Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167838.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_11, 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: 23775123
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 69000 characters in sequence are not A, C, G, or T
File 108 of 129
Found at i:19443887 original size:58 final size:58
Alignment explanation
Indices: 19443767--19443925 Score: 196
Period size: 58 Copynumber: 2.7 Consensus size: 58
19443757 TTTGTACAAG
* *
19443767 GGAAAATTGATACTTTCAACTTTTTTTCCAAAAATATTTTTTGAAAACTTTAATTTTGA
1 GGAAAATTGATACTTTCAACTTTTCTT-CAAAAATATTTTTTGAAAACTTTAATTTTAA
* *
19443826 GGAAAATTGATACTTTCAACTTTTCTTCAAAAGTATTTTTTGGAAAGC-TT-ATTTTCAA
1 GGAAAATTGATACTTTCAACTTTTCTTCAAAAATATTTTTT-GAAAACTTTAATTTT-AA
* ** *
19443884 GGAAAATTTATGTTTTCAACTTTTCCTCAAAAATATATTTTT
1 GGAAAATTGATACTTTCAACTTTTCTTCAAAAATAT-TTTTT
19443926 TTGAATTTTA
Statistics
Matches: 88, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
57 5 0.06
58 47 0.53
59 36 0.41
ACGTcount: A:0.34, C:0.11, G:0.09, T:0.45
Consensus pattern (58 bp):
GGAAAATTGATACTTTCAACTTTTCTTCAAAAATATTTTTTGAAAACTTTAATTTTAA
Found at i:19443991 original size:14 final size:14
Alignment explanation
Indices: 19443954--19443992 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
19443944 CAAAATAAAT
*
19443954 AAATAAA-AAATGA
1 AAATAAATAAAGGA
19443967 AAATAAAATAAAGGA
1 AAAT-AAATAAAGGA
19443982 AAATAAATAAA
1 AAATAAATAAA
19443993 AATAGCAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 4 0.17
14 10 0.43
15 9 0.39
ACGTcount: A:0.77, C:0.00, G:0.08, T:0.15
Consensus pattern (14 bp):
AAATAAATAAAGGA
Found at i:19444057 original size:19 final size:17
Alignment explanation
Indices: 19444027--19444080 Score: 67
Period size: 19 Copynumber: 3.1 Consensus size: 17
19444017 TAATCTAATC
19444027 AATAAATAATAAAAAAA
1 AATAAATAATAAAAAAA
19444044 AATATAATATATAAAAAAA
1 AATA-AATA-ATAAAAAAA
19444063 AATGAAA-AA-AAAAAAA
1 AAT-AAATAATAAAAAAA
19444079 AA
1 AA
19444081 ACATGAAAAC
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
16 9 0.26
17 5 0.15
18 5 0.15
19 14 0.41
20 1 0.03
ACGTcount: A:0.81, C:0.00, G:0.02, T:0.17
Consensus pattern (17 bp):
AATAAATAATAAAAAAA
Found at i:19444899 original size:16 final size:17
Alignment explanation
Indices: 19444878--19444909 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
19444868 TTCAACCGAA
19444878 AAAAAATCAAA-AAAAT
1 AAAAAATCAAATAAAAT
19444894 AAAAAATCAAATAAAA
1 AAAAAATCAAATAAAA
19444910 AATATTAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.81, C:0.06, G:0.00, T:0.12
Consensus pattern (17 bp):
AAAAAATCAAATAAAAT
Found at i:19444956 original size:20 final size:20
Alignment explanation
Indices: 19444931--19444978 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
19444921 ATAATTAAAT
19444931 GAAAATAATCAGATAAACTA
1 GAAAATAATCAGATAAACTA
*
19444951 GAAAATTAA-CAGATAAATTA
1 GAAAA-TAATCAGATAAACTA
19444971 -AAAATAAT
1 GAAAATAAT
19444979 AATAGATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 3 0.12
19 4 0.16
20 15 0.60
21 3 0.12
ACGTcount: A:0.62, C:0.06, G:0.08, T:0.23
Consensus pattern (20 bp):
GAAAATAATCAGATAAACTA
Found at i:19445007 original size:22 final size:22
Alignment explanation
Indices: 19444961--19445047 Score: 81
Period size: 21 Copynumber: 3.9 Consensus size: 22
19444951 GAAAATTAAC
*
19444961 AGATAAATTA-AAAATA-ATAAT
1 AGATAAATTATAATATATA-AAT
19444982 AGATAAATTATAATATATAAAT
1 AGATAAATTATAATATATAAAT
*
19445004 AGATAAATAATAGTAAATATATAACT
1 AGATAAAT--TA-T-AATATATAAAT
*
19445030 AGATAAA-TAAAATATATA
1 AGATAAATTATAATATATA
19445048 TATAAATATT
Statistics
Matches: 57, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
21 18 0.32
22 16 0.28
23 3 0.05
24 2 0.04
25 1 0.02
26 17 0.30
ACGTcount: A:0.62, C:0.01, G:0.06, T:0.31
Consensus pattern (22 bp):
AGATAAATTATAATATATAAAT
Found at i:19445022 original size:26 final size:25
Alignment explanation
Indices: 19444972--19445055 Score: 97
Period size: 26 Copynumber: 3.5 Consensus size: 25
19444962 GATAAATTAA
19444972 AAATA-AT-AATAGATAAAT--TAT
1 AAATATATAAATAGATAAATAATAT
19444993 -AATATATAAATAGATAAATAATAGT
1 AAATATATAAATAGATAAATAATA-T
* *
19445018 AAATATATAACTAGATAAATAAAAT
1 AAATATATAAATAGATAAATAATAT
*
19445043 ATATATATAAATA
1 AAATATATAAATA
19445056 TTAACAGAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
20 4 0.08
21 2 0.04
22 11 0.21
24 2 0.04
25 13 0.25
26 21 0.40
ACGTcount: A:0.62, C:0.01, G:0.05, T:0.32
Consensus pattern (25 bp):
AAATATATAAATAGATAAATAATAT
Found at i:19447112 original size:80 final size:80
Alignment explanation
Indices: 19446979--19447140 Score: 236
Period size: 80 Copynumber: 2.0 Consensus size: 80
19446969 ATCTCCTCAA
*
19446979 TAACTCCTTGTATCTCTCACATGCATCAAACAAAGATTCAACCTCAAATTGTTGAAATACAGTGA
1 TAACTCCTTATATCTCTCACATGCATCAAACAAAGATTCAACCTCAAATTGTTGAAATACAGTGA
*
19447044 TGTTATTCCTTATTT
66 TGATATTCCTTATTT
* ** *
19447059 TAACTCCTTATATCTCTCTCATGCATCAAACAAAGATTCGGCCAT-AAATTGTTGAAATGCAGTG
1 TAACTCCTTATATCTCTCACATGCATCAAACAAAGATTCAACC-TCAAATTGTTGAAATACAGTG
**
19447123 ATGATATTTTTTATTT
65 ATGATATTCCTTATTT
19447139 TA
1 TA
19447141 GTAGTTTTGG
Statistics
Matches: 73, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
80 72 0.99
81 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.11, T:0.38
Consensus pattern (80 bp):
TAACTCCTTATATCTCTCACATGCATCAAACAAAGATTCAACCTCAAATTGTTGAAATACAGTGA
TGATATTCCTTATTT
Found at i:19448558 original size:13 final size:12
Alignment explanation
Indices: 19448544--19448576 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
19448534 ATGAGCTAAA
19448544 AAAAT-AAAAAT
1 AAAATAAAAAAT
19448555 AAAATCAAAAAAT
1 AAAAT-AAAAAAT
19448568 AAAATAAAA
1 AAAATAAAA
19448577 TGGAAAAAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 5 0.25
12 4 0.20
13 11 0.55
ACGTcount: A:0.82, C:0.03, G:0.00, T:0.15
Consensus pattern (12 bp):
AAAATAAAAAAT
Found at i:19448584 original size:19 final size:19
Alignment explanation
Indices: 19448542--19448577 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
19448532 AAATGAGCTA
19448542 AAAAAATAAAAATAAAATC
1 AAAAAATAAAAATAAAATC
19448561 AAAAAAT-AAAATAAAAT
1 AAAAAATAAAAATAAAAT
19448578 GGAAAAAGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.81, C:0.03, G:0.00, T:0.17
Consensus pattern (19 bp):
AAAAAATAAAAATAAAATC
Found at i:19449486 original size:3 final size:3
Alignment explanation
Indices: 19449480--19449504 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
19449470 AATAATAATA
19449480 ATG ATG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG A
19449505 CGATAATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.32, T:0.32
Consensus pattern (3 bp):
ATG
Found at i:19450130 original size:120 final size:120
Alignment explanation
Indices: 19449692--19450189 Score: 484
Period size: 120 Copynumber: 4.2 Consensus size: 120
19449682 AGATAAAGCA
* * * *
19449692 ACCAGGACCGAATCGAGGTAAAAAATAAATGATCGAGATGAAACCATGAGTCATAAGAAATGATT
1 ACCAGGACCGAGTCGAGGTCAAAAATAAATGATCGAGATGAAACCATAAGTCATAAGAAATGATC
* * * *** ** * **
19449757 TGGATTGAGCCATGATTGGGTAATTGGGGTGAAACTACGAGTCAAAAATGAAGCA
66 TGGACTGAGCCAAGATTGAGTAACCAGGACGAAACCACGAGTCAAAAATGAAGTG
* ** * **
19449812 ACCAAGATAGAGTCGAGGTCAAAAGTAAATGA-CTGAGACAAAACCATAAGTCATAAGAAATGAT
1 ACCAGGACCGAGTCGAGGTCAAAAATAAATGATC-GAGATGAAACCATAAGTCATAAGAAATGAT
* * *
19449876 CTGGACTGAGCCAAGATTGGGTAACC-GAGACAAAACCATGAGTCAAAAATGAAGTG
65 CTGGACTGAGCCAAGATTGAGTAACCAG-GACGAAACCACGAGTCAAAAATGAAGTG
* * * * *
19449932 ACCAAGACTGAGTCAAGGTAAAAAATAAATGA-CTGAGATGAAACTATAAGTCATAAGAAATGAT
1 ACCAGGACCGAGTCGAGGTCAAAAATAAATGATC-GAGATGAAACCATAAGTCATAAGAAATGAT
* * * * *
19449996 CTAGACTGGGCCAAGATCGAGTGACCAGGGCGAAACCACGAGTCAAAAATGAAGTG
65 CTGGACTGAGCCAAGATTGAGTAACCAGGACGAAACCACGAGTCAAAAATGAAGTG
* * * * *
19450052 ACCAGGATCGAGTCGAGGTCAAAAATAAATTATCGGGATGAAACCATGAGTCATAAGAAATGATT
1 ACCAGGACCGAGTCGAGGTCAAAAATAAATGATCGAGATGAAACCATAAGTCATAAGAAATGATC
* * * * * * * *
19450117 TGGA-TGAAACCAAGA-TAAATGACCAAGATGAAACCACGAGTCTAAAGATAAAGTG
66 TGGACTG-AGCCAAGATTGAGTAACCAGGACGAAACCACGAGTC-AAAAATGAAGTG
*
19450172 ACCAGGACCAAGTCGAGG
1 ACCAGGACCGAGTCGAGG
19450190 CCTAAAATGA
Statistics
Matches: 312, Mismatches: 60, Indels: 12
0.81 0.16 0.03
Matches are distributed among these distances:
119 25 0.08
120 285 0.91
121 2 0.01
ACGTcount: A:0.43, C:0.15, G:0.24, T:0.18
Consensus pattern (120 bp):
ACCAGGACCGAGTCGAGGTCAAAAATAAATGATCGAGATGAAACCATAAGTCATAAGAAATGATC
TGGACTGAGCCAAGATTGAGTAACCAGGACGAAACCACGAGTCAAAAATGAAGTG
Found at i:19450173 original size:240 final size:240
Alignment explanation
Indices: 19449707--19450175 Score: 541
Period size: 240 Copynumber: 2.0 Consensus size: 240
19449697 GACCGAATCG
* * * * *
19449707 AGGTAAAAAATAAATGATCGAGATGAAACCATGAGTCATAAGAAATGATTTGGATTGAGCCATGA
1 AGGTAAAAAATAAATGATCGAGATGAAACCATAAGTCATAAGAAATGATCTAGACTGAGCCAAGA
* * *** * * *
19449772 TTGGGTAATTGGGGTGAAACTACGAGTCAAAAATGAAGCAACCAAGATAGAGTCGAGGTCAAAAG
66 TCGAGTAACCAGGGCGAAACCACGAGTCAAAAATGAAGCAACCAAGATAGAGTCGAGGTCAAAAA
* ***
19449837 TAAATGACTGAGACAAAACCATAAGTCATAAGAAATGATCTGGACTGAGCCAAGATTGGGTAACC
131 TAAATGACTGAGACAAAACCATAAGTCATAAGAAATGATCTGGACTGAACCAAGATTAAATAACC
* * *
19449902 GAGACAAAACCATGAGTCAAAAATGAAGTGACCAAGACTGAGTCA
196 AAGACAAAACCACGAGTCAAAAATAAAGTGACCAAGACTGAGTCA
* *
19449947 AGGTAAAAAATAAATGA-CTGAGATGAAACTATAAGTCATAAGAAATGATCTAGACTGGGCCAAG
1 AGGTAAAAAATAAATGATC-GAGATGAAACCATAAGTCATAAGAAATGATCTAGACTGAGCCAAG
* ** * *
19450011 ATCGAGTGACCAGGGCGAAACCACGAGTCAAAAATGAAGTGACCAGGATCGAGTCGAGGTCAAAA
65 ATCGAGTAACCAGGGCGAAACCACGAGTCAAAAATGAAGCAACCAAGATAGAGTCGAGGTCAAAA
* * ** * * *
19450076 ATAAATTA-TCGGGATGAAACCATGAGTCATAAGAAATGATTTGGA-TGAAACCAAGA-TAAATG
130 ATAAATGACT-GAGACAAAACCATAAGTCATAAGAAATGATCTGGACTG-AACCAAGATTAAATA
** *
19450138 ACCAAGATGAAACCACGAGTCTAAAGATAAAGTGACCA
193 ACCAAGACAAAACCACGAGTC-AAAAATAAAGTGACCA
19450176 GGACCAAGTC
Statistics
Matches: 188, Mismatches: 37, Indels: 8
0.81 0.16 0.03
Matches are distributed among these distances:
239 23 0.12
240 165 0.88
ACGTcount: A:0.43, C:0.14, G:0.24, T:0.19
Consensus pattern (240 bp):
AGGTAAAAAATAAATGATCGAGATGAAACCATAAGTCATAAGAAATGATCTAGACTGAGCCAAGA
TCGAGTAACCAGGGCGAAACCACGAGTCAAAAATGAAGCAACCAAGATAGAGTCGAGGTCAAAAA
TAAATGACTGAGACAAAACCATAAGTCATAAGAAATGATCTGGACTGAACCAAGATTAAATAACC
AAGACAAAACCACGAGTCAAAAATAAAGTGACCAAGACTGAGTCA
Found at i:19450412 original size:119 final size:119
Alignment explanation
Indices: 19450277--19450512 Score: 301
Period size: 119 Copynumber: 2.0 Consensus size: 119
19450267 GACAAAATCA
* * * * *
19450277 TGAGTCTAAAGATAAAGCGATCAAGATCGAGTCAAGGTCGAAAATGGCTGACTGAGATGGAACCA
1 TGAGTCTAAAGATAAAGCGACCAAGATCGAGTCAAAGTCGAAAACGACTGACCGAGATGGAACCA
* * **
19450342 TGTGTCAAGAAATGATCTGGATGGAACCAAGATCGAATAACTGAGATGAAACTG
66 TGAGTCAAGAAATAATCTGGATGGAACCAAGATCGAATAACCAAGATGAAACTG
* * * ***
19450396 TGAGTCTAAAGATAAAGTGACCAAGATCGAGTCAAAGTTGAAGACGACTGACCGAGATGGAATTG
1 TGAGTCTAAAGATAAAGCGACCAAGATCGAGTCAAAGTCGAAAACGACTGACCGAGATGGAACCA
* * * *
19450461 TGAGTCAAGAAATAATCTGGATTGAGCCGAGATCGAATGACCAAGATGAAAC
66 TGAGTCAAGAAATAATCTGGATGGAACCAAGATCGAATAACCAAGATGAAAC
19450513 ACCAGTTAAA
Statistics
Matches: 98, Mismatches: 19, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
119 98 1.00
ACGTcount: A:0.39, C:0.14, G:0.27, T:0.20
Consensus pattern (119 bp):
TGAGTCTAAAGATAAAGCGACCAAGATCGAGTCAAAGTCGAAAACGACTGACCGAGATGGAACCA
TGAGTCAAGAAATAATCTGGATGGAACCAAGATCGAATAACCAAGATGAAACTG
Found at i:19450884 original size:34 final size:34
Alignment explanation
Indices: 19450842--19450922 Score: 92
Period size: 34 Copynumber: 2.4 Consensus size: 34
19450832 CACGAAAGAA
* *
19450842 AGATTCACAAGATTTCAAATTTCGTAAAGATTCT-
1 AGATTCACAAGA-TTCAAAGTTCGCAAAGATTCTC
* *
19450876 AGATTCACAAGGATTCAAAGTTCGCAAGGATTTTC
1 AGATTCACAA-GATTCAAAGTTCGCAAAGATTCTC
*
19450911 AGACTCACAAGA
1 AGATTCACAAGA
19450923 AAGATTCATA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
34 29 0.73
35 11 0.28
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.28
Consensus pattern (34 bp):
AGATTCACAAGATTCAAAGTTCGCAAAGATTCTC
Found at i:19450937 original size:82 final size:82
Alignment explanation
Indices: 19450837--19451017 Score: 200
Period size: 82 Copynumber: 2.2 Consensus size: 82
19450827 ATTCGCACGA
* ** * *
19450837 AAGAAAGATTCACAAGATTTCAAATTTCGTAAAGATTCTAGATTCACAAGGATTCAAAGTTCGCA
1 AAGAAAGATTCATAAGATTTCAAATTTCACAAAGATTCTAGATTCACAAAGATTCAAAGTTCACA
* *
19450902 AGGATTTTCAGACTCAC
66 AGGACTTTCAAACTCAC
* * * *** * * *
19450919 AAGAAAGATTCATAAGATTTTAAGTTTCACAAAGGTTCTAGATTTGTAAAGATTCTAGGTTCATA
1 AAGAAAGATTCATAAGATTTCAAATTTCACAAAGATTCTAGATTCACAAAGATTCAAAGTTCACA
* *
19450984 AGGACTTTCAAATTCAT
66 AGGACTTTCAAACTCAC
19451001 AAGAAAGATTCATAAGA
1 AAGAAAGATTCATAAGA
19451018 AAGATTCCAA
Statistics
Matches: 81, Mismatches: 18, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
82 81 1.00
ACGTcount: A:0.40, C:0.13, G:0.16, T:0.30
Consensus pattern (82 bp):
AAGAAAGATTCATAAGATTTCAAATTTCACAAAGATTCTAGATTCACAAAGATTCAAAGTTCACA
AGGACTTTCAAACTCAC
Found at i:19451013 original size:13 final size:13
Alignment explanation
Indices: 19450995--19451024 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
19450985 GGACTTTCAA
19450995 ATTCATAAGAAAG
1 ATTCATAAGAAAG
19451008 ATTCATAAGAAAG
1 ATTCATAAGAAAG
19451021 ATTC
1 ATTC
19451025 CAAGATTCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.50, C:0.10, G:0.13, T:0.27
Consensus pattern (13 bp):
ATTCATAAGAAAG
Found at i:19451931 original size:9 final size:8
Alignment explanation
Indices: 19451911--19451995 Score: 75
Period size: 8 Copynumber: 10.1 Consensus size: 8
19451901 TTCCCCTTTG
19451911 TCTTTTTT
1 TCTTTTTT
19451919 TCTTTTTT
1 TCTTTTTT
19451927 CTCTTTTTT
1 -TCTTTTTT
19451936 TCATTTTTTT
1 TC--TTTTTT
19451946 TCATTTTTTT
1 TC--TTTTTT
19451956 TCATTTTTT
1 TC-TTTTTT
19451965 TC--TTTT
1 TCTTTTTT
*
19451971 TCCTTTTT
1 TCTTTTTT
**
19451979 TCTTTTCC
1 TCTTTTTT
19451987 TCTTTTTT
1 TCTTTTTT
19451995 T
1 T
19451996 TTGCACATTT
Statistics
Matches: 66, Mismatches: 6, Indels: 10
0.80 0.07 0.12
Matches are distributed among these distances:
6 6 0.09
8 26 0.39
9 16 0.24
10 18 0.27
ACGTcount: A:0.04, C:0.16, G:0.00, T:0.80
Consensus pattern (8 bp):
TCTTTTTT
Found at i:19451934 original size:10 final size:9
Alignment explanation
Indices: 19451913--19451971 Score: 75
Period size: 9 Copynumber: 6.4 Consensus size: 9
19451903 CCCCTTTGTC
19451913 TTTTTTTCT
1 TTTTTTTCT
*
19451922 TTTTTCTC-
1 TTTTTTTCT
19451930 TTTTTTTCAT
1 TTTTTTTC-T
19451940 TTTTTTTCAT
1 TTTTTTTC-T
*
19451950 TTTTTTTCA
1 TTTTTTTCT
19451959 TTTTTTTCT
1 TTTTTTTCT
19451968 TTTT
1 TTTT
19451972 CCTTTTTTCT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.16
9 19 0.43
10 18 0.41
ACGTcount: A:0.05, C:0.12, G:0.00, T:0.83
Consensus pattern (9 bp):
TTTTTTTCT
Found at i:19451936 original size:20 final size:18
Alignment explanation
Indices: 19451913--19451997 Score: 62
Period size: 18 Copynumber: 4.4 Consensus size: 18
19451903 CCCCTTTGTC
* *
19451913 TTTTTTTCTTTTTTCTCT
1 TTTTTTTTTTTTTTTTCT
**
19451931 TTTTTTCATTTTTTTTCAT
1 TTTTTTTTTTTTTTTTC-T
**
19451950 TTTTTTTCATTTTTTTCT
1 TTTTTTTTTTTTTTTTCT
*
19451968 TTTTCCTTTTTTCTTTTCCTCT
1 TTTT--TTTTTT-TTTT-TTCT
19451990 TTTTTTTT
1 TTTTTTTT
19451998 GCACATTTTT
Statistics
Matches: 53, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
18 19 0.36
19 15 0.28
20 8 0.15
21 4 0.08
22 7 0.13
ACGTcount: A:0.04, C:0.15, G:0.00, T:0.81
Consensus pattern (18 bp):
TTTTTTTTTTTTTTTTCT
Found at i:19451955 original size:13 final size:13
Alignment explanation
Indices: 19451949--19451997 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 13
19451939 TTTTTTTTCA
*
19451949 TTTTTTTTCATTTT
1 TTTTTTTTC-CTTT
19451963 TTTCTTTTTCCTTT
1 TTT-TTTTTCCTTT
*
19451977 TTTCTTTTCCTCTT
1 TTTTTTTTCCT-TT
19451991 TTTTTTT
1 TTTTTTT
19451998 GCACATTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
13 7 0.23
14 17 0.57
15 6 0.20
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82
Consensus pattern (13 bp):
TTTTTTTTCCTTT
Found at i:19455916 original size:19 final size:21
Alignment explanation
Indices: 19455884--19455928 Score: 67
Period size: 19 Copynumber: 2.2 Consensus size: 21
19455874 TTTGTAGGGA
19455884 TTTTTATTTGGAAAAGATTTT
1 TTTTTATTTGGAAAAGATTTT
*
19455905 TTTTTA-TT-GAAAGGATTTT
1 TTTTTATTTGGAAAAGATTTT
19455924 TTTTT
1 TTTTT
19455929 GTTTTTATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 15 0.65
20 2 0.09
21 6 0.26
ACGTcount: A:0.24, C:0.00, G:0.13, T:0.62
Consensus pattern (21 bp):
TTTTTATTTGGAAAAGATTTT
Found at i:19456174 original size:11 final size:11
Alignment explanation
Indices: 19456160--19456185 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
19456150 AATGAGCTAA
19456160 AAAATAAAATC
1 AAAATAAAATC
19456171 AAAATAAAATC
1 AAAATAAAATC
19456182 AAAA
1 AAAA
19456186 AATAAAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.77, C:0.08, G:0.00, T:0.15
Consensus pattern (11 bp):
AAAATAAAATC
Found at i:19457080 original size:3 final size:3
Alignment explanation
Indices: 19457074--19457108 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
19457064 GAAGAAAAAA
19457074 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
19457109 AATAATAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.31, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:19457113 original size:3 final size:3
Alignment explanation
Indices: 19457107--19457148 Score: 68
Period size: 3 Copynumber: 14.0 Consensus size: 3
19457097 GATGATGATG
19457107 ATA ATA ATA ATA ATA ATA ATA GA-A ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA
19457149 TGATGATGAT
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 1 0.03
3 35 0.95
4 1 0.03
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:19464362 original size:24 final size:24
Alignment explanation
Indices: 19464319--19464373 Score: 76
Period size: 24 Copynumber: 2.2 Consensus size: 24
19464309 AAAAATAATA
*
19464319 TAATATTTTTAAATTTTATAAATATT
1 TAATATTTTT-AATTATATAAAT-TT
19464345 TAATATTTTT-ATTATATAAATTT
1 TAATATTTTTAATTATATAAATTT
19464368 TAATAT
1 TAATAT
19464374 AATATTTTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
23 8 0.29
24 10 0.36
26 10 0.36
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (24 bp):
TAATATTTTTAATTATATAAATTT
Found at i:19464379 original size:22 final size:24
Alignment explanation
Indices: 19464327--19464379 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 24
19464317 TATAATATTT
*
19464327 TTAA-ATTTTATAAATATTTAATA
1 TTAATATTATATAAATATTTAATA
**
19464350 TTTTTATTATATAAAT-TTTAATA
1 TTAATATTATATAAATATTTAATA
19464373 -TAATATT
1 TTAATATT
19464380 TTTAATGATC
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
22 5 0.21
23 9 0.38
24 10 0.42
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
TTAATATTATATAAATATTTAATA
Found at i:19464382 original size:14 final size:14
Alignment explanation
Indices: 19464345--19464404 Score: 54
Period size: 14 Copynumber: 4.3 Consensus size: 14
19464335 TATAAATATT
19464345 TAATATTTTTATTATA
1 TAATATTTTTA--ATA
19464361 TAA-A-TTTTAATA
1 TAATATTTTTAATA
19464373 TAATATTTTTAATGA
1 TAATATTTTTAAT-A
* *
19464388 TCAT-TTTTTATTA
1 TAATATTTTTAATA
19464401 TAAT
1 TAAT
19464405 TCATTTTACT
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
12 6 0.16
13 5 0.13
14 19 0.50
15 5 0.13
16 3 0.08
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (14 bp):
TAATATTTTTAATA
Found at i:19464430 original size:18 final size:17
Alignment explanation
Indices: 19464388--19464434 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
19464378 TTTTTAATGA
*
19464388 TCATTTTTTATTATAAT
1 TCATTTTATATTATAAT
*
19464405 TCATTTTACTATTATTAT
1 TCATTTTA-TATTATAAT
19464423 TACA-TTTATATT
1 T-CATTTTATATT
19464435 CAAATACATA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 11 0.42
18 13 0.50
19 2 0.08
ACGTcount: A:0.30, C:0.09, G:0.00, T:0.62
Consensus pattern (17 bp):
TCATTTTATATTATAAT
Found at i:19465005 original size:15 final size:15
Alignment explanation
Indices: 19464987--19465024 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
19464977 TTTATCTTTG
19464987 TATTTTTTATTTAAT
1 TATTTTTTATTTAAT
*
19465002 TATTTTTTATTTCAT
1 TATTTTTTATTTAAT
*
19465017 AATTTTTT
1 TATTTTTT
19465025 TGGAAACAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (15 bp):
TATTTTTTATTTAAT
Found at i:19470678 original size:207 final size:208
Alignment explanation
Indices: 19470296--19470685 Score: 522
Period size: 207 Copynumber: 1.9 Consensus size: 208
19470286 AAGAAAATTA
* *
19470296 TATTGAAGATTTTCTATAAATATTCCAATACACTGATAATATTTTACAAAAAAATCTTCTCACCT
1 TATTGAAAATTTTCTATAAATATTCCAATACACTGATAATATTTTAAAAAAAAATCTTCTCACCT
* *
19470361 AAAGATTTATTAAAGCATCTCTACTCGAAATACTTTTAAAATCCCATCATCGGATAAAATTTCTT
66 AAAGATTTATTAAAGCATCACTACTCGAAATACCTTTAAAATCCCATCATCGGATAAAATTTCTT
* * *
19470426 TTTTCTCATTTTTATCACTTTTTTTTAATATATTAAACAATTTTTAT-TTATTACTAAAAAAAAA
131 TTCTCTCATTTTTATCACTTTGTATTAATATATTAAACAATTTTTATATTATTACTAAAAAAAAA
19470490 AAATTTTTTACTG
196 AAATTTTTTACTG
* * *
19470503 TATTGAAAATTTTTTATAAATATTCCAATACACTGTTAGTA-TTTAAAAAAAAATCTTCTCACCT
1 TATTGAAAATTTTCTATAAATATTCCAATACACTGATAATATTTTAAAAAAAAATCTTCTCACCT
* * * * * *
19470567 AGAGATTTCTT-AGGCATCACTACTCGGAATACCTTT-AAATCTCATCGTCGGATAAAAATTTCC
66 AAAGATTTATTAAAGCATCACTACTCGAAATACCTTTAAAATCCCATCATCGGAT-AAAATTT-C
* **
19470630 TTTTCTCTCATTTTTTATTACTTTAGTATT-AT-TATTAAATTTATTTTTATATTATT
129 TTTTCTCTCA-TTTTTATCACTTT-GTATTAATATATTAAA-CAATTTTTATATTATT
19470686 TTGTTTTTAA
Statistics
Matches: 158, Mismatches: 19, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
204 15 0.09
205 28 0.18
206 48 0.30
207 59 0.37
208 8 0.05
ACGTcount: A:0.36, C:0.15, G:0.06, T:0.44
Consensus pattern (208 bp):
TATTGAAAATTTTCTATAAATATTCCAATACACTGATAATATTTTAAAAAAAAATCTTCTCACCT
AAAGATTTATTAAAGCATCACTACTCGAAATACCTTTAAAATCCCATCATCGGATAAAATTTCTT
TTCTCTCATTTTTATCACTTTGTATTAATATATTAAACAATTTTTATATTATTACTAAAAAAAAA
AAATTTTTTACTG
Found at i:19470817 original size:19 final size:19
Alignment explanation
Indices: 19470793--19470832 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
19470783 CATAAATATT
*
19470793 AATAAAA-TAATATATAAAA
1 AATAAAATTAAAAT-TAAAA
19470812 AATAAAATTAAAATTAAAA
1 AATAAAATTAAAATTAAAA
19470831 AA
1 AA
19470833 AATTTTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (19 bp):
AATAAAATTAAAATTAAAA
Found at i:19482216 original size:30 final size:30
Alignment explanation
Indices: 19482180--19482243 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
19482170 TTAAGGGTTT
*
19482180 TTTAGATATAAATTAAAAATTAAGAACTTA
1 TTTAGATATAAATTAAAAATTAAAAACTTA
* *
19482210 TTTAGATATAAATTAAAAGTTAAAAATTTA
1 TTTAGATATAAATTAAAAATTAAAAACTTA
19482240 TTTA
1 TTTA
19482244 CATGCAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.52, C:0.02, G:0.06, T:0.41
Consensus pattern (30 bp):
TTTAGATATAAATTAAAAATTAAAAACTTA
Found at i:19482271 original size:60 final size:59
Alignment explanation
Indices: 19482189--19482301 Score: 131
Period size: 60 Copynumber: 1.9 Consensus size: 59
19482179 TTTTAGATAT
*
19482189 AAATTAAAAATTAAGAACTTATTTAGATATAAATTAAAAGT-TAAAAATTTATTTACATGCA
1 AAATTAAAAATCAAGAACTTATTTAGATAT-AA-T-AAAGTATAAAAATTTATTTACATGCA
** * * *
19482250 AAATT-AAAATCAAGAGTTTATTTGGGTATAATAAAGTATAAAGATTTATTTA
1 AAATTAAAAATCAAGAACTTATTTAGATATAATAAAGTATAAAAATTTATTTA
19482302 GATAAAATGA
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
57 5 0.11
58 14 0.31
59 2 0.04
60 19 0.42
61 5 0.11
ACGTcount: A:0.50, C:0.04, G:0.10, T:0.37
Consensus pattern (59 bp):
AAATTAAAAATCAAGAACTTATTTAGATATAATAAAGTATAAAAATTTATTTACATGCA
Found at i:19482548 original size:20 final size:19
Alignment explanation
Indices: 19482512--19482549 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
19482502 TCTTTCAATC
*
19482512 TGAAAAGAGATATTTTGTA
1 TGAAAAGAGAAATTTTGTA
19482531 TGAAAAGAGAAAATTTTGT
1 TGAAAAGAG-AAATTTTGT
19482550 CTTATCTGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.45, C:0.00, G:0.21, T:0.34
Consensus pattern (19 bp):
TGAAAAGAGAAATTTTGTA
Found at i:19484635 original size:43 final size:44
Alignment explanation
Indices: 19484566--19484648 Score: 125
Period size: 43 Copynumber: 1.9 Consensus size: 44
19484556 CCACTTCATG
19484566 ATTCAATATCAAATGACAATATTAAGTATATTA-TTGATACGAT
1 ATTCAATATCAAATGACAATATTAAGTATATTATTTGATACGAT
**
19484609 ATTCAATATCAAATGTTGAATA-TAAGTATATTATTTGATA
1 ATTCAATATCAAATG-ACAATATTAAGTATATTATTTGATA
19484649 ACTTGAAATG
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
43 26 0.72
44 10 0.28
ACGTcount: A:0.43, C:0.07, G:0.10, T:0.40
Consensus pattern (44 bp):
ATTCAATATCAAATGACAATATTAAGTATATTATTTGATACGAT
Found at i:19490949 original size:21 final size:21
Alignment explanation
Indices: 19490920--19491003 Score: 82
Period size: 20 Copynumber: 4.0 Consensus size: 21
19490910 ATATCATTTT
* * *
19490920 TAATGTTAAAAAATTATAAAA
1 TAATTTTAAAATATTAAAAAA
19490941 TAATTTTAAAATA-TAAAAAA
1 TAATTTTAAAATATTAAAAAA
* * *
19490961 GAGTTTT-CAATATTAAAAAA
1 TAATTTTAAAATATTAAAAAA
*
19490981 TAATTTTGAAATATCTAAAAAA
1 TAATTTTAAAATAT-TAAAAAA
19491003 T
1 T
19491004 TTTAAAAAAT
Statistics
Matches: 51, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
19 4 0.08
20 23 0.45
21 16 0.31
22 8 0.16
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.36
Consensus pattern (21 bp):
TAATTTTAAAATATTAAAAAA
Found at i:19491398 original size:14 final size:14
Alignment explanation
Indices: 19491360--19491405 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 14
19491350 TTTTAAATTT
19491360 TATAAATATTTAATA
1 TATAAAT-TTTAATA
* *
19491375 TTTAATATTTTATTA
1 TATAA-ATTTTAATA
19491390 TATAAATTTTAATA
1 TATAAATTTTAATA
19491404 TA
1 TA
19491406 ATATTTTTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
14 10 0.38
15 14 0.54
16 2 0.08
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
TATAAATTTTAATA
Found at i:19491413 original size:14 final size:14
Alignment explanation
Indices: 19491339--19491435 Score: 58
Period size: 14 Copynumber: 6.6 Consensus size: 14
19491329 AACAGAAAAA
19491339 TAATATAATATTTT
1 TAATATAATATTTT
*
19491353 TAAATTTTATAA-ATATT
1 T-AA---TATAATATTTT
19491370 TAATATTTAATATTTT
1 TAATA--TAATATTTT
*
19491386 ATTATATAA-A-TTT
1 -TAATATAATATTTT
19491399 TAATATAATATTTT
1 TAATATAATATTTT
*
19491413 TAATGATCAT-TTTT
1 TAAT-ATAATATTTT
*
19491427 TATTATAAT
1 TAATATAAT
19491436 TTATTTTACT
Statistics
Matches: 65, Mismatches: 7, Indels: 23
0.68 0.07 0.24
Matches are distributed among these distances:
12 7 0.11
13 10 0.15
14 16 0.25
15 12 0.18
16 6 0.09
17 9 0.14
18 5 0.08
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (14 bp):
TAATATAATATTTT
Found at i:19492036 original size:15 final size:15
Alignment explanation
Indices: 19492018--19492055 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
19492008 TTTATCTTTG
19492018 TATTTTTTATTTAAT
1 TATTTTTTATTTAAT
*
19492033 TATTTTTTATTTCAT
1 TATTTTTTATTTAAT
*
19492048 GATTTTTT
1 TATTTTTT
19492056 TGGAAACAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.74
Consensus pattern (15 bp):
TATTTTTTATTTAAT
Found at i:19492129 original size:12 final size:12
Alignment explanation
Indices: 19492106--19492139 Score: 50
Period size: 13 Copynumber: 2.7 Consensus size: 12
19492096 TTGTATCTTG
19492106 TATTTGTTTAATT
1 TATTT-TTTAATT
19492119 TATTTTTTAATT
1 TATTTTTTAATT
19492131 TCATTTTTT
1 T-ATTTTTT
19492140 TAACAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 8 0.40
13 12 0.60
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.74
Consensus pattern (12 bp):
TATTTTTTAATT
Found at i:19493561 original size:29 final size:30
Alignment explanation
Indices: 19493529--19493598 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 30
19493519 ATTTCAAATA
*
19493529 AATTGAATCCTAAAAT-TTTATTTTTACTT
1 AATTAAATCCTAAAATATTTATTTTTACTT
** *
19493558 AATTAAATTTTTAAATATTTATTTTTACTCT
1 AATTAAATCCTAAAATATTTATTTTTACT-T
19493589 -ATTAAATCCT
1 AATTAAATCCT
19493599 TGATTAGATA
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
29 12 0.36
30 20 0.61
31 1 0.03
ACGTcount: A:0.36, C:0.10, G:0.01, T:0.53
Consensus pattern (30 bp):
AATTAAATCCTAAAATATTTATTTTTACTT
Found at i:19494310 original size:12 final size:12
Alignment explanation
Indices: 19494293--19494338 Score: 58
Period size: 12 Copynumber: 3.8 Consensus size: 12
19494283 CGATTTTAAT
19494293 TTTTTTAAAAAA
1 TTTTTTAAAAAA
19494305 TTTTTT-AAAAA
1 TTTTTTAAAAAA
19494316 TTATTTTAAAAAAA
1 TT-TTTT-AAAAAA
*
19494330 TTTTATAAA
1 TTTTTTAAA
19494339 TTTTACTTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
11 7 0.23
12 13 0.43
13 3 0.10
14 7 0.23
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
TTTTTTAAAAAA
Found at i:19494314 original size:11 final size:11
Alignment explanation
Indices: 19494293--19494342 Score: 55
Period size: 11 Copynumber: 4.4 Consensus size: 11
19494283 CGATTTTAAT
19494293 TTTTTTAAAAAA
1 TTTTTT-AAAAA
19494305 TTTTTTAAAAA
1 TTTTTTAAAAA
19494316 TTATTTTAAAAA
1 TT-TTTTAAAAA
** *
19494328 AATTTTATAAA
1 TTTTTTAAAAA
19494339 TTTT
1 TTTT
19494343 ACTTAAAGAA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
11 17 0.53
12 15 0.47
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (11 bp):
TTTTTTAAAAA
Found at i:19496725 original size:19 final size:19
Alignment explanation
Indices: 19496688--19496731 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
19496678 AATTAATGTA
*
19496688 ATAATA-ATTTTTAAATTG
1 ATAATATATTTTGAAATTG
*
19496706 ATAATATATTTTGAATTTG
1 ATAATATATTTTGAAATTG
19496725 A-AATATA
1 ATAATATA
19496732 ATAAATCGTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 12 0.52
19 11 0.48
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (19 bp):
ATAATATATTTTGAAATTG
Found at i:19504457 original size:30 final size:30
Alignment explanation
Indices: 19504392--19504524 Score: 105
Period size: 30 Copynumber: 4.6 Consensus size: 30
19504382 ATATTAAGGG
* * *
19504392 TTTATTTAGATATAAATTAAAAATTGAGAA
1 TTTATTTAGATATAAATTAAAAGTTAAAAA
*
19504422 CTTATTTAGATATAAATTAAAAGTTAAAAA
1 TTTATTTAGATATAAATTAAAAGTTAAAAA
* ** * * *
19504452 TTTATTTACATGCAAATTAAAA-TCAAGAG
1 TTTATTTAGATATAAATTAAAAGTTAAAAA
* * *
19504481 TTTATTTGGGTAT-AA-T-AAAGTATAAAGA
1 TTTATTTAGATATAAATTAAAAGT-TAAAAA
19504509 TTTATTTAGATA-AAAT
1 TTTATTTAGATATAAAT
19504525 GATAAAATTT
Statistics
Matches: 77, Mismatches: 22, Indels: 9
0.71 0.20 0.08
Matches are distributed among these distances:
26 3 0.04
27 2 0.03
28 16 0.21
29 12 0.16
30 44 0.57
ACGTcount: A:0.47, C:0.03, G:0.11, T:0.39
Consensus pattern (30 bp):
TTTATTTAGATATAAATTAAAAGTTAAAAA
Found at i:19506025 original size:29 final size:31
Alignment explanation
Indices: 19505992--19506059 Score: 113
Period size: 29 Copynumber: 2.3 Consensus size: 31
19505982 ACGGCTAGCC
19505992 AGTTGCCATATATTTGTTTGGAAG-CA-TTG
1 AGTTGCCATATATTTGTTTGGAAGCCATTTG
19506021 AGTTGCCATATATTTGTTTGGAAGCCATTTG
1 AGTTGCCATATATTTGTTTGGAAGCCATTTG
*
19506052 AGCTGCCA
1 AGTTGCCA
19506060 AAACAAGTTA
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
29 24 0.67
30 2 0.06
31 10 0.28
ACGTcount: A:0.24, C:0.15, G:0.24, T:0.38
Consensus pattern (31 bp):
AGTTGCCATATATTTGTTTGGAAGCCATTTG
Found at i:19507859 original size:17 final size:16
Alignment explanation
Indices: 19507825--19507861 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
19507815 AATTTGTACC
*
19507825 TTTTTTTAAATGTTAA
1 TTTTTTTAAATGTAAA
19507841 TTTTTTTAAATGTAAAA
1 TTTTTTTAAATGT-AAA
19507858 TTTT
1 TTTT
19507862 AAAAGGATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.62
Consensus pattern (16 bp):
TTTTTTTAAATGTAAA
Found at i:19514868 original size:12 final size:12
Alignment explanation
Indices: 19514843--19514879 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
19514833 TAAAGTTTTT
19514843 TAAAATAATTTAA
1 TAAAA-AATTTAA
*
19514856 TAAAAATTTTAA
1 TAAAAAATTTAA
19514868 TAAAAAATTTAA
1 TAAAAAATTTAA
19514880 ATAGATAGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 17 0.77
13 5 0.23
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
TAAAAAATTTAA
Found at i:19521933 original size:2 final size:2
Alignment explanation
Indices: 19521926--19521953 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
19521916 AAGGAAATTA
19521926 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19521954 CAATGGGATC
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19528245 original size:3 final size:3
Alignment explanation
Indices: 19528237--19528283 Score: 69
Period size: 3 Copynumber: 15.7 Consensus size: 3
19528227 AGAAAGAGGA
*
19528237 ATT ATT ATT ATT ATT AATT ATT ATT ATT ATT A-T ACT ATT ATT ATT
1 ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
19528282 AT
1 AT
19528284 CAAAATAAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
2 2 0.05
3 36 0.88
4 3 0.07
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:19528257 original size:16 final size:16
Alignment explanation
Indices: 19528236--19528283 Score: 78
Period size: 16 Copynumber: 2.9 Consensus size: 16
19528226 CAGAAAGAGG
19528236 AATTATTATTATTATT
1 AATTATTATTATTATT
19528252 AATTATTATTATTATT
1 AATTATTATTATTATT
*
19528268 ATACTATTATTATTAT
1 A-ATTATTATTATTAT
19528284 CAAAATAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
16 17 0.57
17 13 0.43
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (16 bp):
AATTATTATTATTATT
Found at i:19532694 original size:41 final size:40
Alignment explanation
Indices: 19532624--19532752 Score: 116
Period size: 41 Copynumber: 3.0 Consensus size: 40
19532614 TTTCAAATAT
19532624 TTAAAAAAATTTT-TATTTTTAAATTTTTTAAGTTTTTTGAA
1 TTAAAAAAATTTTAT-TTTTTAAA-TTTTTAAGTTTTTTGAA
* * **
19532665 TTAAAAAAATTTTATTTTATTAAAATTTTAATTTTTTTCGTT
1 TTAAAAAAATTTTATTTT-TTAAATTTTTAAGTTTTTT-GAA
* **
19532707 TTATAAATTTTTTGGATTTTTTTAAATTTTTAAGATTTTTTGAA
1 TTAAAAAAATTTT--A-TTTTTTAAATTTTTAAG-TTTTTTGAA
19532751 TT
1 TT
19532753 TTTAAAAATA
Statistics
Matches: 70, Mismatches: 11, Indels: 11
0.76 0.12 0.12
Matches are distributed among these distances:
41 28 0.40
42 17 0.24
44 15 0.21
45 10 0.14
ACGTcount: A:0.33, C:0.01, G:0.05, T:0.60
Consensus pattern (40 bp):
TTAAAAAAATTTTATTTTTTAAATTTTTAAGTTTTTTGAA
Found at i:19532745 original size:18 final size:19
Alignment explanation
Indices: 19532705--19532757 Score: 63
Period size: 18 Copynumber: 2.8 Consensus size: 19
19532695 ATTTTTTTCG
* **
19532705 TTTTATAAATTTTTTGGAT
1 TTTTTTAAATTTTTAAGAT
19532724 TTTTTTAAATTTTTAAGA-
1 TTTTTTAAATTTTTAAGAT
*
19532742 TTTTTTGAATTTTTAA
1 TTTTTTAAATTTTTAA
19532758 AAATATTTCA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
18 15 0.50
19 15 0.50
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (19 bp):
TTTTTTAAATTTTTAAGAT
Found at i:19532761 original size:28 final size:28
Alignment explanation
Indices: 19532705--19532775 Score: 74
Period size: 28 Copynumber: 2.5 Consensus size: 28
19532695 ATTTTTTTCG
* **
19532705 TTTTATAA-ATTTTTTGGATTTTTTTAAA
1 TTTT-TAAGATTTTTTGAATTTTTAAAAA
19532733 TTTTTAAGATTTTTTGAATTTTTAAAAA
1 TTTTTAAGATTTTTTGAATTTTTAAAAA
*
19532761 TATTTCAAG-TTTTTT
1 T-TTTTAAGATTTTTT
19532776 AGTGTTTATA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
27 3 0.08
28 28 0.76
29 6 0.16
ACGTcount: A:0.30, C:0.01, G:0.07, T:0.62
Consensus pattern (28 bp):
TTTTTAAGATTTTTTGAATTTTTAAAAA
Found at i:19533596 original size:10 final size:10
Alignment explanation
Indices: 19533573--19533597 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
19533563 AAATTTTGGA
19533573 TTTTAAAATT
1 TTTTAAAATT
19533583 TTTTAAAATT
1 TTTTAAAATT
19533593 TTTTA
1 TTTTA
19533598 TTTTTCTGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (10 bp):
TTTTAAAATT
Found at i:19533680 original size:27 final size:28
Alignment explanation
Indices: 19533623--19533685 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 28
19533613 ATAAAAAATT
*
19533623 TATTTTAATTTTTTAAAGAAGTTATCAA
1 TATTTTAATTTTTTAAACAAGTTATCAA
* *
19533651 TATTTTGAA-TTTTTAAACAA-TTTTCCA
1 TATTTT-AATTTTTTAAACAAGTTATCAA
19533678 TATTTTAA
1 TATTTTAA
19533686 AAATTTTTTG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
26 2 0.06
27 11 0.35
28 16 0.52
29 2 0.06
ACGTcount: A:0.37, C:0.06, G:0.05, T:0.52
Consensus pattern (28 bp):
TATTTTAATTTTTTAAACAAGTTATCAA
Found at i:19533746 original size:19 final size:20
Alignment explanation
Indices: 19533724--19533766 Score: 56
Period size: 18 Copynumber: 2.3 Consensus size: 20
19533714 AAATTTAAGC
*
19533724 CTTTTTCATTTTTTTT-TTA
1 CTTTTTAATTTTTTTTATTA
19533743 C-TTTTAATTTTTTTTATTA
1 CTTTTTAATTTTTTTTATTA
19533762 -TTTTT
1 CTTTTT
19533767 TTTTTGAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 13 0.62
19 8 0.38
ACGTcount: A:0.14, C:0.07, G:0.00, T:0.79
Consensus pattern (20 bp):
CTTTTTAATTTTTTTTATTA
Found at i:19534244 original size:14 final size:15
Alignment explanation
Indices: 19534219--19534253 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
19534209 TAACTAAAAA
19534219 TAAAATATTAAATAT
1 TAAAATATTAAATAT
19534234 TAAAATA-TAAATAT
1 TAAAATATTAAATAT
*
19534248 AAAAAT
1 TAAAAT
19534254 TTATCTTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.63
15 7 0.37
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
TAAAATATTAAATAT
Found at i:19535825 original size:25 final size:27
Alignment explanation
Indices: 19535797--19535861 Score: 84
Period size: 24 Copynumber: 2.6 Consensus size: 27
19535787 TTAATTATCC
19535797 AATGATGAAATTTTTAGAAAATT-C-A
1 AATGATGAAATTTTTAGAAAATTCCTA
*
19535822 AATGAT-AAATTTTTATAAAATTCCTA
1 AATGATGAAATTTTTAGAAAATTCCTA
*
19535848 AGTGA-GAAATTTTT
1 AATGATGAAATTTTT
19535862 TTTAGATTTG
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
24 15 0.43
25 7 0.20
26 13 0.37
ACGTcount: A:0.45, C:0.05, G:0.11, T:0.40
Consensus pattern (27 bp):
AATGATGAAATTTTTAGAAAATTCCTA
Found at i:19538353 original size:55 final size:53
Alignment explanation
Indices: 19538158--19538353 Score: 142
Period size: 55 Copynumber: 3.6 Consensus size: 53
19538148 TGAGATAAGT
* * *
19538158 TTTTC-AGACTTGTGATTCAATCTCAGTCGTTGATCTCGACTTGATCTAGATCA
1 TTTTCTAGACTTGCGGTTCAATCT-AGTCGTTGATCTCGACTCGATCTAGATCA
* * * * * * * **
19538211 TTTTCTTGACCTGCGGTTCAATCACAGTCATTTGAACTCAACTCGATCTAGGTTGG
1 TTTTCTAGACTTGCGGTTCAATC-TAGTC-GTTGATCTCGACTCGATCTA-GATCA
* * * ** * * *
19538267 TTTTTTAGATTTACATTTCAATCTTGATCGTTCGATCTCGACTCGATCCAAATCA
1 TTTTCTAGACTTGCGGTTCAATCTAG-TCGTT-GATCTCGACTCGATCTAGATCA
19538322 TTTTCTAGACTTGCGGTTCAATCCTAGTCGTT
1 TTTTCTAGACTTGCGGTTCAAT-CTAGTCGTT
19538354 TGACCTAGAC
Statistics
Matches: 101, Mismatches: 35, Indels: 12
0.68 0.24 0.08
Matches are distributed among these distances:
53 5 0.05
54 17 0.17
55 42 0.42
56 37 0.37
ACGTcount: A:0.22, C:0.22, G:0.16, T:0.40
Consensus pattern (53 bp):
TTTTCTAGACTTGCGGTTCAATCTAGTCGTTGATCTCGACTCGATCTAGATCA
Found at i:19538415 original size:111 final size:110
Alignment explanation
Indices: 19538157--19538416 Score: 265
Period size: 111 Copynumber: 2.3 Consensus size: 110
19538147 TTGAGATAAG
* * * * * * * *
19538157 TTTTTCAGACTTGTGATTCAATCTCAGTCGTTGATCTCGACTTGATCTAGATCATTTTCTTGACC
1 TTTTTTAGACTTATGTTTCAATCTCGGTCGTTGATCTCGACTCGATCCAAATCATTTTCTAGACC
* * *
19538222 TGCGGTTCAATCACAGTCATTTGAACTCAACTCGATCTAGGTTGG
66 TGCGGTTCAATCACAGTCATTTGAACTCAACTAGATCCAGGTTGA
* ** * *
19538267 TTTTTTAGATTTACATTTCAATCTTGATCGTTCGATCTCGACTCGATCCAAATCATTTTCTAGAC
1 TTTTTTAGACTTATGTTTCAATCTCGGTCGTT-GATCTCGACTCGATCCAAATCATTTTCTAGAC
* * * *
19538332 TTGCGGTTCAATC-CTAGTCGTTTGACCT-AGACTTAG-TCCATGTTGA
65 CTGCGGTTCAATCAC-AGTCATTTGAACTCA-AC-TAGATCCAGGTTGA
*
19538378 TTTTTTAGACTTATGTTTCAATCTCGGTCATGTGATCTC
1 TTTTTTAGACTTATGTTTCAATCTCGGTCGT-TGATCTC
19538417 AGCTTAGTCC
Statistics
Matches: 119, Mismatches: 26, Indels: 9
0.77 0.17 0.06
Matches are distributed among these distances:
110 25 0.21
111 91 0.76
112 3 0.03
ACGTcount: A:0.22, C:0.21, G:0.17, T:0.41
Consensus pattern (110 bp):
TTTTTTAGACTTATGTTTCAATCTCGGTCGTTGATCTCGACTCGATCCAAATCATTTTCTAGACC
TGCGGTTCAATCACAGTCATTTGAACTCAACTAGATCCAGGTTGA
Found at i:19538874 original size:111 final size:111
Alignment explanation
Indices: 19538694--19538954 Score: 254
Period size: 111 Copynumber: 2.4 Consensus size: 111
19538684 TTTGACCTCA
*** * * * **
19538694 ACTCGGTCCAAGTTGGTTTTTTAAACTTAC-AGTTCAATCTCGATCATTCGATCTCAGCTTGATC
1 ACTCGGTCCAAGTCAATTTTTCAAACTTGCGA-TTCAATCCCGATCATTCGATCTCAGCTCAATC
* * *
19538758 CAGATCACTTTCCCAACTTACAATTCAATCTTGATCGTTCGACCTTG
65 CAGATCACTTTCCCAACTTACAATTCAATATCGATCATTCGACCTTG
* * * * * **
19538805 ACTTGGTCTAGGTCAATTTTTCAAACTTGTGATTCAATCCCGATCATTCGATCTTAGCTCAATTT
1 ACTCGGTCCAAGTCAATTTTTCAAACTTGCGATTCAATCCCGATCATTCGATCTCAGCTCAATCC
* **** * ** *
19538870 AGATCATTTTTTTTACTTGCGGTTCAATATCGATCATTCGATCTTG
66 AGATCACTTTCCCAACTTACAATTCAATATCGATCATTCGACCTTG
*
19538916 ACTCGGTCCAAGTCAATTTTTCAAACTTGCGATTTAATC
1 ACTCGGTCCAAGTCAATTTTTCAAACTTGCGATTCAATC
19538955 TTAGTTGTTC
Statistics
Matches: 117, Mismatches: 32, Indels: 2
0.77 0.21 0.01
Matches are distributed among these distances:
111 116 0.99
112 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.14, T:0.39
Consensus pattern (111 bp):
ACTCGGTCCAAGTCAATTTTTCAAACTTGCGATTCAATCCCGATCATTCGATCTCAGCTCAATCC
AGATCACTTTCCCAACTTACAATTCAATATCGATCATTCGACCTTG
Found at i:19539362 original size:3 final size:3
Alignment explanation
Indices: 19539332--19539437 Score: 53
Period size: 3 Copynumber: 37.3 Consensus size: 3
19539322 TTTTCATTTG
* * * * * * *
19539332 TAT TTT TAT TAT TTT TGT TAT TAG TAT TAT TGT TAT TCT TAC TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * *
19539380 TAA TAC TAG TAT TA- TAT TAT TA- TAG TA- TAT TAT TA- TAT TA- TAC
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
19539423 TA- TAT TAT CAT TAT T
1 TAT TAT TAT TAT TAT T
19539438 TTTTTTCTTC
Statistics
Matches: 78, Mismatches: 19, Indels: 12
0.72 0.17 0.11
Matches are distributed among these distances:
2 12 0.15
3 66 0.85
ACGTcount: A:0.31, C:0.05, G:0.05, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:19539410 original size:13 final size:13
Alignment explanation
Indices: 19539392--19539421 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
19539382 ATACTAGTAT
19539392 TATATTATTATAG
1 TATATTATTATAG
*
19539405 TATATTATTATAT
1 TATATTATTATAG
19539418 TATA
1 TATA
19539422 CTATATTATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (13 bp):
TATATTATTATAG
Found at i:19539412 original size:18 final size:18
Alignment explanation
Indices: 19539374--19539437 Score: 76
Period size: 18 Copynumber: 3.4 Consensus size: 18
19539364 TTATTCTTAC
19539374 TATTATTAATACTAGTATTA
1 TATTATT-ATACTA-TATTA
*
19539394 TATTATTATAGTATATTA
1 TATTATTATACTATATTA
19539412 T-TATATTATACTATATTA
1 TAT-TATTATACTATATTA
19539430 TCATTATT
1 T-ATTATT
19539438 TTTTTTCTTC
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
17 1 0.03
18 21 0.54
19 9 0.23
20 8 0.21
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.55
Consensus pattern (18 bp):
TATTATTATACTATATTA
Found at i:19539415 original size:21 final size:21
Alignment explanation
Indices: 19539356--19539420 Score: 64
Period size: 21 Copynumber: 3.1 Consensus size: 21
19539346 TTGTTATTAG
* *
19539356 TATTATTGT-TATTCTTACTAT
1 TATTATAGTATATTATTA-TAT
*
19539377 TATTA-A-TACTAGTATTATAT
1 TATTATAGTA-TATTATTATAT
19539397 TATTATAGTATATTATTATAT
1 TATTATAGTATATTATTATAT
19539418 TAT
1 TAT
19539421 ACTATATTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
19 1 0.03
20 8 0.22
21 25 0.69
22 2 0.06
ACGTcount: A:0.34, C:0.05, G:0.05, T:0.57
Consensus pattern (21 bp):
TATTATAGTATATTATTATAT
Found at i:19539772 original size:21 final size:22
Alignment explanation
Indices: 19539748--19539789 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
19539738 AACTTTTTGT
19539748 TTAA-GTTTCTAGGATTTTGGG
1 TTAAGGTTTCTAGGATTTTGGG
* *
19539769 TTAAGGTTTTTGGGATTTTGG
1 TTAAGGTTTCTAGGATTTTGG
19539790 ATTTAAACTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.17, C:0.02, G:0.31, T:0.50
Consensus pattern (22 bp):
TTAAGGTTTCTAGGATTTTGGG
Found at i:19539873 original size:22 final size:22
Alignment explanation
Indices: 19539831--19539874 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
19539821 TAGGTTAGGG
*
19539831 TTGAATTGCTAGGATTGAGATT
1 TTGAATTGCTAGGATTAAGATT
*
19539853 TTGAATTTCTAGG-TTCAAGATT
1 TTGAATTGCTAGGATT-AAGATT
19539875 GAATTTATGG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 2 0.11
22 17 0.89
ACGTcount: A:0.27, C:0.07, G:0.23, T:0.43
Consensus pattern (22 bp):
TTGAATTGCTAGGATTAAGATT
Found at i:19540297 original size:17 final size:17
Alignment explanation
Indices: 19540245--19540297 Score: 65
Period size: 16 Copynumber: 3.2 Consensus size: 17
19540235 ATTACATGTT
* *
19540245 TTTTTTTTCTTTTTTTGT
1 TTTTTTTT-ATTTTTTGA
19540263 TTTTTTTTA-TTTTT-A
1 TTTTTTTTATTTTTTGA
19540278 TTTTTTTTATTTTTTGA
1 TTTTTTTTATTTTTTGA
19540295 TTT
1 TTT
19540298 GATTTTTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
15 9 0.29
16 10 0.32
17 4 0.13
18 8 0.26
ACGTcount: A:0.08, C:0.02, G:0.04, T:0.87
Consensus pattern (17 bp):
TTTTTTTTATTTTTTGA
Found at i:19540304 original size:35 final size:33
Alignment explanation
Indices: 19540245--19540316 Score: 92
Period size: 35 Copynumber: 2.1 Consensus size: 33
19540235 ATTACATGTT
* *
19540245 TTTTTTTTCTTTTTTTGTTTTTTTTTATTTTTA
1 TTTTTTTTCATTTTTTGTTTTTTTTTATCTTTA
19540278 TTTTTTTT-ATTTTTTGATTTGATTTTTTATCTTTA
1 TTTTTTTTCATTTTTTG-TTT--TTTTTTATCTTTA
19540313 TTTT
1 TTTT
19540317 AGTCTCTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
32 7 0.21
33 11 0.32
35 16 0.47
ACGTcount: A:0.10, C:0.03, G:0.04, T:0.83
Consensus pattern (33 bp):
TTTTTTTTCATTTTTTGTTTTTTTTTATCTTTA
Found at i:19540305 original size:1 final size:1
Alignment explanation
Indices: 19540243--19540292 Score: 55
Period size: 1 Copynumber: 50.0 Consensus size: 1
19540233 TGATTACATG
* * * * *
19540243 TTTTTTTTTTCTTTTTTTGTTTTTTTTTATTTTTATTTTTTTTATTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
19540293 GATTTGATTT
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
1 39 1.00
ACGTcount: A:0.06, C:0.02, G:0.02, T:0.90
Consensus pattern (1 bp):
T
Found at i:19542478 original size:22 final size:22
Alignment explanation
Indices: 19542450--19542521 Score: 74
Period size: 22 Copynumber: 3.3 Consensus size: 22
19542440 TGATTTGTAA
19542450 ATTTTGTGCTAATTTGGTGCAG
1 ATTTTGTGCTAATTTGGTGCAG
* **
19542472 -TGTTTGTGCTGATTTAATGCAG
1 AT-TTTGTGCTAATTTGGTGCAG
** *
19542494 ATTTCATGCTAATTTGGTGCAA
1 ATTTTGTGCTAATTTGGTGCAG
19542516 ATTTTG
1 ATTTTG
19542522 AGTAGTTCTT
Statistics
Matches: 37, Mismatches: 11, Indels: 4
0.71 0.21 0.08
Matches are distributed among these distances:
21 1 0.03
22 35 0.95
23 1 0.03
ACGTcount: A:0.21, C:0.10, G:0.24, T:0.46
Consensus pattern (22 bp):
ATTTTGTGCTAATTTGGTGCAG
Found at i:19542888 original size:20 final size:19
Alignment explanation
Indices: 19542865--19542911 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
19542855 TTTTTTTTGG
19542865 TTTATTTGTTATTTT-ATTA
1 TTTATTT-TTATTTTAATTA
*
19542884 TTTTAAATTTTATTTTAATTA
1 -TTT-ATTTTTATTTTAATTA
19542905 TTTATTT
1 TTTATTT
19542912 ATCTTTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
19 3 0.13
20 13 0.57
21 7 0.30
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (19 bp):
TTTATTTTTATTTTAATTA
Found at i:19543974 original size:6 final size:7
Alignment explanation
Indices: 19543930--19543984 Score: 60
Period size: 7 Copynumber: 7.6 Consensus size: 7
19543920 TAATATTTTC
19543930 AAATAAA
1 AAATAAA
19543937 AAA-AAA
1 AAATAAA
19543943 GAAGA-AAA
1 -AA-ATAAA
19543951 AAATTTAAA
1 AAA--TAAA
19543960 AAATAAA
1 AAATAAA
19543967 AAATAAA
1 AAATAAA
19543974 AAATAAA
1 AAATAAA
19543981 AAAT
1 AAAT
19543985 TGGTTTGAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
6 4 0.09
7 29 0.67
8 4 0.09
9 6 0.14
ACGTcount: A:0.82, C:0.00, G:0.04, T:0.15
Consensus pattern (7 bp):
AAATAAA
Found at i:19551328 original size:51 final size:51
Alignment explanation
Indices: 19551269--19551404 Score: 186
Period size: 51 Copynumber: 2.7 Consensus size: 51
19551259 TAATTCATTC
* *
19551269 TAATTTTTG-AAAGAATTTATTG-AAGGTATTTTTTACATTATACGCCTTGAA
1 TAATTTTTGTACAGAA-TTA-TGAAAGGTATTTTTTACATTATACGCCTTCAA
* *
19551320 TAATTTTTGTACAGAATTATGAAAGGTACTTTTTACATTATATGCCTTCAA
1 TAATTTTTGTACAGAATTATGAAAGGTATTTTTTACATTATACGCCTTCAA
* *
19551371 TAGTTTTTGTACAGAATTATGAAAGCTATTTTTT
1 TAATTTTTGTACAGAATTATGAAAGGTATTTTTT
19551405 GAAAATAAAT
Statistics
Matches: 76, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
50 2 0.03
51 69 0.91
52 5 0.07
ACGTcount: A:0.32, C:0.09, G:0.13, T:0.46
Consensus pattern (51 bp):
TAATTTTTGTACAGAATTATGAAAGGTATTTTTTACATTATACGCCTTCAA
Found at i:19552262 original size:239 final size:236
Alignment explanation
Indices: 19551663--19552230 Score: 669
Period size: 239 Copynumber: 2.4 Consensus size: 236
19551653 CGTAAAATGC
* * ** * * * **
19551663 CTACTAAATTTTTAAGGGGGTTGTTGAAAACGTTTATTCCATAAAAATGCCTTTACTAGTTTGTT
1 CTACTAAAATTTTAAGGGGG-TATTGAAGGCATTTATTCCATAAAAATGCCTTCACTAATTCATT
*
19551728 CTAATTTTTGAAAGAATTTATTGAAGGTGTTTTTTGCATTATACGCCTTTAATAATTTTTGTACA
65 CTAATTTTTGAAAGAATTT-TTGAAGGCGTTTTTTGCATTATACGCCTTTAATAATTTTTGTACA
* * *
19551793 AAATTATCGAAGACGTTTTTTGAAAATAAATACCTTCAATAATTTCTTTTTAAAAATTATTTTGG
129 AAATTATCGAAGA-GTTTTTTAAAAATAAACACCTTCAATAAGTTCTTTTTAAAAATTATTTTGG
*
19551858 ATTATTAAAGGTGTCTTGTAGCAGAAAATGCCTTTAATATTTCA
193 ATTATTAAAGGTGTCTTGTAGCAGAAAACGCCTTTAATATTTCA
* * * * ** *
19551902 CTACTAAAATTTTAAAGGGGTTATTGAAGGGATTTTTTTTCATAAAAACACATTCACTAATTCAT
1 CTACTAAAATTTT-AAGGGGGTATTGAAGGCA-TTTATTCCATAAAAATGCCTTCACTAATTCAT
* * * * * *
19551967 TATAATTTTTAAAAGAATTTTTGAAGGCGTTTTTTGCATTGTATGCCTTCAATAATTTTTGTATA
64 TCTAATTTTTGAAAGAATTTTTGAAGGCGTTTTTTGCATTATACGCCTTTAATAATTTTTGTACA
* ** **
19552032 AAATTATTGAAG-GTGTTTTTAAAGAATAAACGTCTTTGATAAGTTCTTTTTAAAAATTA-TTTG
129 AAATTATCGAAGAGT-TTTTTAAA-AATAAACACCTTCAATAAGTTCTTTTTAAAAATTATTTTG
*
19552095 AGATTATTAAAGGCT-TCTTTTAGCAGAAAACG-CTTTCAATA-TTCTA
192 -GATTATTAAAGG-TGTCTTGTAGCAGAAAACGCCTTT-AATATTTC-A
*
19552141 TTACTAAAATTTTAAGGGGGTATTGAAGGCATTTATTCCATAAAAATGCCTTCACTAATTCATTC
1 CTACTAAAATTTTAAGGGGGTATTGAAGGCATTTATTCCATAAAAATGCCTTCACTAATTCATTC
*
19552206 TAATTTTTTGAAGGAATTTGTTGAA
66 TAA-TTTTTGAAAGAATTT-TTGAA
19552231 TGCATTTTCT
Statistics
Matches: 275, Mismatches: 44, Indels: 20
0.81 0.13 0.06
Matches are distributed among these distances:
237 33 0.12
238 47 0.17
239 147 0.53
240 48 0.17
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.42
Consensus pattern (236 bp):
CTACTAAAATTTTAAGGGGGTATTGAAGGCATTTATTCCATAAAAATGCCTTCACTAATTCATTC
TAATTTTTGAAAGAATTTTTGAAGGCGTTTTTTGCATTATACGCCTTTAATAATTTTTGTACAAA
ATTATCGAAGAGTTTTTTAAAAATAAACACCTTCAATAAGTTCTTTTTAAAAATTATTTTGGATT
ATTAAAGGTGTCTTGTAGCAGAAAACGCCTTTAATATTTCA
Found at i:19552512 original size:13 final size:13
Alignment explanation
Indices: 19552496--19552530 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
19552486 AATTTGCTCT
19552496 AATTTTTTGAAGG
1 AATTTTTTGAAGG
*
19552509 AATTTATTGAAGG
1 AATTTTTTGAAGG
*
19552522 TATTTTTTG
1 AATTTTTTG
19552531 CATAATATGC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.29, C:0.00, G:0.20, T:0.51
Consensus pattern (13 bp):
AATTTTTTGAAGG
Found at i:19553192 original size:28 final size:29
Alignment explanation
Indices: 19553152--19553215 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 29
19553142 TGGTCTTTAA
* * *
19553152 ATATTGTGATTTGCTGAATGGTATTATGTG
1 ATATTGT-ATTTGCTAAATGATATTATATG
*
19553182 ATATTGT-TTTGCTAAATGATATTGTATG
1 ATATTGTATTTGCTAAATGATATTATATG
19553210 ATATTG
1 ATATTG
19553216 GTATGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 23 0.77
30 7 0.23
ACGTcount: A:0.27, C:0.03, G:0.22, T:0.48
Consensus pattern (29 bp):
ATATTGTATTTGCTAAATGATATTATATG
Found at i:19557184 original size:6 final size:6
Alignment explanation
Indices: 19557173--19557223 Score: 59
Period size: 6 Copynumber: 8.3 Consensus size: 6
19557163 AATATTATTT
* *
19557173 TAAATA TAAATA TAAATA TAAATA TATATA -AAATA TATATAA TTAAATA
1 TAAATA TAAATA TAAATA TAAATA TAAATA TAAATA TAAAT-A -TAAATA
19557222 TA
1 TA
19557224 TAATTAAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
5 4 0.11
6 28 0.74
7 2 0.05
8 4 0.11
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (6 bp):
TAAATA
Found at i:19557210 original size:9 final size:10
Alignment explanation
Indices: 19557176--19557214 Score: 51
Period size: 11 Copynumber: 3.6 Consensus size: 10
19557166 ATTATTTTAA
19557176 ATATAAATAT
1 ATATAAATAT
19557186 AAATATAAATAT
1 --ATATAAATAT
19557198 ATATAAAATAT
1 ATAT-AAATAT
19557209 ATATAA
1 ATATAA
19557215 TTAAATATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 6 0.23
11 10 0.38
12 10 0.38
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (10 bp):
ATATAAATAT
Found at i:19557224 original size:12 final size:13
Alignment explanation
Indices: 19557175--19557231 Score: 68
Period size: 12 Copynumber: 4.6 Consensus size: 13
19557165 TATTATTTTA
19557175 AATATAAATATA-
1 AATATAAATATAT
19557187 AATATAAATATAT
1 AATATAAATATAT
*
19557200 -ATAAAATATATAT
1 AATATAA-ATATAT
19557213 AAT-TAAATATAT
1 AATATAAATATAT
19557225 AAT-TAAA
1 AATATAAA
19557232 AAAATAATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
12 30 0.75
13 8 0.20
14 2 0.05
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
AATATAAATATAT
Found at i:19557231 original size:27 final size:28
Alignment explanation
Indices: 19557158--19557237 Score: 80
Period size: 27 Copynumber: 2.9 Consensus size: 28
19557148 ATCCGAAATT
*
19557158 AATA-AAATATTATTTTAAATATAAATATA
1 AATATAAATA-TATATTAAA-ATAAATATA
*
19557187 AATATAAATATATA-TAAAATATATAT-
1 AATATAAATATATATTAAAATAAATATA
19557213 AAT-TAAATATATAATTAAAA-AAATA
1 AATATAAATATAT-ATTAAAATAAATA
19557238 ATTTTTTTAT
Statistics
Matches: 45, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
25 9 0.20
26 8 0.18
27 12 0.27
28 4 0.09
29 7 0.16
30 5 0.11
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (28 bp):
AATATAAATATATATTAAAATAAATATA
Found at i:19562014 original size:186 final size:185
Alignment explanation
Indices: 19561692--19562136 Score: 522
Period size: 186 Copynumber: 2.4 Consensus size: 185
19561682 AATGGAAGGA
* * * *
19561692 GATTATTGAAGGCATTTTTGGCAGAAAATGTCTTGAATAATCCCTTTTAGGAAGG-GATTATTCT
1 GATTATTCAAGGCATTTTTGGCAAAAAATGCCTTGAATAATCCC-TTTAAG-AGGAGATTATTCT
* *
19561756 TAGTTTAAATAATATCTTTTAATTATAAAAATACTAAAGTAGCTTAATCGATTAAAGCATAAGCT
64 TAGTTTAAATAATACCTTTTAATTATAAAAACACTAAAGTAGCTTAATCGATTAAAGCATAAGCT
* * * * *
19561821 ATTAACCATAAGGTCATAGGTTCGATCCCTCTCTCTAGCT-TTTTT-GGGTTTTCAAG
129 ATTAACCATAAGATCATAAGTTCGATCCCTCCCTATAG-TGTTTTTAAGGTTTTCAAG
* ** * *
19561877 GATTATTCAATGTGTTTTCTTGCAAAAAATGCCTTGAATAATCCTCTTTATGAGGAGATTATTCT
1 GATTATTCAAGGCATTTT-TGGCAAAAAATGCCTTGAATAATCC-CTTTAAGAGGAGATTATTCT
* * * * *
19561942 TAGTTTAAATAATACCTTTT-ATTATAAAAACATTGAAGTAGTTTAATCGGTTAGAGCATATAGC
64 TAGTTTAAATAATACCTTTTAATTATAAAAACACTAAAGTAGCTTAATCGATTAAAGCATA-AGC
* * * **
19562006 TGTTAACCATAAGATCGTAAGTTTGATCTTTCCCTATAGTGTTTTTCAAGGTTTTCAAG
128 TATTAACCATAAGATCATAAGTTCGATCCCTCCCTATAGTGTTTTT-AAGGTTTTCAAG
* * *
19562065 GATTATTTAAGGCATTTTTGGCAGAAAA-GCCTTGAATAATCCCTTGTAAGAGAAGATTATTCTT
1 GATTATTCAAGGCATTTTTGGCAAAAAATGCCTTGAATAATCCCTT-TAAGAGGAGATTATTCTT
19562129 AGTTTAAA
65 AGTTTAAA
19562137 ATATTGGAGT
Statistics
Matches: 219, Mismatches: 33, Indels: 15
0.82 0.12 0.06
Matches are distributed among these distances:
185 55 0.25
186 131 0.60
187 9 0.04
188 24 0.11
ACGTcount: A:0.32, C:0.13, G:0.16, T:0.39
Consensus pattern (185 bp):
GATTATTCAAGGCATTTTTGGCAAAAAATGCCTTGAATAATCCCTTTAAGAGGAGATTATTCTTA
GTTTAAATAATACCTTTTAATTATAAAAACACTAAAGTAGCTTAATCGATTAAAGCATAAGCTAT
TAACCATAAGATCATAAGTTCGATCCCTCCCTATAGTGTTTTTAAGGTTTTCAAG
Found at i:19562353 original size:108 final size:108
Alignment explanation
Indices: 19562164--19562379 Score: 378
Period size: 108 Copynumber: 2.0 Consensus size: 108
19562154 TCGATTAGAG
* * *
19562164 CATACAACTGTTAACTATAAAATTATAGGTTCGATCCTTCTCTCTAGTGTTTTTTAGTTTTTTCA
1 CATACAACTGTTAACCATAAAATCATAGGTTCGATCCTTCTCTCTAGTGTTTTTTAGGTTTTTCA
*
19562229 AAATACCTTGAATAATCCCTTTCAATTTTTATGAGAGGATTAT
66 AAATACCTTGAATAATCCCTTTCAATTTTTATAAGAGGATTAT
*
19562272 CATACAACTGTTAACCATAAAATCGTAGGTTCGATCCTTCTCTCTAGTGTTTTTTAGGTTTTTCA
1 CATACAACTGTTAACCATAAAATCATAGGTTCGATCCTTCTCTCTAGTGTTTTTTAGGTTTTTCA
*
19562337 AAATACCTTGAATAATCCCTTTCAATTTTTATAAGGGGATTAT
66 AAATACCTTGAATAATCCCTTTCAATTTTTATAAGAGGATTAT
19562380 TCAATGCGTT
Statistics
Matches: 102, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
108 102 1.00
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (108 bp):
CATACAACTGTTAACCATAAAATCATAGGTTCGATCCTTCTCTCTAGTGTTTTTTAGGTTTTTCA
AAATACCTTGAATAATCCCTTTCAATTTTTATAAGAGGATTAT
Found at i:19565179 original size:27 final size:28
Alignment explanation
Indices: 19565143--19565198 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
19565133 CCATGAATGG
*
19565143 TAACATATTTTG-CAATGATTTATGAAT
1 TAACATATTTTGACAATAATTTATGAAT
*
19565170 TAACATATTTTGACATTAATTTATGAAT
1 TAACATATTTTGACAATAATTTATGAAT
19565198 T
1 T
19565199 TACAAAATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
27 12 0.46
28 14 0.54
ACGTcount: A:0.38, C:0.07, G:0.09, T:0.46
Consensus pattern (28 bp):
TAACATATTTTGACAATAATTTATGAAT
Found at i:19565647 original size:17 final size:17
Alignment explanation
Indices: 19565625--19565659 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
19565615 TTTAGATTTT
19565625 ATTTCAAGGTAATATAA
1 ATTTCAAGGTAATATAA
19565642 ATTTCAAGGTAATATAA
1 ATTTCAAGGTAATATAA
19565659 A
1 A
19565660 CGTTTTGCGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.49, C:0.06, G:0.11, T:0.34
Consensus pattern (17 bp):
ATTTCAAGGTAATATAA
Found at i:19572810 original size:24 final size:22
Alignment explanation
Indices: 19572771--19572815 Score: 63
Period size: 24 Copynumber: 2.0 Consensus size: 22
19572761 TTGATTATTC
*
19572771 ATTTTTTTTTTGTTTATCTTTG
1 ATTTTTTATTTGTTTATCTTTG
19572793 ATTTTTTGATTTGATTTATCTTT
1 ATTTTTT-ATTTG-TTTATCTTT
19572816 TGTTATGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 7 0.35
23 4 0.20
24 9 0.45
ACGTcount: A:0.13, C:0.04, G:0.09, T:0.73
Consensus pattern (22 bp):
ATTTTTTATTTGTTTATCTTTG
Found at i:19583489 original size:7 final size:8
Alignment explanation
Indices: 19583468--19583515 Score: 62
Period size: 8 Copynumber: 6.0 Consensus size: 8
19583458 AATACTATGC
19583468 TTAAAAAA
1 TTAAAAAA
19583476 TTAAAAAA
1 TTAAAAAA
19583484 TTAAAAAAA
1 TT-AAAAAA
19583493 TTAAAAAA
1 TTAAAAAA
* *
19583501 ATGAAAAA
1 TTAAAAAA
19583509 -TAAAAAA
1 TTAAAAAA
19583516 AGAGGACTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
7 6 0.17
8 22 0.61
9 8 0.22
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (8 bp):
TTAAAAAA
Found at i:19583507 original size:17 final size:17
Alignment explanation
Indices: 19583470--19583516 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 17
19583460 TACTATGCTT
*
19583470 AAAAAATTAAAAAATTA
1 AAAAAATTAAAAAAATA
19583487 AAAAAATTAAAAAAAT-
1 AAAAAATTAAAAAAATA
*
19583503 GAAAAA-TAAAAAAA
1 AAAAAATTAAAAAAA
19583517 GAGGACTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
15 8 0.29
16 5 0.18
17 15 0.54
ACGTcount: A:0.81, C:0.00, G:0.02, T:0.17
Consensus pattern (17 bp):
AAAAAATTAAAAAAATA
Found at i:19583516 original size:9 final size:9
Alignment explanation
Indices: 19583470--19583508 Score: 62
Period size: 9 Copynumber: 4.4 Consensus size: 9
19583460 TACTATGCTT
19583470 AAAAAATT-
1 AAAAAATTA
19583478 AAAAAATTA
1 AAAAAATTA
19583487 AAAAAATTA
1 AAAAAATTA
*
19583496 AAAAAATGA
1 AAAAAATTA
19583505 AAAA
1 AAAA
19583509 TAAAAAAAGA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
8 8 0.28
9 21 0.72
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (9 bp):
AAAAAATTA
Found at i:19584298 original size:33 final size:33
Alignment explanation
Indices: 19584248--19584310 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
19584238 TAAGATTTGC
**
19584248 ATAGCATGCATTACATTTTTGAATGTCTAGTGT
1 ATAGCATGCATTACATTTAAGAATGTCTAGTGT
* *
19584281 ATAGTATGCATTGCATTTAAGAATGTCTAG
1 ATAGCATGCATTACATTTAAGAATGTCTAG
19584311 GAAGCAGGGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.19, T:0.40
Consensus pattern (33 bp):
ATAGCATGCATTACATTTAAGAATGTCTAGTGT
Found at i:19584582 original size:19 final size:19
Alignment explanation
Indices: 19584555--19584597 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
19584545 TTGTTAAGCC
*
19584555 TTTAATTAGAGAAGCTTTA
1 TTTATTTAGAGAAGCTTTA
*
19584574 TTTATTTAGAGGAGCTTTA
1 TTTATTTAGAGAAGCTTTA
19584593 TTTAT
1 TTTAT
19584598 CTTTCAAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.30, C:0.05, G:0.16, T:0.49
Consensus pattern (19 bp):
TTTATTTAGAGAAGCTTTA
Found at i:19584940 original size:23 final size:24
Alignment explanation
Indices: 19584905--19584968 Score: 78
Period size: 23 Copynumber: 2.7 Consensus size: 24
19584895 TATTTTATAT
*
19584905 TTTATTTTATTTATTTATGATTCA
1 TTTATTTTATTTATTTATCATTCA
*
19584929 TTTA-TTTATTTATTTATCTTTCA
1 TTTATTTTATTTATTTATCATTCA
*
19584952 TTTTTTTTGATTT-TTTA
1 TTTATTTT-ATTTATTTA
19584969 GTTGATTTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
23 20 0.57
24 11 0.31
25 4 0.11
ACGTcount: A:0.20, C:0.05, G:0.03, T:0.72
Consensus pattern (24 bp):
TTTATTTTATTTATTTATCATTCA
Found at i:19585873 original size:17 final size:16
Alignment explanation
Indices: 19585839--19585884 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 16
19585829 CCAAGTCGAT
*
19585839 TTTTAGTTTTTTTATTA
1 TTTTA-TTTATTTATTA
19585856 TTTTATTTATTTAGTTA
1 TTTTATTTATTTA-TTA
*
19585873 TTATATTTATTT
1 TTTTATTTATTT
19585885 TATAAGTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
16 7 0.27
17 19 0.73
ACGTcount: A:0.22, C:0.00, G:0.04, T:0.74
Consensus pattern (16 bp):
TTTTATTTATTTATTA
Found at i:19586582 original size:43 final size:46
Alignment explanation
Indices: 19586535--19586626 Score: 136
Period size: 43 Copynumber: 2.1 Consensus size: 46
19586525 GGAAAAAAAC
*
19586535 AAAAAAAATTCTAAATAGACCCAAAT-G-A-TAAATTTAGAAATAA
1 AAAAAAAATTCTAAATAGACCCAAATAGTAGAAAATTTAGAAATAA
* *
19586578 AAAAAAAATTGTAAATTGACCCAAATAGTAGAAAATTTAGAAATAA
1 AAAAAAAATTCTAAATAGACCCAAATAGTAGAAAATTTAGAAATAA
19586624 AAA
1 AAA
19586627 TAAATTTCAA
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
43 24 0.56
44 1 0.02
45 1 0.02
46 17 0.40
ACGTcount: A:0.61, C:0.08, G:0.09, T:0.23
Consensus pattern (46 bp):
AAAAAAAATTCTAAATAGACCCAAATAGTAGAAAATTTAGAAATAA
Found at i:19588675 original size:18 final size:18
Alignment explanation
Indices: 19588652--19588690 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
19588642 TCAAATTCTG
19588652 TTTGAATT-TTCCCACGAT
1 TTTGAATTATT-CCACGAT
*
19588670 TTTGAATTATTCGACGAT
1 TTTGAATTATTCCACGAT
19588688 TTT
1 TTT
19588691 TCCCTTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 17 0.89
19 2 0.11
ACGTcount: A:0.23, C:0.15, G:0.13, T:0.49
Consensus pattern (18 bp):
TTTGAATTATTCCACGAT
Found at i:19596704 original size:90 final size:88
Alignment explanation
Indices: 19596534--19596715 Score: 208
Period size: 90 Copynumber: 2.0 Consensus size: 88
19596524 TTTTAGGAAA
*
19596534 TTATAAGGCTTTCCAATATGCGAATAAAATCTTATTTTGAAAAAACATTAGCCCTCCAATCTATT
1 TTATAAGGCTTTCCAATATGCGAATAAAATCTTATTTTGAAAAAAAATTAGCCCTCCAATCTATT
* * *
19596599 GGTAAGGCTTTTTATTTATATATTT
66 AGTAAAGCTTATTATTTA-A-ATTT
* * * * * *
19596624 TTATAAGGTTTTCCAATATGTTG-GTAAAATCTTATTTTTTAAAAAATAATT-GCCTTTCAATCT
1 TTATAAGGCTTTCCAATATG-CGAATAAAATCTTA-TTTTGAAAAAA-AATTAGCCCTCCAATCT
19596687 ATTAGTAAAGC-TATTATTTAAATTT
63 ATTAGTAAAGCTTATTATTTAAATTT
19596712 TTAT
1 TTAT
19596716 TTGGTTATAT
Statistics
Matches: 79, Mismatches: 10, Indels: 8
0.81 0.10 0.08
Matches are distributed among these distances:
88 8 0.10
89 1 0.01
90 37 0.47
91 30 0.38
92 3 0.04
ACGTcount: A:0.34, C:0.12, G:0.10, T:0.45
Consensus pattern (88 bp):
TTATAAGGCTTTCCAATATGCGAATAAAATCTTATTTTGAAAAAAAATTAGCCCTCCAATCTATT
AGTAAAGCTTATTATTTAAATTT
Found at i:19597710 original size:6 final size:6
Alignment explanation
Indices: 19597695--19597735 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
19597685 TTTTTAAAAT
*
19597695 AATT-A AATTAA AATT-A AA-TCA AATTAA AATTAA AATTAA AA
1 AATTAA AATTAA AATTAA AATTAA AATTAA AATTAA AATTAA AA
19597736 AATTCCTGCT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
4 1 0.03
5 10 0.31
6 21 0.66
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (6 bp):
AATTAA
Found at i:19598358 original size:66 final size:67
Alignment explanation
Indices: 19598145--19598373 Score: 202
Period size: 66 Copynumber: 3.5 Consensus size: 67
19598135 ATCGCAGGTT
** * * * * *
19598145 AAAAAACTAAAATGACCTGGACCAAG-C-TGATATAAAAAAA-AGTGACTAGGATTAAA-TAGCA
1 AAAAAACTAAAATGACCTGGACTGAGCCAAGGTA-AAAAAAAGAGTAACCAGGATTAAACCA-CA
19598206 AGTC
64 AGTC
* * *
19598210 AAAAAACTAAAATGACCTAGA-TCGAGCCAAGGTAAAAAAAAGAGTAACCAGGATTAAACCGC-T
1 AAAAAACTAAAATGACCTGGACT-GAGCCAAGGTAAAAAAAAGAGTAACCAGGATTAAACCACAA
19598273 GATC
65 G-TC
* * * * * * * * *
19598277 AAAAGACTAAAATGACTTGGACTGAGCCAAGGT-TAAAAATGAGTGATCATGATTGAACTACAAG
1 AAAAAACTAAAATGACCTGGACTGAGCCAAGGTAAAAAAAAGAGTAACCAGGATTAAACCACAAG
19598341 TC
66 TC
19598343 AAAAAACTAAAATGACCTGGACTGAGCCAAG
1 AAAAAACTAAAATGACCTGGACTGAGCCAAG
19598374 ATTGAAGATA
Statistics
Matches: 132, Mismatches: 24, Indels: 15
0.77 0.14 0.09
Matches are distributed among these distances:
65 22 0.17
66 60 0.45
67 49 0.37
68 1 0.01
ACGTcount: A:0.48, C:0.16, G:0.19, T:0.18
Consensus pattern (67 bp):
AAAAAACTAAAATGACCTGGACTGAGCCAAGGTAAAAAAAAGAGTAACCAGGATTAAACCACAAG
TC
Found at i:19609228 original size:20 final size:21
Alignment explanation
Indices: 19609200--19609245 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
19609190 ATGTGTATGT
* *
19609200 AAATGAATG-ACAAATATATA
1 AAATAAATGAACAAATAAATA
19609220 AAATAAATGAACAAATAAATA
1 AAATAAATGAACAAATAAATA
19609241 AAATA
1 AAATA
19609246 TAAGCAAGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 8 0.35
21 15 0.65
ACGTcount: A:0.67, C:0.04, G:0.07, T:0.22
Consensus pattern (21 bp):
AAATAAATGAACAAATAAATA
Found at i:19612078 original size:39 final size:38
Alignment explanation
Indices: 19612017--19612116 Score: 130
Period size: 39 Copynumber: 2.6 Consensus size: 38
19612007 TTTTCAAAAG
19612017 TTTAAAGTTGTGTGCCTCTATTAT-AAATGAACCCTTATT
1 TTTAAAGTTGTGTGCCTCTATTATGAAA--AACCCTTATT
* * *
19612056 TTTAAAGTTGTGTACCTATATTATGGAAAAGCCCTTATT
1 TTTAAAGTTGTGTGCCTCTATTAT-GAAAAACCCTTATT
*
19612095 TTTAAAATTGTGTGCCTCTATT
1 TTTAAAGTTGTGTGCCTCTATT
19612117 GTTAATGAGT
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
39 50 0.94
41 3 0.06
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.44
Consensus pattern (38 bp):
TTTAAAGTTGTGTGCCTCTATTATGAAAAACCCTTATT
Found at i:19612197 original size:21 final size:21
Alignment explanation
Indices: 19612167--19612211 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
19612157 GTTGAAAAGC
*
19612167 CCTTCTTTTTAAAATTGTGTG
1 CCTTCATTTTAAAATTGTGTG
* *
19612188 CCTTCATTTTTAAGTTGTGTG
1 CCTTCATTTTAAAATTGTGTG
19612209 CCT
1 CCT
19612212 CTATTATGGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.18, G:0.16, T:0.51
Consensus pattern (21 bp):
CCTTCATTTTAAAATTGTGTG
Found at i:19612288 original size:39 final size:38
Alignment explanation
Indices: 19612187--19612370 Score: 194
Period size: 39 Copynumber: 4.8 Consensus size: 38
19612177 AAAATTGTGT
19612187 GCCTTCATTTTT-AAGTTGTGTGCCTCTATTATGGAAAA
1 GCCTT-ATTTTTAAAGTTGTGTGCCTCTATTATGGAAAA
* * *
19612225 GCCCTTA-TTTTAAAGTTGTATGTCTCTATTGTGGAAAA
1 G-CCTTATTTTTAAAGTTGTGTGCCTCTATTATGGAAAA
* * * *
19612263 GCCCTTATTTTTAAAGTTATGTGTCTCTATTATAGAAGA
1 G-CCTTATTTTTAAAGTTGTGTGCCTCTATTATGGAAAA
* * * * *
19612302 GCTTTAGTTTTTAAAGTTATGTACCTCTATTTTGGAGGAA
1 GCCTTA-TTTTTAAAGTTGTGTGCCTCTATTATGGA-AAA
19612342 -CCTTATTTTTAAAGTTGTGTGCCTCTATT
1 GCCTTATTTTTAAAGTTGTGTGCCTCTATT
19612371 TTTGAGGAGC
Statistics
Matches: 123, Mismatches: 18, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
37 4 0.03
38 58 0.47
39 60 0.49
40 1 0.01
ACGTcount: A:0.24, C:0.14, G:0.17, T:0.45
Consensus pattern (38 bp):
GCCTTATTTTTAAAGTTGTGTGCCTCTATTATGGAAAA
Found at i:19612291 original size:77 final size:75
Alignment explanation
Indices: 19612188--19612370 Score: 203
Period size: 77 Copynumber: 2.4 Consensus size: 75
19612178 AAATTGTGTG
*
19612188 CCTTCATTTTT-AAGTTGTGTGCCTCTATTATGGAAAAGCCCTTA-TTTTAAAGTTGTATGT-CT
1 CCTT-ATTTTTAAAGTTGTGTGCCTCTATTATAGAAAAG-CCTTAGTTTTAAAG-T-TATGTACT
19612250 CTATTGTGGA-AAA
62 CTATTGTGGAGAAA
* * * *
19612263 GCCCTTATTTTTAAAGTTATGTGTCTCTATTATAGAAGAGCTTTAGTTTTTAAAGTTATGTACCT
1 --CCTTATTTTTAAAGTTGTGTGCCTCTATTATAGAAAAGCCTTAG-TTTTAAAGTTATGTA-CT
* *
19612328 CTATTTTGGAGGAA
62 CTATTGTGGAGAAA
19612342 CCTTATTTTTAAAGTTGTGTGCCTCTATT
1 CCTTATTTTTAAAGTTGTGTGCCTCTATT
19612371 TTTGAGGAGC
Statistics
Matches: 91, Mismatches: 9, Indels: 12
0.81 0.08 0.11
Matches are distributed among these distances:
76 15 0.16
77 55 0.60
78 19 0.21
79 2 0.02
ACGTcount: A:0.25, C:0.14, G:0.17, T:0.45
Consensus pattern (75 bp):
CCTTATTTTTAAAGTTGTGTGCCTCTATTATAGAAAAGCCTTAGTTTTAAAGTTATGTACTCTAT
TGTGGAGAAA
Found at i:19612378 original size:38 final size:38
Alignment explanation
Indices: 19612188--19612370 Score: 167
Period size: 38 Copynumber: 4.8 Consensus size: 38
19612178 AAATTGTGTG
*
19612188 CCTTCATTTTT-AAGTTGTGTGCCTCTATTATGGAAAAGC
1 CCTT-ATTTTTAAAGTTGTGTGCCTCTATTATGGAGAA-C
* * * *
19612227 CCTTA-TTTTAAAGTTGTATGTCTCTATTGTGGAAAAGC
1 CCTTATTTTTAAAGTTGTGTGCCTCTATTATGGAGAA-C
* * * *
19612265 CCTTATTTTTAAAGTTATGTGTCTCTATTATAGA-AGAG
1 CCTTATTTTTAAAGTTGTGTGCCTCTATTATGGAGA-AC
* * * *
19612303 CTTTAGTTTTTAAAGTTATGTACCTCTATTTTGGAGGAA-
1 CCTTA-TTTTTAAAGTTGTGTGCCTCTATTATGGA-GAAC
19612342 CCTTATTTTTAAAGTTGTGTGCCTCTATT
1 CCTTATTTTTAAAGTTGTGTGCCTCTATT
19612371 TTTGAGGAGC
Statistics
Matches: 122, Mismatches: 16, Indels: 13
0.81 0.11 0.09
Matches are distributed among these distances:
37 4 0.03
38 58 0.48
39 58 0.48
40 1 0.01
41 1 0.01
ACGTcount: A:0.25, C:0.14, G:0.17, T:0.45
Consensus pattern (38 bp):
CCTTATTTTTAAAGTTGTGTGCCTCTATTATGGAGAAC
Found at i:19622237 original size:13 final size:12
Alignment explanation
Indices: 19622180--19622295 Score: 69
Period size: 13 Copynumber: 9.7 Consensus size: 12
19622170 ACCCTTCAGC
*
19622180 AAACCACTCAAA
1 AAACCATTCAAA
* *
19622192 AACAACATTCAAC
1 AA-ACCATTCAAA
*
19622205 AAACCATTC-AG
1 AAACCATTCAAA
*
19622216 CAA-CATTCAAA
1 AAACCATTCAAA
*
19622227 AATACCATTC-AG
1 AA-ACCATTCAAA
*
19622239 CAA-CATTCAAA
1 AAACCATTCAAA
**
19622250 AATACCATTCAGC
1 AA-ACCATTCAAA
19622263 AAACCATTCAGAA
1 AAACCATTCA-AA
* *
19622276 ACACCATTCAAC
1 AAACCATTCAAA
19622288 AAACCATT
1 AAACCATT
19622296 TAACATATGA
Statistics
Matches: 77, Mismatches: 19, Indels: 16
0.69 0.17 0.14
Matches are distributed among these distances:
10 10 0.13
11 8 0.10
12 28 0.36
13 31 0.40
ACGTcount: A:0.49, C:0.29, G:0.03, T:0.18
Consensus pattern (12 bp):
AAACCATTCAAA
Found at i:19622295 original size:25 final size:23
Alignment explanation
Indices: 19622194--19622285 Score: 132
Period size: 23 Copynumber: 4.0 Consensus size: 23
19622184 CACTCAAAAA
*
19622194 CAACATTCAACAA-ACCATTCAG
1 CAACATTCAAAAATACCATTCAG
19622216 CAACATTCAAAAATACCATTCAG
1 CAACATTCAAAAATACCATTCAG
19622239 CAACATTCAAAAATACCATTCAG
1 CAACATTCAAAAATACCATTCAG
* *
19622262 CAAACCATTCAGAAACACCATTCA
1 C-AA-CATTCAAAAATACCATTCA
19622286 ACAAACCATT
Statistics
Matches: 64, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
22 12 0.19
23 33 0.52
24 2 0.03
25 17 0.27
ACGTcount: A:0.47, C:0.29, G:0.04, T:0.20
Consensus pattern (23 bp):
CAACATTCAAAAATACCATTCAG
Found at i:19622925 original size:62 final size:62
Alignment explanation
Indices: 19622802--19622931 Score: 183
Period size: 62 Copynumber: 2.1 Consensus size: 62
19622792 TAGAAAATCA
* *
19622802 CCTTCAATAATTATGTACAAAAATTAAAAGGAATTAGTGAAGGCGTTTGTTCTCAAAAAATG
1 CCTTCAATAATTATGTACAAAAATTAAAAGGAATTAATGAAGGCGTTTGTCCTCAAAAAATG
** *
19622864 CCTTCAATAATTATGTACGTAAATTAGAAGGAATTAATGAAGGCGTTT-TCCT-AGAATAAATG
1 CCTTCAATAATTATGTACAAAAATTAAAAGGAATTAATGAAGGCGTTTGTCCTCA-AA-AAATG
19622926 CCTTCA
1 CCTTCA
19622932 CTAACTGTCT
Statistics
Matches: 61, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
60 1 0.02
61 5 0.08
62 55 0.90
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.32
Consensus pattern (62 bp):
CCTTCAATAATTATGTACAAAAATTAAAAGGAATTAATGAAGGCGTTTGTCCTCAAAAAATG
Found at i:19623037 original size:124 final size:123
Alignment explanation
Indices: 19622903--19623365 Score: 494
Period size: 124 Copynumber: 3.8 Consensus size: 123
19622893 GGAATTAATG
* * *
19622903 AAGGCGTTTTCCTAGAATAAATGCCTTCACTAACTGTCTTAAAATTTGAGTTGTGAAAAATGATG
1 AAGGCATTTTTCTAGAATAAATGCCTTCACTAACTGTCTTAAAATTTGAGTTGTGAAAAATGAAG
* * **
19622968 GCATTTTTCACTAGAAGGCACCTTTAATAATTTTAAAAATTTTAAGAGAAAATTAGTT
66 GCATTTTTCACTAGAAGACGCCTTTAATAATCCTAAAAATTTTAAGAGAAAATTAGTT
* ** *
19623026 AAGGCATTTTTCTAAAATAAATGCCTTCACTAACCATATTAAAATTTGAGTTGTGAAAAATTGAA
1 AAGGCATTTTTCTAGAATAAATGCCTTCACTAACTGTCTTAAAATTTGAGTTGTGAAAAA-TGAA
* * *
19623091 GGCATTTTTCACT-GAAAAACGCCTTTAATAATCCCAAAAATTTTAAGAGAAAATTAGTG
65 GGCATTTTTCACTAG-AAGACGCCTTTAATAATCCTAAAAATTTTAAGAGAAAATTAGTT
* * * * * *
19623150 AAGGCATTTTTTTAGAATAAAAGCTTTCACT-A---TCTTAAAATTTGAGTTATGAAATATTAAA
1 AAGGCATTTTTCTAGAATAAATGCCTTCACTAACTGTCTTAAAATTTGAGTTGTGAAA-AATGAA
* * * *
19623211 GGCGTTTTTCACTAGAAGACGCCTTTAATAATCCTAAAACTTTTAAAAGGAAATTA-TT
65 GGCATTTTTCACTAGAAGACGCCTTTAATAATCCTAAAAATTTTAAGAGAAAATTAGTT
* * * * * * *
19623269 AA-ACATGTTTGTTCTA-AA-AAGATGCCTTCACTAATTGTCCTAAAGTTTGAGTAGTGGAACAT
1 AAGGCA--TTT-TTCTAGAATAA-ATGCCTTCACTAACTGTCTTAAAATTTGAGTTGT-GAAAAA
* *
19623331 TGAATGCATTTTTCACTAGAAGACGCCTTCAATAA
61 TGAAGGCATTTTTCACTAGAAGACGCCTTTAATAA
19623366 AAAAAAAAAA
Statistics
Matches: 285, Mismatches: 42, Indels: 25
0.81 0.12 0.07
Matches are distributed among these distances:
118 2 0.01
119 5 0.02
120 85 0.30
121 7 0.02
123 56 0.20
124 127 0.45
125 3 0.01
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.35
Consensus pattern (123 bp):
AAGGCATTTTTCTAGAATAAATGCCTTCACTAACTGTCTTAAAATTTGAGTTGTGAAAAATGAAG
GCATTTTTCACTAGAAGACGCCTTTAATAATCCTAAAAATTTTAAGAGAAAATTAGTT
Found at i:19626104 original size:12 final size:12
Alignment explanation
Indices: 19626085--19626113 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
19626075 CTTGATGTTC
19626085 AAAG-TGATGAA
1 AAAGATGATGAA
19626096 AAAGATGATGAA
1 AAAGATGATGAA
19626108 AAAGAT
1 AAAGAT
19626114 AACCCCAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 4 0.24
12 13 0.76
ACGTcount: A:0.59, C:0.00, G:0.24, T:0.17
Consensus pattern (12 bp):
AAAGATGATGAA
Found at i:19629802 original size:19 final size:19
Alignment explanation
Indices: 19629775--19629828 Score: 92
Period size: 19 Copynumber: 2.9 Consensus size: 19
19629765 AAATTAAACT
*
19629775 TTTGGATGGCTTTCAATAG
1 TTTGAATGGCTTTCAATAG
19629794 TTTGAATGGCTTTCAATAG
1 TTTGAATGGCTTTCAATAG
19629813 TTTGAATGGC-TTCAAT
1 TTTGAATGGCTTTCAAT
19629829 CCATGATATT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
18 6 0.18
19 28 0.82
ACGTcount: A:0.24, C:0.11, G:0.22, T:0.43
Consensus pattern (19 bp):
TTTGAATGGCTTTCAATAG
Found at i:19630400 original size:107 final size:106
Alignment explanation
Indices: 19630271--19630485 Score: 331
Period size: 107 Copynumber: 2.0 Consensus size: 106
19630261 AGAAAACGAA
19630271 AGAGAAATGACTGTTGAGATTAAAGTAGCATACAATGGTTCTCTCAACATACAAGAATTAAAAAA
1 AGAGAAATGACTGTTGAGATTAAAGTAGCATACAATGGTTCTCTCAACATACAAGAATTAAAAAA
* * *
19630336 TTAGATATTCATAGAAGTTGTTGGAAAAGAAAGGCATGGAT
66 TCAGATATTCATAGAAGTTGCTAGAAAAGAAAGGCATGGAT
* * *** * *
19630377 AGAGAAAATGGCTGTTGAGATTAAAGTAGTATATGGTGGTTCTCTCAACATGCAAGAATTGAAAA
1 AGAG-AAATGACTGTTGAGATTAAAGTAGCATACAATGGTTCTCTCAACATACAAGAATTAAAAA
19630442 ATCAGATATTCATAGAAGTTGCTAGAAAAGAAAGGCATGGAT
65 ATCAGATATTCATAGAAGTTGCTAGAAAAGAAAGGCATGGAT
19630484 AG
1 AG
19630486 GTCTGAGGCC
Statistics
Matches: 98, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
106 4 0.04
107 94 0.96
ACGTcount: A:0.42, C:0.09, G:0.23, T:0.26
Consensus pattern (106 bp):
AGAGAAATGACTGTTGAGATTAAAGTAGCATACAATGGTTCTCTCAACATACAAGAATTAAAAAA
TCAGATATTCATAGAAGTTGCTAGAAAAGAAAGGCATGGAT
Found at i:19632603 original size:23 final size:23
Alignment explanation
Indices: 19632577--19632621 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
19632567 GACCTCCCCT
*
19632577 GTATGCAGACCCATTGTCATTAG
1 GTATGCAGACCCATTGCCATTAG
19632600 GTATGCAGACCCATTGCCATTA
1 GTATGCAGACCCATTGCCATTA
19632622 TCCTTCTTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (23 bp):
GTATGCAGACCCATTGCCATTAG
Found at i:19639073 original size:17 final size:16
Alignment explanation
Indices: 19639042--19639113 Score: 56
Period size: 17 Copynumber: 4.4 Consensus size: 16
19639032 TGGATTAATT
*
19639042 AATAAATTTAATATAA
1 AATAAATTTATTATAA
*
19639058 AATAAATTTTATTATAT
1 AATAAA-TTTATTATAA
* *
19639075 AATCAATTAATT-TATA
1 AATAAATTTATTATA-A
* *
19639091 AATCAATTTTATTATAT
1 AAT-AAATTTATTATAA
19639108 AATAAA
1 AATAAA
19639114 CTAATAAATA
Statistics
Matches: 42, Mismatches: 10, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
15 2 0.05
16 16 0.38
17 22 0.52
18 2 0.05
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (16 bp):
AATAAATTTATTATAA
Found at i:19639100 original size:33 final size:32
Alignment explanation
Indices: 19639049--19639119 Score: 97
Period size: 33 Copynumber: 2.2 Consensus size: 32
19639039 ATTAATAAAT
19639049 TTAATATAAAATAAATTTTATTATATAATCAA
1 TTAATATAAAATAAATTTTATTATATAATCAA
* * *
19639081 TTAATTTATAAATCAATTTTATTATATAATAAA
1 TTAATATA-AAATAAATTTTATTATATAATCAA
*
19639114 CTAATA
1 TTAATA
19639120 AATAATTTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
32 7 0.21
33 26 0.79
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (32 bp):
TTAATATAAAATAAATTTTATTATATAATCAA
Found at i:19639105 original size:16 final size:16
Alignment explanation
Indices: 19639057--19639106 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
19639047 ATTTAATATA
*
19639057 AAATAAATTTTATTAT
1 AAATCAATTTTATTAT
*
19639073 ATAATCAA-TTAATTTAT
1 A-AATCAATTTTA-TTAT
19639090 AAATCAATTTTATTAT
1 AAATCAATTTTATTAT
19639106 A
1 A
19639107 TAATAAACTA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
16 15 0.54
17 13 0.46
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (16 bp):
AAATCAATTTTATTAT
Found at i:19639230 original size:41 final size:39
Alignment explanation
Indices: 19639151--19639231 Score: 92
Period size: 39 Copynumber: 2.0 Consensus size: 39
19639141 AATAAAACTA
** *
19639151 TTATTTTATTTTAAAAATTAATAATTTTTAATTATTTAT
1 TTATTTTATTTTAAAAATTAATAATTTAAAAGTATTTAT
*
19639190 TTATTTTATTTTATAAGTATTAAATAATTTAAAAGT-TTTAT
1 TTATTTTATTTTA-AA-AATT-AATAATTTAAAAGTATTTAT
19639231 T
1 T
19639232 GCATAAAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
39 13 0.37
40 2 0.06
41 9 0.26
42 11 0.31
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.59
Consensus pattern (39 bp):
TTATTTTATTTTAAAAATTAATAATTTAAAAGTATTTAT
Found at i:19647562 original size:16 final size:16
Alignment explanation
Indices: 19647541--19647575 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
19647531 TTTCATTTTT
19647541 TGTTAAGTACAAAAGA
1 TGTTAAGTACAAAAGA
*
19647557 TGTTAAGTATAAAAGA
1 TGTTAAGTACAAAAGA
19647573 TGT
1 TGT
19647576 CAAGAATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.46, C:0.03, G:0.20, T:0.31
Consensus pattern (16 bp):
TGTTAAGTACAAAAGA
Found at i:19650295 original size:17 final size:17
Alignment explanation
Indices: 19650275--19650307 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
19650265 TGTAAAAAAA
*
19650275 TTTTAAGGTCGAAAAGC
1 TTTTAAGGTCAAAAAGC
19650292 TTTTAAGGTCAAAAAG
1 TTTTAAGGTCAAAAAG
19650308 TTCAAATTGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.39, C:0.09, G:0.21, T:0.30
Consensus pattern (17 bp):
TTTTAAGGTCAAAAAGC
Done.