Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167882.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_15, 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: 22478863
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 61000 characters in sequence are not A, C, G, or T
File 67 of 106
Found at i:12145512 original size:2 final size:2
Alignment explanation
Indices: 12145507--12145533 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
12145497 AAAAAAATTA
12145507 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
12145534 AAAGTAGCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12145935 original size:95 final size:95
Alignment explanation
Indices: 12145826--12146025 Score: 400
Period size: 95 Copynumber: 2.1 Consensus size: 95
12145816 TTATTTGATA
12145826 TTTAAATTTTCAATCTATTTAATATTATAAGTTTTTATTATATTTATGTTAATTTTTATTTAAAC
1 TTTAAATTTTCAATCTATTTAATATTATAAGTTTTTATTATATTTATGTTAATTTTTATTTAAAC
12145891 TTTTTATATATTTGATATTGTGAAAAATAT
66 TTTTTATATATTTGATATTGTGAAAAATAT
12145921 TTTAAATTTTCAATCTATTTAATATTATAAGTTTTTATTATATTTATGTTAATTTTTATTTAAAC
1 TTTAAATTTTCAATCTATTTAATATTATAAGTTTTTATTATATTTATGTTAATTTTTATTTAAAC
12145986 TTTTTATATATTTGATATTGTGAAAAATAT
66 TTTTTATATATTTGATATTGTGAAAAATAT
12146016 TTTAAATTTT
1 TTTAAATTTT
12146026 TTTATTAAAA
Statistics
Matches: 105, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
95 105 1.00
ACGTcount: A:0.34, C:0.03, G:0.05, T:0.57
Consensus pattern (95 bp):
TTTAAATTTTCAATCTATTTAATATTATAAGTTTTTATTATATTTATGTTAATTTTTATTTAAAC
TTTTTATATATTTGATATTGTGAAAAATAT
Found at i:12146834 original size:74 final size:74
Alignment explanation
Indices: 12146725--12146870 Score: 292
Period size: 74 Copynumber: 2.0 Consensus size: 74
12146715 TTTATTATCA
12146725 ATTCATTATAAATTATTACTCTAAAATACACCATCAATTTCATCTATATGCACCTTATTCTTTTT
1 ATTCATTATAAATTATTACTCTAAAATACACCATCAATTTCATCTATATGCACCTTATTCTTTTT
12146790 TTACTTTCC
66 TTACTTTCC
12146799 ATTCATTATAAATTATTACTCTAAAATACACCATCAATTTCATCTATATGCACCTTATTCTTTTT
1 ATTCATTATAAATTATTACTCTAAAATACACCATCAATTTCATCTATATGCACCTTATTCTTTTT
12146864 TTACTTT
66 TTACTTT
12146871 TCTTTTTGAT
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 72 1.00
ACGTcount: A:0.32, C:0.21, G:0.01, T:0.47
Consensus pattern (74 bp):
ATTCATTATAAATTATTACTCTAAAATACACCATCAATTTCATCTATATGCACCTTATTCTTTTT
TTACTTTCC
Found at i:12156545 original size:4 final size:4
Alignment explanation
Indices: 12156536--12156591 Score: 60
Period size: 4 Copynumber: 13.8 Consensus size: 4
12156526 TTATTTTGAT
* * *
12156536 TTTA TTTA TTTG TTTA TTTA TTTA -TTA TTTTT TTTG TCTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA -TTTA TTTA T-TTA TTTA TTTA
12156585 TTTA TTT
1 TTTA TTT
12156592 TTCTTTTGGT
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
3 3 0.07
4 36 0.82
5 5 0.11
ACGTcount: A:0.18, C:0.02, G:0.04, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:12156580 original size:25 final size:25
Alignment explanation
Indices: 12156536--12156593 Score: 84
Period size: 25 Copynumber: 2.4 Consensus size: 25
12156526 TTATTTTGAT
*
12156536 TTTA-TTTATTTGTTTATTTATTTA
1 TTTATTTTTTTTGTTTATTTATTTA
12156560 -TTATTTTTTTTGTCTTATTTATTTA
1 TTTATTTTTTTTGT-TTATTTATTTA
12156585 TTTATTTTT
1 TTTATTTTT
12156594 CTTTTGGTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
23 3 0.10
24 8 0.27
25 11 0.37
26 8 0.27
ACGTcount: A:0.17, C:0.02, G:0.03, T:0.78
Consensus pattern (25 bp):
TTTATTTTTTTTGTTTATTTATTTA
Found at i:12156803 original size:14 final size:14
Alignment explanation
Indices: 12156784--12156814 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
12156774 TATTATATTA
12156784 TTTTACATGATAAT
1 TTTTACATGATAAT
*
12156798 TTTTACGTGATAAT
1 TTTTACATGATAAT
12156812 TTT
1 TTT
12156815 GTTTTATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.29, C:0.06, G:0.10, T:0.55
Consensus pattern (14 bp):
TTTTACATGATAAT
Found at i:12157189 original size:103 final size:103
Alignment explanation
Indices: 12156984--12157170 Score: 243
Period size: 103 Copynumber: 1.8 Consensus size: 103
12156974 ATTTTTAAAA
* * * ** * *
12156984 AATCCTACAAACATATTAGAGGATAATTCTTAACAAAAAATCTTATTAATATATTGAAAGATATT
1 AATCCTACAAACAGATTAGAAGATAATGCTTAACAAAAAATCTTAACAACACATTGAAAGATATT
12157049 TCTGAAAATAAATTATTTTCACAAACAAATAAATTTTT
66 TCTGAAAATAAATTATTTTCACAAACAAATAAATTTTT
* * *
12157087 AATCTTACCAACAGATTAGAAGATAATGCTTGACAAAAAATCTTAACAACACATT-AGAAGATAT
1 AATCCTACAAACAGATTAGAAGATAATGCTTAACAAAAAATCTTAACAACACATTGA-AAGATAT
*
12157151 TT-TTAAGAATAAATTATTTT
65 TTCTGAA-AATAAATTATTTT
12157171 TTACAAATAA
Statistics
Matches: 71, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
102 4 0.06
103 67 0.94
ACGTcount: A:0.47, C:0.11, G:0.07, T:0.34
Consensus pattern (103 bp):
AATCCTACAAACAGATTAGAAGATAATGCTTAACAAAAAATCTTAACAACACATTGAAAGATATT
TCTGAAAATAAATTATTTTCACAAACAAATAAATTTTT
Found at i:12157200 original size:18 final size:19
Alignment explanation
Indices: 12157161--12157200 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
12157151 TTTTAAGAAT
*
12157161 AAATTATTTTTTACAAATA
1 AAATTATTTTTTACAAACA
*
12157180 AAATTTTTTTTTAC-AACA
1 AAATTATTTTTTACAAACA
12157198 AAA
1 AAA
12157201 AGATTAAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.45
Consensus pattern (19 bp):
AAATTATTTTTTACAAACA
Found at i:12157640 original size:23 final size:23
Alignment explanation
Indices: 12157613--12157660 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
12157603 AAATCTAGCA
12157613 ATAGGTCCACAGATCTATACGTT
1 ATAGGTCCACAGATCTATACGTT
* * *
12157636 ATAGGTCTACGGATTTATACGTT
1 ATAGGTCCACAGATCTATACGTT
12157659 AT
1 AT
12157661 GACACTATCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (23 bp):
ATAGGTCCACAGATCTATACGTT
Found at i:12163032 original size:27 final size:27
Alignment explanation
Indices: 12163001--12163053 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
12162991 GACATAAAAA
* *
12163001 TAATTTAATAAATTTTAAATTATTTAT
1 TAATTTAATAAATATTAAATAATTTAT
*
12163028 TAATTTTATAAATATTAAATAATTTA
1 TAATTTAATAAATATTAAATAATTTA
12163054 AAATTTTTAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (27 bp):
TAATTTAATAAATATTAAATAATTTAT
Found at i:12163034 original size:18 final size:18
Alignment explanation
Indices: 12162998--12163062 Score: 60
Period size: 19 Copynumber: 3.6 Consensus size: 18
12162988 TTTGACATAA
*
12162998 AAATAATTTAATAAATTTT
1 AAATTATTTAAT-AATTTT
*
12163017 AAATTATTTATTAATTTT
1 AAATTATTTAATAATTTT
* * *
12163035 ATAAATATTAAATAATTTA
1 A-AATTATTTAATAATTTT
12163054 AAATT-TTTA
1 AAATTATTTA
12163063 CTACATATAA
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
17 3 0.08
18 10 0.27
19 24 0.65
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
AAATTATTTAATAATTTT
Found at i:12163062 original size:27 final size:27
Alignment explanation
Indices: 12163002--12163060 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
12162992 ACATAAAAAT
* * * *
12163002 AATTTAATAAATTTTAAATTATTTATT
1 AATTTTATAAATATTAAATAATTTATA
12163029 AATTTTATAAATATTAAATAATTTA-A
1 AATTTTATAAATATTAAATAATTTATA
12163055 AATTTT
1 AATTTT
12163061 TACTACATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 6 0.21
27 22 0.79
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (27 bp):
AATTTTATAAATATTAAATAATTTATA
Found at i:12163486 original size:12 final size:12
Alignment explanation
Indices: 12163466--12163495 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
12163456 AATTTTTTAT
*
12163466 TGGATATAGAGA
1 TGGAGATAGAGA
12163478 TGGAGATAGAGA
1 TGGAGATAGAGA
12163490 TGGAGA
1 TGGAGA
12163496 CAGGTAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.40, T:0.20
Consensus pattern (12 bp):
TGGAGATAGAGA
Found at i:12170047 original size:15 final size:15
Alignment explanation
Indices: 12170029--12170058 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
12170019 TTGCAGCACC
12170029 TTCACCAACATTATT
1 TTCACCAACATTATT
*
12170044 TTCACCACCATTATT
1 TTCACCAACATTATT
12170059 ACTTTCTCTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.30, G:0.00, T:0.40
Consensus pattern (15 bp):
TTCACCAACATTATT
Found at i:12174824 original size:1 final size:1
Alignment explanation
Indices: 12174818--12174843 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
12174808 AGAAAAGACA
12174818 CCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCC
12174844 AAAAGAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:12177736 original size:92 final size:92
Alignment explanation
Indices: 12177616--12177887 Score: 275
Period size: 92 Copynumber: 2.9 Consensus size: 92
12177606 TAAATTTAAT
* * *
12177616 AAAAAATAATCCATAAATATTACGTTTCAAAACTTAAAAACGATGATGTTTTGTTCATGAAAAAC
1 AAAAAATAATCCACAAATACTATGTTTCAAAACTTAAAAACGATGATGTTTTGTTCATGAAAAAC
12177681 GTCGTCGTTGTATTAAAAAAATAGC-AC
66 GTCGTCGTTGTATT-AAAAAATAGCTAC
* * ** *
12177708 AAAAAATAATCCACAAATACTATATTTC-AAATTCTAGAAAATTATGATGTTTTATTCATGAAAA
1 AAAAAATAATCCACAAATACTATGTTTCAAAACT-TA-AAAACGATGATGTTTTGTTCATGAAAA
* * *
12177772 ACGAT-GTTGTTATA-TAAAAAAT-TCTAC
64 ACG-TCGTCGTTGTATTAAAAAATAGCTAC
* * * * * * *
12177799 AAAACAATAATCAACAAATACTTTGTTTCAAATCCTAAAAACGATCACGTTTTGTTCATAAAAAA
1 AAAA-AATAATCCACAAATACTATGTTTCAAAACTTAAAAACGATGATGTTTTGTTCATGAAAAA
* *
12177864 CATCGTCGTTGTATTCACAAAATA
65 CGTCGTCGTTGTATT-AAAAAATA
12177888 TTTTTTTTCA
Statistics
Matches: 143, Mismatches: 27, Indels: 18
0.76 0.14 0.10
Matches are distributed among these distances:
90 2 0.01
91 47 0.33
92 51 0.36
93 42 0.29
94 1 0.01
ACGTcount: A:0.45, C:0.14, G:0.09, T:0.32
Consensus pattern (92 bp):
AAAAAATAATCCACAAATACTATGTTTCAAAACTTAAAAACGATGATGTTTTGTTCATGAAAAAC
GTCGTCGTTGTATTAAAAAATAGCTAC
Found at i:12177774 original size:93 final size:93
Alignment explanation
Indices: 12177640--12177887 Score: 272
Period size: 91 Copynumber: 2.7 Consensus size: 93
12177630 AAATATTACG
* *
12177640 TTTCAAAACTTAAAAACGATGATGTTTTGTTCATGAAAAACGTCGTCGTTGTATTAAAAAAATAG
1 TTTCAAATCCTAAAAACGATGATGTTTTGTTCATGAAAAACGTCGTCGTTGTATT-AAAAAATAG
*
12177705 C-ACAAAA-AATAATCCACAAATACTATA
65 CTACAAAACAATAATCAACAAATACTATA
* ** * * *
12177732 TTTCAAATTCTAGAAAATTATGATGTTTTATTCATGAAAAACGAT-GTTGTTATA-TAAAAAAT-
1 TTTCAAATCCTA-AAAACGATGATGTTTTGTTCATGAAAAACG-TCGTCGTTGTATTAAAAAATA
* * *
12177794 TCTACAAAACAATAATCAACAAATACTTTG
64 GCTACAAAACAATAATCAACAAATACTATA
* * * * *
12177824 TTTCAAATCCTAAAAACGATCACGTTTTGTTCATAAAAAACATCGTCGTTGTATTCACAAAATA
1 TTTCAAATCCTAAAAACGATGATGTTTTGTTCATGAAAAACGTCGTCGTTGTATT-AAAAAATA
12177888 TTTTTTTTCA
Statistics
Matches: 125, Mismatches: 23, Indels: 14
0.77 0.14 0.09
Matches are distributed among these distances:
90 2 0.02
91 43 0.34
92 39 0.31
93 40 0.32
94 1 0.01
ACGTcount: A:0.44, C:0.14, G:0.10, T:0.33
Consensus pattern (93 bp):
TTTCAAATCCTAAAAACGATGATGTTTTGTTCATGAAAAACGTCGTCGTTGTATTAAAAAATAGC
TACAAAACAATAATCAACAAATACTATA
Found at i:12178856 original size:25 final size:25
Alignment explanation
Indices: 12178821--12178889 Score: 77
Period size: 25 Copynumber: 2.8 Consensus size: 25
12178811 ATTTATTTTT
* *
12178821 AATTAAATTTAATATTTTATAATTGA
1 AATT-AATTTAATATTTTAAAATTAA
*
12178847 AATTAATTTAATAATTTAAAATTAA
1 AATTAATTTAATATTTTAAAATTAA
* *
12178872 AAATAATTTTA-ATTTTAA
1 AATTAATTTAATATTTTAA
12178890 TAAATTTCAA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
24 6 0.16
25 27 0.73
26 4 0.11
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (25 bp):
AATTAATTTAATATTTTAAAATTAA
Found at i:12179160 original size:2 final size:2
Alignment explanation
Indices: 12179153--12179218 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
12179143 AGTACTTCAT
12179153 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
12179195 GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA
12179219 TTGTTTTCTG
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:12183153 original size:7 final size:7
Alignment explanation
Indices: 12183141--12183179 Score: 78
Period size: 7 Copynumber: 5.6 Consensus size: 7
12183131 CAAAAGAATA
12183141 AAATTAG
1 AAATTAG
12183148 AAATTAG
1 AAATTAG
12183155 AAATTAG
1 AAATTAG
12183162 AAATTAG
1 AAATTAG
12183169 AAATTAG
1 AAATTAG
12183176 AAAT
1 AAAT
12183180 AAAAAATCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.59, C:0.00, G:0.13, T:0.28
Consensus pattern (7 bp):
AAATTAG
Found at i:12183186 original size:14 final size:14
Alignment explanation
Indices: 12183140--12183186 Score: 67
Period size: 14 Copynumber: 3.4 Consensus size: 14
12183130 ACAAAAGAAT
12183140 AAAATTAGAAATTA
1 AAAATTAGAAATTA
*
12183154 GAAATTAGAAATTA
1 AAAATTAGAAATTA
* *
12183168 GAAATTAGAAATAA
1 AAAATTAGAAATTA
12183182 AAAAT
1 AAAAT
12183187 CAAAGCAGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.64, C:0.00, G:0.11, T:0.26
Consensus pattern (14 bp):
AAAATTAGAAATTA
Found at i:12183186 original size:21 final size:21
Alignment explanation
Indices: 12183140--12183186 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
12183130 ACAAAAGAAT
*
12183140 AAAATTAGAAATTAGAAATTA
1 AAAATTAGAAATTAGAAATAA
*
12183161 GAAATTAGAAATTAGAAATAA
1 AAAATTAGAAATTAGAAATAA
12183182 AAAAT
1 AAAAT
12183187 CAAAGCAGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.64, C:0.00, G:0.11, T:0.26
Consensus pattern (21 bp):
AAAATTAGAAATTAGAAATAA
Found at i:12183557 original size:19 final size:20
Alignment explanation
Indices: 12183535--12183575 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
12183525 TTCCGATCGT
*
12183535 CTTAACCTTT-ACCGAAAAA
1 CTTAAACTTTCACCGAAAAA
*
12183554 CTTAAACTTTCACTGAAAAA
1 CTTAAACTTTCACCGAAAAA
12183574 CT
1 CT
12183576 CATATAAAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.41, C:0.24, G:0.05, T:0.29
Consensus pattern (20 bp):
CTTAAACTTTCACCGAAAAA
Found at i:12184293 original size:21 final size:22
Alignment explanation
Indices: 12184246--12184294 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
12184236 TTTTTTCTTT
*
12184246 TTAAAATAAGTAAAATTAAACA
1 TTAAAATAAATAAAATTAAACA
* *
12184268 -AAAAATAAATCAAATTAAA-A
1 TTAAAATAAATAAAATTAAACA
12184288 TTAAAAT
1 TTAAAAT
12184295 TAAAATTTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
20 1 0.05
21 21 0.95
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.27
Consensus pattern (22 bp):
TTAAAATAAATAAAATTAAACA
Found at i:12184727 original size:18 final size:18
Alignment explanation
Indices: 12184704--12184738 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
12184694 AGATTCGTAA
*
12184704 AAAATTCATAATGATTTC
1 AAAATTCATAAAGATTTC
*
12184722 AAAATTTATAAAGATTT
1 AAAATTCATAAAGATTT
12184739 AAGATTCGTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.49, C:0.06, G:0.06, T:0.40
Consensus pattern (18 bp):
AAAATTCATAAAGATTTC
Found at i:12185216 original size:44 final size:43
Alignment explanation
Indices: 12185166--12185328 Score: 136
Period size: 44 Copynumber: 3.7 Consensus size: 43
12185156 ATTCAAATAC
**
12185166 TTTCATTTGAAAACTTTAGAAATTCACCCCCAAAAGTTAAAGA
1 TTTCATTTGAAAACTTTAGAAATTCACATCCAAAAGTTAAAGA
*
12185209 TCTTCATTTGACAAA-TTTA-AAGATTCACATCCAAAATTTTAAAGA
1 T-TTCATTTGA-AAACTTTAGAA-ATTCACATCCAAAA-GTTAAAGA
* * *
12185254 TTCACATTCAT-AAAATTTTAGAGATTCACATCCAAAAGTTAAAGA
1 TT-TCATT--TGAAAACTTTAGAAATTCACATCCAAAAGTTAAAGA
* * *
12185299 TTTTCCTTCGAAATAC-TTAGAGATTCACAT
1 -TTTCATTTGAAA-ACTTTAGAAATTCACAT
12185329 AAAAAATTTT
Statistics
Matches: 98, Mismatches: 10, Indels: 23
0.75 0.08 0.18
Matches are distributed among these distances:
43 3 0.03
44 43 0.44
45 29 0.30
46 21 0.21
47 2 0.02
ACGTcount: A:0.40, C:0.17, G:0.09, T:0.34
Consensus pattern (43 bp):
TTTCATTTGAAAACTTTAGAAATTCACATCCAAAAGTTAAAGA
Found at i:12185252 original size:22 final size:22
Alignment explanation
Indices: 12185224--12185300 Score: 102
Period size: 22 Copynumber: 3.5 Consensus size: 22
12185214 ATTTGACAAA
12185224 TTTAAAGATTCACATCCAAAAT
1 TTTAAAGATTCACATCCAAAAT
*
12185246 TTTAAAGATTCACATTCATAAAAT
1 TTTAAAGATTCACA-TC-CAAAAT
*
12185270 TTTAGAGATTCACATCCAAAA-
1 TTTAAAGATTCACATCCAAAAT
*
12185291 GTTAAAGATT
1 TTTAAAGATT
12185301 TTCCTTCGAA
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
21 8 0.17
22 18 0.38
23 4 0.08
24 18 0.38
ACGTcount: A:0.44, C:0.14, G:0.08, T:0.34
Consensus pattern (22 bp):
TTTAAAGATTCACATCCAAAAT
Found at i:12185288 original size:46 final size:45
Alignment explanation
Indices: 12185224--12185528 Score: 147
Period size: 46 Copynumber: 6.7 Consensus size: 45
12185214 ATTTGACAAA
*
12185224 TTTAAAGATTCACATCCAAAATTTTAAAGATTCACATTCATAAAAT
1 TTTAGAGATTCACATCCAAAATTTTAAAGATTCACATTCA-AAAAT
* ** * *
12185270 TTTAGAGATTCACATCCAAAA-GTTAAAGATTTTCCTTC-GAAAT
1 TTTAGAGATTCACATCCAAAATTTTAAAGATTCACATTCAAAAAT
* ** * * * *
12185313 ACTTAGAGATTCACATAAAAAATTTTTAAAAAAATCATATTCAAAAAC
1 -TTTAGAGATTCACATCCAAAA-TTTT-AAAGATTCACATTCAAAAAT
* * * * * * *
12185361 TTTA-ATATTTAACAACCAAAATTTCAAAAATAT-TCATCTGAAAAAT
1 TTTAGAGA-TTCACATCCAAAATTTTAAAGAT-TCACAT-TCAAAAAT
* * * * * *
12185407 TTTAGGGTTTCA-ATCTAATATTTTAAATATTCATATTCAAAAAAT
1 TTTAGAGATTCACATCCAAAATTTTAAAGATTCACATTC-AAAAAT
* * * * *** *
12185452 TTTAGAGATTCATATCTAAAGTTTTAAAGGTTCTTTTTC-AAAAC
1 TTTAGAGATTCACATCCAAAATTTTAAAGATTCACATTCAAAAAT
* * *
12185496 TTTATG-GCTTCACATCCAATATTTTAAAAATTC
1 TTTA-GAGATTCACATCCAAAATTTTAAAGATTC
12185529 TTATTTGAAT
Statistics
Matches: 188, Mismatches: 58, Indels: 28
0.69 0.21 0.10
Matches are distributed among these distances:
43 4 0.02
44 48 0.26
45 52 0.28
46 61 0.32
47 20 0.11
48 3 0.02
ACGTcount: A:0.43, C:0.13, G:0.07, T:0.37
Consensus pattern (45 bp):
TTTAGAGATTCACATCCAAAATTTTAAAGATTCACATTCAAAAAT
Found at i:12185289 original size:90 final size:88
Alignment explanation
Indices: 12185175--12185463 Score: 231
Period size: 90 Copynumber: 3.2 Consensus size: 88
12185165 CTTTCATTTG
* ** * *
12185175 AAAACTTTAGAAATTCACCCCCAAAAGTTAAAGATCTTCATTTGACAAATTTAAAGATTCACATC
1 AAAACTTTAGAGATTCACAACCAAAAGTTAAAGATATTCATTTGA-AAATTTAGAGATTCACATC
* * *
12185240 CAAAATTTTAAAGATTCACATTCA
65 AAAAATTTTAAAAATTCATATTCA
* * * * * *
12185264 TAAAATTTTAGAGATTCACATCCAAAAGTTAAAGATTTTCCTTCGAAATACTTAGAGATTCACAT
1 -AAAACTTTAGAGATTCACAACCAAAAGTTAAAGATATTCATTTGAAA-ATTTAGAGATTCACAT
* *
12185329 AAAAAATTTTTAAAAAAATCATATTCA
64 CAAAAA-TTTT-AAAAATTCATATTCA
* * * * * * *
12185356 AAAACTTTA-ATATTTAACAACCAAAATTTCAAAAATATTCATCTGAAAAATTTTAGGGTTTCA-
1 AAAACTTTAGAGA-TTCACAACCAAAAGTT-AAAGATATTCATTTG-AAAA-TTTAGAGATTCAC
* * *
12185419 ATCTAATATTTTAAATATTCATATTCAA
62 ATCAAAAATTTTAAAAATTCATATTC-A
*
12185447 AAAATTTTAGAGATTCA
1 AAAACTTTAGAGATTCA
12185464 TATCTAAAGT
Statistics
Matches: 155, Mismatches: 35, Indels: 17
0.75 0.17 0.08
Matches are distributed among these distances:
89 2 0.01
90 70 0.45
91 41 0.26
92 30 0.19
93 12 0.08
ACGTcount: A:0.45, C:0.14, G:0.07, T:0.34
Consensus pattern (88 bp):
AAAACTTTAGAGATTCACAACCAAAAGTTAAAGATATTCATTTGAAAATTTAGAGATTCACATCA
AAAATTTTAAAAATTCATATTCA
Found at i:12185908 original size:24 final size:23
Alignment explanation
Indices: 12185851--12185912 Score: 63
Period size: 24 Copynumber: 2.7 Consensus size: 23
12185841 ATGTTTTTTA
* *
12185851 CATGATGCAAATGCATATCCAAC
1 CATGAAGCAAATGCATACCCAAC
* *
12185874 CAT-AATACAAATGCATGCCCCAAC
1 CATGAA-GCAAATGCAT-ACCCAAC
12185898 CATGAAGCAAATGCA
1 CATGAAGCAAATGCA
12185913 ATTATCAAGG
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
22 1 0.03
23 12 0.39
24 16 0.52
25 2 0.06
ACGTcount: A:0.42, C:0.27, G:0.13, T:0.18
Consensus pattern (23 bp):
CATGAAGCAAATGCATACCCAAC
Found at i:12186600 original size:12 final size:12
Alignment explanation
Indices: 12186583--12186615 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
12186573 TTAAGTCTTC
*
12186583 CTTTTTTTTATT
1 CTTTTTTTTACT
12186595 CTTTTTTTTACT
1 CTTTTTTTTACT
12186607 -TTTTTTTTA
1 CTTTTTTTTA
12186616 ATTTTTACAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 9 0.45
12 11 0.55
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.82
Consensus pattern (12 bp):
CTTTTTTTTACT
Found at i:12186914 original size:20 final size:20
Alignment explanation
Indices: 12186878--12186915 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
12186868 TATCCCATCA
*
12186878 ATTTTTTTCTTTCTTTCTCT
1 ATTTTTTGCTTTCTTTCTCT
12186898 ATTTTTTGCATTT-TTTCT
1 ATTTTTTGC-TTTCTTTCT
12186916 TTTTCATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.81
21 3 0.19
ACGTcount: A:0.08, C:0.16, G:0.03, T:0.74
Consensus pattern (20 bp):
ATTTTTTGCTTTCTTTCTCT
Found at i:12190558 original size:17 final size:16
Alignment explanation
Indices: 12190531--12190565 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
12190521 TATGCAAATG
*
12190531 AATGATAAATATATAA
1 AATGATAAATAAATAA
12190547 AATGACTAAATAAATAA
1 AATGA-TAAATAAATAA
12190564 AA
1 AA
12190566 CAAATAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.66, C:0.03, G:0.06, T:0.26
Consensus pattern (16 bp):
AATGATAAATAAATAA
Found at i:12191682 original size:14 final size:15
Alignment explanation
Indices: 12191645--12191682 Score: 62
Period size: 14 Copynumber: 2.7 Consensus size: 15
12191635 AAATAAAATT
12191645 AGAAACAAAAAATAA
1 AGAAACAAAAAATAA
12191660 A-AAACAAAAAATAA
1 AGAAACAAAAAATAA
12191674 AGAAA-AAAA
1 AGAAACAAAA
12191683 TCAACAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 18 0.82
15 4 0.18
ACGTcount: A:0.84, C:0.05, G:0.05, T:0.05
Consensus pattern (15 bp):
AGAAACAAAAAATAA
Found at i:12191693 original size:14 final size:12
Alignment explanation
Indices: 12191614--12191702 Score: 56
Period size: 13 Copynumber: 7.2 Consensus size: 12
12191604 AATAGTATAT
*
12191614 AAAAAAAA-CAA
1 AAAAAAAATAAA
*
12191625 AACAAAAAT-AA
1 AAAAAAAATAAA
* *
12191636 AATAAAATTAGAA
1 AAAAAAAATA-AA
*
12191649 ACAAAAAATAAAA
1 AAAAAAAAT-AAA
12191662 AACAAAAAATAAA
1 AA-AAAAAATAAA
*
12191675 GAAAAAAATCAACA
1 AAAAAAAAT-AA-A
*
12191689 AAAAAAAAGAAA
1 AAAAAAAATAAA
12191701 AA
1 AA
12191703 CCTATGGAAT
Statistics
Matches: 61, Mismatches: 10, Indels: 13
0.73 0.12 0.15
Matches are distributed among these distances:
11 16 0.26
12 10 0.16
13 19 0.31
14 16 0.26
ACGTcount: A:0.82, C:0.07, G:0.03, T:0.08
Consensus pattern (12 bp):
AAAAAAAATAAA
Found at i:12193761 original size:212 final size:210
Alignment explanation
Indices: 12193302--12193717 Score: 481
Period size: 212 Copynumber: 2.0 Consensus size: 210
12193292 TATTTCAAGT
* * * * * *
12193302 TCTCAAAATGTAGTATTAGATTACTCAATTTTTTCAAAAAATGATAATGAACAATTACTATGTTT
1 TCTCTAAATGTAG-ATTAGAGTA-TCAATTTTTTTAAAAAATGACAATGAACAATCACTACGTTT
*
12193367 AGCTTAAAAAAAACACAATAATTGCCATACCCATTATAAATACTCATTAAATCAAAAGCCATCAA
64 AGCTTAAAAAAAACACAATAATTGCCATAACCATTATAAATACTCATTAAATCAAAAGCCATCAA
* * * **
12193432 GTAAAATAGATGAAAAAAGTTAAATGCCAAATAATGTGTTTCTATTCAAAAAAATGCAATAATTG
129 GTAAAACAAATGAAAAAAATTAAATGCCAAATAATGCATTTCTATTCAAAAAAATGCAATAATTG
* * *
12193497 TCATACCCATAATAAAT
194 CCATACACATAATAAAG
* * * * *
12193514 TCTCTAAATGTAGTATTATATTACTCATTTTTTTTAAAAAATGACAATGAACAATCATTGCGTTT
1 TCTCTAAATGTAG-ATTAGAGTA-TCAATTTTTTTAAAAAATGACAATGAACAATCACTACGTTT
* * * *
12193579 AGCTTTAAAAAAACACAGTAATTGTCATAACCATTATAAATACTCATTAAATCAAAAGCTATCAA
64 AGCTTAAAAAAAACACAATAATTGCCATAACCATTATAAATACTCATTAAATCAAAAGCCATCAA
** ** * * * * *
12193644 GTCGAACAAATGAAAAAAAAATTAGTTGTCAAATACTGCATTTTTGTTCAATAAAATGCAATAAT
129 GTAAAACAAATG--AAAAAAATTAAATGCCAAATAATGCATTTCTATTCAAAAAAATGCAATAAT
12193709 TGCCATACA
192 TGCCATACA
12193718 TATGGATGAT
Statistics
Matches: 172, Mismatches: 30, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
212 124 0.72
214 48 0.28
ACGTcount: A:0.45, C:0.14, G:0.09, T:0.32
Consensus pattern (210 bp):
TCTCTAAATGTAGATTAGAGTATCAATTTTTTTAAAAAATGACAATGAACAATCACTACGTTTAG
CTTAAAAAAAACACAATAATTGCCATAACCATTATAAATACTCATTAAATCAAAAGCCATCAAGT
AAAACAAATGAAAAAAATTAAATGCCAAATAATGCATTTCTATTCAAAAAAATGCAATAATTGCC
ATACACATAATAAAG
Found at i:12196052 original size:20 final size:21
Alignment explanation
Indices: 12196016--12196067 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
12196006 TCTGAAATTA
12196016 ATAAAATATTATTTTTTAAAAT
1 ATAAAATATTA-TTTTTAAAAT
*
12196038 ATAAAATATTATTTTTTAAAT
1 ATAAAATATTATTTTTAAAAT
12196059 AT-AAATATT
1 ATAAAATATT
12196068 TAAAAATATC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 7 0.24
21 11 0.38
22 11 0.38
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
ATAAAATATTATTTTTAAAAT
Found at i:12196058 original size:21 final size:22
Alignment explanation
Indices: 12196016--12196067 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
12196006 TCTGAAATTA
12196016 ATAAAATATTATTTTTTAAAAT
1 ATAAAATATTATTTTTTAAAAT
12196038 ATAAAATATTATTTTTT-AAAT
1 ATAAAATATTATTTTTTAAAAT
12196059 AT-AAATATT
1 ATAAAATATT
12196068 TAAAAATATC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 7 0.23
21 6 0.20
22 17 0.57
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
ATAAAATATTATTTTTTAAAAT
Found at i:12196063 original size:28 final size:27
Alignment explanation
Indices: 12196032--12196099 Score: 64
Period size: 30 Copynumber: 2.4 Consensus size: 27
12196022 TATTATTTTT
* * *
12196032 TAAAATATAAAATATTATTTTTTAAATA
1 TAAAAT-TAAAATATCATTATATAAATA
12196060 TAAATATTTAAAAATATCATTATATAAATA
1 TAAA-A-TT-AAAATATCATTATATAAATA
*
12196090 AAAAATTAAA
1 TAAAATTAAA
12196100 TAATTAATTA
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
27 3 0.09
28 6 0.18
29 3 0.09
30 21 0.64
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (27 bp):
TAAAATTAAAATATCATTATATAAATA
Found at i:12204220 original size:14 final size:14
Alignment explanation
Indices: 12204201--12204227 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
12204191 AAGATATGTG
12204201 TTAGATCACCCAAC
1 TTAGATCACCCAAC
12204215 TTAGATCACCCAA
1 TTAGATCACCCAA
12204228 GTCTCTTTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.33, G:0.07, T:0.22
Consensus pattern (14 bp):
TTAGATCACCCAAC
Found at i:12211977 original size:30 final size:30
Alignment explanation
Indices: 12211927--12212004 Score: 119
Period size: 30 Copynumber: 2.7 Consensus size: 30
12211917 TTAAATTTTC
12211927 ATTATCACTTAA--TT-TC-TTTTTCAACA
1 ATTATCACTTAATTTTCTCATTTTTCAACA
12211953 ATTATCACTTAATTTTCTCATTTTTCAACA
1 ATTATCACTTAATTTTCTCATTTTTCAACA
*
12211983 ATTATCACTTAATTTACTCATT
1 ATTATCACTTAATTTTCTCATT
12212005 ATCAAATCTG
Statistics
Matches: 47, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
26 12 0.26
28 2 0.04
29 2 0.04
30 31 0.66
ACGTcount: A:0.31, C:0.19, G:0.00, T:0.50
Consensus pattern (30 bp):
ATTATCACTTAATTTTCTCATTTTTCAACA
Found at i:12212517 original size:14 final size:16
Alignment explanation
Indices: 12212488--12212520 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
12212478 CTTAAAATTA
12212488 ATTGTAATTATTTTAT
1 ATTGTAATTATTTTAT
12212504 ATTGTAA-T-TTTTAT
1 ATTGTAATTATTTTAT
12212518 ATT
1 ATT
12212521 TTCAAACCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 9 0.53
15 1 0.06
16 7 0.41
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (16 bp):
ATTGTAATTATTTTAT
Found at i:12214407 original size:2 final size:2
Alignment explanation
Indices: 12214400--12214459 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
12214390 GCTATTTACA
12214400 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
12214442 CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT
12214460 ATATATATAT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:12214877 original size:33 final size:33
Alignment explanation
Indices: 12214813--12214877 Score: 76
Period size: 33 Copynumber: 2.0 Consensus size: 33
12214803 TTGGTGAAGA
* **
12214813 AAATTCTTTGAACTATTCAGATATGGTTTACTT
1 AAATTCTTTGAACTATTCAGAAATGAATTACTT
* * *
12214846 AAATTCTTTGGAGTATTCATAAATGAATTACT
1 AAATTCTTTGAACTATTCAGAAATGAATTACT
12214878 GGACCCAATT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.34, C:0.11, G:0.12, T:0.43
Consensus pattern (33 bp):
AAATTCTTTGAACTATTCAGAAATGAATTACTT
Found at i:12215093 original size:12 final size:11
Alignment explanation
Indices: 12215059--12215097 Score: 53
Period size: 12 Copynumber: 3.5 Consensus size: 11
12215049 ATTAATAAGA
*
12215059 ATATTTAGTTT
1 ATATTTAATTT
12215070 A-ATTTAATTT
1 ATATTTAATTT
12215080 ATATTTATATTT
1 ATATTTA-ATTT
12215092 ATATTT
1 ATATTT
12215098 TAAAGTATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
10 9 0.36
11 6 0.24
12 10 0.40
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (11 bp):
ATATTTAATTT
Found at i:12219282 original size:23 final size:23
Alignment explanation
Indices: 12219239--12219285 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
12219229 TTCAATTAAG
*
12219239 TTAAACGAATTCGTTCGTAAACA
1 TTAAACGAATTAGTTCGTAAACA
*
12219262 TTAAACGAATATATTTC-TAAACA
1 TTAAACGAAT-TAGTTCGTAAACA
12219285 T
1 T
12219286 ATTTACGAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 17 0.81
24 4 0.19
ACGTcount: A:0.43, C:0.15, G:0.09, T:0.34
Consensus pattern (23 bp):
TTAAACGAATTAGTTCGTAAACA
Found at i:12219343 original size:15 final size:15
Alignment explanation
Indices: 12219303--12219345 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
12219293 AATAATAAAC
*
12219303 AAATCATAACCAAAT
1 AAATCATAAACAAAT
*
12219318 AAAT-TTAAACAAAT
1 AAATCATAAACAAAT
*
12219332 AAATCCTAAACAAA
1 AAATCATAAACAAA
12219346 AATAAACAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 12 0.50
15 12 0.50
ACGTcount: A:0.63, C:0.16, G:0.00, T:0.21
Consensus pattern (15 bp):
AAATCATAAACAAAT
Found at i:12219374 original size:18 final size:20
Alignment explanation
Indices: 12219328--12219376 Score: 57
Period size: 18 Copynumber: 2.5 Consensus size: 20
12219318 AAATTTAAAC
12219328 AAATAAATCCTAAACAAAAAT
1 AAATAAA-CCTAAACAAAAAT
* *
12219349 AAACAAACC-AAA-AAATAT
1 AAATAAACCTAAACAAAAAT
12219367 AAATAAACCT
1 AAATAAACCT
12219377 TAAAATAGCA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
18 13 0.54
19 3 0.12
20 2 0.08
21 6 0.25
ACGTcount: A:0.67, C:0.16, G:0.00, T:0.16
Consensus pattern (20 bp):
AAATAAACCTAAACAAAAAT
Found at i:12219458 original size:11 final size:11
Alignment explanation
Indices: 12219444--12219471 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
12219434 ATAATAAATG
12219444 AACAAATTTTA
1 AACAAATTTTA
12219455 AACAAATTTTA
1 AACAAATTTTA
12219466 AACAAA
1 AACAAA
12219472 CTTATTCATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.61, C:0.11, G:0.00, T:0.29
Consensus pattern (11 bp):
AACAAATTTTA
Found at i:12221350 original size:5 final size:5
Alignment explanation
Indices: 12221340--12221367 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
12221330 ATGTGGAAGA
12221340 CAAGG CAAGG CAAGG CAAGG CAAGG CAA
1 CAAGG CAAGG CAAGG CAAGG CAAGG CAA
12221368 AACAGGCCGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.43, C:0.21, G:0.36, T:0.00
Consensus pattern (5 bp):
CAAGG
Found at i:12222349 original size:21 final size:22
Alignment explanation
Indices: 12222324--12222377 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
12222314 GTACTATGTT
12222324 TAAAAATAAT-TATTAAAA-AAA
1 TAAAAATAATATA-TAAAATAAA
* *
12222345 TAAAACTAATATATAAAATTAA
1 TAAAAATAATATATAAAATAAA
*
12222367 TAAAAAAAATA
1 TAAAAATAATA
12222378 AAATTACTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 14 0.52
22 13 0.48
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (22 bp):
TAAAAATAATATATAAAATAAA
Found at i:12223674 original size:21 final size:20
Alignment explanation
Indices: 12223605--12223685 Score: 74
Period size: 21 Copynumber: 4.0 Consensus size: 20
12223595 GTAGCATAGG
* *
12223605 TTTTTTTATTTTTTATTTTA
1 TTTTTTTATCTTTTGTTTTA
*
12223625 TTTTATTT-TACTTTTGTTTTG
1 TTTT-TTTAT-CTTTTGTTTTA
*
12223646 GTTTTTTATCTATTTGTTTTA
1 TTTTTTTATCT-TTTGTTTTA
* *
12223667 TTTTTTTATGTTTGGTTTT
1 TTTTTTTATCTTTTGTTTT
12223686 TGCTTATTAT
Statistics
Matches: 49, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
20 17 0.35
21 32 0.65
ACGTcount: A:0.11, C:0.02, G:0.09, T:0.78
Consensus pattern (20 bp):
TTTTTTTATCTTTTGTTTTA
Found at i:12234834 original size:5 final size:5
Alignment explanation
Indices: 12234824--12234849 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
12234814 TTCTAGGCTC
12234824 CTTTT CTTTT CTTTT CTTTT CTTTT C
1 CTTTT CTTTT CTTTT CTTTT CTTTT C
12234850 CCCCATCTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (5 bp):
CTTTT
Found at i:12235776 original size:15 final size:15
Alignment explanation
Indices: 12235736--12235775 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
12235726 TAATAAAATT
12235736 TTTTTAATTTTAATA
1 TTTTTAATTTTAATA
*
12235751 TATTTAATTTTAA-A
1 TTTTTAATTTTAATA
*
12235765 TTTTAAATTTT
1 TTTTTAATTTT
12235776 TTATAGAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
14 10 0.45
15 12 0.55
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
TTTTTAATTTTAATA
Found at i:12235837 original size:13 final size:14
Alignment explanation
Indices: 12235813--12235841 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
12235803 AATGTCAAAA
12235813 AATTTATAAAATAT
1 AATTTATAAAATAT
12235827 AATTT-TAAAATAT
1 AATTTATAAAATAT
12235840 AA
1 AA
12235842 AAAGTAAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
AATTTATAAAATAT
Found at i:12240649 original size:22 final size:22
Alignment explanation
Indices: 12240618--12240671 Score: 58
Period size: 22 Copynumber: 2.4 Consensus size: 22
12240608 CGGTTGGTTA
12240618 ATTTAAAATTT-TGAATTGATAA-
1 ATTT-AAATTTAT-AATTGATAAG
*
12240640 ATATTAAATTTATAATTTATAAG
1 AT-TTAAATTTATAATTGATAAG
12240663 ATTTAAATT
1 ATTTAAATT
12240672 CAATTTTGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
22 23 0.82
23 5 0.18
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.48
Consensus pattern (22 bp):
ATTTAAATTTATAATTGATAAG
Found at i:12244422 original size:2 final size:2
Alignment explanation
Indices: 12244410--12244486 Score: 57
Period size: 2 Copynumber: 36.5 Consensus size: 2
12244400 TATTATTATC
* * *
12244410 AT AT AT CAT AT AT AA AT AT AT A- AA AT AT CAT AT AT AA AT AT AT
1 AT AT AT -AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT
* *
12244453 AT AA AT AT CAT CAT AT AT CAT AT AT AA AT AT AT A
1 AT AT AT AT -AT -AT AT AT -AT AT AT AT AT AT AT A
12244487 AAAAAAATTT
Statistics
Matches: 61, Mismatches: 9, Indels: 10
0.76 0.11 0.12
Matches are distributed among these distances:
1 1 0.02
2 49 0.80
3 11 0.18
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (2 bp):
AT
Found at i:12244440 original size:22 final size:22
Alignment explanation
Indices: 12244412--12244485 Score: 103
Period size: 22 Copynumber: 3.2 Consensus size: 22
12244402 TTATTATCAT
12244412 ATATCATATATAAATATATAAA
1 ATATCATATATAAATATATAAA
12244434 ATATCATATATAAATATATATAA
1 ATATCATATATAAATATATA-AA
*
12244457 ATATCATCATATATCATATATAAA
1 ATATCAT-ATATA-AATATATAAA
12244481 TATAT
1 -ATAT
12244486 AAAAAAAATT
Statistics
Matches: 47, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
22 20 0.43
23 9 0.19
24 7 0.15
25 11 0.23
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATCATATATAAATATATAAA
Found at i:12244454 original size:10 final size:10
Alignment explanation
Indices: 12244417--12244486 Score: 77
Period size: 10 Copynumber: 6.5 Consensus size: 10
12244407 ATCATATATC
12244417 ATATATAAAT
1 ATATATAAAT
*
12244427 ATATAAAATAT
1 ATATATAA-AT
12244438 CATATATAAAT
1 -ATATATAAAT
12244449 ATATATAAAT
1 ATATATAAAT
*
12244459 ATCATCATATAT
1 AT-AT-ATAAAT
12244471 CATATATAAAT
1 -ATATATAAAT
12244482 ATATA
1 ATATA
12244487 AAAAAAATTT
Statistics
Matches: 51, Mismatches: 4, Indels: 10
0.78 0.06 0.15
Matches are distributed among these distances:
10 24 0.47
11 11 0.22
12 14 0.27
13 2 0.04
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.39
Consensus pattern (10 bp):
ATATATAAAT
Found at i:12244476 original size:33 final size:32
Alignment explanation
Indices: 12244417--12244486 Score: 113
Period size: 33 Copynumber: 2.2 Consensus size: 32
12244407 ATCATATATC
12244417 ATATATAAATATATAAAATATCATATATAAAT
1 ATATATAAATATATAAAATATCATATATAAAT
* *
12244449 ATATATAAATATCATCATATATCATATATAAAT
1 ATATATAAATAT-ATAAAATATCATATATAAAT
12244482 ATATA
1 ATATA
12244487 AAAAAAATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
32 12 0.34
33 23 0.66
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.39
Consensus pattern (32 bp):
ATATATAAATATATAAAATATCATATATAAAT
Found at i:12244681 original size:13 final size:13
Alignment explanation
Indices: 12244663--12244688 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
12244653 CCCCAGTGAC
12244663 CCTCTTTTTATAT
1 CCTCTTTTTATAT
12244676 CCTCTTTTTATAT
1 CCTCTTTTTATAT
12244689 TCGATGTGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.23, G:0.00, T:0.62
Consensus pattern (13 bp):
CCTCTTTTTATAT
Found at i:12245758 original size:25 final size:25
Alignment explanation
Indices: 12245730--12245780 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
12245720 TTCTCATAAT
12245730 TAATTATATTTATATTATAGTTATG
1 TAATTATATTTATATTATAGTTATG
*
12245755 TAATTATATTTATTTTATAGTTATG
1 TAATTATATTTATATTATAGTTATG
12245780 T
1 T
12245781 TCCTTTTTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.59
Consensus pattern (25 bp):
TAATTATATTTATATTATAGTTATG
Found at i:12245915 original size:19 final size:19
Alignment explanation
Indices: 12245893--12245929 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
12245883 GATATTTTAA
*
12245893 TGTTAATCGTGTTTAATCT
1 TGTTAATCATGTTTAATCT
12245912 TGTTAATCATGTTTAATC
1 TGTTAATCATGTTTAATC
12245930 ATATTAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.24, C:0.11, G:0.14, T:0.51
Consensus pattern (19 bp):
TGTTAATCATGTTTAATCT
Found at i:12245936 original size:19 final size:19
Alignment explanation
Indices: 12245895--12245942 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
12245885 TATTTTAATG
* * *
12245895 TTAATCGTGTTTAATCTTG
1 TTAATCATGTTTAATCATA
12245914 TTAATCATGTTTAATCATA
1 TTAATCATGTTTAATCATA
*
12245933 TTAATTATGT
1 TTAATCATGT
12245943 CCTATCATGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.29, C:0.08, G:0.10, T:0.52
Consensus pattern (19 bp):
TTAATCATGTTTAATCATA
Found at i:12246446 original size:14 final size:15
Alignment explanation
Indices: 12246427--12246461 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
12246417 AAATCATGAT
12246427 CAAATAAA-TTTAAA
1 CAAATAAATTTTAAA
12246441 CAAATAAATTTTAAA
1 CAAATAAATTTTAAA
*
12246456 CTAATA
1 CAAATA
12246462 TAAACGAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.42
15 11 0.58
ACGTcount: A:0.60, C:0.09, G:0.00, T:0.31
Consensus pattern (15 bp):
CAAATAAATTTTAAA
Found at i:12246481 original size:20 final size:20
Alignment explanation
Indices: 12246453--12246491 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
12246443 AATAAATTTT
*
12246453 AAACTAATATAAACGAATCC
1 AAACAAATATAAACGAATCC
12246473 AAACAAATATAAACGAATC
1 AAACAAATATAAACGAATC
12246492 TTAAAATAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.59, C:0.18, G:0.05, T:0.18
Consensus pattern (20 bp):
AAACAAATATAAACGAATCC
Found at i:12247965 original size:26 final size:26
Alignment explanation
Indices: 12247936--12247987 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
12247926 AGCAATGGCC
12247936 AAGATTAATATCAATAACAGCAGAGG
1 AAGATTAATATCAATAACAGCAGAGG
12247962 AAGATTAATATCAATAACAGCAGAGG
1 AAGATTAATATCAATAACAGCAGAGG
12247988 CAACCAAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.50, C:0.12, G:0.19, T:0.19
Consensus pattern (26 bp):
AAGATTAATATCAATAACAGCAGAGG
Found at i:12248854 original size:27 final size:29
Alignment explanation
Indices: 12248821--12248874 Score: 76
Period size: 27 Copynumber: 1.9 Consensus size: 29
12248811 ATATTATATT
*
12248821 ATTAATAAAT-AAATATTAAT-TTTTTAA
1 ATTAATAAATAAAAAATTAATATTTTTAA
*
12248848 ATTAATATATAAAAAATTAATATTTTT
1 ATTAATAAATAAAAAATTAATATTTTT
12248875 TAAAATACTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 9 0.39
28 9 0.39
29 5 0.22
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (29 bp):
ATTAATAAATAAAAAATTAATATTTTTAA
Found at i:12255403 original size:38 final size:39
Alignment explanation
Indices: 12255352--12255427 Score: 127
Period size: 39 Copynumber: 2.0 Consensus size: 39
12255342 ACGTTGGATT
12255352 CTCTTGAATTTGAAGAA-AGGATACAGAGCATTTAACTA
1 CTCTTGAATTTGAAGAATAGGATACAGAGCATTTAACTA
* *
12255390 CTCTTGAATTTGAAGAATAGGATACTGGGCATTTAACT
1 CTCTTGAATTTGAAGAATAGGATACAGAGCATTTAACT
12255428 TTATTATTGG
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
38 17 0.49
39 18 0.51
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.32
Consensus pattern (39 bp):
CTCTTGAATTTGAAGAATAGGATACAGAGCATTTAACTA
Found at i:12261035 original size:33 final size:34
Alignment explanation
Indices: 12260971--12261036 Score: 89
Period size: 34 Copynumber: 2.0 Consensus size: 34
12260961 GCGTTTCATA
*
12260971 ATTTTTAAAAATAAATGTCCAAAAAGCTTTAAAG
1 ATTTTTAAAAATAAATGTCCAAAAAGATTTAAAG
* * *
12261005 ATTTTTAAAATTAAATTTTCAAAAA-ATTTAAA
1 ATTTTTAAAAATAAATGTCCAAAAAGATTTAAA
12261037 AAAAAATTGG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
33 6 0.21
34 22 0.79
ACGTcount: A:0.52, C:0.06, G:0.05, T:0.38
Consensus pattern (34 bp):
ATTTTTAAAAATAAATGTCCAAAAAGATTTAAAG
Found at i:12261083 original size:34 final size:34
Alignment explanation
Indices: 12261045--12261110 Score: 98
Period size: 34 Copynumber: 1.9 Consensus size: 34
12261035 AAAAAAAATT
*
12261045 GGAAATTCATTT-TAAAAAACCTTTAAGAACTTCC
1 GGAAATTCATTTCCAAAAAACCTTTAA-AACTTCC
*
12261079 GGAAATTCATTTCCAAAAACCCTTTAAAACTT
1 GGAAATTCATTTCCAAAAAACCTTTAAAACTT
12261111 TTCAAAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.32
Consensus pattern (34 bp):
GGAAATTCATTTCCAAAAAACCTTTAAAACTTCC
Found at i:12261120 original size:35 final size:34
Alignment explanation
Indices: 12261047--12261133 Score: 86
Period size: 35 Copynumber: 2.5 Consensus size: 34
12261037 AAAAAATTGG
* * **
12261047 AAATTCATTTTAAAAAACCTTTAAGAACTTCCGG
1 AAATTCATTTCAAAAACCCTTTAAGAACTTCCAA
*
12261081 AAATTCATTTCCAAAAACCCTTTAA-AACTTTTCAA
1 AAATTCATTT-CAAAAACCCTTTAAGAAC-TTCCAA
*
12261116 AAATTTATTTTCAAAAAC
1 AAATTCA-TTTCAAAAAC
12261134 TTATTTATAA
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
34 13 0.30
35 28 0.64
36 3 0.07
ACGTcount: A:0.44, C:0.18, G:0.03, T:0.34
Consensus pattern (34 bp):
AAATTCATTTCAAAAACCCTTTAAGAACTTCCAA
Found at i:12261128 original size:14 final size:14
Alignment explanation
Indices: 12261109--12261139 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
12261099 CCTTTAAAAC
*
12261109 TTTTCAAAAATTTA
1 TTTTCAAAAACTTA
12261123 TTTTCAAAAACTTA
1 TTTTCAAAAACTTA
12261137 TTT
1 TTT
12261140 ATAAGAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.39, C:0.10, G:0.00, T:0.52
Consensus pattern (14 bp):
TTTTCAAAAACTTA
Found at i:12274120 original size:14 final size:15
Alignment explanation
Indices: 12274098--12274130 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
12274088 GAAAATAATG
*
12274098 ATTTTATTAAA-TTA
1 ATTTGATTAAATTTA
12274112 ATTTGATTAAATTTA
1 ATTTGATTAAATTTA
12274127 ATTT
1 ATTT
12274131 ATTTATAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (15 bp):
ATTTGATTAAATTTA
Found at i:12275544 original size:49 final size:50
Alignment explanation
Indices: 12275478--12275576 Score: 157
Period size: 49 Copynumber: 2.0 Consensus size: 50
12275468 ATTTGATTTT
*
12275478 CCAAGAAAATTGTCATATGCATTTTG-TTGAAATTCTAAAAA-CCTTTGAG
1 CCAAGAAAATTGTCATATGCA-TTTGATTGAAACTCTAAAAATCCTTTGAG
*
12275527 CCAAGAAGATTGTCATATGCATTTGATTGAAACTCTAAAAATCCTTTGAG
1 CCAAGAAAATTGTCATATGCATTTGATTGAAACTCTAAAAATCCTTTGAG
12275577 TACAAAGTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
48 4 0.09
49 34 0.74
50 8 0.17
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.33
Consensus pattern (50 bp):
CCAAGAAAATTGTCATATGCATTTGATTGAAACTCTAAAAATCCTTTGAG
Found at i:12276192 original size:26 final size:25
Alignment explanation
Indices: 12276143--12276208 Score: 89
Period size: 26 Copynumber: 2.6 Consensus size: 25
12276133 TTAACATAAC
12276143 TATTAAAATATTAAAACTTATTTAT
1 TATTAAAATATTAAAACTTATTTAT
*
12276168 TATTAAAGTATATTGAAA-TTATTTAT
1 TATTAAA--ATATTAAAACTTATTTAT
12276194 TATTAAAATTATTAA
1 TATTAAAA-TATTAA
12276209 TATTCTCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
24 1 0.03
25 12 0.33
26 15 0.42
27 8 0.22
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (25 bp):
TATTAAAATATTAAAACTTATTTAT
Found at i:12276264 original size:19 final size:18
Alignment explanation
Indices: 12276229--12276272 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
12276219 TAATTATATT
*
12276229 TTAATAATAATATTTAATA
1 TTAA-AATAATATTTAAAA
*
12276248 TTAAAATATTATATTAAAA
1 TTAAAATAATAT-TTAAAA
12276267 TTAAAA
1 TTAAAA
12276273 AAAACTTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TTAAAATAATATTTAAAA
Found at i:12276395 original size:38 final size:37
Alignment explanation
Indices: 12276348--12276420 Score: 103
Period size: 38 Copynumber: 1.9 Consensus size: 37
12276338 ACTATTCTTA
*
12276348 AATATTATTTTTATTAATA-TTATAATATTAAAATAGC
1 AATATTATTTTTA-AAATATTTATAATATTAAAATAGC
*
12276385 AATATTTATTTTTAAAATATTTATACTATTAAAATA
1 AATA-TTATTTTTAAAATATTTATAATATTAAAATA
12276421 TTTAGATTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
37 8 0.25
38 24 0.75
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.49
Consensus pattern (37 bp):
AATATTATTTTTAAAATATTTATAATATTAAAATAGC
Found at i:12276405 original size:15 final size:16
Alignment explanation
Indices: 12276385--12276424 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 16
12276375 TTAAAATAGC
*
12276385 AATATTTAT-TTTTAA
1 AATATTTATATATTAA
12276400 AATATTTATACTATTAA
1 AATATTTATA-TATTAA
12276417 AATATTTA
1 AATATTTA
12276425 GATTTTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 9 0.41
17 13 0.59
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (16 bp):
AATATTTATATATTAA
Found at i:12276598 original size:17 final size:19
Alignment explanation
Indices: 12276561--12276601 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
12276551 ATATTAAGAA
*
12276561 ATTATTAAAATATATTAAT
1 ATTATGAAAATATATTAAT
12276580 ATTATGAAAATA-A-TAAT
1 ATTATGAAAATATATTAAT
12276597 ATTAT
1 ATTAT
12276602 TTAACGTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 9 0.43
18 1 0.05
19 11 0.52
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (19 bp):
ATTATGAAAATATATTAAT
Found at i:12277662 original size:168 final size:169
Alignment explanation
Indices: 12277324--12277663 Score: 673
Period size: 168 Copynumber: 2.0 Consensus size: 169
12277314 TATTTAAAAT
12277324 TTCTTAAAATTAAGAGTTTTGTTATAAATTTTAAATCACAATTACGTGATTTTAATAAAAGGCAA
1 TTCTTAAAATTAAGAGTTTTGTTATAAATTTTAAATCACAATTACGTGATTTTAATAAAAGGCAA
12277389 TTTAATTTTCTTGTTTTTTTTTTTTTTTAAGAATACTATTTCTCTAATCAAGTATTAAATATATT
66 TTTAATTTTCTTGTTTTTTTTTTTTTTTAAGAATACTATTTCTCTAATCAAGTATTAAATATATT
12277454 TTTTTGTCAATTATTGATCTTATATACTATAATTAAGAG
131 TTTTTGTCAATTATTGATCTTATATACTATAATTAAGAG
12277493 TTCTTAAAATTAAGAGTTTTGTTATAAATTTTAAATCACAATTACGTGATTTTAATAAAAGGCAA
1 TTCTTAAAATTAAGAGTTTTGTTATAAATTTTAAATCACAATTACGTGATTTTAATAAAAGGCAA
12277558 TTTAATTTTCTTG-TTTTTTTTTTTTTTAAGAATACTATTTCTCTAATCAAGTATTAAATATATT
66 TTTAATTTTCTTGTTTTTTTTTTTTTTTAAGAATACTATTTCTCTAATCAAGTATTAAATATATT
12277622 TTTTTGTCAATTATTGATCTTATATACTATAATTAAGAG
131 TTTTTGTCAATTATTGATCTTATATACTATAATTAAGAG
12277661 TTC
1 TTC
12277664 AATATTTTAT
Statistics
Matches: 171, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
168 93 0.54
169 78 0.46
ACGTcount: A:0.34, C:0.08, G:0.08, T:0.50
Consensus pattern (169 bp):
TTCTTAAAATTAAGAGTTTTGTTATAAATTTTAAATCACAATTACGTGATTTTAATAAAAGGCAA
TTTAATTTTCTTGTTTTTTTTTTTTTTTAAGAATACTATTTCTCTAATCAAGTATTAAATATATT
TTTTTGTCAATTATTGATCTTATATACTATAATTAAGAG
Found at i:12278113 original size:21 final size:20
Alignment explanation
Indices: 12278087--12278144 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 20
12278077 TTATATATCA
*
12278087 AACACACTATTGTTTGGTAC
1 AACACACTCTTGTTTGGTAC
* *
12278107 TAACACACCCTTGATTGGTAC
1 -AACACACTCTTGTTTGGTAC
12278128 ATACACACTCTTGTTTG
1 A-ACACACTCTTGTTTG
12278145 ATATATAAGA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
20 1 0.03
21 30 0.97
ACGTcount: A:0.28, C:0.24, G:0.14, T:0.34
Consensus pattern (20 bp):
AACACACTCTTGTTTGGTAC
Found at i:12278197 original size:17 final size:18
Alignment explanation
Indices: 12278170--12278209 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
12278160 ATATGATAGG
12278170 ATAATATAAGATGATATT
1 ATAATATAAGATGATATT
*
12278188 ATAA-ATAAGATTATATT
1 ATAATATAAGATGATATT
12278205 A-AATA
1 ATAATA
12278210 ATGTCACATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 2 0.10
17 14 0.70
18 4 0.20
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (18 bp):
ATAATATAAGATGATATT
Found at i:12278670 original size:16 final size:18
Alignment explanation
Indices: 12278649--12278685 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
12278639 ATTATTATTC
12278649 TTTAAAGT-TT-ATATAA
1 TTTAAAGTATTGATATAA
*
12278665 TTTAAATTATTGATATAA
1 TTTAAAGTATTGATATAA
12278683 TTT
1 TTT
12278686 TTAAAGGTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 7 0.39
17 2 0.11
18 9 0.50
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (18 bp):
TTTAAAGTATTGATATAA
Found at i:12282938 original size:110 final size:111
Alignment explanation
Indices: 12282792--12282995 Score: 342
Period size: 110 Copynumber: 1.8 Consensus size: 111
12282782 TTAAAAATAA
*
12282792 ATTAGAAATAAAAAATACTATCCAAATACAATTTTAAATCG-GGTCTAAATATTTAATAGTCAAA
1 ATTAGAAATAAAAAATACTATCCAAATACAACTTTAAA-CGAGGTCTAAATATTTAATAGTCAAA
12282856 AAATAAAAAGAAATACGTGTGAAATTAATTTGGAAAATTTGAAAACAG
65 AAA-AAAAAGAAATACGTGTGAAATTAATTTGGAAAATTTGAAAACAG
* *
12282904 ATTA-AAA-AAAAAATACTATCCAAATACAACTTTAAACGAGGTCTAAATATTTAATAGTCGAGA
1 ATTAGAAATAAAAAATACTATCCAAATACAACTTTAAACGAGGTCTAAATATTTAATAGTCAAAA
12282967 AAAAAAAGAAATACGTGTGAAATTAATTT
66 AAAAAAAGAAATACGTGTGAAATTAATTT
12282996 TGCATTTGTG
Statistics
Matches: 88, Mismatches: 3, Indels: 5
0.92 0.03 0.05
Matches are distributed among these distances:
109 29 0.33
110 52 0.59
111 3 0.03
112 4 0.05
ACGTcount: A:0.52, C:0.09, G:0.11, T:0.28
Consensus pattern (111 bp):
ATTAGAAATAAAAAATACTATCCAAATACAACTTTAAACGAGGTCTAAATATTTAATAGTCAAAA
AAAAAAAGAAATACGTGTGAAATTAATTTGGAAAATTTGAAAACAG
Found at i:12297542 original size:49 final size:49
Alignment explanation
Indices: 12297470--12297569 Score: 173
Period size: 49 Copynumber: 2.0 Consensus size: 49
12297460 TAGATAGTTT
*
12297470 ATCTTTACTCTAGTTGTAGCTTTTTCATGTCTTGGATAAAGCTAGTCTG
1 ATCTTTACTCTAGTTGTAGCTTTTGCATGTCTTGGATAAAGCTAGTCTG
* *
12297519 ATCTTTGCTCTAGTTGTAGCTTTTGCATGTCTTGGATAAAGCTGGTCTG
1 ATCTTTACTCTAGTTGTAGCTTTTGCATGTCTTGGATAAAGCTAGTCTG
12297568 AT
1 AT
12297570 GCGCATTATT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.19, C:0.16, G:0.21, T:0.44
Consensus pattern (49 bp):
ATCTTTACTCTAGTTGTAGCTTTTGCATGTCTTGGATAAAGCTAGTCTG
Found at i:12314170 original size:21 final size:21
Alignment explanation
Indices: 12314146--12314188 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
12314136 AATGGTGAAA
12314146 AATATATATAAATATAAAATT
1 AATATATATAAATATAAAATT
12314167 AATATATATAAATATAAAATT
1 AATATATATAAATATAAAATT
12314188 A
1 A
12314189 TCTCACTTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (21 bp):
AATATATATAAATATAAAATT
Found at i:12315553 original size:13 final size:13
Alignment explanation
Indices: 12315535--12315565 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
12315525 TCACATATCA
*
12315535 TTTTTCTTTTTCT
1 TTTTTCTTTTGCT
12315548 TTTTTCTTTTGCT
1 TTTTTCTTTTGCT
12315561 TTTTT
1 TTTTT
12315566 AGTTATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.00, C:0.13, G:0.03, T:0.84
Consensus pattern (13 bp):
TTTTTCTTTTGCT
Found at i:12315714 original size:19 final size:19
Alignment explanation
Indices: 12315692--12315730 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
12315682 GTGGACCAAC
*
12315692 TTTTTTTATGTTTT-ATATA
1 TTTTTTAAT-TTTTAATATA
12315711 TTTTTTAATTTTTAATATA
1 TTTTTTAATTTTTAATATA
12315730 T
1 T
12315731 AATAATTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.72
Consensus pattern (19 bp):
TTTTTTAATTTTTAATATA
Found at i:12315917 original size:17 final size:17
Alignment explanation
Indices: 12315897--12315931 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
12315887 TAATAAGATT
**
12315897 TTTTTTTATGTTTTATA
1 TTTTTTTACATTTTATA
12315914 TTTTTTTACATTTTATA
1 TTTTTTTACATTTTATA
12315931 T
1 T
12315932 CAACTATATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.20, C:0.03, G:0.03, T:0.74
Consensus pattern (17 bp):
TTTTTTTACATTTTATA
Found at i:12324565 original size:12 final size:13
Alignment explanation
Indices: 12324548--12324576 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
12324538 GTTCTTTTCA
12324548 TTATTTATTTAT-
1 TTATTTATTTATC
12324560 TTATTTATTTATC
1 TTATTTATTTATC
12324573 TTAT
1 TTAT
12324577 CAACATGAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.72
Consensus pattern (13 bp):
TTATTTATTTATC
Found at i:12324928 original size:34 final size:34
Alignment explanation
Indices: 12324889--12324958 Score: 113
Period size: 34 Copynumber: 2.1 Consensus size: 34
12324879 TCTATCAAAT
12324889 AAATTTTCAAAAATTAATTTATGAAAACTTTTAA
1 AAATTTTCAAAAATTAATTTATGAAAACTTTTAA
* **
12324923 AAATTTTCAAAAATTAATTTTTGAAAGTTTTTAA
1 AAATTTTCAAAAATTAATTTATGAAAACTTTTAA
12324957 AA
1 AA
12324959 TCTTTCGAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.43
Consensus pattern (34 bp):
AAATTTTCAAAAATTAATTTATGAAAACTTTTAA
Found at i:12325324 original size:68 final size:67
Alignment explanation
Indices: 12325246--12325378 Score: 153
Period size: 68 Copynumber: 2.0 Consensus size: 67
12325236 GAATTTTCAA
** *
12325246 AAAATCTT-AAAAGTTCCAAAAATATATTTTTTTGAAG-CTTTTAAGATTTTTCAAAAATTTATT
1 AAAATCTTAAAAAGTTCCAAAAATATA-TTTTCGGAAGTC-TTTAAAATTTTTCAAAAATTTATT
12325309 TTTG
64 TTTG
* ** * *
12325313 AAAATCTTTAAAAATTTTTAAAAATTTATTTTCGGAAGTCTTTAAAATTTTTTAAAAATTTATTT
1 AAAATC-TTAAAAAGTTCCAAAAATATATTTTCGGAAGTCTTTAAAATTTTTCAAAAATTTATTT
12325378 T
65 T
12325379 CAAAAACTTA
Statistics
Matches: 55, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
67 6 0.11
68 34 0.62
69 15 0.27
ACGTcount: A:0.40, C:0.06, G:0.06, T:0.48
Consensus pattern (67 bp):
AAAATCTTAAAAAGTTCCAAAAATATATTTTCGGAAGTCTTTAAAATTTTTCAAAAATTTATTTT
TG
Found at i:12325330 original size:35 final size:33
Alignment explanation
Indices: 12325285--12325384 Score: 128
Period size: 34 Copynumber: 2.9 Consensus size: 33
12325275 TTTTGAAGCT
* *
12325285 TTTAAGATTTTTCAAAAATTTATTTTTGAAAATC
1 TTTAAAATTTTT-AAAAATTTATTTTCGAAAATC
* *
12325319 TTTAAAAATTTTTAAAAATTTATTTTCGGAAGTC
1 TTT-AAAATTTTTAAAAATTTATTTTCGAAAATC
*
12325353 TTTAAAATTTTTTAAAAATTTATTTTCAAAAA
1 TTTAAAA-TTTTTAAAAATTTATTTTCGAAAA
12325385 CTTATTCAAA
Statistics
Matches: 57, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
33 4 0.07
34 45 0.79
35 8 0.14
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (33 bp):
TTTAAAATTTTTAAAAATTTATTTTCGAAAATC
Found at i:12325332 original size:10 final size:10
Alignment explanation
Indices: 12325306--12325339 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
12325296 TCAAAAATTT
*
12325306 ATTTTTGAAA
1 ATTTTTAAAA
*
12325316 ATCTTTAAAA
1 ATTTTTAAAA
12325326 ATTTTTAAAA
1 ATTTTTAAAA
12325336 ATTT
1 ATTT
12325340 ATTTTCGGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (10 bp):
ATTTTTAAAA
Found at i:12329640 original size:23 final size:20
Alignment explanation
Indices: 12329612--12329664 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 20
12329602 ATTTGTTATA
12329612 AATTTATATAAATATATTAAAT
1 AATTTATATAAAT-TA-TAAAT
12329634 AAGTTTATAT-AATTATAAAT
1 AA-TTTATATAAATTATAAAT
*
12329654 AATTTGTATAA
1 AATTTATATAA
12329665 TTGTATATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
19 6 0.21
20 8 0.29
21 2 0.07
22 5 0.18
23 7 0.25
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (20 bp):
AATTTATATAAATTATAAAT
Found at i:12329665 original size:19 final size:20
Alignment explanation
Indices: 12329609--12329666 Score: 64
Period size: 23 Copynumber: 2.8 Consensus size: 20
12329599 ATAATTTGTT
*
12329609 ATAAATTTATATAAATATATTAA
1 ATAAGTTTATAT-AAT-TA-TAA
12329632 ATAAGTTTATATAATTATAA
1 ATAAGTTTATATAATTATAA
*
12329652 ATAA-TTTGTATAATT
1 ATAAGTTTATATAATT
12329667 GTATATAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 10 0.30
20 7 0.21
21 2 0.06
22 3 0.09
23 11 0.33
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (20 bp):
ATAAGTTTATATAATTATAA
Found at i:12329731 original size:23 final size:24
Alignment explanation
Indices: 12329699--12329744 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 24
12329689 TATATAAATT
12329699 TATATAATTATATATTTAAAATAC
1 TATATAATTATATATTTAAAATAC
12329723 TATAT-ATTATATATTTAAAATA
1 TATATAATTATATATTTAAAATA
12329745 TTTTTATCCC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 17 0.77
24 5 0.23
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (24 bp):
TATATAATTATATATTTAAAATAC
Found at i:12330839 original size:10 final size:9
Alignment explanation
Indices: 12330822--12330846 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
12330812 AATATATATA
12330822 AAAATTTTT
1 AAAATTTTT
12330831 AAAATTTTT
1 AAAATTTTT
12330840 AAAATTT
1 AAAATTT
12330847 ATGCACACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (9 bp):
AAAATTTTT
Found at i:12335851 original size:21 final size:22
Alignment explanation
Indices: 12335820--12335860 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
12335810 TTTTTAAAAT
*
12335820 TTTAATAAAAATAATAAATAAA
1 TTTAATAAAAATAAAAAATAAA
12335842 TTTAAT-AAAATAAAAAATA
1 TTTAATAAAAATAAAAAATA
12335861 TATTATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (22 bp):
TTTAATAAAAATAAAAAATAAA
Found at i:12336548 original size:2 final size:2
Alignment explanation
Indices: 12336541--12336568 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
12336531 GAAACGCTTG
12336541 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
12336569 TTGGAAATTT
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:12342521 original size:31 final size:31
Alignment explanation
Indices: 12342483--12342542 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
12342473 TATTTTATAT
*
12342483 TTTAAATTATAATAATAAAATTTTTAAATTA
1 TTTAAATTATAATAATAAAATTTTAAAATTA
12342514 TTTAAATTATAATAATAAAATTTTAAAAT
1 TTTAAATTATAATAATAAAATTTTAAAAT
12342543 CAGTTAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (31 bp):
TTTAAATTATAATAATAAAATTTTAAAATTA
Found at i:12342550 original size:31 final size:31
Alignment explanation
Indices: 12342484--12342550 Score: 107
Period size: 31 Copynumber: 2.2 Consensus size: 31
12342474 ATTTTATATT
* * *
12342484 TTAAATTATAATAATAAAATTTTTAAATTAT
1 TTAAATTATAATAATAAAATTTTAAAATCAG
12342515 TTAAATTATAATAATAAAATTTTAAAATCAG
1 TTAAATTATAATAATAAAATTTTAAAATCAG
12342546 TTAAA
1 TTAAA
12342551 AAATTCAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (31 bp):
TTAAATTATAATAATAAAATTTTAAAATCAG
Found at i:12343618 original size:2 final size:2
Alignment explanation
Indices: 12343611--12343641 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
12343601 TTGAAGTTTT
12343611 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
12343642 TTGCAGCAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:12358953 original size:22 final size:22
Alignment explanation
Indices: 12358928--12358974 Score: 78
Period size: 22 Copynumber: 2.1 Consensus size: 22
12358918 TTGATGAATT
12358928 CACTCATTCACTC-TCAATTACA
1 CACTCATTCACTCTTC-ATTACA
12358950 CACTCATTCACTCTTCATTACA
1 CACTCATTCACTCTTCATTACA
12358972 CAC
1 CAC
12358975 GACAGGCCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 22 0.92
23 2 0.08
ACGTcount: A:0.30, C:0.38, G:0.00, T:0.32
Consensus pattern (22 bp):
CACTCATTCACTCTTCATTACA
Found at i:12365870 original size:4 final size:4
Alignment explanation
Indices: 12365861--12365893 Score: 50
Period size: 4 Copynumber: 8.5 Consensus size: 4
12365851 CATATAATTG
*
12365861 TTTC TTTC TTTC TTTC -TTC TTTC TTTT TTTC TT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TT
12365894 ATCAATTATC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
3 3 0.12
4 23 0.88
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (4 bp):
TTTC
Found at i:12365882 original size:15 final size:15
Alignment explanation
Indices: 12365862--12365893 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
12365852 ATATAATTGT
12365862 TTCTTTCTTTCTTTC
1 TTCTTTCTTTCTTTC
*
12365877 TTCTTTCTTTTTTTC
1 TTCTTTCTTTCTTTC
12365892 TT
1 TT
12365894 ATCAATTATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (15 bp):
TTCTTTCTTTCTTTC
Found at i:12367881 original size:25 final size:27
Alignment explanation
Indices: 12367848--12367905 Score: 75
Period size: 25 Copynumber: 2.2 Consensus size: 27
12367838 AATTATAACA
* *
12367848 AAATATTTAATATCATATAT-AATT-T
1 AAATTTTTAATATAATATATAAATTAT
*
12367873 AAATTTTTAATATAATATTTAAATTAT
1 AAATTTTTAATATAATATATAAATTAT
12367900 AAATTT
1 AAATTT
12367906 AATACGACAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 17 0.61
26 4 0.14
27 7 0.25
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (27 bp):
AAATTTTTAATATAATATATAAATTAT
Found at i:12367908 original size:20 final size:20
Alignment explanation
Indices: 12367869--12367909 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
12367859 ATCATATATA
* *
12367869 ATTTAAATTTTTAATATAAT
1 ATTTAAATTATAAATATAAT
*
12367889 ATTTAAATTATAAATTTAAT
1 ATTTAAATTATAAATATAAT
12367909 A
1 A
12367910 CGACATAAAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
ATTTAAATTATAAATATAAT
Found at i:12368006 original size:30 final size:30
Alignment explanation
Indices: 12367952--12368045 Score: 111
Period size: 30 Copynumber: 3.2 Consensus size: 30
12367942 TTAATAATCA
* *
12367952 TTTAAATTTTTA-TATTAATTAATTAAAAT
1 TTTAAATTTTTATTTTTATTTAATTAAAAT
12367981 TTTAAATTTTTATTTTTATTTAATT-AAAT
1 TTTAAATTTTTATTTTTATTTAATTAAAAT
* * * *
12368010 TCTTATATATTTATTTTTATTCAATTAAACT
1 T-TTAAATTTTTATTTTTATTTAATTAAAAT
12368041 TTTAA
1 TTTAA
12368046 TTAAACTGAA
Statistics
Matches: 55, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
29 17 0.31
30 34 0.62
31 4 0.07
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (30 bp):
TTTAAATTTTTATTTTTATTTAATTAAAAT
Found at i:12368022 original size:24 final size:22
Alignment explanation
Indices: 12367982--12368025 Score: 61
Period size: 24 Copynumber: 1.9 Consensus size: 22
12367972 AATTAAAATT
*
12367982 TTAAATTTTTATTTTTATTTAA
1 TTAAATTTTTATATTTATTTAA
12368004 TTAAATTCTTATATATTTATTT
1 TTAAATT-TT-TATATTTATTT
12368026 TTATTCAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
23 2 0.11
24 10 0.53
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (22 bp):
TTAAATTTTTATATTTATTTAA
Found at i:12368289 original size:16 final size:16
Alignment explanation
Indices: 12368270--12368312 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
12368260 AATACTATAT
12368270 TAATTAATAAATTTTA
1 TAATTAATAAATTTTA
*
12368286 TAATTCAAAAAATTTTA
1 TAATT-AATAAATTTTA
12368303 -AATTTAATAA
1 TAA-TTAATAA
12368313 TATATTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
16 11 0.48
17 12 0.52
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (16 bp):
TAATTAATAAATTTTA
Found at i:12370826 original size:2 final size:2
Alignment explanation
Indices: 12370816--12370854 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
12370806 TGTGTGTGAA
*
12370816 AG AG GG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
12370855 ACCTATGATG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
AG
Found at i:12371795 original size:27 final size:27
Alignment explanation
Indices: 12371757--12371810 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
12371747 GACTATCAGA
12371757 AAAGAACAAGTTGACAATACATACATT
1 AAAGAACAAGTTGACAATACATACATT
12371784 AAAGAACAAGTTGACAATACATACATT
1 AAAGAACAAGTTGACAATACATACATT
12371811 CTATTTGGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.52, C:0.15, G:0.11, T:0.22
Consensus pattern (27 bp):
AAAGAACAAGTTGACAATACATACATT
Found at i:12373902 original size:126 final size:126
Alignment explanation
Indices: 12373677--12373931 Score: 483
Period size: 126 Copynumber: 2.0 Consensus size: 126
12373667 AGCCGATATG
12373677 TCCACTCCACCAAATGTGCAATTGGCATTATAACAATGGCAGGAATCTTTATTTTTGGCCTGAAA
1 TCCACTCCACCAAATGTGCAATTGGCATTATAACAATGGCAGGAATCTTTATTTTTGGCCTGAAA
*
12373742 ATTACAGCAGTTCAGAAGAGAGAAAGATACAAGGTCCAGCAGTTTCATAAGCATCTTTAAT
66 ATTACAGCAGTTCAGAAAAGAGAAAGATACAAGGTCCAGCAGTTTCATAAGCATCTTTAAT
12373803 TCCACTCCACCAAATGTGCAATTGGCATTATAACAATGGCAGGAATCTTTATTTTTGGCCTGAAA
1 TCCACTCCACCAAATGTGCAATTGGCATTATAACAATGGCAGGAATCTTTATTTTTGGCCTGAAA
* *
12373868 ATTACAGCAGTTCAGAAAAGAGGAAGATACAAGGTCCGGCAGTTTCATAAGCATCTTTAAT
66 ATTACAGCAGTTCAGAAAAGAGAAAGATACAAGGTCCAGCAGTTTCATAAGCATCTTTAAT
12373929 TCC
1 TCC
12373932 CAAATTTCCA
Statistics
Matches: 126, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
126 126 1.00
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (126 bp):
TCCACTCCACCAAATGTGCAATTGGCATTATAACAATGGCAGGAATCTTTATTTTTGGCCTGAAA
ATTACAGCAGTTCAGAAAAGAGAAAGATACAAGGTCCAGCAGTTTCATAAGCATCTTTAAT
Found at i:12376189 original size:2 final size:2
Alignment explanation
Indices: 12376184--12376223 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
12376174 TTCTTGCTAA
12376184 AT AT AT AT AT AT 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 AT AT AT AT AT AT
12376224 TGGTTCTATT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12379016 original size:15 final size:15
Alignment explanation
Indices: 12378985--12379048 Score: 56
Period size: 15 Copynumber: 4.2 Consensus size: 15
12378975 AATTTTATTG
**
12378985 TTAGGGTTTTGGGAT
1 TTAGGGTTTTGAAAT
*
12379000 TTGGGGTTTTGAAAT
1 TTAGGGTTTTGAAAT
* *
12379015 TTAGAGTTTTAAAAT
1 TTAGGGTTTTGAAAT
**
12379030 TTATAGTTTTGAAAAT
1 TTAGGGTTTTG-AAAT
12379046 TTA
1 TTA
12379049 AGGTCGAGGG
Statistics
Matches: 40, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
15 33 0.82
16 7 0.17
ACGTcount: A:0.28, C:0.00, G:0.23, T:0.48
Consensus pattern (15 bp):
TTAGGGTTTTGAAAT
Found at i:12379046 original size:16 final size:16
Alignment explanation
Indices: 12379005--12379048 Score: 65
Period size: 15 Copynumber: 2.9 Consensus size: 16
12378995 GGGATTTGGG
12379005 GTTTTG-AAATTTAGA
1 GTTTTGAAAATTTAGA
*
12379020 GTTTT-AAAATTTATA
1 GTTTTGAAAATTTAGA
12379035 GTTTTGAAAATTTA
1 GTTTTGAAAATTTA
12379049 AGGTCGAGGG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 18 0.69
16 8 0.31
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (16 bp):
GTTTTGAAAATTTAGA
Found at i:12380080 original size:188 final size:187
Alignment explanation
Indices: 12379741--12380093 Score: 398
Period size: 189 Copynumber: 1.9 Consensus size: 187
12379731 TAAGTATTAA
**
12379741 TTATCCAATGATGAAATTTATAAAAATTTCAAATGGTAAATTTTTATAAAATTCTTAAGTGAAAA
1 TTATCCAATGATGAAATTTATAAAAATTTCAAATGGTAAATTCCTATAAAATTCTTAAGTGAAAA
* * * * * *
12379806 ATTTTATCTAAATTTATCCCAAATTGTGAAATAATTTAGATAAAGTTTCAATAACAATAATTAAT
66 ATTTTATCTAAATTTATCCAAAATGGTGAAAGAATTTAAATAAAGTTTCAAGAAAAATAATTAAT
12379871 ATTTATTTTCAATAAAAAAAAATAAAA-AAATAAAATTTTGGTTGAAAATATATGACAG
131 ATTTATTTTC-ATAAAAAAAAA-AAAAGAAATAAAATTTTGGTTGAAAATATATGACAG
* *
12379929 TTATCCAATGATGAGATTCT-TAAAAATTTTCAAATGGTAAATTCCTA-AGAAATT-TTTAGATG
1 TTATCCAATGATGAAATT-TATAAAAA-TTTCAAATGGTAAATTCCTATA-AAATTCTTAAG-TG
* * * *
12379991 AGAAATTTCT-T-TAAATTTGTCTCAAAATGGTGGAAGAATTTAAATGAAA-TTTTAAGAAAAAT
62 AAAAATTT-TATCTAAATTTATC-CAAAATGGTGAAAGAATTTAAAT-AAAGTTTCAAGAAAAAT
** **
12380053 AATTTTTATATTATTTTC-TTTAAAAAAAAAAAGAAATAAAA
124 AATTAATAT-TTATTTTCATAAAAAAAAAAAAAGAAATAAAA
12380094 AGAATTTATA
Statistics
Matches: 138, Mismatches: 18, Indels: 18
0.79 0.10 0.10
Matches are distributed among these distances:
187 4 0.03
188 53 0.38
189 69 0.50
190 12 0.09
ACGTcount: A:0.47, C:0.06, G:0.09, T:0.37
Consensus pattern (187 bp):
TTATCCAATGATGAAATTTATAAAAATTTCAAATGGTAAATTCCTATAAAATTCTTAAGTGAAAA
ATTTTATCTAAATTTATCCAAAATGGTGAAAGAATTTAAATAAAGTTTCAAGAAAAATAATTAAT
ATTTATTTTCATAAAAAAAAAAAAAGAAATAAAATTTTGGTTGAAAATATATGACAG
Found at i:12380228 original size:58 final size:57
Alignment explanation
Indices: 12380166--12380355 Score: 178
Period size: 58 Copynumber: 3.4 Consensus size: 57
12380156 AGATTGAACT
* *
12380166 AAATGGAGGAAACTTTAGAAATTAAGATCAAAAAATAAAATAATTTCTAAATTGGCCC
1 AAATGGAGAAAAATTTAGAAATTAAGATCAAAAAATAAAA-AATTTCTAAATTGGCCC
* * * * * * *
12380224 AAATGGTGGAGAATTTAGAAA-T----TCTAAAAA-AAAAAATTTTTAAATTGACTC
1 AAATGGAGAAAAATTTAGAAATTAAGATCAAAAAATAAAAAATTTCTAAATTGGCCC
* **
12380275 AAATGGTA-AAAAATTTAGAAATTAAGATCAAAAAATAAAAAAAATTCTAAATAAGCCC
1 AAATGG-AGAAAAATTTAGAAATTAAGATCAAAAAAT-AAAAAATTTCTAAATTGGCCC
* *
12380333 AAATTGTGAAAAATTTAGAAATT
1 AAATGGAGAAAAATTTAGAAATT
12380356 CAAAAAGAGA
Statistics
Matches: 104, Mismatches: 19, Indels: 18
0.74 0.13 0.13
Matches are distributed among these distances:
51 31 0.30
52 5 0.05
53 7 0.07
56 7 0.07
57 1 0.01
58 53 0.51
ACGTcount: A:0.53, C:0.07, G:0.12, T:0.27
Consensus pattern (57 bp):
AAATGGAGAAAAATTTAGAAATTAAGATCAAAAAATAAAAAATTTCTAAATTGGCCC
Done.