Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13
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: 46006518
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2011935 characters in sequence are not A, C, G, or T
File 127 of 141
Found at i:40569601 original size:18 final size:18
Alignment explanation
Indices: 40569561--40569620 Score: 66
Period size: 19 Copynumber: 3.2 Consensus size: 18
40569551 TTTAACTTTC
* *
40569561 TTTATATATGTTTTAGAATT
1 TTTATAAATATTTT-GAA-T
40569581 TTTATAAATATTTTGAAT
1 TTTATAAATATTTTGAAT
*
40569599 TTTAAAAATTATTTTGAAT
1 TTTATAAA-TATTTTGAAT
40569618 TTT
1 TTT
40569621 TTGTAATTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
18 8 0.22
19 16 0.44
20 12 0.33
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.58
Consensus pattern (18 bp):
TTTATAAATATTTTGAAT
Found at i:40578535 original size:13 final size:13
Alignment explanation
Indices: 40578514--40578544 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
40578504 AGGATGATAT
*
40578514 AATTGCATATCAA
1 AATTACATATCAA
40578527 AATTACATATCAA
1 AATTACATATCAA
40578540 AATTA
1 AATTA
40578545 GAAAAATAAA
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:0.52, C:0.13, G:0.03, T:0.32
Consensus pattern (13 bp):
AATTACATATCAA
Found at i:40583869 original size:19 final size:19
Alignment explanation
Indices: 40583847--40583886 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
40583837 CCAAGGGAAT
40583847 TTTTAATAAATTATT-ATTA
1 TTTTAA-AAATTATTAATTA
*
40583866 TTTTGAAAATTATTAATTA
1 TTTTAAAAATTATTAATTA
40583885 TT
1 TT
40583887 GGTAATAAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (19 bp):
TTTTAAAAATTATTAATTA
Found at i:40588591 original size:3 final size:3
Alignment explanation
Indices: 40588583--40588651 Score: 131
Period size: 3 Copynumber: 23.3 Consensus size: 3
40588573 GACGAGGACG
40588583 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT- ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
40588630 ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA A
40588652 GCTGACGTTA
Statistics
Matches: 65, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 63 0.97
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:40589912 original size:91 final size:92
Alignment explanation
Indices: 40589799--40589981 Score: 359
Period size: 91 Copynumber: 2.0 Consensus size: 92
40589789 TATTTATATA
40589799 TTTAATAATTAAATTTAAATAAAAATATTTATTATTTTATATTATTTCGAATCAAGTCAAATAAA
1 TTTAATAATTAAATTTAAATAAAAATATTTATTATTTTATATTATTTCGAATCAAGTCAAATAAA
40589864 TTTAAAAAATTTACCTAAAATTCAGCT
66 TTTAAAAAATTTACCTAAAATTCAGCT
40589891 TTTAATAATT-AATTTAAATAAAAATATTTATTATTTTATATTATTTCGAATCAAGTCAAATAAA
1 TTTAATAATTAAATTTAAATAAAAATATTTATTATTTTATATTATTTCGAATCAAGTCAAATAAA
40589955 TTTAAAAAATTTACCTAAAATTCAGCT
66 TTTAAAAAATTTACCTAAAATTCAGCT
40589982 CCGGCTATCT
Statistics
Matches: 91, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
91 81 0.89
92 10 0.11
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.43
Consensus pattern (92 bp):
TTTAATAATTAAATTTAAATAAAAATATTTATTATTTTATATTATTTCGAATCAAGTCAAATAAA
TTTAAAAAATTTACCTAAAATTCAGCT
Found at i:40590741 original size:16 final size:16
Alignment explanation
Indices: 40590708--40590740 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
40590698 TTATAATTTT
*
40590708 AATGAACATAAATCAA
1 AATGAACATAAATAAA
40590724 AATGAACA-AAATAAA
1 AATGAACATAAATAAA
40590739 AA
1 AA
40590741 AAAAATAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.70, C:0.09, G:0.06, T:0.15
Consensus pattern (16 bp):
AATGAACATAAATAAA
Found at i:40591109 original size:14 final size:14
Alignment explanation
Indices: 40591092--40591124 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
40591082 ACCTGTCACC
40591092 TCTCTCTCTCTCTT
1 TCTCTCTCTCTCTT
*
40591106 TCTCTCTCTCTTTT
1 TCTCTCTCTCTCTT
40591120 TCTCT
1 TCTCT
40591125 TTGCTTTTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (14 bp):
TCTCTCTCTCTCTT
Found at i:40591111 original size:12 final size:12
Alignment explanation
Indices: 40591094--40591124 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
40591084 CTGTCACCTC
40591094 TCTCTCTCTCTT
1 TCTCTCTCTCTT
40591106 TCTCTCTCTCTT
1 TCTCTCTCTCTT
*
40591118 TTTCTCT
1 TCTCTCT
40591125 TTGCTTTTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (12 bp):
TCTCTCTCTCTT
Found at i:40614623 original size:25 final size:22
Alignment explanation
Indices: 40614579--40614625 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
40614569 ATAATAATTG
*
40614579 ATATTTTAAAATTTTAATTAAA
1 ATATTTTAAAATTTGAATTAAA
40614601 ATATTATTAAAATTTAGAGATTAAA
1 ATATT-TTAAAATTT-GA-ATTAAA
40614626 TTAAAATGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 5 0.24
23 9 0.43
24 1 0.05
25 6 0.29
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (22 bp):
ATATTTTAAAATTTGAATTAAA
Found at i:40615178 original size:15 final size:16
Alignment explanation
Indices: 40615158--40615187 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
40615148 TAAATTAAAA
40615158 AAATT-AAATATTGTC
1 AAATTAAAATATTGTC
40615173 AAATTAAAATATTGT
1 AAATTAAAATATTGT
40615188 TACAATATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.50, C:0.03, G:0.07, T:0.40
Consensus pattern (16 bp):
AAATTAAAATATTGTC
Found at i:40615366 original size:11 final size:11
Alignment explanation
Indices: 40615333--40615381 Score: 50
Period size: 11 Copynumber: 4.6 Consensus size: 11
40615323 AAAATTTTTA
40615333 ATTTTTTA-AT
1 ATTTTTTAGAT
*
40615343 -TTTCTTTATAT
1 ATTT-TTTAGAT
40615354 ATTTTTTAGAT
1 ATTTTTTAGAT
*
40615365 ATTTTTT-GAA
1 ATTTTTTAGAT
40615375 ATTTTTT
1 ATTTTTT
40615382 TATTTTTTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
9 3 0.09
10 13 0.38
11 15 0.44
12 3 0.09
ACGTcount: A:0.24, C:0.02, G:0.04, T:0.69
Consensus pattern (11 bp):
ATTTTTTAGAT
Found at i:40623839 original size:22 final size:22
Alignment explanation
Indices: 40623811--40623856 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
40623801 AAAAAAAGAA
40623811 TGATGATATTGGAGGTCCATGT
1 TGATGATATTGGAGGTCCATGT
*
40623833 TGATGATATTGGAGGTTCATGT
1 TGATGATATTGGAGGTCCATGT
40623855 TG
1 TG
40623857 GAATAGTTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.22, C:0.07, G:0.33, T:0.39
Consensus pattern (22 bp):
TGATGATATTGGAGGTCCATGT
Found at i:40638177 original size:24 final size:24
Alignment explanation
Indices: 40638150--40638195 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
40638140 AACCTAATTC
40638150 TAATCAAAG-TCAAATATATTATGT
1 TAATCAAAGCT-AAATATATTATGT
*
40638174 TAATCAATGCTAAATATATTAT
1 TAATCAAAGCTAAATATATTAT
40638196 ACTCATAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 19 0.95
25 1 0.05
ACGTcount: A:0.46, C:0.09, G:0.07, T:0.39
Consensus pattern (24 bp):
TAATCAAAGCTAAATATATTATGT
Found at i:40640433 original size:51 final size:51
Alignment explanation
Indices: 40640377--40640474 Score: 133
Period size: 51 Copynumber: 1.9 Consensus size: 51
40640367 ATAAATTTAG
** * * *
40640377 CCCTCAACTTTTACATATTATATCAATTGAATCATAATTTTAAAAAATTAA
1 CCCTCAAAATTTACAAATGATATCAATTGAATCATAATTCTAAAAAATTAA
* *
40640428 CCCTCAAAATTTACAAATGATATCAATTTAATCCTAATTCTAAAAAA
1 CCCTCAAAATTTACAAATGATATCAATTGAATCATAATTCTAAAAAA
40640475 ATCAAAAAAT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
51 40 1.00
ACGTcount: A:0.45, C:0.17, G:0.02, T:0.36
Consensus pattern (51 bp):
CCCTCAAAATTTACAAATGATATCAATTGAATCATAATTCTAAAAAATTAA
Found at i:40641027 original size:9 final size:9
Alignment explanation
Indices: 40641000--40641045 Score: 56
Period size: 9 Copynumber: 5.0 Consensus size: 9
40640990 TGTAATTTTT
40641000 AAATTATAA
1 AAATTATAA
* *
40641009 AACTTTTAA
1 AAATTATAA
*
40641018 AAATTGTAA
1 AAATTATAA
40641027 AACATTATAA
1 AA-ATTATAA
40641037 AAATTATAA
1 AAATTATAA
40641046 GAAAATGAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
9 23 0.74
10 8 0.26
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (9 bp):
AAATTATAA
Found at i:40641027 original size:18 final size:19
Alignment explanation
Indices: 40641000--40641045 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 19
40640990 TGTAATTTTT
*
40641000 AAATTATAAAAC-TTTTAA
1 AAATTATAAAACATTATAA
*
40641018 AAATTGTAAAACATTATAA
1 AAATTATAAAACATTATAA
40641037 AAATTATAA
1 AAATTATAA
40641046 GAAAATGAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 11 0.46
19 13 0.54
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (19 bp):
AAATTATAAAACATTATAA
Found at i:40641056 original size:28 final size:28
Alignment explanation
Indices: 40641002--40641057 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
40640992 TAATTTTTAA
* * *
40641002 ATTATAAAACTTTTAAAAATTGTAAAAC
1 ATTATAAAAATTATAAAAAATGTAAAAC
*
40641030 ATTATAAAAATTATAAGAAAATGAAAAA
1 ATTATAAAAATTATAA-AAAATGTAAAA
40641058 GGGTAGTTCT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
28 14 0.61
29 9 0.39
ACGTcount: A:0.61, C:0.04, G:0.05, T:0.30
Consensus pattern (28 bp):
ATTATAAAAATTATAAAAAATGTAAAAC
Found at i:40649809 original size:25 final size:24
Alignment explanation
Indices: 40649781--40649827 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
40649771 TGAGAAAGTT
40649781 TAAACAAAAATATAAAATTAAAAAA
1 TAAACAAAAATA-AAAATTAAAAAA
***
40649806 TAAACTTGAATAAAAATTAAAA
1 TAAACAAAAATAAAAATTAAAA
40649828 CTCGTTTTCT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 10 0.53
25 9 0.47
ACGTcount: A:0.70, C:0.04, G:0.02, T:0.23
Consensus pattern (24 bp):
TAAACAAAAATAAAAATTAAAAAA
Found at i:40663885 original size:2 final size:2
Alignment explanation
Indices: 40663878--40663909 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
40663868 AGCGGCATTC
40663878 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
40663910 GATACTTGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:40664118 original size:2 final size:2
Alignment explanation
Indices: 40664111--40664142 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
40664101 AGCGGCATTC
40664111 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
40664143 GATACTTGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:40664197 original size:233 final size:233
Alignment explanation
Indices: 40663790--40664214 Score: 841
Period size: 233 Copynumber: 1.8 Consensus size: 233
40663780 GAGGTGCTGG
40663790 AGGCCCTGCAAGTGGCGTTTTCGAGCAGCAGGAGTGTCTTGAAATTGCTTATCGCAATAGTCGCA
1 AGGCCCTGCAAGTGGCGTTTTCGAGCAGCAGGAGTGTCTTGAAATTGCTTATCGCAATAGTCGCA
40663855 GTAATACTTCCCTAGCGGCATTCCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTGATACTTGTT
66 GTAATACTTCCCTAGCGGCATTCCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTGATACTTGTT
40663920 CTATTACTAATACTAGTCCATAACTGGAAGCCAAATCAGAGTAAAAGGGGAAAGGTTTCGGTAAA
131 CTATTACTAATACTAGTCCATAACTGGAAGCCAAATCAGAGTAAAAGGGGAAAGGTTTCGGTAAA
40663985 ATTCTGCCGCAGAGCCCGTCGTTGCCGAAAAATGGGGA
196 ATTCTGCCGCAGAGCCCGTCGTTGCCGAAAAATGGGGA
40664023 AGGCCCTGCAAGTGGCGTTTTCGAGCAGCAGGAGTGTCTTGAAATTGCTTATCGCAATAGTCGCA
1 AGGCCCTGCAAGTGGCGTTTTCGAGCAGCAGGAGTGTCTTGAAATTGCTTATCGCAATAGTCGCA
40664088 GTAATACTTCCCTAGCGGCATTCCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTGATACTTGTT
66 GTAATACTTCCCTAGCGGCATTCCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTGATACTTGTT
*
40664153 CTATTACTAATACTAGTCGATAACTGGAAGCCAAATCAGAGTAAAAGGGGAAAGGTTTCGGT
131 CTATTACTAATACTAGTCCATAACTGGAAGCCAAATCAGAGTAAAAGGGGAAAGGTTTCGGT
40664215 TGTTTTCAGT
Statistics
Matches: 191, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
233 191 1.00
ACGTcount: A:0.24, C:0.25, G:0.21, T:0.30
Consensus pattern (233 bp):
AGGCCCTGCAAGTGGCGTTTTCGAGCAGCAGGAGTGTCTTGAAATTGCTTATCGCAATAGTCGCA
GTAATACTTCCCTAGCGGCATTCCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTGATACTTGTT
CTATTACTAATACTAGTCCATAACTGGAAGCCAAATCAGAGTAAAAGGGGAAAGGTTTCGGTAAA
ATTCTGCCGCAGAGCCCGTCGTTGCCGAAAAATGGGGA
Found at i:40679675 original size:18 final size:17
Alignment explanation
Indices: 40679643--40679676 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
40679633 ATAAAAATAA
*
40679643 TATAAAAATTAATTAAT
1 TATAAAAATAAATTAAT
40679660 TATAAAAATAAGATTAA
1 TATAAAAATAA-ATTAA
40679677 AGAAAATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (17 bp):
TATAAAAATAAATTAAT
Found at i:40682140 original size:139 final size:137
Alignment explanation
Indices: 40681889--40682310 Score: 476
Period size: 139 Copynumber: 3.1 Consensus size: 137
40681879 GGAATCTCAT
* * * *
40681889 ACTCAAGGATGTAA-TAGCAATTATCTAACCATCTAACGAAAAAAGCTAATATGTTAGAAATATT
1 ACTCAAGAATGTAATTA-CAACTATCTAACCATCTAACGAAAGAA-CTAATATGTTAAAAATATT
* * *
40681953 AATTAGAA---AAAA-CTTGAAGCAACATGAAATAAAAAATACAAATGTGAGTAGTAGAGGAATC
64 AATTAAAATTTAAAAGCTTGAAGCAACATGAAATAAAAAATACAAATGTGAGTAGAAGAAGAATC
**
40682014 GGACTCGAG
129 AAACTCGAG
* * * * *
40682023 ACTCAAGAATGTACTTACGACTATCTAACTATCTAACGAAAGAATTAAAATGTTAAAAATATTAA
1 ACTCAAGAATGTAATTACAACTATCTAACCATCTAACGAAAGAACTAATATGTTAAAAATATTAA
* * * * * * *
40682088 TTAAAATTTTAAAATGCTTGAAGTAACATGAAATAGAAAATACAAATATGAGTCGGAGATGAATT
66 TTAAAA-TTTAAAA-GCTTGAAGCAACATGAAATAAAAAATACAAATGTGAGTAGAAGAAGAATC
*
40682153 AAACTTGAG
129 AAACTCGAG
* ** * * *
40682162 ACTCAAGGATGTAATTGTAACTATTTAACCATCTAACCAAAGAACTAATATGTTAAAAAAATTAA
1 ACTCAAGAATGTAATTACAACTATCTAACCATCTAACGAAAGAACTAATATGTTAAAAATATTAA
* *
40682227 TTAAAGATTTAAAAAGCTTGAAGCAACGTGAAATAAAAAATACAAATGTCAGTAGAAGAAGAATC
66 TTAAA-ATTT-AAAAGCTTGAAGCAACATGAAATAAAAAATACAAATGTGAGTAGAAGAAGAATC
*
40682292 AAACTCGGG
129 AAACTCGAG
40682301 ACTCAAGAAT
1 ACTCAAGAAT
40682311 AAAAACACTA
Statistics
Matches: 236, Mismatches: 43, Indels: 13
0.81 0.15 0.04
Matches are distributed among these distances:
133 23 0.10
134 35 0.15
135 2 0.01
137 4 0.02
139 167 0.71
140 5 0.02
ACGTcount: A:0.48, C:0.12, G:0.15, T:0.25
Consensus pattern (137 bp):
ACTCAAGAATGTAATTACAACTATCTAACCATCTAACGAAAGAACTAATATGTTAAAAATATTAA
TTAAAATTTAAAAGCTTGAAGCAACATGAAATAAAAAATACAAATGTGAGTAGAAGAAGAATCAA
ACTCGAG
Found at i:40687071 original size:22 final size:22
Alignment explanation
Indices: 40687046--40687088 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
40687036 TAAAATAAAA
**
40687046 TTTTAAATATTTGTAGTTATTAT
1 TTTTAAA-ATTTAAAGTTATTAT
40687069 TTTTAAAATTTAAAGTTATT
1 TTTTAAAATTTAAAGTTATT
40687089 TCATATGTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.58
Consensus pattern (22 bp):
TTTTAAAATTTAAAGTTATTAT
Found at i:40690980 original size:20 final size:20
Alignment explanation
Indices: 40690932--40690982 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 20
40690922 CATGCGGATG
* **
40690932 TTTATAATTTTTTTTATAAT
1 TTTATAAATTTTTGGATAAT
*
40690952 TTTAT-AATTTTTGGATATT
1 TTTATAAATTTTTGGATAAT
40690971 TTTATAAATTTT
1 TTTATAAATTTT
40690983 AAATTAGTTG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
19 15 0.58
20 11 0.42
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (20 bp):
TTTATAAATTTTTGGATAAT
Found at i:40702435 original size:18 final size:18
Alignment explanation
Indices: 40702412--40702449 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
40702402 AAAAATGTAC
40702412 TTATATAATTAAAATAAA
1 TTATATAATTAAAATAAA
* *
40702430 TTATATTATTCAAATAAA
1 TTATATAATTAAAATAAA
40702448 TT
1 TT
40702450 TTAGTCTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (18 bp):
TTATATAATTAAAATAAA
Found at i:40706018 original size:19 final size:18
Alignment explanation
Indices: 40705975--40706018 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
40705965 CTATTTAGAA
* *
40705975 ATTTTTTATCGTGATAAT
1 ATTTTTTATAGTAATAAT
*
40705993 AATTTTTATAGTAATTAAT
1 ATTTTTTATAGTAA-TAAT
40706012 ATTTTTT
1 ATTTTTT
40706019 TAAATATGAA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 11 0.52
19 10 0.48
ACGTcount: A:0.32, C:0.02, G:0.07, T:0.59
Consensus pattern (18 bp):
ATTTTTTATAGTAATAAT
Found at i:40710515 original size:18 final size:18
Alignment explanation
Indices: 40710468--40710515 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
40710458 GTGAAACAAC
*
40710468 ATTTCTAATATTTTATAA
1 ATTTCTAATTTTTTATAA
* *
40710486 ATTTCTATTTTTTTATAT
1 ATTTCTAATTTTTTATAA
*
40710504 ATTTTTAATTTT
1 ATTTCTAATTTT
40710516 AAAATAATAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (18 bp):
ATTTCTAATTTTTTATAA
Found at i:40713245 original size:15 final size:16
Alignment explanation
Indices: 40713220--40713252 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
40713210 TTATAAAAAA
*
40713220 TAAAAAGAAAATAATT
1 TAAAAAGAAAAGAATT
40713236 TAAAAA-AAAAGAATT
1 TAAAAAGAAAAGAATT
40713251 TA
1 TA
40713253 GCATGAAGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.70, C:0.00, G:0.06, T:0.24
Consensus pattern (16 bp):
TAAAAAGAAAAGAATT
Found at i:40717952 original size:18 final size:17
Alignment explanation
Indices: 40717919--40717952 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
40717909 ATTTTGTGTT
*
40717919 ATTTAATAAAAAATTTC
1 ATTTAAAAAAAAATTTC
40717936 ATTTAAAAAAAATATTT
1 ATTTAAAAAAAA-ATTT
40717953 TTAGTAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (17 bp):
ATTTAAAAAAAAATTTC
Found at i:40719958 original size:42 final size:42
Alignment explanation
Indices: 40719906--40719989 Score: 116
Period size: 42 Copynumber: 2.0 Consensus size: 42
40719896 TATATGTTTT
* * *
40719906 CGTTTAACCCTAATGGGTTTTCGTTTAGC-TTCTATGTGCTTC
1 CGTTAAACCCTAACGGGTTTTCGTTTAGCACT-TATGTGCTTC
*
40719948 CGTTAAACCCTTACGGGTTTTCGTTTAGCACTTATGTGCTTC
1 CGTTAAACCCTAACGGGTTTTCGTTTAGCACTTATGTGCTTC
40719990 TGTGCAGCCT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
42 36 0.97
43 1 0.03
ACGTcount: A:0.15, C:0.23, G:0.19, T:0.43
Consensus pattern (42 bp):
CGTTAAACCCTAACGGGTTTTCGTTTAGCACTTATGTGCTTC
Found at i:40721804 original size:38 final size:38
Alignment explanation
Indices: 40721724--40721804 Score: 90
Period size: 38 Copynumber: 2.1 Consensus size: 38
40721714 TTAACAAAAG
* * * * *
40721724 GCATGATTATCATGTATTTAGTTCAATAGTAACAGTAG
1 GCATGATTAACATGTATTCAGTTCAACAATAACAGTAA
* * *
40721762 GCATGTTTAACATGTATTCAGTTTAACAATAACGGTAA
1 GCATGATTAACATGTATTCAGTTCAACAATAACAGTAA
40721800 GCATG
1 GCATG
40721805 CAACCAGTAC
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.35
Consensus pattern (38 bp):
GCATGATTAACATGTATTCAGTTCAACAATAACAGTAA
Found at i:40731282 original size:17 final size:18
Alignment explanation
Indices: 40731260--40731295 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
40731250 TTCATTTTTA
*
40731260 TATAAAATAA-TTTATTT
1 TATAAAACAATTTTATTT
40731277 TATAAAACAATTTTATTT
1 TATAAAACAATTTTATTT
40731295 T
1 T
40731296 CAATTTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (18 bp):
TATAAAACAATTTTATTT
Found at i:40732803 original size:16 final size:17
Alignment explanation
Indices: 40732779--40732821 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
40732769 TAATATTATA
*
40732779 AAATCAAAAAAT-AATT
1 AAATAAAAAAATAAATT
40732795 AAATAAAAAAATCAAATT
1 AAATAAAAAAAT-AAATT
*
40732813 AATTAAAAA
1 AAATAAAAA
40732822 TTCGTCTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 11 0.48
18 12 0.52
ACGTcount: A:0.72, C:0.05, G:0.00, T:0.23
Consensus pattern (17 bp):
AAATAAAAAAATAAATT
Found at i:40734271 original size:31 final size:31
Alignment explanation
Indices: 40734205--40734278 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 31
40734195 TAATTTGATG
* * * *
40734205 AATTTTAATCTTTATATTTTTCGAATTGGTC
1 AATTTTAGTCCTTATACTTTTCGAATTGGTA
*
40734236 AATTTTAGTCCTTATACTTTTCGAATT-TTGA
1 AATTTTAGTCCTTATACTTTTCGAATTGGT-A
40734267 AATTTTAGTCCT
1 AATTTTAGTCCT
40734279 GACTCAATGG
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 1 0.03
31 36 0.97
ACGTcount: A:0.26, C:0.12, G:0.09, T:0.53
Consensus pattern (31 bp):
AATTTTAGTCCTTATACTTTTCGAATTGGTA
Found at i:40743762 original size:25 final size:26
Alignment explanation
Indices: 40743729--40743782 Score: 67
Period size: 25 Copynumber: 2.1 Consensus size: 26
40743719 CTAAATTTTG
*
40743729 AATTACTTT-TAATTCTAATATGGAAC
1 AATTACTTTCTAATTATAA-ATGGAAC
*
40743755 AATT-CTTTCTAATTATAAATTGAAC
1 AATTACTTTCTAATTATAAATGGAAC
40743780 AAT
1 AAT
40743783 GGTAGCAACC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 13 0.52
26 12 0.48
ACGTcount: A:0.41, C:0.11, G:0.06, T:0.43
Consensus pattern (26 bp):
AATTACTTTCTAATTATAAATGGAAC
Found at i:40744651 original size:18 final size:18
Alignment explanation
Indices: 40744620--40744668 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
40744610 TACAAAAAAA
* *
40744620 ATTAAAATATTTATAAAT
1 ATTAAAAAAATTATAAAT
40744638 ATTAAAAAAATTAT--AT
1 ATTAAAAAAATTATAAAT
40744654 -TTAAAAAAA-TATAAA
1 ATTAAAAAAATTATAAA
40744669 AATTCTAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
14 3 0.11
15 9 0.33
16 3 0.11
18 12 0.44
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
ATTAAAAAAATTATAAAT
Found at i:40744679 original size:19 final size:18
Alignment explanation
Indices: 40744655--40744690 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
40744645 AAATTATATT
40744655 TAAAAAAATATAAAAATTC
1 TAAAAAAA-ATAAAAATTC
*
40744674 TAAAAAAAATTAAAATT
1 TAAAAAAAATAAAAATT
40744691 TTTCTAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (18 bp):
TAAAAAAAATAAAAATTC
Found at i:40746297 original size:13 final size:14
Alignment explanation
Indices: 40746268--40746304 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
40746258 TTTATTTTTT
*
40746268 TTTCTTTCTTTCGA
1 TTTCTTTCTTTCAA
40746282 TTTCTTT-TTTCAA
1 TTTCTTTCTTTCAA
40746295 TTT-TTTCTTT
1 TTTCTTTCTTT
40746305 TTCTTTACTG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
12 3 0.14
13 11 0.52
14 7 0.33
ACGTcount: A:0.08, C:0.16, G:0.03, T:0.73
Consensus pattern (14 bp):
TTTCTTTCTTTCAA
Found at i:40749935 original size:263 final size:264
Alignment explanation
Indices: 40749537--40750063 Score: 1047
Period size: 263 Copynumber: 2.0 Consensus size: 264
40749527 TAATTATTCG
40749537 TTGTATGTAAAAAAAAAATTCAACCATTAAATATATATTATTATAGATAATATTTTAGATTGATA
1 TTGTATGTAAAAAAAAAATTCAACCATTAAATATATATTATTATAGATAATATTTTAGATTGATA
40749602 TGAGAGGAATATAGAATCTTTTCATTAATTTACATGCATGACAAATAAAAATATATTAATAAATT
66 TGAGAGGAATATAGAATCTTTTCATTAATTTACATGCATGACAAATAAAAATATATTAATAAATT
40749667 CAATGGTTGGATTGTTAAAATGTTAGTAGTATGAAAAGTTATGGAAGAGTATAAAACTATTCTAA
131 CAATGGTTGGATTGTTAAAATGTTAGTAGTATGAAAAGTTATGGAAGAGTATAAAACTATTCTAA
40749732 TTTTATACCGGTGTAAGTGGATCTCTTCCCTACTTCTTCTACCCTTAACTTCCTTAAATCAGAAT
196 TTTTATACCGGTGTAAGTGGATCTCTTCCCTACTTCTTCTACCCTTAACTTCCTTAAATCAGAAT
40749797 AAAA
261 AAAA
40749801 TTGTATGT-AAAAAAAAATTCAACCATTAAATATATATTATTATAGATAATATTTTAGATTGATA
1 TTGTATGTAAAAAAAAAATTCAACCATTAAATATATATTATTATAGATAATATTTTAGATTGATA
40749865 TGAGAGGAATATAGAATCTTTTCATTAATTTACATGCATGACAAATAAAAATATATTAATAAATT
66 TGAGAGGAATATAGAATCTTTTCATTAATTTACATGCATGACAAATAAAAATATATTAATAAATT
40749930 CAATGGTTGGATTGTTAAAATGTTAGTAGTATGAAAAGTTATGGAAGAGTATAAAACTATTCTAA
131 CAATGGTTGGATTGTTAAAATGTTAGTAGTATGAAAAGTTATGGAAGAGTATAAAACTATTCTAA
40749995 TTTTATACCGGTGTAAGTGGATCTCTTCCCTACTTCTTCTACCCTTAACTTCCTTAAATCAGAAT
196 TTTTATACCGGTGTAAGTGGATCTCTTCCCTACTTCTTCTACCCTTAACTTCCTTAAATCAGAAT
40750060 AAAA
261 AAAA
40750064 ATATGCTTAA
Statistics
Matches: 263, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
263 255 0.97
264 8 0.03
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.37
Consensus pattern (264 bp):
TTGTATGTAAAAAAAAAATTCAACCATTAAATATATATTATTATAGATAATATTTTAGATTGATA
TGAGAGGAATATAGAATCTTTTCATTAATTTACATGCATGACAAATAAAAATATATTAATAAATT
CAATGGTTGGATTGTTAAAATGTTAGTAGTATGAAAAGTTATGGAAGAGTATAAAACTATTCTAA
TTTTATACCGGTGTAAGTGGATCTCTTCCCTACTTCTTCTACCCTTAACTTCCTTAAATCAGAAT
AAAA
Found at i:40752203 original size:7 final size:7
Alignment explanation
Indices: 40752191--40752215 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
40752181 ACAGACAAAT
40752191 AAACCCA
1 AAACCCA
40752198 AAACCCA
1 AAACCCA
40752205 AAACCCA
1 AAACCCA
40752212 AAAC
1 AAAC
40752216 ATAGACAACC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.40, G:0.00, T:0.00
Consensus pattern (7 bp):
AAACCCA
Found at i:40758715 original size:19 final size:19
Alignment explanation
Indices: 40758693--40758732 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
40758683 TAAATATCTT
40758693 TTAAAATAA-TCCATTTTTA
1 TTAAAA-AATTCCATTTTTA
*
40758712 TTAAAAAATTCTATTTTTA
1 TTAAAAAATTCCATTTTTA
40758731 TT
1 TT
40758733 TTTATAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 2 0.11
19 17 0.89
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (19 bp):
TTAAAAAATTCCATTTTTA
Found at i:40768811 original size:16 final size:16
Alignment explanation
Indices: 40768787--40768820 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
40768777 TAATACTAAT
*
40768787 TAATTTTTGATTTTAA
1 TAATGTTTGATTTTAA
40768803 TAATGTTTGATTTTAA
1 TAATGTTTGATTTTAA
40768819 TA
1 TA
40768821 TTTAATAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.09, T:0.59
Consensus pattern (16 bp):
TAATGTTTGATTTTAA
Found at i:40768916 original size:43 final size:43
Alignment explanation
Indices: 40768852--40769072 Score: 259
Period size: 43 Copynumber: 5.2 Consensus size: 43
40768842 ATGATATTTT
* * * *
40768852 TAGCAGCGTTTGT-GATCAAAGCGTCGCTAAAGGTCTTGAGCTA
1 TAGCGGCGTTTGTGGA-AAAAGCGCCGCTAAAGGTCTTGATCTA
* *
40768895 TAGCAGCGTTTGTGGAAAAAGCGCCGCTAAAGGCCTTGATCTA
1 TAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCTTGATCTA
* * *
40768938 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGATCTTGAGCTA
1 TAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCTTGATCTA
* * ** * *
40768981 TAGTGGCGTTTGT-GTAAAAGCGTTGCTAAAGGTCCTGATTTA
1 TAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCTTGATCTA
*
40769023 TAGCGGCGTTTGTGG-AAAAGACGCCGCTAAAGGTCATGATCTA
1 TAGCGGCGTTTGTGGAAAAAG-CGCCGCTAAAGGTCTTGATCTA
40769066 TAGCGGC
1 TAGCGGC
40769073 ATTTATTTCT
Statistics
Matches: 153, Mismatches: 22, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
42 39 0.25
43 112 0.73
44 2 0.01
ACGTcount: A:0.26, C:0.18, G:0.30, T:0.26
Consensus pattern (43 bp):
TAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCTTGATCTA
Found at i:40769048 original size:85 final size:86
Alignment explanation
Indices: 40768869--40769069 Score: 273
Period size: 85 Copynumber: 2.3 Consensus size: 86
40768859 GTTTGTGATC
*
40768869 AAAGCGTCGCTAAAGGTCTTGAGCTATAGCAGCGTTTGTGGAAAAAGCGCCGCTAAAGGCCTTGA
1 AAAGCGCCGCTAAAGGTCTTGAGCTATAGCAGCGTTTGTGGAAAAAGCGCCGCTAAAGGCCTTGA
40768934 TCTATAGCGGCGTTTGTGGGA
66 TCTATAGCGGCGTTTGTGGGA
* ** * **
40768955 AAAGCGCCGCTAAAGATCTTGAGCTATAGTGGCGTTTGT-GTAAAAGCGTTGCTAAAGGTCC-TG
1 AAAGCGCCGCTAAAGGTCTTGAGCTATAGCAGCGTTTGTGGAAAAAGCGCCGCTAAAGG-CCTTG
*
40769018 ATTTATAGCGGCGTTTGT-GGA
65 ATCTATAGCGGCGTTTGTGGGA
* *
40769039 AAAGACGCCGCTAAAGGTCATGATCTATAGC
1 AAAG-CGCCGCTAAAGGTCTTGAGCTATAGC
40769070 GGCATTTATT
Statistics
Matches: 101, Mismatches: 12, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
84 7 0.07
85 57 0.56
86 37 0.37
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.26
Consensus pattern (86 bp):
AAAGCGCCGCTAAAGGTCTTGAGCTATAGCAGCGTTTGTGGAAAAAGCGCCGCTAAAGGCCTTGA
TCTATAGCGGCGTTTGTGGGA
Found at i:40771294 original size:19 final size:19
Alignment explanation
Indices: 40771270--40771315 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
40771260 GACTTCAACC
40771270 GACTAACTAAAACAGTTAT
1 GACTAACTAAAACAGTTAT
*
40771289 GACTAACTAAAACGGTTAT
1 GACTAACTAAAACAGTTAT
40771308 GAGCTAAC
1 GA-CTAAC
40771316 CATCTTATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 20 0.80
20 5 0.20
ACGTcount: A:0.43, C:0.17, G:0.15, T:0.24
Consensus pattern (19 bp):
GACTAACTAAAACAGTTAT
Found at i:40778332 original size:31 final size:29
Alignment explanation
Indices: 40778285--40778342 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 29
40778275 ACCTGAATTT
40778285 TAAAATTTAAAATATAATGAGATTAAATTCC
1 TAAAATTTAAAATATAA-GA-ATTAAATTCC
40778316 TAAAA-TTAAAAGTATAAGAATTAAATT
1 TAAAATTTAAAA-TATAAGAATTAAATT
40778343 ATAATTTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
29 8 0.31
30 8 0.31
31 10 0.38
ACGTcount: A:0.55, C:0.03, G:0.07, T:0.34
Consensus pattern (29 bp):
TAAAATTTAAAATATAAGAATTAAATTCC
Found at i:40782178 original size:19 final size:19
Alignment explanation
Indices: 40782154--40782267 Score: 147
Period size: 19 Copynumber: 5.8 Consensus size: 19
40782144 AATTTTTGAG
40782154 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
40782173 GATATGCAATCCTAGATAT
1 GATATGCAATCTTAGATAT
40782192 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
40782213 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
** *
40782232 GATATATAATATTAGATAT
1 GATATGCAATCTTAGATAT
* *
40782251 GATTTTGTAATCTTAGA
1 GA-TATGCAATCTTAGA
40782268 GATTTAATTT
Statistics
Matches: 84, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
19 55 0.65
20 11 0.13
21 18 0.21
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.39
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:40782199 original size:40 final size:40
Alignment explanation
Indices: 40782155--40782253 Score: 166
Period size: 40 Copynumber: 2.5 Consensus size: 40
40782145 ATTTTTGAGG
40782155 ATATGCAATCTTAGATATGATATGCAATCCTAGATATGAT
1 ATATGCAATCTTAGATATGATATGCAATCCTAGATATGAT
*
40782195 ATATGCAATCTTAGATATGATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGATATGCAATCCTAGATATGAT
*
40782235 ATAT--AATATTAGATATGAT
1 ATATGCAATCTTAGATATGAT
40782254 TTTGTAATCT
Statistics
Matches: 57, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
38 14 0.25
40 43 0.75
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.37
Consensus pattern (40 bp):
ATATGCAATCTTAGATATGATATGCAATCCTAGATATGAT
Found at i:40782221 original size:59 final size:58
Alignment explanation
Indices: 40782154--40782267 Score: 165
Period size: 59 Copynumber: 1.9 Consensus size: 58
40782144 AATTTTTGAG
* *
40782154 GATATGCAATCTTAGATATGATATGCAATCCTAGATATGATATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATATGATATACAATACTAGATATGAT-TATGCAATCTTAGATAT
* * * *
40782213 GATATGCAATCTTAGATATGATATATAATATTAGATATGATTTTGTAATCTTAGA
1 GATATGCAATCTTAGATATGATATACAATACTAGATATGATTATGCAATCTTAGA
40782268 GATTTAATTT
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
58 12 0.24
59 37 0.76
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.39
Consensus pattern (58 bp):
GATATGCAATCTTAGATATGATATACAATACTAGATATGATTATGCAATCTTAGATAT
Found at i:40785685 original size:33 final size:34
Alignment explanation
Indices: 40785644--40785712 Score: 81
Period size: 34 Copynumber: 2.1 Consensus size: 34
40785634 AAAAACTTGC
* *
40785644 AAAATTAT-TTTA-AAAA-TATAAAAATTAGTTT
1 AAAATTTTATTTAGAAAATTATAAAAATTAATTT
* *
40785675 AAAATTTTATTTAGAAAATTTTAAAATTTAATTT
1 AAAATTTTATTTAGAAAATTATAAAAATTAATTT
40785709 AAAA
1 AAAA
40785713 ATATGAAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
31 7 0.23
32 4 0.13
33 4 0.13
34 16 0.52
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (34 bp):
AAAATTTTATTTAGAAAATTATAAAAATTAATTT
Found at i:40785713 original size:21 final size:22
Alignment explanation
Indices: 40785672--40785714 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
40785662 TAAAAATTAG
*
40785672 TTTAAAATTTTATTTAGAAAAT
1 TTTAAAATTTAATTTAGAAAAT
40785694 TTTAAAATTTAATTTA-AAAAT
1 TTTAAAATTTAATTTAGAAAAT
40785715 ATGAAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (22 bp):
TTTAAAATTTAATTTAGAAAAT
Found at i:40785721 original size:21 final size:22
Alignment explanation
Indices: 40785675--40785721 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
40785665 AAATTAGTTT
* * *
40785675 AAAATTTTATTTAGAAAATTTT
1 AAAATTTAATTTAGAAAATATG
40785697 AAAATTTAATTTA-AAAATATG
1 AAAATTTAATTTAGAAAATATG
40785718 AAAA
1 AAAA
40785722 ATATATAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.40
Consensus pattern (22 bp):
AAAATTTAATTTAGAAAATATG
Found at i:40786106 original size:20 final size:20
Alignment explanation
Indices: 40786049--40786108 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
40786039 TAGTTTTAAT
*
40786049 ATTTTTT-GTAATTTTTAAAA
1 ATTTTTTAG-AATTTTTACAA
* * *
40786069 AATTATTATAATTTTTACAA
1 ATTTTTTAGAATTTTTACAA
40786089 ATTTTTTAGAATTTTTACAA
1 ATTTTTTAGAATTTTTACAA
40786109 CTTCAAAATA
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.55
Consensus pattern (20 bp):
ATTTTTTAGAATTTTTACAA
Found at i:40795650 original size:33 final size:34
Alignment explanation
Indices: 40795609--40795677 Score: 81
Period size: 34 Copynumber: 2.1 Consensus size: 34
40795599 AAAAACTTGC
* *
40795609 AAAATTAT-TTTA-AAAA-TATAAAAATTAGTTT
1 AAAATTTTATTTAGAAAATTATAAAAATTAATTT
* *
40795640 AAAATTTTATTTAGAAAATTTTAAAATTTAATTT
1 AAAATTTTATTTAGAAAATTATAAAAATTAATTT
40795674 AAAA
1 AAAA
40795678 ATATGAAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
31 7 0.23
32 4 0.13
33 4 0.13
34 16 0.52
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (34 bp):
AAAATTTTATTTAGAAAATTATAAAAATTAATTT
Found at i:40795678 original size:21 final size:22
Alignment explanation
Indices: 40795637--40795679 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
40795627 TAAAAATTAG
*
40795637 TTTAAAATTTTATTTAGAAAAT
1 TTTAAAATTTAATTTAGAAAAT
40795659 TTTAAAATTTAATTTA-AAAAT
1 TTTAAAATTTAATTTAGAAAAT
40795680 ATGAAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (22 bp):
TTTAAAATTTAATTTAGAAAAT
Found at i:40795686 original size:21 final size:22
Alignment explanation
Indices: 40795640--40795686 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
40795630 AAATTAGTTT
* * *
40795640 AAAATTTTATTTAGAAAATTTT
1 AAAATTTAATTTAGAAAATATG
40795662 AAAATTTAATTTA-AAAATATG
1 AAAATTTAATTTAGAAAATATG
40795683 AAAA
1 AAAA
40795687 ATATATAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.40
Consensus pattern (22 bp):
AAAATTTAATTTAGAAAATATG
Found at i:40795999 original size:20 final size:20
Alignment explanation
Indices: 40795952--40796001 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
40795942 TAATTTTTTT
* *
40795952 ATTTTTAAAAAATTATTATA
1 ATTTTTACAAAATTATTAGA
* *
40795972 ATTTTTACAAATTTTTTAGA
1 ATTTTTACAAAATTATTAGA
40795992 ATTTTTACAA
1 ATTTTTACAA
40796002 CTTAAAAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.52
Consensus pattern (20 bp):
ATTTTTACAAAATTATTAGA
Found at i:40803908 original size:5 final size:5
Alignment explanation
Indices: 40803900--40803934 Score: 70
Period size: 5 Copynumber: 7.0 Consensus size: 5
40803890 CTAAATCTAA
40803900 ATATT ATATT ATATT ATATT ATATT ATATT ATATT
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT
40803935 CTATGTCATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
ATATT
Found at i:40805539 original size:23 final size:23
Alignment explanation
Indices: 40805513--40805557 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
40805503 CTATGTACCT
40805513 TGAAGGAAATAAATTTA-TAAATG
1 TGAAGG-AATAAATTTATTAAATG
*
40805536 TGAAGGATTAAATTTATTAAAT
1 TGAAGGAATAAATTTATTAAAT
40805558 TATTTAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.49, C:0.00, G:0.16, T:0.36
Consensus pattern (23 bp):
TGAAGGAATAAATTTATTAAATG
Found at i:40805859 original size:21 final size:20
Alignment explanation
Indices: 40805813--40805871 Score: 59
Period size: 21 Copynumber: 3.0 Consensus size: 20
40805803 GCTTTTAAAT
*
40805813 AAATTATTATTTAATAAATTT
1 AAATT-TTATTTAATAAATTA
* *
40805834 TAATTTTATATTAATTAATTA
1 AAATTTTAT-TTAATAAATTA
40805855 AAA-TTTATTTAA-AAATT
1 AAATTTTATTTAATAAATT
40805872 TAGAAACCCC
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
18 4 0.12
19 4 0.12
20 9 0.28
21 15 0.47
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
AAATTTTATTTAATAAATTA
Found at i:40841886 original size:31 final size:30
Alignment explanation
Indices: 40841810--40841874 Score: 78
Period size: 30 Copynumber: 2.1 Consensus size: 30
40841800 AAGATTACAT
* *
40841810 ATGAACTTCGATTTAAT-GTGCAATGTTATAC
1 ATGAACTTTGATTT--TCGTGCAATGTTATAA
*
40841841 ATGAACTTTGATTTTCGTGCAATTTTATAA
1 ATGAACTTTGATTTTCGTGCAATGTTATAA
40841871 ATGA
1 ATGA
40841875 CATCTTGATT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
29 1 0.03
30 16 0.53
31 13 0.43
ACGTcount: A:0.32, C:0.11, G:0.15, T:0.42
Consensus pattern (30 bp):
ATGAACTTTGATTTTCGTGCAATGTTATAA
Found at i:40845812 original size:2 final size:2
Alignment explanation
Indices: 40845807--40845838 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
40845797 TATATTGTAT
*
40845807 AC AC AC AC AC AC AC AC AC AC AC AC TC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
40845839 TCAGATTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.50, G:0.00, T:0.03
Consensus pattern (2 bp):
AC
Found at i:40850137 original size:3 final size:3
Alignment explanation
Indices: 40850129--40850154 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
40850119 GTAAGCGTGG
40850129 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
40850155 GTAGACAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:40851567 original size:10 final size:11
Alignment explanation
Indices: 40851547--40851572 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
40851537 TTCTGTTAAC
40851547 TTTCTTTTTTT
1 TTTCTTTTTTT
40851558 TTTCTTTTTTT
1 TTTCTTTTTTT
40851569 TTTC
1 TTTC
40851573 CATTCTCTGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (11 bp):
TTTCTTTTTTT
Found at i:40851615 original size:170 final size:172
Alignment explanation
Indices: 40851330--40851670 Score: 580
Period size: 170 Copynumber: 2.0 Consensus size: 172
40851320 TGATCCCCAT
*
40851330 AATTTTTCGTTTTGAGCAATTTAATTCTTTTATGTTCTTTTAACTTTCTTTCTTTTTTTTTCTTT
1 AATTTTTCGTTTTGAGCAATTTAATTCTTTTATGTTCTGTTAACTTTC-TTCTTTTTTTTTCTTT
** *
40851395 TTTTTTTCCATTCTCTTTTACTTCTCCCTCTATTTTTCTACCTTCTTTATTTCTTTTAACATACC
65 TTTTTTTCCATTCTCTGCTACTTCTCCCTCTATTTTTCTACATTCTTTATTTCTTTTAACATA-C
40851460 T-GGAAGTCGAATTGGTAGTGAAAAAAGAAGCATGGTATGGGGG
129 TAGGAAGTCGAATTGGTAGTGAAAAAAGAAGCATGGTATGGGGG
40851503 AATTTTTCGTTTTGAGCAATTTAATTCTTTTATGTTCTGTTAACTTTC-T-TTTTTTTTTCTTTT
1 AATTTTTCGTTTTGAGCAATTTAATTCTTTTATGTTCTGTTAACTTTCTTCTTTTTTTTTCTTTT
* *
40851566 TTTTTTCCATTCTCTGCTGCTTCTCCCTCTGTTTTTCTACATTCTTTATTTCTTTTAACATACTA
66 TTTTTTCCATTCTCTGCTACTTCTCCCTCTATTTTTCTACATTCTTTATTTCTTTTAACATACTA
*
40851631 GGAAGTCGAATTGGTAGTGAAGAAAGAAGCATGGTATGGG
131 GGAAGTCGAATTGGTAGTGAAAAAAGAAGCATGGTATGGG
40851671 TTTATGGGTT
Statistics
Matches: 160, Mismatches: 7, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
169 2 0.01
170 110 0.69
171 1 0.01
173 47 0.29
ACGTcount: A:0.20, C:0.16, G:0.13, T:0.51
Consensus pattern (172 bp):
AATTTTTCGTTTTGAGCAATTTAATTCTTTTATGTTCTGTTAACTTTCTTCTTTTTTTTTCTTTT
TTTTTTCCATTCTCTGCTACTTCTCCCTCTATTTTTCTACATTCTTTATTTCTTTTAACATACTA
GGAAGTCGAATTGGTAGTGAAAAAAGAAGCATGGTATGGGGG
Found at i:40851693 original size:14 final size:14
Alignment explanation
Indices: 40851672--40851705 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
40851662 TGGTATGGGT
40851672 TTAT-GGGTTTTGG
1 TTATAGGGTTTTGG
40851685 TTATAGGGTTTTGG
1 TTATAGGGTTTTGG
40851699 TTATAGG
1 TTATAGG
40851706 CAAATGATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.20
14 16 0.80
ACGTcount: A:0.15, C:0.00, G:0.35, T:0.50
Consensus pattern (14 bp):
TTATAGGGTTTTGG
Found at i:40851863 original size:25 final size:26
Alignment explanation
Indices: 40851835--40851883 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
40851825 AGAGGAAAGT
40851835 TTAAAGAACATAAAA-GAAAAAAAAA
1 TTAAAGAACATAAAACGAAAAAAAAA
** *
40851860 TTAAATTACTTAAAACGAAAAAAA
1 TTAAAGAACATAAAACGAAAAAAA
40851884 TATGGGAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 12 0.60
26 8 0.40
ACGTcount: A:0.69, C:0.06, G:0.06, T:0.18
Consensus pattern (26 bp):
TTAAAGAACATAAAACGAAAAAAAAA
Found at i:40852032 original size:15 final size:15
Alignment explanation
Indices: 40852012--40852062 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 15
40852002 ACAACATGAT
40852012 AACGTAAATGACTAA
1 AACGTAAATGACTAA
** *
40852027 AACGT-AATGTTTCA
1 AACGTAAATGACTAA
* *
40852041 AACATAAGTGACTAA
1 AACGTAAATGACTAA
40852056 AACGTAA
1 AACGTAA
40852063 CCTAAGGTAA
Statistics
Matches: 26, Mismatches: 9, Indels: 2
0.70 0.24 0.05
Matches are distributed among these distances:
14 10 0.38
15 16 0.62
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (15 bp):
AACGTAAATGACTAA
Found at i:40859652 original size:16 final size:18
Alignment explanation
Indices: 40859626--40859662 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
40859616 CCTTTTAGGC
*
40859626 ATTTTATAATTTATAA-A
1 ATTTTATAATTAATAATA
40859643 ATTTTA-AATTAATAATA
1 ATTTTATAATTAATAATA
40859660 ATT
1 ATT
40859663 AAATAGAACT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
ATTTTATAATTAATAATA
Found at i:40889189 original size:20 final size:21
Alignment explanation
Indices: 40889148--40889191 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
40889138 TTTGGTAAAA
*
40889148 ATATCGATATTTTTGGTCCTAG
1 ATATCGATACTTTT-GTCCTAG
40889170 ATATCGATACTTTT-TCCTAG
1 ATATCGATACTTTTGTCCTAG
40889190 AT
1 AT
40889192 GGTGAAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 8 0.38
22 13 0.62
ACGTcount: A:0.25, C:0.16, G:0.14, T:0.45
Consensus pattern (21 bp):
ATATCGATACTTTTGTCCTAG
Found at i:40898644 original size:18 final size:18
Alignment explanation
Indices: 40898621--40898658 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
40898611 TATTTGATTT
40898621 AATTTAATTTATATATAA
1 AATTTAATTTATATATAA
*
40898639 AATTTAATTTTTATATAA
1 AATTTAATTTATATATAA
40898657 AA
1 AA
40898659 ATAAAATTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
AATTTAATTTATATATAA
Found at i:40900519 original size:13 final size:15
Alignment explanation
Indices: 40900495--40900526 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
40900485 GATAATCATG
40900495 TATTTATTTTATT-A
1 TATTTATTTTATTCA
40900509 TATTT-TTTTATTCA
1 TATTTATTTTATTCA
40900523 TATT
1 TATT
40900527 ATATATATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.41
14 10 0.59
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (15 bp):
TATTTATTTTATTCA
Found at i:40900543 original size:23 final size:22
Alignment explanation
Indices: 40900503--40900549 Score: 67
Period size: 23 Copynumber: 2.1 Consensus size: 22
40900493 TGTATTTATT
* *
40900503 TTATTATATTTTTTTATTCATA
1 TTATTATATTTGTATATTCATA
40900525 TTATATATATTTGTATATTCATA
1 TTAT-TATATTTGTATATTCATA
40900548 TT
1 TT
40900550 GTTTTCTTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 4 0.18
23 18 0.82
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.64
Consensus pattern (22 bp):
TTATTATATTTGTATATTCATA
Found at i:40901406 original size:68 final size:69
Alignment explanation
Indices: 40901305--40901447 Score: 252
Period size: 68 Copynumber: 2.1 Consensus size: 69
40901295 TAAAACTAGT
*
40901305 CCCTATACTTTTATTTTTTTCGAAAAATTTAATTTTTTCTTTTTATTTCTTTATTTTCCTTTTCT
1 CCCT-TACTTTTATTTTTTTCGAAAAATTTAATTTTTCCTTTTTATTTCTTTATTTTCCTTTTCT
40901370 TCTTC
65 TCTTC
*
40901375 CCCTTACTTTTA-TTTTTTCGAACAATTTAATTTTTCCTTTTTATTTCTTTATTTTCCTTTTCTT
1 CCCTTACTTTTATTTTTTTCGAAAAATTTAATTTTTCCTTTTTATTTCTTTATTTTCCTTTTCTT
40901439 CTTC
66 CTTC
40901443 CCCTT
1 CCCTT
40901448 TAGATTTAAC
Statistics
Matches: 71, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
68 59 0.83
69 8 0.11
70 4 0.06
ACGTcount: A:0.15, C:0.20, G:0.01, T:0.63
Consensus pattern (69 bp):
CCCTTACTTTTATTTTTTTCGAAAAATTTAATTTTTCCTTTTTATTTCTTTATTTTCCTTTTCTT
CTTC
Found at i:40908344 original size:19 final size:19
Alignment explanation
Indices: 40908317--40908355 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
40908307 CAAATATGTT
*
40908317 AAAATTATTAATTAAAATA
1 AAAAATATTAATTAAAATA
**
40908336 AAAAATATTTTTTAAAATA
1 AAAAATATTAATTAAAATA
40908355 A
1 A
40908356 TACAAATGTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
AAAAATATTAATTAAAATA
Found at i:40908390 original size:21 final size:21
Alignment explanation
Indices: 40908366--40908409 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
40908356 TACAAATGTG
*
40908366 TTAATATCTA-ATTATAAATAT
1 TTAATAGCTATATT-TAAATAT
*
40908387 TTAATGGCTATATTTAAATAT
1 TTAATAGCTATATTTAAATAT
40908408 TT
1 TT
40908410 GAAATATAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.50
Consensus pattern (21 bp):
TTAATAGCTATATTTAAATAT
Found at i:40910549 original size:17 final size:17
Alignment explanation
Indices: 40910527--40910565 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
40910517 ACTTTGTTTT
* *
40910527 AAATTTTTAAATTTTAA
1 AAATTTTAAAATTATAA
40910544 AAATTTTAAAATTATAA
1 AAATTTTAAAATTATAA
40910561 AAATT
1 AAATT
40910566 ATTTTTAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
AAATTTTAAAATTATAA
Found at i:40913781 original size:25 final size:25
Alignment explanation
Indices: 40913747--40913823 Score: 127
Period size: 25 Copynumber: 3.1 Consensus size: 25
40913737 ATTTGAAGAG
* *
40913747 TTATCTCTTAACTTCGAAATGCACT
1 TTATCCCTTAGCTTCGAAATGCACT
*
40913772 TTATCCCTTAGCTTTGAAATGCACT
1 TTATCCCTTAGCTTCGAAATGCACT
40913797 TTATCCCTTAGCTTCGAAATGCACT
1 TTATCCCTTAGCTTCGAAATGCACT
40913822 TT
1 TT
40913824 GAATCACTCG
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 48 1.00
ACGTcount: A:0.25, C:0.25, G:0.10, T:0.40
Consensus pattern (25 bp):
TTATCCCTTAGCTTCGAAATGCACT
Found at i:40921151 original size:18 final size:19
Alignment explanation
Indices: 40921128--40921166 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
40921118 AAAGAAAAAT
40921128 AAATTGTAAC-TC-AGTTTC
1 AAATTG-AACGTCTAGTTTC
40921146 AAATTGAACGTCTAGTTTC
1 AAATTGAACGTCTAGTTTC
40921165 AA
1 AA
40921167 TCATTATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 3 0.16
18 8 0.42
19 8 0.42
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (19 bp):
AAATTGAACGTCTAGTTTC
Found at i:40922330 original size:240 final size:241
Alignment explanation
Indices: 40921897--40922377 Score: 946
Period size: 240 Copynumber: 2.0 Consensus size: 241
40921887 ATTATATAAA
40921897 ATTATTAAATTTTTTTAAAAAAAGTAAAATTTGTTGTATCTTAATGTAGGGTAAATTACACATAA
1 ATTATTAAATTTTTTTAAAAAAAGTAAAATTTGTTGTATCTTAATGTAGGGTAAATTACACATAA
40921962 AAGCCCTATTTTTTTAAAATTTACCGAAATAGGCTTGGTATTTTATTATTTACCGGAATGGGCCA
66 AAGCCCTATTTTTTTAAAATTTACCGAAATAGGCTTGGTATTTTATTATTTACCGGAATGGGCCA
40922027 TTTTCCATGAAATCGCGTTCACGTCAGCGCGATGTCAGGGGATGTGTCAGCAAATTGTGTCCACG
131 TTTTCCATGAAATCGCGTTCACGTCAGCGCGATGTCAGGGGATGTGTCAGCAAATTGTGTCCACG
40922092 TCAGCGCGATTACTTACATGGCAACAAATTGCGTCCACGTAAGCGC
196 TCAGCGCGATTACTTACATGGCAACAAATTGCGTCCACGTAAGCGC
*
40922138 ATTATTAAA-TTTTTTAAAAAGAGTAAAATTTGTTGTATCTTAATGTAGGGTAAATTACACATAA
1 ATTATTAAATTTTTTTAAAAAAAGTAAAATTTGTTGTATCTTAATGTAGGGTAAATTACACATAA
40922202 AAGCCCTATTTTTTTAAAATTTACCGAAATAGGCTTGGTATTTTATTATTTACCGGAATGGGCCA
66 AAGCCCTATTTTTTTAAAATTTACCGAAATAGGCTTGGTATTTTATTATTTACCGGAATGGGCCA
40922267 TTTTCCATGAAATCGCGTTCACGTCAGCGCGATGTCAGGGGATGTGTCAGCAAATTGTGTCCACG
131 TTTTCCATGAAATCGCGTTCACGTCAGCGCGATGTCAGGGGATGTGTCAGCAAATTGTGTCCACG
40922332 TCAGCGCGATTACTTACATGGCAACAAATTGCGTCCACGTAAGCGC
196 TCAGCGCGATTACTTACATGGCAACAAATTGCGTCCACGTAAGCGC
40922378 GATTTGCTGA
Statistics
Matches: 239, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
240 230 0.96
241 9 0.04
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (241 bp):
ATTATTAAATTTTTTTAAAAAAAGTAAAATTTGTTGTATCTTAATGTAGGGTAAATTACACATAA
AAGCCCTATTTTTTTAAAATTTACCGAAATAGGCTTGGTATTTTATTATTTACCGGAATGGGCCA
TTTTCCATGAAATCGCGTTCACGTCAGCGCGATGTCAGGGGATGTGTCAGCAAATTGTGTCCACG
TCAGCGCGATTACTTACATGGCAACAAATTGCGTCCACGTAAGCGC
Found at i:40923475 original size:13 final size:14
Alignment explanation
Indices: 40923457--40923489 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
40923447 GTATTTTAAG
*
40923457 AATATTTTA-ATAA
1 AATATTTGACATAA
40923470 AATATTTGACATAA
1 AATATTTGACATAA
40923484 AATATT
1 AATATT
40923490 AATATTTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.44
14 10 0.56
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (14 bp):
AATATTTGACATAA
Found at i:40923499 original size:65 final size:65
Alignment explanation
Indices: 40923424--40924056 Score: 1266
Period size: 65 Copynumber: 9.7 Consensus size: 65
40923414 ATACATACGC
40923424 TAATATTTGACATAAAATTGATTGTATTTTAAGAATATTTTAATAAAATATTTGACATAAAATAT
1 TAATATTTGACATAAAATTGATTGTATTTTAAGAATATTTTAATAAAATATTTGACATAAAATAT
40923489 TAATATTTGACATAAAATTGATTGTATTTTAAGAATATTTTAATAAAATATTTGACATAAAATAT
1 TAATATTTGACATAAAATTGATTGTATTTTAAGAATATTTTAATAAAATATTTGACATAAAATAT
40923554 TAATATTTGACATAAAATTGATTGTATTTTAAGAATATTTTAATAAAATATTTGACATAAAATAT
1 TAATATTTGACATAAAATTGATTGTATTTTAAGAATATTTTAATAAAATATTTGACATAAAATAT
40923619 TAATATTTGACATAAAATTGATTGTATTTTAAGAATATTTTAATAAAATATTTGACATAAAATAT
1 TAATATTTGACATAAAATTGATTGTATTTTAAGAATATTTTAATAAAATATTTGACATAAAATAT
40923684 TAATATTTGACATAAAATTGATTGTATTTTAAGAATATTTTAATAAAATATTTGACATAAAATAT
1 TAATATTTGACATAAAATTGATTGTATTTTAAGAATATTTTAATAAAATATTTGACATAAAATAT
40923749 TAATATTTGACATAAAATTGATTGTATTTTAAGAATATTTTAATAAAATATTTGACATAAAATAT
1 TAATATTTGACATAAAATTGATTGTATTTTAAGAATATTTTAATAAAATATTTGACATAAAATAT
40923814 TAATATTTGACATAAAATTGATTGTATTTTAAGAATATTTTAATAAAATATTTGACATAAAATAT
1 TAATATTTGACATAAAATTGATTGTATTTTAAGAATATTTTAATAAAATATTTGACATAAAATAT
40923879 TAATATTTGACATAAAATTGATTGTATTTTAAGAATATTTTAATAAAATATTTGACATAAAATAT
1 TAATATTTGACATAAAATTGATTGTATTTTAAGAATATTTTAATAAAATATTTGACATAAAATAT
40923944 TAATATTTGACATAAAATTGATTGTATTTTAAGAATATTTTAATAAAATATTTGACATAAAATAT
1 TAATATTTGACATAAAATTGATTGTATTTTAAGAATATTTTAATAAAATATTTGACATAAAATAT
40924009 TAATATTTGACATAAAATTGATTGTATTTTAAGAATATTTTAATAAAA
1 TAATATTTGACATAAAATTGATTGTATTTTAAGAATATTTTAATAAAA
40924057 ATTAAATTTT
Statistics
Matches: 568, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 568 1.00
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.43
Consensus pattern (65 bp):
TAATATTTGACATAAAATTGATTGTATTTTAAGAATATTTTAATAAAATATTTGACATAAAATAT
Found at i:40923540 original size:13 final size:14
Alignment explanation
Indices: 40923522--40923554 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
40923512 GTATTTTAAG
*
40923522 AATATTTTA-ATAA
1 AATATTTGACATAA
40923535 AATATTTGACATAA
1 AATATTTGACATAA
40923549 AATATT
1 AATATT
40923555 AATATTTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.44
14 10 0.56
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (14 bp):
AATATTTGACATAA
Found at i:40923605 original size:13 final size:14
Alignment explanation
Indices: 40923587--40923619 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
40923577 GTATTTTAAG
*
40923587 AATATTTTA-ATAA
1 AATATTTGACATAA
40923600 AATATTTGACATAA
1 AATATTTGACATAA
40923614 AATATT
1 AATATT
40923620 AATATTTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.44
14 10 0.56
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (14 bp):
AATATTTGACATAA
Found at i:40923670 original size:13 final size:14
Alignment explanation
Indices: 40923652--40923684 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
40923642 GTATTTTAAG
*
40923652 AATATTTTA-ATAA
1 AATATTTGACATAA
40923665 AATATTTGACATAA
1 AATATTTGACATAA
40923679 AATATT
1 AATATT
40923685 AATATTTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.44
14 10 0.56
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (14 bp):
AATATTTGACATAA
Found at i:40923735 original size:13 final size:14
Alignment explanation
Indices: 40923717--40923749 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
40923707 GTATTTTAAG
*
40923717 AATATTTTA-ATAA
1 AATATTTGACATAA
40923730 AATATTTGACATAA
1 AATATTTGACATAA
40923744 AATATT
1 AATATT
40923750 AATATTTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.44
14 10 0.56
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (14 bp):
AATATTTGACATAA
Found at i:40923800 original size:13 final size:14
Alignment explanation
Indices: 40923782--40923814 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
40923772 GTATTTTAAG
*
40923782 AATATTTTA-ATAA
1 AATATTTGACATAA
40923795 AATATTTGACATAA
1 AATATTTGACATAA
40923809 AATATT
1 AATATT
40923815 AATATTTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.44
14 10 0.56
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (14 bp):
AATATTTGACATAA
Found at i:40923865 original size:13 final size:14
Alignment explanation
Indices: 40923847--40923879 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
40923837 GTATTTTAAG
*
40923847 AATATTTTA-ATAA
1 AATATTTGACATAA
40923860 AATATTTGACATAA
1 AATATTTGACATAA
40923874 AATATT
1 AATATT
40923880 AATATTTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.44
14 10 0.56
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (14 bp):
AATATTTGACATAA
Found at i:40923930 original size:13 final size:14
Alignment explanation
Indices: 40923912--40923944 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
40923902 GTATTTTAAG
*
40923912 AATATTTTA-ATAA
1 AATATTTGACATAA
40923925 AATATTTGACATAA
1 AATATTTGACATAA
40923939 AATATT
1 AATATT
40923945 AATATTTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.44
14 10 0.56
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (14 bp):
AATATTTGACATAA
Found at i:40923995 original size:13 final size:14
Alignment explanation
Indices: 40923977--40924009 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
40923967 GTATTTTAAG
*
40923977 AATATTTTA-ATAA
1 AATATTTGACATAA
40923990 AATATTTGACATAA
1 AATATTTGACATAA
40924004 AATATT
1 AATATT
40924010 AATATTTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.44
14 10 0.56
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (14 bp):
AATATTTGACATAA
Found at i:40929868 original size:103 final size:104
Alignment explanation
Indices: 40929736--40929953 Score: 420
Period size: 103 Copynumber: 2.1 Consensus size: 104
40929726 ATATTATAAA
40929736 TAATTTATTTTTATTTTATTTTGAAGGGATGAATATTAAAATTATACATAAATTTTGATATAATT
1 TAATTTATTTTTATTTTATTTTGAAGGGATGAATATTAAAATTATACATAAATTTTGATATAATT
40929801 TGTAATATTATAAATCAGCTTCAGCTTTTCACATTCCAC
66 TGTAATATTATAAATCAGCTTCAGCTTTTCACATTCCAC
40929840 TAATTTATTTTTA-TTTATTTTGAAGGGATGAATATTAAAATTATACATAAATTTTGATATAATT
1 TAATTTATTTTTATTTTATTTTGAAGGGATGAATATTAAAATTATACATAAATTTTGATATAATT
40929904 TGTAATATTATAAATCAGCTTCAGCTTTTCACATTCCAC
66 TGTAATATTATAAATCAGCTTCAGCTTTTCACATTCCAC
40929943 TAATTTCATTT
1 TAATTT-ATTT
40929954 ATCTGTGTGA
Statistics
Matches: 113, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
103 96 0.85
104 17 0.15
ACGTcount: A:0.35, C:0.10, G:0.08, T:0.47
Consensus pattern (104 bp):
TAATTTATTTTTATTTTATTTTGAAGGGATGAATATTAAAATTATACATAAATTTTGATATAATT
TGTAATATTATAAATCAGCTTCAGCTTTTCACATTCCAC
Found at i:40952214 original size:2 final size:2
Alignment explanation
Indices: 40952207--40952250 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
40952197 TTGCATGCAT
40952207 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
40952249 AG
1 AG
40952251 TTATTAGGCT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:40952275 original size:12 final size:12
Alignment explanation
Indices: 40952258--40952284 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
40952248 GAGTTATTAG
40952258 GCTTGCTACAAA
1 GCTTGCTACAAA
40952270 GCTTGCTACAAA
1 GCTTGCTACAAA
40952282 GCT
1 GCT
40952285 GATGCTTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.26
Consensus pattern (12 bp):
GCTTGCTACAAA
Found at i:40956667 original size:11 final size:11
Alignment explanation
Indices: 40956653--40956678 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
40956643 AAATTAAAAA
40956653 AAAAGTATTTT
1 AAAAGTATTTT
40956664 AAAAGTATTTT
1 AAAAGTATTTT
40956675 AAAA
1 AAAA
40956679 TTTAAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (11 bp):
AAAAGTATTTT
Found at i:40956667 original size:42 final size:40
Alignment explanation
Indices: 40956586--40956688 Score: 143
Period size: 42 Copynumber: 2.4 Consensus size: 40
40956576 AAAAATTTAT
40956586 TTTTAAAATTAAAATTAAAATTAAAAAAAGTATTTTAAAAATA
1 TTTTAAAATT-AAA--AAAATTAAAAAAAGTATTTTAAAAATA
*
40956629 TTTTAAAATTAAAAAAATTAAAAAAAAAGTATTTTAAAAGTA
1 TTTTAAAATTAAAAAAATT--AAAAAAAGTATTTTAAAAATA
40956671 TTTTAAAATTTAAAAAAA
1 TTTTAAAA-TTAAAAAAA
40956689 ATATTTATTA
Statistics
Matches: 56, Mismatches: 1, Indels: 6
0.89 0.02 0.10
Matches are distributed among these distances:
40 6 0.11
42 31 0.55
43 19 0.34
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (40 bp):
TTTTAAAATTAAAAAAATTAAAAAAAGTATTTTAAAAATA
Found at i:40968751 original size:113 final size:114
Alignment explanation
Indices: 40968613--40968833 Score: 282
Period size: 113 Copynumber: 1.9 Consensus size: 114
40968603 GATTAACAAA
* * * ** *
40968613 AAAAAACTATCAAAAACCCCCAAGAGACCCACCGCATCAGTAATGCGCAAAAAGCCACGTTTCAA
1 AAAAAACTATCAAAAACCCCCAAGAGACCCACCACATCAATAATGCACAAAAAGCCAAATCTCAA
* * *
40968678 ATGGCCCATTCTCCTCTTCATCACCTTAGATCTATCACCATCATGGTTG
66 ATGGCCCATCCTCCTCTTCATCACCTCAAATCTATCACCATCATGGTTG
* * * * *
40968727 AAAAAACTGTC-AAAAGCCCCAAGAGACCCACCACATCAATGATGCATAAAAGGCCAAATCTCAA
1 AAAAAACTATCAAAAACCCCCAAGAGACCCACCACATCAATAATGCACAAAAAGCCAAATCTCAA
* * *
40968791 ATGGTCTATCCTCCTCTTCATCACCTCAAATCTATTACCATCA
66 ATGGCCCATCCTCCTCTTCATCACCTCAAATCTATCACCATCA
40968834 CTATGATCAA
Statistics
Matches: 90, Mismatches: 17, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
113 80 0.89
114 10 0.11
ACGTcount: A:0.36, C:0.31, G:0.11, T:0.22
Consensus pattern (114 bp):
AAAAAACTATCAAAAACCCCCAAGAGACCCACCACATCAATAATGCACAAAAAGCCAAATCTCAA
ATGGCCCATCCTCCTCTTCATCACCTCAAATCTATCACCATCATGGTTG
Found at i:40981246 original size:58 final size:58
Alignment explanation
Indices: 40981145--40981258 Score: 160
Period size: 58 Copynumber: 1.9 Consensus size: 58
40981135 GAAATGGTGA
*
40981145 AAAATGGATAAATGGGAAACATTTGGAAATGATTATGGGTTTCTCCAAAATGAAAAACG
1 AAAATGGAGAAAT-GGAAACATTTGGAAATGATTATGGGTTTCTCCAAAATGAAAAACG
* *
40981204 AAAATGGAGAAAT-GAAATCATTTGGAAATGGA-TGTGGTTTTCTCCAAAATGAAAA
1 AAAATGGAGAAATGGAAA-CATTTGGAAAT-GATTATGGGTTTCTCCAAAATGAAAA
40981259 TGAAAAGTGA
Statistics
Matches: 50, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
57 4 0.08
58 32 0.64
59 14 0.28
ACGTcount: A:0.44, C:0.08, G:0.22, T:0.26
Consensus pattern (58 bp):
AAAATGGAGAAATGGAAACATTTGGAAATGATTATGGGTTTCTCCAAAATGAAAAACG
Found at i:40989723 original size:19 final size:18
Alignment explanation
Indices: 40989699--40989737 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
40989689 TTTTTAATTT
40989699 TTTTTAAGAAATAATAAAA
1 TTTTTAA-AAATAATAAAA
**
40989718 TTTTTAAATGTAATAAAA
1 TTTTTAAAAATAATAAAA
40989736 TT
1 TT
40989738 AAAAATTCTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (18 bp):
TTTTTAAAAATAATAAAA
Found at i:40991357 original size:29 final size:30
Alignment explanation
Indices: 40991321--40991383 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 30
40991311 TTTATATTTA
*
40991321 CCACTAAA-TTT-TTATGTGATTGAATTTTG
1 CCACTAAACTTTAATATGT-ATTGAATTTTG
*
40991350 CCACTAAACTTTAAATATGTTTTGAATTTTG
1 CCACTAAACTTT-AATATGTATTGAATTTTG
40991381 CCA
1 CCA
40991384 TCAAATATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 8 0.28
30 3 0.10
31 13 0.45
32 5 0.17
ACGTcount: A:0.30, C:0.14, G:0.11, T:0.44
Consensus pattern (30 bp):
CCACTAAACTTTAATATGTATTGAATTTTG
Found at i:40994154 original size:25 final size:27
Alignment explanation
Indices: 40994118--40994170 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
40994108 GAGCTGAAAT
*
40994118 GAACAATAAAG-TT-ATACAAGTTACA
1 GAACAATAAAGTTTGACACAAGTTACA
40994143 GAACAA-ACAAGTTTGACACAAGTTACA
1 GAACAATA-AAGTTTGACACAAGTTACA
40994170 G
1 G
40994171 TGTGTGATGA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
24 1 0.04
25 9 0.38
26 2 0.08
27 12 0.50
ACGTcount: A:0.49, C:0.15, G:0.15, T:0.21
Consensus pattern (27 bp):
GAACAATAAAGTTTGACACAAGTTACA
Found at i:41000789 original size:30 final size:30
Alignment explanation
Indices: 41000755--41000874 Score: 240
Period size: 30 Copynumber: 4.0 Consensus size: 30
41000745 CTGCTTCCAT
41000755 ATATCAATACCCCATTTAACTCCTTTCCTC
1 ATATCAATACCCCATTTAACTCCTTTCCTC
41000785 ATATCAATACCCCATTTAACTCCTTTCCTC
1 ATATCAATACCCCATTTAACTCCTTTCCTC
41000815 ATATCAATACCCCATTTAACTCCTTTCCTC
1 ATATCAATACCCCATTTAACTCCTTTCCTC
41000845 ATATCAATACCCCATTTAACTCCTTTCCTC
1 ATATCAATACCCCATTTAACTCCTTTCCTC
41000875 TATGCATTCA
Statistics
Matches: 90, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 90 1.00
ACGTcount: A:0.27, C:0.37, G:0.00, T:0.37
Consensus pattern (30 bp):
ATATCAATACCCCATTTAACTCCTTTCCTC
Found at i:41001760 original size:18 final size:18
Alignment explanation
Indices: 41001729--41001779 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
41001719 CCTCTTATAA
41001729 TATAATTTATTGTTTTTTT
1 TATAATTTA-TGTTTTTTT
* * *
41001748 TTTATTTTATGTTTGTTT
1 TATAATTTATGTTTTTTT
41001766 TATAATTTAT-TTTT
1 TATAATTTATGTTTT
41001780 AAGGTTTGAA
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
17 3 0.12
18 16 0.62
19 7 0.27
ACGTcount: A:0.20, C:0.00, G:0.06, T:0.75
Consensus pattern (18 bp):
TATAATTTATGTTTTTTT
Found at i:41009760 original size:17 final size:17
Alignment explanation
Indices: 41009738--41009773 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
41009728 TAAGCAACAT
41009738 AAAACAAACATTCATCA
1 AAAACAAACATTCATCA
*
41009755 AAAACAACCATTCATCA
1 AAAACAAACATTCATCA
41009772 AA
1 AA
41009774 CTTACCAGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.58, C:0.25, G:0.00, T:0.17
Consensus pattern (17 bp):
AAAACAAACATTCATCA
Found at i:41012963 original size:8 final size:8
Alignment explanation
Indices: 41012952--41012979 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
41012942 CTCACTCTGC
41012952 TTTTCTTT
1 TTTTCTTT
41012960 TTTTCTTT
1 TTTTCTTT
41012968 TTTTCTTT
1 TTTTCTTT
41012976 TTTT
1 TTTT
41012980 TTTCTGAATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (8 bp):
TTTTCTTT
Found at i:41016212 original size:18 final size:18
Alignment explanation
Indices: 41016185--41016219 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
41016175 ATTTACAAAG
41016185 GGGTTAATTTACAATGTT
1 GGGTTAATTTACAATGTT
* *
41016203 GGGTTTATTTAGAATGT
1 GGGTTAATTTACAATGT
41016220 AACTGTAGTT
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:0.26, C:0.03, G:0.26, T:0.46
Consensus pattern (18 bp):
GGGTTAATTTACAATGTT
Found at i:41023263 original size:23 final size:24
Alignment explanation
Indices: 41023214--41023263 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 24
41023204 TTTTTAAATT
*
41023214 TTTTAGAAGTTTAAAATGCTAGCA
1 TTTTAGAAGTTCAAAATGCTAGCA
* * *
41023238 TTTTAGAA-TTCATAATGTTAGGA
1 TTTTAGAAGTTCAAAATGCTAGCA
41023261 TTT
1 TTT
41023264 GTAATTGTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
23 14 0.64
24 8 0.36
ACGTcount: A:0.34, C:0.06, G:0.16, T:0.44
Consensus pattern (24 bp):
TTTTAGAAGTTCAAAATGCTAGCA
Found at i:41024278 original size:63 final size:64
Alignment explanation
Indices: 41024205--41024324 Score: 163
Period size: 63 Copynumber: 1.9 Consensus size: 64
41024195 ATATATATCG
*
41024205 AAATTATATTTATGTTAAATAAT-ACTCATTAAAACTTATTAA-ATAATATTTATATTTAGAAAA
1 AAATCATATTTATGTTAAATAATAAC-CATTAAAACTTATTAACATAATATTTATATTTAGAAAA
* * * * *
41024268 AAATCATATTTATTTTAAATAATAACCATTACAAGTTATTAACATAATTTTTGTATT
1 AAATCATATTTATGTTAAATAATAACCATTAAAACTTATTAACATAATATTTATATT
41024325 AAAATAAATA
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
63 35 0.71
64 14 0.29
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.44
Consensus pattern (64 bp):
AAATCATATTTATGTTAAATAATAACCATTAAAACTTATTAACATAATATTTATATTTAGAAAA
Found at i:41032071 original size:128 final size:129
Alignment explanation
Indices: 41031925--41032184 Score: 497
Period size: 128 Copynumber: 2.0 Consensus size: 129
41031915 ATTTTACCTT
41031925 TTATATCTCTTCATTGTTCATGGCGGCATTTCATTATCAGTCCATTTTTATTTTTCTTATTAGTA
1 TTATATCTCTTCATTGTTCATGGCGGCATTTCATTATCAGTCCATTTTTATTTTTCTTATTAGTA
41031990 TTTTATTTAAAATTTTAGTAAAATTAG-TTTTATTTATAAGCAAAATAAAAATAATAATTTTTAA
66 TTTTATTTAAAATTTTAGTAAAATTAGTTTTTA-TTATAAGCAAAATAAAAATAATAATTTTTAA
41032054 TTATATCTCTTCA-TGTTCATGGCGGCATTTCATTATCAGTCCATTTTTATTTTTCTTATTAGTA
1 TTATATCTCTTCATTGTTCATGGCGGCATTTCATTATCAGTCCATTTTTATTTTTCTTATTAGTA
41032118 TTTTATTTAAAATTTTAGTAAAATTAGTTTTTATTATAAGCAAAATAAAAATAATAATTTTTAA
66 TTTTATTTAAAATTTTAGTAAAATTAGTTTTTATTATAAGCAAAATAAAAATAATAATTTTTAA
41032182 TTA
1 TTA
41032185 AAATATCATT
Statistics
Matches: 130, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
128 112 0.86
129 18 0.14
ACGTcount: A:0.33, C:0.09, G:0.08, T:0.50
Consensus pattern (129 bp):
TTATATCTCTTCATTGTTCATGGCGGCATTTCATTATCAGTCCATTTTTATTTTTCTTATTAGTA
TTTTATTTAAAATTTTAGTAAAATTAGTTTTTATTATAAGCAAAATAAAAATAATAATTTTTAA
Found at i:41032581 original size:147 final size:147
Alignment explanation
Indices: 41032313--41033374 Score: 1770
Period size: 147 Copynumber: 7.2 Consensus size: 147
41032303 TATTTAAAAA
* * * *
41032313 GCCAAGATGTAAAAGTCAAGCTTAACATGGAGA-GTCAGCGAAATTATTGTTTCGATTTTTTAAC
1 GCCAAGATGTAAAAGTCAAGCTTATCATGGAGAGGTCAGTGAAATTATAGTTTCGATTTTTGAAC
* * * *
41032377 TACTCAATATATTCTAAATCGATCCGCTCCAAATTAGTACTTAATTTGAAGAATGGAGCTTAAAA
66 TACTCGATATATTCTGAATCGATCCGCTCCAAATTAGTATTTAATTTGAAGAGTGGAGCTTAAAA
*
41032442 ACATCATGATGTTGGAG
131 ACATCATGATGTTTGAG
41032459 GCCAAGATGTAAAAGTCAAGCTTATCATGGAGAGGTCAGTGAAATTATAGTTTCGATTTTTGAAC
1 GCCAAGATGTAAAAGTCAAGCTTATCATGGAGAGGTCAGTGAAATTATAGTTTCGATTTTTGAAC
41032524 TACTCGATATATTCTGAATCGATCCGCTCCAAATTAGTATTTAATTTGAAGAGTGGAGCTTAAAA
66 TACTCGATATATTCTGAATCGATCCGCTCCAAATTAGTATTTAATTTGAAGAGTGGAGCTTAAAA
41032589 ACATCATGATGTTTGAG
131 ACATCATGATGTTTGAG
* * * *
41032606 GCCAAGATGTAAAAGTCAAGCTTAACATGGAGA-GTCAGCGAAATTATTGTTTCGATTTTTTAAC
1 GCCAAGATGTAAAAGTCAAGCTTATCATGGAGAGGTCAGTGAAATTATAGTTTCGATTTTTGAAC
* * * *
41032670 TACTCAATATATTCTAAATCGATCCGCTCCAAATTAGTACTTAATTTGAAGAATGGAGCTTAAAA
66 TACTCGATATATTCTGAATCGATCCGCTCCAAATTAGTATTTAATTTGAAGAGTGGAGCTTAAAA
*
41032735 ACATCATGATGTTGGAG
131 ACATCATGATGTTTGAG
41032752 GCCAAGATGTAAAAGTCAAGCTTATCATGGAGAGGTCAGTGAAATTATAGTTTCGATTTTTGAAC
1 GCCAAGATGTAAAAGTCAAGCTTATCATGGAGAGGTCAGTGAAATTATAGTTTCGATTTTTGAAC
41032817 TACTCGATATATTCTGAATCGATCCGCTCCAAATTAGTATTTAATTTGAAGAGTGGAGCTTAAAA
66 TACTCGATATATTCTGAATCGATCCGCTCCAAATTAGTATTTAATTTGAAGAGTGGAGCTTAAAA
41032882 ACATCATGATGTTTGAG
131 ACATCATGATGTTTGAG
* * * *
41032899 GCCAAGATGTAAAAGTCAAGCTTAACATGGAGA-GTCAGCGAAATTATTGTTTCGATTTTTTAAC
1 GCCAAGATGTAAAAGTCAAGCTTATCATGGAGAGGTCAGTGAAATTATAGTTTCGATTTTTGAAC
* * * *
41032963 TACTCAATATATTCTAAATCGATCCGCTCCAAATTAGTACTTAATTTGAAGAATGGAGCTTAAAA
66 TACTCGATATATTCTGAATCGATCCGCTCCAAATTAGTATTTAATTTGAAGAGTGGAGCTTAAAA
*
41033028 ACATCATGATGTTGGAG
131 ACATCATGATGTTTGAG
41033045 GCCAAGATGTAAAAGTCAAGCTTATCATGGAGAGGTCAGTGAAATTATAGTTTCGATTTTTGAAC
1 GCCAAGATGTAAAAGTCAAGCTTATCATGGAGAGGTCAGTGAAATTATAGTTTCGATTTTTGAAC
* * * *
41033110 TACTCGATATATTCTGAATCGATCCGCTCCAGATTAGTATTTAATTTGAAGAGTGAAGGTTTAAA
66 TACTCGATATATTCTGAATCGATCCGCTCCAAATTAGTATTTAATTTGAAGAGTGGAGCTTAAAA
*
41033175 ATATCATGATGTTTGAG
131 ACATCATGATGTTTGAG
41033192 GCCAAGATGTAAAAGTCAAGCTTATCATGGAGAGGTCAGTGAAATTATAGTTTCGATTTTTGAAC
1 GCCAAGATGTAAAAGTCAAGCTTATCATGGAGAGGTCAGTGAAATTATAGTTTCGATTTTTGAAC
* * * *
41033257 TACTCGATATATTCTGAATCGATCCGCTCCAGATTAGTATTTAATTTGAAGAGTGAAGGTTTAAA
66 TACTCGATATATTCTGAATCGATCCGCTCCAAATTAGTATTTAATTTGAAGAGTGGAGCTTAAAA
*
41033322 ATATCATGATGTTTGAG
131 ACATCATGATGTTTGAG
41033339 GCCAAGATGTAAAAGTCAAGCTTATCATGGAGAGGT
1 GCCAAGATGTAAAAGTCAAGCTTATCATGGAGAGGT
41033375 TTTCATGGCT
Statistics
Matches: 863, Mismatches: 50, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
146 306 0.35
147 557 0.65
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.32
Consensus pattern (147 bp):
GCCAAGATGTAAAAGTCAAGCTTATCATGGAGAGGTCAGTGAAATTATAGTTTCGATTTTTGAAC
TACTCGATATATTCTGAATCGATCCGCTCCAAATTAGTATTTAATTTGAAGAGTGGAGCTTAAAA
ACATCATGATGTTTGAG
Found at i:41032840 original size:293 final size:293
Alignment explanation
Indices: 41032313--41033374 Score: 1944
Period size: 293 Copynumber: 3.6 Consensus size: 293
41032303 TATTTAAAAA
41032313 GCCAAGATGTAAAAGTCAAGCTTAACATGGAGAGTCAGCGAAATTATTGTTTCGATTTTTTAACT
1 GCCAAGATGTAAAAGTCAAGCTTAACATGGAGAGTCAGCGAAATTATTGTTTCGATTTTTTAACT
41032378 ACTCAATATATTCTAAATCGATCCGCTCCAAATTAGTACTTAATTTGAAGAATGGAGCTTAAAAA
66 ACTCAATATATTCTAAATCGATCCGCTCCAAATTAGTACTTAATTTGAAGAATGGAGCTTAAAAA
41032443 CATCATGATGTTGGAGGCCAAGATGTAAAAGTCAAGCTTATCATGGAGAGGTCAGTGAAATTATA
131 CATCATGATGTTGGAGGCCAAGATGTAAAAGTCAAGCTTATCATGGAGAGGTCAGTGAAATTATA
41032508 GTTTCGATTTTTGAACTACTCGATATATTCTGAATCGATCCGCTCCAAATTAGTATTTAATTTGA
196 GTTTCGATTTTTGAACTACTCGATATATTCTGAATCGATCCGCTCCAAATTAGTATTTAATTTGA
41032573 AGAGTGGAGCTTAAAAACATCATGATGTTTGAG
261 AGAGTGGAGCTTAAAAACATCATGATGTTTGAG
41032606 GCCAAGATGTAAAAGTCAAGCTTAACATGGAGAGTCAGCGAAATTATTGTTTCGATTTTTTAACT
1 GCCAAGATGTAAAAGTCAAGCTTAACATGGAGAGTCAGCGAAATTATTGTTTCGATTTTTTAACT
41032671 ACTCAATATATTCTAAATCGATCCGCTCCAAATTAGTACTTAATTTGAAGAATGGAGCTTAAAAA
66 ACTCAATATATTCTAAATCGATCCGCTCCAAATTAGTACTTAATTTGAAGAATGGAGCTTAAAAA
41032736 CATCATGATGTTGGAGGCCAAGATGTAAAAGTCAAGCTTATCATGGAGAGGTCAGTGAAATTATA
131 CATCATGATGTTGGAGGCCAAGATGTAAAAGTCAAGCTTATCATGGAGAGGTCAGTGAAATTATA
41032801 GTTTCGATTTTTGAACTACTCGATATATTCTGAATCGATCCGCTCCAAATTAGTATTTAATTTGA
196 GTTTCGATTTTTGAACTACTCGATATATTCTGAATCGATCCGCTCCAAATTAGTATTTAATTTGA
41032866 AGAGTGGAGCTTAAAAACATCATGATGTTTGAG
261 AGAGTGGAGCTTAAAAACATCATGATGTTTGAG
41032899 GCCAAGATGTAAAAGTCAAGCTTAACATGGAGAGTCAGCGAAATTATTGTTTCGATTTTTTAACT
1 GCCAAGATGTAAAAGTCAAGCTTAACATGGAGAGTCAGCGAAATTATTGTTTCGATTTTTTAACT
41032964 ACTCAATATATTCTAAATCGATCCGCTCCAAATTAGTACTTAATTTGAAGAATGGAGCTTAAAAA
66 ACTCAATATATTCTAAATCGATCCGCTCCAAATTAGTACTTAATTTGAAGAATGGAGCTTAAAAA
41033029 CATCATGATGTTGGAGGCCAAGATGTAAAAGTCAAGCTTATCATGGAGAGGTCAGTGAAATTATA
131 CATCATGATGTTGGAGGCCAAGATGTAAAAGTCAAGCTTATCATGGAGAGGTCAGTGAAATTATA
*
41033094 GTTTCGATTTTTGAACTACTCGATATATTCTGAATCGATCCGCTCCAGATTAGTATTTAATTTGA
196 GTTTCGATTTTTGAACTACTCGATATATTCTGAATCGATCCGCTCCAAATTAGTATTTAATTTGA
* * * *
41033159 AGAGTGAAGGTTTAAAATATCATGATGTTTGAG
261 AGAGTGGAGCTTAAAAACATCATGATGTTTGAG
* * * *
41033192 GCCAAGATGTAAAAGTCAAGCTTATCATGGAGAGGTCAGTGAAATTATAGTTTCGATTTTTGAAC
1 GCCAAGATGTAAAAGTCAAGCTTAACATGGAGA-GTCAGCGAAATTATTGTTTCGATTTTTTAAC
* * * * * * * *
41033257 TACTCGATATATTCTGAATCGATCCGCTCCAGATTAGTATTTAATTTGAAGAGTGAAGGTTTAAA
65 TACTCAATATATTCTAAATCGATCCGCTCCAAATTAGTACTTAATTTGAAGAATGGAGCTTAAAA
* *
41033322 ATATCATGATGTTTGAGGCCAAGATGTAAAAGTCAAGCTTATCATGGAGAGGT
130 ACATCATGATGTTGGAGGCCAAGATGTAAAAGTCAAGCTTATCATGGAGAGGT
41033375 TTTCATGGCT
Statistics
Matches: 749, Mismatches: 19, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
293 613 0.82
294 136 0.18
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.32
Consensus pattern (293 bp):
GCCAAGATGTAAAAGTCAAGCTTAACATGGAGAGTCAGCGAAATTATTGTTTCGATTTTTTAACT
ACTCAATATATTCTAAATCGATCCGCTCCAAATTAGTACTTAATTTGAAGAATGGAGCTTAAAAA
CATCATGATGTTGGAGGCCAAGATGTAAAAGTCAAGCTTATCATGGAGAGGTCAGTGAAATTATA
GTTTCGATTTTTGAACTACTCGATATATTCTGAATCGATCCGCTCCAAATTAGTATTTAATTTGA
AGAGTGGAGCTTAAAAACATCATGATGTTTGAG
Found at i:41033133 original size:440 final size:439
Alignment explanation
Indices: 41032313--41033372 Score: 1762
Period size: 440 Copynumber: 2.4 Consensus size: 439
41032303 TATTTAAAAA
* * * *
41032313 GCCAAGATGTAAAAGTCAAGCTTAACATGGAGA-GTCAGCGAAATTATTGTTTCGATTTTTTAAC
1 GCCAAGATGTAAAAGTCAAGCTTATCATGGAGAGGTCAGTGAAATTATAGTTTCGATTTTTGAAC
* * * *
41032377 TACTCAATATATTCTAAATCGATCCGCTCCAAATTAGTACTTAATTTGAAGAATGGAGCTTAAAA
66 TACTCGATATATTCTGAATCGATCCGCTCCAAATTAGTATTTAATTTGAAGAGTGGAGCTTAAAA
* *
41032442 ACATCATGATGTTGGAGGCCAAGATGTAAAAGTCAAGCTTATCATGGAGAGGTCAGTGAAATTAT
131 ACATCATGATGTTTGAGGCCAAGATGTAAAAGTCAAGCTTATCATGGAGA-GTCAGCGAAATTAT
* * *
41032507 AGTTTCGATTTTTGAACTACTCGATATATTCTGAATCGATCCGCTCCAAATTAGTATTTAATTTG
195 AGTTTCGATTTTTGAACTACTCAATATATTCTAAATCGATCCGCTCCAAATTAGTACTTAATTTG
* *
41032572 AAGAGTGGAGCTTAAAAACATCATGATGTTTGAGGCCAAGATGTAAAAGTCAAGCTTAACATGGA
260 AAGAATGGAGCTTAAAAACATCATGATGTTGGAGGCCAAGATGTAAAAGTCAAGCTTAACATGGA
* *
41032637 GAGTCAGCGAAATTATTGTTTCGATTTTTTAACTACTCAATATATTCTAAATCGATCCGCTCCAA
325 GAGTCAGCGAAATTATAGTTTCGATTTTTGAACTACTCAATATATTCTAAATCGATCCGCTCCAA
*
41032702 ATTAGTACTTAATTTGAAGAATGGAGCTTAAAAACATCATGATGTTGGAG
390 ATTAGTACTTAATTTGAAGAATGAAGCTTAAAAACATCATGATGTTGGAG
41032752 GCCAAGATGTAAAAGTCAAGCTTATCATGGAGAGGTCAGTGAAATTATAGTTTCGATTTTTGAAC
1 GCCAAGATGTAAAAGTCAAGCTTATCATGGAGAGGTCAGTGAAATTATAGTTTCGATTTTTGAAC
41032817 TACTCGATATATTCTGAATCGATCCGCTCCAAATTAGTATTTAATTTGAAGAGTGGAGCTTAAAA
66 TACTCGATATATTCTGAATCGATCCGCTCCAAATTAGTATTTAATTTGAAGAGTGGAGCTTAAAA
* *
41032882 ACATCATGATGTTTGAGGCCAAGATGTAAAAGTCAAGCTTAACATGGAGAGTCAGCGAAATTATT
131 ACATCATGATGTTTGAGGCCAAGATGTAAAAGTCAAGCTTATCATGGAGAGTCAGCGAAATTATA
*
41032947 GTTTCGATTTTTTAACTACTCAATATATTCTAAATCGATCCGCTCCAAATTAGTACTTAATTTGA
196 GTTTCGATTTTTGAACTACTCAATATATTCTAAATCGATCCGCTCCAAATTAGTACTTAATTTGA
*
41033012 AGAATGGAGCTTAAAAACATCATGATGTTGGAGGCCAAGATGTAAAAGTCAAGCTTATCATGGAG
261 AGAATGGAGCTTAAAAACATCATGATGTTGGAGGCCAAGATGTAAAAGTCAAGCTTAACATGGAG
* * * *
41033077 AGGTCAGTGAAATTATAGTTTCGATTTTTGAACTACTCGATATATTCTGAATCGATCCGCTCCAG
326 A-GTCAGCGAAATTATAGTTTCGATTTTTGAACTACTCAATATATTCTAAATCGATCCGCTCCAA
* * * * * *
41033142 ATTAGTATTTAATTTGAAGAGTGAAGGTTTAAAATATCATGATGTTTGAG
390 ATTAGTACTTAATTTGAAGAATGAAGCTTAAAAACATCATGATGTTGGAG
41033192 GCCAAGATGTAAAAGTCAAGCTTATCATGGAGAGGTCAGTGAAATTATAGTTTCGATTTTTGAAC
1 GCCAAGATGTAAAAGTCAAGCTTATCATGGAGAGGTCAGTGAAATTATAGTTTCGATTTTTGAAC
* * * *
41033257 TACTCGATATATTCTGAATCGATCCGCTCCAGATTAGTATTTAATTTGAAGAGTGAAGGTTTAAA
66 TACTCGATATATTCTGAATCGATCCGCTCCAAATTAGTATTTAATTTGAAGAGTGGAGCTTAAAA
*
41033322 ATATCATGATGTTTGAGGCCAAGATGTAAAAGTCAAGCTTATCATGGAGAG
131 ACATCATGATGTTTGAGGCCAAGATGTAAAAGTCAAGCTTATCATGGAGAG
41033373 GTTTTCATGG
Statistics
Matches: 581, Mismatches: 38, Indels: 3
0.93 0.06 0.00
Matches are distributed among these distances:
439 169 0.29
440 412 0.71
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.32
Consensus pattern (439 bp):
GCCAAGATGTAAAAGTCAAGCTTATCATGGAGAGGTCAGTGAAATTATAGTTTCGATTTTTGAAC
TACTCGATATATTCTGAATCGATCCGCTCCAAATTAGTATTTAATTTGAAGAGTGGAGCTTAAAA
ACATCATGATGTTTGAGGCCAAGATGTAAAAGTCAAGCTTATCATGGAGAGTCAGCGAAATTATA
GTTTCGATTTTTGAACTACTCAATATATTCTAAATCGATCCGCTCCAAATTAGTACTTAATTTGA
AGAATGGAGCTTAAAAACATCATGATGTTGGAGGCCAAGATGTAAAAGTCAAGCTTAACATGGAG
AGTCAGCGAAATTATAGTTTCGATTTTTGAACTACTCAATATATTCTAAATCGATCCGCTCCAAA
TTAGTACTTAATTTGAAGAATGAAGCTTAAAAACATCATGATGTTGGAG
Found at i:41035073 original size:121 final size:121
Alignment explanation
Indices: 41034338--41035064 Score: 1400
Period size: 121 Copynumber: 6.0 Consensus size: 121
41034328 TCACGATACT
*
41034338 ATAGTATCGTGACTAAATAAGTTTATAATTGATATGAGAAAACTTAGAACTTAATTATAAAATAT
1 ATAGTATTGTGACTAAATAAGTTTATAATTGATATGAGAAAACTTAGAACTTAATTATAAAATAT
41034403 TTGAGCCCTAATTACATATGTTTAGTCGGTCTCTTCCTTAACTCGTTGAAATCAGA
66 TTGAGCCCTAATTACATATGTTTAGTCGGTCTCTTCCTTAACTCGTTGAAATCAGA
41034459 ATAGTATTGTGACTAAATAAGTTTATAATTGATATGAGAAAACTTAGAACTTAATTATAAAATAT
1 ATAGTATTGTGACTAAATAAGTTTATAATTGATATGAGAAAACTTAGAACTTAATTATAAAATAT
41034524 TTGAGCCCTAATTACATATGTTTAGTCGGTCTCTTCCTTAACTCGTTGAAATCAGA
66 TTGAGCCCTAATTACATATGTTTAGTCGGTCTCTTCCTTAACTCGTTGAAATCAGA
41034580 ATAGTATTGTGACTAAATAAGTTTATAATTGATATGAGAAAACTTAGAACTTAATTATAAAATAT
1 ATAGTATTGTGACTAAATAAGTTTATAATTGATATGAGAAAACTTAGAACTTAATTATAAAATAT
41034645 TTGAGCCCTAATTACATATGTTTAGTCGGTCTCTTCCTTAACTCGTTGAAATCAGA
66 TTGAGCCCTAATTACATATGTTTAGTCGGTCTCTTCCTTAACTCGTTGAAATCAGA
41034701 ATAGTATTGTGACTAAATAAGTTTATAATTGATATGAGAAAACTTAGAACTTAATTATAAAATAT
1 ATAGTATTGTGACTAAATAAGTTTATAATTGATATGAGAAAACTTAGAACTTAATTATAAAATAT
41034766 TTGAGCCCTAATTACATATGTTTAGTCGGTCTCTTCCTTAACTCGTTGAAATCAGA
66 TTGAGCCCTAATTACATATGTTTAGTCGGTCTCTTCCTTAACTCGTTGAAATCAGA
41034822 ATAGTATTGTGACTAAATAAGTTTATAATTGATATGAGAAAACTTAGAACTTAATTATAAAATAT
1 ATAGTATTGTGACTAAATAAGTTTATAATTGATATGAGAAAACTTAGAACTTAATTATAAAATAT
41034887 TTGAGCCCTAATTACATATGTTTAGTCGGTCTCTTCCTTAACTCGTTGAAATCAGA
66 TTGAGCCCTAATTACATATGTTTAGTCGGTCTCTTCCTTAACTCGTTGAAATCAGA
*
41034943 ATAGTATTGTGACTAAATAAGTTTATAATTGATATGAGAAAACTTAAAACTTAATTATAAAATAT
1 ATAGTATTGTGACTAAATAAGTTTATAATTGATATGAGAAAACTTAGAACTTAATTATAAAATAT
* * * *
41035008 TTGAACCCTAATTACATATGTTTAGTTGGTCTCTCCCCTAACTCGTTGAAATCAGA
66 TTGAGCCCTAATTACATATGTTTAGTCGGTCTCTTCCTTAACTCGTTGAAATCAGA
41035064 A
1 A
41035065 ATGAATTGTA
Statistics
Matches: 600, Mismatches: 6, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
121 600 1.00
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.37
Consensus pattern (121 bp):
ATAGTATTGTGACTAAATAAGTTTATAATTGATATGAGAAAACTTAGAACTTAATTATAAAATAT
TTGAGCCCTAATTACATATGTTTAGTCGGTCTCTTCCTTAACTCGTTGAAATCAGA
Found at i:41043412 original size:147 final size:147
Alignment explanation
Indices: 41043045--41043479 Score: 728
Period size: 147 Copynumber: 3.0 Consensus size: 147
41043035 TGTAATGGTA
*
41043045 AAATTATAGTTTCGATTTTTTAATTACTCGATATATTCTGAATCGATCCGCTCCAAATTAGTATT
1 AAATTATAGTTTCGATTTTTTAACTACTCGATATATTCTGAATCGATCCGCTCCAAATTAGTATT
41043110 TAATTTGAAGAGTGGAGCTTAAAAACATCATGATGTTTGAGGCCAAGATGTAAAAGTCAAGCTTA
66 TAATTTGAAGAGTGGAGCTTAAAAACATCATGATGTTTGAGGCCAAGATGTAAAAGTCAAGCTTA
*
41043175 ACATGGAGA-GTCAGCG
131 TCATGGAGAGGTCAGCG
* * * *
41043191 AAATTATTGTTTCGATTTTTTAACTACTCAATATATTCTAAATCGATCCGCTCCAAATTAGTACT
1 AAATTATAGTTTCGATTTTTTAACTACTCGATATATTCTGAATCGATCCGCTCCAAATTAGTATT
* *
41043256 TAATTTGAAGAATGGAGCTTAAAAACATCATGATGTTGGAGGCCAAGATGTAAAAGTCAAGCTTA
66 TAATTTGAAGAGTGGAGCTTAAAAACATCATGATGTTTGAGGCCAAGATGTAAAAGTCAAGCTTA
*
41043321 TCATGGAGAGGTCAGTG
131 TCATGGAGAGGTCAGCG
* *
41043338 AAATTATAGTTTCGATTTTTGAACTACTCGATATATTCTGAATCGATCCGCTCCAGATTAGTATT
1 AAATTATAGTTTCGATTTTTTAACTACTCGATATATTCTGAATCGATCCGCTCCAAATTAGTATT
* * * *
41043403 TAATTTGAAGAGTGAAGGTTTAAAATATCATGATGTTTGAGGCCAAGATGTAAAAGTCAAGCTTA
66 TAATTTGAAGAGTGGAGCTTAAAAACATCATGATGTTTGAGGCCAAGATGTAAAAGTCAAGCTTA
41043468 TCATGGAGAGGT
131 TCATGGAGAGGT
41043480 TTTCATGGCT
Statistics
Matches: 267, Mismatches: 21, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
146 131 0.49
147 136 0.51
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.33
Consensus pattern (147 bp):
AAATTATAGTTTCGATTTTTTAACTACTCGATATATTCTGAATCGATCCGCTCCAAATTAGTATT
TAATTTGAAGAGTGGAGCTTAAAAACATCATGATGTTTGAGGCCAAGATGTAAAAGTCAAGCTTA
TCATGGAGAGGTCAGCG
Found at i:41044640 original size:121 final size:121
Alignment explanation
Indices: 41044443--41044685 Score: 432
Period size: 121 Copynumber: 2.0 Consensus size: 121
41044433 TCACGATACT
*
41044443 ATAGTATCGTGACTAAATAAGTTTATAATTGATATGAGAAAACTTAGAACTTAATTATAAAATAT
1 ATAGTATCGTGACTAAATAAGTTTATAATTGATATGAGAAAACTTAAAACTTAATTATAAAATAT
* * *
41044508 TTGAGCCCTAATTACATATGTTTAGTCGGTCTCTTCCTTAACTCGTTGAAATCAGA
66 TTGAACCCTAATTACATATGTTTAGTCGGTCTCTCCCCTAACTCGTTGAAATCAGA
*
41044564 ATAGTATTGTGACTAAATAAGTTTATAATTGATATGAGAAAACTTAAAACTTAATTATAAAATAT
1 ATAGTATCGTGACTAAATAAGTTTATAATTGATATGAGAAAACTTAAAACTTAATTATAAAATAT
*
41044629 TTGAACCCTAATTACATATGTTTAGTTGGTCTCTCCCCTAACTCGTTGAAATCAGA
66 TTGAACCCTAATTACATATGTTTAGTCGGTCTCTCCCCTAACTCGTTGAAATCAGA
41044685 A
1 A
41044686 ATGAATTGTA
Statistics
Matches: 116, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
121 116 1.00
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.36
Consensus pattern (121 bp):
ATAGTATCGTGACTAAATAAGTTTATAATTGATATGAGAAAACTTAAAACTTAATTATAAAATAT
TTGAACCCTAATTACATATGTTTAGTCGGTCTCTCCCCTAACTCGTTGAAATCAGA
Found at i:41053065 original size:11 final size:11
Alignment explanation
Indices: 41053041--41053073 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
41053031 ATGATAAAAA
*
41053041 ATAAAAATCA-
1 ATAAAAATTAT
41053051 ATAAAAATTAT
1 ATAAAAATTAT
41053062 ATAAAAATTAT
1 ATAAAAATTAT
41053073 A
1 A
41053074 AAATACTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
10 9 0.43
11 12 0.57
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (11 bp):
ATAAAAATTAT
Found at i:41053184 original size:19 final size:19
Alignment explanation
Indices: 41053157--41053193 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
41053147 TATAAAAGTT
*
41053157 TATAAATTTTTTATATTTC
1 TATAAATTTTATATATTTC
*
41053176 TATATATTTTATATATTT
1 TATAAATTTTATATATTT
41053194 TTAATGATTT
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:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (19 bp):
TATAAATTTTATATATTTC
Found at i:41053195 original size:10 final size:10
Alignment explanation
Indices: 41053155--41053214 Score: 65
Period size: 9 Copynumber: 6.3 Consensus size: 10
41053145 TTTATAAAAG
*
41053155 TTTATAAATT
1 TTTATATATT
41053165 TTT-TATATT
1 TTTATATATT
*
41053174 TCTATATA-T
1 TTTATATATT
41053183 TTTATATATT
1 TTTATATATT
41053193 TTTA-ATGATT
1 TTTATAT-ATT
41053203 TTTATA-ATT
1 TTTATATATT
41053212 TTT
1 TTT
41053215 CCTATTTTTA
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
9 23 0.53
10 19 0.44
11 1 0.02
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (10 bp):
TTTATATATT
Found at i:41053203 original size:19 final size:18
Alignment explanation
Indices: 41053164--41053214 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 18
41053154 GTTTATAAAT
*
41053164 TTTTTATATTTCTATATA
1 TTTTTATATTTTTATATA
41053182 TTTTATATATTTTTA-ATGA
1 TTTT-TATATTTTTATAT-A
41053201 TTTTTATAATTTTT
1 TTTTTAT-ATTTTT
41053215 CCTATTTTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 9 0.31
19 20 0.69
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (18 bp):
TTTTTATATTTTTATATA
Found at i:41053248 original size:28 final size:29
Alignment explanation
Indices: 41053179--41053248 Score: 72
Period size: 28 Copynumber: 2.4 Consensus size: 29
41053169 ATATTTCTAT
* **
41053179 ATATTTTATATATTTTTAATGATTTTTATA
1 ATATTTT-TATATTTTTAATAAAATTTATA
**
41053209 AT-TTTTCCTATTTTTAATAAAATTTA-A
1 ATATTTTTATATTTTTAATAAAATTTATA
41053236 ATATTTTTATATT
1 ATATTTTTATATT
41053249 CTTTTATTAA
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
27 3 0.09
28 23 0.72
29 4 0.12
30 2 0.06
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.61
Consensus pattern (29 bp):
ATATTTTTATATTTTTAATAAAATTTATA
Done.