Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D04
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: 52479919
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 336953 characters in sequence are not A, C, G, or T
File 146 of 173
Found at i:44247247 original size:11 final size:11
Alignment explanation
Indices: 44247233--44247287 Score: 60
Period size: 11 Copynumber: 4.9 Consensus size: 11
44247223 TTAAATATGG
44247233 ATTTGAGAGAA
1 ATTTGAGAGAA
*
44247244 ATTTG-GAAGGA
1 ATTTGAG-AGAA
44247255 ATTTGAGAGTAA
1 ATTTGAGAG-AA
44247267 A-TTGAGAGGAA
1 ATTTGAGA-GAA
44247278 ATTTGAGAGA
1 ATTTGAGAGA
44247288 GGATTAGTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
10 1 0.03
11 26 0.70
12 10 0.27
ACGTcount: A:0.42, C:0.00, G:0.31, T:0.27
Consensus pattern (11 bp):
ATTTGAGAGAA
Found at i:44247280 original size:23 final size:22
Alignment explanation
Indices: 44247233--44247287 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
44247223 TTAAATATGG
44247233 ATTTGAGAGAAATTTGGAAGGA
1 ATTTGAGAGAAATTTGGAAGGA
44247255 ATTTGAGAGTAAA-TT-GAGAGGAA
1 ATTTGAGAG-AAATTTGGA-AGG-A
44247278 ATTTGAGAGA
1 ATTTGAGAGA
44247288 GGATTAGTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
21 2 0.07
22 15 0.50
23 13 0.43
ACGTcount: A:0.42, C:0.00, G:0.31, T:0.27
Consensus pattern (22 bp):
ATTTGAGAGAAATTTGGAAGGA
Found at i:44254096 original size:18 final size:17
Alignment explanation
Indices: 44254068--44254102 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
44254058 TCAGATGTAC
*
44254068 TTTATATTTTTTTTATT
1 TTTATATTTTTTATATT
44254085 TTTATGATTTTTTATATT
1 TTTAT-ATTTTTTATATT
44254103 ATGTTTTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.20, C:0.00, G:0.03, T:0.77
Consensus pattern (17 bp):
TTTATATTTTTTATATT
Found at i:44259231 original size:17 final size:17
Alignment explanation
Indices: 44259072--44259224 Score: 70
Period size: 17 Copynumber: 9.0 Consensus size: 17
44259062 TTATTATTAA
44259072 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
44259089 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
* ***
44259106 -TCTTAATATTAAATATTCTT
1 AT-ATAAT-TT-AATA-AAAT
*
44259126 ATATGAATTTACTAAAAT
1 ATAT-AATTTAATAAAAT
* * *
44259144 -CATAATAT-ATAATACT
1 ATATAATTTAATAA-AAT
* *
44259160 ATAAAATATAATTTAAAAT
1 ATATAATTTAA--TAAAAT
* *
44259179 A-ATTA-TT-AT-TAA-
1 ATATAATTTAATAAAAT
44259191 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
44259208 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
44259225 TCTTAATATT
Statistics
Matches: 98, Mismatches: 22, Indels: 32
0.64 0.14 0.21
Matches are distributed among these distances:
12 1 0.01
13 5 0.05
14 3 0.03
15 5 0.05
16 10 0.10
17 47 0.48
18 6 0.06
19 10 0.10
20 7 0.07
21 4 0.04
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:44259263 original size:119 final size:120
Alignment explanation
Indices: 44259052--44259514 Score: 798
Period size: 119 Copynumber: 3.9 Consensus size: 120
44259042 TTAATCATAT
*
44259052 TTTAACATAATTATTATTAAATATAATTTAAT-AAAATATATAATTTAATAAAATTCTTAATATT
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
44259116 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
66 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
44259171 TTTAAAATAATTATTATTAAATATAATTTAAT-AAAATATATAATTTAATAAAATTCTTAATATT
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
* *
44259235 AAATATTCTTATATGAATTTACTAAAATCATAATAGATAATAATATAAAATAT-A
66 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
*
44259289 TTTAAAATAATTATAATTAAATATAATTTAATAAAAATATATAA-TTAATAAAATTCTTAATATT
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
*
44259353 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTACAAAATATAA
66 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
*
44259408 TTT--AA-AACTATTATTAAATATAA-TTAGATAAAAATATATAATTTAATAAAATTCTTAATAT
1 TTTAAAATAATTATTATTAAATATAATTTA-ATAAAAATATATAATTTAATAAAATTCTTAATAT
*
44259469 TAAATATTCTTATATGAATTTACTAAAATTATAATATATAATACTA
65 TAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTA
44259515 AAATCATAAT
Statistics
Matches: 330, Mismatches: 10, Indels: 10
0.94 0.03 0.03
Matches are distributed among these distances:
115 3 0.01
116 30 0.09
117 66 0.20
118 102 0.31
119 129 0.39
ACGTcount: A:0.52, C:0.05, G:0.01, T:0.42
Consensus pattern (120 bp):
TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
Found at i:44259289 original size:41 final size:38
Alignment explanation
Indices: 44259199--44259511 Score: 89
Period size: 38 Copynumber: 8.1 Consensus size: 38
44259189 AAATATAATT
* * *
44259199 TAATA-AAATATATAATTTAATAAAATTCTTAAT-ATTA
1 TAATATAAATATATAATTTACTAAAA-TCATAATAATAA
***
44259236 -AATATTCTTATATGAATTTACTAAAATCATAATAGATAA
1 TAATATAAATATAT-AATTTACTAAAATCATAATA-ATAA
* *
44259275 TAATATAAA-ATAT-ATTTA-AAATAATTATAATTAAATATAA
1 TAATATAAATATATAATTTACTAA-AATCATAA-T--A-ATAA
* * * *
44259315 TTTAATAAAAATATATAA-TTAATAAAATTCTTAAT-ATTA
1 --TAATATAAATATATAATTTACTAAAA-TCATAATAATAA
***
44259354 -AATATTCTTATATGAATTTACTAAAATCATAATATATAA
1 TAATATAAATATAT-AATTTACTAAAATCATAATA-ATAA
* * *
44259393 TACTACAAA-ATATAATTTA--AAACTATTATTAA-ATATAA
1 TAATATAAATATATAATTTACTAAA--ATCA-TAATA-ATAA
* * * *
44259431 TTAGATAAAAATATATAATTTAATAAAATTCTTAAT-ATTA
1 -TA-ATATAAATATATAATTTACTAAAA-TCATAATAATAA
*** *
44259471 -AATATTCTTATATGAATTTACTAAAATTATAATATATAA
1 TAATATAAATATAT-AATTTACTAAAATCATAATA-ATAA
44259510 TA
1 TA
44259512 CTAAAATCAT
Statistics
Matches: 199, Mismatches: 43, Indels: 65
0.65 0.14 0.21
Matches are distributed among these distances:
36 18 0.09
37 44 0.22
38 47 0.24
39 25 0.13
40 22 0.11
41 14 0.07
42 9 0.05
43 13 0.07
44 7 0.04
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.41
Consensus pattern (38 bp):
TAATATAAATATATAATTTACTAAAATCATAATAATAA
Found at i:44259314 original size:16 final size:15
Alignment explanation
Indices: 44259285--44259336 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
44259275 TAATATAAAA
*
44259285 TATATTTAAAATAAT
1 TATAATTAAAATAAT
44259300 TATAATTAAATATAAT
1 TATAATTAAA-ATAAT
*
44259316 T-TAATAAAAAT-A-
1 TATAATTAAAATAAT
44259328 TATAATTAA
1 TATAATTAA
44259337 TAAAATTCTT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
12 1 0.03
13 7 0.22
14 2 0.06
15 16 0.50
16 6 0.19
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
TATAATTAAAATAAT
Found at i:44259511 original size:56 final size:55
Alignment explanation
Indices: 44259309--44259511 Score: 168
Period size: 55 Copynumber: 3.6 Consensus size: 55
44259299 TTATAATTAA
*
44259309 ATATAATTTAATAAAAATAT-ATA-ATTAATAAAATTCTTAATATTAAATATTCTT
1 ATATAATTTAATAAAATTATAATATA-TAATAAAATTCTTAATATTAAATATTCTT
* * * * *
44259363 ATATGAATTTACTAAAATCATAATATATAATACTACAAAAT-ATAAT-TTAAAACTATTATT
1 ATAT-AATTTAATAAAATTATAATATAT-A-A-TA-AAATTCTTAATATT-AAA-TATTCTT
44259423 AAATATAA-TTAGATAAAAATATATAAT-T-TAATAAAATTCTTAATATTAAATATTCTT
1 --ATATAATTTA-AT-AAAAT-TATAATATATAATAAAATTCTTAATATTAAATATTCTT
*
44259480 ATATGAATTTACTAAAATTATAATATATAATA
1 ATAT-AATTTAATAAAATTATAATATATAATA
44259512 CTAAAATCAT
Statistics
Matches: 117, Mismatches: 12, Indels: 38
0.70 0.07 0.23
Matches are distributed among these distances:
54 10 0.09
55 23 0.20
56 12 0.10
57 15 0.13
58 12 0.10
59 12 0.10
60 14 0.12
61 4 0.03
62 10 0.09
63 5 0.04
ACGTcount: A:0.52, C:0.05, G:0.01, T:0.41
Consensus pattern (55 bp):
ATATAATTTAATAAAATTATAATATATAATAAAATTCTTAATATTAAATATTCTT
Found at i:44259533 original size:23 final size:21
Alignment explanation
Indices: 44259489--44259529 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
44259479 TATATGAATT
*
44259489 TACTAAAATTATAATATATAA
1 TACTAAAATCATAATATATAA
44259510 TACTAAAATCATAATATATA
1 TACTAAAATCATAATATATA
44259530 TAATTTAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (21 bp):
TACTAAAATCATAATATATAA
Found at i:44262027 original size:14 final size:14
Alignment explanation
Indices: 44262008--44262036 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
44261998 CTTTTATAGT
44262008 TTAAAAGGTTTGTA
1 TTAAAAGGTTTGTA
44262022 TTAAAAGGTTTGTA
1 TTAAAAGGTTTGTA
44262036 T
1 T
44262037 CAATAACACT
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:0.34, C:0.00, G:0.21, T:0.45
Consensus pattern (14 bp):
TTAAAAGGTTTGTA
Found at i:44263415 original size:8 final size:9
Alignment explanation
Indices: 44263387--44263414 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
44263377 GTATTATCTC
44263387 AATTTTAAA
1 AATTTTAAA
44263396 AATTTTAAA
1 AATTTTAAA
44263405 AATTTTAAA
1 AATTTTAAA
44263414 A
1 A
44263415 TCAAGTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (9 bp):
AATTTTAAA
Found at i:44264561 original size:19 final size:19
Alignment explanation
Indices: 44264537--44264590 Score: 99
Period size: 19 Copynumber: 2.8 Consensus size: 19
44264527 AATCATATCT
44264537 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
44264556 TCTAAGATTACATATCATA
1 TCTAAGATTGCATATCATA
44264575 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
44264591 CTTGAAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.37
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:44264586 original size:38 final size:40
Alignment explanation
Indices: 44264514--44264590 Score: 113
Period size: 38 Copynumber: 1.9 Consensus size: 40
44264504 AAATTAAATC
44264514 TCTAAGATTACAAAATCATATCTTCTAAGATTGCATATCATA
1 TCTAAGATTACAAAATCATA--TTCTAAGATTGCATATCATA
*
44264556 TCTAAGATTAC-ATATCATA-TCTAAGATTGCATATC
1 TCTAAGATTACAAAATCATATTCTAAGATTGCATATC
44264591 CTTGAAAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
38 16 0.47
41 7 0.21
42 11 0.32
ACGTcount: A:0.39, C:0.17, G:0.08, T:0.36
Consensus pattern (40 bp):
TCTAAGATTACAAAATCATATTCTAAGATTGCATATCATA
Found at i:44264921 original size:43 final size:42
Alignment explanation
Indices: 44264874--44264978 Score: 140
Period size: 42 Copynumber: 2.5 Consensus size: 42
44264864 ATAAAAATAT
*
44264874 ATATATGTATGTGTATATA-CATAAAATTATAAACATATGAAAA
1 ATATATGTATGTATATATATCATAAAATTATAAA-ATAT-AAAA
**
44264917 ATATATGTATGTATATATATTTTAAAATTATAAAATATAAAA
1 ATATATGTATGTATATATATCATAAAATTATAAAATATAAAA
* *
44264959 ATATATGTAAGTATGTATAT
1 ATATATGTATGTATATATAT
44264979 ATACATATAT
Statistics
Matches: 56, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
42 22 0.39
43 22 0.39
44 12 0.21
ACGTcount: A:0.50, C:0.02, G:0.09, T:0.40
Consensus pattern (42 bp):
ATATATGTATGTATATATATCATAAAATTATAAAATATAAAA
Found at i:44264979 original size:2 final size:2
Alignment explanation
Indices: 44264974--44265037 Score: 51
Period size: 2 Copynumber: 33.0 Consensus size: 2
44264964 TGTAAGTATG
* * * * *
44264974 TA TA TA TA CA TA TA TA TG TA TA TA AA T- TA -A AA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
44265014 TA TA TA TG TA TA TA TA TG TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA
44265038 AAAATTATGA
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
1 2 0.04
2 45 0.96
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (2 bp):
TA
Found at i:44264996 original size:10 final size:10
Alignment explanation
Indices: 44264970--44265037 Score: 63
Period size: 10 Copynumber: 7.0 Consensus size: 10
44264960 TATATGTAAG
44264970 TATGTATATA
1 TATGTATATA
*
44264980 TA--CATATA
1 TATGTATATA
44264988 TATGTATATA
1 TATGTATATA
* *
44264998 AAT-TA-AAA
1 TATGTATATA
44265006 TATGTATATATA
1 TATG--TATATA
44265018 TATGTATATA
1 TATGTATATA
44265028 TATGTATATA
1 TATGTATATA
44265038 AAAATTATGA
Statistics
Matches: 46, Mismatches: 6, Indels: 12
0.72 0.09 0.19
Matches are distributed among these distances:
8 11 0.24
9 2 0.04
10 25 0.54
11 2 0.04
12 6 0.13
ACGTcount: A:0.46, C:0.01, G:0.07, T:0.46
Consensus pattern (10 bp):
TATGTATATA
Found at i:44265008 original size:18 final size:20
Alignment explanation
Indices: 44264987--44265039 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 20
44264977 ATATACATAT
44264987 ATATGTATATAAAT-TA-AA
1 ATATGTATATAAATGTATAA
*
44265005 ATATGTATATATATATGTATAT
1 ATATGTATATA-A-ATGTATAA
44265027 ATATGTATATAAA
1 ATATGTATATAAA
44265040 AATTATGAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
18 11 0.37
19 1 0.03
20 3 0.10
21 3 0.10
22 12 0.40
ACGTcount: A:0.49, C:0.00, G:0.08, T:0.43
Consensus pattern (20 bp):
ATATGTATATAAATGTATAA
Found at i:44265037 original size:12 final size:12
Alignment explanation
Indices: 44264959--44265030 Score: 57
Period size: 12 Copynumber: 6.3 Consensus size: 12
44264949 AAATATAAAA
44264959 ATATATGTAAGTAT
1 ATATATGT-A-TAT
* * *
44264973 GTATATATACAT
1 ATATATGTATAT
44264985 ATATATGTATAT
1 ATATATGTATAT
44264997 A-A-AT-TA-A-
1 ATATATGTATAT
44265004 A-ATATGTATAT
1 ATATATGTATAT
44265015 ATATATGTATAT
1 ATATATGTATAT
44265027 ATAT
1 ATAT
44265031 GTATATAAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 12
0.72 0.09 0.18
Matches are distributed among these distances:
7 2 0.04
8 3 0.06
9 4 0.09
10 3 0.06
11 2 0.04
12 26 0.55
13 1 0.02
14 6 0.13
ACGTcount: A:0.46, C:0.01, G:0.08, T:0.44
Consensus pattern (12 bp):
ATATATGTATAT
Found at i:44267044 original size:60 final size:60
Alignment explanation
Indices: 44266942--44267073 Score: 183
Period size: 60 Copynumber: 2.2 Consensus size: 60
44266932 TACACTAGTA
* ** *
44266942 GTCAGCCAACTATTAATAAATTTATCTTTTGGTCATTTAACTATGAAAAGTTATAAAATG
1 GTCACCCAACTATTAATAAATTTATCTTTTGGTCATCAAACTATGAAAAGTTACAAAATG
* * * * *
44267002 GTTATCCAACTATTAGTAAATTTCTTTTTTGGTCATCAAACTATGAAAAGTTACAAAATG
1 GTCACCCAACTATTAATAAATTTATCTTTTGGTCATCAAACTATGAAAAGTTACAAAATG
44267062 GTCACCCAACTA
1 GTCACCCAACTA
44267074 CTCAATTTTG
Statistics
Matches: 62, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
60 62 1.00
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.36
Consensus pattern (60 bp):
GTCACCCAACTATTAATAAATTTATCTTTTGGTCATCAAACTATGAAAAGTTACAAAATG
Found at i:44268672 original size:28 final size:29
Alignment explanation
Indices: 44268635--44268694 Score: 86
Period size: 28 Copynumber: 2.1 Consensus size: 29
44268625 TAATAGTGTT
44268635 TAAATTTATTATTATAATTTAAATTGTAA
1 TAAATTTATTATTATAATTTAAATTGTAA
* * *
44268664 TAAA-TTATTATTTTCATTTATATTGTAA
1 TAAATTTATTATTATAATTTAAATTGTAA
44268692 TAA
1 TAA
44268695 CAGATTTTGC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 24 0.86
29 4 0.14
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (29 bp):
TAAATTTATTATTATAATTTAAATTGTAA
Found at i:44270686 original size:98 final size:98
Alignment explanation
Indices: 44270565--44270759 Score: 354
Period size: 98 Copynumber: 2.0 Consensus size: 98
44270555 TTAAAAAAAA
* * *
44270565 TAAAGGAAATATTCCGAGTTTGGGATTTTAAAGGAATTGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACATATTGGGTGTGATTTC
44270630 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
*
44270663 TAAAGGAAATATTCTGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACATATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACATATTGGGTGTGATTTC
44270728 TTAAATCTTGGATAAGTGGATGTTCTTTTAAA
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAA
44270760 AGTTTTATTG
Statistics
Matches: 93, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
98 93 1.00
ACGTcount: A:0.29, C:0.10, G:0.24, T:0.37
Consensus pattern (98 bp):
TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACATATTGGGTGTGATTTC
TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
Found at i:44272912 original size:31 final size:31
Alignment explanation
Indices: 44272869--44272933 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
44272859 AGCCAGCTGG
*
44272869 TGACAAAAAAAGATAA-A-ATTGAATAGTTGGA
1 TGACAAAAAAAGA-AATATACT-AATAGTTGGA
*
44272900 TGACCAAAAAAGAAATATACTAATAGTTGGA
1 TGACAAAAAAAGAAATATACTAATAGTTGGA
44272931 TGA
1 TGA
44272934 TAACTAGATT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
30 2 0.07
31 26 0.87
32 2 0.07
ACGTcount: A:0.52, C:0.06, G:0.18, T:0.23
Consensus pattern (31 bp):
TGACAAAAAAAGAAATATACTAATAGTTGGA
Found at i:44275894 original size:12 final size:12
Alignment explanation
Indices: 44275847--44275905 Score: 52
Period size: 12 Copynumber: 4.9 Consensus size: 12
44275837 ACTTAATTAC
44275847 TTTAATATTAAA
1 TTTAATATTAAA
*
44275859 TTAAAT-TTAAAA
1 TTTAATATT-AAA
*
44275871 TTT-ATCTATAAA
1 TTTAATAT-TAAA
44275883 TATTAA-ATTAAA
1 T-TTAATATTAAA
44275895 TTTAATATTAA
1 TTTAATATTAA
44275906 GATAATCACT
Statistics
Matches: 38, Mismatches: 3, Indels: 12
0.72 0.06 0.23
Matches are distributed among these distances:
11 8 0.21
12 25 0.66
13 4 0.11
14 1 0.03
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (12 bp):
TTTAATATTAAA
Found at i:44281138 original size:42 final size:42
Alignment explanation
Indices: 44281076--44281158 Score: 112
Period size: 42 Copynumber: 2.0 Consensus size: 42
44281066 GATGGTTTTG
* * * *
44281076 TTTCCCATTTGGGATTTTTTGGGTATCTCAAGATTTCCTTTA
1 TTTCCCATTTGGGATATTTTGAGTATCCCAAGATTGCCTTTA
* *
44281118 TTTCCCGTTTGGGATATTTTGAGTATCCCAGGATTGCCTTT
1 TTTCCCATTTGGGATATTTTGAGTATCCCAAGATTGCCTTT
44281159 CTTGCCTGAG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.16, C:0.18, G:0.19, T:0.47
Consensus pattern (42 bp):
TTTCCCATTTGGGATATTTTGAGTATCCCAAGATTGCCTTTA
Found at i:44282036 original size:40 final size:40
Alignment explanation
Indices: 44281961--44282103 Score: 141
Period size: 40 Copynumber: 3.6 Consensus size: 40
44281951 AGCACACCAG
* * *
44281961 TTTGGCACCCAGTGTCTCATCAGA-TAATTCTAAGTAATAA
1 TTTGACACCCAGTGTCTCATC-GACTAATCCAAAGTAATAA
* * *
44282001 TTTGACACCTAGTGTCTCATCGACTAAACCGAAGT-A-AA
1 TTTGACACCCAGTGTCTCATCGACTAATCCAAAGTAATAA
* * * *
44282039 -TTGGCACCCAGTGCCTCATCGAATTAATCCAAAGTAGTAA
1 TTTGACACCCAGTGTCTCATCG-ACTAATCCAAAGTAATAA
*
44282079 ATTGACACCCAGTGTCTCATCGACT
1 TTTGACACCCAGTGTCTCATCGACT
44282104 CGAAGTCGAA
Statistics
Matches: 83, Mismatches: 15, Indels: 10
0.77 0.14 0.09
Matches are distributed among these distances:
37 18 0.22
38 12 0.14
39 3 0.04
40 31 0.37
41 19 0.23
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.28
Consensus pattern (40 bp):
TTTGACACCCAGTGTCTCATCGACTAATCCAAAGTAATAA
Found at i:44288820 original size:13 final size:13
Alignment explanation
Indices: 44288802--44288828 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
44288792 TTTCAGTTTA
44288802 ATTTAAACAATAT
1 ATTTAAACAATAT
44288815 ATTTAAACAATAT
1 ATTTAAACAATAT
44288828 A
1 A
44288829 GTTGTTTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (13 bp):
ATTTAAACAATAT
Found at i:44290400 original size:23 final size:23
Alignment explanation
Indices: 44290365--44290409 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
44290355 CCTTATTTAA
**
44290365 TTCAAATTGATTAT-AATATTATC
1 TTCAAATAAATTATCAA-ATTATC
44290388 TTCAAATAAATTATCAAATTAT
1 TTCAAATAAATTATCAAATTAT
44290410 AAAATGACAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 17 0.89
24 2 0.11
ACGTcount: A:0.44, C:0.09, G:0.02, T:0.44
Consensus pattern (23 bp):
TTCAAATAAATTATCAAATTATC
Found at i:44293688 original size:92 final size:90
Alignment explanation
Indices: 44293531--44293739 Score: 271
Period size: 92 Copynumber: 2.3 Consensus size: 90
44293521 TTGATTTTAG
* *
44293531 TAAATTCATATAAAAACATTTTATTATTAAGAATTTTATGAAATTATATATCACTATTAAATTAT
1 TAAATTCATATAAAAA-A-TTTATTATCAAGAATTTTATGAAATTATATATAACTATTAAATTAT
* *
44293596 ATTTAAT-ATTAATTATTTTAAATTGTA
64 ATGTAATAATT-ATTATTTTAAATTATA
*
44293623 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATT-TAATATTAATTATTAAATTA
1 TAAATTCATATAA-AAAATTTATTATCAAGAATTTTATGAAATTAT-ATA-TAACTATTAAATTA
44293687 TATGTAATAATTATTATTTTAAATTATA
63 TATGTAATAATTATTATTTTAAATTATA
*
44293715 CAAATTCATA-AAATATAATTTATTA
1 TAAATTCATATAAA-A-AATTTATTA
44293740 GTTATAATTA
Statistics
Matches: 105, Mismatches: 6, Indels: 12
0.85 0.05 0.10
Matches are distributed among these distances:
90 2 0.02
91 31 0.30
92 66 0.63
93 6 0.06
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.46
Consensus pattern (90 bp):
TAAATTCATATAAAAAATTTATTATCAAGAATTTTATGAAATTATATATAACTATTAAATTATAT
GTAATAATTATTATTTTAAATTATA
Found at i:44293702 original size:24 final size:25
Alignment explanation
Indices: 44293667--44293714 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
44293657 TTATGAAATT
44293667 TAATATTAATTA-TTAAATTATATG
1 TAATATTAATTATTTAAATTATATG
44293691 TAATAATT-ATTATTTTAAATTATA
1 TAAT-ATTAATTA-TTTAAATTATA
44293715 CAAATTCATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 8 0.38
25 3 0.14
26 10 0.48
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (25 bp):
TAATATTAATTATTTAAATTATATG
Found at i:44293868 original size:66 final size:63
Alignment explanation
Indices: 44293793--44294003 Score: 183
Period size: 66 Copynumber: 3.4 Consensus size: 63
44293783 AAATATATTT
44293793 AATATTAATTATTTCAAATTTTCATTTACAGTATCATATATTATGATTTGAGTAAATTCATATAA
1 AATATTAATTATTT-AAATTTT-ATTTACAGTATCATATATTATGATTTGAGTAAATT-ATATAA
44293858 G
63 G
* * * * **
44293859 AATATTAATTATTAAGAATTTTA-TTA-A--ATTATATATT-TTAATT-A-T-AA-TATAT-TT
1 AATATTAATTATTTA-AATTTTATTTACAGTATCATATATTATGATTTGAGTAAATTATATAAG
* *
44293913 AATAATAATTATGTT-AATTTATATTTTACAGTATCATATATTATGATTTGAGTAAATTTGTATA
1 AATATTAATTAT-TTAAATTT-TA-TTTACAGTATCATATATTATGATTTGAGTAAA-TTATATA
44293977 AG
62 AG
*
44293979 AATATTAATTATTAAGAATTTTATT
1 AATATTAATTATTTA-AATTTTATT
44294004 AAATTATATA
Statistics
Matches: 112, Mismatches: 16, Indels: 35
0.69 0.10 0.21
Matches are distributed among these distances:
53 5 0.04
54 13 0.12
55 5 0.04
56 4 0.04
57 3 0.03
58 1 0.01
59 10 0.09
60 8 0.07
61 10 0.09
62 1 0.01
63 3 0.03
64 3 0.03
65 9 0.08
66 32 0.29
67 5 0.04
ACGTcount: A:0.41, C:0.03, G:0.07, T:0.49
Consensus pattern (63 bp):
AATATTAATTATTTAAATTTTATTTACAGTATCATATATTATGATTTGAGTAAATTATATAAG
Found at i:44293897 original size:120 final size:120
Alignment explanation
Indices: 44293762--44294047 Score: 479
Period size: 120 Copynumber: 2.4 Consensus size: 120
44293752 TTAAATTATT
* * *
44293762 TTAAATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTCAAATTT-TCA-TTTACAG
1 TTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT--AATTTAT-ATTTTACAG
44293824 TATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTA
63 TATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTA
44293882 TTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTAT
1 TTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTAT
**
44293947 CATATATTATGATTTGAGTAAATTTGTATAAGAATATTAATTATTAAGAATTTTA
66 CATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTA
44294002 TTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
1 TTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
44294048 TAAATATGAT
Statistics
Matches: 158, Mismatches: 5, Indels: 6
0.93 0.03 0.04
Matches are distributed among these distances:
119 6 0.04
120 150 0.95
121 2 0.01
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (120 bp):
TTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTAT
CATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTA
Found at i:44293915 original size:15 final size:15
Alignment explanation
Indices: 44293880--44293931 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
44293870 TTAAGAATTT
*
44293880 TATTAAATTAT-ATA
1 TATTTAATTATAATA
44293894 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
44293908 TATTTAATAATAAT-
1 TATTTAATTATAATA
44293922 TATGTTAATT
1 TAT-TTAATT
44293932 TATATTTTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:44294030 original size:16 final size:16
Alignment explanation
Indices: 44294009--44294050 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
44293999 TTATTAAATT
*
44294009 ATATATTTTAATTATA
1 ATATATTTTAATAATA
44294025 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
44294040 AT-TATGTTTAA
1 ATATAT-TTTAA
44294051 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:44294035 original size:15 final size:15
Alignment explanation
Indices: 44294000--44294041 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
44293990 TTAAGAATTT
*
44294000 TATTAAATTAT-ATA
1 TATTTAATTATAATA
44294014 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
44294028 TATTTAATAATAAT
1 TATTTAATTATAAT
44294042 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:44294180 original size:18 final size:17
Alignment explanation
Indices: 44294152--44294186 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
44294142 AATTATAAGA
*
44294152 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
44294169 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
44294187 TTAATAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:44294276 original size:153 final size:156
Alignment explanation
Indices: 44293984--44294296 Score: 560
Period size: 153 Copynumber: 2.0 Consensus size: 156
44293974 ATAAGAATAT
*
44293984 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTT-ATAATAATTATGTTT
*
44294049 AAATATGATTAAATTATTTATTATTGATATTAATAATCTTATTAAAATTTAAATAACAATAACAA
65 AAATATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
44294114 TAATAATTTACCAAAACAAATTTATGC
130 TAATAATTTACCAAAACAAATTTATGC
44294141 TAATTA-TAAGAATTTTATTAAATTATATATTTTAATTAAAATATA-TT-TAATAATTATGTTTA
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTATAATAATTATGTTTA
*
44294203 AATATGATTAAATTATTTATTATTGATAATAATCATCTTATTAAAATTTAAATAACAATAACAAT
66 AATATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAAT
*
44294268 AATCATTTACCAAAACAAATTTATGC
131 AATAATTTACCAAAACAAATTTATGC
44294294 TAA
1 TAA
44294297 GGGTATTCTA
Statistics
Matches: 152, Mismatches: 4, Indels: 4
0.95 0.03 0.03
Matches are distributed among these distances:
153 106 0.70
155 2 0.01
156 38 0.25
157 6 0.04
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.44
Consensus pattern (156 bp):
TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTATAATAATTATGTTTA
AATATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAAT
AATAATTTACCAAAACAAATTTATGC
Found at i:44294427 original size:45 final size:41
Alignment explanation
Indices: 44294329--44294438 Score: 107
Period size: 45 Copynumber: 2.6 Consensus size: 41
44294319 TTTTCCATTA
44294329 TGCTATTACACCTCTATTCCATT-C-AACCAAACACAAGAT
1 TGCTATTACACCTCTATTCCATTACAAACCAAACACAAGAT
* * ***
44294368 TACTATTACGCCTCTATTCCATTACATTTAACCAAACAGTTGATT
1 TGCTATTACACCTCTATTCCATTACA---AACCAAACACAAGA-T
* *
44294413 TGCTATTACACCTCTAATCCAATACA
1 TGCTATTACACCTCTATTCCATTACA
44294439 CCTCTAATCC
Statistics
Matches: 56, Mismatches: 9, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
39 21 0.38
40 1 0.02
44 11 0.20
45 23 0.41
ACGTcount: A:0.34, C:0.28, G:0.05, T:0.33
Consensus pattern (41 bp):
TGCTATTACACCTCTATTCCATTACAAACCAAACACAAGAT
Found at i:44294440 original size:16 final size:16
Alignment explanation
Indices: 44294419--44294454 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
44294409 GATTTGCTAT
44294419 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
44294435 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
44294451 TACA
1 TACA
44294455 GCGAACCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.39, C:0.36, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:44296453 original size:35 final size:35
Alignment explanation
Indices: 44296424--44296492 Score: 102
Period size: 35 Copynumber: 2.0 Consensus size: 35
44296414 GTGTCTCACT
*
44296424 GAAGGGCCTATAAACCGTTTACACAGTGTCGCCTC
1 GAAGGACCTATAAACCGTTTACACAGTGTCGCCTC
* **
44296459 GAAGGACCTATAAATCGTTTACATGGTGTCGCCT
1 GAAGGACCTATAAACCGTTTACACAGTGTCGCCT
44296493 TAAAGGACAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.26, C:0.25, G:0.23, T:0.26
Consensus pattern (35 bp):
GAAGGACCTATAAACCGTTTACACAGTGTCGCCTC
Found at i:44296499 original size:35 final size:35
Alignment explanation
Indices: 44296425--44296500 Score: 98
Period size: 35 Copynumber: 2.2 Consensus size: 35
44296415 TGTCTCACTG
* *
44296425 AAGGGCCTATAAACCGTTTACACAGTGTCGCCTCG
1 AAGGACCTATAAACCGTTTACACAGTGTCGCCTCA
* ** *
44296460 AAGGACCTATAAATCGTTTACATGGTGTCGCCTTA
1 AAGGACCTATAAACCGTTTACACAGTGTCGCCTCA
44296495 AAGGAC
1 AAGGAC
44296501 AAGTCGATAT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.25
Consensus pattern (35 bp):
AAGGACCTATAAACCGTTTACACAGTGTCGCCTCA
Found at i:44298732 original size:44 final size:44
Alignment explanation
Indices: 44298669--44298787 Score: 186
Period size: 44 Copynumber: 2.7 Consensus size: 44
44298659 TCCCATGGAG
**
44298669 TCTTTCATCCATGGTCTTACTA-ATCATACCTAGCTGCCATAGCA
1 TCTTTCATTTATGGTCTTAC-ACATCATACCTAGCTGCCATAGCA
*
44298713 TCTTTCATTTATGGTCTTACACTTCATACCTAGCTGCCATAGCA
1 TCTTTCATTTATGGTCTTACACATCATACCTAGCTGCCATAGCA
*
44298757 TCTTTCATTTATGGTCTTACACTTCATACCT
1 TCTTTCATTTATGGTCTTACACATCATACCT
44298788 TACATCATTT
Statistics
Matches: 71, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
43 1 0.01
44 70 0.99
ACGTcount: A:0.23, C:0.28, G:0.10, T:0.39
Consensus pattern (44 bp):
TCTTTCATTTATGGTCTTACACATCATACCTAGCTGCCATAGCA
Found at i:44307848 original size:3 final size:3
Alignment explanation
Indices: 44307834--44307884 Score: 57
Period size: 3 Copynumber: 16.7 Consensus size: 3
44307824 AAGGGCCCAA
* * * *
44307834 ATT ATC ATT ATT ATT ATT ATT ACT ATT AAT ATT ATT ATT AAAT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT
44307880 ATT AT
1 ATT AT
44307885 CTTTTTTTAC
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
3 37 0.95
4 2 0.05
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (3 bp):
ATT
Found at i:44307855 original size:12 final size:12
Alignment explanation
Indices: 44307840--44307884 Score: 63
Period size: 12 Copynumber: 3.7 Consensus size: 12
44307830 CCAAATTATC
*
44307840 ATTATTATTATT
1 ATTATTATTAAT
*
44307852 ATTACTATTAAT
1 ATTATTATTAAT
44307864 ATTATTATTAAAT
1 ATTATTATT-AAT
44307877 ATTATTAT
1 ATTATTAT
44307885 CTTTTTTTAC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
12 18 0.62
13 11 0.38
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (12 bp):
ATTATTATTAAT
Found at i:44308668 original size:159 final size:158
Alignment explanation
Indices: 44308222--44308692 Score: 685
Period size: 155 Copynumber: 3.0 Consensus size: 158
44308212 TGATTTTATT
* *
44308222 AAAAAGAGAAAATTTAGATTTTAAAAATAAAAATATGTTTTTTAAGTCATTTTAAAGGAAAATTT
1 AAAAAGAGAAAATTTAGATTTTAAAAATAAAAATATGTTTTTTTAGTCATTTTAAAGGAAAGTTT
*
44308287 AAAAATTTAAAACAAAATTTTGA---TTTTTTTCAACTATTTCAATATAAAAGCTTTGATCTTTA
66 -AAAATTTAAAACAAATTTTTGATTTTTTTTTTCAACTATTTCAA-ATAAAAGCTTTGATCTTTA
44308349 AGAAAAGTAGTGATTTTTTT--AAGAAAAA
129 AGAAAAGTAGTGATTTTTTTAAAAGAAAAA
* * *
44308377 AAAAGGAGAAAATTTAAATTTTAAAAATAAAAATATG-TTTTTTAGTTATTTTAAAGGAAAGTTT
1 AAAAAGAGAAAATTTAGATTTTAAAAATAAAAATATGTTTTTTTAGTCATTTTAAAGGAAAGTTT
* *
44308441 AAAATTTTAAAAC-AATTTTT--TTTATTTTTTTCAACTATTTCAAAATAAAAGTTTTTATCTTT
66 AAAA-TTTAAAACAAATTTTTGATTT-TTTTTTTCAACTATTTC-AAATAAAAGCTTTGATCTTT
44308503 AAGAAAAGTAGTGATTATTTTTAAAAGAAAAA
128 AAGAAAAGTAGTGATT-TTTTTAAAAGAAAAA
* *
44308535 AAAAAGAGAAAGTTTAGATTTTAAAAATAAAAATATGTTTTTTTAGTCCTTTTAAAGGAAAGTTT
1 AAAAAGAGAAAATTTAGATTTTAAAAATAAAAATATGTTTTTTTAGTCATTTTAAAGGAAAGTTT
*
44308600 AAAATTTAAAACAAATTTTTGATTTTTTTTTTGAACTATTTCGAAAT-AAAGCTTTGATCTTTAA
66 AAAATTTAAAACAAATTTTTGATTTTTTTTTTCAACTATTTC-AAATAAAAGCTTTGATCTTTAA
* *
44308664 GAAAAGTATTGATTTTTTTTAAA-AAAAA
130 GAAAAGTAGTGATTTTTTTAAAAGAAAAA
44308692 A
1 A
44308693 CTTTGACTTT
Statistics
Matches: 284, Mismatches: 19, Indels: 24
0.87 0.06 0.07
Matches are distributed among these distances:
153 10 0.04
154 32 0.11
155 84 0.30
156 7 0.02
157 6 0.02
158 58 0.20
159 64 0.23
160 20 0.07
161 3 0.01
ACGTcount: A:0.45, C:0.04, G:0.10, T:0.41
Consensus pattern (158 bp):
AAAAAGAGAAAATTTAGATTTTAAAAATAAAAATATGTTTTTTTAGTCATTTTAAAGGAAAGTTT
AAAATTTAAAACAAATTTTTGATTTTTTTTTTCAACTATTTCAAATAAAAGCTTTGATCTTTAAG
AAAAGTAGTGATTTTTTTAAAAGAAAAA
Found at i:44312508 original size:33 final size:33
Alignment explanation
Indices: 44312433--44312535 Score: 111
Period size: 33 Copynumber: 3.1 Consensus size: 33
44312423 CAATGAACTT
* * * *
44312433 GAGCCGGGAGGAGTGGAGTACAGCGGTGGATAC
1 GAGCCGGAAGGAGCGGAGTACTGAGGTGGATAC
*
44312466 -AGGCTGGAAGGAGCGGAGTACTGAGGTGGATAC
1 GA-GCCGGAAGGAGCGGAGTACTGAGGTGGATAC
* *
44312499 GAGCCGGAAGGTA-CGGACTACTGAGGTGGATAT
1 GAGCCGGAAGG-AGCGGAGTACTGAGGTGGATAC
44312532 GAGC
1 GAGC
44312536 TACGATGACT
Statistics
Matches: 59, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
32 1 0.02
33 56 0.95
34 2 0.03
ACGTcount: A:0.26, C:0.15, G:0.45, T:0.15
Consensus pattern (33 bp):
GAGCCGGAAGGAGCGGAGTACTGAGGTGGATAC
Found at i:44315562 original size:60 final size:60
Alignment explanation
Indices: 44315478--44315592 Score: 176
Period size: 60 Copynumber: 1.9 Consensus size: 60
44315468 ATACTAAACT
** * *
44315478 AAACACACCAATTTATAACTTAATCCTAAATTACTAATAAATTAATTTTAAAATATTTAC
1 AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATATTTAC
* *
44315538 AAACACAAAAATTTGTAACATAATCCTAAATTACTAACGAATTAATTTTAAAATA
1 AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATA
44315593 ATTATAAAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
60 49 1.00
ACGTcount: A:0.50, C:0.14, G:0.02, T:0.34
Consensus pattern (60 bp):
AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATATTTAC
Found at i:44315671 original size:7 final size:7
Alignment explanation
Indices: 44315661--44315686 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
44315651 ACTAAACATA
44315661 AATAATT
1 AATAATT
44315668 AATAATT
1 AATAATT
44315675 AATAATT
1 AATAATT
44315682 AATAA
1 AATAA
44315687 CAAAAAATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (7 bp):
AATAATT
Found at i:44315783 original size:3 final size:3
Alignment explanation
Indices: 44315775--44315830 Score: 57
Period size: 3 Copynumber: 19.7 Consensus size: 3
44315765 CTTTCTTTCT
* *
44315775 TTC TTC TTC TTC TTC TTC TTC -TC TTC TTT TTT TTC TTC -TC TT- TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
44315820 TCTC TT- TTC TT
1 T-TC TTC TTC TT
44315831 TCTCTCTTCC
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
2 8 0.17
3 35 0.76
4 3 0.07
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (3 bp):
TTC
Found at i:44315799 original size:20 final size:18
Alignment explanation
Indices: 44315770--44315839 Score: 74
Period size: 19 Copynumber: 3.8 Consensus size: 18
44315760 TTTTTCTTTC
44315770 TTTCTTTCTTCTTCTTCT
1 TTTCTTTCTTCTTCTTCT
44315788 TCTTCTTCTCTTCTT-TT-T
1 T-TTCTT-TCTTCTTCTTCT
44315806 TTTCTTCTCTT-TTCTCTCT
1 TTTCTT-TCTTCTTCT-TCT
44315825 TTTCTTTCTCTCTTC
1 TTTCTTTCT-TCTTC
44315840 CGGTGGATGG
Statistics
Matches: 45, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
16 2 0.04
17 11 0.24
18 7 0.16
19 15 0.33
20 10 0.22
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (18 bp):
TTTCTTTCTTCTTCTTCT
Found at i:44322600 original size:33 final size:33
Alignment explanation
Indices: 44322549--44322617 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 33
44322539 TATCGAATCT
* * *
44322549 ACTTCCTCTAAAGCATACCTGTTAGTTTACTTC
1 ACTTCCCCCAAAGAATACCTGTTAGTTTACTTC
44322582 ACTTCCCCCAAAGAATACCTGTTAGTTTACTTC
1 ACTTCCCCCAAAGAATACCTGTTAGTTTACTTC
44322615 ACT
1 ACT
44322618 ATTTGCTAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.26, C:0.29, G:0.09, T:0.36
Consensus pattern (33 bp):
ACTTCCCCCAAAGAATACCTGTTAGTTTACTTC
Found at i:44323171 original size:26 final size:24
Alignment explanation
Indices: 44323112--44323160 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
44323102 ATAATAAATC
44323112 TCTCTCTCTCTAACCTATTATGAT
1 TCTCTCTCTCTAACCTATTATGAT
44323136 TCTCTCTCTCTAACCTATTATGAT
1 TCTCTCTCTCTAACCTATTATGAT
44323160 T
1 T
44323161 TGAGTACTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.20, C:0.29, G:0.04, T:0.47
Consensus pattern (24 bp):
TCTCTCTCTCTAACCTATTATGAT
Found at i:44323571 original size:2 final size:2
Alignment explanation
Indices: 44323564--44323595 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
44323554 ACTACAGCTG
44323564 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
44323596 ATATGTTCCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:44334521 original size:30 final size:30
Alignment explanation
Indices: 44334481--44334538 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
44334471 GACCATGCCA
44334481 GTCATAGCAAATTGGTACTTATGGTCTTAT
1 GTCATAGCAAATTGGTACTTATGGTCTTAT
*
44334511 GTCATGGCAAATTGGTACTTATGGTCTT
1 GTCATAGCAAATTGGTACTTATGGTCTT
44334539 GTACAAATGC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.24, C:0.14, G:0.22, T:0.40
Consensus pattern (30 bp):
GTCATAGCAAATTGGTACTTATGGTCTTAT
Found at i:44336612 original size:15 final size:15
Alignment explanation
Indices: 44336592--44336623 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
44336582 TCAAATCAAG
44336592 ATGTGAGAGCCTGAT
1 ATGTGAGAGCCTGAT
44336607 ATGTGAGAGCCTGAT
1 ATGTGAGAGCCTGAT
44336622 AT
1 AT
44336624 TCTCAAGACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.28, C:0.12, G:0.31, T:0.28
Consensus pattern (15 bp):
ATGTGAGAGCCTGAT
Found at i:44347248 original size:22 final size:21
Alignment explanation
Indices: 44347223--44347271 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
44347213 AAGAATGCCC
44347223 AACAACTAATCCTTACCAAAGG
1 AACAAC-AATCCTTACCAAAGG
* * *
44347245 AACAACCATGCTTACCTAAGG
1 AACAACAATCCTTACCAAAGG
44347266 AACAAC
1 AACAAC
44347272 CACGAAACAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 18 0.75
22 6 0.25
ACGTcount: A:0.45, C:0.29, G:0.10, T:0.16
Consensus pattern (21 bp):
AACAACAATCCTTACCAAAGG
Found at i:44347260 original size:21 final size:21
Alignment explanation
Indices: 44347234--44347273 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
44347224 ACAACTAATC
44347234 CTTACCAAAGGAACAACCATG
1 CTTACCAAAGGAACAACCATG
*
44347255 CTTACCTAAGGAACAACCA
1 CTTACCAAAGGAACAACCA
44347274 CGAAACATGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.42, C:0.30, G:0.12, T:0.15
Consensus pattern (21 bp):
CTTACCAAAGGAACAACCATG
Found at i:44348354 original size:11 final size:11
Alignment explanation
Indices: 44348338--44348368 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
44348328 TATATATATT
44348338 TAAAAATTATA
1 TAAAAATTATA
*
44348349 TAAAAATAATA
1 TAAAAATTATA
44348360 TAAAAATTA
1 TAAAAATTA
44348369 ATACGGGTGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
TAAAAATTATA
Found at i:44351048 original size:29 final size:29
Alignment explanation
Indices: 44350952--44351098 Score: 154
Period size: 30 Copynumber: 5.0 Consensus size: 29
44350942 CAAAAAATAA
* *
44350952 AAAATTGCATTTTGACCCCTAAATTTTTTT
1 AAAATTACATTTTGACCCCTAAA-ATTTTT
* *
44350982 AAAATTATATTTTGACCCCTAAACTTGTTT
1 AAAATTACATTTTGACCCCTAAAATT-TTT
* *
44351012 AAAATTACATTTTAACCCATAAAATTTTT
1 AAAATTACATTTTGACCCCTAAAATTTTT
*
44351041 AAAATTACGTTTTGACCCC-AAAATTTTCT
1 AAAATTACATTTTGACCCCTAAAATTTT-T
* *
44351070 AAAAATTACGTTTAGACCCC-AGAAATTTT
1 -AAAATTACATTTTGACCCCTA-AAATTTT
44351099 ACTGATATTG
Statistics
Matches: 102, Mismatches: 11, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
28 8 0.08
29 22 0.22
30 65 0.64
31 7 0.07
ACGTcount: A:0.37, C:0.17, G:0.06, T:0.40
Consensus pattern (29 bp):
AAAATTACATTTTGACCCCTAAAATTTTT
Found at i:44351075 original size:59 final size:61
Alignment explanation
Indices: 44350951--44351078 Score: 156
Period size: 59 Copynumber: 2.1 Consensus size: 61
44350941 ACAAAAAATA
* * * * * *
44350951 AAAAATTGCATTTTGACCCCTAAATTTTTTTAAAATTATATTTTGACCCCTAAACTTGTTT
1 AAAAATTACATTTTAACCCATAAATATTTTTAAAATTACATTTTGACCCCTAAAATTGTTT
*
44351012 -AAAATTACATTTTAACCCATAAA-ATTTTTAAAATTACGTTTTGACCCC-AAAATT-TTCT
1 AAAAATTACATTTTAACCCATAAATATTTTTAAAATTACATTTTGACCCCTAAAATTGTT-T
44351070 AAAAATTAC
1 AAAAATTAC
44351079 GTTTAGACCC
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
57 2 0.03
58 6 0.10
59 30 0.52
60 20 0.34
ACGTcount: A:0.38, C:0.16, G:0.05, T:0.41
Consensus pattern (61 bp):
AAAAATTACATTTTAACCCATAAATATTTTTAAAATTACATTTTGACCCCTAAAATTGTTT
Found at i:44352103 original size:18 final size:17
Alignment explanation
Indices: 44352080--44352138 Score: 57
Period size: 18 Copynumber: 3.2 Consensus size: 17
44352070 TCGGGTTTCT
44352080 AAATTTTCGTGTCTTCAA
1 AAATTTTCGTGT-TTCAA
44352098 AAATTTTTCTCGTGTTTC-A
1 AAA--TTT-TCGTGTTTCAA
*
44352117 AAATTCTCGTGTTTTCAA
1 AAATTTTCGTG-TTTCAA
44352135 AAAT
1 AAAT
44352139 AAGGCAACGA
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
16 5 0.14
17 6 0.17
18 8 0.23
19 4 0.11
20 6 0.17
21 6 0.17
ACGTcount: A:0.29, C:0.15, G:0.10, T:0.46
Consensus pattern (17 bp):
AAATTTTCGTGTTTCAA
Found at i:44352125 original size:16 final size:17
Alignment explanation
Indices: 44352104--44352136 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
44352094 TCAAAAATTT
44352104 TTCTCGTG-TTTCAAAA
1 TTCTCGTGTTTTCAAAA
44352120 TTCTCGTGTTTTCAAAA
1 TTCTCGTGTTTTCAAAA
44352137 ATAAGGCAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.24, C:0.18, G:0.12, T:0.45
Consensus pattern (17 bp):
TTCTCGTGTTTTCAAAA
Found at i:44352335 original size:17 final size:17
Alignment explanation
Indices: 44352293--44352562 Score: 215
Period size: 18 Copynumber: 15.4 Consensus size: 17
44352283 TTCCATTTTC
* *
44352293 CAAAATTTTTCGTGTCTT
1 CAAAAATTTCCGTGT-TT
44352311 CTAAAAATTTCCGTGTTT
1 C-AAAAATTTCCGTGTTT
* *
44352329 CAAAAATTTTCTTGTTTT
1 CAAAAATTTCCGTG-TTT
*
44352347 CAAAAATTTCTGTGTTT
1 CAAAAATTTCCGTGTTT
*
44352364 CAAAAATTTTCGTGTTTT
1 CAAAAATTTCCGTG-TTT
* *
44352382 CAAAATTTTGCGTGTTT
1 CAAAAATTTCCGTGTTT
**
44352399 CAAAAATTTTGGTGTTTT
1 CAAAAATTTCCGTG-TTT
44352417 CAAAAA-TTCCGGTGTTT
1 CAAAAATTTCC-GTGTTT
*
44352434 CAAAAAATTCCCGTGTTT
1 C-AAAAATTTCCGTGTTT
*
44352452 TAAAAATTTCCGTGTTTT
1 CAAAAATTTCCGTG-TTT
*
44352470 CAAAATTTTCGCGT-TTT
1 CAAAAATTTC-CGTGTTT
* * * *
44352487 TAAAATTTTTCGTATTT
1 CAAAAATTTCCGTGTTT
*
44352504 CAAAAA-TCCTCGTGTTTT
1 CAAAAATTTC-CGTG-TTT
*
44352522 CAAAAATTTCGGTGTTTT
1 CAAAAATTTCCGTG-TTT
*
44352540 CAAAATTTTCGCGT-TTT
1 CAAAAATTTC-CGTGTTT
44352557 CAAAAA
1 CAAAAA
44352563 AAAAATCTAG
Statistics
Matches: 205, Mismatches: 33, Indels: 29
0.77 0.12 0.11
Matches are distributed among these distances:
16 4 0.02
17 87 0.42
18 92 0.45
19 22 0.11
ACGTcount: A:0.29, C:0.14, G:0.12, T:0.46
Consensus pattern (17 bp):
CAAAAATTTCCGTGTTT
Found at i:44352362 original size:35 final size:35
Alignment explanation
Indices: 44352293--44352562 Score: 305
Period size: 35 Copynumber: 7.7 Consensus size: 35
44352283 TTCCATTTTC
* *
44352293 CAAAATTTTTCGTGTCTTCTAAAAATTTCCGTGTTT
1 CAAAAATTTTCGTGTTTTC-AAAAATTTCCGTGTTT
* *
44352329 CAAAAATTTTCTTGTTTTCAAAAATTTCTGTGTTT
1 CAAAAATTTTCGTGTTTTCAAAAATTTCCGTGTTT
* *
44352364 CAAAAATTTTCGTGTTTTCAAAATTTTGCGTGTTT
1 CAAAAATTTTCGTGTTTTCAAAAATTTCCGTGTTT
*
44352399 CAAAAATTTTGGTGTTTTCAAAAA-TTCCGGTGTTT
1 CAAAAATTTTCGTGTTTTCAAAAATTTCC-GTGTTT
**
44352434 CAAAAAATTCCCGTGTTTT-AAAAATTTCCGTGTTTT
1 C-AAAAATTTTCGTGTTTTCAAAAATTTCCGTG-TTT
* * * * *
44352470 C-AAAATTTTCGCGTTTTTAAAATTTTTCGTATTT
1 CAAAAATTTTCGTGTTTTCAAAAATTTCCGTGTTT
** *
44352504 CAAAAATCCTCGTGTTTTCAAAAATTTCGGTGTTTT
1 CAAAAATTTTCGTGTTTTCAAAAATTTCCGTG-TTT
*
44352540 C-AAAATTTTCGCGTTTTCAAAAA
1 CAAAAATTTTCGTGTTTTCAAAAA
44352563 AAAAATCTAG
Statistics
Matches: 196, Mismatches: 31, Indels: 15
0.81 0.13 0.06
Matches are distributed among these distances:
34 20 0.10
35 134 0.68
36 42 0.21
ACGTcount: A:0.29, C:0.14, G:0.12, T:0.46
Consensus pattern (35 bp):
CAAAAATTTTCGTGTTTTCAAAAATTTCCGTGTTT
Found at i:44353500 original size:17 final size:17
Alignment explanation
Indices: 44353461--44353504 Score: 65
Period size: 17 Copynumber: 2.7 Consensus size: 17
44353451 TTTATTGCTC
*
44353461 TATTAACTAT-TAAAAT
1 TATTAAATATATAAAAT
44353477 T-TTAAATATATAAAAT
1 TATTAAATATATAAAAT
44353493 TATTAAATATAT
1 TATTAAATATAT
44353505 TTAAAATGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
15 7 0.28
16 8 0.32
17 10 0.40
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (17 bp):
TATTAAATATATAAAAT
Found at i:44353509 original size:19 final size:17
Alignment explanation
Indices: 44353468--44353511 Score: 63
Period size: 17 Copynumber: 2.5 Consensus size: 17
44353458 CTCTATTAAC
44353468 TATTAAAATTTTAAATA
1 TATTAAAATTTTAAATA
44353485 TA-TAAAATTATTAAATA
1 TATTAAAATT-TTAAATA
44353502 TATTTAAAAT
1 TA-TTAAAAT
44353512 GAAAGATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 7 0.29
17 11 0.46
19 6 0.25
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
TATTAAAATTTTAAATA
Found at i:44356077 original size:122 final size:125
Alignment explanation
Indices: 44355767--44356149 Score: 515
Period size: 122 Copynumber: 3.0 Consensus size: 125
44355757 TTGGGTTAGT
* *
44355767 ACGAATAACATATAAGTTGTTCAAAGTACTAATGGAAAGAAGTCCATCAAATAAATAAGGTCTTG
1 ACGAATAACATATAAG-TGTTCAAAGTACTAATAGAAAGAAGTCCATCAAATAAATAAGGCCTTG
* * *
44355832 CAAAAGGAATTGCAAATAAGTTGCAATTATGGAATCC-TAGTAGTATTGCAAAAGTTTTCCTTTG
65 C-AAAGGAATTGCAAATAAATTGCAATTATGGAATCCTTA-T-GCA-T-C-AAAG----CC-ATG
* *
44355896 TGTTA-GT
119 T-TCATGA
44355903 ACGAATAACATATAAGTTGTTCAAAGTACTAATAGAAAGAAGTCCATCAAATAAATAAGGCCTTG
1 ACGAATAACATATAAG-TGTTCAAAGTACTAATAGAAAGAAGTCCATCAAATAAATAAGGCCTTG
44355968 CAAAGGAATTGCAAATAAATTGCAATTATGGAATCCTTATGCATCAAAGCCATGTTCATGA
65 CAAAGGAATTGCAAATAAATTGCAATTATGGAATCCTTATGCATCAAAGCCATGTTCATGA
* * *
44356029 AC-AAT-GCTTTTAA-TGTTCAAAGTACTAATAGAAAGAAGTCCATCAAATAAATAAGGCCTTGC
1 ACGAATAACATATAAGTGTTCAAAGTACTAATAGAAAGAAGTCCATCAAATAAATAAGGCCTTGC
44356091 AAAGGAATTGCAAATAAATTGCAATTATGGAATCCTTATGCATCAAAGCCATGTTCATG
66 AAAGGAATTGCAAATAAATTGCAATTATGGAATCCTTATGCATCAAAGCCATGTTCATG
44356150 TTCAATCCGT
Statistics
Matches: 235, Mismatches: 10, Indels: 18
0.89 0.04 0.07
Matches are distributed among these distances:
122 108 0.46
124 5 0.02
125 5 0.02
126 6 0.03
127 2 0.01
131 4 0.02
132 1 0.00
133 1 0.00
134 2 0.01
135 35 0.15
136 66 0.28
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (125 bp):
ACGAATAACATATAAGTGTTCAAAGTACTAATAGAAAGAAGTCCATCAAATAAATAAGGCCTTGC
AAAGGAATTGCAAATAAATTGCAATTATGGAATCCTTATGCATCAAAGCCATGTTCATGA
Found at i:44367027 original size:25 final size:25
Alignment explanation
Indices: 44366999--44367051 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
44366989 CAAGTGAAAA
*
44366999 GTCTGTTCTGACTAGGATAAAATGT
1 GTCTGTTCTGACTAAGATAAAATGT
44367024 GTCTGTTCTGACTAAGATAAAATGT
1 GTCTGTTCTGACTAAGATAAAATGT
44367049 GTC
1 GTC
44367052 GACTTAGTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.28, C:0.13, G:0.23, T:0.36
Consensus pattern (25 bp):
GTCTGTTCTGACTAAGATAAAATGT
Found at i:44384431 original size:7 final size:7
Alignment explanation
Indices: 44384419--44384445 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
44384409 ATATTTTTTT
44384419 ATTTGAC
1 ATTTGAC
44384426 ATTTGAC
1 ATTTGAC
44384433 ATTTGAC
1 ATTTGAC
44384440 ATTTGA
1 ATTTGA
44384446 ATTATCCTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.30, C:0.11, G:0.15, T:0.44
Consensus pattern (7 bp):
ATTTGAC
Found at i:44389980 original size:10 final size:10
Alignment explanation
Indices: 44389857--44389985 Score: 71
Period size: 10 Copynumber: 13.4 Consensus size: 10
44389847 CGAAAAAATG
44389857 ATAAAAAT-T
1 ATAAAAATAT
*
44389866 ATTAAAATCA-
1 ATAAAAAT-AT
44389876 ATAAAAATAT
1 ATAAAAATAT
44389886 -TAAAAAT-T
1 ATAAAAATAT
*
44389894 ATAGAATTATAT
1 ATA-AA-AATAT
*
44389906 ATAGAAATAT
1 ATAAAAATAT
44389916 ATAAAAATAT
1 ATAAAAATAT
** *
44389926 AT-TCAATTT
1 ATAAAAATAT
44389935 ATGAAAAAT-T
1 AT-AAAAATAT
*
44389945 ATTAAAAT-T
1 ATAAAAATAT
*
44389954 -TGAAAAT-T
1 ATAAAAATAT
44389962 ACT-AAAATAT
1 A-TAAAAATAT
44389972 ATAAAAATAT
1 ATAAAAATAT
44389982 ATAA
1 ATAA
44389986 TTTTTTTAAT
Statistics
Matches: 94, Mismatches: 13, Indels: 25
0.71 0.10 0.19
Matches are distributed among these distances:
8 8 0.09
9 35 0.37
10 41 0.44
11 6 0.06
12 4 0.04
ACGTcount: A:0.60, C:0.02, G:0.03, T:0.35
Consensus pattern (10 bp):
ATAAAAATAT
Found at i:44392139 original size:37 final size:37
Alignment explanation
Indices: 44392098--44392176 Score: 158
Period size: 37 Copynumber: 2.1 Consensus size: 37
44392088 TCTCAAGATC
44392098 ATTTAAAACTTGAGTTTGAAAAGATTCGTGCATTTAG
1 ATTTAAAACTTGAGTTTGAAAAGATTCGTGCATTTAG
44392135 ATTTAAAACTTGAGTTTGAAAAGATTCGTGCATTTAG
1 ATTTAAAACTTGAGTTTGAAAAGATTCGTGCATTTAG
44392172 ATTTA
1 ATTTA
44392177 TTGTGAAGAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.35, C:0.08, G:0.18, T:0.39
Consensus pattern (37 bp):
ATTTAAAACTTGAGTTTGAAAAGATTCGTGCATTTAG
Found at i:44393050 original size:16 final size:17
Alignment explanation
Indices: 44393024--44393056 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
44393014 GAAAATAAAA
44393024 GTAATAAATATATATAT
1 GTAATAAATATATATAT
*
44393041 GTAA-AAATATGTATAT
1 GTAATAAATATATATAT
44393057 ATATATTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.52, C:0.00, G:0.09, T:0.39
Consensus pattern (17 bp):
GTAATAAATATATATAT
Found at i:44393236 original size:3 final size:3
Alignment explanation
Indices: 44393228--44393275 Score: 78
Period size: 3 Copynumber: 16.0 Consensus size: 3
44393218 ATAAGAAATT
* *
44393228 ATA ATA ATA ATA ATA ATA ATA GTA ATA ATA ATA ATA ACA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
44393276 TGAAATTTGT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:44399575 original size:39 final size:39
Alignment explanation
Indices: 44399517--44399617 Score: 100
Period size: 39 Copynumber: 2.6 Consensus size: 39
44399507 TGATAAAACT
* * **
44399517 AAAATCA-ATAAAAGTTATAAAAATTATTGAATTTTAATA
1 AAAATCATAAAAAAATTATAAAAATTATAAAATTTT-ATA
* *
44399556 AAAAT-ATTTAAAAAA-TATAAAAAATTGTAAAATTTTATA
1 AAAATCA-TAAAAAAATTAT-AAAAATTATAAAATTTTATA
44399595 AAAATCATAAAAAAATTATAAAA
1 AAAATCATAAAAAAATTATAAAA
44399618 TGCATAAAAA
Statistics
Matches: 50, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
38 1 0.02
39 27 0.54
40 22 0.44
ACGTcount: A:0.62, C:0.02, G:0.03, T:0.33
Consensus pattern (39 bp):
AAAATCATAAAAAAATTATAAAAATTATAAAATTTTATA
Found at i:44399607 original size:20 final size:20
Alignment explanation
Indices: 44399590--44399627 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
44399580 TTGTAAAATT
44399590 TTATAAAAAT-CATAAAAAAA
1 TTAT-AAAATGCATAAAAAAA
44399610 TTATAAAATGCATAAAAA
1 TTATAAAATGCATAAAAA
44399628 GACCATTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.66, C:0.05, G:0.03, T:0.26
Consensus pattern (20 bp):
TTATAAAATGCATAAAAAAA
Found at i:44399624 original size:29 final size:28
Alignment explanation
Indices: 44399566--44399627 Score: 72
Period size: 30 Copynumber: 2.2 Consensus size: 28
44399556 AAAATATTTA
* **
44399566 AAAAATATAAAAAATTGTAAAATTTTAT
1 AAAAATATAAAAAATTATAAAATTGCAT
44399594 AAAAATCATAAAAAAATTATAAAA-TGCAT
1 AAAAAT-AT-AAAAAATTATAAAATTGCAT
44399623 AAAAA
1 AAAAA
44399628 GACCATTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
28 6 0.21
29 10 0.34
30 13 0.45
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.27
Consensus pattern (28 bp):
AAAAATATAAAAAATTATAAAATTGCAT
Found at i:44399955 original size:29 final size:29
Alignment explanation
Indices: 44399883--44399956 Score: 91
Period size: 28 Copynumber: 2.6 Consensus size: 29
44399873 TTATAATTTT
* *
44399883 TTTTTCTAATTTTTAATAAATATTAAGTA
1 TTTTTATAATTTTTATTAAATATTAAGTA
44399912 TTTTTAT-ATTTTTATTAAA-ATTTAA-TAA
1 TTTTTATAATTTTTATTAAATA-TTAAGT-A
44399940 TTTTTATAATTTTTATT
1 TTTTTATAATTTTTATT
44399957 GGTTTTTATT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
27 2 0.05
28 23 0.57
29 15 0.38
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.62
Consensus pattern (29 bp):
TTTTTATAATTTTTATTAAATATTAAGTA
Found at i:44403346 original size:54 final size:54
Alignment explanation
Indices: 44403282--44403387 Score: 212
Period size: 54 Copynumber: 2.0 Consensus size: 54
44403272 ACAAAGAGCA
44403282 ATTAATCAAGTCCGACAATGAGTTTTCCAACAAGTTTTACAAGGAGCTCTAGCG
1 ATTAATCAAGTCCGACAATGAGTTTTCCAACAAGTTTTACAAGGAGCTCTAGCG
44403336 ATTAATCAAGTCCGACAATGAGTTTTCCAACAAGTTTTACAAGGAGCTCTAG
1 ATTAATCAAGTCCGACAATGAGTTTTCCAACAAGTTTTACAAGGAGCTCTAG
44403388 GAACTTTGAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (54 bp):
ATTAATCAAGTCCGACAATGAGTTTTCCAACAAGTTTTACAAGGAGCTCTAGCG
Found at i:44408334 original size:43 final size:43
Alignment explanation
Indices: 44408287--44408504 Score: 201
Period size: 43 Copynumber: 5.1 Consensus size: 43
44408277 ATAAACGTCG
44408287 CTATAGACCATA-ACCTTTAGCGGCGCTTCTACAACAAACGCCA
1 CTATAGACCA-AGACCTTTAGCGGCGCTTCTACAACAAACGCCA
* * * *
44408330 CTATAG-CTCAAGACCTTTAGCGGCGGTTTTCCCACAAACGCCA
1 CTATAGAC-CAAGACCTTTAGCGGCGCTTCTACAACAAACGCCA
* * * *** * *
44408373 CTGTAGATCAAGACCTTTAGCGGCGCTTTTTTTACAAACACCG
1 CTATAGACCAAGACCTTTAGCGGCGCTTCTACAACAAACGCCA
* * * *
44408416 CTATAGATCAAGACCTTTTAGCGGCGCTTATATAAAAAACGCCA
1 CTATAGACCAAGACC-TTTAGCGGCGCTTCTACAACAAACGCCA
* * *
44408460 CTATAGAACAA-ACCTTTAGCGACGCTTCTTGCAA-AAACGCCA
1 CTATAGACCAAGACCTTTAGCGGCGCTTC-TACAACAAACGCCA
44408502 CTA
1 CTA
44408505 AAAACATAAC
Statistics
Matches: 146, Mismatches: 24, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
42 25 0.17
43 89 0.61
44 32 0.22
ACGTcount: A:0.31, C:0.28, G:0.16, T:0.24
Consensus pattern (43 bp):
CTATAGACCAAGACCTTTAGCGGCGCTTCTACAACAAACGCCA
Found at i:44408410 original size:86 final size:86
Alignment explanation
Indices: 44408287--44408504 Score: 242
Period size: 86 Copynumber: 2.5 Consensus size: 86
44408277 ATAAACGTCG
* * *
44408287 CTATAGACCATAACCTTTAGCGGCGCTTCTACAACAAACGCCACTATAGCTCAAGACC-TTTAGC
1 CTATAGAACA-AACCTTTAGCGGCGCTTCTTCAACAAACGCCACTATAGATCAAGACCTTTTAGC
* * * * *
44408351 GGCGGTTTTCCCACAAACGCCA
65 GGCGCTTATACAAAAAACGCCA
* * * ** * *
44408373 CTGTAGATCAAGACCTTTAGCGGCGCTTTTTTTACAAACACCGCTATAGATCAAGACCTTTTAGC
1 CTATAGAACAA-ACCTTTAGCGGCGCTTCTTCAACAAACGCCACTATAGATCAAGACCTTTTAGC
*
44408438 GGCGCTTATATAAAAAACGCCA
65 GGCGCTTATACAAAAAACGCCA
*
44408460 CTATAGAACAAACCTTTAGCGACGCTTCTTGCAA-AAACGCCACTA
1 CTATAGAACAAACCTTTAGCGGCGCTTCTT-CAACAAACGCCACTA
44408505 AAAACATAAC
Statistics
Matches: 106, Mismatches: 23, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
85 1 0.01
86 73 0.69
87 32 0.30
ACGTcount: A:0.31, C:0.28, G:0.16, T:0.24
Consensus pattern (86 bp):
CTATAGAACAAACCTTTAGCGGCGCTTCTTCAACAAACGCCACTATAGATCAAGACCTTTTAGCG
GCGCTTATACAAAAAACGCCA
Found at i:44408551 original size:20 final size:19
Alignment explanation
Indices: 44408521--44408573 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 19
44408511 TAACATTTAA
44408521 AAATA-TTATTTTAATCAA-
1 AAATATTTATTTTAAT-AAT
*
44408539 ATAATATTTATTTTTATAAT
1 A-AATATTTATTTTAATAAT
44408559 AAATATTTTATTTTA
1 AAATA-TTTATTTTA
44408574 TTTTATTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
18 1 0.03
19 10 0.34
20 18 0.62
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (19 bp):
AAATATTTATTTTAATAAT
Found at i:44409377 original size:45 final size:45
Alignment explanation
Indices: 44409319--44409420 Score: 186
Period size: 45 Copynumber: 2.3 Consensus size: 45
44409309 CCCGCTATCA
44409319 CCACATAAAGGTAATTAACTCAATAAGACATACTCAAACAATTAG
1 CCACATAAAGGTAATTAACTCAATAAGACATACTCAAACAATTAG
* *
44409364 CCACATAATGGTAATTAACTCAATAAGGCATACTCAAACAATTAG
1 CCACATAAAGGTAATTAACTCAATAAGACATACTCAAACAATTAG
44409409 CCACATAAAGGT
1 CCACATAAAGGT
44409421 TTAACATTCC
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 54 1.00
ACGTcount: A:0.46, C:0.21, G:0.11, T:0.23
Consensus pattern (45 bp):
CCACATAAAGGTAATTAACTCAATAAGACATACTCAAACAATTAG
Found at i:44417922 original size:45 final size:45
Alignment explanation
Indices: 44417857--44418492 Score: 891
Period size: 45 Copynumber: 14.2 Consensus size: 45
44417847 TTCAGAGAAC
*
44417857 AGATCGAAGATAGCAGATCTTGTCTTCTTGTATTGGCAGCGAAGT
1 AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGT
* *
44417902 AGATCGAAGATAGCATATCTTGTCTTCCTGTATTGGCAACGAAGT
1 AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGT
* *
44417947 AGATCGAAGATAGTAGATCTTGTCTTCCTGTATTGGCAGCAAAGT
1 AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGT
*
44417992 AGATCGAAGATATCAGATCTTGTCTTCCTGTATTGGCAGCGAAGT
1 AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGT
* *
44418037 AGATCGAGGATAGCAGATCTTGTCTTCCTGTATTGGCAGCAAAGT
1 AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGT
* *
44418082 AGATCGAGGATAGTAGATCTTGTCTTCCTGTATTGGCAGCGAAGT
1 AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGT
* *
44418127 AGATCGAGGATAGCAGATTTTGTCTTCCTGTATTGGCAGCGAAGT
1 AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGT
* * *
44418172 AGATCGAAGATAGCAGATTTTGT-ATCCTGTATTAGCAGCGAAGT
1 AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGT
* * * *
44418216 AGATCGAGGATAGCAAATCTTGTCTTCCAGTATTGGCAGCGAAAT
1 AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGT
* *
44418261 AGATCGAAGATAGCAAATCTTGTCTTCCTGTATTGGCAGCAAAGT
1 AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGT
*
44418306 AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGTAGCGAAGT
1 AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGT
** *
44418351 AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGTAAAGC
1 AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGT
* * * * * ** * * *
44418396 AGATCGAAGACACCAG-CCTTGCCTTTCTGTGCTGACAACGAAGC
1 AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGT
* * * *
44418440 AGA-CTGAAGATAGCAGATCATGCCTTCCTGTACTGGCAGCGAAGC
1 AGATC-GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGT
44418485 AGATCGAA
1 AGATCGAA
44418493 AAACAACGAA
Statistics
Matches: 530, Mismatches: 57, Indels: 8
0.89 0.10 0.01
Matches are distributed among these distances:
43 1 0.00
44 70 0.13
45 458 0.86
46 1 0.00
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.28
Consensus pattern (45 bp):
AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGT
Found at i:44426947 original size:3 final size:3
Alignment explanation
Indices: 44426939--44426969 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
44426929 TAAAATCCTT
44426939 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
44426970 CAGGTTGTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:44430664 original size:26 final size:27
Alignment explanation
Indices: 44430635--44430703 Score: 70
Period size: 26 Copynumber: 2.6 Consensus size: 27
44430625 CGATATATGA
44430635 CTCTTCGTGAGCTTCCCGATTAA-AGG
1 CTCTTCGTGAGCTTCCCGATTAATAGG
** * * *
44430661 CTCTTTATGAGCATCCTGATTAATTGG
1 CTCTTCGTGAGCTTCCCGATTAATAGG
*
44430688 CT-TGCGTGAGCTTCCC
1 CTCTTCGTGAGCTTCCC
44430704 TATATGGCTT
Statistics
Matches: 32, Mismatches: 10, Indels: 2
0.73 0.23 0.05
Matches are distributed among these distances:
26 28 0.88
27 4 0.12
ACGTcount: A:0.17, C:0.26, G:0.22, T:0.35
Consensus pattern (27 bp):
CTCTTCGTGAGCTTCCCGATTAATAGG
Found at i:44438721 original size:23 final size:25
Alignment explanation
Indices: 44438681--44438733 Score: 65
Period size: 23 Copynumber: 2.2 Consensus size: 25
44438671 TCTGATTAAT
*
44438681 TGGCTCGCATAAGCTTCCC-A-ATA
1 TGGCTCGCATAAACTTCCCGATATA
* *
44438704 TGGCTCGCTTAAATTTCCCGATATA
1 TGGCTCGCATAAACTTCCCGATATA
44438729 TGGCT
1 TGGCT
44438734 ATCCGAAGCA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 16 0.64
24 1 0.04
25 8 0.32
ACGTcount: A:0.23, C:0.26, G:0.19, T:0.32
Consensus pattern (25 bp):
TGGCTCGCATAAACTTCCCGATATA
Found at i:44439996 original size:42 final size:42
Alignment explanation
Indices: 44439928--44440120 Score: 325
Period size: 42 Copynumber: 4.6 Consensus size: 42
44439918 AAGGGAAGAG
* *
44439928 ACACGGGCGTGTG-CTCAGCTGTGTGTGGCACACGGCCTAGC
1 ACACGGGCGTGTGTCTCAGCCGTGTGTGACACACGGCCTAGC
44439969 ACACGGGCGTGTGTCTCAGCCGTGTGTGACACACGGCCTAGC
1 ACACGGGCGTGTGTCTCAGCCGTGTGTGACACACGGCCTAGC
*
44440011 ACACGGGCGTGTGTCTCAGCCGTGTATGACACACGGCCTAGC
1 ACACGGGCGTGTGTCTCAGCCGTGTGTGACACACGGCCTAGC
*
44440053 ACACGGGCGTGTGTCTCAGCCGTGTATGACACACGGCCTAGC
1 ACACGGGCGTGTGTCTCAGCCGTGTGTGACACACGGCCTAGC
**
44440095 ACACGGGCGTGTGTCTTGGCCGTGTG
1 ACACGGGCGTGTGTCTCAGCCGTGTG
44440121 ACTCCTGTAC
Statistics
Matches: 145, Mismatches: 6, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
41 13 0.09
42 132 0.91
ACGTcount: A:0.16, C:0.30, G:0.34, T:0.20
Consensus pattern (42 bp):
ACACGGGCGTGTGTCTCAGCCGTGTGTGACACACGGCCTAGC
Found at i:44440219 original size:73 final size:73
Alignment explanation
Indices: 44440082--44440219 Score: 165
Period size: 73 Copynumber: 1.9 Consensus size: 73
44440072 CCGTGTATGA
* * * * ** *
44440082 CACACGGCCTAGCACACGGGCGTGTGTCTTGGCCGTGTGACTCCTGTACCTAATTAATGCAAATT
1 CACACAGCCTAGCACACGGGCGTGTGGCTTGGCCGTGTGACTCCAGTACATAACCAATCCAAATT
44440147 AAATTGTT
66 AAATTGTT
44440155 CACACAGCCTAGCACACGGGCGTGTGGCTTGGCCGTGTGAC-CCAAGT-CAATAACCAA-CCTAA
1 CACACAGCCTAGCACACGGGCGTGTGGCTTGGCCGTGTGACTCC-AGTAC-ATAACCAATCC-AA
44440217 ATT
63 ATT
44440220 GGACACGGGC
Statistics
Matches: 55, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
72 4 0.07
73 51 0.93
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (73 bp):
CACACAGCCTAGCACACGGGCGTGTGGCTTGGCCGTGTGACTCCAGTACATAACCAATCCAAATT
AAATTGTT
Found at i:44440280 original size:13 final size:13
Alignment explanation
Indices: 44440262--44440286 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
44440252 TTTTGAAGTC
44440262 CCACACGGCCTAG
1 CCACACGGCCTAG
44440275 CCACACGGCCTA
1 CCACACGGCCTA
44440287 ACCATACGAG
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:0.24, C:0.48, G:0.20, T:0.08
Consensus pattern (13 bp):
CCACACGGCCTAG
Found at i:44446720 original size:14 final size:15
Alignment explanation
Indices: 44446703--44446733 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
44446693 CCTAGTATTG
44446703 TATAAAAAATATTTTA
1 TATAAAAAATA-TTTA
44446719 TATAAAAAATATTTA
1 TATAAAAAATATTTA
44446734 ATACCGTAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
TATAAAAAATATTTA
Found at i:44453185 original size:96 final size:97
Alignment explanation
Indices: 44453020--44453209 Score: 310
Period size: 96 Copynumber: 2.0 Consensus size: 97
44453010 TCTGCCCAAT
* * *
44453020 TTGTAGCAAATCGATGGGAGATATGGCGGTAAGAAAATTATTTTTAAAAGCATATTACTGTTTTA
1 TTGTAGAAAATCGATGGGAGATATGGCAGTAAGAAAATTATTTTTAAAAGCATACTACTGTTTTA
* *
44453085 AGTTATGATTACATATAAAATTGTTTTAGCAG
66 AGTTATGACTACATACAAAATTGTTTTAGCAG
*
44453117 TTGTAGAAAATCGATGGGAGATATGGCAGTAAG-AAATTCTTTTTAAAAGCATACTACTGTTTTA
1 TTGTAGAAAATCGATGGGAGATATGGCAGTAAGAAAATTATTTTTAAAAGCATACTACTGTTTTA
*
44453181 AGTTATGACTACATACAAGATTGTTTTAG
66 AGTTATGACTACATACAAAATTGTTTTAG
44453210 GGGATAGGCA
Statistics
Matches: 86, Mismatches: 7, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
96 55 0.64
97 31 0.36
ACGTcount: A:0.36, C:0.08, G:0.19, T:0.36
Consensus pattern (97 bp):
TTGTAGAAAATCGATGGGAGATATGGCAGTAAGAAAATTATTTTTAAAAGCATACTACTGTTTTA
AGTTATGACTACATACAAAATTGTTTTAGCAG
Found at i:44455595 original size:17 final size:18
Alignment explanation
Indices: 44455573--44455606 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
44455563 ATAATTGTAA
44455573 TTTAAAT-TCTAATTATT
1 TTTAAATGTCTAATTATT
*
44455590 TTTAAATGTGTAATTAT
1 TTTAAATGTCTAATTAT
44455607 CATAACTTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.35, C:0.03, G:0.06, T:0.56
Consensus pattern (18 bp):
TTTAAATGTCTAATTATT
Found at i:44455624 original size:44 final size:44
Alignment explanation
Indices: 44455574--44455663 Score: 135
Period size: 44 Copynumber: 2.0 Consensus size: 44
44455564 TAATTGTAAT
* * *
44455574 TTAAATTCTAATTATTTTTAAATGTGTAATTATCATAACTTCTA
1 TTAAATTATAATTATTTTTAAATGTATAATTATCACAACTTCTA
* *
44455618 TTAAATTATAATTGTTTTTAAATGTATAATTATCACGACTTCTA
1 TTAAATTATAATTATTTTTAAATGTATAATTATCACAACTTCTA
44455662 TT
1 TT
44455664 TTATTTCAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.36, C:0.09, G:0.06, T:0.50
Consensus pattern (44 bp):
TTAAATTATAATTATTTTTAAATGTATAATTATCACAACTTCTA
Found at i:44463713 original size:12 final size:12
Alignment explanation
Indices: 44463688--44463840 Score: 54
Period size: 12 Copynumber: 12.8 Consensus size: 12
44463678 TTTATCAAGA
44463688 TAAATATTAAAT
1 TAAATATTAAAT
44463700 TAAAT-TTAATAT
1 TAAATATTAA-AT
*
44463712 TAAATCTT--AT
1 TAAATATTAAAT
*
44463722 TAAAATAATGTAGA-
1 T-AAAT-AT-TAAAT
*
44463736 TAAACATTAAAT
1 TAAATATTAAAT
44463748 TAAAT-TTAATAT
1 TAAATATTAA-AT
* * *
44463760 TAAGATAATCATT
1 TAA-ATATTAAAT
*
44463773 TTAATATTAAAT
1 TAAATATTAAAT
* * *
44463785 TAATAAAATACTAT
1 TAA-ATATTA-AAT
*
44463799 TAAGATA-AAAAT
1 TAA-ATATTAAAT
44463811 T-AA-ATTAAAT
1 TAAATATTAAAT
*
44463821 TAAATATTAAAA
1 TAAATATTAAAT
44463833 T-AATATTA
1 TAAATATTA
44463841 TTTTTAGAAT
Statistics
Matches: 104, Mismatches: 21, Indels: 33
0.66 0.13 0.21
Matches are distributed among these distances:
9 1 0.01
10 9 0.09
11 25 0.24
12 42 0.40
13 16 0.15
14 10 0.10
15 1 0.01
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.40
Consensus pattern (12 bp):
TAAATATTAAAT
Found at i:44463788 original size:20 final size:18
Alignment explanation
Indices: 44463640--44463789 Score: 60
Period size: 17 Copynumber: 8.7 Consensus size: 18
44463630 TTCAACTATG
44463640 ATTAAACTTAATCACTTTAAT
1 ATTAAA-TTAAT-A-TTTAAT
44463661 ATTAAATTAATA--TAAT
1 ATTAAATTAATATTTAAT
* * * *
44463677 ATT-TATCAAGA-TAAAT
1 ATTAAATTAATATTTAAT
44463693 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
44463710 ATTAAATCT--TA-TTAA-
1 ATTAAAT-TAATATTTAAT
* *
44463725 AAT-AATGTAGATA---AAC
1 ATTAAAT-TA-ATATTTAAT
44463741 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
44463758 ATTAAGA-TAATCATTTTAAT
1 ATTAA-ATTAAT-A-TTTAAT
44463778 ATTAAATTAATA
1 ATTAAATTAATA
44463790 AAATACTATT
Statistics
Matches: 100, Mismatches: 11, Indels: 38
0.67 0.07 0.26
Matches are distributed among these distances:
14 5 0.05
15 10 0.10
16 22 0.22
17 31 0.31
18 2 0.02
19 4 0.04
20 20 0.20
21 6 0.06
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.42
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:44465334 original size:20 final size:21
Alignment explanation
Indices: 44465309--44465357 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
44465299 TATTGATCCA
*
44465309 GTATCGATACT-TTTCTTAAG
1 GTATCGATACTATTTCCTAAG
*
44465329 GTATCGAT-GTATTTCCTAAG
1 GTATCGATACTATTTCCTAAG
44465349 GTATCGATA
1 GTATCGATA
44465358 TTCCTGCTCC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 1 0.04
20 24 0.96
ACGTcount: A:0.27, C:0.14, G:0.18, T:0.41
Consensus pattern (21 bp):
GTATCGATACTATTTCCTAAG
Found at i:44465881 original size:19 final size:19
Alignment explanation
Indices: 44465857--44465894 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
44465847 TAGGGAAATC
44465857 TTTAATTGTGGTAAGCTAA
1 TTTAATTGTGGTAAGCTAA
44465876 TTTAATTGTGGTAAGCTAA
1 TTTAATTGTGGTAAGCTAA
44465895 GTAGTTGAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.05, G:0.21, T:0.42
Consensus pattern (19 bp):
TTTAATTGTGGTAAGCTAA
Found at i:44473203 original size:101 final size:101
Alignment explanation
Indices: 44473036--44473231 Score: 365
Period size: 101 Copynumber: 1.9 Consensus size: 101
44473026 ACAACTATGC
*
44473036 TATTTGCTAAGCAATAAGGAAGATGATAATGGTTGTTATCATATGTTAGAATCGAGTAACTCGAA
1 TATTTGCTAAGCAATAAGGAAGATGATAATGGTTGATATCATATGTTAGAATCGAGTAACTCGAA
*
44473101 TCATTATTTAAATAAAATATAGTGGTAAAACTATAT
66 TCATTATTTAAATAAAATACAGTGGTAAAACTATAT
*
44473137 TATTTGCTAAGCAATAAGGAAGATGATAATGGTTGATATCATCTGTTAGAATCGAGTAACTCGAA
1 TATTTGCTAAGCAATAAGGAAGATGATAATGGTTGATATCATATGTTAGAATCGAGTAACTCGAA
44473202 TCATTATTTAAATAAAATACAGTGGTAAAA
66 TCATTATTTAAATAAAATACAGTGGTAAAA
44473232 TAAAATAAAA
Statistics
Matches: 92, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
101 92 1.00
ACGTcount: A:0.41, C:0.09, G:0.17, T:0.33
Consensus pattern (101 bp):
TATTTGCTAAGCAATAAGGAAGATGATAATGGTTGATATCATATGTTAGAATCGAGTAACTCGAA
TCATTATTTAAATAAAATACAGTGGTAAAACTATAT
Found at i:44476319 original size:15 final size:15
Alignment explanation
Indices: 44476299--44476329 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
44476289 TTAAAACTGT
44476299 ATTTTTACATGAAGA
1 ATTTTTACATGAAGA
44476314 ATTTTTACATGAAGA
1 ATTTTTACATGAAGA
44476329 A
1 A
44476330 CTTGAGGAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.42, C:0.06, G:0.13, T:0.39
Consensus pattern (15 bp):
ATTTTTACATGAAGA
Found at i:44484056 original size:22 final size:22
Alignment explanation
Indices: 44484031--44484162 Score: 65
Period size: 22 Copynumber: 6.0 Consensus size: 22
44484021 GCTTGTATGA
44484031 GTTTAGCACTTCTGTGCTCTCT
1 GTTTAGCACTTCTGTGCTCTCT
** * * *
44484053 GTTTAGTGCTTCGGTACTCTTT
1 GTTTAGCACTTCTGTGCTCTCT
* *
44484075 GTTCAGTC-CTT-TGGTAG-TATCT
1 GTTTAG-CACTTCT-GT-GCTCTCT
* * * *
44484097 GATCAGCAC-TCCGATGCTCTTT
1 GTTTAGCACTTCTG-TGCTCTCT
* *
44484119 GGTTAGCACTTTTGTGCTCTCT
1 GTTTAGCACTTCTGTGCTCTCT
* *
44484141 GTTTAGCACTACGGTGCTCTCT
1 GTTTAGCACTTCTGTGCTCTCT
44484163 AGTGTGGTGT
Statistics
Matches: 78, Mismatches: 24, Indels: 16
0.66 0.20 0.14
Matches are distributed among these distances:
21 4 0.05
22 72 0.92
23 2 0.03
ACGTcount: A:0.12, C:0.24, G:0.21, T:0.42
Consensus pattern (22 bp):
GTTTAGCACTTCTGTGCTCTCT
Found at i:44487744 original size:39 final size:39
Alignment explanation
Indices: 44487701--44487814 Score: 149
Period size: 39 Copynumber: 2.9 Consensus size: 39
44487691 AGTACACCAG
* * * * *
44487701 CACACAGCTTGCTAGGCAAAAAGCCCAAATAATCA-TCGT
1 CACACAACTTGCTAGGCACATAGCCCGAATAATCACT-GA
*
44487740 CACACAACCTGCTAGGCACATAGCCCGAATAATCACTGA
1 CACACAACTTGCTAGGCACATAGCCCGAATAATCACTGA
*
44487779 CACACAACTTACTAGGCACATAGCCCGAATAATCAC
1 CACACAACTTGCTAGGCACATAGCCCGAATAATCAC
44487815 CGTATTTCTA
Statistics
Matches: 66, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
39 65 0.98
40 1 0.02
ACGTcount: A:0.38, C:0.32, G:0.14, T:0.17
Consensus pattern (39 bp):
CACACAACTTGCTAGGCACATAGCCCGAATAATCACTGA
Found at i:44492787 original size:45 final size:44
Alignment explanation
Indices: 44492718--44492974 Score: 241
Period size: 45 Copynumber: 5.8 Consensus size: 44
44492708 AGGAGGAAGA
* * * * *
44492718 ATTGGTGGCTTT-GTCCACAGCCTACACGTCAGCTTGTCTACAGAT
1 ATTGGTGG-TTTCGTCCACAACCTACATGGCAGCTTGTTTGC-GAT
* ** * *
44492763 ATTGGTGGTTTCGGCCACAACCTACATGAAAACTTGTCTGCGAAT
1 ATTGGTGGTTTCGTCCACAACCTACATGGCAGCTTGTTTGCG-AT
* * *
44492808 ATTGGTGGCTTCGTCCACAACCTGCACGGCAGCTTGTTTGCGGAT
1 ATTGGTGGTTTCGTCCACAACCTACATGGCAGCTTGTTTGC-GAT
** * *
44492853 ATTGGTGGTTTCACCCACAACCTACATGGCAACTTGTTTTCGAAT
1 ATTGGTGGTTTCGTCCACAACCTACATGGCAGCTTGTTTGCG-AT
* *
44492898 ATTGGTGGCTTCGTCCACAACCTACATGGCAGCTTGTTTGC-AA
1 ATTGGTGGTTTCGTCCACAACCTACATGGCAGCTTGTTTGCGAT
* * *
44492941 ATTTGGTGGTTT-ATCCGCAACCTACATGGAAGCT
1 A-TTGGTGGTTTCGTCCACAACCTACATGGCAGCT
44492975 ATCTTTAAAT
Statistics
Matches: 175, Mismatches: 32, Indels: 12
0.80 0.15 0.05
Matches are distributed among these distances:
43 21 0.12
44 14 0.08
45 139 0.79
46 1 0.01
ACGTcount: A:0.22, C:0.25, G:0.23, T:0.31
Consensus pattern (44 bp):
ATTGGTGGTTTCGTCCACAACCTACATGGCAGCTTGTTTGCGAT
Found at i:44492871 original size:90 final size:90
Alignment explanation
Indices: 44492718--44493003 Score: 353
Period size: 90 Copynumber: 3.2 Consensus size: 90
44492708 AGGAGGAAGA
* * * * * **
44492718 ATTGGTGGCTTTGTCCACAGCCTACACGTCAGCTTGTCTACAGATATTGGTGGTTTCGGCCACAA
1 ATTGGTGGCTTCGTCCACAACCTACACGGCAGCTTGTTTGCAGATATTGGTGGTTTCACCCACAA
* *
44492783 CCTACATGAAAACTTGTCTGCGAAT
66 CCTACATGGAAACTTGTCTTCGAAT
* *
44492808 ATTGGTGGCTTCGTCCACAACCTGCACGGCAGCTTGTTTGCGGATATTGGTGGTTTCACCCACAA
1 ATTGGTGGCTTCGTCCACAACCTACACGGCAGCTTGTTTGCAGATATTGGTGGTTTCACCCACAA
* *
44492873 CCTACATGGCAACTTGTTTTCGAAT
66 CCTACATGGAAACTTGTCTTCGAAT
* * * *
44492898 ATTGGTGGCTTCGTCCACAACCTACATGGCAGCTTGTTTGCAAAT-TTGGTGGTTT-ATCCGCAA
1 ATTGGTGGCTTCGTCCACAACCTACACGGCAGCTTGTTTGCAGATATTGGTGGTTTCACCCACAA
* * **
44492961 CCTACATGGAAGC-TATCTTTAAAT
66 CCTACATGGAAACTTGTCTTCGAAT
*
44492985 ATTGGTGGCTTCGACCACA
1 ATTGGTGGCTTCGTCCACA
44493004 TCTTTTGTAG
Statistics
Matches: 170, Mismatches: 26, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
87 25 0.15
88 17 0.10
89 10 0.06
90 118 0.69
ACGTcount: A:0.22, C:0.24, G:0.22, T:0.31
Consensus pattern (90 bp):
ATTGGTGGCTTCGTCCACAACCTACACGGCAGCTTGTTTGCAGATATTGGTGGTTTCACCCACAA
CCTACATGGAAACTTGTCTTCGAAT
Found at i:44494286 original size:30 final size:30
Alignment explanation
Indices: 44494240--44494318 Score: 122
Period size: 30 Copynumber: 2.6 Consensus size: 30
44494230 AGCAAATTTG
*
44494240 ACTTGTTTGAAAATCATTTAAAATGATTTTA
1 ACTTGATTG-AAATCATTTAAAATGATTTTA
44494271 ACTTGATTGAAATCATTTAAAATGATTTTA
1 ACTTGATTGAAATCATTTAAAATGATTTTA
* *
44494301 ATTTGATTGAAATTATTT
1 ACTTGATTGAAATCATTT
44494319 GACTTGGTTA
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
30 37 0.82
31 8 0.18
ACGTcount: A:0.38, C:0.05, G:0.10, T:0.47
Consensus pattern (30 bp):
ACTTGATTGAAATCATTTAAAATGATTTTA
Found at i:44494629 original size:18 final size:18
Alignment explanation
Indices: 44494606--44494640 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
44494596 ATGAGTTTAC
44494606 AAATATTTTAAACTATTG
1 AAATATTTTAAACTATTG
*
44494624 AAATATTTTAAATTATT
1 AAATATTTTAAACTATT
44494641 TATGATTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (18 bp):
AAATATTTTAAACTATTG
Found at i:44496050 original size:24 final size:27
Alignment explanation
Indices: 44495994--44496053 Score: 72
Period size: 24 Copynumber: 2.3 Consensus size: 27
44495984 GAGAAAATAT
* *
44495994 ATTTAATTTTCCTGTATTCAACAGTTC
1 ATTTAATTTTCATGTATTCAACACTTC
*
44496021 ACTTAATTTTCAT-T-TTCAA-ACTTC
1 ATTTAATTTTCATGTATTCAACACTTC
44496045 ATTTAATTT
1 ATTTAATTT
44496054 GAAAAAGCGT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
24 12 0.41
25 5 0.17
26 1 0.03
27 11 0.38
ACGTcount: A:0.28, C:0.17, G:0.03, T:0.52
Consensus pattern (27 bp):
ATTTAATTTTCATGTATTCAACACTTC
Found at i:44496572 original size:4 final size:4
Alignment explanation
Indices: 44496563--44496594 Score: 50
Period size: 4 Copynumber: 8.5 Consensus size: 4
44496553 AATTGGAAAT
44496563 TTAA TTAA TTAA TTAA TTAA TTAA --AA TTAA TT
1 TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTAA TT
44496595 TATGATGTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
2 2 0.08
4 24 0.92
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
TTAA
Found at i:44499595 original size:56 final size:56
Alignment explanation
Indices: 44499509--44499625 Score: 227
Period size: 56 Copynumber: 2.1 Consensus size: 56
44499499 TTCTTCACAT
44499509 GTTCCACGAATCAGGCAAGTTCAAGTTGGTCAAATGAGCTTCATTAATCAATTGAC
1 GTTCCACGAATCAGGCAAGTTCAAGTTGGTCAAATGAGCTTCATTAATCAATTGAC
44499565 GTTCCACGAATCAGGCAAGTTCAAGTTGGTCAAATGAGCTTCATTAATCAATTGAC
1 GTTCCACGAATCAGGCAAGTTCAAGTTGGTCAAATGAGCTTCATTAATCAATTGAC
44499621 -TTCCA
1 GTTCCA
44499626 TGGGATTCTC
Statistics
Matches: 61, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
55 5 0.08
56 56 0.92
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.29
Consensus pattern (56 bp):
GTTCCACGAATCAGGCAAGTTCAAGTTGGTCAAATGAGCTTCATTAATCAATTGAC
Found at i:44504931 original size:23 final size:24
Alignment explanation
Indices: 44504887--44504944 Score: 84
Period size: 23 Copynumber: 2.5 Consensus size: 24
44504877 GACATTCTAT
44504887 TATGTATGCATGTGCTGTAGCTGG
1 TATGTATGCATGTGCTGTAGCTGG
*
44504911 TATGTAT-CATGTG-TTTGAGCTGG
1 TATGTATGCATGTGCTGT-AGCTGG
44504934 TATGTATGCAT
1 TATGTATGCAT
44504945 CATTTTCGAC
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
22 2 0.06
23 19 0.61
24 10 0.32
ACGTcount: A:0.19, C:0.10, G:0.29, T:0.41
Consensus pattern (24 bp):
TATGTATGCATGTGCTGTAGCTGG
Found at i:44512117 original size:21 final size:20
Alignment explanation
Indices: 44512091--44512131 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
44512081 TTCGATTTTC
*
44512091 TTTTTTTTCTTATTTTTCAAT
1 TTTTTTTTCTT-TTTTACAAT
44512112 TTTTTTTTCTTTTTTACAAT
1 TTTTTTTTCTTTTTTACAAT
44512132 AATAGATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.15, C:0.10, G:0.00, T:0.76
Consensus pattern (20 bp):
TTTTTTTTCTTTTTTACAAT
Found at i:44513206 original size:5 final size:5
Alignment explanation
Indices: 44513196--44513260 Score: 62
Period size: 5 Copynumber: 12.6 Consensus size: 5
44513186 TAAGAATAAT
* *
44513196 AAATA AAATA AAATA AAA-A TTAGTA AAATA AAA-A GAAATA AAATAA
1 AAATA AAATA AAATA AAATA -AAATA AAATA AAATA -AAATA AAAT-A
44513242 TAAATA AAATA AAATA AAA
1 -AAATA AAATA AAATA AAA
44513261 AAGAAGGGGT
Statistics
Matches: 50, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
4 2 0.04
5 40 0.80
6 4 0.08
7 4 0.08
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (5 bp):
AAATA
Found at i:44513224 original size:15 final size:15
Alignment explanation
Indices: 44513185--44513261 Score: 82
Period size: 15 Copynumber: 4.8 Consensus size: 15
44513175 AAATCTAAGT
44513185 ATAAGAATAATAAATAAA
1 ATAA-AATAA-AAAT-AA
*
44513203 ATAAAATAAAAATTA
1 ATAAAATAAAAATAA
* *
44513218 GTAAAATAAAAAGAA
1 ATAAAATAAAAATAA
44513233 ATAAAATAATAAATAAA
1 ATAAAATAA-AAAT-AA
44513250 ATAAAATAAAAA
1 ATAAAATAAAAA
44513262 AGAAGGGGTG
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
15 21 0.41
16 10 0.20
17 16 0.31
18 4 0.08
ACGTcount: A:0.75, C:0.00, G:0.04, T:0.21
Consensus pattern (15 bp):
ATAAAATAAAAATAA
Found at i:44517552 original size:27 final size:27
Alignment explanation
Indices: 44517520--44517772 Score: 260
Period size: 27 Copynumber: 9.4 Consensus size: 27
44517510 GGCAATTTAT
44517520 CGAAATACCCTCGAAGGGTAAAATTAC
1 CGAAATACCCTCGAAGGGTAAAATTAC
* *
44517547 CGAAATACCTTTC-AAGGGTAAAATTAT
1 CGAAATACC-CTCGAAGGGTAAAATTAC
* * *
44517574 CGAAATACCCCCGAAAGGTAAAATTAT
1 CGAAATACCCTCGAAGGGTAAAATTAC
* * * *
44517601 CGAAATACCC-CCATAGTGTGAAATTAT
1 CGAAATACCCTCGA-AGGGTAAAATTAC
* **
44517628 TGAAATACCCTCGAACAGTAAAATTAC
1 CGAAATACCCTCGAAGGGTAAAATTAC
*
44517655 CGAAATACCCTTGAAGGGTAAAATTAC
1 CGAAATACCCTCGAAGGGTAAAATTAC
* * *
44517682 TGAAATACTCTTGAAGGGTAAAATTAC
1 CGAAATACCCTCGAAGGGTAAAATTAC
* * * *
44517709 TGAAATACCCTTGAAGGGTAAAAGTAT
1 CGAAATACCCTCGAAGGGTAAAATTAC
*
44517736 CGAAATATCCCT-GAAAGGTAAAATTAC
1 CGAAATA-CCCTCGAAGGGTAAAATTAC
*
44517763 CAAAATACCC
1 CGAAATACCC
44517773 ACATAGTGTG
Statistics
Matches: 192, Mismatches: 29, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
26 6 0.03
27 178 0.93
28 8 0.04
ACGTcount: A:0.42, C:0.19, G:0.16, T:0.23
Consensus pattern (27 bp):
CGAAATACCCTCGAAGGGTAAAATTAC
Found at i:44517579 original size:54 final size:54
Alignment explanation
Indices: 44517516--44517772 Score: 306
Period size: 54 Copynumber: 4.8 Consensus size: 54
44517506 CATGGGCAAT
* *
44517516 TTATCGAAATACCCTCGAAGGGTAAAATTACCGAAATACCTTTCAAGGGTAAAA
1 TTATCGAAATACCCTCGAAAGGTAAAATTACCGAAATACCCTTCAAGGGTAAAA
* * * * *
44517570 TTATCGAAATACCCCCGAAAGGTAAAATTATCGAAATACCC-CCATAGTGTGAAA
1 TTATCGAAATACCCTCGAAAGGTAAAATTACCGAAATACCCTTCA-AGGGTAAAA
* *
44517624 TTATTGAAATACCCTCGAACA-GTAAAATTACCGAAATACCCTTGAAGGGTAAAA
1 TTATCGAAATACCCTCGAA-AGGTAAAATTACCGAAATACCCTTCAAGGGTAAAA
* * * * *
44517678 TTA-CTGAAATACTCTTGAAGGGTAAAATTACTGAAATACCCTTGAAGGGTAAAA
1 TTATC-GAAATACCCTCGAAAGGTAAAATTACCGAAATACCCTTCAAGGGTAAAA
* *
44517732 GTATCGAAATATCCCT-GAAAGGTAAAATTACCAAAATACCC
1 TTATCGAAATA-CCCTCGAAAGGTAAAATTACCGAAATACCC
44517773 ACATAGTGTG
Statistics
Matches: 172, Mismatches: 24, Indels: 14
0.82 0.11 0.07
Matches are distributed among these distances:
53 2 0.01
54 164 0.95
55 6 0.03
ACGTcount: A:0.42, C:0.19, G:0.16, T:0.24
Consensus pattern (54 bp):
TTATCGAAATACCCTCGAAAGGTAAAATTACCGAAATACCCTTCAAGGGTAAAA
Found at i:44517798 original size:81 final size:78
Alignment explanation
Indices: 44517550--44517801 Score: 218
Period size: 81 Copynumber: 3.1 Consensus size: 78
44517540 AAATTACCGA
* * * * *
44517550 AATACCTTTCAAGGGTAAAATTATCGAAATACCCCCGAAAGGTAAAATTATCGAAATACCCCCAT
1 AATACCCTTGAAGGGTAAAATTATCGAAATA-CCCTGAAAGGTAAAATTACCGAAATACCCACAT
*
44517615 AGTGTGAAATTATT
65 AGTGTGAAATTCTT
* ** * * * **
44517629 GAAATACCCTCGAACAGTAAAATTACCGAAATACCCTTGAAGGGTAAAATTACTGAAATACTCTT
1 --AATACCCTTGAAGGGTAAAATTATCGAAATACCC-TGAAAGGTAAAATTACCGAAATAC-CCA
* * * *
44517694 GA-AGGGTAAAATTACTGA
62 CATAGTGTGAAATT-CT-T
* *
44517712 AATACCCTTGAAGGGTAAAAGTATCGAAATATCCCTGAAAGGTAAAATTACCAAAATACCCACAT
1 AATACCCTTGAAGGGTAAAATTATCGAAATA-CCCTGAAAGGTAAAATTACCGAAATACCCACAT
44517777 AGTGTGAAATGGTCTT
65 AGTGTGAAAT--TCTT
*
44517793 TATACCCTT
1 AATACCCTT
44517802 AGGAGATGAA
Statistics
Matches: 131, Mismatches: 32, Indels: 16
0.73 0.18 0.09
Matches are distributed among these distances:
80 5 0.04
81 117 0.89
82 8 0.06
83 1 0.01
ACGTcount: A:0.40, C:0.18, G:0.15, T:0.26
Consensus pattern (78 bp):
AATACCCTTGAAGGGTAAAATTATCGAAATACCCTGAAAGGTAAAATTACCGAAATACCCACATA
GTGTGAAATTCTT
Found at i:44518214 original size:28 final size:27
Alignment explanation
Indices: 44518147--44518208 Score: 79
Period size: 28 Copynumber: 2.3 Consensus size: 27
44518137 TTGCATTTTA
* *
44518147 TGTACTGTATTGGGTTAAGGCCCACAC
1 TGTACTGAATTGGGCTAAGGCCCACAC
* *
44518174 TGCTACTGAATTGGGCTAAGGCCCTCAT
1 TG-TACTGAATTGGGCTAAGGCCCACAC
44518202 TGTACTG
1 TGTACTG
44518209 CCATTGAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 7 0.23
28 23 0.77
ACGTcount: A:0.21, C:0.23, G:0.26, T:0.31
Consensus pattern (27 bp):
TGTACTGAATTGGGCTAAGGCCCACAC
Found at i:44530625 original size:20 final size:21
Alignment explanation
Indices: 44530578--44530623 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
44530568 AGTTGATGAG
*
44530578 AAAAAA-TAAATATATATTAT
1 AAAAAATTAAATATAAATTAT
*
44530598 AAAAAATTAAATATAAATTTT
1 AAAAAATTAAATATAAATTAT
44530619 AAAAA
1 AAAAA
44530624 TTTTAAGAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 6 0.26
21 17 0.74
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (21 bp):
AAAAAATTAAATATAAATTAT
Found at i:44532585 original size:19 final size:21
Alignment explanation
Indices: 44532549--44532596 Score: 55
Period size: 19 Copynumber: 2.3 Consensus size: 21
44532539 GAACCAACCT
*
44532549 AATTTTTTTATCATCTTTTCTA
1 AATTTTTTTA-CATCTTTTATA
*
44532571 AATTTTTTTA-A-CTTTTATG
1 AATTTTTTTACATCTTTTATA
44532590 AATTTTT
1 AATTTTT
44532597 AAAAAAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 13 0.54
20 1 0.04
22 10 0.42
ACGTcount: A:0.25, C:0.08, G:0.02, T:0.65
Consensus pattern (21 bp):
AATTTTTTTACATCTTTTATA
Found at i:44537202 original size:26 final size:27
Alignment explanation
Indices: 44537141--44537202 Score: 76
Period size: 26 Copynumber: 2.4 Consensus size: 27
44537131 AGAAGAATAT
*
44537141 TGGAAGC-TTGAAGATGGTAAAAGTAG
1 TGGAAGCTTTGAAGATGATAAAAGTAG
* *
44537167 TTGAAG-TTTGAAGATGATAAAA-TGG
1 TGGAAGCTTTGAAGATGATAAAAGTAG
44537192 TGGAAGCTTTG
1 TGGAAGCTTTG
44537203 CACAAGGAAG
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
25 7 0.23
26 23 0.77
ACGTcount: A:0.35, C:0.03, G:0.32, T:0.29
Consensus pattern (27 bp):
TGGAAGCTTTGAAGATGATAAAAGTAG
Found at i:44538540 original size:11 final size:10
Alignment explanation
Indices: 44538481--44538558 Score: 50
Period size: 10 Copynumber: 7.6 Consensus size: 10
44538471 CTATTAAAAA
*
44538481 TTTTAAAAAT
1 TTTTAATAAT
*
44538491 ATTT-ATAAT
1 TTTTAATAAT
** *
44538500 TTCAAATAAC
1 TTTTAATAAT
*
44538510 TTTTAATTACT
1 TTTTAA-TAAT
*
44538521 TTTAAATAACT
1 TTTTAATAA-T
*
44538532 TTTTTATAAT
1 TTTTAATAAT
44538542 TTTTAATAAT
1 TTTTAATAAT
44538552 TGTTTAA
1 T-TTTAA
44538559 GAAACCACTT
Statistics
Matches: 49, Mismatches: 15, Indels: 7
0.69 0.21 0.10
Matches are distributed among these distances:
9 5 0.10
10 24 0.49
11 20 0.41
ACGTcount: A:0.40, C:0.05, G:0.01, T:0.54
Consensus pattern (10 bp):
TTTTAATAAT
Found at i:44538544 original size:21 final size:20
Alignment explanation
Indices: 44538479--44538550 Score: 67
Period size: 21 Copynumber: 3.6 Consensus size: 20
44538469 AACTATTAAA
*
44538479 AATTTTAAA-AA-TATTTAT
1 AATTTTAAATAACTTTTTAT
* *
44538497 AATTTCAAATAACTTTTAATT
1 AATTTTAAATAACTTTTTA-T
*
44538518 ACTTTTAAATAACTTTTTTAT
1 AATTTTAAATAAC-TTTTTAT
*
44538539 AATTTTTAATAA
1 AATTTTAAATAA
44538551 TTGTTTAAGA
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
18 8 0.19
19 2 0.05
20 4 0.10
21 23 0.55
22 5 0.12
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (20 bp):
AATTTTAAATAACTTTTTAT
Done.