Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 135709677
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: 135709677
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 350 characters in sequence are not A, C, G, or T
File 56 of 438
Found at i:14445913 original size:41 final size:40
Alignment explanation
Indices: 14445845--14446035 Score: 240
Period size: 41 Copynumber: 4.7 Consensus size: 40
14445835 GCAAAAATTT
* * *
14445845 TAAAATACAGAGCAATAGCGACGTTTTTCTTAAAACGCCGT
1 TAAAA-ACAGAGCAATAGCGGCGCTTTTCTTAAAACGCCGC
* * *
14445886 TAAAAACAAAGCAACAGCGGCG-TTTTTTACTAAAACGCCGC
1 TAAAAACAGAGCAATAGCGGCGCTTTTCT--TAAAACGCCGC
14445927 TAAAAACAGAGCAATAGCGGCGCTTTTCTTAAAACGCCGC
1 TAAAAACAGAGCAATAGCGGCGCTTTTCTTAAAACGCCGC
* **
14445967 TAAAAACCAGAGCATTAGCGGCGCTTTTGGTAAAACGCCGC
1 TAAAAA-CAGAGCAATAGCGGCGCTTTTCTTAAAACGCCGC
*
14446008 TAAAAACCAGAGCATTAGCGGCGCTTTT
1 TAAAAA-CAGAGCAATAGCGGCGCTTTT
14446036 GGTAAAATGG
Statistics
Matches: 135, Mismatches: 11, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
39 5 0.04
40 31 0.23
41 94 0.70
42 5 0.04
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.22
Consensus pattern (40 bp):
TAAAAACAGAGCAATAGCGGCGCTTTTCTTAAAACGCCGC
Found at i:14446042 original size:82 final size:81
Alignment explanation
Indices: 14445845--14446035 Score: 258
Period size: 81 Copynumber: 2.3 Consensus size: 81
14445835 GCAAAAATTT
* * * *
14445845 TAAAATACAGAGCAATAGCGACGTTTTTCTTAAAACGCCGTTAAAAACAAAGCAACAGCGGCGTT
1 TAAAA-ACAGAGCAATAGCGGCGCTTTTCTTAAAACGCCGCTAAAAACAAAGCAACAGCGGCGTC
14445910 TTTTACTAAAACGCCGC
65 TTTTACTAAAACGCCGC
* **
14445927 TAAAAACAGAGCAATAGCGGCGCTTTTCTTAAAACGCCGCTAAAAACCAGAGCATTAGCGGCG-C
1 TAAAAACAGAGCAATAGCGGCGCTTTTCTTAAAACGCCGCTAAAAA-CAAAGCAACAGCGGCGTC
**
14445991 TTTTGGTAAAACGCCGC
65 TTTTACTAAAACGCCGC
*
14446008 TAAAAACCAGAGCATTAGCGGCGCTTTT
1 TAAAAA-CAGAGCAATAGCGGCGCTTTT
14446036 GGTAAAATGG
Statistics
Matches: 97, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
81 59 0.61
82 38 0.39
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.22
Consensus pattern (81 bp):
TAAAAACAGAGCAATAGCGGCGCTTTTCTTAAAACGCCGCTAAAAACAAAGCAACAGCGGCGTCT
TTTACTAAAACGCCGC
Found at i:14448434 original size:2 final size:2
Alignment explanation
Indices: 14448427--14448468 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
14448417 AGTTGCACAA
14448427 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
14448469 CCATTTTTAG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:14450276 original size:53 final size:51
Alignment explanation
Indices: 14450136--14450336 Score: 193
Period size: 52 Copynumber: 4.0 Consensus size: 51
14450126 AACGGAATAG
* * *
14450136 ATGTGATATGTGTGCCCGTATAAGACCATAGCAGGGCTATGACATCAGTGCA
1 ATGTGATATGTGT-CCCGTATAAGACCATAGCTGGGCTATGGCATCGGTGCA
* *
14450188 ATATGATACGTGTTCCCGTATAAGACCATAGCTGGGCTATGGCATCGGTGTC-
1 ATGTGATATGTG-TCCCGTATAAGACCATAGCTGGGCTATGGCATCGGTG-CA
* *
14450240 ATGTGATAATGTGATCCCGTATAAGACCATATCTGGGATATGGCATCGGT---
1 ATGTGAT-ATGTG-TCCCGTATAAGACCATAGCTGGGCTATGGCATCGGTGCA
* * *
14450290 A--TGATATGTGAT-CCGTGTAAGACCAT-GGTAGGGCTATGGCTTCGGTG
1 ATGTGATATGTG-TCCCGTATAAGACCATAGCT-GGGCTATGGCATCGGTG
14450337 TGTGGTGTGT
Statistics
Matches: 129, Mismatches: 15, Indels: 15
0.81 0.09 0.09
Matches are distributed among these distances:
45 1 0.01
46 27 0.21
47 7 0.05
48 4 0.03
50 1 0.01
52 49 0.38
53 40 0.31
ACGTcount: A:0.25, C:0.18, G:0.28, T:0.28
Consensus pattern (51 bp):
ATGTGATATGTGTCCCGTATAAGACCATAGCTGGGCTATGGCATCGGTGCA
Found at i:14451177 original size:22 final size:22
Alignment explanation
Indices: 14451135--14451178 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
14451125 GTCGTGTGTC
* *
14451135 AAAATTGTGTGAAAATGGTTTA
1 AAAATTGTGTAAAAATAGTTTA
14451157 AAAATTGTG-AAAAATCAGTTTA
1 AAAATTGTGTAAAAAT-AGTTTA
14451179 CCACATGGCC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.45, C:0.02, G:0.18, T:0.34
Consensus pattern (22 bp):
AAAATTGTGTAAAAATAGTTTA
Found at i:14457812 original size:53 final size:52
Alignment explanation
Indices: 14457686--14457823 Score: 154
Period size: 52 Copynumber: 2.6 Consensus size: 52
14457676 CTTTTGTGCA
* * *
14457686 CCCGTATAAGACCATAGCAGGGCTATGGCATCGGTGCAATGTTATACATGTT
1 CCCGTATAAGACCATAGCTGGGCTATGGCATCGATGCAATGTGATACATGTT
* *
14457738 CCCGTATAAGACCATAGCTGGGCTGTGGCATCGATGTC-ATGTGATAATATGATT
1 CCCGTATAAGACCATAGCTGGGCTATGGCATCGATG-CAATGTGAT-ACATG-TT
* * * *
14457792 -CCGTATAATACCATATCTGGGATATGACATCG
1 CCCGTATAAGACCATAGCTGGGCTATGGCATCG
14457824 GTATGATATG
Statistics
Matches: 73, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
52 39 0.53
53 32 0.44
54 2 0.03
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (52 bp):
CCCGTATAAGACCATAGCTGGGCTATGGCATCGATGCAATGTGATACATGTT
Found at i:14459125 original size:23 final size:22
Alignment explanation
Indices: 14459082--14459134 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
14459072 TATTTTGTTC
*
14459082 TTTTTCTTTCTTTTTTCTGCCA
1 TTTTTCTTTCTTTCTTCTGCCA
14459104 TTTTTGCTTTCTGTTCTT-TGCC-
1 TTTTT-CTTTCT-TTCTTCTGCCA
*
14459126 TTCTTCTTT
1 TTTTTCTTT
14459135 GCAGGTATTC
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
21 4 0.15
22 9 0.33
23 10 0.37
24 4 0.15
ACGTcount: A:0.02, C:0.23, G:0.08, T:0.68
Consensus pattern (22 bp):
TTTTTCTTTCTTTCTTCTGCCA
Found at i:14466476 original size:10 final size:10
Alignment explanation
Indices: 14466461--14466493 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
14466451 TTCATCAATT
14466461 TTTTTTTAGA
1 TTTTTTTAGA
14466471 TTTTTTTA-A
1 TTTTTTTAGA
14466480 TTTTTTTAAGA
1 TTTTTTT-AGA
14466491 TTT
1 TTT
14466494 AAGATAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 8 0.38
10 9 0.43
11 4 0.19
ACGTcount: A:0.21, C:0.00, G:0.06, T:0.73
Consensus pattern (10 bp):
TTTTTTTAGA
Found at i:14466772 original size:19 final size:20
Alignment explanation
Indices: 14466727--14466772 Score: 51
Period size: 18 Copynumber: 2.4 Consensus size: 20
14466717 TCCATACAAG
14466727 TACTTAAATGGTTAAATTTGA
1 TACTT-AATGGTTAAATTTGA
* *
14466748 T-TTTAAT-GTTCAATTTGA
1 TACTTAATGGTTAAATTTGA
14466766 TACTTAA
1 TACTTAA
14466773 GAGTTTCTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 4
0.75 0.11 0.14
Matches are distributed among these distances:
18 11 0.52
19 7 0.33
20 2 0.10
21 1 0.05
ACGTcount: A:0.35, C:0.07, G:0.11, T:0.48
Consensus pattern (20 bp):
TACTTAATGGTTAAATTTGA
Found at i:14466942 original size:19 final size:18
Alignment explanation
Indices: 14466896--14466946 Score: 61
Period size: 19 Copynumber: 2.9 Consensus size: 18
14466886 AACCAAACTT
*
14466896 AAATATCAA-ATTAAAAC
1 AAATATAAATATTAAAAC
*
14466913 AAA-AAAAATATTAAAACC
1 AAATATAAATATTAAAA-C
14466931 AAATATAAATATTAAA
1 AAATATAAATATTAAA
14466947 TAATATATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
16 3 0.11
17 10 0.36
18 4 0.14
19 11 0.39
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.24
Consensus pattern (18 bp):
AAATATAAATATTAAAAC
Found at i:14468688 original size:2 final size:2
Alignment explanation
Indices: 14468681--14468712 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
14468671 GTTAAAAACA
14468681 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
14468713 GATTTAAATT
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):
AT
Found at i:14468810 original size:10 final size:10
Alignment explanation
Indices: 14468795--14468822 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
14468785 GAATGAAAAG
14468795 AGAAAGAAGA
1 AGAAAGAAGA
14468805 AGAAAGAAGA
1 AGAAAGAAGA
14468815 AGAAAGAA
1 AGAAAGAA
14468823 ATTGAGAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (10 bp):
AGAAAGAAGA
Found at i:14472141 original size:19 final size:18
Alignment explanation
Indices: 14472105--14472149 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 18
14472095 GAAATGGCAA
*
14472105 AGATGAGAATTGAATATG
1 AGATGAGAAATGAATATG
14472123 AGATGAGAAATGAAATATG
1 AGATGAGAAATG-AATATG
*
14472142 AAATGAGA
1 AGATGAGA
14472150 TGTGAAACTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 11 0.46
19 13 0.54
ACGTcount: A:0.51, C:0.00, G:0.27, T:0.22
Consensus pattern (18 bp):
AGATGAGAAATGAATATG
Found at i:14474581 original size:35 final size:35
Alignment explanation
Indices: 14474530--14474711 Score: 242
Period size: 35 Copynumber: 5.2 Consensus size: 35
14474520 AGTGCCATGA
* * *
14474530 TTCACAACTCAATATGGTTAATACCATACCTACGT
1 TTCATAACTCAGTATGGATAATACCATACCTACGT
*
14474565 TTCACAACTCAGTATGGGA-AATACCATACCTACGT
1 TTCATAACTCAGTAT-GGATAATACCATACCTACGT
* *
14474600 TTTATAGCTCAGTATGGATAATACCATACCTACGT
1 TTCATAACTCAGTATGGATAATACCATACCTACGT
* *
14474635 ATCATAACTCAGTATGGAAAATACCATACCTACGT
1 TTCATAACTCAGTATGGATAATACCATACCTACGT
*
14474670 ATT-ATAGCTCAGTATGGATAATACCATACCTACGT
1 -TTCATAACTCAGTATGGATAATACCATACCTACGT
*
14474705 ATCATAA
1 TTCATAA
14474712 GTTTTCCATA
Statistics
Matches: 129, Mismatches: 14, Indels: 8
0.85 0.09 0.05
Matches are distributed among these distances:
34 4 0.03
35 122 0.95
36 3 0.02
ACGTcount: A:0.36, C:0.23, G:0.12, T:0.30
Consensus pattern (35 bp):
TTCATAACTCAGTATGGATAATACCATACCTACGT
Found at i:14474657 original size:70 final size:70
Alignment explanation
Indices: 14474537--14474711 Score: 296
Period size: 70 Copynumber: 2.5 Consensus size: 70
14474527 TGATTCACAA
* * * * * *
14474537 CTCAATATGGTTAATACCATACCTACGTTTCACAACTCAGTATGGGAAATACCATACCTACGTTT
1 CTCAGTATGGATAATACCATACCTACGTATCATAACTCAGTATGGAAAATACCATACCTACGTAT
14474602 TATAG
66 TATAG
14474607 CTCAGTATGGATAATACCATACCTACGTATCATAACTCAGTATGGAAAATACCATACCTACGTAT
1 CTCAGTATGGATAATACCATACCTACGTATCATAACTCAGTATGGAAAATACCATACCTACGTAT
14474672 TATAG
66 TATAG
14474677 CTCAGTATGGATAATACCATACCTACGTATCATAA
1 CTCAGTATGGATAATACCATACCTACGTATCATAA
14474712 GTTTTCCATA
Statistics
Matches: 99, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
70 99 1.00
ACGTcount: A:0.35, C:0.22, G:0.13, T:0.30
Consensus pattern (70 bp):
CTCAGTATGGATAATACCATACCTACGTATCATAACTCAGTATGGAAAATACCATACCTACGTAT
TATAG
Found at i:14479021 original size:4 final size:4
Alignment explanation
Indices: 14479006--14479044 Score: 50
Period size: 4 Copynumber: 10.8 Consensus size: 4
14478996 AATATATACT
14479006 TTTA TTTA --TA TTTA TTTA TTTA -TTA TTTA -TTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
14479045 TTATATTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
2 2 0.06
3 6 0.19
4 23 0.74
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:14479033 original size:7 final size:7
Alignment explanation
Indices: 14479007--14479066 Score: 65
Period size: 7 Copynumber: 8.7 Consensus size: 7
14478997 ATATATACTT
14479007 TTATTTA
1 TTATTTA
14479014 -TATTTA
1 TTATTTA
14479020 TTTATTTA
1 -TTATTTA
14479028 TTATTTA
1 TTATTTA
14479035 TTATTTA
1 TTATTTA
14479042 TT-TTTA
1 TTATTTA
14479048 -TATTT-
1 TTATTTA
14479053 TATATTTTA
1 T-TA-TTTA
14479062 TTATT
1 TTATT
14479067 ATTTTTCCAA
Statistics
Matches: 46, Mismatches: 0, Indels: 14
0.77 0.00 0.23
Matches are distributed among these distances:
5 1 0.02
6 13 0.28
7 20 0.43
8 11 0.24
9 1 0.02
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (7 bp):
TTATTTA
Found at i:14480780 original size:75 final size:73
Alignment explanation
Indices: 14480692--14480863 Score: 217
Period size: 75 Copynumber: 2.4 Consensus size: 73
14480682 GGTTTTCCTC
*** * * **
14480692 ATTGAAATACCATACCTACATTTTTTAACTCGGTATGGGA-AATGCCATACCTACATTTCTTAAC
1 ATTGAAATACCATACCTACATTTCACAACTCAGTAT-GGATAATACCATACCTACATTTCACAAC
14480756 TCAGTATGG
65 TCAGTATGG
*
14480765 ATTTGATAATACCATACCTACATTTCACAGCTCAGTATGGATAATACCATACCTACATTTCACAA
1 A-TTGA-AATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACCTACATTTCACAA
14480830 CTCAGTATGG
64 CTCAGTATGG
14480840 A-TG--ATACCATACCTACATTTCACA
1 ATTGAAATACCATACCTACATTTCACA
14480864 CTTTGCCATG
Statistics
Matches: 88, Mismatches: 8, Indels: 9
0.84 0.08 0.09
Matches are distributed among these distances:
70 21 0.24
73 3 0.03
74 7 0.08
75 57 0.65
ACGTcount: A:0.34, C:0.23, G:0.11, T:0.32
Consensus pattern (73 bp):
ATTGAAATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACCTACATTTCACAACT
CAGTATGG
Found at i:14480861 original size:35 final size:35
Alignment explanation
Indices: 14480697--14480863 Score: 192
Period size: 35 Copynumber: 4.6 Consensus size: 35
14480687 TCCTCATTGA
*** *
14480697 AATACCATACCTACATTTTTTAACTCGGTATGGGA-
1 AATACCATACCTACATTTCACAACTCAGTAT-GGAT
* **
14480732 AATGCCATACCTACATTTCTTAACTCAGTATGGATTTGAT
1 AATACCATACCTACATTTCACAACTCAGTAT-G----GAT
*
14480772 AATACCATACCTACATTTCACAGCTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
14480807 AATACCATACCTACATTTCACAACTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
*
14480842 GATACCATACCTACATTTCACA
1 AATACCATACCTACATTTCACA
14480864 CTTTGCCATG
Statistics
Matches: 118, Mismatches: 9, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
35 88 0.75
39 3 0.03
40 27 0.23
ACGTcount: A:0.34, C:0.24, G:0.11, T:0.32
Consensus pattern (35 bp):
AATACCATACCTACATTTCACAACTCAGTATGGAT
Found at i:14486435 original size:13 final size:13
Alignment explanation
Indices: 14486417--14486459 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
14486407 TAGATTTTTC
14486417 CTAAATATTATCA
1 CTAAATATTATCA
14486430 CTAAATA--ATC-
1 CTAAATATTATCA
14486440 CTAAATATTATCA
1 CTAAATATTATCA
14486453 CTAAATA
1 CTAAATA
14486460 ATTTAAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
10 7 0.26
11 3 0.11
12 3 0.11
13 14 0.52
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.35
Consensus pattern (13 bp):
CTAAATATTATCA
Found at i:14486468 original size:23 final size:23
Alignment explanation
Indices: 14486415--14486461 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
14486405 GTTAGATTTT
14486415 TCCTAAATATTATCACTAAATAA
1 TCCTAAATATTATCACTAAATAA
14486438 TCCTAAATATTATCACTAAATAA
1 TCCTAAATATTATCACTAAATAA
14486461 T
1 T
14486462 TTAAAATTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.47, C:0.17, G:0.00, T:0.36
Consensus pattern (23 bp):
TCCTAAATATTATCACTAAATAA
Found at i:14490279 original size:3 final size:3
Alignment explanation
Indices: 14490271--14490300 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
14490261 CCTGACGGCA
*
14490271 ATG ATG ATG GTG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
14490301 TTGCTGCTGC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.30, C:0.00, G:0.37, T:0.33
Consensus pattern (3 bp):
ATG
Found at i:14491072 original size:48 final size:48
Alignment explanation
Indices: 14491017--14491135 Score: 229
Period size: 48 Copynumber: 2.5 Consensus size: 48
14491007 GGTATATATA
*
14491017 TATCTTTGCTTTGTAACCCTCTATATTGCTTTTGTTCTTATTTTCCTT
1 TATCTTTGCTTTGTAACTCTCTATATTGCTTTTGTTCTTATTTTCCTT
14491065 TATCTTTGCTTTGTAACTCTCTATATTGCTTTTGTTCTTATTTTCCTT
1 TATCTTTGCTTTGTAACTCTCTATATTGCTTTTGTTCTTATTTTCCTT
14491113 TATCTTTGCTTTGTAACTCTCTA
1 TATCTTTGCTTTGTAACTCTCTA
14491136 ATCTCATCTG
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
48 70 1.00
ACGTcount: A:0.13, C:0.20, G:0.08, T:0.58
Consensus pattern (48 bp):
TATCTTTGCTTTGTAACTCTCTATATTGCTTTTGTTCTTATTTTCCTT
Found at i:14499561 original size:26 final size:26
Alignment explanation
Indices: 14499525--14499576 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
14499515 ATGAGCCAAA
14499525 CCAGAAAAAAGAAAAGTAAATGCAAT
1 CCAGAAAAAAGAAAAGTAAATGCAAT
14499551 CCAGAAAAAAGAAAAGTAAATGCAAT
1 CCAGAAAAAAGAAAAGTAAATGCAAT
14499577 ATCCCATATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.62, C:0.12, G:0.15, T:0.12
Consensus pattern (26 bp):
CCAGAAAAAAGAAAAGTAAATGCAAT
Found at i:14518346 original size:33 final size:33
Alignment explanation
Indices: 14518250--14518347 Score: 144
Period size: 33 Copynumber: 3.0 Consensus size: 33
14518240 TTTCTTCTTG
* *
14518250 ACATTCCA-CTCTTGTCCAGCAACAAAACACCC
1 ACATTCCAGCTCCTGTCCAGCAACAAAACACTC
* *
14518282 ATATTCCAGCTCCTGTCCAGCAGCAAAACACTC
1 ACATTCCAGCTCCTGTCCAGCAACAAAACACTC
*
14518315 ACATTCCAGCTCCTGTCCAGCAACCAAACACTC
1 ACATTCCAGCTCCTGTCCAGCAACAAAACACTC
14518348 TCACTCAGTT
Statistics
Matches: 58, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
32 7 0.12
33 51 0.88
ACGTcount: A:0.32, C:0.40, G:0.09, T:0.19
Consensus pattern (33 bp):
ACATTCCAGCTCCTGTCCAGCAACAAAACACTC
Found at i:14521334 original size:18 final size:18
Alignment explanation
Indices: 14521311--14521345 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
14521301 GGGGGGTTGG
14521311 TTTTATCTTT-TTATTTTA
1 TTTTAT-TTTATTATTTTA
14521329 TTTTATTTTATTATTTT
1 TTTTATTTTATTATTTT
14521346 TCCCAACATC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (18 bp):
TTTTATTTTATTATTTTA
Found at i:14522813 original size:34 final size:34
Alignment explanation
Indices: 14522770--14522838 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
14522760 AATTCTAGAC
14522770 TAAGAGTTTTGTAAATTTTGGACTCTCTGGACTT
1 TAAGAGTTTTGTAAATTTTGGACTCTCTGGACTT
14522804 TAAGAGTTTTGTAAATTTTGGACTCTCTGGACTT
1 TAAGAGTTTTGTAAATTTTGGACTCTCTGGACTT
14522838 T
1 T
14522839 TGTGTTTTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.23, C:0.12, G:0.20, T:0.45
Consensus pattern (34 bp):
TAAGAGTTTTGTAAATTTTGGACTCTCTGGACTT
Found at i:14525087 original size:61 final size:61
Alignment explanation
Indices: 14525008--14525131 Score: 230
Period size: 61 Copynumber: 2.0 Consensus size: 61
14524998 GTGGAGTATC
*
14525008 GAGTCAGTTCGGATTGTGCTACTAAGAGAGTGATTCTGATATTTGAGGATGATGTGGAGGT
1 GAGTCAGTTCGGACTGTGCTACTAAGAGAGTGATTCTGATATTTGAGGATGATGTGGAGGT
*
14525069 GAGTCAGTTTGGACTGTGCTACTAAGAGAGTGATTCTGATATTTGAGGATGATGTGGAGGT
1 GAGTCAGTTCGGACTGTGCTACTAAGAGAGTGATTCTGATATTTGAGGATGATGTGGAGGT
14525130 GA
1 GA
14525132 TTGTGATCGG
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.25, C:0.08, G:0.35, T:0.32
Consensus pattern (61 bp):
GAGTCAGTTCGGACTGTGCTACTAAGAGAGTGATTCTGATATTTGAGGATGATGTGGAGGT
Found at i:14529204 original size:2 final size:2
Alignment explanation
Indices: 14529197--14529224 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
14529187 AGCATACGTG
14529197 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
14529225 CCTGGTGTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:14529771 original size:18 final size:18
Alignment explanation
Indices: 14529744--14529779 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
14529734 TCTCTGGAAT
* *
14529744 TTTGGGTTTTATTTTGGA
1 TTTGGATTTTAATTTGGA
14529762 TTTGGATTTTAATTTGGA
1 TTTGGATTTTAATTTGGA
14529780 ATTTCTAGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.00, G:0.25, T:0.58
Consensus pattern (18 bp):
TTTGGATTTTAATTTGGA
Found at i:14532576 original size:22 final size:23
Alignment explanation
Indices: 14532524--14532577 Score: 58
Period size: 22 Copynumber: 2.4 Consensus size: 23
14532514 ACACCACACT
* *
14532524 AGTAGGCACCGAAGTGCTTTAAC
1 AGTAGGCACCAAAGTGCTTGAAC
**
14532547 AGTA-GCACCAAAGTG-TTGAGG
1 AGTAGGCACCAAAGTGCTTGAAC
14532568 AGTAGGCACC
1 AGTAGGCACC
14532578 GTAGTGAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 7 0.27
22 15 0.58
23 4 0.15
ACGTcount: A:0.31, C:0.20, G:0.30, T:0.19
Consensus pattern (23 bp):
AGTAGGCACCAAAGTGCTTGAAC
Found at i:14533765 original size:18 final size:17
Alignment explanation
Indices: 14533735--14533769 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
14533725 TTCATTTTCC
14533735 CTTTTTATTTTTTTCTT
1 CTTTTTATTTTTTTCTT
*
14533752 CTTTTTTTTATTTTTCTT
1 CTTTTTATT-TTTTTCTT
14533770 TTCCTTACCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.06, C:0.11, G:0.00, T:0.83
Consensus pattern (17 bp):
CTTTTTATTTTTTTCTT
Found at i:14538634 original size:16 final size:16
Alignment explanation
Indices: 14538613--14538655 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
14538603 ATGATTGTTT
* *
14538613 ATTATTGTATTATTTA
1 ATTATTGTAATAGTTA
14538629 ATTATT-TAATAGTTA
1 ATTATTGTAATAGTTA
*
14538644 ATTTTTGTAATA
1 ATTATTGTAATA
14538656 CAATAATTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 12 0.52
16 11 0.48
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.58
Consensus pattern (16 bp):
ATTATTGTAATAGTTA
Found at i:14549171 original size:2 final size:2
Alignment explanation
Indices: 14549124--14549154 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
14549114 TGTATATATA
14549124 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
14549155 AAGTATGTAT
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:14559931 original size:13 final size:13
Alignment explanation
Indices: 14559913--14559942 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
14559903 TGACAAATGG
14559913 CCATTTGACATCA
1 CCATTTGACATCA
14559926 CCATTTGACATCA
1 CCATTTGACATCA
14559939 CCAT
1 CCAT
14559943 GGTCAATGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.30, C:0.33, G:0.07, T:0.30
Consensus pattern (13 bp):
CCATTTGACATCA
Found at i:14567951 original size:21 final size:20
Alignment explanation
Indices: 14567922--14567986 Score: 58
Period size: 21 Copynumber: 3.1 Consensus size: 20
14567912 TATTAACTCA
*
14567922 TATGAGTTTCCGTTTAACCCT
1 TATG-GTTTCCGTTCAACCCT
* * *
14567943 TATAGGTTTTCGTTCAGCTCT
1 TAT-GGTTTCCGTTCAACCCT
*
14567964 TATGAGCTTCCGTTCAACCCT
1 TATG-GTTTCCGTTCAACCCT
14567985 TA
1 TA
14567987 CGGGTTTCTG
Statistics
Matches: 34, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
20 1 0.03
21 32 0.94
22 1 0.03
ACGTcount: A:0.18, C:0.25, G:0.15, T:0.42
Consensus pattern (20 bp):
TATGGTTTCCGTTCAACCCT
Found at i:14569750 original size:45 final size:45
Alignment explanation
Indices: 14569686--14569776 Score: 164
Period size: 45 Copynumber: 2.0 Consensus size: 45
14569676 GAACTTTAGT
14569686 CTGGCAAACCGTGTGGTCTTAGGTGACTTCTTTGCTTCAAATTTG
1 CTGGCAAACCGTGTGGTCTTAGGTGACTTCTTTGCTTCAAATTTG
**
14569731 CTGGCAAATTGTGTGGTCTTAGGTGACTTCTTTGCTTCAAATTTG
1 CTGGCAAACCGTGTGGTCTTAGGTGACTTCTTTGCTTCAAATTTG
14569776 C
1 C
14569777 CTAAGTCAGT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.18, C:0.19, G:0.24, T:0.40
Consensus pattern (45 bp):
CTGGCAAACCGTGTGGTCTTAGGTGACTTCTTTGCTTCAAATTTG
Found at i:14570974 original size:23 final size:23
Alignment explanation
Indices: 14570930--14570974 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
14570920 ATCAATGCAA
*
14570930 CATATTTTCAAGATAAATTCATG
1 CATATTTTCAAGATAAAGTCATG
*
14570953 CATATTTAT-AAGATAACGTCAT
1 CATATTT-TCAAGATAAAGTCAT
14570975 CACATATCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (23 bp):
CATATTTTCAAGATAAAGTCATG
Found at i:14580166 original size:14 final size:14
Alignment explanation
Indices: 14580147--14580282 Score: 54
Period size: 12 Copynumber: 10.6 Consensus size: 14
14580137 ACATACACAC
14580147 ATATATAAATATAT
1 ATATATAAATATAT
14580161 ATATATAAATA-AT
1 ATATATAAATATAT
14580174 AGTAT-TAGAA-ATAT
1 A-TATATA-AATATAT
*
14580188 ACCATAT-AATAT-T
1 A-TATATAAATATAT
* *
14580201 AGATATATATATA-
1 ATATATAAATATAT
*
14580214 ATAGTATAAA-AGA-
1 ATA-TATAAATATAT
* *
14580227 AAATATAACTA-AT
1 ATATATAAATATAT
*
14580240 A-ATATTAA-A-AT
1 ATATATAAATATAT
14580251 ATATAT-AATA-AT
1 ATATATAAATATAT
14580263 ATATA-AAATATA-
1 ATATATAAATATAT
14580275 ATAT-TAAA
1 ATATATAAA
14580283 AACTTATATA
Statistics
Matches: 96, Mismatches: 11, Indels: 32
0.69 0.08 0.23
Matches are distributed among these distances:
11 6 0.06
12 38 0.40
13 23 0.24
14 28 0.29
15 1 0.01
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.36
Consensus pattern (14 bp):
ATATATAAATATAT
Found at i:14580187 original size:21 final size:21
Alignment explanation
Indices: 14580163--14580275 Score: 88
Period size: 21 Copynumber: 5.3 Consensus size: 21
14580153 AAATATATAT
*
14580163 ATATAAATAATAGTATTAGAA
1 ATATAAATAATAATATTAGAA
* *
14580184 ATATACCAT-ATAATATTAGAT
1 ATATA-AATAATAATATTAGAA
* **
14580205 ATATATATAATAGTATAAAAGAAA
1 ATATAAATAATA--ATATTAG-AA
*
14580229 ATATAACTAATAATATTA-AA
1 ATATAAATAATAATATTAGAA
*
14580249 ATATATATAATAATATATA-AA
1 ATATAAATAATAATAT-TAGAA
14580270 ATATAA
1 ATATAA
14580276 TATTAAAAAC
Statistics
Matches: 72, Mismatches: 14, Indels: 12
0.73 0.14 0.12
Matches are distributed among these distances:
20 18 0.25
21 32 0.44
22 6 0.08
23 5 0.07
24 11 0.15
ACGTcount: A:0.58, C:0.03, G:0.04, T:0.35
Consensus pattern (21 bp):
ATATAAATAATAATATTAGAA
Found at i:14580228 original size:44 final size:46
Alignment explanation
Indices: 14580161--14580270 Score: 124
Period size: 46 Copynumber: 2.5 Consensus size: 46
14580151 ATAAATATAT
* * * *
14580161 ATATATAAATAATAGTAT--TAG-AAATAT-ACCATATAATATT-AG
1 ATATATATATAATAGTATAAAAGAAAATATAACTA-ATAATATTAAA
14580203 ATATATATATAATAGTATAAAAGAAAATATAACTAATAATATTAAA
1 ATATATATATAATAGTATAAAAGAAAATATAACTAATAATATTAAA
14580249 ATATATATAATAATA-TATAAAA
1 ATATATAT-ATAATAGTATAAAA
14580271 TATAATATTA
Statistics
Matches: 58, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
42 17 0.29
44 2 0.03
45 14 0.24
46 19 0.33
47 6 0.10
ACGTcount: A:0.58, C:0.03, G:0.05, T:0.35
Consensus pattern (46 bp):
ATATATATATAATAGTATAAAAGAAAATATAACTAATAATATTAAA
Found at i:14580249 original size:20 final size:20
Alignment explanation
Indices: 14580226--14580277 Score: 79
Period size: 20 Copynumber: 2.5 Consensus size: 20
14580216 AGTATAAAAG
14580226 AAAATATAACTAATAATAT-T
1 AAAATATAA-TAATAATATAT
14580246 AAAATATATATAATAATATAT
1 AAAATATA-ATAATAATATAT
14580267 AAAATATAATA
1 AAAATATAATA
14580278 TTAAAAACTT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
20 20 0.67
21 10 0.33
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (20 bp):
AAAATATAATAATAATATAT
Found at i:14580493 original size:13 final size:14
Alignment explanation
Indices: 14580475--14580505 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
14580465 ATGTATGAAT
14580475 ATATACATATA-TA
1 ATATACATATATTA
14580488 ATATACATATATTA
1 ATATACATATATTA
14580502 ATAT
1 ATAT
14580506 TAATAATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.65
14 6 0.35
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (14 bp):
ATATACATATATTA
Found at i:14580581 original size:21 final size:23
Alignment explanation
Indices: 14580557--14580604 Score: 73
Period size: 21 Copynumber: 2.1 Consensus size: 23
14580547 AATAATACTT
14580557 TAAAAATAAT-TAATA-TATTAA
1 TAAAAATAATATAATAGTATTAA
14580578 TAAAAATAATAGTAATAGTATTAA
1 TAAAAATAATA-TAATAGTATTAA
14580602 TAA
1 TAA
14580605 TATGTAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
21 10 0.42
23 5 0.21
24 9 0.38
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.35
Consensus pattern (23 bp):
TAAAAATAATATAATAGTATTAA
Found at i:14581222 original size:18 final size:18
Alignment explanation
Indices: 14581209--14581244 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
14581199 TTTTTTTTGC
14581209 TTTTTATTTATTTTTATA
1 TTTTTATTTATTTTTATA
14581227 TTTTTATTATATTTTTAT
1 TTTTTATT-TATTTTTAT
14581245 GTATATATGC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTTTATTTATTTTTATA
Found at i:14582349 original size:16 final size:16
Alignment explanation
Indices: 14582330--14582367 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
14582320 GGAAATTTAT
14582330 TTTATAAA-AAATTAAA
1 TTTATAAAGAAA-TAAA
14582346 TTTATAAAGAAATAAA
1 TTTATAAAGAAATAAA
14582362 TTTATA
1 TTTATA
14582368 TAATTAATGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 18 0.86
17 3 0.14
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (16 bp):
TTTATAAAGAAATAAA
Found at i:14583308 original size:11 final size:11
Alignment explanation
Indices: 14583294--14583370 Score: 57
Period size: 11 Copynumber: 7.1 Consensus size: 11
14583284 ATATCTAAGT
14583294 AATAACAACAA
1 AATAACAACAA
* *
14583305 AATAATAATAA
1 AATAACAACAA
* *
14583316 CATAATAACAA
1 AATAACAACAA
*
14583327 AATGACAACAA
1 AATAACAACAA
* *
14583338 AACAACATCAA
1 AATAACAACAA
**
14583349 AATGGCAAC-A
1 AATAACAACAA
*
14583359 AACAACAACAA
1 AATAACAACAA
14583370 A
1 A
14583371 CAACAGTGAA
Statistics
Matches: 48, Mismatches: 17, Indels: 2
0.72 0.25 0.03
Matches are distributed among these distances:
10 7 0.15
11 41 0.85
ACGTcount: A:0.66, C:0.18, G:0.04, T:0.12
Consensus pattern (11 bp):
AATAACAACAA
Found at i:14583349 original size:22 final size:21
Alignment explanation
Indices: 14583322--14583370 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
14583312 ATAACATAAT
14583322 AACAAAATGACAACAAAACAAC
1 AACAAAATGACAAC-AAACAAC
* *
14583344 ATCAAAATGGCAACAAACAAC
1 AACAAAATGACAACAAACAAC
14583365 AACAAA
1 AACAAA
14583371 CAACAGTGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 12 0.50
22 12 0.50
ACGTcount: A:0.65, C:0.22, G:0.06, T:0.06
Consensus pattern (21 bp):
AACAAAATGACAACAAACAAC
Found at i:14583697 original size:2 final size:2
Alignment explanation
Indices: 14583690--14583722 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
14583680 TGGAATTTAA
14583690 TC TC 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 TC TC T
14583723 ATATATATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:14583727 original size:2 final size:2
Alignment explanation
Indices: 14583722--14583760 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
14583712 TCTCTCTCTC
14583722 TA TA TA TA 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 TA TA TA TA T
14583761 CCTATTTTTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 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):
TA
Found at i:14585094 original size:2 final size:2
Alignment explanation
Indices: 14585087--14585113 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
14585077 GTTAAAAATT
14585087 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
14585114 TTGAACATGG
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:14588805 original size:14 final size:15
Alignment explanation
Indices: 14588781--14588810 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
14588771 TTAGTCTAGG
14588781 TTTATGTTTTTATTT
1 TTTATGTTTTTATTT
14588796 TTTA-GTTTTTATTT
1 TTTATGTTTTTATTT
14588810 T
1 T
14588811 ATTTCAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.13, C:0.00, G:0.07, T:0.80
Consensus pattern (15 bp):
TTTATGTTTTTATTT
Found at i:14592245 original size:2 final size:2
Alignment explanation
Indices: 14592233--14592270 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
14592223 ACTTTAATAC
*
14592233 AT AT TT 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
14592271 CCCTTTCAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:14601119 original size:20 final size:21
Alignment explanation
Indices: 14601094--14601136 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
14601084 ATATAAATTC
14601094 AATTC-TTATACTCAATCTCA
1 AATTCATTATACTCAATCTCA
*
14601114 AATTCTATTATATTCAATCTCA
1 AATTC-ATTATACTCAATCTCA
14601136 A
1 A
14601137 GATGGAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 5 0.25
22 15 0.75
ACGTcount: A:0.37, C:0.21, G:0.00, T:0.42
Consensus pattern (21 bp):
AATTCATTATACTCAATCTCA
Found at i:14605972 original size:18 final size:18
Alignment explanation
Indices: 14605945--14605982 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
14605935 CTTTTTTTTC
14605945 ATTTTGAATA-ACACATTT
1 ATTTTGAATATA-ACATTT
*
14605963 ATTTTTAATATAACATTT
1 ATTTTGAATATAACATTT
14605981 AT
1 AT
14605983 CTATTCTTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 17 0.94
19 1 0.06
ACGTcount: A:0.39, C:0.08, G:0.03, T:0.50
Consensus pattern (18 bp):
ATTTTGAATATAACATTT
Found at i:14608128 original size:15 final size:16
Alignment explanation
Indices: 14608099--14608132 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
14608089 TTATAATTTA
14608099 AAACATAAAAAAAAAG
1 AAACATAAAAAAAAAG
*
14608115 AAACA-AAAAGAAAAG
1 AAACATAAAAAAAAAG
14608130 AAA
1 AAA
14608133 GAACAGAAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.82, C:0.06, G:0.09, T:0.03
Consensus pattern (16 bp):
AAACATAAAAAAAAAG
Found at i:14613917 original size:18 final size:18
Alignment explanation
Indices: 14613894--14613949 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
14613884 CCACCACCAA
14613894 CTCCACTAGCCACACTTG
1 CTCCACTAGCCACACTTG
*
14613912 CTCCACCA-CCA-AC-T-
1 CTCCACTAGCCACACTTG
14613926 CT--ACTAGCCACACTTG
1 CTCCACTAGCCACACTTG
*
14613942 CTCTACTA
1 CTCCACTA
14613950 CCTACTCCAC
Statistics
Matches: 30, Mismatches: 2, Indels: 12
0.68 0.05 0.27
Matches are distributed among these distances:
12 3 0.10
13 3 0.10
14 4 0.13
15 2 0.07
16 4 0.13
17 3 0.10
18 11 0.37
ACGTcount: A:0.25, C:0.45, G:0.07, T:0.23
Consensus pattern (18 bp):
CTCCACTAGCCACACTTG
Found at i:14613920 original size:30 final size:30
Alignment explanation
Indices: 14613884--14613969 Score: 136
Period size: 30 Copynumber: 2.9 Consensus size: 30
14613874 CTAGCCTTTG
14613884 CCACCACCAACTCCACTAGCCACACTTGCT
1 CCACCACCAACTCCACTAGCCACACTTGCT
*
14613914 CCACCACCAACTCTACTAGCCACACTTGCT
1 CCACCACCAACTCCACTAGCCACACTTGCT
* * *
14613944 CTACTACCTACTCCACTAGCCACACT
1 CCACCACCAACTCCACTAGCCACACT
14613970 CCACCACCCC
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 51 1.00
ACGTcount: A:0.27, C:0.48, G:0.06, T:0.20
Consensus pattern (30 bp):
CCACCACCAACTCCACTAGCCACACTTGCT
Found at i:14614590 original size:53 final size:50
Alignment explanation
Indices: 14614531--14614630 Score: 128
Period size: 53 Copynumber: 1.9 Consensus size: 50
14614521 CTATATTACG
* *
14614531 TATATATATATATATACTATTTTATGTATATATCTTTAATACTATATTATTTA
1 TATATATATATACATACTATCTTATGTATATAT-TTTAAT--TATATTATTTA
* **
14614584 TATATATATTTACATGTTATCTTATGTATATATTTTAATTATATTAT
1 TATATATATATACATACTATCTTATGTATATATTTTAATTATATTAT
14614631 ATATGCATTT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
50 8 0.19
52 6 0.14
53 28 0.67
ACGTcount: A:0.36, C:0.05, G:0.03, T:0.56
Consensus pattern (50 bp):
TATATATATATACATACTATCTTATGTATATATTTTAATTATATTATTTA
Found at i:14614625 original size:22 final size:23
Alignment explanation
Indices: 14614576--14614665 Score: 71
Period size: 24 Copynumber: 3.9 Consensus size: 23
14614566 TTAATACTAT
*
14614576 ATTAT-TTATATATATA-TTTAC
1 ATTATATTATGTATATATTTTAC
*
14614597 ATGTTATCTTATGTATATATTTTA-
1 A--TTATATTATGTATATATTTTAC
*
14614621 ATTATATTATATATGCAT-TTTTAC
1 ATTATATTATGTAT--ATATTTTAC
* *
14614645 ACTATATTATGTACATATTTT
1 ATTATATTATGTATATATTTT
14614666 TAATATTATC
Statistics
Matches: 55, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
21 1 0.02
22 13 0.24
23 13 0.24
24 24 0.44
25 4 0.07
ACGTcount: A:0.33, C:0.07, G:0.04, T:0.56
Consensus pattern (23 bp):
ATTATATTATGTATATATTTTAC
Found at i:14614671 original size:20 final size:20
Alignment explanation
Indices: 14614648--14614706 Score: 57
Period size: 23 Copynumber: 2.9 Consensus size: 20
14614638 TTTTTACACT
14614648 ATATTATGTACATATTTTTA
1 ATATTATGTACATATTTTTA
** *
14614668 ATATTATCACGTATTTATTTTTT
1 ATATTAT---GTACATATTTTTA
14614691 ATA-TATGTACATATTT
1 ATATTATGTACATATTT
14614707 ATGTAGTATT
Statistics
Matches: 31, Mismatches: 5, Indels: 7
0.72 0.12 0.16
Matches are distributed among these distances:
19 8 0.26
20 7 0.23
22 3 0.10
23 13 0.42
ACGTcount: A:0.32, C:0.07, G:0.05, T:0.56
Consensus pattern (20 bp):
ATATTATGTACATATTTTTA
Found at i:14615521 original size:23 final size:23
Alignment explanation
Indices: 14615495--14615543 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
14615485 ATAAGAAATA
14615495 TAAAAGAAGTAGATATCTAATTC
1 TAAAAGAAGTAGATATCTAATTC
14615518 TAAAAGAAGTAGATATCTAATTC
1 TAAAAGAAGTAGATATCTAATTC
14615541 TAA
1 TAA
14615544 TAACTATTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.49, C:0.08, G:0.12, T:0.31
Consensus pattern (23 bp):
TAAAAGAAGTAGATATCTAATTC
Found at i:14620125 original size:26 final size:27
Alignment explanation
Indices: 14620085--14620156 Score: 94
Period size: 26 Copynumber: 2.7 Consensus size: 27
14620075 GAATTTTCTC
*
14620085 AAAATTTTATTGAGGGTAAAATCG-CA
1 AAAATTTTATCGAGGGTAAAATCGTCA
*
14620111 AAAATTTTATCGAGGGTAAAATTGTCA
1 AAAATTTTATCGAGGGTAAAATCGTCA
* *
14620138 AAAAATTTA-CTAGGGTAAA
1 AAAATTTTATCGAGGGTAAA
14620157 TTTGGGATAA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
26 31 0.76
27 10 0.24
ACGTcount: A:0.44, C:0.07, G:0.18, T:0.31
Consensus pattern (27 bp):
AAAATTTTATCGAGGGTAAAATCGTCA
Found at i:14622384 original size:49 final size:50
Alignment explanation
Indices: 14622302--14622414 Score: 149
Period size: 49 Copynumber: 2.2 Consensus size: 50
14622292 AGTGTTTCAA
* *
14622302 GTGTGTTTCGGGGGAGGATGTAAAGCCTACGGGCTTAGCACTTGGTGCCGAG
1 GTGTGTTTC-GGAGAGGATGTAAAGCCTACGGGCCTAGCACTTGGTGCC-AG
* *
14622354 GTGTGTTTCGGAG-GGATGT-TAGCCTTCGGGCCTAGCACTTGGTGCCAG
1 GTGTGTTTCGGAGAGGATGTAAAGCCTACGGGCCTAGCACTTGGTGCCAG
14622402 GTGTGTTCTCGGA
1 GTGTGTT-TCGGA
14622415 TGGTTATCTC
Statistics
Matches: 56, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
48 9 0.16
49 29 0.52
50 6 0.11
51 3 0.05
52 9 0.16
ACGTcount: A:0.14, C:0.19, G:0.39, T:0.28
Consensus pattern (50 bp):
GTGTGTTTCGGAGAGGATGTAAAGCCTACGGGCCTAGCACTTGGTGCCAG
Found at i:14624233 original size:32 final size:32
Alignment explanation
Indices: 14624193--14624255 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
14624183 AAAAATGTCC
*
14624193 ATGTTCAATAATTATTATCTTAATGCCAATCA
1 ATGTTCAATAATTATCATCTTAATGCCAATCA
*
14624225 ATGTTCAATCATTATCATCTTAATGCCAATC
1 ATGTTCAATAATTATCATCTTAATGCCAATC
14624256 TATGCGTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.35, C:0.19, G:0.06, T:0.40
Consensus pattern (32 bp):
ATGTTCAATAATTATCATCTTAATGCCAATCA
Found at i:14629717 original size:24 final size:25
Alignment explanation
Indices: 14629668--14629723 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 25
14629658 TTTATTAACC
* *
14629668 TTATTTAAATGTTTCATTTATATG-
1 TTATTTAAATATTTCATATATATGT
*
14629692 TTATTTCAAATATTTTATATAT-TGT
1 TTATTT-AAATATTTCATATATATGT
14629717 TTATTTA
1 TTATTTA
14629724 CATCATTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
24 9 0.33
25 18 0.67
ACGTcount: A:0.30, C:0.04, G:0.05, T:0.61
Consensus pattern (25 bp):
TTATTTAAATATTTCATATATATGT
Found at i:14629807 original size:3 final size:3
Alignment explanation
Indices: 14629794--14629838 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
14629784 TTATTGTAGA
*
14629794 TAT TCT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
14629839 ATGCATATAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:14630066 original size:31 final size:31
Alignment explanation
Indices: 14630018--14630082 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
14630008 CCATCCTATG
* * *
14630018 TATATATTTTTTAAATACTATATTGTGTGTA
1 TATATATTTCTTAAATACCATATTGTGTATA
14630049 TATATATATTCTT-AATACCATATTGTGTATA
1 TATATAT-TTCTTAAATACCATATTGTGTATA
14630080 TAT
1 TAT
14630083 CATTATTATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
31 26 0.87
32 4 0.13
ACGTcount: A:0.34, C:0.06, G:0.08, T:0.52
Consensus pattern (31 bp):
TATATATTTCTTAAATACCATATTGTGTATA
Found at i:14634276 original size:8 final size:8
Alignment explanation
Indices: 14634252--14634313 Score: 54
Period size: 8 Copynumber: 7.4 Consensus size: 8
14634242 GACAGTCATG
*
14634252 AAAAGAAA
1 AAAACAAA
14634260 AAGAA-AAA
1 AA-AACAAA
14634268 AAAACAAA
1 AAAACAAA
14634276 AAAACAAA
1 AAAACAAA
*
14634284 AAGAAAAAA
1 AA-AACAAA
*
14634293 AGACAAGAAA
1 A-A-AACAAA
14634303 AAAACAAA
1 AAAACAAA
14634311 AAA
1 AAA
14634314 GAAATCAAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
7 2 0.04
8 28 0.61
9 9 0.20
10 7 0.15
ACGTcount: A:0.85, C:0.06, G:0.08, T:0.00
Consensus pattern (8 bp):
AAAACAAA
Found at i:14634284 original size:24 final size:25
Alignment explanation
Indices: 14634252--14634304 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 25
14634242 GACAGTCATG
*
14634252 AAAAGAAAAAGAAAAAAAAACAA-A
1 AAAACAAAAAGAAAAAAAAACAAGA
*
14634276 AAAACAAAAAGAAAAAAAGACAAGA
1 AAAACAAAAAGAAAAAAAAACAAGA
14634301 AAAA
1 AAAA
14634305 AACAAAAAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 21 0.81
25 5 0.19
ACGTcount: A:0.85, C:0.06, G:0.09, T:0.00
Consensus pattern (25 bp):
AAAACAAAAAGAAAAAAAAACAAGA
Found at i:14636612 original size:72 final size:72
Alignment explanation
Indices: 14636460--14636675 Score: 299
Period size: 72 Copynumber: 3.0 Consensus size: 72
14636450 TTATTTCTGT
* *
14636460 TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCATGCTGAGGTAATTTCA
1 TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCA
*
14636525 ATTTCTG
66 ATTTATG
* ** * * * *
14636532 TTTGTCAAAACTCAACTCATATTGC-AGAAATGAGTCGAGCCTCAAGACACGTTGAGGTATTTTC
1 TTT-TCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTC
14636596 AATTTATG
65 AATTTATG
14636604 CTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTT
1 -TTTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTT
14636669 TCAATTT
63 TCAATTT
14636676 CCGTTTTTCA
Statistics
Matches: 122, Mismatches: 17, Indels: 7
0.84 0.12 0.05
Matches are distributed among these distances:
72 43 0.35
73 23 0.19
74 18 0.15
75 38 0.31
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31
Consensus pattern (72 bp):
TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCA
ATTTATG
Found at i:14636776 original size:16 final size:16
Alignment explanation
Indices: 14636755--14636785 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
14636745 CTGAGGTAAT
*
14636755 TTCAATTTCTGTTTTC
1 TTCAATTTATGTTTTC
14636771 TTCAATTTATGTTTT
1 TTCAATTTATGTTTT
14636786 TCGAAAATCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.16, C:0.13, G:0.06, T:0.65
Consensus pattern (16 bp):
TTCAATTTATGTTTTC
Found at i:14636779 original size:89 final size:90
Alignment explanation
Indices: 14636593--14636937 Score: 468
Period size: 89 Copynumber: 4.0 Consensus size: 90
14636583 TTGAGGTATT
*
14636593 TTCAATTTATGCTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACG
1 TTCAATTTATGCTTTTC-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACG
* *
14636658 CTGAGGTATTTTCAATTTCCG-TTT-
65 CTGAGGTAATTTCAATTTCTGTTTTC
*
14636682 TTCAATTTATGCTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACATGC
1 TTCAATTTATGCTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGC
14636746 TGAGGTAATTTCAATTTCTGTTTTC
66 TGAGGTAATTTCAATTTCTGTTTTC
* * * *
14636771 TTCAATTTATGTTTTTC-GAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGC
1 TTCAATTTATGCTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGC
* *
14636835 TGA-GTATTTTCAA--T-T-TTTGC
66 TGAGGTAATTTCAATTTCTGTTTTC
14636855 TTC------TGCTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACG
1 TTCAATTTATGCTTTTC-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACG
*
14636914 CTGAGGTAATTTCAATTTATGTTT
65 CTGAGGTAATTTCAATTTCTGTTT
14636938 GTCAAAAAAA
Statistics
Matches: 231, Mismatches: 16, Indels: 22
0.86 0.06 0.08
Matches are distributed among these distances:
78 7 0.03
80 47 0.20
81 9 0.04
83 1 0.00
84 8 0.03
85 4 0.02
86 1 0.00
87 63 0.27
88 12 0.05
89 79 0.34
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.36
Consensus pattern (90 bp):
TTCAATTTATGCTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGC
TGAGGTAATTTCAATTTCTGTTTTC
Found at i:14636919 original size:169 final size:172
Alignment explanation
Indices: 14636593--14637002 Score: 532
Period size: 169 Copynumber: 2.4 Consensus size: 172
14636583 TTGAGGTATT
14636593 TTCAATTTATGCTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACG
1 TTCAATTTATGCTTTTC-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACG
*
14636658 CTGAGGTATTTTCAATTTCCGTTTTTCAATTTATGCTTTTCAAAAATCAACTCATATTGCGAGAG
65 CTGAGGTATTTTCAA-TT-C-TTTTGC-A-TTATGCTTTTCAAAAATCAACTCATATTGCGAGAG
* *
14636723 GTGAGTTGAGCCTCAGGACATGCTGAGGTAATTTCAATTTCTGTTTTC
125 GTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTATGTTTTC
* * *
14636771 TTCAATTTATGTTTTTC-GAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGC
1 TTCAATTTATGCTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGC
*
14636835 TGA-GTATTTTCAA-T-TTTTGC-TTCTGCTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGA
66 TGAGGTATTTTCAATTCTTTTGCATTATGCTTTTC--AAAAATCAACTCATATTGCGAGAGGTGA
14636896 GTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTATG-TTT-
129 GTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTATGTTTTC
* * *
14636938 GTCAA---A--------AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCGGGGCACGC
1 TTCAATTTATGCTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGC
14636992 TGAGGTATTTT
66 TGAGGTATTTT
14637003 TAGTTTATGT
Statistics
Matches: 216, Mismatches: 12, Indels: 28
0.84 0.05 0.11
Matches are distributed among these distances:
157 46 0.21
158 7 0.03
164 1 0.00
167 14 0.06
168 3 0.01
169 65 0.30
170 5 0.02
173 1 0.00
175 10 0.05
176 48 0.22
178 16 0.07
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (172 bp):
TTCAATTTATGCTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGC
TGAGGTATTTTCAATTCTTTTGCATTATGCTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGT
TGAGCCTCAGGACACGCTGAGGTAATTTCAATTTATGTTTTC
Found at i:14636991 original size:77 final size:78
Alignment explanation
Indices: 14636789--14637014 Score: 312
Period size: 77 Copynumber: 2.9 Consensus size: 78
14636779 ATGTTTTTCG
* *
14636789 AAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGA-GTATTTTCAATTTTT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTTAT
***
14636853 GCTTCTGCTTTTCAAA
66 G-TT-TGC-TCAAAAA
* *
14636869 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTAT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTTAT
14636934 GTTTG-TCAAAAA
66 GTTTGCTCAAAAA
* * * *
14636946 AAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCGGGGCACGCTGAGGTATTTTTAGTTTAT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTTAT
14637011 GTTT
66 GTTT
14637015 TAAATTGACT
Statistics
Matches: 132, Mismatches: 13, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
77 67 0.51
79 2 0.02
80 49 0.37
81 14 0.11
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.32
Consensus pattern (78 bp):
AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTTAT
GTTTGCTCAAAAA
Found at i:14637289 original size:72 final size:72
Alignment explanation
Indices: 14637054--14637272 Score: 366
Period size: 72 Copynumber: 3.0 Consensus size: 72
14637044 TAAGCCTTTT
* * ** *
14637054 AATTTTTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGTTGAG
1 AATTTCTG-TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAG
14637119 GTAATTTC
65 GTAATTTC
*
14637127 AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGATACGTTGAGG
1 AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
14637192 TAATTTC
66 TAATTTC
14637199 AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
1 AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
*
14637264 TATTTTC
66 TAATTTC
14637271 AA
1 AA
14637273 AATCAACTTT
Statistics
Matches: 138, Mismatches: 8, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
72 131 0.95
73 7 0.05
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (72 bp):
AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
TAATTTC
Found at i:14637604 original size:54 final size:54
Alignment explanation
Indices: 14637299--14637600 Score: 552
Period size: 54 Copynumber: 5.6 Consensus size: 54
14637289 TAAGTTTCAA
14637299 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTTTTAATTTCTGTTTTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTTTTAATTTCTGTTTTTC
* *
14637353 -AAAATCAACTCATATTGCGAGAGGTGGGTTGAACCTTTTAATTTCTATTTTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTTTTAATTTCTGTTTTTC
*
14637406 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTTTTAATTTCTATTTTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTTTTAATTTCTGTTTTTC
*
14637460 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTTTTAATTCCTGTTTTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTTTTAATTTCTGTTTTTC
*
14637514 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAATTTCTGTTTTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTTTTAATTTCTGTTTTTC
14637568 AAAAATCAACTCATATTGCGAGAGGTGAGTTGA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGA
14637601 GCCTCGGGTC
Statistics
Matches: 240, Mismatches: 7, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
53 51 0.21
54 189 0.79
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.37
Consensus pattern (54 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTTTTAATTTCTGTTTTTC
Found at i:14637847 original size:45 final size:45
Alignment explanation
Indices: 14637796--14637884 Score: 106
Period size: 45 Copynumber: 2.0 Consensus size: 45
14637786 AATAAAGACC
* * * * * *
14637796 GGAGCTGGTTGAAGATGCCAGATTTTGTCTCTCTGAAGTTGCAGT
1 GGAGCTGATCGAAGATACAAGATCTTGCCTCTCTGAAGTTGCAGT
* *
14637841 GGAGCTGATCGAAGATATAAGATCTTGCCTTTCTGAAGTTGCAG
1 GGAGCTGATCGAAGATACAAGATCTTGCCTCTCTGAAGTTGCAG
14637885 AAGAAAATAC
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
45 36 1.00
ACGTcount: A:0.24, C:0.16, G:0.29, T:0.31
Consensus pattern (45 bp):
GGAGCTGATCGAAGATACAAGATCTTGCCTCTCTGAAGTTGCAGT
Found at i:14639378 original size:3 final size:3
Alignment explanation
Indices: 14639353--14639412 Score: 93
Period size: 3 Copynumber: 20.0 Consensus size: 3
14639343 TTATTGTAGA
* * *
14639353 TAT TCT TAT TCT TAT TCT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
14639401 TAT TAT TAT TAT
1 TAT TAT TAT TAT
14639413 ATGCATATAT
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:14639637 original size:29 final size:29
Alignment explanation
Indices: 14639592--14639654 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
14639582 CCATCCTATG
* *
14639592 TATATATTTTTTAAATACTATATTGTATA
1 TATATATTTCTTAAATACCATATTGTATA
*
14639621 TATATATATTCTT-AATACCATATTGTGTA
1 TATATAT-TTCTTAAATACCATATTGTATA
14639650 TATAT
1 TATAT
14639655 CATTATTACA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 26 0.87
30 4 0.13
ACGTcount: A:0.37, C:0.06, G:0.05, T:0.52
Consensus pattern (29 bp):
TATATATTTCTTAAATACCATATTGTATA
Found at i:14654558 original size:2 final size:2
Alignment explanation
Indices: 14654551--14654594 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
14654541 CATCACCATA
14654551 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
14654593 AT
1 AT
14654595 CTTAAAAATC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:14659160 original size:55 final size:56
Alignment explanation
Indices: 14659076--14659188 Score: 201
Period size: 55 Copynumber: 2.0 Consensus size: 56
14659066 ACTGGTGAAC
*
14659076 TGGGTATTTACGTTGAGTTGGGAAGGTTTT-TTTGAATCATGTATAATCGATGTAA
1 TGGGTATTTACGTTGAGTTGGAAAGGTTTTGTTTGAATCATGTATAATCGATGTAA
*
14659131 TGGGTATTTGCGTTGAGTTGGAAAGGTTTTGTTTGAATCATGTATAATCGATGTAA
1 TGGGTATTTACGTTGAGTTGGAAAGGTTTTGTTTGAATCATGTATAATCGATGTAA
14659187 TG
1 TG
14659189 TCTACTTCTA
Statistics
Matches: 55, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
55 28 0.51
56 27 0.49
ACGTcount: A:0.25, C:0.05, G:0.28, T:0.42
Consensus pattern (56 bp):
TGGGTATTTACGTTGAGTTGGAAAGGTTTTGTTTGAATCATGTATAATCGATGTAA
Found at i:14660544 original size:47 final size:47
Alignment explanation
Indices: 14660475--14660569 Score: 190
Period size: 47 Copynumber: 2.0 Consensus size: 47
14660465 TATACTACTT
14660475 AGCCATTAGGTAGCTAGACTTCCTAAATGCATGCTTAATCGTTATCC
1 AGCCATTAGGTAGCTAGACTTCCTAAATGCATGCTTAATCGTTATCC
14660522 AGCCATTAGGTAGCTAGACTTCCTAAATGCATGCTTAATCGTTATCC
1 AGCCATTAGGTAGCTAGACTTCCTAAATGCATGCTTAATCGTTATCC
14660569 A
1 A
14660570 TTCACCATAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.32
Consensus pattern (47 bp):
AGCCATTAGGTAGCTAGACTTCCTAAATGCATGCTTAATCGTTATCC
Found at i:14681443 original size:16 final size:16
Alignment explanation
Indices: 14681424--14681459 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
14681414 ATTTAGTTAG
*
14681424 TTTCGTGACACATCAT
1 TTTCGCGACACATCAT
14681440 TTTCGCGACACATCAT
1 TTTCGCGACACATCAT
14681456 TTTC
1 TTTC
14681460 ACTTATAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.22, C:0.28, G:0.11, T:0.39
Consensus pattern (16 bp):
TTTCGCGACACATCAT
Found at i:14693658 original size:42 final size:41
Alignment explanation
Indices: 14693546--14693694 Score: 140
Period size: 42 Copynumber: 3.5 Consensus size: 41
14693536 TGTGATTTCG
* *
14693546 TGTAAGACCATGTTTGGGACGTTGCCATCG-ATTTGAAATTACA
1 TGTAAGACCATGTCTGGGACG-TGACATCGTATTTG--ATTACA
* * * * *
14693589 TGTAAGACCATGACTGGTACTTCGACATCGTATTTGATTTCG
1 TGTAAGACCATGTCTGGGACGT-GACATCGTATTTGATTACA
* *
14693631 TGTAAGACCTTGTCTGGGACAGTGACATTGATATTTGATTACA
1 TGTAAGACCATGTCTGGGAC-GTGACATCG-TATTTGATTACA
*
14693674 TGTAA-ACCATGTCTAGGACGT
1 TGTAAGACCATGTCTGGGACGT
14693695 TGGCATTGTA
Statistics
Matches: 86, Mismatches: 16, Indels: 10
0.77 0.14 0.09
Matches are distributed among these distances:
41 2 0.02
42 40 0.47
43 39 0.45
44 5 0.06
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.34
Consensus pattern (41 bp):
TGTAAGACCATGTCTGGGACGTGACATCGTATTTGATTACA
Found at i:14693678 original size:43 final size:42
Alignment explanation
Indices: 14693546--14693694 Score: 142
Period size: 43 Copynumber: 3.5 Consensus size: 42
14693536 TGTGATTTCG
* * *
14693546 TGTAAGACCATGTTTGGGACGTTGCCATCG-ATTTGAAATTACA
1 TGTAAGACCATGTCTGGGACGTCGACATCGTATTTG--ATTACA
* * * * *
14693589 TGTAAGACCATGACTGGTACTTCGACATCGTATTTGATTTCG
1 TGTAAGACCATGTCTGGGACGTCGACATCGTATTTGATTACA
* *
14693631 TGTAAGACCTTGTCTGGGACAGT-GACATTGATATTTGATTACA
1 TGTAAGACCATGTCTGGGAC-GTCGACATCG-TATTTGATTACA
*
14693674 TGTAA-ACCATGTCTAGGACGT
1 TGTAAGACCATGTCTGGGACGT
14693695 TGGCATTGTA
Statistics
Matches: 86, Mismatches: 17, Indels: 8
0.77 0.15 0.07
Matches are distributed among these distances:
41 2 0.02
42 39 0.45
43 40 0.47
44 5 0.06
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.34
Consensus pattern (42 bp):
TGTAAGACCATGTCTGGGACGTCGACATCGTATTTGATTACA
Found at i:14705595 original size:29 final size:29
Alignment explanation
Indices: 14705561--14705634 Score: 105
Period size: 29 Copynumber: 2.6 Consensus size: 29
14705551 TAATCGATCA
**
14705561 CGCACACTTAGTGCCATGTGATTT-AAGCT
1 CGCACACTTAGTGCCAT-ACATTTCAAGCT
14705590 CGCACACTTAGTGCCATACATTTCAAGCT
1 CGCACACTTAGTGCCATACATTTCAAGCT
*
14705619 TGCACACTTAGTGCCA
1 CGCACACTTAGTGCCA
14705635 ATCTCGTCAC
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
28 4 0.10
29 37 0.90
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.28
Consensus pattern (29 bp):
CGCACACTTAGTGCCATACATTTCAAGCT
Found at i:14709169 original size:45 final size:45
Alignment explanation
Indices: 14709100--14709186 Score: 147
Period size: 45 Copynumber: 1.9 Consensus size: 45
14709090 TATGTAATCT
*
14709100 GAACTCATTGGGTTGTGGTCTGAGTTCATGATATATCTGACATCC
1 GAACTCATTGAGTTGTGGTCTGAGTTCATGATATATCTGACATCC
* *
14709145 GAACTCATTGAGTTGTGGTTTGAGTTCATGATATATGTGACA
1 GAACTCATTGAGTTGTGGTCTGAGTTCATGATATATCTGACA
14709187 CATGTTTTGG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.24, C:0.14, G:0.25, T:0.37
Consensus pattern (45 bp):
GAACTCATTGAGTTGTGGTCTGAGTTCATGATATATCTGACATCC
Found at i:14713822 original size:17 final size:18
Alignment explanation
Indices: 14713775--14713822 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 18
14713765 TGGGTTCGTC
14713775 ATTTGGCAGACTC-CAGG
1 ATTTGGCAGACTCTCAGG
* * *
14713792 ATTTGGTAAACTCTGA-G
1 ATTTGGCAGACTCTCAGG
14713809 ATTTGGCAGACTCT
1 ATTTGGCAGACTCT
14713823 TCTATTAAGT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
17 24 0.96
18 1 0.04
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (18 bp):
ATTTGGCAGACTCTCAGG
Found at i:14720847 original size:6 final size:6
Alignment explanation
Indices: 14720836--14720880 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
14720826 AGGTTTCTAA
** * *
14720836 AAATGG AAATGG AAATGG AAATAA AAATGA AAATGA AAATGG AAA
1 AAATGG AAATGG AAATGG AAATGG AAATGG AAATGG AAATGG AAA
14720881 CTTGCAATCT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.62, C:0.00, G:0.22, T:0.16
Consensus pattern (6 bp):
AAATGG
Found at i:14720853 original size:12 final size:12
Alignment explanation
Indices: 14720835--14720880 Score: 65
Period size: 12 Copynumber: 3.8 Consensus size: 12
14720825 TAGGTTTCTA
14720835 AAAATGGAAATG
1 AAAATGGAAATG
* *
14720847 GAAATGGAAATA
1 AAAATGGAAATG
*
14720859 AAAATGAAAATG
1 AAAATGGAAATG
14720871 AAAATGGAAA
1 AAAATGGAAA
14720881 CTTGCAATCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.63, C:0.00, G:0.22, T:0.15
Consensus pattern (12 bp):
AAAATGGAAATG
Found at i:14720862 original size:24 final size:24
Alignment explanation
Indices: 14720833--14720880 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
14720823 TATAGGTTTC
* *
14720833 TAAAAATGGAAATGGAAATGGAAA
1 TAAAAATGAAAATGAAAATGGAAA
14720857 TAAAAATGAAAATGAAAATGGAAA
1 TAAAAATGAAAATGAAAATGGAAA
14720881 CTTGCAATCT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.62, C:0.00, G:0.21, T:0.17
Consensus pattern (24 bp):
TAAAAATGAAAATGAAAATGGAAA
Found at i:14721082 original size:26 final size:26
Alignment explanation
Indices: 14721024--14721082 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
14721014 GATTTTCTCG
*
14721024 AAATTTTACTAGGGTTAAAATCGTTA
1 AAATTTTACTAGGGTTAAAATCGTCA
*
14721050 AAATTTTACTAAGGG-TAAAATTGTCA
1 AAATTTTACT-AGGGTTAAAATCGTCA
*
14721076 AATTTTT
1 AAATTTT
14721083 GTTGGGATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 25 0.86
27 4 0.14
ACGTcount: A:0.39, C:0.07, G:0.14, T:0.41
Consensus pattern (26 bp):
AAATTTTACTAGGGTTAAAATCGTCA
Found at i:14722934 original size:42 final size:43
Alignment explanation
Indices: 14722875--14722955 Score: 137
Period size: 42 Copynumber: 1.9 Consensus size: 43
14722865 GCCACCTGCT
14722875 CGTGTGCCAGGCCATGTA-CCTTCAAAATAACCCCACACGCAC
1 CGTGTGCCAGGCCATGTACCCTTCAAAATAACCCCACACGCAC
* *
14722917 CGTGTGCCAGGCCATGTACCCTTTAAAATAACCTCACAC
1 CGTGTGCCAGGCCATGTACCCTTCAAAATAACCCCACAC
14722956 ACCTATGTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
42 18 0.50
43 18 0.50
ACGTcount: A:0.28, C:0.36, G:0.16, T:0.20
Consensus pattern (43 bp):
CGTGTGCCAGGCCATGTACCCTTCAAAATAACCCCACACGCAC
Found at i:14722970 original size:42 final size:41
Alignment explanation
Indices: 14722882--14722975 Score: 109
Period size: 42 Copynumber: 2.2 Consensus size: 41
14722872 GCTCGTGTGC
* **
14722882 CAGGCCATGTACCTTCAAAATAACCCCACACGCACCGTGTGC
1 CAGGCCATGTACCTTCAAAATAACCCCACAC-CACCATGTAA
* *
14722924 CAGGCCATGTACCCTTTAAAATAACCTCACA-CACCTATGTAA
1 CAGGCCATGTA-CCTTCAAAATAACCCCACACCACC-ATGTAA
14722966 CAGGCCATGT
1 CAGGCCATGT
14722976 GCTAGGCCGT
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
41 4 0.09
42 24 0.53
43 17 0.38
ACGTcount: A:0.31, C:0.34, G:0.15, T:0.20
Consensus pattern (41 bp):
CAGGCCATGTACCTTCAAAATAACCCCACACCACCATGTAA
Found at i:14728162 original size:26 final size:26
Alignment explanation
Indices: 14728130--14728181 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
14728120 TTATTCACTT
14728130 ACAAACTTACTAAGATATGAAGCTTA
1 ACAAACTTACTAAGATATGAAGCTTA
*
14728156 ACAAACTTACTAAGCTATGAAGCTTA
1 ACAAACTTACTAAGATATGAAGCTTA
14728182 CTTTATGTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.44, C:0.17, G:0.12, T:0.27
Consensus pattern (26 bp):
ACAAACTTACTAAGATATGAAGCTTA
Found at i:14728672 original size:23 final size:22
Alignment explanation
Indices: 14728620--14728676 Score: 57
Period size: 23 Copynumber: 2.6 Consensus size: 22
14728610 TGAATATGGT
*
14728620 ATGAATTGTGTA--TATTGATG
1 ATGAATTGGGTACCTATTGATG
*
14728640 ATGATTTTGGGTACCTATTGTATG
1 ATGA-ATTGGGTACCTATTG-ATG
14728664 ATGAATT-GGTACC
1 ATGAATTGGGTACC
14728677 ATTTTGGTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
20 4 0.13
21 6 0.20
22 6 0.20
23 7 0.23
24 7 0.23
ACGTcount: A:0.26, C:0.07, G:0.25, T:0.42
Consensus pattern (22 bp):
ATGAATTGGGTACCTATTGATG
Found at i:14729207 original size:14 final size:14
Alignment explanation
Indices: 14729188--14729216 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
14729178 TTTTTTAAGT
14729188 TTCTAAAATTTTTA
1 TTCTAAAATTTTTA
14729202 TTCTAAAATTTTTA
1 TTCTAAAATTTTTA
14729216 T
1 T
14729217 ATGTTATCGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.07, G:0.00, T:0.59
Consensus pattern (14 bp):
TTCTAAAATTTTTA
Found at i:14730610 original size:51 final size:54
Alignment explanation
Indices: 14730542--14730710 Score: 154
Period size: 58 Copynumber: 3.1 Consensus size: 54
14730532 ATTTCCAAGT
* * *
14730542 TATTTTTA-TTTAGGAGAAGACCATATTCATTTCCAAATGATTCC-A-CTTC-CC
1 TATTTTCATTTTA-GAGAAAACCATAATCATTTCCAAATGATTCCTATCTTCTCC
* *
14730593 TATTTTCATTTTAGAGAAAACCATAATCATTTCTAAAT-ATTTCCTATTTCTTCATTTC
1 TATTTTCATTTTAGAGAAAACCATAATCATTTCCAAATGA-TTCCTA--TCTTC--TCC
* * * *
14730651 TATTTTCATTTTGGAGAAAACCATAATCATTTCCAAATGTTTCCCAT-TTCACC
1 TATTTTCATTTTAGAGAAAACCATAATCATTTCCAAATGATTCCTATCTTCTCC
14730704 -ATTTTCA
1 TATTTTCA
14730711 CCATTTCTAT
Statistics
Matches: 97, Mismatches: 11, Indels: 19
0.76 0.09 0.15
Matches are distributed among these distances:
50 1 0.01
51 33 0.34
52 12 0.12
53 1 0.01
55 7 0.07
56 1 0.01
58 42 0.43
ACGTcount: A:0.30, C:0.20, G:0.07, T:0.43
Consensus pattern (54 bp):
TATTTTCATTTTAGAGAAAACCATAATCATTTCCAAATGATTCCTATCTTCTCC
Found at i:14730707 original size:58 final size:58
Alignment explanation
Indices: 14730592--14730707 Score: 178
Period size: 58 Copynumber: 2.0 Consensus size: 58
14730582 TTCCACTTCC
* * **
14730592 CTATTTTCATTTTAGAGAAAACCATAATCATTTCTAAATATTTCCTATTTCTTCATTT
1 CTATTTTCATTTTAGAGAAAACCATAATCATTTCCAAATATTTCCCATTTCACCATTT
* *
14730650 CTATTTTCATTTTGGAGAAAACCATAATCATTTCCAAATGTTTCCCATTTCACCATTT
1 CTATTTTCATTTTAGAGAAAACCATAATCATTTCCAAATATTTCCCATTTCACCATTT
14730708 TCACCATTTC
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
58 52 1.00
ACGTcount: A:0.30, C:0.20, G:0.05, T:0.45
Consensus pattern (58 bp):
CTATTTTCATTTTAGAGAAAACCATAATCATTTCCAAATATTTCCCATTTCACCATTT
Found at i:14732284 original size:48 final size:46
Alignment explanation
Indices: 14732227--14732344 Score: 130
Period size: 48 Copynumber: 2.5 Consensus size: 46
14732217 GAGAGCTAGT
* *
14732227 GTAAGACATGTCTGGGACATGCATCGGCTTTGAGATATACCATGC-AAA
1 GTAAGACATGTCTGGGACATGCATCGACTTTGAGAT-GA-CA-GCTAAA
* * * * **
14732275 GTAAGACATGTCTGAGATATGCATCTACTTTGAGATGAGAGCTAGT
1 GTAAGACATGTCTGGGACATGCATCGACTTTGAGATGACAGCTAAA
14732321 GTAAGACATGTCTGGGACATGCAT
1 GTAAGACATGTCTGGGACATGCAT
14732345 TAGCCTCGAG
Statistics
Matches: 59, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
45 2 0.03
46 24 0.41
47 1 0.02
48 32 0.54
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.27
Consensus pattern (46 bp):
GTAAGACATGTCTGGGACATGCATCGACTTTGAGATGACAGCTAAA
Found at i:14741398 original size:9 final size:9
Alignment explanation
Indices: 14741384--14741409 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
14741374 TAAGTATTGT
14741384 TTTTTTTTC
1 TTTTTTTTC
14741393 TTTTTTTTC
1 TTTTTTTTC
14741402 TTTTTTTT
1 TTTTTTTT
14741410 AAGAACAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:14744224 original size:26 final size:26
Alignment explanation
Indices: 14744195--14744302 Score: 198
Period size: 26 Copynumber: 4.2 Consensus size: 26
14744185 TGATACAAAT
*
14744195 TGATAATGGGTTAGGTAAATGTTCTA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
14744221 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
14744247 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
14744273 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
14744299 TGAT
1 TGAT
14744303 GGGAATTTCA
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 79 1.00
ACGTcount: A:0.31, C:0.06, G:0.27, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:14745545 original size:14 final size:15
Alignment explanation
Indices: 14745526--14745581 Score: 60
Period size: 18 Copynumber: 3.5 Consensus size: 15
14745516 AATCTTCAAT
14745526 GATATG-CAATCTTA
1 GATATGACAATCTTA
14745540 GATATGATACAATCTTA
1 GATATG--ACAATCTTA
14745557 GATATGATTGCAATCTTA
1 GATATGA---CAATCTTA
14745575 GATATGA
1 GATATGA
14745582 TATACAATCT
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
14 6 0.17
15 1 0.03
17 14 0.39
18 15 0.42
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.36
Consensus pattern (15 bp):
GATATGACAATCTTA
Found at i:14745552 original size:17 final size:17
Alignment explanation
Indices: 14745532--14745595 Score: 92
Period size: 17 Copynumber: 3.6 Consensus size: 17
14745522 CAATGATATG
14745532 CAATCTTAGATATGATA
1 CAATCTTAGATATGATA
*
14745549 CAATCTTAGATATGATTG
1 CAATCTTAGATATGA-TA
14745567 CAATCTTAGATATGATATA
1 CAATCTTAGATATG--ATA
14745586 CAATCTTAGA
1 CAATCTTAGA
14745596 AGATATGATT
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
17 15 0.36
18 15 0.36
19 11 0.26
20 1 0.02
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.36
Consensus pattern (17 bp):
CAATCTTAGATATGATA
Found at i:14745570 original size:35 final size:37
Alignment explanation
Indices: 14745524--14745602 Score: 121
Period size: 35 Copynumber: 2.2 Consensus size: 37
14745514 ATAATCTTCA
14745524 ATGATATGCAATCTTAGATATG-ATACAATCTTAGAT
1 ATGATATGCAATCTTAGATATGAATACAATCTTAGAT
14745560 ATGAT-TGCAATCTTAGATATGATATACAATCTTAGA-
1 ATGATATGCAATCTTAGATATGA-ATACAATCTTAGAT
14745596 A-GATATG
1 ATGATATG
14745603 ATTTTGTAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
35 19 0.47
36 8 0.20
37 13 0.32
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.35
Consensus pattern (37 bp):
ATGATATGCAATCTTAGATATGAATACAATCTTAGAT
Found at i:14745917 original size:12 final size:11
Alignment explanation
Indices: 14745902--14745935 Score: 50
Period size: 12 Copynumber: 2.9 Consensus size: 11
14745892 TATTTTTAAT
14745902 TTATTATATATA
1 TTATT-TATATA
14745914 TTATTTATTATA
1 TTATTTA-TATA
14745926 TTATTTATAT
1 TTATTTATAT
14745936 TTTCAAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 5 0.24
12 16 0.76
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
TTATTTATATA
Found at i:14745927 original size:21 final size:21
Alignment explanation
Indices: 14745903--14746011 Score: 61
Period size: 21 Copynumber: 5.3 Consensus size: 21
14745893 ATTTTTAATT
14745903 TATTATATATATTATTTATTA
1 TATTATATATATTATTTATTA
* *
14745924 TATTATTTATATT-TTCA--A
1 TATTATATATATTATTTATTA
* * *
14745942 AATT-TGTAAATTA-TTATTA
1 TATTATATATATTATTTATTA
* *
14745961 TA-TATTATATTTTAACTTATATA
1 TATTA-TATATATT-ATTTAT-TA
*
14745984 TCTTATATAT-TTATTTATTTA
1 TATTATATATATTATTTA-TTA
14746005 TATTATA
1 TATTATA
14746012 CATTATTTTG
Statistics
Matches: 65, Mismatches: 13, Indels: 20
0.66 0.13 0.20
Matches are distributed among these distances:
17 8 0.12
18 5 0.08
19 2 0.03
20 8 0.12
21 25 0.38
22 7 0.11
23 8 0.12
24 2 0.03
ACGTcount: A:0.37, C:0.03, G:0.01, T:0.60
Consensus pattern (21 bp):
TATTATATATATTATTTATTA
Found at i:14745933 original size:16 final size:16
Alignment explanation
Indices: 14745900--14745930 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
14745890 CTTATTTTTA
14745900 ATTTATTATATATATT
1 ATTTATTATATATATT
14745916 ATTTATTATAT-TATT
1 ATTTATTATATATATT
14745931 TATATTTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
ATTTATTATATATATT
Found at i:14746032 original size:37 final size:37
Alignment explanation
Indices: 14745991--14746096 Score: 160
Period size: 37 Copynumber: 2.8 Consensus size: 37
14745981 ATATCTTATA
14745991 TATTTATTTATTTATATTATACATTATTTTGAAAACT
1 TATTTATTTATTTATATTATACATTATTTTGAAAACT
14746028 TATTTATTTATTTATATTATACATTATTTTGAAAACT
1 TATTTATTTATTTATATTATACATTATTTTGAAAACT
*
14746065 TACATTT-TTATATTATATATTATAAATTATTT
1 T--ATTTATT-TATT-TATATTATACATTATTT
14746097 CATTTATTAT
Statistics
Matches: 64, Mismatches: 1, Indels: 5
0.91 0.01 0.07
Matches are distributed among these distances:
37 38 0.59
38 2 0.03
39 8 0.12
40 16 0.25
ACGTcount: A:0.36, C:0.05, G:0.02, T:0.58
Consensus pattern (37 bp):
TATTTATTTATTTATATTATACATTATTTTGAAAACT
Found at i:14746435 original size:3 final size:3
Alignment explanation
Indices: 14746427--14746488 Score: 115
Period size: 3 Copynumber: 20.3 Consensus size: 3
14746417 TATGTTACTA
14746427 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
14746475 TAT TAT ATAT TAT T
1 TAT TAT -TAT TAT T
14746489 GTATTTGTTT
Statistics
Matches: 58, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
3 55 0.95
4 3 0.05
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:14750271 original size:31 final size:31
Alignment explanation
Indices: 14750230--14750293 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
14750220 CCTTTTCATA
*
14750230 TTTCATATTTCATAACACTGGGCCGAAGCCT
1 TTTCAAATTTCATAACACTGGGCCGAAGCCT
**
14750261 TTTCAAATTTCATATTACTGGGCCGAAGCCT
1 TTTCAAATTTCATAACACTGGGCCGAAGCCT
14750292 TT
1 TT
14750294 ACTGTAAACG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (31 bp):
TTTCAAATTTCATAACACTGGGCCGAAGCCT
Found at i:14750543 original size:24 final size:24
Alignment explanation
Indices: 14750485--14750626 Score: 191
Period size: 24 Copynumber: 6.0 Consensus size: 24
14750475 GCTTTATCAT
*
14750485 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
* *
14750510 ATAACT-GGGCAAAAGCCCTTTCA
1 ATAACTGGGGCATAAGCCCTTTTA
14750533 ATAACTGGGGCATAAGCCCTTTT-
1 ATAACTGGGGCATAAGCCCTTTTA
* *
14750556 ATAATTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
*
14750580 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
14750604 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
14750627 TCACTTCCTC
Statistics
Matches: 107, Mismatches: 7, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
23 36 0.34
24 65 0.61
25 6 0.06
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.30
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:14750567 original size:47 final size:48
Alignment explanation
Indices: 14750485--14750625 Score: 189
Period size: 47 Copynumber: 3.0 Consensus size: 48
14750475 GCTTTATCAT
* *
14750485 ATAACTGGAGGCCT-AGCCTCTTTTAATAACT-GGGCAAAAGCCCTTTCA
1 ATAACTGG-GGCATAAGCC-CTTTTAATAACTGGGGCATAAGCCCTTTCA
* **
14750533 ATAACTGGGGCATAAGCCCTTTT-ATAATTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTCA
*
14750580 ATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCCTTT
1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTT
14750626 TTCACTTCCT
Statistics
Matches: 84, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
46 5 0.06
47 46 0.55
48 33 0.39
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (48 bp):
ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTCA
Found at i:14750807 original size:25 final size:25
Alignment explanation
Indices: 14750775--14750822 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
14750765 ATACATAAAC
* * *
14750775 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
14750800 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
14750823 CATGGTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:14754939 original size:30 final size:31
Alignment explanation
Indices: 14754899--14754961 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 31
14754889 CCTTTTCATA
14754899 TTTCATATTTCATAACACTGGGCCGAAGCCT
1 TTTCATATTTCATAACACTGGGCCGAAGCCT
**
14754930 TTTCA-ATTTCATATTACTGGGCCGAAGCCT
1 TTTCATATTTCATAACACTGGGCCGAAGCCT
14754960 TT
1 TT
14754962 ACTGTAAACG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 25 0.83
31 5 0.17
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.37
Consensus pattern (31 bp):
TTTCATATTTCATAACACTGGGCCGAAGCCT
Found at i:14755204 original size:24 final size:24
Alignment explanation
Indices: 14755153--14755271 Score: 170
Period size: 24 Copynumber: 5.0 Consensus size: 24
14755143 GCTTTATCAT
*
14755153 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
* *
14755178 ATAACTGGGGCAAAAGCCCTTTCA
1 ATAACTGGGGCATAAGCCCTTTTA
14755202 ATAACTGGGGCATAAGCCCTTTT-
1 ATAACTGGGGCATAAGCCCTTTTA
*
14755225 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
14755249 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
14755272 TCACTTCCTC
Statistics
Matches: 87, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
23 23 0.26
24 52 0.60
25 12 0.14
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.29
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:14755232 original size:47 final size:48
Alignment explanation
Indices: 14755153--14755271 Score: 170
Period size: 47 Copynumber: 2.5 Consensus size: 48
14755143 GCTTTATCAT
*
14755153 ATAACTGGAGGCCT-AGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTCA
1 ATAACTGG-GGCATAAGCC-CTTTTAATAACTGGGGCAAAAGCCCTTTCA
* **
14755202 ATAACTGGGGCATAAGCCCTTTT-ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCAAAAGCCCTTTCA
14755249 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
14755272 TCACTTCCTC
Statistics
Matches: 65, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
47 44 0.68
48 9 0.14
49 12 0.18
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.29
Consensus pattern (48 bp):
ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCAAAAGCCCTTTCA
Found at i:14755352 original size:11 final size:11
Alignment explanation
Indices: 14755322--14755375 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
14755312 TATGATTACC
14755322 TCATGTGCATA
1 TCATGTGCATA
*
14755333 TCA--TACATA
1 TCATGTGCATA
14755342 TCATGTGCATA
1 TCATGTGCATA
*
14755353 TCA--TACAT-
1 TCATGTGCATA
14755361 TCATGTGCATA
1 TCATGTGCATA
14755372 TCAT
1 TCAT
14755376 ACATACCATA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
8 3 0.09
9 12 0.35
10 4 0.12
11 15 0.44
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.37
Consensus pattern (11 bp):
TCATGTGCATA
Found at i:14755366 original size:19 final size:20
Alignment explanation
Indices: 14755322--14755380 Score: 111
Period size: 19 Copynumber: 3.0 Consensus size: 20
14755312 TATGATTACC
14755322 TCATGTGCATATCATACATA
1 TCATGTGCATATCATACATA
14755342 TCATGTGCATATCATACAT-
1 TCATGTGCATATCATACATA
14755361 TCATGTGCATATCATACATA
1 TCATGTGCATATCATACATA
14755381 CCATATTTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
19 19 0.50
20 19 0.50
ACGTcount: A:0.34, C:0.20, G:0.10, T:0.36
Consensus pattern (20 bp):
TCATGTGCATATCATACATA
Done.