Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D05
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: 64368997
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1610000 characters in sequence are not A, C, G, or T
File 49 of 208
Found at i:19025627 original size:20 final size:21
Alignment explanation
Indices: 19025577--19025620 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
19025567 AGTTAAAATT
*
19025577 AATA-TAAATAATTTATAATA
1 AATACTAAGTAATTTATAATA
*
19025597 AATACTAAGTAATTTA-ATTA
1 AATACTAAGTAATTTATAATA
19025617 AATA
1 AATA
19025621 TTTAGTAGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (21 bp):
AATACTAAGTAATTTATAATA
Found at i:19030069 original size:16 final size:16
Alignment explanation
Indices: 19030019--19030069 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
19030009 TATTTTTATT
19030019 TTTTAATTTTAAAATA
1 TTTTAATTTTAAAATA
* * *
19030035 CTTTT--TTTTTAATTT
1 -TTTTAATTTTAAAATA
19030050 TTTTAATTTTAAAATA
1 TTTTAATTTTAAAATA
19030066 TTTT
1 TTTT
19030070 TAAAATACTT
Statistics
Matches: 26, Mismatches: 6, Indels: 5
0.70 0.16 0.14
Matches are distributed among these distances:
14 4 0.15
15 7 0.27
16 11 0.42
17 4 0.15
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTTAATTTTAAAATA
Found at i:19030082 original size:31 final size:29
Alignment explanation
Indices: 19030015--19030122 Score: 100
Period size: 31 Copynumber: 3.7 Consensus size: 29
19030005 TAAATATTTT
**
19030015 TATTTTTTAATTTTAAAATACTTTTTTTTTAA
1 TATTTTTTAATTTTAAAATA---TTTTTAAAA
19030047 T-TTTTTTAATTTTAAAATATTTTTAAAA
1 TATTTTTTAATTTTAAAATATTTTTAAAA
*
19030075 TACTTTTTTAATTTT----TAATTTTAAAA
1 TA-TTTTTTAATTTTAAAATATTTTTAAAA
19030101 TAATTTTTTAATTTTTAAAATA
1 T-ATTTTTTAA-TTTTAAAATA
19030123 AATTTTTGGT
Statistics
Matches: 65, Mismatches: 3, Indels: 17
0.76 0.04 0.20
Matches are distributed among these distances:
26 19 0.29
27 5 0.08
28 8 0.12
30 12 0.18
31 20 0.31
32 1 0.02
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (29 bp):
TATTTTTTAATTTTAAAATATTTTTAAAA
Found at i:19030088 original size:20 final size:19
Alignment explanation
Indices: 19030086--19030129 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 19
19030076 ACTTTTTTAA
19030086 TTTTTAATTTTAAAATAAT
1 TTTTTAATTTTAAAATAAT
19030105 TTTTTAATTTTTAAAATAAAT
1 TTTTTAA-TTTTAAAAT-AAT
19030126 TTTT
1 TTTT
19030130 GGTATTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 7 0.30
20 9 0.39
21 7 0.30
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
TTTTTAATTTTAAAATAAT
Found at i:19030096 original size:26 final size:26
Alignment explanation
Indices: 19030067--19030118 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
19030057 TTTAAAATAT
*
19030067 TTTTAAAATACTTTTTTAATTTTTAA
1 TTTTAAAATAATTTTTTAATTTTTAA
19030093 TTTTAAAATAATTTTTTAATTTTTAA
1 TTTTAAAATAATTTTTTAATTTTTAA
19030119 AATAAATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (26 bp):
TTTTAAAATAATTTTTTAATTTTTAA
Found at i:19030849 original size:7 final size:7
Alignment explanation
Indices: 19030837--19030874 Score: 76
Period size: 7 Copynumber: 5.4 Consensus size: 7
19030827 TAATAAAAAC
19030837 AAATTAG
1 AAATTAG
19030844 AAATTAG
1 AAATTAG
19030851 AAATTAG
1 AAATTAG
19030858 AAATTAG
1 AAATTAG
19030865 AAATTAG
1 AAATTAG
19030872 AAA
1 AAA
19030875 ATAATTTTCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.61, C:0.00, G:0.13, T:0.26
Consensus pattern (7 bp):
AAATTAG
Found at i:19033382 original size:25 final size:26
Alignment explanation
Indices: 19033348--19033396 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
19033338 AGTGGTAGTC
*
19033348 TCTAGGCATA-TTTGTGAAAAGGAAT
1 TCTAGGCATATTTTGCGAAAAGGAAT
19033373 TCTAGGCATATTTTGCGAAAAGGA
1 TCTAGGCATATTTTGCGAAAAGGA
19033397 GTAAGTGTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 10 0.45
26 12 0.55
ACGTcount: A:0.35, C:0.10, G:0.24, T:0.31
Consensus pattern (26 bp):
TCTAGGCATATTTTGCGAAAAGGAAT
Found at i:19056221 original size:21 final size:20
Alignment explanation
Indices: 19056176--19056215 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
19056166 CACGACCAAC
19056176 AAATATATTAATATATAAGCA
1 AAATATATTAATATATAA-CA
*
19056197 AAATATAATTATTATATAA
1 AAATAT-ATTAATATATAA
19056216 ATAAATTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.38
Consensus pattern (20 bp):
AAATATATTAATATATAACA
Found at i:19060556 original size:17 final size:18
Alignment explanation
Indices: 19060536--19060570 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
19060526 TTTATTAATT
*
19060536 TTAAAATTTTAAA-AAAA
1 TTAAAATATTAAATAAAA
19060553 TTAAAATATTAAATAAAA
1 TTAAAATATTAAATAAAA
19060571 AAATTCTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
TTAAAATATTAAATAAAA
Found at i:19064360 original size:19 final size:18
Alignment explanation
Indices: 19064308--19064364 Score: 57
Period size: 19 Copynumber: 3.2 Consensus size: 18
19064298 TTGAAAATAA
19064308 TTATAATTG-TAATAATT
1 TTATAATTGTTAATAATT
*
19064325 TT-TAATCAT-TTATTAATT
1 TTATAAT--TGTTAATAATT
19064343 TTATAATTGTTAAATAATT
1 TTATAATTGTT-AATAATT
19064362 TTA
1 TTA
19064365 AAAATTTCTA
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
16 4 0.12
17 3 0.09
18 12 0.38
19 13 0.41
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.56
Consensus pattern (18 bp):
TTATAATTGTTAATAATT
Found at i:19064495 original size:21 final size:21
Alignment explanation
Indices: 19064471--19064523 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
19064461 CGCTGTTTCT
* *
19064471 AATCTCACTGCTACAGTACCC
1 AATCTCACCGCTACAGTAACC
*
19064492 AATCTCACCGCTACAGTAACT
1 AATCTCACCGCTACAGTAACC
19064513 AATCTCACCGC
1 AATCTCACCGC
19064524 CACCGCTGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.30, C:0.38, G:0.09, T:0.23
Consensus pattern (21 bp):
AATCTCACCGCTACAGTAACC
Found at i:19081342 original size:46 final size:46
Alignment explanation
Indices: 19081277--19081544 Score: 206
Period size: 36 Copynumber: 6.5 Consensus size: 46
19081267 TGAGTACTTT
* * *
19081277 TGATCAAGAGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTGTT
1 TGATCAAGAGAAAAAGTGATAAGTGGTAGCTTTAGCTACACTTATC
*
19081323 TGATCAAGTGAAAAAGTGAT-A-----AG---T-GCTACACTTATC
1 TGATCAAGAGAAAAAGTGATAAGTGGTAGCTTTAGCTACACTTATC
*
19081359 TGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATC
1 TGATCAAGAGAAAAAGTGATAAGTGGTAGCTTTAGCTACACTTATC
*
19081405 TGATCAAGTGAAAAAGTGATAA---GT-G--TTA--T--ACTTATC
1 TGATCAAGAGAAAAAGTGATAAGTGGTAGCTTTAGCTACACTTATC
*
19081441 TGATCAAGTGAAAAAGTGATAA---GT-GC--TA--T--ACTTATC
1 TGATCAAGAGAAAAAGTGATAAGTGGTAGCTTTAGCTACACTTATC
* *
19081477 TGATCAAGTGACAAAGTGATAAGTGGTAGC-TTAGCTACACTTATC
1 TGATCAAGAGAAAAAGTGATAAGTGGTAGCTTTAGCTACACTTATC
* *
19081522 TGGTCAAG-GACAAA-TGATAAGTG
1 TGATCAAGAGAAAAAGTGATAAGTG
19081545 ATCATACGTA
Statistics
Matches: 192, Mismatches: 10, Indels: 43
0.78 0.04 0.18
Matches are distributed among these distances:
36 91 0.47
37 2 0.01
38 1 0.01
39 2 0.01
40 7 0.04
41 2 0.01
42 3 0.02
43 12 0.06
44 6 0.03
45 16 0.08
46 50 0.26
ACGTcount: A:0.36, C:0.12, G:0.22, T:0.29
Consensus pattern (46 bp):
TGATCAAGAGAAAAAGTGATAAGTGGTAGCTTTAGCTACACTTATC
Found at i:19081352 original size:36 final size:36
Alignment explanation
Indices: 19081311--19081501 Score: 220
Period size: 36 Copynumber: 5.0 Consensus size: 36
19081301 GGTAGCTTTA
* *
19081311 GCTACACTTGTTTGATCAAGTGAAAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
* *
19081347 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGAT-A-----AG---T
19081392 AGCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 -GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
* *
19081429 GTTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
* *
19081465 GCTATACTTATCTGATCAAGTGACAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
19081501 G
1 G
19081502 GTAGCTTAGC
Statistics
Matches: 135, Mismatches: 10, Indels: 20
0.82 0.06 0.12
Matches are distributed among these distances:
36 97 0.72
37 2 0.01
40 2 0.01
42 2 0.01
45 2 0.01
46 30 0.22
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.30
Consensus pattern (36 bp):
GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
Found at i:19081414 original size:82 final size:82
Alignment explanation
Indices: 19081277--19081465 Score: 315
Period size: 82 Copynumber: 2.3 Consensus size: 82
19081267 TGAGTACTTT
* * *
19081277 TGATCAAGAGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTGTTTGATCAAGTGAAAAAGTGA
1 TGATCAAGAGAAAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGTGA
19081342 TAAGTGCTACACTTATC
66 TAAGTGCTACACTTATC
*
19081359 TGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGTGA
1 TGATCAAGAGAAAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGTGA
* *
19081424 TAAGTGTTATACTTATC
66 TAAGTGCTACACTTATC
*
19081441 TGATCAAGTGAAAAAGTGATAAGTG
1 TGATCAAGAGAAAAAGTGATAAGTG
19081466 CTATACTTAT
Statistics
Matches: 100, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
82 100 1.00
ACGTcount: A:0.37, C:0.11, G:0.22, T:0.30
Consensus pattern (82 bp):
TGATCAAGAGAAAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGTGA
TAAGTGCTACACTTATC
Found at i:19084205 original size:42 final size:42
Alignment explanation
Indices: 19084059--19084205 Score: 132
Period size: 42 Copynumber: 3.5 Consensus size: 42
19084049 TTGAAGGCTG
* * * * * * *
19084059 AACAGAAGCACATAAGTGCTAAACAGAAACCCCATGAGGGTTG
1 AACAGAAGCTCATAAGAGTTGAACGGAAA-CCCATAAGGGTTA
* * * *
19084102 AACGGAAGCTCATAAGAGCTGAATGAAAACCCATAAGGGTTA
1 AACAGAAGCTCATAAGAGTTGAACGGAAACCCATAAGGGTTA
** * *
19084144 AATTGAAGCTCAAAAGAGTTGAACGGAAACCCATTAGGGTTA
1 AACAGAAGCTCATAAGAGTTGAACGGAAACCCATAAGGGTTA
* *
19084186 AACAGAAACTCATATGAGTT
1 AACAGAAGCTCATAAGAGTT
19084206 AATAGAAGCT
Statistics
Matches: 83, Mismatches: 21, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
42 61 0.73
43 22 0.27
ACGTcount: A:0.42, C:0.17, G:0.22, T:0.18
Consensus pattern (42 bp):
AACAGAAGCTCATAAGAGTTGAACGGAAACCCATAAGGGTTA
Found at i:19085867 original size:31 final size:31
Alignment explanation
Indices: 19085805--19085868 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 31
19085795 CACATTCTAT
** *
19085805 ATATTTTAATTAAGTATTTTTTATTTTTATA
1 ATATTTTAATTAAGTAAATTTTATTTATATA
*
19085836 ATATTTT-ATTATGTAAATTTTATTTAATATA
1 ATATTTTAATTAAGTAAATTTTATTT-ATATA
19085867 AT
1 AT
19085869 TAAAATACTA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 15 0.54
31 13 0.46
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (31 bp):
ATATTTTAATTAAGTAAATTTTATTTATATA
Found at i:19090103 original size:21 final size:22
Alignment explanation
Indices: 19090056--19090109 Score: 65
Period size: 21 Copynumber: 2.4 Consensus size: 22
19090046 AATTATTTTG
19090056 TTCAATTAATAAATTTTTAAAAAT
1 TTCAATT-A-AAATTTTTAAAAAT
* *
19090080 TTCGATTAAAATTTTT-AAAGT
1 TTCAATTAAAATTTTTAAAAAT
19090101 TTCAATTAA
1 TTCAATTAA
19090110 TAATAATTGG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 12 0.44
22 8 0.30
23 1 0.04
24 6 0.22
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (22 bp):
TTCAATTAAAATTTTTAAAAAT
Found at i:19090941 original size:126 final size:126
Alignment explanation
Indices: 19090516--19090981 Score: 756
Period size: 124 Copynumber: 3.7 Consensus size: 126
19090506 CGTCTCTGGT
* * * * *
19090516 CAAATAGTATAAAATCGCTTCTACCAGGATGCTGTTTGAGAATAAATTGTGAAATCGCGCCCCCG
1 CAAATAGTATAAAATCGTTTCTACGAGGATGCTATTTGAGAAGAAATTGTGAAATCGCGCCCTCG
* *
19090581 TGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTTTTTTCTGATTTTTCTGAG
66 TGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAA--TTTTTTTTCTGATGTTTCTAAG
* * *
19090644 CAAATAGTATAAAACCGTTTGTACGAGGATGCTATTTGAGAAGAAATTGTGAAATCGTGCCCTCG
1 CAAATAGTATAAAATCGTTTCTACGAGGATGCTATTTGAGAAGAAATTGTGAAATCGCGCCCTCG
*
19090709 TGGATGCGATTTTGCTACAGTAGGTCATGTAAGAAAT-A-TTTTTTTCTGATGTTTCTAAG
66 TGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTTTTCTGATGTTTCTAAG
* * *
19090768 CAAATAGTATAAAATCGTTTGTACGAGGATGCTATTTGAGAAAAAATTGTGAAATCGTGCCCTCG
1 CAAATAGTATAAAATCGTTTCTACGAGGATGCTATTTGAGAAGAAATTGTGAAATCGCGCCCTCG
* *
19090833 TGGATGCGATTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTTTTCTAATGTTTCTAAG
66 TGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTTTTCTGATGTTTCTAAG
19090894 CAAATAGTATAAAATCGTTTCTACGAGGATGCTATTTGAGAAGAAATTGTGAAATCGCGCCCTCG
1 CAAATAGTATAAAATCGTTTCTACGAGGATGCTATTTGAGAAGAAATTGTGAAATCGCGCCCTCG
19090959 TGGACGCGATTTTGCTACAGTAG
66 TGGACGCGATTTTGCTACAGTAG
19090982 CAAGTTTGGG
Statistics
Matches: 318, Mismatches: 18, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
124 119 0.37
125 1 0.00
126 104 0.33
127 1 0.00
128 93 0.29
ACGTcount: A:0.30, C:0.14, G:0.22, T:0.34
Consensus pattern (126 bp):
CAAATAGTATAAAATCGTTTCTACGAGGATGCTATTTGAGAAGAAATTGTGAAATCGCGCCCTCG
TGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTTTTCTGATGTTTCTAAG
Found at i:19090979 original size:250 final size:251
Alignment explanation
Indices: 19090516--19090981 Score: 781
Period size: 250 Copynumber: 1.9 Consensus size: 251
19090506 CGTCTCTGGT
* *
19090516 CAAATAGTATAAAATCGCTTCTACCAGGATGCTGTTTGAGAATAAATTGTGAAATCGCGCCCCCG
1 CAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAAAAATTGTGAAATCGCGCCCCCG
* * *
19090581 TGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTTTTTTCTGATTTTTCTGAGCA
66 TGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAA-TTTTTTTTTCTAATGTTTCTAAGCA
* *
19090646 AATAGTATAAAACCGTTTGTACGAGGATGCTATTTGAGAAGAAATTGTGAAATCGTGCCCTCGTG
130 AATAGTATAAAACCGTTTCTACGAGGATGCTATTTGAGAAGAAATTGTGAAATCGCGCCCTCGTG
*
19090711 GATGCGATTTTGCTACAGTAGGTCATGTAAGAAATATTTTTTTCTGATGTTTCTAAG
195 GACGCGATTTTGCTACAGTAGGTCATGTAAGAAATATTTTTTTCTGATGTTTCTAAG
* * * * *
19090768 CAAATAGTATAAAATCGTTTGTACGAGGATGCTATTTGAGAAAAAATTGTGAAATCGTGCCCTCG
1 CAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAAAAATTGTGAAATCGCGCCCCCG
*
19090833 TGGATGCGATTTTGCTACAGTAGGTCATGTAAGAAATAA-TTTTTTTTCTAATGTTTCTAAGCAA
66 TGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTTTTTCTAATGTTTCTAAGCAA
*
19090897 ATAGTATAAAATCGTTTCTACGAGGATGCTATTTGAGAAGAAATTGTGAAATCGCGCCCTCGTGG
131 ATAGTATAAAACCGTTTCTACGAGGATGCTATTTGAGAAGAAATTGTGAAATCGCGCCCTCGTGG
19090962 ACGCGATTTTGCTACAGTAG
196 ACGCGATTTTGCTACAGTAG
19090982 CAAGTTTGGG
Statistics
Matches: 199, Mismatches: 15, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
250 103 0.52
252 96 0.48
ACGTcount: A:0.30, C:0.14, G:0.22, T:0.34
Consensus pattern (251 bp):
CAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAAAAATTGTGAAATCGCGCCCCCG
TGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTTTTTCTAATGTTTCTAAGCAA
ATAGTATAAAACCGTTTCTACGAGGATGCTATTTGAGAAGAAATTGTGAAATCGCGCCCTCGTGG
ACGCGATTTTGCTACAGTAGGTCATGTAAGAAATATTTTTTTCTGATGTTTCTAAG
Found at i:19093317 original size:29 final size:29
Alignment explanation
Indices: 19093275--19093337 Score: 90
Period size: 29 Copynumber: 2.2 Consensus size: 29
19093265 GCCATTGATG
* *
19093275 AAAATATAAAAAAATTTAAAATTATTTTA
1 AAAAAATAAAAAAAATTAAAATTATTTTA
* *
19093304 AAAAAATATAAAAAATTATAATTATTTTA
1 AAAAAATAAAAAAAATTAAAATTATTTTA
19093333 AAAAA
1 AAAAA
19093338 TGGATTTGAG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (29 bp):
AAAAAATAAAAAAAATTAAAATTATTTTA
Found at i:19093408 original size:22 final size:22
Alignment explanation
Indices: 19093383--19093433 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
19093373 AAATATGAGT
19093383 TTGAGAGAATTTTGGAAGGAAA
1 TTGAGAGAATTTTGGAAGGAAA
19093405 TTGAGAGAATTTTGGAAGGAAA
1 TTGAGAGAATTTTGGAAGGAAA
19093427 TTGAGAG
1 TTGAGAG
19093434 GATTAGAGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.39, C:0.00, G:0.33, T:0.27
Consensus pattern (22 bp):
TTGAGAGAATTTTGGAAGGAAA
Found at i:19096146 original size:19 final size:20
Alignment explanation
Indices: 19096110--19096149 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
19096100 GATTAATGGG
19096110 AAAAAAAGAAAACAATAATA
1 AAAAAAAGAAAACAATAATA
19096130 AAAAGAAAG-AAAC-ATAATA
1 AAAA-AAAGAAAACAATAATA
19096149 A
1 A
19096150 CAATAACCCT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.37
20 8 0.42
21 4 0.21
ACGTcount: A:0.78, C:0.05, G:0.07, T:0.10
Consensus pattern (20 bp):
AAAAAAAGAAAACAATAATA
Found at i:19102481 original size:7 final size:7
Alignment explanation
Indices: 19102469--19102493 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
19102459 CTCAAATGGG
19102469 TGAAATT
1 TGAAATT
19102476 TGAAATT
1 TGAAATT
19102483 TGAAATT
1 TGAAATT
19102490 TGAA
1 TGAA
19102494 GCCATTGCAA
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:0.44, C:0.00, G:0.16, T:0.40
Consensus pattern (7 bp):
TGAAATT
Found at i:19108963 original size:47 final size:47
Alignment explanation
Indices: 19108897--19109050 Score: 173
Period size: 41 Copynumber: 3.4 Consensus size: 47
19108887 TAGGCAATAA
* *
19108897 GGGATGTGCAGGCAATGGTGGTGGTGGTGGTGGTGGTTTTGGCAGGG
1 GGGAGGTGTAGGCAATGGTGGTGGTGGTGGTGGTGGTTTTGGCAGGG
19108944 GGGAGGTGTAGGCAA------TGGTGGTGGTGGTGGTTTTGGCAGGG
1 GGGAGGTGTAGGCAATGGTGGTGGTGGTGGTGGTGGTTTTGGCAGGG
* * *
19108985 GGGAGGTGTAGGCAATGGTGGT-CT--TGGTGGAGGTTTCGGCAGAGG
1 GGGAGGTGTAGGCAATGGTGGTGGTGGTGGTGGTGGTTTTGGCAG-GG
* *
19109030 GGGAGGTATGGGCAATGGTGG
1 GGGAGGTGTAGGCAATGGTGG
19109051 AACCGGGGGT
Statistics
Matches: 93, Mismatches: 7, Indels: 16
0.80 0.06 0.14
Matches are distributed among these distances:
41 41 0.44
44 16 0.17
45 21 0.23
46 1 0.01
47 14 0.15
ACGTcount: A:0.14, C:0.06, G:0.55, T:0.25
Consensus pattern (47 bp):
GGGAGGTGTAGGCAATGGTGGTGGTGGTGGTGGTGGTTTTGGCAGGG
Found at i:19108969 original size:41 final size:41
Alignment explanation
Indices: 19108918--19109050 Score: 194
Period size: 41 Copynumber: 3.1 Consensus size: 41
19108908 GCAATGGTGG
19108918 TGGTGGTGGTGGTGGTTTTGGCAGGGGGGAGGTGTAGGCAA
1 TGGTGGTGGTGGTGGTTTTGGCAGGGGGGAGGTGTAGGCAA
19108959 TGGTGGTGGTGGTGGTTTTGGCAGGGGGGAGGTGTAGGCAA
1 TGGTGGTGGTGGTGGTTTTGGCAGGGGGGAGGTGTAGGCAA
* * * *
19109000 TGGTGGTCTTGGTGGAGGTTTCGGCAGAGGGGGAGGTATGGGCAA
1 TGGTGG---TGGTGGTGGTTTTGGCAG-GGGGGAGGTGTAGGCAA
19109045 TGGTGG
1 TGGTGG
19109051 AACCGGGGGT
Statistics
Matches: 84, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
41 47 0.56
44 16 0.19
45 21 0.25
ACGTcount: A:0.13, C:0.06, G:0.55, T:0.26
Consensus pattern (41 bp):
TGGTGGTGGTGGTGGTTTTGGCAGGGGGGAGGTGTAGGCAA
Found at i:19117152 original size:57 final size:58
Alignment explanation
Indices: 19117050--19117168 Score: 186
Period size: 57 Copynumber: 2.1 Consensus size: 58
19117040 AAATCAATGT
* * *
19117050 ATTTAATTTGATTTTAGGTTGGTATATTATTTAAATTACATAATTCAATTTGGATTTG
1 ATTTAATTTGATTTTAGGTTGGTATATTATTAAAATCACACAATTCAATTTGGATTTG
* *
19117108 ATTT-ATTTGATTTTAGGTTGGTGTATTATTAAAATCGCACAATTCAATTTGGATTTG
1 ATTTAATTTGATTTTAGGTTGGTATATTATTAAAATCACACAATTCAATTTGGATTTG
19117165 ATTT
1 ATTT
19117169 TTCACATGAA
Statistics
Matches: 56, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
57 52 0.93
58 4 0.07
ACGTcount: A:0.29, C:0.05, G:0.15, T:0.50
Consensus pattern (58 bp):
ATTTAATTTGATTTTAGGTTGGTATATTATTAAAATCACACAATTCAATTTGGATTTG
Found at i:19121816 original size:53 final size:52
Alignment explanation
Indices: 19121758--19121859 Score: 118
Period size: 53 Copynumber: 1.9 Consensus size: 52
19121748 AAATCCCCAG
*
19121758 CCTTTTA-TTTTATCCCCAAAACTTTTACTTCCCCCTAAATCCCT-CAAAATATT
1 CCTTTTACTTTCAT-CCCAAAACTTTTACTTCCCCC-AAA-CCCTCCAAAATATT
** * *
19121811 CCTTTTACTTTCATCTTAAGACTTTTACTTTCCCCAAACCCTCCAAAAT
1 CCTTTTACTTTCATCCCAAAACTTTTACTTCCCCCAAACCCTCCAAAAT
19121860 TTTTTCCTCT
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
51 4 0.10
52 9 0.21
53 24 0.57
54 5 0.12
ACGTcount: A:0.27, C:0.32, G:0.01, T:0.39
Consensus pattern (52 bp):
CCTTTTACTTTCATCCCAAAACTTTTACTTCCCCCAAACCCTCCAAAATATT
Found at i:19123619 original size:6 final size:6
Alignment explanation
Indices: 19123608--19123632 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
19123598 AATGGTTTAA
19123608 TTCAAT TTCAAT TTCAAT TTCAAT T
1 TTCAAT TTCAAT TTCAAT TTCAAT T
19123633 AAATAATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.16, G:0.00, T:0.52
Consensus pattern (6 bp):
TTCAAT
Found at i:19125941 original size:20 final size:21
Alignment explanation
Indices: 19125911--19125959 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
19125901 TATATAAAAA
*
19125911 TATTATTGTAATAA-TATAATT
1 TATT-TTGTAAAAAGTATAATT
*
19125932 TATTTTGTAAAAAGTATGATT
1 TATTTTGTAAAAAGTATAATT
19125953 T-TTTTGT
1 TATTTTGT
19125960 CATTTTCCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 14 0.56
21 11 0.44
ACGTcount: A:0.35, C:0.00, G:0.10, T:0.55
Consensus pattern (21 bp):
TATTTTGTAAAAAGTATAATT
Found at i:19127965 original size:27 final size:27
Alignment explanation
Indices: 19127930--19127982 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
19127920 TAAATAAAAA
* *
19127930 TAAAAAAATTATTTAAAATTTATTTAG
1 TAAAAAAATCACTTAAAATTTATTTAG
* *
19127957 TAAACAAATCACTTAAAGTTTATTTA
1 TAAAAAAATCACTTAAAATTTATTTA
19127983 ATTTTTGGCA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.42
Consensus pattern (27 bp):
TAAAAAAATCACTTAAAATTTATTTAG
Found at i:19130125 original size:23 final size:24
Alignment explanation
Indices: 19130098--19130145 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
19130088 GAACTTCCCG
*
19130098 ATTACAT-CTCTTATGAGCTTCCT
1 ATTACATACTCATATGAGCTTCCT
*
19130121 ATTACATGACTCATATTAGCTTCCT
1 ATTACAT-ACTCATATGAGCTTCCT
19130146 GTTATATGGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 7 0.33
25 14 0.67
ACGTcount: A:0.25, C:0.25, G:0.08, T:0.42
Consensus pattern (24 bp):
ATTACATACTCATATGAGCTTCCT
Found at i:19144758 original size:21 final size:21
Alignment explanation
Indices: 19144732--19144859 Score: 134
Period size: 21 Copynumber: 6.1 Consensus size: 21
19144722 TTACTTTCCA
19144732 TTCAACTCTT-TCGAGCTTCTG
1 TTCAACTCTTAT-GAGCTTCTG
* *
19144753 TTCAACTCTTATAAGTTTCTG
1 TTCAACTCTTATGAGCTTCTG
* * *
19144774 TTCAGCTCTTACGAGTTTCTG
1 TTCAACTCTTATGAGCTTCTG
*
19144795 TTCAACTCTTATGAGTTTCTG
1 TTCAACTCTTATGAGCTTCTG
* * * *
19144816 TTTAGCTCTTACGAGCTTTTG
1 TTCAACTCTTATGAGCTTCTG
19144837 TT-AAGCTCTTATGAGCTTCTG
1 TTCAA-CTCTTATGAGCTTCTG
19144858 TT
1 TT
19144860 AATAATGTAC
Statistics
Matches: 90, Mismatches: 15, Indels: 4
0.83 0.14 0.04
Matches are distributed among these distances:
20 1 0.01
21 88 0.98
22 1 0.01
ACGTcount: A:0.17, C:0.21, G:0.16, T:0.46
Consensus pattern (21 bp):
TTCAACTCTTATGAGCTTCTG
Found at i:19144794 original size:42 final size:42
Alignment explanation
Indices: 19144732--19144859 Score: 170
Period size: 42 Copynumber: 3.0 Consensus size: 42
19144722 TTACTTTCCA
* * * *
19144732 TTCAACTCTTTCGAGCTTCTGTTCAACTCTTATAAGTTTCTG
1 TTCAGCTCTTACGAGTTTCTGTTCAACTCTTATGAGTTTCTG
19144774 TTCAGCTCTTACGAGTTTCTGTTCAACTCTTATGAGTTTCTG
1 TTCAGCTCTTACGAGTTTCTGTTCAACTCTTATGAGTTTCTG
* *
19144816 TTTAGCTCTTACGAGCTTT-TGTT-AAGCTCTTATGAGCTTCTG
1 TTCAGCTCTTACGAG-TTTCTGTTCAA-CTCTTATGAGTTTCTG
19144858 TT
1 TT
19144860 AATAATGTAC
Statistics
Matches: 78, Mismatches: 6, Indels: 4
0.89 0.07 0.05
Matches are distributed among these distances:
41 2 0.03
42 73 0.94
43 3 0.04
ACGTcount: A:0.17, C:0.21, G:0.16, T:0.46
Consensus pattern (42 bp):
TTCAGCTCTTACGAGTTTCTGTTCAACTCTTATGAGTTTCTG
Found at i:19144815 original size:63 final size:63
Alignment explanation
Indices: 19144732--19144859 Score: 152
Period size: 63 Copynumber: 2.0 Consensus size: 63
19144722 TTACTTTCCA
* * *
19144732 TTCAACTCTTTCGAGCTTCTGTTCAACTCTTATAAG-TTTCTGTTCAGCTCTTACGAGTTTCTG
1 TTCAACTCTTTCGAGCTTCTGTTCAACTCTTACAAGCTTT-TGTTAAGCTCTTACGAGCTTCTG
* * * * *
19144795 TTCAACTCTTAT-GAGTTTCTGTTTAGCTCTTACGAGCTTTTGTTAAGCTCTTATGAGCTTCTG
1 TTCAACTCTT-TCGAGCTTCTGTTCAACTCTTACAAGCTTTTGTTAAGCTCTTACGAGCTTCTG
19144858 TT
1 TT
19144860 AATAATGTAC
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
63 51 0.93
64 4 0.07
ACGTcount: A:0.17, C:0.21, G:0.16, T:0.46
Consensus pattern (63 bp):
TTCAACTCTTTCGAGCTTCTGTTCAACTCTTACAAGCTTTTGTTAAGCTCTTACGAGCTTCTG
Found at i:19172270 original size:46 final size:46
Alignment explanation
Indices: 19172203--19172379 Score: 293
Period size: 46 Copynumber: 3.8 Consensus size: 46
19172193 AGTGTGGAAT
19172203 GTAGGTATGGTATTTCAGTAAAGAAAACCATACTGAGTTGTGAAAA
1 GTAGGTATGGTATTTCAGTAAAGAAAACCATACTGAGTTGTGAAAA
* *
19172249 GTAGGTATGATATTTCAGTAAAGAAAACCATACTGAGTTGTGAGAA
1 GTAGGTATGGTATTTCAGTAAAGAAAACCATACTGAGTTGTGAAAA
* *
19172295 GTAGGTATGGTATTTCAATAACA-AAAATCATACTGAGTTGTGAAAA
1 GTAGGTATGGTATTTCAGTAA-AGAAAACCATACTGAGTTGTGAAAA
*
19172341 GTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGTT
1 GTAGGTATGGTATTTCAGTAAAGAAAACCATACTGAGTT
19172380 ATAGCATTGT
Statistics
Matches: 120, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
45 1 0.01
46 118 0.98
47 1 0.01
ACGTcount: A:0.38, C:0.09, G:0.23, T:0.29
Consensus pattern (46 bp):
GTAGGTATGGTATTTCAGTAAAGAAAACCATACTGAGTTGTGAAAA
Found at i:19203974 original size:46 final size:46
Alignment explanation
Indices: 19203907--19204083 Score: 293
Period size: 46 Copynumber: 3.8 Consensus size: 46
19203897 AGTGTGGAAT
19203907 GTAGGTATGGTATTTCAGTAAAGAAAACCATACTGAGTTGTGAAAA
1 GTAGGTATGGTATTTCAGTAAAGAAAACCATACTGAGTTGTGAAAA
* *
19203953 GTAGGTATGATATTTCAGTAAAGAAAACCATACTGAGTTGTGAGAA
1 GTAGGTATGGTATTTCAGTAAAGAAAACCATACTGAGTTGTGAAAA
* *
19203999 GTAGGTATGGTATTTCAATAACA-AAAATCATACTGAGTTGTGAAAA
1 GTAGGTATGGTATTTCAGTAA-AGAAAACCATACTGAGTTGTGAAAA
*
19204045 GTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGTT
1 GTAGGTATGGTATTTCAGTAAAGAAAACCATACTGAGTT
19204084 ATAGCATTGT
Statistics
Matches: 120, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
45 1 0.01
46 118 0.98
47 1 0.01
ACGTcount: A:0.38, C:0.09, G:0.23, T:0.29
Consensus pattern (46 bp):
GTAGGTATGGTATTTCAGTAAAGAAAACCATACTGAGTTGTGAAAA
Found at i:19244966 original size:10 final size:10
Alignment explanation
Indices: 19244953--19245011 Score: 91
Period size: 10 Copynumber: 5.7 Consensus size: 10
19244943 ATGAAAGAAA
19244953 ATGTATAGAT
1 ATGTATAGAT
19244963 ATGTATAGAT
1 ATGTATAGAT
*
19244973 ATGTATATGGAA
1 ATGTATA--GAT
19244985 ATGTATAGAT
1 ATGTATAGAT
19244995 ATGTATAGAT
1 ATGTATAGAT
19245005 ATGTATA
1 ATGTATA
19245012 TGGAAATCGA
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
10 36 0.80
12 9 0.20
ACGTcount: A:0.41, C:0.00, G:0.20, T:0.39
Consensus pattern (10 bp):
ATGTATAGAT
Found at i:19244992 original size:32 final size:32
Alignment explanation
Indices: 19244951--19245018 Score: 136
Period size: 32 Copynumber: 2.1 Consensus size: 32
19244941 GGATGAAAGA
19244951 AAATGTATAGATATGTATAGATATGTATATGG
1 AAATGTATAGATATGTATAGATATGTATATGG
19244983 AAATGTATAGATATGTATAGATATGTATATGG
1 AAATGTATAGATATGTATAGATATGTATATGG
19245015 AAAT
1 AAAT
19245019 CGAAAGAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.43, C:0.00, G:0.21, T:0.37
Consensus pattern (32 bp):
AAATGTATAGATATGTATAGATATGTATATGG
Found at i:19246700 original size:74 final size:74
Alignment explanation
Indices: 19246551--19246960 Score: 497
Period size: 74 Copynumber: 5.4 Consensus size: 74
19246541 ATTAAAAGGT
* * *
19246551 TCAACCCACCTCTCGCAATATGAGTTGATTTTTTGAAAGA-AGAATTTGAAAATACCTCAGCGTG
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGAAATTGAAAATACCTCAGCGTG
* **
19246615 CCCCGAGGC
66 TCTTGAGGC
* *
19246624 TCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGAAATTGAAATTACCTCAGCGTA
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGAAATTGAAAATACCTCAGCGTG
*
19246689 TCCTGAGGC
66 TCTTGAGGC
19246698 TCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAAACATAAATTGAACAGGAATTGAAAAT
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAAC----A--G---A--AATTGAAAAT
*
19246762 ACCTCAACGTGTCTTGAGGC
55 ACCTCAGCGTGTCTTGAGGC
** **
19246782 TCAACTCACCTCTCGCAATATGAGTTGATTTTCTTGAAATGCAGAAATTGAAAATACCTCAATGT
1 TCAACTCACCTCTCGCAATATGAGTTGATTTT-TTGAAAAACAGAAATTGAAAATACCTCAGCGT
19246847 GTCTTGAGGC
65 GTCTTGAGGC
* * *
19246857 TCAACTCACCTCTCGCAATATGAGTTGATTTTTTTG-ACAGCAGAAATTGAAACTACCTCAGC--
1 TCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTGAAAAACAGAAATTGAAAATACCTCAGCGT
19246919 GTCTTGAGGC
65 GTCTTGAGGC
**
19246929 TCAACTCATTTCTCGCAATATGAGTTGATTTT
1 TCAACTCACCTCTCGCAATATGAGTTGATTTT
19246961 CCTTGGAAAG
Statistics
Matches: 301, Mismatches: 21, Indels: 32
0.85 0.06 0.09
Matches are distributed among these distances:
71 4 0.01
72 36 0.12
73 50 0.17
74 77 0.26
75 60 0.20
76 4 0.01
77 2 0.01
79 1 0.00
80 1 0.00
82 2 0.01
84 54 0.18
85 3 0.01
86 7 0.02
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.30
Consensus pattern (74 bp):
TCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGAAATTGAAAATACCTCAGCGTG
TCTTGAGGC
Found at i:19246875 original size:75 final size:73
Alignment explanation
Indices: 19246752--19246972 Score: 336
Period size: 75 Copynumber: 3.0 Consensus size: 73
19246742 ATTGAACAGG
19246752 AATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTCTT
1 AATTGAAAATACCTCAA-GTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTCTT
19246817 GAAATGCAGA
65 GAAA-GCAGA
*
19246827 AATTGAAAATACCTCAATGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTT
1 AATTGAAAATACCTCAA-GTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTCTT
*
19246892 GACAGCAGA
65 GAAAGCAGA
* * **
19246901 AATTGAAACTACCTC-AGCGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTCCTT
1 AATTGAAAATACCTCAAGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT-CTT
19246965 GGAAAGCA
65 -GAAAGCA
19246973 TGAATATTAA
Statistics
Matches: 135, Mismatches: 9, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
72 41 0.30
73 3 0.02
74 25 0.19
75 66 0.49
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (73 bp):
AATTGAAAATACCTCAAGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTCTTG
AAAGCAGA
Found at i:19246881 original size:159 final size:158
Alignment explanation
Indices: 19246596--19246889 Score: 480
Period size: 159 Copynumber: 1.9 Consensus size: 158
19246586 AAAGAAGAAT
*
19246596 TTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAA
1 TTGAAAATACCTCAACGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAA
* *
19246661 AAACAGAAATTGAAATTACCTCAGCGTATCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
66 AAACAGAAATTGAAAATACCTCAACGTATCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
19246726 TTTTTGAAAAACATAAATTGAACAGGAA
131 TTTTTGAAAAACATAAATTGAACAGGAA
* **
19246754 TTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTCTTGA
1 TTGAAAATACCTCAACGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT-TTGA
** * * *
19246819 AATGCAGAAATTGAAAATACCTCAATGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTG
65 AAAACAGAAATTGAAAATACCTCAACGTATCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG
19246884 ATTTTT
130 ATTTTT
19246890 TTGACAGCAG
Statistics
Matches: 124, Mismatches: 11, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
158 56 0.45
159 68 0.55
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.30
Consensus pattern (158 bp):
TTGAAAATACCTCAACGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAA
AAACAGAAATTGAAAATACCTCAACGTATCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
TTTTTGAAAAACATAAATTGAACAGGAA
Found at i:19258463 original size:71 final size:71
Alignment explanation
Indices: 19258348--19258731 Score: 416
Period size: 70 Copynumber: 5.3 Consensus size: 71
19258338 GTAGCTTCAC
* * **
19258348 CCTC-CGCAATATG-G-TGATTTTTGAAAGA-AGAATTTGAAAATACCTCAGCGTGCCCCGAGGC
1 CCTCTCGCAATATGAGTTGATTTTTGAAA-ACAGAAATTGAAAATACCTCAACGTG-CTTGAGGC
19258409 TCAA-TCA
64 TCAACTCA
*
19258416 CCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGAAATTACCTCAACGTG-TCTGAGGCT
1 CCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGAAAATACCTCAACGTGCT-TGAGGCT
19258480 CAACTCA
65 CAACTCA
19258487 CCTCTCGCAATATGAGTTGATTTTTGAAAAACATAAATTGAACAGGAATTGAAAATACCTCAACG
1 CCTCTCGCAATATGAGTTGATTTTTG-AAAAC----A--G---A--AATTGAAAATACCTCAACG
19258552 TGTCTTGAGGCTCAACTCA
54 TG-CTTGAGGCTCAACTCA
*
19258571 --TCTCGCAATATGAGTTGA-TTTTGAAAAGCAAAAATTGAAAATACCTCAACGTGTCTTGAGGC
1 CCTCTCGCAATATGAGTTGATTTTTGAAAA-CAGAAATTGAAAATACCTCAACGTG-CTTGAGGC
19258633 TCAACTCA
64 TCAACTCA
* * *
19258641 --TCTCGCAATATGAGTTGATTTTTG-AAGCAGAAATTGAAACTACCTCAGCGT-CTTGAGGCTC
1 CCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGAAAATACCTCAACGTGCTTGAGGCTC
19258702 AACTCA
66 AACTCA
**
19258708 TTTCTCGCAATATGAGTTGATTTT
1 CCTCTCGCAATATGAGTTGATTTT
19258732 CCTTGGAAAG
Statistics
Matches: 281, Mismatches: 11, Indels: 47
0.83 0.03 0.14
Matches are distributed among these distances:
67 16 0.06
68 4 0.01
69 52 0.19
70 69 0.25
71 67 0.24
72 6 0.02
76 1 0.00
77 1 0.00
78 1 0.00
80 4 0.01
81 7 0.02
82 18 0.06
83 20 0.07
84 14 0.05
85 1 0.00
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (71 bp):
CCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGAAAATACCTCAACGTGCTTGAGGCTC
AACTCA
Found at i:19258606 original size:153 final size:152
Alignment explanation
Indices: 19258381--19258666 Score: 452
Period size: 153 Copynumber: 1.9 Consensus size: 152
19258371 AAAGAAGAAT
*
19258381 TTGAAAATACCTCAGCGTGCCCCGAGGCTCAATCACCTCTCGCAATATGAGTTGATTTTTGAAAA
1 TTGAAAATACCTCAACGTGCCCCGAGGCTCAATCA-CTCTCGCAATATGAGTTGATTTTTGAAAA
* *
19258446 CAGAAATTGAAATTACCTCAACGTGTC-TGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
65 CAAAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCA--TCTCGCAATATGAGTTGATTT
19258510 TTGAAAAACATAAATTGAACAGGAA
128 TTGAAAAACATAAATTGAACAGGAA
* **
19258535 TTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCA-TCTCGCAATATGAGTTGA-TTTTGAAAA
1 TTGAAAATACCTCAACGTGCCCCGAGGCTCAA-TCACTCTCGCAATATGAGTTGATTTTTGAAAA
19258598 GCAAAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATCTCGCAATATGAGTTGATTTT
65 -CAAAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATCTCGCAATATGAGTTGATTTT
19258663 TGAA
129 TGAA
19258667 GCAGAAATTG
Statistics
Matches: 123, Mismatches: 6, Indels: 8
0.90 0.04 0.06
Matches are distributed among these distances:
152 35 0.28
153 43 0.35
154 42 0.34
155 3 0.02
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.29
Consensus pattern (152 bp):
TTGAAAATACCTCAACGTGCCCCGAGGCTCAATCACTCTCGCAATATGAGTTGATTTTTGAAAAC
AAAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATCTCGCAATATGAGTTGATTTTTG
AAAAACATAAATTGAACAGGAA
Found at i:19259561 original size:15 final size:13
Alignment explanation
Indices: 19259542--19259577 Score: 54
Period size: 15 Copynumber: 2.6 Consensus size: 13
19259532 TTCCCTTCCC
19259542 TTTTTTTTTCTTT
1 TTTTTTTTTCTTT
19259555 GTCTTTTTTTTCTTT
1 -T-TTTTTTTTCTTT
19259570 TTTTTTTT
1 TTTTTTTT
19259578 AGCAACTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 7 0.33
14 2 0.10
15 12 0.57
ACGTcount: A:0.00, C:0.08, G:0.03, T:0.89
Consensus pattern (13 bp):
TTTTTTTTTCTTT
Found at i:19286854 original size:21 final size:21
Alignment explanation
Indices: 19286809--19286900 Score: 73
Period size: 21 Copynumber: 4.5 Consensus size: 21
19286799 GAGTACATCG
**
19286809 TTAACAGAAGCTC-GCA-AGC
1 TTAACAGAAGCTCATAAGAGC
* *
19286828 TGAACAGAAGCTCATAATAGC
1 TTAACAGAAGCTCATAAGAGC
* *
19286849 TTAACAGAAACTCTTAAGAG-
1 TTAACAGAAGCTCATAAGAGC
* *
19286869 TTGAATAGAAGCTTATAAGAGC
1 TT-AACAGAAGCTCATAAGAGC
*
19286891 TAAACAGAAG
1 TTAACAGAAG
19286901 TTAAACATAA
Statistics
Matches: 56, Mismatches: 13, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
19 12 0.21
20 3 0.05
21 40 0.71
22 1 0.02
ACGTcount: A:0.43, C:0.16, G:0.20, T:0.21
Consensus pattern (21 bp):
TTAACAGAAGCTCATAAGAGC
Found at i:19286957 original size:21 final size:21
Alignment explanation
Indices: 19286933--19287015 Score: 87
Period size: 21 Copynumber: 4.0 Consensus size: 21
19286923 TGAACGAAAA
*
19286933 CTCATAAGAGTTTAACAGAAG
1 CTCATAAGAGTTAAACAGAAG
* * *
19286954 CTCA-ATAGAGTTGAACGGAAT
1 CTCATA-AGAGTTAAACAGAAG
*
19286975 CTCATATGAGTTAAACAGAAG
1 CTCATAAGAGTTAAACAGAAG
* *
19286996 CTCGTAAGAGCTAAACAGAA
1 CTCATAAGAGTTAAACAGAA
19287016 AGTAAAACAC
Statistics
Matches: 50, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
20 1 0.02
21 48 0.96
22 1 0.02
ACGTcount: A:0.42, C:0.16, G:0.20, T:0.22
Consensus pattern (21 bp):
CTCATAAGAGTTAAACAGAAG
Found at i:19286986 original size:42 final size:42
Alignment explanation
Indices: 19286918--19286998 Score: 117
Period size: 42 Copynumber: 1.9 Consensus size: 42
19286908 TAAACTTGTA
*
19286918 AGAGCTGAACGAAAACTCATAAGAGTTTAACAGAAGCTCAAT
1 AGAGCTGAACGAAAACTCATAAGAGTTAAACAGAAGCTCAAT
* * * *
19286960 AGAGTTGAACGGAATCTCATATGAGTTAAACAGAAGCTC
1 AGAGCTGAACGAAAACTCATAAGAGTTAAACAGAAGCTC
19286999 GTAAGAGCTA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.42, C:0.16, G:0.21, T:0.21
Consensus pattern (42 bp):
AGAGCTGAACGAAAACTCATAAGAGTTAAACAGAAGCTCAAT
Found at i:19289792 original size:37 final size:37
Alignment explanation
Indices: 19289728--19289884 Score: 199
Period size: 37 Copynumber: 4.0 Consensus size: 37
19289718 TACGTATGAT
*
19289728 CACTTATCAC-TTGTCCCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
*
19289764 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
19289801 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGC
1 CACTTATCACTTTGTCTCTTGATCAGATAA--GT-G-T--AGC
*
19289844 TATCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGC
1 ---CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
19289884 C
1 C
19289885 GAAGCTATCA
Statistics
Matches: 107, Mismatches: 4, Indels: 19
0.82 0.03 0.15
Matches are distributed among these distances:
36 10 0.09
37 54 0.50
39 2 0.02
40 4 0.04
41 1 0.01
42 1 0.01
43 3 0.03
44 2 0.02
46 30 0.28
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.37
Consensus pattern (37 bp):
CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
Found at i:19289854 original size:46 final size:46
Alignment explanation
Indices: 19289801--19290167 Score: 437
Period size: 46 Copynumber: 7.6 Consensus size: 46
19289791 TAAGTGTAGC
* **
19289801 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* *
19289847 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
19289893 CACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
1 CACTTATCAC---T---TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
19289945 CACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTAT
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
19289997 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* * *
19290043 AACTTATCACTTTATCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* ** *
19290089 TACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
19290141 CACTTATCACTTTATCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
19290168 AGTACTCAAA
Statistics
Matches: 290, Mismatches: 18, Indels: 26
0.87 0.05 0.08
Matches are distributed among these distances:
46 154 0.53
48 1 0.00
49 1 0.00
50 2 0.01
51 3 0.01
52 129 0.44
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
Found at i:19289920 original size:52 final size:52
Alignment explanation
Indices: 19289844--19290161 Score: 417
Period size: 52 Copynumber: 6.3 Consensus size: 52
19289834 TAGCTAAAGC
* *
19289844 TATCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACT
1 TATCACTTTTCAC-TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
19289897 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
* * *
19289949 TATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
19290001 TATCAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATAACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
19290047 TATCAC-TTT-A----TCACTTGATCAGATAAGTATAGCCGAAGCTATTACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
* * ** *
19290093 TATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
19290145 TATCACTTTATCACTTG
1 TATCACTTT-TCACTTG
19290162 ATCAGAAGTA
Statistics
Matches: 238, Mismatches: 17, Indels: 20
0.87 0.06 0.07
Matches are distributed among these distances:
46 83 0.35
47 2 0.01
48 2 0.01
52 133 0.56
53 18 0.08
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (52 bp):
TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
Found at i:19290109 original size:196 final size:196
Alignment explanation
Indices: 19289801--19290153 Score: 598
Period size: 196 Copynumber: 1.8 Consensus size: 196
19289791 TAAGTGTAGC
* * * * * *
19289801 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCTCT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCAAAGCTATAACTTATCACTTTATCACT
*
19289866 TGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTTCACTTGTCACTTGATCAGATAAGT
66 TGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTCCACTTGTCACTTGATCAGATAAGT
* *
19289931 GTAGCCGAAGCTATCACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTA
131 GTAGCCAAAGCTACCACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTA
19289996 T
196 T
*
19289997 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATAACTTATCACTTTATCACT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCAAAGCTATAACTTATCACTTTATCACT
*
19290062 TGATCAGATAAGTATAGCCGAAGCTATTACTTATCACTTTCCACTTGTCACTTGATCAGATAAGT
66 TGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTCCACTTGTCACTTGATCAGATAAGT
*
19290127 GTAGCTAAAGCTACCACTTATCACTTT
131 GTAGCCAAAGCTACCACTTATCACTTT
19290154 ATCACTTGAT
Statistics
Matches: 145, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
196 145 1.00
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (196 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCAAAGCTATAACTTATCACTTTATCACT
TGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTCCACTTGTCACTTGATCAGATAAGT
GTAGCCAAAGCTACCACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTA
T
Found at i:19290157 original size:98 final size:97
Alignment explanation
Indices: 19289801--19290167 Score: 492
Period size: 98 Copynumber: 3.7 Consensus size: 97
19289791 TAAGTGTAGC
* * * *
19289801 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCTCT
1 CACTT-TCAC-TTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTATCACTTTATCACT
19289866 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
64 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
*
19289900 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTCCACTTG
1 CAC-TTTCACTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTATCACTTT--A----
* *
19289965 TCACTTGATCAGATAAGTGTAGCTGAAGCTATCACTTAT
59 TCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTAT
* * *
19290004 CAC--T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATAACTTATCACTTTATCACTTG
1 CACTTTCACTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTATCACTTTATCACTTG
*
19290064 ATCAGATAAGTATAGCCGAAGCTATTACTTAT
66 ATCAGATAAGTATAGCCGAAGCTATCACTTAT
* *
19290096 CACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTATCACTT
1 CACTTT-CACTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTATCACTTTATCACTT
19290161 GATCAGA
65 GATCAGA
19290168 AGTACTCAAA
Statistics
Matches: 238, Mismatches: 17, Indels: 27
0.84 0.06 0.10
Matches are distributed among these distances:
92 39 0.16
94 1 0.00
96 1 0.00
98 148 0.62
99 7 0.03
100 2 0.01
101 1 0.00
104 39 0.16
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (97 bp):
CACTTTCACTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTATCACTTTATCACTTG
ATCAGATAAGTATAGCCGAAGCTATCACTTAT
Found at i:19292936 original size:17 final size:16
Alignment explanation
Indices: 19292912--19292947 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
19292902 TTCAATATTA
*
19292912 GTTTTAGTTTATTTTT
1 GTTTTAGTTCATTTTT
19292928 GTTTCTAGTTCATTTTT
1 GTTT-TAGTTCATTTTT
19292945 GTT
1 GTT
19292948 AATTGTTCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.11, C:0.06, G:0.14, T:0.69
Consensus pattern (16 bp):
GTTTTAGTTCATTTTT
Found at i:19302626 original size:73 final size:71
Alignment explanation
Indices: 19302535--19302670 Score: 227
Period size: 73 Copynumber: 1.9 Consensus size: 71
19302525 ACCAAAAACT
* * *
19302535 AAAGACAACATTTTAAGTCAAAAGAAAGGTTTGGCTTAGAGATCAAAAATCAAAATAAATATAAC
1 AAAGAAAACATTTTAAGTCAAAA-AAAGCTTTGACTTAGAGAT-AAAAATCAAAATAAATATAAC
19302600 TGCCAAAA
64 TGCCAAAA
19302608 AAAGAAAACATTTTAAGTCAAAAAAAGCTTTGACTTAGAGATAAAAATCAAAATAAATATAAC
1 AAAGAAAACATTTTAAGTCAAAAAAAGCTTTGACTTAGAGATAAAAATCAAAATAAATATAAC
19302671 ACTGAAGATA
Statistics
Matches: 60, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
71 21 0.35
72 17 0.28
73 22 0.37
ACGTcount: A:0.54, C:0.11, G:0.12, T:0.23
Consensus pattern (71 bp):
AAAGAAAACATTTTAAGTCAAAAAAAGCTTTGACTTAGAGATAAAAATCAAAATAAATATAACTG
CCAAAA
Found at i:19305460 original size:30 final size:31
Alignment explanation
Indices: 19305414--19305509 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 31
19305404 TCATTCTATT
* *
19305414 AATTTAATCTTAAATA-TAAAAAATTTAACA
1 AATTTAGTCTTTAATATTAAAAAATTTAACA
* *
19305444 AATTTAGTCTTTAATATTTACAAAATTTATC-
1 AATTTAGTCTTTAATA-TTAAAAAATTTAACA
* * * *
19305475 ATTTTAGT-TCTAATATTAAAAAAATTAATA
1 AATTTAGTCTTTAATATTAAAAAATTTAACA
19305505 AATTT
1 AATTT
19305510 GGCTAGCAAC
Statistics
Matches: 52, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
29 10 0.19
30 24 0.46
31 7 0.13
32 11 0.21
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (31 bp):
AATTTAGTCTTTAATATTAAAAAATTTAACA
Found at i:19316096 original size:20 final size:20
Alignment explanation
Indices: 19316055--19316096 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
19316045 TGTAGGTGTT
* *
19316055 TTTTTAAATCATAATCAGTA
1 TTTTTAAATCATAATAACTA
19316075 TTTTTAATATCA-AATAACTA
1 TTTTTAA-ATCATAATAACTA
19316095 TT
1 TT
19316097 AAGTAAATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.40, C:0.10, G:0.02, T:0.48
Consensus pattern (20 bp):
TTTTTAAATCATAATAACTA
Found at i:19327217 original size:15 final size:16
Alignment explanation
Indices: 19327186--19327218 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
19327176 ATATCCTTTT
*
19327186 AAATTTCAAACACATA
1 AAATTTCAAACAAATA
19327202 AAATTTCAAA-AAATA
1 AAATTTCAAACAAATA
19327217 AA
1 AA
19327219 GACAATATTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.64, C:0.12, G:0.00, T:0.24
Consensus pattern (16 bp):
AAATTTCAAACAAATA
Found at i:19337229 original size:20 final size:20
Alignment explanation
Indices: 19337204--19337253 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
19337194 TGGCTTAAAA
19337204 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
19337224 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
19337241 GTGGTAGTGGATT
1 TTGGTAGTGGATT
19337254 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:19341868 original size:20 final size:20
Alignment explanation
Indices: 19341843--19341892 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
19341833 TGGCTTAAAA
19341843 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
19341863 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
19341880 GTGGTAGTGGATT
1 TTGGTAGTGGATT
19341893 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:19349062 original size:14 final size:14
Alignment explanation
Indices: 19349043--19349069 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
19349033 CATTTTTAGG
19349043 TATTTTTCATTTTT
1 TATTTTTCATTTTT
19349057 TATTTTTCATTTT
1 TATTTTTCATTTT
19349070 CAATTTCATT
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:0.15, C:0.07, G:0.00, T:0.78
Consensus pattern (14 bp):
TATTTTTCATTTTT
Found at i:19349158 original size:51 final size:51
Alignment explanation
Indices: 19349073--19349180 Score: 121
Period size: 51 Copynumber: 2.1 Consensus size: 51
19349063 TCATTTTCAA
* *
19349073 TTTCATTTTGGAGAAAATCATATTCATTTCCAAATAATT-CCATTTCTCCAT
1 TTTCATTTTGGAGAAAACCATAATCATTTCCAAAT-ATTACCATTTCTCCAT
* * * *
19349124 TTTCATTTTGGAG-AAACCAATAATGATTTTCAAATGTTACCCATTTCTTCAT
1 TTTCATTTTGGAGAAAACC-ATAATCATTTCCAAATATTA-CCATTTCTCCAT
19349176 TTTCA
1 TTTCA
19349181 CCATTTCTAT
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
50 6 0.12
51 26 0.54
52 16 0.33
ACGTcount: A:0.31, C:0.19, G:0.07, T:0.44
Consensus pattern (51 bp):
TTTCATTTTGGAGAAAACCATAATCATTTCCAAATATTACCATTTCTCCAT
Found at i:19352130 original size:20 final size:21
Alignment explanation
Indices: 19352105--19352143 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
19352095 CTGACTTCTA
*
19352105 CTTT-AAAAATTAATTTGGCT
1 CTTTAAAAAAATAATTTGGCT
19352125 CTTTAAAAAAATAATTTGG
1 CTTTAAAAAAATAATTTGG
19352144 ATTTTTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.41, C:0.08, G:0.10, T:0.41
Consensus pattern (21 bp):
CTTTAAAAAAATAATTTGGCT
Found at i:19352150 original size:21 final size:21
Alignment explanation
Indices: 19352105--19352151 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
19352095 CTGACTTCTA
* *
19352105 CTTT-AAAAATTAATTTGGCT
1 CTTTAAAAAAATAATTTGGAT
19352125 CTTTAAAAAAATAATTTGGAT
1 CTTTAAAAAAATAATTTGGAT
*
19352146 TTTTAA
1 CTTTAA
19352152 TTTATCAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 4 0.17
21 19 0.83
ACGTcount: A:0.40, C:0.06, G:0.09, T:0.45
Consensus pattern (21 bp):
CTTTAAAAAAATAATTTGGAT
Found at i:19364964 original size:231 final size:231
Alignment explanation
Indices: 19364561--19365719 Score: 2318
Period size: 231 Copynumber: 5.0 Consensus size: 231
19364551 ATTTTATAAA
19364561 AATTGTATAACCAATATAAAAACAACTATGCATTCTAATGACACAATGATATCTACTTTCTACGT
1 AATTGTATAACCAATATAAAAACAACTATGCATTCTAATGACACAATGATATCTACTTTCTACGT
19364626 TACTGGCTTTTAAAACCATAATCCTTTTAGCCATGATGCTCTCATTTTGTTTGATATATGTTCAC
66 TACTGGCTTTTAAAACCATAATCCTTTTAGCCATGATGCTCTCATTTTGTTTGATATATGTTCAC
19364691 TTTGATGTTATTTGAAGAGTAATGCTCTTTGGTTTTCTTCATTCTCTTTATCTTTATTCTTCCAA
131 TTTGATGTTATTTGAAGAGTAATGCTCTTTGGTTTTCTTCATTCTCTTTATCTTTATTCTTCCAA
19364756 ATACAGAGCGCTTCAGATATGGTTTTAGCTGATGAC
196 ATACAGAGCGCTTCAGATATGGTTTTAGCTGATGAC
19364792 AATTGTATAACCAATATAAAAACAACTATGCATTCTAATGACACAATGATATCTACTTTCTACGT
1 AATTGTATAACCAATATAAAAACAACTATGCATTCTAATGACACAATGATATCTACTTTCTACGT
19364857 TACTGGCTTTTAAAACCATAATCCTTTTAGCCATGATGCTCTCATTTTGTTTGATATATGTTCAC
66 TACTGGCTTTTAAAACCATAATCCTTTTAGCCATGATGCTCTCATTTTGTTTGATATATGTTCAC
19364922 TTTGATGTTATTTGAAGAGTAATGCTCTTTGGTTTTCTTCATTCTCTTTATCTTTATTCTTCCAA
131 TTTGATGTTATTTGAAGAGTAATGCTCTTTGGTTTTCTTCATTCTCTTTATCTTTATTCTTCCAA
19364987 ATACAGAGCGCTTCAGATATGGTTTTAGCTGATGAC
196 ATACAGAGCGCTTCAGATATGGTTTTAGCTGATGAC
19365023 AATTGTATAACCAATATAAAAACAACTATGCATTCTAATGACACAATGATATCTACTTTCTACGT
1 AATTGTATAACCAATATAAAAACAACTATGCATTCTAATGACACAATGATATCTACTTTCTACGT
19365088 TACTGGCTTTTAAAACCATAATCCTTTTAGCCATGATGCTCTCATTTTGTTTGATATATGTTCAC
66 TACTGGCTTTTAAAACCATAATCCTTTTAGCCATGATGCTCTCATTTTGTTTGATATATGTTCAC
19365153 TTTGATGTTATTTGAAGAGTAATGCTCTTTGGTTTTCTTCATTCTCTTTATCTTTATTCTTCCAA
131 TTTGATGTTATTTGAAGAGTAATGCTCTTTGGTTTTCTTCATTCTCTTTATCTTTATTCTTCCAA
19365218 ATACAGAGCGCTTCAGATATGGTTTTAGCTGATGAC
196 ATACAGAGCGCTTCAGATATGGTTTTAGCTGATGAC
19365254 AATTGTATAACCAATATAAAAACAACTATGCATTCTAATGACACAATGATATCTACTTTCTACGT
1 AATTGTATAACCAATATAAAAACAACTATGCATTCTAATGACACAATGATATCTACTTTCTACGT
19365319 TACTGGCTTTTAAAACCATAATCCTTTTAGCCATGATGCTCTCATTTTGTTTGATATATGTTCAC
66 TACTGGCTTTTAAAACCATAATCCTTTTAGCCATGATGCTCTCATTTTGTTTGATATATGTTCAC
19365384 TTTGATGTTATTTGAAGAGTAATGCTCTTTGGTTTTCTTCATTCTCTTTATCTTTATTCTTCCAA
131 TTTGATGTTATTTGAAGAGTAATGCTCTTTGGTTTTCTTCATTCTCTTTATCTTTATTCTTCCAA
19365449 ATACAGAGCGCTTCAGATATGGTTTTAGCTGATGAC
196 ATACAGAGCGCTTCAGATATGGTTTTAGCTGATGAC
19365485 AATTGTATAACCAATATAAAAACAACTATGCATTCTAATGACACAATGATATCTACTTTCTACGT
1 AATTGTATAACCAATATAAAAACAACTATGCATTCTAATGACACAATGATATCTACTTTCTACGT
19365550 TACTGGCTTTTAAAACCATAATCCTTTTAGCCATGATGCTCTCATTTTGTTTGATATATGTTCAC
66 TACTGGCTTTTAAAACCATAATCCTTTTAGCCATGATGCTCTCATTTTGTTTGATATATGTTCAC
19365615 TTTGATGTTATTTGAAGAGTAATGCTCTTTGGTTTTCTTCATTCTCTTTATCTTTATTCTTCCAA
131 TTTGATGTTATTTGAAGAGTAATGCTCTTTGGTTTTCTTCATTCTCTTTATCTTTATTCTTCCAA
19365680 ATACAGAGCGCTTCAGATATGGTTTTAGCTGATGAC
196 ATACAGAGCGCTTCAGATATGGTTTTAGCTGATGAC
19365716 AATT
1 AATT
19365720 TTGCTACCAT
Statistics
Matches: 928, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
231 928 1.00
ACGTcount: A:0.28, C:0.18, G:0.13, T:0.41
Consensus pattern (231 bp):
AATTGTATAACCAATATAAAAACAACTATGCATTCTAATGACACAATGATATCTACTTTCTACGT
TACTGGCTTTTAAAACCATAATCCTTTTAGCCATGATGCTCTCATTTTGTTTGATATATGTTCAC
TTTGATGTTATTTGAAGAGTAATGCTCTTTGGTTTTCTTCATTCTCTTTATCTTTATTCTTCCAA
ATACAGAGCGCTTCAGATATGGTTTTAGCTGATGAC
Found at i:19369207 original size:12 final size:12
Alignment explanation
Indices: 19369190--19369214 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
19369180 GGTGTTCATT
19369190 CGGTTAACCGAC
1 CGGTTAACCGAC
19369202 CGGTTAACCGAC
1 CGGTTAACCGAC
19369214 C
1 C
19369215 CGAAATAACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.36, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTTAACCGAC
Found at i:19369399 original size:18 final size:18
Alignment explanation
Indices: 19369387--19369446 Score: 86
Period size: 18 Copynumber: 3.3 Consensus size: 18
19369377 AAATTAACCG
*
19369387 AATTATCCGAATTATCCA
1 AATTAACCGAATTATCCA
*
19369405 AATTAATCGAATTATCCA
1 AATTAACCGAATTATCCA
19369423 AATTAACCGAATTAAT-CA
1 AATTAACCGAATT-ATCCA
19369441 AATTAA
1 AATTAA
19369447 ATCACTACAT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
18 36 0.95
19 2 0.05
ACGTcount: A:0.47, C:0.17, G:0.05, T:0.32
Consensus pattern (18 bp):
AATTAACCGAATTATCCA
Found at i:19369415 original size:27 final size:27
Alignment explanation
Indices: 19369377--19369445 Score: 93
Period size: 27 Copynumber: 2.6 Consensus size: 27
19369367 TTTTGGTTAA
* * *
19369377 AAATTAACCGAATTATCCGAATTATCC
1 AAATTAATCGAATTATCCAAATTAACC
19369404 AAATTAATCGAATTATCCAAATTAACC
1 AAATTAATCGAATTATCCAAATTAACC
* *
19369431 GAATTAATCAAATTA
1 AAATTAATCGAATTA
19369446 AATCACTACA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.46, C:0.17, G:0.06, T:0.30
Consensus pattern (27 bp):
AAATTAATCGAATTATCCAAATTAACC
Found at i:19369437 original size:9 final size:9
Alignment explanation
Indices: 19369378--19369437 Score: 66
Period size: 9 Copynumber: 6.7 Consensus size: 9
19369368 TTTGGTTAAA
19369378 AATTAACCG
1 AATTAACCG
*
19369387 AATTATCCG
1 AATTAACCG
* *
19369396 AATTATCCA
1 AATTAACCG
*
19369405 AATTAATCG
1 AATTAACCG
* *
19369414 AATTATCCA
1 AATTAACCG
19369423 AATTAACCG
1 AATTAACCG
19369432 AATTAA
1 AATTAA
19369438 TCAAATTAAA
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
9 41 1.00
ACGTcount: A:0.45, C:0.18, G:0.07, T:0.30
Consensus pattern (9 bp):
AATTAACCG
Found at i:19369574 original size:18 final size:18
Alignment explanation
Indices: 19369551--19369604 Score: 63
Period size: 18 Copynumber: 3.0 Consensus size: 18
19369541 TAATTTTATG
* **
19369551 ATTGGGTTGGGTTGGGTA
1 ATTGGGTTGAGTTGAATA
19369569 ATTGGGTTGAGTTGAATA
1 ATTGGGTTGAGTTGAATA
* *
19369587 ATTGGGTTTAGGTGAATA
1 ATTGGGTTGAGTTGAATA
19369605 GTGAGCCTAT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.22, C:0.00, G:0.39, T:0.39
Consensus pattern (18 bp):
ATTGGGTTGAGTTGAATA
Found at i:19380585 original size:41 final size:39
Alignment explanation
Indices: 19380454--19380586 Score: 103
Period size: 39 Copynumber: 3.4 Consensus size: 39
19380444 TCCAGTATGG
* * ** *
19380454 CACCCAGTGCCTCATCGGATAATTCGAAG-CAATAGTTGA
1 CACCCAGTGTCTCATCGGAAAACCCGAAGAAAATAG-TGA
* *
19380493 CACCCAGTGTCTCATCGGAAAAGCCGAAGAAAAT--TGG
1 CACCCAGTGTCTCATCGGAAAACCCGAAGAAAATAGTGA
* ** *
19380530 TACCCAGTACCTCATC-GAATCTACCCGAAGAAATATAGTGA
1 CACCCAGTGTCTCATCGGAA--AACCCGAAGAAA-ATAGTGA
19380571 CACCCAGTGTCTCATC
1 CACCCAGTGTCTCATC
19380587 AACTCGAGGT
Statistics
Matches: 73, Mismatches: 15, Indels: 10
0.74 0.15 0.10
Matches are distributed among these distances:
36 3 0.04
37 15 0.21
38 10 0.14
39 27 0.37
40 3 0.04
41 15 0.21
ACGTcount: A:0.32, C:0.28, G:0.19, T:0.21
Consensus pattern (39 bp):
CACCCAGTGTCTCATCGGAAAACCCGAAGAAAATAGTGA
Found at i:19380732 original size:39 final size:39
Alignment explanation
Indices: 19380688--19380771 Score: 91
Period size: 39 Copynumber: 2.2 Consensus size: 39
19380678 TCATTTTTCT
* *
19380688 ATTTCAAATT-CACTTTTGATTCAAT-CACAATTCAATTCA
1 ATTTCAAATTCCACTTTT-AATCAATACACAATTCAAAT-A
** *
19380727 ATTTCACTTTCCACTTTTAATCAATACACAGTTCAAATA
1 ATTTCAAATTCCACTTTTAATCAATACACAATTCAAATA
19380766 ATTTCA
1 ATTTCA
19380772 CTTCGATTCA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
39 21 0.55
40 17 0.45
ACGTcount: A:0.36, C:0.21, G:0.02, T:0.40
Consensus pattern (39 bp):
ATTTCAAATTCCACTTTTAATCAATACACAATTCAAATA
Found at i:19380772 original size:39 final size:40
Alignment explanation
Indices: 19380698--19380774 Score: 104
Period size: 40 Copynumber: 1.9 Consensus size: 40
19380688 ATTTCAAATT
* *
19380698 CACTTTTGATTCAATCACAATTCAATTCAATTTCACTTTC
1 CACTTTTGAATCAATCACAATTCAAATCAATTTCACTTTC
*
19380738 CACTTTT-AATCAATACACAGTTCAAAT-AATTTCACTT
1 CACTTTTGAATCAAT-CACAATTCAAATCAATTTCACTT
19380775 CGATTCAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
39 16 0.48
40 17 0.52
ACGTcount: A:0.34, C:0.23, G:0.03, T:0.40
Consensus pattern (40 bp):
CACTTTTGAATCAATCACAATTCAAATCAATTTCACTTTC
Found at i:19383718 original size:24 final size:24
Alignment explanation
Indices: 19383686--19383736 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
19383676 TACTTGGGTA
19383686 ATTTACCGTCAATTCATCCTTTAC
1 ATTTACCGTCAATTCATCCTTTAC
*
19383710 ATTTTCCGTCAATTCATCCTTTAC
1 ATTTACCGTCAATTCATCCTTTAC
19383734 ATT
1 ATT
19383737 CGTAGTGCCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.24, C:0.27, G:0.04, T:0.45
Consensus pattern (24 bp):
ATTTACCGTCAATTCATCCTTTAC
Found at i:19386122 original size:22 final size:22
Alignment explanation
Indices: 19386077--19386122 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
19386067 TAATATAGAC
* *
19386077 TTAATAGATGCAGGAAAATCTT
1 TTAATAGATGAAAGAAAATCTT
19386099 TTAATAGATGAAAAGAAAAT-TT
1 TTAATAGATG-AAAGAAAATCTT
19386121 TT
1 TT
19386123 GAACTGCTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.46, C:0.04, G:0.15, T:0.35
Consensus pattern (22 bp):
TTAATAGATGAAAGAAAATCTT
Found at i:19392446 original size:21 final size:22
Alignment explanation
Indices: 19392422--19392473 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
19392412 AATATTTTTC
* *
19392422 TCATAAAATTTATTTAAAAA-A
1 TCATAAAATTGATTAAAAAATA
*
19392443 TCATAAAAATGATTAAAAAATA
1 TCATAAAATTGATTAAAAAATA
*
19392465 TCAAAAAAT
1 TCATAAAAT
19392474 ATAAAAATTA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 17 0.68
22 8 0.32
ACGTcount: A:0.62, C:0.06, G:0.02, T:0.31
Consensus pattern (22 bp):
TCATAAAATTGATTAAAAAATA
Found at i:19392451 original size:10 final size:9
Alignment explanation
Indices: 19392436--19392532 Score: 54
Period size: 9 Copynumber: 10.3 Consensus size: 9
19392426 AAAATTTATT
19392436 TAAAAAATCA
1 TAAAAAAT-A
19392446 T-AAAAATGA
1 TAAAAAAT-A
19392455 TTAAAAAATA
1 -TAAAAAATA
19392465 TCAAAAAATA
1 T-AAAAAATA
*
19392475 TAAAAATTA
1 TAAAAAATA
* *
19392484 TTAAATAT-
1 TAAAAAATA
*
19392492 TTAAAAATA
1 TAAAAAATA
* *
19392501 TGAAAATTGA
1 TAAAAAAT-A
* *
19392511 TATGAAATTA
1 TA-AAAAATA
19392521 TAAAAAATA
1 TAAAAAATA
19392530 TAA
1 TAA
19392533 TTTTTTTATA
Statistics
Matches: 69, Mismatches: 12, Indels: 13
0.73 0.13 0.14
Matches are distributed among these distances:
8 7 0.10
9 34 0.49
10 17 0.25
11 11 0.16
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (9 bp):
TAAAAAATA
Found at i:19392480 original size:20 final size:21
Alignment explanation
Indices: 19392437--19392480 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
19392427 AAATTTATTT
19392437 AAAAAATCATAAAAATGATTAA
1 AAAAAATCATAAAAATGA-TAA
*
19392459 AAAATATCA-AAAAAT-ATAA
1 AAAAAATCATAAAAATGATAA
19392478 AAA
1 AAA
19392481 TTATTAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 6 0.29
20 1 0.05
21 6 0.29
22 8 0.38
ACGTcount: A:0.73, C:0.05, G:0.02, T:0.20
Consensus pattern (21 bp):
AAAAAATCATAAAAATGATAA
Found at i:19392820 original size:10 final size:8
Alignment explanation
Indices: 19392792--19392826 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
19392782 TGAACCAATT
19392792 TTTTTTAA
1 TTTTTTAA
19392800 TTTTTTAA
1 TTTTTTAA
19392808 TTTTTTAA
1 TTTTTTAA
* *
19392816 TATTTTGA
1 TTTTTTAA
19392824 TTT
1 TTT
19392827 ATTATGTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (8 bp):
TTTTTTAA
Found at i:19393192 original size:19 final size:19
Alignment explanation
Indices: 19393155--19393225 Score: 58
Period size: 19 Copynumber: 3.7 Consensus size: 19
19393145 AATGTTACAT
*
19393155 TTTTTTAAGAATTACAATATG
1 TTTTTTAA-ATTTA-AATATG
*
19393176 TTTTTTAAATTTAAATAAG
1 TTTTTTAAATTTAAATATG
*
19393195 TTTTATT-AATTT-TATAT-
1 TTTT-TTAAATTTAAATATG
19393212 TTTTTTATAATTTA
1 TTTTTTA-AATTTA
19393226 TTAGAATTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
16 2 0.05
17 4 0.10
18 8 0.19
19 14 0.33
20 6 0.14
21 8 0.19
ACGTcount: A:0.35, C:0.01, G:0.04, T:0.59
Consensus pattern (19 bp):
TTTTTTAAATTTAAATATG
Found at i:19393208 original size:20 final size:19
Alignment explanation
Indices: 19393155--19393208 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
19393145 AATGTTACAT
* *
19393155 TTTTTTAAGAATTACAATATG
1 TTTTTTAA-ATTTA-AATAAG
19393176 TTTTTTAAATTTAAATAAG
1 TTTTTTAAATTTAAATAAG
*
19393195 TTTTATTAATTTTA
1 TTTT-TTAAATTTA
19393209 TATTTTTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
19 9 0.31
20 12 0.41
21 8 0.28
ACGTcount: A:0.37, C:0.02, G:0.06, T:0.56
Consensus pattern (19 bp):
TTTTTTAAATTTAAATAAG
Found at i:19409005 original size:55 final size:55
Alignment explanation
Indices: 19408921--19409031 Score: 186
Period size: 55 Copynumber: 2.0 Consensus size: 55
19408911 CGTTTAACCC
* * *
19408921 TAATGGGTTTTAGTTCAACTCTTTTGAGCTTCGGTTTAACCCTTATGGGTTTCCG
1 TAATGAGTTTCAGTTCAACTCTTTTGAGCTTCAGTTTAACCCTTATGGGTTTCCG
*
19408976 TAATGAGTTTCAGTTCAGCTCTTTTGAGCTTCAGTTTAACCCTTATGGGTTTCCG
1 TAATGAGTTTCAGTTCAACTCTTTTGAGCTTCAGTTTAACCCTTATGGGTTTCCG
19409031 T
1 T
19409032 TCAACTCTTA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
55 52 1.00
ACGTcount: A:0.17, C:0.19, G:0.21, T:0.43
Consensus pattern (55 bp):
TAATGAGTTTCAGTTCAACTCTTTTGAGCTTCAGTTTAACCCTTATGGGTTTCCG
Found at i:19409043 original size:21 final size:21
Alignment explanation
Indices: 19409013--19409074 Score: 88
Period size: 21 Copynumber: 3.0 Consensus size: 21
19409003 GCTTCAGTTT
19409013 AACCCTTATGGGTTTCCGTTC
1 AACCCTTATGGGTTTCCGTTC
* * * *
19409034 AACTCTTATGAGCTTCTGTTC
1 AACCCTTATGGGTTTCCGTTC
19409055 AACCCTTATGGGTTTCCGTT
1 AACCCTTATGGGTTTCCGTT
19409075 TAGCACTTGT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.16, C:0.26, G:0.18, T:0.40
Consensus pattern (21 bp):
AACCCTTATGGGTTTCCGTTC
Found at i:19409046 original size:42 final size:42
Alignment explanation
Indices: 19408982--19409074 Score: 141
Period size: 42 Copynumber: 2.2 Consensus size: 42
19408972 TCCGTAATGA
* * * *
19408982 GTTTCAGTTCAGCTCTTTTGAGCTTCAGTTTAACCCTTATGG
1 GTTTCCGTTCAACTCTTATGAGCTTCAGTTCAACCCTTATGG
*
19409024 GTTTCCGTTCAACTCTTATGAGCTTCTGTTCAACCCTTATGG
1 GTTTCCGTTCAACTCTTATGAGCTTCAGTTCAACCCTTATGG
19409066 GTTTCCGTT
1 GTTTCCGTT
19409075 TAGCACTTGT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.43
Consensus pattern (42 bp):
GTTTCCGTTCAACTCTTATGAGCTTCAGTTCAACCCTTATGG
Found at i:19413138 original size:21 final size:22
Alignment explanation
Indices: 19413104--19413146 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
19413094 ATATTTTTGA
* *
19413104 AATTTTTATATTTTTTAATTTT
1 AATTTTGATATTTTATAATTTT
19413126 AATTTTGAT-TTTTATAATTTT
1 AATTTTGATATTTTATAATTTT
19413147 TGAATTATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (22 bp):
AATTTTGATATTTTATAATTTT
Found at i:19413161 original size:28 final size:27
Alignment explanation
Indices: 19413105--19413161 Score: 62
Period size: 28 Copynumber: 2.0 Consensus size: 27
19413095 TATTTTTGAA
* *
19413105 ATTTTTATATTTTTTAATTTTAATTTTG
1 ATTTTTATATTTTTGAATTTT-ATATTG
19413133 ATTTTTATAATTTTTGAATTATT-TATTG
1 ATTTTTAT-ATTTTTGAATT-TTATATTG
19413161 A
1 A
19413162 CGTGACATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
28 13 0.52
29 10 0.40
30 2 0.08
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (27 bp):
ATTTTTATATTTTTGAATTTTATATTG
Found at i:19416100 original size:23 final size:23
Alignment explanation
Indices: 19416071--19416116 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
19416061 TAATTTTATC
19416071 ATCCTAACTTTATTTGAAGTTTT
1 ATCCTAACTTTATTTGAAGTTTT
19416094 ATCCTAACTTTATTTGAAGTTTT
1 ATCCTAACTTTATTTGAAGTTTT
19416117 CTCGAATCGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.26, C:0.13, G:0.09, T:0.52
Consensus pattern (23 bp):
ATCCTAACTTTATTTGAAGTTTT
Found at i:19417016 original size:30 final size:31
Alignment explanation
Indices: 19416975--19417035 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 31
19416965 GGGTTGGGAG
* * *
19416975 GGGAGAGGAGTAAAAGTTTTGGGGGGAAAGT
1 GGGAGAGGAGTAAAAATTTTGAGGGAAAAGT
19417006 GGGA-AGGAGTAAAAATTTTGAGGGAAAAGT
1 GGGAGAGGAGTAAAAATTTTGAGGGAAAAGT
19417036 AAAAAGGTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 23 0.85
31 4 0.15
ACGTcount: A:0.38, C:0.00, G:0.43, T:0.20
Consensus pattern (31 bp):
GGGAGAGGAGTAAAAATTTTGAGGGAAAAGT
Found at i:19421357 original size:24 final size:23
Alignment explanation
Indices: 19421326--19421372 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
19421316 TATTCACACA
19421326 TATTCTTA-CTTAATTTCAAATGT
1 TATTCTTACCTTAATTT-AAATGT
*
19421349 TATTACTTACCTTACTTTAAATGT
1 TATT-CTTACCTTAATTTAAATGT
19421373 CCCATGATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 4 0.19
24 10 0.48
25 7 0.33
ACGTcount: A:0.30, C:0.15, G:0.04, T:0.51
Consensus pattern (23 bp):
TATTCTTACCTTAATTTAAATGT
Found at i:19421654 original size:22 final size:24
Alignment explanation
Indices: 19421612--19421655 Score: 74
Period size: 22 Copynumber: 1.9 Consensus size: 24
19421602 TAACTAAGCT
19421612 TACTTACTTTTCTAACTTAATTCA
1 TACTTACTTTTCTAACTTAATTCA
19421636 TACTT-CTTTTCT-ACTTAATT
1 TACTTACTTTTCTAACTTAATT
19421656 TCTTGCCATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 8 0.40
23 7 0.35
24 5 0.25
ACGTcount: A:0.25, C:0.20, G:0.00, T:0.55
Consensus pattern (24 bp):
TACTTACTTTTCTAACTTAATTCA
Found at i:19422274 original size:5 final size:5
Alignment explanation
Indices: 19422255--19422325 Score: 62
Period size: 5 Copynumber: 14.6 Consensus size: 5
19422245 TTAGTTTATT
* *
19422255 TAATA T-ATAA TAATA TAATA TAATA TAAT- TAATA TTATA TAATA TTTTATA
1 TAATA TAAT-A TAATA TAATA TAATA TAATA TAATA TAATA TAATA --TAATA
19422306 TAATA -AA-A TAATA T-ATA TAA
1 TAATA TAATA TAATA TAATA TAA
19422326 AACATAAAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 16
0.73 0.05 0.22
Matches are distributed among these distances:
3 1 0.02
4 14 0.26
5 33 0.61
6 2 0.04
7 4 0.07
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (5 bp):
TAATA
Found at i:19422289 original size:19 final size:18
Alignment explanation
Indices: 19422259--19422325 Score: 68
Period size: 19 Copynumber: 3.8 Consensus size: 18
19422249 TTTATTTAAT
19422259 ATATAATAATATAATATA
1 ATATAATAATATAATATA
*
19422277 ATATAATTAATATTATATA
1 ATATAA-TAATATAATATA
* *
19422296 ATAT-TTTATATAATA-A
1 ATATAATAATATAATATA
19422312 A-ATAATATATATAA
1 ATATAATA-ATATAA
19422326 AACATAAAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
15 2 0.05
16 3 0.08
17 14 0.35
18 6 0.15
19 15 0.38
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
ATATAATAATATAATATA
Found at i:19422296 original size:29 final size:28
Alignment explanation
Indices: 19422254--19422325 Score: 83
Period size: 29 Copynumber: 2.5 Consensus size: 28
19422244 TTTAGTTTAT
19422254 TTAATATATAATAATA-TAATATAATATAA
1 TTAATATAT-ATAATATTAATATAATA-AA
*
19422283 TTAATATTATATAATATTTTATATAATAAA
1 TTAATA-TATATAATA-TTAATATAATAAA
*
19422313 ATAATATATATAA
1 TTAATATATATAA
19422326 AACATAAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
29 19 0.50
30 10 0.26
31 9 0.24
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (28 bp):
TTAATATATATAATATTAATATAATAAA
Found at i:19422315 original size:17 final size:17
Alignment explanation
Indices: 19422267--19422325 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
19422257 ATATATAATA
*
19422267 ATATAATATAATATAATTA
1 ATATAATA-AA-ATAATTT
* * *
19422286 ATATTATATAATATTTT
1 ATATAATAAAATAATTT
*
19422303 ATATAATAAAATAATAT
1 ATATAATAAAATAATTT
19422320 ATATAA
1 ATATAA
19422326 AACATAAAAA
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
17 24 0.75
18 1 0.03
19 7 0.22
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
ATATAATAAAATAATTT
Found at i:19423879 original size:21 final size:21
Alignment explanation
Indices: 19423819--19423886 Score: 66
Period size: 21 Copynumber: 3.3 Consensus size: 21
19423809 TTTCGTTGAG
* * *
19423819 CTCTTTTGAGCTTCTGTTTAA
1 CTCTTATGAGCTTCCGTTCAA
* * * *
19423840 CCCTTATG-GTTTCCATTCAG
1 CTCTTATGAGCTTCCGTTCAA
19423860 CTCTTATGAGCTTCCGTTCAA
1 CTCTTATGAGCTTCCGTTCAA
19423881 CTCTTA
1 CTCTTA
19423887 CGGGTTTCTG
Statistics
Matches: 35, Mismatches: 11, Indels: 2
0.73 0.23 0.04
Matches are distributed among these distances:
20 14 0.40
21 21 0.60
ACGTcount: A:0.16, C:0.26, G:0.13, T:0.44
Consensus pattern (21 bp):
CTCTTATGAGCTTCCGTTCAA
Found at i:19426643 original size:37 final size:39
Alignment explanation
Indices: 19426554--19426645 Score: 107
Period size: 41 Copynumber: 2.4 Consensus size: 39
19426544 CCTTGAGTCA
* **
19426554 ATGAGACACTGGGTGTCACTATTTTACTTCGGATAGATTCG
1 ATGAGACACTGGGTATCAC--TTTTACTTCGGATAGAGCCG
* *
19426595 ATGAGATACTGGGTATCAC-TTTACTTCGGCTAG-GCCG
1 ATGAGACACTGGGTATCACTTTTACTTCGGATAGAGCCG
19426632 ATGAGACACTGGGT
1 ATGAGACACTGGGT
19426646 GTCAAATTTG
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
37 15 0.33
38 13 0.29
41 17 0.38
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.30
Consensus pattern (39 bp):
ATGAGACACTGGGTATCACTTTTACTTCGGATAGAGCCG
Found at i:19426660 original size:38 final size:38
Alignment explanation
Indices: 19426554--19426684 Score: 122
Period size: 38 Copynumber: 3.4 Consensus size: 38
19426544 CCTTGAGTCA
* * *
19426554 ATGAGACACTGGGTGTCACTATTTTACTTCGGATAGATTCG
1 ATGAGACACTGGGTGTCA--AATTTACTTCGGCTAG-TCCG
* * * *
19426595 ATGAGATACTGGGTATC-ACTTTACTTCGGCTAGGCCG
1 ATGAGACACTGGGTGTCAAATTTACTTCGGCTAGTCCG
* *
19426632 ATGAGACACTGGGTGTCAAATTTGCTTCGAACTA-TCCG
1 ATGAGACACTGGGTGTCAAATTTACTTCG-GCTAGTCCG
*
19426670 ATGAGGCACTGGGTG
1 ATGAGACACTGGGTG
19426685 CCAATCTGGT
Statistics
Matches: 75, Mismatches: 13, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
37 17 0.23
38 40 0.53
39 3 0.04
41 15 0.20
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30
Consensus pattern (38 bp):
ATGAGACACTGGGTGTCAAATTTACTTCGGCTAGTCCG
Found at i:19434955 original size:37 final size:37
Alignment explanation
Indices: 19434914--19434988 Score: 105
Period size: 37 Copynumber: 2.0 Consensus size: 37
19434904 AGTGAACCAG
* * *
19434914 TTGAGGGTGACACCGACTCAATCAGAAGCTTAAATAA
1 TTGAGGGTGACACCAACTAAATCAAAAGCTTAAATAA
* *
19434951 TTGAGGGTGATACTAACTAAATCAAAAGCTTAAATAA
1 TTGAGGGTGACACCAACTAAATCAAAAGCTTAAATAA
19434988 T
1 T
19434989 AGAATGGATG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.41, C:0.15, G:0.19, T:0.25
Consensus pattern (37 bp):
TTGAGGGTGACACCAACTAAATCAAAAGCTTAAATAA
Found at i:19435466 original size:4 final size:4
Alignment explanation
Indices: 19435457--19435484 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
19435447 ACTCTTATAT
19435457 TTAA TTAA TTAA TTAA TTAA TTAA TTAA
1 TTAA TTAA TTAA TTAA TTAA TTAA TTAA
19435485 AGCGAGCCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
TTAA
Found at i:19440363 original size:9 final size:9
Alignment explanation
Indices: 19440338--19440394 Score: 89
Period size: 9 Copynumber: 6.4 Consensus size: 9
19440328 TTTGGTTCAA
19440338 AATTAACCG
1 AATTAACCG
19440347 AATT-ACCG
1 AATTAACCG
19440355 AATTAACCG
1 AATTAACCG
* *
19440364 GATTACCCG
1 AATTAACCG
19440373 AATTAACCG
1 AATTAACCG
19440382 AATTAACCG
1 AATTAACCG
19440391 AATT
1 AATT
19440395 GAATCACTAC
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
8 8 0.19
9 35 0.81
ACGTcount: A:0.40, C:0.23, G:0.12, T:0.25
Consensus pattern (9 bp):
AATTAACCG
Found at i:19443035 original size:20 final size:19
Alignment explanation
Indices: 19442997--19443035 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
19442987 CGAGTGAAAA
*
19442997 TTTTAAATAACATTAATAT
1 TTTTAAAAAACATTAATAT
*
19443016 TTTTAAAAAATATATAATAT
1 TTTTAAAAAACAT-TAATAT
19443036 ATGATTTCAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTTAAAAAACATTAATAT
Found at i:19456208 original size:17 final size:18
Alignment explanation
Indices: 19456176--19456209 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
19456166 GGTTGAACTG
19456176 ATTTAATACATTTTTTAT
1 ATTTAATACATTTTTTAT
*
19456194 ATTTAATTC-TTTTTTA
1 ATTTAATACATTTTTTA
19456210 CGAATTTTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (18 bp):
ATTTAATACATTTTTTAT
Found at i:19458187 original size:13 final size:13
Alignment explanation
Indices: 19458169--19458193 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19458159 TATTTTTAGA
19458169 TTTTTTATAAATT
1 TTTTTTATAAATT
19458182 TTTTTTATAAAT
1 TTTTTTATAAAT
19458194 AAATTTTTGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TTTTTTATAAATT
Found at i:19458220 original size:19 final size:20
Alignment explanation
Indices: 19458198--19458247 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
19458188 ATAAATAAAT
19458198 TTTTGAA-ATTTAAAAATTA
1 TTTTGAATATTTAAAAATTA
* *
19458217 TTTTGAATTTTTTAAAATTA
1 TTTTGAATATTTAAAAATTA
19458237 TTTT-AATATTT
1 TTTTGAATATTT
19458248 TTTTTGTAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 13 0.48
20 14 0.52
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (20 bp):
TTTTGAATATTTAAAAATTA
Found at i:19464661 original size:50 final size:50
Alignment explanation
Indices: 19464590--19464690 Score: 193
Period size: 50 Copynumber: 2.0 Consensus size: 50
19464580 AAAACCTTAA
19464590 TTTTTTGCTTATTCTTCTCTTTAATCTTTTTCATGGTGCAAGATACTAAT
1 TTTTTTGCTTATTCTTCTCTTTAATCTTTTTCATGGTGCAAGATACTAAT
*
19464640 TTTTTTGCTTATTCTTCTCTTTAATCTTTTTCATGGTGCAAGATTCTAAT
1 TTTTTTGCTTATTCTTCTCTTTAATCTTTTTCATGGTGCAAGATACTAAT
19464690 T
1 T
19464691 GAAACTCACA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.19, C:0.16, G:0.10, T:0.55
Consensus pattern (50 bp):
TTTTTTGCTTATTCTTCTCTTTAATCTTTTTCATGGTGCAAGATACTAAT
Found at i:19472493 original size:15 final size:15
Alignment explanation
Indices: 19472468--19472502 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
19472458 AACTCTATTT
*
19472468 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
19472482 TAATTAATATTAAGA
1 TAATTAATATTAAGA
19472497 TAATTA
1 TAATTA
19472503 TTAAGGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:19473886 original size:18 final size:17
Alignment explanation
Indices: 19473853--19473891 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
19473843 TTGTATAAAT
19473853 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
19473871 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
19473888 TGTG
1 TGTG
19473892 GAAGGAAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:19474144 original size:23 final size:23
Alignment explanation
Indices: 19474117--19474214 Score: 153
Period size: 23 Copynumber: 4.3 Consensus size: 23
19474107 AGTGTTATTG
19474117 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* * *
19474140 TTCAGTGGTAGCTTTGGCTGCAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
19474163 -CCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
19474185 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
19474208 ATCAGTG
1 ATCAGTG
19474215 TGGCACTTAT
Statistics
Matches: 67, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
22 19 0.28
23 48 0.72
ACGTcount: A:0.19, C:0.21, G:0.28, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:19482425 original size:17 final size:15
Alignment explanation
Indices: 19482384--19482428 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 15
19482374 TTTTAAAAAT
19482384 ATTTATATTATTTTAA
1 ATTTATA-TATTTTAA
19482400 ATTTA-ATATTTAATAA
1 ATTTATATATTT--TAA
19482416 ATTTATATATTTT
1 ATTTATATATTTT
19482429 TCTTGATTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
14 5 0.19
15 2 0.08
16 13 0.50
17 6 0.23
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
ATTTATATATTTTAA
Found at i:19489907 original size:25 final size:25
Alignment explanation
Indices: 19489871--19489918 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
19489861 CTTAAAATCA
19489871 CTACCATCTCTATAGATGTTAGACT
1 CTACCATCTCTATAGATGTTAGACT
* *
19489896 CTACCA-CTTCTATGGTTGTTAGA
1 CTACCATC-TCTATAGATGTTAGA
19489919 TGCATCCATC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 1 0.05
25 19 0.95
ACGTcount: A:0.25, C:0.23, G:0.15, T:0.38
Consensus pattern (25 bp):
CTACCATCTCTATAGATGTTAGACT
Found at i:19491328 original size:15 final size:16
Alignment explanation
Indices: 19491308--19491337 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
19491298 CATCATACAA
19491308 TTATTC-TCTTCTTTC
1 TTATTCTTCTTCTTTC
19491323 TTATTCTTCTTCTTT
1 TTATTCTTCTTCTTT
19491338 GCAAATAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.07, C:0.23, G:0.00, T:0.70
Consensus pattern (16 bp):
TTATTCTTCTTCTTTC
Found at i:19495761 original size:21 final size:21
Alignment explanation
Indices: 19495709--19495755 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
19495699 AAATATACAG
19495709 TATATG-GCATTTAAACTATA
1 TATATGAGCATTTAAACTATA
**
19495729 TATATGAGCATTTAATGTATA
1 TATATGAGCATTTAAACTATA
19495750 TATATG
1 TATATG
19495756 CTCATTAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 6 0.25
21 18 0.75
ACGTcount: A:0.38, C:0.06, G:0.13, T:0.43
Consensus pattern (21 bp):
TATATGAGCATTTAAACTATA
Found at i:19496339 original size:9 final size:9
Alignment explanation
Indices: 19496325--19496362 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
19496315 AATTGTAGAG
19496325 TTTAAAAAT
1 TTTAAAAAT
19496334 TTTAAAAAT
1 TTTAAAAAT
* *
19496343 CTTCAAAAT
1 TTTAAAAAT
19496352 TTT-AAAAT
1 TTTAAAAAT
19496360 TTT
1 TTT
19496363 TCATCTGAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
8 8 0.31
9 18 0.69
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (9 bp):
TTTAAAAAT
Found at i:19512328 original size:15 final size:15
Alignment explanation
Indices: 19512310--19512338 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
19512300 AAAAAAAAGA
19512310 AAAGAACAAAAGAAG
1 AAAGAACAAAAGAAG
19512325 AAAGAACAAAAGAA
1 AAAGAACAAAAGAA
19512339 TAGGAGTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.76, C:0.07, G:0.17, T:0.00
Consensus pattern (15 bp):
AAAGAACAAAAGAAG
Found at i:19515320 original size:19 final size:18
Alignment explanation
Indices: 19515256--19515351 Score: 59
Period size: 19 Copynumber: 4.9 Consensus size: 18
19515246 AATTTAAAAT
19515256 ATATATTATATTATATATA
1 ATATATTATATTATAT-TA
* * *
19515275 CGTA-ATTAATGATTATGTTT
1 -ATATATT-AT-ATTATATTA
* *
19515295 TTATATTGTATTATTATTA
1 ATATATTATATTA-TATTA
19515314 ATATATTATATTATATTA
1 ATATATTATATTATATTA
19515332 TATTATATATATATATATAT
1 -A-TATAT-TATAT-TATAT
19515352 AACAAAAGAA
Statistics
Matches: 59, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
18 9 0.15
19 21 0.36
20 13 0.22
21 11 0.19
22 5 0.08
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.55
Consensus pattern (18 bp):
ATATATTATATTATATTA
Found at i:19515330 original size:10 final size:10
Alignment explanation
Indices: 19515257--19515351 Score: 67
Period size: 10 Copynumber: 9.5 Consensus size: 10
19515247 ATTTAAAATA
19515257 TATATTATAT
1 TATATTATAT
*
19515267 TATA-TATACG
1 TATATTATA-T
19515277 TA-ATTAATGAT
1 TATATT-AT-AT
*
19515288 TATGTT-T-T
1 TATATTATAT
*
19515296 TATATTGTAT
1 TATATTATAT
19515306 TATTATTA-A-
1 TA-TATTATAT
19515315 TATATTATAT
1 TATATTATAT
19515325 TATATTATAT
1 TATATTATAT
19515335 TATATATATAT
1 TATAT-TATAT
19515346 ATATAT
1 -TATAT
19515352 AACAAAAGAA
Statistics
Matches: 68, Mismatches: 5, Indels: 22
0.72 0.05 0.23
Matches are distributed among these distances:
8 11 0.16
9 9 0.13
10 27 0.40
11 13 0.19
12 8 0.12
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.56
Consensus pattern (10 bp):
TATATTATAT
Found at i:19515342 original size:2 final size:2
Alignment explanation
Indices: 19515314--19515352 Score: 50
Period size: 2 Copynumber: 21.5 Consensus size: 2
19515304 ATTATTATTA
19515314 AT AT AT -T AT AT -T AT AT -T AT AT -T 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 AT
19515352 A
1 A
19515353 ACAAAAGAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
1 4 0.12
2 29 0.88
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
AT
Found at i:19516237 original size:27 final size:26
Alignment explanation
Indices: 19516193--19516247 Score: 83
Period size: 27 Copynumber: 2.1 Consensus size: 26
19516183 GAATGTCGAT
*
19516193 ATTGAATTAAATGAATTAAAATATGA
1 ATTGAATAAAATGAATTAAAATATGA
*
19516219 ATTGAATAAAAGTGAATTAAATTATGA
1 ATTGAATAAAA-TGAATTAAAATATGA
19516246 AT
1 AT
19516248 ATGTGTGAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 10 0.38
27 16 0.62
ACGTcount: A:0.53, C:0.00, G:0.13, T:0.35
Consensus pattern (26 bp):
ATTGAATAAAATGAATTAAAATATGA
Found at i:19516240 original size:26 final size:27
Alignment explanation
Indices: 19516193--19516247 Score: 78
Period size: 26 Copynumber: 2.1 Consensus size: 27
19516183 GAATGTCGAT
*
19516193 ATTGAATTAAATGAATTAAAA-TATGA
1 ATTGAATAAAATGAATTAAAATTATGA
19516219 ATTGAATAAAAGTGAATT-AAATTATGA
1 ATTGAATAAAA-TGAATTAAAATTATGA
19516246 AT
1 AT
19516248 ATGTGTGAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 13 0.50
27 13 0.50
ACGTcount: A:0.53, C:0.00, G:0.13, T:0.35
Consensus pattern (27 bp):
ATTGAATAAAATGAATTAAAATTATGA
Found at i:19523824 original size:23 final size:22
Alignment explanation
Indices: 19523792--19523853 Score: 79
Period size: 22 Copynumber: 2.7 Consensus size: 22
19523782 TCACCCCATT
*
19523792 TTTTTAATTAAAATTAAAATTATA
1 TTTTT-ATTAAAATTAAAACTA-A
19523816 TTTTTATTAAAATTAAAACTAA
1 TTTTTATTAAAATTAAAACTAA
* *
19523838 TTGTTATCAAAATTAA
1 TTTTTATTAAAATTAA
19523854 TTGTTATCAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
22 15 0.43
23 15 0.43
24 5 0.14
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.47
Consensus pattern (22 bp):
TTTTTATTAAAATTAAAACTAA
Found at i:19523854 original size:16 final size:16
Alignment explanation
Indices: 19523830--19523883 Score: 90
Period size: 16 Copynumber: 3.4 Consensus size: 16
19523820 TATTAAAATT
*
19523830 AAAACTAATTGTTATC
1 AAAATTAATTGTTATC
19523846 AAAATTAATTGTTATC
1 AAAATTAATTGTTATC
*
19523862 AAAATTAATTGTTATT
1 AAAATTAATTGTTATC
19523878 AAAATT
1 AAAATT
19523884 GTATCAAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.46, C:0.06, G:0.06, T:0.43
Consensus pattern (16 bp):
AAAATTAATTGTTATC
Done.