Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr6
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: 44797108
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 921406 characters in sequence are not A, C, G, or T
File 14 of 144
Found at i:3516667 original size:35 final size:35
Alignment explanation
Indices: 3516628--3516696 Score: 120
Period size: 35 Copynumber: 2.0 Consensus size: 35
3516618 ACTTGCCTCT
*
3516628 TCCCACTCTCCCATGCTGTCTGCCACCAACACCAC
1 TCCCACCCTCCCATGCTGTCTGCCACCAACACCAC
*
3516663 TCCCACCCTCCCATGCTGTCTGCCACCAGCACCA
1 TCCCACCCTCCCATGCTGTCTGCCACCAACACCA
3516697 TCACACACCC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.19, C:0.52, G:0.10, T:0.19
Consensus pattern (35 bp):
TCCCACCCTCCCATGCTGTCTGCCACCAACACCAC
Found at i:3516723 original size:34 final size:35
Alignment explanation
Indices: 3516635--3516724 Score: 94
Period size: 35 Copynumber: 2.6 Consensus size: 35
3516625 TCTTCCCACT
* * *
3516635 CTCCCATGCTGTCTGCCACCAACACCACTCCCACC
1 CTCCCATACCGTCTGCCACCAACACCACTCACACC
* * *
3516670 CTCCCATGCTGTCTGCCACCAGCACCA-TCACACAC
1 CTCCCATACCGTCTGCCACCAACACCACTCACAC-C
*
3516705 C-CCCATACCGTCTACCACCA
1 CTCCCATACCGTCTGCCACCA
3516725 CCATGCCTTT
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
34 21 0.43
35 28 0.57
ACGTcount: A:0.22, C:0.52, G:0.09, T:0.17
Consensus pattern (35 bp):
CTCCCATACCGTCTGCCACCAACACCACTCACACC
Found at i:3517228 original size:11 final size:11
Alignment explanation
Indices: 3517214--3517247 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
3517204 CCCTTCCCCT
3517214 TCCCTTCTCTC
1 TCCCTTCTCTC
3517225 TCCCTTCTCTC
1 TCCCTTCTCTC
3517236 TTCCC-TCTCTC
1 -TCCCTTCTCTC
3517247 T
1 T
3517248 TCTTTTTTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 1 0.05
11 17 0.77
12 4 0.18
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (11 bp):
TCCCTTCTCTC
Found at i:3517230 original size:22 final size:22
Alignment explanation
Indices: 3517204--3517247 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
3517194 GGCCGGATTC
3517204 CCCTTC-CCCTTCCCTTCTCTCT
1 CCCTTCTCCCTTCCC-TCTCTCT
*
3517226 CCCTTCTCTCTTCCCTCTCTCT
1 CCCTTCTCCCTTCCCTCTCTCT
3517248 TCTTTTTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.00, C:0.57, G:0.00, T:0.43
Consensus pattern (22 bp):
CCCTTCTCCCTTCCCTCTCTCT
Found at i:3517248 original size:11 final size:11
Alignment explanation
Indices: 3517212--3517249 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
3517202 TCCCCTTCCC
3517212 CTTCCCT-TCT
1 CTTCCCTCTCT
3517222 CTCTCCCTTCTCT
1 CT-TCCC-TCTCT
3517235 CTTCCCTCTCT
1 CTTCCCTCTCT
3517246 CTTC
1 CTTC
3517250 TTTTTTTCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
10 2 0.08
11 13 0.52
12 5 0.20
13 5 0.20
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (11 bp):
CTTCCCTCTCT
Found at i:3531054 original size:29 final size:28
Alignment explanation
Indices: 3531022--3531107 Score: 82
Period size: 31 Copynumber: 2.9 Consensus size: 28
3531012 GTTTTTTATT
3531022 TAATTTGATATATAAATTTTAATTTGGTG
1 TAATTT-ATATATAAATTTTAATTTGGTG
* * *
3531051 TAATTATACATATGAAATTTTAGTTGTGGTT
1 TAATT-TATATAT-AAATTTTAATT-TGGTG
*
3531082 TACATGTATATATTAAATTTTAATTT
1 TA-ATTTATATA-TAAATTTTAATTT
3531108 TGATTTAATC
Statistics
Matches: 46, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
29 10 0.22
30 12 0.26
31 21 0.46
32 3 0.07
ACGTcount: A:0.35, C:0.02, G:0.12, T:0.51
Consensus pattern (28 bp):
TAATTTATATATAAATTTTAATTTGGTG
Found at i:3531593 original size:31 final size:31
Alignment explanation
Indices: 3531515--3531596 Score: 101
Period size: 31 Copynumber: 2.6 Consensus size: 31
3531505 AATGTACAAA
* *
3531515 TTGAATCAAAATCAAAATTTTATATATACAT
1 TTGAATCACAATCAAAGTTTTATATATACAT
* * * *
3531546 TGGAATCGCAATCAAAGTTTTATTTATATAT
1 TTGAATCACAATCAAAGTTTTATATATACAT
*
3531577 TTGAATTACAATCAAAGTTT
1 TTGAATCACAATCAAAGTTT
3531597 CATGTGTATA
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.41, C:0.10, G:0.09, T:0.40
Consensus pattern (31 bp):
TTGAATCACAATCAAAGTTTTATATATACAT
Found at i:3531643 original size:29 final size:30
Alignment explanation
Indices: 3531586--3531643 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
3531576 TTTGAATTAC
*
3531586 AATCAAAGTTTCATGTGTATAATTGCACAA
1 AATCAAAGTTTCATGTGTATAATCGCACAA
*
3531616 AATCAAAGTTT-ATGTAT-TAAATCGCACA
1 AATCAAAGTTTCATGTGTAT-AATCGCACA
3531644 TTGAATCAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 1 0.04
29 13 0.52
30 11 0.44
ACGTcount: A:0.41, C:0.14, G:0.12, T:0.33
Consensus pattern (30 bp):
AATCAAAGTTTCATGTGTATAATCGCACAA
Found at i:3532118 original size:28 final size:28
Alignment explanation
Indices: 3532086--3532142 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
3532076 ACTTAATATT
* * * *
3532086 AGAGGTTTTGATGTAAAATTATATTTTA
1 AGAGGGTTTGACGAAAAATTACATTTTA
3532114 AGAGGGTTTGACGAAAAATTACATTTTA
1 AGAGGGTTTGACGAAAAATTACATTTTA
3532142 A
1 A
3532143 AAATTCAATT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.39, C:0.04, G:0.19, T:0.39
Consensus pattern (28 bp):
AGAGGGTTTGACGAAAAATTACATTTTA
Found at i:3542528 original size:28 final size:29
Alignment explanation
Indices: 3542496--3542551 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
3542486 TAACATTTAA
*
3542496 AAGA-TGATTTTTTTTTTCTGTAAGACTG
1 AAGAGTGATTTTCTTTTTCTGTAAGACTG
*
3542524 AAGATGTGATTTTCTTTTTCTTTAAGAC
1 AAGA-GTGATTTTCTTTTTCTGTAAGAC
3542552 AGAATGCATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 4 0.17
30 20 0.83
ACGTcount: A:0.25, C:0.09, G:0.16, T:0.50
Consensus pattern (29 bp):
AAGAGTGATTTTCTTTTTCTGTAAGACTG
Found at i:3549358 original size:77 final size:77
Alignment explanation
Indices: 3549267--3549412 Score: 256
Period size: 77 Copynumber: 1.9 Consensus size: 77
3549257 TCCCATCAGT
* * *
3549267 ACTACATGCACATAAGTGCATTCACTATTCCATGCAATATCTCATTTGTCACATGCATTACGAAC
1 ACTACATGCACATAAATGCATTCACTATTCCATGCAATATCTCATATGTCACAGGCATTACGAAC
3549332 CTGGTCCCCATC
66 CTGGTCCCCATC
*
3549344 ACTACATGCACATAAATGCATTCATTATTCCATGCAATATCTCATATGTCACAGGCATTACGAAC
1 ACTACATGCACATAAATGCATTCACTATTCCATGCAATATCTCATATGTCACAGGCATTACGAAC
3549409 CTGG
66 CTGG
3549413 ACCATCATCT
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
77 65 1.00
ACGTcount: A:0.31, C:0.27, G:0.12, T:0.29
Consensus pattern (77 bp):
ACTACATGCACATAAATGCATTCACTATTCCATGCAATATCTCATATGTCACAGGCATTACGAAC
CTGGTCCCCATC
Found at i:3556129 original size:50 final size:50
Alignment explanation
Indices: 3556015--3556134 Score: 143
Period size: 50 Copynumber: 2.4 Consensus size: 50
3556005 TTAAGGGAAT
* * *
3556015 GAGATCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGA
1 GAGACCCCATGTAAGACCATGTCTGGGACATGGCATCGGCACCGAGATGA
* ** * *
3556065 GAGGCCCCCCGTAAGACTATGTCTGGGACATGGCATCGGCACCGATATGA
1 GAGACCCCATGTAAGACCATGTCTGGGACATGGCATCGGCACCGAGATGA
*
3556115 GA-ACTCTCATGTAAGACCAT
1 GAGAC-CCCATGTAAGACCAT
3556135 ACCTGAGAAC
Statistics
Matches: 56, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
49 1 0.02
50 55 0.98
ACGTcount: A:0.27, C:0.25, G:0.28, T:0.20
Consensus pattern (50 bp):
GAGACCCCATGTAAGACCATGTCTGGGACATGGCATCGGCACCGAGATGA
Found at i:3557873 original size:16 final size:15
Alignment explanation
Indices: 3557821--3557874 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 15
3557811 TGGTTCGCTA
*
3557821 TAATGGAATAGAGGTG
1 TAATAGAATAGAGG-G
3557837 TAAT-GAAATAGATGGG
1 TAATAG-AATAGA-GGG
3557853 TAATAGAATAGAGGCG
1 TAATAGAATAGAGG-G
3557869 TAATAG
1 TAATAG
3557875 GTAATTCTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
15 3 0.09
16 28 0.82
17 3 0.09
ACGTcount: A:0.43, C:0.02, G:0.31, T:0.24
Consensus pattern (15 bp):
TAATAGAATAGAGGG
Found at i:3557943 original size:44 final size:46
Alignment explanation
Indices: 3557858--3557946 Score: 128
Period size: 44 Copynumber: 2.0 Consensus size: 46
3557848 ATGGGTAATA
*
3557858 GAATAGAGGCGTAATAGGTAATTCTTTTGTTTGATTAAATGGAATG
1 GAATAGAGGCGTAATAGGTAATTCTTGTGTTTGATTAAATGGAATG
* * *
3557904 GAATAGAGGTGTAATA-GT-ATTCTTGTGTTTGGTTGAATGGAAT
1 GAATAGAGGCGTAATAGGTAATTCTTGTGTTTGATTAAATGGAAT
3557947 AGAGGTGTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
44 22 0.56
45 2 0.05
46 15 0.38
ACGTcount: A:0.30, C:0.03, G:0.28, T:0.38
Consensus pattern (46 bp):
GAATAGAGGCGTAATAGGTAATTCTTGTGTTTGATTAAATGGAATG
Found at i:3558213 original size:23 final size:21
Alignment explanation
Indices: 3558169--3558209 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
3558159 TATATGAATT
3558169 TACTAAAATCATAATATATAA
1 TACTAAAATCATAATATATAA
3558190 TACTAAAATCATAATATATA
1 TACTAAAATCATAATATATA
3558210 TAATTTAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.56, C:0.10, G:0.00, T:0.34
Consensus pattern (21 bp):
TACTAAAATCATAATATATAA
Found at i:3571674 original size:25 final size:25
Alignment explanation
Indices: 3571645--3571694 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
3571635 TTAGAATTAA
3571645 TTTTCTTT-TCATT-TTTCTACTTTTC
1 TTTTCTTTCT-ATTCTTTC-ACTTTTC
3571670 TTTTCTTTCTATTCTTTCACTTTTC
1 TTTTCTTTCTATTCTTTCACTTTTC
3571695 CACTCTACCC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 18 0.78
26 5 0.22
ACGTcount: A:0.08, C:0.22, G:0.00, T:0.70
Consensus pattern (25 bp):
TTTTCTTTCTATTCTTTCACTTTTC
Found at i:3573079 original size:24 final size:24
Alignment explanation
Indices: 3573052--3573119 Score: 68
Period size: 24 Copynumber: 2.9 Consensus size: 24
3573042 ATCTTTTAAT
3573052 ATAATAATTATTAAATATAATTTA
1 ATAATAATTATTAAATATAATTTA
* * ** *
3573076 ATAAAAATAACCATATATAATTTA
1 ATAATAATTATTAAATATAATTTA
*
3573100 ATAAT-ATT-TTTAATATAATT
1 ATAATAATTATTAAATATAATT
3573120 ATTTTTTAAA
Statistics
Matches: 33, Mismatches: 11, Indels: 2
0.72 0.24 0.04
Matches are distributed among these distances:
22 8 0.24
23 2 0.06
24 23 0.70
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (24 bp):
ATAATAATTATTAAATATAATTTA
Found at i:3573122 original size:59 final size:59
Alignment explanation
Indices: 3572999--3573118 Score: 143
Period size: 59 Copynumber: 2.0 Consensus size: 59
3572989 TAACAGGATT
* * *
3572999 ATTATTAAAAATAATTTAATAATAAATAATAAATAAATTAGTCATCTTTTAATATAATA
1 ATTATTAAAAATAATTTAATAATAAATAATAAATAAATTAATAATATTTTAATATAATA
* * *
3573058 ATTATTAAATATAATTTAATAA-AAATAACCATATATAATTTAATAATATTTTTAATATAAT
1 ATTATTAAAAATAATTTAATAATAAAT-A--ATAAATAAATTAATAATA-TTTTAATATAAT
3573119 TATTTTTTAA
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
58 4 0.08
59 22 0.43
61 13 0.25
62 12 0.24
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.42
Consensus pattern (59 bp):
ATTATTAAAAATAATTTAATAATAAATAATAAATAAATTAATAATATTTTAATATAATA
Found at i:3577007 original size:18 final size:17
Alignment explanation
Indices: 3576984--3577020 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
3576974 TACATATTAC
3576984 ATAAATAAAAATAATATT
1 ATAAATAAAAATAAT-TT
*
3577002 ATAAATAAAATTAATTT
1 ATAAATAAAAATAATTT
3577019 AT
1 AT
3577021 CGGTATCTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
ATAAATAAAAATAATTT
Found at i:3585937 original size:15 final size:15
Alignment explanation
Indices: 3585917--3585967 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 15
3585907 ATAACACGAT
3585917 AACGTAAGTAACTAA
1 AACGTAAGTAACTAA
* *
3585932 AACGTAA-TATCTCA
1 AACGTAAGTAACTAA
* *
3585946 AACATAAGTGACTAA
1 AACGTAAGTAACTAA
*
3585961 AATGTAA
1 AACGTAA
3585968 TATGAGAAAA
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
14 11 0.41
15 16 0.59
ACGTcount: A:0.51, C:0.14, G:0.12, T:0.24
Consensus pattern (15 bp):
AACGTAAGTAACTAA
Found at i:3586371 original size:58 final size:58
Alignment explanation
Indices: 3586213--3586373 Score: 162
Period size: 58 Copynumber: 2.7 Consensus size: 58
3586203 TTTTAGGGCT
* * * * * * *
3586213 TGAACTTGATAATTATTCTCATATTGGGGTTTGAACTTTTTTAGGGTTCAAGTTAGACTC
1 TGAACTTGATAATTGTTCCCACATTGAGGCTTGAACTTTTTT--TGTTCAAGTTAGACCC
* ** * * * *
3586273 TAAACTTGGCAATTGTTTCCACATTAAGGCCT-AAGTTTTTTTTGTTCAAGTTAGACCC
1 TGAACTTGATAATTGTTCCCACATTGAGGCTTGAA-CTTTTTTTGTTCAAGTTAGACCC
3586331 TGAACTTGATAATTGTTCCCACATTGAGGCTTGAACTTTTTTT
1 TGAACTTGATAATTGTTCCCACATTGAGGCTTGAACTTTTTTT
3586374 CATCCAAGTT
Statistics
Matches: 78, Mismatches: 21, Indels: 6
0.74 0.20 0.06
Matches are distributed among these distances:
58 47 0.60
59 4 0.05
60 27 0.35
ACGTcount: A:0.25, C:0.16, G:0.17, T:0.42
Consensus pattern (58 bp):
TGAACTTGATAATTGTTCCCACATTGAGGCTTGAACTTTTTTTGTTCAAGTTAGACCC
Found at i:3588169 original size:3 final size:3
Alignment explanation
Indices: 3588161--3588191 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
3588151 TCAATTGTCT
3588161 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
3588192 GGGTTTTTAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:3603181 original size:21 final size:21
Alignment explanation
Indices: 3603155--3603195 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3603145 ATCTGCTCAA
* *
3603155 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
3603176 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
3603196 TTGCTCGTCT
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:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:3607601 original size:3 final size:3
Alignment explanation
Indices: 3607593--3607627 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
3607583 TGACGTTGGG
3607593 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
3607628 TGATGATGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:3609114 original size:16 final size:16
Alignment explanation
Indices: 3609093--3609126 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3609083 AGGGTCTAAA
* *
3609093 GAAAATTTGAAGGATT
1 GAAAATTGGAAAGATT
3609109 GAAAATTGGAAAGATT
1 GAAAATTGGAAAGATT
3609125 GA
1 GA
3609127 TGAAATTTTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.47, C:0.00, G:0.26, T:0.26
Consensus pattern (16 bp):
GAAAATTGGAAAGATT
Found at i:3627100 original size:40 final size:40
Alignment explanation
Indices: 3627045--3627122 Score: 129
Period size: 40 Copynumber: 1.9 Consensus size: 40
3627035 AAGAGAGAAT
*
3627045 GAAAATAACTTTATTAAATCCAAATGATACCTTGAAAAAC
1 GAAAATAACTTTATTAAATCCAAATGATAACTTGAAAAAC
* *
3627085 GAAAATCACTTTATTAAATCTAAATGATAACTTGAAAA
1 GAAAATAACTTTATTAAATCCAAATGATAACTTGAAAA
3627123 TTCTTTTAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.50, C:0.13, G:0.08, T:0.29
Consensus pattern (40 bp):
GAAAATAACTTTATTAAATCCAAATGATAACTTGAAAAAC
Found at i:3627117 original size:22 final size:22
Alignment explanation
Indices: 3627049--3627117 Score: 56
Period size: 20 Copynumber: 3.3 Consensus size: 22
3627039 GAGAATGAAA
3627049 ATAACTTTATTAAATCCAAATG
1 ATAACTTTATTAAATCCAAATG
* * * *
3627071 ATACCTTGA--AAAACGAAA--
1 ATAACTTTATTAAATCCAAATG
* *
3627089 ATCACTTTATTAAATCTAAATG
1 ATAACTTTATTAAATCCAAATG
3627111 ATAACTT
1 ATAACTT
3627118 GAAAATTCTT
Statistics
Matches: 33, Mismatches: 10, Indels: 8
0.65 0.20 0.16
Matches are distributed among these distances:
18 6 0.18
20 14 0.42
22 13 0.39
ACGTcount: A:0.46, C:0.14, G:0.06, T:0.33
Consensus pattern (22 bp):
ATAACTTTATTAAATCCAAATG
Found at i:3629384 original size:5 final size:5
Alignment explanation
Indices: 3629374--3629407 Score: 59
Period size: 5 Copynumber: 6.6 Consensus size: 5
3629364 TGGCGGAGCT
3629374 GTGGC GTGGC GTGGC GTGGC GTGGC GTGGGC GTG
1 GTGGC GTGGC GTGGC GTGGC GTGGC GT-GGC GTG
3629408 TCGACTGCAG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 23 0.82
6 5 0.18
ACGTcount: A:0.00, C:0.18, G:0.62, T:0.21
Consensus pattern (5 bp):
GTGGC
Found at i:3630903 original size:19 final size:20
Alignment explanation
Indices: 3630876--3630915 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
3630866 AAATTGATAT
3630876 AAACTTATAAATATT-ATAAA
1 AAACTTATAAAT-TTAATAAA
3630896 AAAC-TATAAATTTAATAAA
1 AAACTTATAAATTTAATAAA
3630915 A
1 A
3630916 TTTATTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 2 0.11
19 13 0.68
20 4 0.21
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (20 bp):
AAACTTATAAATTTAATAAA
Found at i:3631598 original size:16 final size:16
Alignment explanation
Indices: 3631547--3631606 Score: 57
Period size: 17 Copynumber: 3.6 Consensus size: 16
3631537 TAAAATAACC
3631547 AAAATAAAAAATAAAA
1 AAAATAAAAAATAAAA
* * *
3631563 TAAAATAAACATTAAGA
1 -AAAATAAAAAATAAAA
*
3631580 AAAATAAATAATAATAA
1 AAAATAAAAAATAA-AA
3631597 AATAATAAAA
1 AA-AATAAAA
3631607 TGGCACTAAA
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
16 12 0.35
17 16 0.47
18 6 0.18
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.20
Consensus pattern (16 bp):
AAAATAAAAAATAAAA
Found at i:3631871 original size:9 final size:9
Alignment explanation
Indices: 3631869--3631924 Score: 64
Period size: 9 Copynumber: 6.4 Consensus size: 9
3631859 AAAATAATAA
3631869 AAAAATTAT
1 AAAAATTAT
*
3631878 TAAAA-TAT
1 AAAAATTAT
3631886 -AAAATTAT
1 AAAAATTAT
*
3631894 TAAAA-TAT
1 AAAAATTAT
3631902 ATAAAATTAT
1 A-AAAATTAT
3631912 AAAAATTAT
1 AAAAATTAT
3631921 AAAA
1 AAAA
3631925 TATATATTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
7 4 0.10
8 9 0.22
9 24 0.59
10 4 0.10
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (9 bp):
AAAAATTAT
Found at i:3631891 original size:16 final size:16
Alignment explanation
Indices: 3631870--3631925 Score: 76
Period size: 17 Copynumber: 3.3 Consensus size: 16
3631860 AAATAATAAA
3631870 AAAATTATTAAAATAT
1 AAAATTATTAAAATAT
3631886 AAAATTATTAAAATATAT
1 AAAATTATT-AAA-ATAT
*
3631904 AAAATTATAAAAATTAT
1 AAAATTATTAAAA-TAT
3631921 AAAAT
1 AAAAT
3631926 ATATATTTTA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
16 10 0.28
17 14 0.39
18 12 0.33
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
AAAATTATTAAAATAT
Found at i:3631912 original size:26 final size:25
Alignment explanation
Indices: 3631870--3631930 Score: 81
Period size: 26 Copynumber: 2.4 Consensus size: 25
3631860 AAATAATAAA
3631870 AAAAT-TATTAAAATAT-AAAATTATT
1 AAAATATA-TAAAATATAAAAATTA-T
3631895 AAAATATATAAAATTATAAAAATTAT
1 AAAATATATAAAA-TATAAAAATTAT
3631921 AAAATATATA
1 AAAATATATA
3631931 TTTTAATAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
25 10 0.30
26 16 0.48
27 7 0.21
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (25 bp):
AAAATATATAAAATATAAAAATTAT
Found at i:3631958 original size:19 final size:19
Alignment explanation
Indices: 3631931--3631971 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
3631921 AAAATATATA
*
3631931 TTTTAATAATATTTATCAG
1 TTTTAATAATATTTATAAG
* *
3631950 TTTTTATAATTTTTATAAG
1 TTTTAATAATATTTATAAG
3631969 TTT
1 TTT
3631972 ATATCAAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (19 bp):
TTTTAATAATATTTATAAG
Found at i:3638022 original size:3 final size:3
Alignment explanation
Indices: 3638014--3638094 Score: 67
Period size: 3 Copynumber: 26.0 Consensus size: 3
3638004 AAAATAAAAC
* *
3638014 TAA TAA TAA TTAA TAA TGA TAA TAA TAG TAA TAA TAA TAA TAA TAAA
1 TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA
* *
3638061 TGA TAA TACA TTAA -AA TAA TTAA CAA -AA TAA TAA
1 TAA TAA TA-A -TAA TAA TAA -TAA TAA TAA TAA TAA
3638095 GACTGCTAAA
Statistics
Matches: 64, Mismatches: 7, Indels: 14
0.75 0.08 0.16
Matches are distributed among these distances:
2 4 0.06
3 47 0.73
4 11 0.17
5 2 0.03
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:3638876 original size:14 final size:14
Alignment explanation
Indices: 3638857--3638883 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3638847 ATGTAAAAGA
3638857 TAAAATAAAATAAG
1 TAAAATAAAATAAG
3638871 TAAAATAAAATAA
1 TAAAATAAAATAA
3638884 ACAAGCAGAA
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:0.74, C:0.00, G:0.04, T:0.22
Consensus pattern (14 bp):
TAAAATAAAATAAG
Found at i:3640778 original size:44 final size:44
Alignment explanation
Indices: 3640720--3640819 Score: 128
Period size: 44 Copynumber: 2.3 Consensus size: 44
3640710 GGTGGCTTAA
* * * * *
3640720 ATCTGCTTCACTACTGCTTAGGAAGATGAGATTTGCCATTTTCG
1 ATCTGCTCCACTACTGCTTAGGAAGATAAGATCTACCATCTTCG
* *
3640764 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACTATCTTCG
1 ATCTGCTCCACTACTGCTTAGGAAGATAAGATCTACCATCTTCG
*
3640808 ACCTGCTCCACT
1 ATCTGCTCCACT
3640820 GTAACCTCAG
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
44 48 1.00
ACGTcount: A:0.23, C:0.26, G:0.18, T:0.33
Consensus pattern (44 bp):
ATCTGCTCCACTACTGCTTAGGAAGATAAGATCTACCATCTTCG
Found at i:3641131 original size:44 final size:44
Alignment explanation
Indices: 3640760--3641594 Score: 411
Period size: 44 Copynumber: 18.8 Consensus size: 44
3640750 ATTTGCCATT
* * ** *
3640760 TTCGATCTGCTCCACTACT-GCTT-AGGGAGATAAGATCTACTATC
1 TTCGATCTGCTCCACT-GTAACTTCAGGGAGATAAGAT-TTGTGTC
* * *
3640804 TTCGACCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAAT-TC
1 TTCGATCTGCTCCACTGTAACTTCAGGGAGATAAGATTTG---TGTC
* * *
3640850 TTCGGTTTACTCCACTGTAACCTT-AGGGAGATAAGA-TT-TGT-
1 TTCGATCTGCTCCACTGTAA-CTTCAGGGAGATAAGATTTGTGTC
* * * * * *
3640891 TGCGATCTACTCTACTGTAACTTCAGAGAGATGAGATCCTT-TAT-
1 TTCGATCTGCTCCACTGTAACTTCAGGGAGATAAGAT--TTGTGTC
** * * * **
3640935 TTTAATCCGCTCCACTGTAACTTTAGGGAGATAGGATTACTAG-C
1 TTCGATCTGCTCCACTGTAACTTCAGGGAGATAAGATTTGT-GTC
* * * *
3640979 TCCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAAT-TC
1 TTCGATCTGCTCCACTGTAACTTCAGGGAGATAAGATTTG---TGTC
* ** * * ** *
3641025 TTCGGTCCACTCCACTGTAACCTCAGGGAGATAAGACTTGCATA
1 TTCGATCTGCTCCACTGTAACTTCAGGGAGATAAGATTTGTGTC
* * * * *
3641069 TTCAACCTGC-CCTACTGTAACTTTAGGGAGATAAGGTTTGTGGC
1 TTCGATCTGCTCC-ACTGTAACTTCAGGGAGATAAGATTTGTGTC
* * * * *
3641113 TTCGATCTGCTCCTCTGTAA-TCTCACGGAGATAAGATCTCTGGC
1 TTCGATCTGCTCCACTGTAACT-TCAGGGAGATAAGATTTGTGTC
* * * *
3641157 TTCAACCTGCTCCACTGTAACCTCAGGGAGATAAGAATTGAAAT-TC
1 TTCGATCTGCTCCACTGTAACTTCAGGGAGATAAGATTTG---TGTC
* * ***
3641203 TTCGGTCTACTCCACTGTAA-TCTCAGGGAGATAAGACCTAAAAT-TC
1 TTCGATCTGCTCCACTGTAACT-TCAGGGAGATAAGA--T-TTGTGTC
* * * * ** *
3641249 TTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGACTTGCATA
1 TTCGATCTGCTCCACTGTAACTTCAGGGAGATAAGATTTGTGTC
* * * * * * *
3641293 TTCAACCTGCCCCACTGTAACTTCAGGGAAATAAGGTTCGTGGC
1 TTCGATCTGCTCCACTGTAACTTCAGGGAGATAAGATTTGTGTC
* *
3641337 TTCGATCTGCTCCTCTGTAA-TCTCAGGGAGATAAGATCTGAAAT-TC
1 TTCGATCTGCTCCACTGTAACT-TCAGGGAGATAAGATTTG---TGTC
* * * ** *
3641383 TTCGGTCTACTCCACTGTAA-TCTCAGGGAGATAAGACTTGCATA
1 TTCGATCTGCTCCACTGTAACT-TCAGGGAGATAAGATTTGTGTC
* * * * *
3641427 TTCAACCTGCCCCACTGTAACTTCAGGGAGATAAGGTTTGTGGC
1 TTCGATCTGCTCCACTGTAACTTCAGGGAGATAAGATTTGTGTC
** * * *
3641471 TTCGATCTGCTCTTCTGTAACTTCAGAGAGATAGGATCCTT-TAT-
1 TTCGATCTGCTCCACTGTAACTTCAGGGAGATAAGAT--TTGTGTC
** * * *
3641515 TTTAATCTGCTCCACTATAACTTCAGGGAGATAGGA-TAGTGTC
1 TTCGATCTGCTCCACTGTAACTTCAGGGAGATAAGATTTGTGTC
*
3641558 TTCGATCTGCTCCGCTGTAA-TCTCAGGGAGATAAGAT
1 TTCGATCTGCTCCACTGTAACT-TCAGGGAGATAAGAT
3641595 CTCTGACTCT
Statistics
Matches: 587, Mismatches: 160, Indels: 88
0.70 0.19 0.11
Matches are distributed among these distances:
40 3 0.01
41 28 0.05
42 5 0.01
43 35 0.06
44 322 0.55
45 18 0.03
46 170 0.29
47 6 0.01
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.30
Consensus pattern (44 bp):
TTCGATCTGCTCCACTGTAACTTCAGGGAGATAAGATTTGTGTC
Found at i:3641397 original size:134 final size:134
Alignment explanation
Indices: 3641202--3641508 Score: 499
Period size: 134 Copynumber: 2.3 Consensus size: 134
3641192 AATTGAAATT
* * * *
3641202 CTTCGGTCTACTCCACTGTAATCTCAGGGAGATAAGACCTAAAATTCTTCGGTCTACTCCACTGT
1 CTTCGATCTGCTCCTCTGTAATCTCAGGGAGATAAGATCTAAAATTCTTCGGTCTACTCCACTGT
3641267 AACCTCAGGGAGATAAGACTTGCATATTCAACCTGCCCCACTGTAACTTCAGGGAAATAAGGTTC
66 AACCTCAGGGAGATAAGACTTGCATATTCAACCTGCCCCACTGTAACTTCAGGGAAATAAGGTTC
3641332 GTGG
131 GTGG
*
3641336 CTTCGATCTGCTCCTCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTACTCCACTGT
1 CTTCGATCTGCTCCTCTGTAATCTCAGGGAGATAAGATCTAAAATTCTTCGGTCTACTCCACTGT
* * *
3641401 AATCTCAGGGAGATAAGACTTGCATATTCAACCTGCCCCACTGTAACTTCAGGGAGATAAGGTTT
66 AACCTCAGGGAGATAAGACTTGCATATTCAACCTGCCCCACTGTAACTTCAGGGAAATAAGGTTC
3641466 GTGG
131 GTGG
* * *
3641470 CTTCGATCTGCTCTTCTGTAA-CTTCAGAGAGATAGGATC
1 CTTCGATCTGCTCCTCTGTAATC-TCAGGGAGATAAGATC
3641509 CTTTATTTTA
Statistics
Matches: 161, Mismatches: 11, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
133 1 0.01
134 160 0.99
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (134 bp):
CTTCGATCTGCTCCTCTGTAATCTCAGGGAGATAAGATCTAAAATTCTTCGGTCTACTCCACTGT
AACCTCAGGGAGATAAGACTTGCATATTCAACCTGCCCCACTGTAACTTCAGGGAAATAAGGTTC
GTGG
Found at i:3641412 original size:358 final size:350
Alignment explanation
Indices: 3640785--3641594 Score: 1010
Period size: 358 Copynumber: 2.3 Consensus size: 350
3640775 TACTGCTTAG
* *
3640785 GGAGATAAGATCTACTATCTTCGACCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTC
1 GGAGATAAGATCT-CTAACTTCAACCTGCTCCACTGTAACCTCAGGGAGATAAGAT-TGAAATTC
* * * * * *
3640850 TTCGGTTTACTCCACTGTAACCTTAGGGAGATAAGATTTGTTGCGATCTACTCTACTGTAACTTC
64 TTCGGTCTACTCCACTGTAATCTCAGGGAGATAAGATTTCTTGCGATCTACTCCACTGTAACCTC
* * * * * *
3640915 AGAGAGATGAGATCCTTTATTTTAATCCGCTCCACTGTAACTTTAGGGAGATAGGATTACTAGCT
129 AGAGAGATAAGA-CCTTCATTTCAATCCGCCCCACTGTAACTTCAGGGAAATAGGATTACTAGCT
3640980 CCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTTCGGTCCACTCCACTGTAA
193 CCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTTCGGTCCACTCCACTGTAA
* *
3641045 CCTCAGGGAGATAAGACTTGCATATTCAACCTGCCCTACTGTAACTTTAGGGAGATAAGGTTTGT
258 CCTCAGGGAGATAAGACTTGCATATTCAACCTGCCCCACTGTAACTTCAGGGAGATAAGGTTTGT
3641110 GGCTTCGATCTGCTCCTCTGTAA-TCTCA
323 GGCTTCGATCTGCTCCTCTGTAACT-TCA
**
3641138 CGGAGATAAGATCTCTGGCTTCAACCTGCTCCACTGTAACCTCAGGGAGATAAGAATTGAAATTC
1 -GGAGATAAGATCTCTAACTTCAACCTGCTCCACTGTAACCTCAGGGAGATAAG-ATTGAAATTC
*
3641203 TTCGGTCTACTCCACTGTAATCTCAGGGAGATAAGACCTAAAATTCTT-CGGTCTACTCCACTGT
64 TTCGGTCTACTCCACTGTAATCTCAGGGAGATAAGA--T----TTCTTGCGATCTACTCCACTGT
*
3641267 AACCTCAGGGAGATAAGA-CTTGCATATTCAA-CCTGCCCCACTGTAACTTCAGGGAAATAAGG-
123 AACCTCAGAGAGATAAGACCTT-CAT-TTCAATCC-GCCCCACTGTAACTTCAGGGAAAT-AGGA
* * * * * *
3641329 TT-CGTGGCTTCGATCTGCTCCTCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTAC
184 TTAC-TAGCTCCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTTCGGTCCAC
*
3641393 TCCACTGTAATCTCAGGGAGATAAGACTTGCATATTCAACCTGCCCCACTGTAACTTCAGGGAGA
248 TCCACTGTAACCTCAGGGAGATAAGACTTGCATATTCAACCTGCCCCACTGTAACTTCAGGGAGA
*
3641458 TAAGGTTTGTGGCTTCGATCTGCTCTTCTGTAACTTCA
313 TAAGGTTTGTGGCTTCGATCTGCTCCTCTGTAACTTCA
* * * * * * * * *
3641496 GAGAGATAGGATC-CTTTATTTTAATCTGCTCCACTATAACTTCAGGGAGATAGGA-T--AGTGT
1 G-GAGATAAGATCTC-TAACTTCAACCTGCTCCACTGTAACCTCAGGGAGATAAGATTGAAAT-T
* * *
3641557 CTTCGATCTGCTCCGCTGTAATCTCAGGGAGATAAGAT
63 CTTCGGTCTACTCCACTGTAATCTCAGGGAGATAAGAT
3641595 CTCTGACTCT
Statistics
Matches: 400, Mismatches: 40, Indels: 33
0.85 0.08 0.07
Matches are distributed among these distances:
353 79 0.20
354 17 0.04
355 36 0.09
356 4 0.01
357 8 0.02
358 248 0.62
359 8 0.02
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (350 bp):
GGAGATAAGATCTCTAACTTCAACCTGCTCCACTGTAACCTCAGGGAGATAAGATTGAAATTCTT
CGGTCTACTCCACTGTAATCTCAGGGAGATAAGATTTCTTGCGATCTACTCCACTGTAACCTCAG
AGAGATAAGACCTTCATTTCAATCCGCCCCACTGTAACTTCAGGGAAATAGGATTACTAGCTCCA
ATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTTCGGTCCACTCCACTGTAACCT
CAGGGAGATAAGACTTGCATATTCAACCTGCCCCACTGTAACTTCAGGGAGATAAGGTTTGTGGC
TTCGATCTGCTCCTCTGTAACTTCA
Found at i:3642897 original size:13 final size:13
Alignment explanation
Indices: 3642879--3642903 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3642869 TTAGCCTCTC
3642879 CATTTTTCATTTT
1 CATTTTTCATTTT
3642892 CATTTTTCATTT
1 CATTTTTCATTT
3642904 GTTTTCATTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.68
Consensus pattern (13 bp):
CATTTTTCATTTT
Found at i:3643892 original size:39 final size:38
Alignment explanation
Indices: 3643849--3643969 Score: 122
Period size: 39 Copynumber: 3.1 Consensus size: 38
3643839 TTCTTCTTTC
*
3643849 TTTTTTCAGTTTCATTTTCATTTTGATATTGATTTTGAT
1 TTTTTTCACTTTCATTTTCATTTTGAT-TTGATTTTGAT
* * *
3643888 TTTTTTCTTCTTTC-TTCTT-TTTTTTATTTTGATTTTTGAT
1 TTTTTTC-ACTTTCATT-TTCATTTTGA-TTTGA-TTTTGAT
3643928 TTTTTTC-CTTTTCATTTTCATTTTGACTTTGATTTTGAT
1 TTTTTTCAC-TTTCATTTTCATTTTGA-TTTGATTTTGAT
3643967 TTT
1 TTT
3643970 GATTTTTCTT
Statistics
Matches: 68, Mismatches: 7, Indels: 14
0.76 0.08 0.16
Matches are distributed among these distances:
38 1 0.01
39 34 0.50
40 33 0.49
ACGTcount: A:0.12, C:0.10, G:0.07, T:0.70
Consensus pattern (38 bp):
TTTTTTCACTTTCATTTTCATTTTGATTTGATTTTGAT
Found at i:3644653 original size:26 final size:28
Alignment explanation
Indices: 3644624--3644679 Score: 64
Period size: 25 Copynumber: 2.1 Consensus size: 28
3644614 TGAAATAATC
*
3644624 AGAAATAATTATTCAAAAA-GAATG-AA
1 AGAAATAATTACTCAAAAAGGAATGCAA
* *
3644650 AG-AATATTTGCTCAAAAAGGAATGCAA
1 AGAAATAATTACTCAAAAAGGAATGCAA
3644677 AGA
1 AGA
3644680 TGTATTTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
25 13 0.54
26 7 0.29
27 4 0.17
ACGTcount: A:0.55, C:0.07, G:0.16, T:0.21
Consensus pattern (28 bp):
AGAAATAATTACTCAAAAAGGAATGCAA
Found at i:3647072 original size:26 final size:28
Alignment explanation
Indices: 3647043--3647098 Score: 64
Period size: 25 Copynumber: 2.1 Consensus size: 28
3647033 TGAAATAATC
*
3647043 AGAAATAATTATTCAAAAA-GAATG-AA
1 AGAAATAATTACTCAAAAAGGAATGCAA
* *
3647069 AG-AATATTTGCTCAAAAAGGAATGCAA
1 AGAAATAATTACTCAAAAAGGAATGCAA
3647096 AGA
1 AGA
3647099 TGTATTTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
25 13 0.54
26 7 0.29
27 4 0.17
ACGTcount: A:0.55, C:0.07, G:0.16, T:0.21
Consensus pattern (28 bp):
AGAAATAATTACTCAAAAAGGAATGCAA
Found at i:3650211 original size:3 final size:3
Alignment explanation
Indices: 3650203--3650280 Score: 70
Period size: 3 Copynumber: 25.0 Consensus size: 3
3650193 AAAATAAAAC
* *
3650203 TAA TAA TAA TTAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAAA TGA
1 TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA
*
3650250 TAA TACA TTAA -AA TAA TTAA CAA -AA TAA TAA
1 TAA TA-A -TAA TAA TAA -TAA TAA TAA TAA TAA
3650281 GATTGCTAAA
Statistics
Matches: 63, Mismatches: 5, Indels: 14
0.77 0.06 0.17
Matches are distributed among these distances:
2 4 0.06
3 46 0.73
4 11 0.17
5 2 0.03
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:3650226 original size:28 final size:28
Alignment explanation
Indices: 3650203--3650280 Score: 52
Period size: 28 Copynumber: 2.8 Consensus size: 28
3650193 AAAATAAAAC
* *
3650203 TAATAATAATTAATAATGATAAT-AATAA
1 TAATAATAA-TAATAATAATAATAAATGA
* * *
3650231 TAATAATAATAATAAATGATAATACATTA
1 TAATAATAATAAT-AATAATAATAAATGA
* *
3650260 AAATAATTAACAA-AATAATAA
1 TAATAA-TAATAATAATAATAA
3650281 GATTGCTAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
27 4 0.10
28 25 0.60
29 8 0.19
30 5 0.12
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.32
Consensus pattern (28 bp):
TAATAATAATAATAATAATAATAAATGA
Found at i:3651062 original size:14 final size:14
Alignment explanation
Indices: 3651043--3651069 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3651033 ATGTAAAAGA
3651043 TAAAATAAAATAAG
1 TAAAATAAAATAAG
3651057 TAAAATAAAATAA
1 TAAAATAAAATAA
3651070 ACAAGCAGAA
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:0.74, C:0.00, G:0.04, T:0.22
Consensus pattern (14 bp):
TAAAATAAAATAAG
Found at i:3652693 original size:24 final size:25
Alignment explanation
Indices: 3652636--3652695 Score: 65
Period size: 24 Copynumber: 2.5 Consensus size: 25
3652626 AAGAAAAGAG
3652636 AATATATGAAA--AATAGAGAATCA
1 AATATATGAAAGGAATAGAGAATCA
**
3652659 AATATGGGAAAGGAA-AGAGAAT-A
1 AATATATGAAAGGAATAGAGAATCA
3652682 ACATATATGAAAGG
1 A-ATATATGAAAGG
3652696 GAATTTAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
23 11 0.37
24 17 0.57
25 2 0.07
ACGTcount: A:0.57, C:0.03, G:0.22, T:0.18
Consensus pattern (25 bp):
AATATATGAAAGGAATAGAGAATCA
Found at i:3666104 original size:13 final size:13
Alignment explanation
Indices: 3666067--3666111 Score: 67
Period size: 12 Copynumber: 3.6 Consensus size: 13
3666057 ATTTTAATTC
3666067 AAAAT-TAAATAT
1 AAAATATAAATAT
3666079 AAAAT-TAAATAT
1 AAAATATAAATAT
*
3666091 AAAATATCAATAT
1 AAAATATAAATAT
3666104 AAAATATA
1 AAAATATA
3666112 TTTTTATTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
12 17 0.57
13 13 0.43
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (13 bp):
AAAATATAAATAT
Found at i:3674642 original size:25 final size:25
Alignment explanation
Indices: 3674614--3674705 Score: 87
Period size: 25 Copynumber: 3.6 Consensus size: 25
3674604 CTAATTTATG
3674614 GCTCGCATGAGCTTCCCGTTATATA
1 GCTCGCATGAGCTTCCCGTTATATA
* ** *
3674639 GCTCACATGAGCTTTTCGTTATATG
1 GCTCGCATGAGCTTCCCGTTATATA
* * *
3674664 GCTCGAAAGAGCTTCCCGTT-TACA
1 GCTCGCATGAGCTTCCCGTTATATA
*
3674688 TGCTCGTATGAGCATTCC
1 -GCTCGCATGAGC-TTCC
3674706 TAAATATAAA
Statistics
Matches: 52, Mismatches: 13, Indels: 3
0.76 0.19 0.04
Matches are distributed among these distances:
24 2 0.04
25 46 0.88
26 4 0.08
ACGTcount: A:0.21, C:0.26, G:0.21, T:0.33
Consensus pattern (25 bp):
GCTCGCATGAGCTTCCCGTTATATA
Found at i:3682205 original size:56 final size:56
Alignment explanation
Indices: 3682138--3682250 Score: 190
Period size: 56 Copynumber: 2.0 Consensus size: 56
3682128 CAAATAGGGT
** * *
3682138 GAGCTTACCAAACCCTAATTTAGAGTTTACCTAGCTACCAGTATCTTTAGGCCGTA
1 GAGCTTACCAAACCCTAATCCAAAGTCTACCTAGCTACCAGTATCTTTAGGCCGTA
3682194 GAGCTTACCAAACCCTAATCCAAAGTCTACCTAGCTACCAGTATCTTTAGGCCGTA
1 GAGCTTACCAAACCCTAATCCAAAGTCTACCTAGCTACCAGTATCTTTAGGCCGTA
3682250 G
1 G
3682251 CTCAATTCCT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
56 53 1.00
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.27
Consensus pattern (56 bp):
GAGCTTACCAAACCCTAATCCAAAGTCTACCTAGCTACCAGTATCTTTAGGCCGTA
Found at i:3683173 original size:25 final size:26
Alignment explanation
Indices: 3683121--3683173 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 26
3683111 GTCGTTGCTG
** * *
3683121 TTGAAAAATGCTTTTGAAAAATATAA
1 TTGAAAAATGCTCGTGAAAAAAACAA
3683147 TTGAAAAATG-TCGTGAAAAAAACAA
1 TTGAAAAATGCTCGTGAAAAAAACAA
3683172 TT
1 TT
3683174 TATTAAGTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
25 13 0.57
26 10 0.43
ACGTcount: A:0.51, C:0.06, G:0.13, T:0.30
Consensus pattern (26 bp):
TTGAAAAATGCTCGTGAAAAAAACAA
Found at i:3683657 original size:6 final size:6
Alignment explanation
Indices: 3683646--3683673 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
3683636 CCTGCAGCTC
3683646 ACATAT ACATAT ACATAT ACATAT ACAT
1 ACATAT ACATAT ACATAT ACATAT ACAT
3683674 CGTTTACTAG
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:0.18, G:0.00, T:0.32
Consensus pattern (6 bp):
ACATAT
Found at i:3686078 original size:42 final size:42
Alignment explanation
Indices: 3686007--3686143 Score: 166
Period size: 42 Copynumber: 3.3 Consensus size: 42
3685997 TTTAGCTTTC
* * * *
3686007 ATGAGCTTCTGTTTAACTCATATGAGTTTCCGTTCAGCTATT
1 ATGAGCTTCTGTTTAACCCTTATGGGTTTCCGTTCAGCTCTT
*
3686049 TTGAGCTTCTGTTTAACCCTTATGGGTTTCCGTTCAGCTCTT
1 ATGAGCTTCTGTTTAACCCTTATGGGTTTCCGTTCAGCTCTT
* * * * * * *
3686091 ACGAGCTTCCGTTTAACCTTTACGGGTTTCTGTTTAGCTCTC
1 ATGAGCTTCTGTTTAACCCTTATGGGTTTCCGTTCAGCTCTT
3686133 ATGAGCTTCTG
1 ATGAGCTTCTG
3686144 CTCAGCCTTC
Statistics
Matches: 80, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 80 1.00
ACGTcount: A:0.16, C:0.23, G:0.19, T:0.42
Consensus pattern (42 bp):
ATGAGCTTCTGTTTAACCCTTATGGGTTTCCGTTCAGCTCTT
Found at i:3686142 original size:21 final size:21
Alignment explanation
Indices: 3685996--3686143 Score: 84
Period size: 21 Copynumber: 7.0 Consensus size: 21
3685986 TTTACTTTTC
3685996 GTTTAGCT-TTCATGAGCTTCT
1 GTTTAGCTCTT-ATGAGCTTCT
* * * *
3686017 GTTTAACTCATATGAGTTTCC
1 GTTTAGCTCTTATGAGCTTCT
* * *
3686038 GTTCAGCTATTTTGAGCTTCT
1 GTTTAGCTCTTATGAGCTTCT
* * * * *
3686059 GTTTAACCCTTATGGGTTTCC
1 GTTTAGCTCTTATGAGCTTCT
* * *
3686080 GTTCAGCTCTTACGAGCTTCC
1 GTTTAGCTCTTATGAGCTTCT
* * * *
3686101 GTTTAAC-CTTTACGGGTTTCT
1 GTTTAGCTC-TTATGAGCTTCT
*
3686122 GTTTAGCTCTCATGAGCTTCT
1 GTTTAGCTCTTATGAGCTTCT
3686143 G
1 G
3686144 CTCAGCCTTC
Statistics
Matches: 89, Mismatches: 35, Indels: 6
0.68 0.27 0.05
Matches are distributed among these distances:
20 1 0.01
21 86 0.97
22 2 0.02
ACGTcount: A:0.16, C:0.22, G:0.19, T:0.43
Consensus pattern (21 bp):
GTTTAGCTCTTATGAGCTTCT
Found at i:3690915 original size:17 final size:18
Alignment explanation
Indices: 3690888--3690921 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
3690878 ATAAACATTA
3690888 AAAAAATATTTTAAAAAT
1 AAAAAATATTTTAAAAAT
3690906 AAAAAA-ATTTTAAAAA
1 AAAAAATATTTTAAAAA
3690922 AATTATTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (18 bp):
AAAAAATATTTTAAAAAT
Found at i:3690924 original size:19 final size:19
Alignment explanation
Indices: 3690886--3690922 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
3690876 AAATAAACAT
*
3690886 TAAAAAAATATTTTAAAAA
1 TAAAAAAATATTTAAAAAA
3690905 TAAAAAAAT-TTTAAAAAA
1 TAAAAAAATATTTAAAAAA
3690923 ATTATTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (19 bp):
TAAAAAAATATTTAAAAAA
Found at i:3693846 original size:23 final size:23
Alignment explanation
Indices: 3693820--3693867 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
3693810 TTTCTTATTG
*
3693820 TAGTAATTTTCGGGGTATTACAA
1 TAGTAATTTTCGGGATATTACAA
3693843 TAGTAATTTTCGGGATATTACAA
1 TAGTAATTTTCGGGATATTACAA
3693866 TA
1 TA
3693868 ATTAATTGAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.33, C:0.08, G:0.19, T:0.40
Consensus pattern (23 bp):
TAGTAATTTTCGGGATATTACAA
Found at i:3703418 original size:3 final size:3
Alignment explanation
Indices: 3703412--3703471 Score: 120
Period size: 3 Copynumber: 20.0 Consensus size: 3
3703402 GAATAATAAG
3703412 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
3703460 AGA AGA AGA AGA
1 AGA AGA AGA AGA
3703472 GAAAAATGGA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:3703613 original size:49 final size:49
Alignment explanation
Indices: 3703541--3703634 Score: 161
Period size: 49 Copynumber: 1.9 Consensus size: 49
3703531 CCTATTAAAC
*
3703541 TTCAATTTCCCTTTTCATAAATCTTTGGATTTTCATGGAGGAAATCAAT
1 TTCAATTTCCCCTTTCATAAATCTTTGGATTTTCATGGAGGAAATCAAT
* *
3703590 TTCAATTTCCCCTTTCATAAATCTTTGGGTTTTTATGGAGGAAAT
1 TTCAATTTCCCCTTTCATAAATCTTTGGATTTTCATGGAGGAAAT
3703635 ATCAATTAGG
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
49 42 1.00
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.44
Consensus pattern (49 bp):
TTCAATTTCCCCTTTCATAAATCTTTGGATTTTCATGGAGGAAATCAAT
Found at i:3704570 original size:21 final size:21
Alignment explanation
Indices: 3704544--3704584 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3704534 CAATGTGGCA
3704544 AGTTAACTGGCAACATCAGCT
1 AGTTAACTGGCAACATCAGCT
* *
3704565 AGTTAACTTGCCACATCAGC
1 AGTTAACTGGCAACATCAGC
3704585 AATCTTGCCA
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:0.32, C:0.27, G:0.17, T:0.24
Consensus pattern (21 bp):
AGTTAACTGGCAACATCAGCT
Found at i:3707724 original size:6 final size:6
Alignment explanation
Indices: 3707715--3707747 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
3707705 ACCATCAACC
3707715 TATGTA TATGTA TATGTA TATGTA TATGTA TAT
1 TATGTA TATGTA TATGTA TATGTA TATGTA TAT
3707748 ATATCCTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (6 bp):
TATGTA
Found at i:3717394 original size:17 final size:17
Alignment explanation
Indices: 3717369--3717406 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
3717359 TTCTTTAGTC
*
3717369 AAATTAACATAAT-AATA
1 AAATGAACA-AATAAATA
3717386 AAATGAACAAATAAATA
1 AAATGAACAAATAAATA
3717403 AAAT
1 AAAT
3717407 TTCAAATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 3 0.16
17 16 0.84
ACGTcount: A:0.68, C:0.05, G:0.03, T:0.24
Consensus pattern (17 bp):
AAATGAACAAATAAATA
Found at i:3717695 original size:30 final size:31
Alignment explanation
Indices: 3717661--3717743 Score: 98
Period size: 30 Copynumber: 2.7 Consensus size: 31
3717651 ATGTTGAAAC
* *
3717661 AATATATTATTAGCTTAATTTATACT-ATAA
1 AATATATTATTAGCTTAATCTACACTAATAA
* *
3717691 AATATATTA-TAGTCTTAATCTGCATTAATAA
1 AATATATTATTAG-CTTAATCTACACTAATAA
3717722 AATATATTATTAGCTTCAATCT
1 AATATATTATTAGCTT-AATCT
3717744 TTCCTTATTA
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
29 3 0.07
30 18 0.40
31 16 0.36
32 8 0.18
ACGTcount: A:0.41, C:0.10, G:0.05, T:0.45
Consensus pattern (31 bp):
AATATATTATTAGCTTAATCTACACTAATAA
Found at i:3719978 original size:7 final size:7
Alignment explanation
Indices: 3719966--3720009 Score: 52
Period size: 7 Copynumber: 6.3 Consensus size: 7
3719956 GCTAAGCTAC
3719966 CACTTAT
1 CACTTAT
3719973 CACTTAT
1 CACTTAT
*
3719980 CACTTGT
1 CACTTAT
*
3719987 CACTTGT
1 CACTTAT
*
3719994 CACTTGT
1 CACTTAT
*
3720001 CACTGAT
1 CACTTAT
3720008 CA
1 CA
3720010 GATAAGTCTA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.23, C:0.30, G:0.09, T:0.39
Consensus pattern (7 bp):
CACTTAT
Found at i:3719989 original size:14 final size:14
Alignment explanation
Indices: 3719966--3720009 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
3719956 GCTAAGCTAC
*
3719966 CACTTATCACTTAT
1 CACTTGTCACTTAT
*
3719980 CACTTGTCACTTGT
1 CACTTGTCACTTAT
*
3719994 CACTTGTCACTGAT
1 CACTTGTCACTTAT
3720008 CA
1 CA
3720010 GATAAGTCTA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.23, C:0.30, G:0.09, T:0.39
Consensus pattern (14 bp):
CACTTGTCACTTAT
Found at i:3720049 original size:65 final size:65
Alignment explanation
Indices: 3719935--3720113 Score: 324
Period size: 65 Copynumber: 2.8 Consensus size: 65
3719925 CATTTATCTC
3719935 GTCACTGATCAGATAAGTGTAGCT-AAGCTACCACTTATCACTTATCACTTGTCACTTGTCACTT
1 GTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTATCACTTGTCACTTGTCACTT
* *
3719999 GTCACTGATCAGATAAGTCTAGCTAAAGCTACCACTTACCACTTATCACTTGTCACTTGTCACTT
1 GTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTATCACTTGTCACTTGTCACTT
*
3720064 GTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTGTCACT
1 GTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTATCACT
3720114 GATCAGAAGT
Statistics
Matches: 109, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
64 23 0.21
65 86 0.79
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.32
Consensus pattern (65 bp):
GTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTATCACTTGTCACTTGTCACTT
Found at i:3720054 original size:7 final size:7
Alignment explanation
Indices: 3720038--3720069 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
3720028 TACCACTTAC
*
3720038 CACTTAT
1 CACTTGT
3720045 CACTTGT
1 CACTTGT
3720052 CACTTGT
1 CACTTGT
3720059 CACTTGT
1 CACTTGT
3720066 CACT
1 CACT
3720070 GATCAGATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.19, C:0.31, G:0.09, T:0.41
Consensus pattern (7 bp):
CACTTGT
Found at i:3720055 original size:14 final size:14
Alignment explanation
Indices: 3720038--3720074 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
3720028 TACCACTTAC
3720038 CACTTATCACTTGT
1 CACTTATCACTTGT
*
3720052 CACTTGTCACTTGT
1 CACTTATCACTTGT
*
3720066 CACTGATCA
1 CACTTATCA
3720075 GATAAGTGTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.22, C:0.30, G:0.11, T:0.38
Consensus pattern (14 bp):
CACTTATCACTTGT
Found at i:3728086 original size:12 final size:12
Alignment explanation
Indices: 3728069--3728095 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
3728059 ATTAGTATTT
3728069 ATTATTTTCATA
1 ATTATTTTCATA
3728081 ATTATTTTCATA
1 ATTATTTTCATA
3728093 ATT
1 ATT
3728096 TCATATAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.59
Consensus pattern (12 bp):
ATTATTTTCATA
Found at i:3734870 original size:16 final size:17
Alignment explanation
Indices: 3734849--3734888 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
3734839 TTATACGGGT
3734849 AAAATAAAATA-TTAAA
1 AAAATAAAATATTTAAA
*
3734865 AAAAT-AAATATTTTAA
1 AAAATAAAATATTTAAA
3734881 AAAATAAA
1 AAAATAAA
3734889 CATGATAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 5 0.24
16 14 0.67
17 2 0.10
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (17 bp):
AAAATAAAATATTTAAA
Found at i:3735513 original size:23 final size:23
Alignment explanation
Indices: 3735464--3735513 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
3735454 AATAGGTATG
* *
3735464 AAATTAAAATAAAAAATTAGTTA
1 AAATTAAAATAAAAAATAAATTA
*
3735487 AAATTACAAAT-AAAAATAAATTT
1 AAATTA-AAATAAAAAATAAATTA
3735510 AAAT
1 AAAT
3735514 AGATAAATGC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 19 0.83
24 4 0.17
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (23 bp):
AAATTAAAATAAAAAATAAATTA
Found at i:3737223 original size:24 final size:23
Alignment explanation
Indices: 3737182--3737240 Score: 59
Period size: 23 Copynumber: 2.5 Consensus size: 23
3737172 TTTAAAACTT
3737182 AATT-TTTTTAAAAAATTATA-AA
1 AATTATTTTTAAAAAATTA-ACAA
*
3737204 AATTATTTTTAAAATTATTAACAA
1 AATTATTTTTAAAA-AATTAACAA
*
3737228 TATATATTTTTAA
1 AAT-TATTTTTAA
3737241 TATTTTAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
22 4 0.13
23 10 0.32
24 8 0.26
25 9 0.29
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (23 bp):
AATTATTTTTAAAAAATTAACAA
Found at i:3750615 original size:2 final size:2
Alignment explanation
Indices: 3750608--3750634 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3750598 GAGAAAGCAA
3750608 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
3750635 GAATGAAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3759565 original size:16 final size:16
Alignment explanation
Indices: 3759538--3759580 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
3759528 AATTAAAATT
3759538 TTAAATTTTAAATCAAA
1 TTAAATTTTAAAT-AAA
3759555 TTAAA-TTTAAATAAA
1 TTAAATTTTAAATAAA
*
3759570 TATAGATTTTA
1 T-TAAATTTTA
3759581 TTAATATTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 4 0.17
16 10 0.43
17 9 0.39
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (16 bp):
TTAAATTTTAAATAAA
Found at i:3765009 original size:111 final size:111
Alignment explanation
Indices: 3764815--3765036 Score: 444
Period size: 111 Copynumber: 2.0 Consensus size: 111
3764805 CAATACCATG
3764815 CATGTAGTTGTATTGTTGTATTAAAGTTTGTTAATATGTACAGACATTTAGAAAAAGTAGTGTAT
1 CATGTAGTTGTATTGTTGTATTAAAGTTTGTTAATATGTACAGACATTTAGAAAAAGTAGTGTAT
3764880 GTTTATATGGTATACATATATCACTACTCTCTCTCTTAGACAACAA
66 GTTTATATGGTATACATATATCACTACTCTCTCTCTTAGACAACAA
3764926 CATGTAGTTGTATTGTTGTATTAAAGTTTGTTAATATGTACAGACATTTAGAAAAAGTAGTGTAT
1 CATGTAGTTGTATTGTTGTATTAAAGTTTGTTAATATGTACAGACATTTAGAAAAAGTAGTGTAT
3764991 GTTTATATGGTATACATATATCACTACTCTCTCTCTTAGACAACAA
66 GTTTATATGGTATACATATATCACTACTCTCTCTCTTAGACAACAA
3765037 TACTTCATCA
Statistics
Matches: 111, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
111 111 1.00
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (111 bp):
CATGTAGTTGTATTGTTGTATTAAAGTTTGTTAATATGTACAGACATTTAGAAAAAGTAGTGTAT
GTTTATATGGTATACATATATCACTACTCTCTCTCTTAGACAACAA
Found at i:3765454 original size:48 final size:51
Alignment explanation
Indices: 3765341--3765446 Score: 203
Period size: 51 Copynumber: 2.1 Consensus size: 51
3765331 TTTTTCCCAC
*
3765341 TAATAAGAATGCATTTTTTTTCAATTTATAACGATTAATATTGTAGTTTAA
1 TAATAAGAATGTATTTTTTTTCAATTTATAACGATTAATATTGTAGTTTAA
3765392 TAATAAGAATGTATTTTTTTTCAATTTATAACGATTAATATTGTAGTTTAA
1 TAATAAGAATGTATTTTTTTTCAATTTATAACGATTAATATTGTAGTTTAA
3765443 TAAT
1 TAAT
3765447 TGAGTATTAT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 54 1.00
ACGTcount: A:0.38, C:0.05, G:0.09, T:0.48
Consensus pattern (51 bp):
TAATAAGAATGTATTTTTTTTCAATTTATAACGATTAATATTGTAGTTTAA
Found at i:3765650 original size:20 final size:20
Alignment explanation
Indices: 3765625--3765664 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
3765615 AATATTTTTC
*
3765625 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
3765645 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
3765665 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:3765666 original size:34 final size:35
Alignment explanation
Indices: 3765613--3765679 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
3765603 CAAATACCAG
* *
3765613 AAAATATTTTTCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
3765648 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
3765680 TATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.46, C:0.12, G:0.09, T:0.33
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:3779083 original size:21 final size:20
Alignment explanation
Indices: 3779054--3779097 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
3779044 TTAGAGAATG
*
3779054 AAAGGGCAAAAGACTAAATAA
1 AAAGAGCAAAAGACTAAA-AA
*
3779075 AAAGAGCAAAAGAGTAAAAA
1 AAAGAGCAAAAGACTAAAAA
3779095 AAA
1 AAA
3779098 CGCAGGGACA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.68, C:0.07, G:0.18, T:0.07
Consensus pattern (20 bp):
AAAGAGCAAAAGACTAAAAA
Found at i:3779989 original size:20 final size:20
Alignment explanation
Indices: 3779960--3779998 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3779950 AAAAAAGTTT
3779960 TTAATATAAAAAATTAAAAA
1 TTAATATAAAAAATTAAAAA
* *
3779980 TTAATTTAAAATATTAAAA
1 TTAATATAAAAAATTAAAA
3779999 TTTTGTACTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
TTAATATAAAAAATTAAAAA
Found at i:3789844 original size:28 final size:27
Alignment explanation
Indices: 3789791--3789863 Score: 74
Period size: 28 Copynumber: 2.6 Consensus size: 27
3789781 AATTGAAGCC
*
3789791 AAACTCAAATACTTAAATGGGAAAAAGAA
1 AAACTCAAATA-TCAAATGGGAAAAA-AA
* **
3789820 GAACTCAAATATCAAATTTGAAAAAAA
1 AAACTCAAATATCAAATGGGAAAAAAA
*
3789847 AAAGCTCAAGTATCAAA
1 AAA-CTCAAATATCAAA
3789864 CTAAATATTG
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
27 4 0.11
28 23 0.62
29 10 0.27
ACGTcount: A:0.58, C:0.12, G:0.11, T:0.19
Consensus pattern (27 bp):
AAACTCAAATATCAAATGGGAAAAAAA
Found at i:3792360 original size:5 final size:5
Alignment explanation
Indices: 3792350--3792376 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
3792340 TTTATAGTTG
3792350 ATGAC ATGAC ATGAC ATGAC ATGAC AT
1 ATGAC ATGAC ATGAC ATGAC ATGAC AT
3792377 TTGTTCTAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.22
Consensus pattern (5 bp):
ATGAC
Found at i:3795106 original size:15 final size:16
Alignment explanation
Indices: 3795084--3795118 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
3795074 GGTGGTTTGT
**
3795084 ATTTTTTTTTTGAAAA
1 ATTTTTTTTAAGAAAA
3795100 ATTTTTTTTAAGAAAA
1 ATTTTTTTTAAGAAAA
3795116 ATT
1 ATT
3795119 CATTAATTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (16 bp):
ATTTTTTTTAAGAAAA
Found at i:3798783 original size:102 final size:101
Alignment explanation
Indices: 3798671--3798868 Score: 290
Period size: 102 Copynumber: 2.0 Consensus size: 101
3798661 AATTAATATG
* * * *
3798671 AATTTAATTTTAATAATTAACGAAATATCAATTATCAATATTATTACAATTTGAATACAAAAT-T
1 AATTTAATTTTAATAACTAACGAAATATAAATTATCAATATTATTAAAACTTGAATACAAAATAT
3798735 CAAATAAAACTCTATTATTCAATAATATATTTTTTAAA
66 -AAATAAAACTCTATTATTCAATAATAT-TTTTTTAAA
* * *
3798773 AATTTAATTTTAATAACTAATGAAATATAAATTATCCATATTATTAAAACTTGAATATAAAATAT
1 AATTTAATTTTAATAACTAACGAAATATAAATTATCAATATTATTAAAACTTGAATACAAAATAT
* *
3798838 AAATAAGATTCTATTATTCAATAATATTTTT
66 AAATAAAACTCTATTATTCAATAATATTTTT
3798869 CATTAATTTT
Statistics
Matches: 86, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
101 4 0.05
102 81 0.94
103 1 0.01
ACGTcount: A:0.48, C:0.08, G:0.03, T:0.42
Consensus pattern (101 bp):
AATTTAATTTTAATAACTAACGAAATATAAATTATCAATATTATTAAAACTTGAATACAAAATAT
AAATAAAACTCTATTATTCAATAATATTTTTTTAAA
Found at i:3799771 original size:4 final size:4
Alignment explanation
Indices: 3799762--3799786 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
3799752 AATAATAATA
3799762 ATGC ATGC ATGC ATGC ATGC ATGC A
1 ATGC ATGC ATGC ATGC ATGC ATGC A
3799787 CCTACTTTGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.28, C:0.24, G:0.24, T:0.24
Consensus pattern (4 bp):
ATGC
Found at i:3817030 original size:31 final size:31
Alignment explanation
Indices: 3816992--3817056 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
3816982 TTACAGTTCA
3816992 AGACAATATAGGAACATCCATTTCAACTTGT
1 AGACAATATAGGAACATCCATTTCAACTTGT
*
3817023 AGACAATATAGGACCATCCATTTCAACTTGT
1 AGACAATATAGGAACATCCATTTCAACTTGT
3817054 AGA
1 AGA
3817057 GAAGTACTCA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.38, C:0.20, G:0.14, T:0.28
Consensus pattern (31 bp):
AGACAATATAGGAACATCCATTTCAACTTGT
Found at i:3820868 original size:52 final size:52
Alignment explanation
Indices: 3820810--3820911 Score: 152
Period size: 52 Copynumber: 2.0 Consensus size: 52
3820800 CTGTGTATAA
* * *
3820810 TTTTTTCCTAATTATTATATTCTTTGGGT-TATATTAAATTAAATTAATAAGT
1 TTTTTTCCTAATTATCATATTCTTTGGATCAAT-TTAAATTAAATTAATAAGT
*
3820862 TTTTTTCCTAATTATCGTATTCTTTGGATCAATTTAAATTAAATTAATAA
1 TTTTTTCCTAATTATCATATTCTTTGGATCAATTTAAATTAAATTAATAA
3820912 TTTAGATATC
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
52 43 0.96
53 2 0.04
ACGTcount: A:0.33, C:0.08, G:0.07, T:0.52
Consensus pattern (52 bp):
TTTTTTCCTAATTATCATATTCTTTGGATCAATTTAAATTAAATTAATAAGT
Found at i:3821120 original size:3 final size:3
Alignment explanation
Indices: 3821112--3821144 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
3821102 TTAGGGTCAG
3821112 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
3821145 AAAGTGAAGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:3824801 original size:27 final size:27
Alignment explanation
Indices: 3824746--3824798 Score: 88
Period size: 28 Copynumber: 1.9 Consensus size: 27
3824736 TAAGTCATTG
*
3824746 ACCACATTGTGCATGTATTTTCTTTTC
1 ACCACATAGTGCATGTATTTTCTTTTC
3824773 ACCATCATAGTGCATGTATTTTCTTT
1 ACCA-CATAGTGCATGTATTTTCTTT
3824799 CACTTATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
27 4 0.17
28 20 0.83
ACGTcount: A:0.21, C:0.21, G:0.11, T:0.47
Consensus pattern (27 bp):
ACCACATAGTGCATGTATTTTCTTTTC
Found at i:3848612 original size:14 final size:14
Alignment explanation
Indices: 3848593--3848630 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
3848583 ATACCATAAC
3848593 TATATATATGTACA
1 TATATATATGTACA
* *
3848607 TATATAAATATACA
1 TATATATATGTACA
3848621 TATATATATG
1 TATATATATG
3848631 CAGTGTTAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.42
Consensus pattern (14 bp):
TATATATATGTACA
Found at i:3857603 original size:23 final size:24
Alignment explanation
Indices: 3857576--3857632 Score: 64
Period size: 25 Copynumber: 2.4 Consensus size: 24
3857566 CTTTAAAAAA
*
3857576 TAAATATATATTTATTTTCATAT-
1 TAAATATATAATTATTTTCATATG
*
3857599 TAAATTAATATAATTATTTTTATATG
1 TAAA-T-ATATAATTATTTTCATATG
3857625 T-AATATAT
1 TAAATATAT
3857633 CAGCGTAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
23 8 0.28
24 2 0.07
25 18 0.62
26 1 0.03
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (24 bp):
TAAATATATAATTATTTTCATATG
Found at i:3857609 original size:27 final size:25
Alignment explanation
Indices: 3857573--3857623 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
3857563 ACACTTTAAA
3857573 AAATAAATATATATTTATTTTCATATT
1 AAATAAATATA-A-TTATTTTCATATT
* *
3857600 AAATTAATATAATTATTTTTATAT
1 AAATAAATATAATTATTTTCATAT
3857624 GTAATATATC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 11 0.50
26 1 0.05
27 10 0.45
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (25 bp):
AAATAAATATAATTATTTTCATATT
Found at i:3875745 original size:21 final size:22
Alignment explanation
Indices: 3875698--3875738 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
3875688 AAAACGAATC
3875698 CAAAAACAAAAAAGTCAAAATT
1 CAAAAACAAAAAAGTCAAAATT
*
3875720 CAAAAATAAAAAA-TCAAAA
1 CAAAAACAAAAAAGTCAAAA
3875739 CTTAAAAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.73, C:0.12, G:0.02, T:0.12
Consensus pattern (22 bp):
CAAAAACAAAAAAGTCAAAATT
Found at i:3877462 original size:31 final size:30
Alignment explanation
Indices: 3877396--3877466 Score: 99
Period size: 31 Copynumber: 2.3 Consensus size: 30
3877386 AAAATAACAG
*
3877396 TTTAGTGACTTAAATGAAAATTTGCAAATAG
1 TTTAGTGACTTAAATGAAAATTTG-AAATAA
3877427 TTTAGTGACTTAAATGAAAACTTTTG-AATAA
1 TTTAGTGACTTAAATGAAAA--TTTGAAATAA
3877458 TTTAGTGAC
1 TTTAGTGAC
3877467 CAAATTATAA
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
31 33 0.89
33 4 0.11
ACGTcount: A:0.39, C:0.07, G:0.15, T:0.38
Consensus pattern (30 bp):
TTTAGTGACTTAAATGAAAATTTGAAATAA
Found at i:3877754 original size:21 final size:21
Alignment explanation
Indices: 3877724--3877763 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
3877714 TAACGGGATC
3877724 GCTGACGTGGCAAGTTAACCA
1 GCTGACGTGGCAAGTTAACCA
*
3877745 GCTGATGTGGCAAGTTAAC
1 GCTGACGTGGCAAGTTAAC
3877764 TTGCCACGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.20, G:0.30, T:0.23
Consensus pattern (21 bp):
GCTGACGTGGCAAGTTAACCA
Found at i:3878245 original size:12 final size:11
Alignment explanation
Indices: 3878221--3878279 Score: 55
Period size: 12 Copynumber: 5.0 Consensus size: 11
3878211 CAATTTCAAT
*
3878221 TTTAATTTCGA
1 TTTAATTTTGA
3878232 TTCTAATTTTGA
1 TT-TAATTTTGA
*
3878244 TTTTGATTTTGA
1 -TTTAATTTTGA
*
3878256 TTTCGATTTTGA
1 TTT-AATTTTGA
3878268 TTTCAATTTTGA
1 TTT-AATTTTGA
3878280 AACACTCACT
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
11 5 0.12
12 35 0.83
13 2 0.05
ACGTcount: A:0.22, C:0.07, G:0.12, T:0.59
Consensus pattern (11 bp):
TTTAATTTTGA
Found at i:3878246 original size:6 final size:6
Alignment explanation
Indices: 3878237--3878270 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
3878227 TTCGATTCTA
*
3878237 ATTTTG ATTTTG ATTTTG ATTTCG ATTTTG ATTT
1 ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG ATTT
3878271 CAATTTTGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.18, C:0.03, G:0.15, T:0.65
Consensus pattern (6 bp):
ATTTTG
Found at i:3878276 original size:18 final size:18
Alignment explanation
Indices: 3878213--3878279 Score: 73
Period size: 18 Copynumber: 3.7 Consensus size: 18
3878203 GGTTATTTCA
* *
3878213 ATTTCAATTTTAATTTCG
1 ATTTCAATTTTGATTTTG
3878231 A-TTCTAATTTTGATTTTG
1 ATTTC-AATTTTGATTTTG
** *
3878249 ATTTTGATTTCGATTTTG
1 ATTTCAATTTTGATTTTG
3878267 ATTTCAATTTTGA
1 ATTTCAATTTTGA
3878280 AACACTCACT
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
17 3 0.08
18 34 0.87
19 2 0.05
ACGTcount: A:0.24, C:0.07, G:0.10, T:0.58
Consensus pattern (18 bp):
ATTTCAATTTTGATTTTG
Found at i:3878360 original size:12 final size:12
Alignment explanation
Indices: 3878315--3878367 Score: 52
Period size: 12 Copynumber: 4.4 Consensus size: 12
3878305 TTTGATTTCA
* *
3878315 ATTTCAATTTCG
1 ATTTCGATTTAG
*
3878327 ATCTCGATTTAG
1 ATTTCGATTTAG
*
3878339 ATTTAGATTTAG
1 ATTTCGATTTAG
* *
3878351 ATTTCTATTTGG
1 ATTTCGATTTAG
3878363 ATTTC
1 ATTTC
3878368 AGTTTGGTTA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.25, C:0.11, G:0.13, T:0.51
Consensus pattern (12 bp):
ATTTCGATTTAG
Found at i:3880799 original size:65 final size:65
Alignment explanation
Indices: 3880711--3880850 Score: 217
Period size: 65 Copynumber: 2.2 Consensus size: 65
3880701 TACCGCAACA
* * ** *
3880711 CTTTGTGAGCGTCCTGTTATATGATCGGTTGTGATCCTGCATATATTGTGGACACAAACGCAGCT
1 CTTTGTGAGCGTCCTGTTATATGATCGGTTGTAATCCTACATATATTGCAGACACAAACACAGCT
* *
3880776 CTTTGTGAGCGTCCTGTTTTATGATCGGTTGTAATCCTACATATGTTGCAGACACAAACACAGCT
1 CTTTGTGAGCGTCCTGTTATATGATCGGTTGTAATCCTACATATATTGCAGACACAAACACAGCT
3880841 CTTTGTGAGC
1 CTTTGTGAGC
3880851 ATCTTGATAT
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
65 68 1.00
ACGTcount: A:0.22, C:0.21, G:0.23, T:0.34
Consensus pattern (65 bp):
CTTTGTGAGCGTCCTGTTATATGATCGGTTGTAATCCTACATATATTGCAGACACAAACACAGCT
Found at i:3883924 original size:40 final size:40
Alignment explanation
Indices: 3883870--3883966 Score: 194
Period size: 40 Copynumber: 2.4 Consensus size: 40
3883860 TAGTGAGTGC
3883870 TTTTTAATATGCATGCAGTGATTGTTGGTGTGTTGACTAT
1 TTTTTAATATGCATGCAGTGATTGTTGGTGTGTTGACTAT
3883910 TTTTTAATATGCATGCAGTGATTGTTGGTGTGTTGACTAT
1 TTTTTAATATGCATGCAGTGATTGTTGGTGTGTTGACTAT
3883950 TTTTTAATATGCATGCA
1 TTTTTAATATGCATGCA
3883967 TTGAGTATTT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 57 1.00
ACGTcount: A:0.22, C:0.08, G:0.23, T:0.47
Consensus pattern (40 bp):
TTTTTAATATGCATGCAGTGATTGTTGGTGTGTTGACTAT
Found at i:3884003 original size:28 final size:26
Alignment explanation
Indices: 3883943--3884009 Score: 73
Period size: 28 Copynumber: 2.5 Consensus size: 26
3883933 GTTGGTGTGT
* *
3883943 TGACTA-TTTTTTAATATGCATGCAT
1 TGACTATTTTTTTAATATACATGCAG
* *
3883968 TGAGTATTTTTTAATAATATACATGTAG
1 TGACTATTTTTT--TAATATACATGCAG
3883996 TGACTATTTTTTTA
1 TGACTATTTTTTTA
3884010 GGGGTGTGTG
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
25 5 0.15
26 7 0.21
28 22 0.65
ACGTcount: A:0.30, C:0.07, G:0.12, T:0.51
Consensus pattern (26 bp):
TGACTATTTTTTTAATATACATGCAG
Found at i:3885176 original size:23 final size:24
Alignment explanation
Indices: 3885150--3885195 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
3885140 CTATTTTTTA
*
3885150 TGAGTATTGA-AAAAACAAATGTG
1 TGAGCATTGAGAAAAACAAATGTG
*
3885173 TGAGCATTGAGAAATACAAATGT
1 TGAGCATTGAGAAAAACAAATGT
3885196 TTTTTTTTCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.46, C:0.07, G:0.22, T:0.26
Consensus pattern (24 bp):
TGAGCATTGAGAAAAACAAATGTG
Found at i:3885419 original size:20 final size:20
Alignment explanation
Indices: 3885391--3885453 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 20
3885381 AGCAACCATT
*
3885391 TATAACAACATAAGCAACAA
1 TATACCAACATAAGCAACAA
*
3885411 TATACCAAC--AA-C--CATG
1 TATACCAACATAAGCAACA-A
3885427 TATACCAACATAAGCAACAA
1 TATACCAACATAAGCAACAA
3885447 TATACCA
1 TATACCA
3885454 GCAACAATAT
Statistics
Matches: 34, Mismatches: 3, Indels: 12
0.69 0.06 0.24
Matches are distributed among these distances:
15 2 0.06
16 9 0.26
17 1 0.03
18 4 0.12
19 1 0.03
20 15 0.44
21 2 0.06
ACGTcount: A:0.52, C:0.25, G:0.05, T:0.17
Consensus pattern (20 bp):
TATACCAACATAAGCAACAA
Found at i:3885423 original size:36 final size:36
Alignment explanation
Indices: 3885375--3885477 Score: 145
Period size: 36 Copynumber: 2.9 Consensus size: 36
3885365 GTTAGCCATG
3885375 TATACCAGCAACCATTTATAACAACATAAGCAACAA
1 TATACCAGCAACCATTTATAACAACATAAGCAACAA
* * *
3885411 TATACCAACAACCATGTATACCAACATAAGCAACAA
1 TATACCAGCAACCATTTATAACAACATAAGCAACAA
* *
3885447 TATACCAGCAACAATATTACAA-AACATAAGC
1 TATACCAGCAACCAT-TTATAACAACATAAGC
3885478 CGGTTTTCAA
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
36 55 0.95
37 3 0.05
ACGTcount: A:0.50, C:0.25, G:0.06, T:0.18
Consensus pattern (36 bp):
TATACCAGCAACCATTTATAACAACATAAGCAACAA
Found at i:3885792 original size:3 final size:3
Alignment explanation
Indices: 3885777--3885822 Score: 65
Period size: 3 Copynumber: 15.3 Consensus size: 3
3885767 CTATTTTTCC
* * *
3885777 TCT TCT CCT TCT TCT TCT TCT TCT TTT TCT TCT TCT TAT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
3885823 TAACCCTAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.02, C:0.30, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:3892966 original size:2 final size:2
Alignment explanation
Indices: 3892959--3892988 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3892949 GTTGATTTAA
*
3892959 CT CT CT CT CT CT CT CT CT CT CT TT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
3892989 TATATTTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
CT
Found at i:3900664 original size:34 final size:34
Alignment explanation
Indices: 3900621--3900688 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
3900611 GAAAAAGAAA
3900621 AATGAAAGAATCATTGGATAAGAATGACAAAGGG
1 AATGAAAGAATCATTGGATAAGAATGACAAAGGG
3900655 AATGAAAGAATCATTGGATAAGAATGACAAAGGG
1 AATGAAAGAATCATTGGATAAGAATGACAAAGGG
3900689 CCCCTGCATC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.50, C:0.06, G:0.26, T:0.18
Consensus pattern (34 bp):
AATGAAAGAATCATTGGATAAGAATGACAAAGGG
Found at i:3905302 original size:348 final size:348
Alignment explanation
Indices: 3904659--3905507 Score: 1511
Period size: 348 Copynumber: 2.4 Consensus size: 348
3904649 CCAAGTTTAA
* * * *
3904659 AAATGACATCAAGAAAGCTTTTAGTCAAAACTAAGATAGTATTCGAAGCAAAAAATGTCTAACAA
1 AAATGACATCAAGAAAGCCTTTAGTCAAACCTGAGATAGTATTCGAAGCAACAAATGTCTAACAA
* * *
3904724 TACCTTCAGCTGCTCATTTTCAGCAGTAAGTCTATTTATTGATTCATCGTCAATAACGGTAGGTT
66 TACCTTCAGCTGTTCATTTTCAGCAGTAAGTTTATTCATTGATTCATCGTCAATAACGGTAGGTT
3904789 TATTCATTGATTCATTGTCAATAACAGGGATCTCCTGAACCACAGGAACTTGTTGAGATAAGGAA
131 TATTCATTGATTCATTGTCAATAACAGGGATCTCCTGAACCACAGGAACTTGTTGAGATAAGGAA
*
3904854 AGAATTATTCTACTCAATAAAAATAAAAGGAAAGAATGTTGAGATATATCTTACTGCAGATGTCA
196 AGAATTATTCTACTCAATAAAAATAAAAGGAAACAATGTTGAGATATATCTTACTGCAGATGTCA
*
3904919 CCTCTGACATGGTTGTACTCAGTGAACTCGGCATGGCCAGCTGCTGTGGTTTCTGGTCCTCAGCT
261 CCTCTGACATGGTTGTACTCAGTGAACTCGGCATGGCCAGCTGCTGCGGTTTCTGGTCCTCAGCT
3904984 CCCATGTCCAAAATCTTTTTTCC
326 CCCATGTCCAAAATCTTTTTTCC
* *
3905007 AAATGGCATCAAGAAAGCCTTTAGTCAAACCTGAGATAGTATTCAAAGCAACAAATGTCTAACAA
1 AAATGACATCAAGAAAGCCTTTAGTCAAACCTGAGATAGTATTCGAAGCAACAAATGTCTAACAA
* **
3905072 TACCTTCAGCTGTTCTTTTTCAGCAGTAAGTTTATTCATTGATTCATCACCAATAACGGTAGGTT
66 TACCTTCAGCTGTTCATTTTCAGCAGTAAGTTTATTCATTGATTCATCGTCAATAACGGTAGGTT
*
3905137 TATTCTTTGATTCATTGTCAATAACAGGGATCTCCTGAACCACAGGAACTTGTTGAGATAAGGAA
131 TATTCATTGATTCATTGTCAATAACAGGGATCTCCTGAACCACAGGAACTTGTTGAGATAAGGAA
*
3905202 AGAATTATTCTACTCAATAAAAATAAAAGGAAACAATGTTGAGATTTATCTTACTGCAGATGTCA
196 AGAATTATTCTACTCAATAAAAATAAAAGGAAACAATGTTGAGATATATCTTACTGCAGATGTCA
*
3905267 CCTCTGACATGGTTGTACTCAGTGAACTCGGCATGGCCTGCTGCTGCGGTTTCTGGTCCTCAGCT
261 CCTCTGACATGGTTGTACTCAGTGAACTCGGCATGGCCAGCTGCTGCGGTTTCTGGTCCTCAGCT
3905332 CCCATGTCCAAAATCTTTTTTCC
326 CCCATGTCCAAAATCTTTTTTCC
*
3905355 AAATGACATCAAGAAAGCCTTTAGTCAAACCTGAGATAGTATTTGAAGCAACAAATGTCTAACAA
1 AAATGACATCAAGAAAGCCTTTAGTCAAACCTGAGATAGTATTCGAAGCAACAAATGTCTAACAA
*
3905420 TACCTTCAGCTGTTCATTTTCAGCAGTAAGTTTATTCATTGATTCATCGTCAATAATGGTAGGTT
66 TACCTTCAGCTGTTCATTTTCAGCAGTAAGTTTATTCATTGATTCATCGTCAATAACGGTAGGTT
3905485 TATTCATTGATTCATCT-TCAATA
131 TATTCATTGATTCAT-TGTCAATA
3905508 TCGGTAGGTT
Statistics
Matches: 475, Mismatches: 25, Indels: 2
0.95 0.05 0.00
Matches are distributed among these distances:
348 474 1.00
349 1 0.00
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (348 bp):
AAATGACATCAAGAAAGCCTTTAGTCAAACCTGAGATAGTATTCGAAGCAACAAATGTCTAACAA
TACCTTCAGCTGTTCATTTTCAGCAGTAAGTTTATTCATTGATTCATCGTCAATAACGGTAGGTT
TATTCATTGATTCATTGTCAATAACAGGGATCTCCTGAACCACAGGAACTTGTTGAGATAAGGAA
AGAATTATTCTACTCAATAAAAATAAAAGGAAACAATGTTGAGATATATCTTACTGCAGATGTCA
CCTCTGACATGGTTGTACTCAGTGAACTCGGCATGGCCAGCTGCTGCGGTTTCTGGTCCTCAGCT
CCCATGTCCAAAATCTTTTTTCC
Found at i:3905486 original size:33 final size:33
Alignment explanation
Indices: 3905449--3905538 Score: 146
Period size: 33 Copynumber: 2.7 Consensus size: 33
3905439 TCAGCAGTAA
*
3905449 GTTTATTCATTGATTCATCGTCAATAAT-GGTAG
1 GTTTATTCATTGATTCATCATCAAT-ATCGGTAG
*
3905482 GTTTATTCATTGATTCATCTTCAATATCGGTAG
1 GTTTATTCATTGATTCATCATCAATATCGGTAG
3905515 GTTTATTCATTGATTCATCATCAA
1 GTTTATTCATTGATTCATCATCAA
3905539 CAACGGGGAT
Statistics
Matches: 54, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 2 0.04
33 52 0.96
ACGTcount: A:0.27, C:0.14, G:0.14, T:0.44
Consensus pattern (33 bp):
GTTTATTCATTGATTCATCATCAATATCGGTAG
Found at i:3906313 original size:21 final size:21
Alignment explanation
Indices: 3906288--3906337 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
3906278 TTTCTTCAAG
* *
3906288 CTCAAGTTGCATTTTCTGAAA
1 CTCAAGTTGCAGTTCCTGAAA
*
3906309 CTCAACTTGCAGTTCCTGAAA
1 CTCAAGTTGCAGTTCCTGAAA
3906330 CTCAAGTT
1 CTCAAGTT
3906338 CCTTCTTGTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.28, C:0.24, G:0.14, T:0.34
Consensus pattern (21 bp):
CTCAAGTTGCAGTTCCTGAAA
Found at i:3906403 original size:66 final size:66
Alignment explanation
Indices: 3906321--3906469 Score: 253
Period size: 66 Copynumber: 2.3 Consensus size: 66
3906311 CAACTTGCAG
3906321 TTCCTGAAACTCAAGTTCCTTCTTGTACAAAGTAGATTCAAATGTTGCTCTTTCCTGTTTTTTGG
1 TTCCTGAAACTCAAGTTCCTTCTTGTACAAAGTAGATTCAAATGTTGCTCTTTCCTGTTTTTTGG
3906386 A
66 A
* * * *
3906387 TTCCTGAAACTCAAGTTCCTTCTTGTGCAAAGTAGATTCTAGTGTTTCTCTTTCCTGTTTTTTGG
1 TTCCTGAAACTCAAGTTCCTTCTTGTACAAAGTAGATTCAAATGTTGCTCTTTCCTGTTTTTTGG
3906452 A
66 A
*
3906453 TTCCTCAAACTCAAGTT
1 TTCCTGAAACTCAAGTT
3906470 GCAGTTTCTG
Statistics
Matches: 78, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 78 1.00
ACGTcount: A:0.21, C:0.21, G:0.15, T:0.43
Consensus pattern (66 bp):
TTCCTGAAACTCAAGTTCCTTCTTGTACAAAGTAGATTCAAATGTTGCTCTTTCCTGTTTTTTGG
A
Found at i:3906486 original size:21 final size:21
Alignment explanation
Indices: 3906459--3906511 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
3906449 TGGATTCCTC
*
3906459 AAACTCAAGTTGCAGTTTCTG
1 AAACTCAAGTTGCAGTTGCTG
* **
3906480 CAACTCAAACTGCAGTTGCTG
1 AAACTCAAGTTGCAGTTGCTG
*
3906501 AAACTGAAGTT
1 AAACTCAAGTT
3906512 CCTTTCTGTG
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.28
Consensus pattern (21 bp):
AAACTCAAGTTGCAGTTGCTG
Found at i:3906597 original size:174 final size:174
Alignment explanation
Indices: 3906283--3906844 Score: 547
Period size: 174 Copynumber: 3.1 Consensus size: 174
3906273 TTTTGTTTCT
* *
3906283 TCAAGCTCAAGTTGCATTTTCTGAAACTCAACTTGCAGTTCCTGAAACTCAAGTTCCTTCTTGTA
1 TCAAACTCAAGTTGCAGTTTCTGAAACTCAACTTGCAGTTCCTGAAACTCAAGTTCCTTCTTGTA
** * *
3906348 CAAAGTAGATTCAAATGTTGCTCTTTCCTGTTTTTTGGATTCCTGAAACTCAAGTTCCTTCTTGT
66 CAAAGTAGATTCAAACCTTGCTCTTTCCTGTTTTTTGGATTCCTCAAACTCAAGTTCCATCTTGT
* *** *
3906413 GCAAAGTAGATTCTAGTGTTTCTCTTTCCTGTTTTTTGGATTCC
131 GCAAAGTAGATTCAAACCTTTCACTTTCCTGTTTTTTGGATTCC
* * *
3906457 TCAAACTCAAGTTGCAGTTTCTGCAACTCAAAC-TGCAGTTGCTGAAACTGAAGTTCCTT-TCTG
1 TCAAACTCAAGTTGCAGTTTCTGAAACTC-AACTTGCAGTTCCTGAAACTCAAGTTCCTTCT-TG
* *
3906520 TGCAAAGTAGATTCAAACCTTGCTCTTTCCTGTTTTTTGGATTCCTCAAACTCAAGTTGCATCTT
64 TACAAAGTAGATTCAAACCTTGCTCTTTCCTGTTTTTTGGATTCCTCAAACTCAAGTTCCATCTT
* **
3906585 TTGCGTAGTAGATTCAAACCTTTCACTTTCCTGTTTTTTGGATTCC
129 GTGCAAAGTAGATTCAAACCTTTCACTTTCCTGTTTTTTGGATTCC
* * * *
3906631 TCAAACTCAACTTGCA-TCTTGTGGAAAGTAGATTCAAACCTTTCACTTTCCTGTTTCTTGGATT
1 TCAAACTCAAGTTGCAGT-TTCT-G--A--A-ACTC--A------AC--T--TG---C--AG-TT
* * * * * *
3906695 CCTCAAACTCAAGTTGCATCTTGTGCAAAGTAGATTCAAACCTTTCACTTTCCTGTTTTTTGGAT
41 CCTGAAACTCAAGTTCCTTCTTGTACAAAGTAGATTCAAACCTTGCTCTTTCCTGTTTTTTGGAT
* * * *
3906760 TCCTCAAACTCAAGTTCCTTCTTATGCAAAATAGATTCAAACCTTGCACTTTCCT-TTTTCTTGG
106 TCCTCAAACTCAAGTTCCATCTTGTGCAAAGTAGATTCAAACCTTTCACTTTCCTGTTTT-TTGG
3906824 ATTCC
170 ATTCC
3906829 TCAAACTCAAGTTGCA
1 TCAAACTCAAGTTGCA
3906845 TCTTTTGTAA
Statistics
Matches: 320, Mismatches: 39, Indels: 34
0.81 0.10 0.09
Matches are distributed among these distances:
173 2 0.01
174 167 0.52
175 4 0.01
179 1 0.00
180 3 0.01
181 2 0.01
187 2 0.01
192 2 0.01
195 1 0.00
197 5 0.02
198 130 0.41
199 1 0.00
ACGTcount: A:0.24, C:0.23, G:0.14, T:0.39
Consensus pattern (174 bp):
TCAAACTCAAGTTGCAGTTTCTGAAACTCAACTTGCAGTTCCTGAAACTCAAGTTCCTTCTTGTA
CAAAGTAGATTCAAACCTTGCTCTTTCCTGTTTTTTGGATTCCTCAAACTCAAGTTCCATCTTGT
GCAAAGTAGATTCAAACCTTTCACTTTCCTGTTTTTTGGATTCC
Found at i:3906614 original size:66 final size:66
Alignment explanation
Indices: 3906518--3906898 Score: 593
Period size: 66 Copynumber: 5.8 Consensus size: 66
3906508 AGTTCCTTTC
*
3906518 TGTGCAAAGTAGATTCAAACCTTGCTCTTTCCTGTTTTTTGGATTCCTCAAACTCAAGTTGCATC
1 TGTGCAAAGTAGATTCAAACCTTGCACTTTCCTGTTTTTTGGATTCCTCAAACTCAAGTTGCATC
3906583 T
66 T
* ** * *
3906584 TTTGCGTAGTAGATTCAAACCTTTCACTTTCCTGTTTTTTGGATTCCTCAAACTCAACTTGCATC
1 TGTGCAAAGTAGATTCAAACCTTGCACTTTCCTGTTTTTTGGATTCCTCAAACTCAAGTTGCATC
3906649 T
66 T
* * *
3906650 TGTGGAAAGTAGATTCAAACCTTTCACTTTCCTGTTTCTTGGATTCCTCAAACTCAAGTTGCATC
1 TGTGCAAAGTAGATTCAAACCTTGCACTTTCCTGTTTTTTGGATTCCTCAAACTCAAGTTGCATC
3906715 T
66 T
* * *
3906716 TGTGCAAAGTAGATTCAAACCTTTCACTTTCCTGTTTTTTGGATTCCTCAAACTCAAGTTCCTTC
1 TGTGCAAAGTAGATTCAAACCTTGCACTTTCCTGTTTTTTGGATTCCTCAAACTCAAGTTGCATC
3906781 T
66 T
* *
3906782 TATGCAAAATAGATTCAAACCTTGCACTTTCCT-TTTTCTTGGATTCCTCAAACTCAAGTTGCAT
1 TGTGCAAAGTAGATTCAAACCTTGCACTTTCCTGTTTT-TTGGATTCCTCAAACTCAAGTTGCAT
3906846 CT
65 CT
* * *
3906848 TTTGTAAAGTAGATTCAAACCTTGCACTTTCCTGTTTTTTTGATTCCTCAA
1 TGTGCAAAGTAGATTCAAACCTTGCACTTTCCTGTTTTTTGGATTCCTCAA
3906899 GGTCAACCTG
Statistics
Matches: 288, Mismatches: 25, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
65 4 0.01
66 280 0.97
67 4 0.01
ACGTcount: A:0.24, C:0.23, G:0.13, T:0.40
Consensus pattern (66 bp):
TGTGCAAAGTAGATTCAAACCTTGCACTTTCCTGTTTTTTGGATTCCTCAAACTCAAGTTGCATC
T
Found at i:3913510 original size:18 final size:18
Alignment explanation
Indices: 3913487--3913524 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
3913477 GTCTGTTCAG
3913487 AACACTTATTACATCAAT
1 AACACTTATTACATCAAT
3913505 AACACTTATTACATCAAT
1 AACACTTATTACATCAAT
3913523 AA
1 AA
3913525 GCACATGAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.47, C:0.21, G:0.00, T:0.32
Consensus pattern (18 bp):
AACACTTATTACATCAAT
Found at i:3913891 original size:109 final size:105
Alignment explanation
Indices: 3913700--3913919 Score: 309
Period size: 109 Copynumber: 2.1 Consensus size: 105
3913690 AAGGATTTAC
* **
3913700 AGCAATCAATATATTTCCTGTGTAGGTCTGGAATAAACATCAGCACATTTAGCTTCAAACAACAA
1 AGCAACCAATATATTTCCCATGTAGGTCTGGAATAAACATCAGCACATTTAGCTTCAAACAACAA
3913765 TACATATCCCTAGAAAAAAAACAAACAGCCACACAACAAATTAA
66 TACATATCCCTAG---AAAAA-AAACAGCCACACAACAAATTAA
* *
3913809 AGCAACCAATATATTTCCCATGTAGGTCTGGAATATACATCAGCACATTTAGCTTCAAACAA-TA
1 AGCAACCAATATATTTCCCATGTAGGTCTGGAATAAACATCAGCACATTTAGCTTCAAACAACAA
* *
3913873 -ACATGCATCTCTAGAAAAAAAACAGGCACACAACAAATTAA
66 TACAT--ATCCCTAGAAAAAAAACAGCCACACAACAAATTAA
3913914 AGCAAC
1 AGCAAC
3913920 ATATTCACAC
Statistics
Matches: 102, Mismatches: 7, Indels: 8
0.87 0.06 0.07
Matches are distributed among these distances:
105 27 0.26
106 5 0.05
107 4 0.04
108 1 0.01
109 65 0.64
ACGTcount: A:0.45, C:0.22, G:0.11, T:0.22
Consensus pattern (105 bp):
AGCAACCAATATATTTCCCATGTAGGTCTGGAATAAACATCAGCACATTTAGCTTCAAACAACAA
TACATATCCCTAGAAAAAAAACAGCCACACAACAAATTAA
Found at i:3919677 original size:88 final size:87
Alignment explanation
Indices: 3919580--3919771 Score: 224
Period size: 88 Copynumber: 2.2 Consensus size: 87
3919570 ATTGGTGTAC
* * * * *
3919580 TGATAGCATATTTGTTGTATATTGAATATTTGGCCATAAT-AGAAATGTCTTGAATTTAATGGCT
1 TGATGGCATATTAGGTGTAAATTGAATATTTGACCATAATGAGAAATGTCTTGAATTTAATGGCT
*
3919644 TGTGTTTATGGGAAATTGATACAT
66 TATGTTTAT-GG-AATTGATACAT
* * * * *
3919668 TGATGGCATATTAGGTGTAAATTGAATATTTGATCATGATGGAATAAATGTCTTTAATTTGATGG
1 TGATGGCATATTAGGTGTAAATTGAATATTTGACCATAAT-G-AGAAATGTCTTGAATTTAATGG
* *
3919733 CTTATGTTTATGGAATTGGTATAT
64 CTTATGTTTATGGAATTGATACAT
3919757 TGATGGCATATTAGG
1 TGATGGCATATTAGG
3919772 AGTATACTGA
Statistics
Matches: 88, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
88 33 0.38
89 24 0.27
90 2 0.02
91 29 0.33
ACGTcount: A:0.30, C:0.06, G:0.22, T:0.42
Consensus pattern (87 bp):
TGATGGCATATTAGGTGTAAATTGAATATTTGACCATAATGAGAAATGTCTTGAATTTAATGGCT
TATGTTTATGGAATTGATACAT
Found at i:3922330 original size:59 final size:59
Alignment explanation
Indices: 3922267--3922436 Score: 313
Period size: 59 Copynumber: 2.9 Consensus size: 59
3922257 TCAAGTTTGT
*
3922267 TTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATACAATTAATAATTTGATAAA
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATTTGATAAA
*
3922326 TTTACTAATCAAATATTAGATTTTATTACAACAATTAATACAATTAATAATTTGATAAA
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATTTGATAAA
*
3922385 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAACAATT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATT
3922437 AATAATTTGA
Statistics
Matches: 107, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
59 107 1.00
ACGTcount: A:0.45, C:0.09, G:0.05, T:0.41
Consensus pattern (59 bp):
TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATTTGATAAA
Done.