TCATTGTTGTTTCTCGATCTGCAGCTCAATCGC-AGTCA-TTTTTAT-TTTATGA-TTTGTGGTT
66 TCATCATTGTTTCTCGATCTGCAGCTCAATC-CTAGT-AGTATTTATCTTT-TGACTTACT-GTT
* ** *
10352425 TAATCCCAATCATTCTTTATTCTTAACTTGCGGTTTAGTCTTGCTCTTCATTGTTT
127 CAATCCCAATCATTCTTTATTCTTAACTTGCGACTTAGTCTTGCTCATCATTGTTT
10352481 TTTGACTTGT
Statistics
Matches: 152, Mismatches: 26, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
209 6 0.04
210 144 0.95
211 2 0.01
ACGTcount: A:0.18, C:0.20, G:0.15, T:0.47
Consensus pattern (210 bp):
TTTATTTTCTAACTTACGGTTCAATCCTAGTCATTCTTTATTCCTGACTTACAGCTTAGCCTCGA
TCATCATTGTTTCTCGATCTGCAGCTCAATCCTAGTAGTATTTATCTTTTGACTTACTGTTCAAT
CCCAATCATTCTTTATTCTTAACTTGCGACTTAGTCTTGCTCATCATTGTTTCTCAATCTGTAGC
TTAGTCTTGGTAACC
Found at i:10352693 original size:12 final size:12
Alignment explanation
Indices: 10352676--10352700 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
10352666 TTTCAACTTA
10352676 AAAACAAAAAAC
1 AAAACAAAAAAC
10352688 AAAACAAAAAAC
1 AAAACAAAAAAC
10352700 A
1 A
10352701 CAATTTTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAACAAAAAAC
Found at i:10353062 original size:17 final size:17
Alignment explanation
Indices: 10353040--10353076 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
10353030 ACCAAATAAA
*
10353040 AAATATATAATTATTAC
1 AAATATAAAATTATTAC
10353057 AAATATAAAATTATTAC
1 AAATATAAAATTATTAC
10353074 AAA
1 AAA
10353077 ATGATAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.35
Consensus pattern (17 bp):
AAATATAAAATTATTAC
Found at i:10353106 original size:16 final size:16
Alignment explanation
Indices: 10353057--10353107 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
10353047 TAATTATTAC
*
10353057 AAATATAAAATTATTACA
1 AAATATAAAA--ATTAGA
*
10353075 AAATGATAATAA-TAGA
1 AAAT-ATAAAAATTAGA
10353091 AAATATAAAAATTAGA
1 AAATATAAAAATTAGA
10353107 A
1 A
10353108 TGGACTTGGC
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
15 6 0.21
16 12 0.43
17 1 0.04
18 4 0.14
19 5 0.18
ACGTcount: A:0.65, C:0.02, G:0.06, T:0.27
Consensus pattern (16 bp):
AAATATAAAAATTAGA
Found at i:10355159 original size:23 final size:24
Alignment explanation
Indices: 10355106--10355160 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 24
10355096 ATAAAAATAT
* *
10355106 AATATA-AAATATTAATAAGTAAT
1 AATATATAAATATTAATAAGAAAA
*
10355129 AATA-ATAAATTTTAAT-AGAAAA
1 AATATATAAATATTAATAAGAAAA
10355151 AATATATAAA
1 AATATATAAA
10355161 ATATAAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 9 0.33
23 18 0.67
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.33
Consensus pattern (24 bp):
AATATATAAATATTAATAAGAAAA
Found at i:10355361 original size:26 final size:26
Alignment explanation
Indices: 10355330--10355388 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 26
10355320 CCAATCGGAG
* * *
10355330 CCTTAAACTTAAAACCTTAAATGAAA
1 CCTTAAAATTAAAACCATAAATAAAA
* *
10355356 CTTTAAAATTAAAATCATAAATAAAA
1 CCTTAAAATTAAAACCATAAATAAAA
10355382 CCTTAAA
1 CCTTAAA
10355389 TGAAATCTGA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.54, C:0.15, G:0.02, T:0.29
Consensus pattern (26 bp):
CCTTAAAATTAAAACCATAAATAAAA
Found at i:10356706 original size:16 final size:16
Alignment explanation
Indices: 10356664--10356706 Score: 59
Period size: 18 Copynumber: 2.6 Consensus size: 16
10356654 AAATAATTAA
*
10356664 AATAATTAATATTTTT
1 AATAAATAATATTTTT
10356680 ATATCAAATAATATTTTT
1 A-AT-AAATAATATTTTT
10356698 AATAAATAA
1 AATAAATAA
10356707 AAAATTATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 7 0.29
17 4 0.17
18 13 0.54
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (16 bp):
AATAAATAATATTTTT
Found at i:10356795 original size:16 final size:17
Alignment explanation
Indices: 10356770--10356802 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
10356760 AAATTACTAA
*
10356770 ATTTTTTTAT-AATAAT
1 ATTTTGTTATAAATAAT
10356786 ATTTTGTTATAAATAAT
1 ATTTTGTTATAAATAAT
10356803 TGAATATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (17 bp):
ATTTTGTTATAAATAAT
Found at i:10358652 original size:303 final size:304
Alignment explanation
Indices: 10358104--10358685 Score: 864
Period size: 303 Copynumber: 1.9 Consensus size: 304
10358094 CGGATGAAAC
* * * * * *
10358104 TTTTAATGGTTGGATTATTGAAGGTGATTATTTTCATAAATGCCTTCAATAAAATTTTGTTAGGA
1 TTTTAATGGTCGGATTATTAAAGGTGATTATATCCAGAAACGCCTTCAATAAAATTTTGTTAGGA
* * *
10358169 ATTATTCAAGGCGTTACCCGTAGGAAAATGCCCTTTATAATCCATTCGATTAATTTTTAGTTAGT
66 ATTATTAAAGGCGTTACCCATAGGAAAACGCCCTTTATAATCCATTCGATTAATTTTTAGTTAGT
* **
10358234 ATTATTGAAGGTTTTTTTTAAAAATGCCTTCAATAATTTATACAAAAAAGACAAGACAGATTCTT
131 ATTATTGAAGGTTTTTTTTAAAAACGCCTTCAATAATCCATACAAAAAAGACAAGACAGATTCTT
* * * **
10358299 GAAGGTGTTTTTTGCCTAAAATGCCTTTAATATTCCACACAATAAATTTTTGGTG-GATTATTGA
196 GAAGGTATTTTTTCCCCAAAATGCCTTTAATATTCCACACAATAAATTTTTGGTGTGATTATCAA
10358363 AGGCAGTTTTGGTAAAAAAAGCCATTACTATTCCATACGATAAA
261 AGGCAGTTTTGGTAAAAAAAGCCATTACTATTCCATACGATAAA
* * *
10358407 TTTTAATGGTCGGATTATTAAAGGTGGTTATATCCAGAAACGCCTTCAATAACATTTTGTTAGGG
1 TTTTAATGGTCGGATTATTAAAGGTGATTATATCCAGAAACGCCTTCAATAAAATTTTGTTAGGA
*
10358472 ATTATTAAAGGCGTTACCCATAGGGAAACGCCCTTCT-TAATCCATTCGATTAATTTTTAGTTAG
66 ATTATTAAAGGCGTTACCCATAGGAAAACGCCCTT-TATAATCCATTCGATTAATTTTTAGTTAG
* * * *
10358536 TCTTATTGAAGGTGTTTTTTT-AAAACGCCTTTAATAATCCATACAAAAAAGGCACGACAGATTC
130 TATTATTGAAGGT-TTTTTTTAAAAACGCCTTCAATAATCCATACAAAAAAGACAAGACAGATTC
* *
10358600 TTGAAGGTATTTTTTCCCCAAAATGCCTTTAATATTCCATACAATGAATTTTTGGTGTGATTATC
194 TTGAAGGTATTTTTTCCCCAAAATGCCTTTAATATTCCACACAATAAATTTTTGGTGTGATTATC
* *
10358665 AAAGGCGGTTTTGGTTAAAAA
259 AAAGGCAGTTTTGGTAAAAAA
10358686 TGCTTCAAAA
Statistics
Matches: 247, Mismatches: 29, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
303 215 0.87
304 32 0.13
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (304 bp):
TTTTAATGGTCGGATTATTAAAGGTGATTATATCCAGAAACGCCTTCAATAAAATTTTGTTAGGA
ATTATTAAAGGCGTTACCCATAGGAAAACGCCCTTTATAATCCATTCGATTAATTTTTAGTTAGT
ATTATTGAAGGTTTTTTTTAAAAACGCCTTCAATAATCCATACAAAAAAGACAAGACAGATTCTT
GAAGGTATTTTTTCCCCAAAATGCCTTTAATATTCCACACAATAAATTTTTGGTGTGATTATCAA
AGGCAGTTTTGGTAAAAAAAGCCATTACTATTCCATACGATAAA
Found at i:10361969 original size:25 final size:25
Alignment explanation
Indices: 10361941--10362006 Score: 78
Period size: 25 Copynumber: 2.6 Consensus size: 25
10361931 TAATTATGTA
****
10361941 CAGAAACACCATTCAGCAATGTGCT
1 CAGAAACACCATTCAGCAAACCACT
* *
10361966 CAGATACACCATTTAGCAAACCACT
1 CAGAAACACCATTCAGCAAACCACT
10361991 CAGAAACACCATTCAG
1 CAGAAACACCATTCAG
10362007 TATACGATTC
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.39, C:0.30, G:0.12, T:0.18
Consensus pattern (25 bp):
CAGAAACACCATTCAGCAAACCACT
Found at i:10362168 original size:80 final size:81
Alignment explanation
Indices: 10362001--10362311 Score: 328
Period size: 80 Copynumber: 3.9 Consensus size: 81
10361991 CAGAAACACC
* * * * * *
10362001 ATTCAGTATACGATTCAGCCCT-CAATATCATACAAAACCATTTAGCAAAACAATATCAGACAAC
1 ATTCAGCATACGATTCAACCCTCCAATATCATACAATACCATTCAGCAAAACAATATCAAATAAC
**
10362065 AAGGTTT-AGCAAATA
66 AAGGTTTAAGCAAACG
* * * * * *
10362080 ATTTAGCATATGATTC-ATCCTCCCAATATCATACAAAACCATTTAGCAAAACAATATCAAACAA
1 ATTCAGCATACGATTCAACCCT-CCAATATCATACAATACCATTCAGCAAAACAATATCAAATAA
10362144 CAAGGTTTAAG-AAACG
65 CAAGGTTTAAGCAAACG
* * * * * * * *
10362160 ATTCAGCATATGATTTAGCCCTCCAATATCATACAATATCATTCGGTAATACAATATCATATAAC
1 ATTCAGCATACGATTCAACCCTCCAATATCATACAATACCATTCAGCAAAACAATATCAAATAAC
*
10362225 AAGGTTT-AGCAAACT
66 AAGGTTTAAGCAAACG
* * * *
10362240 ATTTAGCATACGATTCAACCCTTCAATATCATACAATACCATTCAGCAAAA-AAAATCAGATAAC
1 ATTCAGCATACGATTCAACCCTCCAATATCATACAATACCATTCAGCAAAACAATATCAAATAAC
10362304 AAGGTTTA
66 AAGGTTTA
10362312 GCTAACCACA
Statistics
Matches: 194, Mismatches: 32, Indels: 11
0.82 0.14 0.05
Matches are distributed among these distances:
78 3 0.02
79 33 0.17
80 153 0.79
81 5 0.03
ACGTcount: A:0.43, C:0.21, G:0.09, T:0.27
Consensus pattern (81 bp):
ATTCAGCATACGATTCAACCCTCCAATATCATACAATACCATTCAGCAAAACAATATCAAATAAC
AAGGTTTAAGCAAACG
Found at i:10362290 original size:160 final size:158
Alignment explanation
Indices: 10362001--10362311 Score: 401
Period size: 160 Copynumber: 2.0 Consensus size: 158
10361991 CAGAAACACC
* *
10362001 ATTCAGTATACGATTCAGCCCTCAATATCATACAAAACCATTTAGCAAAACAATATCAGACAACA
1 ATTCAGCATACGATTCAGCCCTCAATATCATACAAAACCATTCAGCAAAACAATATCAGACAACA
* * *
10362066 AGGTTTAGCAAATAATTTAGCATATGATTCATCCTCCCAATATCATACAAAACCATTTAGCAAAA
66 AGGTTTAGCAAATAATTTAGCATACGATTCACCCTCCCAATATCATACAAAACCATTCAGCAAAA
*
10362131 CAATATCAAACAACAAGGTTTAAGAAACG
131 -AAAATCAAACAACAAGGTTTAAGAAACG
* * * * * * * * *
10362160 ATTCAGCATATGATTTAGCCCTCCAATATCATACAATATCATTCGGTAATACAATATCATATAAC
1 ATTCAGCATACGATTCAGCCCT-CAATATCATACAAAACCATTCAGCAAAACAATATCAGACAAC
* *
10362225 AAGGTTTAGCAAACT-ATTTAGCATACGATTCAACCCT-TCAATATCATACAATACCATTCAGCA
65 AAGGTTTAGCAAA-TAATTTAGCATACGATTC-ACCCTCCCAATATCATACAAAACCATTCAGCA
* *
10362288 AAAAAAATCAGATAACAAGGTTTA
128 AAAAAAATCAAACAACAAGGTTTA
10362312 GCTAACCACA
Statistics
Matches: 130, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
159 37 0.28
160 88 0.68
161 5 0.04
ACGTcount: A:0.43, C:0.21, G:0.09, T:0.27
Consensus pattern (158 bp):
ATTCAGCATACGATTCAGCCCTCAATATCATACAAAACCATTCAGCAAAACAATATCAGACAACA
AGGTTTAGCAAATAATTTAGCATACGATTCACCCTCCCAATATCATACAAAACCATTCAGCAAAA
AAAATCAAACAACAAGGTTTAAGAAACG
Found at i:10371576 original size:14 final size:14
Alignment explanation
Indices: 10371553--10371583 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
10371543 TTTTCTTTTT
*
10371553 AAATATATTTTATA
1 AAATACATTTTATA
10371567 AAATACATTTTATA
1 AAATACATTTTATA
10371581 AAA
1 AAA
10371584 AAAAATAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (14 bp):
AAATACATTTTATA
Found at i:10371755 original size:32 final size:30
Alignment explanation
Indices: 10371670--10371762 Score: 89
Period size: 32 Copynumber: 3.0 Consensus size: 30
10371660 AAATGACTTG
*
10371670 AAAATTTTTATATAATATTTTTAAATGATATG
1 AAAATTTTTAT-TAAT-TTTTTAAATGATATA
* ** *
10371702 GACCTTTTT-TTAATTTCTTAAATCGATATA
1 AAAATTTTTATTAATTTTTTAAAT-GATATA
10371732 AAAATTTTTACTTAATTTTTTAAAATGATAT
1 AAAATTTTTA-TTAATTTTTT-AAATGATAT
10371763 GTAATTTGAA
Statistics
Matches: 48, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
29 8 0.17
30 15 0.31
31 1 0.02
32 20 0.42
33 4 0.08
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.51
Consensus pattern (30 bp):
AAAATTTTTATTAATTTTTTAAATGATATA
Found at i:10371833 original size:17 final size:17
Alignment explanation
Indices: 10371806--10371846 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
10371796 CTTAATTTTA
10371806 ATTTT-TTAAAAATA-T
1 ATTTTATTAAAAATATT
10371821 ATTTCTATTAAAAATATT
1 ATTT-TATTAAAAATATT
10371839 ATTTTATT
1 ATTTTATT
10371847 GATAAATGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 4 0.17
16 1 0.04
17 13 0.57
18 5 0.22
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTTTATTAAAAATATT
Found at i:10374745 original size:2 final size:2
Alignment explanation
Indices: 10374733--10374768 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
10374723 TATGCAATAT
10374733 AG AG AG A- AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
10374769 ATTTTGAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:10380923 original size:15 final size:16
Alignment explanation
Indices: 10380903--10380932 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
10380893 GTAATTTGCC
10380903 AAAC-TTTCTTTGTGG
1 AAACTTTTCTTTGTGG
10380918 AAACTTTTCTTTGTG
1 AAACTTTTCTTTGTG
10380933 CAAGTATTCC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.20, C:0.13, G:0.17, T:0.50
Consensus pattern (16 bp):
AAACTTTTCTTTGTGG
Found at i:10381317 original size:16 final size:16
Alignment explanation
Indices: 10381288--10381321 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
10381278 TTGTTGGGTA
*
10381288 AAACAGCTCCTAGGAT
1 AAACAACTCCTAGGAT
*
10381304 AAACAACTCTTAGGAT
1 AAACAACTCCTAGGAT
10381320 AA
1 AA
10381322 GGTCTATACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.21, G:0.15, T:0.21
Consensus pattern (16 bp):
AAACAACTCCTAGGAT
Found at i:10387996 original size:18 final size:18
Alignment explanation
Indices: 10387975--10388010 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
10387965 TGAAACTCTC
*
10387975 TTTTTTTTT-CCTTTCTT
1 TTTTTTTTTACCCTTCTT
10387992 TTTTTTTTTACCCTTCTT
1 TTTTTTTTTACCCTTCTT
10388010 T
1 T
10388011 CTTTCTTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTTTTTTTACCCTTCTT
Found at i:10388039 original size:31 final size:31
Alignment explanation
Indices: 10387970--10388053 Score: 93
Period size: 31 Copynumber: 2.7 Consensus size: 31
10387960 ACTTTTGAAA
*
10387970 CTCTCTT-TTTTTTTCCTTTCTTTTTTTTTT
1 CTCTCTTCTTTCTTTCCTTTCTTTTTTTTTT
*
10388000 -TACCCTTCTTTCTTT-CTTTCTTTTTTTTCTT
1 CT-CTCTTCTTTCTTTCCTTTCTTTTTTTT-TT
* *
10388031 CTCTCTTCTTTCCTTCCATTCTT
1 CTCTCTTCTTTCTTTCCTTTCTT
10388054 CTTTACACCG
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
29 1 0.02
30 17 0.39
31 19 0.43
32 7 0.16
ACGTcount: A:0.02, C:0.27, G:0.00, T:0.70
Consensus pattern (31 bp):
CTCTCTTCTTTCTTTCCTTTCTTTTTTTTTT
Found at i:10397430 original size:18 final size:17
Alignment explanation
Indices: 10397407--10397453 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 17
10397397 GCATGAATAC
*
10397407 TATTATTTGTAAAAAAGT
1 TATTATTT-AAAAAAAGT
10397425 TATTATTTAAAAAAA--
1 TATTATTTAAAAAAAGT
10397440 T-TTATTTAAAAAAA
1 TATTATTTAAAAAAA
10397454 AAAAAGCAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
14 13 0.46
15 1 0.04
17 6 0.21
18 8 0.29
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (17 bp):
TATTATTTAAAAAAAGT
Found at i:10404552 original size:39 final size:39
Alignment explanation
Indices: 10404501--10404607 Score: 108
Period size: 39 Copynumber: 2.7 Consensus size: 39
10404491 GGGTAAAATC
* * *
10404501 TTAAATCTTTGAATGATCTCTAAGACCTCTAAAC-AAATT
1 TTAAATTTTTGAATGAT-TCTAAGACCTCCAAACAAAACT
* * *
10404540 TTAGATTTTTGAATGATTATCAAGACCTCCAAGCAAAACT
1 TTAAATTTTTGAATGATTCT-AAGACCTCCAAACAAAACT
* *
10404580 TTAAATTTTTAAATGATTTCCAAGACCT
1 TTAAATTTTTGAATGA-TTCTAAGACCT
10404608 TCAGATAAAA
Statistics
Matches: 55, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
38 2 0.04
39 26 0.47
40 25 0.45
41 2 0.04
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.36
Consensus pattern (39 bp):
TTAAATTTTTGAATGATTCTAAGACCTCCAAACAAAACT
Found at i:10404939 original size:41 final size:40
Alignment explanation
Indices: 10404495--10404939 Score: 255
Period size: 40 Copynumber: 11.1 Consensus size: 40
10404485 TTCTTTGGGT
* * * * **
10404495 AAAATCTTAAATCTTTGAATGATCTCTAAGACC-TCTAAAC
1 AAAATCTTAAATTTTTAAATGATTTCCAAGACCTTC-AGGC
* * * * *
10404535 -AAATTTTAGATTTTTGAATGATTAT-CAAGACCTCCAAGC
1 AAAATCTTAAATTTTTAAATGATT-TCCAAGACCTTCAGGC
**
10404574 AAAA-CTTTAAATTTTTAAATGATTTCCAAGACCTTCAGAT
1 AAAATC-TTAAATTTTTAAATGATTTCCAAGACCTTCAGGC
*** * * * **
10404614 AAAATCTTAAACACTTAAATGATCTCTAAAACCTTTGGGC
1 AAAATCTTAAATTTTTAAATGATTTCCAAGACCTTCAGGC
* * * * **
10404654 AAAATTTTAAAATTTT-AATGATTTGCAAAGACTTTTGGGC
1 AAAATCTTAAATTTTTAAATGATTT-CCAAGACCTTCAGGC
* * * * *
10404694 AAAATCTTAAAATTTTGAATGATTCCCAATACCTTCGGGTC
1 AAAATCTTAAATTTTTAAATGATTTCCAAGACCTTCAGG-C
* * *
10404735 -AAATTTTAAATTTTTAAAAGAATTTCAAAGACC-TCTAGGC
1 AAAATCTTAAATTTTTAAATG-ATTTCCAAGACCTTC-AGGC
* * * *
10404775 AAAAT-TTCTAATTTTTAAATGATTTCCAAAGACCTTTAAGA
1 AAAATCTT-AAATTTTTAAATGATTTCC-AAGACCTTCAGGC
* * * * *
10404816 AAAATCTTAAA-TTCTAAATGATCTCTAAGACTTTCAAGC
1 AAAATCTTAAATTTTTAAATGATTTCCAAGACCTTCAGGC
* * * * *
10404855 AAAATTTTAGACTTTTGAATGATTTCTAAAGACCTTC-GAGC
1 AAAATCTTAAATTTTTAAATGATTTC-CAAGACCTTCAG-GC
10404896 AAAATCTTAAATTTTTAAATGATTTTCCAAGA-CTTCCAGGC
1 AAAATCTTAAATTTTTAAATGA-TTTCCAAGACCTT-CAGGC
10404937 AAA
1 AAA
10404940 GACTCAAATG
Statistics
Matches: 311, Mismatches: 72, Indels: 43
0.73 0.17 0.10
Matches are distributed among these distances:
39 55 0.18
40 160 0.51
41 88 0.28
42 8 0.03
ACGTcount: A:0.39, C:0.16, G:0.10, T:0.35
Consensus pattern (40 bp):
AAAATCTTAAATTTTTAAATGATTTCCAAGACCTTCAGGC
Found at i:10406997 original size:18 final size:18
Alignment explanation
Indices: 10406962--10406997 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
10406952 ACTTCATAAT
*
10406962 AGTTTCTCCTATACATCA
1 AGTTTCTCCAATACATCA
*
10406980 AGTTTCTCCAATATATCA
1 AGTTTCTCCAATACATCA
10406998 TCTTATCTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.25, G:0.06, T:0.39
Consensus pattern (18 bp):
AGTTTCTCCAATACATCA
Found at i:10407192 original size:252 final size:249
Alignment explanation
Indices: 10406730--10407209 Score: 712
Period size: 252 Copynumber: 1.9 Consensus size: 249
10406720 AACTTCAGGA
*
10406730 AAGTTTCTCATATACATCACTTATCTCAATTTAAACCAACTTTAAACTAGTTTATCTTTTTTAAT
1 AAGTTTCTCATATACATCACTTATCTCAATTTAAACCAACTTTAAACTAATTTATCTTTTTTAAT
* * * *
10406795 TTATCTGCAGTTAATATGAATATTTAAATTTATCACAAATTTTAAAAATATTATTTAATATCTTT
66 TTATCTACAGTTAACATGAATATTTAAATTTATCACAAATTTTAAAAATATTATTCAATATCTCT
* * *
10406860 AATATTTTTTATAAATAATCTTTATATTATCTTTAGCATTTAAATATATTTCACAAAGGAAATGT
131 AATATTTTTTATAAATAATCATTATATTATCTTCAACATTTAAATATATTTCACAAAGGAAATGT
10406925 GAAAATATATATATAAATACCAAAACAACTTCATAATAGTTTCTCCTATACATC
196 GAAAATATATATATAAATACCAAAACAACTTCATAATAGTTTCTCCTATACATC
* * * **
10406979 AAGTTTCTCCA-ATATATCATCTTATCTCAATTTAAAATCAATTTTAATGTAATTTATCTTTTTT
1 AAGTTTCT-CATATACATCA-CTTATCTCAATTT-AAACCAACTTTAAACTAATTTATCTTTTTT
* * *
10407043 AATTTATCTACATTTAGCAT-AAGTATTTAAATTTATCACAATTTTTAAAAATATTATTCAATAT
63 AATTTATCTACAGTTAACATGAA-TATTTAAATTTATCACAAATTTTAAAAATATTATTCAATAT
** *
10407107 CTCTCCTATTTTTTTATAAATAATCATTATATTATCTTCAACTTTTAAATATATTTCACAAAGGA
127 CTCTAATA-TTTTTTATAAATAATCATTATATTATCTTCAACATTTAAATATATTTCACAAAGGA
* *
10407172 AATGTGAAAATATATATATAAATACTAGAACAACTTCA
191 AATGTGAAAATATATATATAAATACCAAAACAACTTCA
10407210 GGAAATCCTT
Statistics
Matches: 205, Mismatches: 21, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
249 15 0.07
250 17 0.08
251 85 0.41
252 88 0.43
ACGTcount: A:0.40, C:0.13, G:0.04, T:0.44
Consensus pattern (249 bp):
AAGTTTCTCATATACATCACTTATCTCAATTTAAACCAACTTTAAACTAATTTATCTTTTTTAAT
TTATCTACAGTTAACATGAATATTTAAATTTATCACAAATTTTAAAAATATTATTCAATATCTCT
AATATTTTTTATAAATAATCATTATATTATCTTCAACATTTAAATATATTTCACAAAGGAAATGT
GAAAATATATATATAAATACCAAAACAACTTCATAATAGTTTCTCCTATACATC
Found at i:10407425 original size:43 final size:43
Alignment explanation
Indices: 10407355--10407441 Score: 138
Period size: 43 Copynumber: 2.0 Consensus size: 43
10407345 TTCTGATGAT
*
10407355 AGGTATTATTTCACTAAACATACTATTCACTCCATCATGTAAG
1 AGGTATTATTTCACTAAACATACTATTCACTCCATCAGGTAAG
* * *
10407398 AGGTATTATTTCACTAAAGATATTATTCATTCCATCAGGTAAG
1 AGGTATTATTTCACTAAACATACTATTCACTCCATCAGGTAAG
10407441 A
1 A
10407442 TTTTTTTTTC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.36
Consensus pattern (43 bp):
AGGTATTATTTCACTAAACATACTATTCACTCCATCAGGTAAG
Found at i:10409304 original size:7 final size:7
Alignment explanation
Indices: 10409292--10409317 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
10409282 AACTGCATTA
10409292 CTTTTAT
1 CTTTTAT
10409299 CTTTTAT
1 CTTTTAT
10409306 CTTTTAT
1 CTTTTAT
10409313 CTTTT
1 CTTTT
10409318 TCTATTTTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.12, C:0.15, G:0.00, T:0.73
Consensus pattern (7 bp):
CTTTTAT
Found at i:10412243 original size:7 final size:7
Alignment explanation
Indices: 10412231--10412261 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
10412221 GTTGATAGAA
10412231 GTTTGGG
1 GTTTGGG
10412238 GTTTGGG
1 GTTTGGG
10412245 GTTTGGG
1 GTTTGGG
*
10412252 GTTTGAG
1 GTTTGGG
10412259 GTT
1 GTT
10412262 CAAACTAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.03, C:0.00, G:0.52, T:0.45
Consensus pattern (7 bp):
GTTTGGG
Found at i:10413507 original size:34 final size:35
Alignment explanation
Indices: 10413436--10413507 Score: 92
Period size: 34 Copynumber: 2.1 Consensus size: 35
10413426 TGTTAGCGGC
* *
10413436 TTTTGTATATGAAAAATGCCACTAATTTAGTGACA
1 TTTTGTATAGGAAAAATGCCACTAATATAGTGACA
* * *
10413471 TTTT-TATAGGAAAAATGCTACTAATATGGTGGCA
1 TTTTGTATAGGAAAAATGCCACTAATATAGTGACA
10413505 TTT
1 TTT
10413508 ATATGATAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
34 28 0.88
35 4 0.12
ACGTcount: A:0.35, C:0.10, G:0.17, T:0.39
Consensus pattern (35 bp):
TTTTGTATAGGAAAAATGCCACTAATATAGTGACA
Found at i:10416952 original size:20 final size:19
Alignment explanation
Indices: 10416907--10416954 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 19
10416897 TGTTGTTTAG
*
10416907 AATTAAACAAAAATAAAATA
1 AATTAAA-ACAAATAAAATA
*
10416927 AA-TAAAACAAATTAAATCA
1 AATTAAAACAAATAAAAT-A
10416946 AATTAAAAC
1 AATTAAAAC
10416955 CTTTTTAGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
18 9 0.38
19 7 0.29
20 8 0.33
ACGTcount: A:0.71, C:0.08, G:0.00, T:0.21
Consensus pattern (19 bp):
AATTAAAACAAATAAAATA
Found at i:10417393 original size:119 final size:119
Alignment explanation
Indices: 10417148--10417554 Score: 422
Period size: 119 Copynumber: 3.4 Consensus size: 119
10417138 AATGACTAGT
* * * **
10417148 ACGAAACCACAAGTCATAAGAAATGATCTAGACTGAGCCAAGATCTGGTGATTGGGATGAAACCA
1 ACGAAACCACGAGTCATAAGAAATGATCTAGACTGAGCCAAGATCAGGTGATCGGGACAAAACCA
* * * * * **
10417213 C-AAGCAAAAAAAAATGAACAGGATCGATTCGAGGTTGAAAATAAATGACCAAG
66 CGAATCAAAATAAAACGAACAGGATCGAGTCGAGGTTGAAAATAAATAACCGGG
* * * * * *
10417266 ACGGAACCACGAGTCATAAGAAATTATTTGGACTAAGCCAAGATTAGGTGATCGGGACAAAACCA
1 ACGAAACCACGAGTCATAAGAAATGATCTAGACTGAGCCAAGATCAGGTGATCGGGACAAAACCA
* * * *
10417331 CGAATCAAAATAAAGCGACCAGGATCGAGTCGAGGTTGAAATTAAATTACCGGG
66 CGAATCAAAATAAAACGAACAGGATCGAGTCGAGGTTGAAAATAAATAACCGGG
* * * * *
10417385 ATGAAACCACTAGTCATAAGAAATGATCTAGACTGAGCCAAAATCAGGTGA-CTAGAACAAAACC
1 ACGAAACCACGAGTCATAAGAAATGATCTAGACTGAGCCAAGATCAGGTGATC-GGGACAAAACC
* * * * * ** *
10417449 ATGAGTCCAAATAAAACGATCAGGATAGAGTCGAGGTCAAAAATAAATAATCGGG
65 ACGAATCAAAATAAAACGAACAGGATCGAGTCGAGGTTGAAAATAAATAACCGGG
* * * * * *
10417504 ACGAAACCATGAATCATAAGAAATGATTTGGATTGAGCCGAGATCAGGTGA
1 ACGAAACCACGAGTCATAAGAAATGATCTAGACTGAGCCAAGATCAGGTGA
10417555 CTGGGATGAA
Statistics
Matches: 235, Mismatches: 52, Indels: 3
0.81 0.18 0.01
Matches are distributed among these distances:
118 56 0.24
119 179 0.76
ACGTcount: A:0.43, C:0.16, G:0.23, T:0.18
Consensus pattern (119 bp):
ACGAAACCACGAGTCATAAGAAATGATCTAGACTGAGCCAAGATCAGGTGATCGGGACAAAACCA
CGAATCAAAATAAAACGAACAGGATCGAGTCGAGGTTGAAAATAAATAACCGGG
Found at i:10417769 original size:17 final size:18
Alignment explanation
Indices: 10417749--10417792 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
10417739 CGCAAATGTG
10417749 CTAAATTCACAAAGA-TT
1 CTAAATTCACAAAGACTT
* *
10417766 CTAAGTTCACAAGGACTT
1 CTAAATTCACAAAGACTT
*
10417784 TTAAATTCA
1 CTAAATTCA
10417793 TAAGAAAGAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 13 0.59
18 9 0.41
ACGTcount: A:0.41, C:0.18, G:0.09, T:0.32
Consensus pattern (18 bp):
CTAAATTCACAAAGACTT
Found at i:10417978 original size:69 final size:69
Alignment explanation
Indices: 10417897--10418056 Score: 236
Period size: 68 Copynumber: 2.3 Consensus size: 69
10417887 AAAAATTCAC
* *
10417897 AAGATTCCAAGTTTCGCAAAGGTTT-TAGATTCACAAGAACATTCAAATTCGTAAGAAAGAAAGA
1 AAGATTCTAAGTTTCGCAAAGGTTTCTAGATTCACAAGAACATTC-AATTCGCAAGAAAGAAAGA
*
10417961 TTTGT
65 TTTAT
* *
10417966 AAGATTCTAAGTTTCACAAA-GTTTCTAGATTCACAAGAACTTTCAATTCGCAAGAAAGAAAGAT
1 AAGATTCTAAGTTTCGCAAAGGTTTCTAGATTCACAAGAACATTCAATTCGCAAGAAAGAAAGAT
10418030 TTAT
66 TTAT
10418034 AAGATT-TCAAGTTTCGCAAAGGT
1 AAGATTCT-AAGTTTCGCAAAGGT
10418057 GCAAGATTCG
Statistics
Matches: 82, Mismatches: 6, Indels: 6
0.87 0.06 0.06
Matches are distributed among these distances:
67 1 0.01
68 43 0.52
69 38 0.46
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.30
Consensus pattern (69 bp):
AAGATTCTAAGTTTCGCAAAGGTTTCTAGATTCACAAGAACATTCAATTCGCAAGAAAGAAAGAT
TTAT
Found at i:10418046 original size:68 final size:68
Alignment explanation
Indices: 10417897--10418083 Score: 234
Period size: 68 Copynumber: 2.7 Consensus size: 68
10417887 AAAAATTCAC
* * *
10417897 AAGATTCCAAGTTTCGCAAAGGTTT-TAGATTCACAAGAACATTCAAATTCGTAAGAAAGAAAGA
1 AAGATTTCAAGTTTCGCAAA-GTTTCTAGATTCACAAGAACTTTC-AATTCGCAAGAAAGAAAGA
*
10417961 TTTGT
64 TTTAT
*
10417966 AAGA-TTCTAAGTTTCACAAAGTTTCTAGATTCACAAGAACTTTCAATTCGCAAGAAAGAAAGAT
1 AAGATTTC-AAGTTTCGCAAAGTTTCTAGATTCACAAGAACTTTCAATTCGCAAGAAAGAAAGAT
10418030 TTAT
65 TTAT
* * * * *
10418034 AAGATTTCAAGTTTCGCAAAGGTGCAAGATTCGCAAGGACTTTCAGATTC
1 AAGATTTCAAGTTTCGCAAAGTTTCTAGATTCACAAGAACTTTCA-ATTC
10418084 ACAGATTTCA
Statistics
Matches: 103, Mismatches: 11, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
68 63 0.61
69 40 0.39
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.29
Consensus pattern (68 bp):
AAGATTTCAAGTTTCGCAAAGTTTCTAGATTCACAAGAACTTTCAATTCGCAAGAAAGAAAGATT
TAT
Found at i:10418141 original size:51 final size:51
Alignment explanation
Indices: 10418011--10418141 Score: 133
Period size: 51 Copynumber: 2.6 Consensus size: 51
10418001 AGAACTTTCA
10418011 ATTCGCAAGAAAGAAAGATT-TATAAGATTTCAAGTTTCGCAAAGGTGCAAG
1 ATTCGCAAGAAAGAAAGATTCT-TAAGATTTCAAGTTTCGCAAAGGTGCAAG
***** *
10418062 ATTCGCAAGGACTTTCAGATTC--ACAGATTTCAAGTTTTGCAAAGGTGCAAG
1 ATTCGCAA-GAAAGAAAGATTCTTA-AGATTTCAAGTTTCGCAAAGGTGCAAG
* * *
10418113 GTTTGTAAGAAAGAAAGATTCTTAAGATT
1 ATTCGCAAGAAAGAAAGATTCTTAAGATT
10418142 CTATGCTTCA
Statistics
Matches: 61, Mismatches: 14, Indels: 10
0.72 0.16 0.12
Matches are distributed among these distances:
50 9 0.15
51 44 0.72
52 8 0.13
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.29
Consensus pattern (51 bp):
ATTCGCAAGAAAGAAAGATTCTTAAGATTTCAAGTTTCGCAAAGGTGCAAG
Found at i:10418442 original size:72 final size:72
Alignment explanation
Indices: 10418356--10418499 Score: 279
Period size: 72 Copynumber: 2.0 Consensus size: 72
10418346 TGACCTATCT
*
10418356 AGGATGTAAATGTAAACACAATGTATGTAGTGTAGATGTCATGAGATTTCATTGTGGTGATGAGG
1 AGGATGTAAATGTAAACACAATGTATGTAGTGCAGATGTCATGAGATTTCATTGTGGTGATGAGG
10418421 TTCTTAA
66 TTCTTAA
10418428 AGGATGTAAATGTAAACACAATGTATGTAGTGCAGATGTCATGAGATTTCATTGTGGTGATGAGG
1 AGGATGTAAATGTAAACACAATGTATGTAGTGCAGATGTCATGAGATTTCATTGTGGTGATGAGG
10418493 TTCTTAA
66 TTCTTAA
10418500 GACTCCACCA
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 71 1.00
ACGTcount: A:0.32, C:0.08, G:0.26, T:0.34
Consensus pattern (72 bp):
AGGATGTAAATGTAAACACAATGTATGTAGTGCAGATGTCATGAGATTTCATTGTGGTGATGAGG
TTCTTAA
Found at i:10419148 original size:24 final size:24
Alignment explanation
Indices: 10419120--10419179 Score: 67
Period size: 23 Copynumber: 2.6 Consensus size: 24
10419110 TTTTTCCTCA
10419120 TTTGTCTCTTTTTTTTT-TTGT-TT
1 TTTGTCTCTTTTTTTTTATT-TATT
10419143 TCTTGT-T-TTTTTTTTTATTTATT
1 T-TTGTCTCTTTTTTTTTATTTATT
10419166 TTT-TCTCTTTTTTT
1 TTTGTCTCTTTTTTT
10419180 GTACATATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
21 1 0.03
22 13 0.41
23 14 0.44
24 4 0.12
ACGTcount: A:0.03, C:0.08, G:0.05, T:0.83
Consensus pattern (24 bp):
TTTGTCTCTTTTTTTTTATTTATT
Found at i:10423020 original size:21 final size:22
Alignment explanation
Indices: 10422995--10423036 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
10422985 TAAAAAGATT
10422995 TTTTTTAGAAAATAT-TTTTTC
1 TTTTTTAGAAAATATATTTTTC
**
10423016 TTTTTTTTAAAATATATTTTT
1 TTTTTTAGAAAATATATTTTT
10423037 TCAAAAATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (22 bp):
TTTTTTAGAAAATATATTTTTC
Found at i:10423023 original size:23 final size:23
Alignment explanation
Indices: 10422993--10423038 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
10422983 TTTAAAAAGA
10422993 TTTTTTTTAGAAA-ATATTTTTTC
1 TTTTTTTTA-AAATATATTTTTTC
10423016 TTTTTTTTAAAATATATTTTTTC
1 TTTTTTTTAAAATATATTTTTTC
10423039 AAAAATGTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 3 0.14
23 19 0.86
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.67
Consensus pattern (23 bp):
TTTTTTTTAAAATATATTTTTTC
Found at i:10424794 original size:20 final size:19
Alignment explanation
Indices: 10424749--10424796 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 19
10424739 TTACAAGTAG
*
10424749 AATTAAACAAAAATAAAATA
1 AATTAAA-ACAAATAAAATA
*
10424769 AA-TAAAACAAATTAAATCA
1 AATTAAAACAAATAAAAT-A
10424788 AATTAAAAC
1 AATTAAAAC
10424797 CTTTTTATTG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
18 9 0.38
19 7 0.29
20 8 0.33
ACGTcount: A:0.71, C:0.08, G:0.00, T:0.21
Consensus pattern (19 bp):
AATTAAAACAAATAAAATA
Found at i:10425415 original size:140 final size:140
Alignment explanation
Indices: 10425163--10425425 Score: 323
Period size: 140 Copynumber: 1.9 Consensus size: 140
10425153 GACATAAATG
*
10425163 ATAACTTTTTTATACATATCAACCATAAAAATCAAGTTCAATCAATCAAACAAGTTTAATATCAA
1 ATAACTTTTTCATACATATCAACCATAAAAATCAAGTTCAATCAATCAAACAAGTTTAATATCAA
** * * * * *
10425228 GTATTGAAGTTATCCAAACTGTTAAAATAGAACAGTAACAACAAATTTGTATTTTTACCTAAATA
66 GTATTGAAACTATCAAAACTATTAAAATAGAACAATAACAACAAATTTGCATATTTACCTAAATA
10425293 GATGTAAACA
131 GATGTAAACA
* * ** * *
10425303 ATAACTTTTTCATACATATCAACCATGACAA-CTAAGTTCAATACTTTC-GATAAGTTTAATATC
1 ATAACTTTTTCATACATATCAACCATAAAAATC-AAGTTCAAT-CAATCAAACAAGTTTAATATC
* ****
10425366 ATGTATTGAAACTATCAAAACTATTAAAATAGAACAATAACTGTTAATTTGCATATTTAC
64 AAGTATTGAAACTATCAAAACTATTAAAATAGAACAATAACAACAAATTTGCATATTTAC
10425426 ATTTTAACAG
Statistics
Matches: 102, Mismatches: 19, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
139 1 0.01
140 98 0.96
141 3 0.03
ACGTcount: A:0.44, C:0.15, G:0.08, T:0.34
Consensus pattern (140 bp):
ATAACTTTTTCATACATATCAACCATAAAAATCAAGTTCAATCAATCAAACAAGTTTAATATCAA
GTATTGAAACTATCAAAACTATTAAAATAGAACAATAACAACAAATTTGCATATTTACCTAAATA
GATGTAAACA
Found at i:10431820 original size:13 final size:12
Alignment explanation
Indices: 10431797--10431828 Score: 55
Period size: 13 Copynumber: 2.6 Consensus size: 12
10431787 AATTCATTCT
10431797 AATTTTTGAAGG
1 AATTTTTGAAGG
10431809 AATTTATTGAAGG
1 AATTT-TTGAAGG
10431822 AATTTTT
1 AATTTTT
10431829 TGCATTATAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.34, C:0.00, G:0.19, T:0.47
Consensus pattern (12 bp):
AATTTTTGAAGG
Found at i:10432096 original size:186 final size:187
Alignment explanation
Indices: 10431749--10432194 Score: 621
Period size: 186 Copynumber: 2.4 Consensus size: 187
10431739 TTGAAAGAGG
*
10431749 GTTATTGAATGCGTTTATTCCAAAAAAATACCTTCACTAATTCATTCTAATTTTTGAAGGAATTT
1 GTTATTGAATGCGTTTATTCCAAAAAAATACCTTCACTAATTCATTCTAATTTTTGAAAGAATTT
* *
10431814 ATTGAAGGAATTTTTTGCATTATACGCCTTCAATAATTTTTTTAAAAAAATTATTTAAAATTATT
66 ATTGAAAGAATTTTTTGCATTATACGCCTTCAATAATTTTTTTAAAAAAATTATTTAAAACTATT
*
10431879 AAATGCATCTTTTTGTAGAAAACGCCTTCAATATTCTACTACTAAAATTTTAAGGGT
131 AAAGGCATCTTTTTGTAGAAAACGCCTTCAATATTCTACTACTAAAATTTTAAGGGT
* * * *
10431936 GTTATTAAAGGCGTTTATTCCGGAAAAACT-CCTTCACTAATTCATTCTAATTTTTGAAAGAATT
1 GTTATTGAATGCGTTTATTCC-AAAAAAATACCTTCACTAATTCATTCTAATTTTTGAAAGAATT
* * * * **
10432000 TATTGAAAGCA-TTTTTGCATTATATGCCTTCAATAATTTCTTTT-TAAAAATTGTTTAGGACTA
65 TATTGAAAGAATTTTTTGCATTATACGCCTTCAATAATTT-TTTTAAAAAAATTATTTAAAACTA
* *
10432063 TTAAAGGTAT-TTTTTAGTAGAAAACGCCTTCAATATTCTATTACTAAAATTTTAAGGGT
129 TTAAAGGCATCTTTTT-GTAGAAAACGCCTTCAATATTCTACTACTAAAATTTTAAGGGT
* ** * * *
10432122 GTTATTGAATGCGCTTATTCTCAAAAAAATGTCTTCACTAATTTATTATAATTTTTTGAAAAAAT
1 GTTATTGAATGCGTTTATTC-CAAAAAAATACCTTCACTAATTCATTCTAA-TTTTTGAAAGAAT
10432187 TTATTGAA
64 TTATTGAA
10432195 GTATTTCTAT
Statistics
Matches: 228, Mismatches: 25, Indels: 11
0.86 0.09 0.04
Matches are distributed among these distances:
185 5 0.02
186 114 0.50
187 83 0.36
188 26 0.11
ACGTcount: A:0.35, C:0.12, G:0.11, T:0.42
Consensus pattern (187 bp):
GTTATTGAATGCGTTTATTCCAAAAAAATACCTTCACTAATTCATTCTAATTTTTGAAAGAATTT
ATTGAAAGAATTTTTTGCATTATACGCCTTCAATAATTTTTTTAAAAAAATTATTTAAAACTATT
AAAGGCATCTTTTTGTAGAAAACGCCTTCAATATTCTACTACTAAAATTTTAAGGGT
Found at i:10433106 original size:12 final size:12
Alignment explanation
Indices: 10433089--10433128 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
10433079 TGTATGATAT
10433089 TGGTATGCTGAA
1 TGGTATGCTGAA
*
10433101 TGGTATGCTAAA
1 TGGTATGCTGAA
* *
10433113 TGATTTGCTGAA
1 TGGTATGCTGAA
10433125 TGGT
1 TGGT
10433129 GTTTTTGTAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.25, C:0.07, G:0.30, T:0.38
Consensus pattern (12 bp):
TGGTATGCTGAA
Found at i:10437885 original size:6 final size:6
Alignment explanation
Indices: 10437874--10437910 Score: 65
Period size: 6 Copynumber: 6.2 Consensus size: 6
10437864 ATTTTGAAAG
*
10437874 AATAAA AATAAA AGTAAA AATAAA AATAAA AATAAA A
1 AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA A
10437911 GTGCCTTTCT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.16
Consensus pattern (6 bp):
AATAAA
Found at i:10441582 original size:13 final size:13
Alignment explanation
Indices: 10441564--10441588 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
10441554 TAGAATAAAG
10441564 TAAAATTTTTTAA
1 TAAAATTTTTTAA
10441577 TAAAATTTTTTA
1 TAAAATTTTTTA
10441589 TTATATTATT
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TAAAATTTTTTAA
Found at i:10443989 original size:2 final size:2
Alignment explanation
Indices: 10443982--10444009 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
10443972 TGCACACCCT
10443982 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
10444010 ATGCATACAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:10445371 original size:15 final size:15
Alignment explanation
Indices: 10445351--10445409 Score: 73
Period size: 15 Copynumber: 3.6 Consensus size: 15
10445341 CTACTTATTA
10445351 AATTTTATTAATCTT
1 AATTTTATTAATCTT
10445366 AATTTTTAGTTATTAATCTT
1 AA---TT--TTATTAATCTT
10445386 AATTTTATTAATCTT
1 AATTTTATTAATCTT
10445401 AATTTTATT
1 AATTTTATT
10445410 GATCCCAATG
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
15 22 0.56
17 2 0.05
18 2 0.05
20 13 0.33
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.61
Consensus pattern (15 bp):
AATTTTATTAATCTT
Found at i:10458375 original size:9 final size:9
Alignment explanation
Indices: 10458350--10458403 Score: 51
Period size: 9 Copynumber: 6.0 Consensus size: 9
10458340 ATCTGACTTT
10458350 TTAAAAAAA
1 TTAAAAAAA
10458359 TTACAAAAAA
1 TTA-AAAAAA
10458369 TTAAAAAAGA
1 TTAAAAAA-A
*
10458379 --AAGAAAA
1 TTAAAAAAA
10458386 -TAAGAAAAA
1 TTAA-AAAAA
10458395 TTAAAAAAA
1 TTAAAAAAA
10458404 ATCAAAATAC
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
7 1 0.03
8 7 0.18
9 17 0.45
10 13 0.34
ACGTcount: A:0.76, C:0.02, G:0.06, T:0.17
Consensus pattern (9 bp):
TTAAAAAAA
Found at i:10458399 original size:26 final size:25
Alignment explanation
Indices: 10458364--10458432 Score: 84
Period size: 26 Copynumber: 2.7 Consensus size: 25
10458354 AAAAATTACA
10458364 AAAAATTAAAAAAGAAAGAAAATAAG
1 AAAAATTAAAAAA-AAAGAAAATAAG
** **
10458390 AAAAATTAAAAAAAATCAAAATACT
1 AAAAATTAAAAAAAAAGAAAATAAG
10458415 AAAATATTAAAAAAAAAG
1 AAAA-ATTAAAAAAAAAG
10458433 TAAACATTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
25 12 0.33
26 24 0.67
ACGTcount: A:0.75, C:0.03, G:0.06, T:0.16
Consensus pattern (25 bp):
AAAAATTAAAAAAAAAGAAAATAAG
Found at i:10458457 original size:29 final size:28
Alignment explanation
Indices: 10458425--10458493 Score: 70
Period size: 29 Copynumber: 2.4 Consensus size: 28
10458415 AAAATATTAA
*
10458425 AAAAAAAGTAAACATTTTGAAAA-TTTCTT
1 AAAAAAAGTAAACATTTT-AAAATTTTC-G
* *
10458454 AAAAATA-TGAAATATTTTAAAATTTTCG
1 AAAAAAAGT-AAACATTTTAAAATTTTCG
10458482 AAAAAAAGTAAA
1 AAAAAAAGTAAA
10458494 AAATATTAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
28 14 0.42
29 19 0.58
ACGTcount: A:0.57, C:0.04, G:0.07, T:0.32
Consensus pattern (28 bp):
AAAAAAAGTAAACATTTTAAAATTTTCG
Found at i:10458788 original size:16 final size:16
Alignment explanation
Indices: 10458769--10458802 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
10458759 TTTTCCTATG
*
10458769 TTTTATTTTTTATTTT
1 TTTTATTTTTCATTTT
10458785 TTTTATTTTTCATTTT
1 TTTTATTTTTCATTTT
10458801 TT
1 TT
10458803 CATGTTTTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.12, C:0.03, G:0.00, T:0.85
Consensus pattern (16 bp):
TTTTATTTTTCATTTT
Found at i:10458832 original size:12 final size:11
Alignment explanation
Indices: 10458814--10458843 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
10458804 ATGTTTTACT
10458814 ATTTTTTTGGA
1 ATTTTTTTGGA
10458825 ATTTTTTTGGA
1 ATTTTTTTGGA
10458836 ATTTTTTT
1 ATTTTTTT
10458844 AAATATGGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.17, C:0.00, G:0.13, T:0.70
Consensus pattern (11 bp):
ATTTTTTTGGA
Found at i:10458902 original size:17 final size:17
Alignment explanation
Indices: 10458861--10458902 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
10458851 GTAAATTTTA
*
10458861 AGATTTTTTATATTCTT
1 AGATTTTTTATATTATT
*
10458878 ACGATTTTTAAT-TTATT
1 A-GATTTTTTATATTATT
10458895 AGATTTTT
1 AGATTTTT
10458903 GTTAGAGTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 7 0.32
17 6 0.27
18 9 0.41
ACGTcount: A:0.26, C:0.05, G:0.07, T:0.62
Consensus pattern (17 bp):
AGATTTTTTATATTATT
Found at i:10459166 original size:19 final size:20
Alignment explanation
Indices: 10459144--10459188 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
10459134 AATTTTTCTC
*
10459144 TTTTTTTGAGA-TTTTGTGA
1 TTTTTTTGAAATTTTTGTGA
*
10459163 TTTTTTTGAAATTTTTTTGA
1 TTTTTTTGAAATTTTTGTGA
10459183 TTTTTT
1 TTTTTT
10459189 ATACTTTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 10 0.43
20 13 0.57
ACGTcount: A:0.16, C:0.00, G:0.13, T:0.71
Consensus pattern (20 bp):
TTTTTTTGAAATTTTTGTGA
Found at i:10459220 original size:19 final size:19
Alignment explanation
Indices: 10459192--10459240 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
10459182 ATTTTTTATA
* *
10459192 CTTTAATTTTTT-TAATTT
1 CTTTTATTTTTTAGAATTT
10459210 CTTTTAGTTTTTTAGAATTT
1 CTTTTA-TTTTTTAGAATTT
*
10459230 GTTTTATTTTT
1 CTTTTATTTTT
10459241 ACTTTTCATT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
18 5 0.19
19 11 0.42
20 10 0.38
ACGTcount: A:0.18, C:0.04, G:0.06, T:0.71
Consensus pattern (19 bp):
CTTTTATTTTTTAGAATTT
Found at i:10463786 original size:16 final size:16
Alignment explanation
Indices: 10463765--10463795 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
10463755 TCACTAAAAT
*
10463765 ACTAAACACTATTATC
1 ACTAAACAATATTATC
10463781 ACTAAACAATATTAT
1 ACTAAACAATATTAT
10463796 TAATTAGAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.19, G:0.00, T:0.32
Consensus pattern (16 bp):
ACTAAACAATATTATC
Found at i:10470839 original size:3 final size:3
Alignment explanation
Indices: 10470831--10470877 Score: 53
Period size: 3 Copynumber: 16.0 Consensus size: 3
10470821 TAATGAGTAA
* *
10470831 AAT AAT AATT AAG AAT AAT AAT AAT AAT AA- AAT AAA AAT AA- AAT
1 AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
10470875 AAT
1 AAT
10470878 CAAATCAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
2 4 0.11
3 30 0.81
4 3 0.08
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:10470855 original size:19 final size:17
Alignment explanation
Indices: 10470829--10470876 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
10470819 AATAATGAGT
10470829 AAAATAATAATTAAGAATA
1 AAAATAATAA-TAA-AATA
*
10470848 ATAATAATAATAAAATA
1 AAAATAATAATAAAATA
10470865 AAAATAA-AATAA
1 AAAATAATAATAA
10470877 TCAAATCAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
16 5 0.19
17 10 0.37
18 3 0.11
19 9 0.33
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (17 bp):
AAAATAATAATAAAATA
Found at i:10470877 original size:19 final size:19
Alignment explanation
Indices: 10470828--10470906 Score: 61
Period size: 19 Copynumber: 4.0 Consensus size: 19
10470818 AAATAATGAG
* *
10470828 TAAAATAATAATTAAGAATAA
1 TAAAATAATAA--AATAAAAA
10470849 TAATAATAATAAAATAAAAA
1 TAA-AATAATAAAATAAAAA
* *
10470869 TAAAATAATCAAATCAAAA
1 TAAAATAATAAAATAAAAA
* *
10470888 CAAAA-AATAGAATGAAAAA
1 TAAAATAATAAAAT-AAAAA
10470907 AGGAAATAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
18 6 0.12
19 22 0.46
20 9 0.19
21 3 0.06
22 8 0.17
ACGTcount: A:0.71, C:0.04, G:0.04, T:0.22
Consensus pattern (19 bp):
TAAAATAATAAAATAAAAA
Found at i:10473878 original size:31 final size:30
Alignment explanation
Indices: 10473842--10473907 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 30
10473832 TTATTCACCG
*
10473842 AAAAATTCAACCAAACTC-AAAAAAATCTAGA
1 AAAAATTCAA-AAAACTCAAAAAAAATCTA-A
* *
10473873 AAAAATTGAAAAAATTCAAAAAAAATCTAA
1 AAAAATTCAAAAAACTCAAAAAAAATCTAA
10473903 AAAAA
1 AAAAA
10473908 CTCTCAGATG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 11 0.35
31 20 0.65
ACGTcount: A:0.68, C:0.12, G:0.03, T:0.17
Consensus pattern (30 bp):
AAAAATTCAAAAAACTCAAAAAAAATCTAA
Found at i:10474347 original size:3 final size:3
Alignment explanation
Indices: 10474333--10474417 Score: 145
Period size: 3 Copynumber: 28.3 Consensus size: 3
10474323 TAAAAACAGA
*
10474333 AAT AAA AAT AAT AAT AAT AGA- AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT
10474378 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
10474418 GCAAAAGCAT
Statistics
Matches: 78, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
2 1 0.01
3 76 0.97
4 1 0.01
ACGTcount: A:0.68, C:0.00, G:0.01, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:10474866 original size:119 final size:119
Alignment explanation
Indices: 10474726--10475363 Score: 617
Period size: 119 Copynumber: 5.4 Consensus size: 119
10474716 ATTTCGGACC
* * * * * *
10474726 AAACCACAAATCATAAA-AAATGATCTGGACTGAGCTAAGATTAAGTGA-CTAAGATGAAACCAC
1 AAACCACGAATCA-AAAGAAATGATCTGGATTGAGCCAAGATCAAGTGATC-AGGACGAAACCAC
** * **
10474789 AAGTCAAAATAAAGCAACTAGGACTGAGTCGAGGTAAAAAATGAATGATCAGGATG
64 AAGTCAAAATAAAGTGACTAGGACCGAGTCGAGGTCGAAAATGAATGATCAGGATG
* * *
10474845 AAACCACGAATTAAAAGAAATGATCTGGATTAAGCCAAGATC-AGATGATCAGGACAAAACCACA
1 AAACCACGAATCAAAAGAAATGATCTGGATTGAGCCAAGATCAAG-TGATCAGGACGAAACCACA
* * * *
10474909 AGTCGAAATAAAGTGACTAGGACCGAGTTGAGGTTGAAAATGAATGATTAGGATG
65 AGTCAAAATAAAGTGACTAGGACCGAGTCGAGGTCGAAAATGAATGATCAGGATG
* * * * * * *
10474964 GAACCACAAATCATAAGAAATGAT-TGGATTGAACCAAGATCAGGTGATCGGGACAAAACCACAA
1 AAACCACGAATCAAAAGAAATGATCTGGATTGAGCCAAGATCAAGTGATCAGGACGAAACCACAA
* * *
10475028 GTCGAAATAAAAGTGATTAGGACCGAGTCGATGTCGAAAATGAATGATC-GAGATG
66 GTCAAAAT-AAAGTGACTAGGACCGAGTCGAGGTCGAAAATGAATGATCAG-GATG
* * * * * * *
10475083 AAACCATGAATTATAAGAAATGATTTAGATTGAGCCAAGATCAGGTGATC-GAGACGGAACCACA
1 AAACCACGAATCAAAAGAAATGATCTGGATTGAGCCAAGATCAAGTGATCAG-GACGAAACCACA
** * *
10475147 AGTCAAAATAAAACGA-TCAGGACCGAGTCGAGGTCGAAAATAAATGATCAGGACG
65 AGTCAAAATAAAGTGACT-AGGACCGAGTCGAGGTCGAAAATGAATGATCAGGATG
* * * *
10475202 AAACCACGAATCATAAA-AAATGATATGGACTGAGCCAAGATCAAGTGATCAGGATGAAATCACA
1 AAACCACGAATCA-AAAGAAATGATCTGGATTGAGCCAAGATCAAGTGATCAGGACGAAACCACA
* * * * * * * *
10475266 AATTAAAATAGAGTGACTAGGACCGAGGCGAGATCGAAAATGAATGATTAAGACG
65 AGTCAAAATAAAGTGACTAGGACCGAGTCGAGGTCGAAAATGAATGATCAGGATG
* * *** * * *
10475321 GAACCACAAATTTTAAGAAATGATTTAGATTGAGCCAAAATCA
1 AAACCACGAATCAAAAGAAATGATCTGGATTGAGCCAAGATCA
10475364 GGTAGATGTA
Statistics
Matches: 432, Mismatches: 73, Indels: 28
0.81 0.14 0.05
Matches are distributed among these distances:
118 51 0.12
119 334 0.77
120 47 0.11
ACGTcount: A:0.44, C:0.15, G:0.22, T:0.19
Consensus pattern (119 bp):
AAACCACGAATCAAAAGAAATGATCTGGATTGAGCCAAGATCAAGTGATCAGGACGAAACCACAA
GTCAAAATAAAGTGACTAGGACCGAGTCGAGGTCGAAAATGAATGATCAGGATG
Found at i:10475366 original size:238 final size:236
Alignment explanation
Indices: 10474721--10475366 Score: 749
Period size: 238 Copynumber: 2.7 Consensus size: 236
10474711 TGAATATTTC
* * * *
10474721 GGACCAAACCACAAATCATAAAAAATGATCTGGACTGAGCTAAGATTAAGTGA-CTAAGATGAAA
1 GGACGAAACCACAAATCATAAAAAATGAT-TGGACTGAGCCAAGATCAAGTGATC-AGGATGAAA
** * ** *
10474785 CCACAAGTCAAAATAAAGCAACTAGGACTGAGTCGAGGTAAAAAATGAATGATCAGGATGAAACC
64 CCACAAGTCAAAATAAAGTGACTAGGACCGAGTCGA-GTCGAAAATGAATGATCAAGATGAAACC
* * * * * *
10474850 ACGAATTAAAAGAAATGATCTGGATTAAGCCAAGATCAGATGATCAGGACAAAACCACAAGTCGA
128 ACGAATTATAAGAAATGATTTAGATTGAGCCAAGATCAGGTGATCAGGACAAAACCACAAGTCAA
** * * * *
10474915 AATAAAGTGACTAGGACCGAGTTGAGGTTGAAAATGAATGATTA
193 AATAAAACGACTAGGACCGAGTCGAGGTCGAAAATAAATGATCA
* * * * * * * **
10474959 GGATGGAACCACAAATCATAAGAAATGATTGGATTGAACCAAGATCAGGTGATCGGGACAAAACC
1 GGACGAAACCACAAATCATAAAAAATGATTGGACTGAGCCAAGATCAAGTGATCAGGATGAAACC
* * *
10475024 ACAAGTCGAAATAAAAGTGATTAGGACCGAGTCGATGTCGAAAATGAATGATCGAGATGAAACCA
66 ACAAGTCAAAAT-AAAGTGACTAGGACCGAGTCGA-GTCGAAAATGAATGATCAAGATGAAACCA
* **
10475089 TGAATTATAAGAAATGATTTAGATTGAGCCAAGATCAGGTGATC-GAGACGGAACCACAAGTCAA
129 CGAATTATAAGAAATGATTTAGATTGAGCCAAGATCAGGTGATCAG-GACAAAACCACAAGTCAA
10475153 AATAAAACGA-TCAGGACCGAGTCGAGGTCGAAAATAAATGATCA
193 AATAAAACGACT-AGGACCGAGTCGAGGTCGAAAATAAATGATCA
* *
10475197 GGACGAAACCACGAATCATAAAAAATGATATGGACTGAGCCAAGATCAAGTGATCAGGATGAAAT
1 GGACGAAACCACAAATCATAAAAAATGAT-TGGACTGAGCCAAGATCAAGTGATCAGGATGAAAC
* * * * * * *
10475262 CACAAATTAAAATAGAGTGACTAGGACCGAGGCGAGATCGAAAATGAATGATTAAGACGGAACCA
65 CACAAGTCAAAATAAAGTGACTAGGACCGAGTCGAG-TCGAAAATGAATGATCAAGATGAAACCA
* * *
10475327 CAAATTTTAAGAAATGATTTAGATTGAGCCAAAATCAGGT
129 CGAATTATAAGAAATGATTTAGATTGAGCCAAGATCAGGT
10475367 AGATGTAAAT
Statistics
Matches: 339, Mismatches: 63, Indels: 12
0.82 0.15 0.03
Matches are distributed among these distances:
237 39 0.12
238 262 0.77
239 38 0.11
ACGTcount: A:0.44, C:0.15, G:0.23, T:0.19
Consensus pattern (236 bp):
GGACGAAACCACAAATCATAAAAAATGATTGGACTGAGCCAAGATCAAGTGATCAGGATGAAACC
ACAAGTCAAAATAAAGTGACTAGGACCGAGTCGAGTCGAAAATGAATGATCAAGATGAAACCACG
AATTATAAGAAATGATTTAGATTGAGCCAAGATCAGGTGATCAGGACAAAACCACAAGTCAAAAT
AAAACGACTAGGACCGAGTCGAGGTCGAAAATAAATGATCA
Found at i:10475674 original size:33 final size:34
Alignment explanation
Indices: 10475576--10475676 Score: 114
Period size: 34 Copynumber: 3.0 Consensus size: 34
10475566 TGCATTTTTG
* * *
10475576 GCAAAAAAATCATCTTTTATCAGCTTAGAGGCAT
1 GCAAAGAAATCATATTTCATCAGCTTAGAGGCAT
* * ***
10475610 GCAAAGAAATTATTTTTCATCAGCCCGGAGGCAT
1 GCAAAGAAATCATATTTCATCAGCTTAGAGGCAT
*
10475644 GCAAAGAAA-CATATTTCATCATCTTAGAGGCAT
1 GCAAAGAAATCATATTTCATCAGCTTAGAGGCAT
10475677 TTTTTGGTAA
Statistics
Matches: 54, Mismatches: 13, Indels: 1
0.79 0.19 0.01
Matches are distributed among these distances:
33 18 0.33
34 36 0.67
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.28
Consensus pattern (34 bp):
GCAAAGAAATCATATTTCATCAGCTTAGAGGCAT
Found at i:10476241 original size:6 final size:6
Alignment explanation
Indices: 10476221--10476261 Score: 57
Period size: 6 Copynumber: 6.8 Consensus size: 6
10476211 GAACTTCTCT
*
10476221 TTTTTT TTTTGTA TTTTTA -TTTTA TTTTTA TTTTTA TTTTT
1 TTTTTA TTTT-TA TTTTTA TTTTTA TTTTTA TTTTTA TTTTT
10476262 GTATTTTGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
5 5 0.16
6 22 0.69
7 5 0.16
ACGTcount: A:0.12, C:0.00, G:0.02, T:0.85
Consensus pattern (6 bp):
TTTTTA
Found at i:10476248 original size:25 final size:25
Alignment explanation
Indices: 10476220--10476268 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
10476210 TGAACTTCTC
* *
10476220 TTTTTTTTTTTGTATTTT-TATTTTA
1 TTTTTATTTTTAT-TTTTGTATTTTA
10476245 TTTTTATTTTTATTTTTGTATTTT
1 TTTTTATTTTTATTTTTGTATTTT
10476269 GAATCAAGCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 4 0.19
25 17 0.81
ACGTcount: A:0.12, C:0.00, G:0.04, T:0.84
Consensus pattern (25 bp):
TTTTTATTTTTATTTTTGTATTTTA
Found at i:10476252 original size:17 final size:18
Alignment explanation
Indices: 10476222--10476260 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
10476212 AACTTCTCTT
*
10476222 TTTTTTTTTGTATTTTTA
1 TTTTATTTTGTATTTTTA
10476240 TTTTATTTT-TATTTTTA
1 TTTTATTTTGTATTTTTA
10476257 TTTT
1 TTTT
10476261 TGTATTTTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.13, C:0.00, G:0.03, T:0.85
Consensus pattern (18 bp):
TTTTATTTTGTATTTTTA
Found at i:10486537 original size:5 final size:5
Alignment explanation
Indices: 10486527--10486597 Score: 67
Period size: 5 Copynumber: 14.6 Consensus size: 5
10486517 ACCAAAAAAT
** **
10486527 AATAA AATAA AATAA AAT-A AATGG GTTAGA AATAA AATAA AATAA AATAA
1 AATAA AATAA AATAA AATAA AATAA AATA-A AATAA AATAA AATAA AATAA
*
10486577 AAT-C AA-AA AATAA AATAA AAT
1 AATAA AATAA AATAA AATAA AAT
10486598 GGAAAAAAGA
Statistics
Matches: 53, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
4 8 0.15
5 43 0.81
6 2 0.04
ACGTcount: A:0.72, C:0.01, G:0.06, T:0.21
Consensus pattern (5 bp):
AATAA
Found at i:10487601 original size:26 final size:26
Alignment explanation
Indices: 10487570--10487654 Score: 89
Period size: 26 Copynumber: 3.3 Consensus size: 26
10487560 GCTTGATTGG
*
10487570 AATGGGCTTAGTTAGGCTCGAACCAA
1 AATGGGCTTAGTTAGGCTCAAACCAA
* * * * *
10487596 AATGGGCTGAATTTGGCCCAGACCAA
1 AATGGGCTTAGTTAGGCTCAAACCAA
* * *
10487622 AATAGGCCTAGTTGGGCTCAAACCAA
1 AATGGGCTTAGTTAGGCTCAAACCAA
10487648 AATGGGC
1 AATGGGC
10487655 CCAATTGGGC
Statistics
Matches: 45, Mismatches: 14, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
26 45 1.00
ACGTcount: A:0.32, C:0.21, G:0.27, T:0.20
Consensus pattern (26 bp):
AATGGGCTTAGTTAGGCTCAAACCAA
Found at i:10487640 original size:52 final size:52
Alignment explanation
Indices: 10487578--10487676 Score: 144
Period size: 52 Copynumber: 1.9 Consensus size: 52
10487568 GGAATGGGCT
* ** *
10487578 TAGTTAGGCTCGAACCAAAATGGGCTGAATTTGGCCCAGACCAAAATAGGCC
1 TAGTTAGGCTCAAACCAAAATGGGCCCAATTGGGCCCAGACCAAAATAGGCC
* *
10487630 TAGTTGGGCTCAAACCAAAATGGGCCCAATTGGGCCCGGACCAAAAT
1 TAGTTAGGCTCAAACCAAAATGGGCCCAATTGGGCCCAGACCAAAAT
10487677 GGATATTTAC
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
52 41 1.00
ACGTcount: A:0.32, C:0.24, G:0.25, T:0.18
Consensus pattern (52 bp):
TAGTTAGGCTCAAACCAAAATGGGCCCAATTGGGCCCAGACCAAAATAGGCC
Found at i:10487655 original size:26 final size:26
Alignment explanation
Indices: 10487590--10487678 Score: 90
Period size: 26 Copynumber: 3.4 Consensus size: 26
10487580 GTTAGGCTCG
*
10487590 AACCAAAATGGG-CTGAATTTGGCCCA
1 AACCAAAATGGGCCT-AATTGGGCCCA
* * * *
10487616 GACCAAAATAGGCCTAGTTGGGCTCA
1 AACCAAAATGGGCCTAATTGGGCCCA
* *
10487642 AACCAAAATGGGCCCAATTGGGCCCG
1 AACCAAAATGGGCCTAATTGGGCCCA
*
10487668 GACCAAAATGG
1 AACCAAAATGG
10487679 ATATTTACAA
Statistics
Matches: 50, Mismatches: 12, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
26 48 0.96
27 2 0.04
ACGTcount: A:0.34, C:0.25, G:0.26, T:0.16
Consensus pattern (26 bp):
AACCAAAATGGGCCTAATTGGGCCCA
Found at i:10497611 original size:12 final size:12
Alignment explanation
Indices: 10497594--10497621 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
10497584 GAGTCACCAC
10497594 CAATCCCATAAG
1 CAATCCCATAAG
10497606 CAATCCCATAAG
1 CAATCCCATAAG
10497618 CAAT
1 CAAT
10497622 TTCTTCCATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.43, C:0.32, G:0.07, T:0.18
Consensus pattern (12 bp):
CAATCCCATAAG
Found at i:10501139 original size:8 final size:7
Alignment explanation
Indices: 10501126--10501159 Score: 50
Period size: 7 Copynumber: 4.6 Consensus size: 7
10501116 TAGTAAGTTT
10501126 TTTTTTCA
1 TTTTTT-A
10501134 TTTTTTA
1 TTTTTTA
10501141 TTTTTTA
1 TTTTTTA
10501148 TTTTTTGA
1 TTTTTT-A
10501156 TTTT
1 TTTT
10501160 GATTTTATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 14 0.56
8 11 0.44
ACGTcount: A:0.12, C:0.03, G:0.03, T:0.82
Consensus pattern (7 bp):
TTTTTTA
Found at i:10501146 original size:15 final size:15
Alignment explanation
Indices: 10501126--10501159 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
10501116 TAGTAAGTTT
10501126 TTTTTTCATTTTTT-A
1 TTTTTT-ATTTTTTGA
10501141 TTTTTTATTTTTTGA
1 TTTTTTATTTTTTGA
10501156 TTTT
1 TTTT
10501160 GATTTTATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 7 0.39
15 11 0.61
ACGTcount: A:0.12, C:0.03, G:0.03, T:0.82
Consensus pattern (15 bp):
TTTTTTATTTTTTGA
Found at i:10506582 original size:40 final size:40
Alignment explanation
Indices: 10506517--10506605 Score: 124
Period size: 40 Copynumber: 2.2 Consensus size: 40
10506507 GCACCAAGAG
* *
10506517 AAAGGCATTCACATTTACATCATTGCATTTACATCATAAT
1 AAAGGCATTCACATTTACATAATTGCATATACATCATAAT
* * * *
10506557 AAAGGCATTCATATTTGCATAATTGCATATGCATTATAAT
1 AAAGGCATTCACATTTACATAATTGCATATACATCATAAT
10506597 AAAGGCATT
1 AAAGGCATT
10506606 TGTATCATTG
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.35
Consensus pattern (40 bp):
AAAGGCATTCACATTTACATAATTGCATATACATCATAAT
Found at i:10506992 original size:23 final size:21
Alignment explanation
Indices: 10506966--10507009 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 21
10506956 AGAGTCTATC
10506966 AAGAGAAAAAAAAACAAATAAAA
1 AAGAGAAAAAAAAA-AAA-AAAA
10506989 AAGAGAAAAAAAAAAAAAAAA
1 AAGAGAAAAAAAAAAAAAAAA
10507010 GGAAAATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 4 0.19
22 3 0.14
23 14 0.67
ACGTcount: A:0.86, C:0.02, G:0.09, T:0.02
Consensus pattern (21 bp):
AAGAGAAAAAAAAAAAAAAAA
Found at i:10507981 original size:22 final size:22
Alignment explanation
Indices: 10507926--10507983 Score: 68
Period size: 22 Copynumber: 2.6 Consensus size: 22
10507916 ATCTTCAAGT
10507926 ATCA-TTCAAAAGTCCTCAAGGC
1 ATCATTTC-AAAGTCCTCAAGGC
10507948 ATCATATT-AAAGTCCTCTAA-GC
1 ATCAT-TTCAAAGTCCTC-AAGGC
10507970 ATCATTTCAAAGTC
1 ATCATTTCAAAGTC
10507984 TTTTAGGCAT
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
21 2 0.06
22 26 0.81
23 2 0.06
24 2 0.06
ACGTcount: A:0.36, C:0.24, G:0.10, T:0.29
Consensus pattern (22 bp):
ATCATTTCAAAGTCCTCAAGGC
Found at i:10507993 original size:22 final size:22
Alignment explanation
Indices: 10507934--10507993 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
10507924 GTATCATTCA
*
10507934 AAAGTCCTCAAGGCATCATATT
1 AAAGTCCTCTAGGCATCATATT
*
10507956 AAAGTCCTCTAAGCATCAT-TT
1 AAAGTCCTCTAGGCATCATATT
* *
10507977 CAAAGTCTTTTAGGCAT
1 -AAAGTCCTCTAGGCAT
10507994 TATTCTAAAG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
21 2 0.06
22 30 0.94
ACGTcount: A:0.33, C:0.22, G:0.13, T:0.32
Consensus pattern (22 bp):
AAAGTCCTCTAGGCATCATATT
Found at i:10508400 original size:65 final size:66
Alignment explanation
Indices: 10508331--10508531 Score: 149
Period size: 66 Copynumber: 3.1 Consensus size: 66
10508321 TTCTATTTAA
* *
10508331 AGGAATCTTTCAAATACCATAAACTCT-TGTTAGAGGAACCTTTCAAA-AAAATCACTTTTGGTT
1 AGGAATCTTTCAAATACCATAAACTCTGT-TTAGAAGAACCTTTCAAATAAAATCACCTTTGGTT
10508394 AG
65 AG
* * *** * ** * *
10508396 AGGAATAC-TCCAAATGCCATTGCCTCTGTTTAGAAGAATCTTTCAAATACTATTACCTTTGTTT
1 AGGAAT-CTTTCAAATACCATAAACTCTGTTTAGAAGAACCTTTCAAATAAAATCACCTTTGGTT
10508460 AG
65 AG
* *** * * * * **
10508462 AGGAATATTTCAAATACCATTGTCTCTATTTAGAGGAATCC-TTCAACTAACATTGCCTTTGGTT
1 AGGAATCTTTCAAATACCATAAACTCTGTTTAGAAGAA-CCTTTCAAATAAAATCACCTTTGGTT
10508526 AG
65 AG
10508528 AGGA
1 AGGA
10508532 TTTTATTAAA
Statistics
Matches: 107, Mismatches: 24, Indels: 9
0.76 0.17 0.06
Matches are distributed among these distances:
65 36 0.34
66 70 0.65
67 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Consensus pattern (66 bp):
AGGAATCTTTCAAATACCATAAACTCTGTTTAGAAGAACCTTTCAAATAAAATCACCTTTGGTTA
G
Found at i:10508462 original size:98 final size:97
Alignment explanation
Indices: 10508160--10508475 Score: 390
Period size: 98 Copynumber: 3.3 Consensus size: 97
10508150 AAAACACACC
* * * *
10508160 ACCTATTGTTAGAAGAACCTTT-AAAAAAATCACCTCTGGTTAGAGGAATACTACAAA-CCATTG
1 ACCTCTTGTTAGAGGAACCTTTCAAAAAAATCACCTTTGGTTAGAGGAATACTCCAAATCCATTG
* * *
10508223 CCTTTGTTTAG-AGAATCATTCAAATACCATG
66 CCTCTGTTTAGAAGAATCTTTCAAATACCATA
* ** *
10508254 ACCTCTTATTAGATAAACCTTTCAAAATAATCACCTTTGGTTAGAGGAATACTCCAAATACCATT
1 ACCTCTTGTTAGAGGAACCTTTCAAAAAAATCACCTTTGGTTAGAGGAATACTCCAAAT-CCATT
* *
10508319 GCTTCTATTTA-AAGGAATCTTTCAAATACCATA
65 GCCTCTGTTTAGAA-GAATCTTTCAAATACCATA
* *
10508352 AACTCTTGTTAGAGGAACCTTTCAAAAAAATCACTTTTGGTTAGAGGAATACTCCAAATGCCATT
1 ACCTCTTGTTAGAGGAACCTTTCAAAAAAATCACCTTTGGTTAGAGGAATACTCCAAAT-CCATT
* *
10508417 GCCTCTGTTTAGAAGAATCTTTCAAATACTATT
65 GCCTCTGTTTAGAAGAATCTTTCAAATACCATA
**
10508450 ACCT-TTGTTTAGAGGAATATTTCAAA
1 ACCTCTTG-TTAGAGGAACCTTTCAAA
10508476 TACCATTGTC
Statistics
Matches: 189, Mismatches: 26, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
94 18 0.10
95 32 0.17
97 17 0.09
98 120 0.63
99 2 0.01
ACGTcount: A:0.36, C:0.19, G:0.13, T:0.33
Consensus pattern (97 bp):
ACCTCTTGTTAGAGGAACCTTTCAAAAAAATCACCTTTGGTTAGAGGAATACTCCAAATCCATTG
CCTCTGTTTAGAAGAATCTTTCAAATACCATA
Found at i:10508476 original size:66 final size:66
Alignment explanation
Indices: 10508387--10508531 Score: 184
Period size: 66 Copynumber: 2.2 Consensus size: 66
10508377 AAAAATCACT
* * *
10508387 TTTGGTTAGAGGAATACTCCAAATGCCATTGCCTCTGTTTAGAAGAATCTTTCAAAT-ACTATTA
1 TTTGGTTAGAGGAATACTCCAAATACCATTGCCTCTATTTAGAAGAATCCTTCAAATAAC-ATTA
10508451 CC
65 CC
* * * * * * *
10508453 TTTGTTTAGAGGAATATTTCAAATACCATTGTCTCTATTTAGAGGAATCCTTCAACTAACATTGC
1 TTTGGTTAGAGGAATACTCCAAATACCATTGCCTCTATTTAGAAGAATCCTTCAAATAACATTAC
10508518 C
66 C
10508519 TTTGGTTAGAGGA
1 TTTGGTTAGAGGA
10508532 TTTTATTAAA
Statistics
Matches: 67, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
66 65 0.97
67 2 0.03
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.37
Consensus pattern (66 bp):
TTTGGTTAGAGGAATACTCCAAATACCATTGCCTCTATTTAGAAGAATCCTTCAAATAACATTAC
C
Found at i:10508528 original size:33 final size:33
Alignment explanation
Indices: 10508287--10508531 Score: 126
Period size: 33 Copynumber: 7.5 Consensus size: 33
10508277 AAAATAATCA
* * *
10508287 CCTTTGGTTAGAGGAATACTCCAAATACCATTG
1 CCTTTGTTTAGAGGAATACTTCAAATAACATTG
* * * **
10508320 -CTTCTATTTAAAGGAAT-CTTTCAAATACCATAA
1 CCTT-TGTTTAGAGGAATAC-TTCAAATAACATTG
* * * **
10508353 ACTCTTG-TTAGAGGAA-CCTTTCAAA-AAAATCA
1 CCT-TTGTTTAGAGGAATAC-TTCAAATAACATTG
* * * **
10508385 CTTTTGGTTAGAGGAATACTCCAAATGCCATTG
1 CCTTTGTTTAGAGGAATACTTCAAATAACATTG
* * *
10508418 CCTCTGTTTAGAAGAAT-CTTTCAAAT-ACTATTA
1 CCTTTGTTTAGAGGAATAC-TTCAAATAAC-ATTG
* *
10508451 CCTTTGTTTAGAGGAATATTTCAAATACCATTG
1 CCTTTGTTTAGAGGAATACTTCAAATAACATTG
* * * * *
10508484 TCTCTATTTAGAGGAATCCTTCAACTAACATTG
1 CCTTTGTTTAGAGGAATACTTCAAATAACATTG
*
10508517 CCTTTGGTTAGAGGA
1 CCTTTGTTTAGAGGA
10508532 TTTTATTAAA
Statistics
Matches: 157, Mismatches: 43, Indels: 24
0.70 0.19 0.11
Matches are distributed among these distances:
31 3 0.02
32 25 0.16
33 124 0.79
34 4 0.03
35 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (33 bp):
CCTTTGTTTAGAGGAATACTTCAAATAACATTG
Found at i:10508607 original size:34 final size:34
Alignment explanation
Indices: 10508569--10508633 Score: 112
Period size: 34 Copynumber: 1.9 Consensus size: 34
10508559 AGTTAAAGGT
**
10508569 GTTATTTAAAGTGTCATAGCCTTTGGTTAGATGA
1 GTTATTTAAAGTGTCATAGAATTTGGTTAGATGA
10508603 GTTATTTAAAGTGTCATAGAATTTGGTTAGA
1 GTTATTTAAAGTGTCATAGAATTTGGTTAGA
10508634 GGAGCTTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.29, C:0.06, G:0.23, T:0.42
Consensus pattern (34 bp):
GTTATTTAAAGTGTCATAGAATTTGGTTAGATGA
Found at i:10508645 original size:34 final size:34
Alignment explanation
Indices: 10508560--10508645 Score: 111
Period size: 34 Copynumber: 2.5 Consensus size: 34
10508550 ATAACTTTTA
* * **
10508560 GTTAAAGGTGTTATTTAAAGTGTCATAGCCTTTG
1 GTTAGAGGAGTTATTTAAAGTGTCATAGAATTTG
*
10508594 GTTAGATGAGTTATTTAAAGTGTCATAGAATTTG
1 GTTAGAGGAGTTATTTAAAGTGTCATAGAATTTG
10508628 GTTAGAGGAGCTT-TTTAA
1 GTTAGAGGAG-TTATTTAA
10508646 CTTTAAAAGC
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
34 43 0.96
35 2 0.04
ACGTcount: A:0.29, C:0.06, G:0.24, T:0.41
Consensus pattern (34 bp):
GTTAGAGGAGTTATTTAAAGTGTCATAGAATTTG
Found at i:10508784 original size:34 final size:34
Alignment explanation
Indices: 10508741--10508813 Score: 119
Period size: 34 Copynumber: 2.1 Consensus size: 34
10508731 TTTCAAATTC
*
10508741 AAAGTGTCATAACCTCTGGTTAGATGAATTATTT
1 AAAGTGTCATAACCTCTGGTTAGAAGAATTATTT
* *
10508775 AAAGTGTCATAACCTTTGGTTAGAAGAGTTATTT
1 AAAGTGTCATAACCTCTGGTTAGAAGAATTATTT
10508809 AAAGT
1 AAAGT
10508814 TTTATAGTCT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.34, C:0.10, G:0.19, T:0.37
Consensus pattern (34 bp):
AAAGTGTCATAACCTCTGGTTAGAAGAATTATTT
Found at i:10508872 original size:36 final size:34
Alignment explanation
Indices: 10508757--10508877 Score: 100
Period size: 34 Copynumber: 3.5 Consensus size: 34
10508747 TCATAACCTC
* * * * * *
10508757 TGGTTAGATGAATTATTTAAAGTGTCATAACCTT
1 TGGTTAGAGGAGTTTTTTAAAGTGTTATAGCTTT
* * * *
10508791 TGGTTAGAAGAGTTATTTAAAGTTTTATAG-TCTC
1 TGGTTAGAGGAGTTTTTTAAAGTGTTATAGCT-TT
* *
10508825 TAGTTAAAGGAGTTTTTCTCAAAGTGTTATAGCTTT
1 TGGTTAGAGGAGTTTTT-T-AAAGTGTTATAGCTTT
10508861 TGGTTAGAGGAGTTTTT
1 TGGTTAGAGGAGTTTTT
10508878 AAATTTTAAG
Statistics
Matches: 68, Mismatches: 15, Indels: 6
0.76 0.17 0.07
Matches are distributed among these distances:
34 39 0.57
35 1 0.01
36 27 0.40
37 1 0.01
ACGTcount: A:0.28, C:0.07, G:0.21, T:0.44
Consensus pattern (34 bp):
TGGTTAGAGGAGTTTTTTAAAGTGTTATAGCTTT
Found at i:10508950 original size:22 final size:22
Alignment explanation
Indices: 10508925--10508981 Score: 87
Period size: 22 Copynumber: 2.6 Consensus size: 22
10508915 ATTAGGTATG
* *
10508925 ATTTGTAAGACCTATAGGCATA
1 ATTTATAAGAACTATAGGCATA
*
10508947 ATTTATAAAAACTATAGGCATA
1 ATTTATAAGAACTATAGGCATA
10508969 ATTTATAAGAACT
1 ATTTATAAGAACT
10508982 TTTAGAATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.44, C:0.11, G:0.12, T:0.33
Consensus pattern (22 bp):
ATTTATAAGAACTATAGGCATA
Found at i:10509095 original size:34 final size:34
Alignment explanation
Indices: 10509052--10509137 Score: 100
Period size: 34 Copynumber: 2.5 Consensus size: 34
10509042 ATTGCCTCCG
* * *
10509052 GTTAGAGGAGTTATTTAAAGTACCATAACCTTTA
1 GTTACAGGAGTTTTTTAAAGTACCATAACCTCTA
* * * *
10509086 GTTATAGGAGTTTTTTTAAGTATCATAGCCTCTA
1 GTTACAGGAGTTTTTTAAAGTACCATAACCTCTA
*
10509120 GTTACAGAAGTTTTTTAA
1 GTTACAGGAGTTTTTTAA
10509138 TGTCTCATAG
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
34 43 1.00
ACGTcount: A:0.31, C:0.10, G:0.17, T:0.41
Consensus pattern (34 bp):
GTTACAGGAGTTTTTTAAAGTACCATAACCTCTA
Found at i:10510939 original size:8 final size:7
Alignment explanation
Indices: 10510912--10510938 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
10510902 TTTTCTCTAT
10510912 TTTTTTA
1 TTTTTTA
10510919 TTTTTTA
1 TTTTTTA
10510926 TTTTTTA
1 TTTTTTA
10510933 TTTTTT
1 TTTTTT
10510939 TTTGTTAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (7 bp):
TTTTTTA
Found at i:10511537 original size:8 final size:8
Alignment explanation
Indices: 10511526--10511554 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
10511516 AGAAAAAATG
10511526 AAAAAA-A
1 AAAAAACA
10511533 AAAAAACA
1 AAAAAACA
10511541 AAAAAACA
1 AAAAAACA
10511549 AAAAAA
1 AAAAAA
10511555 TAACAATAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
7 6 0.29
8 15 0.71
ACGTcount: A:0.93, C:0.07, G:0.00, T:0.00
Consensus pattern (8 bp):
AAAAAACA
Found at i:10512275 original size:3 final size:3
Alignment explanation
Indices: 10512267--10512406 Score: 78
Period size: 3 Copynumber: 48.3 Consensus size: 3
10512257 TTTTCACGTA
** * * *
10512267 TAT TAT TAT TAT TAT TGC CAT TAC TAT TAT TAT TAT T-T T-T TGT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * ** * *
10512313 TGT TGT TAT TAT TAT TGT TAT TAT TGC TAG TAT TA- TAT TAT TAGGG
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA--T
* * *
10512359 TA- TAT TA- TAT TA- TAT TA- TAT TAT TAT TAT TAT TGT TGT TGT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
10512403 TAT T
1 TAT T
10512407 TTTTTTCCTT
Statistics
Matches: 108, Mismatches: 21, Indels: 16
0.74 0.14 0.11
Matches are distributed among these distances:
2 14 0.13
3 92 0.85
5 2 0.02
ACGTcount: A:0.26, C:0.03, G:0.09, T:0.61
Consensus pattern (3 bp):
TAT
Done.