Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A07
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: 93829987
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4250000 characters in sequence are not A, C, G, or T
File 66 of 295
Found at i:19122387 original size:14 final size:13
Alignment explanation
Indices: 19122367--19122402 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
19122357 CCAACTCAAA
19122367 ATTTTTTTTTTTG
1 ATTTTTTTTTTTG
*
19122380 ACTTTTTTTTTTG
1 ATTTTTTTTTTTG
19122393 ATTTTTTTTT
1 ATTTTTTTTT
19122403 CGTTACAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.08, C:0.03, G:0.06, T:0.83
Consensus pattern (13 bp):
ATTTTTTTTTTTG
Found at i:19124023 original size:30 final size:30
Alignment explanation
Indices: 19123989--19124085 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
19123979 TAAACTAAAA
*
19123989 TGAGCTAAGTTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
* * * * * * *
19124019 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
*
19124049 TGAGCTAAGGTTTAGCTCGTGAACTAAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
19124078 ATGAGCTA
1 -TGAGCTA
19124086 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 16, Indels: 2
0.74 0.24 0.03
Matches are distributed among these distances:
29 1 0.02
30 49 0.98
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
Found at i:19125924 original size:10 final size:11
Alignment explanation
Indices: 19125906--19125936 Score: 55
Period size: 10 Copynumber: 2.9 Consensus size: 11
19125896 TTTCTTCACG
19125906 AATTTTTTTCA
1 AATTTTTTTCA
19125917 AATTTTTTTC-
1 AATTTTTTTCA
19125927 AATTTTTTTC
1 AATTTTTTTC
19125937 TAAAGATACG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.23, C:0.10, G:0.00, T:0.68
Consensus pattern (11 bp):
AATTTTTTTCA
Found at i:19135401 original size:37 final size:37
Alignment explanation
Indices: 19135351--19135429 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
19135341 TTATTACGAA
* * *
19135351 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
19135388 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
19135425 GTCTT
1 GTCTT
19135430 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:19135626 original size:47 final size:47
Alignment explanation
Indices: 19135548--19136170 Score: 1012
Period size: 47 Copynumber: 13.1 Consensus size: 47
19135538 CCCTTCGGGA
* * * * * *
19135548 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
19135595 CCTGTCACATATATATACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
19135642 CCTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
19135691 CCTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
19135740 CTTATCACGTATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
19135787 CTTATCACGTATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
19135834 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
19135881 CCTATCACATATATATACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
19135928 CTTATCACGTATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
19135975 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
19136024 CTTATCACGTATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
19136071 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
19136120 CTTATCACATATATACACTTTCACGTTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
19136167 CTTA
1 CTTA
19136171 CTATCATTTC
Statistics
Matches: 547, Mismatches: 23, Indels: 12
0.94 0.04 0.02
Matches are distributed among these distances:
47 361 0.66
49 186 0.34
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:19136168 original size:96 final size:96
Alignment explanation
Indices: 19135548--19136170 Score: 1042
Period size: 96 Copynumber: 6.5 Consensus size: 96
19135538 CCCTTCGGGA
* * * * * * * *
19135548 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATAT--
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
19135611 ACTTTCACATTCATCACATCGGCCATTAGGC
66 ACTTTCACATTCATCACATCGGCCATTAGGC
* *
19135642 CCTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATAT
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAT
19135707 ACACTTTCACATTCATCACATCGGCCATTAGGC
64 ACACTTTCACATTCATCACATCGGCCATTAGGC
* *
19135740 CTTATCACGTATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--GTATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
19135803 ACTTTCACATTCATCACATCGGCCATTAGGC
66 ACTTTCACATTCATCACATCGGCCATTAGGC
*
19135834 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATAT--
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
19135897 ACTTTCACATTCATCACATCGGCCATTAGGC
66 ACTTTCACATTCATCACATCGGCCATTAGGC
*
19135928 CTTATCACGTATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
19135993 ACTTTCACATTCATCACATCGGCCATTAGGC
66 ACTTTCACATTCATCACATCGGCCATTAGGC
*
19136024 CTTATCACGTATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
19136089 ACTTTCACATTCATCACATCGGCCATTAGGC
66 ACTTTCACATTCATCACATCGGCCATTAGGC
*
19136120 CTTATCACATATATACACTTTCACGTTCATCACATCGGCCATTAGGCCTTA
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
19136171 CTATCATTTC
Statistics
Matches: 502, Mismatches: 19, Indels: 14
0.94 0.04 0.03
Matches are distributed among these distances:
94 190 0.38
96 274 0.55
98 38 0.08
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (96 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
ACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:19141204 original size:30 final size:29
Alignment explanation
Indices: 19141170--19141236 Score: 107
Period size: 30 Copynumber: 2.3 Consensus size: 29
19141160 ATGAATCGGA
19141170 AGCTTTGGCACTAAGTGTGCGATTTAAACT
1 AGCTTTGGCACTAAGTGTGCGATTT-AACT
*
19141200 AGCTTTAGCACTAAGTGTGCGATTTAACT
1 AGCTTTGGCACTAAGTGTGCGATTTAACT
*
19141229 GGCTTTGG
1 AGCTTTGG
19141237 TTACTTGAGG
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
29 10 0.29
30 24 0.71
ACGTcount: A:0.24, C:0.16, G:0.25, T:0.34
Consensus pattern (29 bp):
AGCTTTGGCACTAAGTGTGCGATTTAACT
Found at i:19154154 original size:15 final size:15
Alignment explanation
Indices: 19154131--19154160 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
19154121 CTTTGTATTT
19154131 GGTAATCATTAAGTA
1 GGTAATCATTAAGTA
*
19154146 GGTATTCATTAAGTA
1 GGTAATCATTAAGTA
19154161 TAAGTGATGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.07, G:0.20, T:0.37
Consensus pattern (15 bp):
GGTAATCATTAAGTA
Found at i:19156713 original size:30 final size:30
Alignment explanation
Indices: 19156679--19156775 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
19156669 TAAACTAAAA
*
19156679 TGAGCTAAGTTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
* * * * * * *
19156709 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
19156739 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
19156768 ATGAGCTA
1 -TGAGCTA
19156776 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
Found at i:19165986 original size:42 final size:43
Alignment explanation
Indices: 19165867--19166030 Score: 120
Period size: 43 Copynumber: 3.8 Consensus size: 43
19165857 CATAGGATTC
* * * * *
19165867 CGATATAAGATTTCGTGTAAGACCACGTCTGGGAC-GTTCGCAT
1 CGATATATGATTACATGTAAGACCATGTCTGGGACAG-TAGCAT
* * * *
19165910 CAATTTGA-GATTTATATGTAAAACCATGTCTGGGACA-TCAGCAT
1 CGATAT-ATGA-TTACATGTAAGACCATGTCTGGGACAGT-AGCAT
* * * *
19165954 CG-TATATGATTTCATGTAAGACCCTGTTTGGGACAGTGGCAT
1 CGATATATGATTACATGTAAGACCATGTCTGGGACAGTAGCAT
* * *
19165996 TGATATTTGATTACATGTAAGACCACGTCTGGGAC
1 CGATATATGATTACATGTAAGACCATGTCTGGGAC
19166031 GTTGGCATTG
Statistics
Matches: 92, Mismatches: 22, Indels: 14
0.72 0.17 0.11
Matches are distributed among these distances:
42 27 0.29
43 39 0.42
44 26 0.28
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.31
Consensus pattern (43 bp):
CGATATATGATTACATGTAAGACCATGTCTGGGACAGTAGCAT
Found at i:19168645 original size:27 final size:27
Alignment explanation
Indices: 19168597--19168648 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
19168587 TGTTTGTAGG
* * *
19168597 TACATGCATGGATGGCATTGAAGATAA
1 TACATGCATGGACGACAATGAAGATAA
19168624 TACATGCATGGACGACAATGAAGAT
1 TACATGCATGGACGACAATGAAGAT
19168649 GCTTCAATGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.38, C:0.13, G:0.25, T:0.23
Consensus pattern (27 bp):
TACATGCATGGACGACAATGAAGATAA
Found at i:19175586 original size:12 final size:12
Alignment explanation
Indices: 19175569--19175599 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
19175559 TTGGCTACTT
19175569 AACAAAATGCTA
1 AACAAAATGCTA
19175581 AACAAAATGCTA
1 AACAAAATGCTA
19175593 AACAAAA
1 AACAAAA
19175600 GACTCGAGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.65, C:0.16, G:0.06, T:0.13
Consensus pattern (12 bp):
AACAAAATGCTA
Found at i:19180870 original size:28 final size:28
Alignment explanation
Indices: 19180838--19180966 Score: 102
Period size: 28 Copynumber: 4.6 Consensus size: 28
19180828 TAATTATATG
** *
19180838 TGGCACTTAACGTGCGAAGTATC-AGGGA
1 TGGCACTTAGTGTGCGAAGTAACGA-GGA
*
19180866 TGGCACTTAGTGTACGAAGTAACGAGGA
1 TGGCACTTAGTGTGCGAAGTAACGAGGA
** * * *
19180894 TGGCACTTAGTGTGCGAAACATCCAGAA
1 TGGCACTTAGTGTGCGAAGTAACGAGGA
* * *
19180922 CGGCACTTAGTGTGC-AAGGTATCGAGTA
1 TGGCACTTAGTGTGCGAA-GTAACGAGGA
19180950 TGGCA-TCTAGTGTGCGA
1 TGGCACT-TAGTGTGCGA
19180967 TACATTGAAT
Statistics
Matches: 81, Mismatches: 16, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
27 3 0.04
28 76 0.94
29 2 0.02
ACGTcount: A:0.28, C:0.18, G:0.31, T:0.23
Consensus pattern (28 bp):
TGGCACTTAGTGTGCGAAGTAACGAGGA
Found at i:19181112 original size:32 final size:32
Alignment explanation
Indices: 19181029--19181112 Score: 116
Period size: 32 Copynumber: 2.6 Consensus size: 32
19181019 TACGAGATGA
* *
19181029 TACAGGTATCTACGAAAATTGGTACAATATGG
1 TACAGGTATGTACGAAAATTGGTACAATATAG
*
19181061 TACAGGTATGTAC-AGAAATTTGTACAATATAG
1 TACAGGTATGTACGA-AAATTGGTACAATATAG
*
19181093 TACATGTATGTACGAAAATT
1 TACAGGTATGTACGAAAATT
19181113 CAATTGAGTA
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
31 1 0.02
32 44 0.96
33 1 0.02
ACGTcount: A:0.39, C:0.11, G:0.19, T:0.31
Consensus pattern (32 bp):
TACAGGTATGTACGAAAATTGGTACAATATAG
Found at i:19181737 original size:69 final size:70
Alignment explanation
Indices: 19181626--19181768 Score: 252
Period size: 69 Copynumber: 2.1 Consensus size: 70
19181616 GTTTCAGAAG
19181626 TTTGCTCGGGTTGGAAGTCAACAGAGATCACATCACACTATCCTACTATTGATTTTTGGTATTTT
1 TTTGCTCGGGTTGGAAGTCAACAGAGATCACATCACACTATCCTACTATTGATTTTTGGTATTTT
19181691 TACA-
66 TACAC
* * *
19181695 TTTGCTCTGGTTGGAAGTCAACAGAGATCGCATCACACTATCCTGCTATTGATTTTTGGTATTTT
1 TTTGCTCGGGTTGGAAGTCAACAGAGATCACATCACACTATCCTACTATTGATTTTTGGTATTTT
19181760 TACAC
66 TACAC
19181765 TTTG
1 TTTG
19181769 GGGCTTGGTA
Statistics
Matches: 70, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
69 66 0.94
70 4 0.06
ACGTcount: A:0.24, C:0.19, G:0.18, T:0.39
Consensus pattern (70 bp):
TTTGCTCGGGTTGGAAGTCAACAGAGATCACATCACACTATCCTACTATTGATTTTTGGTATTTT
TACAC
Found at i:19188381 original size:30 final size:30
Alignment explanation
Indices: 19188347--19188443 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
19188337 TAAACTAAAA
19188347 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
19188377 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
19188407 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
19188437 TGAGCTA
1 TGAGCTA
19188444 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 2 0.04
30 42 0.84
31 6 0.12
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:19199693 original size:27 final size:27
Alignment explanation
Indices: 19199662--19199839 Score: 187
Period size: 27 Copynumber: 6.6 Consensus size: 27
19199652 TAAATTGTAC
19199662 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
19199689 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
19199715 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
19199743 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* **
19199771 AGCACTAAGTGTGCGATTTGATTGCGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
19199798 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
* *
19199825 AGCACTGAGTATGCG
1 AGCACTAAGTGTGCG
19199840 GACTCAATAT
Statistics
Matches: 126, Mismatches: 22, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
27 103 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:19207677 original size:40 final size:40
Alignment explanation
Indices: 19207633--19207894 Score: 328
Period size: 39 Copynumber: 6.7 Consensus size: 40
19207623 GCTCCTCGTT
* *
19207633 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
19207673 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
*
19207713 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGTA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
19207752 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
19207791 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* *
19207830 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGT-ATC-TCGCA
19207871 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
19207895 CATCATTCAA
Statistics
Matches: 203, Mismatches: 11, Indels: 17
0.88 0.05 0.07
Matches are distributed among these distances:
38 2 0.01
39 126 0.62
40 64 0.32
41 11 0.05
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:19221259 original size:48 final size:48
Alignment explanation
Indices: 19221204--19221348 Score: 220
Period size: 48 Copynumber: 3.0 Consensus size: 48
19221194 GTCAACAATT
* * *
19221204 ATACATAACATTTAACACATATAGAGTCATATTAACTTACTCTTTTCA
1 ATACATAACATATATCACATACAGAGTCATATTAACTTACTCTTTTCA
*
19221252 ATACATAACATATATCACATACAGAGTTATATTAACTTACT-TTTTGCA
1 ATACATAACATATATCACATACAGAGTCATATTAACTTACTCTTTT-CA
* *
19221300 ATGCATAACATATATCACATACAAAGTCATATTAACTTACTCTTTTCA
1 ATACATAACATATATCACATACAGAGTCATATTAACTTACTCTTTTCA
19221348 A
1 A
19221349 ATATTTCTTT
Statistics
Matches: 88, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
47 4 0.05
48 80 0.91
49 4 0.05
ACGTcount: A:0.40, C:0.19, G:0.05, T:0.37
Consensus pattern (48 bp):
ATACATAACATATATCACATACAGAGTCATATTAACTTACTCTTTTCA
Found at i:19222386 original size:7 final size:8
Alignment explanation
Indices: 19222358--19222386 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
19222348 GCAATTGGGT
19222358 CCACAATC
1 CCACAATC
19222366 CCACAATC
1 CCACAATC
19222374 CCACAAT-
1 CCACAATC
19222381 CCACAA
1 CCACAA
19222387 CTGGCATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
7 6 0.29
8 15 0.71
ACGTcount: A:0.41, C:0.48, G:0.00, T:0.10
Consensus pattern (8 bp):
CCACAATC
Found at i:19230138 original size:16 final size:14
Alignment explanation
Indices: 19230117--19230150 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 14
19230107 AAACTTTTTT
19230117 TTATAAATGTTATATA
1 TTATAAAT-TT-TATA
19230133 TTATAAATTTTATA
1 TTATAAATTTTATA
19230147 TTAT
1 TTAT
19230151 TTTTAACATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 8 0.44
15 2 0.11
16 8 0.44
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (14 bp):
TTATAAATTTTATA
Found at i:19231586 original size:29 final size:28
Alignment explanation
Indices: 19231553--19231690 Score: 150
Period size: 28 Copynumber: 4.9 Consensus size: 28
19231543 GATAGTCCAT
* *
19231553 ATGGACTATCTTTCAAGCAATAGTAGTGC
1 ATGGACTATCTTTCAAGCAAGAGT-CTGC
* *
19231582 ATGGACTATCATTCAAGCAAGAGTCCGC
1 ATGGACTATCTTTCAAGCAAGAGTCTGC
* *
19231610 AGGGACTATATTTCAAGCAAGAGTCTGC
1 ATGGACTATCTTTCAAGCAAGAGTCTGC
* * * **
19231638 ATGGACCAACTTTCAAGAAAGAGTCCAC
1 ATGGACTATCTTTCAAGCAAGAGTCTGC
* *
19231666 ATGGACCAACTTTCAAGCAAGAGTC
1 ATGGACTATCTTTCAAGCAAGAGTC
19231691 CATATGGAGC
Statistics
Matches: 93, Mismatches: 16, Indels: 1
0.85 0.15 0.01
Matches are distributed among these distances:
28 71 0.76
29 22 0.24
ACGTcount: A:0.34, C:0.22, G:0.21, T:0.23
Consensus pattern (28 bp):
ATGGACTATCTTTCAAGCAAGAGTCTGC
Found at i:19231740 original size:28 final size:28
Alignment explanation
Indices: 19231709--19231788 Score: 115
Period size: 28 Copynumber: 2.9 Consensus size: 28
19231699 GCAAGACTCT
*
19231709 GCATGGACTAACTTTTAAGCAAGAGTTC
1 GCATGGACTAACTTTCAAGCAAGAGTTC
* * *
19231737 GCATAGACTACCTTTCAAGCAAGAGTTT
1 GCATGGACTAACTTTCAAGCAAGAGTTC
*
19231765 GCATGGACTATCTTTCAAGCAAGA
1 GCATGGACTAACTTTCAAGCAAGA
19231789 ATCTACAGGA
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 46 1.00
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.28
Consensus pattern (28 bp):
GCATGGACTAACTTTCAAGCAAGAGTTC
Found at i:19231752 original size:73 final size:73
Alignment explanation
Indices: 19231625--19231762 Score: 195
Period size: 73 Copynumber: 1.9 Consensus size: 73
19231615 CTATATTTCA
* *
19231625 AGCAAGAGTCTGCATGGACCAACTTTCAAGAAAGAGTCCACATGGACCAACTTTCAAGCAAGAGT
1 AGCAAGACTCTGCATGGACCAACTTTCAAGAAAGAGTCCACATAGACCAACTTTCAAGCAAGAGT
19231690 CCATATGG
66 CCATATGG
* * * * * * *
19231698 AGCAAGACTCTGCATGGACTAACTTTTAAGCAAGAGTTCGCATAGACTACCTTTCAAGCAAGAGT
1 AGCAAGACTCTGCATGGACCAACTTTCAAGAAAGAGTCCACATAGACCAACTTTCAAGCAAGAGT
19231763 TTGCATGGAC
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
73 56 1.00
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.22
Consensus pattern (73 bp):
AGCAAGACTCTGCATGGACCAACTTTCAAGAAAGAGTCCACATAGACCAACTTTCAAGCAAGAGT
CCATATGG
Found at i:19231772 original size:101 final size:101
Alignment explanation
Indices: 19231597--19231788 Score: 235
Period size: 101 Copynumber: 1.9 Consensus size: 101
19231587 CTATCATTCA
* *
19231597 AGCAAGAGTCCGCAGGGACTATATTTCAAGCAAGAGTCTGCATGGACCAACTTTCAAGAAAGAGT
1 AGCAAGACTCCGCAGGGACTATATTTCAAGCAAGAGTCTGCATAGACCAACTTTCAAGAAAGAGT
19231662 CCACATGGACCAACTTTCAAGCAAGAGTCCATATGG
66 CCACATGGACCAACTTTCAAGCAAGAGTCCATATGG
* * * * * *
19231698 AGCAAGACTCTGCATGGACTA-ACTTTTAAGCAAGAGT-TCGCATAGACTACCTTTCAAGCAAGA
1 AGCAAGACTCCGCAGGGACTATA-TTTCAAGCAAGAGTCT-GCATAGACCAACTTTCAAGAAAGA
*** * *
19231761 GTTTGCATGGACTATCTTTCAAGCAAGA
64 GTCCACATGGACCAACTTTCAAGCAAGA
19231789 ATCTACAGGA
Statistics
Matches: 76, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
100 2 0.03
101 74 0.97
ACGTcount: A:0.34, C:0.22, G:0.21, T:0.23
Consensus pattern (101 bp):
AGCAAGACTCCGCAGGGACTATATTTCAAGCAAGAGTCTGCATAGACCAACTTTCAAGAAAGAGT
CCACATGGACCAACTTTCAAGCAAGAGTCCATATGG
Found at i:19231802 original size:28 final size:28
Alignment explanation
Indices: 19231698--19231795 Score: 81
Period size: 28 Copynumber: 3.5 Consensus size: 28
19231688 GTCCATATGG
* * * *
19231698 AGCAAGACTCTGCATGGACTAACTTTTA
1 AGCAAGAATCTACATGGACTACCTTTCA
* * *
19231726 AGCAAGAGT-TCGCATAGACTACCTTTCA
1 AGCAAGAATCT-ACATGGACTACCTTTCA
* * * *
19231754 AGCAAGAGTTTGCATGGACTATCTTTCA
1 AGCAAGAATCTACATGGACTACCTTTCA
19231782 AGCAAGAATCTACA
1 AGCAAGAATCTACA
19231796 GGAACTAACT
Statistics
Matches: 59, Mismatches: 9, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
27 1 0.02
28 57 0.97
29 1 0.02
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (28 bp):
AGCAAGAATCTACATGGACTACCTTTCA
Found at i:19231922 original size:28 final size:28
Alignment explanation
Indices: 19231891--19231946 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
19231881 CATGCACAAT
** *
19231891 TCCACATCTATTAACTTGCATGTATGAA
1 TCCACATCTACGAACTCGCATGTATGAA
*
19231919 TCCATATCTACGAACTCGCATGTATGAA
1 TCCACATCTACGAACTCGCATGTATGAA
19231947 ATCAATACAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.32, C:0.23, G:0.12, T:0.32
Consensus pattern (28 bp):
TCCACATCTACGAACTCGCATGTATGAA
Found at i:19232234 original size:46 final size:46
Alignment explanation
Indices: 19232162--19232254 Score: 168
Period size: 46 Copynumber: 2.0 Consensus size: 46
19232152 ACATAATAAT
* *
19232162 ATCATGATTGGGTGTGTTATATTAAAAACTCACTAAGTTAATTTTA
1 ATCATGATTGAGTGTGTTATAGTAAAAACTCACTAAGTTAATTTTA
19232208 ATCATGATTGAGTGTGTTATAGTAAAAACTCACTAAGTTAATTTTA
1 ATCATGATTGAGTGTGTTATAGTAAAAACTCACTAAGTTAATTTTA
19232254 A
1 A
19232255 CTTAGATTCT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.37, C:0.09, G:0.15, T:0.40
Consensus pattern (46 bp):
ATCATGATTGAGTGTGTTATAGTAAAAACTCACTAAGTTAATTTTA
Found at i:19233375 original size:16 final size:16
Alignment explanation
Indices: 19233354--19233384 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
19233344 GAGAATTCTT
19233354 TGTAATTACAAGAAAG
1 TGTAATTACAAGAAAG
*
19233370 TGTAATTACTAGAAA
1 TGTAATTACAAGAAA
19233385 AATTTCATCC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.06, G:0.16, T:0.29
Consensus pattern (16 bp):
TGTAATTACAAGAAAG
Found at i:19240584 original size:24 final size:24
Alignment explanation
Indices: 19240538--19240585 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
19240528 ATTCTTAAGG
* * * *
19240538 ATAAGAATAGATAAGTAAGAGAAA
1 ATAAGAAAAGAAAAGAAAAAGAAA
19240562 ATAAGAAAAGAAAAGAAAAAGAAA
1 ATAAGAAAAGAAAAGAAAAAGAAA
19240586 GAGAAAGAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.71, C:0.00, G:0.19, T:0.10
Consensus pattern (24 bp):
ATAAGAAAAGAAAAGAAAAAGAAA
Found at i:19240585 original size:16 final size:17
Alignment explanation
Indices: 19240564--19240601 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
19240554 AAGAGAAAAT
19240564 AAGAAAAGA-AAAGAAA
1 AAGAAAAGAGAAAGAAA
19240580 AAG-AAAGAGAAAGAAA
1 AAGAAAAGAGAAAGAAA
19240596 AA-AAAA
1 AAGAAAA
19240602 TTAAAGAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 5 0.25
16 15 0.75
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (17 bp):
AAGAAAAGAGAAAGAAA
Found at i:19240741 original size:21 final size:19
Alignment explanation
Indices: 19240710--19240762 Score: 56
Period size: 18 Copynumber: 2.7 Consensus size: 19
19240700 TCAATTTTTT
19240710 AAAAAATTAAAAGGAATAAAAG
1 AAAAAA-TAAAAGG-A-AAAAG
*
19240732 AAAAAATAAATGG-AAAAG
1 AAAAAATAAAAGGAAAAAG
19240750 AAAAAA-AAAAGGA
1 AAAAAATAAAAGGA
19240763 GAGCCTAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
17 5 0.18
18 11 0.39
21 6 0.21
22 6 0.21
ACGTcount: A:0.75, C:0.00, G:0.15, T:0.09
Consensus pattern (19 bp):
AAAAAATAAAAGGAAAAAG
Found at i:19240757 original size:22 final size:21
Alignment explanation
Indices: 19240710--19240759 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
19240700 TCAATTTTTT
* *
19240710 AAAAAATTAAAAGGAATAAAA
1 AAAAAAATAAAAGGAAAAAAA
* *
19240731 GAAAAAATAAATGGAAAAGAAA
1 AAAAAAATAAAAGGAAAA-AAA
19240753 AAAAAAA
1 AAAAAAA
19240760 GGAGAGCCTA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
21 14 0.61
22 9 0.39
ACGTcount: A:0.78, C:0.00, G:0.12, T:0.10
Consensus pattern (21 bp):
AAAAAAATAAAAGGAAAAAAA
Found at i:19244302 original size:8 final size:8
Alignment explanation
Indices: 19244291--19244315 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
19244281 AATGGAAAGT
19244291 AAAAGATG
1 AAAAGATG
19244299 AAAAGATG
1 AAAAGATG
19244307 AAAAGATG
1 AAAAGATG
19244315 A
1 A
19244316 TAAATTAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.64, C:0.00, G:0.24, T:0.12
Consensus pattern (8 bp):
AAAAGATG
Found at i:19245339 original size:26 final size:26
Alignment explanation
Indices: 19245308--19245360 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
19245298 ACAGCTCTTA
19245308 TGAGCTTCCCGATTAAAGGCTCTTTG
1 TGAGCTTCCCGATTAAAGGCTCTTTG
*
19245334 TGAGCTTCTCGATTAAAGGCTCTTTG
1 TGAGCTTCCCGATTAAAGGCTCTTTG
19245360 T
1 T
19245361 AAGATTCTCG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.19, C:0.21, G:0.23, T:0.38
Consensus pattern (26 bp):
TGAGCTTCCCGATTAAAGGCTCTTTG
Found at i:19245368 original size:26 final size:26
Alignment explanation
Indices: 19245317--19245372 Score: 94
Period size: 26 Copynumber: 2.2 Consensus size: 26
19245307 ATGAGCTTCC
* *
19245317 CGATTAAAGGCTCTTTGTGAGCTTCT
1 CGATTAAAGGCTCTTTGTAAGATTCT
19245343 CGATTAAAGGCTCTTTGTAAGATTCT
1 CGATTAAAGGCTCTTTGTAAGATTCT
19245369 CGAT
1 CGAT
19245373 ATGGCTCGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.23, C:0.18, G:0.21, T:0.38
Consensus pattern (26 bp):
CGATTAAAGGCTCTTTGTAAGATTCT
Found at i:19248422 original size:24 final size:24
Alignment explanation
Indices: 19248331--19248444 Score: 103
Period size: 22 Copynumber: 4.9 Consensus size: 24
19248321 ACATCTCGTA
* *
19248331 AGAGCTTAGTG-TTTCAGCTCACT
1 AGAGCTTACTGTTTTCAGCTCAAT
* * * *
19248354 GGAG-TTATTGATTT-AGCTCAAA
1 AGAGCTTACTGTTTTCAGCTCAAT
*
19248376 AAAGCTTACTG--TTCAGCTCAAT
1 AGAGCTTACTGTTTTCAGCTCAAT
*
19248398 AGAGCTTACTGTTTTCAGCTTAAT
1 AGAGCTTACTGTTTTCAGCTCAAT
*
19248422 AGAGCTTACTATTTATCAGCTCA
1 AGAGCTTACTGTTT-TCAGCTCA
19248445 GGAGGAGCTT
Statistics
Matches: 73, Mismatches: 12, Indels: 10
0.77 0.13 0.11
Matches are distributed among these distances:
21 2 0.03
22 30 0.41
23 11 0.15
24 23 0.32
25 7 0.10
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (24 bp):
AGAGCTTACTGTTTTCAGCTCAAT
Found at i:19249229 original size:10 final size:10
Alignment explanation
Indices: 19249216--19249244 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
19249206 ATGGTCAATT
19249216 ATGCTTGTAA
1 ATGCTTGTAA
19249226 ATGCTTGTAA
1 ATGCTTGTAA
19249236 ATGCTTGTA
1 ATGCTTGTA
19249245 TTTTTAGGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.28, C:0.10, G:0.21, T:0.41
Consensus pattern (10 bp):
ATGCTTGTAA
Found at i:19253889 original size:36 final size:36
Alignment explanation
Indices: 19253849--19253920 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
19253839 GATGTAACAG
19253849 TCCGTTTTCAGTAAAATCGAAACAGTGGTTTCGAGA
1 TCCGTTTTCAGTAAAATCGAAACAGTGGTTTCGAGA
19253885 TCCGTTTTCAGTAAAATCGAAACAGTGGTTTCGAGA
1 TCCGTTTTCAGTAAAATCGAAACAGTGGTTTCGAGA
19253921 CCACAAATCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.31
Consensus pattern (36 bp):
TCCGTTTTCAGTAAAATCGAAACAGTGGTTTCGAGA
Found at i:19260729 original size:25 final size:27
Alignment explanation
Indices: 19260692--19260745 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 27
19260682 TCAAACATGC
19260692 ATTTAGGTCAATTTAAC-CCTAGGGGT
1 ATTTAGGTCAATTTAACACCTAGGGGT
* *
19260718 ATTTCGGT-AATTTTACACCTAGGGGT
1 ATTTAGGTCAATTTAACACCTAGGGGT
19260744 AT
1 AT
19260746 AACAGTAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.28
26 18 0.72
ACGTcount: A:0.26, C:0.15, G:0.22, T:0.37
Consensus pattern (27 bp):
ATTTAGGTCAATTTAACACCTAGGGGT
Found at i:19260753 original size:26 final size:26
Alignment explanation
Indices: 19260701--19260784 Score: 80
Period size: 28 Copynumber: 3.2 Consensus size: 26
19260691 CATTTAGGTC
* * *
19260701 AATTTAAC-CCTAGGGGTATTTCGGT
1 AATTTTACACCTAGGGGTATTACAGT
*
19260726 AATTTTACACCTAGGGGTATAACAGT
1 AATTTTACACCTAGGGGTATTACAGT
* * *
19260752 AATTTTCCATACATAGGGGTATTATAGT
1 AATTTT--ACACCTAGGGGTATTACAGT
19260780 AATTT
1 AATTT
19260785 AGCTGCTTTT
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
25 7 0.15
26 20 0.42
28 21 0.44
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.37
Consensus pattern (26 bp):
AATTTTACACCTAGGGGTATTACAGT
Found at i:19262262 original size:26 final size:26
Alignment explanation
Indices: 19262231--19262338 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
19262221 TGAAATGCCC
*
19262231 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
19262257 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
19262283 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
19262309 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
19262335 ATCA
1 ATCA
19262339 ATTTGTACCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:19267822 original size:32 final size:32
Alignment explanation
Indices: 19267784--19267942 Score: 221
Period size: 32 Copynumber: 5.0 Consensus size: 32
19267774 TATAACTATG
*
19267784 CTACTTTTTTATATGTAAAACTAATATATGAT
1 CTACTTTTTTATATGTAAAACTAATGTATGAT
* *
19267816 CTACTTTTTCATATGCAAAACTAATGTATGAT
1 CTACTTTTTTATATGTAAAACTAATGTATGAT
* *
19267848 CTACTTTTTTATATGTGAACCTAATGTATGAT
1 CTACTTTTTTATATGTAAAACTAATGTATGAT
* * *
19267880 ATAC-TTTTTATATGCAAAACTAATGTATAAT
1 CTACTTTTTTATATGTAAAACTAATGTATGAT
* *
19267911 CTACTTTTTTATAGGTAAACCTAATGTATGAT
1 CTACTTTTTTATATGTAAAACTAATGTATGAT
19267943 ATTTTTTATG
Statistics
Matches: 109, Mismatches: 17, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
31 26 0.24
32 83 0.76
ACGTcount: A:0.35, C:0.12, G:0.09, T:0.44
Consensus pattern (32 bp):
CTACTTTTTTATATGTAAAACTAATGTATGAT
Found at i:19267904 original size:63 final size:63
Alignment explanation
Indices: 19267784--19267951 Score: 259
Period size: 63 Copynumber: 2.7 Consensus size: 63
19267774 TATAACTATG
* * * *
19267784 CTACTTTTTTATATGTAAAACTAATATATGATCTACTTTTTCATATGCAAAACTAATGTATGAT
1 CTACTTTTTTATATGTAAACCTAATGTATGATATACTTTTT-ATATGCAAAACTAATGTATAAT
*
19267848 CTACTTTTTTATATGTGAACCTAATGTATGATATACTTTTTATATGCAAAACTAATGTATAAT
1 CTACTTTTTTATATGTAAACCTAATGTATGATATACTTTTTATATGCAAAACTAATGTATAAT
*
19267911 CTACTTTTTTATAGGTAAACCTAATGTATGATAT--TTTTTAT
1 CTACTTTTTTATATGTAAACCTAATGTATGATATACTTTTTAT
19267952 GTTTGGTATT
Statistics
Matches: 97, Mismatches: 7, Indels: 3
0.91 0.07 0.03
Matches are distributed among these distances:
61 7 0.07
63 53 0.55
64 37 0.38
ACGTcount: A:0.34, C:0.11, G:0.09, T:0.46
Consensus pattern (63 bp):
CTACTTTTTTATATGTAAACCTAATGTATGATATACTTTTTATATGCAAAACTAATGTATAAT
Found at i:19269970 original size:21 final size:21
Alignment explanation
Indices: 19269944--19269996 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
19269934 CGCTGCTTCT
*
19269944 AATCTCACCGCTACAGTATCC
1 AATCTCACCGCTACAGTAACC
*
19269965 AATCTCACCACTACAGTAACC
1 AATCTCACCGCTACAGTAACC
19269986 AATCTCACCGC
1 AATCTCACCGC
19269997 CACTGCTGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.32, C:0.40, G:0.08, T:0.21
Consensus pattern (21 bp):
AATCTCACCGCTACAGTAACC
Found at i:19277778 original size:34 final size:34
Alignment explanation
Indices: 19277740--19277809 Score: 131
Period size: 34 Copynumber: 2.1 Consensus size: 34
19277730 AGGCAAAGAT
19277740 AATTTTACTATAATGGAAAAAGAACGAATAGTAC
1 AATTTTACTATAATGGAAAAAGAACGAATAGTAC
*
19277774 AATTTTACTATAATGGCAAAAGAACGAATAGTAC
1 AATTTTACTATAATGGAAAAAGAACGAATAGTAC
19277808 AA
1 AA
19277810 AAGATGGAGA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.50, C:0.10, G:0.14, T:0.26
Consensus pattern (34 bp):
AATTTTACTATAATGGAAAAAGAACGAATAGTAC
Found at i:19279180 original size:25 final size:25
Alignment explanation
Indices: 19279148--19279196 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
19279138 AATTTACCAT
19279148 TCCTTAATGTATTTGGGCAAGTTAC
1 TCCTTAATGTATTTGGGCAAGTTAC
19279173 TCCTTAATGTATTTGGGCAAGTTA
1 TCCTTAATGTATTTGGGCAAGTTA
19279197 TACCTCTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.24, C:0.14, G:0.20, T:0.41
Consensus pattern (25 bp):
TCCTTAATGTATTTGGGCAAGTTAC
Found at i:19280542 original size:3 final size:3
Alignment explanation
Indices: 19280534--19280562 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
19280524 CGCGTTTTAT
19280534 ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
19280563 TTGAAGTTCG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.31, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:19284960 original size:13 final size:13
Alignment explanation
Indices: 19284942--19284966 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19284932 ATAGTAAAAC
19284942 TTTTAAAAAAATA
1 TTTTAAAAAAATA
19284955 TTTTAAAAAAAT
1 TTTTAAAAAAAT
19284967 GAGATATATG
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
TTTTAAAAAAATA
Found at i:19285904 original size:19 final size:19
Alignment explanation
Indices: 19285871--19285914 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
19285861 TTATAATTAA
19285871 TAAAAAATTATTAAAAATT-
1 TAAAAAATTATT-AAAATTC
19285890 TAAAAAATTCA-TAAAATTC
1 TAAAAAATT-ATTAAAATTC
19285909 TAAAAA
1 TAAAAA
19285915 GTTGTAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 6 0.26
19 16 0.70
20 1 0.04
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.32
Consensus pattern (19 bp):
TAAAAAATTATTAAAATTC
Found at i:19289939 original size:44 final size:45
Alignment explanation
Indices: 19289879--19290055 Score: 222
Period size: 45 Copynumber: 4.0 Consensus size: 45
19289869 TAGGATTCTA
*
19289879 ATATGTGTTTTCGTGTAAGACCATGTCTGGGACGTT-GCATCAAT
1 ATATGTGTTTTCGTGTAAGACCATGTCTGGGACGTTGGCATCGAT
*
19289923 ATATGTGTTTTCGTGTAAGACCACGTCTGGGACGTTGGCATCGAT
1 ATATGTGTTTTCGTGTAAGACCATGTCTGGGACGTTGGCATCGAT
* ** * *
19289968 ATATGTGGTTAAGTGTAAGACCATGTCGGGGACATTGGCATCG-T
1 ATATGTGTTTTCGTGTAAGACCATGTCTGGGACGTTGGCATCGAT
* *
19290012 AT-T-TG-ATTCGTGTAAGACCCTGTCTGGGACAG-TGGCATCGAT
1 ATATGTGTTTTCGTGTAAGACCATGTCTGGGAC-GTTGGCATCGAT
19290054 AT
1 AT
19290056 GAGATGACAT
Statistics
Matches: 116, Mismatches: 14, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
41 28 0.24
42 5 0.04
43 1 0.01
44 38 0.33
45 44 0.38
ACGTcount: A:0.23, C:0.16, G:0.28, T:0.33
Consensus pattern (45 bp):
ATATGTGTTTTCGTGTAAGACCATGTCTGGGACGTTGGCATCGAT
Found at i:19289984 original size:45 final size:44
Alignment explanation
Indices: 19289879--19290092 Score: 194
Period size: 45 Copynumber: 4.9 Consensus size: 44
19289869 TAGGATTCTA
* * *
19289879 ATATGTGTTTTCGTGTAAGACCATGTCTGGGACGTT-GCATCAAT
1 ATATGTG-ATTCGTGTAAGACCACGTCTGGGACGTTGGCATCGAT
*
19289923 ATATGTGTTTTCGTGTAAGACCACGTCTGGGACGTTGGCATCGAT
1 ATATGTG-ATTCGTGTAAGACCACGTCTGGGACGTTGGCATCGAT
* * * * *
19289968 ATATGTGGTTAAGTGTAAGACCATGTCGGGGACATTGGCATCG-T
1 ATATGTGATT-CGTGTAAGACCACGTCTGGGACGTTGGCATCGAT
19290012 AT-T-TGATTCGTGTAAGACC-CTGTCTGGGACAG-TGGCATCGAT
1 ATATGTGATTCGTGTAAGACCAC-GTCTGGGAC-GTTGGCATCGAT
* * *
19290054 ATGA-GATGA--CATGTAAGACCGCGTCTGGGATGTTGGCAT
1 AT-ATG-TGATTCGTGTAAGACCACGTCTGGGACGTTGGCAT
19290093 TGTTCGATAT
Statistics
Matches: 145, Mismatches: 14, Indels: 23
0.80 0.08 0.13
Matches are distributed among these distances:
41 26 0.18
42 8 0.06
43 25 0.17
44 41 0.28
45 45 0.31
ACGTcount: A:0.23, C:0.16, G:0.29, T:0.31
Consensus pattern (44 bp):
ATATGTGATTCGTGTAAGACCACGTCTGGGACGTTGGCATCGAT
Found at i:19290048 original size:86 final size:89
Alignment explanation
Indices: 19289891--19290055 Score: 225
Period size: 86 Copynumber: 1.9 Consensus size: 89
19289881 ATGTGTTTTC
* * *
19289891 GTGTAAGACCATGTCTGGGACGTTGCATCAATATATGTGTTTTCGTGTAAGACCACGTCTGGGAC
1 GTGTAAGACCATGTCGGGGACATTGCATCAATATATGTGTATTCGTGTAAGACCACGTCTGGGAC
19289956 GTTGGCATCGATATATGTGGTTAA
66 GTTGGCATCGATATATGTGGTTAA
*
19289980 GTGTAAGACCATGTCGGGGACATTGGCATC-GTAT-T-TG-ATTCGTGTAAGACC-CTGTCTGGG
1 GTGTAAGACCATGTCGGGGACATT-GCATCAATATATGTGTATTCGTGTAAGACCAC-GTCTGGG
19290040 ACAG-TGGCATCGATAT
64 AC-GTTGGCATCGATAT
19290056 GAGATGACAT
Statistics
Matches: 69, Mismatches: 4, Indels: 9
0.84 0.05 0.11
Matches are distributed among these distances:
85 1 0.01
86 34 0.49
87 3 0.04
88 1 0.01
89 25 0.36
90 5 0.07
ACGTcount: A:0.23, C:0.17, G:0.29, T:0.31
Consensus pattern (89 bp):
GTGTAAGACCATGTCGGGGACATTGCATCAATATATGTGTATTCGTGTAAGACCACGTCTGGGAC
GTTGGCATCGATATATGTGGTTAA
Found at i:19306414 original size:19 final size:21
Alignment explanation
Indices: 19306386--19306434 Score: 66
Period size: 19 Copynumber: 2.4 Consensus size: 21
19306376 AAACTCCTCG
*
19306386 AGATTAACCACTCGT-C-TCT
1 AGATTGACCACTCGTCCTTCT
19306405 AGATTGACCACTCGTCCTTCT
1 AGATTGACCACTCGTCCTTCT
19306426 AGAGTTGAC
1 AGA-TTGAC
19306435 AATATGTCCC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 14 0.54
20 1 0.04
21 6 0.23
22 5 0.19
ACGTcount: A:0.24, C:0.29, G:0.16, T:0.31
Consensus pattern (21 bp):
AGATTGACCACTCGTCCTTCT
Found at i:19309032 original size:2 final size:2
Alignment explanation
Indices: 19309025--19309049 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
19309015 AATGTTCGAC
19309025 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
19309050 AGATAAGAAC
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:19309138 original size:26 final size:26
Alignment explanation
Indices: 19309109--19309192 Score: 107
Period size: 26 Copynumber: 3.2 Consensus size: 26
19309099 ATTCTTTTTC
19309109 TTAATTTAATATTTAAATTTTTTTAT
1 TTAATTTAATATTTAAATTTTTTTAT
** *
19309135 TTAATTTGGTATATAAATTTGATTTT-T
1 TTAATTTAATATTTAAATTT--TTTTAT
19309162 TTAATTTAATATTTAAATTTTTTTAT
1 TTAATTTAATATTTAAATTTTTTTAT
*
19309188 CTAAT
1 TTAAT
19309193 GTAGCACTTA
Statistics
Matches: 48, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
25 4 0.08
26 22 0.46
27 18 0.38
28 4 0.08
ACGTcount: A:0.33, C:0.01, G:0.04, T:0.62
Consensus pattern (26 bp):
TTAATTTAATATTTAAATTTTTTTAT
Found at i:19309178 original size:27 final size:25
Alignment explanation
Indices: 19309094--19309185 Score: 105
Period size: 26 Copynumber: 3.6 Consensus size: 25
19309084 TGATATATGA
*
19309094 ATTT-AATTCTTTTTCTTAATTTAAT
1 ATTTAAATT-TTTTTTTTAATTTAAT
**
19309119 ATTTAAATTTTTTTATTTAATTTGGT
1 ATTTAAATTTTTTT-TTTAATTTAAT
*
19309145 ATATAAATTTGATTTTTTTAATTTAAT
1 ATTTAAATTT--TTTTTTTAATTTAAT
19309172 ATTTAAATTTTTTT
1 ATTTAAATTTTTTT
19309186 ATCTAATGTA
Statistics
Matches: 56, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
25 13 0.23
26 21 0.38
27 18 0.32
28 4 0.07
ACGTcount: A:0.30, C:0.02, G:0.03, T:0.64
Consensus pattern (25 bp):
ATTTAAATTTTTTTTTTAATTTAAT
Found at i:19309820 original size:25 final size:24
Alignment explanation
Indices: 19309786--19309835 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 24
19309776 TTTGACAAGT
*
19309786 TTAGATACCAAATTAGGTTAAAAAA
1 TTAGATACCAAATTAGG-AAAAAAA
19309811 TTAGATACCAAATTAGGAAAAAAA
1 TTAGATACCAAATTAGGAAAAAAA
19309835 T
1 T
19309836 GTTAAATCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 7 0.29
25 17 0.71
ACGTcount: A:0.54, C:0.08, G:0.12, T:0.26
Consensus pattern (24 bp):
TTAGATACCAAATTAGGAAAAAAA
Found at i:19311316 original size:11 final size:11
Alignment explanation
Indices: 19311300--19311324 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
19311290 AATAATTAAT
19311300 ATTATGTGTTA
1 ATTATGTGTTA
19311311 ATTATGTGTTA
1 ATTATGTGTTA
19311322 ATT
1 ATT
19311325 TCAAGACTTA
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:0.28, C:0.00, G:0.16, T:0.56
Consensus pattern (11 bp):
ATTATGTGTTA
Found at i:19314836 original size:18 final size:19
Alignment explanation
Indices: 19314800--19314837 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
19314790 TGCAAATAAA
*
19314800 TCATTTCTCATTTTAATTT
1 TCATTTCTCATTTCAATTT
*
19314819 TCATTT-TCATTTCCATTT
1 TCATTTCTCATTTCAATTT
19314837 T
1 T
19314838 GAGAAACCTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.18, C:0.18, G:0.00, T:0.63
Consensus pattern (19 bp):
TCATTTCTCATTTCAATTT
Found at i:19316405 original size:99 final size:98
Alignment explanation
Indices: 19316232--19316663 Score: 605
Period size: 99 Copynumber: 4.4 Consensus size: 98
19316222 AAAACATATG
* * *
19316232 AGGTATGAAAGTATTAACATACCATGTTGCGTACTTGTTATTCTGTGTGAGCGATAATGTGTCTG
1 AGGTATGAAAGTATTAACATACCATGTTGCGTACTTGTTATTCTGTGTGATCGATAAAGTGTCCG
* *
19316297 CATTTATTATGTTGAAAATGAATGAGAATGAGTC
66 CATTTA-TATTTTGAAAATGAATGAGAATGAATC
* *
19316331 ATGTATGAAAGTATTAACATACCATGTTGCGTACTTGTTATTCTGTGTGATCGATAAAGTGTTCG
1 AGGTATGAAAGTATTAACATACCATGTTGCGTACTTGTTATTCTGTGTGATCGATAAAGTGTCCG
*
19316396 CATTTATTATTTTGAAAATTAATGAGAATGAATC
66 CATTTA-TATTTTGAAAATGAATGAGAATGAATC
* * * * *
19316430 AGGTATGAAAGAATTAACATACCATGTTGCGTACTTTTTATTCTCTGTGATTGATAAAGTCTCCG
1 AGGTATGAAAGTATTAACATACCATGTTGCGTACTTGTTATTCTGTGTGATCGATAAAGTGTCCG
* ***
19316495 TATTTATATACAGAAAATGAATGAGAATGAATC
66 CATTTATATTTTGAAAATGAATGAGAATGAATC
* * *
19316528 AGGTATGAAAGTATTAACATACCATGTTGTGTACTTGTTATTCTGTGTGATTGATAAAGTGTCCA
1 AGGTATGAAAGTATTAACATACCATGTTGCGTACTTGTTATTCTGTGTGATCGATAAAGTGTCCG
*
19316593 CATTTATACTTTTGAAAATGAATGGGAATGAATC
66 CATTTATA-TTTTGAAAATGAATGAGAATGAATC
* * *
19316627 AGTTATGAAAGTGTTAACATATCAT-TTAGCGTACTTG
1 AGGTATGAAAGTATTAACATACCATGTT-GCGTACTTG
19316664 ATATACAATA
Statistics
Matches: 296, Mismatches: 35, Indels: 4
0.88 0.10 0.01
Matches are distributed among these distances:
98 91 0.31
99 205 0.69
ACGTcount: A:0.33, C:0.11, G:0.20, T:0.37
Consensus pattern (98 bp):
AGGTATGAAAGTATTAACATACCATGTTGCGTACTTGTTATTCTGTGTGATCGATAAAGTGTCCG
CATTTATATTTTGAAAATGAATGAGAATGAATC
Found at i:19316568 original size:197 final size:198
Alignment explanation
Indices: 19316232--19316663 Score: 618
Period size: 197 Copynumber: 2.2 Consensus size: 198
19316222 AAAACATATG
* * * *
19316232 AGGTATGAAAGTATTAACATACCATGTTGCGTACTTGTTATTCTGTGTGAGCGATAATGTGTCTG
1 AGGTATGAAAGTATTAACATACCATGTTGCGTACTTGTTATTCTCTGTGAGCGATAAAGTCTCCG
*** * *
19316297 CATTTATTATGTTGAAAATGAATGAGAATGAGTCATGTATGAAAGTATTAACATACCATGTTGCG
66 CATTTATTATACAGAAAATGAATGAGAATGAATCAGGTATGAAAGTATTAACATACCATGTTGCG
* * *
19316362 TACTTGTTATTCTGTGTGATCGATAAAGTGTTCGCATTTATTA-TTTTGAAAATTAATGAGAATG
131 TACTTGTTATTCTGTGTGATCGATAAAGTGTCCACATTTA-TACTTTTGAAAATGAATGAGAATG
19316426 AATC
195 AATC
* * **
19316430 AGGTATGAAAGAATTAACATACCATGTTGCGTACTTTTTATTCTCTGTGATTGATAAAGTCTCCG
1 AGGTATGAAAGTATTAACATACCATGTTGCGTACTTGTTATTCTCTGTGAGCGATAAAGTCTCCG
* *
19316495 TATTTA-TATACAGAAAATGAATGAGAATGAATCAGGTATGAAAGTATTAACATACCATGTTGTG
66 CATTTATTATACAGAAAATGAATGAGAATGAATCAGGTATGAAAGTATTAACATACCATGTTGCG
* *
19316559 TACTTGTTATTCTGTGTGATTGATAAAGTGTCCACATTTATACTTTTGAAAATGAATGGGAATGA
131 TACTTGTTATTCTGTGTGATCGATAAAGTGTCCACATTTATACTTTTGAAAATGAATGAGAATGA
19316624 ATC
196 ATC
* * *
19316627 AGTTATGAAAGTGTTAACATATCAT-TTAGCGTACTTG
1 AGGTATGAAAGTATTAACATACCATGTT-GCGTACTTG
19316664 ATATACAATA
Statistics
Matches: 207, Mismatches: 25, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
196 4 0.02
197 141 0.68
198 62 0.30
ACGTcount: A:0.33, C:0.11, G:0.20, T:0.37
Consensus pattern (198 bp):
AGGTATGAAAGTATTAACATACCATGTTGCGTACTTGTTATTCTCTGTGAGCGATAAAGTCTCCG
CATTTATTATACAGAAAATGAATGAGAATGAATCAGGTATGAAAGTATTAACATACCATGTTGCG
TACTTGTTATTCTGTGTGATCGATAAAGTGTCCACATTTATACTTTTGAAAATGAATGAGAATGA
ATC
Found at i:19319584 original size:38 final size:39
Alignment explanation
Indices: 19319513--19319598 Score: 97
Period size: 38 Copynumber: 2.3 Consensus size: 39
19319503 TTTAAAATGT
* * * *
19319513 TATTTTTATACAATAGTAATAGTATTTTATTTTTACATA
1 TATTTTTAAAAAATAGTAATAGTATGTTATTTTTACAAA
*
19319552 TATTTTTAAAAAATA-TAATTA-TATGTTATTTTTCCAAA
1 TATTTTTAAAAAATAGTAA-TAGTATGTTATTTTTACAAA
19319590 T-TTTTTAAA
1 TATTTTTAAA
19319599 TAATTTAAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
37 8 0.20
38 18 0.44
39 15 0.37
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.53
Consensus pattern (39 bp):
TATTTTTAAAAAATAGTAATAGTATGTTATTTTTACAAA
Found at i:19339775 original size:284 final size:284
Alignment explanation
Indices: 19339265--19340118 Score: 1618
Period size: 284 Copynumber: 3.0 Consensus size: 284
19339255 TTTCATGTTC
*
19339265 ATATGCAACATTCTTTATAATTCAACTATTATTTATAGTTCATTCAAAGCTGTCTACTTGAGTCA
1 ATATGCAACATTCTCTATAATTCAACTATTATTTATAGTTCATTCAAAGCTGTCTACTTGAGTCA
19339330 TAGTCACTAAATTATTTTTATCTTGAGCTACAGAACTCCAAATTAGTATCTGATAATTTTACATG
66 TAGTCACTAAATTATTTTTATCTTGAGCTACAGAACTCCAAATTAGTATCTGATAATTTTACATG
* * *
19339395 AAACTAGACTCACATATATTCTTACCATAAAATTTTTATAAGTTTTGGTTTTGCCAATTAGTACA
131 AAACTAGACTCACATATCTTCTTACCATAAAATTTTTATAAGTTTTGGTTTAGCCAATCAGTACA
19339460 GTTTATTCTTTAAAGTCACCCCTGTTCTGCTGTTGACAGTTCTAACCCTTCTTCACTAAAAATTA
196 GTTTATTCTTTAAAGTCACCCCTGTTCTGCTGTTGACAGTTCTAACCCTTCTTCACTAAAAATTA
19339525 ATTATCTCTTCATACAGAATTCAA
261 ATTATCTCTTCATACAGAATTCAA
19339549 ATATGCAACATTCTCTATAATTCAACTATTATTTATAGTTCATTCAAAGCTGTCTACTTGAGTCA
1 ATATGCAACATTCTCTATAATTCAACTATTATTTATAGTTCATTCAAAGCTGTCTACTTGAGTCA
*
19339614 TAGTCACTAAATTATTTTTATCTTGAGCTACAGAACTCCAAATTAGTATATGATAATTTTACATG
66 TAGTCACTAAATTATTTTTATCTTGAGCTACAGAACTCCAAATTAGTATCTGATAATTTTACATG
19339679 AAACTAGACTCACATATCTTCTTACCATAAAATTTTTATAAGTTTTGGTTTAGCCAATCAGTACA
131 AAACTAGACTCACATATCTTCTTACCATAAAATTTTTATAAGTTTTGGTTTAGCCAATCAGTACA
19339744 GTTTATTCTTTAAAGTCACCCCTGTTCTGCTGTTGACAGTTCTAACCCTTCTTCACTAAAAATTA
196 GTTTATTCTTTAAAGTCACCCCTGTTCTGCTGTTGACAGTTCTAACCCTTCTTCACTAAAAATTA
19339809 ATTATCTCTTCATACAGAATTCAA
261 ATTATCTCTTCATACAGAATTCAA
*
19339833 ATATGCAACATTCTCTATAATTCAACTATTATTTATAGTTCATTCAAAGCTGTCTACTTGATTCA
1 ATATGCAACATTCTCTATAATTCAACTATTATTTATAGTTCATTCAAAGCTGTCTACTTGAGTCA
* *
19339898 TAGTCACTAAACTATTTTTATCTTGAGCTAAAGAACTCCAAATTAGTATCTGATAATTTTACATG
66 TAGTCACTAAATTATTTTTATCTTGAGCTACAGAACTCCAAATTAGTATCTGATAATTTTACATG
*
19339963 AAACTAGACTCACATATCTTCTTACCATAAAATTTTTGTAAGTTTTGGTTTAGCCAATCAGTACA
131 AAACTAGACTCACATATCTTCTTACCATAAAATTTTTATAAGTTTTGGTTTAGCCAATCAGTACA
*
19340028 GTTTATTCTTTAAAGTCACCCCTGTTCTGCTGTTGACAGTTCTAACTCTTCTTCACTAAAAATTA
196 GTTTATTCTTTAAAGTCACCCCTGTTCTGCTGTTGACAGTTCTAACCCTTCTTCACTAAAAATTA
19340093 ATTATCTCTTCATACAGAATTCAA
261 ATTATCTCTTCATACAGAATTCAA
19340117 AT
1 AT
19340119 GATGTTCTCG
Statistics
Matches: 559, Mismatches: 11, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
284 559 1.00
ACGTcount: A:0.32, C:0.19, G:0.09, T:0.40
Consensus pattern (284 bp):
ATATGCAACATTCTCTATAATTCAACTATTATTTATAGTTCATTCAAAGCTGTCTACTTGAGTCA
TAGTCACTAAATTATTTTTATCTTGAGCTACAGAACTCCAAATTAGTATCTGATAATTTTACATG
AAACTAGACTCACATATCTTCTTACCATAAAATTTTTATAAGTTTTGGTTTAGCCAATCAGTACA
GTTTATTCTTTAAAGTCACCCCTGTTCTGCTGTTGACAGTTCTAACCCTTCTTCACTAAAAATTA
ATTATCTCTTCATACAGAATTCAA
Found at i:19344729 original size:23 final size:22
Alignment explanation
Indices: 19344703--19344777 Score: 69
Period size: 23 Copynumber: 3.2 Consensus size: 22
19344693 TTTATTATTA
*
19344703 ATTTTAAAAATTTCGAAATATAT
1 ATTTTAAAAATTT-TAAATATAT
* **
19344726 ATTTGAAATGTTTTATAATATAT
1 ATTTTAAAAATTTTA-AATATAT
*
19344749 ATTTTTTTAAAATTTTAAATATAT
1 A--TTTTAAAAATTTTAAATATAT
19344773 ATTTT
1 ATTTT
19344778 TGAAATTATT
Statistics
Matches: 41, Mismatches: 8, Indels: 7
0.73 0.14 0.12
Matches are distributed among these distances:
22 5 0.12
23 18 0.44
24 8 0.20
25 10 0.24
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.53
Consensus pattern (22 bp):
ATTTTAAAAATTTTAAATATAT
Found at i:19344788 original size:25 final size:25
Alignment explanation
Indices: 19344720--19344789 Score: 81
Period size: 25 Copynumber: 2.8 Consensus size: 25
19344710 AAATTTCGAA
* *
19344720 ATATATATTTGAAATGTTTTATAAT
1 ATATATTTTTGAAATATTTTATAAT
*
19344745 ATATATTTTTTTAAA-ATTTTA-AAT
1 ATATA-TTTTTGAAATATTTTATAAT
19344769 ATATATTTTTGAAATTATTTT
1 ATATATTTTTGAAA-TATTTT
19344790 TTTTAAATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
23 8 0.21
24 8 0.21
25 15 0.39
26 7 0.18
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (25 bp):
ATATATTTTTGAAATATTTTATAAT
Found at i:19344798 original size:36 final size:35
Alignment explanation
Indices: 19344748--19344818 Score: 115
Period size: 36 Copynumber: 2.0 Consensus size: 35
19344738 TTATAATATA
19344748 TATTTTTTTAAAATTTTAAATATATATTTTTGAAAT
1 TATTTTTTTAAAATTTTAAATAT-TATTTTTGAAAT
* *
19344784 TATTTTTTTTAAATTTTAAATATTATTTTTTAAAT
1 TATTTTTTTAAAATTTTAAATATTATTTTTGAAAT
19344819 ATTAAATATA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
35 11 0.33
36 22 0.67
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (35 bp):
TATTTTTTTAAAATTTTAAATATTATTTTTGAAAT
Found at i:19344812 original size:21 final size:21
Alignment explanation
Indices: 19344775--19344832 Score: 75
Period size: 21 Copynumber: 2.8 Consensus size: 21
19344765 AAATATATAT
19344775 TTTTGAAATTATT-TTTTTTAAA
1 TTTT-AAA-TATTATTTTTTAAA
19344797 TTTTAAATATTATTTTTTAAA
1 TTTTAAATATTATTTTTTAAA
*
19344818 TATTAAATA-TATTTT
1 TTTTAAATATTATTTT
19344833 AATAATATAA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
20 10 0.29
21 20 0.59
22 4 0.12
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (21 bp):
TTTTAAATATTATTTTTTAAA
Found at i:19344934 original size:132 final size:124
Alignment explanation
Indices: 19344817--19345053 Score: 302
Period size: 132 Copynumber: 1.9 Consensus size: 124
19344807 TATTTTTTAA
19344817 ATATTAAA-TAT-ATTTT-AATAATATAAAACAT-TTAAATATTTTAAAGATATGACCTTTCAAA
1 ATATTAAATTATGATTTTAAATAATATAAAACATATT--AT-TTTTAAAGATATGACCTTTCAAA
19344878 TTTATTATTAGTTTTATAATATTTTAAATGTATATTTTAAATTTTAAATATTTTTAATTTGTTTA
63 TTTA-T-TT--TTTTATAATATTTTAAAT-T-T-TTTTAAATTTTAAATATTTTTAATTTGTTTA
19344943 TAAT
121 TAAT
* * * * *
19344947 ATTTTAAATTATGGTTTTTAAATTATTTAAAATATATTATTTTTAAAGATATGACCTTTCAAATT
1 ATATTAAATTAT-GATTTTAAATAATATAAAACATATTATTTTTAAAGATATGACCTTTCAAATT
19345012 TATTTTTTTATAATATTTTAAATTTTTTTAAATTTTAAATAT
65 TATTTTTTTATAATATTTTAAATTTTTTTAAATTTTAAATAT
19345054 AATTTTTATA
Statistics
Matches: 97, Mismatches: 5, Indels: 15
0.83 0.04 0.13
Matches are distributed among these distances:
125 17 0.18
126 1 0.01
127 1 0.01
128 18 0.19
130 9 0.09
131 4 0.04
132 27 0.28
133 6 0.06
134 12 0.12
135 2 0.02
ACGTcount: A:0.40, C:0.03, G:0.04, T:0.54
Consensus pattern (124 bp):
ATATTAAATTATGATTTTAAATAATATAAAACATATTATTTTTAAAGATATGACCTTTCAAATTT
ATTTTTTTATAATATTTTAAATTTTTTTAAATTTTAAATATTTTTAATTTGTTTATAAT
Found at i:19344949 original size:20 final size:19
Alignment explanation
Indices: 19344909--19344956 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
19344899 TTTTAAATGT
19344909 ATATTTTAAA--T-TTTAA
1 ATATTTTAAATTTGTTTAA
*
19344925 ATATTTTTAATTTGTTTATA
1 ATATTTTAAATTTGTTTA-A
19344945 ATATTTTAAATT
1 ATATTTTAAATT
19344957 ATGGTTTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
16 9 0.35
18 1 0.04
19 4 0.15
20 12 0.46
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (19 bp):
ATATTTTAAATTTGTTTAA
Found at i:19345034 original size:24 final size:24
Alignment explanation
Indices: 19344934--19345040 Score: 67
Period size: 24 Copynumber: 4.2 Consensus size: 24
19344924 AATATTTTTA
*
19344934 ATTTGTTTATAATATTTTAAA-TT
1 ATTTTTTTATAATATTTTAAATTT
* * *
19344957 ATGGTTTTTA-AATTATTTAAAATAT
1 AT-TTTTTTATAA-TATTTTAAATTT
*
19344982 ATTATTTTTAAAGATATGACCTTTCAAATTT
1 ATT-TTTTTATA-ATAT----TTT-AAATTT
19345013 ATTTTTTTATAATATTTTAAATTT
1 ATTTTTTTATAATATTTTAAATTT
19345037 -TTTT
1 ATTTT
19345041 AAATTTTAAA
Statistics
Matches: 65, Mismatches: 8, Indels: 22
0.68 0.08 0.23
Matches are distributed among these distances:
23 8 0.12
24 19 0.29
25 12 0.18
26 4 0.06
27 1 0.02
29 4 0.06
30 9 0.14
31 8 0.12
ACGTcount: A:0.35, C:0.03, G:0.05, T:0.58
Consensus pattern (24 bp):
ATTTTTTTATAATATTTTAAATTT
Found at i:19345037 original size:17 final size:17
Alignment explanation
Indices: 19345016--19345051 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
19345006 CAAATTTATT
19345016 TTTTTATAATATTTTAAA
1 TTTTTATAA-ATTTTAAA
*
19345034 TTTTTTTAAATTTTAAA
1 TTTTTATAAATTTTAAA
19345051 T
1 T
19345052 ATAATTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TTTTTATAAATTTTAAA
Found at i:19345059 original size:12 final size:13
Alignment explanation
Indices: 19345042--19345091 Score: 50
Period size: 12 Copynumber: 3.7 Consensus size: 13
19345032 AATTTTTTTA
19345042 AATTTTAAATA-T
1 AATTTTAAATATT
19345054 AATTTTTATAAATTATT
1 AA--TTT-TAAA-TATT
19345071 AATTTTAAA-ATT
1 AATTTTAAATATT
19345083 AATTTTAAA
1 AATTTTAAA
19345092 GATATTCAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
12 14 0.42
14 7 0.21
15 7 0.21
16 2 0.06
17 3 0.09
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
AATTTTAAATATT
Found at i:19345113 original size:31 final size:29
Alignment explanation
Indices: 19345072--19345130 Score: 82
Period size: 31 Copynumber: 2.0 Consensus size: 29
19345062 TAAATTATTA
*
19345072 ATTTTAAAATTAATTTTAAAGATATTCAAAC
1 ATTTTAAAATTAAATTTAAA-AT-TTCAAAC
*
19345103 ATTTTTAAATTAAATTTAAAATTTCAAA
1 ATTTTAAAATTAAATTTAAAATTTCAAA
19345131 AATTAATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 6 0.23
30 2 0.08
31 18 0.69
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (29 bp):
ATTTTAAAATTAAATTTAAAATTTCAAAC
Found at i:19348042 original size:130 final size:132
Alignment explanation
Indices: 19347571--19348224 Score: 486
Period size: 132 Copynumber: 4.9 Consensus size: 132
19347561 AGAAAATACG
* * * ** * *
19347571 AGTGAAATTTCGAAA-AGACATTCAATTATTTTGAACAAACTG-GGGATTGCAACCCAGCACGAT
1 AGTGAAATTTC-AAAGGGATATTCGATTATTTTGAACAAAC-GAGAAATTGCAACCCAACACGTT
* * * ** * *
19347634 AGGGCACTATTCCCCGAATTGCCAAACATTGAACATTT--CTTCCGTTTTCAAGAGTTTTTAGAA
64 AGGGCACGATTCCGCAAATTGCCAAACATCAAAC-TTTGCCTT-CGTTTTAAAGAATTTTTA-AA
***
19347697 A-ACGTG
126 AGACACA
* * * * * ** * *
19347703 AGTGAAATTCCAAAGGGATCTTCGATCATTTTGAACAAATGAAAAAGCGCAACCCAGCACGATAG
1 AGTGAAATTTCAAAGGGATATTCGATTATTTTGAACAAACGAGAAATTGCAACCCAACACGTTAG
* * * * * ** *
19347768 GGCACGATTCTCG--AATTGCCAAACATCGAACATCGCATTTGTTTTAAAGGTTTTTCTTAAAAA
66 GGCACGATTC-CGCAAATTGCCAAACATCAAACTTTGCCTTCGTTTTAAA-GAATTT-TTAAAAG
*
19347831 AAACA
128 ACACA
* * ** * ** * *
19347836 TGAGTGAAAACTT-AAAGGAACGTTCGATTATTTTGAACAAATGAGAAATCACAACCCAGCACGA
1 --AGTG-AAATTTCAAAGGGATATTCGATTATTTTGAACAAACGAGAAATTGCAACCCAACACGT
* * ** * * *
19347900 TAGGGCATGATTCC-CAAATTGTCAAACA-CCGAGTATTGCCTTCGTTTTAAAGGATTTTTAGAA
63 TAGGGCACGATTCCGCAAATTGCCAAACATCAAACT-TTGCCTTCGTTTTAAAGAATTTTTAAAA
*
19347963 GAC-CT
127 GACACA
* *
19347968 AGTGAAATTTCAAAGGGATATTTGATTATTTTGAGCAAACGAGAAATTGCAACCCAACACGTTAG
1 AGTGAAATTTCAAAGGGATATTCGATTATTTTGAACAAACGAGAAATTGCAACCCAACACGTTAG
** * * *
19348033 GGTGCGATTCCGCGAATTGCCAAATATCAAACTTTGCCTTCGTTTTAAAGAATTTTTAAAAGGCA
66 GGCACGATTCCGCAAATTGCCAAACATCAAACTTTGCCTTCGTTTTAAAGAATTTTTAAAAGACA
19348098 CA
131 CA
** *
19348100 AGTGAAATTTTGAAGGGATATTCGATTATTTTGAACAAACGCGAAATTGCAACCCAACACGTTAG
1 AGTGAAATTTCAAAGGGATATTCGATTATTTTGAACAAACGAGAAATTGCAACCCAACACGTTAG
* * * * * * *
19348165 GACACTATTCCGCGAATTGCCAAATATCGAA-TCTCGTCTTCGTTTTAAAGAATTTTTAAA
66 GGCACGATTCCGCAAATTGCCAAACATCAAACT-TTGCCTTCGTTTTAAAGAATTTTTAAA
19348225 TGAATACTTA
Statistics
Matches: 417, Mismatches: 86, Indels: 38
0.77 0.16 0.07
Matches are distributed among these distances:
129 5 0.01
130 57 0.14
131 68 0.16
132 181 0.43
133 11 0.03
134 7 0.02
135 84 0.20
136 4 0.01
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.28
Consensus pattern (132 bp):
AGTGAAATTTCAAAGGGATATTCGATTATTTTGAACAAACGAGAAATTGCAACCCAACACGTTAG
GGCACGATTCCGCAAATTGCCAAACATCAAACTTTGCCTTCGTTTTAAAGAATTTTTAAAAGACA
CA
Found at i:19350518 original size:24 final size:22
Alignment explanation
Indices: 19350469--19350518 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 22
19350459 GCTGTTTTTT
*
19350469 TTTGCTTTGTTTTTGCCTGTTC
1 TTTGCTTTGTGTTTGCCTGTTC
*
19350491 -TTGCTGTTGTGTTTGTCTGTTTC
1 TTTGCT-TTGTGTTTGCCTG-TTC
19350514 TTTGC
1 TTTGC
19350519 AGGTGTGGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
21 5 0.22
22 11 0.48
23 3 0.13
24 4 0.17
ACGTcount: A:0.00, C:0.16, G:0.22, T:0.62
Consensus pattern (22 bp):
TTTGCTTTGTGTTTGCCTGTTC
Found at i:19351161 original size:44 final size:44
Alignment explanation
Indices: 19351089--19351826 Score: 711
Period size: 44 Copynumber: 16.8 Consensus size: 44
19351079 TAGATTCACC
* * *
19351089 ATCTTCGATCTACTCTCTGTCAAC-ACAGAGATGCCAAATCTGCT
1 ATCTTCGATCTGCTCTCTG-CCACTACAGAGACGCCAAATCTGCT
* ** * *
19351133 ATCTTCGATCTGCCCTCTAACAATACAGAGACGTCAAA--T-CT
1 ATCTTCGATCTGCTCTCTGCCACTACAGAGACGCCAAATCTGCT
* * ** * * * * *
19351174 A-CTTGGATTTGCT-TCAACGTA-AACACGTGAAAGCCAAATCAGCT
1 ATCTTCGATCTGCTCTCTGC-CACTACA-GAG-ACGCCAAATCTGCT
* * * * *
19351218 ATGTCTTTGATCTGCTCCCTGCCTAATATAGAGATGCCAAATCATGCT
1 A--TCTTCGATCTGCTCTCTGCC-ACTACAGAGACGCCAAATC-TGCT
* * ** *
19351266 ATCTTCGATCTACTCTCCGCTGCTACAGAGATGCCAAATCATGCT
1 ATCTTCGATCTGCTCTCTGCCACTACAGAGACGCCAAATC-TGCT
* * * *
19351311 -TCTTCGATCTACTCTCCGCCGCTACAGAGACGCCAAATCTGTT
1 ATCTTCGATCTGCTCTCTGCCACTACAGAGACGCCAAATCTGCT
* * * * * *
19351354 ATCTTCGACCTGCTTTCTGCCGCTACAGAAACACCAAATCTGTT
1 ATCTTCGATCTGCTCTCTGCCACTACAGAGACGCCAAATCTGCT
* * * * * * *
19351398 GTCTTCGATCTGCT-TTTCGTCGCTACGGAAACGCCAAATCTGTT
1 ATCTTCGATCTGCTCTCT-GCCACTACAGAGACGCCAAATCTGCT
*
19351442 ATCTTCGATCTGCTCTCTGCCGCTACAGAGACGCCAAATCTGCT
1 ATCTTCGATCTGCTCTCTGCCACTACAGAGACGCCAAATCTGCT
* **
19351486 ATCTTCGATCTGCTCTCCGCCACTACAGAGACGCCAAATCTATT
1 ATCTTCGATCTGCTCTCTGCCACTACAGAGACGCCAAATCTGCT
*
19351530 ATCTTCAATCTGCTCTCTGCCACTACAGAGACGCCAAATCTGCT
1 ATCTTCGATCTGCTCTCTGCCACTACAGAGACGCCAAATCTGCT
* * **
19351574 ATCTTCGATCTACTCTCTGCCACTATAGAGACGCCAAATCTATT
1 ATCTTCGATCTGCTCTCTGCCACTACAGAGACGCCAAATCTGCT
* * **
19351618 ATCTTCGATCTACTCTCCGCCACTACAGAGACGCCAAATCTATT
1 ATCTTCGATCTGCTCTCTGCCACTACAGAGACGCCAAATCTGCT
* * *
19351662 ATCTTCGATCTGCTCTCCGCCACTACAGAGACGCCAAATTTGTT
1 ATCTTCGATCTGCTCTCTGCCACTACAGAGACGCCAAATCTGCT
* *
19351706 ATTTTCGATCTGCTCTCTGCCACTACAGAGACGCCAAATCTACT
1 ATCTTCGATCTGCTCTCTGCCACTACAGAGACGCCAAATCTGCT
* ** **
19351750 ATCTTCGATCTGCTCTCCGCCACTATGGAGACGCCAAATCTATT
1 ATCTTCGATCTGCTCTCTGCCACTACAGAGACGCCAAATCTGCT
*
19351794 ATCTTTGATCTGCTCTCTGCCACTACAGAGACG
1 ATCTTCGATCTGCTCTCTGCCACTACAGAGACG
19351827 TCTGCTCTCT
Statistics
Matches: 586, Mismatches: 91, Indels: 34
0.82 0.13 0.05
Matches are distributed among these distances:
39 6 0.01
40 12 0.02
41 9 0.02
42 1 0.00
43 6 0.01
44 484 0.83
45 23 0.04
46 15 0.03
47 19 0.03
48 9 0.02
49 2 0.00
ACGTcount: A:0.25, C:0.31, G:0.15, T:0.29
Consensus pattern (44 bp):
ATCTTCGATCTGCTCTCTGCCACTACAGAGACGCCAAATCTGCT
Found at i:19351855 original size:113 final size:113
Alignment explanation
Indices: 19351714--19351939 Score: 357
Period size: 113 Copynumber: 2.0 Consensus size: 113
19351704 TTATTTTCGA
*
19351714 TCTGCTCTCTGCCACTACAGAGACGCCAAATCTACTATCTTCGA-TCTGCTCTCCGCCACTATGG
1 TCTGCTCTCTGCCACTACAGAGACGCCAAATCTACTATCTTCGACT-TGCTCTCCGCCACTATAG
* *
19351778 AGACGCCAAATCTATTATCTTTGATCTGCTCT-CTGCCACTACAGAGACG
65 AGACACCAAATCTATTATCTTCGATCTGCTCTCCT-CCACTACAGAGACG
* * *
19351827 TCTGCTCTCTGCCACTACAGATACGCCAAATTTGCTATCTTCGACTTGCTCTCCGCCACTATAGA
1 TCTGCTCTCTGCCACTACAGAGACGCCAAATCTACTATCTTCGACTTGCTCTCCGCCACTATAGA
*
19351892 GACACCAAATCTATTATCTTCGATTTGCTCTCCTCCACTACAGAGACG
66 GACACCAAATCTATTATCTTCGATCTGCTCTCCTCCACTACAGAGACG
19351940 CCAAATCTAC
Statistics
Matches: 104, Mismatches: 7, Indels: 4
0.90 0.06 0.03
Matches are distributed among these distances:
113 101 0.97
114 3 0.03
ACGTcount: A:0.23, C:0.33, G:0.15, T:0.29
Consensus pattern (113 bp):
TCTGCTCTCTGCCACTACAGAGACGCCAAATCTACTATCTTCGACTTGCTCTCCGCCACTATAGA
GACACCAAATCTATTATCTTCGATCTGCTCTCCTCCACTACAGAGACG
Found at i:19351877 original size:69 final size:69
Alignment explanation
Indices: 19351758--19351894 Score: 168
Period size: 69 Copynumber: 2.0 Consensus size: 69
19351748 CTATCTTCGA
** * * *
19351758 TCTGCTCTCCGCCACTATGGAGACGCCAAATCTATTATCTTTGATCTGCTCTCTGCCACTACAGA
1 TCTGCTCTCCGCCACTACAGAGACGCCAAATCTACTATCTTCGATCTGCTCTCCGCCACTACAGA
19351823 GACG
66 GACG
* * * * *
19351827 TCTGCTCTCTGCCACTACAGATACGCCAAATTTGCTATCTTCGA-CTTGCTCTCCGCCACTATAG
1 TCTGCTCTCCGCCACTACAGAGACGCCAAATCTACTATCTTCGATC-TGCTCTCCGCCACTACAG
19351891 AGAC
65 AGAC
19351895 ACCAAATCTA
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
68 1 0.02
69 56 0.98
ACGTcount: A:0.22, C:0.33, G:0.16, T:0.29
Consensus pattern (69 bp):
TCTGCTCTCCGCCACTACAGAGACGCCAAATCTACTATCTTCGATCTGCTCTCCGCCACTACAGA
GACG
Found at i:19351900 original size:44 final size:44
Alignment explanation
Indices: 19351827--19352163 Score: 428
Period size: 44 Copynumber: 7.9 Consensus size: 44
19351817 TACAGAGACG
* * * *
19351827 TCTGCTCTCTGCCACTACAGATACGCCAAATTTGCTATCTTCGA
1 TCTGCTCTCCGCCACTACAGAGACGCCAAATCTGTTATCTTCGA
* * *
19351871 -CTTGCTCTCCGCCACTATAGAGACACCAAATCTATTATCTTCGA
1 TC-TGCTCTCCGCCACTACAGAGACGCCAAATCTGTTATCTTCGA
* * **
19351915 TTTGCTCTCCTCCACTACAGAGACGCCAAATCTACTATCTTCGA
1 TCTGCTCTCCGCCACTACAGAGACGCCAAATCTGTTATCTTCGA
19351959 TCTGCTCTCCGCCACTACAGAGACGCCAAATCTGTTATCTTCGA
1 TCTGCTCTCCGCCACTACAGAGACGCCAAATCTGTTATCTTCGA
19352003 TCTGCTCTCCGCCACTACAGAGACGCCAAATCTGTTATCTTCGA
1 TCTGCTCTCCGCCACTACAGAGACGCCAAATCTGTTATCTTCGA
*
19352047 TCTGCTCT----C-C-AC-----CGCTAAATCTGTTATCTTCGA
1 TCTGCTCTCCGCCACTACAGAGACGCCAAATCTGTTATCTTCGA
* * *
19352080 TCTGCTCTCCACCGCTACAGAGACGCAAAATCTGTTATCTTCGA
1 TCTGCTCTCCGCCACTACAGAGACGCCAAATCTGTTATCTTCGA
* *
19352124 TCTACTCTCCGCCGCTACAGAGACGCCAAATCTGTTATCT
1 TCTGCTCTCCGCCACTACAGAGACGCCAAATCTGTTATCT
19352164 ACTTAAAGGA
Statistics
Matches: 259, Mismatches: 21, Indels: 26
0.85 0.07 0.08
Matches are distributed among these distances:
33 28 0.11
37 1 0.00
38 3 0.01
39 3 0.01
40 1 0.00
43 1 0.00
44 222 0.86
ACGTcount: A:0.23, C:0.33, G:0.14, T:0.29
Consensus pattern (44 bp):
TCTGCTCTCCGCCACTACAGAGACGCCAAATCTGTTATCTTCGA
Found at i:19351961 original size:157 final size:157
Alignment explanation
Indices: 19351670--19351983 Score: 477
Period size: 157 Copynumber: 2.0 Consensus size: 157
19351660 TTATCTTCGA
* * *
19351670 TCTGCTCTCCGCCACTACAGAGACGCCAAATTTGTTATTTTCGATCTGCTCTCTGCCACTACAGA
1 TCTGCTCTCCGCCACTACAGAGACGCCAAATTTGCTATCTTCGATCTGCTCTCCGCCACTACAGA
* ** * *
19351735 GACGCCAAATCTACTATCTTCGATCTGCTCTCCGCCACTATGGAGACGCCAAATCTATTATCTTT
66 GACACCAAATCTACTATCTTCGATCTGCTCTCCGCCACTACAGAGACGCCAAATCTACTATCTTC
*
19351800 GATCTGCTCTCTGCCACTACAGAGACG
131 GATCTGCTCTCCGCCACTACAGAGACG
* * *
19351827 TCTGCTCTCTGCCACTACAGATACGCCAAATTTGCTATCTTCGA-CTTGCTCTCCGCCACTATAG
1 TCTGCTCTCCGCCACTACAGAGACGCCAAATTTGCTATCTTCGATC-TGCTCTCCGCCACTACAG
* * *
19351891 AGACACCAAATCTATTATCTTCGATTTGCTCTCCTCCACTACAGAGACGCCAAATCTACTATCTT
65 AGACACCAAATCTACTATCTTCGATCTGCTCTCCGCCACTACAGAGACGCCAAATCTACTATCTT
19351956 CGATCTGCTCTCCGCCACTACAGAGACG
130 CGATCTGCTCTCCGCCACTACAGAGACG
19351984 CCAAATCTGT
Statistics
Matches: 141, Mismatches: 15, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
156 1 0.01
157 140 0.99
ACGTcount: A:0.24, C:0.33, G:0.15, T:0.29
Consensus pattern (157 bp):
TCTGCTCTCCGCCACTACAGAGACGCCAAATTTGCTATCTTCGATCTGCTCTCCGCCACTACAGA
GACACCAAATCTACTATCTTCGATCTGCTCTCCGCCACTACAGAGACGCCAAATCTACTATCTTC
GATCTGCTCTCCGCCACTACAGAGACG
Found at i:19352016 original size:245 final size:245
Alignment explanation
Indices: 19351586--19352163 Score: 744
Period size: 245 Copynumber: 2.3 Consensus size: 245
19351576 CTTCGATCTA
* * *
19351586 CTCTCTGCCACTATAGAGACGCCAAATCTATTATCTTCGATCTACTCTCCGCCACTACAGAGACG
1 CTCTCTGCCACTACAGAGACGCCAAATCTACTATCTTCGATCTACTCTCCGCCACTACAGAGACA
* ** *
19351651 CCAAATCTATTATCTTCGATCTGCTCTCCGCCACTACAGAGACGCCAAATTTGTTATTTTCGATC
66 CCAAATCTATTATCTTCGATCTGCTCTCCGCCACTACAGAGACGCCAAATCTACTATCTTCGATC
* **
19351716 TGCTCTCTGCCACTACAGAGACGCCAAATCTACTATCTTCGATCTGCTCTCCGCCACTATGGAGA
131 TGCTCTCCGCCACTACAGAGACGCCAAATCTACTATCTTCGATCTGCTCTCCGCCACTACAGAGA
*
19351781 CGCCAAATCTATTATCTTTGATCTGCTCTCTGCCACTACAGAGACGTCTG
196 CGCCAAATCTATTATCTTCGATCTGCTCTCTGCCACTACAGAGACGTCTG
* * * * *
19351831 CTCTCTGCCACTACAGATACGCCAAATTTGCTATCTTCGA-CTTGCTCTCCGCCACTATAGAGAC
1 CTCTCTGCCACTACAGAGACGCCAAATCTACTATCTTCGATC-TACTCTCCGCCACTACAGAGAC
* *
19351895 ACCAAATCTATTATCTTCGATTTGCTCTCCTCCACTACAGAGACGCCAAATCTACTATCTTCGAT
65 ACCAAATCTATTATCTTCGATCTGCTCTCCGCCACTACAGAGACGCCAAATCTACTATCTTCGAT
**
19351960 CTGCTCTCCGCCACTACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCACTACAGAG
130 CTGCTCTCCGCCACTACAGAGACGCCAAATCTACTATCTTCGATCTGCTCTCCGCCACTACAGAG
* ** * * **
19352025 ACGCCAAATCTGTTATCTTCGATCTGCTCTCCACCGCTAAATCTGTTATCTTCGATCTG
195 ACGCCAAATCTATTATCTTCGATCTGCTCTCTGCCACT--A-CAG--A--GACG-TCTG
** * * ** * *
19352084 CTCTCCACCGCTACAGAGACGCAAAATCTGTTATCTTCGATCTACTCTCCGCCGCTACAGAGACG
1 CTCTCTGCCACTACAGAGACGCCAAATCTACTATCTTCGATCTACTCTCCGCCACTACAGAGACA
*
19352149 CCAAATCTGTTATCT
66 CCAAATCTATTATCT
19352164 ACTTAAAGGA
Statistics
Matches: 284, Mismatches: 39, Indels: 12
0.85 0.12 0.04
Matches are distributed among these distances:
244 1 0.00
245 206 0.73
247 1 0.00
248 2 0.01
250 1 0.00
252 2 0.01
253 70 0.25
254 1 0.00
ACGTcount: A:0.24, C:0.33, G:0.14, T:0.29
Consensus pattern (245 bp):
CTCTCTGCCACTACAGAGACGCCAAATCTACTATCTTCGATCTACTCTCCGCCACTACAGAGACA
CCAAATCTATTATCTTCGATCTGCTCTCCGCCACTACAGAGACGCCAAATCTACTATCTTCGATC
TGCTCTCCGCCACTACAGAGACGCCAAATCTACTATCTTCGATCTGCTCTCCGCCACTACAGAGA
CGCCAAATCTATTATCTTCGATCTGCTCTCTGCCACTACAGAGACGTCTG
Found at i:19352072 original size:33 final size:33
Alignment explanation
Indices: 19352030--19352096 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
19352020 CAGAGACGCC
19352030 AAATCTGTTATCTTCGATCTGCTCTCCACCGCT
1 AAATCTGTTATCTTCGATCTGCTCTCCACCGCT
19352063 AAATCTGTTATCTTCGATCTGCTCTCCACCGCT
1 AAATCTGTTATCTTCGATCTGCTCTCCACCGCT
19352096 A
1 A
19352097 CAGAGACGCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.19, C:0.33, G:0.12, T:0.36
Consensus pattern (33 bp):
AAATCTGTTATCTTCGATCTGCTCTCCACCGCT
Found at i:19352079 original size:77 final size:77
Alignment explanation
Indices: 19351986--19352140 Score: 265
Period size: 77 Copynumber: 2.0 Consensus size: 77
19351976 CAGAGACGCC
* * *
19351986 AAATCTGTTATCTTCGATCTGCTCTCCGCCACTACAGAGACGCCAAATCTGTTATCTTCGATCTG
1 AAATCTGTTATCTTCGATCTGCTCTCCACCACTACAGAGACGCAAAATCTGTTATCTTCGATCTA
19352051 CTCTCCACCGCT
66 CTCTCCACCGCT
*
19352063 AAATCTGTTATCTTCGATCTGCTCTCCACCGCTACAGAGACGCAAAATCTGTTATCTTCGATCTA
1 AAATCTGTTATCTTCGATCTGCTCTCCACCACTACAGAGACGCAAAATCTGTTATCTTCGATCTA
*
19352128 CTCTCCGCCGCT
66 CTCTCCACCGCT
19352140 A
1 A
19352141 CAGAGACGCC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
77 73 1.00
ACGTcount: A:0.22, C:0.33, G:0.14, T:0.31
Consensus pattern (77 bp):
AAATCTGTTATCTTCGATCTGCTCTCCACCACTACAGAGACGCAAAATCTGTTATCTTCGATCTA
CTCTCCACCGCT
Found at i:19353437 original size:5 final size:5
Alignment explanation
Indices: 19353427--19353488 Score: 67
Period size: 5 Copynumber: 12.4 Consensus size: 5
19353417 TTGGCCTCTC
*
19353427 CTTTT CTTTT CTTTT CTTCT -TTTT CTTTTT CTTCTT -TATTT C-TTT
1 CTTTT CTTTT CTTTT CTTTT CTTTT C-TTTT CTT-TT CT-TTT CTTTT
19353472 CTTTT CTTTT CTTTT CT
1 CTTTT CTTTT CTTTT CT
19353489 CTTTTTTTTT
Statistics
Matches: 49, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
4 7 0.14
5 34 0.69
6 8 0.16
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (5 bp):
CTTTT
Found at i:19353458 original size:15 final size:15
Alignment explanation
Indices: 19353433--19353496 Score: 64
Period size: 15 Copynumber: 4.3 Consensus size: 15
19353423 TCTCCTTTTC
19353433 TTTTC-TTTTCTTCT
1 TTTTCTTTTTCTTCT
19353447 TTTTCTTTTTCTTCTT
1 TTTTCTTTTTCTTC-T
19353463 TATTTCTTTCTT-TTC-
1 T-TTTCTTT-TTCTTCT
19353478 TTTTCTTTTCTCTT-T
1 TTTTCTTTT-TCTTCT
19353493 TTTT
1 TTTT
19353497 TTGTTGATCT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 1 0.02
14 13 0.30
15 15 0.35
16 2 0.05
17 10 0.23
18 2 0.05
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.80
Consensus pattern (15 bp):
TTTTCTTTTTCTTCT
Found at i:19353474 original size:21 final size:20
Alignment explanation
Indices: 19353429--19353497 Score: 63
Period size: 21 Copynumber: 3.5 Consensus size: 20
19353419 GGCCTCTCCT
*
19353429 TTTC-TTTTCTT-TTCTTCTT
1 TTTCTTTTTCTTCTT-TTCTC
*
19353448 TTTCTTTTTCTTCTTTATTTC
1 TTTCTTTTTCTTCTTT-TCTC
*
19353469 TTTCTTTTCTTTTCTTTTCTC
1 TTTCTTTT-TCTTCTTTTCTC
19353490 TTT-TTTTT
1 TTTCTTTTT
19353498 TGTTGATCTC
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
19 5 0.12
20 12 0.29
21 18 0.43
22 7 0.17
ACGTcount: A:0.01, C:0.19, G:0.00, T:0.80
Consensus pattern (20 bp):
TTTCTTTTTCTTCTTTTCTC
Found at i:19358729 original size:20 final size:20
Alignment explanation
Indices: 19358704--19358759 Score: 58
Period size: 22 Copynumber: 2.6 Consensus size: 20
19358694 AAAAAATTAT
19358704 TTTATTTTAATTAAATAATA
1 TTTATTTTAATTAAATAATA
* *
19358724 TTTATTTCTATTTTAAATATTA
1 TTTATTT-TA-ATTAAATAATA
19358746 TATTATGTTTAATT
1 T-TTAT-TTTAATT
19358760 CTTGAAATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
20 7 0.24
21 2 0.07
22 12 0.41
23 6 0.21
24 2 0.07
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (20 bp):
TTTATTTTAATTAAATAATA
Found at i:19361064 original size:16 final size:15
Alignment explanation
Indices: 19361043--19361081 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
19361033 TAATTTCATG
19361043 AAAAATTTAATACTAA
1 AAAAATTTAATA-TAA
*
19361059 AAAAATGTAATATAA
1 AAAAATTTAATATAA
*
19361074 TAAAATTT
1 AAAAATTT
19361082 GCTATTCAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.33
Consensus pattern (15 bp):
AAAAATTTAATATAA
Found at i:19361973 original size:34 final size:34
Alignment explanation
Indices: 19361926--19361993 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 34
19361916 CAACATTTTT
*
19361926 TATGTAAGGCAACTAAATAGAAGAGGATAGCAAG
1 TATGTAAGACAACTAAATAGAAGAGGATAGCAAG
*
19361960 TATGTAAGACAACTAAATAGAAGAGGATTGCAAG
1 TATGTAAGACAACTAAATAGAAGAGGATAGCAAG
19361994 AATCTTGATA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.47, C:0.09, G:0.25, T:0.19
Consensus pattern (34 bp):
TATGTAAGACAACTAAATAGAAGAGGATAGCAAG
Found at i:19362470 original size:14 final size:15
Alignment explanation
Indices: 19362451--19362479 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
19362441 CGGAAAAGAA
19362451 TAAACCTT-AACCCC
1 TAAACCTTAAACCCC
19362465 TAAACCTTAAACCCC
1 TAAACCTTAAACCCC
19362480 AATCCCTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.38, C:0.41, G:0.00, T:0.21
Consensus pattern (15 bp):
TAAACCTTAAACCCC
Found at i:19362521 original size:7 final size:7
Alignment explanation
Indices: 19362511--19362616 Score: 56
Period size: 7 Copynumber: 14.9 Consensus size: 7
19362501 AACCTTTAAC
19362511 CCATAAA
1 CCATAAA
19362518 CCATAAA
1 CCATAAA
*
19362525 CCATAAT
1 CCATAAA
*
19362532 CCCTAAA
1 CCATAAA
*
19362539 CCCATAAT
1 -CCATAAA
19362547 CCATAAA
1 CCATAAA
*
19362554 CC-T-TA
1 CCATAAA
*
19362559 CAATAGTAA
1 CCATA--AA
19362568 CTCATAAA
1 C-CATAAA
19362576 -CATTAAA
1 CCA-TAAA
* *
19362583 CCCTTAA
1 CCATAAA
*
19362590 CCATATA
1 CCATAAA
19362597 CCATAAA
1 CCATAAA
*
19362604 CCCTAAA
1 CCATAAA
*
19362611 CTATAA
1 CCATAA
19362617 TGATAATTAA
Statistics
Matches: 72, Mismatches: 19, Indels: 16
0.67 0.18 0.15
Matches are distributed among these distances:
5 2 0.03
6 4 0.06
7 53 0.74
8 8 0.11
9 2 0.03
10 3 0.04
ACGTcount: A:0.47, C:0.29, G:0.01, T:0.23
Consensus pattern (7 bp):
CCATAAA
Found at i:19362526 original size:15 final size:15
Alignment explanation
Indices: 19362508--19362555 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
19362498 CACAACCTTT
*
19362508 AACCCATAAACCATA
1 AACCCATAATCCATA
*
19362523 AA-CCATAATCCCTA
1 AACCCATAATCCATA
19362537 AACCCATAATCCATA
1 AACCCATAATCCATA
19362552 AACC
1 AACC
19362556 TTACAATAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
14 12 0.41
15 17 0.59
ACGTcount: A:0.48, C:0.35, G:0.00, T:0.17
Consensus pattern (15 bp):
AACCCATAATCCATA
Found at i:19362645 original size:19 final size:18
Alignment explanation
Indices: 19362621--19362663 Score: 70
Period size: 17 Copynumber: 2.4 Consensus size: 18
19362611 CTATAATGAT
19362621 AATTAATTCAATATTTTAA
1 AATTAATT-AATATTTTAA
19362640 AATTAA-TAATATTTTAA
1 AATTAATTAATATTTTAA
19362657 AATTAAT
1 AATTAAT
19362664 ACTATCTCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 16 0.70
18 1 0.04
19 6 0.26
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (18 bp):
AATTAATTAATATTTTAA
Found at i:19366359 original size:30 final size:30
Alignment explanation
Indices: 19366318--19366411 Score: 161
Period size: 30 Copynumber: 3.1 Consensus size: 30
19366308 GGGTGAAATA
*
19366318 AACTCGAACCGCCTATGTCCGAGTGATATG
1 AACTTGAACCGCCTATGTCCGAGTGATATG
19366348 AACTTGAACCGCCTATGTCCGAGTGATATG
1 AACTTGAACCGCCTATGTCCGAGTGATATG
* *
19366378 AATTTGAACCGCCAATGTCCGAGTGATATG
1 AACTTGAACCGCCTATGTCCGAGTGATATG
19366408 AACT
1 AACT
19366412 GCTCTGCGAC
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 60 1.00
ACGTcount: A:0.29, C:0.23, G:0.22, T:0.26
Consensus pattern (30 bp):
AACTTGAACCGCCTATGTCCGAGTGATATG
Found at i:19368319 original size:18 final size:19
Alignment explanation
Indices: 19368298--19368336 Score: 71
Period size: 18 Copynumber: 2.1 Consensus size: 19
19368288 AAATAAGTAA
19368298 TAATATATTAA-TATATTT
1 TAATATATTAAGTATATTT
19368316 TAATATATTAAGTATATTT
1 TAATATATTAAGTATATTT
19368335 TA
1 TA
19368337 TACTCAACAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (19 bp):
TAATATATTAAGTATATTT
Found at i:19368372 original size:17 final size:16
Alignment explanation
Indices: 19368350--19368419 Score: 59
Period size: 17 Copynumber: 4.1 Consensus size: 16
19368340 TCAACATTTT
19368350 ATTTTAACATATTTAAA
1 ATTTTAA-ATATTTAAA
*
19368367 ATTTTAATATATTTAATT
1 ATTTTAA-ATATTTAA-A
* * *
19368385 TTTTTAAGTTTTTTAAA
1 ATTTTAA-ATATTTAAA
19368402 ATTTTAAATATATTAAA
1 ATTTTAAATAT-TTAAA
19368419 A
1 A
19368420 AATCTTTTTT
Statistics
Matches: 41, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
16 2 0.05
17 27 0.66
18 12 0.29
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (16 bp):
ATTTTAAATATTTAAA
Found at i:19368566 original size:62 final size:62
Alignment explanation
Indices: 19368499--19368617 Score: 220
Period size: 62 Copynumber: 1.9 Consensus size: 62
19368489 ATATATTGAG
*
19368499 TATATTAAAATTTTAAAATTGATTATACTTAACTTTTTTTAATATATTTAATTTTTTAAAAA
1 TATATTAAAATTTTAAAATTGATTATACTTAACGTTTTTTAATATATTTAATTTTTTAAAAA
*
19368561 TATATTAAAATTTTAAAATTGGTTATACTTAACGTTTTTTAATATATTTAATTTTTT
1 TATATTAAAATTTTAAAATTGATTATACTTAACGTTTTTTAATATATTTAATTTTTT
19368618 TAAGTTTTTT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
62 55 1.00
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (62 bp):
TATATTAAAATTTTAAAATTGATTATACTTAACGTTTTTTAATATATTTAATTTTTTAAAAA
Found at i:19368568 original size:19 final size:20
Alignment explanation
Indices: 19368539--19368578 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
19368529 AACTTTTTTT
**
19368539 AATATATTTAATTTTTTAAA
1 AATATATTTAAAATTTTAAA
19368559 AATATA-TTAAAATTTTAAA
1 AATATATTTAAAATTTTAAA
19368578 A
1 A
19368579 TTGGTTATAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
AATATATTTAAAATTTTAAA
Found at i:19369211 original size:20 final size:20
Alignment explanation
Indices: 19369188--19369243 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
19369178 TGACCAATTA
19369188 TAATATATATTTTTAATTTT
1 TAATATATATTTTTAATTTT
* * *
19369208 TAATTTAAATTTTTACTTTT
1 TAATATATATTTTTAATTTT
19369228 TAATATATATTTTTAA
1 TAATATATATTTTTAA
19369244 ATAAATTCAT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (20 bp):
TAATATATATTTTTAATTTT
Found at i:19369327 original size:18 final size:18
Alignment explanation
Indices: 19369306--19369340 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
19369296 TTAATTAATT
19369306 TAAAT-TTACTTTTTTAAA
1 TAAATATTA-TTTTTTAAA
19369324 TAAATATTATTTTTTAA
1 TAAATATTATTTTTTAA
19369341 CTTTTAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 13 0.81
19 3 0.19
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (18 bp):
TAAATATTATTTTTTAAA
Found at i:19369335 original size:23 final size:21
Alignment explanation
Indices: 19369269--19369335 Score: 64
Period size: 21 Copynumber: 3.0 Consensus size: 21
19369259 AATAAAAAAA
* *
19369269 TATTTTTTAACAAATATTTTT
1 TATTTTTTAATAAATATTATT
*
19369290 TATTTTTTAATTAAT-TTAAATT
1 TATTTTTTAATAAATATT--ATT
19369312 TACTTTTTTAAATAAATATTATT
1 TA-TTTTTT-AATAAATATTATT
19369335 T
1 T
19369336 TTTAACTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
20 2 0.05
21 13 0.35
22 4 0.11
23 10 0.27
24 6 0.16
25 2 0.05
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (21 bp):
TATTTTTTAATAAATATTATT
Found at i:19369522 original size:22 final size:21
Alignment explanation
Indices: 19369497--19369558 Score: 83
Period size: 20 Copynumber: 3.0 Consensus size: 21
19369487 TAAATGTTTT
19369497 ATATTATTAAAAAATATATTTA
1 ATATT-TTAAAAAATATATTTA
19369519 ATA-TTTAAAAAATAATATTTA
1 ATATTTTAAAAAAT-ATATTTA
*
19369540 AAATTTTAAAAAATA-ATTT
1 ATATTTTAAAAAATATATTT
19369559 CAAATATATA
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
20 13 0.35
21 11 0.30
22 13 0.35
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
ATATTTTAAAAAATATATTTA
Found at i:19373925 original size:24 final size:24
Alignment explanation
Indices: 19373898--19373954 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 24
19373888 CTATTCGGAG
* *
19373898 CTTCTCGATATGATTCTTTGTGAA
1 CTTCCCGATAAGATTCTTTGTGAA
* *
19373922 CTTCCCGACAAGGTTCTTTGTGAA
1 CTTCCCGATAAGATTCTTTGTGAA
19373946 CTTCCCGAT
1 CTTCCCGAT
19373955 TATGGCTCTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.19, C:0.25, G:0.18, T:0.39
Consensus pattern (24 bp):
CTTCCCGATAAGATTCTTTGTGAA
Found at i:19377943 original size:28 final size:28
Alignment explanation
Indices: 19377903--19377959 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
19377893 ATATTGAACT
19377903 ATCAAAATATTCGAATATTGTTTATAGA
1 ATCAAAATATTCGAATATTGTTTATAGA
19377931 ATCAAAATATTCGAATATTGTTTATAGA
1 ATCAAAATATTCGAATATTGTTTATAGA
19377959 A
1 A
19377960 GTAAGGCTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.44, C:0.07, G:0.11, T:0.39
Consensus pattern (28 bp):
ATCAAAATATTCGAATATTGTTTATAGA
Found at i:19383962 original size:21 final size:22
Alignment explanation
Indices: 19383930--19383978 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 22
19383920 ATAGATTAAA
**
19383930 AAAAATAGTTAAACTAAAACTT
1 AAAAATAGTTAAAAAAAAACTT
*
19383952 AAAAATA-TTAAAAAAAAATTT
1 AAAAATAGTTAAAAAAAAACTT
19383973 AAAAAT
1 AAAAAT
19383979 TTCCAAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 17 0.71
22 7 0.29
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.27
Consensus pattern (22 bp):
AAAAATAGTTAAAAAAAAACTT
Found at i:19384602 original size:20 final size:18
Alignment explanation
Indices: 19384542--19384608 Score: 55
Period size: 20 Copynumber: 3.6 Consensus size: 18
19384532 TTTATTATGG
*
19384542 AATTATAAAGAACATAAAAA
1 AATTATAAA-ATCAT-AAAA
* * *
19384562 AATTATAAAATTATTAGA
1 AATTATAAAATCATAAAA
19384580 AATTGATTAAAATCATAAAA
1 AATT-A-TAAAATCATAAAA
19384600 AATTA-AAAA
1 AATTATAAAA
19384609 AAATTATAAT
Statistics
Matches: 38, Mismatches: 7, Indels: 7
0.73 0.13 0.13
Matches are distributed among these distances:
17 4 0.11
18 6 0.16
19 5 0.13
20 23 0.61
ACGTcount: A:0.64, C:0.03, G:0.04, T:0.28
Consensus pattern (18 bp):
AATTATAAAATCATAAAA
Found at i:19385245 original size:18 final size:19
Alignment explanation
Indices: 19385222--19385260 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
19385212 TATTGAAATT
19385222 ATATTTATATTAAATA-TA
1 ATATTTATATTAAATAGTA
*
19385240 ATATTTATGTTAAATAGTA
1 ATATTTATATTAAATAGTA
19385259 AT
1 AT
19385261 TGCAAATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (19 bp):
ATATTTATATTAAATAGTA
Found at i:19387437 original size:26 final size:27
Alignment explanation
Indices: 19387386--19387437 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 27
19387376 CGAGCTCTGT
*
19387386 ATGCAAACCCCTTATAGGTGAACCCTC
1 ATGCAAACCCCTTATAGGTCAACCCTC
*
19387413 ATGCGAACCCC-TATAGG-CAAGCCCT
1 ATGCAAACCCCTTATAGGTCAA-CCCT
19387438 TGTATGCGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
25 2 0.09
26 10 0.45
27 10 0.45
ACGTcount: A:0.29, C:0.35, G:0.17, T:0.19
Consensus pattern (27 bp):
ATGCAAACCCCTTATAGGTCAACCCTC
Found at i:19387472 original size:15 final size:14
Alignment explanation
Indices: 19387413--19387494 Score: 85
Period size: 14 Copynumber: 5.8 Consensus size: 14
19387403 GTGAACCCTC
*
19387413 ATGCGAACCCCTAT
1 ATGCGAACCCCTGT
* *
19387427 AGGC-AAGCCCTTGT
1 ATGCGAA-CCCCTGT
* *
19387441 ATGCGAGCCCTTGT
1 ATGCGAACCCCTGT
19387455 ATGCGAACACCCTGT
1 ATGCGAAC-CCCTGT
*
19387470 ATGCGAACCCCTAT
1 ATGCGAACCCCTGT
19387484 ATGCGAACCCC
1 ATGCGAACCCC
19387495 CTACATGTGC
Statistics
Matches: 57, Mismatches: 8, Indels: 6
0.80 0.11 0.08
Matches are distributed among these distances:
13 2 0.04
14 41 0.72
15 14 0.25
ACGTcount: A:0.24, C:0.34, G:0.21, T:0.21
Consensus pattern (14 bp):
ATGCGAACCCCTGT
Found at i:19387472 original size:29 final size:29
Alignment explanation
Indices: 19387413--19387496 Score: 91
Period size: 29 Copynumber: 2.9 Consensus size: 29
19387403 GTGAACCCTC
* *
19387413 ATGCGAACCCCTATAGGC-AAGC-CCTTGT
1 ATGCGAACCCCTATATGCGAA-CACCCTGT
* * *
19387441 ATGCGAGCCCTTGTATGCGAACACCCTGT
1 ATGCGAACCCCTATATGCGAACACCCTGT
*
19387470 ATGCGAACCCCTATATGCGAACCCCCT
1 ATGCGAACCCCTATATGCGAACACCCT
19387497 ACATGTGCGA
Statistics
Matches: 45, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
28 15 0.33
29 30 0.67
ACGTcount: A:0.24, C:0.35, G:0.20, T:0.21
Consensus pattern (29 bp):
ATGCGAACCCCTATATGCGAACACCCTGT
Found at i:19387495 original size:15 final size:15
Alignment explanation
Indices: 19387454--19387497 Score: 63
Period size: 15 Copynumber: 3.0 Consensus size: 15
19387444 CGAGCCCTTG
* *
19387454 TATGCGAACACCCTG
1 TATGCGAACCCCCTA
19387469 TATGCGAA-CCCCTA
1 TATGCGAACCCCCTA
19387483 TATGCGAACCCCCTA
1 TATGCGAACCCCCTA
19387498 CATGTGCGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
14 12 0.46
15 14 0.54
ACGTcount: A:0.27, C:0.36, G:0.16, T:0.20
Consensus pattern (15 bp):
TATGCGAACCCCCTA
Found at i:19387754 original size:23 final size:23
Alignment explanation
Indices: 19387684--19387830 Score: 121
Period size: 23 Copynumber: 6.6 Consensus size: 23
19387674 ATGAATATCT
19387684 TGCGAACCCT--ATA-TGTTAATTA
1 TGCGAACCCTACATATTG-TAA-TA
*
19387706 TGCAAACCCTACATA-TGT-ATA
1 TGCGAACCCTACATATTGTAATA
*
19387727 TGCGAACACTACATATTGTAATA
1 TGCGAACCCTACATATTGTAATA
19387750 TGCGAACCCTACATATTGTAATA
1 TGCGAACCCTACATATTGTAATA
* * *
19387773 TGTGAACCCTATATGTT-T-ATCA
1 TGCGAACCCTACATATTGTAAT-A
* * *
19387795 TGCGAGCCCTATATA-TGTATTTA
1 TGCGAACCCTACATATTGTA-ATA
*
19387818 TGTGAACCCTACA
1 TGCGAACCCTACA
19387831 AGTAGTAATA
Statistics
Matches: 103, Mismatches: 14, Indels: 15
0.78 0.11 0.11
Matches are distributed among these distances:
21 18 0.17
22 28 0.27
23 51 0.50
24 6 0.06
ACGTcount: A:0.33, C:0.20, G:0.14, T:0.33
Consensus pattern (23 bp):
TGCGAACCCTACATATTGTAATA
Found at i:19387820 original size:45 final size:42
Alignment explanation
Indices: 19387687--19387828 Score: 140
Period size: 45 Copynumber: 3.2 Consensus size: 42
19387677 AATATCTTGC
* * *
19387687 GAACCCTATATGTTAATTATGCAAACCCTACATATGTATATGC
1 GAACCCTATATGTTTA-TATGCGAACCCTACATATGTATATGT
* * *
19387730 GAACACTACATATTGTAATATGCGAACCCTACATATTGTAATATGT
1 GAACCCTATATGTT-T-ATATGCGAACCCTACATA-TGT-ATATGT
* *
19387776 GAACCCTATATGTTTATCATGCGAGCCCTATATATGTATTTATGT
1 GAACCCTATATGTTTAT-ATGCGAACCCTACATATGTA--TATGT
19387821 GAACCCTA
1 GAACCCTA
19387829 CAAGTAGTAA
Statistics
Matches: 81, Mismatches: 11, Indels: 12
0.78 0.11 0.12
Matches are distributed among these distances:
43 12 0.15
44 21 0.26
45 32 0.40
46 16 0.20
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.34
Consensus pattern (42 bp):
GAACCCTATATGTTTATATGCGAACCCTACATATGTATATGT
Found at i:19387886 original size:15 final size:15
Alignment explanation
Indices: 19387862--19387917 Score: 60
Period size: 15 Copynumber: 3.7 Consensus size: 15
19387852 TGTATTTAAT
19387862 TGTGCGAACCCTGTA
1 TGTGCGAACCCTGTA
* *
19387877 TGTGCAAACCCCAG-A
1 TGTGCGAA-CCCTGTA
*
19387892 TGTGTGAACCCTGTA
1 TGTGCGAACCCTGTA
*
19387907 TGTGTGAACCC
1 TGTGCGAACCC
19387918 AACATGTGCT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
14 4 0.12
15 26 0.76
16 4 0.12
ACGTcount: A:0.23, C:0.27, G:0.25, T:0.25
Consensus pattern (15 bp):
TGTGCGAACCCTGTA
Found at i:19387925 original size:30 final size:30
Alignment explanation
Indices: 19387862--19387926 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 30
19387852 TGTATTTAAT
* *
19387862 TGTGCGAACCCTGTATGTGCAAACCCCAGA
1 TGTGCGAACCCTGTATGTGCAAACCCAACA
* **
19387892 TGTGTGAACCCTGTATGTGTGAACCCAACA
1 TGTGCGAACCCTGTATGTGCAAACCCAACA
19387922 TGTGC
1 TGTGC
19387927 TGTGAACCTG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.25, C:0.26, G:0.25, T:0.25
Consensus pattern (30 bp):
TGTGCGAACCCTGTATGTGCAAACCCAACA
Found at i:19389673 original size:25 final size:25
Alignment explanation
Indices: 19389639--19389687 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
19389629 AGATGACACC
19389639 TAGTTGAAAGATGGAAGTTAGAACG
1 TAGTTGAAAGATGGAAGTTAGAACG
* *
19389664 TAGTTGAAAGGTGGAAGTTGGAAC
1 TAGTTGAAAGATGGAAGTTAGAAC
19389688 ATGAAATAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.37, C:0.04, G:0.35, T:0.24
Consensus pattern (25 bp):
TAGTTGAAAGATGGAAGTTAGAACG
Found at i:19393013 original size:90 final size:90
Alignment explanation
Indices: 19392855--19393087 Score: 240
Period size: 90 Copynumber: 2.6 Consensus size: 90
19392845 ACTACTATTC
* * * **
19392855 AAAATATTTGTATTATTTTGGTATCCATAAATCAATTTTAGTCTGTTTTATTTATTGCTCAAAAT
1 AAAATGTTTGTATTATTTTGGTATCCATAAATAAATTTTAGTCTGTATTATTTACCGCTCAAAAT
*
19392920 TTATATTTTCATATATC-AGTTTTGT
66 TTATATTTTCATATATCAAATTTT-T
* * *
19392945 AAAATGTTTGTATTATTTTTGG-ATCCGTAAA-AATATTTTAGTCTGTATTATTTGCCGGTCAAA
1 AAAATGTTTGTATTA-TTTTGGTATCCATAAATAA-ATTTTAGTCTGTATTATTTACCGCTCAAA
* *
19393008 TTTTATATTTTCGTATATCAAATTTTT
64 ATTTATATTTTCATATATCAAATTTTT
* *** ** *
19393035 AAAATGTTCGTATTAATTTT-GTATATGTAAATAAAAATTAGTCAGTATTATTT
1 AAAATGTTTGTATT-ATTTTGGTATCCATAAATAAATTTTAGTCTGTATTATTT
19393088 GTTAGTCAAT
Statistics
Matches: 120, Mismatches: 17, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
89 2 0.02
90 104 0.87
91 14 0.12
ACGTcount: A:0.32, C:0.08, G:0.11, T:0.50
Consensus pattern (90 bp):
AAAATGTTTGTATTATTTTGGTATCCATAAATAAATTTTAGTCTGTATTATTTACCGCTCAAAAT
TTATATTTTCATATATCAAATTTTT
Found at i:19393088 original size:90 final size:90
Alignment explanation
Indices: 19392913--19393114 Score: 221
Period size: 90 Copynumber: 2.3 Consensus size: 90
19392903 TATTTATTGC
* * * * * *
19392913 TCAAAATTTATATTTTCATATATCAGTTTTGTAAAATGTTTGTATTATTTTTGGATCCGTAAAAA
1 TCAAATTTTATATTTTCGTATATCAATTTTGTAAAATGTTCGTATTAATTTTGGATACGTAAAAA
** * *
19392978 TATTTTAGTCTGTATTATTTGCCGG
66 TAAATTAGTCAGTATTATTTGCCAG
* *
19393003 TCAAATTTTATATTTTCGTATATCAAATTTT-TAAAATGTTCGTATTAATTTTGTATATGTAAAT
1 TCAAATTTTATATTTTCGTATATC-AATTTTGTAAAATGTTCGTATTAATTTTGGATACGTAAA-
**
19393067 AA-AAATTAGTCAGTATTATTTGTTAG
64 AATAAATTAGTCAGTATTATTTGCCAG
* *
19393093 TC-AATTATATATTTTTGTATAT
1 TCAAATTTTATATTTTCGTATAT
19393115 TAGTTTTCTA
Statistics
Matches: 94, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
89 18 0.19
90 69 0.73
91 7 0.07
ACGTcount: A:0.32, C:0.07, G:0.11, T:0.50
Consensus pattern (90 bp):
TCAAATTTTATATTTTCGTATATCAATTTTGTAAAATGTTCGTATTAATTTTGGATACGTAAAAA
TAAATTAGTCAGTATTATTTGCCAG
Found at i:19393737 original size:27 final size:27
Alignment explanation
Indices: 19393697--19393751 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
19393687 GGGGTTTGAG
*
19393697 ATAGATTCTGTGTTCCCGAATGGTGGA
1 ATAGATTCTATGTTCCCGAATGGTGGA
19393724 ATAGATTCTATGTTCCCGAATGGTGGA
1 ATAGATTCTATGTTCCCGAATGGTGGA
19393751 A
1 A
19393752 CTCGATTACG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.25, C:0.15, G:0.27, T:0.33
Consensus pattern (27 bp):
ATAGATTCTATGTTCCCGAATGGTGGA
Done.