Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167960.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_22, 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: 19587844
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 68000 characters in sequence are not A, C, G, or T
File 53 of 105
Found at i:10195734 original size:40 final size:41
Alignment explanation
Indices: 10195639--10195765 Score: 138
Period size: 40 Copynumber: 3.2 Consensus size: 41
10195629 TTCTCGATGG
*
10195639 TGATATCCGAGTGA-TAAAAATCATTT--ATCTT-TTGGTGG
1 TGATATCCGAGT-ATTAAAAATCATTTGCATCTTCTTGGTGA
* *
10195677 TGATATCCGAGTGTTAAAAATCATTTGCATCTTCTTGTTGA
1 TGATATCCGAGTATTAAAAATCATTTGCATCTTCTTGGTGA
* * ** *
10195718 TGATAT-TGAGTATTAAAAGTCATTTGCATCTTCTCAGTGG
1 TGATATCCGAGTATTAAAAATCATTTGCATCTTCTTGGTGA
10195758 TGATATCC
1 TGATATCC
10195766 AAATGTTAAA
Statistics
Matches: 73, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
38 24 0.33
40 38 0.52
41 11 0.15
ACGTcount: A:0.28, C:0.13, G:0.19, T:0.40
Consensus pattern (41 bp):
TGATATCCGAGTATTAAAAATCATTTGCATCTTCTTGGTGA
Found at i:10195849 original size:42 final size:42
Alignment explanation
Indices: 10195759--10195851 Score: 98
Period size: 42 Copynumber: 2.2 Consensus size: 42
10195749 TCTCAGTGGT
* * *
10195759 GATATCCAAATGTTAAAACTGGAATTGTATTTTCTTCGTAGT
1 GATATTCAAATGTTAAAACTGGAATTGGATTTTCTTCGTAGC
* * * * *
10195801 GGTATTCAAGTGTTAAAGCTTGAATTGGATTTTC-TCGATGGC
1 GATATTCAAATGTTAAAACTGGAATTGGATTTTCTTCG-TAGC
10195843 GATATTCAA
1 GATATTCAA
10195852 TTTTCTTTGG
Statistics
Matches: 41, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
41 3 0.07
42 38 0.93
ACGTcount: A:0.29, C:0.12, G:0.20, T:0.39
Consensus pattern (42 bp):
GATATTCAAATGTTAAAACTGGAATTGGATTTTCTTCGTAGC
Found at i:10195967 original size:33 final size:30
Alignment explanation
Indices: 10195925--10195996 Score: 83
Period size: 33 Copynumber: 2.3 Consensus size: 30
10195915 TGTCCTTCAG
10195925 TGGTGATATCTAA-AGTCATTCGCATCTTTTCGA
1 TGGTGATATCTAAGA-TCATTCG--TCTTTT-GA
* *
10195958 TGGTGATATCTGAGATCATTTGTCTTTTGA
1 TGGTGATATCTAAGATCATTCGTCTTTTGA
10195988 TGGTGATAT
1 TGGTGATAT
10195997 TCGAAGTTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
30 11 0.31
31 6 0.17
33 18 0.50
34 1 0.03
ACGTcount: A:0.22, C:0.12, G:0.22, T:0.43
Consensus pattern (30 bp):
TGGTGATATCTAAGATCATTCGTCTTTTGA
Found at i:10196267 original size:15 final size:15
Alignment explanation
Indices: 10196247--10196279 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
10196237 TTATTTATTA
*
10196247 TTTTTCTTTTCTTTT
1 TTTTTCTATTCTTTT
10196262 TTTTTCTATTCTTTT
1 TTTTTCTATTCTTTT
10196277 TTT
1 TTT
10196280 GGCATTTTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.03, C:0.12, G:0.00, T:0.85
Consensus pattern (15 bp):
TTTTTCTATTCTTTT
Found at i:10197133 original size:21 final size:21
Alignment explanation
Indices: 10197104--10197153 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
10197094 AATTTTTTGA
10197104 ATTATT-TTTT-AATATTATT
1 ATTATTATTTTAAATATTATT
* *
10197123 TTTATTATTTTAAATTTTATT
1 ATTATTATTTTAAATATTATT
*
10197144 ATTAGTATTT
1 ATTATTATTT
10197154 ATGCATGTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 5 0.20
20 4 0.16
21 16 0.64
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (21 bp):
ATTATTATTTTAAATATTATT
Found at i:10197398 original size:3 final size:3
Alignment explanation
Indices: 10197390--10197416 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
10197380 ACAAAAAATG
10197390 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
10197417 GTAAGAAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:10202989 original size:22 final size:22
Alignment explanation
Indices: 10202938--10203031 Score: 113
Period size: 22 Copynumber: 4.3 Consensus size: 22
10202928 CCAAAATTTG
* *
10202938 AAACCTTAAAAACTCTAAACCTT
1 AAACCCTAAAATC-CTAAACCTT
10202961 AAA-CCTAAAA-CTCTAAA-CTCT
1 AAACCCTAAAATC-CTAAACCT-T
*
10202982 AAACCCTAAAATCCTAAACCCT
1 AAACCCTAAAATCCTAAACCTT
10203004 AAACCCTAAAATCCTAAACCTT
1 AAACCCTAAAATCCTAAACCTT
10203026 AAACCC
1 AAACCC
10203032 AATCCTTAAA
Statistics
Matches: 64, Mismatches: 3, Indels: 9
0.84 0.04 0.12
Matches are distributed among these distances:
20 2 0.03
21 11 0.17
22 46 0.72
23 5 0.08
ACGTcount: A:0.47, C:0.32, G:0.00, T:0.21
Consensus pattern (22 bp):
AAACCCTAAAATCCTAAACCTT
Found at i:10202999 original size:8 final size:8
Alignment explanation
Indices: 10202964--10203021 Score: 52
Period size: 7 Copynumber: 7.8 Consensus size: 8
10202954 AAACCTTAAA
10202964 CCTAAAAC
1 CCTAAAAC
*
10202972 TCT-AAAC
1 CCTAAAAC
*
10202979 TCT-AAAC
1 CCTAAAAC
*
10202986 CCTAAAAT
1 CCTAAAAC
10202994 CCT-AAAC
1 CCTAAAAC
10203001 CCT-AAAC
1 CCTAAAAC
*
10203008 CCTAAAAT
1 CCTAAAAC
10203016 CCTAAA
1 CCTAAA
10203022 CCTTAAACCC
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
7 26 0.60
8 17 0.40
ACGTcount: A:0.47, C:0.33, G:0.00, T:0.21
Consensus pattern (8 bp):
CCTAAAAC
Found at i:10203440 original size:19 final size:19
Alignment explanation
Indices: 10203413--10203449 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
10203403 CCAAAAACAA
* *
10203413 AATGTTTTATTTTTAAAAG
1 AATGATTTATTTTCAAAAG
10203432 AATGATTTATTTTCAAAA
1 AATGATTTATTTTCAAAA
10203450 AAGAAAGGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.49
Consensus pattern (19 bp):
AATGATTTATTTTCAAAAG
Found at i:10203566 original size:20 final size:20
Alignment explanation
Indices: 10203541--10203580 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
10203531 CAAGGTTAAC
10203541 CTGTAATCAATTGGTACCAT
1 CTGTAATCAATTGGTACCAT
10203561 CTGTAATCAATTGGTACCAT
1 CTGTAATCAATTGGTACCAT
10203581 TTTTTAAGGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (20 bp):
CTGTAATCAATTGGTACCAT
Found at i:10205995 original size:11 final size:11
Alignment explanation
Indices: 10205979--10206003 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
10205969 ATGCACCATT
10205979 GATGGTCAGAA
1 GATGGTCAGAA
10205990 GATGGTCAGAA
1 GATGGTCAGAA
10206001 GAT
1 GAT
10206004 AGTATGCATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.08, G:0.36, T:0.20
Consensus pattern (11 bp):
GATGGTCAGAA
Found at i:10213834 original size:45 final size:45
Alignment explanation
Indices: 10213785--10213870 Score: 102
Period size: 45 Copynumber: 1.9 Consensus size: 45
10213775 AACTATTTGC
10213785 ACCAAAGGCCAACATGTGC-CGATAATGGTCGAGGCATGTGCTAAG
1 ACCAAAGGCCAACATGT-CTCGATAATGGTCGAGGCATGTGCTAAG
* ** * * *
10213830 ACCAAGGGTTAACATGTCTTGATAGTGGTTGAGGCATGTGC
1 ACCAAAGGCCAACATGTCTCGATAATGGTCGAGGCATGTGC
10213871 ATGTGTCACA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
44 1 0.03
45 33 0.97
ACGTcount: A:0.28, C:0.19, G:0.30, T:0.23
Consensus pattern (45 bp):
ACCAAAGGCCAACATGTCTCGATAATGGTCGAGGCATGTGCTAAG
Found at i:10220884 original size:12 final size:12
Alignment explanation
Indices: 10220809--10220878 Score: 54
Period size: 12 Copynumber: 5.9 Consensus size: 12
10220799 AAAATTTCTC
*
10220809 AAAAATAAAACCA
1 AAAAATAAAA-TA
*
10220822 AAAAA-ATAATA
1 AAAAATAAAATA
*
10220833 AAAACTAAAA-A
1 AAAAATAAAATA
* * **
10220844 TAAAATGAGCTA
1 AAAAATAAAATA
10220856 AAAAATAAAATA
1 AAAAATAAAATA
10220868 AAAAATAAAAT
1 AAAAATAAAAT
10220879 GGAAAAAGGA
Statistics
Matches: 42, Mismatches: 13, Indels: 5
0.70 0.22 0.08
Matches are distributed among these distances:
11 11 0.26
12 26 0.62
13 5 0.12
ACGTcount: A:0.76, C:0.06, G:0.03, T:0.16
Consensus pattern (12 bp):
AAAAATAAAATA
Found at i:10221506 original size:18 final size:18
Alignment explanation
Indices: 10221485--10221521 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
10221475 TCTAGGTTTG
10221485 AATCCTAGGATTGGTTCT
1 AATCCTAGGATTGGTTCT
10221503 AATCCTAGGATTGGTTCT
1 AATCCTAGGATTGGTTCT
10221521 A
1 A
10221522 TTTAACCATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.24, C:0.16, G:0.22, T:0.38
Consensus pattern (18 bp):
AATCCTAGGATTGGTTCT
Found at i:10221761 original size:15 final size:15
Alignment explanation
Indices: 10221699--10221795 Score: 58
Period size: 15 Copynumber: 6.4 Consensus size: 15
10221689 AATAATAATA
* *
10221699 ATAATATGATATGAT
1 ATAATATTAAATGAT
* *
10221714 ATACTAAT-AATGAT
1 ATAATATTAAATGAT
10221728 A-AATATATAAAT-AT
1 ATAATAT-TAAATGAT
10221742 AATAATATTAAATGAT
1 -ATAATATTAAATGAT
* *
10221758 ATAATATATTATATTAT
1 AT-A-ATATTAAATGAT
*
10221775 ATTATA-TAATATGAT
1 ATAATATTAA-ATGAT
10221790 ATAATA
1 ATAATA
10221796 ATACTAATAG
Statistics
Matches: 62, Mismatches: 12, Indels: 16
0.69 0.13 0.18
Matches are distributed among these distances:
13 3 0.05
14 11 0.18
15 28 0.45
16 8 0.13
17 12 0.19
ACGTcount: A:0.53, C:0.01, G:0.05, T:0.41
Consensus pattern (15 bp):
ATAATATTAAATGAT
Found at i:10221771 original size:7 final size:7
Alignment explanation
Indices: 10221687--10221798 Score: 60
Period size: 6 Copynumber: 15.9 Consensus size: 7
10221677 AATAATAACA
10221687 ATAATA-
1 ATAATAT
10221693 ATAATA-
1 ATAATAT
10221699 ATAATAT
1 ATAATAT
10221706 GAT-ATGAT
1 -ATAAT-AT
*
10221714 ATACTA-
1 ATAATAT
10221720 ATAATGAT
1 ATAAT-AT
10221728 A-AATAT
1 ATAATAT
10221734 ATAA-AT
1 ATAATAT
10221740 ATAATAAT
1 ATAAT-AT
10221748 ATTAAATGAT
1 A-T-AAT-AT
10221758 ATAATAT
1 ATAATAT
*
10221765 ATTATATT
1 ATAATA-T
*
10221773 ATATTAT
1 ATAATAT
10221780 ATAATAT
1 ATAATAT
10221787 GAT-ATA-
1 -ATAATAT
10221793 ATAATA
1 ATAATA
10221799 CTAATAGTAA
Statistics
Matches: 85, Mismatches: 7, Indels: 28
0.71 0.06 0.23
Matches are distributed among these distances:
5 2 0.02
6 28 0.33
7 28 0.33
8 19 0.22
9 2 0.02
10 6 0.07
ACGTcount: A:0.54, C:0.01, G:0.04, T:0.40
Consensus pattern (7 bp):
ATAATAT
Found at i:10222321 original size:120 final size:119
Alignment explanation
Indices: 10222098--10222518 Score: 459
Period size: 120 Copynumber: 3.5 Consensus size: 119
10222088 CAAGATAAGG
* * * *** *
10222098 TGACCGGGATGAAACCACAAGTCAAAAGAAATGATCTAGACTGAGGTAAGATCGAGTGACCTAGG
1 TGACCAGGATGAAACCACGAGTCATAAGAAATGATCTAGACTGAACCAAGATCGAGTGA-TTAGG
** * * * *
10222163 CAAAACTATGAGTCAAAAATGAAATGACTAGGATCGAGTCAAGGTAAAAAATAAA
65 TGAAACTATGAGTCAAAAATGAAGTGACTAGGACCGAGTCGAGGTCAAAAATAAA
* * *
10222218 TGACCGGGATGAAACCACGAGTCATAAGAAATTATCTAAACTGAACCAAGATCGAGTGATTGAGG
1 TGACCAGGATGAAACCACGAGTCATAAGAAATGATCTAGACTGAACCAAGATCGAGTGATT-AGG
* * *
10222283 TGAAACCATGAGTCAAAAATGAAGTGACCAGGACCGAGTTGAGGTCAAAAATAAA
65 TGAAACTATGAGTCAAAAATGAAGTGACTAGGACCGAGTCGAGGTCAAAAATAAA
* * **
10222338 TGACCAGGATGAAACCATGAGTCATAAGAAATGATCTAGACT-AAGCCAAGAT-TAGGTGACCAG
1 TGACCAGGATGAAACCACGAGTCATAAGAAATGATCTAGACTGAA-CCAAGATCGA-GTGATTAG
* ** *
10222401 AGTGAAACTATGAGTCAAAAAATAAAGCAACTAGGACCAAGTCGAGGTCAAAAATAAA
64 -GTGAAACTATGAGTC-AAAAATGAAGTGACTAGGACCGAGTCGAGGTCAAAAATAAA
* * * * * * * *
10222459 TGACTAAGATGAAACTACGAGTCATTAGAAATGATCTGGATTGAGCCAAGATCTAGTGAT
1 TGACCAGGATGAAACCACGAGTCATAAGAAATGATCTAGACTGAACCAAGATCGAGTGAT
10222519 CAAAATAAAA
Statistics
Matches: 254, Mismatches: 40, Indels: 13
0.83 0.13 0.04
Matches are distributed among these distances:
119 6 0.02
120 164 0.65
121 81 0.32
122 3 0.01
ACGTcount: A:0.43, C:0.15, G:0.23, T:0.19
Consensus pattern (119 bp):
TGACCAGGATGAAACCACGAGTCATAAGAAATGATCTAGACTGAACCAAGATCGAGTGATTAGGT
GAAACTATGAGTCAAAAATGAAGTGACTAGGACCGAGTCGAGGTCAAAAATAAA
Found at i:10222538 original size:121 final size:122
Alignment explanation
Indices: 10222105--10222574 Score: 332
Period size: 120 Copynumber: 3.9 Consensus size: 122
10222095 AGGTGACCGG
* * * ** * * ***
10222105 GATGAAACCACAAGTCAAAAGAAATGATCTAGACTGAGGTAAGA-TCGAGTGACCTAGGCAAAAC
1 GATGAAACCACGAGTCATAAGAAATGATCTAGACTAAGCCAAGATTAG-GTGACCAAAATAAAAC
** * * * * * **
10222169 TATGAGTCAAAAATGA-AATG--ACTAGGATCGAGTCAAGGTAAAAAATAAATGACCGG
65 TACAAGTCAAAAAT-ATAAAGCAACCAGGACCGAGTCGAGGTCAAAAATAAATGACCAA
* * * *** ** *
10222225 GATGAAACCACGAGTCATAAGAAATTATCTAAACTGAA-CCAAGA-TCGAGTGATTGAGGTGAAA
1 GATGAAACCACGAGTCATAAGAAATGATCTAGACT-AAGCCAAGATTAG-GTGACCAAAATAAAA
* ** * ** * *
10222288 CCATGAGTC-AAAA-ATGAAGTGACCAGGACCGAGTTGAGGTCAAAAATAAATGACCAG
64 CTACAAGTCAAAAATATAAAGCAACCAGGACCGAGTCGAGGTCAAAAATAAATGACCAA
* * * *
10222345 GATGAAACCATGAGTCATAAGAAATGATCTAGACTAAGCCAAGATTAGGTGACCAGAGTGAAACT
1 GATGAAACCACGAGTCATAAGAAATGATCTAGACTAAGCCAAGATTAGGTGACCAAAATAAAACT
** * * *
10222410 ATGAGTCAAAAA-ATAAAGCAACTAGGACCAAGTCGAGGTCAAAAATAAATGACTAA
66 ACAAGTCAAAAATATAAAGCAACCAGGACCGAGTCGAGGTCAAAAATAAATGACCAA
* * * * * *
10222466 GATGAAACTACGAGTCATTAGAAATGATCTGGATTGAGCCAAGATCTA-GTGATCAAAATAAAAG
1 GATGAAACCACGAGTCATAAGAAATGATCTAGACTAAGCCAAGAT-TAGGTGACCAAAATAAAA-
* *
10222530 C-ACAAGTCAAAAATATAAAGCGACCAAGACCGAGTCGAGGTCAAA
64 CTACAAGTCAAAAATATAAAGCAACCAGGACCGAGTCGAGGTCAAA
10222575 GATGACTAAT
Statistics
Matches: 285, Mismatches: 55, Indels: 18
0.80 0.15 0.05
Matches are distributed among these distances:
117 1 0.00
118 2 0.01
119 6 0.02
120 143 0.50
121 103 0.36
122 30 0.11
ACGTcount: A:0.44, C:0.15, G:0.22, T:0.18
Consensus pattern (122 bp):
GATGAAACCACGAGTCATAAGAAATGATCTAGACTAAGCCAAGATTAGGTGACCAAAATAAAACT
ACAAGTCAAAAATATAAAGCAACCAGGACCGAGTCGAGGTCAAAAATAAATGACCAA
Found at i:10222540 original size:241 final size:242
Alignment explanation
Indices: 10222098--10222574 Score: 534
Period size: 241 Copynumber: 2.0 Consensus size: 242
10222088 CAAGATAAGG
* * ** *
10222098 TGACCGGGATGAAACCACAAGTCAAAAGAAATGATCTAGACTGAGGTAAGATCGAGTGACCTAGG
1 TGACCAGGATGAAACCACAAGTCAAAAGAAATGATCTAGACTAAGCCAAGATAGAGTGACCTAGG
* * **
10222163 CAAAACTATGAGTCAAAAATGAAATGACTAGGATCGAGTCAAGGTAAAAAATAAATGACCGGGAT
66 CAAAACTATGAGTCAAAAATGAAATGACTAGGACCAAGTCAAGGTAAAAAATAAATGACCAAGAT
* ** ** * **
10222228 GAAACCACGAGTCATAAGAAATTATCTAAACTGAACCAAGATCGAGTGATTGAGGTGAAACCATG
131 GAAACCACGAGTCATAAGAAATGATCTAAACTGAACCAAGATCGAGTGATCAAAATAAAACCACA
* * * *
10222293 AGTC-AAAA-ATGAAGTGACCAGGACCGAGTTGAGGTCAAAAATAAA
196 AGTCAAAAATATAAAGCGACCAAGACCGAGTCGAGGTCAAAAATAAA
** *
10222338 TGACCAGGATGAAACCATGAGTCATAAGAAATGATCTAGACTAAGCCAAGATTAG-GTGACC-AG
1 TGACCAGGATGAAACCACAAGTCAAAAGAAATGATCTAGACTAAGCCAAGA-TAGAGTGACCTAG
** * * *
10222401 AGTGAAACTATGAGTCAAAAAAT-AAA-GCAACTAGGACCAAGTCGAGGTCAAAAATAAATGACT
65 -GCAAAACTATGAGTC-AAAAATGAAATG--ACTAGGACCAAGTCAAGGTAAAAAATAAATGACC
* * ** * * *
10222464 AAGATGAAACTACGAGTCATTAGAAATGATCTGGATTGAGCCAAGATCTAGTGATCAAAATAAAA
126 AAGATGAAACCACGAGTCATAAGAAATGATCTAAACTGAACCAAGATCGAGTGATCAAAATAAAA
*
10222529 GCACAAGTCAAAAATATAAAGCGACCAAGACCGAGTCGAGGTCAAA
191 CCACAAGTCAAAAATATAAAGCGACCAAGACCGAGTCGAGGTCAAA
10222575 GATGACTAAT
Statistics
Matches: 193, Mismatches: 37, Indels: 11
0.80 0.15 0.05
Matches are distributed among these distances:
239 3 0.02
240 66 0.34
241 93 0.48
242 4 0.02
243 27 0.14
ACGTcount: A:0.44, C:0.16, G:0.22, T:0.18
Consensus pattern (242 bp):
TGACCAGGATGAAACCACAAGTCAAAAGAAATGATCTAGACTAAGCCAAGATAGAGTGACCTAGG
CAAAACTATGAGTCAAAAATGAAATGACTAGGACCAAGTCAAGGTAAAAAATAAATGACCAAGAT
GAAACCACGAGTCATAAGAAATGATCTAAACTGAACCAAGATCGAGTGATCAAAATAAAACCACA
AGTCAAAAATATAAAGCGACCAAGACCGAGTCGAGGTCAAAAATAAA
Found at i:10228303 original size:45 final size:45
Alignment explanation
Indices: 10228239--10228324 Score: 136
Period size: 45 Copynumber: 1.9 Consensus size: 45
10228229 CATGACACAT
* *
10228239 GCACATGCCTTGACCATCATCAAGACATGTTGGCCCTTGGTCTTA
1 GCACATGCCTTGACCATCATCAACACATGCTGGCCCTTGGTCTTA
**
10228284 GCACATGTTTTGACCATCATCAACACATGCTGGCCCTTGGT
1 GCACATGCCTTGACCATCATCAACACATGCTGGCCCTTGGT
10228325 GCAAGCAGTT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.22, C:0.29, G:0.20, T:0.29
Consensus pattern (45 bp):
GCACATGCCTTGACCATCATCAACACATGCTGGCCCTTGGTCTTA
Found at i:10237400 original size:132 final size:132
Alignment explanation
Indices: 10237158--10237434 Score: 394
Period size: 132 Copynumber: 2.1 Consensus size: 132
10237148 CGTGTACCCA
* *
10237158 AAGGTAATAACACTGGGTGTACATGACTTCTACTCAGTCATGATCTCAAAAGGACTTTGATTTAT
1 AAGGCAATAACATTGGGTGTACATGACTTCTACTCAGTCATGATCTCAAAAGGACTTTGATTTAT
** * * * *
10237223 AGCCTCGTTTTACTGAATATTGTTTAAGAATTAAGCTACATCCAACAACTTGAGCCAGTCTCATT
66 AGCCTCACTTCACTAAATATTGTATAAGAATTAAGCTACATCCAACAACTTGAGCCAATCTCATT
10237288 AG
131 AG
* *
10237290 AAGGCAATAACATTGGGTGTACATGGCTTCTACTCAGTCATGATCTCAAAGGGACTTTGATTTAT
1 AAGGCAATAACATTGGGTGTACATGACTTCTACTCAGTCATGATCTCAAAAGGACTTTGATTTAT
* * *
10237355 AGCCTTACTTCACTAAATGTTGTATAAGAATTGAA-CTACATCCAACAACTTGGGCCAATCTCAT
66 AGCCTCACTTCACTAAATATTGTATAAGAATT-AAGCTACATCCAACAACTTGAGCCAATCTCAT
*
10237419 TGG
130 TAG
* *
10237422 GAGGCATTAACAT
1 AAGGCAATAACAT
10237435 AATGCCAGAG
Statistics
Matches: 128, Mismatches: 16, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
132 126 0.98
133 2 0.02
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Consensus pattern (132 bp):
AAGGCAATAACATTGGGTGTACATGACTTCTACTCAGTCATGATCTCAAAAGGACTTTGATTTAT
AGCCTCACTTCACTAAATATTGTATAAGAATTAAGCTACATCCAACAACTTGAGCCAATCTCATT
AG
Found at i:10244276 original size:9 final size:9
Alignment explanation
Indices: 10244253--10244287 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
10244243 ATAGTTATAG
10244253 ATAATAAATA
1 ATAA-AAATA
10244263 ATAAAAATA
1 ATAAAAATA
*
10244272 CTAAAAATA
1 ATAAAAATA
10244281 ATAAAAA
1 ATAAAAA
10244288 AAATCCTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 19 0.83
10 4 0.17
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (9 bp):
ATAAAAATA
Found at i:10244289 original size:21 final size:20
Alignment explanation
Indices: 10244258--10244312 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 20
10244248 TATAGATAAT
*
10244258 AAATAATAAAAATACTAAAA
1 AAATAAAAAAAATACTAAAA
*
10244278 ATAATAAAAAAAATCCTAAAA
1 A-AATAAAAAAAATACTAAAA
10244299 AAATGAGAAAAAAA
1 AAAT-A-AAAAAAA
10244313 AAGCTTACAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 4 0.13
21 19 0.63
22 7 0.23
ACGTcount: A:0.75, C:0.05, G:0.04, T:0.16
Consensus pattern (20 bp):
AAATAAAAAAAATACTAAAA
Found at i:10245546 original size:23 final size:23
Alignment explanation
Indices: 10245515--10245558 Score: 72
Period size: 22 Copynumber: 1.9 Consensus size: 23
10245505 GACTTTGGAG
10245515 AATGAAAGAAAGGAAAAAAAAAGA
1 AATGAAAGAAA-GAAAAAAAAAGA
10245539 AATG-AAGAAAGAAAAAAAAA
1 AATGAAAGAAAGAAAAAAAAA
10245559 TAATAATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 10 0.50
23 6 0.30
24 4 0.20
ACGTcount: A:0.77, C:0.00, G:0.18, T:0.05
Consensus pattern (23 bp):
AATGAAAGAAAGAAAAAAAAAGA
Found at i:10246020 original size:21 final size:20
Alignment explanation
Indices: 10245991--10246029 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
10245981 ATTAATATTG
*
10245991 TAATTTAAATATCTTTAAAAA
1 TAATATAAATAT-TTTAAAAA
10246012 TAATATAAATATTTTAAA
1 TAATATAAATATTTTAAA
10246030 TTTAAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (20 bp):
TAATATAAATATTTTAAAAA
Found at i:10246039 original size:20 final size:21
Alignment explanation
Indices: 10245996--10246040 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
10245986 TATTGTAATT
*
10245996 TAAATATCTTTAAAAATAATA
1 TAAATATCTTTAAAAATAAAA
**
10246017 TAAATAT-TTTAAATTTAAAA
1 TAAATATCTTTAAAAATAAAA
10246037 TAAA
1 TAAA
10246041 AACAAAAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATATCTTTAAAAATAAAA
Found at i:10249364 original size:87 final size:88
Alignment explanation
Indices: 10249196--10249380 Score: 246
Period size: 87 Copynumber: 2.1 Consensus size: 88
10249186 TCAGATTTTG
* * *
10249196 GATTGAGTGCTTTCTCACAGCAAGTTCGGGTAAGCATGTACTTTTTTTTTTGTATTAACTGCTAG
1 GATTGAGTGCTTTATCACAGCAAGTTCAGGTAAGCATGTAC--TTTTTTTGGTATTAACTGCTAG
* *
10249261 ATTGAGTGCTGGATTGTATGTACTT
64 ATTGAGTGATGGATTGTAGGTACTT
* * * * *
10249286 GATTGATTGCTTTATCATAGCAATTTCAGGTAAGTATGTAC-TTTTTTGGTATTAACTGCTATAT
1 GATTGAGTGCTTTATCACAGCAAGTTCAGGTAAGCATGTACTTTTTTTGGTATTAACTGCTAGAT
*
10249350 TGAGTGATGGATTGTGGGTACTT
66 TGAGTGATGGATTGTAGGTACTT
10249373 GATTGAGT
1 GATTGAGT
10249381 TTGGAAATCG
Statistics
Matches: 83, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
87 48 0.58
90 35 0.42
ACGTcount: A:0.23, C:0.11, G:0.24, T:0.43
Consensus pattern (88 bp):
GATTGAGTGCTTTATCACAGCAAGTTCAGGTAAGCATGTACTTTTTTTGGTATTAACTGCTAGAT
TGAGTGATGGATTGTAGGTACTT
Found at i:10253701 original size:15 final size:15
Alignment explanation
Indices: 10253655--10253701 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
10253645 TTCAAATGCA
*
10253655 TTTTAT-TATGTAAT
1 TTTTATATATTTAAT
* * *
10253669 TTATAAATAATTAAT
1 TTTTATATATTTAAT
10253684 TTTTATATATTTAAT
1 TTTTATATATTTAAT
10253699 TTT
1 TTT
10253702 CATAATTGAT
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
14 4 0.16
15 21 0.84
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (15 bp):
TTTTATATATTTAAT
Found at i:10254012 original size:21 final size:23
Alignment explanation
Indices: 10253982--10254025 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 23
10253972 CAAGTTCTAT
10253982 GTGAAACAAAT-AT-GAAAAAAA
1 GTGAAACAAATGATGGAAAAAAA
*
10254003 GTGAAGCAAATGATGGAAAAAAA
1 GTGAAACAAATGATGGAAAAAAA
10254026 ATGTAATTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 10 0.50
22 2 0.10
23 8 0.40
ACGTcount: A:0.61, C:0.05, G:0.20, T:0.14
Consensus pattern (23 bp):
GTGAAACAAATGATGGAAAAAAA
Found at i:10255346 original size:6 final size:6
Alignment explanation
Indices: 10255337--10255378 Score: 84
Period size: 6 Copynumber: 7.0 Consensus size: 6
10255327 TTTACATAAA
10255337 ATAATT ATAATT ATAATT ATAATT ATAATT ATAATT ATAATT
1 ATAATT ATAATT ATAATT ATAATT ATAATT ATAATT ATAATT
10255379 GCAATTCTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
ATAATT
Found at i:10255384 original size:18 final size:18
Alignment explanation
Indices: 10255337--10255384 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
10255327 TTTACATAAA
*
10255337 ATAATTATAATTATAATT
1 ATAATTACAATTATAATT
*
10255355 ATAATTATAATTATAATT
1 ATAATTACAATTATAATT
*
10255373 ATAATTGCAATT
1 ATAATTACAATT
10255385 CTATAATTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (18 bp):
ATAATTACAATTATAATT
Found at i:10257472 original size:13 final size:13
Alignment explanation
Indices: 10257454--10257478 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
10257444 ACTCAAAATT
10257454 AGATATTTTTAGG
1 AGATATTTTTAGG
10257467 AGATATTTTTAG
1 AGATATTTTTAG
10257479 AGCTTAAGGC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.20, T:0.48
Consensus pattern (13 bp):
AGATATTTTTAGG
Found at i:10257600 original size:14 final size:15
Alignment explanation
Indices: 10257578--10257616 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
10257568 TTTTTTTCTT
10257578 CTTTAATTTTTTGCA
1 CTTTAATTTTTTGCA
*
10257593 CTTTATTTTTTTGCA
1 CTTTAATTTTTTGCA
*
10257608 -TTTCATTTT
1 CTTTAATTTT
10257617 CCTACATTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 7 0.33
15 14 0.67
ACGTcount: A:0.15, C:0.13, G:0.05, T:0.67
Consensus pattern (15 bp):
CTTTAATTTTTTGCA
Found at i:10261665 original size:16 final size:16
Alignment explanation
Indices: 10261640--10261675 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
10261630 TTTTACTAAG
10261640 TTTGAATAATTTTGAC
1 TTTGAATAATTTTGAC
*
10261656 TTTGACTAATTTTGAC
1 TTTGAATAATTTTGAC
10261672 TTTG
1 TTTG
10261676 TTAATCAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.25, C:0.08, G:0.14, T:0.53
Consensus pattern (16 bp):
TTTGAATAATTTTGAC
Found at i:10261997 original size:25 final size:25
Alignment explanation
Indices: 10261963--10262013 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 25
10261953 ATGAGGGTTC
* *
10261963 TTTTTTTTTTTTTGTTT-GCTTTGT
1 TTTTTTTTTTTTTTTTTAGATTTGT
10261987 TTTTTTTTTTTTTTTTTAGATTTGT
1 TTTTTTTTTTTTTTTTTAGATTTGT
10262012 TT
1 TT
10262014 CAAGAGTCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 16 0.67
25 8 0.33
ACGTcount: A:0.04, C:0.02, G:0.10, T:0.84
Consensus pattern (25 bp):
TTTTTTTTTTTTTTTTTAGATTTGT
Found at i:10262248 original size:51 final size:51
Alignment explanation
Indices: 10262178--10262454 Score: 166
Period size: 51 Copynumber: 5.4 Consensus size: 51
10262168 AAATTCTTTC
* * * *
10262178 AAAAGTTTGGGATTTATACCAAGATGCTTTAAAGGTTTAGAATTCGCATAG
1 AAAAGGTTAGGATTTATACCAAGATGCTTTAAAGGTTTAGAATTCACATTG
* * * * ** *
10262229 AAAATGTTAGGATTCATACCAGGGTTTTTTTAAGGTTT-GAGATTCACATTG
1 AAAAGGTTAGGATTTATACCAAGATGCTTTAAAGGTTTAGA-ATTCACATTG
* * * *
10262280 AAAAGGTTAAGATTTGTACCAA-AAGCTTTCAAAGGTTTAGGATTCACATTG
1 AAAAGGTTAGGATTTATACCAAGATGCTTT-AAAGGTTTAGAATTCACATTG
* * * * * * ***
10262331 AAAAGGTT-GGAGTTTACATCAAGAT-TTTTCAAAGATTTTGGATTCACACCA
1 AAAAGGTTAGGA-TTTATACCAAGATGCTTT-AAAGGTTTAGAATTCACATTG
* * * * * * * * * *
10262382 AAAAGGCTAGGATTCACACTAGGATTCTTCAAAAGTTTAGGAGTCACATTG
1 AAAAGGTTAGGATTTATACCAAGATGCTTTAAAGGTTTAGAATTCACATTG
* *
10262433 AAAAGGATGGGATTTATACCAA
1 AAAAGGTTAGGATTTATACCAA
10262455 AATTCTTCAA
Statistics
Matches: 166, Mismatches: 53, Indels: 14
0.71 0.23 0.06
Matches are distributed among these distances:
50 7 0.04
51 152 0.92
52 7 0.04
ACGTcount: A:0.35, C:0.12, G:0.21, T:0.32
Consensus pattern (51 bp):
AAAAGGTTAGGATTTATACCAAGATGCTTTAAAGGTTTAGAATTCACATTG
Found at i:10262460 original size:51 final size:51
Alignment explanation
Indices: 10262269--10262514 Score: 176
Period size: 51 Copynumber: 4.8 Consensus size: 51
10262259 TAAGGTTTGA
* * ** * *
10262269 GATTCACATTGAAAAGGTTAAGATTTGTACCAAAA-GCTTTCAAAGGTTTAG
1 GATTCACATTGAAAAGGCTAGGATTTACACCAAAATTC-TTCAAAAGTTTAG
* * * * *
10262320 GATTCACATTGAAAAGG-TTGGAGTTTACATCAAGATTTTTC-AAAGATTTTG
1 GATTCACATTGAAAAGGCTAGGA-TTTACACCAAAATTCTTCAAAAG-TTTAG
*** * * **
10262371 GATTCACACCAAAAAGGCTAGGATTCACACTAGGATTCTTCAAAAGTTTAG
1 GATTCACATTGAAAAGGCTAGGATTTACACCAAAATTCTTCAAAAGTTTAG
* * * * * *
10262422 GAGTCACATTGAAAAGGATGGGATTTATACCAAAATTCTTCAAAAGTTCAA
1 GATTCACATTGAAAAGGCTAGGATTTACACCAAAATTCTTCAAAAGTTTAG
* * * * *
10262473 GATTCACATCG-AAAGGCTGGGATTCACACCAACATTTTTCAA
1 GATTCACATTGAAAAGGCTAGGATTTACACCAAAATTCTTCAA
10262515 CATAGAAAAG
Statistics
Matches: 150, Mismatches: 40, Indels: 11
0.75 0.20 0.05
Matches are distributed among these distances:
50 32 0.21
51 110 0.73
52 8 0.05
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.30
Consensus pattern (51 bp):
GATTCACATTGAAAAGGCTAGGATTTACACCAAAATTCTTCAAAAGTTTAG
Found at i:10262477 original size:102 final size:101
Alignment explanation
Indices: 10262307--10262501 Score: 232
Period size: 102 Copynumber: 1.9 Consensus size: 101
10262297 ACCAAAAGCT
* * * * * * ***
10262307 TTCAAAGGTTTAGGATTCACATTGAAAAGGTTGGAGTTTACATCAAGATTTTTCAAAGATTTTGG
1 TTCAAAAGTTTAGGAGTCACATTGAAAAGGTGGGAGTTTACACCAAAATTCTTCAAAGATTCAAG
10262372 ATTCACACCAAAAAGGCTAGGATTCACACTAGGATTC
66 ATTCACACC-AAAAGGCTAGGATTCACACTAGGATTC
*
10262409 TTCAAAAGTTTAGGAGTCACATTGAAAAGGATGGGA-TTTATACCAAAATTCTTCAAA-AGTTCA
1 TTCAAAAGTTTAGGAGTCACATTGAAAAGG-TGGGAGTTTACACCAAAATTCTTCAAAGA-TTCA
* * *
10262472 AGATTCACATCGAAAGGCTGGGATTCACAC
64 AGATTCACACCAAAAGGCTAGGATTCACAC
10262502 CAACATTTTT
Statistics
Matches: 78, Mismatches: 13, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
101 18 0.23
102 56 0.72
103 4 0.05
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.29
Consensus pattern (101 bp):
TTCAAAAGTTTAGGAGTCACATTGAAAAGGTGGGAGTTTACACCAAAATTCTTCAAAGATTCAAG
ATTCACACCAAAAGGCTAGGATTCACACTAGGATTC
Found at i:10264891 original size:15 final size:15
Alignment explanation
Indices: 10264871--10264927 Score: 53
Period size: 15 Copynumber: 3.9 Consensus size: 15
10264861 TATTCCTTCA
10264871 TTTTTTTTCC-TTTT
1 TTTTTTTTCCTTTTT
*
10264885 TTTTTTTTACTTTTT
1 TTTTTTTTCCTTTTT
** **
10264900 TCCTTTCACCTTTTT
1 TTTTTTTTCCTTTTT
*
10264915 TTTCTTTTCCTTT
1 TTTTTTTTCCTTT
10264928 AAGTGGATTC
Statistics
Matches: 31, Mismatches: 11, Indels: 1
0.72 0.26 0.02
Matches are distributed among these distances:
14 9 0.29
15 22 0.71
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTTTTTCCTTTTT
Found at i:10266157 original size:23 final size:24
Alignment explanation
Indices: 10266127--10266185 Score: 77
Period size: 23 Copynumber: 2.5 Consensus size: 24
10266117 ATCCGATAAA
10266127 TTTACTGGTATTTTC-TTGGTATT
1 TTTACTGGTATTTTCTTTGGTATT
* *
10266150 TTTGCTGGTA-TTTCTTTGGTGTT
1 TTTACTGGTATTTTCTTTGGTATT
*
10266173 TTTAATGGTATTT
1 TTTACTGGTATTT
10266186 ATTTTTTGAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
22 4 0.13
23 24 0.80
24 2 0.07
ACGTcount: A:0.12, C:0.07, G:0.20, T:0.61
Consensus pattern (24 bp):
TTTACTGGTATTTTCTTTGGTATT
Found at i:10269997 original size:37 final size:37
Alignment explanation
Indices: 10269956--10270034 Score: 95
Period size: 37 Copynumber: 2.1 Consensus size: 37
10269946 CATGTGCTGC
* * * *
10269956 CTATTAAGATGTATATGGAATGGAATGTATGTACCAT
1 CTATTAACATGTACATGAAATGGAATGCATGTACCAT
* * *
10269993 CTATTAACATGTGCATGAAATGGAATGCATGTTCTAT
1 CTATTAACATGTACATGAAATGGAATGCATGTACCAT
10270030 CTATT
1 CTATT
10270035 GATGTGGATG
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (37 bp):
CTATTAACATGTACATGAAATGGAATGCATGTACCAT
Found at i:10270280 original size:10 final size:9
Alignment explanation
Indices: 10270267--10270306 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
10270257 TCTTTTTCCA
*
10270267 TTTTTGTTG
1 TTTTTGTTT
10270276 TTTTTGTTT
1 TTTTTGTTT
*
10270285 GTTTTGATTT
1 TTTTTG-TTT
10270295 TTTTTGTTT
1 TTTTTGTTT
10270304 TTT
1 TTT
10270307 ATTTAGAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
9 19 0.70
10 8 0.30
ACGTcount: A:0.03, C:0.00, G:0.15, T:0.82
Consensus pattern (9 bp):
TTTTTGTTT
Found at i:10271194 original size:9 final size:9
Alignment explanation
Indices: 10271180--10271222 Score: 59
Period size: 9 Copynumber: 4.7 Consensus size: 9
10271170 AATCAAAACA
*
10271180 TTTTTTCAT
1 TTTTTTAAT
10271189 TTTTTTAAT
1 TTTTTTAAT
*
10271198 TTTTTTGAT
1 TTTTTTAAT
10271207 TTTTTTAAT
1 TTTTTTAAT
10271216 TTCTTTT
1 TT-TTTT
10271223 CAAAATTTCA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
9 26 0.87
10 4 0.13
ACGTcount: A:0.14, C:0.05, G:0.02, T:0.79
Consensus pattern (9 bp):
TTTTTTAAT
Found at i:10271203 original size:18 final size:18
Alignment explanation
Indices: 10271180--10271224 Score: 72
Period size: 18 Copynumber: 2.4 Consensus size: 18
10271170 AATCAAAACA
10271180 TTTTTTCATTTTTTTAAT
1 TTTTTTCATTTTTTTAAT
*
10271198 TTTTTTGATTTTTTTAAT
1 TTTTTTCATTTTTTTAAT
10271216 TTCTTTTCA
1 TT-TTTTCA
10271225 AAATTTCACA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 19 0.79
19 5 0.21
ACGTcount: A:0.16, C:0.07, G:0.02, T:0.76
Consensus pattern (18 bp):
TTTTTTCATTTTTTTAAT
Found at i:10272204 original size:7 final size:7
Alignment explanation
Indices: 10272177--10272267 Score: 52
Period size: 7 Copynumber: 13.6 Consensus size: 7
10272167 GCATGATTGA
*
10272177 TTTAGGG
1 TTTAAGG
10272184 TTTAAGG
1 TTTAAGG
*
10272191 GTT--GG
1 TTTAAGG
10272196 TTTAAGG
1 TTTAAGG
10272203 TTT-AGG
1 TTTAAGG
10272209 -TTATA-G
1 TTTA-AGG
*
10272215 TTTAGGG
1 TTTAAGG
10272222 CTTTAAGG
1 -TTTAAGG
10272230 TTTAAGG
1 TTTAAGG
10272237 TTT-AGG
1 TTTAAGG
*
10272243 ATTTTAGG
1 -TTTAAGG
* *
10272251 GTTAGGG
1 TTTAAGG
10272258 TTTAA-G
1 TTTAAGG
10272264 TTTA
1 TTTA
10272268 CAATTTTAGG
Statistics
Matches: 65, Mismatches: 10, Indels: 19
0.69 0.11 0.20
Matches are distributed among these distances:
5 6 0.09
6 12 0.18
7 38 0.58
8 9 0.14
ACGTcount: A:0.22, C:0.01, G:0.32, T:0.45
Consensus pattern (7 bp):
TTTAAGG
Found at i:10272234 original size:34 final size:35
Alignment explanation
Indices: 10272194--10272295 Score: 104
Period size: 34 Copynumber: 3.0 Consensus size: 35
10272184 TTTAAGGGTT
*
10272194 GGTTTAAGGTTTAGG-TTATA-GTTTAGGGCTTTAA
1 GGTTTAAGGTTTAGGATTATAGGGTTAGGG-TTTAA
*
10272228 GGTTTAAGGTTTAGGATTTTAGGGTTAGGGTTTAA
1 GGTTTAAGGTTTAGGATTATAGGGTTAGGGTTTAA
** * *
10272263 -GTTTACAATTTTAGGGTT-TAGGATTAGGGTTTA
1 GGTTTA-AGGTTTAGGATTATAGGGTTAGGGTTTA
10272296 GATTTAGGAC
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
34 34 0.58
35 18 0.31
36 7 0.12
ACGTcount: A:0.24, C:0.02, G:0.30, T:0.44
Consensus pattern (35 bp):
GGTTTAAGGTTTAGGATTATAGGGTTAGGGTTTAA
Found at i:10272273 original size:27 final size:28
Alignment explanation
Indices: 10272228--10272280 Score: 81
Period size: 27 Copynumber: 1.9 Consensus size: 28
10272218 AGGGCTTTAA
**
10272228 GGTTTAAGGTTTAGGATTTTAGGGTTAG
1 GGTTTAAGGTTTACAATTTTAGGGTTAG
10272256 GGTTTAA-GTTTACAATTTTAGGGTT
1 GGTTTAAGGTTTACAATTTTAGGGTT
10272281 TAGGATTAGG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 16 0.70
28 7 0.30
ACGTcount: A:0.23, C:0.02, G:0.30, T:0.45
Consensus pattern (28 bp):
GGTTTAAGGTTTACAATTTTAGGGTTAG
Found at i:10272283 original size:28 final size:29
Alignment explanation
Indices: 10272215--10272284 Score: 90
Period size: 28 Copynumber: 2.4 Consensus size: 29
10272205 TAGGTTATAG
* **
10272215 TTTAGGGCTTTAAGGTTTAAGGTTTAGGAT
1 TTTAGGG-TTTAGGGTTTAAGGTTTACAAT
10272245 TTTAGGG-TTAGGGTTTAA-GTTTACAAT
1 TTTAGGGTTTAGGGTTTAAGGTTTACAAT
10272272 TTTAGGGTTTAGG
1 TTTAGGGTTTAGG
10272285 ATTAGGGTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
27 14 0.39
28 15 0.42
30 7 0.19
ACGTcount: A:0.23, C:0.03, G:0.30, T:0.44
Consensus pattern (29 bp):
TTTAGGGTTTAGGGTTTAAGGTTTACAAT
Found at i:10272294 original size:28 final size:27
Alignment explanation
Indices: 10272194--10272295 Score: 75
Period size: 27 Copynumber: 3.7 Consensus size: 27
10272184 TTTAAGGGTT
* *
10272194 GGTTTAAGGTTTAGG-TTA-TAGTTTAG
1 GGTTT-AGGTTTAGGTTTACAATTTTAG
**
10272220 GGCTTTAAGGTTTAAGGTTTAGGATTTTAG
1 GG-TTT-AGGTTT-AGGTTTACAATTTTAG
*
10272250 GG-TTAGGGTTTAAGTTTACAATTTTAG
1 GGTTTA-GGTTTAGGTTTACAATTTTAG
*
10272277 GGTTTAGGATTAGGGTTTA
1 GGTTTAGGTTTA-GGTTTA
10272296 GATTTAGGAC
Statistics
Matches: 62, Mismatches: 7, Indels: 12
0.77 0.09 0.15
Matches are distributed among these distances:
26 2 0.03
27 31 0.50
28 18 0.29
29 3 0.05
30 8 0.13
ACGTcount: A:0.24, C:0.02, G:0.30, T:0.44
Consensus pattern (27 bp):
GGTTTAGGTTTAGGTTTACAATTTTAG
Found at i:10272302 original size:13 final size:14
Alignment explanation
Indices: 10272215--10272303 Score: 62
Period size: 13 Copynumber: 6.4 Consensus size: 14
10272205 TAGGTTATAG
10272215 TTTAGGGCTTTAAGG-
1 TTTAGGG-TTT-AGGA
*
10272230 TTTAAGGTTTAGGA
1 TTTAGGGTTTAGGA
*
10272244 TTTTAGGG-TTAGGG
1 -TTTAGGGTTTAGGA
* **
10272258 TTTA-AGTTTACAA
1 TTTAGGGTTTAGGA
10272271 TTTTAGGGTTTAGGA
1 -TTTAGGGTTTAGGA
10272286 -TTAGGGTTTA-GA
1 TTTAGGGTTTAGGA
10272298 TTTAGG
1 TTTAGG
10272304 ACTAGGATTT
Statistics
Matches: 58, Mismatches: 10, Indels: 14
0.71 0.12 0.17
Matches are distributed among these distances:
12 3 0.05
13 25 0.43
14 12 0.21
15 18 0.31
ACGTcount: A:0.24, C:0.02, G:0.30, T:0.44
Consensus pattern (14 bp):
TTTAGGGTTTAGGA
Found at i:10272401 original size:24 final size:24
Alignment explanation
Indices: 10272374--10272424 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
10272364 TTAAGACTTC
*
10272374 ATGGGATTTTAGATTTAGGGTTTG
1 ATGGGATTTAAGATTTAGGGTTTG
10272398 ATGGGATTTAAGATTTAGGGTTTG
1 ATGGGATTTAAGATTTAGGGTTTG
10272422 ATG
1 ATG
10272425 AAATTTGGGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.24, C:0.00, G:0.33, T:0.43
Consensus pattern (24 bp):
ATGGGATTTAAGATTTAGGGTTTG
Found at i:10272430 original size:24 final size:24
Alignment explanation
Indices: 10272379--10272430 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
10272369 ACTTCATGGG
* **
10272379 ATTTTAGATTTAGGGTTTGATGGG
1 ATTTAAGATTTAGGGTTTGATGAA
10272403 ATTTAAGATTTAGGGTTTGATGAA
1 ATTTAAGATTTAGGGTTTGATGAA
10272427 ATTT
1 ATTT
10272431 GGGGTTTTAG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.46
Consensus pattern (24 bp):
ATTTAAGATTTAGGGTTTGATGAA
Found at i:10273483 original size:13 final size:13
Alignment explanation
Indices: 10273452--10273484 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
10273442 GAATTATTTT
10273452 TCAATTTTTTTCA
1 TCAATTTTTTTCA
*
10273465 AC-ATTTTTTTCA
1 TCAATTTTTTTCA
10273477 TCAATTTT
1 TCAATTTT
10273485 CTTCCTTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 2
0.81 0.10 0.10
Matches are distributed among these distances:
12 11 0.65
13 6 0.35
ACGTcount: A:0.24, C:0.15, G:0.00, T:0.61
Consensus pattern (13 bp):
TCAATTTTTTTCA
Found at i:10275816 original size:3 final size:3
Alignment explanation
Indices: 10275808--10275842 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
10275798 AGGCTTTTGC
10275808 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
10275843 CACTAATATG
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:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:10276392 original size:27 final size:26
Alignment explanation
Indices: 10276277--10276450 Score: 93
Period size: 26 Copynumber: 6.5 Consensus size: 26
10276267 AATTAAAACC
* **
10276277 CTAAAAAGAAACCCTAATGC-AAAAT
1 CTAAAATGAAACCCTAAAACTAAAAT
* * * *
10276302 CCTATAGTGAAACCTTAAAACTAAAGTT
1 -CTAAAATGAAACCCTAAAACTAAA-AT
* * * * *
10276330 CTAAATTAAAACCCCAAAA-TGAAAC
1 CTAAAATGAAACCCTAAAACTAAAAT
**
10276355 CTTAATGTGAAACCCTAAAACTAAAACT
1 C-TAAAATGAAACCCTAAAACTAAAA-T
*
10276383 CTAAAATGAAAAACCTTAAAACTAAAAT
1 CTAAAATG--AAACCCTAAAACTAAAAT
*
10276411 CCTAAAACTAAAACCCTAAAA-TAAAAT
1 -CTAAAA-TGAAACCCTAAAACTAAAAT
*
10276438 CTTAAAATAAAAC
1 C-TAAAATGAAAC
10276451 TCCAAAATAA
Statistics
Matches: 112, Mismatches: 26, Indels: 20
0.71 0.16 0.13
Matches are distributed among these distances:
25 1 0.01
26 38 0.34
27 37 0.33
28 13 0.12
29 22 0.20
30 1 0.01
ACGTcount: A:0.54, C:0.20, G:0.05, T:0.21
Consensus pattern (26 bp):
CTAAAATGAAACCCTAAAACTAAAAT
Found at i:10276397 original size:29 final size:27
Alignment explanation
Indices: 10276364--10276449 Score: 104
Period size: 29 Copynumber: 3.1 Consensus size: 27
10276354 CCTTAATGTG
10276364 AAACCCTAAAACTAAAACTCTAAAATGAA
1 AAACCCTAAAACTAAAA-TCTAAAAT-AA
*
10276393 AAACCTTAAAACTAAAATCCTAAAACT-A
1 AAACCCTAAAACTAAAAT-CTAAAA-TAA
10276421 AAACCCTAAAA-TAAAATCTTAAAATAA
1 AAACCCTAAAACTAAAATC-TAAAATAA
10276448 AA
1 AA
10276450 CTCCAAAATA
Statistics
Matches: 51, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
26 2 0.04
27 14 0.27
28 12 0.24
29 22 0.43
30 1 0.02
ACGTcount: A:0.60, C:0.19, G:0.01, T:0.20
Consensus pattern (27 bp):
AAACCCTAAAACTAAAATCTAAAATAA
Found at i:10276457 original size:13 final size:13
Alignment explanation
Indices: 10276368--10276460 Score: 82
Period size: 14 Copynumber: 6.8 Consensus size: 13
10276358 AATGTGAAAC
10276368 CCTAAAACTAAAA-
1 CCTAAAA-TAAAAT
*
10276381 CTCTAAAATGAAAAA
1 C-CTAAAAT-AAAAT
10276396 CCTTAAAACTAAAAT
1 CC-TAAAA-TAAAAT
*
10276411 CCTAAAACTAAAAC
1 CCTAAAA-TAAAAT
10276425 CCTAAAATAAAAT
1 CCTAAAATAAAAT
*
10276438 CTTAAAATAAAACT
1 CCTAAAATAAAA-T
10276452 CC-AAAATAA
1 CCTAAAATAA
10276461 GTGAAACCTT
Statistics
Matches: 69, Mismatches: 5, Indels: 12
0.80 0.06 0.14
Matches are distributed among these distances:
13 25 0.36
14 31 0.45
15 12 0.17
16 1 0.01
ACGTcount: A:0.59, C:0.19, G:0.01, T:0.20
Consensus pattern (13 bp):
CCTAAAATAAAAT
Found at i:10276550 original size:19 final size:19
Alignment explanation
Indices: 10276528--10276568 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
10276518 GTGCAACCTG
*
10276528 AAACCCTAAATGAAACTCT
1 AAACCCTAAATGAAACCCT
*
10276547 AAACCCTAAGTGAAACCCT
1 AAACCCTAAATGAAACCCT
10276566 AAA
1 AAA
10276569 TCTTGTATGC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.49, C:0.27, G:0.07, T:0.17
Consensus pattern (19 bp):
AAACCCTAAATGAAACCCT
Found at i:10279719 original size:8 final size:8
Alignment explanation
Indices: 10279708--10279732 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
10279698 TTGATTACAC
10279708 TAGTATTT
1 TAGTATTT
10279716 TAGTATTT
1 TAGTATTT
10279724 TAGTATTT
1 TAGTATTT
10279732 T
1 T
10279733 CATGCTCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.12, T:0.64
Consensus pattern (8 bp):
TAGTATTT
Found at i:10285042 original size:22 final size:22
Alignment explanation
Indices: 10285000--10285042 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
10284990 TGGAAGTATA
*
10285000 ATTTCTACAATTTCTTCATTGC
1 ATTTCTACAATTTCATCATTGC
*
10285022 ATTTCATACCATTTCAT-ATTG
1 ATTTC-TACAATTTCATCATTG
10285043 TTTATCCTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.26, C:0.21, G:0.05, T:0.49
Consensus pattern (22 bp):
ATTTCTACAATTTCATCATTGC
Found at i:10286464 original size:28 final size:28
Alignment explanation
Indices: 10286427--10286491 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 28
10286417 ATCTTGATTC
* * *
10286427 AAAAAT-AAATTATTTTACTTTTCAAA-
1 AAAAATAAAAATAATTTACTTTTAAAAG
* *
10286453 AAAATTAAAAATAATTTGCTTTTAAAAG
1 AAAAATAAAAATAATTTACTTTTAAAAG
10286481 AAAAATAAAAA
1 AAAAATAAAAA
10286492 ATTCAGCTTT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
26 5 0.16
27 16 0.52
28 10 0.32
ACGTcount: A:0.58, C:0.05, G:0.03, T:0.34
Consensus pattern (28 bp):
AAAAATAAAAATAATTTACTTTTAAAAG
Found at i:10286892 original size:186 final size:186
Alignment explanation
Indices: 10286575--10286946 Score: 496
Period size: 186 Copynumber: 2.0 Consensus size: 186
10286565 AAATCTAAAG
***** *
10286575 ATAATATGCAATTAATTGGTACCATCTTCAATGAGTGTTGTGGGAGTACTAATCTTTCTCCATGT
1 ATAATATGCAATTAATTGGTACCATCTTCAATGAGTGTACAAAGAGTACTAATCCTTCTCCATGT
* * * * *
10286640 ATAACCGACTCTCGAACCCAACTTTAATTTTTGCAAACCGTAAAATATTCTTTTAGTCAGTTTTA
66 ATAACCGACTCTCAAACCCAACTCTAATTTTTACAAACCGTAAAATATTCTTTTAGTAAATTTTA
* *
10286705 AACTCGTTTTAAATATTTTATTAAAAGAACAAACTTTTTAGAGG-CCAATCATACCC
131 AACTCGTTTTAAATATTTTAATAAAAGAACAAAATTTTTAGAGGACCAATC-TACCC
* * * **
10286761 ATAATATGCAATTAATTGGTATCGTCTTCGATGAGTGCTACAAAG-GTACTAATCCTTCTTTATG
1 ATAATATGCAATTAATTGGTACCATCTTCAATGAGTG-TACAAAGAGTACTAATCCTTCTCCATG
* *
10286825 TATAACTGACTCTCAAACCCAACTCTAATTTTTACAGACCGTAAAATATTCTTTTAGTAAATTTT
65 TATAACCGACTCTCAAACCCAACTCTAATTTTTACAAACCGTAAAATATTCTTTTAGTAAATTTT
* * * *
10286890 AAATTTGTTTTAAATATTTTAATAAAAGAACAAAATTTTTGGGGGACCAATCTACCC
130 AAACTCGTTTTAAATATTTTAATAAAAGAACAAAATTTTTAGAGGACCAATCTACCC
10286947 TAAAAAAGAT
Statistics
Matches: 160, Mismatches: 24, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
186 152 0.95
187 8 0.05
ACGTcount: A:0.34, C:0.17, G:0.12, T:0.37
Consensus pattern (186 bp):
ATAATATGCAATTAATTGGTACCATCTTCAATGAGTGTACAAAGAGTACTAATCCTTCTCCATGT
ATAACCGACTCTCAAACCCAACTCTAATTTTTACAAACCGTAAAATATTCTTTTAGTAAATTTTA
AACTCGTTTTAAATATTTTAATAAAAGAACAAAATTTTTAGAGGACCAATCTACCC
Found at i:10288197 original size:19 final size:19
Alignment explanation
Indices: 10288175--10288319 Score: 141
Period size: 19 Copynumber: 7.6 Consensus size: 19
10288165 ATCACCTTCC
*
10288175 AAACCCTAAACCACCTATG
1 AAACCCTAAACCACCCATG
**
10288194 AAACCAAAAACCACCCATG
1 AAACCCTAAACCACCCATG
*
10288213 AAACCTTAAACCACCCATG
1 AAACCCTAAACCACCCATG
* *
10288232 AAACCTTAAACCACTCATG
1 AAACCCTAAACCACCCATG
* *
10288251 AAA-CCTCAAATCACCCCA-C
1 AAACCCT-AAACCA-CCCATG
**
10288270 AAACCCTAAACCACCCACC
1 AAACCCTAAACCACCCATG
* *
10288289 AAACCTTAAACCACCCCTG
1 AAACCCTAAACCACCCATG
*
10288308 AAATCCTAAACC
1 AAACCCTAAACC
10288320 GCAAACCTTA
Statistics
Matches: 105, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
18 6 0.06
19 93 0.89
20 6 0.06
ACGTcount: A:0.43, C:0.40, G:0.03, T:0.13
Consensus pattern (19 bp):
AAACCCTAAACCACCCATG
Found at i:10288310 original size:57 final size:57
Alignment explanation
Indices: 10288173--10288310 Score: 161
Period size: 57 Copynumber: 2.4 Consensus size: 57
10288163 AAATCACCTT
* * * *
10288173 CCAAACCCTAAACCACCTATGAAACCAAAAACCACCCATGAAACCTTAAACCACCCA
1 CCAAACCTTAAACCACCCATGAAACCAAAAACCACCCATCAAACCCTAAACCACCCA
** * ** *
10288230 TGAAACCTTAAACCACTCATGAAACCTCAAATCACCCCA-CAAACCCTAAACCACCCA
1 CCAAACCTTAAACCACCCATGAAACCAAAAACCA-CCCATCAAACCCTAAACCACCCA
*
10288287 CCAAACCTTAAACCACCCCTGAAA
1 CCAAACCTTAAACCACCCATGAAA
10288311 TCCTAAACCG
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
57 62 0.94
58 4 0.06
ACGTcount: A:0.43, C:0.41, G:0.04, T:0.12
Consensus pattern (57 bp):
CCAAACCTTAAACCACCCATGAAACCAAAAACCACCCATCAAACCCTAAACCACCCA
Found at i:10288439 original size:19 final size:19
Alignment explanation
Indices: 10288417--10288457 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
10288407 TACTAACCTT
*
10288417 AAACCCTAAGCCAAACCCC
1 AAACCCTAACCCAAACCCC
10288436 AAACCCTAACCCAAACCCC
1 AAACCCTAACCCAAACCCC
10288455 AAA
1 AAA
10288458 TTAATCCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.46, C:0.46, G:0.02, T:0.05
Consensus pattern (19 bp):
AAACCCTAACCCAAACCCC
Found at i:10293836 original size:15 final size:14
Alignment explanation
Indices: 10293806--10293849 Score: 54
Period size: 15 Copynumber: 3.1 Consensus size: 14
10293796 ACTTTATTTT
*
10293806 TTTTTATTTTT-TA
1 TTTTTATTTTTGAA
10293819 TTTTTATTGTTTGAA
1 TTTTTATT-TTTGAA
10293834 TTTTTATTATTTGAA
1 TTTTTATT-TTTGAA
10293849 T
1 T
10293850 ATTGAAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
13 8 0.30
14 3 0.11
15 16 0.59
ACGTcount: A:0.20, C:0.00, G:0.07, T:0.73
Consensus pattern (14 bp):
TTTTTATTTTTGAA
Found at i:10294563 original size:118 final size:117
Alignment explanation
Indices: 10294358--10294609 Score: 278
Period size: 118 Copynumber: 2.1 Consensus size: 117
10294348 TATCTTTTTA
* * * ** * *
10294358 AAAATCACCACTTGTGATTTTATTATTATTGTTATTTTTTTATGTTTGAAAATTTCTAAAATATT
1 AAAATCACCACTTGTGAATTTATTATTATTATAATTTTTTTATACTTCAAAAATTCTAAAATATT
* * *
10294423 TTCAATATTTTTAGAATGTTTTAAAAAAAAAT-TTTG-GCATGAATATTTTTAAT
66 TTCAACACTTTTAGAATATTTT-AAAAAAAATCTTTGTG--TGAATATTTTTAAT
* *
10294476 AAAATCATCACTTGTGAATTTATTGTTATTAATAATTTTTTTATACTTCAAAAATTCTAAAATA-
1 AAAATCACCACTTGTGAATTTATTATTATT-ATAATTTTTTTATACTTCAAAAATTCTAAAATAT
* **
10294540 TTTCTAACACTTTTA-AATATTTTAGAAAATTTCTTTGTGTGAATATTTTTAAT
65 TTTC-AACACTTTTAGAATATTTTAAAAAAAATCTTTGTGTGAATATTTTTAAT
* *
10294593 AAAATCACAACTAGTGA
1 AAAATCACCACTTGTGA
10294610 CTTCGTTATT
Statistics
Matches: 112, Mismatches: 18, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
117 34 0.30
118 42 0.38
119 36 0.32
ACGTcount: A:0.37, C:0.08, G:0.08, T:0.47
Consensus pattern (117 bp):
AAAATCACCACTTGTGAATTTATTATTATTATAATTTTTTTATACTTCAAAAATTCTAAAATATT
TTCAACACTTTTAGAATATTTTAAAAAAAATCTTTGTGTGAATATTTTTAAT
Found at i:10294816 original size:20 final size:21
Alignment explanation
Indices: 10294779--10294817 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
10294769 CAATTAAAAA
10294779 TATTTTATATTTTATACCATT
1 TATTTTATATTTTATACCATT
*
10294800 TATTTTAT-TTTTCTACCA
1 TATTTTATATTTTATACCA
10294818 AAAGTTTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.26, C:0.13, G:0.00, T:0.62
Consensus pattern (21 bp):
TATTTTATATTTTATACCATT
Found at i:10296178 original size:26 final size:26
Alignment explanation
Indices: 10296150--10296231 Score: 76
Period size: 26 Copynumber: 3.2 Consensus size: 26
10296140 ACCCATTTGT
* *
10296150 GTCTGGGCCCAATTAGGCCCATTGAT
1 GTCTGAGCCCAATTAGGCCCATTGAC
* * *
10296176 GTC-AAGCTCGATTAGGCCCATTGAC
1 GTCTGAGCCCAATTAGGCCCATTGAC
* * * *
10296201 GTCCGAGCCTAATTAGGTCCATTTAC
1 GTCTGAGCCCAATTAGGCCCATTGAC
10296227 GTCTG
1 GTCTG
10296232 GGTCCAATGA
Statistics
Matches: 43, Mismatches: 12, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
25 20 0.47
26 23 0.53
ACGTcount: A:0.21, C:0.27, G:0.24, T:0.28
Consensus pattern (26 bp):
GTCTGAGCCCAATTAGGCCCATTGAC
Found at i:10296302 original size:3 final size:3
Alignment explanation
Indices: 10296294--10296369 Score: 93
Period size: 3 Copynumber: 26.0 Consensus size: 3
10296284 GTTATATTAC
** *
10296294 ATT ATT ATT AGC ATT ATT ATT A-T ATC A-T ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* *
10296340 GTT ATT GTT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
10296370 TTGTTTTTGT
Statistics
Matches: 61, Mismatches: 10, Indels: 4
0.81 0.13 0.05
Matches are distributed among these distances:
2 3 0.05
3 58 0.95
ACGTcount: A:0.32, C:0.03, G:0.04, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:10296310 original size:12 final size:11
Alignment explanation
Indices: 10296288--10296337 Score: 50
Period size: 12 Copynumber: 4.5 Consensus size: 11
10296278 TAAATTGTTA
10296288 TATTACATTAT
1 TATTACATTAT
10296299 TATTAGCATTAT
1 TATTA-CATTAT
*
10296311 TATTATATCATAT
1 TATTACAT--TAT
10296324 TATT--ATTAT
1 TATTACATTAT
10296333 TATTA
1 TATTA
10296338 TTGTTATTGT
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
9 7 0.21
11 9 0.26
12 11 0.32
13 7 0.21
ACGTcount: A:0.36, C:0.06, G:0.02, T:0.56
Consensus pattern (11 bp):
TATTACATTAT
Found at i:10308995 original size:119 final size:120
Alignment explanation
Indices: 10308569--10309031 Score: 436
Period size: 119 Copynumber: 3.9 Consensus size: 120
10308559 ATCCACTCAT
* *
10308569 TTGATCTTGGCTCAATCCAGGTCATTTCTTATTATTCGTGGTTTCATCCT-GATCATTTATTTTT
1 TTGATCTTGGCTCAATCCAGATCATTTCTTATGATTCGTGGTTTCATCCTAGATCATTTATTTTT
* * * * * * *
10308633 AACCTCGACTC-AACCTAGTCACTTTATTTTGACTCATGGTTTTGTCTCGGTCAC
66 GACCTCGACTCGATCCTGGTCATTTTATTTTGACTCATGGTTTTGTCCCGATCAA
* * * * * * *
10308687 TTGATCTTGCCTTAATCTAGATCATTTCTTATGATTCGTGGTTTCATCCCA-ATAATCTATTTTC
1 TTGATCTTGGCTCAATCCAGATCATTTCTTATGATTCGTGGTTTCATCCTAGATCATTTATTTTT
* * * * ** * * *
10308751 GACCTCAACT-TAGTCCTGGTCACTTTT-TTTTTACTTATGGCGTCGTCCTGATCAC
66 GACCTCGACTCGA-TCCTGGTCA-TTTTATTTTGACTCATGGTTTTGTCCCGATCAA
* * * * * * * * *
10308806 CTGATCTTGGCTTAGTCCAAATTATTTCTTATAATTTGTGGTTTTAT-CTTGATCATTTATTTTT
1 TTGATCTTGGCTCAATCCAGATCATTTCTTATGATTCGTGGTTTCATCCTAGATCATTTATTTTT
**
10308870 GACCTCGACTCGATGTTGGTCATTTTATTTTGACTCATGGTTTTGTCCCGATCAA
66 GACCTCGACTCGATCCTGGTCATTTTATTTTGACTCATGGTTTTGTCCCGATCAA
* * * * * * *
10308925 TTTATCTTAGCTCAGTCTAGATCATTTTTTATGATTCATGGTTTCGTCCTAG-TCATTTATTTTT
1 TTGATCTTGGCTCAATCCAGATCATTTCTTATGATTCGTGGTTTCATCCTAGATCATTTATTTTT
* * * *
10308989 GACCTCGACTTGATCCTGGTCATTTCATCTTGACTCGTGGTTT
66 GACCTCGACTCGATCCTGGTCATTTTATTTTGACTCATGGTTT
10309032 AGCCTTGGTA
Statistics
Matches: 270, Mismatches: 67, Indels: 15
0.77 0.19 0.04
Matches are distributed among these distances:
118 68 0.25
119 195 0.72
120 7 0.03
ACGTcount: A:0.19, C:0.21, G:0.15, T:0.46
Consensus pattern (120 bp):
TTGATCTTGGCTCAATCCAGATCATTTCTTATGATTCGTGGTTTCATCCTAGATCATTTATTTTT
GACCTCGACTCGATCCTGGTCATTTTATTTTGACTCATGGTTTTGTCCCGATCAA
Found at i:10309052 original size:237 final size:237
Alignment explanation
Indices: 10308569--10309061 Score: 537
Period size: 238 Copynumber: 2.1 Consensus size: 237
10308559 ATCCACTCAT
* * ** *
10308569 TTGATCTTGGCTCAATCCAGGTCATTTCTTATTATTCGTGGTTTCATCCTGATCATTTATTTTTA
1 TTGATCTTGGCTTAGTCCAAATCATTTCTTATAATTCGTGGTTTCATCCTGATCATTTATTTTTA
* * *
10308634 ACCTCGACTCAACCTAGTCACTTTATTTTGACTCATGGTTTTGTCTCGGTCACTTGATCTTGCCT
66 ACCTCGACTCAACCTAGTCACTTTATTTTGACTCATGGTTTTGTCCCGATCAATTGATCTTGCCT
* *
10308699 TAATCTAGATCATTTCTTATGATTCGTGGTTTCATCCCAATAATCTATTTTCGACCTCAACTTAG
131 CAATCTAGATCATTTCTTATGATTCATGGTTTCATCCCAATAATCTATTTTCGACCTCAACTTAG
* * * * *
10308764 TCCTGGTCACTTTTTTTTTACTTATGGCGTCGTCCTGATCAC
196 TCCTGGTCACTTTATCTTGACTCATGGCGTAGTCCTGATCAC
* * * * * *
10308806 CTGATCTTGGCTTAGTCCAAATTATTTCTTATAATTTGTGGTTTTATCTTGATCATTTATTTTTG
1 TTGATCTTGGCTTAGTCCAAATCATTTCTTATAATTCGTGGTTTCATCCTGATCATTTATTTTTA
*** * * *
10308871 ACCTCGACTCGATGTTGGTCATTTTATTTTGACTCATGGTTTTGTCCCGATCAATTTATCTTAG-
66 ACCTCGACTC-AACCTAGTCACTTTATTTTGACTCATGGTTTTGTCCCGATCAATTGATCTT-GC
* * * * * * * * *
10308935 CTCAGTCTAGATCATTTTTTATGATTCATGGTTTCGTCCTAGTCATTTATTTTTGACCTCGACTT
129 CTCAATCTAGATCATTTCTTATGATTCATGGTTTCATCCCAATAATCTATTTTCGACCTCAACTT
* ** *
10309000 -GATCCTGGTCA-TTTCATCTTGACTCGTGGTTTAG-CCTTGGT-AC
194 AG-TCCTGGTCACTTT-ATCTTGACTCATGGCGTAGTCC-TGATCAC
*
10309043 TTGATCTTGGTTTAGTCCA
1 TTGATCTTGGCTTAGTCCA
10309062 GGTTATTTTT
Statistics
Matches: 209, Mismatches: 42, Indels: 10
0.80 0.16 0.04
Matches are distributed among these distances:
237 89 0.43
238 119 0.57
239 1 0.00
ACGTcount: A:0.18, C:0.21, G:0.15, T:0.45
Consensus pattern (237 bp):
TTGATCTTGGCTTAGTCCAAATCATTTCTTATAATTCGTGGTTTCATCCTGATCATTTATTTTTA
ACCTCGACTCAACCTAGTCACTTTATTTTGACTCATGGTTTTGTCCCGATCAATTGATCTTGCCT
CAATCTAGATCATTTCTTATGATTCATGGTTTCATCCCAATAATCTATTTTCGACCTCAACTTAG
TCCTGGTCACTTTATCTTGACTCATGGCGTAGTCCTGATCAC
Found at i:10309213 original size:26 final size:26
Alignment explanation
Indices: 10309176--10309235 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
10309166 GTTATAGACA
10309176 CCCATTTG-TGTCCAGGCCCAATTAGG
1 CCCA-TTGATGTCCAGGCCCAATTAGG
* * * *
10309202 CCCGTTGATGTCCATGCTCGATTAGG
1 CCCATTGATGTCCAGGCCCAATTAGG
10309228 CCCATTGA
1 CCCATTGA
10309236 CAACCGGGCT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
25 3 0.11
26 25 0.89
ACGTcount: A:0.18, C:0.30, G:0.23, T:0.28
Consensus pattern (26 bp):
CCCATTGATGTCCAGGCCCAATTAGG
Found at i:10309353 original size:12 final size:12
Alignment explanation
Indices: 10309331--10309359 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
10309321 TAAGTTGTTA
10309331 TATTA-CATTAT
1 TATTATCATTAT
10309342 TATTATCATTAT
1 TATTATCATTAT
10309354 TATTAT
1 TATTAT
10309360 ATCATCATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 5 0.29
12 12 0.71
ACGTcount: A:0.34, C:0.07, G:0.00, T:0.59
Consensus pattern (12 bp):
TATTATCATTAT
Found at i:10310272 original size:7 final size:7
Alignment explanation
Indices: 10310260--10310291 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
10310250 CGATTGCAAG
10310260 TTTTCCC
1 TTTTCCC
10310267 TTTTCCC
1 TTTTCCC
10310274 TTTTCCC
1 TTTTCCC
*
10310281 TTTTCCA
1 TTTTCCC
10310288 TTTT
1 TTTT
10310292 TTTTTTATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.03, C:0.34, G:0.00, T:0.62
Consensus pattern (7 bp):
TTTTCCC
Found at i:10310304 original size:13 final size:13
Alignment explanation
Indices: 10310288--10310321 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
10310278 CCCTTTTCCA
10310288 TTTTTTTTTTATT
1 TTTTTTTTTTATT
*
10310301 TTTTTATTTTATT
1 TTTTTTTTTTATT
10310314 TTATTTTT
1 TT-TTTTT
10310322 AACCCATTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 14 0.78
14 4 0.22
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTTTTTTATT
Found at i:10311072 original size:21 final size:22
Alignment explanation
Indices: 10311048--10311091 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
10311038 TTTTTTTTAA
10311048 TGATTAATAA-AAAAATAATAT
1 TGATTAATAATAAAAATAATAT
*
10311069 TGATTAATAATAATAATAATAT
1 TGATTAATAATAAAAATAATAT
10311091 T
1 T
10311092 TGAACCTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.39
Consensus pattern (22 bp):
TGATTAATAATAAAAATAATAT
Found at i:10311147 original size:18 final size:19
Alignment explanation
Indices: 10311124--10311180 Score: 82
Period size: 18 Copynumber: 3.1 Consensus size: 19
10311114 AAAGGTTCGC
10311124 AAAGATTCCAAGATTT-CA
1 AAAGATTCCAAGATTTGCA
*
10311142 AAAGATTTCAAGATTTGC-
1 AAAGATTCCAAGATTTGCA
*
10311160 AAAGATTCTAAGATTTGCA
1 AAAGATTCCAAGATTTGCA
10311179 AA
1 AA
10311181 GGTTTTGGAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
18 31 0.91
19 3 0.09
ACGTcount: A:0.44, C:0.12, G:0.14, T:0.30
Consensus pattern (19 bp):
AAAGATTCCAAGATTTGCA
Found at i:10311164 original size:10 final size:9
Alignment explanation
Indices: 10311123--10311181 Score: 52
Period size: 8 Copynumber: 6.6 Consensus size: 9
10311113 TAAAGGTTCG
10311123 CAAAGA-TT
1 CAAAGATTT
*
10311131 CCAAGATTT
1 CAAAGATTT
10311140 CAAAAGATTT
1 C-AAAGATTT
10311150 C-AAGATTT
1 CAAAGATTT
10311158 GCAAAGA-TT
1 -CAAAGATTT
*
10311167 CTAAGATTT
1 CAAAGATTT
10311176 GCAAAG
1 -CAAAG
10311182 GTTTTGGATT
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
8 17 0.41
9 8 0.20
10 16 0.39
ACGTcount: A:0.42, C:0.14, G:0.15, T:0.29
Consensus pattern (9 bp):
CAAAGATTT
Found at i:10311173 original size:36 final size:37
Alignment explanation
Indices: 10311119--10311305 Score: 140
Period size: 36 Copynumber: 5.2 Consensus size: 37
10311109 TTTGTAAAGG
*
10311119 TTCGCAAAGATTCCAAGATTTCA-AAAGATTTCAAGA
1 TTCGCAAAGATTCTAAGATTTCACAAAGATTTCAAGA
* * * **
10311155 TTTGCAAAGATTCTAAGATTT-GCAAAGGTTT-TGGA
1 TTCGCAAAGATTCTAAGATTTCACAAAGATTTCAAGA
* * *
10311190 TTCGCAAAGGTTC-AA-AATTCACAAAGATTCCAAGA
1 TTCGCAAAGATTCTAAGATTTCACAAAGATTTCAAGA
** * *
10311225 TTCGTGAAGATT-TCAAGA-TTCATAAAGATTTCAAAA
1 TTCGCAAAGATTCT-AAGATTTCACAAAGATTTCAAGA
* * *
10311261 TTCGCAAAGGTT-TCAAGA-TTCACAAAGGTTCCAAGA
1 TTCGCAAAGATTCT-AAGATTTCACAAAGATTTCAAGA
*
10311297 TTCACAAAG
1 TTCGCAAAG
10311306 TTTCACATTT
Statistics
Matches: 117, Mismatches: 28, Indels: 12
0.75 0.18 0.08
Matches are distributed among these distances:
33 3 0.03
34 9 0.08
35 24 0.21
36 80 0.68
37 1 0.01
ACGTcount: A:0.39, C:0.16, G:0.17, T:0.29
Consensus pattern (37 bp):
TTCGCAAAGATTCTAAGATTTCACAAAGATTTCAAGA
Found at i:10311272 original size:88 final size:90
Alignment explanation
Indices: 10311123--10311305 Score: 221
Period size: 88 Copynumber: 2.1 Consensus size: 90
10311113 TAAAGGTTCG
** * * *
10311123 CAAAGATTCCAAGATTTCAAAAGATTTCAAGATTTGCAAAGATTCTAAGATTTGCAAAGGTTT-T
1 CAAAGATTCCAAGATTTCAAAAGATTTCAAGATTCACAAAGATTCTAAAATTCGCAAAGGTTTCA
* *
10311187 GGATTCGCAAAGGTT-CAAAATTCA
66 AGATTCACAAAGGTTCCAAAATTCA
** *
10311211 CAAAGATTCCAAGA-TTCGTGAAGATTTCAAGATTCATAAAGATT-TCAAAATTCGCAAAGGTTT
1 CAAAGATTCCAAGATTTC-AAAAGATTTCAAGATTCACAAAGATTCT-AAAATTCGCAAAGGTTT
*
10311274 CAAGATTCACAAAGGTTCCAAGATTCA
64 CAAGATTCACAAAGGTTCCAAAATTCA
10311301 CAAAG
1 CAAAG
10311306 TTTCACATTT
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
87 4 0.05
88 50 0.62
89 13 0.16
90 13 0.16
ACGTcount: A:0.40, C:0.15, G:0.16, T:0.28
Consensus pattern (90 bp):
CAAAGATTCCAAGATTTCAAAAGATTTCAAGATTCACAAAGATTCTAAAATTCGCAAAGGTTTCA
AGATTCACAAAGGTTCCAAAATTCA
Found at i:10311286 original size:18 final size:18
Alignment explanation
Indices: 10311132--10311310 Score: 116
Period size: 18 Copynumber: 10.1 Consensus size: 18
10311122 GCAAAGATTC
*
10311132 CAAGATTTCA-AAAGATTT
1 CAAGA-TTCACAAAGGTTT
** *
10311150 CAAGATTTGCAAA-GATT
1 CAAGATTCACAAAGGTTT
**
10311167 CTAAGATTTGCAAAGGTTT
1 C-AAGATTCACAAAGGTTT
** *
10311186 -TGGATTCGCAAAGG-TT
1 CAAGATTCACAAAGGTTT
* * *
10311202 CAAAATTCACAAAGATTC
1 CAAGATTCACAAAGGTTT
*** *
10311220 CAAGATTCGTGAAGATTT
1 CAAGATTCACAAAGGTTT
* *
10311238 CAAGATTCATAAAGATTT
1 CAAGATTCACAAAGGTTT
* *
10311256 CAAAATTCGCAAAGGTTT
1 CAAGATTCACAAAGGTTT
*
10311274 CAAGATTCACAAAGGTTC
1 CAAGATTCACAAAGGTTT
10311292 CAAGATTCACAAA-GTTT
1 CAAGATTCACAAAGGTTT
10311309 CA
1 CA
10311311 CATTTGAAAA
Statistics
Matches: 127, Mismatches: 29, Indels: 11
0.76 0.17 0.07
Matches are distributed among these distances:
16 2 0.02
17 30 0.24
18 92 0.72
19 3 0.02
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.30
Consensus pattern (18 bp):
CAAGATTCACAAAGGTTT
Found at i:10311760 original size:23 final size:23
Alignment explanation
Indices: 10311660--10311795 Score: 72
Period size: 23 Copynumber: 6.1 Consensus size: 23
10311650 AACTTTAAGA
* *
10311660 TTCAAATATTCACATTT-GAAAAG
1 TTCAAAGATTCTCATTTAG-AAAG
* *
10311683 CTTAAAAG-TTCTCATTT-GAAACT
1 -TTCAAAGATTCTCATTTAGAAA-G
* * **
10311706 TTTAAAGGTTCTCATCCA-AAA-
1 TTCAAAGATTCTCATTTAGAAAG
* *
10311727 TTCAAATATTCGCATTTAGAAAG
1 TTCAAAGATTCTCATTTAGAAAG
*
10311750 TTCAAAGATTCTC-TTTTGAAA-
1 TTCAAAGATTCTCATTTAGAAAG
*
10311771 CTCAAAGATTCTCATTTCA-AAAG
1 TTCAAAGATTCTCATTT-AGAAAG
10311794 TT
1 TT
10311796 TACATCCAAA
Statistics
Matches: 85, Mismatches: 19, Indels: 17
0.70 0.16 0.14
Matches are distributed among these distances:
21 24 0.28
22 25 0.29
23 31 0.36
24 5 0.06
ACGTcount: A:0.38, C:0.16, G:0.10, T:0.37
Consensus pattern (23 bp):
TTCAAAGATTCTCATTTAGAAAG
Found at i:10312390 original size:72 final size:71
Alignment explanation
Indices: 10312273--10312465 Score: 201
Period size: 72 Copynumber: 2.7 Consensus size: 71
10312263 AAGCTCACCA
* * * * *
10312273 AATGATGCAAATGC-ATAGTTC-TAATAATGATTTAGATACTCACCAAATAAAGCATATGCATGG
1 AATGATGCAAATGCAATA-TTCAAAACAATGATTTAAATTCTCACCAAATAAAGCAGATGCATGG
*
10312336 TACAAAT
65 TACAAAC
* * * * *
10312343 AATGATGCAAATACAATATTTCAAAACAATGATTTAAATTCTTACCAAATAATGTAGATGCTTGG
1 AATGATGCAAATGCAATA-TTCAAAACAATGATTTAAATTCTCACCAAATAAAGCAGATGCATGG
* *
10312408 TACCAGC
65 TACAAAC
* * * *
10312415 AATGATGCAAAGGTAATATTCAAAACAATTATTTAAATTCTCACTAAATAA
1 AATGATGCAAATGCAATATTCAAAACAATGATTTAAATTCTCACCAAATAA
10312466 TGCAAATGTA
Statistics
Matches: 101, Mismatches: 20, Indels: 3
0.81 0.16 0.02
Matches are distributed among these distances:
70 13 0.13
71 36 0.36
72 52 0.51
ACGTcount: A:0.44, C:0.14, G:0.12, T:0.30
Consensus pattern (71 bp):
AATGATGCAAATGCAATATTCAAAACAATGATTTAAATTCTCACCAAATAAAGCAGATGCATGGT
ACAAAC
Found at i:10313502 original size:17 final size:18
Alignment explanation
Indices: 10313467--10313523 Score: 66
Period size: 17 Copynumber: 3.3 Consensus size: 18
10313457 AGAACATGTA
10313467 TTTTCATCTTTCTTT-TTT
1 TTTTCAT-TTTCTTTATTT
10313485 TTTTCATTTT-TTTATTT
1 TTTTCATTTTCTTTATTT
* *
10313502 TTTT-GTTTTCTGTATTT
1 TTTTCATTTTCTTTATTT
10313519 TTTTC
1 TTTTC
10313524 GTATTTAAAC
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
16 7 0.21
17 20 0.59
18 7 0.21
ACGTcount: A:0.07, C:0.11, G:0.04, T:0.79
Consensus pattern (18 bp):
TTTTCATTTTCTTTATTT
Found at i:10315123 original size:25 final size:25
Alignment explanation
Indices: 10315093--10315147 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
10315083 TTCTTTACAA
*
10315093 AAAGGAGGGTTGCTGAAGAAAAGAG
1 AAAGGAGGGTTGCTGAAAAAAAGAG
* *
10315118 GAAGGAGGGTTGTTGAAAAAAAGAG
1 AAAGGAGGGTTGCTGAAAAAAAGAG
10315143 AAAGG
1 AAAGG
10315148 GAGAAGGATC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.45, C:0.02, G:0.40, T:0.13
Consensus pattern (25 bp):
AAAGGAGGGTTGCTGAAAAAAAGAG
Found at i:10316170 original size:3 final size:3
Alignment explanation
Indices: 10316156--10316215 Score: 84
Period size: 3 Copynumber: 20.0 Consensus size: 3
10316146 TGTCATAAAC
* * * *
10316156 TAT TAT TGT TAT TAT TGT TGT TGT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
10316204 TAT TAT TAT TAT
1 TAT TAT TAT TAT
10316216 GGATGCAATT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:10316289 original size:3 final size:3
Alignment explanation
Indices: 10316283--10316318 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
10316273 GAAAAAAAGG
* *
10316283 AAT AAT AAT AAT AAT AGT AAT AAT AAC AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
10316319 GATTTTAAAG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:10318109 original size:4 final size:4
Alignment explanation
Indices: 10318102--10318132 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
10318092 TATTCATTTA
10318102 TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTT
1 TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTT
10318133 ATTAACATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.23, T:0.77
Consensus pattern (4 bp):
TTTG
Found at i:10324076 original size:36 final size:36
Alignment explanation
Indices: 10324029--10324103 Score: 150
Period size: 36 Copynumber: 2.1 Consensus size: 36
10324019 ATAATTAAGA
10324029 TATCAAGTGATTAAAGGATTAAATTATACTAAAAAC
1 TATCAAGTGATTAAAGGATTAAATTATACTAAAAAC
10324065 TATCAAGTGATTAAAGGATTAAATTATACTAAAAAC
1 TATCAAGTGATTAAAGGATTAAATTATACTAAAAAC
10324101 TAT
1 TAT
10324104 GTATGGATAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.49, C:0.08, G:0.11, T:0.32
Consensus pattern (36 bp):
TATCAAGTGATTAAAGGATTAAATTATACTAAAAAC
Found at i:10325310 original size:4 final size:4
Alignment explanation
Indices: 10325301--10325344 Score: 52
Period size: 4 Copynumber: 10.8 Consensus size: 4
10325291 TAATTGTCTG
* * *
10325301 TTTA TTTA TTTA TTTG TTTG TTTA TTTG TTTA GTTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA -TTTA TTTA TTT
10325345 GAGTATTTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
4 31 0.89
5 4 0.11
ACGTcount: A:0.16, C:0.00, G:0.09, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:10325322 original size:20 final size:20
Alignment explanation
Indices: 10325294--10325332 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
10325284 TTTATCATAA
10325294 TTGTCTGTTTATTTATTTAT
1 TTGTCTGTTTATTTATTTAT
* *
10325314 TTGTTTGTTTATTTGTTTA
1 TTGTCTGTTTATTTATTTA
10325333 GTTTATTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.13, C:0.03, G:0.13, T:0.72
Consensus pattern (20 bp):
TTGTCTGTTTATTTATTTAT
Found at i:10329912 original size:8 final size:8
Alignment explanation
Indices: 10329899--10329965 Score: 88
Period size: 8 Copynumber: 8.8 Consensus size: 8
10329889 AATGGATGAA
10329899 AAAAAATG
1 AAAAAATG
10329907 AAAAAA--
1 AAAAAATG
*
10329913 AAAGAA-G
1 AAAAAATG
10329920 AAAAAAATG
1 -AAAAAATG
10329929 -AAAAATG
1 AAAAAATG
10329936 AAAAAATG
1 AAAAAATG
10329944 AAAAAATG
1 AAAAAATG
10329952 AAAAAATG
1 AAAAAATG
10329960 AAAAAA
1 AAAAAA
10329966 AAAAGAAAAA
Statistics
Matches: 53, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
6 5 0.09
7 7 0.13
8 40 0.75
9 1 0.02
ACGTcount: A:0.79, C:0.00, G:0.12, T:0.09
Consensus pattern (8 bp):
AAAAAATG
Found at i:10329938 original size:16 final size:15
Alignment explanation
Indices: 10329900--10329983 Score: 83
Period size: 16 Copynumber: 5.9 Consensus size: 15
10329890 ATGGATGAAA
10329900 AAAAATGAAAAAA--
1 AAAAATGAAAAAATG
10329913 AAAGAA-GAAAAAAATG
1 AAA-AATG-AAAAAATG
10329929 AAAAATGAAAAAATG
1 AAAAATGAAAAAATG
10329944 AAAAAATGAAAAAATG
1 -AAAAATGAAAAAATG
10329960 -AAAA--AAAAAA-G
1 AAAAATGAAAAAATG
*
10329971 AAAAAAGAAAAAA
1 AAAAATGAAAAAA
10329984 AAAAGACTCA
Statistics
Matches: 62, Mismatches: 0, Indels: 17
0.78 0.00 0.22
Matches are distributed among these distances:
11 1 0.02
12 10 0.16
13 4 0.06
14 18 0.29
15 10 0.16
16 19 0.31
ACGTcount: A:0.81, C:0.00, G:0.12, T:0.07
Consensus pattern (15 bp):
AAAAATGAAAAAATG
Found at i:10329983 original size:7 final size:7
Alignment explanation
Indices: 10329899--10329987 Score: 71
Period size: 8 Copynumber: 12.6 Consensus size: 7
10329889 AATGGATGAA
10329899 AAAAAATG
1 AAAAAA-G
10329907 AAAAAA-
1 AAAAAAG
*
10329913 AAAGAAG
1 AAAAAAG
10329920 AAAAAAATG
1 -AAAAAA-G
*
10329929 AAAAATG
1 AAAAAAG
10329936 AAAAAATG
1 AAAAAA-G
10329944 AAAAAATG
1 AAAAAA-G
10329952 AAAAAATG
1 AAAAAA-G
10329960 --AAAA-
1 AAAAAAG
10329964 AAAAAAG
1 AAAAAAG
10329971 AAAAAAG
1 AAAAAAG
10329978 AAAAAA-
1 AAAAAAG
10329984 AAAA
1 AAAA
10329988 GACTCAAATT
Statistics
Matches: 70, Mismatches: 4, Indels: 16
0.78 0.04 0.18
Matches are distributed among these distances:
6 17 0.24
7 19 0.27
8 33 0.47
9 1 0.01
ACGTcount: A:0.82, C:0.00, G:0.11, T:0.07
Consensus pattern (7 bp):
AAAAAAG
Found at i:10329984 original size:16 final size:17
Alignment explanation
Indices: 10329899--10329985 Score: 74
Period size: 19 Copynumber: 4.9 Consensus size: 17
10329889 AATGGATGAA
10329899 AAAAAATGAAAAAAAAAG
1 AAAAAATG-AAAAAAAAG
10329917 AAGAAAA--AAATGAAAAATG
1 AA-AAAATGAAA--AAAAA-G
*
10329936 AAAAAATG-AAAAAATG
1 AAAAAATGAAAAAAAAG
10329952 AAAAAATGAAAAAAAAAAG
1 AAAAAATG--AAAAAAAAG
10329971 AAAAAA-GAAAAAAAA
1 AAAAAATGAAAAAAAA
10329986 AAGACTCAAA
Statistics
Matches: 58, Mismatches: 2, Indels: 20
0.73 0.03 0.25
Matches are distributed among these distances:
16 20 0.34
17 4 0.07
18 12 0.21
19 22 0.38
ACGTcount: A:0.82, C:0.00, G:0.11, T:0.07
Consensus pattern (17 bp):
AAAAAATGAAAAAAAAG
Found at i:10330718 original size:79 final size:79
Alignment explanation
Indices: 10330565--10330718 Score: 193
Period size: 79 Copynumber: 1.9 Consensus size: 79
10330555 ACATAACTTG
* * * * * *
10330565 TGAGTTGTGATCAAGTGATGGAAATAATGTGGATCAATGGATGAAATTAGTTTTGAAATTGCTAG
1 TGAGTCGTGATCAAATAATGGAAATAATGTGGATCAATGGATGAAATTAGTTCTAAAATTGCTAA
**
10330630 TGCTGAGAAGCCTA
66 TGCCAAGAAGCCTA
* * *
10330644 TGAGTCGTGATCAAATAATGGAAATAATAG-GGATCAGTGGATGAAATTTGTTCTAAAATTGTTA
1 TGAGTCGTGATCAAATAATGGAAATAAT-GTGGATCAATGGATGAAATTAGTTCTAAAATTGCTA
10330708 ATGCCAAGAAG
65 ATGCCAAGAAG
10330719 TTAAGAAAGG
Statistics
Matches: 63, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
79 62 0.98
80 1 0.02
ACGTcount: A:0.36, C:0.08, G:0.26, T:0.31
Consensus pattern (79 bp):
TGAGTCGTGATCAAATAATGGAAATAATGTGGATCAATGGATGAAATTAGTTCTAAAATTGCTAA
TGCCAAGAAGCCTA
Found at i:10331253 original size:23 final size:23
Alignment explanation
Indices: 10331210--10331424 Score: 101
Period size: 24 Copynumber: 9.5 Consensus size: 23
10331200 AAGAATCTTT
10331210 GAAGTTTAAATGAGAATTTTTAG
1 GAAGTTTAAATGAGAATTTTTAG
10331233 GAAGTCTTAAATGAGAATTTTTTA-
1 GAAGT-TTAAATGAGAA-TTTTTAG
* * ** *
10331257 G--TTTTAAAAGAGAACCTTTAA
1 GAAGTTTAAATGAGAATTTTTAG
* * *
10331278 AAAGTTTTTAATGAGAATCTTT--
1 GAAG-TTTAAATGAGAATTTTTAG
* *
10331300 GAATTTTAAATGAGAATCTTT--
1 GAAGTTTAAATGAGAATTTTTAG
*
10331321 G-AGCTTTAAATGAGAATATTTAAG
1 GAAG-TTTAAATGAGAAT-TTTTAG
* * * *
10331345 CAACTTTAAATGAGAATATTTAA
1 GAAGTTTAAATGAGAATTTTTAG
* * *
10331368 GAAGTTTTAAGTAAGAATCTTT--
1 GAAG-TTTAAATGAGAATTTTTAG
*
10331390 G-AGTTTTAAATGAGAATCTTTAG
1 GAAG-TTTAAATGAGAATTTTTAG
*
10331413 AAAGTTTTAAAT
1 GAAG-TTTAAAT
10331425 TAAAAACTTT
Statistics
Matches: 149, Mismatches: 28, Indels: 29
0.72 0.14 0.14
Matches are distributed among these distances:
20 5 0.03
21 58 0.39
22 6 0.04
23 10 0.07
24 63 0.42
25 7 0.05
ACGTcount: A:0.40, C:0.05, G:0.16, T:0.39
Consensus pattern (23 bp):
GAAGTTTAAATGAGAATTTTTAG
Found at i:10331270 original size:45 final size:45
Alignment explanation
Indices: 10331201--10331424 Score: 215
Period size: 45 Copynumber: 5.0 Consensus size: 45
10331191 AAAAATGATA
* * *
10331201 AGAATCTTTGAAG-TTTAAATGAGAATTTTTAGGAAGTCTTAAATG
1 AGAATCTTTG-AGTTTTAAATGAGAATCTTTAAGAAGTTTTAAATG
* * * * * *
10331246 AGAATTTTTTAGTTTTAAAAGAGAACCTTTAAAAAGTTTTTAATG
1 AGAATCTTTGAGTTTTAAATGAGAATCTTTAAGAAGTTTTAAATG
* *
10331291 AGAATCTTTGAATTTTAAATGAGAATCTTT--G-AGCTTTAAATG
1 AGAATCTTTGAGTTTTAAATGAGAATCTTTAAGAAGTTTTAAATG
* ** * * *
10331333 AGAATATTTAAGCAACTTTAAATGAGAATATTTAAGAAGTTTTAAGTA
1 AGAATCTTT--G-AGTTTTAAATGAGAATCTTTAAGAAGTTTTAAATG
10331381 AGAATCTTTGAGTTTTAAATGAGAATCTTT-AGAAAGTTTTAAAT
1 AGAATCTTTGAGTTTTAAATGAGAATCTTTAAG-AAGTTTTAAAT
10331425 TAAAAACTTT
Statistics
Matches: 143, Mismatches: 28, Indels: 16
0.76 0.15 0.09
Matches are distributed among these distances:
42 17 0.12
44 5 0.03
45 103 0.72
46 1 0.01
47 1 0.01
48 16 0.11
ACGTcount: A:0.40, C:0.05, G:0.16, T:0.39
Consensus pattern (45 bp):
AGAATCTTTGAGTTTTAAATGAGAATCTTTAAGAAGTTTTAAATG
Found at i:10331308 original size:90 final size:91
Alignment explanation
Indices: 10331199--10331424 Score: 257
Period size: 90 Copynumber: 2.5 Consensus size: 91
10331189 TTAAAAATGA
* * * * *
10331199 TAAGAATCTTTGAAGTTTAAATGAGAATTTTTAGGAAGTCTTAAATGAGAATTTTTTAG-TTTTA
1 TAAGAATCTTTGAATTTTAAATGAGAATCTTTAGGAAGTCTTAAATGAGAATATTTAAGACTTTA
*
10331263 AAAGAGAACCTTTAAAAAGTTTTTAA-
66 AAAGAGAACATTTAAAAAG-TTTTAAG
*
10331289 TGAGAATCTTTGAATTTTAAATGAGAATCTTT--G-AG-CTTTAAATGAGAATATTTAAGCAACT
1 TAAGAATCTTTGAATTTTAAATGAGAATCTTTAGGAAGTC-TTAAATGAGAATATTTAAG--ACT
* * *
10331350 TTAAATGAGAATATTTAAGAAGTTTTAAG
63 TTAAAAGAGAACATTTAAAAAGTTTTAAG
* * *
10331379 TAAGAATCTTTGAGTTTTAAATGAGAATCTTTAGAAAGTTTTAAAT
1 TAAGAATCTTTGAATTTTAAATGAGAATCTTTAGGAAGTCTTAAAT
10331425 TAAAAACTTT
Statistics
Matches: 113, Mismatches: 14, Indels: 15
0.80 0.10 0.11
Matches are distributed among these distances:
86 1 0.01
87 19 0.17
88 1 0.01
89 6 0.05
90 78 0.69
93 8 0.07
ACGTcount: A:0.40, C:0.05, G:0.16, T:0.39
Consensus pattern (91 bp):
TAAGAATCTTTGAATTTTAAATGAGAATCTTTAGGAAGTCTTAAATGAGAATATTTAAGACTTTA
AAAGAGAACATTTAAAAAGTTTTAAG
Found at i:10331441 original size:24 final size:23
Alignment explanation
Indices: 10331349--10331441 Score: 66
Period size: 24 Copynumber: 4.0 Consensus size: 23
10331339 TTTAAGCAAC
* * *
10331349 TTTAAATGAGAATATTTAAGAAGT
1 TTTAAATTAAAATCTTT-AGAAGT
*
10331373 TTT-AAGTAAGAATCTTT-G-AGT
1 TTTAAATTAA-AATCTTTAGAAGT
* *
10331394 TTTAAATGAGAATCTTTAGAAAGT
1 TTTAAATTAAAATCTTTAG-AAGT
*
10331418 TTTAAATTAAAAACTTTAAGAAGT
1 TTTAAATTAAAATCTTT-AGAAGT
10331442 AAGAATCTTT
Statistics
Matches: 53, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
21 13 0.25
22 5 0.09
23 3 0.06
24 30 0.57
25 2 0.04
ACGTcount: A:0.43, C:0.03, G:0.15, T:0.39
Consensus pattern (23 bp):
TTTAAATTAAAATCTTTAGAAGT
Found at i:10331457 original size:38 final size:35
Alignment explanation
Indices: 10331415--10331487 Score: 92
Period size: 38 Copynumber: 2.0 Consensus size: 35
10331405 ATCTTTAGAA
*
10331415 AGTTTTAAATTAAAAACTTTAAGAAGTAAGAATCTTTG
1 AGTTTTAAATGAAAAACTTT--GAA-TAAGAATCTTTG
* *
10331453 AGTTTTAAATGAGAATCTTTGAATAAGAATCTTTG
1 AGTTTTAAATGAAAAACTTTGAATAAGAATCTTTG
10331488 TTTTTGAGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
35 12 0.38
36 3 0.09
38 17 0.53
ACGTcount: A:0.41, C:0.05, G:0.15, T:0.38
Consensus pattern (35 bp):
AGTTTTAAATGAAAAACTTTGAATAAGAATCTTTG
Found at i:10331617 original size:22 final size:22
Alignment explanation
Indices: 10331591--10331664 Score: 71
Period size: 22 Copynumber: 3.4 Consensus size: 22
10331581 ATGAGAAGCA
*
10331591 TTAAAATTTTGGATGTGAAACC
1 TTAAAATTTTAGATGTGAAACC
* * *
10331613 TTAAATTTTTTGA-ATGAGAACC
1 TTAAAATTTTAGATGTGA-AACC
* *
10331635 TTAGAA-TTTAGATGTGAAACT
1 TTAAAATTTTAGATGTGAAACC
10331656 TTAAAATTT
1 TTAAAATTT
10331665 ATCGAATGTG
Statistics
Matches: 40, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
21 16 0.40
22 24 0.60
ACGTcount: A:0.38, C:0.07, G:0.15, T:0.41
Consensus pattern (22 bp):
TTAAAATTTTAGATGTGAAACC
Found at i:10331619 original size:21 final size:21
Alignment explanation
Indices: 10331594--10331665 Score: 58
Period size: 21 Copynumber: 3.4 Consensus size: 21
10331584 AGAAGCATTA
*
10331594 AAATTTTGGATGTGAAACCTT
1 AAATTTTAGATGTGAAACCTT
* *
10331615 AAATTTTTTGA-ATGAGAACCTT
1 AAA-TTTTAGATGTGA-AACCTT
*
10331637 AGAA-TTTAGATGTGAAACTTT
1 A-AATTTTAGATGTGAAACCTT
*
10331658 AAAATTTA
1 AAATTTTA
10331666 TCGAATGTGA
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
20 2 0.05
21 21 0.51
22 16 0.39
23 2 0.05
ACGTcount: A:0.39, C:0.07, G:0.15, T:0.39
Consensus pattern (21 bp):
AAATTTTAGATGTGAAACCTT
Found at i:10331672 original size:44 final size:45
Alignment explanation
Indices: 10331553--10331672 Score: 118
Period size: 43 Copynumber: 2.7 Consensus size: 45
10331543 TAAATTTGAA
* * *
10331553 TTAGATGTGAATCACTAAAAGTTTTCAAATGAGAAGCATTAAAATT
1 TTAGATGTGAAACATTAAAA-TTTTCGAATGAGAAGCATTAAAATT
* * * * * *
10331599 TTGGATGTGAAACCTTAAATTTTTTGAATGAGAA-CCTTAGAA-T
1 TTAGATGTGAAACATTAAAATTTTCGAATGAGAAGCATTAAAATT
*
10331642 TTAGATGTGAAACTTTAAAATTTATCGAATG
1 TTAGATGTGAAACATTAAAATTT-TCGAATG
10331673 TGAATCTTTG
Statistics
Matches: 60, Mismatches: 13, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
43 21 0.35
44 12 0.20
45 12 0.20
46 15 0.25
ACGTcount: A:0.39, C:0.08, G:0.17, T:0.36
Consensus pattern (45 bp):
TTAGATGTGAAACATTAAAATTTTCGAATGAGAAGCATTAAAATT
Found at i:10331736 original size:21 final size:20
Alignment explanation
Indices: 10331700--10331738 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
10331690 ATGAGAAGCT
*
10331700 TTGAAATTTTTGATGAAATC
1 TTGAAATTTTTAATGAAATC
10331720 TTGAAATTTTTAAATGAAA
1 TTGAAATTTTT-AATGAAA
10331739 AATATCAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.41, C:0.03, G:0.13, T:0.44
Consensus pattern (20 bp):
TTGAAATTTTTAATGAAATC
Found at i:10332056 original size:16 final size:16
Alignment explanation
Indices: 10332037--10332102 Score: 50
Period size: 16 Copynumber: 4.2 Consensus size: 16
10332027 GAATTTGAGT
10332037 TTTTATGAATCTAAAA
1 TTTTATGAATCTAAAA
10332053 TTTTGAT-AA--TAAAA
1 TTTT-ATGAATCTAAAA
* *
10332067 TTCTTGTGAAACT-AAA
1 TT-TTATGAATCTAAAA
*
10332083 TTCTTACGAATCTAAAA
1 TT-TTATGAATCTAAAA
10332100 TTT
1 TTT
10332103 CTTATAGAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 12
0.71 0.07 0.21
Matches are distributed among these distances:
14 8 0.20
15 4 0.10
16 20 0.50
17 8 0.20
ACGTcount: A:0.41, C:0.09, G:0.08, T:0.42
Consensus pattern (16 bp):
TTTTATGAATCTAAAA
Found at i:10332311 original size:18 final size:18
Alignment explanation
Indices: 10332260--10332340 Score: 72
Period size: 18 Copynumber: 4.4 Consensus size: 18
10332250 AATTCTTTAT
*
10332260 GAATCTTAGAACCTTTGC
1 GAATCTTATAACCTTTGC
* * * * *
10332278 AAAACTTCTAATCTTTGT
1 GAATCTTATAACCTTTGC
10332296 GAATCTTATAACCTTTGC
1 GAATCTTATAACCTTTGC
* * *
10332314 AAATCTTAAAATCTTTTGC
1 GAATCTTATAA-CCTTTGC
10332333 GAATCTTA
1 GAATCTTA
10332341 AATCATGCGA
Statistics
Matches: 47, Mismatches: 15, Indels: 1
0.75 0.24 0.02
Matches are distributed among these distances:
18 34 0.72
19 13 0.28
ACGTcount: A:0.32, C:0.19, G:0.10, T:0.40
Consensus pattern (18 bp):
GAATCTTATAACCTTTGC
Found at i:10332327 original size:36 final size:36
Alignment explanation
Indices: 10332253--10332340 Score: 113
Period size: 36 Copynumber: 2.4 Consensus size: 36
10332243 TTTTTGAAAT
* **
10332253 TCTTTATGAATCTTAGAACCTTTGCAAAACTTCTAA
1 TCTTTGTGAATCTTAGAACCTTTGCAAAACTTAAAA
* *
10332289 TCTTTGTGAATCTTATAACCTTTGCAAATCTTAAAA
1 TCTTTGTGAATCTTAGAACCTTTGCAAAACTTAAAA
*
10332325 TCTTTTGCGAATCTTA
1 TC-TTTGTGAATCTTA
10332341 AATCATGCGA
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
36 33 0.73
37 12 0.27
ACGTcount: A:0.31, C:0.18, G:0.09, T:0.42
Consensus pattern (36 bp):
TCTTTGTGAATCTTAGAACCTTTGCAAAACTTAAAA
Found at i:10332337 original size:19 final size:18
Alignment explanation
Indices: 10332287--10332373 Score: 79
Period size: 18 Copynumber: 4.9 Consensus size: 18
10332277 CAAAACTTCT
* *
10332287 AATCTTTGTGAATCTTAT
1 AATCTTTGCGAATCTTAA
* *
10332305 AACCTTTGCAAATCTTAA
1 AATCTTTGCGAATCTTAA
10332323 AATCTTTTGCGAATCTT-A
1 AATC-TTTGCGAATCTTAA
* *
10332341 AATC-ATGCGAATCTTTA
1 AATCTTTGCGAATCTTAA
* *
10332358 AATCCTTGCAAATCTT
1 AATCTTTGCGAATCTT
10332374 TTAGTTTTTT
Statistics
Matches: 57, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
16 10 0.18
17 5 0.09
18 31 0.54
19 11 0.19
ACGTcount: A:0.32, C:0.18, G:0.09, T:0.40
Consensus pattern (18 bp):
AATCTTTGCGAATCTTAA
Found at i:10332351 original size:16 final size:17
Alignment explanation
Indices: 10332330--10332361 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
10332320 TAAAATCTTT
10332330 TGCGAATC-TTAAATCA
1 TGCGAATCTTTAAATCA
10332346 TGCGAATCTTTAAATC
1 TGCGAATCTTTAAATC
10332362 CTTGCAAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.34, C:0.19, G:0.12, T:0.34
Consensus pattern (17 bp):
TGCGAATCTTTAAATCA
Found at i:10333302 original size:8 final size:8
Alignment explanation
Indices: 10333280--10333323 Score: 52
Period size: 8 Copynumber: 5.4 Consensus size: 8
10333270 TTTACCATAA
*
10333280 TTGTCTAT
1 TTGTTTAT
*
10333288 TTATTTAT
1 TTGTTTAT
10333296 TTGTTTAT
1 TTGTTTAT
10333304 TTGTTTATT
1 TTGTTTA-T
*
10333313 TTATTTAT
1 TTGTTTAT
10333321 TTG
1 TTG
10333324 ACTATTTATG
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
8 23 0.77
9 7 0.23
ACGTcount: A:0.16, C:0.02, G:0.09, T:0.73
Consensus pattern (8 bp):
TTGTTTAT
Found at i:10337039 original size:16 final size:17
Alignment explanation
Indices: 10337004--10337040 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
10336994 AGCCATTATA
10337004 CCATGCTTTATTATTTC
1 CCATGCTTTATTATTTC
10337021 CCATGTCTTT-TTA-TTC
1 CCATG-CTTTATTATTTC
10337037 CCAT
1 CCAT
10337041 TCTCAAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 7 0.37
17 8 0.42
18 4 0.21
ACGTcount: A:0.16, C:0.27, G:0.05, T:0.51
Consensus pattern (17 bp):
CCATGCTTTATTATTTC
Found at i:10337847 original size:16 final size:16
Alignment explanation
Indices: 10337826--10337883 Score: 73
Period size: 16 Copynumber: 3.7 Consensus size: 16
10337816 GATGAAGTAA
* *
10337826 AAAAAATGAAACAATG
1 AAAAAATAAAAAAATG
* *
10337842 AAAAAA-CAAAAAATA
1 AAAAAATAAAAAAATG
10337857 AAAAAATAAAAAAATG
1 AAAAAATAAAAAAATG
10337873 AAAAAATAAAA
1 AAAAAATAAAA
10337884 CAAAAGAGAA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
15 12 0.33
16 24 0.67
ACGTcount: A:0.81, C:0.03, G:0.05, T:0.10
Consensus pattern (16 bp):
AAAAAATAAAAAAATG
Found at i:10337853 original size:8 final size:8
Alignment explanation
Indices: 10337825--10337883 Score: 66
Period size: 8 Copynumber: 7.5 Consensus size: 8
10337815 GGATGAAGTA
10337825 AAAAAAAT
1 AAAAAAAT
* *
10337833 GAAACAAT
1 AAAAAAAT
*
10337841 GAAAAAA-
1 AAAAAAAT
*
10337848 CAAAAAAT
1 AAAAAAAT
10337856 AAAAAAAT
1 AAAAAAAT
10337864 AAAAAAAT
1 AAAAAAAT
*
10337872 GAAAAAAT
1 AAAAAAAT
10337880 AAAA
1 AAAA
10337884 CAAAAGAGAA
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
7 6 0.14
8 37 0.86
ACGTcount: A:0.81, C:0.03, G:0.05, T:0.10
Consensus pattern (8 bp):
AAAAAAAT
Found at i:10337863 original size:31 final size:31
Alignment explanation
Indices: 10337825--10337883 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
10337815 GGATGAAGTA
* *
10337825 AAAAAAATGAAACAATGAAAAAACAAAAAAT
1 AAAAAAATAAAAAAATGAAAAAACAAAAAAT
*
10337856 AAAAAAATAAAAAAATGAAAAAATAAAA
1 AAAAAAATAAAAAAATGAAAAAACAAAA
10337884 CAAAAGAGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.81, C:0.03, G:0.05, T:0.10
Consensus pattern (31 bp):
AAAAAAATAAAAAAATGAAAAAACAAAAAAT
Found at i:10339143 original size:24 final size:24
Alignment explanation
Indices: 10339103--10339297 Score: 237
Period size: 24 Copynumber: 8.5 Consensus size: 24
10339093 GATAAAAATG
10339103 ATGAGAATCTTT--G-AGTTTTAA
1 ATGAGAATCTTTAAGAAGTTTTAA
*
10339124 ATGAGAATCTTTAAGAAGTTTCAA
1 ATGAGAATCTTTAAGAAGTTTTAA
*
10339148 ATGAGAATATTTAAGAAGTTTTAA
1 ATGAGAATCTTTAAGAAGTTTTAA
10339172 ATGAGAATCTTT--G-AGTTTTAA
1 ATGAGAATCTTTAAGAAGTTTTAA
* * *
10339193 ATAAGAATCTTTAATAAGTTTTGA
1 ATGAGAATCTTTAAGAAGTTTTAA
* *
10339217 ATAAGGATCTTTAAGAAGTTTTAA
1 ATGAGAATCTTTAAGAAGTTTTAA
*
10339241 ATGAGAATCATTAAGAAGTTTTAA
1 ATGAGAATCTTTAAGAAGTTTTAA
*
10339265 ATGACAATCTTT--G-AGTTTTAA
1 ATGAGAATCTTTAAGAAGTTTTAA
*
10339286 ATGAGCATCTTT
1 ATGAGAATCTTT
10339298 GAAAGAGAAT
Statistics
Matches: 151, Mismatches: 17, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
21 49 0.32
22 2 0.01
23 1 0.01
24 99 0.66
ACGTcount: A:0.39, C:0.06, G:0.16, T:0.39
Consensus pattern (24 bp):
ATGAGAATCTTTAAGAAGTTTTAA
Found at i:10339188 original size:69 final size:69
Alignment explanation
Indices: 10339103--10339276 Score: 240
Period size: 69 Copynumber: 2.5 Consensus size: 69
10339093 GATAAAAATG
*
10339103 ATGAGAATCTTTGAGTTTTAAATGAGAATCTTTAAGAAGTTTCAAATGAGAATATTTAAGAAGTT
1 ATGAGAATCTTTGAGTTTTAAATGAGAATCTTTAAGAAGTTTCAAATAAGAATATTTAAGAAGTT
10339168 TTAA
66 TTAA
* * ** * *
10339172 ATGAGAATCTTTGAGTTTTAAATAAGAATCTTTAATAAGTTTTGAATAAGGATCTTTAAGAAGTT
1 ATGAGAATCTTTGAGTTTTAAATGAGAATCTTTAAGAAGTTTCAAATAAGAATATTTAAGAAGTT
10339237 TTAA
66 TTAA
* *
10339241 ATGAGAATCATTAAGAAGTTTTAAATGACAATCTTT
1 ATGAGAATC-TT-TG-AGTTTTAAATGAGAATCTTT
10339277 GAGTTTTAAA
Statistics
Matches: 92, Mismatches: 10, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
69 71 0.77
70 2 0.02
71 1 0.01
72 18 0.20
ACGTcount: A:0.40, C:0.05, G:0.16, T:0.39
Consensus pattern (69 bp):
ATGAGAATCTTTGAGTTTTAAATGAGAATCTTTAAGAAGTTTCAAATAAGAATATTTAAGAAGTT
TTAA
Found at i:10339232 original size:93 final size:93
Alignment explanation
Indices: 10339116--10339297 Score: 285
Period size: 93 Copynumber: 2.0 Consensus size: 93
10339106 AGAATCTTTG
* *
10339116 AGTTTTAAATGAGAATCTTTAAGAAGTTTCAAATGAGAAT-ATTTAAGAAGTTTTAAATGAGAAT
1 AGTTTTAAATAAGAATCTTTAAGAAGTTTCAAATGAGAATCA-TTAAGAAGTTTTAAATGACAAT
10339180 CTTTGAGTTTTAAATAAGAATCTTTAATA
65 CTTTGAGTTTTAAATAAGAATCTTTAATA
* * *
10339209 AGTTTTGAATAAGGATCTTTAAGAAGTTTTAAATGAGAATCATTAAGAAGTTTTAAATGACAATC
1 AGTTTTAAATAAGAATCTTTAAGAAGTTTCAAATGAGAATCATTAAGAAGTTTTAAATGACAATC
* *
10339274 TTTGAGTTTTAAATGAGCATCTTT
66 TTTGAGTTTTAAATAAGAATCTTT
10339298 GAAAGAGAAT
Statistics
Matches: 81, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
93 80 0.99
94 1 0.01
ACGTcount: A:0.40, C:0.05, G:0.16, T:0.39
Consensus pattern (93 bp):
AGTTTTAAATAAGAATCTTTAAGAAGTTTCAAATGAGAATCATTAAGAAGTTTTAAATGACAATC
TTTGAGTTTTAAATAAGAATCTTTAATA
Done.