Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 200 of 226
Found at i:63359940 original size:22 final size:22
Alignment explanation
Indices: 63359915--63359983 Score: 68
Period size: 22 Copynumber: 3.1 Consensus size: 22
63359905 AATACAATAT
63359915 ACATGCATATTTAATTTAAAAC
1 ACATGCATATTTAATTTAAAAC
* * ** * *
63359937 ACAT-TAAATTATAATACAATAT
1 ACATGCATATT-TAATTTAAAAC
63359959 ACATGCATATTTAATTTAAAAC
1 ACATGCATATTTAATTTAAAAC
63359981 ACA
1 ACA
63359984 ATAAATTATA
Statistics
Matches: 33, Mismatches: 12, Indels: 4
0.67 0.24 0.08
Matches are distributed among these distances:
21 4 0.12
22 25 0.76
23 4 0.12
ACGTcount: A:0.49, C:0.13, G:0.03, T:0.35
Consensus pattern (22 bp):
ACATGCATATTTAATTTAAAAC
Found at i:63360072 original size:22 final size:21
Alignment explanation
Indices: 63360047--63360116 Score: 50
Period size: 22 Copynumber: 3.2 Consensus size: 21
63360037 AATACAATAG
63360047 ACATACATGTTTATTTTAAAAC
1 ACATACAT-TTTATTTTAAAAC
* * * ** * *
63360069 ACATTAAATTATAATACAATAT
1 ACA-TACATTTTATTTTAAAAC
63360091 ACATACATATTTATTTTAAAAC
1 ACATACAT-TTTATTTTAAAAC
63360113 ACAT
1 ACAT
63360117 TATATATATT
Statistics
Matches: 32, Mismatches: 14, Indels: 4
0.64 0.28 0.08
Matches are distributed among these distances:
21 4 0.12
22 24 0.75
23 4 0.12
ACGTcount: A:0.47, C:0.13, G:0.01, T:0.39
Consensus pattern (21 bp):
ACATACATTTTATTTTAAAAC
Found at i:63360355 original size:36 final size:36
Alignment explanation
Indices: 63360275--63360360 Score: 109
Period size: 36 Copynumber: 2.4 Consensus size: 36
63360265 TCTTTTAGTG
* * *
63360275 GCTGGCACCAAGGCCTGCCAGAGATGGTCTTACATTG
1 GCTGGCACCAA-GCCTGCCACAGATGGCCTTACATTA
* *
63360312 GCCGGCACTAAGCCTGCCACAGATGGCCTTACATTA
1 GCTGGCACCAAGCCTGCCACAGATGGCCTTACATTA
*
63360348 GTTGGCACCAAGC
1 GCTGGCACCAAGC
63360361 TGAAGCCCGC
Statistics
Matches: 41, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
36 32 0.78
37 9 0.22
ACGTcount: A:0.23, C:0.30, G:0.27, T:0.20
Consensus pattern (36 bp):
GCTGGCACCAAGCCTGCCACAGATGGCCTTACATTA
Found at i:63360560 original size:20 final size:20
Alignment explanation
Indices: 63360532--63360610 Score: 52
Period size: 23 Copynumber: 3.5 Consensus size: 20
63360522 AAAAGACGTA
*
63360532 AATTAAAATGGAAAAAAGAT
1 AATTTAAATGGAAAAAAGAT
63360552 AATTTAAATGAAATGAGAAAAA-ATT
1 AATTTAAATG----GA-AAAAAGA-T
63360577 AAATTTAAATGGAAAAAAAAAGAT
1 -AATTTAAATGG---AAAAAAGAT
63360601 AATTTAAATG
1 AATTTAAATG
63360611 AAATGGAAAT
Statistics
Matches: 47, Mismatches: 1, Indels: 19
0.70 0.01 0.28
Matches are distributed among these distances:
20 9 0.19
22 1 0.02
23 10 0.21
24 9 0.19
25 8 0.17
26 10 0.21
ACGTcount: A:0.62, C:0.00, G:0.13, T:0.25
Consensus pattern (20 bp):
AATTTAAATGGAAAAAAGAT
Found at i:63360571 original size:26 final size:25
Alignment explanation
Indices: 63360537--63360619 Score: 102
Period size: 26 Copynumber: 3.4 Consensus size: 25
63360527 ACGTAAATTA
63360537 AAATGGAAAAAAGATAATTTAAATG
1 AAATGGAAAAAAGATAATTTAAATG
*
63360562 AAATGAGAAAAAA-TTAAATTTAAATGG
1 AAATG-GAAAAAAGAT-AATTTAAAT-G
63360589 AAA---AAAAAAGATAATTTAAATG
1 AAATGGAAAAAAGATAATTTAAATG
63360611 AAATGGAAA
1 AAATGGAAA
63360620 TGAAATGAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
22 4 0.08
23 15 0.31
24 1 0.02
25 9 0.18
26 16 0.33
27 4 0.08
ACGTcount: A:0.63, C:0.00, G:0.14, T:0.23
Consensus pattern (25 bp):
AAATGGAAAAAAGATAATTTAAATG
Found at i:63360576 original size:21 final size:20
Alignment explanation
Indices: 63360555--63360594 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
63360545 AAAAGATAAT
63360555 TTAAA-TGAAATGAGAAAAAA
1 TTAAATTGAAATG-GAAAAAA
*
63360575 TTAAATTTAAATGGAAAAAA
1 TTAAATTGAAATGGAAAAAA
63360595 AAAGATAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.62, C:0.00, G:0.12, T:0.25
Consensus pattern (20 bp):
TTAAATTGAAATGGAAAAAA
Found at i:63360840 original size:25 final size:25
Alignment explanation
Indices: 63360797--63360849 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
63360787 TGAAATGAGA
* *
63360797 AAAATTTTGAATTTAAATGAAATTT
1 AAAATTTTGAAATGAAATGAAATTT
* *
63360822 AAAATTTTGAAATGGAATGATATTT
1 AAAATTTTGAAATGAAATGAAATTT
63360847 AAA
1 AAA
63360850 TTGAGAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.49, C:0.00, G:0.11, T:0.40
Consensus pattern (25 bp):
AAAATTTTGAAATGAAATGAAATTT
Found at i:63360872 original size:22 final size:21
Alignment explanation
Indices: 63360847--63360893 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
63360837 AATGATATTT
63360847 AAAT-TGAGAAAAAATTAAAATA
1 AAATATGA-AAAAAATTAAAA-A
**
63360869 AAATATGAAAAACTTTAAAAA
1 AAATATGAAAAAAATTAAAAA
63360890 AAAT
1 AAAT
63360894 GTAATTGAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 5 0.23
22 14 0.64
23 3 0.14
ACGTcount: A:0.68, C:0.02, G:0.06, T:0.23
Consensus pattern (21 bp):
AAATATGAAAAAAATTAAAAA
Found at i:63360878 original size:21 final size:21
Alignment explanation
Indices: 63360854--63360893 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
63360844 TTTAAATTGA
63360854 GAAAAA-ATTAAAATAAAATAT
1 GAAAAACATTAAAA-AAAATAT
*
63360875 GAAAAACTTTAAAAAAAAT
1 GAAAAACATTAAAAAAAAT
63360894 GTAATTGAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.70, C:0.03, G:0.05, T:0.23
Consensus pattern (21 bp):
GAAAAACATTAAAAAAAATAT
Found at i:63360964 original size:15 final size:15
Alignment explanation
Indices: 63360932--63360976 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
63360922 AAAAAATATG
*
63360932 AAATGAATTGAAAAAA
1 AAATAAATTG-AAAAA
*
63360948 AAATTGAATTGAAAAA
1 AAA-TAAATTGAAAAA
63360964 AAATAAATTGAAA
1 AAATAAATTGAAA
63360977 TGAGACTACT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 9 0.33
16 11 0.41
17 7 0.26
ACGTcount: A:0.67, C:0.00, G:0.11, T:0.22
Consensus pattern (15 bp):
AAATAAATTGAAAAA
Found at i:63361080 original size:5 final size:5
Alignment explanation
Indices: 63361063--63361140 Score: 66
Period size: 5 Copynumber: 14.4 Consensus size: 5
63361053 TGTAATTTGT
63361063 AATGA ATATGA AATGA AATGA AATGTTA AATGA ATATGA AATGA AATGA
1 AATGA A-ATGA AATGA AATGA AATG--A AATGA A-ATGA AATGA AATGA
* * * *
63361112 ATTTGT AATGA TTATGA AATGG AATGA AA
1 A-ATGA AATGA -AATGA AATGA AATGA AA
63361141 GTTTAAATGA
Statistics
Matches: 59, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
5 37 0.63
6 17 0.29
7 5 0.08
ACGTcount: A:0.51, C:0.00, G:0.19, T:0.29
Consensus pattern (5 bp):
AATGA
Found at i:63361084 original size:16 final size:15
Alignment explanation
Indices: 63361063--63361140 Score: 66
Period size: 16 Copynumber: 4.8 Consensus size: 15
63361053 TGTAATTTGT
63361063 AATGAATATGAAATGA
1 AATGAA-ATGAAATGA
63361079 AATGAAATGTTAAATGA
1 AATGAAATG--AAATGA
63361096 ATATGAAATGAAATGA
1 A-ATGAAATGAAATGA
* * *
63361112 ATTTGTAATGATTATGA
1 A-ATGAAATGA-AATGA
*
63361129 AATGGAATGAAA
1 AATGAAATGAAA
63361141 GTTTAAATGA
Statistics
Matches: 52, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
15 4 0.08
16 28 0.54
17 12 0.23
18 8 0.15
ACGTcount: A:0.51, C:0.00, G:0.19, T:0.29
Consensus pattern (15 bp):
AATGAAATGAAATGA
Found at i:63361094 original size:28 final size:28
Alignment explanation
Indices: 63361063--63361151 Score: 112
Period size: 28 Copynumber: 3.2 Consensus size: 28
63361053 TGTAATTTGT
63361063 AATGAATATGAAATGAAATGAAATGTTA
1 AATGAATATGAAATGAAATGAAATGTTA
*
63361091 AATGAATATGAAATGAAATG-AAT-TTGT
1 AATGAATATGAAATGAAATGAAATGTT-A
* *
63361118 AATGATTATGAAATGGAATGAAA-GTTTA
1 AATGAATATGAAATGAAATGAAATG-TTA
63361146 AATGAA
1 AATGAA
63361152 AATAAGTTAT
Statistics
Matches: 52, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
26 2 0.04
27 21 0.40
28 27 0.52
29 2 0.04
ACGTcount: A:0.51, C:0.00, G:0.19, T:0.30
Consensus pattern (28 bp):
AATGAATATGAAATGAAATGAAATGTTA
Found at i:63361249 original size:21 final size:19
Alignment explanation
Indices: 63361225--63361273 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 19
63361215 TTATTAATAT
63361225 GAAAAAAAAAGATTGAAATG
1 GAAAAAAAAA-ATTGAAATG
* *
63361245 AGAAAAAATTAAATTTAAATG
1 -GAAAAAA-AAAATTGAAATG
63361266 GAAAAAAA
1 GAAAAAAA
63361274 GATCATTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
20 7 0.29
21 15 0.62
22 2 0.08
ACGTcount: A:0.67, C:0.00, G:0.14, T:0.18
Consensus pattern (19 bp):
GAAAAAAAAAATTGAAATG
Found at i:63363599 original size:25 final size:25
Alignment explanation
Indices: 63363551--63363599 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
63363541 GTGTATGAAT
*
63363551 ATATATATATATATATTATAAAAAA
1 ATATATATATATATATCATAAAAAA
*
63363576 ATATGTATATATATATGCATAAAA
1 ATATATATATATATAT-CATAAAA
63363600 TACAAAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 15 0.71
26 6 0.29
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.39
Consensus pattern (25 bp):
ATATATATATATATATCATAAAAAA
Found at i:63363785 original size:3 final size:3
Alignment explanation
Indices: 63363777--63363836 Score: 95
Period size: 3 Copynumber: 20.0 Consensus size: 3
63363767 ATGCGTAAAT
*
63363777 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ACA ATAA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA
63363823 ATA AT- ATA ATA ATA
1 ATA ATA ATA ATA ATA
63363837 GTGAAAAATG
Statistics
Matches: 53, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
2 2 0.04
3 48 0.91
4 3 0.06
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:63366420 original size:89 final size:90
Alignment explanation
Indices: 63365983--63366398 Score: 624
Period size: 90 Copynumber: 4.6 Consensus size: 90
63365973 ATTCTAGAAT
* * * * * * *
63365983 ATTAATACACAAAAATATAAAATTAAAAC-AAAAATAATACGCACTAAATTAAATTTAAACACCC
1 ATTAATACACGAAAATTTTAAATTCAAACTACATATAATACGGACTAAATTAAATTTAAACACCC
63366047 AACAAACTACAAACAGATGGGTAAA
66 AACAAACTACAAACAGATGGGTAAA
*
63366072 ATTAATACACGAAAATTTTAAATTCAAACTACATATAATACGGACTAAATTAAATTTAAACCCCC
1 ATTAATACACGAAAATTTTAAATTCAAACTACATATAATACGGACTAAATTAAATTTAAACACCC
63366137 AACAAACTACAAACAGATGGGTAAA
66 AACAAACTACAAACAGATGGGTAAA
* * * * *
63366162 ATTAGA-GCACGAAAATTTTAAATTTAAACTATATATAACACAGACTAAATTAAATTTAAACACC
1 ATTA-ATACACGAAAATTTTAAATTCAAACTACATATAATACGGACTAAATTAAATTTAAACACC
63366226 CAACAAACTACAAACAGATGGGTAAA
65 CAACAAACTACAAACAGATGGGTAAA
* * * * *
63366252 ATTAGA-GCACGAAAATTTTAAATTCAAACTATATATAACACAGACTAAAATAAATTTAAACACC
1 ATTA-ATACACGAAAATTTTAAATTCAAACTACATATAATACGGACTAAATTAAATTTAAACACC
63366316 CAACAAACTACAAACAGATGGGTAAA
65 CAACAAACTACAAACAGATGGGTAAA
63366342 ATTAATACACGAAAA-TTTAAATTCAAACTACATATAATACGGACTAAATTAAATTTA
1 ATTAATACACGAAAATTTTAAATTCAAACTACATATAATACGGACTAAATTAAATTTA
63366399 CAGATACAAA
Statistics
Matches: 303, Mismatches: 21, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
89 64 0.21
90 238 0.79
91 1 0.00
ACGTcount: A:0.53, C:0.16, G:0.07, T:0.24
Consensus pattern (90 bp):
ATTAATACACGAAAATTTTAAATTCAAACTACATATAATACGGACTAAATTAAATTTAAACACCC
AACAAACTACAAACAGATGGGTAAA
Found at i:63367197 original size:110 final size:111
Alignment explanation
Indices: 63367059--63367275 Score: 348
Period size: 111 Copynumber: 2.0 Consensus size: 111
63367049 ATAAAGTTGA
* * * * *
63367059 TGCCGTCCATCAGTGTCCCAAAGT-AAAAAAAAGTTCCTTGGGACCCGAAAAATGTACTTTGTGT
1 TGCCGACCATCAGTGTCCCAAAGTAAAAAAAAAGTGCATTGGGACCCGAAAAATGTACTTGGTGC
63367123 CGGCCATCTACTGGCCAGCACCC-AAATCTTTTTTTAAATGACACTG
66 CGGCCATCTACTGGCCAGCACCCAAAAT-TTTTTTTAAATGACACTG
63367169 TGCCGACCATCAGTGTCCCAAAGTAAAAAAAAAGTGCATTGGGACCCGAAAAATGTACTTGGTGC
1 TGCCGACCATCAGTGTCCCAAAGTAAAAAAAAAGTGCATTGGGACCCGAAAAATGTACTTGGTGC
*
63367234 CGGTCATCTACTGGCCAGCACCCAAAAATTTTTTTTAAATGA
66 CGGCCATCTACTGGCCAGCACCC-AAAATTTTTTTTAAATGA
63367276 TTCTGGTGCC
Statistics
Matches: 98, Mismatches: 6, Indels: 4
0.91 0.06 0.04
Matches are distributed among these distances:
110 23 0.23
111 58 0.59
112 13 0.13
113 4 0.04
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (111 bp):
TGCCGACCATCAGTGTCCCAAAGTAAAAAAAAAGTGCATTGGGACCCGAAAAATGTACTTGGTGC
CGGCCATCTACTGGCCAGCACCCAAAATTTTTTTTAAATGACACTG
Found at i:63371162 original size:29 final size:29
Alignment explanation
Indices: 63371101--63371157 Score: 82
Period size: 27 Copynumber: 2.0 Consensus size: 29
63371091 TTAAACTTGA
* *
63371101 TATATTTAAATATATTAATAATGCATAAT
1 TATATTTAAATATATTAACAAAGCATAAT
63371130 TATATTTAAA-A-ATTAACAAAGCATAAT
1 TATATTTAAATATATTAACAAAGCATAAT
63371157 T
1 T
63371158 CTATAAATTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 15 0.58
28 1 0.04
29 10 0.38
ACGTcount: A:0.51, C:0.05, G:0.04, T:0.40
Consensus pattern (29 bp):
TATATTTAAATATATTAACAAAGCATAAT
Found at i:63372806 original size:24 final size:25
Alignment explanation
Indices: 63372754--63372810 Score: 71
Period size: 27 Copynumber: 2.2 Consensus size: 25
63372744 CATTGACAAC
63372754 ATTATTGAATTAACACCATTTGACAAT
1 ATTATTGAATTAACACCATTT-A-AAT
* *
63372781 ATTATTGAATTAGCACCATTT-TAT
1 ATTATTGAATTAACACCATTTAAAT
63372805 ATTATT
1 ATTATT
63372811 ATATTGTAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 8 0.29
27 20 0.71
ACGTcount: A:0.37, C:0.12, G:0.07, T:0.44
Consensus pattern (25 bp):
ATTATTGAATTAACACCATTTAAAT
Found at i:63372812 original size:27 final size:27
Alignment explanation
Indices: 63372746--63372801 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
63372736 TCACAAATCA
*
63372746 TTGACAACATTATTGAATTAACACCAT
1 TTGACAATATTATTGAATTAACACCAT
*
63372773 TTGACAATATTATTGAATTAGCACCAT
1 TTGACAATATTATTGAATTAACACCAT
63372800 TT
1 TT
63372802 TATATTATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.38
Consensus pattern (27 bp):
TTGACAATATTATTGAATTAACACCAT
Found at i:63375685 original size:22 final size:22
Alignment explanation
Indices: 63375660--63375730 Score: 65
Period size: 22 Copynumber: 3.2 Consensus size: 22
63375650 TAAAACACCA
63375660 AATTCCTTAGATGGATAAGGAC
1 AATTCCTTAGATGGATAAGGAC
*** *
63375682 AATTCGAAAG-TAGACT-AGGTAC
1 AATTCCTTAGATGGA-TAAGG-AC
*
63375704 AAATCCTTAGATGGATAAGGAC
1 AATTCCTTAGATGGATAAGGAC
63375726 AATTC
1 AATTC
63375731 GAAAGTAGAC
Statistics
Matches: 35, Mismatches: 10, Indels: 8
0.66 0.19 0.15
Matches are distributed among these distances:
21 6 0.17
22 23 0.66
23 6 0.17
ACGTcount: A:0.39, C:0.14, G:0.21, T:0.25
Consensus pattern (22 bp):
AATTCCTTAGATGGATAAGGAC
Found at i:63375722 original size:44 final size:44
Alignment explanation
Indices: 63375658--63375767 Score: 211
Period size: 44 Copynumber: 2.5 Consensus size: 44
63375648 ATTAAAACAC
63375658 CAAATTCCTTAGATGGATAAGGACAATTCGAAAGTAGACTAGGTA
1 CAAA-TCCTTAGATGGATAAGGACAATTCGAAAGTAGACTAGGTA
63375703 CAAATCCTTAGATGGATAAGGACAATTCGAAAGTAGACTAGGTA
1 CAAATCCTTAGATGGATAAGGACAATTCGAAAGTAGACTAGGTA
63375747 CAAATCCTTAGATGGATAAGG
1 CAAATCCTTAGATGGATAAGG
63375768 TTAGCTTATT
Statistics
Matches: 65, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
44 61 0.94
45 4 0.06
ACGTcount: A:0.40, C:0.14, G:0.23, T:0.24
Consensus pattern (44 bp):
CAAATCCTTAGATGGATAAGGACAATTCGAAAGTAGACTAGGTA
Found at i:63375749 original size:22 final size:22
Alignment explanation
Indices: 63375680--63375749 Score: 63
Period size: 22 Copynumber: 3.2 Consensus size: 22
63375670 ATGGATAAGG
63375680 ACAATTCGAAAGTAGACTAGGT
1 ACAATTCGAAAGTAGACTAGGT
* *** *
63375702 ACAAATCCTTAGATGGA-TAAGG-
1 ACAATTCGAAAG-TAGACT-AGGT
63375724 ACAATTCGAAAGTAGACTAGGT
1 ACAATTCGAAAGTAGACTAGGT
63375746 ACAA
1 ACAA
63375750 ATCCTTAGAT
Statistics
Matches: 34, Mismatches: 10, Indels: 8
0.65 0.19 0.15
Matches are distributed among these distances:
21 6 0.18
22 22 0.65
23 6 0.18
ACGTcount: A:0.43, C:0.14, G:0.21, T:0.21
Consensus pattern (22 bp):
ACAATTCGAAAGTAGACTAGGT
Found at i:63375768 original size:23 final size:23
Alignment explanation
Indices: 63375698--63375768 Score: 67
Period size: 22 Copynumber: 3.2 Consensus size: 23
63375688 AAAGTAGACT
63375698 AGGTACAAATCCTTAGATGGATA
1 AGGTACAAATCCTTAGATGGATA
* *** *
63375721 AGG-ACAATTCGAAAG-TAGACT-
1 AGGTACAAATCCTTAGATGGA-TA
63375742 AGGTACAAATCCTTAGATGGATA
1 AGGTACAAATCCTTAGATGGATA
63375765 AGGT
1 AGGT
63375769 TAGCTTATTC
Statistics
Matches: 34, Mismatches: 10, Indels: 8
0.65 0.19 0.15
Matches are distributed among these distances:
21 6 0.18
22 18 0.53
23 10 0.29
ACGTcount: A:0.39, C:0.13, G:0.24, T:0.24
Consensus pattern (23 bp):
AGGTACAAATCCTTAGATGGATA
Found at i:63375814 original size:21 final size:22
Alignment explanation
Indices: 63375790--63375840 Score: 54
Period size: 21 Copynumber: 2.4 Consensus size: 22
63375780 TATATAGAAT
*
63375790 ATCCTTAGACT-GACTAAGATA
1 ATCCTTAGAATAGACTAAGATA
*
63375811 ATCC--AGGAATAGACTAGGATA
1 ATCCTTA-GAATAGACTAAGATA
63375832 ATCCTTAGA
1 ATCCTTAGA
63375841 TGGACTAGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 7
0.73 0.06 0.21
Matches are distributed among these distances:
19 1 0.04
20 3 0.12
21 17 0.71
22 2 0.08
23 1 0.04
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.25
Consensus pattern (22 bp):
ATCCTTAGAATAGACTAAGATA
Found at i:63377865 original size:9 final size:9
Alignment explanation
Indices: 63377851--63377878 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
63377841 GACCCCTGTT
63377851 TCCAAATGG
1 TCCAAATGG
63377860 TCCAAATGG
1 TCCAAATGG
63377869 TCCAAATGG
1 TCCAAATGG
63377878 T
1 T
63377879 ACTTAATCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.25
Consensus pattern (9 bp):
TCCAAATGG
Found at i:63380020 original size:50 final size:50
Alignment explanation
Indices: 63379891--63380240 Score: 358
Period size: 50 Copynumber: 6.8 Consensus size: 50
63379881 ATTTGGGTAA
* ** *
63379891 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATAATTGAGATTATC
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGC---ACCGAG---ATG
*
63379947 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * *
63379997 AGAGGTCCCATGTAAGACTATGTCTGGGACATGGCGTTGGCACCAAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * * *
63380047 AGAGGTCCCCCGTAAGACCATGTCTAGGACATGGCATTGGCACCTATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * * *
63380097 AGAACTCTCATGTAAGACCATATGTCTGGGACATGGCGTTGGCACCAAGATG
1 AGAGGTCCCATGTAAGACC--ATGTCTGGGACATGGCATTGGCACCGAGATG
** * * * *
63380149 AGAGGTCCCCCGTAAGACCATGTCTAGGACATGGCATGGGCACCTATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * * **
63380199 AGAACTCTCATGTAAGACCATATCTGGGGTATGGCATTGGCA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
63380241 GTACAAGAAA
Statistics
Matches: 249, Mismatches: 43, Indels: 10
0.82 0.14 0.03
Matches are distributed among these distances:
50 165 0.66
52 41 0.16
53 4 0.02
56 39 0.16
ACGTcount: A:0.27, C:0.22, G:0.28, T:0.23
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:63380163 original size:102 final size:102
Alignment explanation
Indices: 63379947--63380221 Score: 446
Period size: 102 Copynumber: 2.7 Consensus size: 102
63379937 TGAGATTATC
** * * * * ** *
63379947 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCATGTAA
1 AGAGGTCCCCCGTAAGACCATGTCTAGGACATGGCATTGGCACCTATATGAGAACTCTCATGTAA
63380012 GA-C-TATGTCTGGGACATGGCGTTGGCACCAAGATG
66 GACCATATGTCTGGGACATGGCGTTGGCACCAAGATG
63380047 AGAGGTCCCCCGTAAGACCATGTCTAGGACATGGCATTGGCACCTATATGAGAACTCTCATGTAA
1 AGAGGTCCCCCGTAAGACCATGTCTAGGACATGGCATTGGCACCTATATGAGAACTCTCATGTAA
63380112 GACCATATGTCTGGGACATGGCGTTGGCACCAAGATG
66 GACCATATGTCTGGGACATGGCGTTGGCACCAAGATG
*
63380149 AGAGGTCCCCCGTAAGACCATGTCTAGGACATGGCATGGGCACCTATATGAGAACTCTCATGTAA
1 AGAGGTCCCCCGTAAGACCATGTCTAGGACATGGCATTGGCACCTATATGAGAACTCTCATGTAA
63380214 GACCATAT
66 GACCATAT
63380222 CTGGGGTATG
Statistics
Matches: 163, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
100 58 0.36
101 1 0.01
102 104 0.64
ACGTcount: A:0.27, C:0.23, G:0.28, T:0.22
Consensus pattern (102 bp):
AGAGGTCCCCCGTAAGACCATGTCTAGGACATGGCATTGGCACCTATATGAGAACTCTCATGTAA
GACCATATGTCTGGGACATGGCGTTGGCACCAAGATG
Found at i:63380214 original size:152 final size:150
Alignment explanation
Indices: 63379955--63380289 Score: 395
Period size: 152 Copynumber: 2.2 Consensus size: 150
63379945 TCAGAGGTCC
* * *
63379955 CATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCATGTAAGACTATGT
1 CATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGATGAGAGGTCCCACGTAAGACCATGT
* * * ** * *
63380020 CTGGGACATGGCGTTGGCACCAAGATGAGAGGTCCCCCGTAAGACCATGTCTAGGACATGGCATT
66 CTAGGACATGGCATGGGCACCAAGATGAGAACTCCCACGTAAGACCATATCTAGGACATGGCATT
63380085 GGCACCTATATGAGAACTCT
131 GGCACCTATATGAGAACTCT
*
63380105 CATGTAAGACCATATGTCTGGGACATGGCGTTGGCACCAAGATGAGAGGTCCCCCGTAAGACCAT
1 CATGTAAGACC--ATGTCTGGGACATGGCGTTGGCACCAAGATGAGAGGTCCCACGTAAGACCAT
* * * * * **
63380170 GTCTAGGACATGGCATGGGCACCTATATGAGAACTCTCATGTAAGACCATATCTGGGGTATGGCA
64 GTCTAGGACATGGCATGGGCACCAAGATGAGAACTCCCACGTAAGACCATATCTAGGACATGGCA
* * * *
63380235 TTGGCA-GTACAAGA-AACATCC
129 TTGGCACCTATATGAGAAC-TCT
* * * *
63380256 CATGTAAGGCTATGTCTGGGACATAGCTTTGGCA
1 CATGTAAGACCATGTCTGGGACATGGCGTTGGCA
63380290 TGTTATATTC
Statistics
Matches: 156, Mismatches: 26, Indels: 7
0.83 0.14 0.04
Matches are distributed among these distances:
149 21 0.13
150 14 0.09
151 16 0.10
152 105 0.67
ACGTcount: A:0.27, C:0.22, G:0.28, T:0.23
Consensus pattern (150 bp):
CATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGATGAGAGGTCCCACGTAAGACCATGT
CTAGGACATGGCATGGGCACCAAGATGAGAACTCCCACGTAAGACCATATCTAGGACATGGCATT
GGCACCTATATGAGAACTCT
Found at i:63381770 original size:31 final size:31
Alignment explanation
Indices: 63381700--63381771 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 31
63381690 GGCATTAAAT
* * *
63381700 ATTCATATATGCATTTTCATACATTGTAATA
1 ATTCATATTTGCATATTCATACATTGCAATA
*
63381731 ATTCATATTTGCATATTCATAC-TCTGCAATC
1 ATTCATATTTGCATATTCATACAT-TGCAATA
*
63381762 ATTTATATTT
1 ATTCATATTT
63381772 ACCTGTCATA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
30 1 0.03
31 34 0.97
ACGTcount: A:0.32, C:0.15, G:0.06, T:0.47
Consensus pattern (31 bp):
ATTCATATTTGCATATTCATACATTGCAATA
Found at i:63387627 original size:35 final size:35
Alignment explanation
Indices: 63387568--63387637 Score: 106
Period size: 35 Copynumber: 2.0 Consensus size: 35
63387558 CGACATTCAG
* *
63387568 GCAAACAAGTCAAACTCAACAGAGAAATGCAACTT
1 GCAAACAAGTCAAACTAAAAAGAGAAATGCAACTT
63387603 GCAAACCAAGTC-AACTAAAAAGAGAAATGCAACTT
1 GCAAA-CAAGTCAAACTAAAAAGAGAAATGCAACTT
63387638 ATAAGAGATC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
35 26 0.81
36 6 0.19
ACGTcount: A:0.50, C:0.21, G:0.14, T:0.14
Consensus pattern (35 bp):
GCAAACAAGTCAAACTAAAAAGAGAAATGCAACTT
Found at i:63388436 original size:2 final size:2
Alignment explanation
Indices: 63388429--63388471 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
63388419 TTAATCATAC
63388429 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
63388471 A
1 A
63388472 GAGGTGTTTA
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:63393363 original size:4 final size:4
Alignment explanation
Indices: 63393354--63393382 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
63393344 ATATTCGTTA
63393354 AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
63393383 TGTACATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:63396807 original size:18 final size:18
Alignment explanation
Indices: 63396771--63396822 Score: 56
Period size: 16 Copynumber: 3.0 Consensus size: 18
63396761 TTATTATTTT
*
63396771 TAAAATTT-ACTATTAAAA
1 TAAAATTTAAATATT-AAA
63396789 TAAAATTTAAATATTAAA
1 TAAAATTTAAATATTAAA
*
63396807 T--AATTTAATTATTAAA
1 TAAAATTTAAATATTAAA
63396823 ATTTAAATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
16 14 0.45
18 12 0.39
19 5 0.16
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (18 bp):
TAAAATTTAAATATTAAA
Found at i:63396813 original size:16 final size:15
Alignment explanation
Indices: 63396792--63396845 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 15
63396782 ATTAAAATAA
63396792 AATTTAAATATTAAAT
1 AATTTAAATATT-AAT
*
63396808 AATTTAATTATTAA-
1 AATTTAAATATTAAT
63396822 AATTTAAATTATATTAAT
1 AATTT-AA--ATATTAAT
63396840 AATTTA
1 AATTTA
63396846 TTATATGACT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
14 5 0.16
15 4 0.12
16 11 0.34
17 7 0.22
18 5 0.16
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
AATTTAAATATTAAT
Found at i:63396825 original size:30 final size:31
Alignment explanation
Indices: 63396789--63396849 Score: 90
Period size: 30 Copynumber: 2.0 Consensus size: 31
63396779 ACTATTAAAA
63396789 TAAAATTTAAA-TAT-TAAATAATTTAATTAT
1 TAAAATTTAAATTATATAAATAATTT-ATTAT
*
63396819 TAAAATTTAAATTATATTAATAATTTATTAT
1 TAAAATTTAAATTATATAAATAATTTATTAT
63396850 ATGACTAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 11 0.39
31 8 0.29
32 9 0.32
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (31 bp):
TAAAATTTAAATTATATAAATAATTTATTAT
Found at i:63396850 original size:16 final size:16
Alignment explanation
Indices: 63396799--63396851 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
63396789 TAAAATTTAA
*
63396799 ATATTAAATAATTTAAT
1 ATATT-AATAATTTATT
63396816 -TATTAA-AATTTAAATT
1 ATATTAATAATTT--ATT
63396832 ATATTAATAATTTATT
1 ATATTAATAATTTATT
63396848 ATAT
1 ATAT
63396852 GACTAAATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 9
0.76 0.02 0.22
Matches are distributed among these distances:
14 5 0.16
15 2 0.06
16 13 0.42
17 6 0.19
18 5 0.16
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
ATATTAATAATTTATT
Found at i:63396915 original size:13 final size:13
Alignment explanation
Indices: 63396897--63396923 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
63396887 AATATTAAAA
63396897 ATATTAATATTTT
1 ATATTAATATTTT
63396910 ATATTAATATTTT
1 ATATTAATATTTT
63396923 A
1 A
63396924 AATATTTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
ATATTAATATTTT
Found at i:63403652 original size:37 final size:37
Alignment explanation
Indices: 63403599--63403702 Score: 110
Period size: 37 Copynumber: 2.8 Consensus size: 37
63403589 ATTCCAAAAA
*
63403599 TAATATTATTTTAATAGTTTAATATTAAATTAA-ATT
1 TAATATTATCTTAATAGTTTAATATTAAATTAATATT
*
63403635 TAATACTTATCTTAATAGTATT-ATATTAATTTAATATT
1 TAATA-TTATCTTAATAGT-TTAATATTAAATTAATATT
*
63403673 AAAGTAATTATCTTAATA--TTAA-ATTAAATT
1 TAA-T-ATTATCTTAATAGTTTAATATTAAATT
63403703 TAATGCTTAT
Statistics
Matches: 58, Mismatches: 4, Indels: 12
0.78 0.05 0.16
Matches are distributed among these distances:
36 14 0.24
37 24 0.41
38 7 0.12
39 12 0.21
40 1 0.02
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (37 bp):
TAATATTATCTTAATAGTTTAATATTAAATTAATATT
Found at i:63403682 original size:25 final size:24
Alignment explanation
Indices: 63403646--63403700 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 24
63403636 AATACTTATC
63403646 TTAATAGTATTATATTAAT-TTAATA
1 TTAA-AGTATTATATTAATATTAA-A
*
63403671 TTAAAGTAATTATCTTAATATTAAA
1 TTAAAGT-ATTATATTAATATTAAA
63403696 TTAAA
1 TTAAA
63403701 TTTAATGCTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
24 3 0.11
25 20 0.74
26 4 0.15
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (24 bp):
TTAAAGTATTATATTAATATTAAA
Found at i:63403793 original size:32 final size:33
Alignment explanation
Indices: 63403730--63403805 Score: 91
Period size: 32 Copynumber: 2.3 Consensus size: 33
63403720 ATAATTATTT
*
63403730 TATTATTTTAATAAGATTTAATATTAAATTAATA
1 TATTA-TTTAATAAGATTAAATATTAAATTAATA
* * *
63403764 TATTATTTATTAAGA-TAAATATTATATTAATT
1 TATTATTTAATAAGATTAAATATTAAATTAATA
*
63403796 TAATATTTAA
1 TATTATTTAA
63403806 GTGATTGAGT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
32 22 0.61
33 9 0.25
34 5 0.14
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (33 bp):
TATTATTTAATAAGATTAAATATTAAATTAATA
Found at i:63409253 original size:22 final size:23
Alignment explanation
Indices: 63409225--63409268 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
63409215 ATGTAATCTT
*
63409225 AGATATGATT-TGTAATCTTAGA
1 AGATATGATTCTGTAATATTAGA
63409247 AGATATGATTCTGTAATATTAG
1 AGATATGATTCTGTAATATTAG
63409269 TGATTTGATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.36, C:0.05, G:0.18, T:0.41
Consensus pattern (23 bp):
AGATATGATTCTGTAATATTAGA
Found at i:63409283 original size:22 final size:23
Alignment explanation
Indices: 63409225--63409283 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 23
63409215 ATGTAATCTT
*
63409225 AGATATGA-TTTGTAATCTTAGA
1 AGATATGATTTTGTAATATTAGA
*
63409247 AGATATGATTCTGTAATATTAG-
1 AGATATGATTTTGTAATATTAGA
* *
63409269 TGATTTGATTTTGTA
1 AGATATGATTTTGTA
63409284 GATAGCTTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
22 20 0.65
23 11 0.35
ACGTcount: A:0.32, C:0.03, G:0.19, T:0.46
Consensus pattern (23 bp):
AGATATGATTTTGTAATATTAGA
Found at i:63410067 original size:9 final size:9
Alignment explanation
Indices: 63410050--63410086 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
63410040 TGAGTTTTCA
63410050 AATTCGAAT
1 AATTCGAAT
*
63410059 AACTCGAAT
1 AATTCGAAT
63410068 AATTCGAAT
1 AATTCGAAT
63410077 AATTCGAAT
1 AATTCGAAT
63410086 A
1 A
63410087 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:63411199 original size:6 final size:6
Alignment explanation
Indices: 63411188--63411217 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
63411178 GGCTTCCATC
63411188 TCACCT TCACCT TCACCT TCACCT TCACCT
1 TCACCT TCACCT TCACCT TCACCT TCACCT
63411218 AATTTCCACC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.50, G:0.00, T:0.33
Consensus pattern (6 bp):
TCACCT
Found at i:63415571 original size:33 final size:33
Alignment explanation
Indices: 63415524--63415685 Score: 113
Period size: 33 Copynumber: 4.8 Consensus size: 33
63415514 GTTAACCGTT
*
63415524 ATCGGTGGATTCAGCACTTAGCAACCACCAATGA
1 ATCGG-GGAATCAGCACTTAGCAACCACCAATGA
**
63415558 ATCGGGGAATCAGCACACAGCAACC-CC-----
1 ATCGGGGAATCAGCACTTAGCAACCACCAATGA
* *
63415585 -TCGGGGGAATCAGCACTTAGCAACCCCCTCTCACATTTAAA
1 ATC-GGGGAATCAGCACTTAGCAA---CCAC-CA-A--T-GA
63415626 ATACGGTGGAATCAGCACTTAGCAACCACCAATGA
1 AT-CGG-GGAATCAGCACTTAGCAACCACCAATGA
*
63415661 ATAGGGGAATCAGCACTTAGCAACC
1 ATCGGGGAATCAGCACTTAGCAACC
63415686 CCTCGGGGGA
Statistics
Matches: 102, Mismatches: 8, Indels: 37
0.69 0.05 0.25
Matches are distributed among these distances:
26 2 0.02
27 18 0.18
30 2 0.02
31 1 0.01
32 3 0.03
33 37 0.36
34 7 0.07
35 3 0.03
36 1 0.01
38 1 0.01
39 2 0.02
40 3 0.03
42 3 0.03
43 19 0.19
ACGTcount: A:0.33, C:0.29, G:0.20, T:0.17
Consensus pattern (33 bp):
ATCGGGGAATCAGCACTTAGCAACCACCAATGA
Found at i:63415705 original size:103 final size:103
Alignment explanation
Indices: 63415526--63415755 Score: 424
Period size: 103 Copynumber: 2.2 Consensus size: 103
63415516 TAACCGTTAT
* *
63415526 CGGTGGATTCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCTCGGGG
1 CGGTGGAATCAGCACTTAGCAACCACCAATGAATAGGGGAATCAGCACACAGCAACCCCTCGGGG
63415591 GAATCAGCACTTAGCAACCCCCTCTCACATTTAAAATA
66 GAATCAGCACTTAGCAACCCCCTCTCACATTTAAAATA
**
63415629 CGGTGGAATCAGCACTTAGCAACCACCAATGAATAGGGGAATCAGCACTTAGCAACCCCTCGGGG
1 CGGTGGAATCAGCACTTAGCAACCACCAATGAATAGGGGAATCAGCACACAGCAACCCCTCGGGG
63415694 GAATCAGCACTTAGCAACCCCCTCTCACATTTAAAATA
66 GAATCAGCACTTAGCAACCCCCTCTCACATTTAAAATA
63415732 CGGTGGAATCAGCACTTAGCAACC
1 CGGTGGAATCAGCACTTAGCAACC
63415756 CCCTTTCACA
Statistics
Matches: 123, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 123 1.00
ACGTcount: A:0.32, C:0.30, G:0.20, T:0.18
Consensus pattern (103 bp):
CGGTGGAATCAGCACTTAGCAACCACCAATGAATAGGGGAATCAGCACACAGCAACCCCTCGGGG
GAATCAGCACTTAGCAACCCCCTCTCACATTTAAAATA
Found at i:63415754 original size:43 final size:43
Alignment explanation
Indices: 63415693--63415798 Score: 194
Period size: 43 Copynumber: 2.5 Consensus size: 43
63415683 ACCCCTCGGG
63415693 GGAATCAGCACTTAGCAACCCCCTCTCACATTTAAAATACGGT
1 GGAATCAGCACTTAGCAACCCCCTCTCACATTTAAAATACGGT
*
63415736 GGAATCAGCACTTAGCAACCCCCTTTCACATTTAAAATACGGT
1 GGAATCAGCACTTAGCAACCCCCTCTCACATTTAAAATACGGT
*
63415779 GGGATCAGCACTTAGCAACC
1 GGAATCAGCACTTAGCAACC
63415799 ACCAATGAAT
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
43 61 1.00
ACGTcount: A:0.32, C:0.29, G:0.16, T:0.23
Consensus pattern (43 bp):
GGAATCAGCACTTAGCAACCCCCTCTCACATTTAAAATACGGT
Found at i:63423173 original size:33 final size:33
Alignment explanation
Indices: 63423136--63423285 Score: 107
Period size: 33 Copynumber: 4.4 Consensus size: 33
63423126 CGGTGGATTT
63423136 AGCACTTAGCAACCACCAATGAATCGGGGAATC
1 AGCACTTAGCAACCACCAATGAATCGGGGAATC
**
63423169 AGCACACAGCAACC-CC------TCGGGGGAATC
1 AGCACTTAGCAACCACCAATGAATC-GGGGAATC
* *
63423196 AGCACTTAGCAACCCCCTCTCACATTTAAAATACGGTGGAATC
1 AGCACTTAGCAA---CCAC-CA-A--T-GAAT-CGG-GGAATC
*
63423239 AGCACTTAGCAACCACCAATGAATAGGGGAATC
1 AGCACTTAGCAACCACCAATGAATCGGGGAATC
63423272 AGCACTTAGCAACC
1 AGCACTTAGCAACC
63423286 CCTCGGGGGA
Statistics
Matches: 92, Mismatches: 7, Indels: 36
0.68 0.05 0.27
Matches are distributed among these distances:
26 2 0.02
27 18 0.20
30 2 0.02
31 1 0.01
32 3 0.03
33 32 0.35
34 2 0.02
35 3 0.03
36 1 0.01
38 1 0.01
39 2 0.02
40 3 0.03
42 3 0.03
43 19 0.21
ACGTcount: A:0.35, C:0.30, G:0.19, T:0.16
Consensus pattern (33 bp):
AGCACTTAGCAACCACCAATGAATCGGGGAATC
Found at i:63423298 original size:27 final size:28
Alignment explanation
Indices: 63423264--63423317 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 28
63423254 CCAATGAATA
63423264 GGGGAATCAGCACTTAGCAA-CCCCTCG
1 GGGGAATCAGCACTTAGCAATCCCCTCG
63423291 GGGGAATCAGCACTTAGCAATCCCCTC
1 GGGGAATCAGCACTTAGCAATCCCCTC
63423318 TCACATTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
27 20 0.77
28 6 0.23
ACGTcount: A:0.26, C:0.33, G:0.24, T:0.17
Consensus pattern (28 bp):
GGGGAATCAGCACTTAGCAATCCCCTCG
Found at i:63423420 original size:28 final size:27
Alignment explanation
Indices: 63423367--63423418 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
63423357 CCAATAATTA
*
63423367 GGGGAAATCATCACTTAGCAACCCCTC
1 GGGGAAATCAGCACTTAGCAACCCCTC
*
63423394 GGGGGAATCAGCACTTAGCAACCCC
1 GGGGAAATCAGCACTTAGCAACCCC
63423419 CTTTCACATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.29, C:0.33, G:0.23, T:0.15
Consensus pattern (27 bp):
GGGGAAATCAGCACTTAGCAACCCCTC
Found at i:63423432 original size:104 final size:103
Alignment explanation
Indices: 63423126--63423433 Score: 519
Period size: 103 Copynumber: 3.0 Consensus size: 103
63423116 TAACCGTTAT
* * * **
63423126 CGGTGGATTTAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCTCGGGG
1 CGGTGGAATCAGCACTTAGCAACCACCAATGAATAGGGGAATCAGCACTTAGCAACCCCTCGGGG
63423191 GAATCAGCACTTAGCAACCCCCTCTCACATTTAAAATA
66 GAATCAGCACTTAGCAACCCCCTCTCACATTTAAAATA
63423229 CGGTGGAATCAGCACTTAGCAACCACCAATGAATAGGGGAATCAGCACTTAGCAACCCCTCGGGG
1 CGGTGGAATCAGCACTTAGCAACCACCAATGAATAGGGGAATCAGCACTTAGCAACCCCTCGGGG
*
63423294 GAATCAGCACTTAGCAATCCCCTCTCACATTTAAAATA
66 GAATCAGCACTTAGCAACCCCCTCTCACATTTAAAATA
*
63423332 CGGTGGAATCAGCACTTAGCAACCACCAAT-AATTAGGGGAAATCATCACTTAGCAACCCCTCGG
1 CGGTGGAATCAGCACTTAGCAACCACCAATGAA-TAGGGG-AATCAGCACTTAGCAACCCCTCGG
*
63423396 GGGAATCAGCACTTAGCAACCCCCTTTCACATTTAAAA
64 GGGAATCAGCACTTAGCAACCCCCTCTCACATTTAAAA
63423434 CTCGTCCACC
Statistics
Matches: 194, Mismatches: 9, Indels: 3
0.94 0.04 0.01
Matches are distributed among these distances:
102 2 0.01
103 133 0.69
104 59 0.30
ACGTcount: A:0.33, C:0.29, G:0.19, T:0.19
Consensus pattern (103 bp):
CGGTGGAATCAGCACTTAGCAACCACCAATGAATAGGGGAATCAGCACTTAGCAACCCCTCGGGG
GAATCAGCACTTAGCAACCCCCTCTCACATTTAAAATA
Found at i:63441081 original size:14 final size:14
Alignment explanation
Indices: 63441062--63441094 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
63441052 GTAAAGACAT
63441062 TTAGAAATCAGTTC
1 TTAGAAATCAGTTC
63441076 TTAGAAATCAGTTC
1 TTAGAAATCAGTTC
63441090 TTAGA
1 TTAGA
63441095 TACCACTGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.36
Consensus pattern (14 bp):
TTAGAAATCAGTTC
Found at i:63441769 original size:18 final size:20
Alignment explanation
Indices: 63441746--63441787 Score: 61
Period size: 18 Copynumber: 2.2 Consensus size: 20
63441736 CTTGGCCCAT
63441746 TATAGTAACA-ATAAT-CAG
1 TATAGTAACAGATAATACAG
*
63441764 TATAGTAACAGATTATACAG
1 TATAGTAACAGATAATACAG
63441784 TATA
1 TATA
63441788 CAGGTCCTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 10 0.48
19 4 0.19
20 7 0.33
ACGTcount: A:0.48, C:0.10, G:0.12, T:0.31
Consensus pattern (20 bp):
TATAGTAACAGATAATACAG
Found at i:63442245 original size:18 final size:17
Alignment explanation
Indices: 63442219--63442252 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
63442209 CATGTTGCAT
63442219 GCTCATGTGGGCCCACAA
1 GCTCATGT-GGCCCACAA
*
63442237 GCTCGTGTGGCCCACA
1 GCTCATGTGGCCCACA
63442253 TGGCCCAAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.18, C:0.35, G:0.29, T:0.18
Consensus pattern (17 bp):
GCTCATGTGGCCCACAA
Found at i:63447635 original size:30 final size:29
Alignment explanation
Indices: 63447601--63447665 Score: 103
Period size: 29 Copynumber: 2.2 Consensus size: 29
63447591 GGCCTAACGG
63447601 CCCAAATCCACTACCCAGAAACAACTTTAA
1 CCCAAATCCACTACCC-GAAACAACTTTAA
* *
63447631 CCCAAATCCACTACCCTAAACAGCTTTAA
1 CCCAAATCCACTACCCGAAACAACTTTAA
63447660 CCCAAA
1 CCCAAA
63447666 CACAACTACC
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
29 17 0.52
30 16 0.48
ACGTcount: A:0.42, C:0.38, G:0.03, T:0.17
Consensus pattern (29 bp):
CCCAAATCCACTACCCGAAACAACTTTAA
Found at i:63447674 original size:30 final size:29
Alignment explanation
Indices: 63447601--63447681 Score: 110
Period size: 30 Copynumber: 2.7 Consensus size: 29
63447591 GGCCTAACGG
*
63447601 CCCAAATCCACTACCCAGAAACAACTTTAA
1 CCCAAATCCACTACCC-TAAACAACTTTAA
*
63447631 CCCAAATCCACTACCCTAAACAGCTTTAA
1 CCCAAATCCACTACCCTAAACAACTTTAA
63447660 CCCAAA-CACAACTACCCTAAAC
1 CCCAAATC-C-ACTACCCTAAAC
63447682 CCAAATCCAA
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
28 1 0.02
29 18 0.38
30 28 0.60
ACGTcount: A:0.42, C:0.40, G:0.02, T:0.16
Consensus pattern (29 bp):
CCCAAATCCACTACCCTAAACAACTTTAA
Found at i:63455246 original size:25 final size:26
Alignment explanation
Indices: 63455215--63455282 Score: 79
Period size: 25 Copynumber: 2.7 Consensus size: 26
63455205 TCTTAAAGTA
63455215 TCCCGATATATGGCTCTTTG-GAGCT
1 TCCCGATATATGGCTCTTTGTGAGCT
*
63455240 TCCCGAT-TAAAGGCTCTTTGTGAGCT
1 TCCCGATAT-ATGGCTCTTTGTGAGCT
*
63455266 TCCTGACTA-ATGGCTCT
1 TCCCGA-TATATGGCTCT
63455283 CCCGATTAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
24 1 0.03
25 17 0.47
26 17 0.47
27 1 0.03
ACGTcount: A:0.18, C:0.25, G:0.22, T:0.35
Consensus pattern (26 bp):
TCCCGATATATGGCTCTTTGTGAGCT
Found at i:63455280 original size:26 final size:25
Alignment explanation
Indices: 63455215--63455282 Score: 84
Period size: 26 Copynumber: 2.7 Consensus size: 25
63455205 TCTTAAAGTA
63455215 TCCCGA-TATATGGCTCTTTGGAGCT
1 TCCCGACTA-ATGGCTCTTTGGAGCT
* *
63455240 TCCCGATTAAAGGCTCTTTGTGAGCT
1 TCCCGACTAATGGCTCTTTG-GAGCT
*
63455266 TCCTGACTAATGGCTCT
1 TCCCGACTAATGGCTCT
63455283 CCCGATTAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
25 16 0.43
26 21 0.57
ACGTcount: A:0.18, C:0.25, G:0.22, T:0.35
Consensus pattern (25 bp):
TCCCGACTAATGGCTCTTTGGAGCT
Found at i:63458944 original size:27 final size:27
Alignment explanation
Indices: 63458906--63458959 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
63458896 TCAAAGAAGT
63458906 TGAATTTTCTATAGATCTTGTTCTGGG
1 TGAATTTTCTATAGATCTTGTTCTGGG
63458933 TGAATTTTCTATAGATCTTGTTCTGGG
1 TGAATTTTCTATAGATCTTGTTCTGGG
63458960 AACAACACCG
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:0.19, C:0.11, G:0.22, T:0.48
Consensus pattern (27 bp):
TGAATTTTCTATAGATCTTGTTCTGGG
Found at i:63463062 original size:25 final size:25
Alignment explanation
Indices: 63463034--63463105 Score: 90
Period size: 26 Copynumber: 2.8 Consensus size: 25
63463024 CCCGATATAT
63463034 GGCTCTTCGGAGCTTCCCGATTAAA
1 GGCTCTTCGGAGCTTCCCGATTAAA
* ** *
63463059 GGCTCTTTGTGAGCTTCCTAACTAAA
1 GGCTCTTCG-GAGCTTCCCGATTAAA
*
63463085 GGCTCTCCGGAGCTTCCCGAT
1 GGCTCTTCGGAGCTTCCCGAT
63463106 ATGGCTTGCT
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
25 17 0.46
26 20 0.54
ACGTcount: A:0.18, C:0.29, G:0.24, T:0.29
Consensus pattern (25 bp):
GGCTCTTCGGAGCTTCCCGATTAAA
Found at i:63464131 original size:13 final size:13
Alignment explanation
Indices: 63464113--63464145 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
63464103 GCCGTGTAAG
63464113 CCACACGGCTTGA
1 CCACACGGCTTGA
63464126 CCACACGGCTTGA
1 CCACACGGCTTGA
63464139 CCACACG
1 CCACACG
63464146 AGCGTGTGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.24, C:0.42, G:0.21, T:0.12
Consensus pattern (13 bp):
CCACACGGCTTGA
Found at i:63488313 original size:33 final size:33
Alignment explanation
Indices: 63488271--63488337 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
63488261 ATTTGAGAAG
63488271 TAAGTGTGTGGTATACCGACCCTCCGGTGCCGA
1 TAAGTGTGTGGTATACCGACCCTCCGGTGCCGA
63488304 TAAGTGTGTGGTATACCGACCCTCCGGTGCCGA
1 TAAGTGTGTGGTATACCGACCCTCCGGTGCCGA
63488337 T
1 T
63488338 CCTATAAGTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.18, C:0.27, G:0.30, T:0.25
Consensus pattern (33 bp):
TAAGTGTGTGGTATACCGACCCTCCGGTGCCGA
Found at i:63493893 original size:29 final size:29
Alignment explanation
Indices: 63493845--63493912 Score: 100
Period size: 29 Copynumber: 2.3 Consensus size: 29
63493835 CCAAAATTGG
63493845 GGCCTGTGTGCGACAAACTGCCATGTGATA
1 GGCC-GTGTGCGACAAACTGCCATGTGATA
* *
63493875 GGCCGTGTGCGACACACTGGCATGTGATA
1 GGCCGTGTGCGACAAACTGCCATGTGATA
*
63493904 GGCCATGTG
1 GGCCGTGTG
63493913 TGAGGCCGTG
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
29 31 0.89
30 4 0.11
ACGTcount: A:0.21, C:0.24, G:0.34, T:0.22
Consensus pattern (29 bp):
GGCCGTGTGCGACAAACTGCCATGTGATA
Found at i:63507083 original size:4 final size:4
Alignment explanation
Indices: 63507074--63507100 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
63507064 TATACGAAGC
63507074 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
63507101 TGAAAATTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:63510348 original size:18 final size:18
Alignment explanation
Indices: 63510322--63510357 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
63510312 CAACCCTACG
63510322 AGGTCTATCTACAGTTTT
1 AGGTCTATCTACAGTTTT
*
63510340 AGGTTTATCTACAGTTTT
1 AGGTCTATCTACAGTTTT
63510358 TATTCAAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.22, C:0.14, G:0.17, T:0.47
Consensus pattern (18 bp):
AGGTCTATCTACAGTTTT
Found at i:63512343 original size:43 final size:44
Alignment explanation
Indices: 63512291--63512407 Score: 114
Period size: 44 Copynumber: 2.7 Consensus size: 44
63512281 CGTACAATGC
* * ** *
63512291 CAACATCCCAAACGTGGTCTTACATGT-AATCACATATCGATG-
1 CAACGTCCCAGACGTGGTCTTACACATAAATCACAAATCGATGT
* *
63512333 CCACTGTCCCAGACAG-GGTCTTACACATAAATCATAAATCGATGT
1 CAAC-GTCCCAGAC-GTGGTCTTACACATAAATCACAAATCGATGT
*
63512378 CAACGTCCCAGATGTGGTCTTACACGATAA
1 CAACGTCCCAGACGTGGTCTTACAC-ATAA
63512408 CACACAACAG
Statistics
Matches: 60, Mismatches: 9, Indels: 9
0.77 0.12 0.12
Matches are distributed among these distances:
42 3 0.05
43 18 0.30
44 32 0.53
45 7 0.12
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.25
Consensus pattern (44 bp):
CAACGTCCCAGACGTGGTCTTACACATAAATCACAAATCGATGT
Found at i:63512866 original size:15 final size:14
Alignment explanation
Indices: 63512829--63512872 Score: 54
Period size: 15 Copynumber: 3.1 Consensus size: 14
63512819 TTTTATTATA
63512829 ATAACTTTATAATAT
1 ATAACTTTATAAT-T
*
63512844 ATAA-TTTATTATT
1 ATAACTTTATAATT
63512857 ATAACCTTTATAATT
1 ATAA-CTTTATAATT
63512872 A
1 A
63512873 ATATAAAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
13 5 0.20
14 7 0.28
15 13 0.52
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (14 bp):
ATAACTTTATAATT
Found at i:63516875 original size:22 final size:23
Alignment explanation
Indices: 63516844--63516918 Score: 82
Period size: 24 Copynumber: 3.2 Consensus size: 23
63516834 CGGCCCGAAT
*
63516844 TATATATTAAATATATATATTTT
1 TATATATTAAATATATATATTTA
* *
63516867 TAT-TTTTAATCAAATATATATATTA
1 TATATATTAA--ATATATATAT-TTA
63516892 TATATATTAAATATATATATTTA
1 TATATATTAAATATATATATTTA
63516915 -ATAT
1 TATAT
63516919 GGGACGGGTC
Statistics
Matches: 43, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
22 9 0.21
23 6 0.14
24 18 0.42
25 5 0.12
26 5 0.12
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.53
Consensus pattern (23 bp):
TATATATTAAATATATATATTTA
Found at i:63516901 original size:26 final size:26
Alignment explanation
Indices: 63516852--63516914 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 26
63516842 ATTATATATT
* *
63516852 AAATATATATATTTTTATTTTTAATC
1 AAATATATATATTTATATTATTAATC
*
63516878 AAATATATATA-TTATA-TA-T-ATT
1 AAATATATATATTTATATTATTAATC
63516900 AAATATATATATTTA
1 AAATATATATATTTA
63516915 ATATGGGACG
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
22 13 0.39
23 4 0.12
24 1 0.03
25 4 0.12
26 11 0.33
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (26 bp):
AAATATATATATTTATATTATTAATC
Found at i:63521141 original size:17 final size:19
Alignment explanation
Indices: 63521119--63521155 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
63521109 TTTTACTGAT
63521119 AAAAAAAT-A-TATAGTTG
1 AAAAAAATCATTATAGTTG
63521136 AAAAAAATCATTATAGTTG
1 AAAAAAATCATTATAGTTG
63521155 A
1 A
63521156 TCATTTCCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 8 0.44
18 1 0.06
19 9 0.50
ACGTcount: A:0.57, C:0.03, G:0.11, T:0.30
Consensus pattern (19 bp):
AAAAAAATCATTATAGTTG
Found at i:63529418 original size:18 final size:19
Alignment explanation
Indices: 63529395--63529431 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
63529385 CAAAAAAAAA
63529395 TATAAAT-TTTGGAATTTT
1 TATAAATATTTGGAATTTT
*
63529413 TATAAATATTTTGAATTTT
1 TATAAATATTTGGAATTTT
63529432 AATTTTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.57
Consensus pattern (19 bp):
TATAAATATTTGGAATTTT
Found at i:63531071 original size:16 final size:16
Alignment explanation
Indices: 63531029--63531063 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
63531019 ATGCATATAC
* *
63531029 AATGCAATCATTCTTT
1 AATGCATTCAATCTTT
63531045 AATGCATTCAATCTTT
1 AATGCATTCAATCTTT
63531061 AAT
1 AAT
63531064 TCTTTCAACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.34, C:0.17, G:0.06, T:0.43
Consensus pattern (16 bp):
AATGCATTCAATCTTT
Found at i:63539636 original size:23 final size:22
Alignment explanation
Indices: 63539593--63539636 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
63539583 TTCTAAGTCG
63539593 ATATTCAATTCAATTCCACACCT
1 ATATTCAATTCAATT-CACACCT
63539616 ATATTCATGATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
63539637 TTAGTCAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.36, C:0.25, G:0.02, T:0.36
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACCT
Found at i:63539745 original size:45 final size:45
Alignment explanation
Indices: 63539681--63539774 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 45
63539671 AACAGATACT
* *
63539681 CGGTGGATTCAGCACATAGCAACCACCTTAT-TAATCAATGATGTC
1 CGGTGGAATCAACACATAGCAACCACCTT-TCTAATCAATGATGTC
* *
63539726 CGGTGGAATCAACATATAGCAACCACCTTTCTAATCAATGATGTT
1 CGGTGGAATCAACACATAGCAACCACCTTTCTAATCAATGATGTC
63539771 CGGT
1 CGGT
63539775 TCACATAGTA
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
44 1 0.02
45 43 0.98
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (45 bp):
CGGTGGAATCAACACATAGCAACCACCTTTCTAATCAATGATGTC
Found at i:63539842 original size:51 final size:51
Alignment explanation
Indices: 63539771--63539957 Score: 198
Period size: 51 Copynumber: 3.7 Consensus size: 51
63539761 CAATGATGTT
* * *
63539771 CGGTTCACATAGTAGCCTGCACATAGTATTACACATGTGACCAATACCATC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACCAATACCATC
* * * * * * *
63539822 CGATACACGTGGTAGCCTGCATATAGTACTACACACGTGATCAAAACTATC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACCAATACCATC
* * * ** *
63539873 CGGTACGCATAGTAACCTGCACATAGTACTACACATGCAACC--TATCATTC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACCAATACCA-TC
*
63539923 CGGTACACGTAGTAGCTTGCACATAGTACTACACA
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACA
63539958 CGTAACCATC
Statistics
Matches: 108, Mismatches: 27, Indels: 3
0.78 0.20 0.02
Matches are distributed among these distances:
49 2 0.02
50 33 0.31
51 73 0.68
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.24
Consensus pattern (51 bp):
CGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACCAATACCATC
Found at i:63539986 original size:101 final size:99
Alignment explanation
Indices: 63539777--63539965 Score: 236
Period size: 101 Copynumber: 1.9 Consensus size: 99
63539767 TGTTCGGTTC
* * ** *
63539777 ACATAGTAGCCTGCACATAGTATTACACATGTGACCAATACCATCCGATACACGTGGTAGCCTGC
1 ACATAGTAACCTGCACATAGTACTACACATGCAACC-ATACCATCCGATACACGTAGTAGCCTGC
* * *
63539842 ATATAGTACTACACACGTGATCAAAACTATCCGGT
65 ACATAGTACTACACACGTAACCAAAACTATCCGGT
* * *
63539877 ACGCATAGTAACCTGCACATAGTACTACACATGCAACC-TATCATTCCGGTACACGTAGTAGCTT
1 A--CATAGTAACCTGCACATAGTACTACACATGCAACCATACCA-TCCGATACACGTAGTAGCCT
63539941 GCACATAGTACTACACACGTAACCA
63 GCACATAGTACTACACACGTAACCA
63539966 TCACTTTCAC
Statistics
Matches: 75, Mismatches: 11, Indels: 5
0.82 0.12 0.05
Matches are distributed among these distances:
100 5 0.07
101 39 0.52
102 31 0.41
ACGTcount: A:0.33, C:0.28, G:0.16, T:0.23
Consensus pattern (99 bp):
ACATAGTAACCTGCACATAGTACTACACATGCAACCATACCATCCGATACACGTAGTAGCCTGCA
CATAGTACTACACACGTAACCAAAACTATCCGGT
Found at i:63543617 original size:138 final size:138
Alignment explanation
Indices: 63543454--63543734 Score: 465
Period size: 138 Copynumber: 2.0 Consensus size: 138
63543444 TAGATATAAT
*
63543454 TAATTAATATATGAATTTGATTCATACAAAATACTAATTGTATATATTTTACCGAATTTATTAAT
1 TAATTAATATATGAATTTGATTCATACAAAATACTAATTGTATATATTTTACCAAATTTATTAAT
* *
63543519 AAAAATAATTATATTAATTAATTTCAGTCAAAATATAAAAGACATGGAAATTAATATTCTTTTGG
66 AAAAACAATTATATTAATTAATTTCAGTCAAAATATAAAAGACATGAAAATTAATATTCTTTTGG
*
63543584 AAGGAATA
131 AAAGAATA
* *
63543592 TAATTAATATATGAACTTT-ATTCATACAAAATATTAATTGTATATATTTTCCCAAATTTATTAA
1 TAATTAATATATGAA-TTTGATTCATACAAAATACTAATTGTATATATTTTACCAAATTTATTAA
* *
63543656 TATAAACAATTATATTAATTAATTTCGGTCAAAATATAAAAGACATGAAAATTAATATTCTTTTG
65 TAAAAACAATTATATTAATTAATTTCAGTCAAAATATAAAAGACATGAAAATTAATATTCTTTTG
*
63543721 GAAAGAATG
130 GAAAGAATA
63543730 TAATT
1 TAATT
63543735 CATTTTTCTA
Statistics
Matches: 133, Mismatches: 9, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
138 130 0.98
139 3 0.02
ACGTcount: A:0.45, C:0.07, G:0.08, T:0.40
Consensus pattern (138 bp):
TAATTAATATATGAATTTGATTCATACAAAATACTAATTGTATATATTTTACCAAATTTATTAAT
AAAAACAATTATATTAATTAATTTCAGTCAAAATATAAAAGACATGAAAATTAATATTCTTTTGG
AAAGAATA
Found at i:63545805 original size:3 final size:3
Alignment explanation
Indices: 63545797--63545839 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
63545787 ATTTATAGTT
63545797 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
63545840 CAACAACAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:63556729 original size:23 final size:23
Alignment explanation
Indices: 63556703--63556778 Score: 134
Period size: 23 Copynumber: 3.3 Consensus size: 23
63556693 ATAAGTGCCA
63556703 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
63556726 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
63556749 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
63556772 TACTGAT
1 CACTGAT
63556779 CAATAACACT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 50 1.00
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.22
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:63562107 original size:25 final size:26
Alignment explanation
Indices: 63562079--63562130 Score: 63
Period size: 24 Copynumber: 2.0 Consensus size: 26
63562069 TTTAAATATC
63562079 TAAAATTCTAAAATTTT-TA-ATAAAA
1 TAAAATT-TAAAATTTTATATATAAAA
* *
63562104 TAAACTTTCAAATTTTATATATAAAA
1 TAAAATTTAAAATTTTATATATAAAA
63562130 T
1 T
63562131 TTTACAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 8 0.35
25 8 0.35
26 7 0.30
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (26 bp):
TAAAATTTAAAATTTTATATATAAAA
Found at i:63566740 original size:17 final size:17
Alignment explanation
Indices: 63566714--63566750 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
63566704 GGTGTAACAT
63566714 ACGCCCGTATGACCCAC
1 ACGCCCGTATGACCCAC
* *
63566731 ACGCCTGTATGGCCCAC
1 ACGCCCGTATGACCCAC
63566748 ACG
1 ACG
63566751 AGCCAAATAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.22, C:0.43, G:0.22, T:0.14
Consensus pattern (17 bp):
ACGCCCGTATGACCCAC
Found at i:63567594 original size:22 final size:22
Alignment explanation
Indices: 63567566--63567608 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
63567556 TGTACAAGCC
63567566 ACCACATAATTGCT-GATAAACA
1 ACCACATAATTG-TAGATAAACA
63567588 ACCACATAATTGTAGATAAAC
1 ACCACATAATTGTAGATAAAC
63567609 TGCTATATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 1 0.05
22 19 0.95
ACGTcount: A:0.47, C:0.21, G:0.09, T:0.23
Consensus pattern (22 bp):
ACCACATAATTGTAGATAAACA
Found at i:63567885 original size:18 final size:19
Alignment explanation
Indices: 63567855--63567891 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
63567845 TTTGCACAAA
*
63567855 CATCACAATCACATAATAT
1 CATCACAATCACACAATAT
63567874 CATCAC-ATCACACAATAT
1 CATCACAATCACACAATAT
63567892 ACTTTTCGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.46, C:0.30, G:0.00, T:0.24
Consensus pattern (19 bp):
CATCACAATCACACAATAT
Found at i:63572879 original size:16 final size:16
Alignment explanation
Indices: 63572860--63572894 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
63572850 TTAAATAGGA
63572860 TTGTAATGGAATAAAG
1 TTGTAATGGAATAAAG
* *
63572876 TTGTAGTGGAATAGAG
1 TTGTAATGGAATAAAG
63572892 TTG
1 TTG
63572895 CAATCAGTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.34, C:0.00, G:0.31, T:0.34
Consensus pattern (16 bp):
TTGTAATGGAATAAAG
Found at i:63573030 original size:61 final size:61
Alignment explanation
Indices: 63572935--63573050 Score: 189
Period size: 61 Copynumber: 1.9 Consensus size: 61
63572925 TTGTTATTAA
63572935 ATTTTAATAAGATTACTATTAAATATAATTTAATAAAAATAAAAATAAATAATTTTATCAT
1 ATTTTAATAAGATTACTATTAAATATAATTTAATAAAAATAAAAATAAATAATTTTATCAT
* * *
63572996 ATTTTAATATA-ATTATTATTAAATATAATTTAATAAAAATAATAATATATAATTT
1 ATTTTAATA-AGATTACTATTAAATATAATTTAATAAAAATAAAAATAAATAATTT
63573051 AATAACACCC
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
61 50 0.98
62 1 0.02
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.44
Consensus pattern (61 bp):
ATTTTAATAAGATTACTATTAAATATAATTTAATAAAAATAAAAATAAATAATTTTATCAT
Found at i:63573116 original size:24 final size:24
Alignment explanation
Indices: 63573071--63573157 Score: 70
Period size: 24 Copynumber: 3.6 Consensus size: 24
63573061 TTAATATATA
* * *
63573071 TTTTAATATAATTTAAAATAAAATG
1 TTTTAA-ATATTTTATATTAAAATG
63573096 TTTTAAATATTTTATATT-AAAT-
1 TTTTAAATATTTTATATTAAAATG
* * *
63573118 TTATTTAATACTTTATATTAAATTG
1 TT-TTAAATATTTTATATTAAAATG
* *
63573143 TTTCAAATATATTAT
1 TTTTAAATATTTTAT
63573158 TTTTATATTT
Statistics
Matches: 49, Mismatches: 10, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
22 2 0.04
23 18 0.37
24 21 0.43
25 8 0.16
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (24 bp):
TTTTAAATATTTTATATTAAAATG
Found at i:63573117 original size:23 final size:23
Alignment explanation
Indices: 63573091--63573157 Score: 73
Period size: 23 Copynumber: 2.9 Consensus size: 23
63573081 ATTTAAAATA
63573091 AAATGTTTTAAATATTTTATATT
1 AAATGTTTTAAATATTTTATATT
* *
63573114 AAAT-TTATTTAATACTTTATATT
1 AAATGTT-TTAAATATTTTATATT
* *
63573137 AAATTGTTTCAAATATATTAT
1 AAA-TGTTTTAAATATTTTAT
63573158 TTTTATATTT
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
22 2 0.06
23 21 0.60
24 10 0.29
25 2 0.06
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.54
Consensus pattern (23 bp):
AAATGTTTTAAATATTTTATATT
Found at i:63576345 original size:15 final size:15
Alignment explanation
Indices: 63576314--63576354 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
63576304 CGTTTAGTAA
63576314 TTAA-ATTTTCAAAAC
1 TTAATATTTT-AAAAC
*
63576329 TTAATATTTTAACAC
1 TTAATATTTTAAAAC
63576344 TTAAT-TTTTAA
1 TTAATATTTTAA
63576355 TTTATTTATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 6 0.25
15 13 0.54
16 5 0.21
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.49
Consensus pattern (15 bp):
TTAATATTTTAAAAC
Found at i:63577788 original size:18 final size:18
Alignment explanation
Indices: 63577765--63577862 Score: 99
Period size: 18 Copynumber: 5.0 Consensus size: 18
63577755 GGCTTCACCA
*
63577765 CCGCCTTCTTTCTTCTCC
1 CCGCCTTCCTTCTTCTCC
63577783 CCGCCTTCCTTCTTCTCTCC
1 CCGCCTTCCTTC-T-TCTCC
63577803 GCCGCCTTCCTTCTTCTCC
1 -CCGCCTTCCTTCTTCTCC
63577822 CCGCCTCCTCCTTCCTTCTTCTC
1 CCGCCT--TCCTT-CTTC-TC-C
63577845 GCCGCCTTCCTTC-TCTCC
1 -CCGCCTTCCTTCTTCTCC
63577863 ACCTCCTCCT
Statistics
Matches: 70, Mismatches: 1, Indels: 18
0.79 0.01 0.20
Matches are distributed among these distances:
18 18 0.26
19 8 0.11
20 13 0.19
21 17 0.24
22 7 0.10
23 1 0.01
24 6 0.09
ACGTcount: A:0.00, C:0.54, G:0.07, T:0.39
Consensus pattern (18 bp):
CCGCCTTCCTTCTTCTCC
Found at i:63577807 original size:21 final size:21
Alignment explanation
Indices: 63577765--63577893 Score: 108
Period size: 21 Copynumber: 6.3 Consensus size: 21
63577755 GGCTTCACCA
*
63577765 CCGCCTTCTTTC-T-TCTCC-
1 CCGCCTTCCTTCTTCTCTCCG
63577783 CCGCCTTCCTTCTTCTCTCCG
1 CCGCCTTCCTTCTTCTCTCCG
*
63577804 CCGCCTTCCTTCTTCTCCCCG
1 CCGCCTTCCTTCTTCTCTCCG
*
63577825 CCTCC-TCCTTCCTTCT-TCTCG
1 CCGCCTTCCTT-CTTCTCTC-CG
* *
63577846 CCGCCTTCCTTC-TCTCCACCT
1 CCGCCTTCCTTCTTCT-CTCCG
* * * *
63577867 CCTCCTCCCTTCTTCCCGCCG
1 CCGCCTTCCTTCTTCTCTCCG
63577888 CCGCCT
1 CCGCCT
63577894 GCAGCAGCAG
Statistics
Matches: 89, Mismatches: 13, Indels: 15
0.76 0.11 0.13
Matches are distributed among these distances:
18 11 0.12
19 1 0.01
20 14 0.16
21 55 0.62
22 8 0.09
ACGTcount: A:0.01, C:0.56, G:0.08, T:0.36
Consensus pattern (21 bp):
CCGCCTTCCTTCTTCTCTCCG
Found at i:63577817 original size:39 final size:41
Alignment explanation
Indices: 63577765--63577889 Score: 145
Period size: 39 Copynumber: 3.1 Consensus size: 41
63577755 GGCTTCACCA
*
63577765 CCGCCTTCTTTCTTCTCCCCGCCT-TCCTT-CTTC-TCTCCG
1 CCGCCTTCCTTCTTCTCCCCGCCTCTCCTTCCTTCTTCT-CG
63577804 CCGCCTTCCTTCTTCTCCCCGCCTCCTCCTTCCTTCTTCTCG
1 CCGCCTTCCTTCTTCTCCCCGCCT-CTCCTTCCTTCTTCTCG
* * *
63577846 CCGCCTTCCTTC-TCT--CCACCTCCTCCTCCCTTCTTCCCG
1 CCGCCTTCCTTCTTCTCCCCGCCT-CTCCTTCCTTCTTCTCG
63577885 CCGCC
1 CCGCC
63577890 GCCTGCAGCA
Statistics
Matches: 78, Mismatches: 4, Indels: 8
0.87 0.04 0.09
Matches are distributed among these distances:
39 49 0.63
41 8 0.10
42 18 0.23
43 3 0.04
ACGTcount: A:0.01, C:0.56, G:0.07, T:0.36
Consensus pattern (41 bp):
CCGCCTTCCTTCTTCTCCCCGCCTCTCCTTCCTTCTTCTCG
Found at i:63577834 original size:24 final size:24
Alignment explanation
Indices: 63577783--63577851 Score: 90
Period size: 24 Copynumber: 3.0 Consensus size: 24
63577773 TTTCTTCTCC
*
63577783 CCGCCTTCCTTCTTCTCTCCG---
1 CCGCCTTCCTTCTTCTCCCCGCCT
63577804 CCGCCTTCCTTCTTCTCCCCGCCT
1 CCGCCTTCCTTCTTCTCCCCGCCT
* *
63577828 CCTCCTTCCTTCTTCTCGCCGCCT
1 CCGCCTTCCTTCTTCTCCCCGCCT
63577852 TCCTTCTCTC
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
21 20 0.48
24 22 0.52
ACGTcount: A:0.00, C:0.55, G:0.09, T:0.36
Consensus pattern (24 bp):
CCGCCTTCCTTCTTCTCCCCGCCT
Found at i:63577878 original size:63 final size:63
Alignment explanation
Indices: 63577768--63577889 Score: 158
Period size: 63 Copynumber: 1.9 Consensus size: 63
63577758 TTCACCACCG
* * *
63577768 CCTTCTTTCTTCTCCCCGCCTTCCTTCTTCTCTCCGCCGCCTTCCTTCTTCTCC-CCGCCTCCT
1 CCTTCCTTCTTCTCCCCGCCTTCCTTCTTCTCACCGCCGCCTCCCTTCTTC-CCGCCGCCTCCT
* * *
63577831 CCTTCCTTCTTCTCGCCGCCTTCCTTC-TCTCCACCTCCTCCTCCCTTCTTCCCGCCGCC
1 CCTTCCTTCTTCTCCCCGCCTTCCTTCTTCT-CACCGCCGCCTCCCTTCTTCCCGCCGCC
63577890 GCCTGCAGCA
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
62 5 0.10
63 46 0.90
ACGTcount: A:0.01, C:0.56, G:0.07, T:0.37
Consensus pattern (63 bp):
CCTTCCTTCTTCTCCCCGCCTTCCTTCTTCTCACCGCCGCCTCCCTTCTTCCCGCCGCCTCCT
Found at i:63577890 original size:42 final size:40
Alignment explanation
Indices: 63577765--63577893 Score: 147
Period size: 42 Copynumber: 3.1 Consensus size: 40
63577755 GGCTTCACCA
*
63577765 CCGCCTTCTTTCTTCTCCCCGCCT--TCCTTCTTCTCTCCG
1 CCGCCTTCCTTCTTCTCCCCGCCTCCTCCTTCTTCTC-CCG
*
63577804 CCGCCTTCCTTCTTCTCCCCGCCTCCTCCTTCCTTCTTCTCG
1 CCGCCTTCCTTCTTCTCCCCGCCTCCTCCTT-CTTC-TCCCG
* *
63577846 CCGCCTTCCTTC-TCTCCACCTCCTCCTCCCTTCTTCCCGCCG
1 CCGCCTTCCTTCTTCTCC-CCGCCTCCT-CCTTCTTCTC-CCG
63577888 CCGCCT
1 CCGCCT
63577894 GCAGCAGCAG
Statistics
Matches: 78, Mismatches: 5, Indels: 11
0.83 0.05 0.12
Matches are distributed among these distances:
39 23 0.29
41 11 0.14
42 38 0.49
43 6 0.08
ACGTcount: A:0.01, C:0.56, G:0.08, T:0.36
Consensus pattern (40 bp):
CCGCCTTCCTTCTTCTCCCCGCCTCCTCCTTCTTCTCCCG
Found at i:63577978 original size:18 final size:18
Alignment explanation
Indices: 63577942--63577984 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
63577932 GCCGGCGTCA
* *
63577942 TTCTTCTCTCCGCCGTCT
1 TTCTTCTCACCGCCATCT
*
63577960 TTCTTCTCACCGGCATCT
1 TTCTTCTCACCGCCATCT
*
63577978 TCCTTCT
1 TTCTTCT
63577985 TAGGGGGAAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.05, C:0.42, G:0.09, T:0.44
Consensus pattern (18 bp):
TTCTTCTCACCGCCATCT
Found at i:63596882 original size:16 final size:17
Alignment explanation
Indices: 63596863--63596902 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
63596853 TTCAATTAAG
*
63596863 TTAATTTTAAAGTT-TT
1 TTAATTTTAAAATTATT
63596879 TTAATTTTAAAATTATT
1 TTAATTTTAAAATTATT
63596896 TT-ATTTT
1 TTAATTTT
63596903 GTTGATATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 18 0.82
17 4 0.18
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.65
Consensus pattern (17 bp):
TTAATTTTAAAATTATT
Found at i:63597217 original size:17 final size:17
Alignment explanation
Indices: 63597195--63597227 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
63597185 GGGAAATGGT
63597195 GGTCATTCCCGGTAAGG
1 GGTCATTCCCGGTAAGG
*
63597212 GGTCATTCCTGGTAAG
1 GGTCATTCCCGGTAAG
63597228 AAGGACCTTT
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:0.18, C:0.21, G:0.33, T:0.27
Consensus pattern (17 bp):
GGTCATTCCCGGTAAGG
Found at i:63602813 original size:21 final size:20
Alignment explanation
Indices: 63602787--63602825 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
63602777 TAACAGAGGC
*
63602787 TTTTTTAATTTCTAAAAATA
1 TTTTTTTATTTCTAAAAATA
*
63602807 TTTTTTTATTTTTAAAAAT
1 TTTTTTTATTTCTAAAAAT
63602826 TTAAATCTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTTTTTATTTCTAAAAATA
Found at i:63616070 original size:2 final size:2
Alignment explanation
Indices: 63616065--63616114 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
63616055 TATATTGATG
63616065 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
63616107 TA TA TA TA
1 TA TA TA TA
63616115 AAAGAGAACA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:63618353 original size:44 final size:44
Alignment explanation
Indices: 63618289--63618530 Score: 257
Period size: 44 Copynumber: 5.6 Consensus size: 44
63618279 AATTTTCAAT
* ** *
63618289 CTATTTCACTGCTGCCCAGGGAGATAGAATTCTCAATCTTTAAC
1 CTATTCCACTGCTGATCAGGGAGATAGGATTCTCAATCTTTAAC
*
63618333 CTATTCCACTGCTGATCAGGGAGATAGGATTCACAATCTTTAAC
1 CTATTCCACTGCTGATCAGGGAGATAGGATTCTCAATCTTTAAC
* * *
63618377 CTATTCCACTACTG-TCCAGGGAAATAGGA---T---TCTTTAAT
1 CTATTCCACTGCTGAT-CAGGGAGATAGGATTCTCAATCTTTAAC
** * * *
63618415 CTATTCCACTGCTGCCCAAGGAGATAGAATTCTCAATCTTCAAC
1 CTATTCCACTGCTGATCAGGGAGATAGGATTCTCAATCTTTAAC
** *
63618459 CTATTCCACTGCTGATCAGGGAGATAGGATTCAAAATCTGTAAC
1 CTATTCCACTGCTGATCAGGGAGATAGGATTCTCAATCTTTAAC
*
63618503 CTATTCCACTGTTGA-CTAGGGAGATAGG
1 CTATTCCACTGCTGATC-AGGGAGATAGG
63618531 GCTGGGGTTA
Statistics
Matches: 164, Mismatches: 25, Indels: 18
0.79 0.12 0.09
Matches are distributed among these distances:
38 30 0.18
41 1 0.01
43 2 0.01
44 131 0.80
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (44 bp):
CTATTCCACTGCTGATCAGGGAGATAGGATTCTCAATCTTTAAC
Found at i:63618420 original size:38 final size:38
Alignment explanation
Indices: 63618369--63618447 Score: 104
Period size: 38 Copynumber: 2.1 Consensus size: 38
63618359 GGATTCACAA
* * *
63618369 TCTTTAACCTATTCCACTACTGTCCAGGGAAATAGGAT
1 TCTTTAACCTATTCCACTACTGCCCAAGGAAATAGAAT
* * *
63618407 TCTTTAATCTATTCCACTGCTGCCCAAGGAGATAGAAT
1 TCTTTAACCTATTCCACTACTGCCCAAGGAAATAGAAT
63618445 TCT
1 TCT
63618448 CAATCTTCAA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.28, C:0.24, G:0.15, T:0.33
Consensus pattern (38 bp):
TCTTTAACCTATTCCACTACTGCCCAAGGAAATAGAAT
Found at i:63618438 original size:82 final size:82
Alignment explanation
Indices: 63618325--63618490 Score: 235
Period size: 82 Copynumber: 2.0 Consensus size: 82
63618315 GAATTCTCAA
* * * *
63618325 TCTTTAACCTATTCCACTGCTGATCAGGGAGATAGGATTCACAATCTTTAACCTATTCCACTACT
1 TCTTTAACCTATTCCACTGCTGACCAAGGAGATAGAATTCACAATCTTCAACCTATTCCACTACT
63618390 G-TCCAGGGAAATAGGAT
66 GAT-CAGGGAAATAGGAT
* * * *
63618407 TCTTTAATCTATTCCACTGCTGCCCAAGGAGATAGAATTCTCAATCTTCAACCTATTCCACTGCT
1 TCTTTAACCTATTCCACTGCTGACCAAGGAGATAGAATTCACAATCTTCAACCTATTCCACTACT
*
63618472 GATCAGGGAGATAGGAT
66 GATCAGGGAAATAGGAT
63618489 TC
1 TC
63618491 AAAATCTGTA
Statistics
Matches: 74, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
82 73 0.99
83 1 0.01
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.31
Consensus pattern (82 bp):
TCTTTAACCTATTCCACTGCTGACCAAGGAGATAGAATTCACAATCTTCAACCTATTCCACTACT
GATCAGGGAAATAGGAT
Found at i:63618438 original size:126 final size:126
Alignment explanation
Indices: 63618286--63618512 Score: 409
Period size: 126 Copynumber: 1.8 Consensus size: 126
63618276 TACAATTTTC
* * *
63618286 AATCTATTTCACTGCTGCCCAGGGAGATAGAATTCTCAATCTTTAACCTATTCCACTGCTGATCA
1 AATCTATTCCACTGCTGCCCAAGGAGATAGAATTCTCAATCTTCAACCTATTCCACTGCTGATCA
* *
63618351 GGGAGATAGGATTCACAATCTTTAACCTATTCCACTACTGTCCAGGGAAATAGGATTCTTT
66 GGGAGATAGGATTCAAAATCTGTAACCTATTCCACTACTGTCCAGGGAAATAGGATTCTTT
63618412 AATCTATTCCACTGCTGCCCAAGGAGATAGAATTCTCAATCTTCAACCTATTCCACTGCTGATCA
1 AATCTATTCCACTGCTGCCCAAGGAGATAGAATTCTCAATCTTCAACCTATTCCACTGCTGATCA
63618477 GGGAGATAGGATTCAAAATCTGTAACCTATTCCACT
66 GGGAGATAGGATTCAAAATCTGTAACCTATTCCACT
63618513 GTTGACTAGG
Statistics
Matches: 96, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
126 96 1.00
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.30
Consensus pattern (126 bp):
AATCTATTCCACTGCTGCCCAAGGAGATAGAATTCTCAATCTTCAACCTATTCCACTGCTGATCA
GGGAGATAGGATTCAAAATCTGTAACCTATTCCACTACTGTCCAGGGAAATAGGATTCTTT
Found at i:63618656 original size:88 final size:88
Alignment explanation
Indices: 63618541--63619028 Score: 782
Period size: 88 Copynumber: 5.5 Consensus size: 88
63618531 GCTGGGGTTA
* * * *
63618541 TCGATCTGCTTCACTGTCGGTGCAGGAAGGCAAGATCTACTATTTTTAGCCTGCTCCACTGCAAC
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAAC
63618606 CCAGGGAGGCAAGGCTGGTGTCT
66 CCAGGGAGGCAAGGCTGGTGTCT
63618629 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAAC
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAAC
* * *
63618694 CCAGGGAGGAAAGGTTGATGTCT
66 CCAGGGAGGCAAGGCTGGTGTCT
* *
63618717 TCGATCTGCTTCGCTG-CTGGCGTAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAA
1 TCGATCTGCTTCGCTGTC-GGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAA
63618781 CCTCA-GGAGGCAAGGCTGGTGTCT
65 CC-CAGGGAGGCAAGGCTGGTGTCT
* * * * *
63618805 TCGATCTGCTTCGCTATCGGCGCAAGAAGGTAAGATCTGCTATTTTTAACCTGCTTCGCTGCAAC
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAAC
*
63618870 CCAGGGAGGCAAGGCTGATGTCT
66 CCAGGGAGGCAAGGCTGGTGTCT
* *
63618893 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCACTACAAC
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAAC
63618958 CCAGGGAGGCAAGGCTGGTGTCT
66 CCAGGGAGGCAAGGCTGGTGTCT
*
63618981 TCGATCTGCTTCGCTGTCGGTGCAAGAAGGCAAGATCTGCTATTTTTA
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTA
63619029 CCGATCTGCT
Statistics
Matches: 369, Mismatches: 27, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
87 3 0.01
88 363 0.98
89 3 0.01
ACGTcount: A:0.20, C:0.25, G:0.27, T:0.27
Consensus pattern (88 bp):
TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAAC
CCAGGGAGGCAAGGCTGGTGTCT
Found at i:63618732 original size:43 final size:43
Alignment explanation
Indices: 63618599--63618996 Score: 141
Period size: 44 Copynumber: 9.1 Consensus size: 43
63618589 GCCTGCTCCA
* *
63618599 CTGCAACCCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCG
1 CTGCAACCCAGGGAGGCAAGGTTGATGTCTTCGATCTGCTTCG
**** * * * * * ** * *
63618642 CTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCG
1 CTG-CAACCCAGGGAGGCAAGGT-TGATGTCTTCGATCTGCTTCG
*
63618687 CTGCAACCCAGGGAGGAAAGGTTGATGTCTTCGATCTGCTTCG
1 CTGCAACCCAGGGAGGCAAGGTTGATGTCTTCGATCTGCTTCG
** ** * * * * * ** * *
63618730 CTGCTGGCGTAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCG
1 CTGC-AACCCAGGGAGGCAAGGT-TGATGTCTTCGATCTGCTTCG
* *
63618775 CTGCAACCTCA-GGAGGCAAGGCTGGTGTCTTCGATCTGCTTCG
1 CTGCAACC-CAGGGAGGCAAGGTTGATGTCTTCGATCTGCTTCG
* ** * * * * * * * * ** *
63618818 CTATCGGCGCAAGAAGGTAAGATCTGCTATTTTTAACCTGCTTCG
1 CT-GCAACCCAGGGAGGCAAGGT-TGATGTCTTCGATCTGCTTCG
*
63618863 CTGCAACCCAGGGAGGCAAGGCTGATGTCTTCGATCTGCTTCG
1 CTGCAACCCAGGGAGGCAAGGTTGATGTCTTCGATCTGCTTCG
**** * * * * * ** * * *
63618906 CTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCA
1 CTG-CAACCCAGGGAGGCAAGGT-TGATGTCTTCGATCTGCTTCG
* * *
63618951 CTACAACCCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCG
1 CTGCAACCCAGGGAGGCAAGGTTGATGTCTTCGATCTGCTTCG
63618994 CTG
1 CTG
63618997 TCGGTGCAAG
Statistics
Matches: 228, Mismatches: 117, Indels: 20
0.62 0.32 0.05
Matches are distributed among these distances:
43 72 0.32
44 88 0.39
45 68 0.30
ACGTcount: A:0.20, C:0.26, G:0.28, T:0.27
Consensus pattern (43 bp):
CTGCAACCCAGGGAGGCAAGGTTGATGTCTTCGATCTGCTTCG
Found at i:63623834 original size:6 final size:6
Alignment explanation
Indices: 63623819--63623849 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
63623809 TAATGAATTT
63623819 TAAAAA -AAAAA TAAAAA TAAAAA TAAAAA TA
1 TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TA
63623850 TTTTTTCGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.21
6 19 0.79
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
TAAAAA
Found at i:63625135 original size:2 final size:2
Alignment explanation
Indices: 63625130--63625155 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
63625120 TATATTGATG
63625130 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
63625156 AAAGAACATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:63637046 original size:27 final size:27
Alignment explanation
Indices: 63637016--63637078 Score: 108
Period size: 27 Copynumber: 2.3 Consensus size: 27
63637006 GCAAAAAATA
*
63637016 CTTCCATTTCTTAGATTACCGCAAAGG
1 CTTCCATTTCTTAGATTACCACAAAGG
*
63637043 CTTCCATTTCTTAGATTGCCACAAAGG
1 CTTCCATTTCTTAGATTACCACAAAGG
63637070 CTTCCATTT
1 CTTCCATTT
63637079 TTTGACATGT
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:0.24, C:0.27, G:0.13, T:0.37
Consensus pattern (27 bp):
CTTCCATTTCTTAGATTACCACAAAGG
Found at i:63641208 original size:8 final size:8
Alignment explanation
Indices: 63641195--63641219 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
63641185 ACATGGCCTA
63641195 GGCCGTGT
1 GGCCGTGT
63641203 GGCCGTGT
1 GGCCGTGT
63641211 GGCCGTGT
1 GGCCGTGT
63641219 G
1 G
63641220 ACCCCTGTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.00, C:0.24, G:0.52, T:0.24
Consensus pattern (8 bp):
GGCCGTGT
Found at i:63642542 original size:8 final size:8
Alignment explanation
Indices: 63642531--63642566 Score: 54
Period size: 8 Copynumber: 4.4 Consensus size: 8
63642521 TTTTTCAACA
63642531 TTTCTAAT
1 TTTCTAAT
63642539 TTTCTAAT
1 TTTCTAAT
*
63642547 TTTCTAAA
1 TTTCTAAT
63642555 TTTCTAAGT
1 TTTCTAA-T
63642564 TTT
1 TTT
63642567 TCATTGTTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
8 22 0.88
9 3 0.12
ACGTcount: A:0.25, C:0.11, G:0.03, T:0.61
Consensus pattern (8 bp):
TTTCTAAT
Found at i:63649236 original size:67 final size:67
Alignment explanation
Indices: 63649133--63649388 Score: 431
Period size: 67 Copynumber: 3.8 Consensus size: 67
63649123 CAATTGCATT
* *
63649133 AGTAATTAAATGTATGTATTTAATTAAATTGATTATATATACGTGATTTGAGAAAGTATGCGAAT
1 AGTATTTAAATGTATGTATTTAATTAAATTGATTATATATATGTGATTTGAGAAAGTATGCGAAT
63649198 TG
66 TG
*
63649200 AGTATTTAAATGTATGTAGTTAATTAAATTGATTATATATATGTGATTTGAGAAAGTATGCGAAT
1 AGTATTTAAATGTATGTATTTAATTAAATTGATTATATATATGTGATTTGAGAAAGTATGCGAAT
63649265 TG
66 TG
** *
63649267 AGTATTTAAATGTATGTATTTAATTAAATCAATTATATATATATGATTTGAGAAAGTATGCGAAT
1 AGTATTTAAATGTATGTATTTAATTAAATTGATTATATATATGTGATTTGAGAAAGTATGCGAAT
63649332 TG
66 TG
* * *
63649334 AGTATTTAAATGTATGTATTTAAATGAATAGATTATATATATGTGATTTGAGAAA
1 AGTATTTAAATGTATGTATTTAATTAAATTGATTATATATATGTGATTTGAGAAA
63649389 TTGAATTATT
Statistics
Matches: 177, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
67 177 1.00
ACGTcount: A:0.39, C:0.02, G:0.17, T:0.41
Consensus pattern (67 bp):
AGTATTTAAATGTATGTATTTAATTAAATTGATTATATATATGTGATTTGAGAAAGTATGCGAAT
TG
Found at i:63650710 original size:13 final size:13
Alignment explanation
Indices: 63650692--63650716 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
63650682 ATATGTTTGG
63650692 ATATGAAATTGAT
1 ATATGAAATTGAT
63650705 ATATGAAATTGA
1 ATATGAAATTGA
63650717 CATTGAATTT
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:0.48, C:0.00, G:0.16, T:0.36
Consensus pattern (13 bp):
ATATGAAATTGAT
Found at i:63653882 original size:18 final size:20
Alignment explanation
Indices: 63653844--63653883 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
63653834 AGGGGGAGGA
*
63653844 TTCTTAGGTTTTTATTCTAG
1 TTCTTAGGTTTTTACTCTAG
63653864 TTCTTA-GTTTTTACT-TAG
1 TTCTTAGGTTTTTACTCTAG
63653882 TT
1 TT
63653884 TAAGTTATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 5 0.26
19 8 0.42
20 6 0.32
ACGTcount: A:0.15, C:0.10, G:0.12, T:0.62
Consensus pattern (20 bp):
TTCTTAGGTTTTTACTCTAG
Found at i:63655881 original size:42 final size:42
Alignment explanation
Indices: 63655732--63655888 Score: 140
Period size: 42 Copynumber: 3.7 Consensus size: 42
63655722 TTACTTTCCC
* *
63655732 TTTAGCTCTCACGAGCTTCTGTTCAA-CTCATATGAGTTT-TCA
1 TTTAGCTCTCACGAGCTTCTGTTCAACCT-TTATGGGTTTCT-A
* * *** * * **
63655774 TTCAACTCTTTTGAACTTCTGTTTAAACC-TTATGGGTTTCCG
1 TTTAGCTCTCACGAGCTTCTG-TTCAACCTTTATGGGTTTCTA
*
63655816 TTTAGCTCTTACGAGCTTCTGTTCAACCTTTATGGGTTTCTA
1 TTTAGCTCTCACGAGCTTCTGTTCAACCTTTATGGGTTTCTA
* *
63655858 TTTAGCTCTCATGAGCTTCTGTTCAGCCTTT
1 TTTAGCTCTCACGAGCTTCTGTTCAACCTTT
63655889 GGGCTTCTGA
Statistics
Matches: 89, Mismatches: 22, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
41 6 0.07
42 78 0.88
43 4 0.04
44 1 0.01
ACGTcount: A:0.18, C:0.23, G:0.15, T:0.44
Consensus pattern (42 bp):
TTTAGCTCTCACGAGCTTCTGTTCAACCTTTATGGGTTTCTA
Found at i:63662249 original size:42 final size:41
Alignment explanation
Indices: 63662168--63662318 Score: 158
Period size: 42 Copynumber: 3.6 Consensus size: 41
63662158 TTACTTTCCA
* *** *
63662168 TTTAGCTCTTACGAGCTTCTGTTCAACTGATACGAGTTTTCG
1 TTTAGCTCTTATGAGCTTCTGTTCAACCCTTATG-GTTTTCG
* * * *
63662210 TTCAGCTCTTTTGAGCTTTTGTTTAACCCTTATAGGTTTTCG
1 TTTAGCTCTTATGAGCTTCTGTTCAACCCTTAT-GGTTTTCG
* * *
63662252 TTTAGCTCTTACGAGCTTCTATTCAACCCTTATGGGTTTCTG
1 TTTAGCTCTTATGAGCTTCTGTTCAACCCTTATGGTTTTC-G
*
63662294 TTTAGCTCTCATGAGCTTCTGTTCA
1 TTTAGCTCTTATGAGCTTCTGTTCA
63662319 GCCTTCGGGC
Statistics
Matches: 88, Mismatches: 19, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
41 6 0.07
42 81 0.92
43 1 0.01
ACGTcount: A:0.17, C:0.22, G:0.17, T:0.44
Consensus pattern (41 bp):
TTTAGCTCTTATGAGCTTCTGTTCAACCCTTATGGTTTTCG
Found at i:63662262 original size:21 final size:22
Alignment explanation
Indices: 63662203--63662262 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 22
63662193 ACTGATACGA
* *
63662203 GTTTTCGTTCAGCTCTTTTGAG
1 GTTTTCGTTTAGCTCTTATGAG
* * *
63662225 CTTTT-GTTTAACCCTTAT-AG
1 GTTTTCGTTTAGCTCTTATGAG
63662245 GTTTTCGTTTAGCTCTTA
1 GTTTTCGTTTAGCTCTTA
63662263 CGAGCTTCTA
Statistics
Matches: 29, Mismatches: 8, Indels: 3
0.73 0.20 0.08
Matches are distributed among these distances:
20 6 0.21
21 19 0.66
22 4 0.14
ACGTcount: A:0.13, C:0.18, G:0.17, T:0.52
Consensus pattern (22 bp):
GTTTTCGTTTAGCTCTTATGAG
Found at i:63668397 original size:35 final size:35
Alignment explanation
Indices: 63668349--63668420 Score: 92
Period size: 35 Copynumber: 2.1 Consensus size: 35
63668339 GTCTAAATGC
* * *
63668349 TAACAAATGATGAATTGAACA-ACTAGTTTTTAGAG
1 TAACAAATCATGAACTGAACAGA-TAGTTTTAAGAG
*
63668384 TAACAAATCATGAACTGAATAGATAGTTTTAAGAG
1 TAACAAATCATGAACTGAACAGATAGTTTTAAGAG
63668419 TA
1 TA
63668421 GAGTAAGTTC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
35 31 0.97
36 1 0.03
ACGTcount: A:0.44, C:0.08, G:0.17, T:0.31
Consensus pattern (35 bp):
TAACAAATCATGAACTGAACAGATAGTTTTAAGAG
Found at i:63671686 original size:11 final size:11
Alignment explanation
Indices: 63671666--63671752 Score: 54
Period size: 11 Copynumber: 7.8 Consensus size: 11
63671656 CAACTAATTA
63671666 AAAATAAAATG
1 AAAATAAAATG
* *
63671677 AAATTAAAATT
1 AAAATAAAATG
* *
63671688 AAGATTAAGAT-
1 AA-AATAAAATG
*
63671699 TAAAT-AAATG
1 AAAATAAAATG
*
63671709 AAAATAAGATG
1 AAAATAAAATG
*
63671720 AAAATAAAAATA
1 AAAAT-AAAATG
63671732 AAAATAAACAT-
1 AAAATAAA-ATG
63671743 AAACATAAAA
1 AAA-ATAAAA
63671753 CTTATTTATT
Statistics
Matches: 60, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
9 3 0.05
10 6 0.10
11 28 0.47
12 23 0.38
ACGTcount: A:0.69, C:0.02, G:0.07, T:0.22
Consensus pattern (11 bp):
AAAATAAAATG
Done.