Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397260.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_51.0, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 10072460
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Warning! 70252 characters in sequence are not A, C, G, or T
File 11 of 20
Found at i:4084460 original size:210 final size:218
Alignment explanation
Indices: 4083866--4084423 Score: 769
Period size: 210 Copynumber: 2.6 Consensus size: 218
4083856 TAATTGTATA
* *
4083866 AATATATTATATATACATATATTTAATTTATACATAAATATTACTATAATTTA-AATAAACTTTA
1 AATATATTATATATACATATATTTAATTTATACATAAGTATTACTATAACTTATAATAAACTTTA
* * * *
4083930 TTTATATAATTATACTTAATAACTTTATTAGTTATCACTTTAAATTTTATAACATATTGTTTATA
66 TTTATATGATTATACTTAATAACTTTATTAGCTATCACTTTAGATTTTATAACATATTATTTATA
* * **
4083995 ATTAATTATTATTTATACAAACTTTGATATAAAACATTATAACATCTAAGTTATGTCATTAATTT
131 ATTAATTATTATTTATACAAACATTGATATAAAACATTATAACACCTAAACTATGTCATTAATTT
4084060 CATATATATATATATAATAAAAT
196 CATATATATATATATAATAAAAT
* * *
4084083 CATATATTATATGTACATATATTTAATTTATACATAAGTATTACTATAACTTATAATAGACTTTA
1 AATATATTATATATACATATATTTAATTTATACATAAGTATTACTATAACTTATAATAAACTTTA
* *
4084148 TTTATATGATTACACTTAATAACTTTATTAGCTATCACTTTAGATTTTATGACATATTGA-TTAT
66 TTTATATGATTATACTTAATAACTTTATTAGCTATCACTTTAGATTTTATAACATATT-ATTTAT
* * * *
4084212 AATTAGTTATTATTTCTATAAACATTGATATAAAACATT-TAA-ACCTATAACT-TGT-A-TCA-
130 AATTAATTATTATTTATACAAACATTGATATAAAACATTATAACACCTA-AACTATGTCATTAAT
*
4084271 TT-A-AT-TATATATATAATAAAGT
194 TTCATATATATATATATAATAAAAT
* * * *
4084293 AATATATTAGACATACATATATTTAATTTATACATAAGCATTACCATAACTTATAATAAACTTTA
1 AATATATTATATATACATATATTTAATTTATACATAAGTATTACTATAACTTATAATAAACTTTA
* * * *
4084358 TTTATATGATTATACTTAATAAGTTTATTAACTATCAGTTTAGATTTTATAATATATTATTTATA
66 TTTATATGATTATACTTAATAACTTTATTAGCTATCACTTTAGATTTTATAACATATTATTTATA
4084423 A
131 A
4084424 NNNNNNNNNN
Statistics
Matches: 304, Mismatches: 33, Indels: 15
0.86 0.09 0.04
Matches are distributed among these distances:
209 1 0.00
210 132 0.43
211 2 0.01
212 1 0.00
213 2 0.01
214 2 0.01
215 1 0.00
216 7 0.02
217 54 0.18
218 102 0.34
ACGTcount: A:0.42, C:0.08, G:0.04, T:0.46
Consensus pattern (218 bp):
AATATATTATATATACATATATTTAATTTATACATAAGTATTACTATAACTTATAATAAACTTTA
TTTATATGATTATACTTAATAACTTTATTAGCTATCACTTTAGATTTTATAACATATTATTTATA
ATTAATTATTATTTATACAAACATTGATATAAAACATTATAACACCTAAACTATGTCATTAATTT
CATATATATATATATAATAAAAT
Found at i:4084486 original size:210 final size:210
Alignment explanation
Indices: 4083866--4084497 Score: 764
Period size: 210 Copynumber: 3.0 Consensus size: 210
4083856 TAATTGTATA
* *
4083866 AATATATTATATATACATATATTTAATTTATACATAAATATTACTATAATTTA-AATAAACTTTA
1 AATATATTATATATACATATATTTAATTTATACATAAGTATTACTATAACTTATAATAAACTTTA
* * * *
4083930 TTTATATAATTATACTTAATAACTTTATTAGTTATCACTTTAAATTTTATAACATATTGTTTATA
66 TTTATATGATTATACTTAATAACTTTATTAGCTATCACTTTAGATTTTATAACATATTATTTATA
* *
4083995 ATTAATTATTATTTATACAAACTTTGATATAAAACATTATAACATCTAAGTTATGTCATTAATTT
131 ATTAATTATTATTTATACAAACTTTGATATAAAACATTAAAACATATAAGTTA--T-A-TAA-TT
4084060 CATATATATATATATAATAAAAT
191 -A-AT-TATATATATAATAAAAT
* * *
4084083 CATATATTATATGTACATATATTTAATTTATACATAAGTATTACTATAACTTATAATAGACTTTA
1 AATATATTATATATACATATATTTAATTTATACATAAGTATTACTATAACTTATAATAAACTTTA
* *
4084148 TTTATATGATTACACTTAATAACTTTATTAGCTATCACTTTAGATTTTATGACATATTGA-TTAT
66 TTTATATGATTATACTTAATAACTTTATTAGCTATCACTTTAGATTTTATAACATATT-ATTTAT
* * * * * * * * *
4084212 AATTAGTTATTATTTCTATAAACATTGATATAAAACATTTAAACCTATAACTTGTATCATTAATT
130 AATTAATTATTATTTATACAAACTTTGATATAAAACATTAAAACATATAAGTTATATAATTAATT
*
4084277 ATATATATAATAAAGT
195 ATATATATAATAAAAT
* * * *
4084293 AATATATTAGACATACATATATTTAATTTATACATAAGCATTACCATAACTTATAATAAACTTTA
1 AATATATTATATATACATATATTTAATTTATACATAAGTATTACTATAACTTATAATAAACTTTA
* * * *
4084358 TTTATATGATTATACTTAATAAGTTTATTAACTATCAGTTTAGATTTTATAATATATTATTTATA
66 TTTATATGATTATACTTAATAACTTTATTAGCTATCACTTTAGATTTTATAACATATTATTTATA
********** * *
4084423 ANNNNNNNNNNTTTATACAAACTTTGATATAAAACATTAAAATATAAAAGTTATATAATTAATTT
131 ATTAATTATTATTTATACAAACTTTGATATAAAACATTAAAACATATAAGTTATATAATTAA-TT
4084488 CATATATATA
195 -ATATATATA
4084498 TAATTATGGA
Statistics
Matches: 354, Mismatches: 56, Indels: 15
0.83 0.13 0.04
Matches are distributed among these distances:
209 1 0.00
210 173 0.49
211 4 0.01
212 10 0.03
213 2 0.01
214 2 0.01
215 1 0.00
216 1 0.00
217 49 0.14
218 111 0.31
ACGTcount: A:0.42, C:0.08, G:0.04, T:0.44
Consensus pattern (210 bp):
AATATATTATATATACATATATTTAATTTATACATAAGTATTACTATAACTTATAATAAACTTTA
TTTATATGATTATACTTAATAACTTTATTAGCTATCACTTTAGATTTTATAACATATTATTTATA
ATTAATTATTATTTATACAAACTTTGATATAAAACATTAAAACATATAAGTTATATAATTAATTA
TATATATAATAAAAT
Found at i:4085244 original size:30 final size:31
Alignment explanation
Indices: 4085193--4085267 Score: 93
Period size: 31 Copynumber: 2.5 Consensus size: 31
4085183 TTAAGTGATA
4085193 ATGTA-TAAATATTATACAGTAA-CAATGTAT
1 ATGTATTAAATATTATACAGTAATC-ATGTAT
4085223 ATGTATTAAATATTATA-AGTAATCATGTAT
1 ATGTATTAAATATTATACAGTAATCATGTAT
**
4085253 AAATAATTAAATATT
1 ATGT-ATTAAATATT
4085268 GTAGGAGTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
30 18 0.45
31 22 0.55
ACGTcount: A:0.48, C:0.04, G:0.08, T:0.40
Consensus pattern (31 bp):
ATGTATTAAATATTATACAGTAATCATGTAT
Found at i:4085839 original size:28 final size:28
Alignment explanation
Indices: 4085803--4085879 Score: 136
Period size: 28 Copynumber: 2.7 Consensus size: 28
4085793 AAATTAAATT
4085803 AAATAAAATTTTTGAAAAATTTTTTAAA
1 AAATAAAATTTTTGAAAAATTTTTTAAA
4085831 AAATAAAATTTTTGAAAAATTTTTTAAA
1 AAATAAAATTTTTGAAAAATTTTTTAAA
*
4085859 AAATAAATTTTTTTGAAAAAT
1 AAATAAA-ATTTTTGAAAAAT
4085880 AAAATTTTTT
Statistics
Matches: 47, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
28 35 0.74
29 12 0.26
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (28 bp):
AAATAAAATTTTTGAAAAATTTTTTAAA
Found at i:4085840 original size:17 final size:17
Alignment explanation
Indices: 4085818--4085905 Score: 91
Period size: 17 Copynumber: 5.5 Consensus size: 17
4085808 AAATTTTTGA
4085818 AAAATTTTTTAAAAAAT
1 AAAATTTTTTAAAAAAT
*
4085835 AAAA-TTTTT----GA-
1 AAAATTTTTTAAAAAAT
4085846 AAAATTTTTTAAAAAAT
1 AAAATTTTTTAAAAAAT
* *
4085863 AAATTTTTTTGAAAAAT
1 AAAATTTTTTAAAAAAT
4085880 AAAATTTTTTTAAAAAAT
1 AAAA-TTTTTTAAAAAAT
4085898 -AAATTTTT
1 AAAATTTTT
4085906 CTNNNNNNNN
Statistics
Matches: 58, Mismatches: 6, Indels: 15
0.73 0.08 0.19
Matches are distributed among these distances:
11 4 0.07
12 6 0.10
16 11 0.19
17 25 0.43
18 12 0.21
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (17 bp):
AAAATTTTTTAAAAAAT
Found at i:4088561 original size:19 final size:19
Alignment explanation
Indices: 4088539--4088577 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
4088529 ATAAATTATA
*
4088539 TTTTTTAAAAAAAATTCTC
1 TTTTTTAAAAAAAATACTC
*
4088558 TTTTTTTAAAAAAATACTC
1 TTTTTTAAAAAAAATACTC
4088577 T
1 T
4088578 CAACCAATCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.49
Consensus pattern (19 bp):
TTTTTTAAAAAAAATACTC
Found at i:4090080 original size:22 final size:21
Alignment explanation
Indices: 4090040--4090080 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
4090030 ATTTATAACT
*
4090040 AATAATTTTTTTCACTTAATA
1 AATAATTTTTTTAACTTAATA
*
4090061 AATATATTTTTTTAATTTAA
1 AATA-ATTTTTTTAACTTAA
4090081 AATATGAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (21 bp):
AATAATTTTTTTAACTTAATA
Found at i:4092071 original size:99 final size:99
Alignment explanation
Indices: 4091950--4092144 Score: 363
Period size: 99 Copynumber: 2.0 Consensus size: 99
4091940 GAAGAAAGAA
*
4091950 TTTGATTTAATGAAATTTATTTCATATTGAAGAAATGAAGTATCACCTTTATCTGTTTATGCAGC
1 TTTGATTTAATGAAATTTATTTCATATTGAAGAAATGAAGTATCACCTTCATCTGTTTATGCAGC
* *
4092015 TTTAAAAAGTGTTGATTGAACTTAGATTTAGCAC
66 ATTAAAAAGTGTAGATTGAACTTAGATTTAGCAC
4092049 TTTGATTTAATGAAATTTATTTCATATTGAAGAAATGAAGTATCACCTTCATCTGTTTATGCAGC
1 TTTGATTTAATGAAATTTATTTCATATTGAAGAAATGAAGTATCACCTTCATCTGTTTATGCAGC
4092114 ATTAAAAAGTGTAGATTGAACTTAGATTTAG
66 ATTAAAAAGTGTAGATTGAACTTAGATTTAG
4092145 TTGAGGCTAA
Statistics
Matches: 93, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
99 93 1.00
ACGTcount: A:0.34, C:0.10, G:0.15, T:0.41
Consensus pattern (99 bp):
TTTGATTTAATGAAATTTATTTCATATTGAAGAAATGAAGTATCACCTTCATCTGTTTATGCAGC
ATTAAAAAGTGTAGATTGAACTTAGATTTAGCAC
Found at i:4097287 original size:30 final size:30
Alignment explanation
Indices: 4097253--4097318 Score: 105
Period size: 30 Copynumber: 2.2 Consensus size: 30
4097243 CAAAAAATCG
*
4097253 TATTTTTATTTTAAATTAAATAAATTTTTA
1 TATTTATATTTTAAATTAAATAAATTTTTA
* *
4097283 TATTTATATTTTAAATTAAATAATTTTTTT
1 TATTTATATTTTAAATTAAATAAATTTTTA
4097313 TATTTA
1 TATTTA
4097319 ATCAAAATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (30 bp):
TATTTATATTTTAAATTAAATAAATTTTTA
Found at i:4102775 original size:25 final size:24
Alignment explanation
Indices: 4102747--4102810 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 24
4102737 AAAATTGAAT
* *
4102747 AAAAAGAAAAAGTAAAAAATCTTTA
1 AAAAAGAAAAAGAAAAAAAT-TATA
*
4102772 AAAATGAAAATAGAAAAAAATTATA
1 AAAAAGAAAA-AGAAAAAAATTATA
4102797 AAAAAGGAAAAAGA
1 AAAAA-GAAAAAGA
4102811 GTGGGAAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
25 19 0.58
26 14 0.42
ACGTcount: A:0.72, C:0.02, G:0.11, T:0.16
Consensus pattern (24 bp):
AAAAAGAAAAAGAAAAAAATTATA
Found at i:4103029 original size:2 final size:2
Alignment explanation
Indices: 4103022--4103048 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4103012 ATAGAAAATA
4103022 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
4103049 AAGTACCCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4104289 original size:3 final size:3
Alignment explanation
Indices: 4104281--4104312 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
4104271 AGCTAATAGT
4104281 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
4104313 GCGAATTTAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:4107866 original size:6 final size:6
Alignment explanation
Indices: 4107855--4107892 Score: 67
Period size: 6 Copynumber: 6.3 Consensus size: 6
4107845 ATGGCTACAA
*
4107855 CTATGG CTATGG CTATGG CTATGG CCATGG CTATGG CT
1 CTATGG CTATGG CTATGG CTATGG CTATGG CTATGG CT
4107893 TTGAATACCC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.16, C:0.21, G:0.32, T:0.32
Consensus pattern (6 bp):
CTATGG
Found at i:4125406 original size:14 final size:15
Alignment explanation
Indices: 4125389--4125422 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
4125379 TATTATCTTC
*
4125389 TTATTTTTATT-TAT
1 TTATTTCTATTCTAT
4125403 TTATTTCTATTCTAT
1 TTATTTCTATTCTAT
4125418 TTATT
1 TTATT
4125423 CATATATTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.74
Consensus pattern (15 bp):
TTATTTCTATTCTAT
Found at i:4126249 original size:2 final size:2
Alignment explanation
Indices: 4126242--4126267 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4126232 CCATTTAGTC
4126242 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
4126268 GACACCATCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4127123 original size:15 final size:14
Alignment explanation
Indices: 4127105--4127157 Score: 61
Period size: 14 Copynumber: 3.7 Consensus size: 14
4127095 ATGTTATAAT
4127105 TAAAATAAAAAATA
1 TAAAATAAAAAATA
*
4127119 TTAAAATAAAATATA
1 -TAAAATAAAAAATA
* *
4127134 TAATATAAAAATTA
1 TAAAATAAAAAATA
*
4127148 AAAAATAAAA
1 TAAAATAAAA
4127158 TAAAATATAA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
14 19 0.59
15 13 0.41
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (14 bp):
TAAAATAAAAAATA
Found at i:4127167 original size:7 final size:7
Alignment explanation
Indices: 4127105--4127167 Score: 53
Period size: 7 Copynumber: 9.4 Consensus size: 7
4127095 ATGTTATAAT
4127105 TAAAATA
1 TAAAATA
*
4127112 AAAAATA
1 TAAAATA
*
4127119 TTAAA-A
1 TAAAATA
4127125 TAAAATA
1 TAAAATA
*
4127132 TATAATA
1 TAAAATA
4127139 TAAAA-A
1 TAAAATA
*
4127145 TTAAAAAA
1 -TAAAATA
4127153 T-AAA-A
1 TAAAATA
4127158 TAAAATA
1 TAAAATA
4127165 TAA
1 TAA
4127168 GAAATTAAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
5 2 0.04
6 12 0.27
7 30 0.67
8 1 0.02
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (7 bp):
TAAAATA
Found at i:4127178 original size:33 final size:35
Alignment explanation
Indices: 4127102--4127179 Score: 99
Period size: 33 Copynumber: 2.3 Consensus size: 35
4127092 ATAATGTTAT
*
4127102 AATTAAAATAAAAAATATTAAAATAAAATATATAA
1 AATTAAAATTAAAAATATTAAAATAAAATATATAA
* *
4127137 TATAAAAATTAAAAA-A-TAAAATAAAATATA-AGA
1 AATTAAAATTAAAAATATTAAAATAAAATATATA-A
4127170 AATTAAAATT
1 AATTAAAATT
4127180 TATATAATAT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
32 1 0.03
33 23 0.62
34 1 0.03
35 12 0.32
ACGTcount: A:0.71, C:0.00, G:0.01, T:0.28
Consensus pattern (35 bp):
AATTAAAATTAAAAATATTAAAATAAAATATATAA
Found at i:4127241 original size:56 final size:55
Alignment explanation
Indices: 4127118--4127245 Score: 127
Period size: 56 Copynumber: 2.3 Consensus size: 55
4127108 AATAAAAAAT
* * * *
4127118 ATTAAAA-TAAAATATATA-ATATAAAAATTAAAAAATAAAATAAAATATAAGAA
1 ATTAAAATTAATATATATAGGTAAAAAAATTAAAAAATAAAACAAAATATAAGAA
* * * * *
4127171 ATTAAAATTTATATAATATAGGTAAAAAAATTAAAATATAATACATAATATAAGCA
1 ATTAAAATTAATAT-ATATAGGTAAAAAAATTAAAAAATAAAACAAAATATAAGAA
*
4127227 ATT-ATATTAAATATATATA
1 ATTAAAATT-AATATATATA
4127246 AGATTATAAT
Statistics
Matches: 60, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
53 7 0.12
54 4 0.07
55 14 0.23
56 35 0.58
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.32
Consensus pattern (55 bp):
ATTAAAATTAATATATATAGGTAAAAAAATTAAAAAATAAAACAAAATATAAGAA
Found at i:4127519 original size:15 final size:15
Alignment explanation
Indices: 4127495--4127528 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
4127485 TTTTTCTTAT
*
4127495 AATCACATTACTAGC
1 AATCACATTACCAGC
*
4127510 AATCATATTACCAGC
1 AATCACATTACCAGC
4127525 AATC
1 AATC
4127529 TAGTGAACAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.41, C:0.26, G:0.06, T:0.26
Consensus pattern (15 bp):
AATCACATTACCAGC
Found at i:4128161 original size:22 final size:21
Alignment explanation
Indices: 4128121--4128177 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 21
4128111 TAAAGCAAAC
4128121 AAATCGAAAAAAAAG-AAAAGA
1 AAAT-GAAAAAAAAGAAAAAGA
*
4128142 ACAATGAAAAAAGAGCAAAAAGA
1 A-AATGAAAAAAAAG-AAAAAGA
*
4128165 AAATTAAAAAAAA
1 AAATGAAAAAAAA
4128178 ATAGAGAAAG
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
21 10 0.33
22 13 0.43
23 7 0.23
ACGTcount: A:0.75, C:0.05, G:0.12, T:0.07
Consensus pattern (21 bp):
AAATGAAAAAAAAGAAAAAGA
Found at i:4128360 original size:16 final size:16
Alignment explanation
Indices: 4128325--4128359 Score: 63
Period size: 15 Copynumber: 2.2 Consensus size: 16
4128315 TAAAACCATC
4128325 AAAAGATAGAGAAAGG
1 AAAAGATAGAGAAAGG
4128341 AAAAGA-AGAGAAAGG
1 AAAAGATAGAGAAAGG
4128356 AAAA
1 AAAA
4128360 AAATTTAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.69, C:0.00, G:0.29, T:0.03
Consensus pattern (16 bp):
AAAAGATAGAGAAAGG
Found at i:4134659 original size:3 final size:3
Alignment explanation
Indices: 4134651--4134686 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
4134641 GACTGGGAAC
* *
4134651 AAG AAG AAG AAG AAG AGG AAG AGG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
4134687 CTGTTGAGTG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:4139966 original size:5 final size:5
Alignment explanation
Indices: 4139956--4139985 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
4139946 CCATCAGATT
4139956 AATTA AATTA AATTA AATTA AATTA AATTA
1 AATTA AATTA AATTA AATTA AATTA AATTA
4139986 TGCACGTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
AATTA
Found at i:4154578 original size:2 final size:2
Alignment explanation
Indices: 4154536--4154566 Score: 53
Period size: 2 Copynumber: 15.0 Consensus size: 2
4154526 ATGTATACGA
4154536 AT AT GAT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT
4154567 GTATGAATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 26 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4159593 original size:2 final size:2
Alignment explanation
Indices: 4159586--4159622 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
4159576 GGTCCTTGGG
4159586 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4159623 TAATTCATGT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:4161191 original size:2 final size:2
Alignment explanation
Indices: 4161184--4161211 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4161174 GATTGTTGGC
4161184 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4161212 TGCAATTGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4162742 original size:19 final size:19
Alignment explanation
Indices: 4162720--4162763 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
4162710 AATTTAAGAA
*
4162720 TTTTTAAAACATTATGCTT
1 TTTTTAAAACATAATGCTT
*
4162739 TTTTT-AATCATAATGCTT
1 TTTTTAAAACATAATGCTT
4162757 TTCTTTA
1 TT-TTTA
4162764 GTGTCCAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 13 0.62
19 8 0.38
ACGTcount: A:0.27, C:0.11, G:0.05, T:0.57
Consensus pattern (19 bp):
TTTTTAAAACATAATGCTT
Found at i:4163795 original size:2 final size:2
Alignment explanation
Indices: 4163788--4163816 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4163778 CATTAACCCA
4163788 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4163817 CAAAAAACAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4164259 original size:2 final size:2
Alignment explanation
Indices: 4164252--4164284 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
4164242 TATGTGTATG
4164252 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4164285 TTATTACGGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4173504 original size:23 final size:25
Alignment explanation
Indices: 4173447--4173505 Score: 68
Period size: 26 Copynumber: 2.4 Consensus size: 25
4173437 TTTATTAATT
*
4173447 TATAAAATAAATATTACAATTCTAAA
1 TATAAAAT-AATATTAAAATTCTAAA
*
4173473 TATTTAAATAATATTAAAATT-TAAA
1 TA-TAAAATAATATTAAAATTCTAAA
4173498 TA-AAAATA
1 TATAAAATA
4173506 TTTTAAATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
23 5 0.17
25 6 0.21
26 13 0.45
27 5 0.17
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.37
Consensus pattern (25 bp):
TATAAAATAATATTAAAATTCTAAA
Found at i:4174249 original size:20 final size:20
Alignment explanation
Indices: 4174212--4174269 Score: 57
Period size: 20 Copynumber: 3.0 Consensus size: 20
4174202 CAAACATTTT
*
4174212 TATATGTTTTAT-AT-TTAA
1 TATATTTTTTATAATATTAA
*
4174230 TTTATTTTTTATAATATTAA
1 TATATTTTTTATAATATTAA
***
4174250 TATATTAAATATAATATTAA
1 TATATTTTTTATAATATTAA
4174270 AAAAACTTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
18 10 0.31
19 2 0.06
20 20 0.62
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (20 bp):
TATATTTTTTATAATATTAA
Found at i:4179982 original size:71 final size:72
Alignment explanation
Indices: 4179907--4180061 Score: 170
Period size: 74 Copynumber: 2.1 Consensus size: 72
4179897 GTAAGATATC
* * * *
4179907 TAAAATTTATAC-TTATAAATATGTATTCATTAAATAATAATTATTAAAAT-TATTTTTATTATA
1 TAAAATTTATACTTTATAAATATATATTCATCAAATAATAATCATTAAAATAT-TTTTTATAATA
4179970 ATTATTAG
65 ATTATTAG
* * * * * *
4179978 TAAAATTAAAACTTTTTATAAATGTATATTCATCAAATGATGATCATTGAAATATTTTTTATAAT
1 TAAAATTTATAC--TTTATAAATATATATTCATCAAATAATAATCATTAAAATATTTTTTATAAT
4180043 AATTATTAG
64 AATTATTAG
*
4180052 TAAGATTTAT
1 TAAAATTTAT
4180062 TTTATTTATA
Statistics
Matches: 67, Mismatches: 13, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
71 10 0.15
74 56 0.84
75 1 0.01
ACGTcount: A:0.44, C:0.04, G:0.05, T:0.47
Consensus pattern (72 bp):
TAAAATTTATACTTTATAAATATATATTCATCAAATAATAATCATTAAAATATTTTTTATAATAA
TTATTAG
Found at i:4180147 original size:20 final size:22
Alignment explanation
Indices: 4180110--4180156 Score: 80
Period size: 20 Copynumber: 2.2 Consensus size: 22
4180100 TTTATTAAAA
4180110 TAATATTTTATAATTTAAATAT
1 TAATATTTTATAATTTAAATAT
4180132 TAATATTTTA-AA-TTAAATAT
1 TAATATTTTATAATTTAAATAT
4180152 TAATA
1 TAATA
4180157 CTCATCAAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 13 0.52
21 2 0.08
22 10 0.40
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
TAATATTTTATAATTTAAATAT
Found at i:4181166 original size:25 final size:28
Alignment explanation
Indices: 4181108--4181171 Score: 80
Period size: 28 Copynumber: 2.4 Consensus size: 28
4181098 CTCTTTTTTA
* *
4181108 AATTTTTTGTTATTATTTTTTTAATGTTT
1 AATTTTTTGTTATTATATTTATAA-GTTT
4181137 AATTTTTT-TTATTATATTTATAA-TTT
1 AATTTTTTGTTATTATATTTATAAGTTT
4181163 -ATTTTTTGT
1 AATTTTTTGT
4181172 AACTTTTTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
25 7 0.22
26 4 0.12
28 13 0.41
29 8 0.25
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.72
Consensus pattern (28 bp):
AATTTTTTGTTATTATATTTATAAGTTT
Found at i:4186181 original size:16 final size:16
Alignment explanation
Indices: 4186146--4186178 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
4186136 AAATTTTGTT
*
4186146 AATAAATTATTAGTTC
1 AATAAATTATTAGTTA
4186162 AATAAATTATTA-TTA
1 AATAAATTATTAGTTA
4186177 AA
1 AA
4186179 ATATTAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (16 bp):
AATAAATTATTAGTTA
Found at i:4186733 original size:14 final size:14
Alignment explanation
Indices: 4186707--4186747 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
4186697 ATAGATAAAC
*
4186707 AAAAAAAAGGAAGG
1 AAAAAAAAAGAAGG
**
4186721 AGGAAAAAAGAAGG
1 AAAAAAAAAGAAGG
4186735 AAAAAAAAAGAAG
1 AAAAAAAAAGAAG
4186748 AAAGGATTAC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAGAAGG
Found at i:4187517 original size:2 final size:2
Alignment explanation
Indices: 4187510--4187539 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4187500 NNNNNNNNNN
4187510 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4187540 CACTGTTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4192630 original size:59 final size:60
Alignment explanation
Indices: 4192554--4192672 Score: 168
Period size: 59 Copynumber: 2.0 Consensus size: 60
4192544 AGTTAAACAG
* * * **
4192554 GAAAACAATAAGCAGTTTGGTAGCATTCAAATTAGATCAATGT-CTATTGACTAGAATAA
1 GAAAAAAATAAGCAGTTTGGCAGCATTCAAATTAAATCAATGTAAAATTGACTAGAATAA
* *
4192613 GAAAAAAATAAGTAGTTTGGCAGCATTCTAATTAAATCAATGTAAAATTGACTAGAATAA
1 GAAAAAAATAAGCAGTTTGGCAGCATTCAAATTAAATCAATGTAAAATTGACTAGAATAA
4192673 AATCCAATCA
Statistics
Matches: 52, Mismatches: 7, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
59 38 0.73
60 14 0.27
ACGTcount: A:0.45, C:0.10, G:0.16, T:0.29
Consensus pattern (60 bp):
GAAAAAAATAAGCAGTTTGGCAGCATTCAAATTAAATCAATGTAAAATTGACTAGAATAA
Found at i:4195095 original size:40 final size:40
Alignment explanation
Indices: 4195051--4195132 Score: 128
Period size: 40 Copynumber: 2.0 Consensus size: 40
4195041 TGCATTTTGT
4195051 AGCATCTCAATCTTAATTGCCCTATAACAAGATATTGCTA
1 AGCATCTCAATCTTAATTGCCCTATAACAAGATATTGCTA
* * * *
4195091 AGCATTTTAATCTTAATTGCCCTTTAATAAGATATTGCTA
1 AGCATCTCAATCTTAATTGCCCTATAACAAGATATTGCTA
4195131 AG
1 AG
4195133 GTTATAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.37
Consensus pattern (40 bp):
AGCATCTCAATCTTAATTGCCCTATAACAAGATATTGCTA
Found at i:4213977 original size:15 final size:15
Alignment explanation
Indices: 4213953--4213982 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
4213943 TCAAATTTTG
4213953 TTAATCATGATAATT
1 TTAATCATGATAATT
*
4213968 TTAATTATGATAATT
1 TTAATCATGATAATT
4213983 ATTTTATATC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.03, G:0.07, T:0.50
Consensus pattern (15 bp):
TTAATCATGATAATT
Found at i:4228869 original size:33 final size:33
Alignment explanation
Indices: 4228810--4228880 Score: 92
Period size: 33 Copynumber: 2.2 Consensus size: 33
4228800 TCATTAATTG
* *
4228810 TTTTA-AAATTTAATTTTAAGTTTTAATTTATT
1 TTTTATAAATTTAACTTTAAGTTTTAATTTAAT
*
4228842 TTTTATAAA-TTAACTTTAATTTATTAATTTAAT
1 TTTTATAAATTTAACTTTAAGTT-TTAATTTAAT
4228875 TTTTAT
1 TTTTAT
4228881 TAATAATATA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
32 16 0.47
33 18 0.53
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.62
Consensus pattern (33 bp):
TTTTATAAATTTAACTTTAAGTTTTAATTTAAT
Found at i:4228873 original size:19 final size:18
Alignment explanation
Indices: 4228816--4228876 Score: 51
Period size: 18 Copynumber: 3.6 Consensus size: 18
4228806 ATTGTTTTAA
*
4228816 AATTTAATTTTAAGTT-TT
1 AATTTAA-TTTAATTTATT
4228834 AATTT-ATTT--TTTA-T
1 AATTTAATTTAATTTATT
*
4228848 AAATTAACTTTAATTTATT
1 AATTTAA-TTTAATTTATT
4228867 AATTTAATTT
1 AATTTAATTT
4228877 TTATTAATAA
Statistics
Matches: 34, Mismatches: 3, Indels: 12
0.69 0.06 0.24
Matches are distributed among these distances:
14 7 0.21
15 1 0.03
16 6 0.18
17 1 0.03
18 12 0.35
19 7 0.21
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (18 bp):
AATTTAATTTAATTTATT
Found at i:4230608 original size:17 final size:18
Alignment explanation
Indices: 4230581--4230622 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
4230571 CTTGTTTGAA
*
4230581 TTTCTTTTCTTCTTTTTT
1 TTTCTTTTCTTATTTTTT
4230599 TTTC-TTTCTTATTTTTT
1 TTTCTTTTCTTATTTTTT
4230616 TTT-TTTT
1 TTTCTTTT
4230623 TTCATAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 18 0.82
18 4 0.18
ACGTcount: A:0.02, C:0.12, G:0.00, T:0.86
Consensus pattern (18 bp):
TTTCTTTTCTTATTTTTT
Found at i:4231065 original size:17 final size:18
Alignment explanation
Indices: 4231039--4231073 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
4231029 TAGAAAGATT
*
4231039 AAATTAAAATAATTTTTA
1 AAATTAAAATAATATTTA
4231057 AAATT-AAATAATATTTA
1 AAATTAAAATAATATTTA
4231074 GATTTTAAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
AAATTAAAATAATATTTA
Found at i:4270423 original size:208 final size:207
Alignment explanation
Indices: 4269885--4270510 Score: 857
Period size: 208 Copynumber: 3.0 Consensus size: 207
4269875 TTTATCCATA
*
4269885 ATTATATATATATGAAATTAATAATATAACTTATATGTTATAATGTTTTATATCACAA-TTTGTA
1 ATTATATATATATGAAATTAATGATATAACTTATATGTTATAATGTTTTATATCA-AAGTTTGTA
* * * * * *
4269949 TAAATTATAACTAATTATAGATAATATGTTATAAAATCTAAGGTAATAGCTAATAAATTTATTAA
65 TAAATAATAACTAATTATAAACAATATGTTATAAAATCTAAGGTGATAACTAATAAAGTTATT-A
*
4270014 ATGTAATCATAAAAATAAAATTTATTATAAGTTATAGTAA-AGCTTATATATAAATTAAATATAT
129 ATGTAATCATATAAATAAAATTTATTATAAGTTATAGTAATA-CTTATATATAAATTAAATATAT
4270078 GTATATATAATATATT
193 GTATATAT-ATATATT
* * * *
4270094 ACTTAT-TATTTAT-ATAATTAATGATACAAATTATATGTTAAAATGTTTTATATCAAAGTTTGT
1 A-TTATATATATATGA-AATTAATGATATAACTTATATGTTATAATGTTTTATATCAAAGTTTGT
* * *
4270157 ATAAATAATAACTAATTATAAACAACATGTTATAAAATCTAATGTGACAACTAATAAAGTTATTA
64 ATAAATAATAACTAATTATAAACAATATGTTATAAAATCTAAGGTGATAACTAATAAAGTTATTA
* * * *
4270222 AGTGTAATCATATAAATAAAGTCTATTATAAGTTAGAGCAATACTTATATATAAATTAAATATAT
129 A-TGTAATCATATAAATAAAATTTATTATAAGTTATAGTAATACTTATATATAAATTAAATATAT
* *
4270287 ATA-ATATATGATTTT
193 GTATATATAT-ATATT
*
4270302 ATTATATATATATGAAATTAATGACATAACTTATATGTTATAATGTTTTATATCAAAGTTTGTAT
1 ATTATATATATATGAAATTAATGATATAACTTATATGTTATAATGTTTTATATCAAAGTTTGTAT
* * * *
4270367 AAATAATAATTAATTATAAACAATATGTTATAAAATATAAGGTGATAACAAATAAAGTTACCTAA
66 AAATAATAACTAATTATAAACAATATGTTATAAAATCTAAGGTGATAACTAATAAAGTTA-TTAA
* * * *
4270432 TATAATCATATAAATAAAATTTATTATAAATTATAGTAATGCTTATGTATAAATTAAATATATGT
130 TGTAATCATATAAATAAAATTTATTATAAGTTATAGTAATACTTATATATAAATTAAATATATGT
4270497 ATATATAATATATT
195 ATATAT-ATATATT
4270511 TATACAATTG
Statistics
Matches: 363, Mismatches: 43, Indels: 22
0.85 0.10 0.05
Matches are distributed among these distances:
207 6 0.02
208 177 0.49
209 173 0.48
210 7 0.02
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.41
Consensus pattern (207 bp):
ATTATATATATATGAAATTAATGATATAACTTATATGTTATAATGTTTTATATCAAAGTTTGTAT
AAATAATAACTAATTATAAACAATATGTTATAAAATCTAAGGTGATAACTAATAAAGTTATTAAT
GTAATCATATAAATAAAATTTATTATAAGTTATAGTAATACTTATATATAAATTAAATATATGTA
TATATATATATT
Found at i:4298957 original size:30 final size:29
Alignment explanation
Indices: 4298892--4298960 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 29
4298882 ATGTATTTTG
4298892 TTTAATTTAATTTTTATATTTAAAATTAA
1 TTTAATTTAATTTTTATATTTAAAATTAA
** *
4298921 AATAATTTAATTTTT-TATTTTAAAAATTAT
1 TTTAATTTAATTTTTATA-TTT-AAAATTAA
4298951 TTTAATTTAA
1 TTTAATTTAA
4298961 CATTTCTTTC
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
28 2 0.06
29 16 0.48
30 15 0.45
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (29 bp):
TTTAATTTAATTTTTATATTTAAAATTAA
Found at i:4300311 original size:18 final size:19
Alignment explanation
Indices: 4300288--4300333 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 19
4300278 ATATAATTTG
*
4300288 AAATATTAAACA-AAATAA
1 AAATATTAAAAATAAATAA
4300306 AAATA-TAAAAATAAATAA
1 AAATATTAAAAATAAATAA
4300324 AAA-ATTAAAA
1 AAATATTAAAA
4300334 GGATGGAGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 6 0.24
18 19 0.76
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (19 bp):
AAATATTAAAAATAAATAA
Found at i:4303396 original size:20 final size:21
Alignment explanation
Indices: 4303352--4303396 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 21
4303342 AATTTTGAAG
4303352 AAAGAAAAAAAATAAGAAAGAA
1 AAAGAAAAAAAATAAG-AAGAA
4303374 AAAGAAAAAAAGATAAG-AGAA
1 AAAGAAAAAAA-ATAAGAAGAA
4303395 AA
1 AA
4303397 TAAAACACAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 6 0.27
22 11 0.50
23 5 0.23
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.04
Consensus pattern (21 bp):
AAAGAAAAAAAATAAGAAGAA
Found at i:4310702 original size:36 final size:36
Alignment explanation
Indices: 4310655--4310729 Score: 141
Period size: 36 Copynumber: 2.1 Consensus size: 36
4310645 GCTTTAGTGG
4310655 TAGCTGATACTTCTCATACCCTTGTAGAACATACAT
1 TAGCTGATACTTCTCATACCCTTGTAGAACATACAT
*
4310691 TAGCTGATACTTCTCATGCCCTTGTAGAACATACAT
1 TAGCTGATACTTCTCATACCCTTGTAGAACATACAT
4310727 TAG
1 TAG
4310730 TTATTGGGCA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.29, C:0.24, G:0.13, T:0.33
Consensus pattern (36 bp):
TAGCTGATACTTCTCATACCCTTGTAGAACATACAT
Found at i:4320686 original size:8 final size:8
Alignment explanation
Indices: 4320663--4320710 Score: 60
Period size: 8 Copynumber: 6.0 Consensus size: 8
4320653 TTTCTCTTAC
*
4320663 ATACATAC
1 ATACATAT
4320671 ATACATAT
1 ATACATAT
4320679 ATACATAT
1 ATACATAT
*
4320687 ATATATAT
1 ATACATAT
*
4320695 ATATATAT
1 ATACATAT
*
4320703 ATATATAT
1 ATACATAT
4320711 GGAAAGAGAG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 38 1.00
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (8 bp):
ATACATAT
Found at i:4320688 original size:2 final size:2
Alignment explanation
Indices: 4320675--4320710 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
4320665 ACATACATAC
*
4320675 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4320711 GGAAAGAGAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:4320690 original size:12 final size:12
Alignment explanation
Indices: 4320667--4320710 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
4320657 TCTTACATAC
*
4320667 ATACATACATAT
1 ATACATATATAT
4320679 ATACATATATAT
1 ATACATATATAT
*
4320691 ATATATATATAT
1 ATACATATATAT
*
4320703 ATATATAT
1 ATACATAT
4320711 GGAAAGAGAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (12 bp):
ATACATATATAT
Found at i:4334217 original size:44 final size:44
Alignment explanation
Indices: 4334149--4334234 Score: 129
Period size: 44 Copynumber: 2.0 Consensus size: 44
4334139 ATTAAACTAT
*
4334149 ATAGAGAAGCATACTGATCATTAAAGCACTTTCATTTTGTTTAG
1 ATAGAGAAGCATACTGATCATTAAAGCACTTGCATTTTGTTTAG
* *
4334193 ATAGAGAAGCATATTGATTC-TTAAAGCCCTTGCATTTTGTTT
1 ATAGAGAAGCATACTGA-TCATTAAAGCACTTGCATTTTGTTT
4334235 GTCTAACATT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
44 36 0.95
45 2 0.05
ACGTcount: A:0.31, C:0.14, G:0.16, T:0.38
Consensus pattern (44 bp):
ATAGAGAAGCATACTGATCATTAAAGCACTTGCATTTTGTTTAG
Found at i:4339426 original size:25 final size:25
Alignment explanation
Indices: 4339398--4339453 Score: 103
Period size: 25 Copynumber: 2.2 Consensus size: 25
4339388 ATATTTGCTC
4339398 TCAACATCCAAAACAAAGTTAACAA
1 TCAACATCCAAAACAAAGTTAACAA
4339423 TCAACATCCAAAACAAAGTTAACAA
1 TCAACATCCAAAACAAAGTTAACAA
*
4339448 TGAACA
1 TCAACA
4339454 ATAACCAGGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.55, C:0.23, G:0.05, T:0.16
Consensus pattern (25 bp):
TCAACATCCAAAACAAAGTTAACAA
Found at i:4348743 original size:3 final size:3
Alignment explanation
Indices: 4348735--4348762 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
4348725 TGAAACTGAA
4348735 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
4348763 TGCTTGGTGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:4359883 original size:18 final size:18
Alignment explanation
Indices: 4359856--4359935 Score: 90
Period size: 18 Copynumber: 4.5 Consensus size: 18
4359846 GAGTGACGAA
*
4359856 GAAGAGGAAGAGGAAGAT
1 GAAGATGAAGAGGAAGAT
*
4359874 GAAGATGAAGATGAAGAT
1 GAAGATGAAGAGGAAGAT
* *
4359892 GAAGTTGAAGATGAAGAT
1 GAAGATGAAGAGGAAGAT
* * *
4359910 GAAGAGGAGGAGGAAGAA
1 GAAGATGAAGAGGAAGAT
4359928 GAAG-TGAA
1 GAAGATGAA
4359936 ACCCAAAAAG
Statistics
Matches: 52, Mismatches: 10, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
17 2 0.04
18 50 0.96
ACGTcount: A:0.49, C:0.00, G:0.40, T:0.11
Consensus pattern (18 bp):
GAAGATGAAGAGGAAGAT
Found at i:4359931 original size:6 final size:6
Alignment explanation
Indices: 4359856--4359914 Score: 91
Period size: 6 Copynumber: 9.8 Consensus size: 6
4359846 GAGTGACGAA
* * *
4359856 GAAGAG GAAGAG GAAGAT GAAGAT GAAGAT GAAGAT GAAGTT GAAGAT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
4359904 GAAGAT GAAGA
1 GAAGAT GAAGA
4359915 GGAGGAGGAA
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 50 1.00
ACGTcount: A:0.49, C:0.00, G:0.37, T:0.14
Consensus pattern (6 bp):
GAAGAT
Found at i:4364245 original size:27 final size:27
Alignment explanation
Indices: 4364214--4364277 Score: 67
Period size: 27 Copynumber: 2.4 Consensus size: 27
4364204 AATTTATATA
*
4364214 ATTATAA-TTATATAATTTTATTATTTT
1 ATTATAATTTATAT-ATATTATTATTTT
* * *
4364241 ATTATTATTTTTATATATTGTTATTTT
1 ATTATAATTTATATATATTATTATTTT
*
4364268 ATTATTATTT
1 ATTATAATTT
4364278 TGGTGCATCT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 27 0.84
28 5 0.16
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (27 bp):
ATTATAATTTATATATATTATTATTTT
Found at i:4364247 original size:11 final size:11
Alignment explanation
Indices: 4364231--4364278 Score: 51
Period size: 11 Copynumber: 3.9 Consensus size: 11
4364221 TTATATAATT
4364231 TTATTATTTTA
1 TTATTATTTTA
4364242 TTATTATTTTTA
1 TTATTA-TTTTA
4364254 TATATTGTTATTTTA
1 T-TA---TTATTTTA
4364269 TTATTATTTT
1 TTATTATTTT
4364279 GGTGCATCTG
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
11 13 0.41
12 6 0.19
13 2 0.06
14 2 0.06
15 6 0.19
16 3 0.09
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (11 bp):
TTATTATTTTA
Found at i:4368366 original size:2 final size:2
Alignment explanation
Indices: 4368359--4368389 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4368349 TAGCTGACGC
4368359 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
4368390 AACAAGACAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4369186 original size:5 final size:5
Alignment explanation
Indices: 4369163--4369201 Score: 53
Period size: 5 Copynumber: 8.0 Consensus size: 5
4369153 TCTTAACCCC
* *
4369163 AAAA- AAAAG AAAAT CAAAG AAAAG AAAAG AAAAG AAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG
4369202 GGTTTTCGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
4 4 0.13
5 26 0.87
ACGTcount: A:0.79, C:0.03, G:0.15, T:0.03
Consensus pattern (5 bp):
AAAAG
Found at i:4369653 original size:19 final size:18
Alignment explanation
Indices: 4369629--4369664 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
4369619 AAAATTCAAA
4369629 TATTAATAAAATATATTTT
1 TATTAATAAAATA-ATTTT
*
4369648 TATTAATATAATAATTT
1 TATTAATAAAATAATTT
4369665 AAATAGGTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TATTAATAAAATAATTTT
Found at i:4395937 original size:13 final size:14
Alignment explanation
Indices: 4395914--4395942 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
4395904 ATTTTGTAGT
4395914 AAAATATTTTTTAA
1 AAAATATTTTTTAA
4395928 AAAATA-TTTTTAA
1 AAAATATTTTTTAA
4395941 AA
1 AA
4395943 TTTATATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
AAAATATTTTTTAA
Found at i:4396098 original size:20 final size:21
Alignment explanation
Indices: 4396073--4396137 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 21
4396063 TAAATTATAC
4396073 AATATTATTAAAATTAAAA-A
1 AATATTATTAAAATTAAAATA
*
4396093 AATATTTTTTAAAA-TAAAATA
1 AATA-TTATTAAAATTAAAATA
* *
4396114 AATATTACTAATAATTATAATA
1 AATATTATTAA-AATTAAAATA
4396136 AA
1 AA
4396138 AAATATTTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
20 14 0.38
21 15 0.41
22 8 0.22
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (21 bp):
AATATTATTAAAATTAAAATA
Found at i:4399457 original size:143 final size:143
Alignment explanation
Indices: 4399163--4399455 Score: 534
Period size: 143 Copynumber: 2.1 Consensus size: 143
4399153 TAGCACTCTT
* *
4399163 CTGATTTTATCACACTAGTATTAAACTTGAGATTTGGTTTCTCAAAAGTAAAGGTAGACTAGCAA
1 CTGATTTTATCACACTAGTATTAAACTTGAGATTTGGCTTCCCAAAAGTAAAGGTAGACTAGCAA
*
4399228 ATATGAAGCTATTAAATATTAGGGTCAGATAATTAACTGTCAAGCAGACTTATCAAACAACTACA
66 ATATGAAGCTATTAAATATTAGGGTCAGATAATTAACTGTCAAGCAGACTAATCAAACAACTACA
*
4399293 CTGCTTAAGACAA
131 CTACTTAAGACAA
4399306 CTGATTTTATCACACTAGTATTAAACTTGAGATTTGGCTTCCCAAAAGTAAAGGTAGACTAGCAA
1 CTGATTTTATCACACTAGTATTAAACTTGAGATTTGGCTTCCCAAAAGTAAAGGTAGACTAGCAA
*
4399371 ATATGAAGCTATTAAATGTTAGGGTCAGATAATTAACTGTCAAGCAGACTAATCAAACAACTACA
66 ATATGAAGCTATTAAATATTAGGGTCAGATAATTAACTGTCAAGCAGACTAATCAAACAACTACA
4399436 CTACTTAAGACAA
131 CTACTTAAGACAA
4399449 CT-ATTTT
1 CTGATTTT
4399456 TAAAAAAAGG
Statistics
Matches: 145, Mismatches: 5, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
142 5 0.03
143 140 0.97
ACGTcount: A:0.39, C:0.16, G:0.15, T:0.30
Consensus pattern (143 bp):
CTGATTTTATCACACTAGTATTAAACTTGAGATTTGGCTTCCCAAAAGTAAAGGTAGACTAGCAA
ATATGAAGCTATTAAATATTAGGGTCAGATAATTAACTGTCAAGCAGACTAATCAAACAACTACA
CTACTTAAGACAA
Found at i:4402881 original size:22 final size:20
Alignment explanation
Indices: 4402855--4402904 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 20
4402845 TTAATCATTA
4402855 ATAATTAAAATATTTATAATAT
1 ATAA-TAAAAT-TTTATAATAT
4402877 ATAAT--AATTTTATAATAT
1 ATAATAAAATTTTATAATAT
*
4402895 CTAAATAAAA
1 AT-AATAAAA
4402905 AAAACTTATA
Statistics
Matches: 24, Mismatches: 1, Indels: 7
0.75 0.03 0.22
Matches are distributed among these distances:
18 11 0.46
19 6 0.25
21 3 0.12
22 4 0.17
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (20 bp):
ATAATAAAATTTTATAATAT
Found at i:4403148 original size:28 final size:29
Alignment explanation
Indices: 4403096--4403151 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 29
4403086 TTAAGTTTAT
4403096 AATACTAAATATTAAACTATAATATATAA
1 AATACTAAATATTAAACTATAATATATAA
*
4403125 AATA-TAAATAGTTAAA-TATGATATATA
1 AATACTAAATA-TTAAACTATAATATATA
4403152 TAATTAATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 16 0.64
29 9 0.36
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.36
Consensus pattern (29 bp):
AATACTAAATATTAAACTATAATATATAA
Found at i:4403385 original size:15 final size:16
Alignment explanation
Indices: 4403354--4403388 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
4403344 ATAATTTTTT
*
4403354 AATTTTTAAAAATTAA
1 AATTATTAAAAATTAA
4403370 AATTATTAAAAA-TAA
1 AATTATTAAAAATTAA
4403385 AATT
1 AATT
4403389 CACATAACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
AATTATTAAAAATTAA
Found at i:4409269 original size:6 final size:6
Alignment explanation
Indices: 4409258--4409284 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
4409248 GGTTTTCATG
4409258 CCTATT CCTATT CCTATT CCTATT CCT
1 CCTATT CCTATT CCTATT CCTATT CCT
4409285 TTTCGCAGGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.37, G:0.00, T:0.48
Consensus pattern (6 bp):
CCTATT
Found at i:4421307 original size:22 final size:23
Alignment explanation
Indices: 4421256--4421309 Score: 58
Period size: 26 Copynumber: 2.3 Consensus size: 23
4421246 TGTTTTAATT
*
4421256 AATAATAATTATTTAATTATTAA
1 AATAAAAATTATTTAATTATTAA
4421279 ATTATAAAAATTTATTTAA-T-TTAA
1 A--ATAAAAA-TTATTTAATTATTAA
4421303 AATAAAA
1 AATAAAA
4421310 TATAAAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
22 6 0.22
23 1 0.04
24 5 0.19
25 7 0.26
26 8 0.30
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (23 bp):
AATAAAAATTATTTAATTATTAA
Found at i:4421315 original size:29 final size:27
Alignment explanation
Indices: 4421276--4421354 Score: 77
Period size: 28 Copynumber: 2.8 Consensus size: 27
4421266 ATTTAATTAT
*
4421276 TAAATTATAAAAATTTATTTAATTTAAAA
1 TAAAATATAAAAATTTATTTAA--TAAAA
* *
4421305 TAAAATATAAAAATTAGATTGAATAAAA
1 TAAAATATAAAAATT-TATTTAATAAAA
* **
4421333 TAAAAAATAAGTATTTATTTAA
1 TAAAATATAAAAATTTATTTAA
4421355 ATTTTTTAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
27 5 0.12
28 17 0.41
29 14 0.34
30 5 0.12
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (27 bp):
TAAAATATAAAAATTTATTTAATAAAA
Found at i:4422276 original size:56 final size:56
Alignment explanation
Indices: 4422216--4422324 Score: 139
Period size: 56 Copynumber: 1.9 Consensus size: 56
4422206 TGTAATTATA
* * * *
4422216 TTTTTTAATAATCTGATTTTATTTATT-TTTCATTCACATCATCAATAAATTAAGGTT
1 TTTTTTAATAATC-GATATCATTTATTATTT-ATACACACCATCAATAAATTAAGGTT
* *
4422273 TTTTTTAATTATCGATATCATTTATTATTTATACACACCATCAATAAGTTAA
1 TTTTTTAATAATCGATATCATTTATTATTTATACACACCATCAATAAATTAA
4422325 TTATTTAAAC
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
56 30 0.67
57 15 0.33
ACGTcount: A:0.34, C:0.12, G:0.05, T:0.50
Consensus pattern (56 bp):
TTTTTTAATAATCGATATCATTTATTATTTATACACACCATCAATAAATTAAGGTT
Found at i:4424684 original size:6 final size:7
Alignment explanation
Indices: 4424662--4424690 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
4424652 ACATTGTTGC
4424662 TTTGATT
1 TTTGATT
4424669 TTTGATT
1 TTTGATT
4424676 TTTGATT
1 TTTGATT
4424683 TTTG-TT
1 TTTGATT
4424689 TT
1 TT
4424691 AGGTTTCATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 4 0.18
7 18 0.82
ACGTcount: A:0.10, C:0.00, G:0.14, T:0.76
Consensus pattern (7 bp):
TTTGATT
Found at i:4443325 original size:19 final size:19
Alignment explanation
Indices: 4443290--4443326 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
4443280 AAATGACTCA
*
4443290 AAAAAATAAAAATAAAAAT
1 AAAAAATAAAAAGAAAAAT
*
4443309 AAAAAATAATAAGAAAAA
1 AAAAAATAAAAAGAAAAA
4443327 AATAGTTCAA
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:0.84, C:0.00, G:0.03, T:0.14
Consensus pattern (19 bp):
AAAAAATAAAAAGAAAAAT
Found at i:4443866 original size:14 final size:14
Alignment explanation
Indices: 4443847--4443875 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
4443837 TATATATATA
4443847 TATATTTGTTATTT
1 TATATTTGTTATTT
4443861 TATATTTGTTATTT
1 TATATTTGTTATTT
4443875 T
1 T
4443876 CAAATTTCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.00, G:0.07, T:0.72
Consensus pattern (14 bp):
TATATTTGTTATTT
Found at i:4446207 original size:15 final size:15
Alignment explanation
Indices: 4446189--4446226 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
4446179 GTAAGTAACG
4446189 TGATTGCAAGCAATA
1 TGATTGCAAGCAATA
4446204 TGATTGCAAGCAATA
1 TGATTGCAAGCAATA
4446219 TGATTGCA
1 TGATTGCA
4446227 GGGAACATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.29
Consensus pattern (15 bp):
TGATTGCAAGCAATA
Found at i:4446470 original size:31 final size:31
Alignment explanation
Indices: 4446430--4446489 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
4446420 CTCTTAAATA
* *
4446430 TATTTTTAATGTCATATATTTTATTTTTATT
1 TATTATTAATCTCATATATTTTATTTTTATT
*
4446461 TATTATTAATCTTATATATTTTATTTTTA
1 TATTATTAATCTCATATATTTTATTTTTA
4446490 ATATATTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.28, C:0.03, G:0.02, T:0.67
Consensus pattern (31 bp):
TATTATTAATCTCATATATTTTATTTTTATT
Found at i:4446480 original size:16 final size:15
Alignment explanation
Indices: 4446427--4446497 Score: 52
Period size: 16 Copynumber: 4.5 Consensus size: 15
4446417 CATCTCTTAA
* *
4446427 ATATATTTTTAATGTC
1 ATATA-TTTTAATCTT
* *
4446443 ATATATTTTATTTTT
1 ATATATTTTAATCTT
*
4446458 ATTTATTATTAATCTT
1 ATATATT-TTAATCTT
* *
4446474 ATATATTTTATTTTT
1 ATATATTTTAATCTT
4446489 AATATATTT
1 -ATATATTT
4446498 ATATTTTTTA
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
15 19 0.43
16 25 0.57
ACGTcount: A:0.31, C:0.03, G:0.01, T:0.65
Consensus pattern (15 bp):
ATATATTTTAATCTT
Found at i:4446485 original size:21 final size:22
Alignment explanation
Indices: 4446459--4446510 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 22
4446449 TTTATTTTTA
*
4446459 TTTATTATTAATCT-TATATAT
1 TTTATTATTAATATATATATAT
* *
4446480 TTTATTTTTAATATATTTATAT
1 TTTATTATTAATATATATATAT
4446502 TTT-TTATTA
1 TTTATTATTA
4446511 TTAATTTTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 17 0.65
22 9 0.35
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (22 bp):
TTTATTATTAATATATATATAT
Found at i:4446504 original size:16 final size:16
Alignment explanation
Indices: 4446443--4446505 Score: 67
Period size: 16 Copynumber: 3.9 Consensus size: 16
4446433 TTTTAATGTC
4446443 ATATATTTTATTTTT-
1 ATATATTTTATTTTTA
* * *
4446458 ATTTATTATTAATCTT-
1 ATATATT-TTATTTTTA
4446474 ATATATTTTATTTTTA
1 ATATATTTTATTTTTA
4446490 ATATATTTATATTTTT
1 ATATATTT-TATTTTT
4446506 TATTATTAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
15 12 0.31
16 20 0.51
17 7 0.18
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (16 bp):
ATATATTTTATTTTTA
Found at i:4446506 original size:24 final size:24
Alignment explanation
Indices: 4446443--4446523 Score: 82
Period size: 24 Copynumber: 3.5 Consensus size: 24
4446433 TTTTAATGTC
4446443 ATATATTT-TA-TTTTTATTTATTA
1 ATATATTTATATTTTTTATTT-TTA
* *
4446466 TTA-ATCTTATATATTTTATTTTTA
1 ATATAT-TTATATTTTTTATTTTTA
*
4446490 ATATATTTATATTTTTTATTATTA
1 ATATATTTATATTTTTTATTTTTA
4446514 AT-T-TTTATAT
1 ATATATTTATAT
4446524 AATATCATCT
Statistics
Matches: 49, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
22 9 0.18
23 5 0.10
24 25 0.51
25 10 0.20
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.68
Consensus pattern (24 bp):
ATATATTTATATTTTTTATTTTTA
Found at i:4446543 original size:49 final size:46
Alignment explanation
Indices: 4446443--4446546 Score: 111
Period size: 46 Copynumber: 2.2 Consensus size: 46
4446433 TTTTAATGTC
* * * *
4446443 ATATATTTTATTTTTATTTATTATTAATCTTATATATTTTATTTTTA
1 ATATA-TTTATATTTATTTATTATTAATCTTATATATATCATTTTAA
*
4446490 ATATATTTATATTT-TTTATTATTAATTTTTATATAATATCATCTCTTAA
1 ATATATTTATATTTATTTATTATTAA-TCTTATAT-ATATCAT-T-TTAA
4446539 ATATATTT
1 ATATATTT
4446547 TTAATGTCAT
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
45 11 0.23
46 15 0.31
47 10 0.21
48 1 0.02
49 11 0.23
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (46 bp):
ATATATTTATATTTATTTATTATTAATCTTATATATATCATTTTAA
Found at i:4446585 original size:19 final size:19
Alignment explanation
Indices: 4446540--4446615 Score: 71
Period size: 21 Copynumber: 3.8 Consensus size: 19
4446530 ATCTCTTAAA
*
4446540 TATATTTTTAATGTCATATAT
1 TATATTTTT-AT-TTATATAT
* * *
4446561 TTTATTTTTATTTCTTTAT
1 TATATTTTTATTTATATAT
4446580 TATATTTTTTATATTATATAT
1 TATA-TTTTTAT-TTATATAT
*
4446601 TATATTTTAATTTAT
1 TATATTTTTATTTAT
4446616 TTTACCTATA
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
19 12 0.27
20 15 0.33
21 18 0.40
ACGTcount: A:0.29, C:0.03, G:0.01, T:0.67
Consensus pattern (19 bp):
TATATTTTTATTTATATAT
Found at i:4446594 original size:14 final size:14
Alignment explanation
Indices: 4446475--4446598 Score: 67
Period size: 14 Copynumber: 8.7 Consensus size: 14
4446465 ATTAATCTTA
*
4446475 TATATTTTATTTTT
1 TATATTATATTTTT
4446489 AATATATTTATATTTTT
1 --TATA-TTATATTTTT
4446506 TATTATTA-ATTTTT
1 TA-TATTATATTTTT
* * *
4446520 ATATAATATCATCTCT
1 -TATATTAT-ATTTTT
*
4446536 TA-AATATATTTTT
1 TATATTATATTTTT
* * * *
4446549 AATGTCATATATTT
1 TATATTATATTTTT
* *
4446563 TAT-TTTTATTTCT
1 TATATTATATTTTT
4446576 T-TATTATATTTTT
1 TATATTATATTTTT
4446589 TATATTATAT
1 TATATTATAT
4446599 ATTATATTTT
Statistics
Matches: 82, Mismatches: 18, Indels: 18
0.69 0.15 0.15
Matches are distributed among these distances:
12 1 0.01
13 21 0.26
14 32 0.39
15 9 0.11
16 10 0.12
17 9 0.11
ACGTcount: A:0.31, C:0.04, G:0.01, T:0.65
Consensus pattern (14 bp):
TATATTATATTTTT
Found at i:4446619 original size:112 final size:112
Alignment explanation
Indices: 4446375--4446613 Score: 378
Period size: 112 Copynumber: 2.2 Consensus size: 112
4446365 AAATATAAGT
*
4446375 TTAATATATTTATATTTTTTATTATTAATTTTTATATGATATCATCTCTTAAATATATTTTTAAT
1 TTAATATATTTATATTTTTTATTATTAATTTTTATATAATATCATCTCTTAAATATATTTTTAAT
* *
4446440 GTCATATATTTTATTTTTATTTATTATTAATCTTATATATTTTATTT
66 GTCATATATTTTATTTTTATTTATTATTAATCTTATATATTATATTA
4446487 TTAATATATTTATATTTTTTATTATTAATTTTTATATAATATCATCTCTTAAATATATTTTTAAT
1 TTAATATATTTATATTTTTTATTATTAATTTTTATATAATATCATCTCTTAAATATATTTTTAAT
* * *
4446552 GTCATATATTTTATTTTTATTTCTTTATTATATTTTTTATATTATA-TA
66 GTCATATATTTTATTTTTATTT-ATTATTA-ATCTTATATATTATATTA
4446600 TT-ATAT-TTTA-ATTT
1 TTAATATATTTATATTT
4446614 ATTTTACCTA
Statistics
Matches: 119, Mismatches: 6, Indels: 6
0.91 0.05 0.05
Matches are distributed among these distances:
110 4 0.03
111 4 0.03
112 90 0.76
113 9 0.08
114 12 0.10
ACGTcount: A:0.31, C:0.04, G:0.01, T:0.63
Consensus pattern (112 bp):
TTAATATATTTATATTTTTTATTATTAATTTTTATATAATATCATCTCTTAAATATATTTTTAAT
GTCATATATTTTATTTTTATTTATTATTAATCTTATATATTATATTA
Found at i:4450136 original size:101 final size:104
Alignment explanation
Indices: 4449956--4450163 Score: 287
Period size: 101 Copynumber: 2.0 Consensus size: 104
4449946 ACGTCCAACA
* * * * **
4449956 ATCATGCAATGTGTTAGATTTCCGTCTGACCTACAACCACAATTATTTGACATTTTTAATGTTTT
1 ATCATGCAATATGTTAGATTTCAGTCTGACCTACAACCAC-AGTATTTGAAATTTTTAATGTCCT
*
4450021 AGAAAAGTAAGCTTGGGACCTGATGGAGATCTCTAAATCT
65 AGAAAAGTAAGCTTGGAACCTGATGGAGATCTCTAAATCT
**
4450061 ATCATGCAATATGTTAGATTTCAGTCTGATGTACAA-C-C-GTATTTGAAATTTTTAATGTCCTA
1 ATCATGCAATATGTTAGATTTCAGTCTGACCTACAACCACAGTATTTGAAATTTTTAATGTCCTA
**
4450123 GAAAAGTAAGCTTGGAATTTGATGGAGATCTCTAAATCT
66 GAAAAGTAAGCTTGGAACCTGATGGAGATCTCTAAATCT
4450162 AT
1 AT
4450164 ATTCTGCAAA
Statistics
Matches: 92, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
101 58 0.63
103 1 0.01
104 1 0.01
105 32 0.35
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (104 bp):
ATCATGCAATATGTTAGATTTCAGTCTGACCTACAACCACAGTATTTGAAATTTTTAATGTCCTA
GAAAAGTAAGCTTGGAACCTGATGGAGATCTCTAAATCT
Found at i:4456268 original size:21 final size:21
Alignment explanation
Indices: 4456233--4456273 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
4456223 AAATGATAAC
* *
4456233 ATGATATAGTGATGTGATATT
1 ATGATATAATGATGTAATATT
*
4456254 ATGATATAATTATGTAATAT
1 ATGATATAATGATGTAATAT
4456274 ATTCACCTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.39, C:0.00, G:0.17, T:0.44
Consensus pattern (21 bp):
ATGATATAATGATGTAATATT
Found at i:4457610 original size:2 final size:2
Alignment explanation
Indices: 4457603--4457631 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4457593 ATTAGTCTAC
4457603 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4457632 AGTGGAAAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4473346 original size:43 final size:43
Alignment explanation
Indices: 4473262--4473348 Score: 104
Period size: 43 Copynumber: 2.0 Consensus size: 43
4473252 CCACAACAGC
* * * *
4473262 ATAAACAAAATTCACTATACTTCTAGAAATAGACAGTAAAAAA
1 ATAAACAAAATTCACCATAATTCTAGAAATACACAGCAAAAAA
* *
4473305 ATAAACAGAATTCACCATAATTC-AGAAATACCCAAGCAAAAAA
1 ATAAACAAAATTCACCATAATTCTAGAAATACAC-AGCAAAAAA
4473348 A
1 A
4473349 AAAATCACTA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
42 8 0.22
43 29 0.78
ACGTcount: A:0.56, C:0.17, G:0.07, T:0.20
Consensus pattern (43 bp):
ATAAACAAAATTCACCATAATTCTAGAAATACACAGCAAAAAA
Found at i:4473413 original size:41 final size:41
Alignment explanation
Indices: 4473348--4473459 Score: 174
Period size: 41 Copynumber: 2.8 Consensus size: 41
4473338 AAGCAAAAAA
* *
4473348 AAAAATCACTAG-AA-TCTTTAAATACCTAGTAATAGCACAG
1 AAAAATCACT-GTAATTCTTGAAATACCCAGTAATAGCACAG
*
4473388 AAAAATCACTGTAATTCTTGCAATACCCAGTAATAGCACAG
1 AAAAATCACTGTAATTCTTGAAATACCCAGTAATAGCACAG
4473429 AAAAATCACTGTAATTCTTGAAATACCCAGT
1 AAAAATCACTGTAATTCTTGAAATACCCAGT
4473460 TTAAAAAAAA
Statistics
Matches: 66, Mismatches: 4, Indels: 3
0.90 0.05 0.04
Matches are distributed among these distances:
39 1 0.02
40 12 0.18
41 53 0.80
ACGTcount: A:0.44, C:0.20, G:0.11, T:0.26
Consensus pattern (41 bp):
AAAAATCACTGTAATTCTTGAAATACCCAGTAATAGCACAG
Found at i:4474115 original size:11 final size:10
Alignment explanation
Indices: 4474095--4474144 Score: 50
Period size: 10 Copynumber: 4.9 Consensus size: 10
4474085 TTCTCTTTTG
4474095 TTCC-TTTCT
1 TTCCTTTTCT
4474104 TCTCCTTTTCT
1 T-TCCTTTTCT
4474115 TTCAC-TTTCTT
1 TTC-CTTTTC-T
4474126 TTCCTTTTCT
1 TTCCTTTTCT
*
4474136 TTCCCTTTC
1 TTCCTTTTC
4474145 CCTCTCTCAG
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
9 1 0.03
10 19 0.54
11 15 0.43
ACGTcount: A:0.02, C:0.34, G:0.00, T:0.64
Consensus pattern (10 bp):
TTCCTTTTCT
Found at i:4474122 original size:21 final size:21
Alignment explanation
Indices: 4474098--4474144 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
4474088 TCTTTTGTTC
4474098 CTTTCTTCTCCTTTTCTTTCA
1 CTTTCTTCTCCTTTTCTTTCA
* *
4474119 CTTTCTTTTCCTTTTCTTTCC
1 CTTTCTTCTCCTTTTCTTTCA
4474140 CTTTC
1 CTTTC
4474145 CCTCTCTCAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.02, C:0.34, G:0.00, T:0.64
Consensus pattern (21 bp):
CTTTCTTCTCCTTTTCTTTCA
Found at i:4474784 original size:22 final size:21
Alignment explanation
Indices: 4474743--4474785 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
4474733 ATAAAATTTA
* *
4474743 TAAATAATAATTAATTATTAT
1 TAAATAAAAATTAATAATTAT
4474764 TAAATAAAATATTAATAATTAT
1 TAAATAAAA-ATTAATAATTAT
4474786 ATTATATTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
TAAATAAAAATTAATAATTAT
Found at i:4474979 original size:17 final size:16
Alignment explanation
Indices: 4474959--4474992 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
4474949 TATACAATAA
*
4474959 AAATTAATATTTTAATT
1 AAATTAAT-TATTAATT
4474976 AAATTAATTATTAATT
1 AAATTAATTATTAATT
4474992 A
1 A
4474993 TAAAAATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
AAATTAATTATTAATT
Found at i:4475027 original size:30 final size:30
Alignment explanation
Indices: 4474991--4475058 Score: 102
Period size: 30 Copynumber: 2.3 Consensus size: 30
4474981 AATTATTAAT
* *
4474991 TATAAAAATTTATTT-GATTTCAAATAAAAA
1 TATAAAAATTGATTTAG-TTTAAAATAAAAA
4475021 TATAAAAATTGATTTAGTTTAAAATAAAAA
1 TATAAAAATTGATTTAGTTTAAAATAAAAA
4475051 TATAAAAA
1 TATAAAAA
4475059 CTTAATTAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
30 34 0.97
31 1 0.03
ACGTcount: A:0.57, C:0.01, G:0.04, T:0.37
Consensus pattern (30 bp):
TATAAAAATTGATTTAGTTTAAAATAAAAA
Found at i:4475945 original size:26 final size:25
Alignment explanation
Indices: 4475890--4475948 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
4475880 TCACTATAAT
*
4475890 ATTATAAAAATACTAATATTTATCA
1 ATTATAAAAATACTAAAATTTATCA
*
4475915 ATTATATAAAATATTCAAAATTTAT-A
1 ATTATA-AAAATACT-AAAATTTATCA
*
4475941 TTTATAAA
1 ATTATAAA
4475949 TATGTATTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
25 8 0.28
26 13 0.45
27 8 0.28
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (25 bp):
ATTATAAAAATACTAAAATTTATCA
Found at i:4476215 original size:21 final size:21
Alignment explanation
Indices: 4476191--4476230 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
4476181 CTTACAAAAT
* *
4476191 CATAAGACATTTTATGTGAGG
1 CATAACACATTTTACGTGAGG
*
4476212 CATAACATATTTTACGTGA
1 CATAACACATTTTACGTGA
4476231 TCCGTGGATA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.35
Consensus pattern (21 bp):
CATAACACATTTTACGTGAGG
Found at i:4477208 original size:13 final size:13
Alignment explanation
Indices: 4477190--4477231 Score: 59
Period size: 13 Copynumber: 3.3 Consensus size: 13
4477180 ATTTTACAAT
4477190 ATATCAAATAGAA
1 ATATCAAATAGAA
4477203 ATATCAAA-AGAA
1 ATATCAAATAGAA
* *
4477215 AAATCAAATACAA
1 ATATCAAATAGAA
4477228 ATAT
1 ATAT
4477232 TTCTCCTAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
12 11 0.44
13 14 0.56
ACGTcount: A:0.64, C:0.10, G:0.05, T:0.21
Consensus pattern (13 bp):
ATATCAAATAGAA
Found at i:4477220 original size:12 final size:13
Alignment explanation
Indices: 4477192--4477224 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
4477182 TTTACAATAT
*
4477192 ATCAAATAGAAAT
1 ATCAAATAGAAAA
4477205 ATCAAA-AGAAAA
1 ATCAAATAGAAAA
4477217 ATCAAATA
1 ATCAAATA
4477225 CAAATATTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.67, C:0.09, G:0.06, T:0.18
Consensus pattern (13 bp):
ATCAAATAGAAAA
Found at i:4478674 original size:3 final size:3
Alignment explanation
Indices: 4478660--4478690 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
4478650 GGCACGTCAA
4478660 AAT AAT ATAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT
4478691 GGTAAAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:4491531 original size:24 final size:25
Alignment explanation
Indices: 4491493--4491560 Score: 66
Period size: 28 Copynumber: 2.6 Consensus size: 25
4491483 GAATAATAAA
*
4491493 AAATATTACAAATAAATAAATTATACT
1 AAATA-TA-AAATAAATAAATTACACT
*
4491520 AAATATAAATAAGTAAATAAATTACATT
1 AAATAT-AA-AA-TAAATAAATTACACT
4491548 AAATAT-AAATAAA
1 AAATATAAAATAAA
4491561 GTTTCAATCT
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
24 4 0.11
25 2 0.06
26 3 0.08
27 8 0.22
28 19 0.53
ACGTcount: A:0.63, C:0.04, G:0.01, T:0.31
Consensus pattern (25 bp):
AAATATAAAATAAATAAATTACACT
Found at i:4491536 original size:28 final size:28
Alignment explanation
Indices: 4491505--4491559 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
4491495 ATATTACAAA
*
4491505 TAAATAAATTATACTAAATATAAATAAG
1 TAAATAAATTACACTAAATATAAATAAG
*
4491533 TAAATAAATTACATTAAATATAAATAA
1 TAAATAAATTACACTAAATATAAATAA
4491560 AGTTTCAATC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.33
Consensus pattern (28 bp):
TAAATAAATTACACTAAATATAAATAAG
Found at i:4494030 original size:12 final size:12
Alignment explanation
Indices: 4494013--4494039 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
4494003 TGCAAAAGTA
4494013 ATATATATGTAT
1 ATATATATGTAT
4494025 ATATATATGTAT
1 ATATATATGTAT
4494037 ATA
1 ATA
4494040 ATTTGGAATT
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:0.44, C:0.00, G:0.07, T:0.48
Consensus pattern (12 bp):
ATATATATGTAT
Found at i:4507592 original size:21 final size:22
Alignment explanation
Indices: 4507557--4507599 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
4507547 CTCTTAAAGT
4507557 AATTTAAAATAAAATAACTTAA
1 AATTTAAAATAAAATAACTTAA
*
4507579 AATTT-AACTAAAATAACTTAA
1 AATTTAAAATAAAATAACTTAA
4507600 TTAAACACTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (22 bp):
AATTTAAAATAAAATAACTTAA
Found at i:4509479 original size:33 final size:33
Alignment explanation
Indices: 4509437--4509513 Score: 120
Period size: 33 Copynumber: 2.3 Consensus size: 33
4509427 CGTTAAGAGC
*
4509437 TTTGGAACGACGAAT-AAATTTAATATTTCAATG
1 TTTGGAACGACGAATGAAA-TTAATATTCCAATG
*
4509470 TTTGGAACGACGAATGAAATTCATATTCCAATG
1 TTTGGAACGACGAATGAAATTAATATTCCAATG
4509503 TTTGGAACGAC
1 TTTGGAACGAC
4509514 ATTTTGAAGA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
33 38 0.93
34 3 0.07
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.32
Consensus pattern (33 bp):
TTTGGAACGACGAATGAAATTAATATTCCAATG
Found at i:4528239 original size:17 final size:16
Alignment explanation
Indices: 4528217--4528249 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
4528207 TTTTTTCATT
4528217 TTATTTATAGTATTTAA
1 TTATTTATA-TATTTAA
4528234 TTATTTATATATTTAA
1 TTATTTATATATTTAA
4528250 CATTGTGTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (16 bp):
TTATTTATATATTTAA
Found at i:4540829 original size:2 final size:2
Alignment explanation
Indices: 4540824--4540852 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4540814 CCCCCTACAT
4540824 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
4540853 TGGATTTGCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4546734 original size:210 final size:200
Alignment explanation
Indices: 4546301--4546734 Score: 500
Period size: 210 Copynumber: 2.1 Consensus size: 200
4546291 TATATACAAA
* * *
4546301 TTATGTATAAATTAAATATAGGTATATATAATAGATTACTTTATTATATATATAAAATTAATGAT
1 TTATGTATAAATTAAATATA--TATATATAATAGATAACTTTATTATATATATAAAATTAAAGAC
* *
4546366 ACAACTTGTATGTTATAATATTTTAATTTTTATATCAAAGTTTATATAAATAATATGTTATAAAA
64 ACAACTTATATGTTATAATATTTTAATTTTTATATCAAAGTATATATAAATAATATGTTATAAAA
* * *
4546431 ATTAAAGTAATAACTAAAAAATTTATTAAGTGTAATCATATAAATAAAGTCTATTATAAGTTATA
129 ACTAAAGTAATAACTAAAAAATTTATTAAATGTAATCATATAAATAAAATCTATTATAAGTTATA
4546496 GTAATAC
194 GTAATAC
* * * *
4546503 TTAATATATGAA-TATATATATATATATATATATGCATAACTTTATTATGTATATATGAAATTAA
1 TT-ATGTATAAATTAAATATATATATATA-ATA-G-ATAACTTTATTA--TATATATAAAATTAA
* * * * *
4546567 AGACACAATTTATATGTTATAATATTTTATATTAAAGTTTGTGT-AAA-TA-ATAACTAATTAGG
60 AGACACAACTTATATGTTATAATATTTTA-ATT----TTTATATCAAAGTATAT-A-TAAATA-A
* * *
4546629 TATGTTATAAAAACTAAAGTGATAATTAATAAAA-TTATTAAATGTAATCATATAAATAAAATTT
117 TATGTTATAAAAACTAAAGTAATAACTAA-AAAATTTATTAAATGTAATCATATAAATAAAATCT
4546693 ATTATAAGTTATAGTAATAC
181 ATTATAAGTTATAGTAATAC
4546713 TTATGTATAAATTAAATATATA
1 TTATGTATAAATTAAATATATA
4546735 ATGTTTATAC
Statistics
Matches: 193, Mismatches: 23, Indels: 24
0.80 0.10 0.10
Matches are distributed among these distances:
200 8 0.04
201 3 0.02
202 10 0.05
203 18 0.09
205 39 0.20
206 3 0.02
207 2 0.01
208 2 0.01
209 15 0.08
210 89 0.46
211 4 0.02
ACGTcount: A:0.47, C:0.04, G:0.08, T:0.42
Consensus pattern (200 bp):
TTATGTATAAATTAAATATATATATATAATAGATAACTTTATTATATATATAAAATTAAAGACAC
AACTTATATGTTATAATATTTTAATTTTTATATCAAAGTATATATAAATAATATGTTATAAAAAC
TAAAGTAATAACTAAAAAATTTATTAAATGTAATCATATAAATAAAATCTATTATAAGTTATAGT
AATAC
Found at i:4547008 original size:16 final size:16
Alignment explanation
Indices: 4546987--4547020 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
4546977 TTAATATATT
*
4546987 TTAAGTATATTATTAA
1 TTAAGTATACTATTAA
*
4547003 TTAAGTTTACTATTAA
1 TTAAGTATACTATTAA
4547019 TT
1 TT
4547021 CTTTGTAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.03, G:0.06, T:0.53
Consensus pattern (16 bp):
TTAAGTATACTATTAA
Found at i:4551019 original size:13 final size:13
Alignment explanation
Indices: 4550998--4551062 Score: 64
Period size: 13 Copynumber: 5.2 Consensus size: 13
4550988 ATATATTATT
4550998 AATAA-AAATTAA
1 AATAATAAATTAA
*
4551010 ATTAATAAATTAA
1 AATAATAAATTAA
**
4551023 AATTAATTGA-TAA
1 AA-TAATAAATTAA
*
4551036 AAGAATAAATTAA
1 AATAATAAATTAA
4551049 AATAAT-AATTAA
1 AATAATAAATTAA
4551061 AA
1 AA
4551063 CAATTAATGA
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
12 16 0.38
13 21 0.50
14 5 0.12
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (13 bp):
AATAATAAATTAA
Found at i:4551108 original size:20 final size:20
Alignment explanation
Indices: 4551058--4551108 Score: 50
Period size: 20 Copynumber: 2.5 Consensus size: 20
4551048 AAATAATAAT
* *
4551058 TAAAACAATT-AATGAATTT
1 TAAAAAAATTAAATGAATTG
* *
4551077 TAACAAATATTAAATTAATTG
1 TAA-AAAAATTAAATGAATTG
4551098 TAAAAAAATTA
1 TAAAAAAATTA
4551109 TAAATAAAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
19 3 0.12
20 12 0.48
21 10 0.40
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.35
Consensus pattern (20 bp):
TAAAAAAATTAAATGAATTG
Found at i:4566884 original size:18 final size:18
Alignment explanation
Indices: 4566840--4566891 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
4566830 TTGTTCTGGT
* *
4566840 TGTTGCTCCTTTTGCTTC
1 TGTTGCTGCTGTTGCTTC
*
4566858 T-TCTTCTGCTGTTGCTTC
1 TGT-TGCTGCTGTTGCTTC
*
4566876 TGTTGCTGCTGCTGCT
1 TGTTGCTGCTGTTGCT
4566892 GCACTTGCTT
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
17 1 0.04
18 25 0.93
19 1 0.04
ACGTcount: A:0.00, C:0.27, G:0.21, T:0.52
Consensus pattern (18 bp):
TGTTGCTGCTGTTGCTTC
Found at i:4566893 original size:27 final size:27
Alignment explanation
Indices: 4566840--4566913 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
4566830 TTGTTCTGGT
* * * * *
4566840 TGTTGCTCCTTTTGCTTCTTCTTCTGC
1 TGTTGCTTCTGTTGCTGCTGCTGCTGC
4566867 TGTTGCTTCTGTTGCTGCTGCTGCTGC
1 TGTTGCTTCTGTTGCTGCTGCTGCTGC
** *
4566894 ACTTGCTTTTGTTGCTGCTG
1 TGTTGCTTCTGTTGCTGCTG
4566914 ATGTTGTTTT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.01, C:0.26, G:0.23, T:0.50
Consensus pattern (27 bp):
TGTTGCTTCTGTTGCTGCTGCTGCTGC
Found at i:4566909 original size:21 final size:22
Alignment explanation
Indices: 4566885--4566936 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 22
4566875 CTGTTGCTGC
4566885 TGCTGCTGCA-CTTGCTTTTGT
1 TGCTGCTGCATCTTGCTTTTGT
* *
4566906 TGCTGCTG-ATGTTGTTTTTGT
1 TGCTGCTGCATCTTGCTTTTGT
*
4566927 TGCAGCTGCA
1 TGCTGCTGCA
4566937 GCTGCTGCTG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 1 0.04
21 24 0.92
22 1 0.04
ACGTcount: A:0.08, C:0.19, G:0.27, T:0.46
Consensus pattern (22 bp):
TGCTGCTGCATCTTGCTTTTGT
Found at i:4567698 original size:15 final size:15
Alignment explanation
Indices: 4567670--4567728 Score: 64
Period size: 15 Copynumber: 3.9 Consensus size: 15
4567660 ATTACAATAC
*
4567670 AATGTGATTACAAGT
1 AATGTGATTGCAAGT
*
4567685 AATGTAATTGCAAGT
1 AATGTGATTGCAAGT
* *
4567700 AATATGATTGCAAGC
1 AATGTGATTGCAAGT
* *
4567715 AATATGATTACAAG
1 AATGTGATTGCAAG
4567729 AAAAATAACA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 38 1.00
ACGTcount: A:0.42, C:0.08, G:0.19, T:0.31
Consensus pattern (15 bp):
AATGTGATTGCAAGT
Found at i:4567972 original size:21 final size:22
Alignment explanation
Indices: 4567948--4568013 Score: 79
Period size: 21 Copynumber: 3.1 Consensus size: 22
4567938 TCATATATTT
4567948 TATTTT-TATTTATTATTATAA
1 TATTTTATATTTATTATTATAA
4567969 TATTTTATATTTTATT-TT-TAA
1 TATTTTATA-TTTATTATTATAA
4567990 TATATTTATATTT-TTA-TATAA
1 TAT-TTTATATTTATTATTATAA
4568011 TAT
1 TAT
4568014 CATATTTTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
20 3 0.08
21 21 0.52
22 10 0.25
23 6 0.15
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (22 bp):
TATTTTATATTTATTATTATAA
Found at i:4567978 original size:33 final size:33
Alignment explanation
Indices: 4567941--4568125 Score: 116
Period size: 33 Copynumber: 5.5 Consensus size: 33
4567931 TTTAATGTCA
4567941 TATATTTTATTTTTATTTATTATTATAATATTT
1 TATATTTTATTTTTATTTATTATTATAATATTT
*
4567974 TATATTTTATTTTTA-ATA-TATT-T-ATATTTT
1 TATATTTTATTTTTATTTATTATTATAATA-TTT
* * **
4568004 TATATAATATCATATTTTAAATATATT-TT-TAATGA-CA
1 TATAT--T-T--TATTTT-TATTTATTATTATAAT-ATTT
* * *
4568041 TATATTTTATTTTTATTTATTACTATAATCTTA
1 TATATTTTATTTTTATTTATTATTATAATATTT
* * *
4568074 TATATTTTATTTTTATTTCTT-TAATATATTTTT
1 TATATTTTATTTTTATTTATTATTATA-ATATTT
*
4568107 TATATTATATATTTTATTT
1 TATATTTTAT-TTTTATTT
4568126 TAATTTATTT
Statistics
Matches: 121, Mismatches: 15, Indels: 31
0.72 0.09 0.19
Matches are distributed among these distances:
29 3 0.02
30 9 0.07
31 10 0.08
32 13 0.11
33 54 0.45
34 9 0.07
35 7 0.06
36 1 0.01
37 11 0.09
38 3 0.02
39 1 0.01
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.65
Consensus pattern (33 bp):
TATATTTTATTTTTATTTATTATTATAATATTT
Found at i:4567997 original size:22 final size:24
Alignment explanation
Indices: 4567948--4568003 Score: 75
Period size: 22 Copynumber: 2.5 Consensus size: 24
4567938 TCATATATTT
*
4567948 TATTTTTA-TTTATTATTATAATA
1 TATTTATATTTTATTATTATAATA
4567971 T-TTTATATTTTATT-TT-TAATA
1 TATTTATATTTTATTATTATAATA
4567992 TATTTATATTTT
1 TATTTATATTTT
4568004 TATATAATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
21 6 0.20
22 17 0.57
23 7 0.23
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (24 bp):
TATTTATATTTTATTATTATAATA
Found at i:4568010 original size:99 final size:100
Alignment explanation
Indices: 4567900--4568122 Score: 319
Period size: 100 Copynumber: 2.2 Consensus size: 100
4567890 TTTATTATTA
*
4567900 ATTTTTATATAATATCAT-TTCTTAAATAT-TTTTTAATGTCATATATTTTATTTTTATTTATTA
1 ATTTTTATATAATATCATATT-TTAAATATATTTTTAATGACATATATTTTATTTTTATTTATTA
* *
4567963 TTATAATATTTTATATTTTATTTTTAATATATTTAT
65 CTATAATATTATATATTTTATTTTTAATATATTTAT
4567999 ATTTTTATATAATATCATATTTTAAATATATTTTTAATGACATATATTTTATTTTTATTTATTAC
1 ATTTTTATATAATATCATATTTTAAATATATTTTTAATGACATATATTTTATTTTTATTTATTAC
* * *
4568064 TATAATCTTATATATTTTATTTTT-ATTTCTTTAAT
66 TATAATATTATATATTTTATTTTTAATATATTT-AT
* *
4568099 ATATTTTTTATATTAT-ATATTTTA
1 AT-TTTTATATAATATCATATTTTA
4568123 TTTTAATTTA
Statistics
Matches: 112, Mismatches: 8, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
99 32 0.29
100 69 0.62
101 11 0.10
ACGTcount: A:0.33, C:0.04, G:0.01, T:0.63
Consensus pattern (100 bp):
ATTTTTATATAATATCATATTTTAAATATATTTTTAATGACATATATTTTATTTTTATTTATTAC
TATAATATTATATATTTTATTTTTAATATATTTAT
Done.