Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D02
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: 67659327
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 461372 characters in sequence are not A, C, G, or T
File 211 of 216
Found at i:65390262 original size:13 final size:13
Alignment explanation
Indices: 65390246--65390295 Score: 59
Period size: 13 Copynumber: 3.9 Consensus size: 13
65390236 TTCCTTTCCC
*
65390246 TTTCTTCTTCCTT
1 TTTCTTCTTCTTT
65390259 TTTCTTCTTTCTTT
1 TTTCTTC-TTCTTT
65390273 TTTC-TC-TCTTT
1 TTTCTTCTTCTTT
*
65390284 TTTATTCTTCTT
1 TTTCTTCTTCTT
65390296 CGGCAACCCC
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
11 8 0.25
12 2 0.06
13 13 0.41
14 9 0.28
ACGTcount: A:0.02, C:0.24, G:0.00, T:0.74
Consensus pattern (13 bp):
TTTCTTCTTCTTT
Found at i:65390272 original size:24 final size:25
Alignment explanation
Indices: 65390245--65390292 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
65390235 TTTCCTTTCC
*
65390245 CTTTCTTCT-TCCTTTTTCTTCTTT
1 CTTTCTTCTCTCCTTTTTATTCTTT
* *
65390269 CTTTTTTCTCTCTTTTTTATTCTT
1 CTTTCTTCTCTCCTTTTTATTCTT
65390293 CTTCGGCAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.02, C:0.25, G:0.00, T:0.73
Consensus pattern (25 bp):
CTTTCTTCTCTCCTTTTTATTCTTT
Found at i:65390407 original size:16 final size:16
Alignment explanation
Indices: 65390375--65390419 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
65390365 TCTCCTCCCC
*
65390375 TTTTCCTTTTC-TTCT
1 TTTTCTTTTTCTTTCT
65390390 TTTTCTTTTTCTTTCT
1 TTTTCTTTTTCTTTCT
* *
65390406 TTGTCTTTGTCTTT
1 TTTTCTTTTTCTTT
65390420 TATTTTTGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
15 10 0.38
16 16 0.62
ACGTcount: A:0.00, C:0.20, G:0.04, T:0.76
Consensus pattern (16 bp):
TTTTCTTTTTCTTTCT
Found at i:65390943 original size:30 final size:30
Alignment explanation
Indices: 65390860--65390955 Score: 106
Period size: 29 Copynumber: 3.3 Consensus size: 30
65390850 TTAGGAACCC
*
65390860 AAATGT-AATTTATAAAAAATTAGGGGTCA
1 AAATGTAAATTTATAAAAATTTAGGGGTCA
* * *
65390889 ATATGAAAATTCA-AAAAATTTAGGGGTCA
1 AAATGTAAATTTATAAAAATTTAGGGGTCA
* * **
65390918 AAATGTAAATTTGTAAAAGTTTAGGGACCA
1 AAATGTAAATTTATAAAAATTTAGGGGTCA
65390948 AAATGTAA
1 AAATGTAA
65390956 TTTTTTTTAT
Statistics
Matches: 54, Mismatches: 11, Indels: 3
0.79 0.16 0.04
Matches are distributed among these distances:
29 28 0.52
30 26 0.48
ACGTcount: A:0.48, C:0.05, G:0.18, T:0.29
Consensus pattern (30 bp):
AAATGTAAATTTATAAAAATTTAGGGGTCA
Found at i:65390958 original size:29 final size:29
Alignment explanation
Indices: 65390827--65390958 Score: 95
Period size: 29 Copynumber: 4.5 Consensus size: 29
65390817 AAATATGAGG
* * * *
65390827 CCAAAATGTAATTTTTGGAAAGTTTAGGAA
1 CCAAAATGTAATTTAT-AAAAATTTAGGGA
* * *
65390857 CCCAAATGTAATTTATAAAAAATTAGGGG
1 CCAAAATGTAATTTATAAAAATTTAGGGA
* * * * *
65390886 TCAATATGAAAATTCA-AAAAATTTAGGGG
1 CCAAAATG-TAATTTATAAAAATTTAGGGA
* * *
65390915 TCAAAATGTAAATTTGTAAAAGTTTAGGGA
1 CCAAAATGT-AATTTATAAAAATTTAGGGA
65390945 CCAAAATGTAATTT
1 CCAAAATGTAATTT
65390959 TTTTTATATT
Statistics
Matches: 79, Mismatches: 20, Indels: 7
0.75 0.19 0.07
Matches are distributed among these distances:
29 41 0.52
30 38 0.48
ACGTcount: A:0.44, C:0.08, G:0.17, T:0.31
Consensus pattern (29 bp):
CCAAAATGTAATTTATAAAAATTTAGGGA
Found at i:65391162 original size:5 final size:5
Alignment explanation
Indices: 65391152--65391184 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
65391142 ATATATATAT
65391152 AATAA AATAA AATAA AAT-A AATAA AATAA AATA
1 AATAA AATAA AATAA AATAA AATAA AATAA AATA
65391185 CGAAGAATGG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 23 0.85
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
AATAA
Found at i:65391175 original size:9 final size:9
Alignment explanation
Indices: 65391152--65391181 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
65391142 ATATATATAT
65391152 AATAAAATAA
1 AATAAAAT-A
65391162 AATAAAATA
1 AATAAAATA
65391171 AATAAAATA
1 AATAAAATA
65391180 AA
1 AA
65391182 ATACGAAGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 12 0.60
10 8 0.40
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (9 bp):
AATAAAATA
Found at i:65391175 original size:14 final size:14
Alignment explanation
Indices: 65391156--65391184 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
65391146 ATATATAATA
65391156 AAATAAAATAAAAT
1 AAATAAAATAAAAT
65391170 AAATAAAATAAAAT
1 AAATAAAATAAAAT
65391184 A
1 A
65391185 CGAAGAATGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (14 bp):
AAATAAAATAAAAT
Found at i:65402412 original size:31 final size:31
Alignment explanation
Indices: 65402345--65402414 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 31
65402335 TTGAAATTTA
* *
65402345 AAATTCAAAAATTAAATGGACTAAAATTAAC
1 AAATTTAAAAATTAAATGGACGAAAATTAAC
* * *
65402376 CAATTTAAAAATTACAT-GACGAAAATTGATC
1 AAATTTAAAAATTAAATGGACGAAAATT-AAC
65402407 AAATTTAA
1 AAATTTAA
65402415 GTATATGGCC
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
30 9 0.28
31 23 0.72
ACGTcount: A:0.54, C:0.10, G:0.07, T:0.29
Consensus pattern (31 bp):
AAATTTAAAAATTAAATGGACGAAAATTAAC
Found at i:65402590 original size:21 final size:21
Alignment explanation
Indices: 65402566--65402607 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
65402556 TCATACATTG
* *
65402566 CATAATTTTATTAAAAAAAAT
1 CATAATGTAATTAAAAAAAAT
*
65402587 CATAATGTAATTATAAAAAAT
1 CATAATGTAATTAAAAAAAAT
65402608 ATTTAAGTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.36
Consensus pattern (21 bp):
CATAATGTAATTAAAAAAAAT
Found at i:65404780 original size:3 final size:3
Alignment explanation
Indices: 65404774--65404804 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
65404764 TGCTCCTCAG
65404774 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
65404805 ACAATCTGAA
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:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:65411223 original size:20 final size:21
Alignment explanation
Indices: 65411185--65411228 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
65411175 AAAAAATATA
* *
65411185 TAAAATTTAGTCTTTAATT-T
1 TAAAATTTAGGCTTCAATTGT
*
65411205 TAAAATTTAGGGTTCAATTGT
1 TAAAATTTAGGCTTCAATTGT
65411226 TAA
1 TAA
65411229 TACTGTTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.36, C:0.05, G:0.11, T:0.48
Consensus pattern (21 bp):
TAAAATTTAGGCTTCAATTGT
Found at i:65415671 original size:19 final size:19
Alignment explanation
Indices: 65415644--65415710 Score: 55
Period size: 19 Copynumber: 3.5 Consensus size: 19
65415634 GAAATTAGAA
*
65415644 AGATCAAATTATAGTAAAG
1 AGATTAAATTATAGTAAAG
* * *
65415663 AGATTAAATTCGTA-AAAAA
1 AGATTAAATT-ATAGTAAAG
*
65415682 AAATTAAATTATAGTAAAG
1 AGATTAAATTATAGTAAAG
* *
65415701 GGATTCAATT
1 AGATTAAATT
65415711 CGTGAAAAAT
Statistics
Matches: 35, Mismatches: 11, Indels: 4
0.70 0.22 0.08
Matches are distributed among these distances:
18 2 0.06
19 31 0.89
20 2 0.06
ACGTcount: A:0.52, C:0.04, G:0.13, T:0.30
Consensus pattern (19 bp):
AGATTAAATTATAGTAAAG
Found at i:65417066 original size:3 final size:3
Alignment explanation
Indices: 65417060--65417088 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
65417050 ACCCCACCAC
65417060 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
65417089 AAATCTCACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:65421296 original size:47 final size:48
Alignment explanation
Indices: 65421182--65421315 Score: 139
Period size: 47 Copynumber: 2.8 Consensus size: 48
65421172 AACAAGAGGA
* *
65421182 GAACATTCTTAATCAGTTGGCAACTAATTTATGAACATGAGGATAAGG
1 GAACATTATTAATCAGTTGGCAACTAATTTATGAACATGAAGATAAGG
* * * * *
65421230 GAACATCACTAATCGGTTGGCAACTAATTT-TGAGCTTGAA-AGT-AGG
1 GAACATTATTAATCAGTTGGCAACTAATTTATGAACATGAAGA-TAAGG
* * *
65421276 GAAACATTGTTAATCAGTTGGAAACTAATTTAGGAACATG
1 G-AACATTATTAATCAGTTGGCAACTAATTTATGAACATG
65421316 TGACATATCT
Statistics
Matches: 68, Mismatches: 15, Indels: 6
0.76 0.17 0.07
Matches are distributed among these distances:
46 5 0.07
47 32 0.47
48 31 0.46
ACGTcount: A:0.37, C:0.13, G:0.22, T:0.29
Consensus pattern (48 bp):
GAACATTATTAATCAGTTGGCAACTAATTTATGAACATGAAGATAAGG
Found at i:65442835 original size:16 final size:15
Alignment explanation
Indices: 65442799--65442833 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
65442789 ATTTTAATAG
65442799 AAAAATGAATATTGT
1 AAAAATGAATATTGT
* *
65442814 GAAAATGAATGTTGT
1 AAAAATGAATATTGT
65442829 AAAAA
1 AAAAA
65442834 ATTTGGTTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (15 bp):
AAAAATGAATATTGT
Found at i:65444273 original size:33 final size:33
Alignment explanation
Indices: 65444227--65444293 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
65444217 CCTTCACTCC
*
65444227 TTAGCCTTTTCTTTTCCCTTTTCTTCAATTAGG
1 TTAGCCTTCTCTTTTCCCTTTTCTTCAATTAGG
*
65444260 TTAGCCTTCTCTTTTCCTTTTTCTTCAATTAGG
1 TTAGCCTTCTCTTTTCCCTTTTCTTCAATTAGG
65444293 T
1 T
65444294 CCTCTCCTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.12, C:0.24, G:0.09, T:0.55
Consensus pattern (33 bp):
TTAGCCTTCTCTTTTCCCTTTTCTTCAATTAGG
Found at i:65444307 original size:28 final size:32
Alignment explanation
Indices: 65444239--65444308 Score: 85
Period size: 33 Copynumber: 2.3 Consensus size: 32
65444229 AGCCTTTTCT
* *
65444239 TTTCCCTTTTCTTCAATTAGGTTAGCCTTCTCT
1 TTTCCTTTTTCTTCAATTAGGTTA-CCTTCTCC
65444272 TTTCCTTTTTCTTCAATTAGG-T-CC-TCTCC
1 TTTCCTTTTTCTTCAATTAGGTTACCTTCTCC
65444301 TTT-CTTTT
1 TTTCCTTTT
65444309 ATTTCTCTTC
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
28 5 0.14
29 7 0.20
30 2 0.06
32 1 0.03
33 20 0.57
ACGTcount: A:0.10, C:0.27, G:0.07, T:0.56
Consensus pattern (32 bp):
TTTCCTTTTTCTTCAATTAGGTTACCTTCTCC
Found at i:65446636 original size:22 final size:22
Alignment explanation
Indices: 65446575--65446638 Score: 74
Period size: 22 Copynumber: 2.9 Consensus size: 22
65446565 TGCTGATCAA
* **
65446575 AGAGCATCAAAGTGCTAAGTAG
1 AGAGCACCAAAGTGCTAAACAG
*
65446597 AGAGCACCAAAGTACTAAACAG
1 AGAGCACCAAAGTGCTAAACAG
* *
65446619 AGAGCACCGAGGTGCTAAAC
1 AGAGCACCAAAGTGCTAAAC
65446639 CCGTACAAGT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.42, C:0.20, G:0.25, T:0.12
Consensus pattern (22 bp):
AGAGCACCAAAGTGCTAAACAG
Found at i:65448019 original size:25 final size:25
Alignment explanation
Indices: 65447991--65448039 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
65447981 AAAATTGGTA
65447991 AGACATTTTCCATTCT-TCTCTAAGT
1 AGACATTTTCCATTCTCT-TCTAAGT
65448016 AGACATTTTCCATTCTCTTCTAAG
1 AGACATTTTCCATTCTCTTCTAAG
65448040 CAGCAGACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 22 0.96
26 1 0.04
ACGTcount: A:0.24, C:0.24, G:0.08, T:0.43
Consensus pattern (25 bp):
AGACATTTTCCATTCTCTTCTAAGT
Found at i:65450056 original size:22 final size:21
Alignment explanation
Indices: 65450028--65450071 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 21
65450018 TGCAGTGAAA
65450028 TTTATGCTTGAGATTTTGAGAC
1 TTTATGCTTGAGATTTTG-GAC
65450050 TTTATGCTTGAGATTTTGGAC
1 TTTATGCTTGAGATTTTGGAC
65450071 T
1 T
65450072 CGTTTTCATA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.20, C:0.09, G:0.23, T:0.48
Consensus pattern (21 bp):
TTTATGCTTGAGATTTTGGAC
Found at i:65450503 original size:14 final size:14
Alignment explanation
Indices: 65450484--65450511 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
65450474 ATAATTTATT
65450484 AATATATATTAATA
1 AATATATATTAATA
65450498 AATATATATTAATA
1 AATATATATTAATA
65450512 TATGTAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
AATATATATTAATA
Found at i:65450667 original size:14 final size:14
Alignment explanation
Indices: 65450644--65450683 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
65450634 ACAGAAAAGT
*
65450644 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
65450658 AAATCATTTTACGG
1 AAAACATTTTACAG
65450672 AAAACATTTTAC
1 AAAACATTTTAC
65450684 TGCCAAACAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:65450675 original size:34 final size:35
Alignment explanation
Indices: 65450609--65450675 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
65450599 CAAACACCAG
* *
65450609 AAAATATTTTCCAGTAAATTATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
65450644 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
65450676 CATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 16 0.55
35 13 0.45
ACGTcount: A:0.46, C:0.12, G:0.09, T:0.33
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:65458221 original size:275 final size:269
Alignment explanation
Indices: 65457588--65458363 Score: 837
Period size: 275 Copynumber: 2.8 Consensus size: 269
65457578 TTCATGTGAG
* * *
65457588 CCATCAACTCATTC-TCACACTAGTAGTAAACATTATTTTCAGCTATCATTTTCGAAAC-GCTCG
1 CCATCAACTCATTCACCATAC-AGTAGTTAACATTATTTTCAGCTATCATTTTCGAAACAGCTC-
* * * * ** *
65457651 GA-TCCCAAACCAAACCACTTCTTGCTGACATCGTATCCTTTATTCCCCATCC-CAATAACTAAA
64 CACCCCCAAACCAAACCACTTCTAGCTGATATTATATCC-TTATTTCCCATCCTCAATAACT-AA
* * * *
65457714 AC-TAAATCTTACTTTTCCACAAACAATTACTTTTGATTGCCAAAAGGAAGTCCTAAAATAAACC
127 ACTTAAATCTTCCTTTTCCACAAACAATCACTTTTGATTGCCAAAA-TAAGTCTTAAAATAAA-C
* * * * *
65457778 CCATTCGAATACCCCAATAATACAATTATCAGTCATTACCACTCTTTCAACAAGTCACATCTTCC
190 CCATTCAAACACCCCAATAATACAATTATCAGTCATTACCACTCTTCCAACAAGTCACATCTACA
65457843 ATGTGTTCTATGTAA
255 ATGTGTTCTATGTAA
* * * * *
65457858 -GATCAATTCATTCACCATACCAGTAGTTAACATTATTGTCGGCTATCATTTTCGAAACAACTCC
1 CCATCAACTCATTCACCATA-CAGTAGTTAACATTATTTTCAGCTATCATTTTCGAAACAGCTCC
* *
65457922 ACCCCCAAACCAAACCATTTCTAGCTGATATTATATCCTTACTTTCCCATCCTCAATAACTGAAC
65 ACCCCCAAACCAAACCACTTCTAGCTGATATTATATCCTTA-TTTCCCATCCTCAATAACTAAAC
* * * *
65457987 TTAAATCTTCCTTTTCCACAGACAATGACTTTTGGTTGCCAAATTATAGTCTTAAAATAAACCCA
129 TTAAATCTTCCTTTTCCACAAACAATCACTTTTGATTGCCAAAATA-AGTCTTAAAATAAACCCA
* * * *
65458052 TTCAAACGCCCCAATAATAGAATTATCACAGTCATTATCACTCTTCCAACAAG-CTGCATCTACA
193 TTCAAACACCCCAATAATACAATTAT--CAGTCATTACCACTCTTCCAACAAGTC-ACATCTACA
*
65458116 ATGTGTTCTTTGTAA
255 ATGTGTTCTATGTAA
* * *
65458131 TCCATCAACTCATTCACCATATCAGTAGTTAACTTTCTTTTCAGCTATCATTTTTGAAACAGCTC
1 -CCATCAACTCATTCACCATA-CAGTAGTTAACATTATTTTCAGCTATCATTTTCGAAACAGCTC
* *
65458196 CACCCCCAAACCTAACCACTTCTAGCTGATATTATATGATTATATCCTTATTTTTCCATCCTCAA
64 CACCCCCAAACCAAACCACTTCTAGCTG-------AT-ATTATATCCTTA-TTTCCCATCCTCAA
* * * * *
65458261 TAACTAAAATTAGATCTTCCCTTTCCACAAACAACCACTTTTGATTGCCAAAATACAGTTCTAAA
120 TAACTAAACTTAAATCTTCCTTTTCCACAAACAATCACTTTTGATTGCCAAAATA-AG-TCTTAA
* * * *
65458326 AATAAACCCATTCAAAAACCCTAATGATACAATCATCA
183 AATAAACCCATTCAAACACCCCAATAATACAATTATCA
65458364 CAATCATTAG
Statistics
Matches: 420, Mismatches: 64, Indels: 32
0.81 0.12 0.06
Matches are distributed among these distances:
269 11 0.03
270 41 0.10
271 73 0.17
272 60 0.14
273 43 0.10
275 80 0.19
282 4 0.01
283 73 0.17
284 35 0.08
ACGTcount: A:0.34, C:0.27, G:0.07, T:0.32
Consensus pattern (269 bp):
CCATCAACTCATTCACCATACAGTAGTTAACATTATTTTCAGCTATCATTTTCGAAACAGCTCCA
CCCCCAAACCAAACCACTTCTAGCTGATATTATATCCTTATTTCCCATCCTCAATAACTAAACTT
AAATCTTCCTTTTCCACAAACAATCACTTTTGATTGCCAAAATAAGTCTTAAAATAAACCCATTC
AAACACCCCAATAATACAATTATCAGTCATTACCACTCTTCCAACAAGTCACATCTACAATGTGT
TCTATGTAA
Found at i:65460026 original size:32 final size:29
Alignment explanation
Indices: 65459990--65460054 Score: 76
Period size: 29 Copynumber: 2.1 Consensus size: 29
65459980 TTAATAAATG
*
65459990 AATATACATAATTATTAAATATTAAATTAAAA
1 AATATAAAT-ATTATTAAA-A-TAAATTAAAA
* *
65460022 AATATAAATATTTTTAAAATAAATTTAAA
1 AATATAAATATTATTAAAATAAATTAAAA
65460051 AATA
1 AATA
65460055 ATATGAGTGG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
29 13 0.43
30 1 0.03
31 8 0.27
32 8 0.27
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (29 bp):
AATATAAATATTATTAAAATAAATTAAAA
Found at i:65460058 original size:32 final size:34
Alignment explanation
Indices: 65459972--65460058 Score: 85
Period size: 32 Copynumber: 2.6 Consensus size: 34
65459962 TTATTTATTT
* *
65459972 ATATAATTTTAATAAATGAATATACATAATTATTAA
1 ATATAAATTTAA-AAAT-AATATAAATAATTATTAA
*
65460008 ATATTAAA-TT-AAAA-AATATAAAT-ATTTTTAA
1 ATA-TAAATTTAAAAATAATATAAATAATTATTAA
65460039 A-ATAAATTTAAAAATAATAT
1 ATATAAATTTAAAAATAATAT
65460059 GAGTGGACTT
Statistics
Matches: 44, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
29 4 0.09
30 3 0.07
31 12 0.27
32 13 0.30
34 3 0.07
35 1 0.02
36 5 0.11
37 3 0.07
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.40
Consensus pattern (34 bp):
ATATAAATTTAAAAATAATATAAATAATTATTAA
Found at i:65469349 original size:10 final size:10
Alignment explanation
Indices: 65469334--65469385 Score: 52
Period size: 10 Copynumber: 5.0 Consensus size: 10
65469324 CATTAATTTG
65469334 TATTTTAAAT
1 TATTTTAAAT
*
65469344 TATTTTTTATAT
1 TA--TTTTAAAT
65469356 GTATTTTAAAT
1 -TATTTTAAAT
*
65469367 TATTTT-TAT
1 TATTTTAAAT
65469376 TATTTTAAAT
1 TATTTTAAAT
65469386 ATAAAATATT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
9 8 0.24
10 10 0.29
11 7 0.21
12 7 0.21
13 2 0.06
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (10 bp):
TATTTTAAAT
Found at i:65469412 original size:21 final size:21
Alignment explanation
Indices: 65469378--65469419 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
65469368 ATTTTTATTA
* *
65469378 TTTTAAATATAAAATATTTAT
1 TTTTAAATAAAAAATAGTTAT
*
65469399 TTTTACATAAAAAATAGTTAT
1 TTTTAAATAAAAAATAGTTAT
65469420 AAAAACTATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (21 bp):
TTTTAAATAAAAAATAGTTAT
Found at i:65472379 original size:6 final size:6
Alignment explanation
Indices: 65472363--65472392 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
65472353 GGGCCTTAAG
65472363 AGAAAA A-AAAA AGAAAA AGAAAA AGAAAA A
1 AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA A
65472393 AAGGTGTTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.22
6 18 0.78
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (6 bp):
AGAAAA
Found at i:65472380 original size:12 final size:12
Alignment explanation
Indices: 65472360--65472394 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
65472350 AAGGGGCCTT
65472360 AAGAGAAAAAAAA
1 AAGA-AAAAAAAA
*
65472373 AAGAAAAAGAAA
1 AAGAAAAAAAAA
65472385 AAGAAAAAAA
1 AAGAAAAAAA
65472395 GGTGTTGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 16 0.80
13 4 0.20
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (12 bp):
AAGAAAAAAAAA
Found at i:65478497 original size:26 final size:26
Alignment explanation
Indices: 65478468--65478519 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
65478458 ATAGATTATG
65478468 GTGCATTGTAATGAGCTAGCGGCACT
1 GTGCATTGTAATGAGCTAGCGGCACT
65478494 GTGCATTGTAATGAGCTAGCGGCACT
1 GTGCATTGTAATGAGCTAGCGGCACT
65478520 CTCTTAAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.23, C:0.19, G:0.31, T:0.27
Consensus pattern (26 bp):
GTGCATTGTAATGAGCTAGCGGCACT
Found at i:65483847 original size:16 final size:17
Alignment explanation
Indices: 65483826--65483858 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
65483816 GACTCGAGTA
65483826 ATTTTAAATTT-AAATT
1 ATTTTAAATTTGAAATT
*
65483842 ATTTTAAGTTTGAAATT
1 ATTTTAAATTTGAAATT
65483859 TAAGTTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (17 bp):
ATTTTAAATTTGAAATT
Found at i:65493530 original size:223 final size:230
Alignment explanation
Indices: 65493120--65493738 Score: 715
Period size: 223 Copynumber: 2.7 Consensus size: 230
65493110 CAACTAGTTT
*
65493120 ATTGGCCACATTGAAAGGAAATATAAATGCCACCAAGGAA-GCTATAGAGCTGGTTTTCCTCTAG
1 ATTGGCCACATTGAAAGGAAATATAAATGCCACCAA-GAAGGCTATAGAGCTGATTTTCCTCTAG
* * * *
65493184 TGTACTTGAAGAATCCAGACAATGTGTTCGTTATTGGGAACATATACAAACATGGGT-CGGGATA
65 TGTACTTGAAGAATCCAGACAACGTGTTCGATATCGGGAACATATACAAACATGGGTACAGGATA
** * *** * * * * * * *
65493248 TGACAGTCCAACAACTTTGTATATACACAGAAAAGCATAGGAATAATTTGAATATATCCATGTTG
130 TGACCCTCCAAAAACTTACCATATACA-TGAAAAGAATAGAAAAAAATCGAACATATCCATGTTG
**
65493313 GACATATATCTGACAC-T-C-AA-C-GC-CA-AATTC
194 GACATATATCCAACACTTCCAAATCAGCACATAATTC
**
65493343 ATTGGCCATGTTGAAAGGAAATATAAATGCCACCAAGAAGGCTATAGAGCTGATTTTCCTCTAGT
1 ATTGGCCACATTGAAAGGAAATATAAATGCCACCAAGAAGGCTATAGAGCTGATTTTCCTCTAGT
* * * * *
65493408 GTGCTTTAAGCATCTAGACAACGTGTTCGATATCGGGAACACATACAAACATGGGTACAGGATAT
66 GTACTTGAAGAATCCAGACAACGTGTTCGATATCGGGAACATATACAAACATGGGTACAGGATAT
65493473 GACCCTCCAAAAACTTACCATATACATGGAAAA-AATAGAAAAAAATCGAACATATCCATGTTGG
131 GACCCTCCAAAAACTTACCATATACAT-GAAAAGAATAGAAAAAAATCGAACATATCCATGTTGG
* *
65493537 ACATATATCCAACACTTGCACCAAATTCAAGCAACATAGTTT
195 ACATATATCCAACACTT---CCAAA-TC-AGC-ACATAATTC
* * * * * *
65493579 ATTGGCCACATGGAAAGGAAATATAAATGCCGA-TAAGGAGGCAATAGAGCTGATTTGCATCTAG
1 ATTGGCCACATTGAAAGGAAATATAAATGCC-ACCAAGAAGGCTATAGAGCTGATTTTCCTCTAG
* * *
65493643 TGTACTTGAAGAATCCAGAAAACGTGTTCGATATCGGAAACATATACAAACATGGG-A-AGAATA
65 TGTACTTGAAGAATCCAGACAACGTGTTCGATATCGGGAACATATACAAACATGGGTACAGGATA
65493706 TGACCCTCCAAAAACTTACCATATACATGAAAA
130 TGACCCTCCAAAAACTTACCATATACATGAAAA
65493739 TGCATAGAGA
Statistics
Matches: 334, Mismatches: 45, Indels: 24
0.83 0.11 0.06
Matches are distributed among these distances:
222 3 0.01
223 144 0.43
224 33 0.10
228 1 0.00
229 2 0.01
231 1 0.00
233 7 0.02
234 33 0.10
235 3 0.01
236 106 0.32
237 1 0.00
ACGTcount: A:0.38, C:0.18, G:0.19, T:0.25
Consensus pattern (230 bp):
ATTGGCCACATTGAAAGGAAATATAAATGCCACCAAGAAGGCTATAGAGCTGATTTTCCTCTAGT
GTACTTGAAGAATCCAGACAACGTGTTCGATATCGGGAACATATACAAACATGGGTACAGGATAT
GACCCTCCAAAAACTTACCATATACATGAAAAGAATAGAAAAAAATCGAACATATCCATGTTGGA
CATATATCCAACACTTCCAAATCAGCACATAATTC
Found at i:65497240 original size:27 final size:27
Alignment explanation
Indices: 65497188--65497240 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 27
65497178 ATTTAGGTCT
* * *
65497188 ATTTATGATTTTAGTCCCTCTATTAAA
1 ATTTAAGATTTTAATCCCTCCATTAAA
65497215 ATTTAAGA-TTTAATCCCTCCACTTAA
1 ATTTAAGATTTTAATCCCTCCA-TTAA
65497241 TTTGATCATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 11 0.50
27 11 0.50
ACGTcount: A:0.32, C:0.19, G:0.06, T:0.43
Consensus pattern (27 bp):
ATTTAAGATTTTAATCCCTCCATTAAA
Found at i:65502814 original size:12 final size:12
Alignment explanation
Indices: 65502797--65502826 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
65502787 TATTTTATAT
65502797 AAATTCTTTAAA
1 AAATTCTTTAAA
65502809 AAATTCTTTAAA
1 AAATTCTTTAAA
65502821 AAATTC
1 AAATTC
65502827 ATGTCATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (12 bp):
AAATTCTTTAAA
Found at i:65505806 original size:46 final size:46
Alignment explanation
Indices: 65505739--65505896 Score: 195
Period size: 46 Copynumber: 3.6 Consensus size: 46
65505729 TTTGAGTACT
* * *
65505739 TCTGATCAAGAGATAAAGTGATAAGTGGTAGCTTTAGCTACATTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
*
65505785 TCTGATCAAGTGACAAAGTGATAA---GT-G-TTAAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
* *
65505826 TCTAATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
* *
65505872 TTTGATC-AGGGAC-AAGTGATAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTG
65505897 ATCATACGTA
Statistics
Matches: 97, Mismatches: 10, Indels: 12
0.82 0.08 0.10
Matches are distributed among these distances:
41 35 0.36
42 1 0.01
43 2 0.02
44 14 0.14
45 6 0.06
46 39 0.40
ACGTcount: A:0.35, C:0.13, G:0.22, T:0.30
Consensus pattern (46 bp):
TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
Found at i:65505820 original size:41 final size:41
Alignment explanation
Indices: 65505774--65505852 Score: 140
Period size: 41 Copynumber: 1.9 Consensus size: 41
65505764 TGGTAGCTTT
* *
65505774 AGCTACATTTATCTGATCAAGTGACAAAGTGATAAGTGTTA
1 AGCTACACTTATCTAATCAAGTGACAAAGTGATAAGTGTTA
65505815 AGCTACACTTATCTAATCAAGTGACAAAGTGATAAGTG
1 AGCTACACTTATCTAATCAAGTGACAAAGTGATAAGTG
65505853 GTAGCCTTAG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (41 bp):
AGCTACACTTATCTAATCAAGTGACAAAGTGATAAGTGTTA
Found at i:65507575 original size:17 final size:17
Alignment explanation
Indices: 65507553--65507586 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
65507543 CGTAAACCAA
*
65507553 ACCATGTCAGATTAAAG
1 ACCATGTCAAATTAAAG
65507570 ACCATGTCAAATTAAAG
1 ACCATGTCAAATTAAAG
65507587 TATAGATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.18, G:0.15, T:0.24
Consensus pattern (17 bp):
ACCATGTCAAATTAAAG
Found at i:65514011 original size:21 final size:21
Alignment explanation
Indices: 65513993--65514036 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
65513983 AAAATTAATT
65513993 AATTTA-TTTTTATTTTTAAG
1 AATTTATTTTTTATTTTTAAG
65514013 AATTTATTTTTTA-TTTTAA-
1 AATTTATTTTTTATTTTTAAG
65514032 AATTT
1 AATTT
65514037 TAAAATGTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 5 0.22
20 12 0.52
21 6 0.26
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (21 bp):
AATTTATTTTTTATTTTTAAG
Found at i:65514214 original size:23 final size:21
Alignment explanation
Indices: 65514173--65514220 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
65514163 TTTAAATTTA
65514173 AAAATTTAAAAATAAAATAACT
1 AAAATTTAAAAATAAAATAA-T
* *
65514195 AAAATTTAAAAGTATTAATAAT
1 AAAATTTAAAAATA-AAATAAT
65514217 AAAA
1 AAAA
65514221 GGATTTAGAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (21 bp):
AAAATTTAAAAATAAAATAAT
Found at i:65515363 original size:21 final size:21
Alignment explanation
Indices: 65515323--65515362 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
65515313 AATTAAATTA
*
65515323 TACAAATAGAAACTTTAAAAT
1 TACAAAAAGAAACTTTAAAAT
65515344 TACAAAAAGAAA-TTTAAAA
1 TACAAAAAGAAACTTTAAAA
65515363 AATATATCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.62, C:0.07, G:0.05, T:0.25
Consensus pattern (21 bp):
TACAAAAAGAAACTTTAAAAT
Found at i:65518591 original size:25 final size:26
Alignment explanation
Indices: 65518563--65518612 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
65518553 GAATGTAAAA
*
65518563 TTTTTTAACT-ATTAATCGAACCGAT
1 TTTTTTAAATAATTAATCGAACCGAT
65518588 TTTTTTAAATACATTAATCGAACCG
1 TTTTTTAAATA-ATTAATCGAACCG
65518613 GAATATTTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 9 0.41
27 13 0.59
ACGTcount: A:0.34, C:0.16, G:0.08, T:0.42
Consensus pattern (26 bp):
TTTTTTAAATAATTAATCGAACCGAT
Found at i:65518784 original size:21 final size:20
Alignment explanation
Indices: 65518745--65518787 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
65518735 AAATAATGTT
65518745 TAAAAAATATATTACTAATA
1 TAAAAAATATATTACTAATA
65518765 TAAAAAATACTATATA-TAATA
1 TAAAAAATA-TAT-TACTAATA
65518786 TA
1 TA
65518788 TATTATTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 9 0.43
21 10 0.48
22 2 0.10
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (20 bp):
TAAAAAATATATTACTAATA
Found at i:65521969 original size:24 final size:24
Alignment explanation
Indices: 65521920--65521970 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
65521910 ATTTGATATT
**
65521920 TATTAGAATAAGGAGTTTCACTCC
1 TATTAGAATAAGGAGTTTCAAGCC
*
65521944 TATTAGAATAAGG-TTTTACAAGCC
1 TATTAGAATAAGGAGTTT-CAAGCC
65521968 TAT
1 TAT
65521971 AAATAGACAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 3 0.13
24 20 0.87
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (24 bp):
TATTAGAATAAGGAGTTTCAAGCC
Found at i:65522486 original size:39 final size:38
Alignment explanation
Indices: 65522445--65522583 Score: 149
Period size: 40 Copynumber: 3.5 Consensus size: 38
65522435 AATTTATTTT
* *
65522445 AAAAATTAAAATAAAAATTAAAAAAAGTATTTTAAAATTAA
1 AAAAATTAAAA-AAATATT-TAAAAAGTATTTTAAAATT-A
65522486 AAAAATTAAAAAAAGTATTTTAAAAA--ATTTTAAAATTAA
1 AAAAATTAAAAAAA-TA-TTTAAAAAGTATTTTAAAATT-A
* *
65522525 AAAAATTAAAAAATGTATTTTAAAAGTATTTTAAAATTAA
1 AAAAATTAAAAAA-ATATTTAAAAAGTATTTTAAAATT-A
65522565 AAAAATTAAAAAAA-ATTTA
1 AAAAATTAAAAAAATATTTA
65522584 TTATTCGGGC
Statistics
Matches: 87, Mismatches: 6, Indels: 13
0.82 0.06 0.12
Matches are distributed among these distances:
38 11 0.13
39 28 0.32
40 29 0.33
41 17 0.20
42 2 0.02
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (38 bp):
AAAAATTAAAAAAATATTTAAAAAGTATTTTAAAATTA
Found at i:65522496 original size:8 final size:9
Alignment explanation
Indices: 65522478--65522537 Score: 50
Period size: 9 Copynumber: 6.3 Consensus size: 9
65522468 AAAGTATTTT
65522478 AAAATTAAA
1 AAAATTAAA
65522487 AAAATTAAAA
1 AAAATT-AAA
*
65522497 AAAGTATTTTAA
1 AAA--A-TTAAA
**
65522509 AAAATT-TT
1 AAAATTAAA
65522517 AAAATTAAA
1 AAAATTAAA
65522526 AAAATTAAA
1 AAAATTAAA
65522535 AAA
1 AAA
65522538 TGTATTTTAA
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
8 6 0.15
9 20 0.49
10 7 0.17
12 6 0.15
13 2 0.05
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (9 bp):
AAAATTAAA
Found at i:65522499 original size:29 final size:31
Alignment explanation
Indices: 65522439--65522569 Score: 113
Period size: 29 Copynumber: 4.0 Consensus size: 31
65522429 ACCAAAAATT
65522439 TATTTTAAAAATTAAAATAAAAATTAAAAAAAG
1 TATTTT-AAAATT-AAATAAAAATTAAAAAAAG
65522472 TATTTTAAAATT-AA-AAAAATTAAAAAAAG
1 TATTTTAAAATTAAATAAAAATTAAAAAAAG
*
65522501 TATTTTAAAAAATTTTAAAATTAAAAAAATTAAAAAATG
1 TATTTT--AAAA--TT-AAA-T--AAAAATTAAAAAAAG
* ** *
65522540 TATTTTAAAAGTATTTTAAAATTAAAAAAA
1 TATTTTAAAATTAAATAAAAATTAAAAAAA
65522570 TTAAAAAAAA
Statistics
Matches: 82, Mismatches: 6, Indels: 22
0.75 0.05 0.20
Matches are distributed among these distances:
29 21 0.26
30 2 0.02
31 16 0.20
32 6 0.07
33 9 0.11
34 1 0.01
35 3 0.04
37 4 0.05
39 20 0.24
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (31 bp):
TATTTTAAAATTAAATAAAAATTAAAAAAAG
Found at i:65522528 original size:40 final size:40
Alignment explanation
Indices: 65522467--65522578 Score: 190
Period size: 39 Copynumber: 2.8 Consensus size: 40
65522457 AAAAATTAAA
*
65522467 AAAAGTATTTTAAAATTAAAAAAATTAAAAAAAGTATTTT
1 AAAAGAATTTTAAAATTAAAAAAATTAAAAAAAGTATTTT
*
65522507 AAAA-AATTTTAAAATTAAAAAAATTAAAAAATGTATTTT
1 AAAAGAATTTTAAAATTAAAAAAATTAAAAAAAGTATTTT
*
65522546 AAAAGTATTTTAAAATTAAAAAAATTAAAAAAA
1 AAAAGAATTTTAAAATTAAAAAAATTAAAAAAA
65522579 ATTTATTATT
Statistics
Matches: 67, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
39 37 0.55
40 30 0.45
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (40 bp):
AAAAGAATTTTAAAATTAAAAAAATTAAAAAAAGTATTTT
Found at i:65538018 original size:381 final size:381
Alignment explanation
Indices: 65537315--65538203 Score: 1652
Period size: 381 Copynumber: 2.3 Consensus size: 381
65537305 AGAAAGCTTG
65537315 AGGACAGAATGAAGATGGCTGAAGATGACCTGAGAAATGCATCTACTTGTGCAACTGTTGCTTTT
1 AGGACAGAATGAAGATGGCTGAAGATGACCTGAGAAATGCATCTACTTGTGCAACTGTTGCTTTT
65537380 GTACTTGTGAATAGATTATCAGAGGCAAACCATAATCATCTCAATGCATTGAAGGGTAAGGACGA
66 GTACTTGTGAATAGATTATCAGAGGCAAACCATAATCATCTCAATGCATTGAAGGGTAAGGACGA
* *
65537445 ACAATTTGCAGAATCAGCGGAGGCGATCTTGAGTAAGGATGCTCTTTTGATCAACCAAGCTACCA
131 ACAACTTGCAGAATCAGCAGAGGCGATCTTGAGTAAGGATGCTCTTTTGATCAACCAAGCTACCA
65537510 TGATTGAAGAAGCAGAAAAACATATTCATTCCCTTGAAACTGAAGTTGAAAAGTCAGAGGAAGCT
196 TGATTGAAGAAGCAGAAAAACATATTCATTCCCTTGAAACTGAAGTTGAAAAGTCAGAGGAAGCT
*
65537575 TGCACTGAACTTAGCCAGAGGCTTCTGGAGGAGGAGCAGCGTGCTGCTGCTATTGAACAAAAGCT
261 TGCACTGAACTTAGCAAGAGGCTTCTGGAGGAGGAGCAGCGTGCTGCTGCTATTGAACAAAAGCT
* *
65537640 TGAAGATATGGTGGAGAATGACATTTTGAAGACACAGGAGGAGCTGTCTAATCTTA
326 TGAAGATATGGTGGAGAATGACATTTTGAACACACAGGAGGAGCTGTCTAAACTTA
* *
65537696 AGGACAGAATGAAGATGGCTGAAGATGACCTGAGAAATGCATCTACTTGCGCAACCGTTGCTTTT
1 AGGACAGAATGAAGATGGCTGAAGATGACCTGAGAAATGCATCTACTTGTGCAACTGTTGCTTTT
65537761 GTACTTGTGAATAGATTATCAGAGGCAAACCATAATCATCTCAATGCATTGAAGGGTAAGGACGA
66 GTACTTGTGAATAGATTATCAGAGGCAAACCATAATCATCTCAATGCATTGAAGGGTAAGGACGA
65537826 ACAACTTGCAGAATCAGCAGAGGCGATCTTGAGTAAGGATGCTCTTTTGATCAACCAAGCTACCA
131 ACAACTTGCAGAATCAGCAGAGGCGATCTTGAGTAAGGATGCTCTTTTGATCAACCAAGCTACCA
* *
65537891 TGATTGAAGAAGCAGAAACACGTATTCATTCCCTTGAAACTGAAGTTGAAAAGTCAGAGGAAGCT
196 TGATTGAAGAAGCAGAAAAACATATTCATTCCCTTGAAACTGAAGTTGAAAAGTCAGAGGAAGCT
* *
65537956 TGCACTGAACTTCGCAAGAGGCTTCTGGAGGAGGAGCAGTGTGCTGCTGCTATTGAACAAAAGCT
261 TGCACTGAACTTAGCAAGAGGCTTCTGGAGGAGGAGCAGCGTGCTGCTGCTATTGAACAAAAGCT
* *
65538021 TGAAGATATGGTGGAGAATGACTTTTTGAACACACAGGAGGAGCTGTCTAAACTTG
326 TGAAGATATGGTGGAGAATGACATTTTGAACACACAGGAGGAGCTGTCTAAACTTA
*
65538077 AGGACAGAATGAAGATGGCTGAAGATGACCTAAGAAATGCATCTACTTGTGCAACTGTTGCTTTT
1 AGGACAGAATGAAGATGGCTGAAGATGACCTGAGAAATGCATCTACTTGTGCAACTGTTGCTTTT
65538142 GTACTTGTGAATAGATTATCAGAGGCAAACCATAATCATCTCAATGCATTGAAGGGTAAGGA
66 GTACTTGTGAATAGATTATCAGAGGCAAACCATAATCATCTCAATGCATTGAAGGGTAAGGA
65538204 TGCTCTTCTA
Statistics
Matches: 492, Mismatches: 16, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
381 492 1.00
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Consensus pattern (381 bp):
AGGACAGAATGAAGATGGCTGAAGATGACCTGAGAAATGCATCTACTTGTGCAACTGTTGCTTTT
GTACTTGTGAATAGATTATCAGAGGCAAACCATAATCATCTCAATGCATTGAAGGGTAAGGACGA
ACAACTTGCAGAATCAGCAGAGGCGATCTTGAGTAAGGATGCTCTTTTGATCAACCAAGCTACCA
TGATTGAAGAAGCAGAAAAACATATTCATTCCCTTGAAACTGAAGTTGAAAAGTCAGAGGAAGCT
TGCACTGAACTTAGCAAGAGGCTTCTGGAGGAGGAGCAGCGTGCTGCTGCTATTGAACAAAAGCT
TGAAGATATGGTGGAGAATGACATTTTGAACACACAGGAGGAGCTGTCTAAACTTA
Found at i:65540782 original size:222 final size:222
Alignment explanation
Indices: 65540503--65541066 Score: 844
Period size: 222 Copynumber: 2.5 Consensus size: 222
65540493 TTGTCCACTT
*
65540503 AGCTGACTCTGGGAAAAAGCTTACCAATGCTTATGCTGTC-CTTGATGGTTTAAAGAAAGAAATG
1 AGCTGACTCTGGAAAAAAGCTTACCAATGCTTATGCTGTCAC-TGATGGTTTAAAGAAAGAAATG
* * *
65540567 ACTTTTACAAAATTAGATGCATGTTTGAAAGAGCAGCTATTGGTGGAGCGGGAAAGTGAGTTGTC
65 ATTTTTGCAAAATTAGATGCATGTTTGAAAGAGCAGCTATTGGTGGAGCAGGAAAGTGAGTTGTC
* * * * * *
65540632 TTTTCTCCAAGAAAAAGTTGAAGAAGCACAGATTGAGTTAAGAATGTTGAAGAAAGAGAACGGTC
130 TTTTCTACAAGAAAAAGTTGAAGAAGCACAAATTGAGGTAAGAAAGATGAAGAAAGAAAACGGTC
* * *
65540697 TACTTCTCCAGGATTTGGAGGAGCAGAA
195 TACTTCTCCAGAATTTGGACGAGAAGAA
* *
65540725 AGCTGACTCTGGAAAAAAGCTTGCCAATGCTTATTCTGTCACTGATGGTTTAAAGAAAGAAATGA
1 AGCTGACTCTGGAAAAAAGCTTACCAATGCTTATGCTGTCACTGATGGTTTAAAGAAAGAAATGA
* *
65540790 TTTTTGCAAAATTAGATGCATGCTTGAAAGGGCAGCTATTGGTGGAGCAGGACAA-TGAGTTGTC
66 TTTTTGCAAAATTAGATGCATGTTTGAAAGAGCAGCTATTGGTGGAGCAGGA-AAGTGAGTTGTC
* *
65540854 TTTTCTACAAGAAAAAGTTGAAGAAGCACAAATTGAGGTAAGAAAGATGCAGAAAGAAAACTGTC
130 TTTTCTACAAGAAAAAGTTGAAGAAGCACAAATTGAGGTAAGAAAGATGAAGAAAGAAAACGGTC
* *
65540919 TGCTTCTCCAGAATTTGGACGAGAAGGA
195 TACTTCTCCAGAATTTGGACGAGAAGAA
* * * * *
65540947 AGCAGACACCGGAAAAAAGCTTACCAATGCTTATGCTGTCATTGATGGTTTAAAGAAAGAAATAA
1 AGCTGACTCTGGAAAAAAGCTTACCAATGCTTATGCTGTCACTGATGGTTTAAAGAAAGAAATGA
* *
65541012 TTTTTGCAAAAGTAGATGCATGTTTGAAAGAGCAACTATTGGTGGAGCAGGAAAG
66 TTTTTGCAAAATTAGATGCATGTTTGAAAGAGCAGCTATTGGTGGAGCAGGAAAG
65541067 GATATCAAAG
Statistics
Matches: 307, Mismatches: 32, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
221 2 0.01
222 302 0.98
223 3 0.01
ACGTcount: A:0.36, C:0.13, G:0.25, T:0.26
Consensus pattern (222 bp):
AGCTGACTCTGGAAAAAAGCTTACCAATGCTTATGCTGTCACTGATGGTTTAAAGAAAGAAATGA
TTTTTGCAAAATTAGATGCATGTTTGAAAGAGCAGCTATTGGTGGAGCAGGAAAGTGAGTTGTCT
TTTCTACAAGAAAAAGTTGAAGAAGCACAAATTGAGGTAAGAAAGATGAAGAAAGAAAACGGTCT
ACTTCTCCAGAATTTGGACGAGAAGAA
Found at i:65545620 original size:166 final size:163
Alignment explanation
Indices: 65545374--65545821 Score: 439
Period size: 158 Copynumber: 2.7 Consensus size: 163
65545364 TGTCTGATAG
* * * *
65545374 AAGTGTGTAAATATAACAGACACACT-AGCTTTTTACTGGATTATATTGTTAGACACTGAAAGCC
1 AAGTGTGT-AA-ATAACAGACACACTAAGCTTTTTACTTGATTATATTGTTA-AAATTG-AAGCT
* * * *
65545438 GGTTTCCGAGTTAATTCAATCAACATTAAATTTCTGATGATAGCAAGTGTGTAATTACATTAGAT
62 GATTTTCGAGTTAATTCAATCTACATTAAATTTCTGATGATAGCAAGTGTGTAATTACATTACAT
* * *
65545503 GCTT-TCAATATGCCCGAACTCATGATCAGGGTTGAATAA
127 GCTTGT-AATATACACG--CTCATGATCAGGGTCGAATAA
* * *
65545542 AAGTGTGTAAATAACAGACAGA-TAAGCCTTTTACTTGATTATATTGTTAAATATTGAATGTTGA
1 AAGTGTGTAAATAACAGACACACTAAGCTTTTTACTTGATTATATTGTTAAA-ATTGAA-GCTGA
* *
65545606 TTTTCGAATTAATTCAATCTACA-TAAATTTCTGATGATAGC-A---TGTAACTA-ATTACATGC
64 TTTTCGAGTTAATTCAATCTACATTAAATTTCTGATGATAGCAAGTGTGTAATTACATTACATGC
* * * ** * * * *
65545665 TTGTGATTTACATGCTTGTGATGAGTGTCGGATAG
129 TTGTAATATACACGCTCATGATCAGGGTCGAATAA
* * * *
65545700 AAGTATGTAAATAATAAACACACTAA-CTTTTTACTTGATTATATTGTTATAAACTGGAAGCTGA
1 AAGTGTGTAAATAACAGACACACTAAGCTTTTTACTTGATTATATTGTTA-AAA-TTGAAGCTGA
* * *
65545764 TTTTCGAGTTAATTCAATTTACATTAAATTTTTTATGATAGCAAGTGTGTAATTACAT
64 TTTTCGAGTTAATTCAATCTACATTAAATTTCTGATGATAGCAAGTGTGTAATTACAT
65545822 GCAAGTTTCA
Statistics
Matches: 230, Mismatches: 37, Indels: 30
0.77 0.12 0.10
Matches are distributed among these distances:
158 80 0.35
159 25 0.11
160 16 0.07
161 8 0.03
163 7 0.03
164 3 0.01
165 22 0.10
166 59 0.26
167 2 0.01
168 8 0.03
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.37
Consensus pattern (163 bp):
AAGTGTGTAAATAACAGACACACTAAGCTTTTTACTTGATTATATTGTTAAAATTGAAGCTGATT
TTCGAGTTAATTCAATCTACATTAAATTTCTGATGATAGCAAGTGTGTAATTACATTACATGCTT
GTAATATACACGCTCATGATCAGGGTCGAATAA
Found at i:65545677 original size:15 final size:15
Alignment explanation
Indices: 65545657--65545686 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
65545647 ATGTAACTAA
65545657 TTACATGCTTGTGAT
1 TTACATGCTTGTGAT
65545672 TTACATGCTTGTGAT
1 TTACATGCTTGTGAT
65545687 GAGTGTCGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.13, G:0.20, T:0.47
Consensus pattern (15 bp):
TTACATGCTTGTGAT
Found at i:65552495 original size:42 final size:42
Alignment explanation
Indices: 65552432--65552515 Score: 143
Period size: 42 Copynumber: 2.0 Consensus size: 42
65552422 AAGTTAAACC
*
65552432 GATTTATCAGTTTTT-AGTTTTTTACACTTTTTATGAATTTTT
1 GATTTATCAGTTTTTAATTTTTTTACA-TTTTTATGAATTTTT
65552474 GATTTATCAGTTTTTAATTTTTTTACATTTTTATGAATTTTT
1 GATTTATCAGTTTTTAATTTTTTTACATTTTTATGAATTTTT
65552516 AAGTATTTAT
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
42 30 0.75
43 10 0.25
ACGTcount: A:0.23, C:0.06, G:0.08, T:0.63
Consensus pattern (42 bp):
GATTTATCAGTTTTTAATTTTTTTACATTTTTATGAATTTTT
Found at i:65554263 original size:4 final size:4
Alignment explanation
Indices: 65554254--65554279 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
65554244 TACTTTTAGT
65554254 TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TT
65554280 AATTAAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:65554526 original size:27 final size:27
Alignment explanation
Indices: 65554494--65554585 Score: 78
Period size: 27 Copynumber: 3.2 Consensus size: 27
65554484 ATTTGATCCT
65554494 AAAAAAAAGCTTAGGTACCAAATTAGG
1 AAAAAAAAGCTTAGGTACCAAATTAGG
* *
65554521 AAAAAAAAGGTCAAGTTCAAGTACCAAATTGAGC
1 AAAAAAAA-G-C---TT-AGGTACCAAATT-AGG
* *
65554555 TAAAAAAA-TTTAGGTACCAAATTAGG
1 AAAAAAAAGCTTAGGTACCAAATTAGG
65554581 AAAAA
1 AAAAA
65554586 GTGTCAAGTT
Statistics
Matches: 51, Mismatches: 7, Indels: 15
0.70 0.10 0.21
Matches are distributed among these distances:
26 6 0.12
27 19 0.37
28 3 0.06
29 1 0.02
32 2 0.04
33 11 0.22
34 9 0.18
ACGTcount: A:0.53, C:0.11, G:0.16, T:0.20
Consensus pattern (27 bp):
AAAAAAAAGCTTAGGTACCAAATTAGG
Found at i:65554575 original size:60 final size:61
Alignment explanation
Indices: 65554495--65554669 Score: 191
Period size: 60 Copynumber: 2.9 Consensus size: 61
65554485 TTTGATCCTA
* *
65554495 AAAAAAAGCTTAGGTACCAAATTAGGAAAAAAAAGGTCAAGTTCAAGTACCAAATTGAGCT
1 AAAAAAAGTTTAGGTACCAAATTAGGAAAAAAAAGGTCAAGTTCAAGTACCAAATTGAGCC
* * *
65554556 AAAAAAA-TTTAGGTACCAAATTAGG---AAAAAGTGTCAAGTTCAGGTACCAATTTGGGCC
1 AAAAAAAGTTTAGGTACCAAATTAGGAAAAAAAAG-GTCAAGTTCAAGTACCAAATTGAGCC
* * * *
65554614 AAATAAAAGTTCATGTACCAAAATA-GAAAAAAAA-ATACAAAGTTCAAGTACCAAAT
1 AAA-AAAAGTTTAGGTACCAAATTAGGAAAAAAAAGGT-C-AAGTTCAAGTACCAAAT
65554670 GTTATATTAA
Statistics
Matches: 95, Mismatches: 11, Indels: 15
0.79 0.09 0.12
Matches are distributed among these distances:
57 6 0.06
58 25 0.26
59 5 0.05
60 31 0.33
61 8 0.08
62 20 0.21
ACGTcount: A:0.50, C:0.13, G:0.16, T:0.21
Consensus pattern (61 bp):
AAAAAAAGTTTAGGTACCAAATTAGGAAAAAAAAGGTCAAGTTCAAGTACCAAATTGAGCC
Found at i:65559766 original size:66 final size:66
Alignment explanation
Indices: 65559660--65559852 Score: 241
Period size: 66 Copynumber: 3.0 Consensus size: 66
65559650 TGAAGACAAC
* *
65559660 GATGATTCTGCATCCATGAATGCTGAAAGTGCGAAGGGAGAAGTGAAAGAAGAGGAAAAGG-AGA
1 GATGATTCTGAATCCATGAATGCTGAAAGTGCGAAGGGAGAAGAGAAAGAAGAGGAAAAGGAAG-
65559724 AA
65 AA
* * *
65559726 GATGATTCTGTATCCATGAATGCTGAAAGTGCGAAGGGAGAAGAGAACGAAGAGGGAAAGGAAGA
1 GATGATTCTGAATCCATGAATGCTGAAAGTGCGAAGGGAGAAGAGAAAGAAGAGGAAAAGGAAGA
65559791 A
66 A
* ** * * * *
65559792 GATGACTCTGAATCTTTAAATGCTGAAAATTC-AA--AAGAAGAGAAAGAAGAGGAAAAGGAAG
1 GATGATTCTGAATCCATGAATGCTGAAAGTGCGAAGGGAGAAGAGAAAGAAGAGGAAAAGGAAG
65559853 GGGAGCAGGA
Statistics
Matches: 112, Mismatches: 14, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
63 24 0.21
65 2 0.02
66 84 0.75
67 2 0.02
ACGTcount: A:0.44, C:0.09, G:0.31, T:0.16
Consensus pattern (66 bp):
GATGATTCTGAATCCATGAATGCTGAAAGTGCGAAGGGAGAAGAGAAAGAAGAGGAAAAGGAAGA
A
Found at i:65564429 original size:16 final size:16
Alignment explanation
Indices: 65564408--65564438 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
65564398 AAATATTAAA
65564408 TTTATCAAGATATTTT
1 TTTATCAAGATATTTT
65564424 TTTATCAAGATATTT
1 TTTATCAAGATATTT
65564439 GTATGTTATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.06, G:0.06, T:0.55
Consensus pattern (16 bp):
TTTATCAAGATATTTT
Found at i:65567541 original size:6 final size:6
Alignment explanation
Indices: 65567532--65567565 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
65567522 GTTGTAGTAG
* *
65567532 TGGTAA TGGTAA TGGTAA TGGCAA TGGCAA TGGT
1 TGGTAA TGGTAA TGGTAA TGGTAA TGGTAA TGGT
65567566 GTGACGTTCA
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:0.29, C:0.06, G:0.35, T:0.29
Consensus pattern (6 bp):
TGGTAA
Found at i:65571101 original size:29 final size:30
Alignment explanation
Indices: 65571040--65571171 Score: 149
Period size: 30 Copynumber: 4.4 Consensus size: 30
65571030 AAAAATTTTG
** *
65571040 CATTTTGACCCCTAATTTTTTTTCAAAATTA
1 CATTTTGACCCCTAA-ACTTTCTCAAAATTA
* **
65571071 CATTTTTACCCCTAAACTTT-TTGAAATTA
1 CATTTTGACCCCTAAACTTTCTCAAAATTA
*
65571100 CATTTTGACCCCTAAAATTTCTCAAAATTA
1 CATTTTGACCCCTAAACTTTCTCAAAATTA
* *
65571130 CATTTTGACCCCTAAACTTCCTCTAAATTA
1 CATTTTGACCCCTAAACTTTCTCAAAATTA
* *
65571160 CGTTTTGGCCCC
1 CATTTTGACCCC
65571172 AAAAATTTTC
Statistics
Matches: 86, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
29 25 0.29
30 47 0.55
31 14 0.16
ACGTcount: A:0.29, C:0.25, G:0.05, T:0.41
Consensus pattern (30 bp):
CATTTTGACCCCTAAACTTTCTCAAAATTA
Found at i:65571158 original size:60 final size:59
Alignment explanation
Indices: 65571040--65571179 Score: 174
Period size: 60 Copynumber: 2.3 Consensus size: 59
65571030 AAAAATTTTG
** * * *
65571040 CATTTTGACCCCTAATTTTTTTTCAAAATTACATTTTTACCCCTAAACTTTTTGAAATTA
1 CATTTTGACCCCTAA-AATTTCTCAAAATTACATTTTGACCCCTAAACTTTCTGAAATTA
65571100 CATTTTGACCCCTAAAATTTCTCAAAATTACATTTTGACCCCTAAACTTCCTCT-AAATTA
1 CATTTTGACCCCTAAAATTTCTCAAAATTACATTTTGACCCCTAAACTT--TCTGAAATTA
* * *
65571160 CGTTTTGGCCCCAAAAATTT
1 CATTTTGACCCCTAAAATTT
65571180 TCCTGTGTTT
Statistics
Matches: 70, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
59 30 0.43
60 38 0.54
61 2 0.03
ACGTcount: A:0.31, C:0.24, G:0.05, T:0.41
Consensus pattern (59 bp):
CATTTTGACCCCTAAAATTTCTCAAAATTACATTTTGACCCCTAAACTTTCTGAAATTA
Found at i:65571590 original size:24 final size:24
Alignment explanation
Indices: 65571544--65571590 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
65571534 AAGAAGAAGA
* * * *
65571544 AGGAAGAATAAGGAAGAAGAAAAG
1 AGGAAGAAGAAAGAAAAAAAAAAG
65571568 AGGAAGAAGAAAGAAAAAAAAAA
1 AGGAAGAAGAAAGAAAAAAAAAA
65571591 AGAAAAATCC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.70, C:0.00, G:0.28, T:0.02
Consensus pattern (24 bp):
AGGAAGAAGAAAGAAAAAAAAAAG
Found at i:65571698 original size:15 final size:14
Alignment explanation
Indices: 65571676--65571715 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 14
65571666 GCAGCCCAAG
65571676 AAAAAAACAACAAAA
1 AAAAAAACAA-AAAA
*
65571691 ACAAAAACAAAAAA
1 AAAAAAACAAAAAA
65571705 AAAAGAAACAA
1 AAAA-AAACAA
65571716 GCCCAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 7 0.32
15 15 0.68
ACGTcount: A:0.85, C:0.12, G:0.03, T:0.00
Consensus pattern (14 bp):
AAAAAAACAAAAAA
Found at i:65571884 original size:15 final size:16
Alignment explanation
Indices: 65571864--65571933 Score: 58
Period size: 16 Copynumber: 4.4 Consensus size: 16
65571854 GGCCCAGCAG
65571864 AGAAAAAAA-AAGAAA
1 AGAAAAAAAGAAGAAA
65571879 AGAAAAAGAAGAA-AAA
1 AGAAAAA-AAGAAGAAA
*
65571895 GAGAAGGAAAA-AAG-AA
1 -AGAA-AAAAAGAAGAAA
* *
65571911 GGAAAAAAAGAAAAAA
1 AGAAAAAAAGAAGAAA
65571927 AGAAAAA
1 AGAAAAA
65571934 GAGGTTCAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 13
0.70 0.08 0.21
Matches are distributed among these distances:
14 4 0.09
15 12 0.28
16 17 0.40
17 8 0.19
18 2 0.05
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (16 bp):
AGAAAAAAAGAAGAAA
Found at i:65571886 original size:11 final size:11
Alignment explanation
Indices: 65571864--65571932 Score: 51
Period size: 11 Copynumber: 6.5 Consensus size: 11
65571854 GGCCCAGCAG
65571864 AGAAAA-AAAA
1 AGAAAAGAAAA
65571874 AGAAAAGAAAA
1 AGAAAAGAAAA
65571885 AG--AAGAAAA
1 AGAAAAGAAAA
*
65571894 AGAGAAGGAAAA
1 AGA-AAAGAAAA
*
65571906 A-AGAAGGAAAA
1 AGA-AAAGAAAA
65571917 A-AAGAA-AAAA
1 AGAA-AAGAAAA
65571927 AGAAAA
1 AGAAAA
65571933 AGAGGTTCAA
Statistics
Matches: 51, Mismatches: 2, Indels: 12
0.78 0.03 0.18
Matches are distributed among these distances:
9 9 0.18
10 14 0.27
11 21 0.41
12 7 0.14
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (11 bp):
AGAAAAGAAAA
Found at i:65571925 original size:31 final size:33
Alignment explanation
Indices: 65571869--65571930 Score: 92
Period size: 31 Copynumber: 1.9 Consensus size: 33
65571859 AGCAGAGAAA
*
65571869 AAAAAAGAAAAGAAAAAGAAGAAAAAGAGAAGG
1 AAAAAAGAAAAGAAAAAGAAGAAAAAAAGAAGG
*
65571902 AAAAAAG-AAGGAAAAA-AAGAAAAAAAGAA
1 AAAAAAGAAAAGAAAAAGAAGAAAAAAAGAA
65571931 AAAGAGGTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 12 0.44
32 8 0.30
33 7 0.26
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (33 bp):
AAAAAAGAAAAGAAAAAGAAGAAAAAAAGAAGG
Found at i:65571927 original size:22 final size:21
Alignment explanation
Indices: 65571864--65571927 Score: 76
Period size: 22 Copynumber: 3.0 Consensus size: 21
65571854 GGCCCAGCAG
65571864 AGAA-AAAAAAAGAAAAGAAAA
1 AGAAGAAAAAAAGAAAA-AAAA
* *
65571885 AGAAGAAAAAGAGAAGGAAAAA
1 AGAAGAAAAAAAGAA-AAAAAA
65571907 AGAAGGAAAAAAAGAAAAAAA
1 AGAA-GAAAAAAAGAAAAAAA
65571928 GAAAAAGAGG
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
21 4 0.11
22 21 0.58
23 11 0.31
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (21 bp):
AGAAGAAAAAAAGAAAAAAAA
Found at i:65572098 original size:12 final size:12
Alignment explanation
Indices: 65572067--65572108 Score: 50
Period size: 11 Copynumber: 3.4 Consensus size: 12
65572057 CATTTTATGC
65572067 ATTTTTATATTTAT
1 ATTTTTA-ATTT-T
*
65572081 ATTTTTAATTTG
1 ATTTTTAATTTT
65572093 ATTTTT-ATTTT
1 ATTTTTAATTTT
65572104 ATTTT
1 ATTTT
65572109 ATTTTAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
11 9 0.35
12 6 0.23
13 4 0.15
14 7 0.27
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (12 bp):
ATTTTTAATTTT
Found at i:65572312 original size:21 final size:20
Alignment explanation
Indices: 65572280--65572321 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
65572270 TCGGGTTTCG
65572280 AAATTTTCGTGTCTTCAAAA
1 AAATTTTCGTGTCTTCAAAA
*
65572300 AAATTTCTCGTGTTTTCAAAA
1 AAATTT-TCGTGTCTTCAAAA
65572321 A
1 A
65572322 TAATGTAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (20 bp):
AAATTTTCGTGTCTTCAAAA
Found at i:65572322 original size:19 final size:19
Alignment explanation
Indices: 65572280--65572321 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 19
65572270 TCGGGTTTCG
65572280 AAATTTTCGTGTCTTCAAAA
1 AAATTTTCGTGTCTTC-AAA
*
65572300 AAATTTCTCGTGTTTTCAAA
1 AAATTT-TCGTGTCTTCAAA
65572320 AA
1 AA
65572322 TAATGTAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (19 bp):
AAATTTTCGTGTCTTCAAA
Found at i:65572480 original size:36 final size:36
Alignment explanation
Indices: 65572426--65572495 Score: 106
Period size: 36 Copynumber: 1.9 Consensus size: 36
65572416 AAAAAAATCG
*
65572426 AAAAATTTTTCGTGTTTTCAAAAATTCCCGTGTTGC
1 AAAAATTTTTCATGTTTTCAAAAATTCCCGTGTTGC
*
65572462 AAAAA-TTTTCATGTTTTTCAAAAATTCTCGTGTT
1 AAAAATTTTTCATG-TTTTCAAAAATTCCCGTGTT
65572496 TTCAAAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
35 7 0.23
36 24 0.77
ACGTcount: A:0.30, C:0.14, G:0.11, T:0.44
Consensus pattern (36 bp):
AAAAATTTTTCATGTTTTCAAAAATTCCCGTGTTGC
Found at i:65572516 original size:36 final size:35
Alignment explanation
Indices: 65572476--65572607 Score: 115
Period size: 36 Copynumber: 3.7 Consensus size: 35
65572466 ATTTTCATGT
*
65572476 TTTTCAAAAATTCTCGTGTTTTCAAAAAAATTCCAA
1 TTTTCAAAAATTTTCGTGTTTTCAAAAAAATT-CAA
* * * **
65572512 TTTTCAAAATTTTTCGTGTTTTCTAAAAACTTCTG
1 TTTTCAAAAATTTTCGTGTTTTCAAAAAAATTCAA
* ** *
65572547 TGTTTCAAAAATTTTCGTG-TTTCTAAAATTTTCGCA
1 T-TTTCAAAAATTTTCGTGTTTTCAAAAAAATTC-AA
* *
65572583 -TTTCAAACATTTTCTTGTTTTCAAA
1 TTTTCAAAAATTTTCGTGTTTTCAAA
65572608 TTTTTCGTAT
Statistics
Matches: 79, Mismatches: 14, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
34 15 0.19
35 20 0.25
36 44 0.56
ACGTcount: A:0.30, C:0.15, G:0.08, T:0.47
Consensus pattern (35 bp):
TTTTCAAAAATTTTCGTGTTTTCAAAAAAATTCAA
Found at i:65572566 original size:17 final size:17
Alignment explanation
Indices: 65572426--65572778 Score: 182
Period size: 17 Copynumber: 19.9 Consensus size: 17
65572416 AAAAAAATCG
65572426 AAAAATTTTTCGTGTTTTC
1 AAAAA-TTTTCGTG-TTTC
** *
65572445 AAAAATTCCCGTGTTGC
1 AAAAATTTTCGTGTTTC
*
65572462 AAAAATTTTCATGTTTTTC
1 AAAAATTTTC--GTGTTTC
*
65572481 AAAAATTCTCGTGTTTTC
1 AAAAATTTTCGTG-TTTC
* * *
65572499 AAAAAAATTCCAAT-TTTC
1 -AAAAATTTTC-GTGTTTC
*
65572517 AAAATTTTTCGTGTTTTC
1 AAAAATTTTCGTG-TTTC
*
65572535 TAAAAA-CTTCTGTGTTTC
1 -AAAAATTTTC-GTGTTTC
65572553 AAAAATTTTCGTGTTTC
1 AAAAATTTTCGTGTTTC
* **
65572570 TAAAATTTTCGCATTTC
1 AAAAATTTTCGTGTTTC
* *
65572587 AAACATTTTCTTGTTTTC
1 AAAAATTTTCGTG-TTTC
* * *
65572605 -AAATTTTTCGTATTTA
1 AAAAATTTTCGTGTTTC
**
65572621 AAAAATCCTCGTGTTTTC
1 AAAAATTTTCGTG-TTTC
*
65572639 -AAAA-TTCCAGTGTTTC
1 AAAAATTTTC-GTGTTTC
*
65572655 AAAATTTTTCGTGTTTC
1 AAAAATTTTCGTGTTTC
* *
65572672 AAAAAAAAATTTCCGTTTTTC
1 ----AAAAATTTTCGTGTTTC
* *
65572693 AAAAACTTTCGCGCTTT-
1 AAAAATTTTCGTG-TTTC
**
65572710 AAGAAATTGACCGTGTTTC
1 AA-AAATT-TTCGTGTTTC
*
65572729 ATAAATTTTCGTGTTTC
1 AAAAATTTTCGTGTTTC
*
65572746 GAAGAAA-TCTCGTGTTTC
1 -AA-AAATTTTCGTGTTTC
65572764 -AAAATTTTCGTGTTT
1 AAAAATTTTCGTGTTT
65572779 TTTTAAAAAT
Statistics
Matches: 247, Mismatches: 60, Indels: 57
0.68 0.16 0.16
Matches are distributed among these distances:
15 3 0.01
16 19 0.08
17 106 0.43
18 64 0.26
19 40 0.16
20 1 0.00
21 14 0.06
ACGTcount: A:0.30, C:0.15, G:0.11, T:0.44
Consensus pattern (17 bp):
AAAAATTTTCGTGTTTC
Found at i:65572679 original size:21 final size:21
Alignment explanation
Indices: 65572655--65572697 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
65572645 CCAGTGTTTC
* *
65572655 AAAATTTTTCGTGTTTCAAAA
1 AAAAATTTCCGTGTTTCAAAA
*
65572676 AAAAATTTCCGTTTTTCAAAA
1 AAAAATTTCCGTGTTTCAAAA
65572697 A
1 A
65572698 CTTTCGCGCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.42, C:0.12, G:0.07, T:0.40
Consensus pattern (21 bp):
AAAAATTTCCGTGTTTCAAAA
Found at i:65572793 original size:18 final size:18
Alignment explanation
Indices: 65572770--65572829 Score: 63
Period size: 18 Copynumber: 3.5 Consensus size: 18
65572760 TTTCAAAATT
65572770 TTCGTGTTTTTTTAAAAA
1 TTCGTGTTTTTTTAAAAA
*
65572788 TTCGTG--TTTCT-AAAA
1 TTCGTGTTTTTTTAAAAA
* * *
65572803 TTCTTGTATTTTAAAAAA
1 TTCGTGTTTTTTTAAAAA
65572821 TTCGTGTTT
1 TTCGTGTTT
65572830 AAAAAAAAGG
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
15 9 0.27
16 4 0.12
17 3 0.09
18 17 0.52
ACGTcount: A:0.27, C:0.08, G:0.12, T:0.53
Consensus pattern (18 bp):
TTCGTGTTTTTTTAAAAA
Found at i:65572793 original size:34 final size:33
Alignment explanation
Indices: 65572477--65572834 Score: 152
Period size: 34 Copynumber: 10.2 Consensus size: 33
65572467 TTTTCATGTT
* * *
65572477 TTTCAAAAATTCTCGTGTTTTCAAAAAAATTCCAAT-
1 TTTC-AAAATTTTCGTGTTTT-TAAAAAATT-C-GTG
*
65572513 TTTCAAAATTTTTCGTGTTTTCTAAAAACTTCTGTG
1 TTTCAAAA-TTTTCGTGTTTT-TAAAAAATTC-GTG
* ** **
65572549 TTTCAAAAATTTTCGTGTTTCTAAAATTTTCGCA
1 TTTC-AAAATTTTCGTGTTTTTAAAAAATTCGTG
* * *** *
65572583 TTTCAAACATTTTCTTGTTTTCAAATTTTTCGTA
1 TTTCAAA-ATTTTCGTGTTTTTAAAAAATTCGTG
* ** *
65572617 TTTAAAAAATCCTCGTG-TTTT-CAAAATTCCAGTG
1 TTT-CAAAATTTTCGTGTTTTTAAAAAATT-C-GTG
** *
65572651 TTTCAAAATTTTTCGTGTTTCAAAAAAAAATTTCCGTT
1 TTTCAAAA-TTTTCGTGTTT--TTAAAAAA-TT-CGTG
* * * *
65572689 TTTCAAAAACTTTCGCG-CTTTAAGAAATTGACCGTG
1 TTTC-AAAATTTTCGTGTTTTTAAAAAATT---CGTG
** *
65572725 TTTCATAAATTTTCGTGTTTCGAAGAAATCTCGTG
1 TTTCA-AAATTTTCGTGTTTTTAAAAAAT-TCGTG
*
65572760 TTTCAAAATTTTCGTGTTTTTTTAAAAATTCGTG
1 TTTCAAAATTTTCGTG-TTTTTAAAAAATTCGTG
*
65572794 TTTCTAAAATTCTT-GT-ATTTTAAAAAATTCGTG
1 TTTC-AAAATT-TTCGTGTTTTTAAAAAATTCGTG
*
65572827 TTTAAAAA
1 TTTCAAAA
65572835 AAAGGAAAAA
Statistics
Matches: 249, Mismatches: 51, Indels: 48
0.72 0.15 0.14
Matches are distributed among these distances:
32 7 0.03
33 29 0.12
34 68 0.27
35 50 0.20
36 57 0.23
37 13 0.05
38 17 0.07
39 8 0.03
ACGTcount: A:0.31, C:0.14, G:0.10, T:0.45
Consensus pattern (33 bp):
TTTCAAAATTTTCGTGTTTTTAAAAAATTCGTG
Found at i:65572824 original size:33 final size:33
Alignment explanation
Indices: 65572721--65572834 Score: 106
Period size: 33 Copynumber: 3.4 Consensus size: 33
65572711 AGAAATTGAC
** *
65572721 CGTGTTTCATAAATTTTCGTGT-TTCGAAGAAATCT
1 CGTGTTTCA-AAA-TTTCGTGTATTTTAAAAAAT-T
* *
65572756 CGTGTTTCAAAATTTTCGTGTTTTTTTAAAAATT
1 CGTGTTTCAAAA-TTTCGTGTATTTTAAAAAATT
*
65572790 CGTGTTTCTAAAA-TTCTTGTATTTTAAAAAATT
1 CGTGTTTC-AAAATTTCGTGTATTTTAAAAAATT
*
65572823 CGTGTTTAAAAA
1 CGTGTTTCAAAA
65572835 AAAGGAAAAA
Statistics
Matches: 69, Mismatches: 8, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
32 4 0.06
33 24 0.35
34 21 0.30
35 20 0.29
ACGTcount: A:0.30, C:0.11, G:0.13, T:0.46
Consensus pattern (33 bp):
CGTGTTTCAAAATTTCGTGTATTTTAAAAAATT
Found at i:65572832 original size:15 final size:15
Alignment explanation
Indices: 65572783--65572835 Score: 52
Period size: 15 Copynumber: 3.3 Consensus size: 15
65572773 GTGTTTTTTT
*
65572783 AAAAATTCGTGTTTC
1 AAAAATTCGTGTTTA
* *
65572798 TAAAATTCTTGTATTTTA
1 AAAAATTC--GT-GTTTA
65572816 AAAAATTCGTGTTTA
1 AAAAATTCGTGTTTA
65572831 AAAAA
1 AAAAA
65572836 AAGGAAAAAG
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
15 16 0.53
16 2 0.07
17 2 0.07
18 10 0.33
ACGTcount: A:0.42, C:0.08, G:0.09, T:0.42
Consensus pattern (15 bp):
AAAAATTCGTGTTTA
Found at i:65574823 original size:4 final size:4
Alignment explanation
Indices: 65574814--65574849 Score: 63
Period size: 4 Copynumber: 9.0 Consensus size: 4
65574804 CATTTACTTG
*
65574814 TCAT TCAT TCAT TCAT TCAT TCAT TCAT TTAT TCAT
1 TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT
65574850 GTATTGCATG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.25, C:0.22, G:0.00, T:0.53
Consensus pattern (4 bp):
TCAT
Found at i:65578825 original size:9 final size:9
Alignment explanation
Indices: 65578811--65578882 Score: 63
Period size: 9 Copynumber: 7.8 Consensus size: 9
65578801 TATTATGCTT
65578811 AAAAAAACAA
1 AAAAAAAC-A
*
65578821 AAAAAAAAA
1 AAAAAAACA
65578830 GAAAAAAACA
1 -AAAAAAACA
* *
65578840 GAAAAAATA
1 AAAAAAACA
*
65578849 GAAAAAACA
1 AAAAAAACA
* *
65578858 GACAAAACA
1 AAAAAAACA
*
65578867 AAAACAACA
1 AAAAAAACA
65578876 AAAAAAA
1 AAAAAAA
65578883 AGAAAGAAAA
Statistics
Matches: 51, Mismatches: 10, Indels: 3
0.80 0.16 0.05
Matches are distributed among these distances:
9 36 0.71
10 15 0.29
ACGTcount: A:0.83, C:0.10, G:0.06, T:0.01
Consensus pattern (9 bp):
AAAAAAACA
Found at i:65578844 original size:18 final size:18
Alignment explanation
Indices: 65578823--65578892 Score: 72
Period size: 18 Copynumber: 3.8 Consensus size: 18
65578813 AAAAACAAAA
65578823 AAAAAAAGAAAAAAACAG
1 AAAAAAAGAAAAAAACAG
65578841 AAAAAATAG-AAAAAACAG
1 AAAAAA-AGAAAAAAACAG
* * *
65578859 ACAAAACA-AAAACAACAA
1 A-AAAAAAGAAAAAAACAG
65578877 AAAAAAAGAAAGAAAA
1 AAAAAAAGAAA-AAAA
65578893 ATCAAGATGA
Statistics
Matches: 42, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
17 5 0.12
18 28 0.67
19 9 0.21
ACGTcount: A:0.81, C:0.09, G:0.09, T:0.01
Consensus pattern (18 bp):
AAAAAAAGAAAAAAACAG
Found at i:65578892 original size:10 final size:9
Alignment explanation
Indices: 65578812--65578893 Score: 60
Period size: 10 Copynumber: 8.6 Consensus size: 9
65578802 ATTATGCTTA
*
65578812 AAAAAACAAA
1 AAAAAA-AAG
65578822 AAAAAAAAG
1 AAAAAAAAG
65578831 AAAAAAACAG
1 AAAAAAA-AG
*
65578841 AAAAAATAG
1 AAAAAAAAG
*
65578850 AAAAAACAG
1 AAAAAAAAG
65578859 ACAAAACAAA-
1 A-AAAA-AAAG
65578869 AACAACAAAA-
1 AA-AA-AAAAG
65578879 AAAAAGAAAG
1 AAAAA-AAAG
65578889 AAAAA
1 AAAAA
65578894 TCAAGATGAA
Statistics
Matches: 61, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
8 1 0.02
9 26 0.43
10 31 0.51
11 3 0.05
ACGTcount: A:0.83, C:0.09, G:0.07, T:0.01
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:65579973 original size:77 final size:77
Alignment explanation
Indices: 65579747--65580435 Score: 958
Period size: 77 Copynumber: 8.8 Consensus size: 77
65579737 TTTCAAGAAA
* * * *
65579747 TATTTTTTAAAATTCTATTTTTTTCAAAAAATCAATTCATAATACAGAGGTGAGTTGAGCCTCGG
1 TATTTTTTTAATTTCTGTTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGG
65579812 GTCACGCTGAGG
66 GTCACGCTGAGG
65579824 TATTTTTTTAATTTAATTTCTG-TTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGC
1 TA---TTTT--TTTAATTTCTGTTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGC
65579888 CTCGGGTCACGCTGAGG
61 CTCGGGTCACGCTGAGG
*
65579905 TATTTTTTTAATTTCTGTTTTTTTCAAAAAATCAACTCATAATATAGAGGTGAGTTGAGCCTCGG
1 TATTTTTTTAATTTCTGTTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGG
65579970 GTCACGCTGAGG
66 GTCACGCTGAGG
* *
65579982 TATTTTTTAAATTTTTGCTTTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTC
1 TATTTTTTTAATTTCTG--TTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTC
65580047 GGGTCACGCTGAGG
64 GGGTCACGCTGAGG
* * * ***
65580061 TATTTTTAATTTATGTCTTTTTTTTTTCTTTCAAATCAACTCATAATACAGAGGTGAGTTGAGCC
1 TATTTTT--TTAATTTC-TGTTTTTTTC-AAAAAATCAACTCATAATACAGAGGTGAGTTGAGCC
65580126 TCGGGTCACGCTGAGG
62 TCGGGTCACGCTGAGG
* *
65580142 TATTTTTTTTAATTTCT-ATTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTTG
1 TA-TTTTTTTAATTTCTGTTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCG
65580206 GGTCACGCTGAGG
65 GGTCACGCTGAGG
* **
65580219 TATTTTTTAAATTTCTACTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGG
1 TATTTTTTTAATTTCTGTTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGG
65580284 GTCACGCTGAGG
66 GTCACGCTGAGG
* * * *
65580296 TATTTTTTTTAAATTTCTGTTTTTTTCAAAAAAATCAACTCATATTGCGAGAAGTGAGTTAAGCC
1 TA-TTTTTTT-AATTTCTGTTTTTTTC-AAAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCC
65580361 TCGGGTCACGCTGAGG
62 TCGGGTCACGCTGAGG
* * *
65580377 TA-TTTTTCAATTTCTG--TTTTTC-AAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCT
1 TATTTTTTTAATTTCTGTTTTTTTCAAAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCT
65580436 TGGGCCACAT
Statistics
Matches: 557, Mismatches: 37, Indels: 39
0.88 0.06 0.06
Matches are distributed among these distances:
74 34 0.06
76 30 0.05
77 185 0.33
78 25 0.04
79 86 0.15
80 36 0.06
81 147 0.26
82 14 0.03
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.39
Consensus pattern (77 bp):
TATTTTTTTAATTTCTGTTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGG
GTCACGCTGAGG
Found at i:65580084 original size:158 final size:156
Alignment explanation
Indices: 65579750--65580435 Score: 930
Period size: 158 Copynumber: 4.4 Consensus size: 156
65579740 CAAGAAATAT
* *
65579750 TTTTTAA-AATTCTATTTTTTTCAAAAAATCAATTCATAATACAGAGGTGAGTTGAGCCTCGGGT
1 TTTTTAATATTTCT-TTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGT
* *
65579814 CACGCTGAGGTATTTTTTT-AATTTAATTTCTGTTTTTTCAAAAAATCAACTCATAATACAGAGG
65 CACGCTGAGGTATTTTTTTAAATTT--TTGCTTTTTTTTCAAAAAATCAACTCATAATACAGAGG
65579878 TGAGTTGAGCCTCGGGTCACGCTGAGGTA
128 TGAGTTGAGCCTCGGGTCACGCTGAGGTA
* *
65579907 TTTTT-TTAATTTCTGTTTTTTTCAAAAAATCAACTCATAATATAGAGGTGAGTTGAGCCTCGGG
1 TTTTTAAT-ATTTCT-TTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGG
65579971 TCACGCTGAGGTA-TTTTTTAAATTTTTGCTTTTTTTTCAAAAAATCAACTCATAATACAGAGGT
64 TCACGCTGAGGTATTTTTTTAAATTTTTGCTTTTTTTTCAAAAAATCAACTCATAATACAGAGGT
65580035 GAGTTGAGCCTCGGGTCACGCTGAGGTA
129 GAGTTGAGCCTCGGGTCACGCTGAGGTA
* ***
65580063 TTTTTAATTTATGTCTTTTTTTTTTCTTTCAAATCAACTCATAATACAGAGGTGAGTTGAGCCTC
1 TTTTTAA--TAT-T-TCTTTTTTTTC-AAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTC
* *
65580128 GGGTCACGCTGAGGTATTTTTTTTAA--TTT-CTATTTTTTCAAAAAATCAACTCATAATACAGA
61 GGGTCACGCTGAGGTATTTTTTTAAATTTTTGCTTTTTTTTCAAAAAATCAACTCATAATACAGA
*
65580190 GGTGAGTTGAGCCTTGGGTCACGCTGAGGTA
126 GGTGAGTTGAGCCTCGGGTCACGCTGAGGTA
*
65580221 TTTTTTAA-ATTTCTACTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGG
1 -TTTTTAATATTTCT-TTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGG
* * *
65580285 TCACGCTGAGGTATTTTTTTTAAATTTCTG--TTTTTTTCAAAAAAATCAACTCATATTGCGAGA
64 TCACGCTGAGGTA-TTTTTTTAAATTTTTGCTTTTTTTTC-AAAAAATCAACTCATAATAC-AGA
* *
65580348 AGTGAGTTAAGCCTCGGGTCACGCTGAGGTA
126 GGTGAGTTGAGCCTCGGGTCACGCTGAGGTA
* * * *
65580379 TTTTTCA-ATTTC-TGTTTTTC-AAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCT
1 TTTTTAATATTTCTTTTTTTTCAAAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCT
65580436 TGGGCCACAT
Statistics
Matches: 476, Mismatches: 34, Indels: 40
0.87 0.06 0.07
Matches are distributed among these distances:
154 70 0.15
155 40 0.08
156 79 0.17
157 42 0.09
158 165 0.35
159 20 0.04
160 52 0.11
161 8 0.02
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.38
Consensus pattern (156 bp):
TTTTTAATATTTCTTTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTC
ACGCTGAGGTATTTTTTTAAATTTTTGCTTTTTTTTCAAAAAATCAACTCATAATACAGAGGTGA
GTTGAGCCTCGGGTCACGCTGAGGTA
Found at i:65580179 original size:237 final size:233
Alignment explanation
Indices: 65579747--65580435 Score: 1009
Period size: 237 Copynumber: 2.9 Consensus size: 233
65579737 TTTCAAGAAA
* *
65579747 TATTTTTTAAAATTCTA-TTTTTTTCAAAAAATCAATTCATAATACAGAGGTGAGTTGAGCCTCG
1 TATTTTTTAAATTTCTACTTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCG
* *
65579811 GGTCACGCTGAGGTATTTTTTTAATTTAATT-TCTGTTTTTTCAAAAAATCAACTCATAATACAG
66 GGTCACGCTGAGGTA--TTTTTAATTTAATTCTTTTTTTTTTCAAAAAATCAACTCATAATACAG
65579875 AGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTTTAATTTCTGTTTTTTTCAAAAAATCAA
129 AGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTTTAATTTC--TTTTTTTCAAAAAATCAA
65579940 CTCATAATATAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGG
192 CTCATAATATAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGG
* *
65579982 TATTTTTTAAATTTTTGCTTTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTC
1 TATTTTTTAAATTTCTAC-TTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTC
***
65580047 GGGTCACGCTGAGGTATTTTTAATTT-ATGTCTTTTTTTTTTCTTTCAAATCAACTCATAATACA
65 GGGTCACGCTGAGGTATTTTTAATTTAAT-TCTTTTTTTTTTC-AAAAAATCAACTCATAATACA
65580111 GAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTTTTAATTTCTATTTTTTCAAAAAATCA
128 GAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTA-TTTTTTTAATTTCT-TTTTTTCAAAAAATCA
* *
65580176 ACTCATAATACAGAGGTGAGTTGAGCCTTGGGTCACGCTGAGG
191 ACTCATAATATAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGG
65580219 TATTTTTTAAATTTCTAC-TTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCG
1 TATTTTTTAAATTTCTACTTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCG
* * *
65580283 GGTCACGCTGAGGTATTTTT--TTTAAATT-TCTGTTTTTTTCAAAAAAATCAACTCATATTGCG
66 GGTCACGCTGAGGTATTTTTAATTT-AATTCT-TTTTTTTTTC-AAAAAATCAACTCATAATAC-
* * * *
65580345 AGAAGTGAGTTAAGCCTCGGGTCACGCTGAGGTA-TTTTTCAATTTCTGTTTTTC-AAAAATCAA
127 AGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTTTAATTTCTTTTTTTCAAAAAATCAA
* *
65580408 CTCATATTGCTAGAGGTGAGTTGAGCCT
192 CTCATAAT-ATAGAGGTGAGTTGAGCCT
65580436 TGGGCCACAT
Statistics
Matches: 415, Mismatches: 27, Indels: 27
0.88 0.06 0.06
Matches are distributed among these distances:
231 16 0.04
232 23 0.06
233 16 0.04
234 27 0.07
235 125 0.30
236 10 0.02
237 185 0.45
238 13 0.03
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.39
Consensus pattern (233 bp):
TATTTTTTAAATTTCTACTTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCG
GGTCACGCTGAGGTATTTTTAATTTAATTCTTTTTTTTTTCAAAAAATCAACTCATAATACAGAG
GTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTTTAATTTCTTTTTTTCAAAAAATCAACTCA
TAATATAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGG
Found at i:65580655 original size:30 final size:30
Alignment explanation
Indices: 65580620--65580759 Score: 192
Period size: 30 Copynumber: 4.7 Consensus size: 30
65580610 AAAAAATTTG
*
65580620 CATTTTGACCCCTAAATTTTTTCAAAATTA
1 CATTTTGACCCCTAAACTTTTTCAAAATTA
65580650 CATTTTGACCCCTAAACTTTTT-AAAATTA
1 CATTTTGACCCCTAAACTTTTTCAAAATTA
*
65580679 CATTTTGACCCCTAAACTTTCTCAAAATTA
1 CATTTTGACCCCTAAACTTTTTCAAAATTA
* ** *
65580709 CATTTTGACCCCTCAACTTCCTCGAAATTA
1 CATTTTGACCCCTAAACTTTTTCAAAATTA
* * *
65580739 CGTTTTGACCCCAAAAATTTT
1 CATTTTGACCCCTAAACTTTT
65580760 CCTATGTTTG
Statistics
Matches: 98, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
29 28 0.29
30 70 0.71
ACGTcount: A:0.31, C:0.25, G:0.05, T:0.39
Consensus pattern (30 bp):
CATTTTGACCCCTAAACTTTTTCAAAATTA
Found at i:65580690 original size:59 final size:60
Alignment explanation
Indices: 65580620--65580759 Score: 192
Period size: 59 Copynumber: 2.4 Consensus size: 60
65580610 AAAAAATTTG
* * *
65580620 CATTTTGACCCCTAAATTTTTTCAAAATTACATTTTGACCCCTAAACTT-TTTAAAATTA
1 CATTTTGACCCCTAAAATTTTTCAAAATTACATTTTGACCCCTAAACTTCCTCAAAATTA
* * * *
65580679 CATTTTGACCCCTAAACTTTCTCAAAATTACATTTTGACCCCTCAACTTCCTCGAAATTA
1 CATTTTGACCCCTAAAATTTTTCAAAATTACATTTTGACCCCTAAACTTCCTCAAAATTA
* *
65580739 CGTTTTGACCCCAAAAATTTT
1 CATTTTGACCCCTAAAATTTT
65580760 CCTATGTTTG
Statistics
Matches: 70, Mismatches: 10, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
59 46 0.66
60 24 0.34
ACGTcount: A:0.31, C:0.25, G:0.05, T:0.39
Consensus pattern (60 bp):
CATTTTGACCCCTAAAATTTTTCAAAATTACATTTTGACCCCTAAACTTCCTCAAAATTA
Found at i:65581121 original size:3 final size:3
Alignment explanation
Indices: 65581113--65581158 Score: 58
Period size: 3 Copynumber: 15.0 Consensus size: 3
65581103 GCTAGACTTT
*
65581113 GAA GAA GAA GAA GGAA GAA GAA GGAA GAA GAA -AA GAG GAA GAA GAA
1 GAA GAA GAA GAA -GAA GAA GAA -GAA GAA GAA GAA GAA GAA GAA GAA
65581159 AGAAAAAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
2 2 0.05
3 30 0.79
4 6 0.16
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:65581131 original size:10 final size:10
Alignment explanation
Indices: 65581116--65581144 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
65581106 AGACTTTGAA
65581116 GAAGAAGAAG
1 GAAGAAGAAG
65581126 GAAGAAGAAG
1 GAAGAAGAAG
65581136 GAAGAAGAA
1 GAAGAAGAA
65581145 AAGAGGAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (10 bp):
GAAGAAGAAG
Found at i:65581131 original size:13 final size:13
Alignment explanation
Indices: 65581113--65581158 Score: 62
Period size: 13 Copynumber: 3.7 Consensus size: 13
65581103 GCTAGACTTT
65581113 GAAGAAGAAGAAG
1 GAAGAAGAAGAAG
65581126 GAAGAAGAAGGAA-
1 GAAGAAGAA-GAAG
65581139 GAAGAA-AAG-AG
1 GAAGAAGAAGAAG
65581150 GAAGAAGAA
1 GAAGAAGAA
65581159 AGAAAAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
10 1 0.03
11 7 0.23
12 4 0.13
13 15 0.50
14 3 0.10
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (13 bp):
GAAGAAGAAGAAG
Found at i:65581273 original size:6 final size:6
Alignment explanation
Indices: 65581262--65581296 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
65581252 AGAAAAAAAC
65581262 AACAAA AACAAA AACAAA AACAAA AA-AAGA AACAA
1 AACAAA AACAAA AACAAA AACAAA AACAA-A AACAA
65581297 GCCCAAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
5 2 0.07
6 23 0.85
7 2 0.07
ACGTcount: A:0.83, C:0.14, G:0.03, T:0.00
Consensus pattern (6 bp):
AACAAA
Found at i:65581283 original size:18 final size:18
Alignment explanation
Indices: 65581251--65581296 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 18
65581241 CCAGCAGCCC
*
65581251 AAGAAAAAAACAACAAAAA
1 AAGAAACAAA-AACAAAAA
65581270 CAA-AAACAAAAACAAAAA
1 -AAGAAACAAAAACAAAAA
65581288 AAGAAACAA
1 AAGAAACAA
65581297 GCCCAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 2 0.08
18 14 0.58
19 6 0.25
20 2 0.08
ACGTcount: A:0.83, C:0.13, G:0.04, T:0.00
Consensus pattern (18 bp):
AAGAAACAAAAACAAAAA
Found at i:65581466 original size:11 final size:11
Alignment explanation
Indices: 65581444--65581513 Score: 60
Period size: 11 Copynumber: 6.5 Consensus size: 11
65581434 GGCCCAGCAG
65581444 AGAAAA-AAAA
1 AGAAAAGAAAA
65581454 AGAAAAGAAAA
1 AGAAAAGAAAA
65581465 AG--AAGAAAA
1 AGAAAAGAAAA
*
65581474 AGAGAAGGAAAA
1 AGA-AAAGAAAA
*
65581486 A-AGAAGGAAAA
1 AGA-AAAGAAAA
65581497 A-AAAAGAAAAA
1 AGAAAAG-AAAA
65581508 AGAAAA
1 AGAAAA
65581514 AAGAGGTTCA
Statistics
Matches: 52, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
9 9 0.17
10 9 0.17
11 23 0.44
12 11 0.21
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (11 bp):
AGAAAAGAAAA
Found at i:65581470 original size:14 final size:13
Alignment explanation
Indices: 65581456--65581517 Score: 54
Period size: 14 Copynumber: 4.5 Consensus size: 13
65581446 AAAAAAAAAG
65581456 AAAAGAAAAAGAAGA
1 AAAAGAAAAAG-A-A
* *
65581471 AAAAGAGAAGGAA
1 AAAAGAAAAAGAA
65581484 AAAAGAAGGAAA-AA
1 AAAAGAA--AAAGAA
65581498 AAAAGAAAAAAGAA
1 AAAAG-AAAAAGAA
65581512 AAAAGA
1 AAAAGA
65581518 GGTTCAATTC
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
13 11 0.28
14 15 0.38
15 13 0.33
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (13 bp):
AAAAGAAAAAGAA
Found at i:65581665 original size:10 final size:9
Alignment explanation
Indices: 65581638--65581662 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
65581628 AATATTATTA
65581638 GCATTTTAT
1 GCATTTTAT
65581647 GCATTTTAT
1 GCATTTTAT
65581656 GCATTTT
1 GCATTTT
65581663 TATATTTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.20, C:0.12, G:0.12, T:0.56
Consensus pattern (9 bp):
GCATTTTAT
Found at i:65581698 original size:21 final size:21
Alignment explanation
Indices: 65581674--65581713 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
65581664 ATATTTATAT
65581674 TTTTAATTTAATTTAATTTGA
1 TTTTAATTTAATTTAATTTGA
* * *
65581695 TTTTTATTTTATTTTATTT
1 TTTTAATTTAATTTAATTT
65581714 TAAATAATTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (21 bp):
TTTTAATTTAATTTAATTTGA
Found at i:65581913 original size:21 final size:20
Alignment explanation
Indices: 65581881--65581922 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 20
65581871 TCGGGTTTCG
65581881 AAATTTTCGTGTCTTCAAAA
1 AAATTTTCGTGTCTTCAAAA
65581901 AAATTTCTCGTGTCTTCAAAA
1 AAATTT-TCGTGTCTTCAAAA
65581922 A
1 A
65581923 TAAGGTAACA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.38
Consensus pattern (20 bp):
AAATTTTCGTGTCTTCAAAA
Found at i:65581923 original size:19 final size:19
Alignment explanation
Indices: 65581881--65581922 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 19
65581871 TCGGGTTTCG
65581881 AAATTTTCGTGTCTTCAAAA
1 AAATTTTCGTGTCTTC-AAA
65581901 AAATTTCTCGTGTCTTCAAA
1 AAATTT-TCGTGTCTTCAAA
65581921 AA
1 AA
65581923 TAAGGTAACA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.38
Consensus pattern (19 bp):
AAATTTTCGTGTCTTCAAA
Found at i:65582058 original size:18 final size:18
Alignment explanation
Indices: 65582036--65582424 Score: 167
Period size: 17 Copynumber: 22.0 Consensus size: 18
65582026 AGAAAATTTT
65582036 TCGTGTTTTCAAAAATTC
1 TCGTGTTTTCAAAAATTC
* * *
65582054 CCGTG-TTGCAAAAATTT
1 TCGTGTTTTCAAAAATTC
*
65582071 TCATGTTTTTCAAAAATTC
1 TCGTG-TTTTCAAAAATTC
65582090 TCGTGTTTTCAAAAAAATTC
1 TCGTGTTTTC--AAAAATTC
** * *
65582110 -C-AATTTTCAAAATTTT
1 TCGTGTTTTCAAAAATTC
65582126 TCGTGTTTTCTAAAAACTTC
1 TCGTGTTTTC-AAAAA-TTC
*
65582146 T-GTG-TTTCAAAAATTT
1 TCGTGTTTTCAAAAATTC
* *
65582162 TCGTG-TTTCTAAAATTT
1 TCGTGTTTTCAAAAATTC
* *
65582179 TCGT-ATTTCAAAAATTT
1 TCGTGTTTTCAAAAATTC
* * *
65582196 TCTTGTTTTC-AAATTTT
1 TCGTGTTTTCAAAAATTC
* * *
65582213 TCGT-ATTTAAAAAATCC
1 TCGTGTTTTCAAAAATTC
65582230 TCGTGTTTTC-AAAATTC
1 TCGTGTTTTCAAAAATTC
* * *
65582247 TAGTG-TTTCAAAATTTT
1 TCGTGTTTTCAAAAATTC
*
65582264 TTGTG-TTTCAAAAAAAAATTC
1 TCGTGTTTTC----AAAAATTC
*
65582285 CCGT-TTTTCAAAAACTT-
1 TCGTGTTTTCAAAAA-TTC
*
65582302 TCGCGTTTT-AAGAAATTGAC
1 TCGTGTTTTCAA-AAATT--C
* *
65582322 -CGTG-TTTCATAAATTT
1 TCGTGTTTTCAAAAATTC
*
65582338 TCGTG-TTTCAAAGAAATC
1 TCGTGTTTTCAAA-AATTC
*
65582356 TCGTG-TTTC-AAAATTT
1 TCGTGTTTTCAAAAATTC
*
65582372 TCGTGTTTTTTTAAAAA-T-
1 TCGTG--TTTTCAAAAATTC
*
65582390 TCGTG-TTTCTAAAATTC
1 TCGTGTTTTCAAAAATTC
* * *
65582407 TTGTATTTTAAAAAATTC
1 TCGTGTTTTCAAAAATTC
65582425 GTGTTAAAAA
Statistics
Matches: 280, Mismatches: 56, Indels: 70
0.69 0.14 0.17
Matches are distributed among these distances:
15 7 0.03
16 25 0.09
17 117 0.42
18 74 0.26
19 30 0.11
20 15 0.05
21 12 0.04
ACGTcount: A:0.30, C:0.14, G:0.10, T:0.46
Consensus pattern (18 bp):
TCGTGTTTTCAAAAATTC
Found at i:65582081 original size:36 final size:35
Alignment explanation
Indices: 65582028--65582096 Score: 102
Period size: 36 Copynumber: 1.9 Consensus size: 35
65582018 AAAAAATCAG
* *
65582028 AAAATTTTTCGTGTTTTCAAAAATTCCCGTGTTGC
1 AAAAATTTTCATGTTTTCAAAAATTCCCGTGTTGC
*
65582063 AAAAATTTTCATGTTTTTCAAAAATTCTCGTGTT
1 AAAAATTTTCATG-TTTTCAAAAATTCCCGTGTT
65582097 TTCAAAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 11 0.37
36 19 0.63
ACGTcount: A:0.29, C:0.14, G:0.12, T:0.45
Consensus pattern (35 bp):
AAAAATTTTCATGTTTTCAAAAATTCCCGTGTTGC
Found at i:65582167 original size:17 final size:17
Alignment explanation
Indices: 65582028--65582379 Score: 201
Period size: 17 Copynumber: 19.9 Consensus size: 17
65582018 AAAAAATCAG
*
65582028 AAAATTTTTCGTGTTTTC
1 AAAAATTTTCGTG-TTTC
** *
65582046 AAAAATTCCCGTGTTGC
1 AAAAATTTTCGTGTTTC
*
65582063 AAAAATTTTCATGTTTTTC
1 AAAAATTTTC--GTGTTTC
*
65582082 AAAAATTCTCGTGTTTTC
1 AAAAATTTTCGTG-TTTC
* * *
65582100 AAAAAAATTCCAAT-TTTC
1 -AAAAATTTTC-GTGTTTC
*
65582118 AAAATTTTTCGTGTTTTC
1 AAAAATTTTCGTG-TTTC
*
65582136 TAAAAA-CTTCTGTGTTTC
1 -AAAAATTTTC-GTGTTTC
65582154 AAAAATTTTCGTGTTTC
1 AAAAATTTTCGTGTTTC
* *
65582171 TAAAATTTTCGTATTTC
1 AAAAATTTTCGTGTTTC
*
65582188 AAAAATTTTCTTGTTTTC
1 AAAAATTTTCGTG-TTTC
* * *
65582206 -AAATTTTTCGTATTTA
1 AAAAATTTTCGTGTTTC
**
65582222 AAAAATCCTCGTGTTTTC
1 AAAAATTTTCGTG-TTTC
* *
65582240 -AAAATTCTAGTGTTTC
1 AAAAATTTTCGTGTTTC
* *
65582256 AAAATTTTTTGTGTTTC
1 AAAAATTTTCGTGTTTC
** *
65582273 AAAAAAAAATTCCCGTTTTTC
1 ----AAAAATTTTCGTGTTTC
* * *
65582294 AAAAACTTTCGCGTTTT
1 AAAAATTTTCGTGTTTC
**
65582311 AAGAAATTGACCGTGTTTC
1 AA-AAATT-TTCGTGTTTC
*
65582330 ATAAATTTTCGTGTTTC
1 AAAAATTTTCGTGTTTC
* *
65582347 AAAGAAATCTCGTGTTTC
1 AAA-AATTTTCGTGTTTC
65582365 -AAAATTTTCGTGTTT
1 AAAAATTTTCGTGTTT
65582380 TTTTAAAAAT
Statistics
Matches: 249, Mismatches: 64, Indels: 44
0.70 0.18 0.12
Matches are distributed among these distances:
16 19 0.08
17 122 0.49
18 60 0.24
19 35 0.14
20 1 0.00
21 12 0.05
ACGTcount: A:0.30, C:0.14, G:0.11, T:0.45
Consensus pattern (17 bp):
AAAAATTTTCGTGTTTC
Found at i:65582425 original size:33 final size:33
Alignment explanation
Indices: 65582322--65582429 Score: 105
Period size: 33 Copynumber: 3.2 Consensus size: 33
65582312 AGAAATTGAC
*
65582322 CGTGTTTCATAAATTTTCGTG--TTTCAAAGAAATCT
1 CGTGTTTCA-AAA-TTTCGTGTATTTTAAA-AAAT-T
* *
65582357 CGTGTTTCAAAATTTTCGTGTTTTTTTAAAAATT
1 CGTGTTTCAAAA-TTTCGTGTATTTTAAAAAATT
*
65582391 CGTGTTTCTAAAA-TTCTTGTATTTTAAAAAATT
1 CGTGTTTC-AAAATTTCGTGTATTTTAAAAAATT
65582424 CGTGTT
1 CGTGTT
65582430 AAAAAAAAAG
Statistics
Matches: 65, Mismatches: 5, Indels: 8
0.83 0.06 0.10
Matches are distributed among these distances:
33 23 0.35
34 20 0.31
35 17 0.26
36 5 0.08
ACGTcount: A:0.28, C:0.11, G:0.13, T:0.48
Consensus pattern (33 bp):
CGTGTTTCAAAATTTCGTGTATTTTAAAAAATT
Found at i:65584482 original size:34 final size:35
Alignment explanation
Indices: 65584438--65584504 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
65584428 CAGTAAAATA
*
65584438 TTTTCCGTAAAATGATCT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATCTACTGGAAAATATTTTAC
* *
65584472 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATCTACTGGAAAATATTTT
65584505 CTGCTGCTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 16 0.55
35 13 0.45
ACGTcount: A:0.31, C:0.10, G:0.13, T:0.45
Consensus pattern (35 bp):
TTTTCCGTAAAATGATCTACTGGAAAATATTTTAC
Found at i:65584483 original size:20 final size:20
Alignment explanation
Indices: 65584455--65584492 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
65584445 TAAAATGATC
*
65584455 TCTGGAAAATGTTTTACTTT
1 TCTGGAAAATGATTTACTTT
*
65584475 TCTGTAAAATGATTTACT
1 TCTGGAAAATGATTTACT
65584493 GGAAAATATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.29, C:0.11, G:0.13, T:0.47
Consensus pattern (20 bp):
TCTGGAAAATGATTTACTTT
Found at i:65590094 original size:30 final size:29
Alignment explanation
Indices: 65590046--65590113 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 29
65590036 AATTGATGAG
* * *
65590046 AATTGGATCAAATAAAAATTTTATGTATAA
1 AATTGTATAAAATAAAAATTAT-TGTATAA
*
65590076 AATTGTATAAAATCAAAATTATTGTATAA
1 AATTGTATAAAATAAAAATTATTGTATAA
*
65590105 AAGTGTATA
1 AATTGTATA
65590114 TTAGACCAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
29 15 0.45
30 18 0.55
ACGTcount: A:0.50, C:0.03, G:0.10, T:0.37
Consensus pattern (29 bp):
AATTGTATAAAATAAAAATTATTGTATAA
Found at i:65590111 original size:29 final size:30
Alignment explanation
Indices: 65590055--65590113 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
65590045 GAATTGGATC
* *
65590055 AAATAAAAATTTTATGTATAAAATTGTATA
1 AAATAAAAATTATATGTATAAAAGTGTATA
*
65590085 AAATCAAAATTAT-TGTATAAAAGTGTATA
1 AAATAAAAATTATATGTATAAAAGTGTATA
65590114 TTAGACCAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 15 0.58
30 11 0.42
ACGTcount: A:0.53, C:0.02, G:0.08, T:0.37
Consensus pattern (30 bp):
AAATAAAAATTATATGTATAAAAGTGTATA
Found at i:65597385 original size:35 final size:35
Alignment explanation
Indices: 65597339--65597409 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
65597329 GATATGGATA
65597339 TGTGTATGATGTTATGTTGTTTTTCTTATGATTTT
1 TGTGTATGATGTTATGTTGTTTTTCTTATGATTTT
65597374 TGTGTATGATGTTATGTTGTTTTTCTTATGATTTT
1 TGTGTATGATGTTATGTTGTTTTTCTTATGATTTT
65597409 T
1 T
65597410 CATAGTCCTC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.14, C:0.03, G:0.20, T:0.63
Consensus pattern (35 bp):
TGTGTATGATGTTATGTTGTTTTTCTTATGATTTT
Found at i:65600536 original size:32 final size:32
Alignment explanation
Indices: 65600456--65600542 Score: 79
Period size: 32 Copynumber: 2.7 Consensus size: 32
65600446 TTAGAGGGTT
*
65600456 TTAAACTATAAATTTACCATTTTTAAAGGGAGG
1 TTAAA-TATAAATTTACAATTTTTAAAGGGAGG
* * **
65600489 TCAAATACAGTTTTACATAATTTTTAAA-GG-GG
1 TTAAATATAAATTTAC--AATTTTTAAAGGGAGG
*
65600521 TTAAATATAAATTTACCATTTT
1 TTAAATATAAATTTACAATTTT
65600543 AGAGAGGCAA
Statistics
Matches: 42, Mismatches: 10, Indels: 7
0.71 0.17 0.12
Matches are distributed among these distances:
30 5 0.12
32 22 0.52
33 6 0.14
34 9 0.21
ACGTcount: A:0.39, C:0.09, G:0.11, T:0.40
Consensus pattern (32 bp):
TTAAATATAAATTTACAATTTTTAAAGGGAGG
Found at i:65604856 original size:17 final size:19
Alignment explanation
Indices: 65604830--65604868 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 19
65604820 CCCGACCTTT
65604830 AAATAAATTT-AATTAA-A
1 AAATAAATTTAAATTAAGA
*
65604847 AAATATATTTAAATTAAGA
1 AAATAAATTTAAATTAAGA
65604866 AAA
1 AAA
65604869 CAATAAGGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 9 0.47
18 6 0.32
19 4 0.21
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (19 bp):
AAATAAATTTAAATTAAGA
Found at i:65606979 original size:3 final size:3
Alignment explanation
Indices: 65606971--65607009 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
65606961 TTTTCTTTCT
** *
65606971 TTC TTC TTC TTC TTC TTC TTC TAG ATC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
65607010 CTTTACAATG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.05, C:0.31, G:0.03, T:0.62
Consensus pattern (3 bp):
TTC
Found at i:65608561 original size:204 final size:205
Alignment explanation
Indices: 65608137--65608659 Score: 782
Period size: 204 Copynumber: 2.6 Consensus size: 205
65608127 GCTCAGCCGA
* * *
65608137 AAAAAAAAACAAATGGTTTGTGTTGTAGTTGATTGCAAACCATTATCCGGGTTTGGTACCATTCA
1 AAAAAAAAACAAATGGTTTGTGTTGTAGTTGATTGCAAATCGTTATCCGGGTTTGGTACCGTTCA
* * * *
65608202 TTCGTATGATAAAAGCG--TGTGTTTTTGGTTGTCGAGGTGTCCGTTTATTCTAGGAAATCAACG
66 TTCATATGATAAAAGTGTTTGTGTTTTTGGTAGTCGAGGTGTCCGTTTATTCTAGGAAATAAACG
* *
65608265 ACGTTGTTGTGATAATTATAGCCTGTTAACCAATACGGTGTTTTCTTTTACCAGCTTGTCCTTAA
131 ACGTTATTGTGATAATTATAGCCTGTTAACCAATACGGTGTTTTCTTTTACCAGCTTGTACTTAA
*
65608330 GGCTTAACCCC
196 GCCTTAA-CCC
** *
65608341 CCAAAAATACAAATGGTTTGTGTTGTAGTTGATTGCAAATCGTTATCCGGGTTTGGTACCGTTCA
1 AAAAAAAAACAAATGGTTTGTGTTGTAGTTGATTGCAAATCGTTATCCGGGTTTGGTACCGTTCA
* *
65608406 TTCATATGATAAAAGTGTTTGTGTTTTTGGTAGTCGAGGTGTCGGTTTATTCTAGGAAATAAAGG
66 TTCATATGATAAAAGTGTTTGTGTTTTTGGTAGTCGAGGTGTCCGTTTATTCTAGGAAATAAACG
* * *
65608471 ACGTTATTGTGATAATTATAGCCTGTTAACTAATACGGTGTTTTCTTTTACCGGCTTGTACTTAT
131 ACGTTATTGTGATAATTATAGCCTGTTAACCAATACGGTGTTTTCTTTTACCAGCTTGTACTTAA
65608536 GCCTTAA-CC
196 GCCTTAACCC
* * *
65608545 AAAAAAAAAGAAATGGTTTGTGTTGTAGTTGATTGCAAATTGTTATCCGGGTTTGGTACCGGTCA
1 AAAAAAAAACAAATGGTTTGTGTTGTAGTTGATTGCAAATCGTTATCCGGGTTTGGTACCGTTCA
* * * *
65608610 TTCACATGATAAAAGTGTTTGTGTTTTTTGCTAGTCGAGGTATCCATTTA
66 TTCATATGATAAAAGTGTTTGTG-TTTTTGGTAGTCGAGGTGTCCGTTTA
65608660 GGAAATAAAG
Statistics
Matches: 287, Mismatches: 29, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
204 157 0.55
205 22 0.08
206 108 0.38
ACGTcount: A:0.26, C:0.14, G:0.22, T:0.38
Consensus pattern (205 bp):
AAAAAAAAACAAATGGTTTGTGTTGTAGTTGATTGCAAATCGTTATCCGGGTTTGGTACCGTTCA
TTCATATGATAAAAGTGTTTGTGTTTTTGGTAGTCGAGGTGTCCGTTTATTCTAGGAAATAAACG
ACGTTATTGTGATAATTATAGCCTGTTAACCAATACGGTGTTTTCTTTTACCAGCTTGTACTTAA
GCCTTAACCC
Found at i:65612028 original size:31 final size:31
Alignment explanation
Indices: 65611969--65612029 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
65611959 ACTTATTTTA
**
65611969 GGCTTCAATGTTTAATTTGGTATTTGAGTTC
1 GGCTTCAATGTTTAATTTGGTACATGAGTTC
*
65612000 GGCTTCAATGTTTAGTTTGGTACATGAGTT
1 GGCTTCAATGTTTAATTTGGTACATGAGTT
65612030 TTTTCAAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.20, C:0.10, G:0.25, T:0.46
Consensus pattern (31 bp):
GGCTTCAATGTTTAATTTGGTACATGAGTTC
Found at i:65624079 original size:19 final size:19
Alignment explanation
Indices: 65624030--65624079 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
65624020 ATATATAAAC
*
65624030 AAAACATGAAAAATAGTTT
1 AAAACATGAAAAATAGTTA
* *
65624049 AAAGCATTAAAAATA-TATA
1 AAAACATGAAAAATAGT-TA
65624068 AAAACATGAAAA
1 AAAACATGAAAA
65624080 TCTCTTTCAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
18 1 0.04
19 24 0.96
ACGTcount: A:0.64, C:0.06, G:0.08, T:0.22
Consensus pattern (19 bp):
AAAACATGAAAAATAGTTA
Found at i:65625401 original size:96 final size:96
Alignment explanation
Indices: 65625234--65625420 Score: 266
Period size: 96 Copynumber: 1.9 Consensus size: 96
65625224 AACTGAACTA
* * * * * *
65625234 ATACTCTCAGTAGACCGGAAGCTTGCATTTTTCACATCCTCCGATTCTTTCCTAGACAAAACGGC
1 ATACTCTCAGTAGACCGAAAACTTGCACTCTGCACATCCTCCGATTCTTTCCTAGACAAAACAGC
65625299 ACAATTCAACTCGTGAACCGAAACCGAACCG
66 ACAATTCAACTCGTGAACCGAAACCGAACCG
* * * *
65625330 ATACTCTCGGTAGACCGAAAACTTGCACTCTGCACATCCTCCGATTCTTTCCTATACAGAACATC
1 ATACTCTCAGTAGACCGAAAACTTGCACTCTGCACATCCTCCGATTCTTTCCTAGACAAAACAGC
* *
65625395 ATAATTCAACTCGTGAGCCGAAACCG
66 ACAATTCAACTCGTGAACCGAAACCG
65625421 GTCTTCTCCT
Statistics
Matches: 79, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
96 79 1.00
ACGTcount: A:0.30, C:0.30, G:0.15, T:0.25
Consensus pattern (96 bp):
ATACTCTCAGTAGACCGAAAACTTGCACTCTGCACATCCTCCGATTCTTTCCTAGACAAAACAGC
ACAATTCAACTCGTGAACCGAAACCGAACCG
Found at i:65625494 original size:123 final size:122
Alignment explanation
Indices: 65625318--65625724 Score: 532
Period size: 123 Copynumber: 3.3 Consensus size: 122
65625308 CTCGTGAACC
* * * * *
65625318 GAAACCGAACCGATACTCTCGGTAGACCGAAAACTTGCACTCTGCACATCCTCCGATTCTTTCCT
1 GAAACCGAACCGATACTCTCAGTAGACCGAAAACTTACATTCTTCACATCCTCCGGTTCTTTCCT
*
65625383 ATACAGAACATCATAATTCAACTCGTGAGCCGAAACCGGTCTTCTCCTCCTTGAGTTA
66 ATACAAAACATCATAATTCAACTCGTGAGCCGAAACCGGTC-TCTCCTCCTTGAGTTA
* * * * *
65625441 GAAACCAAACCGATACTCTCACTAGACCGAAAGCTTACATTTTTTACATCCTCCGGTTCTTTCCT
1 GAAACCGAACCGATACTCTCAGTAGACCGAAAACTTACATTCTTCACATCCTCCGGTTCTTTCCT
* * * *
65625506 ATACAAAACAGCACAATTCAACTCGTGAGCCGAATCCGGTC-CT-CTCC-TCAGTCTA
66 ATACAAAACATCATAATTCAACTCGTGAGCCGAAACCGGTCTCTCCTCCTTGAGT-TA
* *
65625561 GAAACCGAACCGATACTCTCAGTAGACCGAAAACTTGCATTCTTCACATCCTCCGGTTCTTTCCC
1 GAAACCGAACCGATACTCTCAGTAGACCGAAAACTTACATTCTTCACATCCTCCGGTTCTTTCCT
* * * *
65625626 ATACAAAACATCATGATTCAACTCGTGAGCCGAAACCGGTCCTCTCCTCCTCGAGCTC
66 ATACAAAACATCATAATTCAACTCGTGAGCCGAAACCGGT-CTCTCCTCCTTGAGTTA
* * * * *
65625684 GAAACTGAACCTATACTCTCAGTGGACCGGAAGCTTACATT
1 GAAACCGAACCGATACTCTCAGTAGACCGAAAACTTACATT
65625725 TTTCCTACAC
Statistics
Matches: 243, Mismatches: 36, Indels: 10
0.84 0.12 0.03
Matches are distributed among these distances:
119 4 0.02
120 100 0.41
121 3 0.01
122 2 0.01
123 132 0.54
124 2 0.01
ACGTcount: A:0.28, C:0.31, G:0.15, T:0.26
Consensus pattern (122 bp):
GAAACCGAACCGATACTCTCAGTAGACCGAAAACTTACATTCTTCACATCCTCCGGTTCTTTCCT
ATACAAAACATCATAATTCAACTCGTGAGCCGAAACCGGTCTCTCCTCCTTGAGTTA
Found at i:65625618 original size:120 final size:119
Alignment explanation
Indices: 65625318--65625674 Score: 516
Period size: 120 Copynumber: 3.0 Consensus size: 119
65625308 CTCGTGAACC
* * * *
65625318 GAAACCGAACCGATACTCTCGGTAGACCGAAAACTTGCACTCTGCACATCCTCCGATTCTTTCCT
1 GAAACCGAACCGATACTCTCAGTAGACCGAAAACTTGCATTCTTCACATCCTCCGGTTCTTTCCT
* *
65625383 ATACAGAACATCATAATTCAACTCGTGAGCCGAAACCGGTCTTCTCCTCCTTGAGTTA
66 ATACAAAACATCATAATTCAACTCGTGAGCCGAAACCGGTC--CT-CTCC-TCAGTTA
* * * * * *
65625441 GAAACCAAACCGATACTCTCACTAGACCGAAAGCTTACATTTTTTACATCCTCCGGTTCTTTCCT
1 GAAACCGAACCGATACTCTCAGTAGACCGAAAACTTGCATTCTTCACATCCTCCGGTTCTTTCCT
* * *
65625506 ATACAAAACAGCACAATTCAACTCGTGAGCCGAATCCGGTCCTCTCCTCAGTCTA
66 ATACAAAACATCATAATTCAACTCGTGAGCCGAAACCGGTCCTCTCCTCAGT-TA
*
65625561 GAAACCGAACCGATACTCTCAGTAGACCGAAAACTTGCATTCTTCACATCCTCCGGTTCTTTCCC
1 GAAACCGAACCGATACTCTCAGTAGACCGAAAACTTGCATTCTTCACATCCTCCGGTTCTTTCCT
*
65625626 ATACAAAACATCATGATTCAACTCGTGAGCCGAAACCGGTCCTCTCCTC
66 ATACAAAACATCATAATTCAACTCGTGAGCCGAAACCGGTCCTCTCCTC
65625675 CTCGAGCTCG
Statistics
Matches: 207, Mismatches: 26, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
119 4 0.02
120 109 0.53
121 2 0.01
123 92 0.44
ACGTcount: A:0.28, C:0.32, G:0.14, T:0.26
Consensus pattern (119 bp):
GAAACCGAACCGATACTCTCAGTAGACCGAAAACTTGCATTCTTCACATCCTCCGGTTCTTTCCT
ATACAAAACATCATAATTCAACTCGTGAGCCGAAACCGGTCCTCTCCTCAGTTA
Found at i:65626620 original size:23 final size:22
Alignment explanation
Indices: 65626591--65626639 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
65626581 TTTTGCTAAA
65626591 AAAAATTATCCATTTATACTGTT
1 AAAAATTA-CCATTTATACTGTT
* *
65626614 AAAAATTAGCTTTTATACTGTT
1 AAAAATTACCATTTATACTGTT
65626636 AAAA
1 AAAA
65626640 CTTAGCTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 16 0.67
23 8 0.33
ACGTcount: A:0.43, C:0.10, G:0.06, T:0.41
Consensus pattern (22 bp):
AAAAATTACCATTTATACTGTT
Found at i:65626628 original size:22 final size:22
Alignment explanation
Indices: 65626603--65626649 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
65626593 AAATTATCCA
65626603 TTTATACTGTTAAAAATTAGCT
1 TTTATACTGTTAAAAATTAGCT
*
65626625 TTTATACTGTTAAAACTTAGCT
1 TTTATACTGTTAAAAATTAGCT
65626647 TTT
1 TTT
65626650 GTATGCTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.32, C:0.11, G:0.09, T:0.49
Consensus pattern (22 bp):
TTTATACTGTTAAAAATTAGCT
Found at i:65634176 original size:90 final size:85
Alignment explanation
Indices: 65634009--65634320 Score: 286
Period size: 90 Copynumber: 3.5 Consensus size: 85
65633999 TTACACCACA
* * * * *
65634009 ATACTCAAGCTCAAGTGCCCCAGAAATGAAATATAATAAATAACAAAATTTATAATTATCTCGAA
1 ATACTCAAGCCCAAGTGCCCCA-AAATGAAATATAATAAATAA-TAATTTTATAGTTATCCCG--
* *
65634074 AAAATTTTAAAAAA-TTGCATCATC
62 AAAA-TTAAAAAAACTTGCATCACC
* *
65634098 ATACTCAAAGCTCAAGTGCTCCAAAAGTGAAATATAATAAATAATAATTTTAATAGTTATCCCGA
1 ATACTC-AAGCCCAAGTGCCCCAAAA-TGAAATATAATAAATAATAATTTT-ATAGTTATCCCGA
* **
65634163 AAGTATTCAAAAAAAATTTG-GGCACC
63 AA--ATT--AAAAAAACTTGCATCACC
* * *
65634189 ATATTCAAGCCCAAGTACCCCGAAAATGAAATATAATAAATAATAATTTTTATAGTTATCCTGAA
1 ATACTCAAGCCCAAGTGCCCC-AAAATGAAATATAATAAATAATAA-TTTTATAGTTATCCCGAA
**
65634254 AATTAAAAAAACAAGCATCACC
64 AATTAAAAAAACTTGCATCACC
* * *
65634276 GTACTCAAGCCCAAGTGCCTCAAAAAATGAAATGTAATAAATAAT
1 ATACTCAAGCCCAAGTGCC-C-CAAAATGAAATATAATAAATAAT
65634321 TTTAGCACCA
Statistics
Matches: 186, Mismatches: 24, Indels: 27
0.78 0.10 0.11
Matches are distributed among these distances:
86 8 0.04
87 20 0.11
88 28 0.15
89 16 0.09
90 89 0.48
91 22 0.12
92 3 0.02
ACGTcount: A:0.47, C:0.16, G:0.10, T:0.27
Consensus pattern (85 bp):
ATACTCAAGCCCAAGTGCCCCAAAATGAAATATAATAAATAATAATTTTATAGTTATCCCGAAAA
TTAAAAAAACTTGCATCACC
Done.