Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10
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: 48586650
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2183483 characters in sequence are not A, C, G, or T
File 13 of 145
Found at i:4370985 original size:9 final size:9
Alignment explanation
Indices: 4370897--4370986 Score: 53
Period size: 9 Copynumber: 10.2 Consensus size: 9
4370887 TTAGTTTTTT
4370897 TTTTTAAAA
1 TTTTTAAAA
*
4370906 --TTTATAA
1 TTTTTAAAA
4370913 TTTTTAAAA
1 TTTTTAAAA
** *
4370922 AATAT-AAA
1 TTTTTAAAA
*
4370930 -TTTTAGAA
1 TTTTTAAAA
4370938 TTTTTATAAA
1 TTTTTA-AAA
* *
4370948 TATTTAGAA
1 TTTTTAAAA
*
4370957 TTTTAAAAA
1 TTTTTAAAA
*
4370966 TTATTTTAAA
1 TT-TTTAAAA
4370976 TTTTTAAAA
1 TTTTTAAAA
4370985 TT
1 TT
4370987 GTTTTAATTT
Statistics
Matches: 58, Mismatches: 17, Indels: 12
0.67 0.20 0.14
Matches are distributed among these distances:
7 8 0.14
8 5 0.09
9 31 0.53
10 14 0.24
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (9 bp):
TTTTTAAAA
Found at i:4370986 original size:19 final size:20
Alignment explanation
Indices: 4370929--4370992 Score: 80
Period size: 19 Copynumber: 3.3 Consensus size: 20
4370919 AAAAATATAA
4370929 ATTTTAGAATTTTTATAAA-T
1 ATTTTAGAATTTTTA-AAATT
*
4370949 A-TTTAGAATTTTAAAAATT
1 ATTTTAGAATTTTTAAAATT
4370968 ATTTTA-AATTTTTAAAATT
1 ATTTTAGAATTTTTAAAATT
*
4370987 GTTTTA
1 ATTTTA
4370993 ATTTTTTTGC
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
18 3 0.08
19 31 0.79
20 5 0.13
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.55
Consensus pattern (20 bp):
ATTTTAGAATTTTTAAAATT
Found at i:4375150 original size:21 final size:21
Alignment explanation
Indices: 4375107--4375151 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
4375097 AATATAAAAG
*
4375107 AAAAATCAAAATTTAAATCTT
1 AAAAATCAAAATTTAAAGCTT
* *
4375128 AAAAATCAAAGTTTAAAGGTT
1 AAAAATCAAAATTTAAAGCTT
4375149 AAA
1 AAA
4375152 TTTTAGTAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.58, C:0.07, G:0.07, T:0.29
Consensus pattern (21 bp):
AAAAATCAAAATTTAAAGCTT
Found at i:4383222 original size:2 final size:2
Alignment explanation
Indices: 4383215--4383245 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4383205 TGTGGATGAT
4383215 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
4383246 TTAATTAATA
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:4385155 original size:20 final size:19
Alignment explanation
Indices: 4385108--4385154 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
4385098 GTTTCTTTTA
4385108 TAAATTTTGTTAATAATTT
1 TAAATTTTGTTAATAATTT
* *
4385127 TATGATTTTTTTAATAATTT
1 TA-AATTTTGTTAATAATTT
4385147 TAAATTTT
1 TAAATTTT
4385155 TAAAAGGGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 7 0.29
20 17 0.71
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (19 bp):
TAAATTTTGTTAATAATTT
Found at i:4392200 original size:25 final size:25
Alignment explanation
Indices: 4392172--4392219 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
4392162 ATTTTTTAAA
*
4392172 ATTTATATATTTT-TGTAATTTTTAC
1 ATTTATACATTTTCT-TAATTTTTAC
*
4392197 ATTTTTACATTTTCTTAATTTTT
1 ATTTATACATTTTCTTAATTTTT
4392220 TTTATAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 19 0.95
26 1 0.05
ACGTcount: A:0.25, C:0.06, G:0.02, T:0.67
Consensus pattern (25 bp):
ATTTATACATTTTCTTAATTTTTAC
Found at i:4392266 original size:18 final size:18
Alignment explanation
Indices: 4392153--4392268 Score: 58
Period size: 17 Copynumber: 6.3 Consensus size: 18
4392143 AAGATATAAT
* *
4392153 ATTTTTAATATTTTTTAAA
1 ATTTCTAATA-TTTTTATA
* *
4392172 ATTTAT-ATATTTTTGTA
1 ATTTCTAATATTTTTATA
* * *
4392189 ATTT-TTACATTTTTACA
1 ATTTCTAATATTTTTATA
* *
4392206 TTTTCTTAATTTTTTTTATAA
1 ATTTC-TAA-TATTTTTAT-A
* *
4392227 ATTTTATAATAATTTTCA-A
1 A-TTTCTAAT-ATTTTTATA
4392246 ATTTCTAATATTTTTATA
1 ATTTCTAATATTTTTATA
4392264 ATTTC
1 ATTTC
4392269 GACAAATATA
Statistics
Matches: 72, Mismatches: 17, Indels: 17
0.68 0.16 0.16
Matches are distributed among these distances:
16 1 0.01
17 27 0.38
18 16 0.22
19 9 0.12
20 7 0.10
21 9 0.12
22 3 0.04
ACGTcount: A:0.32, C:0.05, G:0.01, T:0.62
Consensus pattern (18 bp):
ATTTCTAATATTTTTATA
Found at i:4395108 original size:31 final size:32
Alignment explanation
Indices: 4395070--4395144 Score: 100
Period size: 31 Copynumber: 2.4 Consensus size: 32
4395060 TCAACGGCTC
*
4395070 AGTGACTAAAATGTTACAACATATT-AA-CATA
1 AGTGACTAAAATGTAACAACAT-TTCAAGCATA
*
4395101 AGTGACTAAAATGTAACAATATTTCAAGCATA
1 AGTGACTAAAATGTAACAACATTTCAAGCATA
*
4395133 GGTGACTAAAAT
1 AGTGACTAAAAT
4395145 ATAATATGAG
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
30 2 0.05
31 22 0.56
32 15 0.38
ACGTcount: A:0.47, C:0.12, G:0.13, T:0.28
Consensus pattern (32 bp):
AGTGACTAAAATGTAACAACATTTCAAGCATA
Found at i:4400836 original size:21 final size:21
Alignment explanation
Indices: 4400795--4400865 Score: 63
Period size: 21 Copynumber: 3.3 Consensus size: 21
4400785 ACGTTATAAA
**
4400795 ATATAAAAAATGGA-AATAAAT
1 ATATAAAAAATCTAGAA-AAAT
*
4400816 ATATAAAAAATTTAGAAAAAT
1 ATATAAAAAATCTAGAAAAAT
* * *
4400837 GTATAAATAATCTAGAAAAAAA
1 ATATAAAAAATCTAG-AAAAAT
4400859 ATATAAA
1 ATATAAA
4400866 TTATAAAAAG
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
21 28 0.68
22 13 0.32
ACGTcount: A:0.66, C:0.01, G:0.07, T:0.25
Consensus pattern (21 bp):
ATATAAAAAATCTAGAAAAAT
Found at i:4401748 original size:109 final size:110
Alignment explanation
Indices: 4401519--4401808 Score: 442
Period size: 109 Copynumber: 2.6 Consensus size: 110
4401509 GTTAAACGTG
* *
4401519 AAATCGAAACCCAGCACCTTAGGGCACGTTTCTCGAATTCCCAAACGCAAAACATTGCCTTATTT
1 AAATCGACACCCAGCACCTTAGGGCACGTTTCTCGAATTTCCAAACGCAAAACATTGCCTTA-TT
* * *
4401584 TTGAAAAGTTTTTTTAAAGGATATTTAGCTATTTGGTTGAATGAGAA
65 TTGAAAAG-TTTTTAAAAGGATATTGAGCTATTTGGTTGAACGAGAA
4401631 AAATCGACACCCAGCACCTTAGGGCACGCTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATT
1 AAATCGACACCCAGCACCTTAGGGCACG-TTTCTCGAATTTCCAAACGCAAAACATTGCCTTATT
*
4401696 TT-AAAA-TTTTTAAAAGGATATTGAG-TCATTTGGTTTAACGAGAA
65 TTGAAAAGTTTTTAAAAGGATATTGAGCT-ATTTGGTTGAACGAGAA
*
4401740 AAATCGACACCCAGCACCTTAGGGCACGTTTTTCTCGAATCTCCAAACGCAAAACATTGCCTTAT
1 AAATCGACACCCAGCACCTTAGGGCACG--TTTCTCGAATTTCCAAACGCAAAACATTGCCTTAT
4401805 TTTG
64 TTTG
4401809 GAACAATTTC
Statistics
Matches: 166, Mismatches: 8, Indels: 9
0.91 0.04 0.05
Matches are distributed among these distances:
108 1 0.01
109 60 0.36
110 37 0.22
111 4 0.02
112 31 0.19
113 33 0.20
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.30
Consensus pattern (110 bp):
AAATCGACACCCAGCACCTTAGGGCACGTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATTT
TGAAAAGTTTTTAAAAGGATATTGAGCTATTTGGTTGAACGAGAA
Found at i:4401858 original size:54 final size:54
Alignment explanation
Indices: 4401773--4401876 Score: 181
Period size: 54 Copynumber: 1.9 Consensus size: 54
4401763 GCACGTTTTT
*
4401773 CTCGAATCTCCAAACGCAAAACATTGCCTTATTTTGGAACAATTTCCTTTGTTC
1 CTCGAATCTCCAAACGAAAAACATTGCCTTATTTTGGAACAATTTCCTTTGTTC
* *
4401827 CTCGAATTTCCAAACGAAAAACATTGTCTTATTTTGGAACAATTTCCTTT
1 CTCGAATCTCCAAACGAAAAACATTGCCTTATTTTGGAACAATTTCCTTT
4401877 TTTGAAATAT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 47 1.00
ACGTcount: A:0.30, C:0.23, G:0.11, T:0.37
Consensus pattern (54 bp):
CTCGAATCTCCAAACGAAAAACATTGCCTTATTTTGGAACAATTTCCTTTGTTC
Found at i:4401949 original size:14 final size:14
Alignment explanation
Indices: 4401917--4401950 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 14
4401907 AATAATAAAT
4401917 AAAATAATATGACTA
1 AAAATAATATGAC-A
4401932 AAAATAATATGAACA
1 AAAATAATATG-ACA
4401947 AAAA
1 AAAA
4401951 AACGAATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 16 0.89
16 2 0.11
ACGTcount: A:0.68, C:0.06, G:0.06, T:0.21
Consensus pattern (14 bp):
AAAATAATATGACA
Found at i:4403668 original size:21 final size:23
Alignment explanation
Indices: 4403642--4403688 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
4403632 NNNNNNNTAA
*
4403642 TTTTTTTATA-A-TTTATATGTT
1 TTTTTTTATAGATTTTATATATT
*
4403663 TTTTTTTCTAGATTTTATATATT
1 TTTTTTTATAGATTTTATATATT
4403686 TTT
1 TTT
4403689 ATGAAATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 9 0.41
22 1 0.05
23 12 0.55
ACGTcount: A:0.21, C:0.02, G:0.04, T:0.72
Consensus pattern (23 bp):
TTTTTTTATAGATTTTATATATT
Found at i:4409187 original size:29 final size:30
Alignment explanation
Indices: 4409149--4409258 Score: 98
Period size: 29 Copynumber: 3.7 Consensus size: 30
4409139 ATATTTTGAC
* *
4409149 CCCCTAAACTTT-TTGAAATTGCATTTTCA
1 CCCCTAAACTTTCTTAAAATTACATTTTCA
**
4409178 CCCCTAAACTTTCTTAAAATTACATTTTTG
1 CCCCTAAACTTTCTTAAAATTACATTTTCA
** * * * *
4409208 CCTATCAAC-TTCTTGAAATTATATTTTGA
1 CCCCTAAACTTTCTTAAAATTACATTTTCA
* *
4409237 CCCCTAAATTTTCTCAAAATTA
1 CCCCTAAACTTTCTTAAAATTA
4409259 TGCTTGGCCC
Statistics
Matches: 62, Mismatches: 17, Indels: 3
0.76 0.21 0.04
Matches are distributed among these distances:
29 33 0.53
30 29 0.47
ACGTcount: A:0.31, C:0.23, G:0.05, T:0.42
Consensus pattern (30 bp):
CCCCTAAACTTTCTTAAAATTACATTTTCA
Found at i:4409259 original size:30 final size:30
Alignment explanation
Indices: 4409132--4409259 Score: 91
Period size: 30 Copynumber: 4.3 Consensus size: 30
4409122 ACAAAAAATA
*
4409132 AAAATTTATATTTTGACCCCCTAAACTTT-TT
1 AAAA-TTATATTTTGA-CCCCTAAATTTTCTT
* ** * *
4409163 GAAATTGCATTTTCACCCCTAAACTTTCTT
1 AAAATTATATTTTGACCCCTAAATTTTCTT
* ** * *
4409193 AAAATTACATTTTTG-CCTATCAA-CTTCTT
1 AAAATTATA-TTTTGACCCCTAAATTTTCTT
* *
4409222 GAAATTATATTTTGACCCCTAAATTTTCTC
1 AAAATTATATTTTGACCCCTAAATTTTCTT
4409252 AAAATTAT
1 AAAATTAT
4409260 GCTTGGCCCC
Statistics
Matches: 74, Mismatches: 19, Indels: 9
0.73 0.19 0.09
Matches are distributed among these distances:
28 5 0.07
29 29 0.39
30 33 0.45
31 7 0.09
ACGTcount: A:0.32, C:0.20, G:0.05, T:0.43
Consensus pattern (30 bp):
AAAATTATATTTTGACCCCTAAATTTTCTT
Found at i:4409836 original size:13 final size:13
Alignment explanation
Indices: 4409814--4409847 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
4409804 AACCCAAAGG
4409814 AAAAAG-AGAGAA
1 AAAAAGAAGAGAA
4409826 AAAAAGAAGAGAA
1 AAAAAGAAGAGAA
4409839 AAGAAAGAA
1 AA-AAAGAA
4409848 AAGAGGAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 6 0.30
13 8 0.40
14 6 0.30
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (13 bp):
AAAAAGAAGAGAA
Found at i:4409840 original size:22 final size:22
Alignment explanation
Indices: 4409815--4409860 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
4409805 ACCCAAAGGA
*
4409815 AAAAGAGAGAAAAAAAGAAGAG
1 AAAAGAAAGAAAAAAAGAAGAG
* *
4409837 AAAAGAAAGAAAAGAGGAAGAG
1 AAAAGAAAGAAAAAAAGAAGAG
4409859 AA
1 AA
4409861 GGGGAGGCGC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (22 bp):
AAAAGAAAGAAAAAAAGAAGAG
Found at i:4409970 original size:19 final size:21
Alignment explanation
Indices: 4409945--4410008 Score: 78
Period size: 23 Copynumber: 3.0 Consensus size: 21
4409935 CCGAGGAAGA
4409945 AGAAG-AAAAAGAAAAAAAAG
1 AGAAGAAAAAAGAAAAAAAAG
4409965 -GAAGAAAAAGAGAGAAGAAAAAG
1 AGAAGAAAAA-AGA-AA-AAAAAG
4409988 AGAAAGAAAAAAGAAAAAAAA
1 AG-AAGAAAAAAGAAAAAAAA
4410009 TAAAAAGCTA
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
19 4 0.11
20 4 0.11
21 3 0.08
22 7 0.18
23 8 0.21
24 4 0.11
25 8 0.21
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (21 bp):
AGAAGAAAAAAGAAAAAAAAG
Found at i:4409971 original size:13 final size:12
Alignment explanation
Indices: 4409937--4409998 Score: 61
Period size: 12 Copynumber: 5.0 Consensus size: 12
4409927 GATTCGGCCC
*
4409937 GAGGAAGAAGAA
1 GAGGAAGAAAAA
**
4409949 GAAAAAGAAAAAA
1 GAGGAAG-AAAAA
*
4409962 AAGGAAGAAAAA
1 GAGGAAGAAAAA
4409974 GAGAGAAGAAAAA
1 GAG-GAAGAAAAA
*
4409987 GAGAAAGAAAAA
1 GAGGAAGAAAAA
4409999 AGAAAAAAAA
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
12 20 0.50
13 20 0.50
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (12 bp):
GAGGAAGAAAAA
Found at i:4409981 original size:32 final size:31
Alignment explanation
Indices: 4409941--4410005 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 31
4409931 CGGCCCGAGG
4409941 AAGAAGAAGAAAAAGA-AAA-AAAAGGAAGAAA
1 AAGAAGAAGAAAAAGAGAAAGAAAA--AAGAAA
4409972 AAGAGAGAAGAAAAAGAGAAAGAAAAAAGAAA
1 AAGA-AGAAGAAAAAGAGAAAGAAAAAAGAAA
4410004 AA
1 AA
4410006 AAATAAAAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
31 4 0.13
32 20 0.65
33 3 0.10
34 4 0.13
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (31 bp):
AAGAAGAAGAAAAAGAGAAAGAAAAAAGAAA
Found at i:4409998 original size:26 final size:23
Alignment explanation
Indices: 4409954--4410008 Score: 69
Period size: 25 Copynumber: 2.4 Consensus size: 23
4409944 AAGAAGAAAA
*
4409954 AGAAAAAAAAGGAAGAAAAAGAG
1 AGAAAAAAAAGAAAGAAAAAGAG
4409977 AGAAGAAAAAGAGAAAGAAAAA-AG
1 AGAA-AAAAA-AGAAAGAAAAAGAG
4410001 A-AAAAAAA
1 AGAAAAAAA
4410009 TAAAAAGCTA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
22 5 0.17
23 6 0.21
24 8 0.28
25 10 0.34
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (23 bp):
AGAAAAAAAAGAAAGAAAAAGAG
Found at i:4409999 original size:13 final size:12
Alignment explanation
Indices: 4409941--4410008 Score: 68
Period size: 13 Copynumber: 5.7 Consensus size: 12
4409931 CGGCCCGAGG
* *
4409941 AAGAAGAAGAAA
1 AAGAAAAAGAGA
* *
4409953 AAGAAAAAAAAGG
1 AAG-AAAAAGAGA
4409966 AAGAAAAAGAGA
1 AAGAAAAAGAGA
4409978 GAAGAAAAAGAGA
1 -AAGAAAAAGAGA
4409991 AAGAAAAA-AGA
1 AAGAAAAAGAGA
4410002 AA-AAAAA
1 AAGAAAAA
4410009 TAAAAAGCTA
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
10 5 0.10
11 5 0.10
12 18 0.38
13 20 0.42
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (12 bp):
AAGAAAAAGAGA
Found at i:4410215 original size:19 final size:19
Alignment explanation
Indices: 4410170--4410217 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
4410160 AAAAAAAAGG
* *
4410170 CCAGCAGGCCTGTCCAAGC
1 CCAGCAAGCCTGACCAAGC
* * *
4410189 CCAACAAGCCTGACCCAGT
1 CCAGCAAGCCTGACCAAGC
4410208 CCAGCAAGCC
1 CCAGCAAGCC
4410218 CAGAACAGCA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.27, C:0.44, G:0.21, T:0.08
Consensus pattern (19 bp):
CCAGCAAGCCTGACCAAGC
Found at i:4410793 original size:17 final size:17
Alignment explanation
Indices: 4410773--4410850 Score: 75
Period size: 17 Copynumber: 4.4 Consensus size: 17
4410763 TACGGTATTA
4410773 AAAAAAATTCGTGTTTC
1 AAAAAAATTCGTGTTTC
**
4410790 AAAAATTTTCGTGTTTTC
1 AAAAAAATTCGTG-TTTC
4410808 AAAAAAATTGACCGTGTTTC
1 AAAAAAATT---CGTGTTTC
* **
4410828 ATAAATTTTCGTGTTTC
1 AAAAAAATTCGTGTTTC
4410845 AAAAAA
1 AAAAAA
4410851 TCCTCGTGTT
Statistics
Matches: 48, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
17 23 0.48
18 11 0.23
20 10 0.21
21 4 0.08
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (17 bp):
AAAAAAATTCGTGTTTC
Found at i:4410815 original size:20 final size:20
Alignment explanation
Indices: 4410790--4410968 Score: 69
Period size: 19 Copynumber: 9.1 Consensus size: 20
4410780 TTCGTGTTTC
4410790 AAAAATTTTCGTGTTTTCAA
1 AAAAATTTTCGTGTTTTCAA
**
4410810 AAAAATTGACCGTG-TTTC--
1 AAAAATT-TTCGTGTTTTCAA
*
4410828 ATAAATTTTCGTG-TTTCAA
1 AAAAATTTTCGTGTTTTCAA
* * *
4410847 AAAATCCTCGTGTTTCGTATTTT-ATC
1 AAAA-----AT-TTTCGTGTTTTCA-A
*
4410873 AAAAATTTT-ATGTTTTCAA
1 AAAAATTTTCGTGTTTTCAA
4410892 AAAAATTTT-GTGTTTT---
1 AAAAATTTTCGTGTTTTCAA
*
4410908 AAAAATTTTCGT-ATTTCAA
1 AAAAATTTTCGTGTTTTCAA
** *
4410927 AAAGAAAATTCGTGTTTCCTAA
1 AAA-AATTTTCGTGTTTTC-AA
*
4410949 AAAAA-TCTCGTG-TTTCAA
1 AAAAATTTTCGTGTTTTCAA
4410967 AA
1 AA
4410969 TTTTTTTTTT
Statistics
Matches: 118, Mismatches: 22, Indels: 40
0.66 0.12 0.22
Matches are distributed among these distances:
16 12 0.10
17 10 0.08
18 10 0.08
19 29 0.25
20 27 0.23
21 10 0.08
22 5 0.04
24 1 0.01
25 7 0.06
26 7 0.06
ACGTcount: A:0.36, C:0.12, G:0.11, T:0.42
Consensus pattern (20 bp):
AAAAATTTTCGTGTTTTCAA
Found at i:4410851 original size:18 final size:17
Alignment explanation
Indices: 4410780--4410849 Score: 77
Period size: 17 Copynumber: 3.9 Consensus size: 17
4410770 TTAAAAAAAA
4410780 TTCGTGTTTCAAAAATT
1 TTCGTGTTTCAAAAATT
4410797 TTCGTGTTTTCAAAAAAATT
1 TTCGTG-TTTC--AAAAATT
** *
4410817 GACCGTGTTTCATAAATT
1 -TTCGTGTTTCAAAAATT
4410835 TTCGTGTTTCAAAAA
1 TTCGTGTTTCAAAAA
4410850 ATCCTCGTGT
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
17 18 0.42
18 10 0.23
20 11 0.26
21 4 0.09
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.43
Consensus pattern (17 bp):
TTCGTGTTTCAAAAATT
Found at i:4417911 original size:7 final size:7
Alignment explanation
Indices: 4417830--4417901 Score: 58
Period size: 7 Copynumber: 9.9 Consensus size: 7
4417820 ATTATGCTTA
4417830 AAAAAAC
1 AAAAAAC
4417837 AAAAAA-
1 AAAAAAC
*
4417843 AAAACAGTC
1 AAAA-A-AC
4417852 AAAACAA-
1 AAAA-AAC
*
4417859 AAAACAAA
1 AAAA-AAC
4417867 AAAAAAC
1 AAAAAAC
4417874 AAAAAAC
1 AAAAAAC
*
4417881 AAAAAAGG
1 AAAAAA-C
4417889 AAAAAAC
1 AAAAAAC
4417896 AAAAAA
1 AAAAAA
4417902 AAAGAAAAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
6 4 0.07
7 35 0.64
8 10 0.18
9 6 0.11
ACGTcount: A:0.83, C:0.11, G:0.04, T:0.01
Consensus pattern (7 bp):
AAAAAAC
Found at i:4419075 original size:80 final size:80
Alignment explanation
Indices: 4418782--4419288 Score: 906
Period size: 80 Copynumber: 6.2 Consensus size: 80
4418772 GTTTTTCAAA
* *
4418782 AATCAGCTCATATTGCGAGAGGTGAGTTGAGCCCCGGGTCACACGCCGAGGTATTTTTCAATTAC
1 AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCCGAGGTATTTTTCAATTAC
*
4418847 TACTTTTCAAAAAAAAA
66 TACTTTT--AAAAAAAC
4418864 AATTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCCGAGGTATTTTTCAATT
1 AA--TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCCGAGGTATTTTTCAATT
*
4418929 ACTACTTTTCAAAAAAAAA
64 ACTACTTTT--AAAAAAAC
4418948 AATTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCCGAGGTATTTTTCAATT
1 AA--TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCCGAGGTATTTTTCAATT
4419013 ACTACTTTTAAAAAAAC
64 ACTACTTTTAAAAAAAC
4419030 AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCCGAGGTATTTTTCAATTAC
1 AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCCGAGGTATTTTTCAATTAC
4419095 TACTTTTAAAAAAAC
66 TACTTTTAAAAAAAC
4419110 AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCCGAGGTATTTTTCAATTAC
1 AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCCGAGGTATTTTTCAATTAC
4419175 TACTTTTAAAAAAAC
66 TACTTTTAAAAAAAC
4419190 AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCCGAGGTATTTTTCAATTAC
1 AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCCGAGGTATTTTTCAATTAC
4419255 TACTTTTAAAAAAAC
66 TACTTTTAAAAAAAC
4419270 AATCAACTCATATTGCGAG
1 AATCAACTCATATTGCGAG
4419289 CCTGTTTTTA
Statistics
Matches: 420, Mismatches: 3, Indels: 6
0.98 0.01 0.01
Matches are distributed among these distances:
80 257 0.61
82 11 0.03
84 152 0.36
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.29
Consensus pattern (80 bp):
AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCCGAGGTATTTTTCAATTAC
TACTTTTAAAAAAAC
Found at i:4419621 original size:9 final size:9
Alignment explanation
Indices: 4419607--4419640 Score: 52
Period size: 10 Copynumber: 3.8 Consensus size: 9
4419597 GCTTTTTTTA
4419607 AAAAAATAC
1 AAAAAATAC
4419616 AAAAAAATAC
1 -AAAAAATAC
4419626 AAAAAATA-
1 AAAAAATAC
4419634 AAAAAAT
1 AAAAAAT
4419641 TATATTTTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 7 0.29
9 8 0.33
10 9 0.38
ACGTcount: A:0.82, C:0.06, G:0.00, T:0.12
Consensus pattern (9 bp):
AAAAAATAC
Found at i:4419621 original size:10 final size:10
Alignment explanation
Indices: 4419606--4419639 Score: 54
Period size: 9 Copynumber: 3.6 Consensus size: 10
4419596 TGCTTTTTTT
4419606 AAAAAAATAC
1 AAAAAAATAC
4419616 AAAAAAATAC
1 AAAAAAATAC
4419626 -AAAAAATA-
1 AAAAAAATAC
4419634 AAAAAA
1 AAAAAA
4419640 TTATATTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 13 0.57
10 10 0.43
ACGTcount: A:0.85, C:0.06, G:0.00, T:0.09
Consensus pattern (10 bp):
AAAAAAATAC
Found at i:4419760 original size:30 final size:30
Alignment explanation
Indices: 4419636--4419762 Score: 109
Period size: 30 Copynumber: 4.3 Consensus size: 30
4419626 AAAAAATAAA
4419636 AAAATTATATTTTGACCCCCTAAACTTTT-T
1 AAAATTATATTTTGA-CCCCTAAACTTTTCT
* ** * *
4419666 GAAATTGCATTTTCACCCCTAAACTTTACT
1 AAAATTATATTTTGACCCCTAAACTTTTCT
* * * *
4419696 AAAATTACATTTTTG-CCCATCAACTTCT-T
1 AAAATTATA-TTTTGACCCCTAAACTTTTCT
*
4419725 GAAATTATATTTTGACCCCTAAA-TTTTCT
1 AAAATTATATTTTGACCCCTAAACTTTTCT
4419754 CAAAATTAT
1 -AAAATTAT
4419763 GCTTGGCCCC
Statistics
Matches: 74, Mismatches: 18, Indels: 10
0.73 0.18 0.10
Matches are distributed among these distances:
28 8 0.11
29 27 0.36
30 35 0.47
31 4 0.05
ACGTcount: A:0.33, C:0.21, G:0.05, T:0.41
Consensus pattern (30 bp):
AAAATTATATTTTGACCCCTAAACTTTTCT
Found at i:4420347 original size:13 final size:13
Alignment explanation
Indices: 4420325--4420358 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
4420315 AACCCAAAGG
4420325 AAAAAG-AGAGAA
1 AAAAAGAAGAGAA
4420337 AAAAAGAAGAGAA
1 AAAAAGAAGAGAA
4420350 AAGAAAGAA
1 AA-AAAGAA
4420359 AAGAGGAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 6 0.30
13 8 0.40
14 6 0.30
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (13 bp):
AAAAAGAAGAGAA
Found at i:4420351 original size:22 final size:22
Alignment explanation
Indices: 4420326--4420371 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
4420316 ACCCAAAGGA
*
4420326 AAAAGAGAGAAAAAAAGAAGAG
1 AAAAGAAAGAAAAAAAGAAGAG
* *
4420348 AAAAGAAAGAAAAGAGGAAGAG
1 AAAAGAAAGAAAAAAAGAAGAG
4420370 AA
1 AA
4420372 GGGGAGGCGC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (22 bp):
AAAAGAAAGAAAAAAAGAAGAG
Found at i:4420481 original size:19 final size:21
Alignment explanation
Indices: 4420456--4420519 Score: 78
Period size: 23 Copynumber: 3.0 Consensus size: 21
4420446 CCGAGGAAGA
4420456 AGAAG-AAAAAGAAAAAAAAG
1 AGAAGAAAAAAGAAAAAAAAG
4420476 -GAAGAAAAAGAGAGAAGAAAAAG
1 AGAAGAAAAA-AGA-AA-AAAAAG
4420499 AGAAAGAAAAAAGAAAAAAAA
1 AG-AAGAAAAAAGAAAAAAAA
4420520 ATAAAAAGCT
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
19 4 0.11
20 4 0.11
21 3 0.08
22 7 0.18
23 8 0.21
24 4 0.11
25 8 0.21
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (21 bp):
AGAAGAAAAAAGAAAAAAAAG
Found at i:4420492 original size:32 final size:31
Alignment explanation
Indices: 4420452--4420516 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 31
4420442 CGGCCCGAGG
4420452 AAGAAGAAGAAAAAGA-AAA-AAAAGGAAGAAA
1 AAGAAGAAGAAAAAGAGAAAGAAAA--AAGAAA
4420483 AAGAGAGAAGAAAAAGAGAAAGAAAAAAGAAA
1 AAGA-AGAAGAAAAAGAGAAAGAAAAAAGAAA
4420515 AA
1 AA
4420517 AAAATAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
31 4 0.13
32 20 0.65
33 3 0.10
34 4 0.13
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (31 bp):
AAGAAGAAGAAAAAGAGAAAGAAAAAAGAAA
Found at i:4420509 original size:26 final size:23
Alignment explanation
Indices: 4420465--4420520 Score: 71
Period size: 25 Copynumber: 2.4 Consensus size: 23
4420455 AAGAAGAAAA
*
4420465 AGAAAAAAAAGGAAGAAAAAGAG
1 AGAAAAAAAAGAAAGAAAAAGAG
4420488 AGAAGAAAAAGAGAAAGAAAAA-AG
1 AGAA-AAAAA-AGAAAGAAAAAGAG
4420512 A-AAAAAAAA
1 AGAAAAAAAA
4420521 TAAAAAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
21 1 0.03
22 5 0.17
23 6 0.20
24 8 0.27
25 10 0.33
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (23 bp):
AGAAAAAAAAGAAAGAAAAAGAG
Found at i:4420510 original size:13 final size:13
Alignment explanation
Indices: 4420458--4420520 Score: 62
Period size: 13 Copynumber: 5.1 Consensus size: 13
4420448 GAGGAAGAAG
*
4420458 AAGAAAAAGAAAA
1 AAGAGAAAGAAAA
* *
4420471 AAAAGGAAG-AAA
1 AAGAGAAAGAAAA
4420483 AAGAGAGAAG-AAA
1 AAGAGA-AAGAAAA
4420496 AAGAGAAAGAAAA
1 AAGAGAAAGAAAA
4420509 AAGA-AAA-AAAA
1 AAGAGAAAGAAAA
4420520 A
1 A
4420521 TAAAAAGCTA
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
11 5 0.12
12 13 0.30
13 25 0.58
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (13 bp):
AAGAGAAAGAAAA
Found at i:4420515 original size:6 final size:6
Alignment explanation
Indices: 4420452--4420520 Score: 61
Period size: 6 Copynumber: 11.2 Consensus size: 6
4420442 CGGCCCGAGG
* * *
4420452 AAGAAG AAGAAA AAGAAA AA-AAA GGAAGAAA AAGAGAG AAGAAA AAGAGA
1 AAGAAA AAGAAA AAGAAA AAGAAA --AAGAAA AAGA-AA AAGAAA AAGAAA
4420502 AAGAAAA AAGAAA AA-AAA A
1 AAG-AAA AAGAAA AAGAAA A
4420521 TAAAAAGCTA
Statistics
Matches: 53, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
5 7 0.13
6 31 0.58
7 12 0.23
8 3 0.06
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (6 bp):
AAGAAA
Found at i:4420519 original size:11 final size:11
Alignment explanation
Indices: 4420461--4420520 Score: 50
Period size: 11 Copynumber: 5.4 Consensus size: 11
4420451 GAAGAAGAAG
4420461 AAAAAGAAAAA
1 AAAAAGAAAAA
4420472 AAAGGAAG-AAAA
1 AAA--AAGAAAAA
* * *
4420484 AGAGAGAAGAA
1 AAAAAGAAAAA
* *
4420495 AAAGAGAAAGA
1 AAAAAGAAAAA
4420506 AAAAAGAAAAA
1 AAAAAGAAAAA
4420517 AAAA
1 AAAA
4420521 TAAAAAGCTA
Statistics
Matches: 38, Mismatches: 8, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
10 2 0.05
11 27 0.71
12 6 0.16
13 3 0.08
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAA
Found at i:4420725 original size:19 final size:19
Alignment explanation
Indices: 4420680--4420727 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
4420670 GAAAAAAAGG
*
4420680 CCAGCAAGCCTGTCCAAGC
1 CCAGCAAGCCTGACCAAGC
* * *
4420699 CCAACAAGCCTGACCCAGT
1 CCAGCAAGCCTGACCAAGC
4420718 CCAGCAAGCC
1 CCAGCAAGCC
4420728 CAGAACAGCA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.29, C:0.44, G:0.19, T:0.08
Consensus pattern (19 bp):
CCAGCAAGCCTGACCAAGC
Found at i:4421320 original size:17 final size:17
Alignment explanation
Indices: 4421293--4421338 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
4421283 AAAAGAATCG
4421293 TGTTTCAAAAATTT-TCA
1 TGTTTC-AAAATTTCTCA
*
4421310 TGTCTTCAAAATTTCTCG
1 TGT-TTCAAAATTTCTCA
4421328 TGTTTCAAAAT
1 TGTTTCAAAAT
4421339 AATAATAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 18 0.69
18 8 0.31
ACGTcount: A:0.30, C:0.15, G:0.09, T:0.46
Consensus pattern (17 bp):
TGTTTCAAAATTTCTCA
Found at i:4421601 original size:44 final size:46
Alignment explanation
Indices: 4421523--4421612 Score: 139
Period size: 44 Copynumber: 2.0 Consensus size: 46
4421513 TTGATGTTAT
*
4421523 CGTGTTTTCAAAAAAAAATTCCCGTGTTTGAAAAATTTTCATGTTTC
1 CGTGTTTTCAAAAAAAAATT-CCGTGTTTCAAAAATTTTCATGTTTC
*
4421570 CGTGTTTT-AAAAAAAAATT-CGTGTTTCAAAAATTTTCGTGTTT
1 CGTGTTTTCAAAAAAAAATTCCGTGTTTCAAAAATTTTCATGTTT
4421613 TCAAAAAAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
44 22 0.54
46 11 0.27
47 8 0.20
ACGTcount: A:0.32, C:0.12, G:0.13, T:0.42
Consensus pattern (46 bp):
CGTGTTTTCAAAAAAAAATTCCGTGTTTCAAAAATTTTCATGTTTC
Found at i:4421607 original size:17 final size:17
Alignment explanation
Indices: 4421587--4421656 Score: 77
Period size: 17 Copynumber: 3.9 Consensus size: 17
4421577 TAAAAAAAAA
4421587 TTCGTGTTTCAAAAATT
1 TTCGTGTTTCAAAAATT
4421604 TTCGTGTTTTCAAAAAAATT
1 TTCGTG-TTTC--AAAAATT
** *
4421624 GACCGTGTTTCATAAATT
1 -TTCGTGTTTCAAAAATT
4421642 TTCGTGTTTCAAAAA
1 TTCGTGTTTCAAAAA
4421657 ATCCTCGTGT
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
17 18 0.42
18 10 0.23
20 11 0.26
21 4 0.09
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.43
Consensus pattern (17 bp):
TTCGTGTTTCAAAAATT
Found at i:4421658 original size:18 final size:18
Alignment explanation
Indices: 4421587--4421775 Score: 84
Period size: 20 Copynumber: 9.8 Consensus size: 18
4421577 TAAAAAAAAA
4421587 TTCGTGTTTC-AAAAATT
1 TTCGTGTTTCAAAAAATT
4421604 TTCGTGTTTTCAAAAAAATT
1 TTCGTG-TTTC-AAAAAATT
** *
4421624 GACCGTGTTTC-ATAAATT
1 -TTCGTGTTTCAAAAAATT
4421642 TTCGTGTTTCAAAAAATCCTCGTGT
1 TTCGTGTTTCAAAAAA------T-T
*
4421667 TTCGTATTTTATCAAAAAATT
1 TTCG--TGTT-TCAAAAAATT
4421688 TAT-GT-TTTCAAAAAAATT
1 T-TCGTGTTTC-AAAAAATT
*
4421706 TT-GTGTTT-TAAAAATT
1 TTCGTGTTTCAAAAAATT
**
4421722 TTCGTGTTTCAAAAAGAAAA
1 TTCGTGTTTC-AAAA-AATT
*
4421742 TTCGTGTTTCCTAAAAAAAT
1 TTCGTGTTT-C-AAAAAATT
*
4421762 CTCGTGTTTCAAAA
1 TTCGTGTTTCAAAA
4421776 TTTTTGTTTT
Statistics
Matches: 135, Mismatches: 14, Indels: 45
0.70 0.07 0.23
Matches are distributed among these distances:
16 9 0.07
17 25 0.19
18 32 0.24
19 5 0.04
20 33 0.24
21 12 0.09
22 2 0.01
24 1 0.01
25 5 0.04
27 3 0.02
28 8 0.06
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.42
Consensus pattern (18 bp):
TTCGTGTTTCAAAAAATT
Found at i:4421700 original size:17 final size:17
Alignment explanation
Indices: 4421678--4421736 Score: 68
Period size: 18 Copynumber: 3.4 Consensus size: 17
4421668 TCGTATTTTA
4421678 TCAAAAAATTTATGT-TT
1 TCAAAAAATTT-TGTGTT
4421695 TCAAAAAAATTTTGTGTT
1 TC-AAAAAATTTTGTGTT
*
4421713 T-TAAAAATTTTCGTGTT
1 TCAAAAAATTTT-GTGTT
4421730 TCAAAAA
1 TCAAAAA
4421737 GAAAATTCGT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
16 9 0.25
17 11 0.31
18 16 0.44
ACGTcount: A:0.41, C:0.07, G:0.08, T:0.44
Consensus pattern (17 bp):
TCAAAAAATTTTGTGTT
Found at i:4421718 original size:16 final size:17
Alignment explanation
Indices: 4421699--4421736 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
4421689 ATGTTTTCAA
*
4421699 AAAAATTTT-GTGTTTT
1 AAAAATTTTCGTGTTTC
4421715 AAAAATTTTCGTGTTTC
1 AAAAATTTTCGTGTTTC
4421732 AAAAA
1 AAAAA
4421737 GAAAATTCGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 9 0.45
17 11 0.55
ACGTcount: A:0.39, C:0.05, G:0.11, T:0.45
Consensus pattern (17 bp):
AAAAATTTTCGTGTTTC
Found at i:4421833 original size:19 final size:19
Alignment explanation
Indices: 4421811--4421852 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
4421801 TCGCGTTTCT
4421811 AAAATGCTTGTATTTT-AAA
1 AAAAT-CTTGTATTTTCAAA
* *
4421830 AAAATTTTGTGTTTTCAAA
1 AAAATCTTGTATTTTCAAA
4421849 AAAA
1 AAAA
4421853 AAAGGAAAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.45, C:0.05, G:0.10, T:0.40
Consensus pattern (19 bp):
AAAATCTTGTATTTTCAAA
Found at i:4424912 original size:22 final size:23
Alignment explanation
Indices: 4424870--4424912 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
4424860 TAAATTGATG
* *
4424870 AAATTACATTTTTATTATTGTAA
1 AAATTACAATTTAATTATTGTAA
4424893 AAATTACAATTTAATT-TTGT
1 AAATTACAATTTAATTATTGT
4424913 TCTTTCTAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.51
Consensus pattern (23 bp):
AAATTACAATTTAATTATTGTAA
Found at i:4425168 original size:12 final size:12
Alignment explanation
Indices: 4425151--4425176 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
4425141 AATTTTTTTT
4425151 ATTTTAGAAATA
1 ATTTTAGAAATA
4425163 ATTTTAGAAATA
1 ATTTTAGAAATA
4425175 AT
1 AT
4425177 AGATATGTTA
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:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (12 bp):
ATTTTAGAAATA
Found at i:4425207 original size:45 final size:41
Alignment explanation
Indices: 4425120--4425227 Score: 112
Period size: 45 Copynumber: 2.5 Consensus size: 41
4425110 CTAATACTTT
* * *
4425120 TAATTTTAGTAATAAAATTTTAATTTTTTTTATTTTAGAAA
1 TAATTTTAGAAATAAAATTTTAATTTTTTTAATTTTAAAAA
*
4425161 TAATTTTAGAAATAATAGATATGTTACTTTTTTTAATTTTAAAAA
1 TAATTTTAGAAATAA-A-AT-T-TTAATTTTTTTAATTTTAAAAA
4425206 TAAAGTTTT--AAATAAAATTTTA
1 T-AA-TTTTAGAAATAAAATTTTA
4425228 CTTATGGAAA
Statistics
Matches: 57, Mismatches: 4, Indels: 12
0.78 0.05 0.16
Matches are distributed among these distances:
41 17 0.30
42 2 0.04
43 4 0.07
44 2 0.04
45 26 0.46
46 2 0.04
47 4 0.07
ACGTcount: A:0.43, C:0.01, G:0.06, T:0.51
Consensus pattern (41 bp):
TAATTTTAGAAATAAAATTTTAATTTTTTTAATTTTAAAAA
Found at i:4426563 original size:18 final size:18
Alignment explanation
Indices: 4426535--4426602 Score: 66
Period size: 19 Copynumber: 3.7 Consensus size: 18
4426525 TATGTCAATC
*
4426535 TTAATTCTTTTAATATTT
1 TTAATTTTTTTAATATTT
*
4426553 ATAATTTTTTTACA-ATTT
1 TTAATTTTTTTA-ATATTT
* *
4426571 TTCTATTTTTTTAATTTTT
1 TT-AATTTTTTTAATATTT
4426590 TTAATTATTTTTA
1 TTAATT-TTTTTA
4426603 TTGGAAATAT
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
18 19 0.47
19 21 0.52
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.69
Consensus pattern (18 bp):
TTAATTTTTTTAATATTT
Found at i:4426580 original size:9 final size:9
Alignment explanation
Indices: 4426535--4426602 Score: 66
Period size: 9 Copynumber: 7.3 Consensus size: 9
4426525 TATGTCAATC
*
4426535 TTAATTCTT
1 TTAATTTTT
*
4426544 TTAATATTT
1 TTAATTTTT
*
4426553 ATAATTTTT
1 TTAATTTTT
4426562 TTACAATTTTT
1 TT--AATTTTT
*
4426573 CT-ATTTTT
1 TTAATTTTT
4426581 TTAATTTTT
1 TTAATTTTT
4426590 TTAATTATTT
1 TTAATT-TTT
4426600 TTA
1 TTA
4426603 TTGGAAATAT
Statistics
Matches: 48, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
8 7 0.15
9 27 0.56
10 6 0.12
11 8 0.17
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.69
Consensus pattern (9 bp):
TTAATTTTT
Found at i:4450798 original size:2 final size:2
Alignment explanation
Indices: 4450791--4450826 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
4450781 CCTCACTTAA
*
4450791 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT CT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4450827 AATTTTAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:4455816 original size:58 final size:58
Alignment explanation
Indices: 4455726--4455838 Score: 217
Period size: 58 Copynumber: 1.9 Consensus size: 58
4455716 ACTATAGCGA
*
4455726 TACTGTAGTGTGAGACAAAAAGTAAACTAAACGCACCGCACCGCACCCAATCGCCTAT
1 TACTGTAGCGTGAGACAAAAAGTAAACTAAACGCACCGCACCGCACCCAATCGCCTAT
4455784 TACTGTAGCGTGAGACAAAAAGTAAACTAAACGCACCGCACCGCACCCAATCGCC
1 TACTGTAGCGTGAGACAAAAAGTAAACTAAACGCACCGCACCGCACCCAATCGCC
4455839 CATCCAAACC
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 54 1.00
ACGTcount: A:0.36, C:0.31, G:0.18, T:0.15
Consensus pattern (58 bp):
TACTGTAGCGTGAGACAAAAAGTAAACTAAACGCACCGCACCGCACCCAATCGCCTAT
Found at i:4456110 original size:22 final size:20
Alignment explanation
Indices: 4456078--4456119 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 20
4456068 TTTTGTTTTG
4456078 TTGTTTTATTT-TCTTTGGGC
1 TTGTTTTATTTAT-TTTGGGC
4456098 TTGTTTCTCATTTATTTTGGGC
1 TTGTTT-T-ATTTATTTTGGGC
4456120 CTTTGAACTT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
20 6 0.32
21 1 0.05
22 11 0.58
23 1 0.05
ACGTcount: A:0.07, C:0.12, G:0.19, T:0.62
Consensus pattern (20 bp):
TTGTTTTATTTATTTTGGGC
Found at i:4456542 original size:80 final size:80
Alignment explanation
Indices: 4456410--4456833 Score: 717
Period size: 80 Copynumber: 5.3 Consensus size: 80
4456400 TAATCTTTTT
* * *
4456410 ACTCTATCAAGTAAAATCTAAATATCATACACACCTCCCTCCGCCGCCAACACTTAACACCAATT
1 ACTCTATCAAGTAAAACCTAAATATCATACACACCTCTCTCCGCCGCCAACACTTAACACCAATC
*
4456475 CTAAAACTCCTTAAT
66 CTAAAACTCCTTAAC
4456490 ACTCTATCAAGTAAAACCTAAATATCATACACACCTCTCTCCGCCGCCAACACTTAACACCAATC
1 ACTCTATCAAGTAAAACCTAAATATCATACACACCTCTCTCCGCCGCCAACACTTAACACCAATC
*
4456555 CTAAAACTCTTTAAC
66 CTAAAACTCCTTAAC
* * *
4456570 ACTCTATCTAGTAAAACCTAAATATCATACACACCTCCCTCCGCCGCCAACACTTAACACCAATT
1 ACTCTATCAAGTAAAACCTAAATATCATACACACCTCTCTCCGCCGCCAACACTTAACACCAATC
*
4456635 CTAAAACTCCTTAAT
66 CTAAAACTCCTTAAC
4456650 ACTCTATCAAGTAAAACCTAAATATCATACACACCTCTCTCCGCCGCCAACACTTAACACCAATC
1 ACTCTATCAAGTAAAACCTAAATATCATACACACCTCTCTCCGCCGCCAACACTTAACACCAATC
*
4456715 CTAAAACTCTTTAAC
66 CTAAAACTCCTTAAC
*
4456730 ACTCTATCTAGTAAAACCTAAATATCATACACACCT-TCCTCCGCCGCCAACACTT-ACACCAAT
1 ACTCTATCAAGTAAAACCTAAATATCATACACACCTCT-CTCCGCCGCCAACACTTAACACCAAT
*
4456793 ACTAAAACTCCTTAAC
65 CCTAAAACTCCTTAAC
4456809 ACTCTATCAAGTAAAACCTAAATAT
1 ACTCTATCAAGTAAAACCTAAATAT
4456834 TCCTTGATAC
Statistics
Matches: 324, Mismatches: 19, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
79 47 0.15
80 277 0.85
ACGTcount: A:0.38, C:0.34, G:0.04, T:0.25
Consensus pattern (80 bp):
ACTCTATCAAGTAAAACCTAAATATCATACACACCTCTCTCCGCCGCCAACACTTAACACCAATC
CTAAAACTCCTTAAC
Found at i:4456674 original size:160 final size:160
Alignment explanation
Indices: 4456410--4456833 Score: 796
Period size: 160 Copynumber: 2.7 Consensus size: 160
4456400 TAATCTTTTT
* *
4456410 ACTCTATCAAGTAAAATCTAAATATCATACACACCTCCCTCCGCCGCCAACACTTAACACCAATT
1 ACTCTATCTAGTAAAACCTAAATATCATACACACCTCCCTCCGCCGCCAACACTTAACACCAATT
4456475 CTAAAACTCCTTAATACTCTATCAAGTAAAACCTAAATATCATACACACCTCTCTCCGCCGCCAA
66 CTAAAACTCCTTAATACTCTATCAAGTAAAACCTAAATATCATACACACCTCTCTCCGCCGCCAA
4456540 CACTTAACACCAATCCTAAAACTCTTTAAC
131 CACTTAACACCAATCCTAAAACTCTTTAAC
4456570 ACTCTATCTAGTAAAACCTAAATATCATACACACCTCCCTCCGCCGCCAACACTTAACACCAATT
1 ACTCTATCTAGTAAAACCTAAATATCATACACACCTCCCTCCGCCGCCAACACTTAACACCAATT
4456635 CTAAAACTCCTTAATACTCTATCAAGTAAAACCTAAATATCATACACACCTCTCTCCGCCGCCAA
66 CTAAAACTCCTTAATACTCTATCAAGTAAAACCTAAATATCATACACACCTCTCTCCGCCGCCAA
4456700 CACTTAACACCAATCCTAAAACTCTTTAAC
131 CACTTAACACCAATCCTAAAACTCTTTAAC
* *
4456730 ACTCTATCTAGTAAAACCTAAATATCATACACACCTTCCTCCGCCGCCAACACTT-ACACCAATA
1 ACTCTATCTAGTAAAACCTAAATATCATACACACCTCCCTCCGCCGCCAACACTTAACACCAATT
*
4456794 CTAAAACTCCTTAACACTCTATCAAGTAAAACCTAAATAT
66 CTAAAACTCCTTAATACTCTATCAAGTAAAACCTAAATAT
4456834 TCCTTGATAC
Statistics
Matches: 259, Mismatches: 5, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
159 47 0.18
160 212 0.82
ACGTcount: A:0.38, C:0.34, G:0.04, T:0.25
Consensus pattern (160 bp):
ACTCTATCTAGTAAAACCTAAATATCATACACACCTCCCTCCGCCGCCAACACTTAACACCAATT
CTAAAACTCCTTAATACTCTATCAAGTAAAACCTAAATATCATACACACCTCTCTCCGCCGCCAA
CACTTAACACCAATCCTAAAACTCTTTAAC
Found at i:4456838 original size:33 final size:33
Alignment explanation
Indices: 4456801--4456863 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
4456791 ATACTAAAAC
4456801 TCCTTAACACTCTATCAAGTAAAACCTAAATAT
1 TCCTTAACACTCTATCAAGTAAAACCTAAATAT
* * *
4456834 TCCTTGATACTCTATTAAGTAAAACCTAAA
1 TCCTTAACACTCTATCAAGTAAAACCTAAA
4456864 GATCATTCAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.41, C:0.22, G:0.05, T:0.32
Consensus pattern (33 bp):
TCCTTAACACTCTATCAAGTAAAACCTAAATAT
Found at i:4456861 original size:112 final size:113
Alignment explanation
Indices: 4456730--4456946 Score: 305
Period size: 112 Copynumber: 1.9 Consensus size: 113
4456720 ACTCTTTAAC
* * * * *
4456730 ACTCTATCTAGTAAAACCTAAATATCATACACACCTTCCTCCGCCGCCAACACTT-ACACCAATA
1 ACTCTATCTAGTAAAACCTAAAGATCATACACACCTCCCTCAGCCGCCAACACTTAAAAACAAT-
4456794 C-TAAAACTCCTTAACACTCTATCAAGTAAAACCTAAATATTCCTTGAT
65 CGTAAAACTCCTTAACACTCTATCAAGTAAAACCTAAATATTCCTTGAT
* *
4456842 ACTCTAT-TAAGTAAAACCTAAAGATCATTCACACCTCCCTCAGCCGTCAACACTTAAAAACAAT
1 ACTCTATCT-AGTAAAACCTAAAGATCATACACACCTCCCTCAGCCGCCAACACTTAAAAACAAT
* * *
4456906 CGTAAAACTCCTTAATACTTTATCAAGTGAAACCTAAATAT
65 CGTAAAACTCCTTAACACTCTATCAAGTAAAACCTAAATAT
4456947 CATGCGAACC
Statistics
Matches: 92, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
111 1 0.01
112 49 0.53
113 42 0.46
ACGTcount: A:0.39, C:0.29, G:0.06, T:0.27
Consensus pattern (113 bp):
ACTCTATCTAGTAAAACCTAAAGATCATACACACCTCCCTCAGCCGCCAACACTTAAAAACAATC
GTAAAACTCCTTAACACTCTATCAAGTAAAACCTAAATATTCCTTGAT
Found at i:4456973 original size:80 final size:80
Alignment explanation
Indices: 4456825--4457002 Score: 205
Period size: 80 Copynumber: 2.2 Consensus size: 80
4456815 TCAAGTAAAA
* * * * *
4456825 CCTAAATATTCCTTGATACTCTATTAAGTAAAACCTAAAGATCATTCACACCTCCCTCAGCCGTC
1 CCTAAA-ACTCCTTAATACTCTATCAAGTAAAACCTAAAGATCATGCACACCTCCCTCAGCCGCC
4456890 AACACTTAAAAACAAT
65 AACACTTAAAAACAAT
* * * * * *
4456906 CGTAAAACTCCTTAATACTTTATCAAGTGAAACCTAAATATCATGCGA-ACCTTCCTCCGCCGCC
1 CCTAAAACTCCTTAATACTCTATCAAGTAAAACCTAAAGATCATGC-ACACCTCCCTCAGCCGCC
* *
4456970 AACACTTAACACCAAT
65 AACACTTAAAAACAAT
*
4456986 CCTCAAACTCCTTAATA
1 CCTAAAACTCCTTAATA
4457003 ACATAAGACA
Statistics
Matches: 81, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
80 75 0.93
81 6 0.07
ACGTcount: A:0.37, C:0.30, G:0.07, T:0.26
Consensus pattern (80 bp):
CCTAAAACTCCTTAATACTCTATCAAGTAAAACCTAAAGATCATGCACACCTCCCTCAGCCGCCA
ACACTTAAAAACAAT
Found at i:4456975 original size:192 final size:193
Alignment explanation
Indices: 4456642--4457000 Score: 533
Period size: 192 Copynumber: 1.9 Consensus size: 193
4456632 ATTCTAAAAC
* * *
4456642 TCCTTAATACTCTATCAAGTAAAACCTAAATATCATACACACCTCTCTCCGCCGCCAACACTTAA
1 TCCTTAATACTCTATCAAGTAAAACCTAAAGATCATACACACCTCCCTCAGCCGCCAACACTTAA
* * * *
4456707 CACCAATCCTAAAACTCTTTAACACTCTATCTAGTAAAACCTAAATATCATACACACCTTCCTCC
66 AAACAATCCTAAAACTCCTTAACACTCTATCAAGTAAAACCTAAATATCATACACACCTTCCTCC
4456772 GCCGCCAACACTT-ACACCAATACTAAAACTCCTTAACACTCTATCAAGTAAAACCTAAATAT
131 GCCGCCAACACTTAACACCAATACTAAAACTCCTTAACACTCTATCAAGTAAAACCTAAATAT
* * * *
4456834 TCCTTGATACTCTATTAAGTAAAACCTAAAGATCATTCACACCTCCCTCAGCCGTCAACACTTAA
1 TCCTTAATACTCTATCAAGTAAAACCTAAAGATCATACACACCTCCCTCAGCCGCCAACACTTAA
* * * * *
4456899 AAACAATCGTAAAACTCCTTAATACTTTATCAAGTGAAACCTAAATATCATGCGA-ACCTTCCTC
66 AAACAATCCTAAAACTCCTTAACACTCTATCAAGTAAAACCTAAATATCATAC-ACACCTTCCTC
* *
4456963 CGCCGCCAACACTTAACACCAATCCTCAAACTCCTTAA
130 CGCCGCCAACACTTAACACCAATACTAAAACTCCTTAA
4457001 TAACATAAGA
Statistics
Matches: 147, Mismatches: 18, Indels: 3
0.88 0.11 0.02
Matches are distributed among these distances:
192 125 0.85
193 22 0.15
ACGTcount: A:0.37, C:0.32, G:0.05, T:0.26
Consensus pattern (193 bp):
TCCTTAATACTCTATCAAGTAAAACCTAAAGATCATACACACCTCCCTCAGCCGCCAACACTTAA
AAACAATCCTAAAACTCCTTAACACTCTATCAAGTAAAACCTAAATATCATACACACCTTCCTCC
GCCGCCAACACTTAACACCAATACTAAAACTCCTTAACACTCTATCAAGTAAAACCTAAATAT
Found at i:4460193 original size:23 final size:26
Alignment explanation
Indices: 4460167--4460220 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 26
4460157 CTTTAATTTT
4460167 TTTATTCGAAAAATAA-AATA-TT-A
1 TTTATTCGAAAAATAAGAATAGTTAA
*
4460190 TTTA-T-GATAAATAAGAATAGTTAA
1 TTTATTCGAAAAATAAGAATAGTTAA
4460214 TTTATTC
1 TTTATTC
4460221 ATGAGGTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 8 0.32
22 5 0.20
23 6 0.24
24 5 0.20
25 1 0.04
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.43
Consensus pattern (26 bp):
TTTATTCGAAAAATAAGAATAGTTAA
Found at i:4472054 original size:142 final size:142
Alignment explanation
Indices: 4471798--4472077 Score: 533
Period size: 142 Copynumber: 2.0 Consensus size: 142
4471788 CAGCAATGAA
4471798 TGTCCACTGAAATAGCTTGAAGCTAAAGTTTGGATCCTTAAAAGGGTAAACTGTTGAAATTGCAG
1 TGTCCACTGAAATAGCTTGAAGCTAAAGTTTGGATCCTTAAAAGGGTAAACTGTTGAAATTGCAG
* *
4471863 TCAATGCACTTGCCCTGCTTTAGTACAACAGGGTTCTATAGAGAGAAAAATGCTCTTAACCGCAC
66 TCAATGCACCTGCCCTGCTTTAGTACAACAGGGTTCTATAGAGAGAAAAATACTCTTAACCGCAC
4471928 TCAAATTCACGT
131 TCAAATTCACGT
*
4471940 TGTCCGCTGAAATAGCTTGAAGCTAAAGTTTGGATCCTTAAAAGGGTAAACTGTTGAAATTGCAG
1 TGTCCACTGAAATAGCTTGAAGCTAAAGTTTGGATCCTTAAAAGGGTAAACTGTTGAAATTGCAG
4472005 TCAATGCACCTGCCCTGCTTTAGTACAACAGGGTTCTATAGAGAGAAAAATACTCTTAACCGCAC
66 TCAATGCACCTGCCCTGCTTTAGTACAACAGGGTTCTATAGAGAGAAAAATACTCTTAACCGCAC
4472070 TCAAATTC
131 TCAAATTC
4472078 TCAAGCTCGG
Statistics
Matches: 135, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
142 135 1.00
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.28
Consensus pattern (142 bp):
TGTCCACTGAAATAGCTTGAAGCTAAAGTTTGGATCCTTAAAAGGGTAAACTGTTGAAATTGCAG
TCAATGCACCTGCCCTGCTTTAGTACAACAGGGTTCTATAGAGAGAAAAATACTCTTAACCGCAC
TCAAATTCACGT
Found at i:4478985 original size:2 final size:2
Alignment explanation
Indices: 4478978--4479006 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4478968 TAACCTCTGC
4478978 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4479007 AAAAAAATAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4480544 original size:9 final size:9
Alignment explanation
Indices: 4480530--4480575 Score: 67
Period size: 9 Copynumber: 5.2 Consensus size: 9
4480520 TTTGGTTAAA
4480530 AATTACCCG
1 AATTACCCG
4480539 AATTACCCG
1 AATTACCCG
*
4480548 -ATTAACCG
1 AATTACCCG
*
4480556 AATTAACCG
1 AATTACCCG
4480565 AATTACCCG
1 AATTACCCG
4480574 AA
1 AA
4480576 AATTACCCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
8 7 0.21
9 27 0.79
ACGTcount: A:0.39, C:0.28, G:0.11, T:0.22
Consensus pattern (9 bp):
AATTACCCG
Found at i:4480556 original size:17 final size:18
Alignment explanation
Indices: 4480530--4480575 Score: 67
Period size: 17 Copynumber: 2.6 Consensus size: 18
4480520 TTTGGTTAAA
*
4480530 AATTACCCGAATTACCCG
1 AATTACCCGAATTAACCG
*
4480548 -ATTAACCGAATTAACCG
1 AATTACCCGAATTAACCG
4480565 AATTACCCGAA
1 AATTACCCGAA
4480576 AATTACCCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 15 0.62
18 9 0.38
ACGTcount: A:0.39, C:0.28, G:0.11, T:0.22
Consensus pattern (18 bp):
AATTACCCGAATTAACCG
Found at i:4481412 original size:29 final size:30
Alignment explanation
Indices: 4481380--4481452 Score: 78
Period size: 30 Copynumber: 2.4 Consensus size: 30
4481370 ATATTTACTA
*
4481380 AAAAATTAAAATTTTAT-AAAATAATA-TCC
1 AAAAATCAAAATTTTATCAAAATAA-AGTCC
* * *
4481409 AAAACTCATAATTTTCTCAAAATAAAGTCC
1 AAAAATCAAAATTTTATCAAAATAAAGTCC
4481439 AAAAATCCAAAATT
1 AAAAAT-CAAAATT
4481453 AATATGAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
29 14 0.40
30 15 0.43
31 6 0.17
ACGTcount: A:0.55, C:0.14, G:0.01, T:0.30
Consensus pattern (30 bp):
AAAAATCAAAATTTTATCAAAATAAAGTCC
Found at i:4486801 original size:3 final size:3
Alignment explanation
Indices: 4486795--4486819 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
4486785 ATATATATCC
4486795 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
4486820 AGGGTACGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:4492686 original size:18 final size:19
Alignment explanation
Indices: 4492658--4492699 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
4492648 AGGATACTCT
* *
4492658 CTACTAAACCAAGTAACTA
1 CTACTAAACCAAATAACAA
4492677 CTAC-AAACCAAATAACAA
1 CTACTAAACCAAATAACAA
4492695 CTACT
1 CTACT
4492700 TGACTATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.50, C:0.29, G:0.02, T:0.19
Consensus pattern (19 bp):
CTACTAAACCAAATAACAA
Found at i:4496695 original size:2 final size:2
Alignment explanation
Indices: 4496690--4496721 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
4496680 AGTGTGTGTG
4496690 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
4496722 CACGAGACAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4504136 original size:21 final size:21
Alignment explanation
Indices: 4504096--4504136 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
4504086 AGGGTAATAG
*
4504096 GGTGGAGGAGGGTAAGCGCCT
1 GGTGGAGGAGGGTAACCGCCT
*
4504117 GGTGGAGGAGGGTATCCGCC
1 GGTGGAGGAGGGTAACCGCC
4504137 ATATGGGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.17, G:0.51, T:0.15
Consensus pattern (21 bp):
GGTGGAGGAGGGTAACCGCCT
Found at i:4509247 original size:21 final size:21
Alignment explanation
Indices: 4509207--4509247 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
4509197 AGGGTAATAG
*
4509207 GGTGGAGGAGGGTAAGCGCCT
1 GGTGGAGGAGGGTAACCGCCT
*
4509228 GGTGGAGGAGGGTATCCGCC
1 GGTGGAGGAGGGTAACCGCC
4509248 ATATGGGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.17, G:0.51, T:0.15
Consensus pattern (21 bp):
GGTGGAGGAGGGTAACCGCCT
Found at i:4514402 original size:18 final size:18
Alignment explanation
Indices: 4514379--4514414 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
4514369 AGGAGGAACC
4514379 GGCTCTTCCAACAAATTA
1 GGCTCTTCCAACAAATTA
*
4514397 GGCTCTTCCTACAAATTA
1 GGCTCTTCCAACAAATTA
4514415 TCCTCTGCCA
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:0.31, C:0.28, G:0.11, T:0.31
Consensus pattern (18 bp):
GGCTCTTCCAACAAATTA
Found at i:4514420 original size:18 final size:18
Alignment explanation
Indices: 4514381--4514420 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
4514371 GAGGAACCGG
*
4514381 CTCTTCCAACAAATTAGG
1 CTCTTCCAACAAATTAGC
* *
4514399 CTCTTCCTACAAATTATC
1 CTCTTCCAACAAATTAGC
4514417 CTCT
1 CTCT
4514421 GCCAGCAACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.28, C:0.33, G:0.05, T:0.35
Consensus pattern (18 bp):
CTCTTCCAACAAATTAGC
Found at i:4526359 original size:6 final size:6
Alignment explanation
Indices: 4526348--4526397 Score: 55
Period size: 6 Copynumber: 8.3 Consensus size: 6
4526338 TACATTTCCC
* * * * *
4526348 CCACCT CCACCT CCTCCT CCGCCA CCACCT CCACCT CCTCCT CCGCCT
1 CCACCT CCACCT CCACCT CCACCT CCACCT CCACCT CCACCT CCACCT
4526396 CC
1 CC
4526398 TTGTAAGTTC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.10, C:0.68, G:0.04, T:0.18
Consensus pattern (6 bp):
CCACCT
Found at i:4526377 original size:24 final size:24
Alignment explanation
Indices: 4526348--4526394 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
4526338 TACATTTCCC
4526348 CCACCTCCACCTCCTCCTCCGCCA
1 CCACCTCCACCTCCTCCTCCGCCA
4526372 CCACCTCCACCTCCTCCTCCGCC
1 CCACCTCCACCTCCTCCTCCGCC
4526395 TCCTTGTAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.11, C:0.68, G:0.04, T:0.17
Consensus pattern (24 bp):
CCACCTCCACCTCCTCCTCCGCCA
Found at i:4528831 original size:27 final size:27
Alignment explanation
Indices: 4528792--4528863 Score: 99
Period size: 27 Copynumber: 2.6 Consensus size: 27
4528782 ACTTACCACT
* *
4528792 AAACTGTGGCTAAAATGTTACAACACGA
1 AAAC-GTGACTAAAACGTTACAACACGA
*
4528820 AAACGTGACTAAAACGTTATAACACGA
1 AAACGTGACTAAAACGTTACAACACGA
*
4528847 AAACATGACTAAAACGT
1 AAACGTGACTAAAACGT
4528864 AAGATTTCAA
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
27 36 0.90
28 4 0.10
ACGTcount: A:0.47, C:0.18, G:0.15, T:0.19
Consensus pattern (27 bp):
AAACGTGACTAAAACGTTACAACACGA
Found at i:4529815 original size:36 final size:36
Alignment explanation
Indices: 4529774--4529846 Score: 110
Period size: 36 Copynumber: 2.0 Consensus size: 36
4529764 TTATTGAAAC
*
4529774 TTTTATATGATCATCTTAACATTATTTTAATATTTA
1 TTTTATATGATCATCGTAACATTATTTTAATATTTA
* * *
4529810 TTTTATATGGTCATCGTAACATTTTTTTAATGTTTA
1 TTTTATATGATCATCGTAACATTATTTTAATATTTA
4529846 T
1 T
4529847 ATTAGAGCAG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.29, C:0.08, G:0.07, T:0.56
Consensus pattern (36 bp):
TTTTATATGATCATCGTAACATTATTTTAATATTTA
Found at i:4531780 original size:11 final size:11
Alignment explanation
Indices: 4531764--4531820 Score: 53
Period size: 11 Copynumber: 5.1 Consensus size: 11
4531754 ATATATACTG
4531764 AATAAAATAAT
1 AATAAAATAAT
4531775 AATAAAATAAT
1 AATAAAATAAT
*
4531786 ATTTAAAATCAA-
1 A-ATAAAAT-AAT
* *
4531798 ATTAAAATATT
1 AATAAAATAAT
*
4531809 AATAAACTAAT
1 AATAAAATAAT
4531820 A
1 A
4531821 TTTATTTATT
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
10 1 0.03
11 28 0.74
12 7 0.18
13 2 0.05
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.32
Consensus pattern (11 bp):
AATAAAATAAT
Found at i:4532294 original size:23 final size:23
Alignment explanation
Indices: 4532268--4532314 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
4532258 TTTCTTACTG
*
4532268 TAGTAATTTTCGGGGTATTACAA
1 TAGTAATTTTCGGGATATTACAA
*
4532291 TAGTAATTTTTGGGATATTACAA
1 TAGTAATTTTCGGGATATTACAA
4532314 T
1 T
4532315 TAGGGTTTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.32, C:0.06, G:0.19, T:0.43
Consensus pattern (23 bp):
TAGTAATTTTCGGGATATTACAA
Found at i:4533290 original size:14 final size:14
Alignment explanation
Indices: 4533271--4533297 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
4533261 AAGAAAGACG
4533271 TATGAAAATTTTAT
1 TATGAAAATTTTAT
4533285 TATGAAAATTTTA
1 TATGAAAATTTTA
4533298 CCAATTTCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.48
Consensus pattern (14 bp):
TATGAAAATTTTAT
Found at i:4534768 original size:25 final size:25
Alignment explanation
Indices: 4534708--4534771 Score: 65
Period size: 25 Copynumber: 2.6 Consensus size: 25
4534698 TTACGGCTCT
* *
4534708 CATGAGCTTCCCGTTATATGACCCA
1 CATGAGCTTCCCGTAACATGACCCA
* * * * *
4534733 GATAAGTTTCCTGTAACATGACTCA
1 CATGAGCTTCCCGTAACATGACCCA
4534758 CATGAGCTTCCCGT
1 CATGAGCTTCCCGT
4534772 TATATGGCTT
Statistics
Matches: 28, Mismatches: 11, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.25, C:0.28, G:0.17, T:0.30
Consensus pattern (25 bp):
CATGAGCTTCCCGTAACATGACCCA
Found at i:4551239 original size:3 final size:3
Alignment explanation
Indices: 4551231--4551270 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
4551221 TGAATCTTTT
4551231 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 A
4551271 AAGACTTGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:4551862 original size:27 final size:28
Alignment explanation
Indices: 4551808--4551868 Score: 88
Period size: 27 Copynumber: 2.2 Consensus size: 28
4551798 TTGAACCTCG
* *
4551808 AACTCCGAACTTAGAACCTTGAATCCTA
1 AACTCCGAACCTAGAACCTTGAACCCTA
*
4551836 AACTCCGAACCT-GAATCTTGAACCCTA
1 AACTCCGAACCTAGAACCTTGAACCCTA
4551863 AACTCC
1 AACTCC
4551869 AAAATCGAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 19 0.63
28 11 0.37
ACGTcount: A:0.34, C:0.33, G:0.10, T:0.23
Consensus pattern (28 bp):
AACTCCGAACCTAGAACCTTGAACCCTA
Found at i:4551886 original size:20 final size:20
Alignment explanation
Indices: 4551863--4551900 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
4551853 TTGAACCCTA
4551863 AACTCCAA-AATCGAACCTCG
1 AACTCCAATAAT-GAACCTCG
*
4551883 AACTCGAATAATGAACCT
1 AACTCCAATAATGAACCT
4551901 TGAGCCTTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.81
21 3 0.19
ACGTcount: A:0.42, C:0.29, G:0.11, T:0.18
Consensus pattern (20 bp):
AACTCCAATAATGAACCTCG
Found at i:4552698 original size:6 final size:6
Alignment explanation
Indices: 4552682--4552715 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
4552672 TTTAGTGATC
4552682 TTTTA- TTTTAT TTTTAT TTTTAT TTTTAT TTTTA
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTA
4552716 AATTAATAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.18
6 23 0.82
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTTAT
Found at i:4559087 original size:3 final size:3
Alignment explanation
Indices: 4559079--4559119 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
4559069 AACACCCATC
4559079 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
4559120 CATTTTGCAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:4565982 original size:64 final size:64
Alignment explanation
Indices: 4565909--4566036 Score: 238
Period size: 64 Copynumber: 2.0 Consensus size: 64
4565899 TTGCAAATTC
* *
4565909 AAATATATTTTAATTTATATGTCATAATTTTAGAATTTCTTTTTTAGGTTAGAATTAACTTGGG
1 AAATATATTTTAATTTATATATCATAATTTTAGAATTTCTTTTGTAGGTTAGAATTAACTTGGG
4565973 AAATATATTTTAATTTATATATCATAATTTTAGAATTTCTTTTGTAGGTTAGAATTAACTTGGG
1 AAATATATTTTAATTTATATATCATAATTTTAGAATTTCTTTTGTAGGTTAGAATTAACTTGGG
4566037 GTTTCACCTA
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
64 62 1.00
ACGTcount: A:0.34, C:0.05, G:0.12, T:0.49
Consensus pattern (64 bp):
AAATATATTTTAATTTATATATCATAATTTTAGAATTTCTTTTGTAGGTTAGAATTAACTTGGG
Found at i:4581432 original size:22 final size:22
Alignment explanation
Indices: 4581404--4581450 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
4581394 AGATATTTCC
4581404 TGACAAAGAGAAAAACCAGACA
1 TGACAAAGAGAAAAACCAGACA
4581426 TGACAAAGAGAAAAACCAGACA
1 TGACAAAGAGAAAAACCAGACA
4581448 TGA
1 TGA
4581451 TGGGCAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.57, C:0.17, G:0.19, T:0.06
Consensus pattern (22 bp):
TGACAAAGAGAAAAACCAGACA
Found at i:4585421 original size:22 final size:23
Alignment explanation
Indices: 4585395--4585440 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
4585385 AAATATTAGC
*
4585395 ATTATAA-AAATTGAATGATAAA
1 ATTATAATAAATTAAATGATAAA
*
4585417 ATTATAATAAATTAAATTATAAA
1 ATTATAATAAATTAAATGATAAA
4585440 A
1 A
4585441 ATTTGAACAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 7 0.33
23 14 0.67
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (23 bp):
ATTATAATAAATTAAATGATAAA
Found at i:4586810 original size:171 final size:171
Alignment explanation
Indices: 4586525--4587031 Score: 1005
Period size: 171 Copynumber: 3.0 Consensus size: 171
4586515 ATTGAAACTA
4586525 ATAATAATATATACGTAATGAGCGTCAGACGATATCAAATGATATTATAATAACATATAATAAGT
1 ATAATAATATATACGTAATGAGCGTCAGACGATATCAAATGATATTATAATAACATATAATAAGT
4586590 AATGAAATGTATTGTTTGAAATTGAACCCGTGTACTTGTCAGATGGTTAGAGTGTTCATTGCCCC
66 AATGAAATGTATTGTTTGAAATTGAACCCGTGTACTTGTCAGATGGTTAGAGTGTTCATTGCCCC
4586655 ATGTGTGACATGGGTTTGAGTCGCGTTGCTGTTAATAATAT
131 ATGTGTGACATGGGTTTGAGTCGCGTTGCTGTTAATAATAT
4586696 ATAATAATATATACGTAATGAGCGTCAGACGATATCAAATGATATTATAATAACATATAATAAGT
1 ATAATAATATATACGTAATGAGCGTCAGACGATATCAAATGATATTATAATAACATATAATAAGT
4586761 AATGAAATGTATTGTTTGAAATTGAACCCGTGTACTTGTCAGATGGTTAGAGTGTTCATTGCCCC
66 AATGAAATGTATTGTTTGAAATTGAACCCGTGTACTTGTCAGATGGTTAGAGTGTTCATTGCCCC
4586826 ATGTGTGACATGGGTTTGAGTCGCGTTGCTGTTAATAATAT
131 ATGTGTGACATGGGTTTGAGTCGCGTTGCTGTTAATAATAT
4586867 ATAATAATATATACGTAATGAGCGTCAGACGATATCAAATGATATTATAATAACATATAATAAGT
1 ATAATAATATATACGTAATGAGCGTCAGACGATATCAAATGATATTATAATAACATATAATAAGT
*
4586932 AATGAAATGTATTGTTTGAAATTGAACCCGTGTATTTGTCAGATGGTTAGAGTGTTCATTGCCCC
66 AATGAAATGTATTGTTTGAAATTGAACCCGTGTACTTGTCAGATGGTTAGAGTGTTCATTGCCCC
4586997 ATGTGTGACATGGGTTTGAGTCGCGTTGCTGTTAA
131 ATGTGTGACATGGGTTTGAGTCGCGTTGCTGTTAA
4587032 GGCTTTATCC
Statistics
Matches: 335, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
171 335 1.00
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.35
Consensus pattern (171 bp):
ATAATAATATATACGTAATGAGCGTCAGACGATATCAAATGATATTATAATAACATATAATAAGT
AATGAAATGTATTGTTTGAAATTGAACCCGTGTACTTGTCAGATGGTTAGAGTGTTCATTGCCCC
ATGTGTGACATGGGTTTGAGTCGCGTTGCTGTTAATAATAT
Found at i:4588774 original size:18 final size:15
Alignment explanation
Indices: 4588733--4588776 Score: 61
Period size: 18 Copynumber: 2.7 Consensus size: 15
4588723 AAGCTAATTA
4588733 AAAAAAATTAAAACC
1 AAAAAAATTAAAACC
4588748 AAAAAAATTAATTAATCC
1 AAAAAAATTAA--AA-CC
4588766 AAAAAAATTAA
1 AAAAAAATTAA
4588777 CCCAGCGCGA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
15 11 0.42
17 2 0.08
18 13 0.50
ACGTcount: A:0.70, C:0.09, G:0.00, T:0.20
Consensus pattern (15 bp):
AAAAAAATTAAAACC
Found at i:4614121 original size:42 final size:43
Alignment explanation
Indices: 4614074--4614183 Score: 120
Period size: 42 Copynumber: 2.6 Consensus size: 43
4614064 AGCTGCATAA
* *
4614074 TTGGCAAGAAAGCTCGTCCAACTGAG-C-AAGTTTTTTACACAG
1 TTGGCAAGAAAGCTCATCCAACTGAGACGAA-TTTTCTACACAG
*
4614116 TTGGC-AGAAAAGCTCATCCAA-TTAGACGAATTTTCTACACAG
1 TTGGCAAG-AAAGCTCATCCAACTGAGACGAATTTTCTACACAG
* * *
4614158 TTGACAGGAAAGCTCTTCCAACTGAG
1 TTGGCAAGAAAGCTCATCCAACTGAG
4614184 TGAGCTTTCA
Statistics
Matches: 56, Mismatches: 7, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
41 5 0.09
42 45 0.80
43 6 0.11
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.25
Consensus pattern (43 bp):
TTGGCAAGAAAGCTCATCCAACTGAGACGAATTTTCTACACAG
Found at i:4616082 original size:107 final size:108
Alignment explanation
Indices: 4615892--4616092 Score: 314
Period size: 107 Copynumber: 1.8 Consensus size: 108
4615882 AAGACACTGG
* *
4615892 TTCCCAAACTACTTATGTTCGACTCAAGAAAAACTTGAACTCGGCTCAATAACTATCGAGCCAAG
1 TTCCCAAACTACTTATGTTCG---CAAGAAAAACTTGAACTCGACTCAATAACTATCAAGCCAAG
4615957 CTCAAACTATTGGTCAAGCTGAATTTGAGACTTCGTAATGCTCAGC
63 CTCAAACTATTGGTCAAGCTGAATTTGAGACTTCGTAATGCTCAGC
* * *
4616003 TTCCCAAACTACTTATGTTCG-AAGAAAAACTTGAACTTGACTCAATAATTATCAAGCCAAGCTT
1 TTCCCAAACTACTTATGTTCGCAAGAAAAACTTGAACTCGACTCAATAACTATCAAGCCAAGCTC
*
4616067 GAACTATTGGTCAAGCTGAATTTGAG
66 AAACTATTGGTCAAGCTGAATTTGAG
4616093 CTTAATTATA
Statistics
Matches: 84, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
107 63 0.75
111 21 0.25
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.28
Consensus pattern (108 bp):
TTCCCAAACTACTTATGTTCGCAAGAAAAACTTGAACTCGACTCAATAACTATCAAGCCAAGCTC
AAACTATTGGTCAAGCTGAATTTGAGACTTCGTAATGCTCAGC
Found at i:4618621 original size:3 final size:3
Alignment explanation
Indices: 4618613--4618638 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
4618603 ACTGAGTAGC
4618613 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
4618639 TTAAAATATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:4619766 original size:42 final size:42
Alignment explanation
Indices: 4619718--4619885 Score: 336
Period size: 42 Copynumber: 4.0 Consensus size: 42
4619708 AGTCTATATT
4619718 TTTACTCAAATTCTTTCACTTTTTATAAAAGTTTCGGCCTAA
1 TTTACTCAAATTCTTTCACTTTTTATAAAAGTTTCGGCCTAA
4619760 TTTACTCAAATTCTTTCACTTTTTATAAAAGTTTCGGCCTAA
1 TTTACTCAAATTCTTTCACTTTTTATAAAAGTTTCGGCCTAA
4619802 TTTACTCAAATTCTTTCACTTTTTATAAAAGTTTCGGCCTAA
1 TTTACTCAAATTCTTTCACTTTTTATAAAAGTTTCGGCCTAA
4619844 TTTACTCAAATTCTTTCACTTTTTATAAAAGTTTCGGCCTAA
1 TTTACTCAAATTCTTTCACTTTTTATAAAAGTTTCGGCCTAA
4619886 CCCTTGGACA
Statistics
Matches: 126, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 126 1.00
ACGTcount: A:0.29, C:0.19, G:0.07, T:0.45
Consensus pattern (42 bp):
TTTACTCAAATTCTTTCACTTTTTATAAAAGTTTCGGCCTAA
Found at i:4625093 original size:21 final size:20
Alignment explanation
Indices: 4625047--4625094 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
4625037 AACCCTACTG
* * *
4625047 TTTTCGTTGTTGTTTTTTCA
1 TTTTTGTTGTTATTTTATCA
4625067 TATTTTGTTGTTATTTTATCA
1 T-TTTTGTTGTTATTTTATCA
4625088 CTTTTTG
1 -TTTTTG
4625095 CCACTATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 21 0.91
22 1 0.04
ACGTcount: A:0.10, C:0.08, G:0.12, T:0.69
Consensus pattern (20 bp):
TTTTTGTTGTTATTTTATCA
Found at i:4625338 original size:18 final size:16
Alignment explanation
Indices: 4625317--4625351 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
4625307 TATATTTTAA
4625317 AAAATTTATATAAAAAAT
1 AAAATTT-TA-AAAAAAT
4625335 AAAATTTTAAAAAAAT
1 AAAATTTTAAAAAAAT
4625351 A
1 A
4625352 CGAGTCCGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 2 0.12
18 7 0.41
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
AAAATTTTAAAAAAAT
Found at i:4626076 original size:15 final size:13
Alignment explanation
Indices: 4626050--4626084 Score: 52
Period size: 15 Copynumber: 2.5 Consensus size: 13
4626040 TTTATTAGTA
4626050 TTTATTTTAAATT
1 TTTATTTTAAATT
4626063 TTTATTTGTAAAATT
1 TTTATTT-T-AAATT
4626078 TTTATTT
1 TTTATTT
4626085 AATATATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 7 0.35
14 1 0.05
15 12 0.60
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.69
Consensus pattern (13 bp):
TTTATTTTAAATT
Found at i:4633118 original size:16 final size:17
Alignment explanation
Indices: 4633097--4633132 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
4633087 TATTCTTCAA
4633097 TTTGAT-CATTTTTAAT
1 TTTGATACATTTTTAAT
4633113 TTTGATACATTTTTAAT
1 TTTGATACATTTTTAAT
4633130 TTT
1 TTT
4633133 AAAATTTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.25, C:0.06, G:0.06, T:0.64
Consensus pattern (17 bp):
TTTGATACATTTTTAAT
Found at i:4637031 original size:12 final size:12
Alignment explanation
Indices: 4637014--4637047 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
4637004 ACGGAAGGAA
4637014 AGCCACGGCCAC
1 AGCCACGGCCAC
4637026 AGCCACGGCCAC
1 AGCCACGGCCAC
4637038 AGCCACGGCC
1 AGCCACGGCC
4637048 TCCGCCGATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.24, C:0.50, G:0.26, T:0.00
Consensus pattern (12 bp):
AGCCACGGCCAC
Found at i:4646522 original size:47 final size:47
Alignment explanation
Indices: 4646453--4646546 Score: 161
Period size: 47 Copynumber: 2.0 Consensus size: 47
4646443 CAAGTGCCCT
*
4646453 AATCGATACGTATCTCTCGTTTGTGACAAGGAAAGATGGAAAGCATG
1 AATCGATACGTAGCTCTCGTTTGTGACAAGGAAAGATGGAAAGCATG
* *
4646500 AATCGATACGTAGCTCTGGTTTGTGACAAGGAAATATGGAAAGCATG
1 AATCGATACGTAGCTCTCGTTTGTGACAAGGAAAGATGGAAAGCATG
4646547 GGTCAGCCGA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 44 1.00
ACGTcount: A:0.34, C:0.14, G:0.27, T:0.26
Consensus pattern (47 bp):
AATCGATACGTAGCTCTCGTTTGTGACAAGGAAAGATGGAAAGCATG
Found at i:4650424 original size:26 final size:26
Alignment explanation
Indices: 4650395--4650451 Score: 80
Period size: 25 Copynumber: 2.2 Consensus size: 26
4650385 AGAAAATTTT
* *
4650395 AAATTTAGGTACTAAATTAAATAAAA
1 AAATTTAGGTACCAAATTAAAAAAAA
*
4650421 AAA-TTAGGTGCCAAATTAAAAAAAA
1 AAATTTAGGTACCAAATTAAAAAAAA
4650446 AAATTT
1 AAATTT
4650452 GTCAAGTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 22 0.81
26 5 0.19
ACGTcount: A:0.58, C:0.05, G:0.09, T:0.28
Consensus pattern (26 bp):
AAATTTAGGTACCAAATTAAAAAAAA
Found at i:4651478 original size:302 final size:303
Alignment explanation
Indices: 4650907--4651520 Score: 752
Period size: 302 Copynumber: 2.0 Consensus size: 303
4650897 AATAGTACAT
* * * * *
4650907 ATATACAACTGATGGAAATAGTAAATTGTGCATATTAAAATAAAAATGTATAGAATATACAAAAA
1 ATATACAACTGATGGAAATAATAAAATGTGCATAGTAAAATAAAAATGCATAAAATATACAAAAA
* * *
4650972 TGAAATTTCAGTTGAGTGGTACATTTAAAATTTTACTAATGCAATTGGTGAGGTTCAATTTTCAC
66 TGAAATTTCAGTTGAGTGGTAAATTTAAAATTTTACTAATGCAATTAGTGAGGTTCAA-TATCAC
* * * *
4651037 CTTATGCAAATTTTTATTAGTTTTTGTCAGAATGAAATGGCTAAAATACTCTCGAATAATACGAG
130 CCTATGCAAATTTTAATTAGTTTTTGTCAAAATGAAAT-G-TAAAATACTCTCGAATAATACGAC
** * **** *
4651102 TTACTTTAATTACGAAAGGACATTTTTGTAATTTTTCTAATCGAGTTTGTGTTTGGTTGACTTAT
193 TTACTTTAATTACGAAAGGACATTTTCATAATTTTTCTAATCGAGTTGGTGCCCAGTTGACTCAT
* *
4651167 GACACCAACTCAGTTAGAGGTTTTATTAAAATTAAGTAT-ATATAG
258 GACACCAACTCAGTTAGAGATTTTATTAAAAGTAAGTATAATATAG
* **
4651212 ATATACAACTGAT-GAAGATAATAAAATGTGCATAGTAAAATAAGAATGCATAAAATATATTAAA
1 ATATACAACTGATGGAA-ATAATAAAATGTGCATAGTAAAATAAAAATGCATAAAATATACAAAA
* ** * * * *
4651276 ATGAAGTTTTGGTTGAGTGGTAAATTTAAGATTTTACTAATGCAATTATTGCGGGTTCAA-ATCC
65 ATGAAATTTCAGTTGAGTGGTAAATTTAAAATTTTACTAATGCAATTAGTG-AGGTTCAATATCA
* * * *
4651340 CCCTATGCAAATTTTAATTGGTTTTTGTTAAAATGAAAAT-TAAAATGC-CTTCGAATAATATGA
129 CCCTATGCAAATTTTAATTAGTTTTTGTCAAAATG-AAATGTAAAATACTC-TCGAATAATACGA
* *
4651403 CTTACTTTAATTACGAAAGGGCATTTTCATAATTTTTCTAATCGAGTTGGTGCCCAGTTGACTCG
192 CTTACTTTAATTACGAAAGGACATTTTCATAATTTTTCTAATCGAGTTGGTGCCCAGTTGACTCA
* * *
4651468 TGACACCAACTTAGTTAGCGATTTTATTAATAGTAAGTATAGATATAG
257 TGACACCAACTCAGTTAGAGATTTTATTAAAAGTAAGTATA-ATATAG
4651516 ATATA
1 ATATA
4651521 GATATAGATA
Statistics
Matches: 262, Mismatches: 41, Indels: 13
0.83 0.13 0.04
Matches are distributed among these distances:
301 1 0.00
302 108 0.41
304 46 0.18
305 100 0.38
306 7 0.03
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.37
Consensus pattern (303 bp):
ATATACAACTGATGGAAATAATAAAATGTGCATAGTAAAATAAAAATGCATAAAATATACAAAAA
TGAAATTTCAGTTGAGTGGTAAATTTAAAATTTTACTAATGCAATTAGTGAGGTTCAATATCACC
CTATGCAAATTTTAATTAGTTTTTGTCAAAATGAAATGTAAAATACTCTCGAATAATACGACTTA
CTTTAATTACGAAAGGACATTTTCATAATTTTTCTAATCGAGTTGGTGCCCAGTTGACTCATGAC
ACCAACTCAGTTAGAGATTTTATTAAAAGTAAGTATAATATAG
Found at i:4651516 original size:6 final size:6
Alignment explanation
Indices: 4651505--4651532 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
4651495 TAATAGTAAG
4651505 TATAGA TATAGA TATAGA TATAGA TATA
1 TATAGA TATAGA TATAGA TATAGA TATA
4651533 CAACTAATGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.14, T:0.36
Consensus pattern (6 bp):
TATAGA
Found at i:4662936 original size:36 final size:36
Alignment explanation
Indices: 4662886--4662961 Score: 134
Period size: 36 Copynumber: 2.1 Consensus size: 36
4662876 AAATAGAAAA
4662886 TTAAAAAAAATCACAATTAACATTGAATTTATTCTG
1 TTAAAAAAAATCACAATTAACATTGAATTTATTCTG
* *
4662922 TTAAAAAAATTCACAATTAGCATTGAATTTATTCTG
1 TTAAAAAAAATCACAATTAACATTGAATTTATTCTG
4662958 TTAA
1 TTAA
4662962 CATGATAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.45, C:0.11, G:0.07, T:0.38
Consensus pattern (36 bp):
TTAAAAAAAATCACAATTAACATTGAATTTATTCTG
Found at i:4669037 original size:131 final size:133
Alignment explanation
Indices: 4668801--4669069 Score: 382
Period size: 131 Copynumber: 2.0 Consensus size: 133
4668791 TTAAAACATT
* * * *
4668801 TGAAAAGCTATCGATTCGAAAACGAGATAGTGTGAGCTTCTGAACAATCCGCCTGATATATTCCA
1 TGAAAAGCTACCGATTCGAAAACGAGAGAGTGTGAGCTTCTGAACAATCCGCCTAACATATTCCA
* * **
4668866 CAAAGTGACAATGCACAAGGAAAGAGGAAACATTGGAGTAAGCACATTGAATGCTTAGTAAGTTT
66 CAAAGTGACAATGCACAAGGAAAGAGGAAACATCGAAGTAAGCACATTGAATGCTTAGTAAGTCC
4668931 ATA
131 ATA
* * * *
4668934 TGAAAAGCTACCGATTCGAAAAC-AG-GAGTTTGAGCTTCTGAACGATCCGTCTAACATATTCTA
1 TGAAAAGCTACCGATTCGAAAACGAGAGAGTGTGAGCTTCTGAACAATCCGCCTAACATATTCCA
* *
4668997 CAAAGTGACAATGTACAAGGAAA-AGGGAAACATCGAAGTAAGCATATTGAATGCTTAGTAAGTC
66 CAAAGTGACAATGCACAAGGAAAGA-GGAAACATCGAAGTAAGCACATTGAATGCTTAGTAAGTC
4669061 CATA
130 CATA
4669065 TGAAA
1 TGAAA
4669070 TTTACTTAGC
Statistics
Matches: 121, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
130 1 0.01
131 96 0.79
132 2 0.02
133 22 0.18
ACGTcount: A:0.39, C:0.16, G:0.21, T:0.24
Consensus pattern (133 bp):
TGAAAAGCTACCGATTCGAAAACGAGAGAGTGTGAGCTTCTGAACAATCCGCCTAACATATTCCA
CAAAGTGACAATGCACAAGGAAAGAGGAAACATCGAAGTAAGCACATTGAATGCTTAGTAAGTCC
ATA
Found at i:4670558 original size:4 final size:4
Alignment explanation
Indices: 4670549--4670576 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
4670539 TTAATAAATC
4670549 TTAA TTAA TTAA TTAA TTAA TTAA TTAA
1 TTAA TTAA TTAA TTAA TTAA TTAA TTAA
4670577 ACATTAAACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
TTAA
Found at i:4671238 original size:39 final size:39
Alignment explanation
Indices: 4671182--4671298 Score: 119
Period size: 39 Copynumber: 3.0 Consensus size: 39
4671172 TTAAATCTCG
* * *
4671182 TTACCCGAGGATATGCAACAAAGGCTAGATCTTATTATA
1 TTACCCAAGGATCTGCAACAAAGGCTAGATCTCATTATA
* * * *
4671221 TTACCCAAGGGTCTGCAACGAATGCTAGATCTCGTTATA
1 TTACCCAAGGATCTGCAACAAAGGCTAGATCTCATTATA
* * * *
4671260 TTACCTAAGGATCTACAA-AAAGTGCTAAATCTCGTTATA
1 TTACCCAAGGATCTGCAACAAAG-GCTAGATCTCATTATA
4671299 ATCTATACAA
Statistics
Matches: 64, Mismatches: 13, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
38 2 0.03
39 62 0.97
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (39 bp):
TTACCCAAGGATCTGCAACAAAGGCTAGATCTCATTATA
Found at i:4681813 original size:21 final size:20
Alignment explanation
Indices: 4681789--4681839 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
4681779 TTGATCCTAA
4681789 TTATAAAAAAATCAAAGAA-AT
1 TTATAAAAAAA-CAAA-AATAT
*
4681810 TTATAAAAATACAAAAATAT
1 TTATAAAAAAACAAAAATAT
*
4681830 TTTTAAAAAA
1 TTATAAAAAA
4681840 TATAATAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
19 2 0.08
20 14 0.54
21 10 0.38
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.29
Consensus pattern (20 bp):
TTATAAAAAAACAAAAATAT
Found at i:4681840 original size:21 final size:21
Alignment explanation
Indices: 4681806--4681873 Score: 82
Period size: 21 Copynumber: 3.1 Consensus size: 21
4681796 AAAATCAAAG
*
4681806 AAATTTATAAAAATACAAAAAT
1 AAATTTA-AAAAATATAAAAAT
** *
4681828 ATTTTTAAAAAATATAATAAT
1 AAATTTAAAAAATATAAAAAT
4681849 AAATTTAAAAATATATAAAAAT
1 AAATTTAAAAA-ATATAAAAAT
4681871 AAA
1 AAA
4681874 AATATTGTTG
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
21 21 0.55
22 17 0.45
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.32
Consensus pattern (21 bp):
AAATTTAAAAAATATAAAAAT
Found at i:4681859 original size:22 final size:22
Alignment explanation
Indices: 4681806--4681873 Score: 75
Period size: 22 Copynumber: 3.1 Consensus size: 22
4681796 AAAATCAAAG
* *
4681806 AAATTTATAAAAATACAAAAAT
1 AAATTTAAAAAAATATAAAAAT
* * *
4681828 -ATTTTTAAAAAATATAATAAT
1 AAATTTAAAAAAATATAAAAAT
*
4681849 AAATTTAAAAATATATAAAAAT
1 AAATTTAAAAAAATATAAAAAT
4681871 AAA
1 AAA
4681874 AATATTGTTG
Statistics
Matches: 36, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
21 16 0.44
22 20 0.56
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.32
Consensus pattern (22 bp):
AAATTTAAAAAAATATAAAAAT
Found at i:4686561 original size:21 final size:19
Alignment explanation
Indices: 4686520--4686562 Score: 50
Period size: 21 Copynumber: 2.2 Consensus size: 19
4686510 AACATCAACA
*
4686520 TAAAATTTAAAAGAGTAAT
1 TAAAATTTAAAAGAATAAT
*
4686539 TAAAATTTTCAAAAGAATGAT
1 TAAAA-TTT-AAAAGAATAAT
4686560 TAA
1 TAA
4686563 GTGTATTATG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 5 0.25
20 3 0.15
21 12 0.60
ACGTcount: A:0.56, C:0.02, G:0.09, T:0.33
Consensus pattern (19 bp):
TAAAATTTAAAAGAATAAT
Found at i:4690381 original size:60 final size:59
Alignment explanation
Indices: 4690264--4690382 Score: 141
Period size: 60 Copynumber: 2.0 Consensus size: 59
4690254 CAATAAAATA
* * * *
4690264 TCAGGGACTAACTTGGACAAAAAAAAATTCAAGTCCCAATGTGAGAACAATTTCCAAGT
1 TCAGGGACTAAATTGAACAAAAAAAAATTCAAGACCCAATGTGAGAACAATTGCCAAGT
* * * *
4690323 TCAGGGACTAAATTGAACGAAAAAATAATT-TAGACCCTATTGTGGGAACAATTGCCAAGT
1 TCAGGGACTAAATTGAAC-AAAAAAAAATTCAAGACCC-AATGTGAGAACAATTGCCAAGT
4690383 CCAAAGACTA
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
59 21 0.42
60 29 0.58
ACGTcount: A:0.41, C:0.17, G:0.18, T:0.24
Consensus pattern (59 bp):
TCAGGGACTAAATTGAACAAAAAAAAATTCAAGACCCAATGTGAGAACAATTGCCAAGT
Found at i:4695149 original size:21 final size:21
Alignment explanation
Indices: 4695125--4695165 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
4695115 TCATACATTG
* *
4695125 CATAATTTTATTATAAAAAAT
1 CATAATGTAATTATAAAAAAT
4695146 CATAATGTAATTATAAAAAA
1 CATAATGTAATTATAAAAAA
4695166 AAATATTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.37
Consensus pattern (21 bp):
CATAATGTAATTATAAAAAAT
Found at i:4697339 original size:3 final size:3
Alignment explanation
Indices: 4697333--4697366 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
4697323 TGCTCCTCAG
4697333 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
4697367 ACAATCTGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:4703767 original size:20 final size:21
Alignment explanation
Indices: 4703729--4703772 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
4703719 AAAAAATATA
* *
4703729 TAAAATTTAGTCTTTAATT-T
1 TAAAATTTAGGCTTCAATTGT
*
4703749 TAAAATTTAGGGTTCAATTGT
1 TAAAATTTAGGCTTCAATTGT
4703770 TAA
1 TAA
4703773 TACTGTTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.36, C:0.05, G:0.11, T:0.48
Consensus pattern (21 bp):
TAAAATTTAGGCTTCAATTGT
Found at i:4708229 original size:19 final size:19
Alignment explanation
Indices: 4708202--4708268 Score: 55
Period size: 19 Copynumber: 3.5 Consensus size: 19
4708192 GAAATTAGAA
*
4708202 AGATCAAATTATAGTAAAG
1 AGATTAAATTATAGTAAAG
* * *
4708221 AGATTAAATTCGTA-AAAAA
1 AGATTAAATT-ATAGTAAAG
*
4708240 AAATTAAATTATAGTAAAG
1 AGATTAAATTATAGTAAAG
* *
4708259 GGATTCAATT
1 AGATTAAATT
4708269 CGTGAAAAAT
Statistics
Matches: 35, Mismatches: 11, Indels: 4
0.70 0.22 0.08
Matches are distributed among these distances:
18 2 0.06
19 31 0.89
20 2 0.06
ACGTcount: A:0.52, C:0.04, G:0.13, T:0.30
Consensus pattern (19 bp):
AGATTAAATTATAGTAAAG
Found at i:4708507 original size:111 final size:110
Alignment explanation
Indices: 4708289--4708498 Score: 255
Period size: 111 Copynumber: 1.9 Consensus size: 110
4708279 GCATAGTATG
* * * * *
4708289 GAATTAATATAAAGAAAGTTAACCTCATGAGTATCGAAAATACACAGCTTGAGAGCTAGCGACAC
1 GAATTAATAGAAAGAAAGTAAACCTCATGAGTATCGAAAATACACAGCTTGAGAACGAGCAACAC
* *
4708354 TAGAAATGATCAAATTATAGTAAATGGATTAAACTAGTTAAAATGC
66 TAGAAATGATCAAATTATAGTAAATGAACTAAACTAG-TAAAATGC
* ** *
4708400 GAATTAATAGAAAGAAAG-AAAGCCTCATGAGTATTGAAAATACACATTTTCGGGAACGA-CAAA
1 GAATTAATAGAAAGAAAGTAAA-CCTCATGAGTATCGAAAATACACAGCTT-GAGAACGAGC-AA
4708463 CACTAGAAATGATCAAATTATAGTAACAT-AACTAAA
63 CACTAGAAATGATCAAATTATAGTAA-ATGAACTAAA
4708499 TTCATAAAAG
Statistics
Matches: 84, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
110 2 0.02
111 43 0.51
112 37 0.44
113 2 0.02
ACGTcount: A:0.47, C:0.13, G:0.16, T:0.24
Consensus pattern (110 bp):
GAATTAATAGAAAGAAAGTAAACCTCATGAGTATCGAAAATACACAGCTTGAGAACGAGCAACAC
TAGAAATGATCAAATTATAGTAAATGAACTAAACTAGTAAAATGC
Found at i:4709499 original size:2 final size:2
Alignment explanation
Indices: 4709492--4709520 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4709482 ACTAGCTAGG
4709492 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
4709521 ATATATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Done.