Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr9
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: 38630433
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2298367 characters in sequence are not A, C, G, or T
File 7 of 97
Found at i:3409988 original size:41 final size:42
Alignment explanation
Indices: 3409910--3409988 Score: 115
Period size: 41 Copynumber: 1.9 Consensus size: 42
3409900 GCTATCTCTA
** *
3409910 GCTGTCAGATTTCAGCAAGAAATTATTGATATTATGCTTCAT
1 GCTGTCAGATTTCAGCAAGAAATTATAAATATAATGCTTCAT
*
3409952 GCTGTCA-ATTTCAGCCAGAAATTATAAATATAATGCT
1 GCTGTCAGATTTCAGCAAGAAATTATAAATATAATGCT
3409989 GCAAGTGTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
41 26 0.79
42 7 0.21
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.35
Consensus pattern (42 bp):
GCTGTCAGATTTCAGCAAGAAATTATAAATATAATGCTTCAT
Found at i:3412472 original size:13 final size:14
Alignment explanation
Indices: 3412449--3412477 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
3412439 ATCCACAAAC
3412449 TACATAAAATTAAA
1 TACATAAAATTAAA
3412463 TACA-AAAATTAAA
1 TACATAAAATTAAA
3412476 TA
1 TA
3412478 AACAAATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.66, C:0.07, G:0.00, T:0.28
Consensus pattern (14 bp):
TACATAAAATTAAA
Found at i:3431474 original size:201 final size:200
Alignment explanation
Indices: 3431110--3431535 Score: 728
Period size: 201 Copynumber: 2.1 Consensus size: 200
3431100 TCGACCAACC
* * * * *
3431110 ATAATCTCCTAACTCAA-ATCCTTATAGGATAGTAAGATCGTTTGTTTTGATATCACTTGATGTA
1 ATAATCTTCTACCT-AAGATCCTTATAGGATAGTAAGATCGTTTGCTCTGATACCACTTGATGTA
3431174 GCCGAAAGGTTTAGGGCAATTAGAACTCAACAATTAGGGCTAGAATAGGGTTGATTGTGTTGGAA
65 GCCGAAAGGTTTAGGGCAATTAGAACTCAACAATTAGGGCTAGAATAGGGTTGATTGTGTTGGAA
3431239 CAATAAAAAGATAATTGGGTTTACAAAGAAACCTCTTGAATAAATATTCAAAATAACAAAAAATG
130 CAATAAAAAGATAATTGGGTTTACAAAGAAACCTCTTGAATAAATATTCAAAATAACAAAAAATG
3431304 ATAATA
195 ATAATA
* *
3431310 ATAATCTTCTATCTAAGATNCCTTATAGGATAGTAAGATCGTTTGCTCTGATACCATTTGATGTA
1 ATAATCTTCTACCTAAGAT-CCTTATAGGATAGTAAGATCGTTTGCTCTGATACCACTTGATGTA
3431375 GCCGAAAGGTTTAGGGCAATTAGAACTCAACAATTAGGGCTAGAATAGGGTTGATTGTGTTGGAA
65 GCCGAAAGGTTTAGGGCAATTAGAACTCAACAATTAGGGCTAGAATAGGGTTGATTGTGTTGGAA
* *
3431440 CAATAAAAAGATAATTGGGTTTTCAAAGAAACCTCTTGAATAAATATTCAAAATAACAAAAGATG
130 CAATAAAAAGATAATTGGGTTTACAAAGAAACCTCTTGAATAAATATTCAAAATAACAAAAAATG
*
3431505 ATAATG
195 ATAATA
*
3431511 ATAATCTTCTACCTAAGATACTTAT
1 ATAATCTTCTACCTAAGATCCTTAT
3431536 TTATAATAGT
Statistics
Matches: 213, Mismatches: 11, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
199 2 0.01
200 19 0.09
201 192 0.90
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.31
Consensus pattern (200 bp):
ATAATCTTCTACCTAAGATCCTTATAGGATAGTAAGATCGTTTGCTCTGATACCACTTGATGTAG
CCGAAAGGTTTAGGGCAATTAGAACTCAACAATTAGGGCTAGAATAGGGTTGATTGTGTTGGAAC
AATAAAAAGATAATTGGGTTTACAAAGAAACCTCTTGAATAAATATTCAAAATAACAAAAAATGA
TAATA
Found at i:3434622 original size:32 final size:34
Alignment explanation
Indices: 3434573--3434636 Score: 80
Period size: 34 Copynumber: 1.9 Consensus size: 34
3434563 ACCGGATAAG
3434573 TTCTATTTATGG-GTTTT-TATTCATACCTTACA
1 TTCTATTTATGGTGTTTTCTATTCATACCTTACA
* *
3434605 TTCTA-TTATGGCTTTTTTCTTTTCATACCTTA
1 TTCTATTTATGG-TGTTTTCTATTCATACCTTA
3434637 TGGAAGACAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
31 6 0.22
32 5 0.19
33 4 0.15
34 12 0.44
ACGTcount: A:0.19, C:0.17, G:0.08, T:0.56
Consensus pattern (34 bp):
TTCTATTTATGGTGTTTTCTATTCATACCTTACA
Found at i:3439026 original size:64 final size:63
Alignment explanation
Indices: 3438936--3439063 Score: 238
Period size: 64 Copynumber: 2.0 Consensus size: 63
3438926 TGGTAAATGC
3438936 ACCTTTTTTTTTCTTTTTTGCATAACATCCTATATGGTGCATTTCCAGTCAAATTTTGGATAA
1 ACCTTTTTTTTTCTTTTTTGCATAACATCCTATATGGTGCATTTCCAGTCAAATTTTGGATAA
*
3438999 ACCTTTTTCTTTTTTTTTTTGCATAACATCCTATATGGTGCATTTCCAGTCAAATTTTGGATAA
1 ACCTTTTT-TTTTCTTTTTTGCATAACATCCTATATGGTGCATTTCCAGTCAAATTTTGGATAA
3439063 A
1 A
3439064 GGATTAAGGT
Statistics
Matches: 63, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
63 8 0.13
64 55 0.87
ACGTcount: A:0.24, C:0.17, G:0.11, T:0.48
Consensus pattern (63 bp):
ACCTTTTTTTTTCTTTTTTGCATAACATCCTATATGGTGCATTTCCAGTCAAATTTTGGATAA
Found at i:3447058 original size:26 final size:25
Alignment explanation
Indices: 3446981--3447059 Score: 79
Period size: 26 Copynumber: 3.0 Consensus size: 25
3446971 ATTCAATTAT
*
3446981 AATAAATTTAAAATCAAATTTTATATAAA
1 AATAAA-TTAAAAT--AATTTCATA-AAA
*
3447010 AATAAATTAAAATTATTTCATAAAA
1 AATAAATTAAAATAATTTCATAAAA
3447035 AATAAAATTAAAA-AATTTCAATAAA
1 AAT-AAATTAAAATAATTTC-ATAAA
3447060 TATTACACTA
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
25 11 0.24
26 21 0.47
28 7 0.16
29 6 0.13
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (25 bp):
AATAAATTAAAATAATTTCATAAAA
Found at i:3451897 original size:2 final size:2
Alignment explanation
Indices: 3451890--3451925 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3451880 AGGATAAGAA
3451890 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
3451926 GTGTGTGTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3472183 original size:33 final size:36
Alignment explanation
Indices: 3472109--3472187 Score: 94
Period size: 33 Copynumber: 2.3 Consensus size: 36
3472099 AAAAAATTAA
* *
3472109 AAAAAATATATAATACATAAAATTATATTTAGAAAT
1 AAAAAATATATAATACATAAAATTATATATAAAAAT
* *
3472145 -GAAAATA-A-AATATATAAAATTATA-ATAAAAAT
1 AAAAAATATATAATACATAAAATTATATATAAAAAT
3472177 AAAAAATATAT
1 AAAAAATATAT
3472188 GATGTTAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
32 6 0.17
33 21 0.60
34 2 0.06
35 6 0.17
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.30
Consensus pattern (36 bp):
AAAAAATATATAATACATAAAATTATATATAAAAAT
Found at i:3479643 original size:16 final size:16
Alignment explanation
Indices: 3479624--3479664 Score: 82
Period size: 16 Copynumber: 2.6 Consensus size: 16
3479614 GAACAGCAGA
3479624 AAGAAAGAACCCAACT
1 AAGAAAGAACCCAACT
3479640 AAGAAAGAACCCAACT
1 AAGAAAGAACCCAACT
3479656 AAGAAAGAA
1 AAGAAAGAA
3479665 AAGAAGCAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.61, C:0.20, G:0.15, T:0.05
Consensus pattern (16 bp):
AAGAAAGAACCCAACT
Found at i:3480054 original size:220 final size:219
Alignment explanation
Indices: 3479640--3480167 Score: 738
Period size: 220 Copynumber: 2.4 Consensus size: 219
3479630 GAACCCAACT
* *
3479640 AAGAAAGAACCCAACTAAGAAAGAAAAGAAGCAGAGAAGACTTAAAGAGAAGATGAAAGGCTTTC
1 AAGAAAGAACCCAGCTAAGAAAGAAAGGAAGCAGAGAAGACTT-AAGAGAAGATGAAAGGCTTT-
* *
3479705 GTGTGTGTTGTGACTGAGGGTGTGAGACTATATTTATAGGCAGAGAGTGAAAAACAAGATAAACA
64 GTGTGTGTTGTGAGTGAGGGTGTGAGACTATATTTATAAGCAGAGAGTGAAAAACAAGATAAACA
* * * *
3479770 TTGGAGCAAAATCAGGAAAGCTAGGTAAATCAAAGGTTTGACCTTTCTTTATAATGTGCACAAAC
129 TTGGAGCAAAACCAGGAAAGCTAGGTAAATCAAAGGCTTGACCTTTCCTTATAATGTACACAAAC
3479835 TAATAAG-GAACGACATGAACAGCAGA
194 TAATAAGAG-ACGACATGAACAGCAGA
* * * *
3479861 AAGAAAAAACCCAGCTAAGAAAGAAAGGAAGCAGAAAAGACTTAAGAGAAAATGACAA-ACTTTG
1 AAGAAAGAACCCAGCTAAGAAAGAAAGGAAGCAGAGAAGACTTAAGAGAAGATGA-AAGGCTTTG
* * * * *
3479925 TTGTGTGTTGTGAGTGAGGGTGTGAGATTGTATTTATAAGCAGGGAGTGAAAACCAAGATAAACG
65 -TGTGTGTTGTGAGTGAGGGTGTGAGACTATATTTATAAGCAGAGAGTGAAAAACAAGATAAACA
* * * *
3479990 TTTGAGCAAAACCAGGAGAGCTAGGTAAATCAAAGGCTTGACGC-TTCCTTATAGTTTACACAAA
129 TTGGAGCAAAACCAGGAAAGCTAGGTAAATCAAAGGCTTGAC-CTTTCCTTATAATGTACACAAA
* *
3480054 CTAATAAGAGATGACATGAAGAGCAGA
193 CTAATAAGAGACGACATGAACAGCAGA
*
3480081 AAGAAAGAACCCGGCTAAGAAAGAAAGGAAGCAGAGAAGACTTAAGAGAAGATGAAAGGCTTTGG
1 AAGAAAGAACCCAGCTAAGAAAGAAAGGAAGCAGAGAAGACTTAAGAGAAGATGAAAGGCTTT-G
* *
3480146 TGTGTGTTGTTAGTAAGGGTGT
65 TGTGTGTTGTGAGTGAGGGTGT
3480168 AAAGCTGAAT
Statistics
Matches: 271, Mismatches: 30, Indels: 13
0.86 0.10 0.04
Matches are distributed among these distances:
219 3 0.01
220 224 0.83
221 44 0.16
ACGTcount: A:0.42, C:0.12, G:0.26, T:0.20
Consensus pattern (219 bp):
AAGAAAGAACCCAGCTAAGAAAGAAAGGAAGCAGAGAAGACTTAAGAGAAGATGAAAGGCTTTGT
GTGTGTTGTGAGTGAGGGTGTGAGACTATATTTATAAGCAGAGAGTGAAAAACAAGATAAACATT
GGAGCAAAACCAGGAAAGCTAGGTAAATCAAAGGCTTGACCTTTCCTTATAATGTACACAAACTA
ATAAGAGACGACATGAACAGCAGA
Found at i:3480323 original size:139 final size:139
Alignment explanation
Indices: 3480068--3480326 Score: 342
Period size: 139 Copynumber: 1.9 Consensus size: 139
3480058 TAAGAGATGA
** * *
3480068 CATGAAGAGCAGAAAGAAAGAACCCGGCTAAGAAAGAAAGGAAGCAGAGAAGACTTAAGAGAAGA
1 CATGAAGAGCAGAAAGAAAGAACCCAACTAAGAAAGAAAAGAAGCAGAGAAGACTAAAGAGAAGA
* * *
3480133 TGAAAGGCTTTGGTGTGTGTTGTTAGTAAGGGTGTAAAGCTGAATTCATAAGCAAGGTAACTAAA
66 TGAAAGACTTTGGTGTGTGTTGTGAGTAAGGATGTAAAGCTGAATTCATAAGCAAGGTAACTAAA
3480198 AAGGAATGG
131 AAGGAATGG
* * *
3480207 CATGAATAGCA-AAAGGAAAGAGCCCAACTAATAAA-AAAAGAAGCAGAGAAGACTAAAAGAGAA
1 CATGAAGAGCAGAAA-GAAAGAACCCAACTAAGAAAGAAAAGAAGCAGAGAAGACT-AAAGAGAA
* * * * * *
3480270 GATGAAAGACTTTGTTGTGTGTTGTGAGTGAGGATGTGAGGCTGTATTTATAAGCAA
64 GATGAAAGACTTTGGTGTGTGTTGTGAGTAAGGATGTAAAGCTGAATTCATAAGCAA
3480327 AGAGTGAAAT
Statistics
Matches: 102, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
138 21 0.21
139 81 0.79
ACGTcount: A:0.43, C:0.09, G:0.29, T:0.19
Consensus pattern (139 bp):
CATGAAGAGCAGAAAGAAAGAACCCAACTAAGAAAGAAAAGAAGCAGAGAAGACTAAAGAGAAGA
TGAAAGACTTTGGTGTGTGTTGTGAGTAAGGATGTAAAGCTGAATTCATAAGCAAGGTAACTAAA
AAGGAATGG
Found at i:3483165 original size:30 final size:31
Alignment explanation
Indices: 3483060--3483163 Score: 158
Period size: 31 Copynumber: 3.4 Consensus size: 31
3483050 TTTTAAAAAT
* *
3483060 TTAAATAAATTTTTATA-TTTTTATTAT-AT
1 TTAAATAAATTTTTATATTTTTTATTTTAAA
*
3483089 TTAATTAAATTTTTATATTTTTTATTTTAAA
1 TTAAATAAATTTTTATATTTTTTATTTTAAA
*
3483120 TCAAATAAATTTTTATATTTTTTATTTTAAA
1 TTAAATAAATTTTTATATTTTTTATTTTAAA
3483151 TTAAATAAATTTT
1 TTAAATAAATTTT
3483164 ATTATTAACG
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
29 16 0.24
30 9 0.13
31 42 0.63
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (31 bp):
TTAAATAAATTTTTATATTTTTTATTTTAAA
Found at i:3483264 original size:33 final size:33
Alignment explanation
Indices: 3483222--3483300 Score: 113
Period size: 33 Copynumber: 2.4 Consensus size: 33
3483212 ATGACGTTAT
*
3483222 TGTGATATATTAAAATATTATAATTAATTATGA
1 TGTGATATATTAAAATATCATAATTAATTATGA
* *
3483255 TGTGATATATTAATATATCATAATTGATTATGA
1 TGTGATATATTAAAATATCATAATTAATTATGA
**
3483288 CATGATATATTAA
1 TGTGATATATTAA
3483301 TTTAATATAA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.43, C:0.03, G:0.10, T:0.44
Consensus pattern (33 bp):
TGTGATATATTAAAATATCATAATTAATTATGA
Found at i:3483662 original size:29 final size:29
Alignment explanation
Indices: 3483621--3483766 Score: 106
Period size: 29 Copynumber: 5.2 Consensus size: 29
3483611 AACGCACATG
*
3483621 TTACACGTCATGTTTAAAAAATATTATTA
1 TTACACATCATGTTTAAAAAATATTATTA
* * * *
3483650 TTATATATCATG-TTAAAAAA-A-AATTG
1 TTACACATCATGTTTAAAAAATATTATTA
* ** *
3483676 TTATACATCATAATTAAAAAATATTGTTGA
1 TTACACATCATGTTTAAAAAATATTATT-A
* * *
3483706 -TACACACCATGTTGAAAAAA-A-AATTA
1 TTACACATCATGTTTAAAAAATATTATTA
** *
3483732 TTACATGTCATGTTTAAAAAATATTATTG
1 TTACACATCATGTTTAAAAAATATTATTA
3483761 TTACAC
1 TTACAC
3483767 GCTATGTTCA
Statistics
Matches: 86, Mismatches: 24, Indels: 14
0.69 0.19 0.11
Matches are distributed among these distances:
26 14 0.16
27 27 0.31
28 11 0.13
29 34 0.40
ACGTcount: A:0.45, C:0.10, G:0.08, T:0.38
Consensus pattern (29 bp):
TTACACATCATGTTTAAAAAATATTATTA
Found at i:3483679 original size:26 final size:26
Alignment explanation
Indices: 3483650--3483730 Score: 74
Period size: 26 Copynumber: 3.0 Consensus size: 26
3483640 AATATTATTA
*
3483650 TTATATATCATGTTAAAAAAAAATTG
1 TTATACATCATGTTAAAAAAAAATTG
* *
3483676 TTATACATCATAATT-AAAAAATATTG
1 TTATACATCAT-GTTAAAAAAAAATTG
*
3483702 TTGATACACACCATGTTGAAAAAAAAATT
1 TT-AT--ACATCATGTT-AAAAAAAAATT
3483731 ATTACATGTC
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
26 22 0.51
27 4 0.09
28 2 0.05
29 6 0.14
30 9 0.21
ACGTcount: A:0.49, C:0.09, G:0.07, T:0.35
Consensus pattern (26 bp):
TTATACATCATGTTAAAAAAAAATTG
Found at i:3483749 original size:56 final size:55
Alignment explanation
Indices: 3483619--3483812 Score: 176
Period size: 56 Copynumber: 3.5 Consensus size: 55
3483609 TAAACGCACA
* * * *
3483619 TGTTACACGTCATGTTTAAAAAATATTATT-ATTATATATCATGTTAAAAAAAAAT
1 TGTTACACGTCATATTTAAAAAATATTATTGA-TACACACCATGTTAAAAAAAAAT
* * * *
3483674 TGTTATACATCATAATTAAAAAATATTGTTGATACACACCATGTTGAAAAAAAAAT
1 TGTTACACGTCATATTTAAAAAATATTATTGATACACACCATGTT-AAAAAAAAAT
* * * * * * **
3483730 TATTACATGTCATGTTTAAAAAATATTATTGTTACACGCTATGTTCAAAAAAATTT
1 TGTTACACGTCATATTTAAAAAATATTATTGATACACACCATGTT-AAAAAAAAAT
**
3483786 TGTTACTTG-CTATATTTAAAAAATATT
1 TGTTACACGTC-ATATTTAAAAAATATT
3483813 GTTGTTATAC
Statistics
Matches: 112, Mismatches: 24, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
55 36 0.32
56 76 0.68
ACGTcount: A:0.43, C:0.09, G:0.08, T:0.39
Consensus pattern (55 bp):
TGTTACACGTCATATTTAAAAAATATTATTGATACACACCATGTTAAAAAAAAAT
Found at i:3483773 original size:29 final size:29
Alignment explanation
Indices: 3483689--3483837 Score: 110
Period size: 29 Copynumber: 5.3 Consensus size: 29
3483679 TACATCATAA
* * * *
3483689 TTAAAAAATATTGTTGATACACACCATGT
1 TTAAAAAATATTATTGTTACACGCTATGT
* * * *
3483718 TGAAAAAA-A-AATTATTACATG-TCATGT
1 TTAAAAAATATTATTGTTACACGCT-ATGT
3483745 TTAAAAAATATTATTGTTACACGCTATGT
1 TTAAAAAATATTATTGTTACACGCTATGT
* ** *
3483774 TCAAAAAA-ATT-TTGTTACTTGCTATAT
1 TTAAAAAATATTATTGTTACACGCTATGT
* * *
3483801 TTAAAAAATATTGTTGTTATACGTTATGT
1 TTAAAAAATATTATTGTTACACGCTATGT
*
3483830 TCAAAAAA
1 TTAAAAAA
3483838 AATTTTACTA
Statistics
Matches: 91, Mismatches: 23, Indels: 12
0.72 0.18 0.10
Matches are distributed among these distances:
27 37 0.41
28 8 0.09
29 45 0.49
30 1 0.01
ACGTcount: A:0.42, C:0.09, G:0.10, T:0.39
Consensus pattern (29 bp):
TTAAAAAATATTATTGTTACACGCTATGT
Found at i:3483818 original size:56 final size:56
Alignment explanation
Indices: 3483666--3483865 Score: 194
Period size: 56 Copynumber: 3.6 Consensus size: 56
3483656 ATCATGTTAA
* * * * *
3483666 AAAAAAATTGTTA-TACA--TCATAATTAAAAAATATTGTTGATACACACCATGTTG
1 AAAAAAATT-TTATTACATGTCATATTTAAAAAATATTGTTGTTACACGCTATGTTC
** * *
3483720 AAAAAAAAATTATTACATGTCATGTTTAAAAAATATTATTGTTACACGCTATGTTC
1 AAAAAAATTTTATTACATGTCATATTTAAAAAATATTGTTGTTACACGCTATGTTC
* * * *
3483776 AAAAAAATTTTGTTACTTG-CTATATTTAAAAAATATTGTTGTTATACGTTATGTTC
1 AAAAAAATTTTATTACATGTC-ATATTTAAAAAATATTGTTGTTACACGCTATGTTC
* *
3483832 AAAAAAAATTTTACTATATGTCAT-TTTGAAAAAA
1 -AAAAAAATTTTATTACATGTCATATTT-AAAAAA
3483866 AAAATATTAT
Statistics
Matches: 118, Mismatches: 21, Indels: 11
0.79 0.14 0.07
Matches are distributed among these distances:
53 3 0.03
54 11 0.09
55 1 0.01
56 79 0.67
57 23 0.19
58 1 0.01
ACGTcount: A:0.43, C:0.09, G:0.09, T:0.39
Consensus pattern (56 bp):
AAAAAAATTTTATTACATGTCATATTTAAAAAATATTGTTGTTACACGCTATGTTC
Found at i:3483893 original size:29 final size:29
Alignment explanation
Indices: 3483720--3483893 Score: 77
Period size: 29 Copynumber: 6.1 Consensus size: 29
3483710 CACCATGTTG
* *
3483720 AAAAAAAA-ATTATTACATGTCATGTTTA
1 AAAAAAAATATTATTACATGTTATGTTCA
* * * * *
3483748 AAAAATATTATTGTTACACGCTATGTTC-
1 AAAAAAAATATTATTACATGTTATGTTCA
* * * * * *
3483776 -AAAAAAATTTTGTTACTTGCTATATTTA
1 AAAAAAAATATTATTACATGTTATGTTCA
* * * * * *
3483804 AAAAATATTGTTGTTATACGTTATGTTC-
1 AAAAAAAATATTATTACATGTTATGTTCA
* * * * * *
3483832 AAAAAAAATTTTACTATATGTCATTTTGAA
1 AAAAAAAATATTATTACATGTTATGTT-CA
*
3483862 AAAAAAAATATTATTACATGTTATATTCA
1 AAAAAAAATATTATTACATGTTATGTTCA
3483891 AAA
1 AAA
3483894 TAATTTTGCT
Statistics
Matches: 103, Mismatches: 38, Indels: 9
0.69 0.25 0.06
Matches are distributed among these distances:
27 20 0.19
28 25 0.24
29 36 0.35
30 22 0.21
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (29 bp):
AAAAAAAATATTATTACATGTTATGTTCA
Found at i:3484558 original size:23 final size:23
Alignment explanation
Indices: 3484532--3484575 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
3484522 TGTTAGTGAA
*
3484532 CCTCTATCATTAGGCGTTAACAG
1 CCTCTATCACTAGGCGTTAACAG
*
3484555 CCTCTATTACTAGGCGTTAAC
1 CCTCTATCACTAGGCGTTAAC
3484576 GTTAATTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.25, C:0.27, G:0.16, T:0.32
Consensus pattern (23 bp):
CCTCTATCACTAGGCGTTAACAG
Found at i:3486990 original size:45 final size:45
Alignment explanation
Indices: 3486941--3487040 Score: 107
Period size: 45 Copynumber: 2.2 Consensus size: 45
3486931 TTTAACAAAT
**
3486941 TATTATTAAAATATAAT-ATATGATATTTTTGT-CTTTTAA-ATAAAA
1 TATTATTAAAATATAATGA-AAAATATTTTT-TACTTTTAATA-AAAA
* * *
3486986 TATTACTAAAATGTAATGAAAAATATTTTTTACTTTTGATAAAAA
1 TATTATTAAAATATAATGAAAAATATTTTTTACTTTTAATAAAAA
3487031 TATTATTAAA
1 TATTATTAAA
3487041 TTACAATAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
44 1 0.02
45 43 0.93
46 2 0.04
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (45 bp):
TATTATTAAAATATAATGAAAAATATTTTTTACTTTTAATAAAAA
Found at i:3487121 original size:43 final size:45
Alignment explanation
Indices: 3487013--3487321 Score: 207
Period size: 45 Copynumber: 6.9 Consensus size: 45
3487003 GAAAAATATT
* * *
3487013 TTTTA-CTTTTGATAAAAATATTATTAAATTACAATAAAAGGGT-G
1 TTTTATCTTTTGTTAAAAATATTATTAAATTATAATAAAA-GGTAA
* * * *
3487057 TTTTATGTTTTGGTGAAAATATTATTAAATTAT-GT-AAAGGATAA
1 TTTTATCTTTTGTTAAAAATATTATTAAATTATAATAAAAGG-TAA
* * * *
3487101 TTTCATCTTTTG-TATAAATATTATTAAGTTATAATAAAAGGTAT
1 TTTTATCTTTTGTTAAAAATATTATTAAATTATAATAAAAGGTAA
* *
3487145 TTTTGTATTTTGTTAAAAATATTATTAAATTATAATAAAAGGTAA
1 TTTTATCTTTTGTTAAAAATATTATTAAATTATAATAAAAGGTAA
*** * * * * *
3487190 TTTTATCTTTTACCATAGATACTATAAAATTATAATAATGAAGGGTAT
1 TTTTATCTTTTGTTAAAAATATTATTAAATTATAATAA--AA-GGTAA
* * * * * * *
3487238 TTTTGTATATTGGTGAAAATATTATTAACTTATAGT-AAAGGTTAA
1 TTTTATCTTTTGTTAAAAATATTATTAAATTATAATAAAAGG-TAA
* * * ** * *
3487283 TTTTTTCCTATGACATAAATATTACTAAATTATAATAAA
1 TTTTATCTTTTGTTAAAAATATTATTAAATTATAATAAA
3487322 GTTTATCTTT
Statistics
Matches: 199, Mismatches: 55, Indels: 20
0.73 0.20 0.07
Matches are distributed among these distances:
42 2 0.01
43 21 0.11
44 30 0.15
45 114 0.57
46 2 0.01
47 3 0.02
48 27 0.14
ACGTcount: A:0.41, C:0.04, G:0.11, T:0.44
Consensus pattern (45 bp):
TTTTATCTTTTGTTAAAAATATTATTAAATTATAATAAAAGGTAA
Found at i:3487183 original size:22 final size:22
Alignment explanation
Indices: 3487116--3487184 Score: 57
Period size: 22 Copynumber: 3.1 Consensus size: 22
3487106 TCTTTTGTAT
*
3487116 AAATATTATTAAGTTATAATAA
1 AAATATTATTAAATTATAATAA
* * ** * **
3487138 AAGGTATTTTTGTATTTTGTTAA
1 AA-ATATTATTAAATTATAATAA
3487161 AAATATTATTAAATTATAATAA
1 AAATATTATTAAATTATAATAA
3487183 AA
1 AA
3487185 GGTAATTTTA
Statistics
Matches: 31, Mismatches: 15, Indels: 2
0.65 0.31 0.04
Matches are distributed among these distances:
22 17 0.55
23 14 0.45
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (22 bp):
AAATATTATTAAATTATAATAA
Found at i:3487245 original size:93 final size:89
Alignment explanation
Indices: 3487028--3487321 Score: 265
Period size: 93 Copynumber: 3.3 Consensus size: 89
3487018 CTTTTGATAA
* * * * *
3487028 AAATATTATTAAATTACAATAAAAGGGTGTTTTATGT-T-TTGGTGAAAATATTATTAAATTAT-
1 AAATACTATAAAATTATAATAAAA-GGTATTTT-TGTATATTGGTAAAAATATTATTAAATTATA
* **
3487090 GTAAAGGATAATTTCATCTTTTGTAT
64 GTAAAGGATAATTTTATCTTTTCCAT
* * * * * *
3487116 AAATATTATTAAGTTATAATAAAAGGTATTTTTGTATTTTGTTAAAAATATTATTAAATTATAAT
1 AAATACTATAAAATTATAATAAAAGGTATTTTTGTATATTGGTAAAAATATTATTAAATTATAGT
3487181 AAAAGG-TAATTTTATCTTTTACCAT
66 -AAAGGATAATTTTATCTTTT-CCAT
* * *
3487206 AGATACTATAAAATTATAATAATGAAGGGTATTTTTGTATATTGGTGAAAATATTATTAACTTAT
1 AAATACTATAAAATTATAATAA--AA-GGTATTTTTGTATATTGGTAAAAATATTATTAAATTAT
* * * **
3487271 AGTAAAGGTTAATTTTTTCCTATGACAT
63 AGTAAAGGATAATTTTAT-CTTTTCCAT
*
3487299 AAATATTACT-AAATTATAATAAA
1 AAATACTA-TAAAATTATAATAAA
3487322 GTTTATCTTT
Statistics
Matches: 171, Mismatches: 24, Indels: 19
0.80 0.11 0.09
Matches are distributed among these distances:
86 3 0.02
87 8 0.05
88 44 0.26
89 14 0.08
90 25 0.15
91 1 0.01
92 7 0.04
93 65 0.38
94 4 0.02
ACGTcount: A:0.41, C:0.04, G:0.11, T:0.44
Consensus pattern (89 bp):
AAATACTATAAAATTATAATAAAAGGTATTTTTGTATATTGGTAAAAATATTATTAAATTATAGT
AAAGGATAATTTTATCTTTTCCAT
Found at i:3490922 original size:2 final size:2
Alignment explanation
Indices: 3490915--3490952 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
3490905 CACGCAAATC
*
3490915 AG AG AG AG AG AG AG AG AG AA 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
3490953 CAAAGATTCT
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:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3499927 original size:9 final size:9
Alignment explanation
Indices: 3499913--3499969 Score: 80
Period size: 9 Copynumber: 6.4 Consensus size: 9
3499903 CATCCCGATT
3499913 TTTTTTTTA
1 TTTTTTTTA
3499922 TTTTTTTTA
1 TTTTTTTTA
3499931 TTTTTTTTA
1 TTTTTTTTA
*
3499940 TTTTATTTA
1 TTTTTTTTA
**
3499949 TTTAATTTA
1 TTTTTTTTA
3499958 TTTTTTTT-
1 TTTTTTTTA
3499966 TTTT
1 TTTT
3499970 AATTTATGTG
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
8 4 0.09
9 40 0.91
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:3499948 original size:27 final size:26
Alignment explanation
Indices: 3499911--3499976 Score: 89
Period size: 27 Copynumber: 2.5 Consensus size: 26
3499901 GCCATCCCGA
**
3499911 TTTTTTT-TTTATTTTTTTTATTTTT
1 TTTTTTTATTTATTTAATTTATTTTT
3499936 TTTATTTTATTTATTTAATTTATTTTT
1 TTT-TTTTATTTATTTAATTTATTTTT
3499963 TTTTTTTAATTTAT
1 TTTTTTT-ATTTAT
3499977 GTGTCTACAG
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
25 3 0.08
26 8 0.22
27 25 0.69
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (26 bp):
TTTTTTTATTTATTTAATTTATTTTT
Found at i:3499970 original size:18 final size:18
Alignment explanation
Indices: 3499918--3499976 Score: 75
Period size: 18 Copynumber: 3.3 Consensus size: 18
3499908 CGATTTTTTT
*
3499918 TTTATTTTTTTTATTTT-T
1 TTTATTTTTTTT-TTTTAA
* *
3499936 TTTATTTTATTTATTTAA
1 TTTATTTTTTTTTTTTAA
3499954 TTTATTTTTTTTTTTTAA
1 TTTATTTTTTTTTTTTAA
3499972 TTTAT
1 TTTAT
3499977 GTGTCTACAG
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
17 3 0.09
18 32 0.91
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (18 bp):
TTTATTTTTTTTTTTTAA
Found at i:3502299 original size:17 final size:17
Alignment explanation
Indices: 3502274--3502308 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
3502264 AAATTGTCTG
*
3502274 TTCTCCTCTTCACCATT
1 TTCTCCTCTTCAACATT
*
3502291 TTCTTCTCTTCAACATT
1 TTCTCCTCTTCAACATT
3502308 T
1 T
3502309 GCTCTCAACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.14, C:0.34, G:0.00, T:0.51
Consensus pattern (17 bp):
TTCTCCTCTTCAACATT
Found at i:3514757 original size:11 final size:11
Alignment explanation
Indices: 3514712--3514761 Score: 50
Period size: 11 Copynumber: 4.6 Consensus size: 11
3514702 TATAAAAGAT
*
3514712 AAATATTTATTT
1 AAATATTT-TTA
3514724 AAA-ATTTTT-
1 AAATATTTTTA
* *
3514733 AAATAATTTAA
1 AAATATTTTTA
3514744 AAATATTTTTA
1 AAATATTTTTA
3514755 AAATATT
1 AAATATT
3514762 ATATCAATAA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
9 3 0.09
10 6 0.19
11 20 0.62
12 3 0.09
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
AAATATTTTTA
Found at i:3515592 original size:7 final size:7
Alignment explanation
Indices: 3515578--3515647 Score: 58
Period size: 7 Copynumber: 10.4 Consensus size: 7
3515568 AAAAATGAAA
3515578 ATAAAAT
1 ATAAAAT
*
3515585 ATATAAT
1 ATAAAAT
*
3515592 ATAAAAA
1 ATAAAAT
3515599 ATAAAA-
1 ATAAAAT
3515605 ATAAAAT
1 ATAAAAT
*
3515612 ATACAAT
1 ATAAAAT
*
3515619 ATTATAAT
1 A-TAAAAT
*
3515627 A-AGAA-
1 ATAAAAT
3515632 ATAAAA-
1 ATAAAAT
3515638 ATAAAAT
1 ATAAAAT
3515645 ATA
1 ATA
3515648 TGATATTAAA
Statistics
Matches: 52, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
5 1 0.02
6 18 0.35
7 27 0.52
8 6 0.12
ACGTcount: A:0.70, C:0.01, G:0.01, T:0.27
Consensus pattern (7 bp):
ATAAAAT
Found at i:3515654 original size:33 final size:30
Alignment explanation
Indices: 3515561--3515659 Score: 107
Period size: 33 Copynumber: 3.3 Consensus size: 30
3515551 ATATTATCTT
*
3515561 TTATAAAAAAAATGAAAATAAAATATATA-A
1 TTAT-AAAAAAATAAAAATAAAATATATATA
*
3515591 -TAT-AAAAAATAAAAATAAAATATACAATA
1 TTATAAAAAAATAAAAATAAAATATA-TATA
3515620 TTATAATAAGAAATAAAAATAAAATATATGATA
1 TTATAA-AA-AAATAAAAATAAAATATAT-ATA
3515653 TTA-AAAA
1 TTATAAAA
3515660 TATATTTAAG
Statistics
Matches: 59, Mismatches: 3, Indels: 13
0.79 0.04 0.17
Matches are distributed among these distances:
27 20 0.34
28 1 0.02
29 4 0.07
30 3 0.05
31 3 0.05
32 4 0.07
33 24 0.41
ACGTcount: A:0.69, C:0.01, G:0.03, T:0.27
Consensus pattern (30 bp):
TTATAAAAAAATAAAAATAAAATATATATA
Found at i:3518221 original size:50 final size:50
Alignment explanation
Indices: 3518146--3518247 Score: 195
Period size: 50 Copynumber: 2.0 Consensus size: 50
3518136 TACGTTCATA
*
3518146 AATATTCTAGTTTCAATACGTCGTTATTGAAATAAAGTCAAATAAAAATT
1 AATATTCTAGTTTCAATACGCCGTTATTGAAATAAAGTCAAATAAAAATT
3518196 AATATTCTAGTTTCAATACGCCGTTATTGAAATAAAGTCAAATAAAAATT
1 AATATTCTAGTTTCAATACGCCGTTATTGAAATAAAGTCAAATAAAAATT
3518246 AA
1 AA
3518248 ATGGATATTG
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.45, C:0.11, G:0.10, T:0.34
Consensus pattern (50 bp):
AATATTCTAGTTTCAATACGCCGTTATTGAAATAAAGTCAAATAAAAATT
Found at i:3520278 original size:18 final size:19
Alignment explanation
Indices: 3520241--3520278 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
3520231 CTTTGAATTA
* *
3520241 TTTATTTATTTTTTATATT
1 TTTATTTATGTTTAATATT
3520260 TTTATTT-TGTTTAATATT
1 TTTATTTATGTTTAATATT
3520278 T
1 T
3520279 CAAGTTATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (19 bp):
TTTATTTATGTTTAATATT
Found at i:3520571 original size:23 final size:23
Alignment explanation
Indices: 3520537--3520582 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
3520527 CAAAAGAATG
3520537 TGTATTTATAAATTGTGAAAGTT
1 TGTATTTATAAATTGTGAAAGTT
*
3520560 TGTATTTGTAAATTGTGAAAGTT
1 TGTATTTATAAATTGTGAAAGTT
3520583 GTAACTAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.33, C:0.00, G:0.20, T:0.48
Consensus pattern (23 bp):
TGTATTTATAAATTGTGAAAGTT
Found at i:3520814 original size:15 final size:17
Alignment explanation
Indices: 3520784--3520817 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
3520774 ATTTATATAT
3520784 ATTTTTTAACACCATAA
1 ATTTTTTAACACCATAA
3520801 ATTTTTT-ACA-CATAA
1 ATTTTTTAACACCATAA
3520816 AT
1 AT
3520818 ATTTGGCTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 3 0.18
17 7 0.41
ACGTcount: A:0.41, C:0.15, G:0.00, T:0.44
Consensus pattern (17 bp):
ATTTTTTAACACCATAA
Found at i:3520821 original size:17 final size:18
Alignment explanation
Indices: 3520782--3520821 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
3520772 GTATTTATAT
3520782 ATATTTTTTAACACCATA
1 ATATTTTTTAACACCATA
3520800 A-ATTTTTT-ACA-CATAA
1 ATATTTTTTAACACCAT-A
3520816 ATATTT
1 ATATTT
3520822 GGCTTATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
15 3 0.15
16 5 0.25
17 11 0.55
18 1 0.05
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.47
Consensus pattern (18 bp):
ATATTTTTTAACACCATA
Found at i:3521099 original size:31 final size:30
Alignment explanation
Indices: 3521045--3521116 Score: 81
Period size: 31 Copynumber: 2.4 Consensus size: 30
3521035 GTCAACACTA
*
3521045 CCATGTCATCACATAATGCCACGTGGTATTG
1 CCATGTCATCACATAATGCCACGTGGCA-TG
* ** *
3521076 CCATGTCATCACTTGGTGTCACGTGGCATG
1 CCATGTCATCACATAATGCCACGTGGCATG
*
3521106 CCACGTCATCA
1 CCATGTCATCA
3521117 TCTCAAATGT
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
30 12 0.34
31 23 0.66
ACGTcount: A:0.22, C:0.29, G:0.21, T:0.28
Consensus pattern (30 bp):
CCATGTCATCACATAATGCCACGTGGCATG
Found at i:3524628 original size:11 final size:12
Alignment explanation
Indices: 3524603--3524632 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
3524593 ATTTGAGTAT
3524603 TTAATTTATTAA
1 TTAATTTATTAA
3524615 TTAATTTA-TAA
1 TTAATTTATTAA
3524626 TTAATTT
1 TTAATTT
3524633 TTTACTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 10 0.56
12 8 0.44
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TTAATTTATTAA
Found at i:3526928 original size:48 final size:48
Alignment explanation
Indices: 3526876--3526967 Score: 130
Period size: 48 Copynumber: 1.9 Consensus size: 48
3526866 GCGTAACTAA
* *
3526876 TTTTTGACAAGACATTGCCTGACTAGTTAATATGCATTACGTGATTAG
1 TTTTTGACAAGACATTGCCTAACTAGTTAATAGGCATTACGTGATTAG
* * * *
3526924 TTTTTGATAAGACATTGCGTAACTAGTTGATAGGCATTGCGTGA
1 TTTTTGACAAGACATTGCCTAACTAGTTAATAGGCATTACGTGA
3526968 CTTGTTAGTA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
48 38 1.00
ACGTcount: A:0.28, C:0.13, G:0.22, T:0.37
Consensus pattern (48 bp):
TTTTTGACAAGACATTGCCTAACTAGTTAATAGGCATTACGTGATTAG
Found at i:3526950 original size:26 final size:26
Alignment explanation
Indices: 3526863--3526951 Score: 69
Period size: 26 Copynumber: 3.6 Consensus size: 26
3526853 GTTTTTAGGT
* *
3526863 ATTGCGTAACTAATTTTTGACAAGAC
1 ATTGCGTAACTAGTTTTTGATAAGAC
* * * *
3526889 ATTGCCTGACTAG---TTAATATG-C
1 ATTGCGTAACTAGTTTTTGATAAGAC
* * *
3526911 ATTACGTGATTAGTTTTTGATAAGAC
1 ATTGCGTAACTAGTTTTTGATAAGAC
3526937 ATTGCGTAACTAGTT
1 ATTGCGTAACTAGTT
3526952 GATAGGCATT
Statistics
Matches: 45, Mismatches: 14, Indels: 8
0.67 0.21 0.12
Matches are distributed among these distances:
22 11 0.24
23 5 0.11
25 6 0.13
26 23 0.51
ACGTcount: A:0.30, C:0.13, G:0.18, T:0.38
Consensus pattern (26 bp):
ATTGCGTAACTAGTTTTTGATAAGAC
Found at i:3526990 original size:23 final size:23
Alignment explanation
Indices: 3526955--3527032 Score: 120
Period size: 23 Copynumber: 3.4 Consensus size: 23
3526945 ACTAGTTGAT
3526955 AGGCATTGCGTGACTTGTTAGTA
1 AGGCATTGCGTGACTTGTTAGTA
* *
3526978 AGGTATTGTGTGACTTGTTAGTA
1 AGGCATTGCGTGACTTGTTAGTA
* *
3527001 AGACATTGCGTGACTAGTTAGTA
1 AGGCATTGCGTGACTTGTTAGTA
3527024 AGGCATTGC
1 AGGCATTGC
3527033 TTAAAAATTA
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 48 1.00
ACGTcount: A:0.24, C:0.12, G:0.29, T:0.35
Consensus pattern (23 bp):
AGGCATTGCGTGACTTGTTAGTA
Found at i:3527075 original size:22 final size:22
Alignment explanation
Indices: 3527034--3527111 Score: 86
Period size: 22 Copynumber: 3.6 Consensus size: 22
3527024 AGGCATTGCT
* * *
3527034 TAAAAATTAGTCACGCAATGTC
1 TAAAAACTAGTCACGTAATGAC
* *
3527056 TAAAAACTAGTCACATAATGCC
1 TAAAAACTAGTCACGTAATGAC
* *
3527078 T-AAAACCAATCACGTAATGAC
1 TAAAAACTAGTCACGTAATGAC
3527099 TAAAAACTAGTCA
1 TAAAAACTAGTCA
3527112 TACGGTGATT
Statistics
Matches: 45, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
21 17 0.38
22 28 0.62
ACGTcount: A:0.46, C:0.21, G:0.10, T:0.23
Consensus pattern (22 bp):
TAAAAACTAGTCACGTAATGAC
Found at i:3528766 original size:214 final size:213
Alignment explanation
Indices: 3528529--3529157 Score: 876
Period size: 214 Copynumber: 3.0 Consensus size: 213
3528519 TAATTGTATA
* * *
3528529 AATATTTTATATATACATATATTTAATTTATAAATAAACATTACTATAATTTATAATAAACTTTA
1 AATATATTATATATAC-TATATTTAATTTATACATAAGCATTACTATAATTTATAATAAACTTTA
* * *
3528594 TTTATATTATTACACTTAATAACTTTATTAGTTATCACCTTAGATTTTGTAACATATTGTTTCTA
65 TTTATATGATTACACTTAATAACTTTATTAGTTATCACCTTAGATTTTATAACATATTGTTTATA
* *
3528659 ATTAGTTATTATTTATATAAACTTTGATTTAAAACATTATAATATATAAGTTATGTCATCAATTT
130 ATTAGTTATTATTTATACAAACTTTGATATAAAACATTATAATATATAAGTTATGTCAT-AATTT
3528724 CATATATATATA-ATAAAGT
194 CATATATATATACATAAAGT
* * *
3528743 CATATATTATATATACGTATATTTAATTTATACATAAGCATTACTATAACTTATAATAGACTTTA
1 AATATATTATATATAC-TATATTTAATTTATACATAAGCATTACTATAATTTATAATAAACTTTA
* * *
3528808 TTTATATGATTACTCTTAATAACTTTATTAGTTATCACCTTAAATGTTATAACATATTGTTTATA
65 TTTATATGATTACACTTAATAACTTTATTAGTTATCACCTTAGATTTTATAACATATTGTTTATA
* * * *
3528873 ATTAGTTATTATTTATACAAACTTTGATATAAAACATTTTAACATATAA-TT-TGT-ATTA-TTA
130 ATTAGTTATTATTTATACAAACTTTGATATAAAACATTATAATATATAAGTTATGTCATAATTTC
3528934 AT-TATATATACATAAAGT
195 ATATATATATACATAAAGT
** * * *
3528952 AATGCATTATCTATA-TATATTTAATTTATACATAAGCATTATTATAATTTATAATAAATTTTAT
1 AATATATTATATATACTATATTTAATTTATACATAAGCATTACTATAATTTATAATAAACTTTAT
* * **
3529016 TTATATGATTATACTTAATAAGTTTATTAGTTATCATTTTAGATTTTATAACATATTGTTTATAA
66 TTATATGATTACACTTAATAACTTTATTAGTTATCACCTTAGATTTTATAACATATTGTTTATAA
* * * **
3529081 TTAGTTATTTTTTTATACAAACTTTGATATAAAATATTATAATATATAAGTTATATCATTGGTTT
131 TTAGTTA-TTATTTATACAAACTTTGATATAAAACATTATAATATATAAGTTATGTCA-TAATTT
3529146 CATATATATATA
194 CATATATATATA
3529158 TATGTAAAAT
Statistics
Matches: 365, Mismatches: 42, Indels: 16
0.86 0.10 0.04
Matches are distributed among these distances:
207 110 0.30
208 45 0.12
209 24 0.07
210 3 0.01
211 3 0.01
212 4 0.01
213 6 0.02
214 170 0.47
ACGTcount: A:0.40, C:0.07, G:0.05, T:0.48
Consensus pattern (213 bp):
AATATATTATATATACTATATTTAATTTATACATAAGCATTACTATAATTTATAATAAACTTTAT
TTATATGATTACACTTAATAACTTTATTAGTTATCACCTTAGATTTTATAACATATTGTTTATAA
TTAGTTATTATTTATACAAACTTTGATATAAAACATTATAATATATAAGTTATGTCATAATTTCA
TATATATATACATAAAGT
Found at i:3531421 original size:9 final size:9
Alignment explanation
Indices: 3531395--3531424 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
3531385 GAAGATGGCT
*
3531395 CAACAACAA
1 CAACAACAG
3531404 CAACAACAG
1 CAACAACAG
3531413 CAACAACAG
1 CAACAACAG
3531422 CAA
1 CAA
3531425 GAGGAGCTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.60, C:0.33, G:0.07, T:0.00
Consensus pattern (9 bp):
CAACAACAG
Found at i:3534570 original size:9 final size:9
Alignment explanation
Indices: 3534556--3534585 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
3534546 TTAATTCGAG
3534556 TTTTTATTT
1 TTTTTATTT
3534565 TTTTTATTTT
1 TTTTTA-TTT
3534575 TTTTTATTT
1 TTTTTATTT
3534584 TT
1 TT
3534586 AATAGTAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (9 bp):
TTTTTATTT
Found at i:3534575 original size:10 final size:10
Alignment explanation
Indices: 3534556--3534585 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
3534546 TTAATTCGAG
3534556 TTTTTA-TTT
1 TTTTTATTTT
3534565 TTTTTATTTT
1 TTTTTATTTT
3534575 TTTTTATTTT
1 TTTTTATTTT
3534585 T
1 T
3534586 AATAGTAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 6 0.30
10 14 0.70
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (10 bp):
TTTTTATTTT
Found at i:3557393 original size:20 final size:20
Alignment explanation
Indices: 3557368--3557408 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
3557358 GCTAGTTTGT
3557368 GCTTTGGTCAAGTGGATTAG
1 GCTTTGGTCAAGTGGATTAG
3557388 GCTTTGGTCAAGTGGATTAG
1 GCTTTGGTCAAGTGGATTAG
3557408 G
1 G
3557409 TTGAAGGACC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.20, C:0.10, G:0.37, T:0.34
Consensus pattern (20 bp):
GCTTTGGTCAAGTGGATTAG
Found at i:3564820 original size:2 final size:2
Alignment explanation
Indices: 3564813--3564847 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
3564803 GTGTCACAGG
*
3564813 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TT TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
3564848 TTCATGCACT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (2 bp):
TC
Found at i:3586066 original size:66 final size:66
Alignment explanation
Indices: 3585960--3586099 Score: 226
Period size: 66 Copynumber: 2.1 Consensus size: 66
3585950 AGGTCTTCTA
* * ** * *
3585960 ATTTGTTAAAAAGTTTCTTTACTTTTATATTTGTACGTATGGGTTGATGCGCAATTGTACATCCT
1 ATTTGTTAAAAAGTTTCTCTACGTTTATATTTCCACGTATGGGTTGATGCGCAATCGGACATCCT
3586025 C
66 C
3586026 ATTTGTTAAAAAGTTTCTCTACGTTTATATTTCCACGTATGGGTTGATGCGCAATCGGACATCCT
1 ATTTGTTAAAAAGTTTCTCTACGTTTATATTTCCACGTATGGGTTGATGCGCAATCGGACATCCT
3586091 C
66 C
3586092 ATTTGTTA
1 ATTTGTTA
3586100 CATTAAGGAA
Statistics
Matches: 68, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
66 68 1.00
ACGTcount: A:0.24, C:0.16, G:0.17, T:0.43
Consensus pattern (66 bp):
ATTTGTTAAAAAGTTTCTCTACGTTTATATTTCCACGTATGGGTTGATGCGCAATCGGACATCCT
C
Found at i:3604156 original size:19 final size:18
Alignment explanation
Indices: 3604124--3604162 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
3604114 TCGTGTTCCC
*
3604124 TTTATTTTTCAGCCGTGT
1 TTTATTTTTAAGCCGTGT
*
3604142 TTTATTTTTTAAGCCTTGT
1 TTTA-TTTTTAAGCCGTGT
3604161 TT
1 TT
3604163 CAATAGTGGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.13, C:0.13, G:0.13, T:0.62
Consensus pattern (18 bp):
TTTATTTTTAAGCCGTGT
Found at i:3619674 original size:23 final size:21
Alignment explanation
Indices: 3619646--3619690 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 21
3619636 TTTTTTAAAA
*
3619646 TTAATATTTTAATATTATATTAT
1 TTAATAATTTAA-A-TATATTAT
3619669 TTAATAATTTAAATATATTAT
1 TTAATAATTTAAATATATTAT
3619690 T
1 T
3619691 ATTAAAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 9 0.43
22 1 0.05
23 11 0.52
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
TTAATAATTTAAATATATTAT
Found at i:3619678 original size:24 final size:23
Alignment explanation
Indices: 3619646--3619693 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 23
3619636 TTTTTTAAAA
*
3619646 TTAATATTTTAATAT-TATATTAT
1 TTAATATTTAAATATAT-TATTAT
3619669 TTAATAATTTAAATATATTATTAT
1 TTAAT-ATTTAAATATATTATTAT
3619693 T
1 T
3619694 AAAATATGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 5 0.23
24 16 0.73
25 1 0.05
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (23 bp):
TTAATATTTAAATATATTATTAT
Found at i:3619684 original size:32 final size:29
Alignment explanation
Indices: 3619633--3619694 Score: 70
Period size: 32 Copynumber: 2.0 Consensus size: 29
3619623 TTATTACAAA
* *
3619633 ATATTTTTTAAAATTAATATTTTAATATT
1 ATATTATTTAAAATTAATATATTAATATT
*
3619662 ATATTATTTAATAATTTAAATATATTATTATT
1 ATATTATTTAA-AA-TT-AATATATTAATATT
3619694 A
1 A
3619695 AAATATGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 10 0.37
30 2 0.07
31 2 0.07
32 13 0.48
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (29 bp):
ATATTATTTAAAATTAATATATTAATATT
Found at i:3627268 original size:13 final size:13
Alignment explanation
Indices: 3627250--3627274 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3627240 CTCTGTTTTG
3627250 GCTCTGTTTTTCT
1 GCTCTGTTTTTCT
3627263 GCTCTGTTTTTC
1 GCTCTGTTTTTC
3627275 AGTTCAAAGA
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:0.00, C:0.24, G:0.16, T:0.60
Consensus pattern (13 bp):
GCTCTGTTTTTCT
Found at i:3636047 original size:18 final size:18
Alignment explanation
Indices: 3636024--3636061 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
3636014 GTACCAATAT
3636024 CATGATCATTATGTATGG
1 CATGATCATTATGTATGG
3636042 CATGATCATTATGTATGG
1 CATGATCATTATGTATGG
3636060 CA
1 CA
3636062 GGACCATGCA
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:0.29, C:0.13, G:0.21, T:0.37
Consensus pattern (18 bp):
CATGATCATTATGTATGG
Found at i:3642140 original size:22 final size:22
Alignment explanation
Indices: 3642113--3642179 Score: 64
Period size: 25 Copynumber: 2.9 Consensus size: 22
3642103 TCATAATTCT
3642113 TAATAAAATATTATAATTTTTA
1 TAATAAAATATTATAATTTTTA
*
3642135 TAATAAAA-ATTTAATATACTTCTTA
1 TAATAAAATA-TT-ATA-A-TTTTTA
*
3642160 TAATAAAGTATTACTAATTT
1 TAATAAAATATTA-TAATTT
3642180 ATAATTTATT
Statistics
Matches: 36, Mismatches: 3, Indels: 11
0.72 0.06 0.22
Matches are distributed among these distances:
21 1 0.03
22 10 0.28
23 5 0.14
24 3 0.08
25 16 0.44
26 1 0.03
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.46
Consensus pattern (22 bp):
TAATAAAATATTATAATTTTTA
Found at i:3642246 original size:24 final size:24
Alignment explanation
Indices: 3642201--3642246 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
3642191 AAAATATAAT
*
3642201 TTTTTATTTTTTTCTTTATTTTCA
1 TTTTTATTTTTTTCTTCATTTTCA
*
3642225 TTTTTACTTTTTTT-TTCCTTTT
1 TTTTTA-TTTTTTTCTTCATTTT
3642247 TCTTTCTTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 12 0.63
25 7 0.37
ACGTcount: A:0.09, C:0.11, G:0.00, T:0.80
Consensus pattern (24 bp):
TTTTTATTTTTTTCTTCATTTTCA
Found at i:3653427 original size:11 final size:11
Alignment explanation
Indices: 3653413--3653438 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
3653403 GTAAAACGAT
3653413 GAGAAAATGGG
1 GAGAAAATGGG
3653424 GAGAAAATGGG
1 GAGAAAATGGG
3653435 GAGA
1 GAGA
3653439 GGCTATTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.46, T:0.08
Consensus pattern (11 bp):
GAGAAAATGGG
Found at i:3665215 original size:5 final size:5
Alignment explanation
Indices: 3665205--3665232 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
3665195 GGAGAGATCT
3665205 GAAAA GAAAA GAAAA GAAAA GAAAA GAA
1 GAAAA GAAAA GAAAA GAAAA GAAAA GAA
3665233 GAGACGCAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (5 bp):
GAAAA
Found at i:3673931 original size:2 final size:2
Alignment explanation
Indices: 3673918--3673959 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
3673908 TTATACCATA
* * *
3673918 AT AT AC AT AT AT AT AT AC AT AT AT AT AC 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
3673960 TCCAAACTCC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:3673934 original size:22 final size:22
Alignment explanation
Indices: 3673909--3673956 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
3673899 ACATTTTCTT
3673909 TATACCATA-ATATACATATATA
1 TATA-CATATATATACATATATA
3673931 TATACATATATATACATATATA
1 TATACATATATATACATATATA
3673953 TATA
1 TATA
3673957 TATTCCAAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 4 0.16
22 21 0.84
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (22 bp):
TATACATATATATACATATATA
Found at i:3673935 original size:12 final size:12
Alignment explanation
Indices: 3673918--3673956 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
3673908 TTATACCATA
3673918 ATATACATATAT
1 ATATACATATAT
3673930 ATATAC--ATAT
1 ATATACATATAT
3673940 ATATACATATAT
1 ATATACATATAT
3673952 ATATA
1 ATATA
3673957 TATTCCAAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 10 0.40
12 15 0.60
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (12 bp):
ATATACATATAT
Found at i:3686260 original size:45 final size:45
Alignment explanation
Indices: 3686140--3686260 Score: 125
Period size: 45 Copynumber: 2.7 Consensus size: 45
3686130 GTACATGGCG
* * *
3686140 TGTCACATGTTTTTGTACATGGCGTGTAACACGATAACCATAATT
1 TGTCACAGGTTTTTGTACATGGCGTGTCACACGATAACCATAACT
* * * * * ** * *
3686185 TATTACAGATTTTTATATATGATGTGTCACACGCTAACCATAGCT
1 TGTCACAGGTTTTTGTACATGGCGTGTCACACGATAACCATAACT
*
3686230 TGTCACAGGTTTTTGTACATGGCGTATCACA
1 TGTCACAGGTTTTTGTACATGGCGTGTCACA
3686261 TATTTTTGTA
Statistics
Matches: 56, Mismatches: 20, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
45 56 1.00
ACGTcount: A:0.28, C:0.18, G:0.17, T:0.36
Consensus pattern (45 bp):
TGTCACAGGTTTTTGTACATGGCGTGTCACACGATAACCATAACT
Found at i:3686266 original size:24 final size:24
Alignment explanation
Indices: 3686239--3686284 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
3686229 TTGTCACAGG
*
3686239 TTTTTGTACATGGCGTATCACATA
1 TTTTTGTACATGACGTATCACATA
* *
3686263 TTTTTGTATATGACGTGTCACA
1 TTTTTGTACATGACGTATCACA
3686285 CGCTAACTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.24, C:0.15, G:0.17, T:0.43
Consensus pattern (24 bp):
TTTTTGTACATGACGTATCACATA
Found at i:3686311 original size:45 final size:45
Alignment explanation
Indices: 3686256--3686357 Score: 141
Period size: 45 Copynumber: 2.3 Consensus size: 45
3686246 ACATGGCGTA
* * * * **
3686256 TCACATATTTTTGTATATGACGTGTCACACGCTAACTATGGTTTG
1 TCACAAATTTTTGTACATGACGTGTAACACGCTAACCATGACTTG
*
3686301 TCACAGATTTTTGTACATGACGTGTAACACGCTAACCATGACTTG
1 TCACAAATTTTTGTACATGACGTGTAACACGCTAACCATGACTTG
3686346 TCACAAATTTTT
1 TCACAAATTTTT
3686358 ATGCATGGCA
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 50 1.00
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.37
Consensus pattern (45 bp):
TCACAAATTTTTGTACATGACGTGTAACACGCTAACCATGACTTG
Found at i:3686331 original size:114 final size:114
Alignment explanation
Indices: 3686120--3686350 Score: 311
Period size: 114 Copynumber: 2.0 Consensus size: 114
3686110 TTGAAGTTTT
* * *
3686120 ACAGGTTTTTGTACATGGCGTGTCACATGTTTTTGTACATGGCGTGTAACACGATAACCATAATT
1 ACAGGTTTTTGTACATGGCGTATCACATATTTTTGTACATGACGTGTAACACGATAACCATAATT
* * * *
3686185 TATTACAGATTTTTATATATGATGTGTCACACGCTAACCAT-AGCTTGTC
66 TATCACAGATTTTTATACATGACGTGTAACACGCTAACCATGA-CTTGTC
* * * * **
3686234 ACAGGTTTTTGTACATGGCGTATCACATATTTTTGTATATGACGTGTCACACGCTAACTATGGTT
1 ACAGGTTTTTGTACATGGCGTATCACATATTTTTGTACATGACGTGTAACACGATAACCATAATT
* *
3686299 TGTCACAGATTTTTGTACATGACGTGTAACACGCTAACCATGACTTGTC
66 TATCACAGATTTTTATACATGACGTGTAACACGCTAACCATGACTTGTC
3686348 ACA
1 ACA
3686351 AATTTTTATG
Statistics
Matches: 101, Mismatches: 15, Indels: 2
0.86 0.13 0.02
Matches are distributed among these distances:
114 100 0.99
115 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.36
Consensus pattern (114 bp):
ACAGGTTTTTGTACATGGCGTATCACATATTTTTGTACATGACGTGTAACACGATAACCATAATT
TATCACAGATTTTTATACATGACGTGTAACACGCTAACCATGACTTGTC
Found at i:3686372 original size:45 final size:45
Alignment explanation
Indices: 3686256--3686374 Score: 121
Period size: 45 Copynumber: 2.6 Consensus size: 45
3686246 ACATGGCGTA
* * * * * * **
3686256 TCACATATTTTTGTATATGACGTGTCACACGCTAACTATGGTTTG
1 TCACAAATTTTTATACATGACATGTAACACGCTAACCATGACTTG
* * *
3686301 TCACAGATTTTTGTACATGACGTGTAACACGCTAACCATGACTTG
1 TCACAAATTTTTATACATGACATGTAACACGCTAACCATGACTTG
* *
3686346 TCACAAATTTTTATGCATGGCATGTAACA
1 TCACAAATTTTTATACATGACATGTAACA
3686375 TCATAGCGTG
Statistics
Matches: 63, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 63 1.00
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (45 bp):
TCACAAATTTTTATACATGACATGTAACACGCTAACCATGACTTG
Found at i:3697405 original size:18 final size:19
Alignment explanation
Indices: 3697382--3697424 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
3697372 ACAAGTATAT
*
3697382 ATCCACTAT-TGGTGGGTG
1 ATCCACTATATGATGGGTG
*
3697400 ATCCAC-ATATGATGGGTT
1 ATCCACTATATGATGGGTG
3697418 ATCCACT
1 ATCCACT
3697425 TCTGGTGGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 2 0.10
18 19 0.90
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (19 bp):
ATCCACTATATGATGGGTG
Found at i:3697841 original size:37 final size:37
Alignment explanation
Indices: 3697800--3697874 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
3697790 TTAAGAGACA
3697800 TAATATAATATATACTATATGATAGTAAAATTCATAT
1 TAATATAATATATACTATATGATAGTAAAATTCATAT
3697837 TAATATAATATATACTATATGATAGTAAAATTCATAT
1 TAATATAATATATACTATATGATAGTAAAATTCATAT
3697874 T
1 T
3697875 CAAGTTGATT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.41
Consensus pattern (37 bp):
TAATATAATATATACTATATGATAGTAAAATTCATAT
Found at i:3699145 original size:14 final size:13
Alignment explanation
Indices: 3699121--3699163 Score: 52
Period size: 14 Copynumber: 3.2 Consensus size: 13
3699111 ATTATCAATT
3699121 AAAAATT-ATTAA
1 AAAAATTAATTAA
*
3699133 AAAAATTTGATTATA
1 AAAAA-TTAATTA-A
3699148 AAAAATTAATTAA
1 AAAAATTAATTAA
3699161 AAA
1 AAA
3699164 TTTTATATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
12 5 0.19
13 6 0.22
14 10 0.37
15 6 0.22
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (13 bp):
AAAAATTAATTAA
Found at i:3699793 original size:19 final size:19
Alignment explanation
Indices: 3699769--3699811 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
3699759 AATTTTATAT
*
3699769 ATTAA-TAATAAAAATTAAA
1 ATTAATTAATAAAAAAT-AA
*
3699788 ATTAATTCATAAAAAATAA
1 ATTAATTAATAAAAAATAA
3699807 ATTAA
1 ATTAA
3699812 AATTTAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
ATTAATTAATAAAAAATAA
Found at i:3699814 original size:25 final size:27
Alignment explanation
Indices: 3699753--3699847 Score: 90
Period size: 27 Copynumber: 3.6 Consensus size: 27
3699743 ATAAAATTTA
* *
3699753 AAATTAAATTTTATAT-ATTAATAATAA-
1 AAATTAAAATTAATATCA-TAA-AATAAT
3699780 AAATTAAAATTAAT-TCATAAAA-AAT
1 AAATTAAAATTAATATCATAAAATAAT
3699805 AAATTAAAATTTAATATCATAAAATAAT
1 AAATTAAAA-TTAATATCATAAAATAAT
* * *
3699833 TAATCAAATTTAATA
1 AAATTAAAATTAATA
3699848 AATATTACAT
Statistics
Matches: 58, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
24 2 0.03
25 11 0.19
26 9 0.16
27 27 0.47
28 9 0.16
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (27 bp):
AAATTAAAATTAATATCATAAAATAAT
Found at i:3707413 original size:2 final size:2
Alignment explanation
Indices: 3707406--3707438 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3707396 TTTTTCTACT
3707406 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 T
3707439 TTAGCAGAGA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3708636 original size:17 final size:17
Alignment explanation
Indices: 3708614--3708663 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
3708604 ATTTATTTAA
3708614 AATTTTTAAATAATTAT
1 AATTTTTAAATAATTAT
*
3708631 AATTTTTTAAAAACATTAT
1 AA-TTTTTAAATA-ATTAT
* *
3708650 ACTTTTTGAATAAT
1 AATTTTTAAATAAT
3708664 AAATATTGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
17 4 0.15
18 17 0.63
19 6 0.22
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.50
Consensus pattern (17 bp):
AATTTTTAAATAATTAT
Found at i:3708639 original size:18 final size:19
Alignment explanation
Indices: 3708616--3708656 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
3708606 TTATTTAAAA
*
3708616 TTTTTAAATA-ATTATAAT
1 TTTTTAAAAACATTATAAT
*
3708634 TTTTTAAAAACATTATACT
1 TTTTTAAAAACATTATAAT
3708653 TTTT
1 TTTT
3708657 GAATAATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (19 bp):
TTTTTAAAAACATTATAAT
Found at i:3721013 original size:113 final size:113
Alignment explanation
Indices: 3720776--3720999 Score: 371
Period size: 113 Copynumber: 2.0 Consensus size: 113
3720766 ACTACACTGG
* *
3720776 TTTCAATTTCTAGCAAAAGAGTTTACATTATTGAGGCTGGCTATAAATTCTAAGATAGTATTACA
1 TTTCCATTTGTAGCAAAAGAGTTTACATTATTGAGGCTGGCTATAAATTCTAAGATAGTATTACA
* *
3720841 AAACCTGTACCGCTCTCATTTTAGTGTATGCAAGTAAAAATGGTCTGG
66 AAACCTGTACCGCTCTCATTTTAGTGTATGCAAGTAAAAATGGTCAGA
3720889 TTTCCATTTGTAGCAAAAGAGTTTACATTATTGAGGCTGGCTATAAATTCTAAGATAGTATTACA
1 TTTCCATTTGTAGCAAAAGAGTTTACATTATTGAGGCTGGCTATAAATTCTAAGATAGTATTACA
* *
3720954 AAA-CTGTACTGGC-CTCATTTTAGTGTATGCAAGTAACAATGGTCAG
66 AAACCTGTAC-CGCTCTCATTTTAGTGTATGCAAGTAAAAATGGTCAG
3721000 CATGTTCTGT
Statistics
Matches: 105, Mismatches: 5, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
112 37 0.35
113 68 0.65
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Consensus pattern (113 bp):
TTTCCATTTGTAGCAAAAGAGTTTACATTATTGAGGCTGGCTATAAATTCTAAGATAGTATTACA
AAACCTGTACCGCTCTCATTTTAGTGTATGCAAGTAAAAATGGTCAGA
Found at i:3726057 original size:88 final size:88
Alignment explanation
Indices: 3725899--3726073 Score: 271
Period size: 88 Copynumber: 2.0 Consensus size: 88
3725889 TTTGTGAGAT
* * * *
3725899 AAAACCGTGAGGTCAACTGGCCAAAATAGACAATACCTCATGAAAGTTGGTGTGGACCGTGGCAC
1 AAAACCGTGAGGCCAACAGACCAAAATAGACAATACCTCATGAAAGTTGGTGTGGACCGTGACAC
3725964 CTATCATCTAACTCTCTTTAGAC
66 CTATCATCTAACTCTCTTTAGAC
* *
3725987 AAAACCGTGAGGCCAACAGACCAAAGTAGACAATACCTCAT-AAATGTTGGTGTGGATCGTGACA
1 AAAACCGTGAGGCCAACAGACCAAAATAGACAATACCTCATGAAA-GTTGGTGTGGACCGTGACA
*
3726051 CTTATCATCTAACTCTCTTTAGA
65 CCTATCATCTAACTCTCTTTAGA
3726074 TGCAATTTTC
Statistics
Matches: 79, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
87 3 0.04
88 76 0.96
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.25
Consensus pattern (88 bp):
AAAACCGTGAGGCCAACAGACCAAAATAGACAATACCTCATGAAAGTTGGTGTGGACCGTGACAC
CTATCATCTAACTCTCTTTAGAC
Found at i:3726668 original size:3 final size:3
Alignment explanation
Indices: 3726654--3726689 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
3726644 AAATCAATGA
3726654 AAT AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
3726690 TATTTACTCT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:3727354 original size:88 final size:88
Alignment explanation
Indices: 3727196--3727370 Score: 237
Period size: 88 Copynumber: 2.0 Consensus size: 88
3727186 TTTGTGAGAT
* * * * *
3727196 AAAATCGTGAGGCCAACTGGCCAAAATATACAATACCTCATGAAAGTTGGTGTAGACCGTAGCAC
1 AAAATCATGAGGCCAACAGACCAAAATAAACAATACCTCATGAAAGGTGGTGTAGACCGTAGCAC
*
3727261 CTATCATCTAACTTTCTTTAGAC
66 CTATCATCTAACTCTCTTTAGAC
* *
3727284 AAAATCATGAGGCCAACAGACCAAAATAAACAATACCTCAT-AAGGGGTGGTGTGGACCGT-GAC
1 AAAATCATGAGGCCAACAGACCAAAATAAACAATACCTCATGAA-AGGTGGTGTAGACCGTAG-C
*
3727347 ACTTATCATCTAACTCTCTTTAGA
64 ACCTATCATCTAACTCTCTTTAGA
3727371 TGCAATTTTC
Statistics
Matches: 76, Mismatches: 9, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
87 3 0.04
88 73 0.96
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.25
Consensus pattern (88 bp):
AAAATCATGAGGCCAACAGACCAAAATAAACAATACCTCATGAAAGGTGGTGTAGACCGTAGCAC
CTATCATCTAACTCTCTTTAGAC
Found at i:3727965 original size:3 final size:3
Alignment explanation
Indices: 3727952--3728006 Score: 83
Period size: 3 Copynumber: 17.3 Consensus size: 3
3727942 AAAATCAATG
3727952 AAT AAT AAAT AAT AAT AAT AAT ATAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT -AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT
3727999 ATAT AAT A
1 A-AT AAT A
3728007 TATNACTAAA
Statistics
Matches: 49, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
3 40 0.82
4 9 0.18
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:3727973 original size:16 final size:16
Alignment explanation
Indices: 3727952--3728006 Score: 85
Period size: 16 Copynumber: 3.4 Consensus size: 16
3727942 AAAATCAATG
3727952 AATAATAAATAATAAT
1 AATAATAAATAATAAT
*
3727968 AATAATATATAATAAT
1 AATAATAAATAATAAT
3727984 AATAAT-AATAATAAT
1 AATAATAAATAATAAT
3727999 ATATAATA
1 A-ATAATA
3728007 TATNACTAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
15 9 0.26
16 26 0.74
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
AATAATAAATAATAAT
Found at i:3727993 original size:25 final size:26
Alignment explanation
Indices: 3727953--3728006 Score: 101
Period size: 25 Copynumber: 2.1 Consensus size: 26
3727943 AAATCAATGA
3727953 ATAATAAATAATAATAATAATATATA
1 ATAATAAATAATAATAATAATATATA
3727979 ATAAT-AATAATAATAATAATATATA
1 ATAATAAATAATAATAATAATATATA
3728004 ATA
1 ATA
3728007 TATNACTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
25 23 0.82
26 5 0.18
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (26 bp):
ATAATAAATAATAATAATAATATATA
Found at i:3728053 original size:16 final size:16
Alignment explanation
Indices: 3728029--3728067 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
3728019 TAAATGAACT
3728029 AAATGAAAATTGCAATA
1 AAAT-AAAATTGCAATA
* *
3728046 AAATAAAATTTCAATG
1 AAATAAAATTGCAATA
3728062 AAATAA
1 AAATAA
3728068 TTACTAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 16 0.80
17 4 0.20
ACGTcount: A:0.62, C:0.05, G:0.08, T:0.26
Consensus pattern (16 bp):
AAATAAAATTGCAATA
Found at i:3728670 original size:34 final size:31
Alignment explanation
Indices: 3728632--3728694 Score: 90
Period size: 31 Copynumber: 1.9 Consensus size: 31
3728622 TGTCGCCAGA
*
3728632 AAGGGAAAGAGGATAAAAGAGAAAGAAGAAATGG
1 AAGGGAAAGA-GA-AAAAGA-AAAGAAAAAATGG
3728666 AAGGGAAAGAGAAAAAGAAAAGAAAAAAT
1 AAGGGAAAGAGAAAAAGAAAAGAAAAAAT
3728695 ATTTTTACCT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 10 0.36
32 6 0.21
33 2 0.07
34 10 0.36
ACGTcount: A:0.65, C:0.00, G:0.30, T:0.05
Consensus pattern (31 bp):
AAGGGAAAGAGAAAAAGAAAAGAAAAAATGG
Found at i:3729921 original size:16 final size:17
Alignment explanation
Indices: 3729902--3729937 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
3729892 GCTTTTTTTT
3729902 AAATTCT-TTTTTTAAA
1 AAATTCTGTTTTTTAAA
*
3729918 AAATTTTGTTTTTTAAA
1 AAATTCTGTTTTTTAAA
3729935 AAA
1 AAA
3729938 ATTATTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 6 0.33
17 12 0.67
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (17 bp):
AAATTCTGTTTTTTAAA
Found at i:3729946 original size:17 final size:16
Alignment explanation
Indices: 3729902--3729946 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 16
3729892 GCTTTTTTTT
*
3729902 AAATTCTTTTTTTAAA
1 AAATTATTTTTTTAAA
*
3729918 AAATTTTGTTTTTTAAAA
1 AAATTAT-TTTTTT-AAA
3729936 AAATTATTTTT
1 AAATTATTTTT
3729947 AAGAGTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 6 0.24
17 10 0.40
18 9 0.36
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (16 bp):
AAATTATTTTTTTAAA
Found at i:3746642 original size:27 final size:28
Alignment explanation
Indices: 3746612--3746666 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
3746602 ATTAATCTTT
3746612 CAAATAAT-ATT-AAAAATAAAAAATTAA
1 CAAATAATCATTAAAAAAT-AAAAATTAA
* *
3746639 CAAATTATCTTTAAAAAATAAAAATTAA
1 CAAATAATCATTAAAAAATAAAAATTAA
3746667 AATGATATGT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 7 0.29
28 11 0.46
29 6 0.25
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.29
Consensus pattern (28 bp):
CAAATAATCATTAAAAAATAAAAATTAA
Found at i:3747268 original size:15 final size:14
Alignment explanation
Indices: 3747248--3747277 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3747238 AAATTACATC
3747248 GAAAAAGTAAAAAAA
1 GAAAAAG-AAAAAAA
3747263 GAAAAAGAAAAAAA
1 GAAAAAGAAAAAAA
3747277 G
1 G
3747278 GTGAAAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (14 bp):
GAAAAAGAAAAAAA
Found at i:3752579 original size:3 final size:3
Alignment explanation
Indices: 3752573--3752608 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
3752563 ACAGCAGCAG
*
3752573 CAA CAA CAA CAG CAA CAA CAA CAA CAA CAA CAA CAA
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA
3752609 AGACAACAGC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.64, C:0.33, G:0.03, T:0.00
Consensus pattern (3 bp):
CAA
Found at i:3752588 original size:9 final size:9
Alignment explanation
Indices: 3752576--3752624 Score: 50
Period size: 9 Copynumber: 5.8 Consensus size: 9
3752566 GCAGCAGCAA
3752576 CAACAACAG
1 CAACAACAG
*
3752585 CAACAACAA
1 CAACAACAG
*
3752594 CAACAACAA
1 CAACAACAG
3752603 CAACAA-AG
1 CAACAACAG
3752611 --ACAACAG
1 CAACAACAG
*
3752618 CCACAAC
1 CAACAAC
3752625 TGCAGCAGCA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
6 4 0.11
7 2 0.06
8 1 0.03
9 28 0.80
ACGTcount: A:0.59, C:0.35, G:0.06, T:0.00
Consensus pattern (9 bp):
CAACAACAG
Found at i:3752902 original size:21 final size:21
Alignment explanation
Indices: 3752884--3752953 Score: 122
Period size: 21 Copynumber: 3.3 Consensus size: 21
3752874 TCATACAGAG
3752884 GCAGCAGCAACAGACACAGTT
1 GCAGCAGCAACAGACACAGTT
*
3752905 GCAGCAACAACAGACACAGTT
1 GCAGCAGCAACAGACACAGTT
*
3752926 GCAGCAGCAACAAACACAGTT
1 GCAGCAGCAACAGACACAGTT
3752947 GCAGCAG
1 GCAGCAG
3752954 TCACCACTGC
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 46 1.00
ACGTcount: A:0.40, C:0.29, G:0.23, T:0.09
Consensus pattern (21 bp):
GCAGCAGCAACAGACACAGTT
Found at i:3753097 original size:3 final size:3
Alignment explanation
Indices: 3753076--3753112 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
3753066 TACAAAAATT
* *
3753076 GCA GCA ACA GCA ACA GCA GCA GCA GCA GCA GCA GCA G
1 GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA G
3753113 TCGTCTCAAC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.38, C:0.32, G:0.30, T:0.00
Consensus pattern (3 bp):
GCA
Found at i:3756374 original size:42 final size:45
Alignment explanation
Indices: 3756309--3756398 Score: 123
Period size: 43 Copynumber: 2.1 Consensus size: 45
3756299 GAAAAATTAA
* * *
3756309 AAAAAAATTTTATATAACAAAATTTATAATTAATA-ATAAATCAT
1 AAAAAAAGTTTATATAACAAAATTTATAAATAAGACATAAATCAT
*
3756353 AAAAAAAGTTT-TATAA-AAAATTTATAAATAAGACATAATTCAT
1 AAAAAAAGTTTATATAACAAAATTTATAAATAAGACATAAATCAT
3756396 AAA
1 AAA
3756399 TAATTGGTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
42 15 0.37
43 16 0.39
44 10 0.24
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.33
Consensus pattern (45 bp):
AAAAAAAGTTTATATAACAAAATTTATAAATAAGACATAAATCAT
Found at i:3760199 original size:62 final size:59
Alignment explanation
Indices: 3760101--3760228 Score: 141
Period size: 62 Copynumber: 2.1 Consensus size: 59
3760091 AAAATATTAG
* *
3760101 TTTTTTATAATTTATTTAAAATATTAATAGAATATAATTTAAAATTTTAATATGATTATTT
1 TTTTTTATAATTTATTTAAAATATTAATAGAATATAA-TTAAAACTTTAAGATGATT-TTT
* ** * * *
3760162 ATTTTTTATAGTTTATTTAACGTATTGATA-ATTTATAATTAACACTTTAAGATGATTTTT
1 -TTTTTTATAATTTATTTAAAATATTAATAGA-ATATAATTAAAACTTTAAGATGATTTTT
3760222 TTTTTTA
1 TTTTTTA
3760229 AACTTTCAGT
Statistics
Matches: 57, Mismatches: 8, Indels: 5
0.81 0.11 0.07
Matches are distributed among these distances:
59 7 0.12
60 3 0.05
61 17 0.30
62 30 0.53
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.55
Consensus pattern (59 bp):
TTTTTTATAATTTATTTAAAATATTAATAGAATATAATTAAAACTTTAAGATGATTTTT
Found at i:3763923 original size:37 final size:37
Alignment explanation
Indices: 3763877--3763955 Score: 158
Period size: 37 Copynumber: 2.1 Consensus size: 37
3763867 ATGTTATAGT
3763877 TTATTTTTTTATATAGATTTCGATTGATGTCTTTTTA
1 TTATTTTTTTATATAGATTTCGATTGATGTCTTTTTA
3763914 TTATTTTTTTATATAGATTTCGATTGATGTCTTTTTA
1 TTATTTTTTTATATAGATTTCGATTGATGTCTTTTTA
3763951 TTATT
1 TTATT
3763956 CTTAGTGATC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.22, C:0.05, G:0.10, T:0.63
Consensus pattern (37 bp):
TTATTTTTTTATATAGATTTCGATTGATGTCTTTTTA
Found at i:3764103 original size:33 final size:33
Alignment explanation
Indices: 3764018--3764103 Score: 118
Period size: 33 Copynumber: 2.6 Consensus size: 33
3764008 AAAGAACTTA
* * *
3764018 AAATAAAATATATAATATAGAAAATTATATTAAG
1 AAATAAAA-ATAAAATATATAAAATTATAATAAG
* *
3764052 AAATGAAAATAAAATATATAAGATTATAATAAG
1 AAATAAAAATAAAATATATAAAATTATAATAAG
3764085 AAATAAAAATAAAATATAT
1 AAATAAAAATAAAATATAT
3764104 GACATTAAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
33 39 0.85
34 7 0.15
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (33 bp):
AAATAAAAATAAAATATATAAAATTATAATAAG
Found at i:3765323 original size:12 final size:11
Alignment explanation
Indices: 3765296--3765330 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
3765286 AGGTGAGAAG
*
3765296 AAAGAGAAAAA
1 AAAGAAAAAAA
3765307 AAAGAAAAAAGA
1 AAAGAAAAAA-A
3765319 AAAGAAAAAAA
1 AAAGAAAAAAA
3765330 A
1 A
3765331 CCAATATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.50
12 11 0.50
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (11 bp):
AAAGAAAAAAA
Found at i:3765773 original size:124 final size:127
Alignment explanation
Indices: 3765568--3765817 Score: 346
Period size: 124 Copynumber: 2.0 Consensus size: 127
3765558 ATTTTGACCA
** * * * *
3765568 CAAAAAAAATTATCAAATTTTGTTATTATGTTGTTGGGTTTTTTTGTTTTTTTTTCTAATAATCT
1 CAAAAAAAATTATCAAATTTTGCAATTATGTTGCTGAGTTCTTTTATTTTTTTTTCTAATAATCT
* * * *
3765633 TTGTAGAGAGAAGTATTATAAGACTAAATTATTACGATTTTGATTTGAGGGGATAAATTGTTG
66 TTGTAGAGAGAAGTATTAAAAAACTAAATTATTACGATTTTGAGTT-AAGGGATAAATTGTTG
3765696 CAAAAAAAA-T-TC-AATTTTGCAATTATGTTGCTGAG-TCTTTTATTTTTTTTTCTAATAATCT
1 CAAAAAAAATTATCAAATTTTGCAATTATGTTGCTGAGTTCTTTTATTTTTTTTTCTAATAATCT
* * *
3765757 TTGTAGAGAGAGGTATTAAAAAACTAAATTGTTACGATTTTGAGTTAATGGATAAATTGTT
66 TTGTAGAGAGAAGTATTAAAAAACTAAATTATTACGATTTTGAGTTAAGGGATAAATTGTT
3765818 ACGATTTTGA
Statistics
Matches: 109, Mismatches: 13, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
123 13 0.12
124 65 0.60
125 19 0.17
126 2 0.02
127 1 0.01
128 9 0.08
ACGTcount: A:0.33, C:0.06, G:0.16, T:0.45
Consensus pattern (127 bp):
CAAAAAAAATTATCAAATTTTGCAATTATGTTGCTGAGTTCTTTTATTTTTTTTTCTAATAATCT
TTGTAGAGAGAAGTATTAAAAAACTAAATTATTACGATTTTGAGTTAAGGGATAAATTGTTG
Found at i:3765938 original size:10 final size:11
Alignment explanation
Indices: 3765908--3765945 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
3765898 GACACCCTAA
*
3765908 ACCATCCCCTC
1 ACCATCCCTTC
3765919 ACCATCCCTTC
1 ACCATCCCTTC
*
3765930 ACCATCCTTTC
1 ACCATCCCTTC
3765941 -CCATC
1 ACCATC
3765946 AAGTCCCCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
10 5 0.20
11 20 0.80
ACGTcount: A:0.18, C:0.55, G:0.00, T:0.26
Consensus pattern (11 bp):
ACCATCCCTTC
Found at i:3777844 original size:25 final size:23
Alignment explanation
Indices: 3777809--3777856 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 23
3777799 AAAAAAAAAA
3777809 AAGTTTATTTTGAAAACTTTTATTT
1 AAGTTTATTTT-AAAA-TTTTATTT
*
3777834 AAGTTTTTTTTAAAATTTTATTT
1 AAGTTTATTTTAAAATTTTATTT
3777857 TTTTAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 8 0.36
24 4 0.18
25 10 0.45
ACGTcount: A:0.31, C:0.02, G:0.06, T:0.60
Consensus pattern (23 bp):
AAGTTTATTTTAAAATTTTATTT
Found at i:3777859 original size:17 final size:17
Alignment explanation
Indices: 3777837--3777878 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
3777827 TTTATTTAAG
* **
3777837 TTTTTTTTAAAATTTTA
1 TTTTTTTAAAAAAATTA
3777854 TTTTTTTAAAAAAATTA
1 TTTTTTTAAAAAAATTA
3777871 TTTTTTTA
1 TTTTTTTA
3777879 GAGTTTTTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTTTTTAAAAAAATTA
Found at i:3781131 original size:22 final size:22
Alignment explanation
Indices: 3781090--3781136 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
3781080 CCTTTTGCTT
***
3781090 TATATTCAATATTTTGCAAAAA
1 TATATTCAATATTCCACAAAAA
3781112 TATATTCAATATTCCACAAAAA
1 TATATTCAATATTCCACAAAAA
3781134 TAT
1 TAT
3781137 GATTTGATCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.47, C:0.13, G:0.02, T:0.38
Consensus pattern (22 bp):
TATATTCAATATTCCACAAAAA
Found at i:3782594 original size:8 final size:8
Alignment explanation
Indices: 3782572--3782605 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
3782562 GCTCTAGGAG
3782572 TTTTCTTT
1 TTTTCTTT
3782580 CTTTTCTTT
1 -TTTTCTTT
3782589 TTTTCTTT
1 TTTTCTTT
*
3782597 TTTTGTTT
1 TTTTCTTT
3782605 T
1 T
3782606 GTTTTGAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
8 16 0.67
9 8 0.33
ACGTcount: A:0.00, C:0.12, G:0.03, T:0.85
Consensus pattern (8 bp):
TTTTCTTT
Found at i:3784909 original size:2 final size:2
Alignment explanation
Indices: 3784902--3784931 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3784892 CATTTGATAA
3784902 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
3784932 GGGCAGGATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:3799181 original size:22 final size:22
Alignment explanation
Indices: 3799154--3799228 Score: 68
Period size: 22 Copynumber: 3.5 Consensus size: 22
3799144 AACTTTTAAT
3799154 TTAATATTAATATTTTAAAATA
1 TTAATATTAATATTTTAAAATA
* *
3799176 TTAATACTAA-ATTAT-AAATA
1 TTAATATTAATATTTTAAAATA
* *
3799196 -AAATATTAATA-TTTAAATTA
1 TTAATATTAATATTTTAAAATA
*
3799216 TCAATTATTAATA
1 TTAA-TATTAATA
3799229 AAATAAATTA
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
19 9 0.21
20 10 0.24
21 6 0.14
22 17 0.40
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (22 bp):
TTAATATTAATATTTTAAAATA
Found at i:3799590 original size:21 final size:21
Alignment explanation
Indices: 3799563--3799624 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
3799553 TAATATTTAA
3799563 ATAAAATAAAATATTAATATT
1 ATAAAATAAAATATTAATATT
*
3799584 TTAAAATATAAATTATTAA-ATT
1 ATAAAATA-AAA-TATTAATATT
*
3799606 AT-GAAT-AAATATTAATATT
1 ATAAAATAAAATATTAATATT
3799625 GAAATTATCA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
18 6 0.17
19 6 0.17
21 10 0.29
22 7 0.20
23 6 0.17
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (21 bp):
ATAAAATAAAATATTAATATT
Found at i:3799686 original size:15 final size:14
Alignment explanation
Indices: 3799640--3799707 Score: 54
Period size: 12 Copynumber: 4.9 Consensus size: 14
3799630 TATCAATTAT
*
3799640 TAAT-ATATTTAAA
1 TAATAATATTAAAA
3799653 -AATAA-ATTAAAA
1 TAATAATATTAAAA
3799665 TAA-AATATTAATAA
1 TAATAATATTAA-AA
*
3799679 TAATAATATTTAAAT
1 TAATAATA-TTAAAA
3799694 TAAATAAATATTAA
1 T-AAT-AATATTAA
3799708 TATATTAAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
12 11 0.24
13 8 0.18
14 5 0.11
15 6 0.13
16 11 0.24
17 4 0.09
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
TAATAATATTAAAA
Found at i:3799726 original size:65 final size:65
Alignment explanation
Indices: 3799485--3799726 Score: 194
Period size: 65 Copynumber: 3.7 Consensus size: 65
3799475 TATCTATTAT
* * *
3799485 TAATATTTTAAA-TAAATAATCAATTATTAAT-T-TTCAAAAATAAAATAAAATAAAATAATTGA
1 TAATA-TTTAAATTAAATAA--AA-TATTAATATATT-AAATATAAATTAAAATAAAAT-ATTAA
* *
3799547 TCATCA
60 TAATAA
* * * * *
3799553 TAATATTTAAATAAAATAAAATATTAATATTTTAAAATATAAATT--ATTAAATTATGAATAAAT
1 TAATATTTAAATTAAATAAAATATTAATATATT-AAATATAAATTAAAATAAAATATTAAT-AAT
*
3799616 AT
64 AA
* * * *
3799618 TAATATTGAAATT--ATCAATTATTAATATATTTAAAAATAAATTAAAATAAAATATTAATAATA
1 TAATATTTAAATTAAATAAAATATTAATATA-TTAAATATAAATTAAAATAAAATATTAATAATA
3799681 A
65 A
*
3799682 TAATATTTAAATTAAAT-AAATATTAATATATTAAATTATTAATTA
1 TAATATTTAAATTAAATAAAATATTAATATATTAAA-TATAAATTA
3799727 TTAATATTTT
Statistics
Matches: 139, Mismatches: 25, Indels: 23
0.74 0.13 0.12
Matches are distributed among these distances:
63 23 0.17
64 27 0.19
65 56 0.40
66 5 0.04
67 17 0.12
68 11 0.08
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.40
Consensus pattern (65 bp):
TAATATTTAAATTAAATAAAATATTAATATATTAAATATAAATTAAAATAAAATATTAATAATAA
Found at i:3799726 original size:128 final size:128
Alignment explanation
Indices: 3799413--3799730 Score: 366
Period size: 128 Copynumber: 2.6 Consensus size: 128
3799403 NNNNNNNNNN
* *
3799413 AAAATAAAATAAAA-AATTAATCATAATAATATTTAAATTAAATAAAATATTAATAT-TT-AAAT
1 AAAATAAAATAAAATAATTAATAATAATAATATTTAAATAAAATAAAATATTAATATATTAAAAT
*
3799475 -T--ATCTATT--A-T-T-AAT--ATTTTAA-A-T-AAATAATCAATTATTAATTTTCAAAAAT
66 ATAAAT-TATTAAATTATGAATAAATATTAATATTGAAATAATCAATTATTAATTTTCAAAAAT
* * * *
3799526 AAAATAAAATAAAATAATTGATCATCATAATATTTAAATAAAATAAAATATTAATATTTTAAAAT
1 AAAATAAAATAAAATAATTAATAATAATAATATTTAAATAAAATAAAATATTAATATATTAAAAT
* *
3799591 ATAAATTATTAAATTATGAATAAATATTAATATTGAAATTATCAATTATTAATATATTTAAAAAT
66 ATAAATTATTAAATTATGAATAAATATTAATATTGAAATAATCAATTATTAAT-T-TTCAAAAAT
* * *
3799656 AAATTAAAATAAAAT-ATTAATAATAATAATATTTAAATTAAAT-AAATATTAATATATTAAATT
1 AAAATAAAATAAAATAATTAATAATAATAATATTTAAATAAAATAAAATATTAATATATTAAAAT
*
3799719 ATTAATTATTAA
66 ATAAATTATTAA
3799731 TATTTTAATT
Statistics
Matches: 173, Mismatches: 14, Indels: 21
0.83 0.07 0.10
Matches are distributed among these distances:
113 14 0.08
114 39 0.23
115 2 0.01
116 4 0.02
117 1 0.01
118 4 0.02
119 2 0.01
120 1 0.01
121 1 0.01
122 1 0.01
123 3 0.02
125 6 0.03
126 1 0.01
127 1 0.01
128 46 0.27
129 25 0.14
130 22 0.13
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.40
Consensus pattern (128 bp):
AAAATAAAATAAAATAATTAATAATAATAATATTTAAATAAAATAAAATATTAATATATTAAAAT
ATAAATTATTAAATTATGAATAAATATTAATATTGAAATAATCAATTATTAATTTTCAAAAAT
Found at i:3799728 original size:15 final size:15
Alignment explanation
Indices: 3799698--3799741 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 15
3799688 TTAAATTAAA
3799698 TAAA-TATTAATATAT
1 TAAATTATTAAT-TAT
3799713 TAAATTATTAATTAT
1 TAAATTATTAATTAT
3799728 TAATATT-TTAATTA
1 TAA-ATTATTAATTA
3799742 AATTCTAGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
15 17 0.63
16 10 0.37
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TAAATTATTAATTAT
Found at i:3802573 original size:33 final size:33
Alignment explanation
Indices: 3802526--3802602 Score: 127
Period size: 33 Copynumber: 2.3 Consensus size: 33
3802516 CCGTTGACAG
*
3802526 CAGTGGCAGCAGGGACAGAGGCAACATTAGGAA
1 CAGTGGCAGCAGGGACAAAGGCAACATTAGGAA
* *
3802559 CAGTGGCAGTAGGGACAAAGGCAGCATTAGGAA
1 CAGTGGCAGCAGGGACAAAGGCAACATTAGGAA
3802592 CAGTGGCAGCA
1 CAGTGGCAGCA
3802603 ACATTATCAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.35, C:0.18, G:0.36, T:0.10
Consensus pattern (33 bp):
CAGTGGCAGCAGGGACAAAGGCAACATTAGGAA
Found at i:3802599 original size:18 final size:18
Alignment explanation
Indices: 3802540--3802602 Score: 60
Period size: 18 Copynumber: 3.7 Consensus size: 18
3802530 GGCAGCAGGG
*
3802540 ACAGAGGCAACATTAGGA
1 ACAGAGGCAGCATTAGGA
* *
3802558 ACAGTGGCAG---TAGGG
1 ACAGAGGCAGCATTAGGA
*
3802573 ACAAAGGCAGCATTAGGA
1 ACAGAGGCAGCATTAGGA
*
3802591 ACAGTGGCAGCA
1 ACAGAGGCAGCA
3802603 ACATTATCAA
Statistics
Matches: 34, Mismatches: 8, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
15 12 0.35
18 22 0.65
ACGTcount: A:0.38, C:0.17, G:0.33, T:0.11
Consensus pattern (18 bp):
ACAGAGGCAGCATTAGGA
Found at i:3804083 original size:16 final size:16
Alignment explanation
Indices: 3804058--3804096 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
3804048 CATGAAAATT
3804058 TATTAATTAATCAATA
1 TATTAATTAATCAATA
*
3804074 TATTATTTAATCAATA
1 TATTAATTAATCAATA
*
3804090 AATTAAT
1 TATTAAT
3804097 AATTTATTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (16 bp):
TATTAATTAATCAATA
Found at i:3804528 original size:17 final size:18
Alignment explanation
Indices: 3804506--3804539 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
3804496 TTAAAATTAG
3804506 TTAAAAATATT-ATTTAA
1 TTAAAAATATTAATTTAA
*
3804523 TTAAAATTATTAATTTA
1 TTAAAAATATTAATTTA
3804540 TAAAGATTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TTAAAAATATTAATTTAA
Found at i:3808350 original size:16 final size:17
Alignment explanation
Indices: 3808329--3808366 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 17
3808319 ATTTAAAGTA
3808329 ATAAAAG-ATAAAATTT
1 ATAAAAGAATAAAATTT
3808345 ATAAAAGAATAAAATTT
1 ATAAAAGAATAAAATTT
3808362 -TAAAA
1 ATAAAA
3808367 TTACCATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 12 0.57
17 9 0.43
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (17 bp):
ATAAAAGAATAAAATTT
Found at i:3809691 original size:22 final size:19
Alignment explanation
Indices: 3809674--3809710 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
3809664 TTATTTTGAT
*
3809674 AAATAATTTAATAAATTTA
1 AAATAATATAATAAATTTA
3809693 AAATAATATAAT-AATTTA
1 AAATAATATAATAAATTTA
3809711 TTAACAAGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
AAATAATATAATAAATTTA
Found at i:3812046 original size:23 final size:21
Alignment explanation
Indices: 3812005--3812049 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 21
3811995 GTTTTGTAAT
*
3812005 TTAAAAAATTTTAAAATTTTA
1 TTAAAAAATTGTAAAATTTTA
3812026 TTAAAATAATTGTACAAATTTTA
1 TTAAAA-AATTGTA-AAATTTTA
3812049 T
1 T
3812050 AGTACAGTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 6 0.29
22 6 0.29
23 9 0.43
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (21 bp):
TTAAAAAATTGTAAAATTTTA
Found at i:3819198 original size:23 final size:23
Alignment explanation
Indices: 3819172--3819227 Score: 96
Period size: 23 Copynumber: 2.4 Consensus size: 23
3819162 AAATGAAAAC
3819172 AAAAAAGAAAGGGAAAAAAAAGGA
1 AAAAAAGAAA-GGAAAAAAAAGGA
3819196 AAAAAAGAAAGGAAAAAAAAGG-
1 AAAAAAGAAAGGAAAAAAAAGGA
3819218 AAAAAAGAAA
1 AAAAAAGAAA
3819228 CCCCTCGAGC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
22 10 0.31
23 12 0.38
24 10 0.31
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (23 bp):
AAAAAAGAAAGGAAAAAAAAGGA
Found at i:3819223 original size:9 final size:10
Alignment explanation
Indices: 3819173--3819223 Score: 57
Period size: 10 Copynumber: 4.6 Consensus size: 10
3819163 AATGAAAACA
3819173 AAAAAGAAAGGG
1 AAAAA-AAA-GG
3819185 AAAAAAAAGG
1 AAAAAAAAGG
3819195 AAAAAAAGAAAGG
1 --AAAAA-AAAGG
3819208 AAAAAAAAGG
1 AAAAAAAAGG
3819218 AAAAAA
1 AAAAAA
3819224 GAAACCCCTC
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
10 13 0.36
11 8 0.22
12 10 0.28
13 5 0.14
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (10 bp):
AAAAAAAAGG
Done.