Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A09
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: 81831061
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 3560000 characters in sequence are not A, C, G, or T
File 185 of 259
Found at i:59716691 original size:20 final size:21
Alignment explanation
Indices: 59716642--59716692 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 21
59716632 TGGAATCAGG
*
59716642 TTTTATAATTTTTAATATAAT
1 TTTTATAATTTTTAATAGAAT
59716663 TTTTA-AATTTTT-AT-GAAT
1 TTTTATAATTTTTAATAGAAT
59716681 TTTTAATAATTT
1 TTTT-ATAATTT
59716693 ATTTAATTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 7 0.26
19 3 0.11
20 12 0.44
21 5 0.19
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (21 bp):
TTTTATAATTTTTAATAGAAT
Found at i:59718818 original size:16 final size:17
Alignment explanation
Indices: 59718791--59718834 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 17
59718781 TATATTTAAT
*
59718791 TTTAGCTTTTATCTT-TA
1 TTTATCTTTTAT-TTGTA
59718808 TTTAT-TTTTATTTGTA
1 TTTATCTTTTATTTGTA
59718824 TTTATCTTTTA
1 TTTATCTTTTA
59718835 GAATTTAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 2 0.08
16 13 0.54
17 9 0.38
ACGTcount: A:0.18, C:0.07, G:0.05, T:0.70
Consensus pattern (17 bp):
TTTATCTTTTATTTGTA
Found at i:59724774 original size:18 final size:19
Alignment explanation
Indices: 59724753--59724789 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
59724743 TTTCTTTGCT
59724753 TTTTTTCCTTTTG-AATAA
1 TTTTTTCCTTTTGTAATAA
*
59724771 TTTTTTTCTTTTGTAATAA
1 TTTTTTCCTTTTGTAATAA
59724790 CCATATGGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.22, C:0.08, G:0.05, T:0.65
Consensus pattern (19 bp):
TTTTTTCCTTTTGTAATAA
Found at i:59724774 original size:19 final size:19
Alignment explanation
Indices: 59724752--59724789 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
59724742 TTTTCTTTGC
59724752 TTTTTTTCCTTTTG-AATAA
1 TTTTTTT-CTTTTGTAATAA
59724771 TTTTTTTCTTTTGTAATAA
1 TTTTTTTCTTTTGTAATAA
59724790 CCATATGGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.21, C:0.08, G:0.05, T:0.66
Consensus pattern (19 bp):
TTTTTTTCTTTTGTAATAA
Found at i:59725557 original size:31 final size:31
Alignment explanation
Indices: 59725522--59725598 Score: 86
Period size: 31 Copynumber: 2.5 Consensus size: 31
59725512 AAGTCTATGA
* * *
59725522 TTGAATCAAAATTAAATTTTCATGTATATAT
1 TTGAATCAAAATCAAAGTTTAATGTATATAT
* *
59725553 TTGAATCACAATCAAAGTTTAATGTATATAA
1 TTGAATCAAAATCAAAGTTTAATGTATATAT
59725584 TT-ACATC-AAATCAAA
1 TTGA-ATCAAAATCAAA
59725599 ATTCACGTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
30 8 0.21
31 31 0.79
ACGTcount: A:0.45, C:0.10, G:0.06, T:0.38
Consensus pattern (31 bp):
TTGAATCAAAATCAAAGTTTAATGTATATAT
Found at i:59725608 original size:29 final size:29
Alignment explanation
Indices: 59725576--59725643 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 29
59725566 AAAGTTTAAT
59725576 GTATATAATT-ACATCAAATCAAAATTCA
1 GTATATAATTCACATCAAATCAAAATTCA
59725604 CGTATCA-AATTGCACATCAAATCAAAATTCA
1 -GTAT-ATAATT-CACATCAAATCAAAATTCA
59725635 -TATATAATT
1 GTATATAATT
59725644 TCGGTATTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
28 1 0.03
29 15 0.43
30 1 0.03
31 18 0.51
ACGTcount: A:0.47, C:0.16, G:0.04, T:0.32
Consensus pattern (29 bp):
GTATATAATTCACATCAAATCAAAATTCA
Found at i:59736950 original size:27 final size:27
Alignment explanation
Indices: 59736916--59736969 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
59736906 TTTATAAGGG
59736916 GATTGAGATTGAGTTATATATATTTTT
1 GATTGAGATTGAGTTATATATATTTTT
59736943 GATTGAGATTGAGTTATATATATTTTT
1 GATTGAGATTGAGTTATATATATTTTT
59736970 ATAAAAGTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.30, C:0.00, G:0.19, T:0.52
Consensus pattern (27 bp):
GATTGAGATTGAGTTATATATATTTTT
Found at i:59740104 original size:31 final size:30
Alignment explanation
Indices: 59740061--59740119 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 30
59740051 TAACAGTATT
*
59740061 TTTGGGTTAATATACAATTAGGTACCTATA
1 TTTGGCTTAATATACAATTAGGTACCTATA
* * *
59740091 TTTGGCTTCAATATTCAGTTTGGTACCTA
1 TTTGGCTT-AATATACAATTAGGTACCTA
59740120 AGTTTTTTCT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 7 0.29
31 17 0.71
ACGTcount: A:0.27, C:0.14, G:0.17, T:0.42
Consensus pattern (30 bp):
TTTGGCTTAATATACAATTAGGTACCTATA
Found at i:59744926 original size:51 final size:51
Alignment explanation
Indices: 59744850--59744952 Score: 152
Period size: 51 Copynumber: 2.0 Consensus size: 51
59744840 GATGCCCAAC
* *
59744850 ATAAGTCCTTAAACGATAAAGTTGACGAAAGATGCAAGTTGTTTGATACCA
1 ATAAGTCCTTAAACGATAAAGTTGACGAAAGATACAAGTTGCTTGATACCA
** **
59744901 ATAAGTCCTTAATTGATAAAGTTGACGATGGATACAAGTTGCTTGATACCA
1 ATAAGTCCTTAAACGATAAAGTTGACGAAAGATACAAGTTGCTTGATACCA
59744952 A
1 A
59744953 GCATGATACC
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 46 1.00
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (51 bp):
ATAAGTCCTTAAACGATAAAGTTGACGAAAGATACAAGTTGCTTGATACCA
Found at i:59748431 original size:31 final size:31
Alignment explanation
Indices: 59748376--59748453 Score: 88
Period size: 31 Copynumber: 2.5 Consensus size: 31
59748366 TTTTCCTTAA
* *
59748376 TGGCTTGGATAAGCCTT--GATGCAATCGAGT
1 TGGCTT-GAGAAGCCTTGAGATGCAATCGAAT
* **
59748406 TGGCTTGAGTAGCCTTGAGATGCAATTTAAT
1 TGGCTTGAGAAGCCTTGAGATGCAATCGAAT
59748437 TGGCTTGAGAAGCCTTG
1 TGGCTTGAGAAGCCTTG
59748454 TGGCAAATGA
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
29 8 0.20
30 6 0.15
31 26 0.65
ACGTcount: A:0.23, C:0.15, G:0.29, T:0.32
Consensus pattern (31 bp):
TGGCTTGAGAAGCCTTGAGATGCAATCGAAT
Found at i:59750742 original size:163 final size:165
Alignment explanation
Indices: 59750465--59750764 Score: 428
Period size: 163 Copynumber: 1.8 Consensus size: 165
59750455 TTTCTCATAA
* ** ** * *
59750465 TTGCATTAGTGTACAAGTTTGTTGCTTGTGGGGAGTTTTTAACATAATTATTTAGTTGTTGAAAT
1 TTGCATTAGTGTACAAATCAGTTGCTTGTGGGGAGTTCATAACATAATTATGTAGTTGTTGAAAA
* *
59750530 TGTGAGTAATTAGGCTTTTGAAGAAGATTGACTTATGTTTCTGGATTTACCAATGTATCTGGCTG
66 TGTGAATAATTAGGCTTTTGAAGAAGATTGACTTATGTTTCTGGATTTACCAATGTATCTGACTG
59750595 AGAAATTCTCAACCGGAATCTGTTAACTCTCTTAG
131 AGAAATTCTCAACCGGAATCTGTTAACTCTCTTAG
*
59750630 TTGCATTAGTGTACAAATCAGTTGCTTGT-GGGAG-TCATAACATGCA-TATGTAGTTGTTGAAA
1 TTGCATTAGTGTACAAATCAGTTGCTTGTGGGGAGTTCATAACAT-AATTATGTAGTTGTTGAAA
* * * *
59750692 ATGCTGAAT-ATTAGGCTTTTGAAGAATATTGACTTATGTTTCTTGATTTACTAATGTGTCTGAC
65 ATG-TGAATAATTAGGCTTTTGAAGAAGATTGACTTATGTTTCTGGATTTACCAATGTATCTGAC
59750756 TGAGAAATT
129 TGAGAAATT
59750765 GTTAACCAAA
Statistics
Matches: 119, Mismatches: 14, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
163 83 0.70
164 10 0.08
165 26 0.22
ACGTcount: A:0.27, C:0.11, G:0.22, T:0.40
Consensus pattern (165 bp):
TTGCATTAGTGTACAAATCAGTTGCTTGTGGGGAGTTCATAACATAATTATGTAGTTGTTGAAAA
TGTGAATAATTAGGCTTTTGAAGAAGATTGACTTATGTTTCTGGATTTACCAATGTATCTGACTG
AGAAATTCTCAACCGGAATCTGTTAACTCTCTTAG
Found at i:59756126 original size:39 final size:40
Alignment explanation
Indices: 59756065--59756140 Score: 145
Period size: 39 Copynumber: 1.9 Consensus size: 40
59756055 AAAGTGAAAC
59756065 TATAGTAAAAAACAGAAAAAGAATGTGCTTAGATAAGCCT
1 TATAGTAAAAAACAGAAAAAGAATGTGCTTAGATAAGCCT
59756105 TATAGTAAAAAACAG-AAAAGAATGTGCTTAGATAAG
1 TATAGTAAAAAACAGAAAAAGAATGTGCTTAGATAAG
59756141 ACTTCATAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
39 21 0.58
40 15 0.42
ACGTcount: A:0.51, C:0.08, G:0.18, T:0.22
Consensus pattern (40 bp):
TATAGTAAAAAACAGAAAAAGAATGTGCTTAGATAAGCCT
Found at i:59759512 original size:11 final size:12
Alignment explanation
Indices: 59759484--59759517 Score: 52
Period size: 11 Copynumber: 2.8 Consensus size: 12
59759474 TTTTGAAACT
59759484 TTTTATATATTCA
1 TTTTA-ATATTCA
59759497 TTTTAATATT-A
1 TTTTAATATTCA
59759508 TTTTAATATT
1 TTTTAATATT
59759518 TACATTAGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.52
12 5 0.24
13 5 0.24
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (12 bp):
TTTTAATATTCA
Found at i:59762347 original size:26 final size:26
Alignment explanation
Indices: 59762311--59762362 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
59762301 CAGAACTGGT
59762311 GATCGATTCAACCAATATGTATTTAC
1 GATCGATTCAACCAATATGTATTTAC
59762337 GATCGATTCAACCAATATGTATTTAC
1 GATCGATTCAACCAATATGTATTTAC
59762363 AACTCAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.35
Consensus pattern (26 bp):
GATCGATTCAACCAATATGTATTTAC
Found at i:59763821 original size:35 final size:35
Alignment explanation
Indices: 59763781--59763850 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
59763771 TTACTTAAAA
59763781 GTTATAATTACTTTATTATTTATTTCTTAAATTTT
1 GTTATAATTACTTTATTATTTATTTCTTAAATTTT
59763816 GTTATAATTACTTTATTATTTATTTCTTAAATTTT
1 GTTATAATTACTTTATTATTTATTTCTTAAATTTT
59763851 TAAAGCTTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.29, C:0.06, G:0.03, T:0.63
Consensus pattern (35 bp):
GTTATAATTACTTTATTATTTATTTCTTAAATTTT
Found at i:59768675 original size:25 final size:21
Alignment explanation
Indices: 59768629--59768671 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
59768619 ATCGCAAAAG
59768629 TATGAAAGAACATATATTTCC
1 TATGAAAGAACATATATTTCC
59768650 TATGAAAGAACATATATTTCC
1 TATGAAAGAACATATATTTCC
59768671 T
1 T
59768672 TCCTTTTTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.42, C:0.14, G:0.09, T:0.35
Consensus pattern (21 bp):
TATGAAAGAACATATATTTCC
Found at i:59770402 original size:14 final size:14
Alignment explanation
Indices: 59770379--59770408 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
59770369 TTACGAGGGA
*
59770379 CATTGTCAAATAGT
1 CATTGCCAAATAGT
59770393 CATTGCCAAATAGT
1 CATTGCCAAATAGT
59770407 CA
1 CA
59770409 GTGCAACATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.37, C:0.20, G:0.13, T:0.30
Consensus pattern (14 bp):
CATTGCCAAATAGT
Found at i:59771929 original size:24 final size:24
Alignment explanation
Indices: 59771891--59771945 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
59771881 TATAATTATG
* * *
59771891 TTTTAAATATGATTTCTTTGCT-AT
1 TTTTAATTATAATTTATTTG-TAAT
59771915 TTTTAATTATAATTTATTTGTAAT
1 TTTTAATTATAATTTATTTGTAAT
59771939 TTTTAAT
1 TTTTAAT
59771946 GATGGTGTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 1 0.04
24 26 0.96
ACGTcount: A:0.29, C:0.04, G:0.05, T:0.62
Consensus pattern (24 bp):
TTTTAATTATAATTTATTTGTAAT
Found at i:59774744 original size:34 final size:33
Alignment explanation
Indices: 59774684--59774748 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 33
59774674 CAGTAAAATG
59774684 TTTTCCGGAAAATGATTTCTAAAAAATGATTTAC
1 TTTTCCGGAAAATGATTTCTAAAAAAT-ATTTAC
* *
59774718 TTTTCTGGAAAATGATTTACT-GAAAATATTT
1 TTTTCCGGAAAATGATTT-CTAAAAAATATTT
59774749 TCTGGTGTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 4 0.14
34 22 0.79
35 2 0.07
ACGTcount: A:0.37, C:0.09, G:0.12, T:0.42
Consensus pattern (33 bp):
TTTTCCGGAAAATGATTTCTAAAAAATATTTAC
Found at i:59774878 original size:22 final size:23
Alignment explanation
Indices: 59774826--59774878 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 23
59774816 CGTAAAAGTT
59774826 ATTTTTAT-TACATATATTAATAA
1 ATTTTTATATACA-ATATTAATAA
59774849 A--TTTATATAC-ATATTAATAA
1 ATTTTTATATACAATATTAATAA
59774869 ATTTTTATAT
1 ATTTTTATAT
59774879 TTTAAATTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
20 11 0.41
21 5 0.19
22 10 0.37
23 1 0.04
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (23 bp):
ATTTTTATATACAATATTAATAA
Found at i:59778175 original size:16 final size:16
Alignment explanation
Indices: 59778085--59778180 Score: 84
Period size: 16 Copynumber: 5.9 Consensus size: 16
59778075 CACATATTTT
59778085 CACAGCTCACACATTA
1 CACAGCTCACACATTA
*
59778101 CTACGGCTCACACATTA
1 C-ACAGCTCACACATTA
* **
59778118 CATAGCTTGCACATTA
1 CACAGCTCACACATTA
* * *
59778134 CACAACTCGCACATCA
1 CACAGCTCACACATTA
***
59778150 TTGTAGCTCACACATTA
1 -CACAGCTCACACATTA
59778167 CACAGCTCACACAT
1 CACAGCTCACACAT
59778181 CACTATGACT
Statistics
Matches: 60, Mismatches: 18, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
16 35 0.58
17 25 0.42
ACGTcount: A:0.33, C:0.34, G:0.09, T:0.23
Consensus pattern (16 bp):
CACAGCTCACACATTA
Found at i:59789152 original size:24 final size:24
Alignment explanation
Indices: 59789122--59789169 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
59789112 GTAGTGAGTT
59789122 AAATTCAAAGTGATATTGAAGTAG
1 AAATTCAAAGTGATATTGAAGTAG
59789146 AAATTCAAAGTGATATTGAAGTAG
1 AAATTCAAAGTGATATTGAAGTAG
59789170 GATCTATATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.46, C:0.04, G:0.21, T:0.29
Consensus pattern (24 bp):
AAATTCAAAGTGATATTGAAGTAG
Found at i:59792881 original size:24 final size:23
Alignment explanation
Indices: 59792849--59793001 Score: 80
Period size: 24 Copynumber: 6.4 Consensus size: 23
59792839 GCATTGTAAT
* *
59792849 GGGAAGCTCACACAGAGCCATTTC
1 GGGAAGCTCACAAAGAGCC-TATC
*
59792873 GGGAAGCTCATAAAGAGCCTATC
1 GGGAAGCTCACAAAGAGCCTATC
* * *
59792896 GGGAAGC-CTATC--CGGGCTATATAAC
1 GGGAAGCTC-A-CAAAGAGC-CTAT--C
* *
59792921 GGAAAGCTCA-TAAGAGCCATAATC
1 GGGAAGCTCACAAAGAGCC-T-ATC
* *
59792945 GGGAAGTTCACAAAGAACCTTATC
1 GGGAAGCTCACAAAGAGCC-TATC
* *
59792969 GGGAAGTTCACAAAGAACCATATC
1 GGGAAGCTCACAAAGAGCC-TATC
59792993 GGGAAGCTC
1 GGGAAGCTC
59793002 CGGATAGCCA
Statistics
Matches: 100, Mismatches: 18, Indels: 22
0.71 0.13 0.16
Matches are distributed among these distances:
22 4 0.04
23 14 0.14
24 60 0.60
25 19 0.19
26 3 0.03
ACGTcount: A:0.35, C:0.23, G:0.25, T:0.18
Consensus pattern (23 bp):
GGGAAGCTCACAAAGAGCCTATC
Found at i:59793184 original size:25 final size:24
Alignment explanation
Indices: 59793156--59793202 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
59793146 TCGGAACGCT
*
59793156 CTGAAGAACTATAACGGGAAGCTCG
1 CTGAACAA-TATAACGGGAAGCTCG
* *
59793181 CTGAACCATATAAGGGGAAGCT
1 CTGAACAATATAACGGGAAGCT
59793203 TGAGAGGGCT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 13 0.68
25 6 0.32
ACGTcount: A:0.36, C:0.19, G:0.28, T:0.17
Consensus pattern (24 bp):
CTGAACAATATAACGGGAAGCTCG
Found at i:59796434 original size:45 final size:45
Alignment explanation
Indices: 59796382--59796484 Score: 134
Period size: 45 Copynumber: 2.3 Consensus size: 45
59796372 TAACAGTAAT
* ** * *
59796382 AGTAACAGTAACAATATTCAACATACAAAGTGTTGAATTGGTAAC
1 AGTAACAGTAACAATATTCAACACACAAAGTGCCGAATCGATAAC
* * *
59796427 GGTAACAGTAATAATATTCGACACACAAAGTGCCGAATCGATAAC
1 AGTAACAGTAACAATATTCAACACACAAAGTGCCGAATCGATAAC
59796472 AGTAACAGTAACA
1 AGTAACAGTAACA
59796485 GTAACAGTAA
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
45 48 1.00
ACGTcount: A:0.45, C:0.17, G:0.17, T:0.22
Consensus pattern (45 bp):
AGTAACAGTAACAATATTCAACACACAAAGTGCCGAATCGATAAC
Found at i:59796437 original size:51 final size:51
Alignment explanation
Indices: 59796371--59796490 Score: 126
Period size: 45 Copynumber: 2.5 Consensus size: 51
59796361 ATCCGGAACA
* * ** *
59796371 GTAACAGTAATAGTAACAGTAACAATATTCAACATACAAAGTGTTGAATTG
1 GTAACAGTAACAGTAACAGTAACAATATTCAACACACAAAGTGCCGAATCG
* *
59796422 GTAAC-G-----GTAACAGTAATAATATTCGACACACAAAGTGCCGAATCG
1 GTAACAGTAACAGTAACAGTAACAATATTCAACACACAAAGTGCCGAATCG
*
59796467 ATAACAGTAACAGTAACAGTAACA
1 GTAACAGTAACAGTAACAGTAACA
59796491 GTAACAGTAT
Statistics
Matches: 55, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
45 37 0.67
46 1 0.02
50 1 0.02
51 16 0.29
ACGTcount: A:0.45, C:0.16, G:0.17, T:0.23
Consensus pattern (51 bp):
GTAACAGTAACAGTAACAGTAACAATATTCAACACACAAAGTGCCGAATCG
Found at i:59796479 original size:6 final size:6
Alignment explanation
Indices: 59796468--59796499 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
59796458 GCCGAATCGA
59796468 TAACAG TAACAG TAACAG TAACAG TAACAG TA
1 TAACAG TAACAG TAACAG TAACAG TAACAG TA
59796500 TGGCACACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.50, C:0.16, G:0.16, T:0.19
Consensus pattern (6 bp):
TAACAG
Found at i:59799391 original size:46 final size:46
Alignment explanation
Indices: 59799341--59799510 Score: 195
Period size: 46 Copynumber: 3.7 Consensus size: 46
59799331 TTGAGCATCT
59799341 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCC
* * * *
59799387 GAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--AATG-TAACTAGGCATCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G--TCC
* *
59799434 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCC
* *
59799480 GAGCTCGTTGAGTTAAGTCCGAGTTCACTTA
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTA
59799511 GGGGCGGGTT
Statistics
Matches: 103, Mismatches: 12, Indels: 18
0.77 0.09 0.14
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 3 0.03
46 57 0.55
47 29 0.28
48 3 0.03
50 3 0.03
51 2 0.02
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.29
Consensus pattern (46 bp):
GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCC
Found at i:59799499 original size:93 final size:93
Alignment explanation
Indices: 59799335--59799505 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
59799325 GGATGGTTGA
* * *
59799335 GCATCTGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
*
59799400 TGAGTCCGAGTTCGTGAAATGTAACTAG
66 TAAGTCCGAGTTCGTGAAATGTAACTAG
*
59799428 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
59799493 TAAGTCCGAGTTC
66 TAAGTCCGAGTTC
59799506 ACTTAGGGGC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TAAGTCCGAGTTCGTGAAATGTAACTAG
Found at i:59800260 original size:14 final size:14
Alignment explanation
Indices: 59800241--59800271 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
59800231 AATAATGAGT
59800241 AAGTTATGAAATTG
1 AAGTTATGAAATTG
59800255 AAGTTATGAAATTG
1 AAGTTATGAAATTG
59800269 AAG
1 AAG
59800272 CTTAATAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.23, T:0.32
Consensus pattern (14 bp):
AAGTTATGAAATTG
Found at i:59803370 original size:23 final size:23
Alignment explanation
Indices: 59803344--59803441 Score: 144
Period size: 23 Copynumber: 4.3 Consensus size: 23
59803334 ATAAGTGCCA
59803344 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
59803367 CACTGATATGTAGCCGAAGCTAA
1 CACTGATATGTAGCCGAAGCTAC
* *
59803390 CACTG-GATGTAGCCAAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
59803412 CACTGAAATGTAACCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
59803435 CACTGAT
1 CACTGAT
59803442 CAATAACACT
Statistics
Matches: 66, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
22 19 0.29
23 47 0.71
ACGTcount: A:0.34, C:0.26, G:0.20, T:0.20
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:59803409 original size:45 final size:45
Alignment explanation
Indices: 59803351--59803439 Score: 142
Period size: 45 Copynumber: 2.0 Consensus size: 45
59803341 CCACACTGAT
* * *
59803351 ATGTAGCCGAAGCTACCACTGATATGTAGCCGAAGCTAACACTGG
1 ATGTAGCCAAAGCTACCACTGAAATGTAACCGAAGCTAACACTGG
*
59803396 ATGTAGCCAAAGCTACCACTGAAATGTAACCGAAGCTACCACTG
1 ATGTAGCCAAAGCTACCACTGAAATGTAACCGAAGCTAACACTG
59803440 ATCAATAACA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.34, C:0.26, G:0.21, T:0.19
Consensus pattern (45 bp):
ATGTAGCCAAAGCTACCACTGAAATGTAACCGAAGCTAACACTGG
Found at i:59806651 original size:23 final size:23
Alignment explanation
Indices: 59806597--59806650 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
59806587 AAGAGTAAGA
59806597 TTCAAAAATCTTTTCCAACCATT
1 TTCAAAAATCTTTTCCAACCATT
*
59806620 TTCAAAAATCTTTTCCAATCATT
1 TTCAAAAATCTTTTCCAACCATT
59806643 TATCAAAA
1 T-TCAAAA
59806651 TACCAAAACT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 23 0.79
24 6 0.21
ACGTcount: A:0.39, C:0.22, G:0.00, T:0.39
Consensus pattern (23 bp):
TTCAAAAATCTTTTCCAACCATT
Found at i:59809769 original size:24 final size:24
Alignment explanation
Indices: 59809742--59809810 Score: 70
Period size: 24 Copynumber: 2.9 Consensus size: 24
59809732 AGATTTATTC
59809742 ATTATATAAATATCT-TATAATATA
1 ATTA-ATAAATATCTATATAATATA
* * **
59809766 ATTAATTAATATATATATTTTATA
1 ATTAATAAATATCTATATAATATA
*
59809790 AATAATAAATATCTAT-TAATA
1 ATTAATAAATATCTATATAATA
59809811 ATTAAATACA
Statistics
Matches: 35, Mismatches: 9, Indels: 3
0.74 0.19 0.06
Matches are distributed among these distances:
23 11 0.31
24 24 0.69
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (24 bp):
ATTAATAAATATCTATATAATATA
Found at i:59809925 original size:20 final size:20
Alignment explanation
Indices: 59809900--59809937 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
59809890 CTATTTATTT
* *
59809900 TATTTATTTATATAAAAATC
1 TATTTACTTAAATAAAAATC
59809920 TATTTACTTAAATAAAAA
1 TATTTACTTAAATAAAAA
59809938 GTAATTAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (20 bp):
TATTTACTTAAATAAAAATC
Found at i:59810302 original size:20 final size:20
Alignment explanation
Indices: 59810256--59810303 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
59810246 AGTCTTTTTT
*
59810256 CCTAATTACTCTTAATTAAG
1 CCTAATTACACTTAATTAAG
59810276 -CTAAATT-CACTTAATTAAAG
1 CCT-AATTACACTTAATT-AAG
59810296 CCTAATTA
1 CCTAATTA
59810304 ACCACTCGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
19 10 0.43
20 11 0.48
21 2 0.09
ACGTcount: A:0.40, C:0.19, G:0.04, T:0.38
Consensus pattern (20 bp):
CCTAATTACACTTAATTAAG
Found at i:59811722 original size:69 final size:69
Alignment explanation
Indices: 59811611--59811748 Score: 276
Period size: 69 Copynumber: 2.0 Consensus size: 69
59811601 TAGTGTCACC
59811611 ATGCCGCATCCAAAGAATCTTAACTTGTTGTTTCCAAAACACCTCTTCTTCAAAGGCGAATCTAA
1 ATGCCGCATCCAAAGAATCTTAACTTGTTGTTTCCAAAACACCTCTTCTTCAAAGGCGAATCTAA
59811676 GGGG
66 GGGG
59811680 ATGCCGCATCCAAAGAATCTTAACTTGTTGTTTCCAAAACACCTCTTCTTCAAAGGCGAATCTAA
1 ATGCCGCATCCAAAGAATCTTAACTTGTTGTTTCCAAAACACCTCTTCTTCAAAGGCGAATCTAA
59811745 GGGG
66 GGGG
59811749 GCGGCAGGGG
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 69 1.00
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (69 bp):
ATGCCGCATCCAAAGAATCTTAACTTGTTGTTTCCAAAACACCTCTTCTTCAAAGGCGAATCTAA
GGGG
Found at i:59812676 original size:14 final size:14
Alignment explanation
Indices: 59812652--59812691 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
59812642 TATTTAAATA
*
59812652 AATAATGTTATTTT
1 AATAATATTATTTT
*
59812666 AATATTATTATTTT
1 AATAATATTATTTT
59812680 AATAATATTATT
1 AATAATATTATT
59812692 ATTTAAGTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (14 bp):
AATAATATTATTTT
Found at i:59812912 original size:23 final size:23
Alignment explanation
Indices: 59812886--59812955 Score: 60
Period size: 23 Copynumber: 3.2 Consensus size: 23
59812876 GAGGGAAGTT
59812886 AAAGTAGTATATATATGTTCACG
1 AAAGTAGTATATATATGTTCACG
* *
59812909 AAAG--GCTATAGTA-A--TTGAGG
1 AAAGTAG-TATA-TATATGTTCACG
*
59812929 GAAGTAGTATATATATGTTCACG
1 AAAGTAGTATATATATGTTCACG
59812952 AAAG
1 AAAG
59812956 GCTATAGGTA
Statistics
Matches: 34, Mismatches: 6, Indels: 14
0.63 0.11 0.26
Matches are distributed among these distances:
20 9 0.26
21 6 0.18
22 6 0.18
23 13 0.38
ACGTcount: A:0.40, C:0.07, G:0.23, T:0.30
Consensus pattern (23 bp):
AAAGTAGTATATATATGTTCACG
Found at i:59818050 original size:222 final size:220
Alignment explanation
Indices: 59817311--59818099 Score: 722
Period size: 222 Copynumber: 3.5 Consensus size: 220
59817301 ACATGATCAG
* *
59817311 TTTTTCTTTGCCTATATCTGGATATATAACTCTATTTGAGCCATGCTTATTACTATCGAATACTG
1 TTTTTCTTTGCATATATCTGG--ATATAACTCTATTTGAGCCATGCTTATTACTATCAAATACTG
* * * ** * * * *
59817376 TTGTT-CAGGATAGCTTAATGGGTGATATTTCTGTTTTCGGTATGATTTTTCCATACAATGGTTT
64 TTGTTCCGGGA-AGCTTAATAGATGATATTTCTGTTTTCCATACGGTTTTGCCATGCAATGGTTT
* * * *
59817440 TGGTATTAGCCCTGTGGCTATTATTGTATCGAAGTTTCCGATATGCTCTTTCTTTTGGGAATTCT
128 TGGTATTAACCC--T-G---TTATTGCATTGAAGCTTCCGATATGCTCTTTCTTTTGGG-A--CT
59817505 TTTTTATGGTTATATGATATAATGATCTTTGGTTTCA
184 TTTTTATGGTTATATGATATAATGATCTTTGGTTTCA
** * *
59817542 TTTTTTCTTTGCATATATCTGGATATAACTCTATTTGAGCCATGCTTACCACGATCAAATACAGT
1 -TTTTTCTTTGCATATATCTGGATATAACTCTATTTGAGCCATGCTTATTACTATCAAATACTGT
* * ***
59817607 TGTTCGGGGTAGCTTAATAGATGATATTTCTGTTTTTTGGTACGGTTTTGCCATGCAA------T
65 TGTTCCGGGAAGCTTAATAGATGATATTTCTG-TTTTCCATACGGTTTTGCCATGCAATGGTTTT
* * * * *
59817666 GGTATTAACTCTGTTATTGCATCT-AAGCTGCTGATATGCTCTTTCTTTCGGGACTTTTTTTTTT
129 GGTATTAACCCTGTTATTGCAT-TGAAGCTTCCGATATGCTCTTTCTTTTGGGAC---TTTTTTA
* * *
59817730 TGGTTATATTATATAATGATCTTTGGATTCG
190 TGGTTATATGATATAATGATCTTTGGTTTCA
* * * * *
59817761 TTTTTCTTTGCAGAT-TGCTGGATATAACTCTATTAGAGCCTTGCTTATTACTATAAAATATTGT
1 TTTTTCTTTGCATATAT-CTGGATATAACTCTATTTGAGCCATGCTTATTACTATCAAATACTGT
** * * *
59817825 TGTTTGGGGAAGCTTAATTGATGATCTTTTTGTTTTCCATACGGTTTTGCCATGCAATGGTTTTG
65 TGTTCCGGGAAGCTTAATAGATGATATTTCTGTTTTCCATACGGTTTTGCCATGCAATGGTTTTG
* * *
59817890 GTATTAACCCTGTTACTGCATTGAAGCTTCCAATATGCTCTTTCTTTTAGGACTTTTTTATGGTT
130 GTATTAACCCTGTTATTGCATTGAAGCTTCCGATATGCTCTTTCTTTTGGGACTTTTTTATGGTT
*
59817955 GACTATGATATAATGATCTATGGGCTTTC-
195 -A-TATGATATAATGATCT-TTGG-TTTCA
* * * * * * **
59817984 TTTTT-TATGCCTATATCTAGATATTACTCTATTTGAGCTATTCTTATTA-TGATCAAATTTTGT
1 TTTTTCTTTGCATATATCTGGATATAACTCTATTTGAGCCATGCTTATTACT-ATCAAATACTGT
* * * * * *
59818047 TGTTCCTGGTAGCTTAATCA-ATGATTTTTGTGTTTTCCATATGGTTTTTCCAT
65 TGTTCCGGGAAGCTTAAT-AGATGATATTTCTGTTTTCCATACGGTTTTGCCAT
59818100 TATACTTGCT
Statistics
Matches: 460, Mismatches: 76, Indels: 52
0.78 0.13 0.09
Matches are distributed among these distances:
216 1 0.00
217 23 0.05
218 81 0.18
219 66 0.14
220 11 0.02
221 2 0.00
222 103 0.22
223 56 0.12
224 3 0.01
225 10 0.02
230 62 0.13
231 22 0.05
232 20 0.04
ACGTcount: A:0.22, C:0.14, G:0.17, T:0.47
Consensus pattern (220 bp):
TTTTTCTTTGCATATATCTGGATATAACTCTATTTGAGCCATGCTTATTACTATCAAATACTGTT
GTTCCGGGAAGCTTAATAGATGATATTTCTGTTTTCCATACGGTTTTGCCATGCAATGGTTTTGG
TATTAACCCTGTTATTGCATTGAAGCTTCCGATATGCTCTTTCTTTTGGGACTTTTTTATGGTTA
TATGATATAATGATCTTTGGTTTCA
Found at i:59820444 original size:18 final size:19
Alignment explanation
Indices: 59820423--59820466 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
59820413 TAAAAAATTC
*
59820423 AAATTTTTA-TTTTGATAG
1 AAATTTTTATTTTTAATAG
*
59820441 AAA-TTTTATTTTTAATAT
1 AAATTTTTATTTTTAATAG
59820459 AAATTTTT
1 AAATTTTT
59820467 CATATTTTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 5 0.23
18 13 0.59
19 4 0.18
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (19 bp):
AAATTTTTATTTTTAATAG
Found at i:59820883 original size:22 final size:23
Alignment explanation
Indices: 59820836--59820883 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 23
59820826 TGGACACCTT
*
59820836 AAATAACTTCAATTTTCCATTAAAA
1 AAATAACTACAATTTT-C-TTAAAA
59820861 AAATAACTACAATTTT-TTAAAA
1 AAATAACTACAATTTTCTTAAAA
59820883 A
1 A
59820884 GAATTCAACT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 7 0.32
25 15 0.68
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.35
Consensus pattern (23 bp):
AAATAACTACAATTTTCTTAAAA
Found at i:59831234 original size:40 final size:40
Alignment explanation
Indices: 59831179--59831260 Score: 155
Period size: 40 Copynumber: 2.0 Consensus size: 40
59831169 CTGAAAAATG
*
59831179 ATTGTTTTTCTCTTATTCATGCTTGATTATAGGTTGTACA
1 ATTGTTTTTCTCTTATTAATGCTTGATTATAGGTTGTACA
59831219 ATTGTTTTTCTCTTATTAATGCTTGATTATAGGTTGTACA
1 ATTGTTTTTCTCTTATTAATGCTTGATTATAGGTTGTACA
59831259 AT
1 AT
59831261 GGGGTTGGAT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.22, C:0.11, G:0.15, T:0.52
Consensus pattern (40 bp):
ATTGTTTTTCTCTTATTAATGCTTGATTATAGGTTGTACA
Found at i:59834346 original size:26 final size:28
Alignment explanation
Indices: 59834290--59834346 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 28
59834280 TTTTAAAAAA
* *
59834290 TATATATGTTATAAAATAATGTGTATTT
1 TATATATGTTATAAAATAAAGTGTATAT
59834318 TATA-ATGTTATAACAA-AAAGT-TATAT
1 TATATATGTTATAA-AATAAAGTGTATAT
59834344 TAT
1 TAT
59834347 TTAAATCATA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
26 7 0.27
27 13 0.50
28 6 0.23
ACGTcount: A:0.44, C:0.02, G:0.09, T:0.46
Consensus pattern (28 bp):
TATATATGTTATAAAATAAAGTGTATAT
Found at i:59836639 original size:3 final size:3
Alignment explanation
Indices: 59836631--59836655 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
59836621 ACTATTTAGT
59836631 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
59836656 AAAACAACTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:59844899 original size:15 final size:15
Alignment explanation
Indices: 59844879--59844908 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
59844869 ATTGATGGCT
*
59844879 AATATTTTTCTGAAA
1 AATATTTGTCTGAAA
59844894 AATATTTGTCTGAAA
1 AATATTTGTCTGAAA
59844909 TTCTGCTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.43
Consensus pattern (15 bp):
AATATTTGTCTGAAA
Found at i:59847709 original size:33 final size:33
Alignment explanation
Indices: 59847672--59847735 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
59847662 GGAACGGAGG
59847672 TATCTCCTCTGTTTTATTGCTCATGGATATTAA
1 TATCTCCTCTGTTTTATTGCTCATGGATATTAA
* *
59847705 TATCTTCTCTGTTTTATTGTTCATGGATATT
1 TATCTCCTCTGTTTTATTGCTCATGGATATT
59847736 TAAGATTTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.19, C:0.16, G:0.12, T:0.53
Consensus pattern (33 bp):
TATCTCCTCTGTTTTATTGCTCATGGATATTAA
Found at i:59848214 original size:21 final size:22
Alignment explanation
Indices: 59848189--59848236 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 22
59848179 GATTTAAACA
59848189 AAAATTT-ATATTTATATAAT-T
1 AAAATTTCATATTT-TATAATAT
*
59848210 AAAATTTCATATTTTGTAATAT
1 AAAATTTCATATTTTATAATAT
59848232 AAAAT
1 AAAAT
59848237 ATTAATTACA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 12 0.50
22 12 0.50
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (22 bp):
AAAATTTCATATTTTATAATAT
Found at i:59852416 original size:3 final size:3
Alignment explanation
Indices: 59852401--59852462 Score: 61
Period size: 3 Copynumber: 20.0 Consensus size: 3
59852391 TTATTTCTTA
* * * *
59852401 TAT TAT TAG TAT TAT TAG TAT TAC TAT TAT TAT TAT TAT GTAT TAG
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT
*
59852447 TAT ATAT TTT TAT TAT
1 TAT -TAT TAT TAT TAT
59852463 GTACGTGTAT
Statistics
Matches: 47, Mismatches: 10, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
3 41 0.87
4 6 0.13
ACGTcount: A:0.32, C:0.02, G:0.06, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:59852459 original size:23 final size:22
Alignment explanation
Indices: 59852404--59852465 Score: 81
Period size: 23 Copynumber: 2.8 Consensus size: 22
59852394 TTTCTTATAT
*
59852404 TATTAGTATTATTA-GTATTAC
1 TATTATTATTATTATGTATTAC
*
59852425 TATTATTATTATTATGTATTAG
1 TATTATTATTATTATGTATTAC
*
59852447 TATATATTTTTATTATGTA
1 TAT-TATTATTATTATGTA
59852466 CGTGTATACA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
21 13 0.36
22 9 0.25
23 14 0.39
ACGTcount: A:0.32, C:0.02, G:0.08, T:0.58
Consensus pattern (22 bp):
TATTATTATTATTATGTATTAC
Found at i:59852472 original size:23 final size:23
Alignment explanation
Indices: 59852399--59852473 Score: 64
Period size: 23 Copynumber: 3.2 Consensus size: 23
59852389 TGTTATTTCT
* *
59852399 TATATTATTAGTATTAT-TAGTAT
1 TATA-TATTATTATTATGTAGTAG
*
59852422 TACTATTATTATTATTATGTATTAG
1 TA-TA-TATTATTATTATGTAGTAG
*
59852447 TATATATTTTTATTATGTACGT-G
1 TATATATTATTATTATGTA-GTAG
59852470 TATA
1 TATA
59852474 CATATATATA
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
23 21 0.48
24 17 0.39
25 6 0.14
ACGTcount: A:0.32, C:0.03, G:0.09, T:0.56
Consensus pattern (23 bp):
TATATATTATTATTATGTAGTAG
Found at i:59852852 original size:16 final size:16
Alignment explanation
Indices: 59852792--59852851 Score: 57
Period size: 19 Copynumber: 3.4 Consensus size: 16
59852782 TATGTTGTAT
59852792 TATTATATTTTAATATTA
1 TATTATATTTT-ATA-TA
59852810 TATTATATATTTATATA
1 TATTATAT-TTTATATA
*
59852827 TACATATATCTTTTATATA
1 T--AT-TATATTTTATATA
59852846 TATTAT
1 TATTAT
59852852 CATGTATATA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
16 3 0.08
17 5 0.14
18 11 0.30
19 14 0.38
20 4 0.11
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.58
Consensus pattern (16 bp):
TATTATATTTTATATA
Found at i:59852923 original size:63 final size:63
Alignment explanation
Indices: 59852791--59852925 Score: 147
Period size: 63 Copynumber: 2.2 Consensus size: 63
59852781 TTATGTTGTA
* *
59852791 TTAT-TATATTTTAATATTATATTATATATTTATATATACATATATCTTTTATATATATTATC
1 TTATATATATTTTAATATTATATTATATATCTATATATACATATATCTTCTATATATATTATC
* *
59852853 ATGTATATATTTTAATATTATCAGTTATATATCT-T-TATACTATATGATC-TCTA-ATACTATT
1 TTATATATATTTTAATATTAT-A-TTATATATCTATATATAC-ATAT-ATCTTCTATATA-TATT
59852914 AT-
61 ATC
59852916 TTATATATAT
1 TTATATATAT
59852926 ATGTGTATAA
Statistics
Matches: 61, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
62 2 0.03
63 32 0.52
64 15 0.25
65 12 0.20
ACGTcount: A:0.36, C:0.07, G:0.02, T:0.55
Consensus pattern (63 bp):
TTATATATATTTTAATATTATATTATATATCTATATATACATATATCTTCTATATATATTATC
Found at i:59858778 original size:113 final size:111
Alignment explanation
Indices: 59858618--59858841 Score: 430
Period size: 113 Copynumber: 2.0 Consensus size: 111
59858608 CAATACCATG
59858618 CATGTAGTTGTATTGTTGTATTAAAGTTTGTTAATATGTACAGACATTTAGAAAAAGTAGTGTAT
1 CATGTAGTTGTATTGTTGTATTAAAGTTTGTTAATATGTACAGACATTTAGAAAAAGTAGTGTAT
59858683 GTTTATATGGTATACATATATCACTACTCTCTCTCTCTTAGACAACAA
66 GTTTATATGGTATACATATATCACTA--CTCTCTCTCTTAGACAACAA
59858731 CATGTAGTTGTATTGTTGTATTAAAGTTTGTTAATATGTACAGACATTTAGAAAAAGTAGTGTAT
1 CATGTAGTTGTATTGTTGTATTAAAGTTTGTTAATATGTACAGACATTTAGAAAAAGTAGTGTAT
59858796 GTTTATATGGTATACATATATCACTACTCTCTCTCTTAGACAACAA
66 GTTTATATGGTATACATATATCACTACTCTCTCTCTTAGACAACAA
59858842 TACTTCATCA
Statistics
Matches: 111, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
111 20 0.18
113 91 0.82
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (111 bp):
CATGTAGTTGTATTGTTGTATTAAAGTTTGTTAATATGTACAGACATTTAGAAAAAGTAGTGTAT
GTTTATATGGTATACATATATCACTACTCTCTCTCTTAGACAACAA
Found at i:59859176 original size:25 final size:25
Alignment explanation
Indices: 59859134--59859227 Score: 59
Period size: 25 Copynumber: 3.7 Consensus size: 25
59859124 TTCTCTTCAC
* * *
59859134 TTTTTTTCCAACTAATAAGAATGCA
1 TTTTTTTTCAATTAATAAGAATGAA
* *
59859159 TTTTTTTTCAATTTATAACG-ATTAA
1 TTTTTTTTCAATTAATAA-GAATGAA
* *
59859184 TATTGTAGTTT-AA-TAATAAGAATGTA
1 T-TT-T-TTTTCAATTAATAAGAATGAA
*
59859210 TTTTTTTTCAATTTATAA
1 TTTTTTTTCAATTAATAA
59859228 CGATTAATAT
Statistics
Matches: 51, Mismatches: 11, Indels: 14
0.67 0.14 0.18
Matches are distributed among these distances:
23 3 0.06
24 3 0.06
25 27 0.53
26 12 0.24
27 3 0.06
28 3 0.06
ACGTcount: A:0.35, C:0.07, G:0.07, T:0.50
Consensus pattern (25 bp):
TTTTTTTTCAATTAATAAGAATGAA
Found at i:59859259 original size:48 final size:51
Alignment explanation
Indices: 59859146--59859251 Score: 203
Period size: 51 Copynumber: 2.1 Consensus size: 51
59859136 TTTTTCCAAC
*
59859146 TAATAAGAATGCATTTTTTTTCAATTTATAACGATTAATATTGTAGTTTAA
1 TAATAAGAATGTATTTTTTTTCAATTTATAACGATTAATATTGTAGTTTAA
59859197 TAATAAGAATGTATTTTTTTTCAATTTATAACGATTAATATTGTAGTTTAA
1 TAATAAGAATGTATTTTTTTTCAATTTATAACGATTAATATTGTAGTTTAA
59859248 TAAT
1 TAAT
59859252 TGAGTATTAT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 54 1.00
ACGTcount: A:0.38, C:0.05, G:0.09, T:0.48
Consensus pattern (51 bp):
TAATAAGAATGTATTTTTTTTCAATTTATAACGATTAATATTGTAGTTTAA
Found at i:59859484 original size:34 final size:35
Alignment explanation
Indices: 59859418--59859484 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
59859408 CAAACACCAG
* *
59859418 AAAATATTTTTCAGTAAATCATTTTATAGAAAAGT
1 AAAACATTTTTCAGTAAATCATTTTACAGAAAAGT
*
59859453 AAAACATTTTTCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTTCAGTAAATCATTTTACAGAAAA
59859485 TATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 16 0.55
35 13 0.45
ACGTcount: A:0.46, C:0.09, G:0.09, T:0.36
Consensus pattern (35 bp):
AAAACATTTTTCAGTAAATCATTTTACAGAAAAGT
Found at i:59859814 original size:2 final size:2
Alignment explanation
Indices: 59859807--59859840 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
59859797 GAGTTTTTCT
*
59859807 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
59859841 ATTAGTAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:59862631 original size:31 final size:31
Alignment explanation
Indices: 59862572--59862632 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
59862562 AATTATACAA
* *
59862572 ATAAAAATTTAATTGTGGTTTAAATGTATAG
1 ATAAAAATTTAATTGTGATTCAAATGTATAG
* * *
59862603 ATAAAACTTTAATTTTGATTCAATTGTATA
1 ATAAAAATTTAATTGTGATTCAAATGTATA
59862633 CATTTAAATA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.11, T:0.44
Consensus pattern (31 bp):
ATAAAAATTTAATTGTGATTCAAATGTATAG
Found at i:59862794 original size:30 final size:30
Alignment explanation
Indices: 59862759--59862832 Score: 78
Period size: 29 Copynumber: 2.4 Consensus size: 30
59862749 AAAATTAAAT
59862759 TAAATCAAAATTTCATATATAAAATTACACA
1 TAAATCAAAATTT-ATATATAAAATTACACA
* * * *
59862790 -AAATCAAACTTTTTGTATAACATTACACA
1 TAAATCAAAATTTATATATAAAATTACACA
*
59862819 TTAAATAAAAATTT
1 -TAAATCAAAATTT
59862833 TTGCGCTGTT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
29 14 0.40
30 11 0.31
31 10 0.29
ACGTcount: A:0.51, C:0.12, G:0.01, T:0.35
Consensus pattern (30 bp):
TAAATCAAAATTTATATATAAAATTACACA
Found at i:59865411 original size:21 final size:21
Alignment explanation
Indices: 59865382--59865428 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
59865372 ATTTTTACAT
* *
59865382 TTTTTACCTTATGCAATTATA
1 TTTTGACCTAATGCAATTATA
*
59865403 TTTTGACCTAATGGAATTATA
1 TTTTGACCTAATGCAATTATA
59865424 TTTTG
1 TTTTG
59865429 TCTTGTCTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.28, C:0.11, G:0.11, T:0.51
Consensus pattern (21 bp):
TTTTGACCTAATGCAATTATA
Found at i:59873505 original size:31 final size:31
Alignment explanation
Indices: 59873447--59873505 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 31
59873437 GGTGCAATTA
*
59873447 TATACGTGAAACTCTAATTGCAGTTTAAATG
1 TATACGTGAAACTCTAATTGCAATTTAAATG
* * **
59873478 TATACTTGAAACTTTAATTTTAATTTAA
1 TATACGTGAAACTCTAATTGCAATTTAA
59873506 CCATATACAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 23 1.00
ACGTcount: A:0.37, C:0.10, G:0.10, T:0.42
Consensus pattern (31 bp):
TATACGTGAAACTCTAATTGCAATTTAAATG
Found at i:59877981 original size:38 final size:36
Alignment explanation
Indices: 59877922--59878004 Score: 96
Period size: 38 Copynumber: 2.3 Consensus size: 36
59877912 AAATACATTC
*
59877922 TAAAATTA-TAAAAATTATAAAAAAATCAAAATTTA
1 TAAAATTATTAAAAATTATAAAAAAATAAAAATTTA
* * *
59877957 TGAAATTATTATAAATTAATTAAAAACATAAAAATTTA
1 TAAAATTATTAAAAATT-A-TAAAAAAATAAAAATTTA
*
59877995 TAAAAATATT
1 TAAAATTATT
59878005 TATTTTTATA
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
35 7 0.18
36 7 0.18
37 1 0.03
38 24 0.62
ACGTcount: A:0.61, C:0.02, G:0.01, T:0.35
Consensus pattern (36 bp):
TAAAATTATTAAAAATTATAAAAAAATAAAAATTTA
Found at i:59880743 original size:44 final size:44
Alignment explanation
Indices: 59880695--59880917 Score: 138
Period size: 44 Copynumber: 5.1 Consensus size: 44
59880685 ACAAATCTAT
* * *
59880695 TCTCCCTAAAATGGCACTGGAGAGGCTCGAAGCCAGCATTCGTA
1 TCTCCCTGAAATGCCACTGGAGAGGCTCGAAGCCACCATTCGTA
* * * * *
59880739 TCTCCTTGAAGTTCCAGC-GGAGTA-GATCGAAGCTACCAATCTC-T-
1 TCTCCCTGAAATGCCA-CTGGAG-AGGCTCGAAGCCACC-AT-TCGTA
* *
59880783 TCTCCCTGAAATGACACTAGAGAGGCTCGAAGCCACCATTCGTA
1 TCTCCCTGAAATGCCACTGGAGAGGCTCGAAGCCACCATTCGTA
** * * * *
59880827 TCTCTTTGAAGTTCCAGC-GGAGTA-GATCGAAGCTACCAATCTC-T-
1 TCTCCCTGAAATGCCA-CTGGAG-AGGCTCGAAGCCACC-AT-TCGTA
* * * *
59880871 TCTCCCTAAAATGGCACTGGAAAGGCTTGAAGCCACCATTCGTA
1 TCTCCCTGAAATGCCACTGGAGAGGCTCGAAGCCACCATTCGTA
59880915 TCT
1 TCT
59880918 TCTTGAAGTT
Statistics
Matches: 130, Mismatches: 33, Indels: 32
0.67 0.17 0.16
Matches are distributed among these distances:
42 4 0.03
43 10 0.08
44 102 0.78
45 10 0.08
46 4 0.03
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (44 bp):
TCTCCCTGAAATGCCACTGGAGAGGCTCGAAGCCACCATTCGTA
Found at i:59880772 original size:88 final size:88
Alignment explanation
Indices: 59880582--59880979 Score: 518
Period size: 88 Copynumber: 4.6 Consensus size: 88
59880572 TCTCCTTCAA
* * ** ** **
59880582 CGGAGTAGATTGAGGCTATAAATCTCTTCTCCCTGAAATGGCGTTAAAGCA-GCTCGAAGCCA-C
1 CGGAGTAGATCGAAGCTACCAATCTCTTCTCCCTGAAATGGCACTGGAG-AGGCTCGAAGCCACC
*
59880645 A-GCAG-ATCTCCTTGAAGTTCCAG
65 ATTC-GTATCTCCTTGAAGTTCCAG
** * * * * *
59880668 TAGAGTAAATCGAAGCTACAAATCTATTCTCCCTAAAATGGCACTGGAGAGGCTCGAAGCCAGCA
1 CGGAGTAGATCGAAGCTACCAATCTCTTCTCCCTGAAATGGCACTGGAGAGGCTCGAAGCCACCA
59880733 TTCGTATCTCCTTGAAGTTCCAG
66 TTCGTATCTCCTTGAAGTTCCAG
* *
59880756 CGGAGTAGATCGAAGCTACCAATCTCTTCTCCCTGAAATGACACTAGAGAGGCTCGAAGCCACCA
1 CGGAGTAGATCGAAGCTACCAATCTCTTCTCCCTGAAATGGCACTGGAGAGGCTCGAAGCCACCA
*
59880821 TTCGTATCTCTTTGAAGTTCCAG
66 TTCGTATCTCCTTGAAGTTCCAG
* * *
59880844 CGGAGTAGATCGAAGCTACCAATCTCTTCTCCCTAAAATGGCACTGGAAAGGCTTGAAGCCACCA
1 CGGAGTAGATCGAAGCTACCAATCTCTTCTCCCTGAAATGGCACTGGAGAGGCTCGAAGCCACCA
* *
59880909 TTCGTATCTTCTTGAAGTT-TAG
66 TTCGTATCTCCTTGAAGTTCCAG
*
59880931 CGGAGTAGATCGAAGCTACCAATCTCTTCTCCCTGAAATGGCATTGGAG
1 CGGAGTAGATCGAAGCTACCAATCTCTTCTCCCTGAAATGGCACTGGAG
59880980 CGATCAAAAT
Statistics
Matches: 274, Mismatches: 34, Indels: 7
0.87 0.11 0.02
Matches are distributed among these distances:
85 1 0.00
86 48 0.18
87 51 0.19
88 174 0.64
ACGTcount: A:0.28, C:0.25, G:0.22, T:0.25
Consensus pattern (88 bp):
CGGAGTAGATCGAAGCTACCAATCTCTTCTCCCTGAAATGGCACTGGAGAGGCTCGAAGCCACCA
TTCGTATCTCCTTGAAGTTCCAG
Found at i:59882897 original size:18 final size:16
Alignment explanation
Indices: 59882874--59882916 Score: 50
Period size: 18 Copynumber: 2.6 Consensus size: 16
59882864 TGTCATTATT
*
59882874 CTTATTTTTTTCTCGTTG
1 CTTATTTTTTTCT--TTA
*
59882892 CTTATTTATTTCTTTA
1 CTTATTTTTTTCTTTA
59882908 CTTATTTTT
1 CTTATTTTT
59882917 ATACCTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 10 0.45
18 12 0.55
ACGTcount: A:0.12, C:0.14, G:0.05, T:0.70
Consensus pattern (16 bp):
CTTATTTTTTTCTTTA
Found at i:59883002 original size:21 final size:21
Alignment explanation
Indices: 59882976--59883190 Score: 68
Period size: 21 Copynumber: 9.8 Consensus size: 21
59882966 TTTTAATCAT
59882976 TTATTATTACTATTACTTTTA
1 TTATTATTACTATTACTTTTA
* * *
59882997 TTATTATTACTGTTTCTATTA
1 TTATTATTACTATTACTTTTA
* * *
59883018 TTGTT-TTTCTATTATTATTTA
1 TTATTATTACTATTACT-TTTA
*
59883039 TGTTATTGTTGGCACTATT-C-TTTA
1 --TTATTATT---ACTATTACTTTTA
* *
59883063 TT-TTATTATTATTATTTTTTA
1 TTATTATTACTATTA-CTTTTA
59883084 TTATT-TTA-TCATTACTTTCTA
1 TTATTATTACT-ATTACTTT-TA
* * * *
59883105 TTATTGTTATTATTAATATACTA
1 TTATTATTACTATTACT-T-TTA
*
59883128 TTATTATT-CTTATTAACCTATTA
1 TTATTATTAC-TATT-A-CTTTTA
* *
59883151 TTATTATTATTATTTTCTACTTTA
1 TTATTATTACTA-TTACT--TTTA
*
59883175 TTATTA-TATTATTACT
1 TTATTATTACTATTACT
59883191 ATTGCTATCA
Statistics
Matches: 143, Mismatches: 27, Indels: 47
0.66 0.12 0.22
Matches are distributed among these distances:
18 5 0.03
20 11 0.08
21 49 0.34
22 18 0.13
23 36 0.25
24 18 0.13
25 1 0.01
27 5 0.03
ACGTcount: A:0.26, C:0.08, G:0.03, T:0.63
Consensus pattern (21 bp):
TTATTATTACTATTACTTTTA
Found at i:59883073 original size:3 final size:3
Alignment explanation
Indices: 59883060--59883193 Score: 86
Period size: 3 Copynumber: 45.7 Consensus size: 3
59883050 GCACTATTCT
*
59883060 TTA TT- TTA TTA TTA TTA TT- TT- TTA TTA TT- TTA TCA TTA CTT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA
* * * * *
59883101 TCTA TTA TTG TTA TTA TTA ATA -TA CTA TTA TTA TTC TTA TTAA CCTA
1 T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A -TTA
* * *
59883148 TTA TTA TTA TTA TTA TTT TCTA CT- TTA TTA TTA -TA TTA TTA CTA
1 TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA
59883192 TT
1 TT
59883194 GCTATCATCA
Statistics
Matches: 103, Mismatches: 16, Indels: 24
0.72 0.11 0.17
Matches are distributed among these distances:
2 14 0.14
3 82 0.80
4 6 0.06
5 1 0.01
ACGTcount: A:0.28, C:0.07, G:0.01, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:59883084 original size:16 final size:15
Alignment explanation
Indices: 59883063--59883092 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
59883053 CTATTCTTTA
59883063 TTTTATTATTATTATT
1 TTTTATTATT-TTATT
59883079 TTTTATTATTTTAT
1 TTTTATTATTTTAT
59883093 CATTACTTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTATTATTTTATT
Found at i:59883086 original size:13 final size:14
Alignment explanation
Indices: 59883060--59883193 Score: 71
Period size: 14 Copynumber: 9.4 Consensus size: 14
59883050 GCACTATTCT
59883060 TTATTTTATTATTA
1 TTATTTTATTATTA
59883074 TTATTTT-TTATTA
1 TTATTTTATTATTA
*
59883087 TT-TTATCATTACTT-
1 TTATT-TTATTA-TTA
*
59883101 TCTATTATTGTTATTA
1 T-TATT-TTATTATTA
* * *
59883117 TTAATATACTATTA
1 TTATTTTATTATTA
*
59883131 TTATTCTTATTAACCTA
1 TTATT-TTATT-A-TTA
59883148 TTATTATTATTATTA
1 TTATT-TTATTATTA
* *
59883163 TT-TTCTACT-TTA
1 TTATTTTATTATTA
*
59883175 TTATTATATTATTA
1 TTATTTTATTATTA
*
59883189 CTATT
1 TTATT
59883194 GCTATCATCA
Statistics
Matches: 91, Mismatches: 18, Indels: 22
0.69 0.14 0.17
Matches are distributed among these distances:
12 7 0.08
13 17 0.19
14 30 0.33
15 15 0.16
16 10 0.11
17 12 0.13
ACGTcount: A:0.28, C:0.07, G:0.01, T:0.63
Consensus pattern (14 bp):
TTATTTTATTATTA
Found at i:59883132 original size:23 final size:23
Alignment explanation
Indices: 59883102--59883185 Score: 84
Period size: 23 Copynumber: 3.8 Consensus size: 23
59883092 TCATTACTTT
* *
59883102 CTATTATTGTTATTATTAATATA
1 CTATTATTATTATTATTAACATA
* *
59883125 CTATTATTATTCTTATTAACCTA
1 CTATTATTATTATTATTAACATA
* **
59883148 TTATTATTATTATTATTTTC-TA
1 CTATTATTATTATTATTAACATA
59883170 CT-TTATTATTA-TATTA
1 CTATTATTATTATTATTA
59883186 TTACTATTGC
Statistics
Matches: 51, Mismatches: 10, Indels: 3
0.80 0.16 0.05
Matches are distributed among these distances:
20 4 0.08
21 9 0.18
22 3 0.06
23 35 0.69
ACGTcount: A:0.31, C:0.08, G:0.01, T:0.60
Consensus pattern (23 bp):
CTATTATTATTATTATTAACATA
Found at i:59883160 original size:20 final size:20
Alignment explanation
Indices: 59883066--59883163 Score: 76
Period size: 20 Copynumber: 4.9 Consensus size: 20
59883056 TTCTTTATTT
* *
59883066 TATTATTATTATT-TTTTAT
1 TATTATTATTATTATTATAC
* * *
59883085 TATT-TTATCATTACTTTCTAT
1 TATTATTATTATTA--TTATAC
* *
59883106 TATTGTTATTATTAATATAC
1 TATTATTATTATTATTATAC
*
59883126 TATTATTATTCTTATTA-ACC
1 TATTATTATTATTATTATA-C
59883146 TATTATTATTATTATTAT
1 TATTATTATTATTATTAT
59883164 TTTCTACTTT
Statistics
Matches: 63, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
18 7 0.11
19 5 0.08
20 34 0.54
21 9 0.14
22 8 0.13
ACGTcount: A:0.30, C:0.07, G:0.01, T:0.62
Consensus pattern (20 bp):
TATTATTATTATTATTATAC
Found at i:59883394 original size:26 final size:26
Alignment explanation
Indices: 59883337--59883432 Score: 79
Period size: 28 Copynumber: 3.6 Consensus size: 26
59883327 ATTATTATCA
*
59883337 ATTTTAAA-TATTTTACATATGTTATTT
1 ATTTTAAATTATTATACATA--TTATTT
* *
59883364 CTTTTAAATTATTATACGTATTATTT
1 ATTTTAAATTATTATACATATTATTT
* * *
59883390 ATTTTGAAATTTTTATATACATCTT-TGT
1 ATTTT-AAA-TTAT-TATACATATTATTT
59883418 ATTTTAAATTATTAT
1 ATTTTAAATTATTAT
59883433 GTATATATAC
Statistics
Matches: 56, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
25 3 0.05
26 13 0.23
27 13 0.23
28 19 0.34
29 8 0.14
ACGTcount: A:0.32, C:0.05, G:0.04, T:0.58
Consensus pattern (26 bp):
ATTTTAAATTATTATACATATTATTT
Found at i:59885643 original size:15 final size:15
Alignment explanation
Indices: 59885619--59885648 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
59885609 ATAGTTTCCC
*
59885619 TTTATTTTATTTTTA
1 TTTATGTTATTTTTA
59885634 TTTATGTTATTTTTA
1 TTTATGTTATTTTTA
59885649 ATAATTAGAT
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:0.20, C:0.00, G:0.03, T:0.77
Consensus pattern (15 bp):
TTTATGTTATTTTTA
Found at i:59885885 original size:18 final size:19
Alignment explanation
Indices: 59885864--59885907 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
59885854 TAATTTTATA
59885864 ATTTATTTTAAT-TAAAAT
1 ATTTATTTTAATATAAAAT
* *
59885882 ATTTATTATAATATAAATT
1 ATTTATTTTAATATAAAAT
59885901 A-TTATTT
1 ATTTATTT
59885908 ATATTTATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 16 0.73
19 6 0.27
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
ATTTATTTTAATATAAAAT
Found at i:59885914 original size:6 final size:6
Alignment explanation
Indices: 59885903--59885956 Score: 60
Period size: 6 Copynumber: 9.5 Consensus size: 6
59885893 TATAAATTAT
***
59885903 TATTTA TATTTA TATTTA TATTTA TATTT- T-TTTA -ACAAA TATTTA
1 TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA
59885948 TATTTA TAT
1 TATTTA TAT
59885957 AAAAGAGAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
4 3 0.08
5 2 0.05
6 34 0.87
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (6 bp):
TATTTA
Found at i:59886161 original size:19 final size:19
Alignment explanation
Indices: 59886137--59886184 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
59886127 TTTATATAAG
59886137 AAAATAAAGAA-TAAAAGAA
1 AAAATAAAGAATTAAAA-AA
* *
59886156 AAAAT-AAGAATTGAAACA
1 AAAATAAAGAATTAAAAAA
59886174 AAAATAAAGAA
1 AAAATAAAGAA
59886185 GTACGCAAGG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
18 11 0.44
19 14 0.56
ACGTcount: A:0.75, C:0.02, G:0.10, T:0.12
Consensus pattern (19 bp):
AAAATAAAGAATTAAAAAA
Found at i:59888734 original size:24 final size:24
Alignment explanation
Indices: 59888707--59888760 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
59888697 GTATTCCTCG
59888707 CTCGTTA-AGCGATGGTACTCCTTC
1 CTCGTTAGA-CGATGGTACTCCTTC
* *
59888731 CTCGTTAGACGTTGGTACTCTTTC
1 CTCGTTAGACGATGGTACTCCTTC
59888755 CTCGTT
1 CTCGTT
59888761 GATTGATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
24 26 0.96
25 1 0.04
ACGTcount: A:0.13, C:0.28, G:0.20, T:0.39
Consensus pattern (24 bp):
CTCGTTAGACGATGGTACTCCTTC
Found at i:59889239 original size:21 final size:21
Alignment explanation
Indices: 59889215--59889257 Score: 52
Period size: 20 Copynumber: 2.0 Consensus size: 21
59889205 TTTGTTGATT
59889215 TTTTAAAAATATTTATT-ATTA
1 TTTT-AAAATATTTATTAATTA
* *
59889236 TTTTTAAATTTTTATTAATTA
1 TTTTAAAATATTTATTAATTA
59889257 T
1 T
59889258 ATGTAGATTG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (21 bp):
TTTTAAAATATTTATTAATTA
Found at i:59895448 original size:43 final size:42
Alignment explanation
Indices: 59895387--59895624 Score: 224
Period size: 43 Copynumber: 5.4 Consensus size: 42
59895377 GTTATAGATT
* *
59895387 ACGCCGCTAAAAGTCATGATCTTTAGCGGCGTTTTCCCCACAA
1 ACGCCGCTAAAAGTCATGGTCTTTAGCGGCGTTTT-TCCACAA
* * *
59895430 ACGCCGCTAAAGGTCATGATCTTTAGCTTTAGCGGCGCTTTATCCACAA
1 ACGCCGCTAAAAGTCATG----GT--CTTTAGCGGCG-TTTTTCCACAA
* * ** *
59895479 ACGCCGCTAAAGGCCATGGTCTTTAGCAACACTTTTTCCACAA
1 ACGCCGCTAAAAGTCATGGTCTTTAGCGGC-GTTTTTCCACAA
* *
59895522 ACGACGCTAAAAGTCATGGCCTTTAGCGGCGCTTTTTCCACAA
1 ACGCCGCTAAAAGTCATGGTCTTTAGCGGCG-TTTTTCCACAA
* * * *
59895565 ACGCCGCTAAAAGTCATGGCCTTTAGTGGCGCTTTTCCCAAAA
1 ACGCCGCTAAAAGTCATGGTCTTTAGCGGCG-TTTTTCCACAA
*
59895608 ACGCCGCTAAAGGTCAT
1 ACGCCGCTAAAAGTCAT
59895625 AAAATTTAAA
Statistics
Matches: 164, Mismatches: 22, Indels: 18
0.80 0.11 0.09
Matches are distributed among these distances:
43 125 0.76
45 1 0.01
47 1 0.01
49 34 0.21
50 3 0.02
ACGTcount: A:0.26, C:0.29, G:0.20, T:0.26
Consensus pattern (42 bp):
ACGCCGCTAAAAGTCATGGTCTTTAGCGGCGTTTTTCCACAA
Found at i:59895479 original size:49 final size:49
Alignment explanation
Indices: 59895407--59895505 Score: 153
Period size: 49 Copynumber: 2.0 Consensus size: 49
59895397 AAGTCATGAT
* * *
59895407 CTTTAGCGGCGTTTTCCCCACAAACGCCGCTAAAGGTCATGATCTTTAG
1 CTTTAGCGGCGCTTTACCCACAAACGCCGCTAAAGGCCATGATCTTTAG
* *
59895456 CTTTAGCGGCGCTTTATCCACAAACGCCGCTAAAGGCCATGGTCTTTAG
1 CTTTAGCGGCGCTTTACCCACAAACGCCGCTAAAGGCCATGATCTTTAG
59895505 C
1 C
59895506 AACACTTTTT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
49 45 1.00
ACGTcount: A:0.22, C:0.29, G:0.21, T:0.27
Consensus pattern (49 bp):
CTTTAGCGGCGCTTTACCCACAAACGCCGCTAAAGGCCATGATCTTTAG
Found at i:59895600 original size:86 final size:88
Alignment explanation
Indices: 59895387--59895624 Score: 284
Period size: 86 Copynumber: 2.7 Consensus size: 88
59895377 GTTATAGATT
* *
59895387 ACGCCGCTAAAAGTCATGATCTTTAGCGGCG-TTTTCCCCACAAACGCCGCTAAAGGTCATGATC
1 ACGCCGCTAAAAGTCATGGTCTTTAGCGGCGCTTTT-CCCACAAACGCCGCTAAAGGTCATGAGC
59895451 TTTAGCTTTAGCGGCGCTTTATCCACAA
65 --T--CTTTAGCGGCGCTTTATCCACAA
* * ** * * * *
59895479 ACGCCGCTAAAGGCCATGGTCTTTAGCAACACTTTTTCCACAAACGACGCTAAAAGTCATG-GC-
1 ACGCCGCTAAAAGTCATGGTCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGGTCATGAGCT
*
59895542 CTTTAGCGGCGCTTTTTCCACAA
66 CTTTAGCGGCGCTTTATCCACAA
* * *
59895565 ACGCCGCTAAAAGTCATGGCCTTTAGTGGCGCTTTTCCCAAAAACGCCGCTAAAGGTCAT
1 ACGCCGCTAAAAGTCATGGTCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGGTCAT
59895625 AAAATTTAAA
Statistics
Matches: 123, Mismatches: 22, Indels: 8
0.80 0.14 0.05
Matches are distributed among these distances:
86 71 0.58
91 1 0.01
92 47 0.38
93 4 0.03
ACGTcount: A:0.26, C:0.29, G:0.20, T:0.26
Consensus pattern (88 bp):
ACGCCGCTAAAAGTCATGGTCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGGTCATGAGCT
CTTTAGCGGCGCTTTATCCACAA
Found at i:59895802 original size:19 final size:19
Alignment explanation
Indices: 59895757--59895803 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
59895747 TTCATTATTA
*
59895757 AATAAAAATAAAAATATAG
1 AATAAAAATAAAAATAAAG
* *
59895776 AATCAAAACT-AAAATAAAT
1 AAT-AAAAATAAAAATAAAG
59895795 AATAAAAAT
1 AATAAAAAT
59895804 TAGATTAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 5 0.22
19 13 0.57
20 5 0.22
ACGTcount: A:0.72, C:0.04, G:0.02, T:0.21
Consensus pattern (19 bp):
AATAAAAATAAAAATAAAG
Found at i:59898641 original size:46 final size:46
Alignment explanation
Indices: 59898607--59898724 Score: 191
Period size: 46 Copynumber: 2.6 Consensus size: 46
59898597 TATATCTTAG
*
59898607 ATTAGCCATTTGGCTTTACCACATATCCATCTCATACACGTTTCGC
1 ATTAGCCATTTGGCTTTACCACATATCCATCTCATACACATTTCGC
*
59898653 ATTAGCCATTTGGCTTTACCTCATATCCATCTCATACACATTTCGC
1 ATTAGCCATTTGGCTTTACCACATATCCATCTCATACACATTTCGC
* **
59898699 ATTAGCCATTCGGCTTCGCCACATAT
1 ATTAGCCATTTGGCTTTACCACATAT
59898725 ATACACTTCC
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 66 1.00
ACGTcount: A:0.24, C:0.31, G:0.11, T:0.35
Consensus pattern (46 bp):
ATTAGCCATTTGGCTTTACCACATATCCATCTCATACACATTTCGC
Found at i:59898769 original size:47 final size:47
Alignment explanation
Indices: 59898734--59899211 Score: 694
Period size: 47 Copynumber: 10.2 Consensus size: 47
59898724 TATACACTTC
* ** *
59898734 CACGTTCATCACATTGGTCATTCTACCTTATCACATTTATGCATGTT
1 CACGTTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTT
*** *
59898781 CGTATTCATCACATTGGCCATTCGGCCTTATCACATATTTGCATGTT
1 CACGTTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTT
* *
59898828 CACATTCATCACATTGGCCATTCGGCCTTATCACATATTTGCATGTT
1 CACGTTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTT
*
59898875 CACGTTCATCACATTGGCCATTCGGCCTTATCACACATATGCATGTT
1 CACGTTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTT
** *
59898922 CACGTTCATCACATTGGCCATTCTACCTTATCACATGTATGCATGTT
1 CACGTTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTT
*
59898969 --CGTATCCATCACATTGGCCATTCGGCCTTATCACATATTTGCATGTT
1 CACGT-T-CATCACATTGGCCATTCGGCCTTATCACATATATGCATGTT
*
59899016 CACGTCCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTT
1 CACGTTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTT
* * *
59899063 CACATTCATCACATTAGCCATTCGGCCTTATCACATATTTGCATGTT
1 CACGTTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTT
* * *
59899110 CACGTTTATCACATTGGCCATTCGGCTTTATCACACATATGCATGTT
1 CACGTTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTT
*
59899157 CACGTTCACCACATTGGCCATTCGGCCTTATCAC--ATATGCATGTT
1 CACGTTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTT
*
59899202 CACATTCATC
1 CACGTTCATC
59899212 TCATACAATC
Statistics
Matches: 389, Mismatches: 38, Indels: 10
0.89 0.09 0.02
Matches are distributed among these distances:
45 22 0.06
46 1 0.00
47 363 0.93
49 3 0.01
ACGTcount: A:0.23, C:0.28, G:0.13, T:0.35
Consensus pattern (47 bp):
CACGTTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTT
Found at i:59898813 original size:22 final size:22
Alignment explanation
Indices: 59898788--59898909 Score: 72
Period size: 22 Copynumber: 5.3 Consensus size: 22
59898778 GTTCGTATTC
59898788 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
* * *
59898810 ATCACATATTTG-CATGTTC-ACATT
1 ATCAC--ATTGGCCA--TTCGGCCTT
59898834 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
* * *
59898857 ATCACATATTTG-CATGTTC-ACGTT
1 ATCAC--ATTGGCCA--TTCGGCCTT
59898881 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
59898904 ATCACA
1 ATCACA
59898910 CATATGCATG
Statistics
Matches: 74, Mismatches: 12, Indels: 28
0.65 0.11 0.25
Matches are distributed among these distances:
22 22 0.30
23 18 0.24
24 18 0.24
25 16 0.22
ACGTcount: A:0.23, C:0.29, G:0.14, T:0.34
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:59899001 original size:22 final size:22
Alignment explanation
Indices: 59898976--59899051 Score: 59
Period size: 22 Copynumber: 3.3 Consensus size: 22
59898966 GTTCGTATCC
59898976 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
* *
59898998 ATCACATATTTG-CATGTTCACGTCC--
1 ATCAC--ATTGGCCA--TT--CGGCCTT
59899023 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
59899045 ATCACAT
1 ATCACAT
59899052 ATATGCATGT
Statistics
Matches: 41, Mismatches: 4, Indels: 18
0.65 0.06 0.29
Matches are distributed among these distances:
20 4 0.10
22 14 0.34
23 6 0.15
24 6 0.15
25 7 0.17
27 4 0.10
ACGTcount: A:0.22, C:0.30, G:0.14, T:0.33
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:59899098 original size:22 final size:22
Alignment explanation
Indices: 59899023--59899098 Score: 66
Period size: 22 Copynumber: 3.3 Consensus size: 22
59899013 GTTCACGTCC
*
59899023 ATCACATTGGCCATTCGGCCTT
1 ATCACATTAGCCATTCGGCCTT
* *
59899045 ATCACATATATG-CATGTTC-ACATT
1 ATCACAT-TA-GCCA--TTCGGCCTT
59899069 CATCACATTAGCCATTCGGCCTT
1 -ATCACATTAGCCATTCGGCCTT
59899092 ATCACAT
1 ATCACAT
59899099 ATTTGCATGT
Statistics
Matches: 42, Mismatches: 5, Indels: 14
0.69 0.08 0.23
Matches are distributed among these distances:
22 17 0.40
23 7 0.17
24 8 0.19
25 10 0.24
ACGTcount: A:0.26, C:0.29, G:0.12, T:0.33
Consensus pattern (22 bp):
ATCACATTAGCCATTCGGCCTT
Found at i:59901977 original size:12 final size:12
Alignment explanation
Indices: 59901960--59901984 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
59901950 TAAAAATAAC
59901960 AATTTAACACTA
1 AATTTAACACTA
59901972 AATTTAACACTA
1 AATTTAACACTA
59901984 A
1 A
59901985 TTTGAAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (12 bp):
AATTTAACACTA
Found at i:59904863 original size:17 final size:17
Alignment explanation
Indices: 59904841--59904873 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
59904831 AACGAAGGAT
59904841 CGAGAGAAAAACAGTAA
1 CGAGAGAAAAACAGTAA
*
59904858 CGAGAGAAAAAGAGTA
1 CGAGAGAAAAACAGTA
59904874 GCTAAATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.58, C:0.09, G:0.27, T:0.06
Consensus pattern (17 bp):
CGAGAGAAAAACAGTAA
Found at i:59905255 original size:7 final size:7
Alignment explanation
Indices: 59905245--59905305 Score: 104
Period size: 7 Copynumber: 8.7 Consensus size: 7
59905235 ATATTTAAGT
59905245 TTTTTAA
1 TTTTTAA
59905252 TTTTTAA
1 TTTTTAA
59905259 TTTTTAA
1 TTTTTAA
59905266 TTTTTAA
1 TTTTTAA
59905273 TTTTTAA
1 TTTTTAA
*
59905280 TTTTAAA
1 TTTTTAA
59905287 TTTTTAA
1 TTTTTAA
*
59905294 ATTTTAA
1 TTTTTAA
59905301 TTTTT
1 TTTTT
59905306 TTTGAAGATT
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 50 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (7 bp):
TTTTTAA
Found at i:59905678 original size:37 final size:37
Alignment explanation
Indices: 59905618--59905748 Score: 201
Period size: 37 Copynumber: 3.5 Consensus size: 37
59905608 CTATGCAGCA
* *
59905618 GATGCACAGGGCGAAGGCGATGGAGGAGATGGGTTGC
1 GATGCACGGGGCGAAGGCGATGGAGGGGATGGGTTGC
* *
59905655 G-TCGCACGGGGCGAAGGCAATGGAGGGGCTGGGTTGC
1 GAT-GCACGGGGCGAAGGCGATGGAGGGGATGGGTTGC
*
59905692 GATGCACGGGGCAAAGGCGATGGAGGGGATGGGTTGC
1 GATGCACGGGGCGAAGGCGATGGAGGGGATGGGTTGC
59905729 GATGCACGGGGCGAAGGCGA
1 GATGCACGGGGCGAAGGCGA
59905749 CAAACGAAAA
Statistics
Matches: 84, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
36 1 0.01
37 82 0.98
38 1 0.01
ACGTcount: A:0.21, C:0.16, G:0.50, T:0.12
Consensus pattern (37 bp):
GATGCACGGGGCGAAGGCGATGGAGGGGATGGGTTGC
Found at i:59905884 original size:23 final size:23
Alignment explanation
Indices: 59905840--59905884 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
59905830 CTACCCATGG
* * *
59905840 CCATTAAACCTTAAACTATAAAA
1 CCATAAAACCCTAAACCATAAAA
*
59905863 CCATAAAACCCTAAACCCTAAA
1 CCATAAAACCCTAAACCATAAA
59905885 CCTTAAATCT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.51, C:0.29, G:0.00, T:0.20
Consensus pattern (23 bp):
CCATAAAACCCTAAACCATAAAA
Found at i:59906144 original size:46 final size:46
Alignment explanation
Indices: 59906020--59906146 Score: 166
Period size: 48 Copynumber: 2.7 Consensus size: 46
59906010 ATCCATATAA
* ***
59906020 TGTTTTTTTGGGTTTAGGGTTTTAAAAGTTATAGATTAGTGTTTAG
1 TGTTTTTTTGGGTTTAGGATTTTAGGGGTTATAGATTAGTGTTTAG
* *
59906066 TGTTTTTTAGGGGGTTAGGGATTTTAGGGGTTATAGATTAGTGTTTA-
1 TGTTTTTT-TGGGTTTA-GGATTTTAGGGGTTATAGATTAGTGTTTAG
59906113 TGATTTTTTTGGGTTTAGGATTTTAGGGGTTATA
1 TG-TTTTTTTGGGTTTAGGATTTTAGGGGTTATA
59906147 TGACTTTTTG
Statistics
Matches: 70, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
46 25 0.36
47 14 0.20
48 31 0.44
ACGTcount: A:0.20, C:0.00, G:0.30, T:0.50
Consensus pattern (46 bp):
TGTTTTTTTGGGTTTAGGATTTTAGGGGTTATAGATTAGTGTTTAG
Found at i:59906196 original size:41 final size:41
Alignment explanation
Indices: 59906151--59906409 Score: 416
Period size: 41 Copynumber: 6.4 Consensus size: 41
59906141 GTTATATGAC
* *
59906151 TTTTT-GCGGCGTTTTGAGCAAAAACGCCGCTATTGCTCAGT
1 TTTTTAGCGGCG-TTTGACCAAAAACGCCGCTATTGCTCTGT
59906192 TTTTTAGCGGCGTTTGACCAAAAACGCCGCTATTGCTCTGT
1 TTTTTAGCGGCGTTTGACCAAAAACGCCGCTATTGCTCTGT
*
59906233 TTTTTAGCGGCGTTTGACCAAAAACGCCACTATTGCTCTG-
1 TTTTTAGCGGCGTTTGACCAAAAACGCCGCTATTGCTCTGT
*
59906273 TTTTTAGCGGCGTTTGACCAAAAACGCTGCTATTGCTCTGT
1 TTTTTAGCGGCGTTTGACCAAAAACGCCGCTATTGCTCTGT
* *
59906314 TTTTTAGGGGCGTTTGACCAAAAACGCCGCTATTACTCTGT
1 TTTTTAGCGGCGTTTGACCAAAAACGCCGCTATTGCTCTGT
* *
59906355 TTTTTAGCAGCGTTTGACTAAAAACGCCGCTATTGCTCTG-
1 TTTTTAGCGGCGTTTGACCAAAAACGCCGCTATTGCTCTGT
59906395 TTTTTAGCGGCGTTT
1 TTTTTAGCGGCGTTT
59906410 TTGGTCAAAC
Statistics
Matches: 203, Mismatches: 13, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
40 52 0.26
41 145 0.71
42 6 0.03
ACGTcount: A:0.20, C:0.22, G:0.22, T:0.36
Consensus pattern (41 bp):
TTTTTAGCGGCGTTTGACCAAAAACGCCGCTATTGCTCTGT
Found at i:59906296 original size:81 final size:82
Alignment explanation
Indices: 59906151--59906409 Score: 416
Period size: 81 Copynumber: 3.2 Consensus size: 82
59906141 GTTATATGAC
* *
59906151 TTTTT-GCGGCGTTTTGAGCAAAAACGCCGCTATTGCTCAGTTTTTTAGCGGCGTTTGACCAAAA
1 TTTTTAGCGGCG-TTTGACCAAAAACGCCGCTATTGCTCTGTTTTTTAGCGGCGTTTGACCAAAA
59906215 ACGCCGCTATTGCTCTGT
65 ACGCCGCTATTGCTCTGT
*
59906233 TTTTTAGCGGCGTTTGACCAAAAACGCCACTATTGCTCTG-TTTTTAGCGGCGTTTGACCAAAAA
1 TTTTTAGCGGCGTTTGACCAAAAACGCCGCTATTGCTCTGTTTTTTAGCGGCGTTTGACCAAAAA
*
59906297 CGCTGCTATTGCTCTGT
66 CGCCGCTATTGCTCTGT
* * * *
59906314 TTTTTAGGGGCGTTTGACCAAAAACGCCGCTATTACTCTGTTTTTTAGCAGCGTTTGACTAAAAA
1 TTTTTAGCGGCGTTTGACCAAAAACGCCGCTATTGCTCTGTTTTTTAGCGGCGTTTGACCAAAAA
59906379 CGCCGCTATTGCTCTG-
66 CGCCGCTATTGCTCTGT
59906395 TTTTTAGCGGCGTTT
1 TTTTTAGCGGCGTTT
59906410 TTGGTCAAAC
Statistics
Matches: 164, Mismatches: 11, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
81 91 0.55
82 67 0.41
83 6 0.04
ACGTcount: A:0.20, C:0.22, G:0.22, T:0.36
Consensus pattern (82 bp):
TTTTTAGCGGCGTTTGACCAAAAACGCCGCTATTGCTCTGTTTTTTAGCGGCGTTTGACCAAAAA
CGCCGCTATTGCTCTGT
Found at i:59906298 original size:122 final size:122
Alignment explanation
Indices: 59906151--59906409 Score: 430
Period size: 122 Copynumber: 2.1 Consensus size: 122
59906141 GTTATATGAC
*
59906151 TTTTT-GCGGCGTTTTGAGCAAAAACGCCGCTATTGCTCAGTTTTTTAGCGGCGTTTGACCAAAA
1 TTTTTAGCGGCG-TTTGACCAAAAACGCCGCTATTGCTCAGTTTTTTAGCGGCGTTTGACCAAAA
* *
59906215 ACGCCGCTATTGCTCTGTTTTTTAGCGGCGTTTGACCAAAAACGCCACTATTGCTCTG
65 ACGCCGCTATTACTCTGTTTTTTAGCAGCGTTTGACCAAAAACGCCACTATTGCTCTG
* * *
59906273 TTTTTAGCGGCGTTTGACCAAAAACGCTGCTATTGCTCTGTTTTTTAGGGGCGTTTGACCAAAAA
1 TTTTTAGCGGCGTTTGACCAAAAACGCCGCTATTGCTCAGTTTTTTAGCGGCGTTTGACCAAAAA
* *
59906338 CGCCGCTATTACTCTGTTTTTTAGCAGCGTTTGACTAAAAACGCCGCTATTGCTCTG
66 CGCCGCTATTACTCTGTTTTTTAGCAGCGTTTGACCAAAAACGCCACTATTGCTCTG
59906395 TTTTTAGCGGCGTTT
1 TTTTTAGCGGCGTTT
59906410 TTGGTCAAAC
Statistics
Matches: 128, Mismatches: 8, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
122 122 0.95
123 6 0.05
ACGTcount: A:0.20, C:0.22, G:0.22, T:0.36
Consensus pattern (122 bp):
TTTTTAGCGGCGTTTGACCAAAAACGCCGCTATTGCTCAGTTTTTTAGCGGCGTTTGACCAAAAA
CGCCGCTATTACTCTGTTTTTTAGCAGCGTTTGACCAAAAACGCCACTATTGCTCTG
Found at i:59906439 original size:122 final size:121
Alignment explanation
Indices: 59906151--59906439 Score: 361
Period size: 122 Copynumber: 2.4 Consensus size: 121
59906141 GTTATATGAC
* * *
59906151 TTTTT-GCGGCGTTTTGAGCAAAAACGCCGCTATTGCTCA-GTTTTTTAGCGGCGTTTGACCAAA
1 TTTTTAGCGGCG-TTTGA-CCAAAACGCCGCTAATGCT-ATATTTTTTAGCGGCGTTTGACCAAA
* *
59906214 AACGCCGCTATTGCTCTGTTTTTTAGCGGCGTTTGACCAAAAACGCCACTATTGCTCTG
63 AACGCCGCTATTACTCTGTTTTTTAGCAGCGTTTGACCAAAAACGCCACTATTGCTCTG
* * * * *
59906273 TTTTTAGCGGCGTTTGACCAAAAACGCTGCTATTGCTCTGTTTTTTAGGGGCGTTTGACCAAAAA
1 TTTTTAGCGGCGTTTGACC-AAAACGCCGCTAATGCTATATTTTTTAGCGGCGTTTGACCAAAAA
* *
59906338 CGCCGCTATTACTCTGTTTTTTAGCAGCGTTTGACTAAAAACGCCGCTATTGCTCTG
65 CGCCGCTATTACTCTGTTTTTTAGCAGCGTTTGACCAAAAACGCCACTATTGCTCTG
** *
59906395 TTTTTAGCGGCGTTTTTGGTC-AAACGCCGCTAATG-TATAATTTTT
1 TTTTTAGCGGCG--TTTGACCAAAACGCCGCTAATGCTATATTTTTT
59906440 GTGGCATTTT
Statistics
Matches: 147, Mismatches: 15, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
121 8 0.05
122 128 0.87
123 6 0.04
124 5 0.03
ACGTcount: A:0.21, C:0.22, G:0.21, T:0.36
Consensus pattern (121 bp):
TTTTTAGCGGCGTTTGACCAAAACGCCGCTAATGCTATATTTTTTAGCGGCGTTTGACCAAAAAC
GCCGCTATTACTCTGTTTTTTAGCAGCGTTTGACCAAAAACGCCACTATTGCTCTG
Found at i:59907089 original size:12 final size:13
Alignment explanation
Indices: 59907072--59907101 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
59907062 GTCTATATTT
59907072 TTTTC-TTTTTTC
1 TTTTCTTTTTTTC
59907084 TTTTCTTTTTTTC
1 TTTTCTTTTTTTC
59907097 TTTTC
1 TTTTC
59907102 GGCATTTGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (13 bp):
TTTTCTTTTTTTC
Found at i:59909095 original size:131 final size:130
Alignment explanation
Indices: 59908857--59909321 Score: 543
Period size: 131 Copynumber: 3.6 Consensus size: 130
59908847 TAATTATCTG
* * * *
59908857 TTTAAAGATTCCTTAAAACGAAGGCAATATTTGATGTTTGGCAATTCGGGGAATCGTGCCCTACC
1 TTTAAAAATTCCTTAAAACGAAGGCAATGTTCGATGTTTGGCAATTCGGGGAATCGTGCCCTACT
*
59908922 GTGCTGGGTTGCAATTTCCTGTTTGCTCGAAACGATTGAATATTCCTTTGGTATTTCACTCATGT
66 GTGCTGGGTTGCAATTT-CTGTTTGCTCGAAACGATCGAATATTCCTTTGGTATTTCACTCATGT
59908987 C
130 C
* * *
59908988 TTTAAAAATTCCTTAAAACGAAGGCAATGTTCGATGTTTGGCTATTCAGGGAATCGTGCCTTACT
1 TTTAAAAATTCCTTAAAACGAAGGCAATGTTCGATGTTTGGCAATTCGGGGAATCGTGCCCTACT
*
59909053 GTGCTGGGTTGCAATTTCATGTTTGCTCGAAACGATCCAATATTCCTTTGGTATTTCACTCATGT
66 GTGCTGGGTTGCAATTTC-TGTTTGCTCGAAACGATCGAATATTCCTTTGGTATTTCACTCATGT
59909118 C
130 C
* * * * * *
59909119 TTTAAAAATTCTTTAAAACGAAGGAAATGTTCGATGCTTAGCGATTCGGGGAATTGTGCCCTATC
1 TTTAAAAATTCCTTAAAACGAAGGCAATGTTCGATGTTTGGCAATTCGGGGAATCGTGCCCTA-C
* * * * * *
59909184 ATGT--TGGGTTGCAATTTTCTCGTTTGTTCAAAACAATCGAATATTCCTTTAGAATTTCATTCG
65 -TGTGCTGGGTTGCAA-TTTCT-GTTTGCTCGAAACGATCGAATATTCCTTTGGTATTTCACTC-
59909247 TAT-TC
126 -ATGTC
* * * * *
59909252 TTT--AAATT-C-TAAAAC-AAAGCAATGTTCAATGTTTGG-AAGTTCGAGGAATCATGCCCAAC
1 TTTAAAAATTCCTTAAAACGAAGGCAATGTTCGATGTTTGGCAA-TTCGGGGAATCGTGCCCTAC
*
59909311 CGTGCTGGGTT
65 TGTGCTGGGTT
59909322 TCGGTTTTTT
Statistics
Matches: 288, Mismatches: 36, Indels: 23
0.83 0.10 0.07
Matches are distributed among these distances:
126 2 0.01
127 2 0.01
128 37 0.13
129 6 0.02
130 1 0.00
131 191 0.66
132 39 0.14
133 8 0.03
134 2 0.01
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.36
Consensus pattern (130 bp):
TTTAAAAATTCCTTAAAACGAAGGCAATGTTCGATGTTTGGCAATTCGGGGAATCGTGCCCTACT
GTGCTGGGTTGCAATTTCTGTTTGCTCGAAACGATCGAATATTCCTTTGGTATTTCACTCATGTC
Found at i:59920979 original size:45 final size:45
Alignment explanation
Indices: 59920911--59921255 Score: 211
Period size: 45 Copynumber: 7.6 Consensus size: 45
59920901 AAGTCACAAG
* *
59920911 TCTTATCTCCTTGAAGTTCCAGTGGAGCAGACTAAATAAAGCAAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAATAAAGCAAA
* * *
59920956 TCTTATTTCCCTGAAGTTGCAGTGGAACAGATTGAATCTATAAAGCACAGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-AA---ATAAAGCA-A-A
* ** * * *
59921007 TCTCATCTCTTTGAAGTTGCAGTAGAGCAGA-T-CA-AAA-CAAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAATAAAGCAAA
* * * * *
59921048 TCTTATCACCCTGAAATTGTAGTGGAGCAGACTAAAGATAGCAAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAATAAAGCAAA
* * * *
59921093 TCTTATTTCCCTGAAGTTGCAGTGGAACAGATTGAAGCTATAAACCACAGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-AA---ATAAAGCA-A-A
* * * * * *
59921144 TCTCATCTCTCTGAAGTTGTAGTAGAGCAGA-T-CA-AAA-CAAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAATAAAGCAAA
* ** * * * *
59921185 TCTTATCTTCCAAAAGTTGCAGTGGAACAAACTAAAGATAGCAAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAATAAAGCAAA
* *
59921230 TCTTATTTCCTTGAAGTTGCAGTGGA
1 TCTTATCTCCCTGAAGTTGCAGTGGA
59921256 ACCGATTAAA
Statistics
Matches: 223, Mismatches: 57, Indels: 40
0.70 0.18 0.12
Matches are distributed among these distances:
41 46 0.21
42 4 0.02
43 6 0.03
44 10 0.04
45 84 0.38
46 4 0.02
49 13 0.06
50 4 0.02
51 52 0.23
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (45 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAATAAAGCAAA
Found at i:59921152 original size:137 final size:137
Alignment explanation
Indices: 59920906--59921345 Score: 648
Period size: 137 Copynumber: 3.2 Consensus size: 137
59920896 GATTGAAGTC
* * * * *
59920906 ACAAGTCTTATCTCCTTGAAGTTCCAGTGGAGCAGACTAAATAAAGCAAATCTTATTTCCCTGAA
1 ACAAGTCTTATCTCCCTGAAATTGCAGTGGAGCAGACTAAAGATAGCAAATCTTATTTCCCTGAA
* *
59920971 GTTGCAGTGGAACAGATTGAATCTATAAAGCACAGATCTCATCTCTTTGAAGTTGCAGTAGAGCA
66 GTTGCAGTGGAACAGATTGAAGCTATAAAGCACAGATCTCATCTCTCTGAAGTTGCAGTAGAGCA
59921036 GATCAAA
131 GATCAAA
* *
59921043 ACAAGTCTTATCACCCTGAAATTGTAGTGGAGCAGACTAAAGATAGCAAATCTTATTTCCCTGAA
1 ACAAGTCTTATCTCCCTGAAATTGCAGTGGAGCAGACTAAAGATAGCAAATCTTATTTCCCTGAA
* *
59921108 GTTGCAGTGGAACAGATTGAAGCTATAAACCACAGATCTCATCTCTCTGAAGTTGTAGTAGAGCA
66 GTTGCAGTGGAACAGATTGAAGCTATAAAGCACAGATCTCATCTCTCTGAAGTTGCAGTAGAGCA
59921173 GATCAAA
131 GATCAAA
* * * * *
59921180 ACAAGTCTTATCTTCC-AAAAGTTGCAGTGGAACAAACTAAAGATAGCAAATCTTATTTCCTTGA
1 ACAAGTCTTATCTCCCTGAAA-TTGCAGTGGAGCAGACTAAAGATAGCAAATCTTATTTCCCTGA
* * *
59921244 AGTTGCAGTGGAACCGATTAAAGCTATAAAGCTCAGATCTCATCTCTCTGAAGTTGCAGTAGAGC
65 AGTTGCAGTGGAACAGATTGAAGCTATAAAGCACAGATCTCATCTCTCTGAAGTTGCAGTAGAGC
59921309 AGATCAAA
130 AGATCAAA
** * * *
59921317 ACAAACCTTATTTCCTTGAAGTTGCAGTG
1 ACAAGTCTTATCTCCCTGAAATTGCAGTG
59921346 AAGCGATAGA
Statistics
Matches: 271, Mismatches: 30, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
136 3 0.01
137 266 0.98
138 2 0.01
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.28
Consensus pattern (137 bp):
ACAAGTCTTATCTCCCTGAAATTGCAGTGGAGCAGACTAAAGATAGCAAATCTTATTTCCCTGAA
GTTGCAGTGGAACAGATTGAAGCTATAAAGCACAGATCTCATCTCTCTGAAGTTGCAGTAGAGCA
GATCAAA
Found at i:59923968 original size:131 final size:131
Alignment explanation
Indices: 59923718--59924181 Score: 613
Period size: 131 Copynumber: 3.6 Consensus size: 131
59923708 TAATTATCTG
*
59923718 TTTAAAGATTCCTTAAAACGAAGGCAATGTTCGATGTTTGGCAATTCGGGGAATCGTG-CCTACC
1 TTTAAAAATTCCTTAAAACGAAGGCAATGTTCGATGTTTGGCAATTCGGGGAATCGTGCCCTACC
*
59923782 ATGCTGGGTTGCAATTTTCTGTTTGCTCGAAACGATCGAATATTCCTTTGGTATTTCACTCATGT
66 GTGCTGGGTTGCAATTTTCTGTTTGCTCGAAACGATCGAATATTCCTTTGGTATTTCACTCATGT
59923847 C
131 C
*
59923848 TTTAAAAATTCCTTAAAACGAAGGCAATGTTCGATGTTTGGCAATTCGGGGAATCGTGCCCTACT
1 TTTAAAAATTCCTTAAAACGAAGGCAATGTTCGATGTTTGGCAATTCGGGGAATCGTGCCCTACC
*
59923913 GTGCTGGGTTGCAATTTCCTGTTTGCTCGAAACGATCGAATATTCCTTTGGTATTTCACTCATGT
66 GTGCTGGGTTGCAATTTTCTGTTTGCTCGAAACGATCGAATATTCCTTTGGTATTTCACTCATGT
59923978 C
131 C
* * * * * * *
59923979 TTTAAAAATTCTTTAAAACGAAGG-ATATTTTCGATGCTTAGCGATTCGGGGAATTGTGCCCTAT
1 TTTAAAAATTCCTTAAAACGAAGGCA-ATGTTCGATGTTTGGCAATTCGGGGAATCGTGCCCTAC
* * * * * * *
59924043 CGTGTTGGGTTGCAATTTTCTCGTTTGTTCAAAACAATCGAATATTCCTTTAGAATTTCATTCGT
65 CGTGCTGGGTTGCAATTTTCT-GTTTGCTCGAAACGATCGAATATTCCTTTGGTATTTCACTC--
59924108 AT-TC
127 ATGTC
* * * * *
59924112 TTT--AAATT-C-TAAAAC-AAAGCAATGTTCAATGTTTGG-AAGTTCGAGGAATCATGCCCAAC
1 TTTAAAAATTCCTTAAAACGAAGGCAATGTTCGATGTTTGGCAA-TTCGGGGAATCGTGCCCTAC
59924171 CGTGCTGGGTT
65 CGTGCTGGGTT
59924182 TCGGTTTTTC
Statistics
Matches: 294, Mismatches: 33, Indels: 16
0.86 0.10 0.05
Matches are distributed among these distances:
127 1 0.00
128 39 0.13
129 7 0.02
130 58 0.20
131 147 0.50
132 35 0.12
133 5 0.02
134 2 0.01
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.36
Consensus pattern (131 bp):
TTTAAAAATTCCTTAAAACGAAGGCAATGTTCGATGTTTGGCAATTCGGGGAATCGTGCCCTACC
GTGCTGGGTTGCAATTTTCTGTTTGCTCGAAACGATCGAATATTCCTTTGGTATTTCACTCATGT
C
Found at i:59930847 original size:60 final size:60
Alignment explanation
Indices: 59930774--59930892 Score: 202
Period size: 60 Copynumber: 2.0 Consensus size: 60
59930764 ATACTAAACT
* *
59930774 AAACACAACAATTTATAACATAATCCTAAATTACTAATAAACTAATTTTAAAATAATTAC
1 AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAACTAATTTTAAAATAATTAC
* *
59930834 AAACATAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTA
1 AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAACTAATTTTAAAATAATTA
59930893 TAAAAAAATT
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
60 55 1.00
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.33
Consensus pattern (60 bp):
AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAACTAATTTTAAAATAATTAC
Found at i:59931066 original size:3 final size:3
Alignment explanation
Indices: 59931060--59931107 Score: 55
Period size: 3 Copynumber: 16.3 Consensus size: 3
59931050 TTTTTTTTCT
* *
59931060 TTC TTC TTC TTC TTC TTC TCTC TCC TTC TTC TTC TT- TT- TTT TTC
1 TTC TTC TTC TTC TTC TTC T-TC TTC TTC TTC TTC TTC TTC TTC TTC
59931104 TTC T
1 TTC T
59931108 CCTTTCTCTC
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
2 4 0.10
3 33 0.82
4 3 0.08
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:59931122 original size:19 final size:19
Alignment explanation
Indices: 59931066--59931134 Score: 56
Period size: 19 Copynumber: 3.7 Consensus size: 19
59931056 TTCTTTCTTC
*
59931066 TTCTTCTTCTTCTCTCTCC-
1 TTCTTCTCCTT-TCTCTCCT
* *
59931085 TTCTTCTTCTTT-T-T-TT
1 TTCTTCTCCTTTCTCTCCT
59931101 TTCTTCTCCTTTCTCTCCT
1 TTCTTCTCCTTTCTCTCCT
59931120 TTCTTTCTCTCTTTC
1 TTC-TTCTC-CTTTC
59931135 GGTGGCTGCT
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
16 12 0.29
17 2 0.05
18 2 0.05
19 15 0.37
20 5 0.12
21 5 0.12
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (19 bp):
TTCTTCTCCTTTCTCTCCT
Found at i:59939999 original size:43 final size:42
Alignment explanation
Indices: 59939917--59940085 Score: 157
Period size: 43 Copynumber: 4.0 Consensus size: 42
59939907 AGCTCGTACA
* * * *
59939917 ATGTCAACATCCCAGACGTGGTCTTACATGTAATCAAATATCG
1 ATGTCAACGTCCCAGACATGGTCTTACACGAAATCAAATAT-G
* * *
59939960 ATG-CCACTGTCTCAGACA-GCGTCTTACACGAAATTAAATATG
1 ATGTCAAC-GTCCCAGACATG-GTCTTACACGAAATCAAATATG
*
59940002 ATGTCAACGTCCCAGACATGGTCTTACATGTAAATCACAA-ATTG
1 ATGTCAACGTCCCAGACATGGTCTTACACG-AAATCA-AATA-TG
* * *
59940046 ATG-CAACGTCACAGACATGGTCTTACACAAAATCACATAT
1 ATGTCAACGTCCCAGACATGGTCTTACACGAAATCAAATAT
59940086 CGGAATCCTA
Statistics
Matches: 103, Mismatches: 15, Indels: 18
0.76 0.11 0.13
Matches are distributed among these distances:
41 2 0.02
42 33 0.32
43 61 0.59
44 7 0.07
ACGTcount: A:0.35, C:0.24, G:0.15, T:0.26
Consensus pattern (42 bp):
ATGTCAACGTCCCAGACATGGTCTTACACGAAATCAAATATG
Found at i:59940061 original size:85 final size:85
Alignment explanation
Indices: 59939917--59940078 Score: 222
Period size: 85 Copynumber: 1.9 Consensus size: 85
59939907 AGCTCGTACA
* * *
59939917 ATGTCAACATCCCAGACGTGGTCTTACATGTAATCAAATATCGATGCCACTGTCTCAGACA-GCG
1 ATGTCAACATCCCAGACATGGTCTTACATGTAATCAAATATCGATGCAACTGTCACAGACATG-G
*
59939981 TCTTACACGAAATTAAATATG
65 TCTTACACAAAATTAAATATG
* *
59940002 ATGTCAACGTCCCAGACATGGTCTTACATGTAAATCACAA-ATTGATGCAAC-GTCACAGACATG
1 ATGTCAACATCCCAGACATGGTCTTACATGT-AATCA-AATATCGATGCAACTGTCACAGACATG
59940065 GTCTTACACAAAAT
64 GTCTTACACAAAAT
59940079 CACATATCGG
Statistics
Matches: 68, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
85 51 0.75
86 15 0.22
87 2 0.03
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.26
Consensus pattern (85 bp):
ATGTCAACATCCCAGACATGGTCTTACATGTAATCAAATATCGATGCAACTGTCACAGACATGGT
CTTACACAAAATTAAATATG
Found at i:59942277 original size:18 final size:18
Alignment explanation
Indices: 59942254--59942356 Score: 80
Period size: 18 Copynumber: 5.4 Consensus size: 18
59942244 ACATCGTGAT
59942254 CTGAAGCCCGAAGTCTAA
1 CTGAAGCCCGAAGTCTAA
**
59942272 CTGAAGCACATAAGTGCTAA
1 CTGAAGC-CCGAAGT-CTAA
* *
59942292 ATGGAAGCCCGAAGGCTAA
1 CT-GAAGCCCGAAGTCTAA
**
59942311 CTGAAGCACATAAGTGCTAAA
1 CTGAAGC-CCGAAGT-CT-AA
* *
59942332 CGGAAGCCCGAAGGCTAA
1 CTGAAGCCCGAAGTCTAA
59942350 CTGAAGC
1 CTGAAGC
59942357 TCACCAGAGC
Statistics
Matches: 64, Mismatches: 15, Indels: 12
0.70 0.16 0.13
Matches are distributed among these distances:
18 20 0.31
19 16 0.25
20 15 0.23
21 13 0.20
ACGTcount: A:0.37, C:0.23, G:0.25, T:0.15
Consensus pattern (18 bp):
CTGAAGCCCGAAGTCTAA
Found at i:59942298 original size:21 final size:21
Alignment explanation
Indices: 59942274--59942338 Score: 73
Period size: 19 Copynumber: 3.2 Consensus size: 21
59942264 AAGTCTAACT
59942274 GAAGCACATAAGTGCTAAATG
1 GAAGCACATAAGTGCTAAATG
** *
59942295 GAAGC-CCGAAG-GCTAACT-
1 GAAGCACATAAGTGCTAAATG
*
59942313 GAAGCACATAAGTGCTAAACG
1 GAAGCACATAAGTGCTAAATG
59942334 GAAGC
1 GAAGC
59942339 CCGAAGGCTA
Statistics
Matches: 34, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
18 5 0.15
19 10 0.29
20 9 0.26
21 10 0.29
ACGTcount: A:0.40, C:0.20, G:0.26, T:0.14
Consensus pattern (21 bp):
GAAGCACATAAGTGCTAAATG
Found at i:59942311 original size:39 final size:39
Alignment explanation
Indices: 59942256--59942356 Score: 184
Period size: 39 Copynumber: 2.6 Consensus size: 39
59942246 ATCGTGATCT
* *
59942256 GAAGCCCGAAGTCTAACTGAAGCACATAAGTGCTAAATG
1 GAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAACG
59942295 GAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAACG
1 GAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAACG
59942334 GAAGCCCGAAGGCTAACTGAAGC
1 GAAGCCCGAAGGCTAACTGAAGC
59942357 TCACCAGAGC
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 60 1.00
ACGTcount: A:0.38, C:0.23, G:0.26, T:0.14
Consensus pattern (39 bp):
GAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAACG
Found at i:59943605 original size:16 final size:18
Alignment explanation
Indices: 59943574--59943608 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
59943564 CAATTAACCC
59943574 CTCAATTAAGATAATTTT
1 CTCAATTAAGATAATTTT
59943592 CTCAATT-A-ATAATTTT
1 CTCAATTAAGATAATTTT
59943608 C
1 C
59943609 ATAAAAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.53
17 1 0.06
18 7 0.41
ACGTcount: A:0.37, C:0.14, G:0.03, T:0.46
Consensus pattern (18 bp):
CTCAATTAAGATAATTTT
Found at i:59945449 original size:18 final size:18
Alignment explanation
Indices: 59945426--59945492 Score: 62
Period size: 18 Copynumber: 3.6 Consensus size: 18
59945416 ACATCGTGAT
*
59945426 CTGAAGCTCGAAGTCTAA
1 CTGAAGCTCAAAGTCTAA
*
59945444 CTGAAGCACATAAGTGCTAAA
1 CTGAAGCTCA-AAGT-CT-AA
* * *
59945465 CGGAAGCCCAAAGGCTAA
1 CTGAAGCTCAAAGTCTAA
59945483 CTGAAGCTCA
1 CTGAAGCTCA
59945493 CCAGAGCTGA
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
18 18 0.46
19 6 0.15
20 5 0.13
21 10 0.26
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.16
Consensus pattern (18 bp):
CTGAAGCTCAAAGTCTAA
Found at i:59947545 original size:20 final size:20
Alignment explanation
Indices: 59947520--59947559 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
59947510 CACTATTCAC
59947520 TATATCAAAATTTTTCCTAA
1 TATATCAAAATTTTTCCTAA
59947540 TATATCAAAATTTTTCCTAA
1 TATATCAAAATTTTTCCTAA
59947560 CTTCACATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.15, G:0.00, T:0.45
Consensus pattern (20 bp):
TATATCAAAATTTTTCCTAA
Found at i:59949784 original size:40 final size:40
Alignment explanation
Indices: 59949740--59950020 Score: 472
Period size: 40 Copynumber: 7.0 Consensus size: 40
59949730 AGAATTGAGA
59949740 GTTACATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGT
1 GTTACATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGT
59949780 GTTACATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGT
1 GTTACATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGT
*
59949820 GTTATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGT
1 GTTACATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGT
* *
59949860 GTTACATCCGGGCTAAGTCCCGAAGAGCATTCATACTGGT
1 GTTACATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGT
*
59949900 GTTATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGT
1 GTTACATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGT
* *
59949940 GTTATATCCGGGCTAAGTCTCGAAGAGCATTCGTGCTGGT
1 GTTACATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGT
* * * *
59949980 GTTACATCCGGGCTAAGTCCTGGAGGGCATTCGTGCCGGT
1 GTTACATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGT
59950020 G
1 G
59950021 ATGTGTAATC
Statistics
Matches: 227, Mismatches: 14, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 227 1.00
ACGTcount: A:0.20, C:0.23, G:0.30, T:0.26
Consensus pattern (40 bp):
GTTACATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGT
Found at i:59950079 original size:43 final size:43
Alignment explanation
Indices: 59950012--59950108 Score: 122
Period size: 43 Copynumber: 2.3 Consensus size: 43
59950002 GAGGGCATTC
*
59950012 GTGCCGGTGATGTGTAATCAGGCCTTCATGCCTAGCAGGCTTT
1 GTGCCGGTGATGTGTAATCAGGCCTTCATGCCTAACAGGCTTT
* * * * * *
59950055 GTGCTGGTGATGTGTATTCGGGCCTTCGTTCCTAACAGGCTTA
1 GTGCCGGTGATGTGTAATCAGGCCTTCATGCCTAACAGGCTTT
*
59950098 ATGCCGGTGAT
1 GTGCCGGTGAT
59950109 TCGAGCAAAG
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.15, C:0.22, G:0.31, T:0.32
Consensus pattern (43 bp):
GTGCCGGTGATGTGTAATCAGGCCTTCATGCCTAACAGGCTTT
Found at i:59950266 original size:25 final size:25
Alignment explanation
Indices: 59950227--59950281 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 25
59950217 TGTGAAATAA
59950227 CGAATGAATATAGGCACTATGTGTG
1 CGAATGAATATAGGCACTATGTGTG
*
59950252 CGAATGAAT-TGAGGCACTGTGTGTG
1 CGAATGAATAT-AGGCACTATGTGTG
59950277 CGAAT
1 CGAAT
59950282 TCTTTAACCG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
24 1 0.04
25 27 0.96
ACGTcount: A:0.29, C:0.13, G:0.31, T:0.27
Consensus pattern (25 bp):
CGAATGAATATAGGCACTATGTGTG
Found at i:59950304 original size:28 final size:28
Alignment explanation
Indices: 59950265--59950363 Score: 101
Period size: 28 Copynumber: 3.5 Consensus size: 28
59950255 ATGAATTGAG
* *
59950265 GCACTGTGTGTGCGAATTCTTTAACCGA
1 GCACTATGTGTGTGAATTCTTTAACCGA
** * ** *
59950293 GCACTATGTGTGTGAGA-TCGGTCAGTGG
1 GCACTATGTGTGTGA-ATTCTTTAACCGA
*
59950321 GCACTGTGTGTGTGAATTCTTTAACCGA
1 GCACTATGTGTGTGAATTCTTTAACCGA
59950349 GCACTATGTGTGTGA
1 GCACTATGTGTGTGA
59950364 GATCGGTCAG
Statistics
Matches: 53, Mismatches: 16, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
27 1 0.02
28 51 0.96
29 1 0.02
ACGTcount: A:0.20, C:0.17, G:0.30, T:0.32
Consensus pattern (28 bp):
GCACTATGTGTGTGAATTCTTTAACCGA
Found at i:59950331 original size:56 final size:56
Alignment explanation
Indices: 59950264--59950390 Score: 245
Period size: 56 Copynumber: 2.3 Consensus size: 56
59950254 AATGAATTGA
59950264 GGCACTGTGTGTGCGAATTCTTTAACCGAGCACTATGTGTGTGAGATCGGTCAGTG
1 GGCACTGTGTGTGCGAATTCTTTAACCGAGCACTATGTGTGTGAGATCGGTCAGTG
*
59950320 GGCACTGTGTGTGTGAATTCTTTAACCGAGCACTATGTGTGTGAGATCGGTCAGTG
1 GGCACTGTGTGTGCGAATTCTTTAACCGAGCACTATGTGTGTGAGATCGGTCAGTG
59950376 GGCACTGTGTGTGCG
1 GGCACTGTGTGTGCG
59950391 GATTTCGTTT
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
56 69 1.00
ACGTcount: A:0.18, C:0.17, G:0.34, T:0.31
Consensus pattern (56 bp):
GGCACTGTGTGTGCGAATTCTTTAACCGAGCACTATGTGTGTGAGATCGGTCAGTG
Found at i:59950380 original size:28 final size:28
Alignment explanation
Indices: 59950293--59950388 Score: 104
Period size: 28 Copynumber: 3.4 Consensus size: 28
59950283 CTTTAACCGA
59950293 GCACTATGTGTGTGAGATCGGTCAGTGG
1 GCACTATGTGTGTGAGATCGGTCAGTGG
* ** * ** *
59950321 GCACTGTGTGTGTGA-ATTCTTTAACCGA
1 GCACTATGTGTGTGAGA-TCGGTCAGTGG
59950349 GCACTATGTGTGTGAGATCGGTCAGTGG
1 GCACTATGTGTGTGAGATCGGTCAGTGG
*
59950377 GCACTGTGTGTG
1 GCACTATGTGTG
59950389 CGGATTTCGT
Statistics
Matches: 51, Mismatches: 15, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
27 1 0.02
28 49 0.96
29 1 0.02
ACGTcount: A:0.18, C:0.16, G:0.35, T:0.31
Consensus pattern (28 bp):
GCACTATGTGTGTGAGATCGGTCAGTGG
Done.