Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold496
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: 765014
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.36
File 3 of 7
Found at i:173000 original size:43 final size:44
Alignment explanation
Indices: 172878--173000 Score: 112
Period size: 43 Copynumber: 2.8 Consensus size: 44
172868 AATTTTAATT
* *
172878 ATTTAAAATAT-TTTATATAATATAAATAAATATATTTATGTAATA
1 ATTTAAAATATATTTATATAATATAAAT-AATATA-TTATATAAGA
** * *
172923 ATTTAAAAT-TATACAATATAATATATCAT-TTATATTATAT-AGA
1 ATTTAAAATATAT-TTATATAATATA-AATAATATATTATATAAGA
172966 ATTTAAAATAATATTTA-ATAATATAAATAATATAT
1 ATTTAAAAT-ATATTTATATAATATAAATAATATAT
173001 AATTAAAAAT
Statistics
Matches: 62, Mismatches: 10, Indels: 14
0.72 0.12 0.16
Matches are distributed among these distances:
42 2 0.03
43 24 0.39
44 7 0.11
45 17 0.27
46 10 0.16
47 2 0.03
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (44 bp):
ATTTAAAATATATTTATATAATATAAATAATATATTATATAAGA
Found at i:173434 original size:11 final size:10
Alignment explanation
Indices: 173414--173442 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
173404 TCTTTTCCCA
173414 TTTTTCTTTT
1 TTTTTCTTTT
173424 TTTTTCTTTT
1 TTTTTCTTTT
173434 TTTTT-TTTT
1 TTTTTCTTTT
173443 CATTCAATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 4 0.21
10 15 0.79
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (10 bp):
TTTTTCTTTT
Found at i:173437 original size:14 final size:15
Alignment explanation
Indices: 173415--173443 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
173405 CTTTTCCCAT
173415 TTTTCTTTTTTTTTC
1 TTTTCTTTTTTTTTC
173430 TTTT-TTTTTTTTTC
1 TTTTCTTTTTTTTTC
173444 ATTCAATGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (15 bp):
TTTTCTTTTTTTTTC
Found at i:173664 original size:24 final size:22
Alignment explanation
Indices: 173619--173666 Score: 60
Period size: 24 Copynumber: 2.1 Consensus size: 22
173609 TTATTGTTGT
173619 TATTTATAATTAATTATAATAA
1 TATTTATAATTAATTATAATAA
* *
173641 TATTTATTACATTTATTATTATAA
1 TATTTA-TA-ATTAATTATAATAA
173665 TA
1 TA
173667 AAATGACATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 6 0.27
23 2 0.09
24 14 0.64
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (22 bp):
TATTTATAATTAATTATAATAA
Found at i:176838 original size:2 final size:2
Alignment explanation
Indices: 176831--176871 Score: 73
Period size: 2 Copynumber: 20.0 Consensus size: 2
176821 GTATCTGAAT
176831 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA GTA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
176872 CGGGTATTGC
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 36 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:177484 original size:26 final size:26
Alignment explanation
Indices: 177436--177486 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
177426 TATTACGTCG
*
177436 TTAAATTTTAAAATTAATATGATTAT
1 TTAAATTTTAAAATTAACATGATTAT
*
177462 TTAAATTTTAAAATTAACGTGATTA
1 TTAAATTTTAAAATTAACATGATTA
177487 ATATTTTAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.47
Consensus pattern (26 bp):
TTAAATTTTAAAATTAACATGATTAT
Found at i:179487 original size:23 final size:22
Alignment explanation
Indices: 179444--179489 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
179434 TTAATCTAAT
**
179444 TAATTTATACTATAATTTTTAA
1 TAATTTATACTATAAAATTTAA
*
179466 TAATTTATATTTATAAAATTTAA
1 TAATTTATA-CTATAAAATTTAA
179489 T
1 T
179490 TTAATGAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.54
Consensus pattern (22 bp):
TAATTTATACTATAAAATTTAA
Found at i:180402 original size:22 final size:22
Alignment explanation
Indices: 180352--180396 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
180342 GTCTATTTAA
*
180352 ATAA-AAATATAATTTAATTTT
1 ATAATAAATATAAGTTAATTTT
180373 ATAATAAATA-AAGTTAATTTT
1 ATAATAAATATAAGTTAATTTT
180394 ATA
1 ATA
180397 GTTAAAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (22 bp):
ATAATAAATATAAGTTAATTTT
Found at i:181798 original size:3 final size:3
Alignment explanation
Indices: 181790--181814 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
181780 TTAAATAAAC
181790 ACA ACA ACA ACA ACA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA A
181815 AAAATTAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:188062 original size:15 final size:16
Alignment explanation
Indices: 188042--188080 Score: 62
Period size: 15 Copynumber: 2.5 Consensus size: 16
188032 ATAACATAAA
*
188042 ATATTTTTAATATT-T
1 ATATTTATAATATTAT
188057 ATATTTATAATATTAT
1 ATATTTATAATATTAT
188073 ATATTTAT
1 ATATTTAT
188081 TTTTTATATG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
ATATTTATAATATTAT
Found at i:188094 original size:20 final size:22
Alignment explanation
Indices: 188051--188095 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 22
188041 AATATTTTTA
*
188051 ATATTTATATTTATAATATTAT
1 ATATTTATATTTATAATATGAT
*
188073 ATATTTAT-TTT-TTATATGAT
1 ATATTTATATTTATAATATGAT
188093 ATA
1 ATA
188096 AATTATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 10 0.48
21 3 0.14
22 8 0.38
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (22 bp):
ATATTTATATTTATAATATGAT
Found at i:189263 original size:18 final size:17
Alignment explanation
Indices: 189217--189263 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
189207 TTATTTTTTG
189217 TATATTTAA-AAAATTA
1 TATATTTAATAAAATTA
* *
189233 TAAATTTATATAAAATTT
1 TATATTTA-ATAAAATTA
189251 TATATGTTAATAA
1 TATAT-TTAATAA
189264 TTTATTTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
16 7 0.28
17 1 0.04
18 14 0.56
19 3 0.12
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (17 bp):
TATATTTAATAAAATTA
Found at i:189294 original size:14 final size:14
Alignment explanation
Indices: 189257--189295 Score: 50
Period size: 12 Copynumber: 3.1 Consensus size: 14
189247 ATTTTATATG
189257 TTAATA-ATTTATT
1 TTAATATATTTATT
189270 TT-ATATA--TATT
1 TTAATATATTTATT
189281 TTAATATATTTATT
1 TTAATATATTTATT
189295 T
1 T
189296 ATGTTATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 7
0.76 0.00 0.24
Matches are distributed among these distances:
11 6 0.27
12 8 0.36
13 3 0.14
14 5 0.23
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
TTAATATATTTATT
Found at i:189296 original size:24 final size:23
Alignment explanation
Indices: 189251--189342 Score: 75
Period size: 24 Copynumber: 3.9 Consensus size: 23
189241 TATAAAATTT
*
189251 TATATGTTAATA-ATTTATTTTATA
1 TATATTTTAATATA-TT-TTTTATA
*
189275 TATATTTTAATATATTTATTTATG
1 TATATTTTAATATATTT-TTTATA
*
189299 T-TATATTT-ATATTATTTTTCATA
1 TATAT-TTTAATA-TATTTTTTATA
189322 CTATATTTTAAT-TATTTTTTA
1 -TATATTTTAATATATTTTTTA
189343 AGTTGTGTTA
Statistics
Matches: 56, Mismatches: 5, Indels: 15
0.74 0.07 0.20
Matches are distributed among these distances:
23 19 0.34
24 31 0.55
25 6 0.11
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (23 bp):
TATATTTTAATATATTTTTTATA
Found at i:189343 original size:11 final size:12
Alignment explanation
Indices: 189268--189342 Score: 50
Period size: 11 Copynumber: 6.4 Consensus size: 12
189258 TAATAATTTA
*
189268 TTTTATA-TATA
1 TTTTATATTATT
189279 TTTTA-ATATATT
1 TTTTATAT-TATT
*
189291 TATTTATGTTA-T
1 T-TTTATATTATT
*
189303 ATTTATATTATT
1 TTTTATATTATT
* * *
189315 TTTCATACTATA
1 TTTTATATTATT
189327 TTTTA-ATTATT
1 TTTTATATTATT
189338 TTTTA
1 TTTTA
189343 AGTTGTGTTA
Statistics
Matches: 48, Mismatches: 11, Indels: 10
0.70 0.16 0.14
Matches are distributed among these distances:
10 1 0.02
11 22 0.46
12 18 0.38
13 6 0.12
14 1 0.02
ACGTcount: A:0.31, C:0.03, G:0.01, T:0.65
Consensus pattern (12 bp):
TTTTATATTATT
Found at i:193837 original size:34 final size:34
Alignment explanation
Indices: 193787--193890 Score: 136
Period size: 34 Copynumber: 3.0 Consensus size: 34
193777 AGATAAGTTT
193787 ACCTAACACACCTAATATGTTTACCTAACACACC
1 ACCTAACACACCTAATATGTTTACCTAACACACC
* * * *
193821 ACCTAACATACTTAATATATTACTCACCTAACATACC
1 ACCTAACACACCTAATATGTT--T-ACCTAACACACC
*
193858 ATCTAACACACCTAATATGTTTACCTAACACAC
1 ACCTAACACACCTAATATGTTTACCTAACACAC
193891 TTAATAAAGA
Statistics
Matches: 58, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
34 28 0.48
35 1 0.02
36 1 0.02
37 28 0.48
ACGTcount: A:0.39, C:0.32, G:0.02, T:0.27
Consensus pattern (34 bp):
ACCTAACACACCTAATATGTTTACCTAACACACC
Found at i:194443 original size:25 final size:25
Alignment explanation
Indices: 194414--194471 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 25
194404 AATTTTAAAA
194414 AATAAATAT-AAATAAT-TATATTTTT
1 AATAAA-ATCAAATAATATA-ATTTTT
*
194439 AATAAAATCACATAATATAATTTTT
1 AATAAAATCAAATAATATAATTTTT
*
194464 AAAAAAAT
1 AATAAAAT
194472 TATATTTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 2 0.07
25 25 0.86
26 2 0.07
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (25 bp):
AATAAAATCAAATAATATAATTTTT
Found at i:195310 original size:19 final size:19
Alignment explanation
Indices: 195250--195319 Score: 72
Period size: 20 Copynumber: 3.6 Consensus size: 19
195240 AAAAAATAAA
*
195250 TTAATTAAATAAAGTATTT
1 TTAATAAAATAAAGTATTT
*
195269 TTGAATAAAATAAATTGATTT
1 TT-AATAAAATAAAGT-ATTT
*
195290 TTATTAATAATAAA-TATTT
1 TTAATAA-AATAAAGTATTT
195309 TTAA-AAAATAA
1 TTAATAAAATAA
195320 TAAAATAATA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
17 5 0.11
18 2 0.05
19 9 0.20
20 16 0.36
21 12 0.27
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.44
Consensus pattern (19 bp):
TTAATAAAATAAAGTATTT
Found at i:195679 original size:23 final size:23
Alignment explanation
Indices: 195635--195685 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
195625 TAATACGTTT
*
195635 GTTATAATAATTCATATATTTAA
1 GTTATAATAATTAATATATTTAA
* *
195658 TTTATAA-AATTAATTATTTTTAA
1 GTTATAATAATTAA-TATATTTAA
195681 GTTAT
1 GTTAT
195686 TATCGAAAAC
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 5 0.22
23 18 0.78
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (23 bp):
GTTATAATAATTAATATATTTAA
Found at i:195991 original size:9 final size:10
Alignment explanation
Indices: 195971--196010 Score: 53
Period size: 10 Copynumber: 3.8 Consensus size: 10
195961 TTATTTCAAA
195971 TAAAATATAT
1 TAAAATATAT
195981 TAAAAATATTAT
1 T-AAAATA-TAT
*
195993 TAAAATTTAT
1 TAAAATATAT
196003 TAAAATAT
1 TAAAATAT
196011 TTCACAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
10 11 0.42
11 11 0.42
12 4 0.15
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (10 bp):
TAAAATATAT
Found at i:195996 original size:22 final size:21
Alignment explanation
Indices: 195971--196011 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
195961 TTATTTCAAA
195971 TAAAATATATTAAAAATATTAT
1 TAAAATATATT-AAAATATTAT
*
195993 TAAAATTTATTAAAATATT
1 TAAAATATATTAAAATATT
196012 TCACAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
TAAAATATATTAAAATATTAT
Found at i:197662 original size:17 final size:16
Alignment explanation
Indices: 197610--197701 Score: 75
Period size: 17 Copynumber: 5.6 Consensus size: 16
197600 AGATATATTT
*
197610 TAAAATTTATTTAATA
1 TAAAATTTATTAAATA
197626 T-AAA-TTATTAACATA
1 TAAAATTTATTAA-ATA
197641 TTAAAATTTATATAAATA
1 -TAAAATTTAT-TAAATA
*
197659 TAAATTTTATTAATATA
1 TAAAATTTATTAA-ATA
*
197676 TAAATATGTGA-TAAATA
1 TAAA-AT-TTATTAAATA
197693 -AAAATTTAT
1 TAAAATTTAT
197702 ATTACCTATA
Statistics
Matches: 62, Mismatches: 5, Indels: 19
0.72 0.06 0.22
Matches are distributed among these distances:
14 8 0.13
15 8 0.13
16 8 0.13
17 22 0.35
18 11 0.18
19 5 0.08
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.45
Consensus pattern (16 bp):
TAAAATTTATTAAATA
Found at i:197960 original size:13 final size:13
Alignment explanation
Indices: 197944--197991 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
197934 TTTAATTAAA
197944 AAAATTAAAATAT
1 AAAATTAAAATAT
197957 AAAATTAAAAT-T
1 AAAATTAAAATAT
197969 ATAAA-TATAAA-AT
1 A-AAATTA-AAATAT
197982 AAAATTAAAA
1 AAAATTAAAA
197992 ATATTTAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
12 10 0.32
13 21 0.68
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (13 bp):
AAAATTAAAATAT
Found at i:197965 original size:6 final size:6
Alignment explanation
Indices: 197944--197991 Score: 62
Period size: 6 Copynumber: 7.7 Consensus size: 6
197934 TTTAATTAAA
197944 AAAATT AAAATAT AAAATT AAAATT ATAAATAT AAAA-T AAAATT AAAA
1 AAAATT AAAAT-T AAAATT AAAATT A-AAAT-T AAAATT AAAATT AAAA
197992 ATATTTAAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
5 5 0.13
6 18 0.47
7 13 0.34
8 2 0.05
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (6 bp):
AAAATT
Found at i:197993 original size:19 final size:20
Alignment explanation
Indices: 197944--197995 Score: 81
Period size: 19 Copynumber: 2.7 Consensus size: 20
197934 TTTAATTAAA
197944 AAAATT-AAAATATAAAATT
1 AAAATTAAAAATATAAAATT
*
197963 AAAATTATAAATATAAAA-T
1 AAAATTAAAAATATAAAATT
197982 AAAATTAAAAATAT
1 AAAATTAAAAATAT
197996 TTAAATCTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 20 0.67
20 10 0.33
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (20 bp):
AAAATTAAAAATATAAAATT
Found at i:198402 original size:19 final size:19
Alignment explanation
Indices: 198360--198402 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
198350 ATTCATTAAT
*
198360 TTAATATATTATTTAAAAA
1 TTAAAATATTATTTAAAAA
* * *
198379 ATAAAATATTATTTTATAA
1 TTAAAATATTATTTAAAAA
198398 TTAAA
1 TTAAA
198403 TTTAAATAAA
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
TTAAAATATTATTTAAAAA
Found at i:198431 original size:29 final size:29
Alignment explanation
Indices: 198377--198432 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 29
198367 ATTATTTAAA
*
198377 AAATAAAATATTATTTTATAATTAAATTT
1 AAATAAAATATTATTTTATAAATAAATTT
198406 AAATAAAA-A-TATTTTTATTAAATAAAT
1 AAATAAAATATTA-TTTTA-TAAATAAAT
198433 AATAATTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 2 0.08
28 6 0.25
29 16 0.67
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (29 bp):
AAATAAAATATTATTTTATAAATAAATTT
Found at i:198441 original size:19 final size:19
Alignment explanation
Indices: 198404--198441 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
198394 ATAATTAAAT
*
198404 TTAAATAAAAATATTTTTA
1 TTAAATAAAAATATATTTA
198423 TTAAATAAATAATA-ATTTA
1 TTAAATAAA-AATATATTTA
198442 AATTAAGTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
TTAAATAAAAATATATTTA
Found at i:199380 original size:23 final size:22
Alignment explanation
Indices: 199354--199459 Score: 65
Period size: 23 Copynumber: 4.8 Consensus size: 22
199344 ATAACATATT
*
199354 TATTTTATTTTTTATTATAATTA
1 TATTTTATTTATTA-TATAATTA
* * *
199377 TATTTAAATTATTATATAAATA
1 TATTTTATTTATTATATAATTA
**
199399 TAATTTTAAATATTA-ATAATT-
1 T-ATTTTATTTATTATATAATTA
* * * *
199420 TATATTATATATTTTTTAA-TA
1 TATTTTATTTATTATATAATTA
199441 TATTTATATTATATTATAT
1 TATTT-TATT-TATTATAT
199460 TTTTTAAAAA
Statistics
Matches: 63, Mismatches: 15, Indels: 10
0.72 0.17 0.11
Matches are distributed among these distances:
20 11 0.17
21 8 0.13
22 16 0.25
23 28 0.44
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
TATTTTATTTATTATATAATTA
Found at i:199394 original size:22 final size:21
Alignment explanation
Indices: 199369--199454 Score: 65
Period size: 22 Copynumber: 4.1 Consensus size: 21
199359 TATTTTTTAT
199369 TATAATTATATTTAAATTATTA
1 TATAATTATATTTAAA-TATTA
*
199391 TATAAATATAATTTTAAATATTA
1 TATAATTAT-A-TTTAAATATTA
* *
199414 -ATAATT-TATATTATATATTT
1 TATAATTATAT-TTAAATATTA
*
199434 TTTAA-TATATTT--ATATTA
1 TATAATTATATTTAAATATTA
199452 TAT
1 TAT
199455 TATATTTTTT
Statistics
Matches: 52, Mismatches: 7, Indels: 14
0.71 0.10 0.19
Matches are distributed among these distances:
18 7 0.13
19 1 0.02
20 12 0.23
21 7 0.13
22 13 0.25
23 6 0.12
24 6 0.12
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TATAATTATATTTAAATATTA
Found at i:199441 original size:30 final size:30
Alignment explanation
Indices: 199386--199467 Score: 87
Period size: 30 Copynumber: 2.7 Consensus size: 30
199376 ATATTTAAAT
* *
199386 TATTATATAAATATAATTTTAAATATTAATAA
1 TATTATAT-TATATATTTTTAAATA-TAATAA
* * *
199418 T-TTATATTATATATTTTTTAATATATTTA
1 TATTATATTATATATTTTTAAATATAATAA
199447 TATTATATTATAT-TTTTTAAA
1 TATTATATTATATATTTTTAAA
199468 AAATAAAATA
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
29 12 0.28
30 24 0.56
31 6 0.14
32 1 0.02
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (30 bp):
TATTATATTATATATTTTTAAATATAATAA
Found at i:199445 original size:25 final size:26
Alignment explanation
Indices: 199411--199463 Score: 83
Period size: 25 Copynumber: 2.1 Consensus size: 26
199401 ATTTTAAATA
199411 TTAATAATTTATATTATA-TAT-TTT
1 TTAATAATTTATATTATATTATATTT
199435 TTAATATATTTATATTATATTATATTT
1 TTAATA-ATTTATATTATATTATATTT
199462 TT
1 TT
199464 TAAAAAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
24 6 0.23
25 12 0.46
26 3 0.12
27 5 0.19
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (26 bp):
TTAATAATTTATATTATATTATATTT
Found at i:204037 original size:16 final size:17
Alignment explanation
Indices: 203999--204051 Score: 65
Period size: 17 Copynumber: 3.1 Consensus size: 17
203989 AATAAGTTAC
203999 TTTTTTAAAAAAATATTA
1 TTTTTTAAAAAAATA-TA
204017 TTTTTTAAATAAAATA-A
1 TTTTTTAAA-AAAATATA
*
204034 TTTTTAAAAAAAAT-TA
1 TTTTTTAAAAAAATATA
204050 TT
1 TT
204052 AAGAGTTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
16 8 0.25
17 9 0.28
18 9 0.28
19 6 0.19
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TTTTTTAAAAAAATATA
Found at i:204176 original size:27 final size:25
Alignment explanation
Indices: 204130--204199 Score: 72
Period size: 27 Copynumber: 2.7 Consensus size: 25
204120 TTGATTTAAT
204130 TTATTTTT-TAA-AAATATTAAAATA
1 TTATTTTTATAATAAATATTAAAA-A
*
204154 TTATTTTTATAATTAAATTTTAAAAA
1 TTATTTTTATAA-TAAATATTAAAAA
*
204180 ATATTTTTATTAAATAAATA
1 TTATTTTTA-T-AATAAATA
204200 ATAATTTAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
24 8 0.21
25 3 0.08
26 9 0.24
27 16 0.42
28 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (25 bp):
TTATTTTTATAATAAATATTAAAAA
Found at i:204905 original size:20 final size:21
Alignment explanation
Indices: 204875--204931 Score: 75
Period size: 20 Copynumber: 2.8 Consensus size: 21
204865 TCGATTTTTA
204875 ATATATTTATTAAATATATTT
1 ATATATTTATTAAATATATTT
204896 ATAT-TTTATTAAATATATTT
1 ATATATTTATTAAATATATTT
*
204916 -TAAATATT-TTAAATAT
1 ATATAT-TTATTAAATAT
204932 TAATTCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
19 2 0.06
20 25 0.76
21 6 0.18
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
ATATATTTATTAAATATATTT
Found at i:205040 original size:9 final size:9
Alignment explanation
Indices: 205026--205085 Score: 52
Period size: 9 Copynumber: 6.7 Consensus size: 9
205016 TGATCAAAAT
205026 TTAATTAAA
1 TTAATTAAA
*
205035 TTAATTGAA
1 TTAATTAAA
*
205044 TCAATTAAA
1 TTAATTAAA
*
205053 TTAAATTTAA
1 TT-AATTAAA
*
205063 TTAATCT--T
1 TTAAT-TAAA
205071 TTAATTAAA
1 TTAATTAAA
205080 TTAATT
1 TTAATT
205086 TTAACTAATT
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
7 1 0.03
8 5 0.12
9 25 0.62
10 9 0.22
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48
Consensus pattern (9 bp):
TTAATTAAA
Found at i:205089 original size:23 final size:23
Alignment explanation
Indices: 205023--205086 Score: 78
Period size: 23 Copynumber: 2.8 Consensus size: 23
205013 AATTGATCAA
*
205023 AATTTAATTAAATTAATTGAATC
1 AATTTAATTAAATTAATTTAATC
*
205046 AATTAAATTAAATTTAA-TTAATC
1 AATTTAATTAAA-TTAATTTAATC
*
205069 -TTTTAATTAAATTAATTT
1 AATTTAATTAAATTAATTT
205087 TAACTAATTG
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
21 4 0.11
22 11 0.31
23 16 0.46
24 4 0.11
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48
Consensus pattern (23 bp):
AATTTAATTAAATTAATTTAATC
Found at i:205437 original size:25 final size:23
Alignment explanation
Indices: 205391--205451 Score: 68
Period size: 24 Copynumber: 2.6 Consensus size: 23
205381 AAAATTTTAA
*
205391 ATTAAAATGTATATATAATAAATT
1 ATTAAAATATATATATAATAAA-T
* *
205415 ATTAAAATTATATTTATATTAAAT
1 ATTAAAA-TATATATATAATAAAT
*
205439 AATAAAATATATA
1 ATTAAAATATATA
205452 AAAAAATTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
23 5 0.16
24 14 0.45
25 12 0.39
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (23 bp):
ATTAAAATATATATATAATAAAT
Found at i:205491 original size:33 final size:34
Alignment explanation
Indices: 205405--205517 Score: 108
Period size: 35 Copynumber: 3.3 Consensus size: 34
205395 AAATGTATAT
205405 ATAAT-AAAT-TATTAAAATTATATTTATATTAA
1 ATAATAAAATATATTAAAATTATATTTATATTAA
* * *
205437 ATAATAAAATATATAAAAAAATT-TATTTATTTTGA
1 ATAATAAAATATAT--TAAAATTATATTTATATTAA
* * *
205472 TTGATAAAATATATTAAAATTATATTCTA-GTTAA
1 ATAATAAAATATATTAAAATTATATT-TATATTAA
205506 ATAATAATAATA
1 ATAATAA-AATA
205518 ATTTAATTTA
Statistics
Matches: 64, Mismatches: 10, Indels: 11
0.75 0.12 0.13
Matches are distributed among these distances:
32 5 0.08
33 10 0.16
34 15 0.23
35 28 0.44
36 6 0.09
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.43
Consensus pattern (34 bp):
ATAATAAAATATATTAAAATTATATTTATATTAA
Found at i:205531 original size:43 final size:40
Alignment explanation
Indices: 205483--205563 Score: 110
Period size: 43 Copynumber: 1.9 Consensus size: 40
205473 TGATAAAATA
205483 TATTAAAATTATATTCTA-GTTAAATAATAATAATAATTTAATT
1 TATTAAAATTAT-TTCTATGTTAAA-AAT-A-AATAATTTAATT
*
205526 TATTAAAATTATTTTTATGTTAAAAATAAATAATTTAA
1 TATTAAAATTATTTCTATGTTAAAAATAAATAATTTAA
205564 ACTTTTGAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
40 10 0.28
41 1 0.03
42 7 0.19
43 18 0.50
ACGTcount: A:0.49, C:0.01, G:0.02, T:0.47
Consensus pattern (40 bp):
TATTAAAATTATTTCTATGTTAAAAATAAATAATTTAATT
Found at i:205916 original size:22 final size:21
Alignment explanation
Indices: 205891--205955 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 21
205881 TATTTTTTAT
205891 TATAATTATATTTAAATTATTA
1 TATAATTATATTTAAA-TATTA
* *
205913 TATAAATATAATTTTAATATTA
1 TATAATTAT-ATTTAAATATTA
*
205935 -ATAATTTATATTATATATATT
1 TATAA-TTATATT-TAAATATT
205956 TTACGTTATA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
21 7 0.20
22 22 0.63
23 6 0.17
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
TATAATTATATTTAAATATTA
Found at i:205940 original size:15 final size:16
Alignment explanation
Indices: 205918--205958 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 16
205908 TATTATATAA
205918 ATATAATTTTAATATT
1 ATATAATTTTAATATT
205934 A-ATAA-TTT-ATATT
1 ATATAATTTTAATATT
205947 ATATATATTTTA
1 ATATA-ATTTTA
205959 CGTTATACTT
Statistics
Matches: 21, Mismatches: 0, Indels: 7
0.75 0.00 0.25
Matches are distributed among these distances:
13 6 0.29
14 6 0.29
15 5 0.24
16 4 0.19
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
ATATAATTTTAATATT
Found at i:208690 original size:17 final size:18
Alignment explanation
Indices: 208660--208699 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
208650 TAACCTATTG
*
208660 TTTTTTAATTAAAATAAT
1 TTTTTTAATAAAAATAAT
*
208678 TTTTTTAA-AAAAATTAT
1 TTTTTTAATAAAAATAAT
208695 TTTTT
1 TTTTT
208700 CACAAGTGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTTTTAATAAAAATAAT
Found at i:208931 original size:13 final size:13
Alignment explanation
Indices: 208884--208935 Score: 56
Period size: 12 Copynumber: 4.2 Consensus size: 13
208874 TTTATGAGAC
*
208884 TTAAATTAATTTA
1 TTAAATTATTTTA
*
208897 -TAATTTATTTT-
1 TTAAATTATTTTA
*
208908 TAAAATT-TTTTA
1 TTAAATTATTTTA
208920 TTAAATTATTTTA
1 TTAAATTATTTTA
208933 TTA
1 TTA
208936 TTTAAAAAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
11 4 0.13
12 19 0.61
13 8 0.26
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TTAAATTATTTTA
Found at i:209014 original size:21 final size:20
Alignment explanation
Indices: 208961--209025 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 20
208951 TATTATTCAT
208961 ATAA-TTAAATTTAAATAA-A
1 ATAATTTAAA-TTAAATAATA
208980 ATATATTT--ATTAAATAAATA
1 ATA-ATTTAAATTAAAT-AATA
209000 ATAATTTAAATTAAATTAATA
1 ATAATTTAAATTAAA-TAATA
*
209021 TTAAT
1 ATAAT
209026 AAAATATTTG
Statistics
Matches: 38, Mismatches: 1, Indels: 12
0.75 0.02 0.24
Matches are distributed among these distances:
18 6 0.16
19 10 0.26
20 5 0.13
21 16 0.42
22 1 0.03
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
ATAATTTAAATTAAATAATA
Found at i:209691 original size:21 final size:20
Alignment explanation
Indices: 209667--209716 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
209657 GACTGTAACG
*
209667 TTAATTATTATAATAATAAAA
1 TTAAATATTAT-ATAATAAAA
*
209688 TTAAATATTATATGATAAAA
1 TTAAATATTATATAATAAAA
209708 TTAAA-ATTA
1 TTAAATATTA
209717 ACAGAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 4 0.15
20 13 0.48
21 10 0.37
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (20 bp):
TTAAATATTATATAATAAAA
Found at i:210090 original size:21 final size:21
Alignment explanation
Indices: 210042--210090 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
210032 TGGCAGACGC
*
210042 CAGTAGATTGGCACCGAGGTG
1 CAGTAGATTGACACCGAGGTG
* *
210063 TATTAGATTGACACCG-GTGTG
1 CAGTAGATTGACACCGAG-GTG
210084 CAGTAGA
1 CAGTAGA
210091 CTAGCATTGG
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
20 1 0.05
21 21 0.95
ACGTcount: A:0.27, C:0.16, G:0.33, T:0.24
Consensus pattern (21 bp):
CAGTAGATTGACACCGAGGTG
Found at i:210300 original size:19 final size:18
Alignment explanation
Indices: 210267--210312 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 18
210257 ATTTATTTTT
210267 ATATATATTTAATTATATA
1 ATATATATTTAATTA-ATA
210286 ATATA-ATTTATATTAATA
1 ATATATATTTA-ATTAATA
210304 ATTATATAT
1 A-TATATAT
210313 ATAAATTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 9 0.38
19 13 0.54
20 2 0.08
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
ATATATATTTAATTAATA
Found at i:210316 original size:12 final size:12
Alignment explanation
Indices: 210268--210316 Score: 55
Period size: 13 Copynumber: 3.9 Consensus size: 12
210258 TTTATTTTTA
*
210268 TATATATTTAAT
1 TATATATATAAT
210280 TATATAATATAAT
1 TATAT-ATATAAT
210293 T-TATATTAATAAT
1 TATATA-T-ATAAT
210306 TATATATATAA
1 TATATATATAA
210317 ATTTTAATAT
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
11 1 0.03
12 13 0.41
13 14 0.44
14 4 0.12
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (12 bp):
TATATATATAAT
Found at i:210336 original size:28 final size:28
Alignment explanation
Indices: 210263--210336 Score: 73
Period size: 26 Copynumber: 2.7 Consensus size: 28
210253 TCATATTTAT
*
210263 TTTTATATATATTTAATTATATAATATAA
1 TTTTA-ATATTTTTAATTATATAATATAA
**
210292 -TTT-ATATTAATAATTATAT-ATATAAA
1 TTTTAATATTTTTAATTATATAATAT-AA
*
210318 TTTTAATATTTTTATTTAT
1 TTTTAATATTTTTAATTAT
210337 TCATGTCATT
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
25 4 0.11
26 15 0.42
27 3 0.08
28 14 0.39
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (28 bp):
TTTTAATATTTTTAATTATATAATATAA
Found at i:212594 original size:2 final size:2
Alignment explanation
Indices: 212587--212631 Score: 74
Period size: 2 Copynumber: 22.5 Consensus size: 2
212577 TGCCCTTGTA
212587 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GAT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT
212629 AT A
1 AT A
212632 ATTTGCAGAT
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 1 0.02
2 38 0.93
3 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:213576 original size:41 final size:41
Alignment explanation
Indices: 213509--213596 Score: 99
Period size: 41 Copynumber: 2.1 Consensus size: 41
213499 TAATATATTT
* *
213509 ATTTAATATTAAAAATAATAAATAAAATTATTAATT-ATTAA
1 ATTTAATATTAAAAATAATAAATAAAA-AATAAATTAATTAA
* * *
213550 ATTTAATA-TAAAATTATTAATTTAAAAAATAAATTAATTAA
1 ATTTAATATTAAAAATAATAA-ATAAAAAATAAATTAATTAA
213591 ATTTAA
1 ATTTAA
213597 AAAAAAATGC
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
40 16 0.40
41 24 0.60
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (41 bp):
ATTTAATATTAAAAATAATAAATAAAAAATAAATTAATTAA
Found at i:213589 original size:21 final size:20
Alignment explanation
Indices: 213541--213604 Score: 85
Period size: 20 Copynumber: 3.1 Consensus size: 20
213531 TAAAATTATT
* *
213541 AATTATTAAATTTAATATAA
1 AATTATTAAATTTAAAAAAA
213561 AATTATT-AATTTAAAAAATA
1 AATTATTAAATTTAAAAAA-A
213581 AATTAATTAAATTTAAAAAAA
1 AATT-ATTAAATTTAAAAAAA
213602 AAT
1 AAT
213605 GCCCTGAAAG
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
19 9 0.23
20 12 0.31
21 7 0.18
22 11 0.28
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
AATTATTAAATTTAAAAAAA
Found at i:214503 original size:8 final size:8
Alignment explanation
Indices: 214490--214523 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
214480 TTTTTTAGTA
214490 AATTTAAT
1 AATTTAAT
214498 AATTTAAT
1 AATTTAAT
214506 AATTT-AT
1 AATTTAAT
*
214513 ATTTTAAT
1 AATTTAAT
214521 AAT
1 AAT
214524 ATATTTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
7 6 0.26
8 17 0.74
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (8 bp):
AATTTAAT
Found at i:214520 original size:15 final size:15
Alignment explanation
Indices: 214490--214533 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
214480 TTTTTTAGTA
*
214490 AATTTAATAATTTAAT
1 AATTT-ATATTTTAAT
214506 AATTTATATTTTAAT
1 AATTTATATTTTAAT
* *
214521 AATATATTTTTTA
1 AATTTATATTTTA
214534 TTTTATAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
15 20 0.80
16 5 0.20
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
AATTTATATTTTAAT
Found at i:215018 original size:11 final size:11
Alignment explanation
Indices: 215002--215027 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
214992 TTTATAATTT
215002 TAAATATAATA
1 TAAATATAATA
215013 TAAATATAATA
1 TAAATATAATA
215024 TAAA
1 TAAA
215028 AAAATTAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
TAAATATAATA
Found at i:215168 original size:19 final size:20
Alignment explanation
Indices: 215144--215185 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
215134 GTGTCAAAAT
*
215144 TTATATAAATAA-TGTAATA
1 TTATATAAATAATTATAATA
*
215163 TTATATATATAATTATAATA
1 TTATATAAATAATTATAATA
215183 TTA
1 TTA
215186 AAAAATATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (20 bp):
TTATATAAATAATTATAATA
Found at i:216984 original size:78 final size:76
Alignment explanation
Indices: 216874--217140 Score: 249
Period size: 78 Copynumber: 3.4 Consensus size: 76
216864 TGAAAAATCG
* * * *
216874 ATATTTT-AGAAATAGAAACAGGGATTGGAGTATCCCATTGGAAATAACAGGATTAGACTATCCC
1 ATATTTTGA-AAATAAAAATAGGGATTGGAGTATCCC-TTGGAAATAAC-GGATTGGAGTATCCC
216938 GAGATGAAAATTTTA
63 GAGATGAAAA-TTTA
* * *
216953 ATATTTTGAAAATAAAAATAGGG-TTGGAGTATTCTCTTGAAAATAACGGAGTGGAGTATCCTC-
1 ATATTTTGAAAATAAAAATAGGGATTGGAGTA-TCCCTTGGAAATAACGGATTGGAGTATCC-CG
217016 ACGATGAAGAATTTA
64 A-GATGAA-AATTTA
* * * * **
217031 ATATTTTGAAAATAAAAAT-GGGATTAGAGTATTCCTTCAGAATTGATGGGATTGGAGTATCCCC
1 ATATTTTGAAAATAAAAATAGGGATTGGAGTATCCCTT-GGAAAT-AACGGATTGGAGTAT-CCC
217095 GAGATGAAAATTTA
63 GAGATGAAAATTTA
* *
217109 ATATTTTTG-AAATAAAAAT-GGGGTTTGAGTAT
1 ATA-TTTTGAAAATAAAAATAGGGATTGGAGTAT
217141 TTCCTCGGAA
Statistics
Matches: 159, Mismatches: 18, Indels: 23
0.80 0.09 0.12
Matches are distributed among these distances:
77 19 0.12
78 88 0.55
79 48 0.30
80 4 0.03
ACGTcount: A:0.39, C:0.09, G:0.21, T:0.31
Consensus pattern (76 bp):
ATATTTTGAAAATAAAAATAGGGATTGGAGTATCCCTTGGAAATAACGGATTGGAGTATCCCGAG
ATGAAAATTTA
Found at i:217145 original size:79 final size:78
Alignment explanation
Indices: 216935--217169 Score: 264
Period size: 78 Copynumber: 3.0 Consensus size: 78
216925 ATTAGACTAT
* * * *
216935 CCCGAGATGAAAATTTTAATATTTTGAAAATAAAAATAGGGTTGGAGTATTCTCTTGA-AAAT-A
1 CCCGAGATGAAAA-TTTAATATTTTGAAAATAAAAATGGGGTTAGAGTATTC-CTTCAGAATTGA
** *
216998 ACGGAGTGGAGTATC
64 TGGGATTGGAGTATC
* *
217013 CTC-ACGATGAAGAATTTAATATTTTGAAAATAAAAATGGGATTAGAGTATTCCTTCAGAATTGA
1 CCCGA-GATGAA-AATTTAATATTTTGAAAATAAAAATGGGGTTAGAGTATTCCTTCAGAATTGA
217077 TGGGATTGGAGTATC
64 TGGGATTGGAGTATC
* * *
217092 CCCGAGATGAAAATTTAATATTTTTG-AAATAAAAATGGGGTTTGAGTATTTCC-TCGGAATGGA
1 CCCGAGATGAAAATTTAATA-TTTTGAAAATAAAAATGGGGTTAGAGTA-TTCCTTCAGAATTGA
*
217155 TGGGGTTGGAGTATC
64 TGGGATTGGAGTATC
217170 TTTGAGATGA
Statistics
Matches: 135, Mismatches: 15, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
77 5 0.04
78 97 0.72
79 32 0.24
80 1 0.01
ACGTcount: A:0.35, C:0.09, G:0.23, T:0.32
Consensus pattern (78 bp):
CCCGAGATGAAAATTTAATATTTTGAAAATAAAAATGGGGTTAGAGTATTCCTTCAGAATTGATG
GGATTGGAGTATC
Found at i:217191 original size:156 final size:155
Alignment explanation
Indices: 216787--217193 Score: 353
Period size: 156 Copynumber: 2.6 Consensus size: 155
216777 CTTTAGATAA
* * * * * * *
216787 AAAATTTAATGTTTTGGAAGTGAAAATGAGGTTGGAGTATCTT-CTCAGAATTGATGGGGTTAGA
1 AAAATTTAATATTTTTGAAATAAAAATGGGGTTGGAGTAT-TTCCTCGGAA-TGATGGGGTTGGA
* * * *
216851 GTATCTTCAATAGTGAAAAATCGATATTTTAGAAATAGAAACAGGGATTGGAGTATCCCATTGGA
64 GTATCTTTAAGA-TGAAAAATCGATATTTTAGAAATAGAAACAGGGATTAGAGTATCCCATTAGA
216916 AATAACAGGATTAGACTATCCCGAGATG
128 AATAACAGGATTAGACTATCCCGAGATG
* * * * * *
216944 AAAATTTTAATA-TTTTGAAAATAAAAATAGGGTTGGAGTA-TTCTCTTGAAAATAACGGAG-TG
1 AAAA-TTTAATATTTTTG-AAATAAAAATGGGGTTGGAGTATTTC-CTCG-GAATGATGGGGTTG
* * * * ** *
217006 GAGTATCCTCACGATGAAGAATTTAATATTTT-GAAAATA-AAA-ATGGGATTAGAGTATTCC-T
62 GAGTATCTTTAAGATGAA-AAATCGATATTTTAG-AAATAGAAACA-GGGATTAGAGTATCCCAT
* * ** * *
217067 TCAGAATTGATGGGATTGGAGTATCCCCGAGATG
124 T-AGAAATAACAGGATTAGACTAT-CCCGAGATG
*
217101 AAAATTTAATATTTTTGAAATAAAAATGGGGTTTGAGTATTTCCTCGGAATGGATGGGGTTGGAG
1 AAAATTTAATATTTTTGAAATAAAAATGGGGTTGGAGTATTTCCTCGGAAT-GATGGGGTTGGAG
*
217166 TATCTTTGAGATGAAAAATCGATATTTT
65 TATCTTTAAGATGAAAAATCGATATTTT
217194 TGGAAGGAAA
Statistics
Matches: 194, Mismatches: 42, Indels: 29
0.73 0.16 0.11
Matches are distributed among these distances:
155 6 0.03
156 83 0.43
157 72 0.37
158 31 0.16
159 2 0.01
ACGTcount: A:0.36, C:0.08, G:0.23, T:0.32
Consensus pattern (155 bp):
AAAATTTAATATTTTTGAAATAAAAATGGGGTTGGAGTATTTCCTCGGAATGATGGGGTTGGAGT
ATCTTTAAGATGAAAAATCGATATTTTAGAAATAGAAACAGGGATTAGAGTATCCCATTAGAAAT
AACAGGATTAGACTATCCCGAGATG
Found at i:220810 original size:4 final size:4
Alignment explanation
Indices: 220803--220831 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
220793 AAAAAAATGG
220803 AAGA AAGA AAGA AAGA AAGA AAGA AAGA A
1 AAGA AAGA AAGA AAGA AAGA AAGA AAGA A
220832 GGCGCCCTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:221290 original size:20 final size:20
Alignment explanation
Indices: 221262--221301 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
221252 AGTTAAATAT
* *
221262 TTATTTTTATTAATTATTAA
1 TTATATTTAATAATTATTAA
*
221282 TTATATTTAATATTTATTAA
1 TTATATTTAATAATTATTAA
221302 ACATTAAACT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TTATATTTAATAATTATTAA
Found at i:221307 original size:27 final size:26
Alignment explanation
Indices: 221258--221308 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
221248 ATTAAGTTAA
* **
221258 ATATTTATTTTTATTAATTATTAATT
1 ATATTTATATTTATTAAACATTAATT
221284 ATATTTAATATTTATTAAACATTAA
1 ATATTT-ATATTTATTAAACATTAA
221309 ACTTAGTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 6 0.29
27 15 0.71
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (26 bp):
ATATTTATATTTATTAAACATTAATT
Found at i:222519 original size:16 final size:15
Alignment explanation
Indices: 222494--222574 Score: 76
Period size: 16 Copynumber: 5.3 Consensus size: 15
222484 CACATTTCAT
222494 AAAAATTTAAATTTA
1 AAAAATTTAAATTTA
*
222509 AAAATATTTAAAATTA
1 AAAA-ATTTAAATTTA
* *
222525 AAAAA-ATAAATTCA
1 AAAAATTTAAATTTA
*
222539 ATGAAA-TTAAATTTA
1 A-AAAATTTAAATTTA
*
222554 AAAAATTTTAAATCTA
1 AAAAA-TTTAAATTTA
222570 AAAAA
1 AAAAA
222575 AAAATTGAAA
Statistics
Matches: 53, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
14 10 0.19
15 16 0.30
16 27 0.51
ACGTcount: A:0.63, C:0.02, G:0.01, T:0.33
Consensus pattern (15 bp):
AAAAATTTAAATTTA
Found at i:222590 original size:18 final size:19
Alignment explanation
Indices: 222553--222590 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
222543 AATTAAATTT
* *
222553 AAAAAATTTTAAATCTAAA
1 AAAAAAATTGAAATCTAAA
222572 AAAAAAATTGAAATC-AAA
1 AAAAAAATTGAAATCTAAA
222590 A
1 A
222591 TGATTCAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.68, C:0.05, G:0.03, T:0.24
Consensus pattern (19 bp):
AAAAAAATTGAAATCTAAA
Found at i:222816 original size:33 final size:32
Alignment explanation
Indices: 222746--222816 Score: 99
Period size: 33 Copynumber: 2.2 Consensus size: 32
222736 GGGTCTTGAT
*
222746 ATATTTTCTTTTTGGTACACATATGATTTTGAT
1 ATATTTTCTTTTTGGTACACATATGATTTT-AC
222779 ATATTTTCTTTTTGGTACACATATATGATTTT-C
1 ATATTTTCTTTTTGGTACAC--ATATGATTTTAC
222812 ATATT
1 ATATT
222817 CAATAAGTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
33 25 0.71
35 10 0.29
ACGTcount: A:0.25, C:0.10, G:0.10, T:0.55
Consensus pattern (32 bp):
ATATTTTCTTTTTGGTACACATATGATTTTAC
Found at i:222954 original size:20 final size:21
Alignment explanation
Indices: 222916--222955 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
222906 AATTAATATA
*
222916 TTTTATCAGTTTAATTCAATT
1 TTTTATCAGTTGAATTCAATT
*
222937 TTTTATTAGTTGAA-TCAAT
1 TTTTATCAGTTGAATTCAAT
222956 ATCTTACTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.55
Consensus pattern (21 bp):
TTTTATCAGTTGAATTCAATT
Found at i:223425 original size:28 final size:28
Alignment explanation
Indices: 223366--223426 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
223356 TAACAATCTC
** *
223366 AAATTAAATTTAATTGATTTATATTATT
1 AAATTAAATTTAATAAATTTAAATTATT
223394 -AATTAATATTTAATAAATTTAAATT-TT
1 AAATTAA-ATTTAATAAATTTAAATTATT
223421 AAATTA
1 AAATTA
223427 TAAAATTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
27 8 0.29
28 20 0.71
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (28 bp):
AAATTAAATTTAATAAATTTAAATTATT
Found at i:223439 original size:16 final size:14
Alignment explanation
Indices: 223396--223442 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 14
223386 ATATTATTAA
223396 TTAATATTTAATAAAT
1 TTAA-ATTT-ATAAAT
223412 TTAAATTT-TAAAT
1 TTAAATTTATAAAT
223425 TATAAAATTTATAAAT
1 T-T-AAATTTATAAAT
223441 TT
1 TT
223443 TTTTCTTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
13 6 0.21
14 1 0.04
15 11 0.39
16 10 0.36
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
TTAAATTTATAAAT
Found at i:223899 original size:20 final size:19
Alignment explanation
Indices: 223874--223947 Score: 61
Period size: 19 Copynumber: 4.1 Consensus size: 19
223864 TTACTTTTTA
223874 TTTATTTTATATTAATATTT
1 TTTATTTTATATTAA-ATTT
223894 TTTA--TTATA--AAATTT
1 TTTATTTTATATTAAATTT
*
223909 TTTATTTTAT-TTAAAATAT
1 TTTATTTTATATT-AAATTT
*
223928 TATATATTTATA-TAAATTT
1 TTTAT-TTTATATTAAATTT
223947 T
1 T
223948 GATATATTAA
Statistics
Matches: 44, Mismatches: 3, Indels: 15
0.71 0.05 0.24
Matches are distributed among these distances:
15 8 0.18
16 2 0.05
17 4 0.09
18 5 0.11
19 15 0.34
20 10 0.23
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
TTTATTTTATATTAAATTT
Found at i:223935 original size:21 final size:22
Alignment explanation
Indices: 223882--223943 Score: 62
Period size: 20 Copynumber: 3.0 Consensus size: 22
223872 TATTTATTTT
*
223882 ATATTAATATTTTTTATTATAAA
1 ATATT-ATATATTTTATTATAAA
*
223905 AT-TT-TTTATTTTATT-TAAA
1 ATATTATATATTTTATTATAAA
223924 ATATTATATA-TTTA-TATAAA
1 ATATTATATATTTTATTATAAA
223944 TTTTGATATA
Statistics
Matches: 33, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
19 7 0.21
20 19 0.58
21 3 0.09
22 2 0.06
23 2 0.06
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
ATATTATATATTTTATTATAAA
Found at i:223987 original size:32 final size:33
Alignment explanation
Indices: 223919--224005 Score: 95
Period size: 32 Copynumber: 2.6 Consensus size: 33
223909 TTTATTTTAT
* * *
223919 TTAAAATATTATATATTTATATAAATTTTGATATA
1 TTAATATATT-TATA-TTATATAAATTTTAAAATA
223954 TTAATA-ATTTATATTATATAAATTTTAAAATA
1 TTAATATATTTATATTATATAAATTTTAAAATA
** *
223986 TTTTTATGTTTATATTATAT
1 TTAATATATTTATATTATAT
224006 TTATTTATAT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
32 21 0.47
33 16 0.36
34 3 0.07
35 5 0.11
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (33 bp):
TTAATATATTTATATTATATAAATTTTAAAATA
Found at i:224008 original size:28 final size:27
Alignment explanation
Indices: 223977--224054 Score: 65
Period size: 28 Copynumber: 2.9 Consensus size: 27
223967 TTATATAAAT
223977 TTTAAAATATTTTTAT-GTTTATATTATA
1 TTTAAAATATTTTTATAG--TATATTATA
** *
224005 TTTATTTATATTTTTATAGTATGTTATA
1 TTTA-AAATATTTTTATAGTATATTATA
224033 TTTAATAAT-TTTTTA-A-TATATT
1 TTTAA-AATATTTTTATAGTATATT
224055 TAAATATTGT
Statistics
Matches: 41, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
25 5 0.12
26 1 0.02
27 6 0.15
28 18 0.44
29 10 0.24
30 1 0.02
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (27 bp):
TTTAAAATATTTTTATAGTATATTATA
Found at i:225147 original size:17 final size:16
Alignment explanation
Indices: 225125--225178 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 16
225115 ATTCGTTTAT
225125 ATATTTTTATTATGTTC
1 ATATTTTTATTAT-TTC
* *
225142 ATATTTTTTTTATATTT
1 ATATTTTTATTAT-TTC
225159 ATATTTTATAATTATTTC
1 ATATTTT-T-ATTATTTC
225177 AT
1 AT
225179 GTTTAAAATT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
17 21 0.70
18 5 0.17
19 4 0.13
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.67
Consensus pattern (16 bp):
ATATTTTTATTATTTC
Found at i:225609 original size:13 final size:13
Alignment explanation
Indices: 225593--225633 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
225583 TTATTTATTT
225593 TTTAAATTATATA
1 TTTAAATTATATA
225606 TTTAAA--ATA-A
1 TTTAAATTATATA
*
225616 TTTAAATTTTATA
1 TTTAAATTATATA
225629 TTTAA
1 TTTAA
225634 TTTGTTAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
10 7 0.29
11 3 0.12
12 2 0.08
13 12 0.50
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TTTAAATTATATA
Found at i:226354 original size:41 final size:40
Alignment explanation
Indices: 226266--226354 Score: 110
Period size: 40 Copynumber: 2.2 Consensus size: 40
226256 TAAATTTGAA
*
226266 TTAAAATTTTATAAACATATTTAAAAAATTATTTAATACAT
1 TTAAAA-TTTATAAACAAATTTAAAAAATTATTTAATACAT
* *
226307 TT-AAATTTATAATCAAATATTAAAAAATTATCTTAATA-TT
1 TTAAAATTTATAAACAAAT-TTAAAAAATTAT-TTAATACAT
226347 TTAAAATT
1 TTAAAATT
226355 AAATTTAAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
39 11 0.26
40 18 0.43
41 13 0.31
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (40 bp):
TTAAAATTTATAAACAAATTTAAAAAATTATTTAATACAT
Found at i:226472 original size:15 final size:15
Alignment explanation
Indices: 226436--226474 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
226426 AATTTTATAT
226436 TATAATTTTATTTAA
1 TATAATTTTATTTAA
* *
226451 AAT-ATTTTATTTTA
1 TATAATTTTATTTAA
226465 TATAATTTTA
1 TATAATTTTA
226475 AAACATGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TATAATTTTATTTAA
Found at i:227482 original size:7 final size:7
Alignment explanation
Indices: 227478--227509 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
227468 TTCCTTTTTC
227478 TTTTTAT
1 TTTTTAT
227485 TTTTTAT
1 TTTTTAT
227492 TTTTTAT
1 TTTTTAT
*
227499 ATTTTAT
1 TTTTTAT
227506 TTTT
1 TTTT
227510 GGGTACATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (7 bp):
TTTTTAT
Found at i:227939 original size:11 final size:11
Alignment explanation
Indices: 227923--227947 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
227913 TTTAATAGGT
227923 AAAAAATTAAA
1 AAAAAATTAAA
227934 AAAAAATTAAA
1 AAAAAATTAAA
227945 AAA
1 AAA
227948 TATTTTATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (11 bp):
AAAAAATTAAA
Found at i:228706 original size:2 final size:2
Alignment explanation
Indices: 228699--228733 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
228689 CAACTATCCA
228699 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
228734 ATATATATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:228738 original size:2 final size:2
Alignment explanation
Indices: 228733--228772 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
228723 TCTCTCTCTC
228733 TA TA TA TA TA 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 TA TA TA TA TA
228773 CACACACATT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:229094 original size:22 final size:20
Alignment explanation
Indices: 229059--229135 Score: 59
Period size: 22 Copynumber: 3.6 Consensus size: 20
229049 TATTAAAATA
*
229059 TTTTTTAAAGAGATTACTCAT
1 TTTTTTAAAAAGATTA-TCAT
229080 TTTTTTAAGAAAGATTAAT-ACT
1 TTTTTTAA-AAAGATT-ATCA-T
*
229102 TTTTTTAAAAA-ATCATCGAT
1 TTTTTTAAAAAGATTATC-AT
*
229122 TTATTTAAGAAAGA
1 TTTTTTAA-AAAGA
229136 ATAACCTTTT
Statistics
Matches: 46, Mismatches: 3, Indels: 13
0.74 0.05 0.21
Matches are distributed among these distances:
19 2 0.04
20 10 0.22
21 16 0.35
22 17 0.37
23 1 0.02
ACGTcount: A:0.40, C:0.06, G:0.09, T:0.44
Consensus pattern (20 bp):
TTTTTTAAAAAGATTATCAT
Found at i:229659 original size:23 final size:23
Alignment explanation
Indices: 229633--229688 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
229623 TAATTTATTT
*
229633 TAATATTTAA-AAATATTAAAAAA
1 TAATATTTAATAAATA-AAAAAAA
229656 TAAT-TTTATATAAATAAAAAAAA
1 TAATATTTA-ATAAATAAAAAAAA
229679 TAA-ATTTAAT
1 TAATATTTAAT
229689 TAAACCGATA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
22 6 0.21
23 18 0.62
24 5 0.17
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (23 bp):
TAATATTTAATAAATAAAAAAAA
Found at i:229972 original size:18 final size:18
Alignment explanation
Indices: 229935--229971 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
229925 AATTCTGTTC
*
229935 TTATTTATTTATTTTATT
1 TTATATATTTATTTTATT
229953 TTATATATTTA-TTTATT
1 TTATATATTTATTTTATT
229970 TT
1 TT
229972 TCCTGCAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (18 bp):
TTATATATTTATTTTATT
Found at i:230524 original size:21 final size:19
Alignment explanation
Indices: 230498--230546 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 19
230488 TTTGATTTAT
230498 ATTTAATTATTTTAAATATAA
1 ATTTAATTA-TTTAAAT-TAA
230519 ATTTAATTATTTAAATTAA
1 ATTTAATTATTTAAATTAA
*
230538 ATTAAATTA
1 ATTTAATTA
230547 AATTATTATT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 11 0.41
20 7 0.26
21 9 0.33
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
ATTTAATTATTTAAATTAA
Found at i:230537 original size:5 final size:5
Alignment explanation
Indices: 230509--230551 Score: 52
Period size: 5 Copynumber: 8.6 Consensus size: 5
230499 TTTAATTATT
* *
230509 TTAAA TATAAA TTTAA TT-AT TTAAA TTAAA TTAAA TTAAA TTA
1 TTAAA T-TAAA TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA TTA
230552 TTATTTATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
4 3 0.09
5 25 0.76
6 5 0.15
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (5 bp):
TTAAA
Found at i:230574 original size:12 final size:13
Alignment explanation
Indices: 230557--230618 Score: 55
Period size: 12 Copynumber: 5.2 Consensus size: 13
230547 AATTATTATT
230557 TATTTAATA-AAA
1 TATTTAATATAAA
* *
230569 TATTTATTATTAA
1 TATTTAATATAAA
230582 -ATTTAATTATAAA
1 TATTTAA-TATAAA
230595 T-TTT-ATATAAA
1 TATTTAATATAAA
230606 TA-TTAATA-AAA
1 TATTTAATATAAA
230617 TA
1 TA
230619 ATAATTTATT
Statistics
Matches: 41, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
11 14 0.34
12 17 0.41
13 10 0.24
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TATTTAATATAAA
Found at i:231257 original size:20 final size:22
Alignment explanation
Indices: 231215--231258 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
231205 TCAATTTAAT
231215 AAACATAATATATTAAATGTAAA
1 AAACATAATATATTAAA-GTAAA
*
231238 AAAC-TAATATTTTAAA-TAAA
1 AAACATAATATATTAAAGTAAA
231258 A
1 A
231259 TAAATTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 5 0.25
22 11 0.55
23 4 0.20
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (22 bp):
AAACATAATATATTAAAGTAAA
Found at i:231382 original size:3 final size:3
Alignment explanation
Indices: 231374--231399 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
231364 TTCACAAAAA
231374 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
231400 CTACTACAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:232147 original size:20 final size:20
Alignment explanation
Indices: 232082--232147 Score: 52
Period size: 20 Copynumber: 3.5 Consensus size: 20
232072 TATAAAATAA
232082 AATATAATATAAAAATATTTT
1 AATATAATATAAAAA-ATTTT
* **
232103 AA-AT--TTTTTAAAA-TTT
1 AATATAATATAAAAAATTTT
232119 -ATATAAATATAAAAAATTTT
1 AATAT-AATATAAAAAATTTT
232139 AATATAATA
1 AATATAATA
232148 AAATATATAA
Statistics
Matches: 33, Mismatches: 6, Indels: 13
0.63 0.12 0.25
Matches are distributed among these distances:
15 1 0.03
16 5 0.15
17 1 0.03
18 5 0.15
19 6 0.18
20 9 0.27
21 6 0.18
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
AATATAATATAAAAAATTTT
Found at i:232148 original size:18 final size:18
Alignment explanation
Indices: 232127--232179 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
232117 TTATATAAAT
* *
232127 ATAAAAAATTTTAATATA
1 ATAAAAAATATAAATATA
* *
232145 ATAAAATATATAAATATT
1 ATAAAAAATATAAATATA
*
232163 ATAAAAATAAATAAATA
1 ATAAAAA-ATATAAATA
232180 GCTATTGTCC
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
18 20 0.71
19 8 0.29
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
ATAAAAAATATAAATATA
Found at i:238273 original size:17 final size:17
Alignment explanation
Indices: 238251--238299 Score: 50
Period size: 17 Copynumber: 3.1 Consensus size: 17
238241 AGTAATATCG
238251 ATTTAATTAATAAAATT
1 ATTTAATTAATAAAATT
**
238268 ATTTAAAAAATAAAA-T
1 ATTTAATTAATAAAATT
*
238284 A--AAATTAATAAAATT
1 ATTTAATTAATAAAATT
238299 A
1 A
238300 AAAAATTATA
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
14 9 0.35
15 2 0.08
16 2 0.08
17 13 0.50
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
ATTTAATTAATAAAATT
Found at i:239372 original size:15 final size:13
Alignment explanation
Indices: 239352--239387 Score: 54
Period size: 15 Copynumber: 2.6 Consensus size: 13
239342 AATTATAAAT
239352 ATAATAAATATTA
1 ATAATAAATATTA
239365 TCATAATAAATATTA
1 --ATAATAAATATTA
239380 ATAATAAA
1 ATAATAAA
239388 AAATTAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 8 0.38
15 13 0.62
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (13 bp):
ATAATAAATATTA
Found at i:239668 original size:21 final size:22
Alignment explanation
Indices: 239631--239678 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 22
239621 AAAAATATAT
* *
239631 TATTTTTAATATTTTAATTAAA
1 TATTTTTAATATATTAAATAAA
239653 TATTTTTAA-ATATTAAATAAA
1 TATTTTTAATATATTAAATAAA
239674 T-TTTT
1 TATTTT
239679 ACACTTAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 4 0.17
21 11 0.46
22 9 0.38
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
TATTTTTAATATATTAAATAAA
Found at i:239911 original size:22 final size:20
Alignment explanation
Indices: 239876--239917 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 20
239866 CAAGAATTGA
239876 TAATTTATTTAATCAAATTT
1 TAATTTATTTAATCAAATTT
239896 TAATTTATATTAAATCAAATTT
1 TAATTTAT-TT-AATCAAATTT
239918 AAATAAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 8 0.40
21 2 0.10
22 10 0.50
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (20 bp):
TAATTTATTTAATCAAATTT
Found at i:239929 original size:22 final size:22
Alignment explanation
Indices: 239886--239929 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
239876 TAATTTATTT
* ** *
239886 AATCAAATTTTAATTTATATTA
1 AATCAAATTTAAATAAAAATTA
239908 AATCAAATTTAAATAAAAATTA
1 AATCAAATTTAAATAAAAATTA
239930 TGATAATTAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.41
Consensus pattern (22 bp):
AATCAAATTTAAATAAAAATTA
Found at i:240614 original size:13 final size:13
Alignment explanation
Indices: 240596--240621 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
240586 ATGATGTAAG
240596 CAAAATAAATAAA
1 CAAAATAAATAAA
240609 CAAAATAAATAAA
1 CAAAATAAATAAA
240622 TAATGTAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.08, G:0.00, T:0.15
Consensus pattern (13 bp):
CAAAATAAATAAA
Found at i:241543 original size:15 final size:15
Alignment explanation
Indices: 241519--241553 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
241509 AACTTGAGCA
241519 TAAA-TAATTAAATT
1 TAAAGTAATTAAATT
241533 TAAAGTAATTAAATT
1 TAAAGTAATTAAATT
241548 TAAAGT
1 TAAAGT
241554 CGGGGATGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 4 0.20
15 16 0.80
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.40
Consensus pattern (15 bp):
TAAAGTAATTAAATT
Found at i:243601 original size:19 final size:18
Alignment explanation
Indices: 243551--243603 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 18
243541 TATAACTACT
*
243551 TTTTATATATTTTAATTAG
1 TTTTATTTATTTT-ATTAG
243570 TGTTT-TTTAATTTTATTAG
1 T-TTTATTT-ATTTTATTAG
243589 ATTTTATTTATTTTA
1 -TTTTATTTATTTTA
243604 ACTGATAGAT
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (18 bp):
TTTTATTTATTTTATTAG
Found at i:246757 original size:19 final size:19
Alignment explanation
Indices: 246733--246770 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
246723 GGCAAACGGG
*
246733 AAACTTTTGGCACGTGCAA
1 AAACTTTTCGCACGTGCAA
246752 AAACTTTTCGCACGTGCAA
1 AAACTTTTCGCACGTGCAA
246771 GAGATGTTCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (19 bp):
AAACTTTTCGCACGTGCAA
Found at i:246928 original size:18 final size:18
Alignment explanation
Indices: 246897--246938 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
246887 GATTTAAGAT
246897 TATTAATTTAATTGATTTA
1 TATT-ATTTAATTGATTTA
246916 -ATTATTTAGATTGATTTA
1 TATTATTTA-ATTGATTTA
246934 TATTA
1 TATTA
246939 AAAGTTTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
17 5 0.24
18 12 0.57
19 4 0.19
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.57
Consensus pattern (18 bp):
TATTATTTAATTGATTTA
Found at i:246983 original size:16 final size:16
Alignment explanation
Indices: 246946--247001 Score: 62
Period size: 16 Copynumber: 3.6 Consensus size: 16
246936 TTAAAAGTTT
246946 AATA-TTAAATATAGTA
1 AATATTTAAATATA-TA
246962 AATATTTAAATATATA
1 AATATTTAAATATATA
** *
246978 TTTATTTAAATGTAT-
1 AATATTTAAATATATA
246993 AATATTTAA
1 AATATTTAA
247002 TAAAAATTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
15 7 0.21
16 18 0.53
17 9 0.26
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (16 bp):
AATATTTAAATATATA
Found at i:248374 original size:14 final size:13
Alignment explanation
Indices: 248348--248383 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
248338 TCAAACATGC
*
248348 TTAATTTTATTTT
1 TTAAATTTATTTT
248361 TTAAATTTATTTT
1 TTAAATTTATTTT
248374 TTAAAATTTA
1 TT-AAATTTA
248384 ATATTTTTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 14 0.67
14 7 0.33
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (13 bp):
TTAAATTTATTTT
Found at i:248383 original size:20 final size:20
Alignment explanation
Indices: 248360--248398 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
248350 AATTTTATTT
*
248360 TTTAA-ATTTATTTTTTAAAA
1 TTTAATATTT-TTGTTTAAAA
248380 TTTAATATTTTTGTTTAAA
1 TTTAATATTTTTGTTTAAA
248399 TTTTTTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (20 bp):
TTTAATATTTTTGTTTAAAA
Found at i:248718 original size:6 final size:6
Alignment explanation
Indices: 248708--248742 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
248698 ATAAAATGTA
* *
248708 AAAAAA AAAAAG AAAAGG AAAAAG AAAAAG AAAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAA
248743 AACCCAAGGT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:259022 original size:2 final size:2
Alignment explanation
Indices: 259017--259041 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
259007 TTTTTTCCTT
259017 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 T
259042 TAATTTTCGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:259306 original size:21 final size:20
Alignment explanation
Indices: 259282--259328 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 20
259272 ATTTAATCGA
259282 TTAATATAATATATTTAGTT-T
1 TTAAT-TAA-ATATTTAGTTAT
*
259303 TTAATTAAATATTTATTTAT
1 TTAATTAAATATTTAGTTAT
259323 TTAATT
1 TTAATT
259329 TATTTAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 9 0.38
20 10 0.42
21 5 0.21
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (20 bp):
TTAATTAAATATTTAGTTAT
Found at i:259402 original size:19 final size:19
Alignment explanation
Indices: 259364--259414 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
259354 ATAAATTTAT
* *
259364 TTAAATTA-ATTTACTTAA
1 TTAAATTATATTAAATTAA
*
259382 TTAAATTTTATTAAATTAA
1 TTAAATTATATTAAATTAA
259401 TTAAATTATATTAA
1 TTAAATTATATTAA
259415 CTAAATAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
18 7 0.25
19 21 0.75
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (19 bp):
TTAAATTATATTAAATTAA
Found at i:259408 original size:14 final size:14
Alignment explanation
Indices: 259343--259424 Score: 52
Period size: 14 Copynumber: 6.3 Consensus size: 14
259333 TAAAAATAAA
*
259343 AAATTAATCAAA-T
1 AAATTAATTAAATT
*
259356 AAATTTATTTAAATT
1 AAA-TTAATTAAATT
* *
259371 AATTTACTT-AATT
1 AAATTAATTAAATT
259384 AAATT--TT--ATT
1 AAATTAATTAAATT
259394 AAATTAATTAAATT
1 AAATTAATTAAATT
* *
259408 ATATTAACTAAA-T
1 AAATTAATTAAATT
259421 AAAT
1 AAAT
259425 AAAAATAAAT
Statistics
Matches: 55, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
10 8 0.15
11 2 0.04
12 2 0.04
13 15 0.27
14 25 0.45
15 3 0.05
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (14 bp):
AAATTAATTAAATT
Found at i:259589 original size:2 final size:2
Alignment explanation
Indices: 259582--259617 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
259572 TTTGAAATGA
259582 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
259618 TTGATTAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:261721 original size:13 final size:13
Alignment explanation
Indices: 261703--261798 Score: 56
Period size: 13 Copynumber: 7.4 Consensus size: 13
261693 TTATTCGAAT
261703 TTAAATATAAATA
1 TTAAATATAAATA
261716 TTAAATATAAATA
1 TTAAATATAAATA
* * * *
261729 TGATATATTTAATT
1 TTAAATA-TAAATA
261743 TTAAA-A-AATTATA
1 TTAAATATAA--ATA
** **
261756 TTTTATATTTATA
1 TTAAATATAAATA
261769 TTTAAATAT--ATA
1 -TTAAATATAAATA
261781 TTAAATATAAATA
1 TTAAATATAAATA
261794 TTAAA
1 TTAAA
261799 AAAATAAAAA
Statistics
Matches: 61, Mismatches: 14, Indels: 16
0.67 0.15 0.18
Matches are distributed among these distances:
11 9 0.15
12 3 0.05
13 35 0.57
14 14 0.23
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (13 bp):
TTAAATATAAATA
Found at i:262927 original size:21 final size:22
Alignment explanation
Indices: 262883--262953 Score: 92
Period size: 22 Copynumber: 3.2 Consensus size: 22
262873 AATATAATAT
*
262883 TTTTATTTAAATTAATTTAAAA
1 TTTTATTTAAATTAATTAAAAA
262905 TTATTA-TTAAATTAA-TAAAAA
1 TT-TTATTTAAATTAATTAAAAA
262926 TTTTATTTAAATTTAATTATAAAA
1 TTTTATTTAAA-TTAATTA-AAAA
262950 TTTT
1 TTTT
262954 TTATCTTAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
20 3 0.07
21 12 0.28
22 15 0.35
23 5 0.12
24 8 0.19
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
TTTTATTTAAATTAATTAAAAA
Found at i:262969 original size:26 final size:25
Alignment explanation
Indices: 262910--262970 Score: 70
Period size: 26 Copynumber: 2.4 Consensus size: 25
262900 TAAAATTATT
262910 ATTAAATTAATAAAAATTTTATTTAA
1 ATTAAATT-ATAAAAATTTTATTTAA
* *
262936 ATTTAATTATAAAATTTTTTATCTTAA
1 ATTAAATTATAAAA-ATTTTAT-TTAA
262963 A-TAAATTA
1 ATTAAATTA
262971 GCGTATAAAG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
25 6 0.20
26 19 0.63
27 5 0.17
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (25 bp):
ATTAAATTATAAAAATTTTATTTAA
Found at i:263714 original size:18 final size:18
Alignment explanation
Indices: 263688--263723 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
263678 TAAAATTAAA
*
263688 TTATTTAATTTTATATAT
1 TTATATAATTTTATATAT
*
263706 TTATATAATTTTTTATAT
1 TTATATAATTTTATATAT
263724 GATATATATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TTATATAATTTTATATAT
Found at i:263729 original size:19 final size:18
Alignment explanation
Indices: 263693--263731 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
263683 TTAAATTATT
*
263693 TAATTTTATATATTTATA
1 TAATTTTATATATATATA
*
263711 TAATTTTTTATATGATATA
1 TAATTTTATATAT-ATATA
263730 TA
1 TA
263732 TTTATTTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (18 bp):
TAATTTTATATATATATA
Found at i:265146 original size:21 final size:21
Alignment explanation
Indices: 265122--265223 Score: 116
Period size: 23 Copynumber: 4.7 Consensus size: 21
265112 AAAAATTTCA
265122 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
265143 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
*
265164 AATGTATATCGATACATTTGTGG
1 AATG--TATCGATACATTTGTAG
* *
265187 AATGTATATCGATACA-TTCTACA
1 AATG--TATCGATACATTTGTA-G
265210 AATGTATCGATACA
1 AATGTATCGATACA
265224 GGGTCCCAAC
Statistics
Matches: 74, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
21 34 0.46
22 3 0.04
23 37 0.50
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:265177 original size:23 final size:23
Alignment explanation
Indices: 265126--265204 Score: 135
Period size: 23 Copynumber: 3.5 Consensus size: 23
265116 ATTTCAAATG
*
265126 TATCGATACATTTGTAGAATG--
1 TATCGATACATTTGTGGAATGTA
265147 TATCGATACATTTGTGGAATGTA
1 TATCGATACATTTGTGGAATGTA
265170 TATCGATACATTTGTGGAATGTA
1 TATCGATACATTTGTGGAATGTA
265193 TATCGATACATT
1 TATCGATACATT
265205 CTACAAATGT
Statistics
Matches: 55, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
21 20 0.36
23 35 0.64
ACGTcount: A:0.32, C:0.10, G:0.19, T:0.39
Consensus pattern (23 bp):
TATCGATACATTTGTGGAATGTA
Found at i:265218 original size:44 final size:42
Alignment explanation
Indices: 265120--265223 Score: 120
Period size: 44 Copynumber: 2.4 Consensus size: 42
265110 AAAAAAATTT
*
265120 CAAATGTATCGATACATTTGTAGAATGTATCGATACATTTGT
1 CAAATGTATCGATACATTTGTAGAATGTATCGATACATTTGA
** *
265162 GGAATGTATATCGATACATTTGTGGAATGTATATCGATACATTCT-A
1 CAAATG--TATCGATACATTTGTAGAATG--TATCGATACATT-TGA
265208 CAAATGTATCGATACA
1 CAAATGTATCGATACA
265224 GGGTCCCAAC
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
42 4 0.08
44 30 0.59
46 16 0.31
47 1 0.02
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.36
Consensus pattern (42 bp):
CAAATGTATCGATACATTTGTAGAATGTATCGATACATTTGA
Found at i:265285 original size:19 final size:19
Alignment explanation
Indices: 265261--265328 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
265251 AATTCAACAA
265261 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
265280 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
265295 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
265312 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
265329 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:265300 original size:13 final size:13
Alignment explanation
Indices: 265282--265306 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
265272 ACATAAGTTT
265282 TGTATCGATACAA
1 TGTATCGATACAA
265295 TGTATCGATACA
1 TGTATCGATACA
265307 TAAGTATTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Done.