Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 ID=Chr08-JGI_221_v2.0
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: 57128820
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 677448 characters in sequence are not A, C, G, or T
File 184 of 190
Found at i:54500794 original size:18 final size:18
Alignment explanation
Indices: 54500756--54500796 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
54500746 GCTGTATCTT
***
54500756 TAATTAAATTATTATCCA
1 TAATTAAATTATTAAAAA
54500774 TAATTAAATTATTAAAAA
1 TAATTAAATTATTAAAAA
54500792 TAATT
1 TAATT
54500797 TTTTAGTATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (18 bp):
TAATTAAATTATTAAAAA
Found at i:54502473 original size:12 final size:12
Alignment explanation
Indices: 54502456--54502485 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
54502446 CCAAATCAAT
54502456 GGAGAACAAAAG
1 GGAGAACAAAAG
*
54502468 GGAGAACGAAAG
1 GGAGAACAAAAG
54502480 GGAGAA
1 GGAGAA
54502486 GGGAGAACGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.53, C:0.07, G:0.40, T:0.00
Consensus pattern (12 bp):
GGAGAACAAAAG
Found at i:54502489 original size:19 final size:19
Alignment explanation
Indices: 54502465--54502504 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
54502455 TGGAGAACAA
54502465 AAGGGAGAACGAAAGGGAG
1 AAGGGAGAACGAAAGGGAG
*
54502484 AAGGGAGAACGAACGGGAG
1 AAGGGAGAACGAAAGGGAG
54502503 AA
1 AA
54502505 CGAAACCAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.47, C:0.07, G:0.45, T:0.00
Consensus pattern (19 bp):
AAGGGAGAACGAAAGGGAG
Found at i:54511211 original size:21 final size:21
Alignment explanation
Indices: 54511185--54511229 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
54511175 GATGGAAAGC
*
54511185 AAAAACAAGATAAAAACCTAA
1 AAAAACAAGAGAAAAACCTAA
*
54511206 AAAAACAAGAGAAAACCCTAA
1 AAAAACAAGAGAAAAACCTAA
54511227 AAA
1 AAA
54511230 CTGCAAGAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.71, C:0.16, G:0.07, T:0.07
Consensus pattern (21 bp):
AAAAACAAGAGAAAAACCTAA
Found at i:54513023 original size:12 final size:11
Alignment explanation
Indices: 54513006--54513038 Score: 50
Period size: 10 Copynumber: 3.0 Consensus size: 11
54512996 AACAAATCCT
54513006 CTCTCATATTTC
1 CTCTCA-ATTTC
54513018 CTCTCAA-TTC
1 CTCTCAATTTC
54513028 CTCTCAATTTC
1 CTCTCAATTTC
54513039 TTTCCAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 10 0.50
11 4 0.20
12 6 0.30
ACGTcount: A:0.18, C:0.36, G:0.00, T:0.45
Consensus pattern (11 bp):
CTCTCAATTTC
Found at i:54513053 original size:22 final size:22
Alignment explanation
Indices: 54513023--54513078 Score: 94
Period size: 22 Copynumber: 2.5 Consensus size: 22
54513013 ATTTCCTCTC
*
54513023 AATTCCTCTCAATTTCTTTCCAA
1 AATT-CTCTCAATTTCCTTCCAA
54513046 AATTCTCTCAATTTCCTTCCAA
1 AATTCTCTCAATTTCCTTCCAA
54513068 AATTCTCTCAA
1 AATTCTCTCAA
54513079 ATCCATATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 28 0.88
23 4 0.12
ACGTcount: A:0.29, C:0.30, G:0.00, T:0.41
Consensus pattern (22 bp):
AATTCTCTCAATTTCCTTCCAA
Found at i:54513104 original size:29 final size:29
Alignment explanation
Indices: 54513072--54513131 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
54513062 TTCCAAAATT
54513072 CTCTCAAATCCATATTTAATTTCAATTTC
1 CTCTCAAATCCATATTTAATTTCAATTTC
54513101 CTCTCAAATCCATATTTAATTTCAATTTC
1 CTCTCAAATCCATATTTAATTTCAATTTC
54513130 CT
1 CT
54513132 TTTTAAAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.30, C:0.25, G:0.00, T:0.45
Consensus pattern (29 bp):
CTCTCAAATCCATATTTAATTTCAATTTC
Found at i:54525265 original size:3 final size:3
Alignment explanation
Indices: 54525257--54525286 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
54525247 AAATCAAATT
54525257 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
54525287 CAAACAGGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:54525822 original size:19 final size:20
Alignment explanation
Indices: 54525774--54525823 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
54525764 TTTTTTTACT
* *
54525774 TTTTAAATT-TATTATTAAT
1 TTTTAAATTATTTTATTAAA
54525793 TTTTAAA-TATTTTA-TAAA
1 TTTTAAATTATTTTATTAAA
54525811 TTTTAAATTATTT
1 TTTTAAATTATTT
54525824 GTTGACGTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 11 0.41
19 16 0.59
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTTAAATTATTTTATTAAA
Found at i:54527720 original size:7 final size:7
Alignment explanation
Indices: 54527684--54527719 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
54527674 TTATTGCAAC
54527684 TTTACAT
1 TTTACAT
54527691 TTTACAT
1 TTTACAT
54527698 TTTACAT
1 TTTACAT
54527705 TTTAC-T
1 TTTACAT
54527711 TTTAC-T
1 TTTACAT
54527717 TTT
1 TTT
54527720 TTTTTTTATG
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 10 0.34
7 19 0.66
ACGTcount: A:0.22, C:0.14, G:0.00, T:0.64
Consensus pattern (7 bp):
TTTACAT
Found at i:54528471 original size:29 final size:29
Alignment explanation
Indices: 54528416--54528471 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
54528406 CAACATTTTA
* *
54528416 AATTATTTTTACTATATAAAATATAAAGT
1 AATTATTTTTAATATAAAAAATATAAAGT
54528445 AATTATTTTTAATCATAAAAAAT-TAAA
1 AATTATTTTTAAT-ATAAAAAATATAAA
54528472 CAAGTTATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 16 0.67
30 8 0.33
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.43
Consensus pattern (29 bp):
AATTATTTTTAATATAAAAAATATAAAGT
Found at i:54532464 original size:13 final size:14
Alignment explanation
Indices: 54532434--54532474 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
54532424 TTTTTTTGTT
54532434 TTATAAATGTTATATA
1 TTATAAAT-TT-TATA
54532450 TTAT-AATTTTATA
1 TTATAAATTTTATA
54532463 TTATAAATTTTA
1 TTATAAATTTTA
54532475 CTTAACTTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 8 0.33
14 9 0.38
15 3 0.12
16 4 0.17
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (14 bp):
TTATAAATTTTATA
Found at i:54535733 original size:14 final size:14
Alignment explanation
Indices: 54535714--54535742 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
54535704 TTGACTCCTA
54535714 CTACTTTCACCCTG
1 CTACTTTCACCCTG
54535728 CTACTTTCACCCTG
1 CTACTTTCACCCTG
54535742 C
1 C
54535743 AAGGTGCTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.45, G:0.07, T:0.34
Consensus pattern (14 bp):
CTACTTTCACCCTG
Found at i:54551395 original size:2 final size:2
Alignment explanation
Indices: 54551388--54551412 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
54551378 TGTTCGAACA
54551388 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
54551413 ATATATATAT
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:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:54567763 original size:24 final size:23
Alignment explanation
Indices: 54567736--54567783 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
54567726 TATACGTTAG
*
54567736 ATTAAAATAATAAATTAATTTTTT
1 ATTAAAAAAAT-AATTAATTTTTT
*
54567760 ATTAAAAAAATTATTAATTTTTT
1 ATTAAAAAAATAATTAATTTTTT
54567783 A
1 A
54567784 CTATTAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
ATTAAAAAAATAATTAATTTTTT
Found at i:54567778 original size:23 final size:25
Alignment explanation
Indices: 54567749--54567797 Score: 75
Period size: 23 Copynumber: 2.0 Consensus size: 25
54567739 AAAATAATAA
54567749 ATTAATTTTTTA-T-TAAAAAAATT
1 ATTAATTTTTTACTATAAAAAAATT
*
54567772 ATTAATTTTTTACTATTAAAAAATT
1 ATTAATTTTTTACTATAAAAAAATT
54567797 A
1 A
54567798 ATCATTGTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 12 0.52
24 1 0.04
25 10 0.43
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (25 bp):
ATTAATTTTTTACTATAAAAAAATT
Found at i:54571344 original size:25 final size:26
Alignment explanation
Indices: 54571297--54571370 Score: 87
Period size: 26 Copynumber: 2.9 Consensus size: 26
54571287 ATACCACTAT
* *
54571297 GTTTTAACTTTATCTTGAATTTTGCA
1 GTTTTAACTTTTTATTGAATTTTGCA
* *
54571323 GTTTTAA-TTTTTATTGATTTTTGTA
1 GTTTTAACTTTTTATTGAATTTTGCA
* *
54571348 GCTTTAATTTTTTATTGAATTTT
1 GTTTTAACTTTTTATTGAATTTT
54571371 ATCACTAAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
25 20 0.49
26 21 0.51
ACGTcount: A:0.22, C:0.05, G:0.11, T:0.62
Consensus pattern (26 bp):
GTTTTAACTTTTTATTGAATTTTGCA
Found at i:54576229 original size:16 final size:16
Alignment explanation
Indices: 54576204--54576234 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
54576194 AAAAAAATTT
54576204 ATAAACTTTTTAAATC
1 ATAAACTTTTTAAATC
*
54576220 ATAAATTTTTTAAAT
1 ATAAACTTTTTAAAT
54576235 AATTAGAAAA
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:0.45, C:0.06, G:0.00, T:0.48
Consensus pattern (16 bp):
ATAAACTTTTTAAATC
Found at i:54578166 original size:20 final size:20
Alignment explanation
Indices: 54578118--54578166 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
54578108 AAAAATAAAT
54578118 AAAA-AGAAA-GAAAGAAAG
1 AAAAGAGAAAGGAAAGAAAG
*
54578136 AAAAGAAAAAGGAAAGAAAG
1 AAAAGAGAAAGGAAAGAAAG
* *
54578156 GAAGGAGAAAG
1 AAAAGAGAAAG
54578167 CCACGGTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
18 4 0.16
19 4 0.16
20 17 0.68
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (20 bp):
AAAAGAGAAAGGAAAGAAAG
Found at i:54581758 original size:11 final size:11
Alignment explanation
Indices: 54581742--54581766 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
54581732 GCGATTATTG
54581742 TATTTATTGTA
1 TATTTATTGTA
54581753 TATTTATTGTA
1 TATTTATTGTA
54581764 TAT
1 TAT
54581767 AAAGGGACCC
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:0.08, T:0.64
Consensus pattern (11 bp):
TATTTATTGTA
Found at i:54584450 original size:45 final size:45
Alignment explanation
Indices: 54584365--54584546 Score: 215
Period size: 45 Copynumber: 4.1 Consensus size: 45
54584355 TTTTGCCGTC
* * * * * *
54584365 TTACTGATTAGGCAC-TTATGTGCCGACTACTGTTACTGTTACTC
1 TTACCGATTCGGCACTTTGTGTGTCGAATACTGTTACTGTTACTG
* *
54584409 TTACCGATTCGGCACATTGTGTGTCGAATAATGTTACTGTTACTG
1 TTACCGATTCGGCACTTTGTGTGTCGAATACTGTTACTGTTACTG
* * * *
54584454 TTACCGATTCGGTACTTTGTGTGTCAAATACTGTTACCG-TATTG
1 TTACCGATTCGGCACTTTGTGTGTCGAATACTGTTACTGTTACTG
* * *
54584498 TTACAGATTCGGCACTTTGTGTGTTGAATATTGTTACTGTTACTG
1 TTACCGATTCGGCACTTTGTGTGTCGAATACTGTTACTGTTACTG
54584543 TTAC
1 TTAC
54584547 TGCTACCTTT
Statistics
Matches: 116, Mismatches: 20, Indels: 3
0.83 0.14 0.02
Matches are distributed among these distances:
44 50 0.43
45 66 0.57
ACGTcount: A:0.21, C:0.18, G:0.20, T:0.41
Consensus pattern (45 bp):
TTACCGATTCGGCACTTTGTGTGTCGAATACTGTTACTGTTACTG
Found at i:54592932 original size:3 final size:3
Alignment explanation
Indices: 54592924--54592951 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
54592914 CATGAGTACT
54592924 TCA TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA T
54592952 AATAATAGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.36
Consensus pattern (3 bp):
TCA
Found at i:54604043 original size:16 final size:17
Alignment explanation
Indices: 54604017--54604065 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 17
54604007 TTAAAATGAT
54604017 AAATTTT-TAATTTA-A
1 AAATTTTATAATTTATA
*
54604032 AATTTTTATAATTTATA
1 AAATTTTATAATTTATA
*
54604049 AAATTTTA-AATTAATA
1 AAATTTTATAATTTATA
54604065 A
1 A
54604066 CAAAATTACA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
15 6 0.21
16 15 0.52
17 8 0.28
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
AAATTTTATAATTTATA
Found at i:54605988 original size:14 final size:15
Alignment explanation
Indices: 54605958--54605990 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
54605948 AATAATATTA
54605958 TAATAAACCTAAATT
1 TAATAAACCTAAATT
*
54605973 TAATAAA-CTAATTT
1 TAATAAACCTAAATT
54605987 TAAT
1 TAAT
54605991 GTTATCTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (15 bp):
TAATAAACCTAAATT
Found at i:54616789 original size:46 final size:46
Alignment explanation
Indices: 54616722--54616857 Score: 209
Period size: 46 Copynumber: 3.0 Consensus size: 46
54616712 TGCTATAACC
* * *
54616722 CAGTATGGTTTCCTTCACTGAAATACCATACCTACTTTTCACATCT
1 CAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCACAACT
* *
54616768 CAGTATGGTTTTCTTCACTGAAACACTATTCCTACTTTTCACAACT
1 CAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCACAACT
* *
54616814 CAGTATGGCTTTCTTCACTGAAACACCAAACCTACTTTTCACAA
1 CAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCACAA
54616858 TTTTCCATGG
Statistics
Matches: 81, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 81 1.00
ACGTcount: A:0.28, C:0.28, G:0.09, T:0.35
Consensus pattern (46 bp):
CAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCACAACT
Found at i:54619977 original size:125 final size:123
Alignment explanation
Indices: 54619749--54620150 Score: 587
Period size: 125 Copynumber: 3.2 Consensus size: 123
54619739 TTATTTCGAG
**
54619749 TTGACGTTTCTG-GTCAAATAGTATAAAATCGCTTCTACCAGGATGCTATCA-GAGAAGAAATTG
1 TTGACGTTTCTGAG-CAAATAGTATAAAATCGCTGATACCAGGATGCTAT-ATGAGAAGAAATTG
* * * *
54619812 TGAAATCGTGCCCTCGTGGATGCCATTTCAGC-ACAGTTGGTCATGTAAGAAGTAATTTTTT
64 TGAAATCGCGCCCTCGTGGACGCGATTTC-GCTACAGTTGGTCATGTAGGAA-TAATTTTTT
54619873 TTGACGTTTTCTGAGCAAATAGTATAAAATCGCTGATACCAGGATGCTATATGAGAAGAAATTGT
1 TTGACG-TTTCTGAGCAAATAGTATAAAATCGCTGATACCAGGATGCTATATGAGAAGAAATTGT
* *
54619938 GAAATTGCGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAGGAA-ATTTTTTT
65 GAAATCGCGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAGGAATAATTTTTT
* * * *
54619996 TTTACATTTCTGAGCAAATAGTGTAAAAACGCTGATACCAGGATGCTATATGAGAAGAAATTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTGATACCAGGATGCTATATGAGAAGAAATTGTG
*
54620061 AAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTTGGTCATGTAGGAAATAATTTTTTT
66 AAATCGCGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAGG-AATAA-TTTTTT
*
54620121 TTGACGTTTCTGAGCAAATAGTGTAAAATC
1 TTGACGTTTCTGAGCAAATAGTATAAAATC
54620151 ATGCCCTCGT
Statistics
Matches: 253, Mismatches: 18, Indels: 13
0.89 0.06 0.05
Matches are distributed among these distances:
122 102 0.40
123 13 0.05
124 10 0.04
125 127 0.50
126 1 0.00
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (123 bp):
TTGACGTTTCTGAGCAAATAGTATAAAATCGCTGATACCAGGATGCTATATGAGAAGAAATTGTG
AAATCGCGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAGGAATAATTTTTT
Found at i:54622949 original size:23 final size:26
Alignment explanation
Indices: 54622922--54623072 Score: 85
Period size: 29 Copynumber: 5.2 Consensus size: 26
54622912 TAAGATTATC
54622922 AAATTAGGTTAGGG-T-TTTA-AATT
1 AAATTAGGTTAGGGTTATTTATAATT
54622945 AAATTAGGTTAGGGTTAGAGTTTATAATT
1 AAATTAGGTTAGGGTT--A-TTTATAATT
*
54622974 AAATTAGGTTAGGGCTAGGGTTTTATAATTAAATT
1 AAATTAGGTTAGGG-T----TATT-T-A-T-AATT
54623009 AAATTAGGTTA-GGTTAGGGTTTTATAATT
1 AAATTAGGTTAGGGTTA----TTTATAATT
*
54623038 GAATTAGGTTAGGGTTAGGGTTTATAATT
1 AAATTAGGTTAGGGTTA---TTTATAATT
54623067 AAATTA
1 AAATTA
54623073 AATTAGGTTT
Statistics
Matches: 103, Mismatches: 5, Indels: 34
0.73 0.04 0.24
Matches are distributed among these distances:
23 14 0.14
24 1 0.01
28 4 0.04
29 49 0.48
30 7 0.07
31 3 0.03
32 2 0.02
33 4 0.04
34 4 0.04
35 15 0.15
ACGTcount: A:0.34, C:0.01, G:0.24, T:0.42
Consensus pattern (26 bp):
AAATTAGGTTAGGGTTATTTATAATT
Found at i:54623006 original size:64 final size:63
Alignment explanation
Indices: 54622938--54623146 Score: 261
Period size: 64 Copynumber: 3.4 Consensus size: 63
54622928 GGTTAGGGTT
*
54622938 TTAAATTAAATTAGGTTAGGGTTAGAGTTTATAATTAAATTAGGTTAGGGCTAGGGTTTTATAA
1 TTAAATTAAATTAGGTTAGGGTTAGAGTTTATAATTAAATTAGGTTAGGGTTAGGG-TTTATAA
* *
54623002 TTAAATTAAATTAGGTTA-GGTTAGGGTTTTATAATTGAATTAGGTTAGGGTTAGGGTTTATAA
1 TTAAATTAAATTAGGTTAGGGTTAGAG-TTTATAATTAAATTAGGTTAGGGTTAGGGTTTATAA
* ** * *
54623065 TTAAATTAAATTAGGTTTGGGTTTTTA-ATTA-AATTAAATTAGGTTAGAGTTTA-GG--T-TAA
1 TTAAATTAAATTAGGTTAGGG-TTAGAGTTTATAATTAAATTAGGTTAG-GGTTAGGGTTTATAA
54623124 TTAAATTAAATTAGGTTAGGGTT
1 TTAAATTAAATTAGGTTAGGGTT
54623147 TAGGGTCTTC
Statistics
Matches: 130, Mismatches: 11, Indels: 14
0.84 0.07 0.09
Matches are distributed among these distances:
58 2 0.02
59 23 0.18
60 1 0.01
62 17 0.13
63 38 0.29
64 47 0.36
65 2 0.02
ACGTcount: A:0.34, C:0.00, G:0.22, T:0.43
Consensus pattern (63 bp):
TTAAATTAAATTAGGTTAGGGTTAGAGTTTATAATTAAATTAGGTTAGGGTTAGGGTTTATAA
Found at i:54623052 original size:93 final size:90
Alignment explanation
Indices: 54622925--54623146 Score: 320
Period size: 93 Copynumber: 2.4 Consensus size: 90
54622915 GATTATCAAA
**
54622925 TTAGGTTAGGGTTTTAAATTAAATTAGGTTAGGGTTAGAGTTTATAATTAAATTAGGTTAGGGCT
1 TTAGGTTAGGGTTTTAAATTAAATTAGGTTAGGGTTAGAGTTTATAATTAAATTAAATTA-GGCT
54622990 AGGGTTTTATAATTAAATTAAATTAGG
65 AGGGTTTT-TAATTAAATTAAATTAGG
* * *
54623017 TTAGGTTAGGGTTTTATAATTGAATTAGGTTAGGGTTAGGGTTTATAATTAAATTAAATTAGGTT
1 TTAGGTTAGGGTTTTA-AATTAAATTAGGTTAGGGTTAGAGTTTATAATTAAATTAAATTAGGCT
*
54623082 TGGGTTTTTAATTAAATTAAATTAGG
65 AGGGTTTTTAATTAAATTAAATTAGG
54623108 TTAGAGTTTA-GGTTAATTAAATTAAATTAGGTTAGGGTT
1 TTAG-G-TTAGGGTT--TTAAATTAAATTAGGTTAGGGTT
54623147 TAGGGTCTTC
Statistics
Matches: 118, Mismatches: 7, Indels: 9
0.88 0.05 0.07
Matches are distributed among these distances:
91 22 0.19
92 31 0.26
93 62 0.53
94 3 0.03
ACGTcount: A:0.33, C:0.00, G:0.23, T:0.43
Consensus pattern (90 bp):
TTAGGTTAGGGTTTTAAATTAAATTAGGTTAGGGTTAGAGTTTATAATTAAATTAAATTAGGCTA
GGGTTTTTAATTAAATTAAATTAGG
Found at i:54623079 original size:23 final size:23
Alignment explanation
Indices: 54623052--54623107 Score: 58
Period size: 28 Copynumber: 2.2 Consensus size: 23
54623042 TAGGTTAGGG
54623052 TTAGGGTTTATAATTAAATTAAA
1 TTAGGGTTTATAATTAAATTAAA
*
54623075 TTAGGTTTGGGTTTTTAATTAAATTAAA
1 TTA-----GGGTTTATAATTAAATTAAA
54623103 TTAGG
1 TTAGG
54623108 TTAGAGTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 10
0.71 0.03 0.26
Matches are distributed among these distances:
23 5 0.19
28 22 0.81
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (23 bp):
TTAGGGTTTATAATTAAATTAAA
Found at i:54632646 original size:29 final size:29
Alignment explanation
Indices: 54632609--54632684 Score: 134
Period size: 29 Copynumber: 2.6 Consensus size: 29
54632599 TTCTTTTTTT
* *
54632609 ATATTAATGGGGTTTGGTCCTTTTGGTAC
1 ATATAAATGGAGTTTGGTCCTTTTGGTAC
54632638 ATATAAATGGAGTTTGGTCCTTTTGGTAC
1 ATATAAATGGAGTTTGGTCCTTTTGGTAC
54632667 ATATAAATGGAGTTTGGT
1 ATATAAATGGAGTTTGGT
54632685 GGGTATCCAC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 45 1.00
ACGTcount: A:0.24, C:0.08, G:0.26, T:0.42
Consensus pattern (29 bp):
ATATAAATGGAGTTTGGTCCTTTTGGTAC
Found at i:54642142 original size:2 final size:2
Alignment explanation
Indices: 54642135--54642161 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
54642125 CTACGTGTTC
54642135 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
54642162 CACAACTGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:54650889 original size:38 final size:38
Alignment explanation
Indices: 54650847--54650922 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
54650837 CTTATTCTTG
54650847 AGGATTTTAACTGTACCCTCTTTATTAATTTAACCATT
1 AGGATTTTAACTGTACCCTCTTTATTAATTTAACCATT
54650885 AGGATTTTAACTGTACCCTCTTTATTAATTTAACCATT
1 AGGATTTTAACTGTACCCTCTTTATTAATTTAACCATT
54650923 CTCTCATTCT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.29, C:0.18, G:0.08, T:0.45
Consensus pattern (38 bp):
AGGATTTTAACTGTACCCTCTTTATTAATTTAACCATT
Found at i:54667277 original size:12 final size:12
Alignment explanation
Indices: 54667260--54667291 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
54667250 CAGTGTCTTC
54667260 TAATTACACAAT
1 TAATTACACAAT
54667272 TAATTACACAAT
1 TAATTACACAAT
*
54667284 TAAGTACA
1 TAATTACA
54667292 TATGGTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.50, C:0.16, G:0.03, T:0.31
Consensus pattern (12 bp):
TAATTACACAAT
Found at i:54674896 original size:24 final size:24
Alignment explanation
Indices: 54674855--54674909 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 24
54674845 CAAATTAATC
*
54674855 TTTTTTAAAAATAATTATATTT-TAT
1 TTTTTTAAAAAT-ATTAT-TTTGAAT
54674880 TTTTTTATAAAAT-TTATTTTGAAT
1 TTTTTTA-AAAATATTATTTTGAAT
54674904 TTTTTT
1 TTTTTT
54674910 TAATTATTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
23 3 0.11
24 12 0.44
25 7 0.26
26 5 0.19
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (24 bp):
TTTTTTAAAAATATTATTTTGAAT
Found at i:54677815 original size:2 final size:2
Alignment explanation
Indices: 54677808--54677848 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
54677798 GAAATAGACA
54677808 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
54677849 GAGGATAATA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:54682691 original size:13 final size:14
Alignment explanation
Indices: 54682626--54682694 Score: 52
Period size: 13 Copynumber: 4.8 Consensus size: 14
54682616 TTATTGCTTT
54682626 ATATAAATATAATAA
1 ATATAAAT-TAATAA
*
54682641 ATAT-AAGTAATAA
1 ATATAAATTAATAA
* **
54682654 TGTCATTAAAAGAATAA
1 -AT-A-TAAATTAATAA
54682671 ATATAAATTAATAA
1 ATATAAATTAATAA
54682685 A-ATAAATTAA
1 ATATAAATTAA
54682695 AAGCAAAATG
Statistics
Matches: 43, Mismatches: 7, Indels: 10
0.72 0.12 0.17
Matches are distributed among these distances:
13 15 0.35
14 13 0.30
15 6 0.14
16 2 0.05
17 7 0.16
ACGTcount: A:0.62, C:0.01, G:0.04, T:0.32
Consensus pattern (14 bp):
ATATAAATTAATAA
Found at i:54696378 original size:5 final size:5
Alignment explanation
Indices: 54696368--54696395 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
54696358 ACCATAATAT
54696368 TTTAA TTTAA TTTAA TTTAA TTTAA TTT
1 TTTAA TTTAA TTTAA TTTAA TTTAA TTT
54696396 TATATAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (5 bp):
TTTAA
Found at i:54698124 original size:8 final size:8
Alignment explanation
Indices: 54698105--54698134 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
54698095 AAATATATTT
54698105 ATTTTTTAA
1 ATTTTTT-A
54698114 ATTTTTTA
1 ATTTTTTA
54698122 ATTTTTTA
1 ATTTTTTA
54698130 ATTTT
1 ATTTT
54698135 AAAAATATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 14 0.67
9 7 0.33
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (8 bp):
ATTTTTTA
Found at i:54698149 original size:13 final size:14
Alignment explanation
Indices: 54698131--54698163 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
54698121 AATTTTTTAA
54698131 TTTTAAAAATA-TT
1 TTTTAAAAATACTT
54698144 TTTT-AAAATACTT
1 TTTTAAAAATACTT
54698157 TTTTAAA
1 TTTTAAA
54698164 TTTTTAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 6 0.33
13 10 0.56
14 2 0.11
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (14 bp):
TTTTAAAAATACTT
Found at i:54698151 original size:12 final size:13
Alignment explanation
Indices: 54698131--54698163 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
54698121 AATTTTTTAA
*
54698131 TTTTAAAAATA-T
1 TTTTTAAAATACT
54698143 TTTTTAAAATACT
1 TTTTTAAAATACT
54698156 TTTTTAAA
1 TTTTTAAA
54698164 TTTTTAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 10 0.53
13 9 0.47
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (13 bp):
TTTTTAAAATACT
Found at i:54700015 original size:16 final size:16
Alignment explanation
Indices: 54699996--54700036 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
54699986 AATTTGATAC
54699996 AATTTTAATAACAATT
1 AATTTTAATAACAATT
*
54700012 AATTTTGATAACAATT
1 AATTTTAATAACAATT
*
54700028 AGTTTTAAT
1 AATTTTAAT
54700037 TTTAATAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (16 bp):
AATTTTAATAACAATT
Found at i:54700038 original size:22 final size:23
Alignment explanation
Indices: 54700010--54700071 Score: 81
Period size: 22 Copynumber: 2.7 Consensus size: 23
54700000 TTAATAACAA
* * *
54700010 TTAATTTTGATAACAAT-TAGTT
1 TTAATTTTAATAAAAATATAATT
54700032 TTAATTTTAATAAAAATATAATT
1 TTAATTTTAATAAAAATATAATT
54700055 TTAATTTTAATTAAAAA
1 TTAATTTTAA-TAAAAA
54700072 ACTGGCCGAG
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
22 15 0.43
23 14 0.40
24 6 0.17
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (23 bp):
TTAATTTTAATAAAAATATAATT
Found at i:54701690 original size:6 final size:6
Alignment explanation
Indices: 54701679--54701707 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
54701669 GGAACAAAAT
54701679 CCAAAC CCAAAC CCAAAC CCAAAC CCAAA
1 CCAAAC CCAAAC CCAAAC CCAAAC CCAAA
54701708 GCCTCTGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (6 bp):
CCAAAC
Found at i:54712063 original size:19 final size:17
Alignment explanation
Indices: 54712039--54712073 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
54712029 TACTCCGTTC
54712039 TAATTTTTATGATTTTTTA
1 TAATTTTT-T-ATTTTTTA
54712058 TAATTTTTTATTTTTT
1 TAATTTTTTATTTTTT
54712074 GTATTGTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 1 0.06
19 8 0.50
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (17 bp):
TAATTTTTTATTTTTTA
Found at i:54712801 original size:34 final size:35
Alignment explanation
Indices: 54712757--54712823 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
54712747 CAGTAAAATA
54712757 TTTTCCGTAAAATGATTT-CGGGAAAATATTTTAC
1 TTTTCCGTAAAATGATTTACGGGAAAATATTTTAC
* *
54712791 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACGGGAAAATATTTT
54712824 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.33, C:0.09, G:0.13, T:0.45
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACGGGAAAATATTTTAC
Found at i:54717445 original size:27 final size:27
Alignment explanation
Indices: 54717381--54717435 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
54717371 GTGTTCAAGT
*
54717381 AAAAAAAAAACATAGGTACTTAATTTG
1 AAAAAAAAAGCATAGGTACTTAATTTG
54717408 AAAAAAAAAGCATAGGTACTTAATTTG
1 AAAAAAAAAGCATAGGTACTTAATTTG
54717435 A
1 A
54717436 TCATTAAAGC
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:0.55, C:0.07, G:0.13, T:0.25
Consensus pattern (27 bp):
AAAAAAAAAGCATAGGTACTTAATTTG
Found at i:54717559 original size:31 final size:32
Alignment explanation
Indices: 54717517--54717580 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
54717507 AGGTATAGAT
*
54717517 TTGAATATTGAAACC-AAATTCAAGTACTAAA
1 TTGAATATTGAAACCAAAACTCAAGTACTAAA
* *
54717548 TTGAATTTTGAAGCCAAAACTCAAGTACTAAA
1 TTGAATATTGAAACCAAAACTCAAGTACTAAA
54717580 T
1 T
54717581 AAAAATATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
31 13 0.45
32 16 0.55
ACGTcount: A:0.45, C:0.14, G:0.11, T:0.30
Consensus pattern (32 bp):
TTGAATATTGAAACCAAAACTCAAGTACTAAA
Found at i:54723398 original size:27 final size:27
Alignment explanation
Indices: 54723357--54723425 Score: 102
Period size: 27 Copynumber: 2.6 Consensus size: 27
54723347 GAAAATCGGA
*
54723357 TGCCAGAGGCGGCACCAAAGGTGTCTG
1 TGCCAGAGGCGGCACCAAAGGTGCCTG
* *
54723384 TGGCAGAGGCGGCACCAAAGGTGCCTT
1 TGCCAGAGGCGGCACCAAAGGTGCCTG
*
54723411 TGCCAGATGCGGCAC
1 TGCCAGAGGCGGCAC
54723426 AAGACTAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.22, C:0.28, G:0.36, T:0.14
Consensus pattern (27 bp):
TGCCAGAGGCGGCACCAAAGGTGCCTG
Found at i:54724270 original size:27 final size:27
Alignment explanation
Indices: 54724232--54724294 Score: 108
Period size: 27 Copynumber: 2.3 Consensus size: 27
54724222 TTTTAGTCCT
*
54724232 GTGCCGCCTCTGGCAAAGGCACCTTTG
1 GTGCCGCCTCTGCCAAAGGCACCTTTG
*
54724259 GTGCCGCCTCTGCCACAGGCACCTTTG
1 GTGCCGCCTCTGCCAAAGGCACCTTTG
54724286 GTGCCGCCT
1 GTGCCGCCT
54724295 GTGACATCCG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.11, C:0.38, G:0.29, T:0.22
Consensus pattern (27 bp):
GTGCCGCCTCTGCCAAAGGCACCTTTG
Found at i:54724576 original size:12 final size:12
Alignment explanation
Indices: 54724559--54724585 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
54724549 GGATAAGGAT
54724559 GTTTTAATTATA
1 GTTTTAATTATA
54724571 GTTTTAATTATA
1 GTTTTAATTATA
54724583 GTT
1 GTT
54724586 GTACTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.59
Consensus pattern (12 bp):
GTTTTAATTATA
Found at i:54725647 original size:25 final size:25
Alignment explanation
Indices: 54725599--54725649 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
54725589 GTAACTTATA
*
54725599 AATATTAAGTTAAATAATTGTAAAT
1 AATATTAAGTTAAATAATAGTAAAT
*
54725624 AATATTAA-TTAAATTATAGATAAAT
1 AATATTAAGTTAAATAATAG-TAAAT
54725649 A
1 A
54725650 CATAAAGTAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 9 0.39
25 14 0.61
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (25 bp):
AATATTAAGTTAAATAATAGTAAAT
Found at i:54725900 original size:12 final size:13
Alignment explanation
Indices: 54725874--54725902 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
54725864 TTGTTTTTAG
54725874 TTATGATTAATAC
1 TTATGATTAATAC
54725887 TTATGATT-ATAC
1 TTATGATTAATAC
54725899 TTAT
1 TTAT
54725903 AAACTCGTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.50
13 8 0.50
ACGTcount: A:0.34, C:0.07, G:0.07, T:0.52
Consensus pattern (13 bp):
TTATGATTAATAC
Found at i:54728266 original size:114 final size:114
Alignment explanation
Indices: 54728080--54728667 Score: 712
Period size: 117 Copynumber: 4.9 Consensus size: 114
54728070 GAAAAACAAC
* * * **
54728080 AACAACAACAAGAAAACTATTGGTGGTGAACATATTATTGAAGGGTTAAGTGATAATAAGGTTGA
1 AACAAGAAGAAGAAAACTATTGGTGGTGAACAGATTATTGAAGGGTTAAGTGATAGCAAGGTTGA
*
54728145 AATGGAAGATCCCCTTAAGCCTAAACGTGGTCGGCCAAAGGGTGCAATG
66 AATGGAAGATCCCCTTAAGCCTAAACGTGGTCGGCCAAAGGGTACAATG
* *
54728194 AACAAGAAGAAGAAAACTATTGGTGGTGAACAGATTCTTGAAGGGTTAAGTGATAACAAGGTTGA
1 AACAAGAAGAAGAAAACTATTGGTGGTGAACAGATTATTGAAGGGTTAAGTGATAGCAAGGTTGA
54728259 AATGGAAGATCCCCTTAAGCCTAAACGTGGTCGGCCAAAGGGTACAATGAAGAAG
66 AATGGAAGATCCCCTTAAGCCTAAACGTGGTCGGCCAAAGGGTACAAT------G
* * * *
54728314 AAGAAGAGGAAGAAAAAGAAAACTATTGGTAGTGAACA-TTGTATTGTAGGGTTAAGTGATAGCA
1 AA-CA-A-GAAG---AAGAAAACTATTGGTGGTGAACAGAT-TATTGAAGGGTTAAGTGATAGCA
* * *
54728378 GGGTTGAAATGGAAAACCCCCTTAAGCCTAAACGTGGTCGGCCAAAGGGTTCAACGAA-G
59 AGGTTGAAATGGAAGATCCCCTTAAGCCTAAACGTGGTCGGCCAAAGGG-T--AC-AATG
* * *
54728437 AAGAAGAAGAAGAAAACTATTGGTGGTGAACAAAGTATTGAAGGGTTAAGTGATAGCAAGGTTGA
1 AACAAGAAGAAGAAAACTATTGGTGGTGAACAGATTATTGAAGGGTTAAGTGATAGCAAGGTTGA
54728502 AATGGAAGATCCCCTTAAGCCTAAACGTGGTCGGCCAAAGGGTACAATG
66 AATGGAAGATCCCCTTAAGCCTAAACGTGGTCGGCCAAAGGGTACAATG
* * * * * *
54728551 AACAAGAAGAAGAAGAAAACTATTGGTGGTGAGCAGAGTATTGAAGTGTTTAGTAATAGCATGGT
1 AAC---AAGAAGAAGAAAACTATTGGTGGTGAACAGATTATTGAAGGGTTAAGTGATAGCAAGGT
54728616 TGAAATGGAAGATCCCCTTAAAGCCAAGCCTAAACGTGGTCGGCCAAAGGGT
63 TGAAATGGAAGATCCCCTT------AAGCCTAAACGTGGTCGGCCAAAGGGT
54728668 TCAAAGAATA
Statistics
Matches: 416, Mismatches: 30, Indels: 47
0.84 0.06 0.10
Matches are distributed among these distances:
113 2 0.00
114 112 0.27
116 1 0.00
117 162 0.39
120 7 0.02
121 2 0.00
122 2 0.00
123 34 0.08
125 1 0.00
126 88 0.21
127 1 0.00
129 2 0.00
130 2 0.00
ACGTcount: A:0.38, C:0.13, G:0.28, T:0.21
Consensus pattern (114 bp):
AACAAGAAGAAGAAAACTATTGGTGGTGAACAGATTATTGAAGGGTTAAGTGATAGCAAGGTTGA
AATGGAAGATCCCCTTAAGCCTAAACGTGGTCGGCCAAAGGGTACAATG
Found at i:54728568 original size:240 final size:236
Alignment explanation
Indices: 54728047--54728672 Score: 805
Period size: 240 Copynumber: 2.6 Consensus size: 236
54728037 TAAGGGTAAG
* * * * * *
54728047 CGTGGTAGGCCAAAGGGTTCAAAGAAAAACAACAACAACAACAAGAAAACTATTGGTGGTGAACA
1 CGTGGTCGGCCAAAGGGTACAATGAAAAA-AAGAAGAAGAA-AAGAAAACTATTGGTGGTGAACA
**
54728112 TAT-TATTGAAGGGTTAAGTGATAATAAGGTTGAAATGGAAGATCCCCTTAAGCCTAAACGTGGT
64 T-TGTATTGAAGGGTTAAGTGATAGCAAGGTTGAAATGGAAGATCCCCTTAAGCCTAAACGTGGT
* * * * *
54728176 CGGCCAAAGGGTGC-AATGAACAAGAAGAAGAAAACTATTGGTGGTGAACAGATTCTTGAAGGGT
128 CGGCCAAAGGGTTCAAAAGAACAAGAAGAAGAAAACTATTGGTGGTGAACAAAGTATTGAAGGGT
54728240 TAAGTGATAACAAGGTTGAAATGGAAGATCCCCTTAAGCCTAAA
193 TAAGTGATAACAAGGTTGAAATGGAAGATCCCCTTAAGCCTAAA
* *
54728284 CGTGGTCGGCCAAAGGGTACAATGAAGAAGAAGAAGAGGAAGAAAAAGAAAACTATTGGTAGTGA
1 CGTGGTCGGCCAAAGGGTACAATG-A-AA-AA-AAGAAGAAG-AAAAGAAAACTATTGGTGGTGA
* * * *
54728349 ACATTGTATTGTAGGGTTAAGTGATAGCAGGGTTGAAATGGAAAACCCCCTTAAGCCTAAACGTG
61 ACATTGTATTGAAGGGTTAAGTGATAGCAAGGTTGAAATGGAAGATCCCCTTAAGCCTAAACGTG
*
54728414 GTCGGCCAAAGGGTTCAACGAAGAAGAAGAAGAAGAAAACTATTGGTGGTGAACAAAGTATTGAA
126 GTCGGCCAAAGGGTTCAA--AAGAACAAGAAGAAGAAAACTATTGGTGGTGAACAAAGTATTGAA
*
54728479 GGGTTAAGTGATAGCAAGGTTGAAATGGAAGATCCCCTTAAGCCTAAA
189 GGGTTAAGTGATAACAAGGTTGAAATGGAAGATCCCCTTAAGCCTAAA
* * **
54728527 CGTGGTCGGCCAAAGGGTACAATG--AACAAGAAGAAG--AAGAAAACTATTGGTGGTGAGCAGA
1 CGTGGTCGGCCAAAGGGTACAATGAAAAAAAGAAGAAGAAAAGAAAACTATTGGTGGTGAACATT
* * * *
54728588 GTATTGAAGTGTTTAGTAATAGCATGGTTGAAATGGAAGATCCCCTTAAAGCCAAGCCTAAACGT
66 GTATTGAAGGGTTAAGTGATAGCAAGGTTGAAATGGAAGATCCCCTT------AAGCCTAAACGT
54728653 GGTCGGCCAAAGGGTTCAAA
125 GGTCGGCCAAAGGGTTCAAA
54728673 GAATAAACAG
Statistics
Matches: 340, Mismatches: 35, Indels: 27
0.85 0.09 0.07
Matches are distributed among these distances:
234 61 0.18
237 29 0.09
238 3 0.01
239 4 0.01
240 129 0.38
241 3 0.01
243 111 0.33
ACGTcount: A:0.38, C:0.14, G:0.27, T:0.20
Consensus pattern (236 bp):
CGTGGTCGGCCAAAGGGTACAATGAAAAAAAGAAGAAGAAAAGAAAACTATTGGTGGTGAACATT
GTATTGAAGGGTTAAGTGATAGCAAGGTTGAAATGGAAGATCCCCTTAAGCCTAAACGTGGTCGG
CCAAAGGGTTCAAAAGAACAAGAAGAAGAAAACTATTGGTGGTGAACAAAGTATTGAAGGGTTAA
GTGATAACAAGGTTGAAATGGAAGATCCCCTTAAGCCTAAA
Found at i:54737650 original size:3 final size:3
Alignment explanation
Indices: 54737644--54737669 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
54737634 CGGCGGAGCT
54737644 GGA GGA GGA GGA GGA GGA GGA GGA GG
1 GGA GGA GGA GGA GGA GGA GGA GGA GG
54737670 GCCGACTGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.69, T:0.00
Consensus pattern (3 bp):
GGA
Found at i:54743049 original size:7 final size:7
Alignment explanation
Indices: 54743037--54743066 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
54743027 TTTCACTGGG
54743037 CATGTAT
1 CATGTAT
54743044 CATGTAT
1 CATGTAT
54743051 CATGTAT
1 CATGTAT
*
54743058 CAAGTAT
1 CATGTAT
54743065 CA
1 CA
54743067 AGTAGTAATC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (7 bp):
CATGTAT
Found at i:54754716 original size:18 final size:18
Alignment explanation
Indices: 54754693--54754729 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
54754683 TAGTTGTGTT
*
54754693 TGAATCCAAACTCATATC
1 TGAATCCAAACCCATATC
54754711 TGAATCCAAACCCATATC
1 TGAATCCAAACCCATATC
54754729 T
1 T
54754730 CACCGATGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.38, C:0.30, G:0.05, T:0.27
Consensus pattern (18 bp):
TGAATCCAAACCCATATC
Found at i:54754788 original size:21 final size:21
Alignment explanation
Indices: 54754741--54754791 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
54754731 ACCGATGTTT
* * *
54754741 CTAATCTCATTACTACAGTAT
1 CTAATCTCATCACTACAATAA
* *
54754762 CAAATCTCATCGCTACAATAA
1 CTAATCTCATCACTACAATAA
54754783 CTAATCTCA
1 CTAATCTCA
54754792 CTGTCACTAC
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.37, C:0.27, G:0.04, T:0.31
Consensus pattern (21 bp):
CTAATCTCATCACTACAATAA
Found at i:54764467 original size:3 final size:3
Alignment explanation
Indices: 54764459--54764494 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
54764449 ATAGACGTAT
54764459 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
54764495 TTATTATTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:54764527 original size:9 final size:8
Alignment explanation
Indices: 54764457--54764542 Score: 55
Period size: 9 Copynumber: 9.8 Consensus size: 8
54764447 AAATAGACGT
54764457 ATATAATA
1 ATATAATA
54764465 ATAATAATA
1 AT-ATAATA
54764474 ATAATAATA
1 AT-ATAATA
54764483 ATAATAATA
1 AT-ATAATA
*
54764492 ATATTATTA
1 ATA-TAATA
* *
54764501 TTATTATTA
1 ATA-TAATA
54764510 ATATTAATA
1 ATA-TAATA
54764519 ATATCAATAA
1 ATAT-AAT-A
*
54764529 ATAGAATA
1 ATATAATA
*
54764537 AAATAA
1 ATATAA
54764543 AAAAATGACA
Statistics
Matches: 67, Mismatches: 7, Indels: 8
0.82 0.09 0.10
Matches are distributed among these distances:
8 9 0.13
9 54 0.81
10 4 0.06
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.38
Consensus pattern (8 bp):
ATATAATA
Found at i:54764629 original size:15 final size:14
Alignment explanation
Indices: 54764609--54764638 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
54764599 AGAATGGGGC
54764609 AAATTTAAAATAAAA
1 AAATTTAAAA-AAAA
54764624 AAATTTAAAAAAAA
1 AAATTTAAAAAAAA
54764638 A
1 A
54764639 GAAAAAGGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (14 bp):
AAATTTAAAAAAAA
Found at i:54769159 original size:24 final size:24
Alignment explanation
Indices: 54769120--54769181 Score: 74
Period size: 24 Copynumber: 2.6 Consensus size: 24
54769110 ATAGTATATT
54769120 AATATATATAAGTAATAAAATTATAA
1 AATA-ATATAA-TAATAAAATTATAA
* *
54769146 AATAATATAATAATAAATTTATAT
1 AATAATATAATAATAAAATTATAA
54769170 AAT-ATA-AATAAT
1 AATAATATAATAAT
54769182 TTAATTTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
22 6 0.18
23 3 0.09
24 15 0.44
25 6 0.18
26 4 0.12
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (24 bp):
AATAATATAATAATAAAATTATAA
Found at i:54769161 original size:16 final size:16
Alignment explanation
Indices: 54769104--54769186 Score: 53
Period size: 16 Copynumber: 5.0 Consensus size: 16
54769094 AATAAAAAGA
54769104 AATAAAATAGTATATTAAT
1 AATAAAATA--ATA-TAAT
* *
54769123 ATATATAAGTAATAAAAT
1 A-ATA-AAATAATATAAT
*
54769141 TATAAAATAATATAAT
1 AATAAAATAATATAAT
* *
54769157 AATAAATTTATATAAT
1 AATAAAATAATATAAT
*
54769173 -AT-AAATAATTTAAT
1 AATAAAATAATATAAT
54769187 TTTTTAATAA
Statistics
Matches: 51, Mismatches: 11, Indels: 9
0.72 0.15 0.13
Matches are distributed among these distances:
14 9 0.18
15 2 0.04
16 23 0.45
17 3 0.06
18 3 0.06
19 4 0.08
20 3 0.06
21 4 0.08
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (16 bp):
AATAAAATAATATAAT
Found at i:54769173 original size:37 final size:38
Alignment explanation
Indices: 54769105--54769178 Score: 89
Period size: 37 Copynumber: 2.0 Consensus size: 38
54769095 ATAAAAAGAA
* * *
54769105 ATAAAATAGTATATTAATATATATAAGTAATA-AAATT
1 ATAAAATAATATAATAATAAATATAAGTAATATAAATT
*
54769142 ATAAAATAATATAATAATAAATTTATA-TAATATAAAT
1 ATAAAATAATATAATAATAAATATA-AGTAATATAAAT
54769179 AATTTAATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
37 26 0.84
38 5 0.16
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (38 bp):
ATAAAATAATATAATAATAAATATAAGTAATATAAATT
Found at i:54769184 original size:18 final size:21
Alignment explanation
Indices: 54769121--54769181 Score: 61
Period size: 21 Copynumber: 2.7 Consensus size: 21
54769111 TAGTATATTA
54769121 ATAT-ATATAAGTAATAAAATTAT
1 ATATAATATAA-TAAT-AAATT-T
*
54769144 AAAATAATATAATAATAAATTT
1 -ATATAATATAATAATAAATTT
54769166 ATATAATATAAATAAT
1 ATATAATAT-AATAAT
54769182 TTAATTTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
21 8 0.24
22 7 0.21
23 5 0.15
24 7 0.21
25 6 0.18
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (21 bp):
ATATAATATAATAATAAATTT
Found at i:54769621 original size:20 final size:19
Alignment explanation
Indices: 54769596--54769636 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
54769586 AACATAATGA
* *
54769596 TATATAATATATATTTTTAT
1 TATATAAT-TACATATTTAT
54769616 TATATAATTACATATTTAT
1 TATATAATTACATATTTAT
54769635 TA
1 TA
54769637 GTTGATTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.56
Consensus pattern (19 bp):
TATATAATTACATATTTAT
Found at i:54774930 original size:50 final size:50
Alignment explanation
Indices: 54774799--54775048 Score: 268
Period size: 50 Copynumber: 4.9 Consensus size: 50
54774789 TGATAATAAC
* * ** * *
54774799 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGAT-G
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCAT-CTCG
* * *
54774850 GTGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCG
* * *
54774900 ATGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCG
* * *
54774950 GTGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T--CG
* *
54775006 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
54775049 TTACCCAAAT
Statistics
Matches: 167, Mismatches: 25, Indels: 9
0.83 0.12 0.04
Matches are distributed among these distances:
49 1 0.01
50 90 0.54
51 33 0.20
53 2 0.01
54 1 0.01
56 40 0.24
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (50 bp):
ATGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCG
Found at i:54774979 original size:100 final size:103
Alignment explanation
Indices: 54774799--54775048 Score: 355
Period size: 100 Copynumber: 2.4 Consensus size: 103
54774789 TGATAATAAC
**
54774799 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGATGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCGTGATGGTGCCCATGCCATG
*
54774864 TCCCAGACATGGTCTTATAGGGGACCTCTC-ATC-T-CG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTACG
* *
54774900 ATGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGT-CTCGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGAT-GGTGCCCATGCCATG
*
54774964 TCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCA--ATCTT-ACG
* *
54775006 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
54775049 TTACCCAAAT
Statistics
Matches: 134, Mismatches: 8, Indels: 9
0.89 0.05 0.06
Matches are distributed among these distances:
99 1 0.01
100 50 0.37
101 37 0.28
103 3 0.02
104 1 0.01
106 42 0.31
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (103 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGATGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTCAATCTTACG
Found at i:54775164 original size:13 final size:13
Alignment explanation
Indices: 54775143--54775174 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
54775133 GCTTGGATCA
*
54775143 TCATCAAATAAAT
1 TCATAAAATAAAT
54775156 TCATAAAATAAAT
1 TCATAAAATAAAT
54775169 TCATAA
1 TCATAA
54775175 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:54775447 original size:29 final size:30
Alignment explanation
Indices: 54775388--54775444 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
54775378 CCTCGACTCT
*
54775388 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
54775418 AACTTTTACATAATTACATTTTTGCCC
1 AACTTTTACAAAATTACAATTTTGCCC
54775445 TAAGGCTCGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.32, C:0.23, G:0.04, T:0.42
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:54778496 original size:23 final size:23
Alignment explanation
Indices: 54778470--54778637 Score: 214
Period size: 23 Copynumber: 7.3 Consensus size: 23
54778460 ATAAGTGGCA
54778470 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
54778493 CACTGATATGTAGCCGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
54778516 CATTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* * *
54778539 CACTGATACGTAG-CTATAGCTAG
1 CACTGATATGTAGCCGA-AGCTAC
* *
54778562 CACTAAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
54778585 CACTGATATGTAGCC-ATAGCTAC
1 CACTGATATGTAGCCGA-AGCTAC
* *
54778608 CACTGAAATATAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
54778631 CACTGAT
1 CACTGAT
54778638 CAATAACACT
Statistics
Matches: 122, Mismatches: 19, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
22 3 0.02
23 116 0.95
24 3 0.02
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.23
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:54778544 original size:46 final size:46
Alignment explanation
Indices: 54778470--54778637 Score: 264
Period size: 46 Copynumber: 3.7 Consensus size: 46
54778460 ATAAGTGGCA
* *
54778470 CACTGATATGTAGCCGAAGCTACCACTGATATGTAGCCGTAGCTAC
1 CACTGAAATGTAGCCGAAGCTACCACTGATATGTAGCCATAGCTAC
* * * *
54778516 CATTGAAATGTAGCCGAAGCTACCACTGATACGTAGCTATAGCTAG
1 CACTGAAATGTAGCCGAAGCTACCACTGATATGTAGCCATAGCTAC
*
54778562 CACTAAAATGTAGCCGAAGCTACCACTGATATGTAGCCATAGCTAC
1 CACTGAAATGTAGCCGAAGCTACCACTGATATGTAGCCATAGCTAC
*
54778608 CACTGAAATATAGCCGAAGCTACCACTGAT
1 CACTGAAATGTAGCCGAAGCTACCACTGAT
54778638 CAATAACACT
Statistics
Matches: 109, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 109 1.00
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.23
Consensus pattern (46 bp):
CACTGAAATGTAGCCGAAGCTACCACTGATATGTAGCCATAGCTAC
Found at i:54780679 original size:17 final size:17
Alignment explanation
Indices: 54780657--54780719 Score: 65
Period size: 17 Copynumber: 3.5 Consensus size: 17
54780647 AATAATATAA
54780657 CATACAATAACTATAGT
1 CATACAATAACTATAGT
*
54780674 CATACAATTAAAATAATA-T
1 CATACAA-T-AACT-ATAGT
54780693 AACATACAATAACTATAGT
1 --CATACAATAACTATAGT
54780712 CATACAAT
1 CATACAAT
54780720 TATTCAATTC
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
17 15 0.39
18 4 0.11
19 8 0.21
20 4 0.11
21 7 0.18
ACGTcount: A:0.52, C:0.16, G:0.03, T:0.29
Consensus pattern (17 bp):
CATACAATAACTATAGT
Found at i:54780695 original size:38 final size:38
Alignment explanation
Indices: 54780644--54780721 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
54780634 TTGTTAAAAG
54780644 TAAAATAATATAACATACAATAACTATAGTCATACAAT
1 TAAAATAATATAACATACAATAACTATAGTCATACAAT
54780682 TAAAATAATATAACATACAATAACTATAGTCATACAAT
1 TAAAATAATATAACATACAATAACTATAGTCATACAAT
54780720 TA
1 TA
54780722 TTCAATTCAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.55, C:0.13, G:0.03, T:0.29
Consensus pattern (38 bp):
TAAAATAATATAACATACAATAACTATAGTCATACAAT
Found at i:54786172 original size:25 final size:25
Alignment explanation
Indices: 54786144--54786192 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
54786134 CATTTATATG
54786144 TTTAAAAATAATAAAA-AATATTTTA
1 TTTAAAAAT-ATAAAATAATATTTTA
* *
54786169 TTTAAATATATAAAATTATATTTT
1 TTTAAAAATATAAAATAATATTTT
54786193 TGTTATCTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 6 0.29
25 15 0.71
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (25 bp):
TTTAAAAATATAAAATAATATTTTA
Found at i:54786300 original size:14 final size:14
Alignment explanation
Indices: 54786281--54786311 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
54786271 GAAACTTGAA
54786281 AAGAAAGATTCTGG
1 AAGAAAGATTCTGG
54786295 AAGAAAGATTCTGG
1 AAGAAAGATTCTGG
54786309 AAG
1 AAG
54786312 TCTCGCTCGA
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:0.06, G:0.29, T:0.19
Consensus pattern (14 bp):
AAGAAAGATTCTGG
Found at i:54791997 original size:11 final size:11
Alignment explanation
Indices: 54791983--54792040 Score: 53
Period size: 11 Copynumber: 5.3 Consensus size: 11
54791973 ATATCCAAAT
54791983 AATAACAACAA
1 AATAACAACAA
* **
54791994 AATAATAGTAA
1 AATAACAACAA
* *
54792005 TATAATAACAA
1 AATAACAACAA
54792016 AATAACAACAA
1 AATAACAACAA
* *
54792027 AACAACAACGA
1 AATAACAACAA
54792038 AAT
1 AAT
54792041 TAGAGCAAAA
Statistics
Matches: 36, Mismatches: 11, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
11 36 1.00
ACGTcount: A:0.67, C:0.14, G:0.03, T:0.16
Consensus pattern (11 bp):
AATAACAACAA
Found at i:54792764 original size:21 final size:22
Alignment explanation
Indices: 54792740--54792780 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
54792730 TATTTTAGTC
54792740 ATTTAATTA-TTAATTTTTTCG
1 ATTTAATTACTTAATTTTTTCG
54792761 ATTTAATTACTTAATTTTTT
1 ATTTAATTACTTAATTTTTT
54792781 GAAATTAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.63
Consensus pattern (22 bp):
ATTTAATTACTTAATTTTTTCG
Found at i:54792788 original size:22 final size:21
Alignment explanation
Indices: 54792742--54792788 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
54792732 TTTTAGTCAT
*
54792742 TTAATTATTAATTTTTTCGAT
1 TTAATTATTAATTTTTTCGAA
54792763 TTAATTACTTAATTTTTT-GAAA
1 TTAATTA-TTAATTTTTTCG-AA
54792785 TTAA
1 TTAA
54792789 ATTTTGTAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 8 0.35
22 15 0.65
ACGTcount: A:0.34, C:0.04, G:0.04, T:0.57
Consensus pattern (21 bp):
TTAATTATTAATTTTTTCGAA
Found at i:54794876 original size:11 final size:13
Alignment explanation
Indices: 54794852--54794883 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
54794842 TAGTTTATTA
54794852 ATATTTTAATATG
1 ATATTTTAATATG
54794865 AT-TTTTAA-ATG
1 ATATTTTAATATG
54794876 ATATTTTA
1 ATATTTTA
54794884 TTAATTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 5 0.28
12 11 0.61
13 2 0.11
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (13 bp):
ATATTTTAATATG
Found at i:54796514 original size:46 final size:46
Alignment explanation
Indices: 54796447--54796748 Score: 359
Period size: 46 Copynumber: 6.6 Consensus size: 46
54796437 TTTGAGTACT
* *
54796447 TCTGATCAAGAGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
* *
54796493 TCTGATCAAGTGAAAAAGTGATAAGTGCTACACTTATTTGATAGCTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTA-GC----TT--TAGCTACACTTA
* *
54796546 TCTGATCAAGTGATAAAGTGATAAGTGGTAGCATTAGCTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
* *
54796592 TCTGATCAAGTGAGAAAGTGATAAGTGGTAGCATTAGCTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
* *
54796638 TCTGATCAAGTG--ACA---ATAAGTGGTAGTTTTAGCTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
* *
54796679 TCTGATCAAGTGACAAAGTGATAAGTGGTAGC-CTAGCTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
* *
54796724 TCTGATC-AG-GGACAAGTGATAAGTG
1 TCTGATCAAGTGAAAAAGTGATAAGTG
54796749 ATTATAAGTA
Statistics
Matches: 226, Mismatches: 18, Indels: 27
0.83 0.07 0.10
Matches are distributed among these distances:
41 36 0.16
43 15 0.07
44 4 0.02
45 19 0.08
46 107 0.47
47 1 0.00
48 1 0.00
51 2 0.01
52 1 0.00
53 40 0.18
ACGTcount: A:0.34, C:0.14, G:0.22, T:0.30
Consensus pattern (46 bp):
TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
Found at i:54796541 original size:17 final size:17
Alignment explanation
Indices: 54796519--54796551 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
54796509 AGTGATAAGT
*
54796519 GCTACACTTATTTGATA
1 GCTACACTTATCTGATA
54796536 GCTACACTTATCTGAT
1 GCTACACTTATCTGAT
54796552 CAAGTGATAA
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:0.27, C:0.21, G:0.12, T:0.39
Consensus pattern (17 bp):
GCTACACTTATCTGATA
Found at i:54796576 original size:99 final size:92
Alignment explanation
Indices: 54796534--54796748 Score: 266
Period size: 87 Copynumber: 2.4 Consensus size: 92
54796524 ACTTATTTGA
*
54796534 TAGCTACACTTATCTGATCAAGTGATAAAGTGATAAGTGGTAGCATTAGCTACACTTATCTGATC
1 TAGCTACACTTATCTGATCAAGTGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATC
* * *
54796599 AAGTGAGAAAGTGATAAGTGGTAGCAT
66 AAGTGAAAAAGTGATAAGTGCTAACAT
* *
54796626 TAGCTACACTTATCTGATCAAGTG--ACA---ATAAGTGGTAGTTTTAGCTACACTTATCTGATC
1 TAGCTACACTTATCTGATCAAGTGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATC
* * * *
54796686 AAGTGACAAAGTGATAAGTGGTAGC-C
66 AAGTGAAAAAGTGATAAGTGCTAACAT
* *
54796712 TAGCTACACTTATCTGATC-AGGGA-CAAGTGATAAGTG
1 TAGCTACACTTATCTGATCAAGTGATAAAGTGATAAGTG
54796749 ATTATAAGTA
Statistics
Matches: 111, Mismatches: 8, Indels: 11
0.85 0.06 0.08
Matches are distributed among these distances:
85 3 0.03
86 20 0.18
87 55 0.50
89 7 0.06
90 2 0.02
92 24 0.22
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.29
Consensus pattern (92 bp):
TAGCTACACTTATCTGATCAAGTGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATC
AAGTGAAAAAGTGATAAGTGCTAACAT
Found at i:54796684 original size:87 final size:86
Alignment explanation
Indices: 54796566--54796731 Score: 287
Period size: 87 Copynumber: 1.9 Consensus size: 86
54796556 TGATAAAGTG
* *
54796566 ATAAGTGGTAGCATTAGCTACACTTATCTGATCAAGTGAGAAAGTGATAAGTGGTAGCATTAGCT
1 ATAAGTGGTAGCATTAGCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGC-CTAGCT
54796631 ACACTTATCTGATCAAGTGACA
65 ACACTTATCTGATCAAGTGACA
**
54796653 ATAAGTGGTAGTTTTAGCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTAGCTA
1 ATAAGTGGTAGCATTAGCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTAGCTA
54796718 CACTTATCTGATCA
66 CACTTATCTGATCA
54796732 GGGACAAGTG
Statistics
Matches: 75, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
86 20 0.27
87 55 0.73
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30
Consensus pattern (86 bp):
ATAAGTGGTAGCATTAGCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTAGCTA
CACTTATCTGATCAAGTGACA
Found at i:54797545 original size:20 final size:20
Alignment explanation
Indices: 54797520--54797560 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
54797510 GGTGGTACGT
*
54797520 ACATATT-TACAATTTGATCC
1 ACATATTGTA-AATATGATCC
54797540 ACATATTGTAAATATGATCC
1 ACATATTGTAAATATGATCC
54797560 A
1 A
54797561 TGTCGCTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 17 0.89
21 2 0.11
ACGTcount: A:0.39, C:0.17, G:0.07, T:0.37
Consensus pattern (20 bp):
ACATATTGTAAATATGATCC
Found at i:54798441 original size:31 final size:31
Alignment explanation
Indices: 54798406--54798481 Score: 93
Period size: 31 Copynumber: 2.5 Consensus size: 31
54798396 GTGTAAATTG
54798406 ATACAT-AAACTTTGATT-CGGTGCAATTATAT
1 ATACATAAAACTTTGATTGCGGTGCAA--ATAT
* * *
54798437 ATACATGAAACTTTGATTGTGGTTCAAATAT
1 ATACATAAAACTTTGATTGCGGTGCAAATAT
54798468 ATACATAAAACTTT
1 ATACATAAAACTTT
54798482 CATTTTAGTT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
31 23 0.57
32 11 0.28
33 6 0.15
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (31 bp):
ATACATAAAACTTTGATTGCGGTGCAAATAT
Found at i:54798493 original size:31 final size:31
Alignment explanation
Indices: 54798433--54798504 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 31
54798423 CGGTGCAATT
* * *
54798433 ATATATACATGAAACTTTGATTGTGGTTCAA
1 ATATATACATAAAACTTTCATTGTAGTTCAA
*
54798464 ATATATACATAAAACTTTCATTTTAGTTCAA
1 ATATATACATAAAACTTTCATTGTAGTTCAA
* *
54798495 TTATACACAT
1 ATATATACAT
54798505 GTAAAGAAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.39, C:0.12, G:0.08, T:0.40
Consensus pattern (31 bp):
ATATATACATAAAACTTTCATTGTAGTTCAA
Found at i:54803733 original size:39 final size:39
Alignment explanation
Indices: 54803679--54803756 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
54803669 TTGATTTTCA
54803679 ATGTCACCAGTTCCGTGTTCTTGAAGATTTCTTCCATTT
1 ATGTCACCAGTTCCGTGTTCTTGAAGATTTCTTCCATTT
54803718 ATGTCACCAGTTCCGTGTTCTTGAAGATTTCTTCCATTT
1 ATGTCACCAGTTCCGTGTTCTTGAAGATTTCTTCCATTT
54803757 TCTTCAACTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.18, C:0.23, G:0.15, T:0.44
Consensus pattern (39 bp):
ATGTCACCAGTTCCGTGTTCTTGAAGATTTCTTCCATTT
Found at i:54809157 original size:14 final size:14
Alignment explanation
Indices: 54809140--54809172 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
54809130 ATCTTAAATT
54809140 TTAAATCCTGAATA
1 TTAAATCCTGAATA
*
54809154 TTAAATCCTGAATC
1 TTAAATCCTGAATA
54809168 TTAAA
1 TTAAA
54809173 CCTTAAACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.42, C:0.15, G:0.06, T:0.36
Consensus pattern (14 bp):
TTAAATCCTGAATA
Found at i:54825874 original size:2 final size:2
Alignment explanation
Indices: 54825867--54825909 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
54825857 TGTTATGCGC
54825867 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
54825909 A
1 A
54825910 ATAATAATAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:54825950 original size:3 final size:3
Alignment explanation
Indices: 54825942--54825973 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
54825932 TAAATATTAC
54825942 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
54825974 TATATATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:54826929 original size:21 final size:18
Alignment explanation
Indices: 54826883--54826938 Score: 51
Period size: 19 Copynumber: 2.9 Consensus size: 18
54826873 TCTTTTTGAT
*
54826883 ATTATTATAAATATTTTA
1 ATTATTATAAATATTTAA
54826901 ATTAATTATATAATCAATTTAA
1 ATT-ATTATA-AAT--ATTTAA
*
54826923 ATTATTA-AATTATTTA
1 ATTATTATAAATATTTA
54826939 TTAGATAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
17 5 0.16
18 3 0.09
19 8 0.25
20 4 0.12
21 4 0.12
22 8 0.25
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (18 bp):
ATTATTATAAATATTTAA
Found at i:54835393 original size:21 final size:20
Alignment explanation
Indices: 54835359--54835397 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
54835349 AAAAATCAAT
54835359 ATATATATAATATAGAAAAAA
1 ATATATATAATATA-AAAAAA
54835380 ATATATA-AATTATAAAAA
1 ATATATATAA-TATAAAAA
54835398 TTTATGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (20 bp):
ATATATATAATATAAAAAAA
Found at i:54839944 original size:9 final size:9
Alignment explanation
Indices: 54839926--54839962 Score: 58
Period size: 9 Copynumber: 4.2 Consensus size: 9
54839916 TTGGGTAATT
54839926 TTCGGGTAA
1 TTCGGGTAA
*
54839935 TTCGGTTAA
1 TTCGGGTAA
54839944 -TCGGGTAA
1 TTCGGGTAA
54839952 TTCGGGTAA
1 TTCGGGTAA
54839961 TT
1 TT
54839963 TTTAATCAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
8 7 0.28
9 18 0.72
ACGTcount: A:0.22, C:0.11, G:0.30, T:0.38
Consensus pattern (9 bp):
TTCGGGTAA
Found at i:54839949 original size:17 final size:17
Alignment explanation
Indices: 54839927--54839961 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
54839917 TGGGTAATTT
*
54839927 TCGGGTAATTCGGTTAA
1 TCGGGTAATTCGGGTAA
54839944 TCGGGTAATTCGGGTAA
1 TCGGGTAATTCGGGTAA
54839961 T
1 T
54839962 TTTTAATCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.23, C:0.11, G:0.31, T:0.34
Consensus pattern (17 bp):
TCGGGTAATTCGGGTAA
Found at i:54846589 original size:76 final size:76
Alignment explanation
Indices: 54846463--54846614 Score: 304
Period size: 76 Copynumber: 2.0 Consensus size: 76
54846453 GAACTTGGGC
54846463 GCTAAATACATCTTCATTTTGCTAATTTTACTGGCTGGTTTGTAGGGATGTATATAAGATGCTGG
1 GCTAAATACATCTTCATTTTGCTAATTTTACTGGCTGGTTTGTAGGGATGTATATAAGATGCTGG
54846528 TTTCCTTCCTG
66 TTTCCTTCCTG
54846539 GCTAAATACATCTTCATTTTGCTAATTTTACTGGCTGGTTTGTAGGGATGTATATAAGATGCTGG
1 GCTAAATACATCTTCATTTTGCTAATTTTACTGGCTGGTTTGTAGGGATGTATATAAGATGCTGG
54846604 TTTCCTTCCTG
66 TTTCCTTCCTG
54846615 TTTTTATATA
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 76 1.00
ACGTcount: A:0.21, C:0.16, G:0.21, T:0.42
Consensus pattern (76 bp):
GCTAAATACATCTTCATTTTGCTAATTTTACTGGCTGGTTTGTAGGGATGTATATAAGATGCTGG
TTTCCTTCCTG
Found at i:54858913 original size:20 final size:20
Alignment explanation
Indices: 54858890--54858927 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
54858880 AATACAATTT
54858890 ATATTTTAATAA-TAAATAAA
1 ATATTTT-ATAATTAAATAAA
54858910 ATATTTTATAATTAAATA
1 ATATTTTATAATTAAATA
54858928 GATTTTTGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
ATATTTTATAATTAAATAAA
Found at i:54860471 original size:2 final size:2
Alignment explanation
Indices: 54860464--54860488 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
54860454 TCAATAAATC
54860464 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
54860489 CAATTTAAGG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:54870835 original size:41 final size:39
Alignment explanation
Indices: 54870749--54870837 Score: 115
Period size: 39 Copynumber: 2.2 Consensus size: 39
54870739 AAAAATTATA
* * * *
54870749 TTTAATACAATAAAATATTTATTATATTTGTTTGTGTTT
1 TTTAATATAATAAAACATTTATTATATTTGGTAGTGTTT
*
54870788 TTTAATATAATTAAACATTTATTATATTTATGGTAGTGTTT
1 TTTAATATAATAAAACATTTATTATA-TT-TGGTAGTGTTT
54870829 TTTAATATA
1 TTTAATATA
54870838 TTTCTAATGT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
39 23 0.53
40 2 0.05
41 18 0.42
ACGTcount: A:0.35, C:0.02, G:0.08, T:0.55
Consensus pattern (39 bp):
TTTAATATAATAAAACATTTATTATATTTGGTAGTGTTT
Found at i:54872517 original size:51 final size:51
Alignment explanation
Indices: 54872462--54872559 Score: 153
Period size: 51 Copynumber: 1.9 Consensus size: 51
54872452 AAAAAATTAA
54872462 AAATAGGGATTTAAGAGAAATTTA-AGAGGAAATTGAGAGCAAATTGAAATT
1 AAATAGGGATTTAAGAGAAATTTAGA-AGGAAATTGAGAGCAAATTGAAATT
* * *
54872513 AAATATGGATTTGAGAGAAATTTGGAAGGAAATTGAGAGCAAATTGA
1 AAATAGGGATTTAAGAGAAATTTAGAAGGAAATTGAGAGCAAATTGA
54872560 GAGGAAATTG
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
51 42 0.98
52 1 0.02
ACGTcount: A:0.47, C:0.02, G:0.26, T:0.26
Consensus pattern (51 bp):
AAATAGGGATTTAAGAGAAATTTAGAAGGAAATTGAGAGCAAATTGAAATT
Found at i:54872548 original size:22 final size:22
Alignment explanation
Indices: 54872523--54872585 Score: 69
Period size: 22 Copynumber: 2.8 Consensus size: 22
54872513 AAATATGGAT
54872523 TTGAGAGAAATTTG-GAAGGAAA
1 TTGAGAGAAATTTGAG-AGGAAA
54872545 TTGAGAGCAAA-TTGAGAGGAAA
1 TTGAGAG-AAATTTGAGAGGAAA
54872567 TTGAGA-AAATAATTGAGAG
1 TTGAGAGAAAT--TTGAGAG
54872586 AGGATTAGTT
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
20 3 0.08
22 22 0.61
23 11 0.31
ACGTcount: A:0.46, C:0.02, G:0.30, T:0.22
Consensus pattern (22 bp):
TTGAGAGAAATTTGAGAGGAAA
Found at i:54879705 original size:2 final size:2
Alignment explanation
Indices: 54879698--54879733 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
54879688 CTTTCCACTC
54879698 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
54879734 ATCCATCTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:54885170 original size:25 final size:25
Alignment explanation
Indices: 54885120--54885170 Score: 61
Period size: 25 Copynumber: 2.0 Consensus size: 25
54885110 AAAATAAAAA
*
54885120 TATAAAAAAATTATTTTTATGGTTT
1 TATAAAAAAATTATTTTTATGATTT
54885145 TATAAATAAAA-TATTTTGTAT-ATTT
1 TATAAA-AAAATTATTTT-TATGATTT
54885170 T
1 T
54885171 TAGAAAATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
25 16 0.70
26 7 0.30
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (25 bp):
TATAAAAAAATTATTTTTATGATTT
Found at i:54885171 original size:26 final size:25
Alignment explanation
Indices: 54885120--54885177 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 25
54885110 AAAATAAAAA
*
54885120 TATAAAAAAATTATTTTTATGGTTT
1 TATAAAAAAATTATTTTTATAGTTT
*
54885145 TATAAATAAAA-TATTTTGTATATTTT
1 TATAAA-AAAATTATTTT-TATAGTTT
*
54885171 TAGAAAA
1 TATAAAA
54885178 TTCATGTCAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
25 13 0.46
26 15 0.54
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (25 bp):
TATAAAAAAATTATTTTTATAGTTT
Found at i:54890070 original size:19 final size:19
Alignment explanation
Indices: 54890033--54890070 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
54890023 TTTAAGTATC
*
54890033 TATTTCAATTTTAATAGTA
1 TATTTCAATTTTAAAAGTA
54890052 TATTT-AATTTGTAAAAGTA
1 TATTTCAATTT-TAAAAGTA
54890071 GTGATAAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.39, C:0.03, G:0.08, T:0.50
Consensus pattern (19 bp):
TATTTCAATTTTAAAAGTA
Found at i:54899725 original size:16 final size:16
Alignment explanation
Indices: 54899704--54899742 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
54899694 ATAATCTTAG
54899704 TTTTTTTAGATATGAT
1 TTTTTTTAGATATGAT
* *
54899720 TTTTTTTAGCTATTAT
1 TTTTTTTAGATATGAT
*
54899736 CTTTTTT
1 TTTTTTT
54899743 CTTAATTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.18, C:0.05, G:0.08, T:0.69
Consensus pattern (16 bp):
TTTTTTTAGATATGAT
Found at i:54901239 original size:4 final size:4
Alignment explanation
Indices: 54901230--54901261 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
54901220 ATTCAAGGTG
*
54901230 CATA CATA CATA CATA CATA CATC CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA
54901262 TTAGTATTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.47, C:0.28, G:0.00, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:54904856 original size:15 final size:16
Alignment explanation
Indices: 54904829--54904858 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
54904819 TAAATCGATA
54904829 ACTTTATTTTTATTTC
1 ACTTTATTTTTATTTC
54904845 ACTTTA-TTTTATTT
1 ACTTTATTTTTATTT
54904859 TTACATATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.20, C:0.10, G:0.00, T:0.70
Consensus pattern (16 bp):
ACTTTATTTTTATTTC
Found at i:54905750 original size:2 final size:2
Alignment explanation
Indices: 54905738--54905786 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
54905728 GATATGAAAG
*
54905738 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
54905780 TA TA TA T
1 TA TA TA T
54905787 TGTCCATGGC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:54915388 original size:13 final size:13
Alignment explanation
Indices: 54915370--54915394 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54915360 GATCGCGACA
54915370 ATTTTAATTTTTT
1 ATTTTAATTTTTT
54915383 ATTTTAATTTTT
1 ATTTTAATTTTT
54915395 ACTTTCTTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
ATTTTAATTTTTT
Found at i:54915939 original size:90 final size:91
Alignment explanation
Indices: 54915826--54915995 Score: 315
Period size: 90 Copynumber: 1.9 Consensus size: 91
54915816 GGCCACCACC
*
54915826 AAATTTTTTTTTACTTTTTTCGTATACTGATACCTGATACTGACACGAAAAAAAAT-AATTTTTT
1 AAATTTTTTTTTACTTTTTTCGTATACTGATACCTGATACTGACACGAAAAAAAATAAAATTTTT
54915890 TTACTGTACTGGGTGCTGGCTTGTCA
66 TTACTGTACTGGGTGCTGGCTTGTCA
*
54915916 AAATTTTTTTTTACTTTTTTCGTATACTGATACCTGATACTGACACGAAAAAAAGTAAAATTTTT
1 AAATTTTTTTTTACTTTTTTCGTATACTGATACCTGATACTGACACGAAAAAAAATAAAATTTTT
54915981 TTACTGTACTGGGTG
66 TTACTGTACTGGGTG
54915996 TCGGCCATTG
Statistics
Matches: 77, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
90 55 0.71
91 22 0.29
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (91 bp):
AAATTTTTTTTTACTTTTTTCGTATACTGATACCTGATACTGACACGAAAAAAAATAAAATTTTT
TTACTGTACTGGGTGCTGGCTTGTCA
Found at i:54916026 original size:105 final size:105
Alignment explanation
Indices: 54915915--54916155 Score: 270
Period size: 105 Copynumber: 2.3 Consensus size: 105
54915905 CTGGCTTGTC
* * *
54915915 AAAATTTTTTTTTAC-TTTTTTCGTA-TACTGATACCTGATACTGACACGAAAAAAAGTAAAATT
1 AAAATTTTTTTTTACTTTTTTTCGTACT-CTGATACCGGACACTGACA-GAAAAAAACTAAAATT
*
54915978 TTTTTACTGTACTGGGTGTCGGCCATTGACAGGCCAGCACTT
64 TTTTTACTGTACTGGGTGCCGGCCATTGACAGGCCAGCACTT
* * * * ** * *
54916020 AAAATTTTTTTTTACTTTTTTTCGTACTCTGGTGCCGGCCATTGACAGACCAAAACTCAATTTTT
1 AAAATTTTTTTTTACTTTTTTTCGTACTCTGATACCGGACACTGACAGAAAAAAACTAAAATTTT
***
54916085 TTTACTGTACTGGGTGCCGGCCATTGACAGGCCAGTACAAAAA
66 TTTACTGTACTGGGTGCCGGCCATTGACAGGCCAG--C-ACTT
* *
54916128 AAAATTATTTTTTCCTTTTTTTCGTACT
1 AAAATTTTTTTTTACTTTTTTTCGTACT
54916156 GAGTGTCAGC
Statistics
Matches: 114, Mismatches: 17, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
105 62 0.54
106 23 0.20
107 2 0.02
108 27 0.24
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.39
Consensus pattern (105 bp):
AAAATTTTTTTTTACTTTTTTTCGTACTCTGATACCGGACACTGACAGAAAAAAACTAAAATTTT
TTTACTGTACTGGGTGCCGGCCATTGACAGGCCAGCACTT
Found at i:54916028 original size:47 final size:48
Alignment explanation
Indices: 54915971--54916119 Score: 138
Period size: 58 Copynumber: 2.9 Consensus size: 48
54915961 CGAAAAAAAG
* *
54915971 TAAAATTTTTTTACTGTACTGGGTGTCGGCCATTGACAGGCCAGCACT
1 TAAAATTTTTTTACTGTACTGGGTGCCGGCCATTGACAGGCCAGAACT
* * *
54916019 TAAAATTTTTTTTTACTTTTTTTCGTACTCTGGTGCCGGCCATTGACAGACCAAAAC-
1 TAAAA--TTTTTTTAC------T-GTACT-GGGTGCCGGCCATTGACAGGCCAGAACT
* *
54916076 TCAATTTTTTTTACTGTACTGGGTGCCGGCCATTGACAGGCCAG
1 TAAAATTTTTTTACTGTACTGGGTGCCGGCCATTGACAGGCCAG
54916120 TACAAAAAAA
Statistics
Matches: 81, Mismatches: 10, Indels: 21
0.72 0.09 0.19
Matches are distributed among these distances:
47 21 0.26
48 10 0.12
49 1 0.01
50 9 0.11
55 9 0.11
56 1 0.01
57 8 0.10
58 22 0.27
ACGTcount: A:0.22, C:0.21, G:0.20, T:0.36
Consensus pattern (48 bp):
TAAAATTTTTTTACTGTACTGGGTGCCGGCCATTGACAGGCCAGAACT
Found at i:54916188 original size:107 final size:104
Alignment explanation
Indices: 54915976--54916194 Score: 296
Period size: 105 Copynumber: 2.1 Consensus size: 104
54915966 AAAAGTAAAA
* *** *
54915976 TTTTTTTACTGTACTGGGTGTCGGCCATTGACAGGCCAGCACTTAAAATTTTTTTTTACTTTTTT
1 TTTTTTTACTGTACTGGGTGCCGGCCATTGACAGGCCAGCAAAAAAAATTATTTTTTACTTTTTT
* *
54916041 TCGTACTCTGGTGCCGGCCATTGACAGACCAAAACTCAAT
66 TCGTAC-CTGGTGCCAGCCATTGACAGACCAAAACCCAAT
*
54916081 TTTTTTTACTGTACTGGGTGCCGGCCATTGACAGGCCAGTACAAAAAAAAATTATTTTTTCCTTT
1 TTTTTTTACTGTACTGGGTGCCGGCCATTGACAGGCCAG--C-AAAAAAAATTATTTTTTACTTT
* *
54916146 TTTTCGTA-CTGAGTGTCAGCCATTGACAGGCCAAAACCCAAT
63 TTTTCGTACCTG-GTGCCAGCCATTGACAGACCAAAACCCAAT
54916188 TTTTTTT
1 TTTTTTT
54916195 TAAAGTCTGA
Statistics
Matches: 100, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
105 38 0.38
106 3 0.03
107 34 0.34
108 25 0.25
ACGTcount: A:0.24, C:0.21, G:0.17, T:0.38
Consensus pattern (104 bp):
TTTTTTTACTGTACTGGGTGCCGGCCATTGACAGGCCAGCAAAAAAAATTATTTTTTACTTTTTT
TCGTACCTGGTGCCAGCCATTGACAGACCAAAACCCAAT
Found at i:54923987 original size:3 final size:3
Alignment explanation
Indices: 54923979--54924018 Score: 64
Period size: 3 Copynumber: 13.3 Consensus size: 3
54923969 ATATGTAGGT
54923979 ATA ATA ATA ATAA ATA AT- ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA A
54924019 CAAAATTAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.06
3 30 0.86
4 3 0.09
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:54924276 original size:19 final size:21
Alignment explanation
Indices: 54924238--54924276 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
54924228 TCTTTTTTAA
*
54924238 AATCGTAAATAAGTAAAAAAT
1 AATCGTAAATAAGAAAAAAAT
54924259 AATCG-AAA-AAGAAAAAAA
1 AATCGTAAATAAGAAAAAAA
54924277 ACAGTAAGCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 3 0.18
21 5 0.29
ACGTcount: A:0.69, C:0.05, G:0.10, T:0.15
Consensus pattern (21 bp):
AATCGTAAATAAGAAAAAAAT
Found at i:54924477 original size:23 final size:22
Alignment explanation
Indices: 54924434--54924491 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
54924424 AAAGGGTATC
* *
54924434 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
54924455 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
*
54924478 TACATATCATATCT
1 TACAAATCATATCT
54924492 AAGATTGCAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 3 0.09
22 18 0.56
23 11 0.34
ACGTcount: A:0.43, C:0.17, G:0.03, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:54924494 original size:19 final size:20
Alignment explanation
Indices: 54924447--54924504 Score: 64
Period size: 19 Copynumber: 2.8 Consensus size: 20
54924437 AAATTAAATC
*
54924447 TCTAAGATTACAAAATCATATCT
1 TCTAAGATTAC-ATATCATA--T
54924470 TCTAAGATTACATATCATA-
1 TCTAAGATTACATATCATAT
*
54924489 TCTAAGATTGCATATC
1 TCTAAGATTACATATC
54924505 CTCGCAGATT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 15 0.45
22 7 0.21
23 11 0.33
ACGTcount: A:0.40, C:0.17, G:0.07, T:0.36
Consensus pattern (20 bp):
TCTAAGATTACATATCATAT
Found at i:54927459 original size:3 final size:3
Alignment explanation
Indices: 54927451--54927476 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
54927441 ATGGTTTTGT
54927451 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
54927477 TTTTTGTGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Done.