Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-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: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 14 of 199
Found at i:4409311 original size:33 final size:33
Alignment explanation
Indices: 4409271--4409336 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
4409261 GTCAATTTTT
4409271 TTAATTTCCATTTTAAAATTGCCGCAAAAACAA
1 TTAATTTCCATTTTAAAATTGCCGCAAAAACAA
*
4409304 TTAATTTCCATTTTAAAATTGCCTCAAAAACAA
1 TTAATTTCCATTTTAAAATTGCCGCAAAAACAA
4409337 CTCTTTTTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.42, C:0.18, G:0.05, T:0.35
Consensus pattern (33 bp):
TTAATTTCCATTTTAAAATTGCCGCAAAAACAA
Found at i:4409768 original size:9 final size:9
Alignment explanation
Indices: 4409750--4409970 Score: 180
Period size: 9 Copynumber: 24.0 Consensus size: 9
4409740 AAATATATAT
4409750 CATAACTTA
1 CATAACTTA
*
4409759 CATAATTTA
1 CATAACTTA
4409768 CATAACTTA
1 CATAACTTA
4409777 CATAACTTA
1 CATAACTTA
4409786 CATAACTTA
1 CATAACTTA
4409795 -ATAACTTA
1 CATAACTTA
* *
4409803 TATATATCATA
1 CATA-A-CTTA
*
4409814 CCATAGCTTA
1 -CATAACTTA
* *
4409824 AATAACTCA
1 CATAACTTA
4409833 CATAACTTA
1 CATAACTTA
*
4409842 CTTAACTTA
1 CATAACTTA
4409851 -ATAACTTA
1 CATAACTTA
* **
4409859 TATATATCAGA
1 CATA-A-CTTA
4409870 CCATAACTTA
1 -CATAACTTA
* *
4409880 AATAACTCA
1 CATAACTTA
4409889 CATAACTTA
1 CATAACTTA
*
4409898 CTTAACTTA
1 CATAACTTA
4409907 -ATAACTTA
1 CATAACTTA
* *
4409915 TATATATCATA
1 CATA-A-CTTA
4409926 CCATAACTTA
1 -CATAACTTA
* *
4409936 AATAACTCA
1 CATAACTTA
4409945 CATAACTTA
1 CATAACTTA
4409954 CATAACTTA
1 CATAACTTA
4409963 -ATAACTTA
1 CATAACTTA
4409971 TATATATATT
Statistics
Matches: 169, Mismatches: 31, Indels: 25
0.75 0.14 0.11
Matches are distributed among these distances:
8 30 0.18
9 109 0.64
10 11 0.07
11 10 0.06
12 9 0.05
ACGTcount: A:0.45, C:0.19, G:0.01, T:0.35
Consensus pattern (9 bp):
CATAACTTA
Found at i:4409836 original size:56 final size:56
Alignment explanation
Indices: 4409759--4409977 Score: 375
Period size: 56 Copynumber: 3.9 Consensus size: 56
4409749 TCATAACTTA
* * *
4409759 CATAATTTACATAACTTACATAACTTACATAACTTAATAACTTATATATATCATAC
1 CATAACTTAAATAACTCACATAACTTACATAACTTAATAACTTATATATATCATAC
* * *
4409815 CATAGCTTAAATAACTCACATAACTTACTTAACTTAATAACTTATATATATCAGAC
1 CATAACTTAAATAACTCACATAACTTACATAACTTAATAACTTATATATATCATAC
*
4409871 CATAACTTAAATAACTCACATAACTTACTTAACTTAATAACTTATATATATCATAC
1 CATAACTTAAATAACTCACATAACTTACATAACTTAATAACTTATATATATCATAC
4409927 CATAACTTAAATAACTCACATAACTTACATAACTTAATAACTTATATATAT
1 CATAACTTAAATAACTCACATAACTTACATAACTTAATAACTTATATATAT
4409978 ATTGTCGAAA
Statistics
Matches: 154, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
56 154 1.00
ACGTcount: A:0.45, C:0.19, G:0.01, T:0.36
Consensus pattern (56 bp):
CATAACTTAAATAACTCACATAACTTACATAACTTAATAACTTATATATATCATAC
Found at i:4411243 original size:21 final size:21
Alignment explanation
Indices: 4411219--4411315 Score: 63
Period size: 23 Copynumber: 4.4 Consensus size: 21
4411209 AGATATTAAA
*
4411219 AAAATAATAT-ATGATAAATTT
1 AAAATAATATAATAAT-AATTT
*
4411240 AAAA-CATATCAATAATAATTT
1 AAAATAATAT-AATAATAATTT
** *
4411261 AAAATAATAGCATATTACATTTT
1 AAAATAATATAATAATA-A-TTT
*
4411284 AAAATTATACTAATAATAAGTTT
1 AAAATAATA-TAATAATAA-TTT
4411307 AAAAGTAAT
1 AAAA-TAAT
4411316 GTCAAACTAA
Statistics
Matches: 57, Mismatches: 12, Indels: 11
0.71 0.15 0.14
Matches are distributed among these distances:
20 4 0.07
21 18 0.32
22 8 0.14
23 19 0.33
24 8 0.14
ACGTcount: A:0.55, C:0.05, G:0.04, T:0.36
Consensus pattern (21 bp):
AAAATAATATAATAATAATTT
Found at i:4411519 original size:20 final size:20
Alignment explanation
Indices: 4411474--4411528 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
4411464 GAATTCAAAT
*
4411474 AAAAATAAAAATAAAAAACT
1 AAAAATAAAAATAAAAAACA
* * *
4411494 ACAAATAGAAATAAAAAAGA
1 AAAAATAAAAATAAAAAACA
*
4411514 AAAAATAAAGATAAA
1 AAAAATAAAAATAAA
4411529 CTAAATTGGT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.78, C:0.04, G:0.05, T:0.13
Consensus pattern (20 bp):
AAAAATAAAAATAAAAAACA
Found at i:4412855 original size:56 final size:56
Alignment explanation
Indices: 4412794--4413102 Score: 410
Period size: 56 Copynumber: 5.5 Consensus size: 56
4412784 GGATTATTAC
*
4412794 ATATATTATACCATAACTTAAATAACTCACATAACTTACTTAACTTAATAACTTAT
1 ATATATCATACCATAACTTAAATAACTCACATAACTTACTTAACTTAATAACTTAT
*
4412850 ATATATCATACAATAACTTAAATAACTCACATAACTTACTTAACTTAATAACTTAT
1 ATATATCATACCATAACTTAAATAACTCACATAACTTACTTAACTTAATAACTTAT
4412906 ATATATCATACCATAACTTAAAATAACTCACAT-A---ACTTAACTTAATAACTTAT
1 ATATATCATACCATAACTT-AAATAACTCACATAACTTACTTAACTTAATAACTTAT
* * * *
4412959 ATATATCATAACATAATTTACATAACTCACATAACTTACATAACTTAATAACTTAT
1 ATATATCATACCATAACTTAAATAACTCACATAACTTACTTAACTTAATAACTTAT
* * * * * *
4413015 ATATATCATATCATAACTTACATAACTCACAGAACTTACATAACTTGCATAATACATAAAT
1 ATATATCATACCATAACTTAAATAACTCACATAACTTACTTAACTT-AAT-A-AC-T-TAT
* *
4413076 ATATATCATATCATAACTTACATAACT
1 ATATATCATACCATAACTTAAATAACT
4413103 TAATTATACT
Statistics
Matches: 231, Mismatches: 12, Indels: 15
0.90 0.05 0.06
Matches are distributed among these distances:
52 12 0.05
53 37 0.16
56 134 0.58
57 15 0.06
58 1 0.00
59 2 0.01
60 1 0.00
61 29 0.13
ACGTcount: A:0.46, C:0.18, G:0.01, T:0.35
Consensus pattern (56 bp):
ATATATCATACCATAACTTAAATAACTCACATAACTTACTTAACTTAATAACTTAT
Found at i:4412965 original size:109 final size:108
Alignment explanation
Indices: 4412794--4413052 Score: 394
Period size: 109 Copynumber: 2.4 Consensus size: 108
4412784 GGATTATTAC
*
4412794 ATATATTATACCATAACTTAAATAACTCACATAACTTACTTAACTTAATAACTTATATATATCAT
1 ATATATCATACCATAACTTAAATAACTCACAT-A---ACTTAACTTAATAACTTATATATATCAT
*
4412859 -ACAATAACTTAAATAACTCACATAACTTACTTAACTTAATAACTTAT
62 AAC-ATAACTTAAATAACTCACATAACTTACATAACTTAATAACTTAT
4412906 ATATATCATACCATAACTTAAAATAACTCACATAACTTAACTTAATAACTTATATATATCATAAC
1 ATATATCATACCATAACTT-AAATAACTCACATAACTTAACTTAATAACTTATATATATCATAAC
* *
4412971 ATAATTTACATAACTCACATAACTTACATAACTTAATAACTTAT
65 ATAACTTAAATAACTCACATAACTTACATAACTTAATAACTTAT
* * *
4413015 ATATATCATATCATAACTTACATAACTCACAGAACTTA
1 ATATATCATACCATAACTTAAATAACTCACATAACTTA
4413053 CATAACTTGC
Statistics
Matches: 138, Mismatches: 7, Indels: 8
0.90 0.05 0.05
Matches are distributed among these distances:
108 17 0.12
109 87 0.63
110 2 0.01
112 19 0.14
113 13 0.09
ACGTcount: A:0.46, C:0.19, G:0.00, T:0.35
Consensus pattern (108 bp):
ATATATCATACCATAACTTAAATAACTCACATAACTTAACTTAATAACTTATATATATCATAACA
TAACTTAAATAACTCACATAACTTACATAACTTAATAACTTAT
Found at i:4412970 original size:24 final size:24
Alignment explanation
Indices: 4412890--4412975 Score: 59
Period size: 24 Copynumber: 3.4 Consensus size: 24
4412880 ATAACTTACT
4412890 TAACTTAATAACTTATATATATCATACCA
1 TAACTTAATAAC-T-TATATAT-AT--CA
* * *
4412919 TAACTTAAAATAACTCACATA-A-CT
1 TAACTT--AATAACTTATATATATCA
4412943 TAACTTAATAACTTATATATATCA
1 TAACTTAATAACTTATATATATCA
*
4412967 TAACATAAT
1 TAACTTAAT
4412976 TTACATAACT
Statistics
Matches: 46, Mismatches: 7, Indels: 13
0.70 0.11 0.20
Matches are distributed among these distances:
22 11 0.24
23 1 0.02
24 16 0.35
27 1 0.02
29 10 0.22
30 1 0.02
31 6 0.13
ACGTcount: A:0.48, C:0.16, G:0.00, T:0.36
Consensus pattern (24 bp):
TAACTTAATAACTTATATATATCA
Found at i:4413038 original size:9 final size:9
Alignment explanation
Indices: 4412805--4413104 Score: 172
Period size: 9 Copynumber: 33.0 Consensus size: 9
4412795 TATATTATAC
4412805 CATAACTTA
1 CATAACTTA
* *
4412814 AATAACTCA
1 CATAACTTA
4412823 CATAACTTA
1 CATAACTTA
*
4412832 CTTAACTTA
1 CATAACTTA
4412841 -ATAACTTA
1 CATAACTTA
* *
4412849 TATATATCATA
1 CATA-A-CTTA
4412860 CAATAACTTA
1 C-ATAACTTA
* *
4412870 AATAACTCA
1 CATAACTTA
4412879 CATAACTTA
1 CATAACTTA
*
4412888 CTTAACTTA
1 CATAACTTA
4412897 -ATAACTTA
1 CATAACTTA
* *
4412905 TATATATCATA
1 CATA-A-CTTA
4412916 CCATAACTTAA
1 -CATAACTT-A
* *
4412927 AATAACTCA
1 CATAACTTA
4412936 CATAAC-T-
1 CATAACTTA
4412943 --TAACTTA
1 CATAACTTA
4412950 -ATAACTTA
1 CATAACTTA
* *
4412958 TATATATCATAA
1 CATA-A-C-TTA
*
4412970 CATAATTTA
1 CATAACTTA
*
4412979 CATAACTCA
1 CATAACTTA
4412988 CATAACTTA
1 CATAACTTA
4412997 CATAACTTA
1 CATAACTTA
4413006 -ATAACTTA
1 CATAACTTA
* *
4413014 TATATATCATA
1 CATA-A-CTTA
4413025 TCATAACTTA
1 -CATAACTTA
*
4413035 CATAACTCA
1 CATAACTTA
*
4413044 CAGAACTTA
1 CATAACTTA
*
4413053 CATAACTTG
1 CATAACTTA
4413062 CATAA--TA
1 CATAACTTA
*
4413069 CATAA-ATA
1 CATAACTTA
* * *
4413077 TATATCATA
1 CATAACTTA
4413086 TCATAACTTA
1 -CATAACTTA
4413096 CATAACTTA
1 CATAACTTA
4413105 ATTATACTTA
Statistics
Matches: 225, Mismatches: 43, Indels: 46
0.72 0.14 0.15
Matches are distributed among these distances:
5 4 0.02
6 1 0.00
7 6 0.03
8 34 0.15
9 127 0.56
10 24 0.11
11 15 0.07
12 14 0.06
ACGTcount: A:0.46, C:0.19, G:0.01, T:0.35
Consensus pattern (9 bp):
CATAACTTA
Found at i:4413143 original size:165 final size:163
Alignment explanation
Indices: 4412805--4413125 Score: 399
Period size: 165 Copynumber: 2.0 Consensus size: 163
4412795 TATATTATAC
* * *
4412805 CATAACTTAAATAACTCACATAACTTACTTAACTTAATAACTTATATATATCATACAATAACTTA
1 CATAATTTACATAACTCACATAACTTACATAACTTAATAACTTATATATATCATACAATAACTTA
* * * *
4412870 AATAACTCACATAACTTACTTAACTTAATAACTTATATATATCATACCATAACTTAAAATAACTC
66 AATAACTCACAGAACTTACATAACTTAATAACTCATAAATATCATACCATAAC-T-AAATAACTC
* *
4412935 ACATAACTTAACTTAATAACTTATATATATCATAA
129 ACATAACTTAACTTAATAACTTATAAATACCATAA
4412970 CATAATTTACATAACTCACATAACTTACATAACTTAATAACTTATATATATCATATC-ATAACTT
1 CATAATTTACATAACTCACATAACTTACATAACTTAATAACTTATATATATCATA-CAATAACTT
* * * *
4413034 ACATAACTCACAGAACTTACATAACTTGCATAA-TACATAAATAT-ATATCAT-A-T-CATAACT
65 AAATAACTCACAGAACTTACATAACTT-AATAACT-CATAAATATCATACCATAACTAAATAACT
*
4413094 TACATAACTTAA-TT-AT-ACTTATAAATAACCAT
128 CACATAACTTAACTTAATAACTTATAAAT-ACCAT
4413126 GACTACCCGT
Statistics
Matches: 138, Mismatches: 14, Indels: 15
0.83 0.08 0.09
Matches are distributed among these distances:
157 9 0.07
158 6 0.04
159 2 0.01
160 17 0.12
162 1 0.01
164 1 0.01
165 90 0.65
166 12 0.09
ACGTcount: A:0.46, C:0.18, G:0.01, T:0.35
Consensus pattern (163 bp):
CATAATTTACATAACTCACATAACTTACATAACTTAATAACTTATATATATCATACAATAACTTA
AATAACTCACAGAACTTACATAACTTAATAACTCATAAATATCATACCATAACTAAATAACTCAC
ATAACTTAACTTAATAACTTATAAATACCATAA
Found at i:4414841 original size:12 final size:12
Alignment explanation
Indices: 4414824--4414849 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
4414814 AAGATTAAGA
4414824 GATGAATCTGAT
1 GATGAATCTGAT
4414836 GATGAATCTGAT
1 GATGAATCTGAT
4414848 GA
1 GA
4414850 AGAGGATGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.08, G:0.27, T:0.31
Consensus pattern (12 bp):
GATGAATCTGAT
Found at i:4418944 original size:43 final size:43
Alignment explanation
Indices: 4418876--4419099 Score: 290
Period size: 43 Copynumber: 5.2 Consensus size: 43
4418866 TCTGCCAAAA
* * *
4418876 TTAGTGGCGTTTTCAATAAAAGCGCCGCTAAAGAATATGACAT
1 TTAGCGGCGTTTTCTATAAAAGCGCCGCTAAAGAACATGACAT
* *
4418919 TTAGCGTCGTTTTCTATAAAAGCGCCGCTAAAGAACATGACCT
1 TTAGCGGCGTTTTCTATAAAAGCGCCGCTAAAGAACATGACAT
*
4418962 TTAGCGGCG-TTTCTTATAAAAGC-CCAGCTAAAGAATATGACAT
1 TTAGCGGCGTTTTC-TATAAAAGCGCC-GCTAAAGAACATGACAT
* * *
4419005 TTAGCGGCGTTTGCTATAAAGGCGCCGCTAAAGAACATGACCT
1 TTAGCGGCGTTTTCTATAAAAGCGCCGCTAAAGAACATGACAT
* * * *
4419048 TTAACGGCGTTTGCTATAAAAGCGGCGATAAAGAACATGACAT
1 TTAGCGGCGTTTTCTATAAAAGCGCCGCTAAAGAACATGACAT
*
4419091 TTAGTGGCG
1 TTAGCGGCG
4419100 CTTATCTTTA
Statistics
Matches: 158, Mismatches: 19, Indels: 8
0.85 0.10 0.04
Matches are distributed among these distances:
42 6 0.04
43 147 0.93
44 5 0.03
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.26
Consensus pattern (43 bp):
TTAGCGGCGTTTTCTATAAAAGCGCCGCTAAAGAACATGACAT
Found at i:4419614 original size:12 final size:13
Alignment explanation
Indices: 4419592--4419620 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
4419582 AGGTAATTCC
4419592 TTTTCTATTTTCT
1 TTTTCTATTTTCT
4419605 TTTTCT-TTTTCT
1 TTTTCTATTTTCT
4419617 TTTT
1 TTTT
4419621 ATTATATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.03, C:0.14, G:0.00, T:0.83
Consensus pattern (13 bp):
TTTTCTATTTTCT
Found at i:4422603 original size:4 final size:4
Alignment explanation
Indices: 4422596--4422621 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
4422586 ATCACATGTT
4422596 CATA CATA CATA CATA CATA CATA CA
1 CATA CATA CATA CATA CATA CATA CA
4422622 GAAAAAGGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.50, C:0.27, G:0.00, T:0.23
Consensus pattern (4 bp):
CATA
Found at i:4423699 original size:15 final size:15
Alignment explanation
Indices: 4423679--4423729 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
4423669 TAAGTATAAA
4423679 TATTTTTTAAAATTT
1 TATTTTTTAAAATTT
* **
4423694 TA-TTTTTAATATAAA
1 TATTTTTTAAAAT-TT
*
4423709 TATTTTTTAAAAATT
1 TATTTTTTAAAATTT
4423724 TATTTT
1 TATTTT
4423730 CAATTTATTG
Statistics
Matches: 27, Mismatches: 7, Indels: 4
0.71 0.18 0.11
Matches are distributed among these distances:
14 9 0.33
15 10 0.37
16 8 0.30
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TATTTTTTAAAATTT
Found at i:4423709 original size:30 final size:31
Alignment explanation
Indices: 4423668--4423729 Score: 108
Period size: 30 Copynumber: 2.0 Consensus size: 31
4423658 TTAGTGTTAG
*
4423668 TTAAGTATAAATATTTTTTAAAATTTTATTT
1 TTAAGTATAAATATTTTTTAAAAATTTATTT
4423699 TTAA-TATAAATATTTTTTAAAAATTTATTT
1 TTAAGTATAAATATTTTTTAAAAATTTATTT
4423729 T
1 T
4423730 CAATTTATTG
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 26 0.87
31 4 0.13
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (31 bp):
TTAAGTATAAATATTTTTTAAAAATTTATTT
Found at i:4427503 original size:111 final size:111
Alignment explanation
Indices: 4427303--4427514 Score: 284
Period size: 111 Copynumber: 1.9 Consensus size: 111
4427293 CAGCTCCGGG
* * * *
4427303 AAGCCTTTCATTTGCTCTCAAACTTTGCCTGCTTGAACTGCTAACACCATCTGCATTTAATCCAT
1 AAGCCTCTCACTTGATCTCAAACTTTGCCTGCTTGAACTGCTAACACCATCTGCATTTAACCCAT
*
4427368 AGCTCGAACTGAGCTCGCCAGTACCTTCATCAAACCCTTCTCTAGC
66 AGCTCGAACTAAGCTCGCCAGTACCTTCATCAAACCCTTCTCTAGC
* * * *
4427414 AAGCCTCTCACTTGATCTCAAACTTTGCCTTCTTGCATTGCTTACACCGA-CTGCATTTAACCCA
1 AAGCCTCTCACTTGATCTCAAACTTTGCCTGCTTGAACTGCTAACACC-ATCTGCATTTAACCCA
* **
4427478 TTGCTCGATAC-AAGCTCGCTGGTACCTTCATCAAACC
65 TAGCTCGA-ACTAAGCTCGCCAGTACCTTCATCAAACC
4427515 GCACTGATGA
Statistics
Matches: 87, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
111 84 0.97
112 3 0.03
ACGTcount: A:0.24, C:0.33, G:0.13, T:0.31
Consensus pattern (111 bp):
AAGCCTCTCACTTGATCTCAAACTTTGCCTGCTTGAACTGCTAACACCATCTGCATTTAACCCAT
AGCTCGAACTAAGCTCGCCAGTACCTTCATCAAACCCTTCTCTAGC
Found at i:4429290 original size:89 final size:87
Alignment explanation
Indices: 4429156--4429322 Score: 205
Period size: 89 Copynumber: 1.9 Consensus size: 87
4429146 AATTCTATGC
* * **
4429156 TTTTTTCACTCAATTGAGTATTTTAACTTTCAAAAATGT-ATAAAAAGG-CTCTCAAACTTTTTC
1 TTTTTTCACTCAATTGAGTACTTGAACTTTCAAAAACATAATAAAAAGGCCT-TCAAACTTTTTC
4429219 AAAAAAAGCAATTAAGGCCCTACTT
65 --AAAAAGCAATTAAGGCCCTACTT
* * *
4429244 TTTTTTACGCTCAATTGGGTACTTGAACTTTCAAAATACATAA-AAAAATGCCTTCAAACTTTTT
1 TTTTTT-CACTCAATTGAGTACTTGAACTTTCAAAA-ACATAATAAAAAGGCCTTCAAACTTTTT
4429308 CAAAAAGCAATTAAG
64 CAAAAAGCAATTAAG
4429323 CCCGTGCTCT
Statistics
Matches: 68, Mismatches: 7, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
88 20 0.29
89 25 0.37
90 20 0.29
91 3 0.04
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.35
Consensus pattern (87 bp):
TTTTTTCACTCAATTGAGTACTTGAACTTTCAAAAACATAATAAAAAGGCCTTCAAACTTTTTCA
AAAAGCAATTAAGGCCCTACTT
Found at i:4429336 original size:2 final size:2
Alignment explanation
Indices: 4429329--4429376 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
4429319 TAAGCCCGTG
4429329 CT CT CT 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 CT CT CT
4429371 CT CT CT
1 CT CT CT
4429377 ATCTATCTAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:4429381 original size:4 final size:4
Alignment explanation
Indices: 4429374--4429400 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
4429364 TCTCTCTCTC
4429374 TCTA TCTA TCTA TCTA TCTA TCTA TCT
1 TCTA TCTA TCTA TCTA TCTA TCTA TCT
4429401 TCCTTACTCC
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:0.26, G:0.00, T:0.52
Consensus pattern (4 bp):
TCTA
Found at i:4430146 original size:4 final size:4
Alignment explanation
Indices: 4430137--4430163 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
4430127 NNNNNNNNNN
4430137 CTAA CTAA CTAA CTAA CTAA CTAA CTA
1 CTAA CTAA CTAA CTAA CTAA CTAA CTA
4430164 CTACTACTAC
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:0.48, C:0.26, G:0.00, T:0.26
Consensus pattern (4 bp):
CTAA
Found at i:4430189 original size:2 final size:2
Alignment explanation
Indices: 4430182--4430249 Score: 136
Period size: 2 Copynumber: 34.0 Consensus size: 2
4430172 ACTACTACTA
4430182 CT CT CT 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 CT CT CT
4430224 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
4430250 TTTTTGCACT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:4430342 original size:20 final size:20
Alignment explanation
Indices: 4430304--4430343 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
4430294 AAAAAATAAC
* **
4430304 ATTTGATCGTTAACTTTAAT
1 ATTTGACCGTTAAAATTAAT
4430324 ATTTGACCGTTAAAATTAAT
1 ATTTGACCGTTAAAATTAAT
4430344 TGTCTCTAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.35, C:0.10, G:0.10, T:0.45
Consensus pattern (20 bp):
ATTTGACCGTTAAAATTAAT
Found at i:4430490 original size:37 final size:36
Alignment explanation
Indices: 4430419--4430507 Score: 112
Period size: 37 Copynumber: 2.4 Consensus size: 36
4430409 AATTATAAAA
4430419 AATAAAAATCAATAAAAGTTATAAAAATATTAAATTTT
1 AATAAAAAT-AAT-AAAGTTATAAAAATATTAAATTTT
4430457 AATAAAAAT-ATAAAGTTTATTAAAAAT-TGTAAATTTT
1 AATAAAAATAATAAAG-TTA-TAAAAATAT-TAAATTTT
4430494 -ATAAAAATAATAAA
1 AATAAAAATAATAAA
4430508 TAATTATAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 9
0.84 0.00 0.16
Matches are distributed among these distances:
35 4 0.09
36 14 0.30
37 20 0.43
38 9 0.19
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.35
Consensus pattern (36 bp):
AATAAAAATAATAAAGTTATAAAAATATTAAATTTT
Found at i:4430514 original size:19 final size:18
Alignment explanation
Indices: 4430420--4430518 Score: 92
Period size: 18 Copynumber: 5.3 Consensus size: 18
4430410 ATTATAAAAA
**
4430420 ATAAAAATCAATAAAAGTT
1 ATAAAAAT-AATAAATTTT
*
4430439 ATAAAAATATTAAATTTT
1 ATAAAAATAATAAATTTT
*
4430457 AATAAAAAT-ATAAAGTTT
1 -ATAAAAATAATAAATTTT
**
4430475 ATTAAAAATTGTAAATTTT
1 A-TAAAAATAATAAATTTT
*
4430494 ATAAAAATAATAAATAATT
1 ATAAAAATAATAAAT-TTT
4430513 ATAAAA
1 ATAAAA
4430519 TGTATCAAAA
Statistics
Matches: 66, Mismatches: 10, Indels: 8
0.79 0.12 0.10
Matches are distributed among these distances:
17 1 0.02
18 33 0.50
19 32 0.48
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.35
Consensus pattern (18 bp):
ATAAAAATAATAAATTTT
Found at i:4430697 original size:22 final size:22
Alignment explanation
Indices: 4430672--4430715 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
4430662 AAAGTTATAG
4430672 AAAAATTATAAAATGCTTCTTT
1 AAAAATTATAAAATGCTTCTTT
4430694 AAAAATTATAAAATGCTTCTTT
1 AAAAATTATAAAATGCTTCTTT
4430716 TGATACGATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.45, C:0.09, G:0.05, T:0.41
Consensus pattern (22 bp):
AAAAATTATAAAATGCTTCTTT
Found at i:4430807 original size:19 final size:18
Alignment explanation
Indices: 4430758--4430837 Score: 63
Period size: 19 Copynumber: 4.2 Consensus size: 18
4430748 TTTTTATTTC
*
4430758 TTTACATTTTTTATAATTT
1 TTTACA-TTTTTATAAATT
*
4430777 TCTTACAATTTTATAAATT
1 T-TTACATTTTTATAAATT
*
4430796 TTTACCATTTTTGT-AATT
1 TTTA-CATTTTTATAAATT
* *
4430814 GTTTATGATTTTTATAATTT
1 -TTTA-CATTTTTATAAATT
4430834 TTTA
1 TTTA
4430838 ATAATTTTTA
Statistics
Matches: 49, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
18 7 0.14
19 34 0.69
20 8 0.16
ACGTcount: A:0.28, C:0.06, G:0.04, T:0.62
Consensus pattern (18 bp):
TTTACATTTTTATAAATT
Found at i:4430845 original size:10 final size:10
Alignment explanation
Indices: 4430821--4430904 Score: 59
Period size: 10 Copynumber: 8.7 Consensus size: 10
4430811 ATTGTTTATG
4430821 ATTTTT-ATA
1 ATTTTTAATA
4430830 ATTTTTTAATA
1 A-TTTTTAATA
4430841 ATTTTTAATA
1 ATTTTTAATA
4430851 A-TTTT-ATA
1 ATTTTTAATA
* *
4430859 TTTTTTATTA
1 ATTTTTAATA
**
4430869 AAATTTAATA
1 ATTTTTAATA
*
4430879 ATGTTT-ATA
1 ATTTTTAATA
* * *
4430888 ACTTTTATTG
1 ATTTTTAATA
4430898 ATTTTTA
1 ATTTTTA
4430905 TTTTTTATCA
Statistics
Matches: 57, Mismatches: 13, Indels: 9
0.72 0.16 0.11
Matches are distributed among these distances:
8 3 0.05
9 16 0.28
10 34 0.60
11 4 0.07
ACGTcount: A:0.35, C:0.01, G:0.02, T:0.62
Consensus pattern (10 bp):
ATTTTTAATA
Found at i:4430845 original size:19 final size:19
Alignment explanation
Indices: 4430723--4430855 Score: 62
Period size: 19 Copynumber: 6.8 Consensus size: 19
4430713 TTTTGATACG
4430723 ATAATTTT-TATATCTTTTTA
1 ATAATTTTATA-AT-TTTTTA
4430743 ATGAATTTT-T-ATTTCTTTA
1 AT-AATTTTATAATTT-TTTA
*
4430762 CAT-TTTTTATAATTTTCTT-
1 -ATAATTTTATAATTTT-TTA
* *
4430781 ACAATTTTATAAATTTTTA
1 ATAATTTTATAATTTTTTA
** * * *
4430800 CCATTTTTGTAATTGTTT-
1 ATAATTTTATAATTTTTTA
*
4430818 ATGATTTTTATAATTTTTTA
1 AT-AATTTTATAATTTTTTA
4430838 ATAATTTTTAATAATTTT
1 ATAA-TTTT-ATAATTTT
4430856 ATATTTTTTA
Statistics
Matches: 87, Mismatches: 14, Indels: 23
0.70 0.11 0.19
Matches are distributed among these distances:
18 9 0.10
19 47 0.54
20 16 0.18
21 15 0.17
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.62
Consensus pattern (19 bp):
ATAATTTTATAATTTTTTA
Found at i:4430857 original size:38 final size:37
Alignment explanation
Indices: 4430815--4430905 Score: 96
Period size: 38 Copynumber: 2.4 Consensus size: 37
4430805 TTTGTAATTG
** *
4430815 TTTATGATTTTTATAATTTTTTAATAATTTTTAATAA-T
1 TTTATGATTTTTATAA-AATTTAATAATGTTT-ATAACT
4430853 TTTAT-ATTTTTTATTAAAATTTAATAATGTTTATAACT
1 TTTATGA-TTTTTA-TAAAATTTAATAATGTTTATAACT
4430891 TTTATTGATTTTTAT
1 TTTA-TGATTTTTAT
4430906 TTTTTATCAT
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
37 5 0.11
38 29 0.64
39 10 0.22
40 1 0.02
ACGTcount: A:0.33, C:0.01, G:0.03, T:0.63
Consensus pattern (37 bp):
TTTATGATTTTTATAAAATTTAATAATGTTTATAACT
Found at i:4430885 original size:29 final size:28
Alignment explanation
Indices: 4430823--4430896 Score: 85
Period size: 28 Copynumber: 2.6 Consensus size: 28
4430813 TGTTTATGAT
* **
4430823 TTTTATAATTTTTTAATAATTTTTAATAA
1 TTTTAT-ATTTTTTATTAAAATTTAATAA
4430852 TTTTATATTTTTTATTAAAATTTAATAA
1 TTTTATATTTTTTATTAAAATTTAATAA
**
4430880 TGTTTATAACTTTTATT
1 T-TTTATATTTTTTATT
4430897 GATTTTTATT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
28 20 0.51
29 19 0.49
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.62
Consensus pattern (28 bp):
TTTTATATTTTTTATTAAAATTTAATAA
Found at i:4432521 original size:2 final size:2
Alignment explanation
Indices: 4432514--4432545 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
4432504 ATAAAATAGC
*
4432514 TA TA TA TA TA TA TA AA 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
4432546 AATTGTCCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:4434480 original size:31 final size:30
Alignment explanation
Indices: 4434445--4434504 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
4434435 AATCATTTTT
** *
4434445 AAAATTCAAAATTTATATTTAAAAAATTATA
1 AAAATTCAAAA-GAATATATAAAAAATTATA
*
4434476 AAAATTCTAAAGAATATATAAAAAATTAT
1 AAAATTCAAAAGAATATATAAAAAATTAT
4434505 TCTTTTTAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 15 0.60
31 10 0.40
ACGTcount: A:0.60, C:0.03, G:0.02, T:0.35
Consensus pattern (30 bp):
AAAATTCAAAAGAATATATAAAAAATTATA
Found at i:4435207 original size:17 final size:18
Alignment explanation
Indices: 4435176--4435215 Score: 73
Period size: 17 Copynumber: 2.3 Consensus size: 18
4435166 TTTATGAAAA
4435176 TATAAAAATCAATTTTTT
1 TATAAAAATCAATTTTTT
4435194 TATAAAAATC-ATTTTTT
1 TATAAAAATCAATTTTTT
4435211 TATAA
1 TATAA
4435216 TTTTATTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 12 0.55
18 10 0.45
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (18 bp):
TATAAAAATCAATTTTTT
Found at i:4437353 original size:29 final size:29
Alignment explanation
Indices: 4437310--4437376 Score: 107
Period size: 29 Copynumber: 2.3 Consensus size: 29
4437300 ACAACACTTT
*
4437310 AACATAAGTGACTGAAATGTAACAATTCA
1 AACATAAGTGACTGAAATATAACAATTCA
* *
4437339 AACATAAGTGGCTGAAATATAACAATTGA
1 AACATAAGTGACTGAAATATAACAATTCA
4437368 AACATAAGT
1 AACATAAGT
4437377 AACTATTTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.49, C:0.12, G:0.15, T:0.24
Consensus pattern (29 bp):
AACATAAGTGACTGAAATATAACAATTCA
Found at i:4441689 original size:544 final size:544
Alignment explanation
Indices: 4440661--4441752 Score: 2067
Period size: 544 Copynumber: 2.0 Consensus size: 544
4440651 TTGCGTATAG
*
4440661 TGAATCTTGAATTTCGGTACTTGAAGTTAAGAATTTATTGGAAAATAATATATGAGATTTAAATC
1 TGAATCTTAAATTTCGGTACTTGAAGTTAAGAATTTATTGGAAAATAATATATGAGATTTAAATC
4440726 AAAATATATTGTAACAGCTCGTTTTTCAGTGGTGTCGGAAACAGTGGTTTTAGGGCCACCAAATT
66 AAAATATATTGTAACAGCTCGTTTTTCAGTGGTGTCGGAAACAGTGGTTTTAGGGCCACCAAATT
*
4440791 CGACGAGTAAGGTCGTAAATATTATTATTTAATATTTACGAGTCAAATGTGTCTTAGGCTGTGTG
131 CGACGAGTAAGGTCGTAAATATTATTATTTAATATTTACGAGTCAAATGTGTCTTAGGCCGTGTG
4440856 AGCATTCGAAATAGGGACACACGGCCATGTCCCAGCCCGTGTGAGTATACTAACTTGGGTCACAC
196 AGCATTCGAAATAGGGACACACGGCCATGTCCCAGCCCGTGTGAGTATACTAACTTGGGTCACAC
4440921 GTATGAGTCACACGACCATGTGACCCCTGTAGTGTTGAAAATTTTAAGTGTTTCTGAAAAATTCT
261 GTATGAGTCACACGACCATGTGACCCCTGTAGTGTTGAAAATTTTAAGTGTTTCTGAAAAATTCT
*
4440986 CTAAGTTTCTGATTTAGTCCCGATCTGTTTCTAATGTGTATTTTGGGCTTCGAGGGCTCATATAA
326 CTAAGTTTCTGATTTAGTCCCGATCTGTTTCTAATGTGTATTTTGGGCTTCGAGGGCTCATACAA
*
4441051 GAGACAATATGTATTATTTTAATCGGTTTTTGACATGAATGCTATATGATATGAAATGTTTGCAT
391 GAGACAATATGTATTATTTTAATCAGTTTTTGACATGAATGCTATATGATATGAAATGTTTGCAT
4441116 TTTCTGTATGTTTAATTTGTAAACTCTGGTAATGCTTCGTAACCCTATTCTAGAGATGGATTCGG
456 TTTCTGTATGTTTAATTTGTAAACTCTGGTAATGCTTCGTAACCCTATTCTAGAGATGGATTCGG
*
4441181 GTTAGGGGTATTACAGTGTGGGCT
521 GTTAGGGGTACTACAGTGTGGGCT
4441205 TGAATCTTAAATTTCGGTACTTGAAGTTAAGAATTTATTGGAAAATAATATATGAGATTTAAATC
1 TGAATCTTAAATTTCGGTACTTGAAGTTAAGAATTTATTGGAAAATAATATATGAGATTTAAATC
*
4441270 AAAATATATTGTAACAGCTCGTTTTTCAGTGGTGTCGGAAACAGTGGTTTTGGGGCCACCAAATT
66 AAAATATATTGTAACAGCTCGTTTTTCAGTGGTGTCGGAAACAGTGGTTTTAGGGCCACCAAATT
* *
4441335 CGACGAGTAAGTTTGTAAATATTATTATTTAATATTTACGAGTCAAATGTGTCTTAGGCCGTGTG
131 CGACGAGTAAGGTCGTAAATATTATTATTTAATATTTACGAGTCAAATGTGTCTTAGGCCGTGTG
*
4441400 AGCATTCGAAATAGGGACACACGGCCATGTCCCAGCCTGTGTGAGTATACTAACTTGGGTCACAC
196 AGCATTCGAAATAGGGACACACGGCCATGTCCCAGCCCGTGTGAGTATACTAACTTGGGTCACAC
4441465 GTATGAGTCACACGACCATGTGACCCCTGTAGTGTTGAAAATTTTAAGTGTTTCTGAAAAATTCT
261 GTATGAGTCACACGACCATGTGACCCCTGTAGTGTTGAAAATTTTAAGTGTTTCTGAAAAATTCT
* * *
4441530 CTAAGTTTTTTATTTAGTCCCGATCTGTTTCTAATGTGTATTTTGGGCTTCGAGGGCTCTTACAA
326 CTAAGTTTCTGATTTAGTCCCGATCTGTTTCTAATGTGTATTTTGGGCTTCGAGGGCTCATACAA
4441595 GAGACAATATGTATTATTTTAATCAGTTTTTGACATGAATGCTATATGATATGAAATGTTTGCAT
391 GAGACAATATGTATTATTTTAATCAGTTTTTGACATGAATGCTATATGATATGAAATGTTTGCAT
*
4441660 TTTCTGTATGTTTAATTTGTAAACTCTGGTAATGCTTCGTAACCCTGTTCTAGAGATGGATTCGG
456 TTTCTGTATGTTTAATTTGTAAACTCTGGTAATGCTTCGTAACCCTATTCTAGAGATGGATTCGG
4441725 GTTAGGGGTACTACAGTGTGGGCT
521 GTTAGGGGTACTACAGTGTGGGCT
4441749 TGAA
1 TGAA
4441753 CTAGAGGTAC
Statistics
Matches: 535, Mismatches: 13, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
544 535 1.00
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.36
Consensus pattern (544 bp):
TGAATCTTAAATTTCGGTACTTGAAGTTAAGAATTTATTGGAAAATAATATATGAGATTTAAATC
AAAATATATTGTAACAGCTCGTTTTTCAGTGGTGTCGGAAACAGTGGTTTTAGGGCCACCAAATT
CGACGAGTAAGGTCGTAAATATTATTATTTAATATTTACGAGTCAAATGTGTCTTAGGCCGTGTG
AGCATTCGAAATAGGGACACACGGCCATGTCCCAGCCCGTGTGAGTATACTAACTTGGGTCACAC
GTATGAGTCACACGACCATGTGACCCCTGTAGTGTTGAAAATTTTAAGTGTTTCTGAAAAATTCT
CTAAGTTTCTGATTTAGTCCCGATCTGTTTCTAATGTGTATTTTGGGCTTCGAGGGCTCATACAA
GAGACAATATGTATTATTTTAATCAGTTTTTGACATGAATGCTATATGATATGAAATGTTTGCAT
TTTCTGTATGTTTAATTTGTAAACTCTGGTAATGCTTCGTAACCCTATTCTAGAGATGGATTCGG
GTTAGGGGTACTACAGTGTGGGCT
Found at i:4441944 original size:11 final size:11
Alignment explanation
Indices: 4441928--4441953 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
4441918 AAAAATTAAA
4441928 AAAAGTATTTT
1 AAAAGTATTTT
4441939 AAAAGTATTTT
1 AAAAGTATTTT
4441950 AAAA
1 AAAA
4441954 TTTTAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (11 bp):
AAAAGTATTTT
Found at i:4442000 original size:5 final size:5
Alignment explanation
Indices: 4441990--4442026 Score: 65
Period size: 5 Copynumber: 7.2 Consensus size: 5
4441980 TTTATTATAT
4441990 CGGGC CGGGC CGGGC CGGGC CGGGC CGGGCC CGGGC C
1 CGGGC CGGGC CGGGC CGGGC CGGGC CGGG-C CGGGC C
4442027 AAAAAAGTGG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 26 0.84
6 5 0.16
ACGTcount: A:0.00, C:0.43, G:0.57, T:0.00
Consensus pattern (5 bp):
CGGGC
Found at i:4443514 original size:9 final size:9
Alignment explanation
Indices: 4443502--4443534 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
4443492 GAATTATTCG
4443502 AATCGAGTT
1 AATCGAGTT
*
4443511 AATCAAGTT
1 AATCGAGTT
4443520 AATCGAGTT
1 AATCGAGTT
4443529 AATCGA
1 AATCGA
4443535 ATCAATTCGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.30
Consensus pattern (9 bp):
AATCGAGTT
Found at i:4443661 original size:29 final size:29
Alignment explanation
Indices: 4443621--4443679 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
4443611 GAATATAAAC
*
4443621 TATATTTTTTATTTTTAAAATACACCACA
1 TATATTTTTTATTTTTAAAAAACACCACA
*
4443650 TATATTTTTTATTTTTAAAAAACACTACA
1 TATATTTTTTATTTTTAAAAAACACCACA
4443679 T
1 T
4443680 TTAAAAATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.39, C:0.12, G:0.00, T:0.49
Consensus pattern (29 bp):
TATATTTTTTATTTTTAAAAAACACCACA
Found at i:4448594 original size:9 final size:9
Alignment explanation
Indices: 4448577--4448613 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
4448567 TGAGTTTTCG
4448577 AATTCGAAT
1 AATTCGAAT
*
4448586 AACTCGAAT
1 AATTCGAAT
4448595 AATTCGAAT
1 AATTCGAAT
4448604 AATTCGAAT
1 AATTCGAAT
4448613 A
1 A
4448614 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:4449548 original size:5 final size:5
Alignment explanation
Indices: 4449538--4449563 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
4449528 GAACAAATAT
4449538 ATTCG ATTCG ATTCG ATTCG ATTCG A
1 ATTCG ATTCG ATTCG ATTCG ATTCG A
4449564 ATTCCATCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.38
Consensus pattern (5 bp):
ATTCG
Found at i:4450971 original size:20 final size:18
Alignment explanation
Indices: 4450921--4450972 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 18
4450911 TTATAGGATA
4450921 AATATTAAATTAA-ATTT
1 AATATTAAATTAATATTT
4450938 AATATTAAGA-TAATTACTTT
1 AATATTAA-ATTAA-TA-TTT
4450958 AATATTAAATTAATA
1 AATATTAAATTAATA
4450973 AAATACTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
17 11 0.37
18 1 0.03
19 4 0.13
20 14 0.47
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (18 bp):
AATATTAAATTAATATTT
Found at i:4454065 original size:16 final size:16
Alignment explanation
Indices: 4454032--4454070 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
4454022 TATAATTAAC
*
4454032 TTAATT-AACCTAAGT
1 TTAATTAAACCTAAAT
*
4454047 TTAATTAAAGCTAAAT
1 TTAATTAAACCTAAAT
4454063 TTAATTAA
1 TTAATTAA
4454071 CAATTTTGGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 6 0.29
16 15 0.71
ACGTcount: A:0.46, C:0.08, G:0.05, T:0.41
Consensus pattern (16 bp):
TTAATTAAACCTAAAT
Found at i:4455989 original size:20 final size:20
Alignment explanation
Indices: 4455964--4456012 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
4455954 TCATTTCCAA
4455964 GTGTTT-ATAACTTGGGTTTT
1 GTGTTTAATAA-TTGGGTTTT
*
4455984 GTGTTTAATTATTGGGTTTT
1 GTGTTTAATAATTGGGTTTT
*
4456004 -TTTTTAATA
1 GTGTTTAATA
4456013 GGATGTTCCG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 7 0.28
20 15 0.60
21 3 0.12
ACGTcount: A:0.18, C:0.02, G:0.20, T:0.59
Consensus pattern (20 bp):
GTGTTTAATAATTGGGTTTT
Found at i:4461607 original size:20 final size:19
Alignment explanation
Indices: 4461569--4461607 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
4461559 CTGTAATGAG
4461569 ATTATTCAAAAAAAATATT
1 ATTATTCAAAAAAAATATT
* *
4461588 ATTATCTCATAAATAATATT
1 ATTAT-TCAAAAAAAATATT
4461608 TTGACCCTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (19 bp):
ATTATTCAAAAAAAATATT
Found at i:4465754 original size:30 final size:30
Alignment explanation
Indices: 4465718--4465786 Score: 120
Period size: 30 Copynumber: 2.3 Consensus size: 30
4465708 AATATCTCGT
4465718 TACCCATATCTTTGACTTTCCAATATTTGA
1 TACCCATATCTTTGACTTTCCAATATTTGA
* *
4465748 TACCCATATCTTTGACTTTCTATTATTTGA
1 TACCCATATCTTTGACTTTCCAATATTTGA
4465778 TACCCATAT
1 TACCCATAT
4465787 TTTTTATTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.26, C:0.23, G:0.06, T:0.45
Consensus pattern (30 bp):
TACCCATATCTTTGACTTTCCAATATTTGA
Found at i:4465761 original size:15 final size:16
Alignment explanation
Indices: 4465718--4465764 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 16
4465708 AATATCTCGT
4465718 TACCCATATCTTTGAC
1 TACCCATATCTTTGAC
** *
4465734 TTTCCA-ATATTTGA-
1 TACCCATATCTTTGAC
4465748 TACCCATATCTTTGAC
1 TACCCATATCTTTGAC
4465764 T
1 T
4465765 TTCTATTATT
Statistics
Matches: 23, Mismatches: 6, Indels: 4
0.70 0.18 0.12
Matches are distributed among these distances:
14 4 0.17
15 14 0.61
16 5 0.22
ACGTcount: A:0.26, C:0.26, G:0.06, T:0.43
Consensus pattern (16 bp):
TACCCATATCTTTGAC
Found at i:4467729 original size:18 final size:19
Alignment explanation
Indices: 4467703--4467740 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
4467693 GACGCAATTT
*
4467703 ATTTTTAAAAAATTA-TAA
1 ATTTATAAAAAATTACTAA
*
4467721 ATTTATAAAATATTACTAA
1 ATTTATAAAAAATTACTAA
4467740 A
1 A
4467741 AATATAATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (19 bp):
ATTTATAAAAAATTACTAA
Found at i:4468277 original size:18 final size:20
Alignment explanation
Indices: 4468235--4468277 Score: 54
Period size: 18 Copynumber: 2.2 Consensus size: 20
4468225 TTCATTAACA
*
4468235 TTTTTATAAATATTAATAAT
1 TTTTTACAAATATTAATAAT
*
4468255 ATTTTACAAAT-TT-ATAAT
1 TTTTTACAAATATTAATAAT
4468273 TTTTT
1 TTTTT
4468278 TATAATTTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 9 0.45
19 2 0.10
20 9 0.45
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (20 bp):
TTTTTACAAATATTAATAAT
Found at i:4470328 original size:2 final size:2
Alignment explanation
Indices: 4470321--4470345 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4470311 TGCTATAGTA
4470321 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
4470346 AGTACTGAAT
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:4475274 original size:2 final size:2
Alignment explanation
Indices: 4475261--4475307 Score: 85
Period size: 2 Copynumber: 23.0 Consensus size: 2
4475251 ACATCATAAG
4475261 TA TA TCA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4475304 TA TA
1 TA TA
4475308 CTACTATAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 42 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:4485091 original size:2 final size:2
Alignment explanation
Indices: 4485084--4485113 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
4485074 ATTCACATTC
*
4485084 AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4485114 GTCAATATGC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:4486562 original size:13 final size:13
Alignment explanation
Indices: 4486546--4486571 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4486536 AAAATGGGTG
4486546 GTCAAAAGTCAAA
1 GTCAAAAGTCAAA
4486559 GTCAAAAGTCAAA
1 GTCAAAAGTCAAA
4486572 TGATTTTATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.15, G:0.15, T:0.15
Consensus pattern (13 bp):
GTCAAAAGTCAAA
Found at i:4489306 original size:2 final size:2
Alignment explanation
Indices: 4489301--4489327 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4489291 AACAGATCAT
4489301 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
4489328 GTAATTATCT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4493268 original size:125 final size:123
Alignment explanation
Indices: 4493035--4493286 Score: 414
Period size: 125 Copynumber: 2.0 Consensus size: 123
4493025 AAATCCTTGT
* *
4493035 AACTCGTTCATACAACTGTTTTCAACTATCTGATCATGGTTTTAACTTCGTATTTATCAATTCAT
1 AACTCGTTCATACAACTGTTTTCAACTATCTGATCATGGTTTTAACTTCGAATTTATCAAATCAT
* *
4493100 AGCCATGCTTTCATAGACAACATTGTTAGGAATTAATATGATGAGAATGAAATCATCA
66 AGCCATGCTCTCATAGACAACATTGTTAGGAATTAATATGATGAGAATGAAACCATCA
* *
4493158 AACTCGTTCATAGACAACTGTTTTCAACTATCTGATCATGGTTTTAGCTTCGAATTTATTAAATC
1 AACTCGTTCAT--ACAACTGTTTTCAACTATCTGATCATGGTTTTAACTTCGAATTTATCAAATC
* *
4493223 ATATCCATGCTCTCATAGACAACATTGTTAGGAATTAGTATGATGAGAATGAAACCATCA
64 ATAGCCATGCTCTCATAGACAACATTGTTAGGAATTAATATGATGAGAATGAAACCATCA
4493283 AACT
1 AACT
4493287 AGGACCTGGT
Statistics
Matches: 119, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
123 11 0.09
125 108 0.91
ACGTcount: A:0.34, C:0.17, G:0.13, T:0.35
Consensus pattern (123 bp):
AACTCGTTCATACAACTGTTTTCAACTATCTGATCATGGTTTTAACTTCGAATTTATCAAATCAT
AGCCATGCTCTCATAGACAACATTGTTAGGAATTAATATGATGAGAATGAAACCATCA
Found at i:4496378 original size:19 final size:20
Alignment explanation
Indices: 4496354--4496392 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
4496344 ACTTAATTTT
*
4496354 TTAAATTAA-AATAGAGTTA
1 TTAAATAAAGAATAGAGTTA
*
4496373 TTAAATAAAGAATTGAGTTA
1 TTAAATAAAGAATAGAGTTA
4496393 AAGGGGAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.51, C:0.00, G:0.13, T:0.36
Consensus pattern (20 bp):
TTAAATAAAGAATAGAGTTA
Found at i:4496634 original size:19 final size:19
Alignment explanation
Indices: 4496610--4496678 Score: 95
Period size: 19 Copynumber: 3.7 Consensus size: 19
4496600 TAATATTTTG
4496610 TTAAATTAAAATAGAGTTA
1 TTAAATTAAAATAGAGTTA
* * *
4496629 TTAAATGAGAATAG-TTTA
1 TTAAATTAAAATAGAGTTA
4496647 TTAAATTAAAATAGAGTTA
1 TTAAATTAAAATAGAGTTA
*
4496666 TTAAATAAAAATA
1 TTAAATTAAAATA
4496679 ATAAATAAGG
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
18 15 0.36
19 27 0.64
ACGTcount: A:0.54, C:0.00, G:0.10, T:0.36
Consensus pattern (19 bp):
TTAAATTAAAATAGAGTTA
Found at i:4496652 original size:37 final size:37
Alignment explanation
Indices: 4496601--4496671 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
4496591 AGTATTAATT
* *
4496601 AATATTTTGTTAAATTAAAATAGAGTTATTAAATGAG
1 AATAGTTTATTAAATTAAAATAGAGTTATTAAATGAG
4496638 AATAGTTTATTAAATTAAAATAGAGTTATTAAAT
1 AATAGTTTATTAAATTAAAATAGAGTTATTAAAT
4496672 AAAAATAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.48, C:0.00, G:0.11, T:0.41
Consensus pattern (37 bp):
AATAGTTTATTAAATTAAAATAGAGTTATTAAATGAG
Found at i:4496780 original size:27 final size:27
Alignment explanation
Indices: 4496725--4496809 Score: 104
Period size: 27 Copynumber: 3.2 Consensus size: 27
4496715 TTTTTTTTCC
*
4496725 TTTGGCACCA-TGGTG-CGCCAA-TGA
1 TTTGGCACCATTGGTGCCGCCAATTTA
*
4496749 CTTTGGCACCATTGGTGCCACCAATTTA
1 -TTTGGCACCATTGGTGCCGCCAATTTA
*
4496777 TTTGGCACCTTTGGTGCCGCCAATTTA
1 TTTGGCACCATTGGTGCCGCCAATTTA
*
4496804 ATTGGC
1 TTTGGC
4496810 CTGATCAGGC
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
25 10 0.19
26 5 0.10
27 35 0.67
28 2 0.04
ACGTcount: A:0.19, C:0.26, G:0.24, T:0.32
Consensus pattern (27 bp):
TTTGGCACCATTGGTGCCGCCAATTTA
Found at i:4496918 original size:27 final size:23
Alignment explanation
Indices: 4496857--4496904 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
4496847 GTTTTTTTTG
*
4496857 ATATATTTTGATAAATAAAAAAA
1 ATATATTTTGGTAAATAAAAAAA
4496880 ATATATTTTGGTAAATAAAAAAA
1 ATATATTTTGGTAAATAAAAAAA
4496903 AT
1 AT
4496905 TATAACATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.35
Consensus pattern (23 bp):
ATATATTTTGGTAAATAAAAAAA
Found at i:4501338 original size:4 final size:4
Alignment explanation
Indices: 4501329--4501366 Score: 67
Period size: 4 Copynumber: 9.5 Consensus size: 4
4501319 AAATATCTAT
*
4501329 ATCC ATCC ATCC ATCC ATCC ATCC GTCC ATCC ATCC AT
1 ATCC ATCC ATCC ATCC ATCC ATCC ATCC ATCC ATCC AT
4501367 ACATGTGTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.24, C:0.47, G:0.03, T:0.26
Consensus pattern (4 bp):
ATCC
Found at i:4505355 original size:27 final size:27
Alignment explanation
Indices: 4505300--4505363 Score: 76
Period size: 27 Copynumber: 2.3 Consensus size: 27
4505290 AAAATATTAT
4505300 AATTAAATTATAAAATTTTAAATGGTTA
1 AATT-AATTATAAAATTTTAAATGGTTA
**
4505328 AATTAATT-TAAAATTTTACAATTTTTA
1 AATTAATTATAAAATTTTA-AATGGTTA
*
4505355 AAATAATTA
1 AATTAATTA
4505364 AATTATAAGG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
26 10 0.32
27 17 0.55
28 4 0.13
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (27 bp):
AATTAATTATAAAATTTTAAATGGTTA
Found at i:4506581 original size:18 final size:19
Alignment explanation
Indices: 4506560--4506595 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
4506550 AACTTGAGCT
*
4506560 TTAAATTGA-ATATTAAAA
1 TTAAATTCATATATTAAAA
4506578 TTAAATTCATATATTAAA
1 TTAAATTCATATATTAAA
4506596 TGATATATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (19 bp):
TTAAATTCATATATTAAAA
Found at i:4510337 original size:2 final size:2
Alignment explanation
Indices: 4510326--4510392 Score: 127
Period size: 2 Copynumber: 34.0 Consensus size: 2
4510316 AAGGAAGTTC
4510326 AT AT -T 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
4510367 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
4510393 GAAGGGACCC
Statistics
Matches: 64, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 63 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:4510678 original size:15 final size:16
Alignment explanation
Indices: 4510654--4510702 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 16
4510644 AGTTTAGAAT
4510654 AATAAGTATAACTATA
1 AATAAGTATAACTATA
*
4510670 AATAA-TATATGCTAT-
1 AATAAGTATA-ACTATA
*
4510685 AATAATTATAACTA-A
1 AATAAGTATAACTATA
4510700 AAT
1 AAT
4510703 TAGATTAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
15 15 0.54
16 13 0.46
ACGTcount: A:0.55, C:0.06, G:0.04, T:0.35
Consensus pattern (16 bp):
AATAAGTATAACTATA
Found at i:4521952 original size:71 final size:70
Alignment explanation
Indices: 4521791--4521957 Score: 182
Period size: 70 Copynumber: 2.4 Consensus size: 70
4521781 CTTTACACAA
* *
4521791 CGCTAGTCGGATAACCGACAATAGTTGTGCCCAACACTAGTTGAACGGATCGACAAATTATTGCA
1 CGCTAGTCGGATAACCAACAATAGTTGTGCCCAACACTAGTTAAACGGATCGACAAATTATTGCA
4521856 CCCAG
66 CCCAG
* * * *
4521861 CACT-GATCGGATAACCAACAATAGTTGTGCCTAGCACTAGTCAAATAAACTGA-CAGA-AAA-T
1 CGCTAG-TCGGATAACCAACAATAGTTGTGCCCAACACTAGT----TAAACGGATC-GACAAATT
*
4521922 -TTGCGCCCAG
60 ATTGCACCCAG
4521932 CGCTAGTCGGATAACCAACAATAGTT
1 CGCTAGTCGGATAACCAACAATAGTT
4521958 ACTCAATCAA
Statistics
Matches: 82, Mismatches: 8, Indels: 13
0.80 0.08 0.13
Matches are distributed among these distances:
69 1 0.01
70 35 0.43
71 32 0.39
72 2 0.02
73 4 0.05
74 8 0.10
ACGTcount: A:0.34, C:0.25, G:0.20, T:0.22
Consensus pattern (70 bp):
CGCTAGTCGGATAACCAACAATAGTTGTGCCCAACACTAGTTAAACGGATCGACAAATTATTGCA
CCCAG
Found at i:4522860 original size:54 final size:54
Alignment explanation
Indices: 4522760--4522906 Score: 243
Period size: 54 Copynumber: 2.8 Consensus size: 54
4522750 AAGTTGAAGG
4522760 ACCAATGGTGTAAATATTTTAAGGGTGGTATGATCTAG------AAACTAAGGAA
1 ACCAAT-GTGTAAATATTTTAAGGGTGGTATGATCTAGAAACTAAAACTAAGGAA
4522809 ACCAATGTGTAAATATTTTAAGGGTGGTATGATCTAGAAACTAAAACTAAGGAA
1 ACCAATGTGTAAATATTTTAAGGGTGGTATGATCTAGAAACTAAAACTAAGGAA
4522863 ACCAATGTGTAAATATTTTAAGGGTGGTATGATCTAGAAACTAA
1 ACCAATGTGTAAATATTTTAAGGGTGGTATGATCTAGAAACTAA
4522907 GGAAAATGGA
Statistics
Matches: 92, Mismatches: 0, Indels: 7
0.93 0.00 0.07
Matches are distributed among these distances:
48 31 0.34
49 6 0.07
54 55 0.60
ACGTcount: A:0.40, C:0.09, G:0.22, T:0.29
Consensus pattern (54 bp):
ACCAATGTGTAAATATTTTAAGGGTGGTATGATCTAGAAACTAAAACTAAGGAA
Found at i:4523765 original size:16 final size:16
Alignment explanation
Indices: 4523714--4523758 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 16
4523704 GGGTGAGAAG
4523714 TAAAAGTTTTGGGGAAAAA
1 TAAAAGTTTTGGGG---AA
4523733 TAAAAAGTTTTGGGGAA
1 T-AAAAGTTTTGGGGAA
4523750 TAAAAGTTT
1 TAAAAGTTT
4523759 GAGGGAAAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 8 0.32
17 3 0.12
19 1 0.04
20 13 0.52
ACGTcount: A:0.44, C:0.00, G:0.24, T:0.31
Consensus pattern (16 bp):
TAAAAGTTTTGGGGAA
Found at i:4525065 original size:22 final size:22
Alignment explanation
Indices: 4525040--4525082 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
4525030 ATCATGAGAT
* *
4525040 ATAATAAATTTGAATAAAAATC
1 ATAAAAAAATTGAATAAAAATC
4525062 ATAAAAAAATTGAATAAAAAT
1 ATAAAAAAATTGAATAAAAAT
4525083 AATTAGAGGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.65, C:0.02, G:0.05, T:0.28
Consensus pattern (22 bp):
ATAAAAAAATTGAATAAAAATC
Found at i:4531163 original size:20 final size:20
Alignment explanation
Indices: 4531138--4531181 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
4531128 CGTGCGTCTC
4531138 TTCTTTCTCCCTTT-CTTTCT
1 TTCTTTCT-CCTTTCCTTTCT
*
4531158 TTCTTTCTCTTTTCCTTTCT
1 TTCTTTCTCCTTTCCTTTCT
4531178 TTCT
1 TTCT
4531182 AATTTGTATG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (20 bp):
TTCTTTCTCCTTTCCTTTCT
Found at i:4532325 original size:18 final size:20
Alignment explanation
Indices: 4532287--4532325 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
4532277 CCCGGAAATG
*
4532287 AAAAATTTTCTAATATTTAT
1 AAAAATTTTCAAATATTTAT
4532307 AAAAA-TTTCAAAT-TTTAT
1 AAAAATTTTCAAATATTTAT
4532325 A
1 A
4532326 TTTTTAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
19 7 0.39
20 5 0.28
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (20 bp):
AAAAATTTTCAAATATTTAT
Found at i:4535676 original size:3 final size:3
Alignment explanation
Indices: 4535668--4535705 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
4535658 ACGCTACCGC
* *
4535668 TGT TGT TGT TAT TTT TGT TGT TGT TGT TGT TGT TGT TG
1 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TG
4535706 CCACCTTCGT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.03, C:0.00, G:0.29, T:0.68
Consensus pattern (3 bp):
TGT
Found at i:4554034 original size:21 final size:20
Alignment explanation
Indices: 4554008--4554054 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
4553998 AAAAAGTAGC
4554008 TTTTTTTCACATTTTCAATT
1 TTTTTTTCACATTTTCAATT
* * *
4554028 TTTTTTTGACTTTTTCAAAT
1 TTTTTTTCACATTTTCAATT
4554048 TTTTTTT
1 TTTTTTT
4554055 ATTGTTAGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.17, C:0.11, G:0.02, T:0.70
Consensus pattern (20 bp):
TTTTTTTCACATTTTCAATT
Found at i:4563795 original size:2 final size:2
Alignment explanation
Indices: 4563790--4563816 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4563780 TTTTTTTACT
4563790 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
4563817 CTAATTCGAC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4567974 original size:19 final size:20
Alignment explanation
Indices: 4567934--4567976 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
4567924 CTATACCAAC
*
4567934 AAATAATTTAAAAATTATAA
1 AAATAATTTAAAAATTAAAA
4567954 AAAT-ATTTAATAAA-TAAAA
1 AAATAATTTAA-AAATTAAAA
4567973 AAAT
1 AAAT
4567977 TCAAAGTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
AAATAATTTAAAAATTAAAA
Found at i:4567975 original size:20 final size:20
Alignment explanation
Indices: 4567934--4567975 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
4567924 CTATACCAAC
* *
4567934 AAATAATTTAAAAATTATAA
1 AAATAATTTAAAAATAAAAA
4567954 AAAT-ATTTAATAAATAAAAA
1 AAATAATTTAA-AAATAAAAA
4567974 AA
1 AA
4567976 TTCAAAGTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (20 bp):
AAATAATTTAAAAATAAAAA
Found at i:4567991 original size:2 final size:2
Alignment explanation
Indices: 4567986--4568010 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4567976 TTCAAAGTTA
4567986 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
4568011 AAGTTCATAA
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:4570303 original size:51 final size:51
Alignment explanation
Indices: 4570195--4570525 Score: 466
Period size: 51 Copynumber: 6.4 Consensus size: 51
4570185 TGATCATTTA
* *
4570195 TCACTTGTCCCTGATCAGATAAGTGTAGCT-AAGCTACCACTTATCACTTG
1 TCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTATCACTTATCACTTG
* * * *
4570245 CCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCACTTG
1 TCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTATCACTTATCACTTG
*
4570296 TAACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTATCACTTATCACTTG
1 TCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTATCACTTATCACTTG
* * * *
4570347 TCATTTGTCACTAATCAAATAAGTGTAGTTGAAGCTATCACTTATCACTTGCCACTTG
1 TCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTATCAC-T-T-A--T--CACTTG
4570405 TCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTATCACTTATCACTTG
1 TCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTATCACTTATCACTTG
* * *
4570456 CCATTTGTCACTGATCAGATAAGTGTAGCTGAAGCTATCACTTATCACTTA
1 TCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTATCACTTATCACTTG
4570507 TCACTTGTCACTGATCAGA
1 TCACTTGTCACTGATCAGA
4570526 AGTACTCAAA
Statistics
Matches: 251, Mismatches: 22, Indels: 15
0.87 0.08 0.05
Matches are distributed among these distances:
50 28 0.11
51 172 0.69
52 1 0.00
53 2 0.01
54 1 0.00
55 1 0.00
56 2 0.01
57 1 0.00
58 43 0.17
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.33
Consensus pattern (51 bp):
TCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTATCACTTATCACTTG
Found at i:4570432 original size:109 final size:109
Alignment explanation
Indices: 4570195--4570518 Score: 493
Period size: 109 Copynumber: 3.0 Consensus size: 109
4570185 TGATCATTTA
* * *
4570195 TCACTTGTCCCTGATCAGATAAGTGTAGCT-AAGCTACCACTTATCACTTGCCACTTGTCACTGA
1 TCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTATCACTTATCACTTGCCATTTGTCACTGA
*
4570259 TCAGATAAGTGTAGCT-AA---A--AC-TACCACTTATCACTTG
66 TCAGATAAGTGTAGCTGAAGCTATCACTTATCACTTATCACTTG
* * *
4570296 TAACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTATCACTTATCACTTGTCATTTGTCACTAA
1 TCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTATCACTTATCACTTGCCATTTGTCACTGA
* * **
4570361 TCAAATAAGTGTAGTTGAAGCTATCACTTATCACTTGCCACTTG
66 TCAGATAAGTGTAGCTGAAGCTATCACTTATCACTTATCACTTG
4570405 TCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTATCACTTATCACTTGCCATTTGTCACTGA
1 TCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTATCACTTATCACTTGCCATTTGTCACTGA
4570470 TCAGATAAGTGTAGCTGAAGCTATCACTTATCACTTATCACTTG
66 TCAGATAAGTGTAGCTGAAGCTATCACTTATCACTTATCACTTG
4570514 TCACT
1 TCACT
4570519 GATCAGAAGT
Statistics
Matches: 197, Mismatches: 18, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
101 28 0.14
102 44 0.22
103 2 0.01
106 1 0.01
108 2 0.01
109 120 0.61
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.33
Consensus pattern (109 bp):
TCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTATCACTTATCACTTGCCATTTGTCACTGA
TCAGATAAGTGTAGCTGAAGCTATCACTTATCACTTATCACTTG
Found at i:4572265 original size:17 final size:18
Alignment explanation
Indices: 4572239--4572273 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
4572229 TAGTGGGAGA
*
4572239 TTATTTTGGGAT-TTTTT
1 TTATTATGGGATATTTTT
4572256 TTATTATGGGATATTTTT
1 TTATTATGGGATATTTTT
4572274 CCTTAATTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.17, C:0.00, G:0.17, T:0.66
Consensus pattern (18 bp):
TTATTATGGGATATTTTT
Found at i:4579732 original size:17 final size:17
Alignment explanation
Indices: 4579710--4579743 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
4579700 GACCGGCCAA
4579710 AGAAAAAAAATCTTTTT
1 AGAAAAAAAATCTTTTT
4579727 AGAAAAAAAATCTTTTT
1 AGAAAAAAAATCTTTTT
4579744 CAAACTCTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.06, G:0.06, T:0.35
Consensus pattern (17 bp):
AGAAAAAAAATCTTTTT
Found at i:4585967 original size:19 final size:19
Alignment explanation
Indices: 4585938--4585990 Score: 63
Period size: 18 Copynumber: 2.8 Consensus size: 19
4585928 ATTTTACAAC
* *
4585938 TTTTTAGAAAATGAAAATTA
1 TTTTTA-AAAATCAAAAATA
4585958 TTTTTAAAAA-CAAAAATA
1 TTTTTAAAAATCAAAAATA
*
4585976 TTTTTCAAAATCAAA
1 TTTTTAAAAATCAAA
4585991 GGAAGGATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
18 15 0.52
19 8 0.28
20 6 0.21
ACGTcount: A:0.53, C:0.06, G:0.04, T:0.38
Consensus pattern (19 bp):
TTTTTAAAAATCAAAAATA
Found at i:4587411 original size:10 final size:10
Alignment explanation
Indices: 4587377--4587411 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
4587367 AAATGGCATG
4587377 AAAATAAATA
1 AAAATAAATA
**
4587387 AAACGAAATA
1 AAAATAAATA
4587397 AAAATAAATA
1 AAAATAAATA
4587407 AAAAT
1 AAAAT
4587412 TATACAAGTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.77, C:0.03, G:0.03, T:0.17
Consensus pattern (10 bp):
AAAATAAATA
Found at i:4588199 original size:20 final size:21
Alignment explanation
Indices: 4588174--4588218 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
4588164 GTAGTTGAAA
4588174 AAAAAATCAAAACTTTT-TTT
1 AAAAAATCAAAACTTTTCTTT
**
4588194 AAAAAATTTAAACTTTTCTTT
1 AAAAAATCAAAACTTTTCTTT
4588215 AAAA
1 AAAA
4588219 TAACTAAGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 15 0.68
21 7 0.32
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (21 bp):
AAAAAATCAAAACTTTTCTTT
Found at i:4588405 original size:153 final size:154
Alignment explanation
Indices: 4587984--4588416 Score: 530
Period size: 154 Copynumber: 2.8 Consensus size: 154
4587974 AAATCATTAA
* **
4587984 TTTTCTTAAAAATCAAAAC-TTTA-TTTCGAAATAGTT----AAAAAATCAAAAAATTATTTTAA
1 TTTTCTTAAAAATTAAAACTTTTACTTT-GAAATAGTTGAAAAAAAAATCAAAACTTTATTTTAA
* * * * * *
4588043 AATTTTAAACTTTCCTCTAAAATGACTTAAAAAACATATTTTTATTTTTCAAAATCTAAATTTTC
65 AATTTTAAACTTTCTTTTAAAATAACTAAAAAAACAGATTTTTATTTTTCAAAATCTAAACTTTC
* *
4588108 TCCCTTTTTTTTAAAAAAATACTAT
130 TCCCTTTTTGTTAAAAAAACACTAT
* * *
4588133 TTTTCTTAAAAATTAAAATTTTTATTTTGAAGTAGTTGAAAAAAAAATCAAAACTTT-TTTTAAA
1 TTTTCTTAAAAATTAAAACTTTTACTTTGAAATAGTTGAAAAAAAAATCAAAACTTTATTTT-AA
* *
4588197 AAATTTAAACTTT-TCTTTAAAATAACTAAGAAAAACAGATTTTTATTTTTCAAAATATAAACTT
65 AATTTTAAACTTTCT-TTTAAAATAACTAA-AAAAACAGATTTTTATTTTTCAAAATCTAAACTT
4588261 TCT-CCTTTTTGTTAAAAAAACACTAT
128 TCTCCCTTTTTGTTAAAAAAACACTAT
* *
4588287 TTTTCTTAAAGATTAAAGCTTTTACTTTGAAAT-GATTG-AAAAAAAATCAAAACTTTATTTTAA
1 TTTTCTTAAAAATTAAAACTTTTACTTTGAAATAG-TTGAAAAAAAAATCAAAACTTTATTTTAA
* * *
4588350 AATTTTAAACTTTCTTTTAAACTAACTAAAAAAAAAGGAATTTTATTTGTT-AAAATCTAAACTT
65 AATTTTAAACTTTCTTTTAAAATAACTAAAAAAACA-GATTTTTATTT-TTCAAAATCTAAACTT
4588414 TCT
128 TCT
4588417 ATTTTGCAGA
Statistics
Matches: 245, Mismatches: 25, Indels: 24
0.83 0.09 0.08
Matches are distributed among these distances:
149 17 0.07
150 12 0.05
151 3 0.01
152 6 0.02
153 75 0.31
154 98 0.40
155 34 0.14
ACGTcount: A:0.43, C:0.10, G:0.04, T:0.42
Consensus pattern (154 bp):
TTTTCTTAAAAATTAAAACTTTTACTTTGAAATAGTTGAAAAAAAAATCAAAACTTTATTTTAAA
ATTTTAAACTTTCTTTTAAAATAACTAAAAAAACAGATTTTTATTTTTCAAAATCTAAACTTTCT
CCCTTTTTGTTAAAAAAACACTAT
Found at i:4588728 original size:151 final size:152
Alignment explanation
Indices: 4588569--4588960 Score: 488
Period size: 153 Copynumber: 2.6 Consensus size: 152
4588559 CTAAATAGTT
* * * *
4588569 AAAAAAATCAAAAATTTATTTTAAAATTTTAAACTTTCCTCTAAAATGACTTAAAAAACATATTT
1 AAAAAAATCAAAACTTTATTTTAAAATTTTAAACTTTCCTTTAAAATAACTTAAAAAACAGATTT
4588634 TTATTTTTCAAAATCTAAATTTTATCTTT-TAAAAAAAAAACACTATTTTTCTTAAAAATTAAAA
66 TTATTTTTCAAAATCTAAATTTTATCTTTGTAAAAAAAAAACACTATTTTTCTTAAAAATTAAAA
* * * *
4588698 TTTTTATTTTGAAGT-AGTTGAA
131 CTTTCACTTTGAAATGA-TTGAA
* * *
4588720 AAAAAAATCAAAACTTT-TTTTAAAAAATTTAAACTTTTCTTTAAAATAACTAAAAAAACAGATT
1 AAAAAAATCAAAACTTTATTTT-AAAATTTTAAACTTTCCTTTAAAATAACTTAAAAAACAGATT
* * ** * * *
4588784 TTTATTTTTCAAAATATAAACTCTCCTTTTTGTTAAAAAAAAACACTATTTTTCTTAAAGATTAA
65 TTTATTTTTCAAAATCTAAA-TTTTATCTTTGTAAAAAAAAAACACTATTTTTCTTAAAAATTAA
*
4588849 AGCTTTCACTTTGAAATGATTGAA
129 AACTTTCACTTTGAAATGATTGAA
* * * * *
4588873 AATAAAATTAAAACTTTATTTTAAAATTTTAAACTTTCTTTTAAAATAAC-TAAAAAAAAGGAAT
1 AAAAAAATCAAAACTTTATTTTAAAATTTTAAACTTTCCTTTAAAATAACTTAAAAAACA-GATT
4588937 TTTATTTGTT-AAAATCTAAATTTT
65 TTTATTT-TTCAAAATCTAAATTTT
4588961 CTATTTTGCA
Statistics
Matches: 204, Mismatches: 30, Indels: 13
0.83 0.12 0.05
Matches are distributed among these distances:
150 4 0.02
151 71 0.35
152 15 0.07
153 107 0.52
154 7 0.03
ACGTcount: A:0.46, C:0.09, G:0.04, T:0.41
Consensus pattern (152 bp):
AAAAAAATCAAAACTTTATTTTAAAATTTTAAACTTTCCTTTAAAATAACTTAAAAAACAGATTT
TTATTTTTCAAAATCTAAATTTTATCTTTGTAAAAAAAAAACACTATTTTTCTTAAAAATTAAAA
CTTTCACTTTGAAATGATTGAA
Found at i:4588746 original size:20 final size:21
Alignment explanation
Indices: 4588721--4588765 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
4588711 GTAGTTGAAA
4588721 AAAAAATCAAAACTTTT-TTT
1 AAAAAATCAAAACTTTTCTTT
**
4588741 AAAAAATTTAAACTTTTCTTT
1 AAAAAATCAAAACTTTTCTTT
4588762 AAAA
1 AAAA
4588766 TAACTAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 15 0.68
21 7 0.32
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (21 bp):
AAAAAATCAAAACTTTTCTTT
Found at i:4588870 original size:546 final size:545
Alignment explanation
Indices: 4588012--4589099 Score: 1952
Period size: 546 Copynumber: 2.0 Consensus size: 545
4588002 CTTTATTTCG
4588012 AAATAGTTAAAAAATCAAAAAATTATTTTAAAATTTTAAACTTTCCTCTAAAATGACTTAAAAAA
1 AAATAGTTAAAAAATCAAAAAATTATTTTAAAATTTTAAACTTTCCTCTAAAATGACTTAAAAAA
* *** *
4588077 CATATTTTTATTTTTCAAAATCTAAATTTTCTCCCTTTTTTTTAAAAAAATACTATTTTTCTTAA
66 CATATTTTTATTTTTCAAAATCTAAATTTTAT-CCTTTTTAAAAAAAAAACACTATTTTTCTTAA
4588142 AAATTAAAATTTTTATTTTGAAGTAGTTGAAAAAAAAATCAAAACTTTTTTTAAAAAATTTAAAC
130 AAATTAAAATTTTTATTTTGAAGTAGTTGAAAAAAAAATCAAAACTTTTTTTAAAAAATTTAAAC
4588207 TTTTCTTTAAAATAACTAAGAAAAACAGATTTTTATTTTTCAAAATATAAACTTTCTCCTTTTTG
195 TTTTCTTTAAAATAACTAAGAAAAACAGATTTTTATTTTTCAAAATATAAAC-TTCTCCTTTTTG
*
4588272 TTAAAAAAACACTATTTTTCTTAAAGATTAAAGCTTTTACTTTGAAATGATTGAAAA-AAAATCA
259 TTAAAAAAACACTATTTTTCTTAAAGATTAAAGCTTTCACTTTGAAATGATTGAAAATAAAATCA
*
4588336 AAACTTTATTTTAAAATTTTAAACTTTCTTTTAAACTAACTAAAAAAAAAGGAATTTTATTTGTT
324 AAACTTTATTTTAAAATTTTAAACTTTCTTTTAAAATAACT-AAAAAAAAGGAATTTTATTTGTT
*
4588401 AAAATCTAAACTTTCTATTTTGCAGAAAAAATTCAAAACTTTTTCCAAAATCAAGCCATTTAAAA
388 AAAATCTAAACTTTCTATTTTGCAGAAAAAATTCAAAACTTTTCCCAAAATCAAGCCATTT--AA
4588466 AAAAAACCTTTATTTTAGAAAGGGGAGAGAAAAAACAAGATTTTTGGGGCTTCCTAGGGGAGGAG
451 AAAAAACCTTTATTTTAGAAAGGGGAGAGAAAAAACAAGATTTTTGGGGCTTCCTAGGGGAGGAG
* *
4588531 AACCGATGTCCGGTGACGTCCCCTTTATCT
516 AACCAACGTCCGGTGACGTCCCCTTTATCT
*
4588561 AAATAGTTAAAAAAATCAAAAATTTATTTTAAAATTTTAAACTTTCCTCTAAAATGACTTAAAAA
1 AAATAGTT-AAAAAATCAAAAAATTATTTTAAAATTTTAAACTTTCCTCTAAAATGACTTAAAAA
4588626 ACATATTTTTATTTTTCAAAATCTAAATTTTAT-C-TTTTAAAAAAAAAACACTATTTTTCTTAA
65 ACATATTTTTATTTTTCAAAATCTAAATTTTATCCTTTTTAAAAAAAAAACACTATTTTTCTTAA
4588689 AAATTAAAATTTTTATTTTGAAGTAGTTGAAAAAAAAATCAAAACTTTTTTTAAAAAATTTAAAC
130 AAATTAAAATTTTTATTTTGAAGTAGTTGAAAAAAAAATCAAAACTTTTTTTAAAAAATTTAAAC
4588754 TTTTCTTTAAAATAACTAA-AAAAACAGATTTTTATTTTTCAAAATATAAAC-TCTCCTTTTTGT
195 TTTTCTTTAAAATAACTAAGAAAAACAGATTTTTATTTTTCAAAATATAAACTTCTCCTTTTTGT
*
4588817 TAAAAAAAAACACTATTTTTCTTAAAGATTAAAGCTTTCACTTTGAAATGATTGAAAATAAAATT
260 T--AAAAAAACACTATTTTTCTTAAAGATTAAAGCTTTCACTTTGAAATGATTGAAAATAAAATC
4588882 AAAACTTTATTTTAAAATTTTAAACTTTCTTTTAAAATAACTAAAAAAAAGGAATTTTATTTGTT
323 AAAACTTTATTTTAAAATTTTAAACTTTCTTTTAAAATAACTAAAAAAAAGGAATTTTATTTGTT
*
4588947 AAAATCTAAATTTTCTATTTTGCAGAAAAAATTCAAAACTTTTCCCAAAATCAAGCCATTTAAAA
388 AAAATCTAAACTTTCTATTTTGCAGAAAAAATTCAAAACTTTTCCCAAAATCAAGCCATTTAAAA
4589012 AAAACCTTTATTTTAGAAAGGGGAGAGAAAAAACAAGATTTTTGGGGCTTCCTAGGGGAGGAGAA
453 AAAACCTTTATTTTAGAAAGGGGAGAGAAAAAACAAGATTTTTGGGGCTTCCTAGGGGAGGAGAA
4589077 CCAACGTCCGGTGACGTCCCCTT
518 CCAACGTCCGGTGACGTCCCCTT
4589100 CATCGAAACC
Statistics
Matches: 522, Mismatches: 13, Indels: 13
0.95 0.02 0.02
Matches are distributed among these distances:
544 103 0.20
546 168 0.32
547 155 0.30
548 1 0.00
549 8 0.02
550 87 0.17
ACGTcount: A:0.43, C:0.11, G:0.08, T:0.38
Consensus pattern (545 bp):
AAATAGTTAAAAAATCAAAAAATTATTTTAAAATTTTAAACTTTCCTCTAAAATGACTTAAAAAA
CATATTTTTATTTTTCAAAATCTAAATTTTATCCTTTTTAAAAAAAAAACACTATTTTTCTTAAA
AATTAAAATTTTTATTTTGAAGTAGTTGAAAAAAAAATCAAAACTTTTTTTAAAAAATTTAAACT
TTTCTTTAAAATAACTAAGAAAAACAGATTTTTATTTTTCAAAATATAAACTTCTCCTTTTTGTT
AAAAAAACACTATTTTTCTTAAAGATTAAAGCTTTCACTTTGAAATGATTGAAAATAAAATCAAA
ACTTTATTTTAAAATTTTAAACTTTCTTTTAAAATAACTAAAAAAAAGGAATTTTATTTGTTAAA
ATCTAAACTTTCTATTTTGCAGAAAAAATTCAAAACTTTTCCCAAAATCAAGCCATTTAAAAAAA
ACCTTTATTTTAGAAAGGGGAGAGAAAAAACAAGATTTTTGGGGCTTCCTAGGGGAGGAGAACCA
ACGTCCGGTGACGTCCCCTTTATCT
Found at i:4588899 original size:19 final size:19
Alignment explanation
Indices: 4588875--4588919 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
4588865 TGATTGAAAA
4588875 TAAAATTAAAACTTTATTT
1 TAAAATTAAAACTTTATTT
* *
4588894 TAAAATTTTAAACTTTCTTT
1 TAAAA-TTAAAACTTTATTT
4588914 TAAAAT
1 TAAAAT
4588920 AACTAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (19 bp):
TAAAATTAAAACTTTATTT
Found at i:4593648 original size:120 final size:120
Alignment explanation
Indices: 4593514--4593782 Score: 416
Period size: 122 Copynumber: 2.2 Consensus size: 120
4593504 TCAGTTTTTT
* * *
4593514 AATCAGTTTTTAGTTTTAATTTATTTATAAAATC-TT-TAAGTTTTTTTTTTCCTTTTTGCCAAA
1 AATCACTTTTTAGTTTTAATTTATTTATAAAATCTTTATAAG-ATTCTTTTTCCTTTTTGCCAAA
**
4593577 AGTATTTAAGAGTTTTAATAAATATCTATCACTACAAATAACCATTCAATGCAAAAA
65 AGTATTTAAGAGTTGCAATAAATATCTATCACTACAAATAACCATTCAAT-CAAAAA
4593634 AATCACTTTTTAGTTTTAATTTATTTATAAAATCTTTTATAAGATTCTTTTTCCTTTTTGCCAAA
1 AATCACTTTTTAGTTTTAATTTATTTATAAAATC-TTTATAAGATTCTTTTTCCTTTTTGCCAAA
* * *
4593699 GGTATTTAAGAGTTGCAATAAATATCTATCACTACAAATAACCATTTAATTAAAAA
65 AGTATTTAAGAGTTGCAATAAATATCTATCACTACAAATAACCATTCAATCAAAAA
*
4593755 AATCACTTTTTAGTTTTAATTTCTTTAT
1 AATCACTTTTTAGTTTTAATTTATTTAT
4593783 GAATAATAAA
Statistics
Matches: 137, Mismatches: 9, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
120 33 0.24
121 32 0.23
122 68 0.50
123 4 0.03
ACGTcount: A:0.36, C:0.12, G:0.06, T:0.46
Consensus pattern (120 bp):
AATCACTTTTTAGTTTTAATTTATTTATAAAATCTTTATAAGATTCTTTTTCCTTTTTGCCAAAA
GTATTTAAGAGTTGCAATAAATATCTATCACTACAAATAACCATTCAATCAAAAA
Found at i:4597792 original size:30 final size:29
Alignment explanation
Indices: 4597737--4597805 Score: 88
Period size: 30 Copynumber: 2.4 Consensus size: 29
4597727 AACTTCTAAA
4597737 AAATC-ATTAACCAACATTCAACCGAATT
1 AAATCGATTAACCAACATTCAACCGAATT
*
4597765 AGATCGATTAACCAACCAATT-AACCGAATT
1 AAATCGATTAACCAA-C-ATTCAACCGAATT
*
4597795 AAATCGGTTAA
1 AAATCGATTAA
4597806 TTCAGTTTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
28 4 0.11
29 9 0.26
30 19 0.54
31 3 0.09
ACGTcount: A:0.45, C:0.22, G:0.09, T:0.25
Consensus pattern (29 bp):
AAATCGATTAACCAACATTCAACCGAATT
Found at i:4600680 original size:17 final size:18
Alignment explanation
Indices: 4600650--4600683 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
4600640 AAAATTTGTG
4600650 ATAATTACACATTTAAAA
1 ATAATTACACATTTAAAA
*
4600668 ATAATTAGA-ATTTAAA
1 ATAATTACACATTTAAA
4600684 TTACAATTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.56, C:0.06, G:0.03, T:0.35
Consensus pattern (18 bp):
ATAATTACACATTTAAAA
Found at i:4601337 original size:21 final size:23
Alignment explanation
Indices: 4601287--4601337 Score: 56
Period size: 21 Copynumber: 2.3 Consensus size: 23
4601277 ATTGTATTTT
*
4601287 TAATATGTAAAAATATTTTAATTA
1 TAATAT-TTAAAATATTTTAATTA
4601311 T-A-ATTTAAAAT-TTTT-ATTA
1 TAATATTTAAAATATTTTAATTA
4601330 TAATATTT
1 TAATATTT
4601338 GAATTGATGA
Statistics
Matches: 24, Mismatches: 1, Indels: 7
0.75 0.03 0.22
Matches are distributed among these distances:
19 5 0.21
20 5 0.21
21 10 0.42
22 2 0.08
23 1 0.04
24 1 0.04
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (23 bp):
TAATATTTAAAATATTTTAATTA
Found at i:4607303 original size:11 final size:11
Alignment explanation
Indices: 4607289--4607346 Score: 53
Period size: 11 Copynumber: 5.2 Consensus size: 11
4607279 TTTTTTACTG
4607289 TTTTGTTGTTA
1 TTTTGTTGTTA
*
4607300 TTTTCTTGTTA
1 TTTTGTTGTTA
* **
4607311 TTTTTTTCACTA
1 TTTTGTT-GTTA
**
4607323 TTTTGTTACTA
1 TTTTGTTGTTA
4607334 TTTTGTTGTTA
1 TTTTGTTGTTA
4607345 TT
1 TT
4607347 GTTTGGATAT
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
11 31 0.79
12 8 0.21
ACGTcount: A:0.12, C:0.07, G:0.10, T:0.71
Consensus pattern (11 bp):
TTTTGTTGTTA
Found at i:4607315 original size:34 final size:34
Alignment explanation
Indices: 4607271--4607346 Score: 98
Period size: 34 Copynumber: 2.2 Consensus size: 34
4607261 TTTTTTCTCA
* * * **
4607271 TTGTTTTTTTTTTTACTGTTTTGTTGTTATTTTC
1 TTGTTATTTTTTTCACTATTTTGTTACTATTTTC
*
4607305 TTGTTATTTTTTTCACTATTTTGTTACTATTTTG
1 TTGTTATTTTTTTCACTATTTTGTTACTATTTTC
4607339 TTGTTATT
1 TTGTTATT
4607347 GTTTGGATAT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.11, C:0.07, G:0.11, T:0.72
Consensus pattern (34 bp):
TTGTTATTTTTTTCACTATTTTGTTACTATTTTC
Found at i:4608730 original size:28 final size:28
Alignment explanation
Indices: 4608683--4608757 Score: 143
Period size: 28 Copynumber: 2.7 Consensus size: 28
4608673 ATAGTTGGCC
4608683 ATATTAT-TTTTTTTAACTTTTTAAAAA
1 ATATTATATTTTTTTAACTTTTTAAAAA
4608710 ATATTATATTTTTTTAACTTTTTAAAAA
1 ATATTATATTTTTTTAACTTTTTAAAAA
4608738 ATATTATATTTTTTTAACTT
1 ATATTATATTTTTTTAACTT
4608758 AAAATTTAAT
Statistics
Matches: 47, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
27 7 0.15
28 40 0.85
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (28 bp):
ATATTATATTTTTTTAACTTTTTAAAAA
Found at i:4615944 original size:26 final size:26
Alignment explanation
Indices: 4615889--4615945 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
4615879 AATTTAAATG
* *
4615889 AATTTCATTTTTTGATGATATATAAT
1 AATTTCATTTATTGATGATATATAAA
* *
4615915 AATTTGATTTATTGATGGTACT-TAAA
1 AATTTCATTTATTGATGATA-TATAAA
4615941 AATTT
1 AATTT
4615946 ATGTTTTCAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
26 25 0.96
27 1 0.04
ACGTcount: A:0.35, C:0.04, G:0.11, T:0.51
Consensus pattern (26 bp):
AATTTCATTTATTGATGATATATAAA
Found at i:4622618 original size:19 final size:19
Alignment explanation
Indices: 4622580--4622619 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
4622570 TCTTGTTGTT
* *
4622580 TTTCACTATTTTGTTACTA
1 TTTCACTATTATATTACTA
*
4622599 TTTCACTATTATATTGCTA
1 TTTCACTATTATATTACTA
4622618 TT
1 TT
4622620 ATTTTGTTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.23, C:0.15, G:0.05, T:0.57
Consensus pattern (19 bp):
TTTCACTATTATATTACTA
Found at i:4623171 original size:7 final size:7
Alignment explanation
Indices: 4623136--4623167 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
4623126 ACAAAAACTT
4623136 AAAATAA
1 AAAATAA
4623143 AAAATAA
1 AAAATAA
4623150 AAAATAA
1 AAAATAA
*
4623157 AAAACAA
1 AAAATAA
4623164 AAAA
1 AAAA
4623168 CAAACTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.88, C:0.03, G:0.00, T:0.09
Consensus pattern (7 bp):
AAAATAA
Found at i:4628132 original size:17 final size:17
Alignment explanation
Indices: 4628110--4628144 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
4628100 AGTGCACAGC
4628110 TTCATTGAATAATTGAT
1 TTCATTGAATAATTGAT
4628127 TTCATTGAATAATTGAT
1 TTCATTGAATAATTGAT
4628144 T
1 T
4628145 GTTGGAAGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.34, C:0.06, G:0.11, T:0.49
Consensus pattern (17 bp):
TTCATTGAATAATTGAT
Found at i:4634909 original size:38 final size:38
Alignment explanation
Indices: 4634867--4634957 Score: 105
Period size: 38 Copynumber: 2.4 Consensus size: 38
4634857 GTATGAGAAA
* *
4634867 ATGCCTACTATTCTGTATTTACTAATTGCATG-TAAAAC
1 ATGCC-ACTATTCTGTAATTACTAATCGCATGTTAAAAC
* * *
4634905 ATGCCACTGTTACTG-AATTACTGATCGTATGTTAAAAC
1 ATGCCACTATT-CTGTAATTACTAATCGCATGTTAAAAC
4634943 ATGCCACTATTCTGT
1 ATGCCACTATTCTGT
4634958 GTTGTACCTA
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
37 20 0.45
38 24 0.55
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (38 bp):
ATGCCACTATTCTGTAATTACTAATCGCATGTTAAAAC
Found at i:4640241 original size:23 final size:23
Alignment explanation
Indices: 4640215--4640259 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
4640205 CAAGACCAAA
4640215 TGCCCAAATTTTTGTATTTACTT
1 TGCCCAAATTTTTGTATTTACTT
4640238 TGCCCAAATTTTTGTATTTACT
1 TGCCCAAATTTTTGTATTTACT
4640260 ATTCCTGGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.22, C:0.18, G:0.09, T:0.51
Consensus pattern (23 bp):
TGCCCAAATTTTTGTATTTACTT
Found at i:4643206 original size:12 final size:10
Alignment explanation
Indices: 4643180--4643204 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
4643170 AAATTAAAAG
4643180 ATATAATAGT
1 ATATAATAGT
4643190 ATATAATAGT
1 ATATAATAGT
4643200 ATATA
1 ATATA
4643205 TATTTATCCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (10 bp):
ATATAATAGT
Found at i:4643710 original size:24 final size:24
Alignment explanation
Indices: 4643683--4643729 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
4643673 TATAAACATA
* *
4643683 CCAATATTCAAATTTAAAAATTAC
1 CCAATAGTCAAATGTAAAAATTAC
*
4643707 CCAATAGTCAAATGTCAAAATTA
1 CCAATAGTCAAATGTAAAAATTA
4643730 TTTTTTTATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.49, C:0.17, G:0.04, T:0.30
Consensus pattern (24 bp):
CCAATAGTCAAATGTAAAAATTAC
Found at i:4651896 original size:33 final size:33
Alignment explanation
Indices: 4651859--4651944 Score: 102
Period size: 33 Copynumber: 2.6 Consensus size: 33
4651849 CGAGATTTAA
*
4651859 GGTTCAAGGTTTGG-GTTAGTGTTTGGGGTTCAT
1 GGTTCAAGGTTTGGAGTTAG-GTTTGGGGTTCAC
* * * *
4651892 GGTTCATGGTTTGGATTTAGGTTTTGGGTTTAC
1 GGTTCAAGGTTTGGAGTTAGGTTTGGGGTTCAC
4651925 GGTTCAAGTGTTTGGAGTTA
1 GGTTCAAG-GTTTGGAGTTA
4651945 CGGGTTTGAG
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
33 30 0.68
34 14 0.32
ACGTcount: A:0.14, C:0.06, G:0.36, T:0.44
Consensus pattern (33 bp):
GGTTCAAGGTTTGGAGTTAGGTTTGGGGTTCAC
Found at i:4675378 original size:19 final size:20
Alignment explanation
Indices: 4675354--4675399 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
4675344 GTGTTCATCG
4675354 TTTATTTCTGTTCATTTT-T
1 TTTATTTCTGTTCATTTTCT
* *
4675373 TTTATTTCTTTTTATTTTCT
1 TTTATTTCTGTTCATTTTCT
4675393 TTTATTT
1 TTTATTT
4675400 TCATTTTGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 16 0.67
20 8 0.33
ACGTcount: A:0.11, C:0.09, G:0.02, T:0.78
Consensus pattern (20 bp):
TTTATTTCTGTTCATTTTCT
Found at i:4675384 original size:10 final size:9
Alignment explanation
Indices: 4675367--4675400 Score: 50
Period size: 10 Copynumber: 3.6 Consensus size: 9
4675357 ATTTCTGTTC
4675367 ATTTTTTTT
1 ATTTTTTTT
4675376 ATTTCTTTTT
1 ATTT-TTTTT
4675386 ATTTTCTTTT
1 ATTTT-TTTT
4675396 ATTTT
1 ATTTT
4675401 CATTTTGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 5 0.22
10 18 0.78
ACGTcount: A:0.12, C:0.06, G:0.00, T:0.82
Consensus pattern (9 bp):
ATTTTTTTT
Found at i:4676248 original size:2 final size:2
Alignment explanation
Indices: 4676197--4676237 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
4676187 TTTTACATTC
*
4676197 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4676238 CACACATATA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:4676472 original size:2 final size:2
Alignment explanation
Indices: 4676465--4676495 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4676455 CTTTATATTT
4676465 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4676496 TAATACATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4680858 original size:132 final size:132
Alignment explanation
Indices: 4680641--4681134 Score: 704
Period size: 132 Copynumber: 3.7 Consensus size: 132
4680631 GTGGAGCAGG
*
4680641 TTGAAGATTTCAGATCTTGCCTCCCTAAGCAGTAGTGGAGTAGATCAAAGATGGTGGATTTTACC
1 TTGAAGATTTCAGATCTTGCCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGGATTTTACC
* *
4680706 TCCCTGTGGTTACAGCGGAGTACATTGAAGCCAATAATTCTACTTCCCTGGGCAGCAGTGGAATA
66 TCCCTGAGGTTACAGTGGAGTACATTGAAGCCAATAATTCTACTTCCCTGGGCAGCAGTGGAATA
4680771 GA
131 GA
** * * * ***
4680773 TTGAAGATTTTGGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATTAAAGACGACAGATTTTACC
1 TTGAAGATTTCAGATCTTGCCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGGATTTTACC
* * * *
4680838 T-CCTCGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTTTACTTCCCTGGACAGCAGTGGAAT
66 TCCCT-GAGGTTACAGTGGAGTACATTGAAGCCAATAATTCTACTTCCCTGGGCAGCAGTGGAAT
4680902 AGA
130 AGA
* * *
4680905 TTGAAGATTTTAGATCTTGCCTCTCTAAGCAGTAGTGGAGAAGATCAAAGATGGTGGATTTTACC
1 TTGAAGATTTCAGATCTTGCCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGGATTTTACC
** *
4680970 TCCCTGAGGTTACAGTGGAGTACATTGAAGCCAATAATTCTA-TCTCCCTCAGCAACAGTGGAAT
66 TCCCTGAGGTTACAGTGGAGTACATTGAAGCCAATAATTCTACT-TCCCTGGGCAGCAGTGGAAT
*
4681034 AAA
130 AGA
* ** * *
4681037 TTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAAATCGAAGATGGTGGATTTTACC
1 TTGAAGATTTCAGATCTTGCCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGGATTTTACC
*
4681102 TCCCTGAGGTTACAGTAGAGTACATTGAAGCCA
66 TCCCTGAGGTTACAGTGGAGTACATTGAAGCCA
4681135 GTTATCCTAT
Statistics
Matches: 320, Mismatches: 39, Indels: 6
0.88 0.11 0.02
Matches are distributed among these distances:
131 4 0.01
132 313 0.98
133 3 0.01
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.29
Consensus pattern (132 bp):
TTGAAGATTTCAGATCTTGCCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGGATTTTACC
TCCCTGAGGTTACAGTGGAGTACATTGAAGCCAATAATTCTACTTCCCTGGGCAGCAGTGGAATA
GA
Found at i:4681184 original size:132 final size:132
Alignment explanation
Indices: 4680652--4681191 Score: 628
Period size: 132 Copynumber: 4.1 Consensus size: 132
4680642 TGAAGATTTC
* * * *
4680652 AGATCTTGCCTCCCTAAGCAGTAGTGGAGTAGATCAAAGATGGTGGATTTTACCTCCCTGTGGTT
1 AGATCTTGTCTCCCTAAGCAGTAGTGGAGCAAATCAAAGATGGTGGATTTTACCTCCCTGAGGTT
* * *
4680717 ACAGCGGAGTACATTGAAGCCAATAATTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATT
66 ACAGTGGAGTACATTGAAGCCAATAATTCTACTTCCCTGAGCAGCAGTGGAATAGATTGAA-AAT
*
4680782 TTG
130 TAG
* * * *** *
4680785 -GATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATTAAAGACGACAGATTTTACCT-CCTCGTGGT
1 AGATCTTGTCTCCCTAAGCAGTAGTGGAGCAAATCAAAGATGGTGGATTTTACCTCCCT-GAGGT
* * *
4680848 TACAGTGGAGTACATTGAAGCCAGTAATTTTACTTCCCTG-GACAGCAGTGGAATAGATTGAAGA
65 TACAGTGGAGTACATTGAAGCCAATAATTCTACTTCCCTGAG-CAGCAGTGGAATAGATTGAAAA
**
4680912 TTTT
129 TTAG
* *
4680916 AGATCTTGCCTCTCTAAGCAGTAGTGGAG-AAGATCAAAGATGGTGGATTTTACCTCCCTGAGGT
1 AGATCTTGTCTCCCTAAGCAGTAGTGGAGCAA-ATCAAAGATGGTGGATTTTACCTCCCTGAGGT
* * * *
4680980 TACAGTGGAGTACATTGAAGCCAATAATTCTA-TCTCCCTCAGCAACAGTGGAATAAATTGAAGA
65 TACAGTGGAGTACATTGAAGCCAATAATTCTACT-TCCCTGAGCAGCAGTGGAATAGATTGAAAA
*
4681044 TTAC
129 TTAG
* *
4681048 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAAATCGAAGATGGTGGATTTTACCTCCCTGAGGTT
1 AGATCTTGTCTCCCTAAGCAGTAGTGGAGCAAATCAAAGATGGTGGATTTTACCTCCCTGAGGTT
* * * * * *
4681113 ACAGTAGAGTACATTGAAGCCAGTTATCCTATTTCCCTGA-TATCGCAGT-GAAGTAGATT-AAA
66 ACAGTGGAGTACATTGAAGCCAATAATTCTACTTCCCTGAGCA--GCAGTGGAA-TAGATTGAAA
*
4681175 ATGAG
128 ATTAG
4681180 AGATCTTGTCTC
1 AGATCTTGTCTC
4681192 TCTGAAGTTG
Statistics
Matches: 350, Mismatches: 45, Indels: 25
0.83 0.11 0.06
Matches are distributed among these distances:
131 10 0.03
132 324 0.93
133 16 0.05
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (132 bp):
AGATCTTGTCTCCCTAAGCAGTAGTGGAGCAAATCAAAGATGGTGGATTTTACCTCCCTGAGGTT
ACAGTGGAGTACATTGAAGCCAATAATTCTACTTCCCTGAGCAGCAGTGGAATAGATTGAAAATT
AG
Found at i:4681186 original size:264 final size:264
Alignment explanation
Indices: 4680652--4681194 Score: 727
Period size: 264 Copynumber: 2.1 Consensus size: 264
4680642 TGAAGATTTC
* * *
4680652 AGATCTTGCCTCCCTAAGCAGTAGTGGAGTAGATCAAAGATGGTGGATTTTACCTCCCTGTGGTT
1 AGATCTTGCCTCTCTAAGCAGTAGTGGAGAAGATCAAAGATGGTGGATTTTACCTCCCTGAGGTT
** * *
4680717 ACAGCGGAGTACATTGAAGCCAATAATTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATT
66 ACAGCGGAGTACATTGAAGCCAATAATTCTACTTCCCTCAGCAACAGTGGAATAAATTGAAGATT
*** * * * *
4680782 TTGGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATTAAAGACGACAGATTTTACCTCCTCGTGG
131 ACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAAATCAAAGACGACAGATTTTACCTCCTCGAGG
* ** *
4680847 TTACAGTGGAGTACATTGAAGCCAGTAATTTTACTTCCCTGGACAGCAGTGGAATAGATTGAAGA
196 TTACAGTAGAGTACATTGAAGCCAGTAATCCTACTTCCCTGGACAGCAGTGGAATAGATTGAAAA
***
4680912 TTTT
261 TGAG
4680916 AGATCTTGCCTCTCTAAGCAGTAGTGGAGAAGATCAAAGATGGTGGATTTTACCTCCCTGAGGTT
1 AGATCTTGCCTCTCTAAGCAGTAGTGGAGAAGATCAAAGATGGTGGATTTTACCTCCCTGAGGTT
*
4680981 ACAGTGGAGTACATTGAAGCCAATAATTCTA-TCTCCCTCAGCAACAGTGGAATAAATTGAAGAT
66 ACAGCGGAGTACATTGAAGCCAATAATTCTACT-TCCCTCAGCAACAGTGGAATAAATTGAAGAT
* * ***
4681045 TACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAAATCGAAGATGGTGGATTTTACCTCC-CTGA
130 TACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAAATCAAAGACGACAGATTTTACCTCCTC-GA
* * *
4681109 GGTTACAGTAGAGTACATTGAAGCCAGTTATCCTATTTCCCT-GATATCGCAGT-GAAGTAGATT
194 GGTTACAGTAGAGTACATTGAAGCCAGTAATCCTACTTCCCTGGACA--GCAGTGGAA-TAGATT
4681172 -AAAATGAG
256 GAAAATGAG
*
4681180 AGATCTTGTCTCTCT
1 AGATCTTGCCTCTCT
4681195 GAAGTTGCAG
Statistics
Matches: 243, Mismatches: 31, Indels: 10
0.86 0.11 0.04
Matches are distributed among these distances:
263 5 0.02
264 227 0.93
265 11 0.05
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (264 bp):
AGATCTTGCCTCTCTAAGCAGTAGTGGAGAAGATCAAAGATGGTGGATTTTACCTCCCTGAGGTT
ACAGCGGAGTACATTGAAGCCAATAATTCTACTTCCCTCAGCAACAGTGGAATAAATTGAAGATT
ACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAAATCAAAGACGACAGATTTTACCTCCTCGAGG
TTACAGTAGAGTACATTGAAGCCAGTAATCCTACTTCCCTGGACAGCAGTGGAATAGATTGAAAA
TGAG
Found at i:4682005 original size:19 final size:20
Alignment explanation
Indices: 4681981--4682026 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
4681971 GTGTTCATCG
4681981 TTTATTTCTGTTCATTTT-T
1 TTTATTTCTGTTCATTTTCT
* *
4682000 TTTATTTCTTTTTATTTTCT
1 TTTATTTCTGTTCATTTTCT
4682020 TTTATTT
1 TTTATTT
4682027 TCATTTTGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 16 0.67
20 8 0.33
ACGTcount: A:0.11, C:0.09, G:0.02, T:0.78
Consensus pattern (20 bp):
TTTATTTCTGTTCATTTTCT
Found at i:4682011 original size:10 final size:9
Alignment explanation
Indices: 4681994--4682027 Score: 50
Period size: 10 Copynumber: 3.6 Consensus size: 9
4681984 ATTTCTGTTC
4681994 ATTTTTTTT
1 ATTTTTTTT
4682003 ATTTCTTTTT
1 ATTT-TTTTT
4682013 ATTTTCTTTT
1 ATTTT-TTTT
4682023 ATTTT
1 ATTTT
4682028 CATTTTGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 5 0.22
10 18 0.78
ACGTcount: A:0.12, C:0.06, G:0.00, T:0.82
Consensus pattern (9 bp):
ATTTTTTTT
Found at i:4683148 original size:44 final size:43
Alignment explanation
Indices: 4683094--4683183 Score: 110
Period size: 44 Copynumber: 2.1 Consensus size: 43
4683084 ATATACATAC
* **
4683094 TTTGTGAATATATGTACATATACTTATACATTTT-ATTTTTCTAT
1 TTTGTAAATATATACACATATAC--ATACATTTTCATTTTTCTAT
* *
4683138 TTTGTAAATATATACGCATATACATACATTTTCATTTTTTTAT
1 TTTGTAAATATATACACATATACATACATTTTCATTTTTCTAT
4683181 TTT
1 TTT
4683184 TATTTTTATT
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
42 9 0.22
43 12 0.30
44 19 0.47
ACGTcount: A:0.30, C:0.10, G:0.06, T:0.54
Consensus pattern (43 bp):
TTTGTAAATATATACACATATACATACATTTTCATTTTTCTAT
Found at i:4683230 original size:22 final size:22
Alignment explanation
Indices: 4683188--4683230 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
4683178 TATTTTTATT
* *
4683188 TTTATTTTTTACTTTATTATAC
1 TTTATATTTTACTATATTATAC
4683210 TTTATATTTTA-TATATATATA
1 TTTATATTTTACTATAT-TATA
4683231 TATATTAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (22 bp):
TTTATATTTTACTATATTATAC
Found at i:4688578 original size:14 final size:14
Alignment explanation
Indices: 4688559--4688589 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
4688549 TGATGAGTTT
4688559 TAAACTAATTTAAC
1 TAAACTAATTTAAC
*
4688573 TAAACTGATTTAAC
1 TAAACTAATTTAAC
4688587 TAA
1 TAA
4688590 GAACTCAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.48, C:0.13, G:0.03, T:0.35
Consensus pattern (14 bp):
TAAACTAATTTAAC
Found at i:4690807 original size:29 final size:31
Alignment explanation
Indices: 4690774--4690836 Score: 87
Period size: 29 Copynumber: 2.1 Consensus size: 31
4690764 ATTACTAAAA
4690774 AAATTCAAAATAATTT-T-AAA-TAATTTTTT
1 AAATTCAAAAT-ATTTATAAAATTAATTTTTT
*
4690803 AAATTCAAAATATTTATAAAATTTATTTTTT
1 AAATTCAAAATATTTATAAAATTAATTTTTT
4690834 AAA
1 AAA
4690837 AAAACATAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
28 4 0.13
29 12 0.40
30 3 0.10
31 11 0.37
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (31 bp):
AAATTCAAAATATTTATAAAATTAATTTTTT
Found at i:4694424 original size:25 final size:26
Alignment explanation
Indices: 4694360--4694430 Score: 76
Period size: 25 Copynumber: 2.8 Consensus size: 26
4694350 CTGACATATT
4694360 TGGCTGCTCACACAAGCTTCATATCA
1 TGGCTGCTCACACAAGCTTCATATCA
* * * *
4694386 TGGTTACT-ATACAAGCTTTAT-TCGA
1 TGGCTGCTCACACAAGCTTCATATC-A
4694411 T-GCTGCTCACACAAGCTTCA
1 TGGCTGCTCACACAAGCTTCA
4694431 AAGAATCCAC
Statistics
Matches: 35, Mismatches: 8, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
24 6 0.17
25 23 0.66
26 6 0.17
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.31
Consensus pattern (26 bp):
TGGCTGCTCACACAAGCTTCATATCA
Done.