Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr10
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 21822658
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.32
Warning! 1067834 characters in sequence are not A, C, G, or T
File 40 of 59
Found at i:14445186 original size:35 final size:33
Alignment explanation
Indices: 14445078--14445189 Score: 86
Period size: 35 Copynumber: 3.3 Consensus size: 33
14445068 TAACCCAAAG
* *
14445078 TGGTTTTTCAAAAGCTCAACCATAACTTTTC-ACAA
1 TGGTTTTTCAAAGGCTCAACCAT-AC--CTCAACAA
** * * *
14445113 TGGTTTTTCACGGGCTCGACCAAAACC-CAA-AG
1 TGGTTTTTCAAAGGCTCAACC-ATACCTCAACAA
14445145 TGGTTTTTCAAAGGCTCAACCACTACCTACAACAA
1 TGGTTTTTCAAAGGCTCAACCA-TACCT-CAACAA
14445180 TGGTTTTTCA
1 TGGTTTTTCA
14445190 CGGGATCAAC
Statistics
Matches: 59, Mismatches: 12, Indels: 12
0.71 0.14 0.14
Matches are distributed among these distances:
31 1 0.02
32 23 0.39
33 1 0.02
34 3 0.05
35 30 0.51
36 1 0.02
ACGTcount: A:0.30, C:0.25, G:0.14, T:0.30
Consensus pattern (33 bp):
TGGTTTTTCAAAGGCTCAACCATACCTCAACAA
Found at i:14445199 original size:35 final size:33
Alignment explanation
Indices: 14445109--14445212 Score: 120
Period size: 32 Copynumber: 3.1 Consensus size: 33
14445099 ATAACTTTTC
*
14445109 ACAATGGTTTTTCACGGGCTCGACCAAAACCCA
1 ACAATGGTTTTTCACGGGCTCAACCAAAACCCA
* ** **
14445142 A-AGTGGTTTTTCAAAGGCTCAACCACTACCTACA
1 ACAATGGTTTTTCACGGGCTCAACCAAAACC--CA
*
14445176 ACAATGGTTTTTCACGGGATCAACCAAAACCCA
1 ACAATGGTTTTTCACGGGCTCAACCAAAACCCA
14445209 ACAA
1 ACAA
14445213 CTAAATTTTC
Statistics
Matches: 56, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
32 23 0.41
33 7 0.12
34 3 0.05
35 23 0.41
ACGTcount: A:0.35, C:0.28, G:0.15, T:0.22
Consensus pattern (33 bp):
ACAATGGTTTTTCACGGGCTCAACCAAAACCCA
Found at i:14447885 original size:20 final size:20
Alignment explanation
Indices: 14447857--14447895 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
14447847 CTTCAAGCAC
* *
14447857 TATTCTCAATTATCATCAAG
1 TATTATCAATCATCATCAAG
14447877 TATTATCAATCATCATCAA
1 TATTATCAATCATCATCAA
14447896 ACATTCATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.21, G:0.03, T:0.38
Consensus pattern (20 bp):
TATTATCAATCATCATCAAG
Found at i:14453146 original size:35 final size:36
Alignment explanation
Indices: 14453092--14453160 Score: 95
Period size: 35 Copynumber: 1.9 Consensus size: 36
14453082 TAACCCAAAG
* *
14453092 TGGTTTTTCAAAGGCTCAACCACAACCT-ACAACAA
1 TGGTTTTTCAAAGGATCAACCAAAACCTAACAACAA
**
14453127 TGGTTTTTCACGGGATCAACCAAAACCTAACAAC
1 TGGTTTTTCAAAGGATCAACCAAAACCTAACAAC
14453161 TAACTTTTCA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
35 24 0.83
36 5 0.17
ACGTcount: A:0.36, C:0.28, G:0.13, T:0.23
Consensus pattern (36 bp):
TGGTTTTTCAAAGGATCAACCAAAACCTAACAACAA
Found at i:14459232 original size:30 final size:30
Alignment explanation
Indices: 14459198--14459259 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
14459188 GTTGAGTCTA
* *
14459198 TTTTATTCAAATTGTAGCAATAGTTTGAAT
1 TTTTATTCAAATTGTAACAATAGTTTAAAT
*
14459228 TTTTATTGAAATTGTAACAATAGTTTAAAT
1 TTTTATTCAAATTGTAACAATAGTTTAAAT
14459258 TT
1 TT
14459260 GCATTATGGA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.35, C:0.05, G:0.11, T:0.48
Consensus pattern (30 bp):
TTTTATTCAAATTGTAACAATAGTTTAAAT
Found at i:14463198 original size:12 final size:12
Alignment explanation
Indices: 14463181--14463206 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
14463171 CTCATTAAAC
14463181 TCGCTAATAGAT
1 TCGCTAATAGAT
14463193 TCGCTAATAGAT
1 TCGCTAATAGAT
14463205 TC
1 TC
14463207 TCTCTTACAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Consensus pattern (12 bp):
TCGCTAATAGAT
Found at i:14464094 original size:30 final size:30
Alignment explanation
Indices: 14464035--14464099 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
14464025 AACTGATTTT
*
14464035 ATTT-TATTCAAATTGTAACAACAATTTGA
1 ATTTGTATTCAAATTGTAACAACAACTTGA
* * *
14464064 ATTTGTATTCAAATTGTAATAATAGCTTGA
1 ATTTGTATTCAAATTGTAACAACAACTTGA
14464094 ATTTGT
1 ATTTGT
14464100 GTTCTGGATA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 4 0.13
30 27 0.87
ACGTcount: A:0.37, C:0.08, G:0.11, T:0.45
Consensus pattern (30 bp):
ATTTGTATTCAAATTGTAACAACAACTTGA
Found at i:14470793 original size:12 final size:13
Alignment explanation
Indices: 14470776--14470804 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
14470766 TAAGAAAATG
14470776 TAATA-TTTTATT
1 TAATATTTTTATT
14470788 TAATATTTTTATT
1 TAATATTTTTATT
14470801 TAAT
1 TAAT
14470805 TTGAATAGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.31
13 11 0.69
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (13 bp):
TAATATTTTTATT
Found at i:14476785 original size:37 final size:36
Alignment explanation
Indices: 14476697--14476810 Score: 174
Period size: 37 Copynumber: 3.1 Consensus size: 36
14476687 CATATGCATT
* *
14476697 CATCATCATGTGTGCACTCCCTACTTGCACACTTCA
1 CATCATCATGTGTGCACTCCCTACTCGCACACTTAA
*
14476733 CATCATCATGTGTGCATTCCCTACTCGCACACTCTAA
1 CATCATCATGTGTGCACTCCCTACTCGCACACT-TAA
*
14476770 CATCATCATGCGTGCACTCCCTACTCGCACACTTTAA
1 CATCATCATGTGTGCACTCCCTACTCGCACAC-TTAA
14476807 CATC
1 CATC
14476811 CTCACGCAAC
Statistics
Matches: 71, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
36 31 0.44
37 39 0.55
38 1 0.01
ACGTcount: A:0.24, C:0.37, G:0.11, T:0.29
Consensus pattern (36 bp):
CATCATCATGTGTGCACTCCCTACTCGCACACTTAA
Found at i:14486285 original size:42 final size:41
Alignment explanation
Indices: 14486224--14486348 Score: 160
Period size: 42 Copynumber: 3.0 Consensus size: 41
14486214 CATCTCATAT
* *
14486224 GCAACGGCTTATGCGCACTCCTACTCGCACATAGTCGGGTCA
1 GCAAC-GCTTATGTGCACTCCTACTCGCACATAGCCGGGTCA
* * * *
14486266 GCAACTGCTTATGTTCACTCCCAGTCGCACATAACCGGGTCA
1 GCAAC-GCTTATGTGCACTCCTACTCGCACATAGCCGGGTCA
*
14486308 GCAACGACTTATGTGCACTCTTACTCGCACATAGCCGGGTC
1 GCAACG-CTTATGTGCACTCCTACTCGCACATAGCCGGGTC
14486349 CACATCAACA
Statistics
Matches: 70, Mismatches: 12, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
41 1 0.01
42 69 0.99
ACGTcount: A:0.22, C:0.33, G:0.22, T:0.23
Consensus pattern (41 bp):
GCAACGCTTATGTGCACTCCTACTCGCACATAGCCGGGTCA
Found at i:14488376 original size:22 final size:22
Alignment explanation
Indices: 14488337--14488382 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
14488327 AACTTTTGAG
* **
14488337 TTTTTTTTTCTTTTTTTTATTC
1 TTTTATTTTCTTGGTTTTATTC
*
14488359 TTTTATTTTCTTGGTTTTGTTC
1 TTTTATTTTCTTGGTTTTATTC
14488381 TT
1 TT
14488383 AATGTTTAAC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.04, C:0.09, G:0.07, T:0.80
Consensus pattern (22 bp):
TTTTATTTTCTTGGTTTTATTC
Found at i:14492978 original size:21 final size:21
Alignment explanation
Indices: 14492954--14493006 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
14492944 TTTAAAGAAC
*
14492954 ATAGTCGACCCTAAGAGCCTT
1 ATAGTTGACCCTAAGAGCCTT
14492975 ATAGTTGACCCTAAGAGCCTT
1 ATAGTTGACCCTAAGAGCCTT
14492996 ATAGTTGACCC
1 ATAGTTGACCC
14493007 CCATGCTTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.26
Consensus pattern (21 bp):
ATAGTTGACCCTAAGAGCCTT
Found at i:14493451 original size:36 final size:36
Alignment explanation
Indices: 14493371--14493451 Score: 119
Period size: 36 Copynumber: 2.2 Consensus size: 36
14493361 GGTCGAGCTT
* *
14493371 GTGAAAAACCATTGTTGAAGGGTTTTGCTTGATCTC
1 GTGAAAAAGCATTCTTGAAGGGTTTTGCTTGATCTC
14493407 GTGAAAAAGCATTCTTGAAGGGTTTCT-CTTGATCTC
1 GTGAAAAAGCATTCTTGAAGGGTTT-TGCTTGATCTC
*
14493443 GTGGAAAAG
1 GTGAAAAAG
14493452 AAATGTAAGT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
36 40 0.98
37 1 0.02
ACGTcount: A:0.27, C:0.14, G:0.26, T:0.33
Consensus pattern (36 bp):
GTGAAAAAGCATTCTTGAAGGGTTTTGCTTGATCTC
Found at i:14504207 original size:22 final size:22
Alignment explanation
Indices: 14504175--14504216 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
14504165 AAATACGACG
14504175 ATGAATCTTCGCTGCAGCGAGA
1 ATGAATCTTCGCTGCAGCGAGA
* *
14504197 ATGAATTTTCGTTGCAGCGA
1 ATGAATCTTCGCTGCAGCGA
14504217 CGTTGGGATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (22 bp):
ATGAATCTTCGCTGCAGCGAGA
Found at i:14504549 original size:60 final size:60
Alignment explanation
Indices: 14504390--14504550 Score: 214
Period size: 60 Copynumber: 2.7 Consensus size: 60
14504380 TAGGAGACAA
* * * *
14504390 AAACAGAAGGTTTTTCGCTGTAGCGAGATTGAATCTCGCTGCAACAAAATTATGACCCAG
1 AAACAGAAAGTTTCTCGCTGCAGCGAGATTGAATCTCGCTGCAACAAAATTATAACCCAG
* * * ** *
14504450 AAACAGAATGTTTCTCGCTACAGCGAGATTCAATCTCGCTGCAATGAAATTGTAACCCAG
1 AAACAGAAAGTTTCTCGCTGCAGCGAGATTGAATCTCGCTGCAACAAAATTATAACCCAG
* *
14504510 AAACAGAAAGTTTCTCGCTGCAGCGAGAATGAATTTCGCTG
1 AAACAGAAAGTTTCTCGCTGCAGCGAGATTGAATCTCGCTG
14504551 TAGCGAGAAG
Statistics
Matches: 87, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
60 87 1.00
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.25
Consensus pattern (60 bp):
AAACAGAAAGTTTCTCGCTGCAGCGAGATTGAATCTCGCTGCAACAAAATTATAACCCAG
Found at i:14504961 original size:43 final size:43
Alignment explanation
Indices: 14504913--14505044 Score: 151
Period size: 43 Copynumber: 3.1 Consensus size: 43
14504903 CCCATCATCA
* ** *
14504913 TCATCACCAGCTCATGCGCACTCCCTACTCACACATGGCTGGG
1 TCATCACCAGCTTATGCGCACTCCCTACTCACACATAACCGGG
*
14504956 TCATCACCGAG-TTATGCGCACTCCCTACTCGCACATAACCGGG
1 TCATCACC-AGCTTATGCGCACTCCCTACTCACACATAACCGGG
* * * *
14504999 TTATC-CTCGGCTTATGCGCACTCCCTACTCACACATAGCCGAG
1 TCATCAC-CAGCTTATGCGCACTCCCTACTCACACATAACCGGG
14505042 TCA
1 TCA
14505045 ATATAATTAC
Statistics
Matches: 75, Mismatches: 11, Indels: 6
0.82 0.12 0.07
Matches are distributed among these distances:
42 2 0.03
43 71 0.95
44 2 0.03
ACGTcount: A:0.22, C:0.38, G:0.17, T:0.23
Consensus pattern (43 bp):
TCATCACCAGCTTATGCGCACTCCCTACTCACACATAACCGGG
Found at i:14515665 original size:22 final size:22
Alignment explanation
Indices: 14515640--14515681 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
14515630 AACATAATGA
14515640 GCTTTGAAA-ATGAATGAAAAAT
1 GCTTTGAAATATGAA-GAAAAAT
*
14515662 GCTTTTAAATATGAAGAAAA
1 GCTTTGAAATATGAAGAAAA
14515682 TCCTCAAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.50, C:0.05, G:0.17, T:0.29
Consensus pattern (22 bp):
GCTTTGAAATATGAAGAAAAAT
Found at i:14522111 original size:103 final size:103
Alignment explanation
Indices: 14521923--14522131 Score: 348
Period size: 103 Copynumber: 2.0 Consensus size: 103
14521913 AAAAAAATGA
14521923 TGCAAAGAATTTTTATTGTTTTCTTTGCTTGATAACCTGAGCCATAAATGGAATTAGGCATAAAA
1 TGCAAAGAATTTTTATTGTTTTCTTTGCTTGATAACCTGAGCCATAAATGGAATTAGGCATAAAA
* * *
14521988 ATTCTTCAAAACGTTCTGCAACATTTATATAGGTCACT
66 ATTCTTCAAAACCTTATGCAACATTTATACAGGTCACT
* * *
14522026 TGCAGAGAATTTTTATTGTTTTCTTTAG-TTGATAACCTGAGCCATCAATGGAATTAGGCGTAAA
1 TGCAAAGAATTTTTATTGTTTTCTTT-GCTTGATAACCTGAGCCATAAATGGAATTAGGCATAAA
14522090 AATTCTTCAAAACCTTATGCAACATTTATACAGGTCACT
65 AATTCTTCAAAACCTTATGCAACATTTATACAGGTCACT
14522129 TGC
1 TGC
14522132 TCAAATAATA
Statistics
Matches: 99, Mismatches: 6, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
103 98 0.99
104 1 0.01
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.36
Consensus pattern (103 bp):
TGCAAAGAATTTTTATTGTTTTCTTTGCTTGATAACCTGAGCCATAAATGGAATTAGGCATAAAA
ATTCTTCAAAACCTTATGCAACATTTATACAGGTCACT
Found at i:14522195 original size:16 final size:16
Alignment explanation
Indices: 14522170--14522200 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
14522160 AAATAATCAT
*
14522170 TAAAATAAAAAAAAAG
1 TAAAAAAAAAAAAAAG
14522186 TAAAAAAAAAAAAAA
1 TAAAAAAAAAAAAAA
14522201 AGAAAACAGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.87, C:0.00, G:0.03, T:0.10
Consensus pattern (16 bp):
TAAAAAAAAAAAAAAG
Found at i:14522206 original size:16 final size:17
Alignment explanation
Indices: 14522171--14522206 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
14522161 AATAATCATT
*
14522171 AAAATAAAAAAAAAGTA
1 AAAAAAAAAAAAAAGTA
14522188 AAAAAAAAAAAAAAG-A
1 AAAAAAAAAAAAAAGTA
14522204 AAA
1 AAA
14522207 CAGATACACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.89, C:0.00, G:0.06, T:0.06
Consensus pattern (17 bp):
AAAAAAAAAAAAAAGTA
Found at i:14526984 original size:82 final size:83
Alignment explanation
Indices: 14526835--14526999 Score: 314
Period size: 82 Copynumber: 2.0 Consensus size: 83
14526825 TTCACACAGG
14526835 ATTCTTTGGACAATTTAGCAAAAAGGAAAAAACCCCAATTAGAACATGAAAAAACTAACAAAACA
1 ATTCTTTGGACAATTTAGCAAAAAGGAAAAAACCCCAATTAGAACATGAAAAAACTAACAAAACA
14526900 ATAAATAAAGCAATATAT
66 ATAAATAAAGCAATATAT
14526918 ATTCTTTGGACAATTTAGCAAAAAGGAAAAAA-CCCAATTAGAACATGAAAAAACTAACAAAACA
1 ATTCTTTGGACAATTTAGCAAAAAGGAAAAAACCCCAATTAGAACATGAAAAAACTAACAAAACA
*
14526982 ATAACTAAAGCAATATAT
66 ATAAATAAAGCAATATAT
14527000 GTACTATGTA
Statistics
Matches: 81, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
82 49 0.60
83 32 0.40
ACGTcount: A:0.55, C:0.15, G:0.10, T:0.21
Consensus pattern (83 bp):
ATTCTTTGGACAATTTAGCAAAAAGGAAAAAACCCCAATTAGAACATGAAAAAACTAACAAAACA
ATAAATAAAGCAATATAT
Found at i:14533002 original size:156 final size:156
Alignment explanation
Indices: 14532718--14533025 Score: 485
Period size: 156 Copynumber: 2.0 Consensus size: 156
14532708 TATGATTCAA
* *
14532718 CCAAAGAAAAAGAATTATGTTCATGTATATTTGTTTGTTTTAATTCATTATTAAGAAGACAAAAA
1 CCAAAGAAAAAGAATTATATTCATGTATATTTGTTTGTTTTAATTCATCATTAAGAAGACAAAAA
** * *
14532783 TGAAGATTTTGACTGTGTGAAGAAGATAAGACTGATTTTAGCAATGATTTTCAGAATGTGAGACA
66 TGAAGATTTTGACTGCATAAAAAAGATAAGACTGATTTTAGCAATGATTTTCAGAATGTGAGACA
*
14532848 AAAAGTATTCGATCATAAACATTTAG
131 AAAAGTATTCAATCATAAACATTTAG
*
14532874 CCAAAGAAAAAGAATTCTATTCATGTATATTTGTTTGTTTTAATTCATCATTAAGAAGACAAAAA
1 CCAAAGAAAAAGAATTATATTCATGTATATTTGTTTGTTTTAATTCATCATTAAGAAGACAAAAA
* * *
14532939 TGAAGATTTTGATTGCATAAAAAAGAT-AGAACT-AGTTTTAGTAGTGATTTTCAGAATGTGAGA
66 TGAAGATTTTGACTGCATAAAAAAGATAAG-ACTGA-TTTTAGCAATGATTTTCAGAATGTGAGA
14533002 CAAAAAGTATTCAATCATAAACAT
129 CAAAAAGTATTCAATCATAAACAT
14533026 CTATATTCTA
Statistics
Matches: 139, Mismatches: 11, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
155 3 0.02
156 136 0.98
ACGTcount: A:0.42, C:0.09, G:0.16, T:0.34
Consensus pattern (156 bp):
CCAAAGAAAAAGAATTATATTCATGTATATTTGTTTGTTTTAATTCATCATTAAGAAGACAAAAA
TGAAGATTTTGACTGCATAAAAAAGATAAGACTGATTTTAGCAATGATTTTCAGAATGTGAGACA
AAAAGTATTCAATCATAAACATTTAG
Found at i:14543142 original size:17 final size:17
Alignment explanation
Indices: 14543120--14543153 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
14543110 GTTCTTGATA
14543120 AAATAA-AACTCCTTATT
1 AAATAATAACT-CTTATT
14543137 AAATAATAACTCTTATT
1 AAATAATAACTCTTATT
14543154 TTATTATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.47, C:0.15, G:0.00, T:0.38
Consensus pattern (17 bp):
AAATAATAACTCTTATT
Found at i:14543357 original size:28 final size:28
Alignment explanation
Indices: 14543295--14543468 Score: 152
Period size: 29 Copynumber: 6.0 Consensus size: 28
14543285 TTAAGACAAC
* *
14543295 TCTTGTCTTTAATTAAGAC-AACAATATTTT
1 TCTTGTC-TAAATTAAGACAAAC-AT-GTTT
* * *
14543325 ATCTTGTTTAAATTGAGACAAATATGTTT
1 -TCTTGTCTAAATTAAGACAAACATGTTT
* * * *
14543354 TCTTGCCTAGATTAAGACAAAAAATATTTT
1 TCTTGTCTAAATTAAGAC-AAACAT-GTTT
* * *
14543384 TCTTATCTTAAATTAAGATAAACATATTT
1 TCTTGTC-TAAATTAAGACAAACATGTTT
*
14543413 TCTTATCTAAATTAAGACCAAACATGTTT
1 TCTTGTCTAAATTAAGA-CAAACATGTTT
14543442 TCTTGTCTAAATTAAGACAAACATGTT
1 TCTTGTCTAAATTAAGACAAACATGTT
14543469 AAAGCTGTCA
Statistics
Matches: 118, Mismatches: 20, Indels: 13
0.78 0.13 0.09
Matches are distributed among these distances:
28 34 0.29
29 43 0.36
30 24 0.20
31 17 0.14
ACGTcount: A:0.37, C:0.13, G:0.09, T:0.41
Consensus pattern (28 bp):
TCTTGTCTAAATTAAGACAAACATGTTT
Found at i:14543358 original size:59 final size:56
Alignment explanation
Indices: 14543295--14543468 Score: 170
Period size: 59 Copynumber: 3.0 Consensus size: 56
14543285 TTAAGACAAC
* *
14543295 TCTTGTCTTTAATTAAGACAACAATATTTTATCTTGTTTAAATTGAGACAAATATGTTT
1 TCTTGTC-TTAATTAAGACAA-AATATTTT-TCTTGTTTAAATTAAGACAAACATGTTT
* * * *
14543354 TCTTG-CCTAGATTAAGACAAAAAATATTTTTCTTATCTTAAATTAAGATAAACATATTT
1 TCTTGTCTTA-ATTAAGAC--AAAATATTTTTCTTGT-TTAAATTAAGACAAACATGTTT
* * * * *
14543413 TCTTATCTAAATTAAGACCAAACATGTTTTCTTGTCTAAATTAAGACAAACATGTT
1 TCTTGTCTTAATTAAGACAAAATAT-TTTTCTTGTTTAAATTAAGACAAACATGTT
14543469 AAAGCTGTCA
Statistics
Matches: 94, Mismatches: 15, Indels: 14
0.76 0.12 0.11
Matches are distributed among these distances:
57 25 0.27
58 22 0.23
59 43 0.46
60 4 0.04
ACGTcount: A:0.37, C:0.13, G:0.09, T:0.41
Consensus pattern (56 bp):
TCTTGTCTTAATTAAGACAAAATATTTTTCTTGTTTAAATTAAGACAAACATGTTT
Found at i:14544452 original size:20 final size:20
Alignment explanation
Indices: 14544427--14544472 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
14544417 TTTTGGCCCC
* *
14544427 ATTTGACTTATTGGAGTATG
1 ATTTGACTAATTGAAGTATG
*
14544447 ATTTGAGTAATTGAAGTATG
1 ATTTGACTAATTGAAGTATG
14544467 ATTTGA
1 ATTTGA
14544473 GGTGTGAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.02, G:0.24, T:0.43
Consensus pattern (20 bp):
ATTTGACTAATTGAAGTATG
Found at i:14544473 original size:20 final size:20
Alignment explanation
Indices: 14544436--14544473 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
14544426 CATTTGACTT
*
14544436 ATTGGAGTATGATTTGAGTA
1 ATTGAAGTATGATTTGAGTA
14544456 ATTGAAGTATGATTTGAG
1 ATTGAAGTATGATTTGAG
14544474 GTGTGAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.29, T:0.39
Consensus pattern (20 bp):
ATTGAAGTATGATTTGAGTA
Found at i:14549435 original size:32 final size:31
Alignment explanation
Indices: 14549365--14549457 Score: 105
Period size: 32 Copynumber: 2.9 Consensus size: 31
14549355 AAAATTCTTT
* * * *
14549365 CTAATAAACTTATACTAAAACACACTAACTTC
1 CTAATAGAGTTATA-TAAAACATACCAACTTC
*
14549397 TTAATAGAGTTATAGTAAAACATACCAACTTC
1 CTAATAGAGTTATA-TAAAACATACCAACTTC
*
14549429 CTAATAGAGTTATATCAAAACATATCAAC
1 CTAATAGAGTTATAT-AAAACATACCAAC
14549458 AAACTACTTA
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
31 1 0.02
32 51 0.98
ACGTcount: A:0.46, C:0.19, G:0.05, T:0.29
Consensus pattern (31 bp):
CTAATAGAGTTATATAAAACATACCAACTTC
Found at i:14551221 original size:223 final size:224
Alignment explanation
Indices: 14550814--14551299 Score: 724
Period size: 223 Copynumber: 2.2 Consensus size: 224
14550804 ACTTTAGATA
* * *
14550814 TTTCGACTTTGGAATAATAATGAAAACTAAATAATACCAACGTTTGAGAGATTAGAGAATCGTGC
1 TTTCGACTTTGGGATAA-AATGAAAACTAAATAATACCAAAGCTTGAGAGATTAGAGAATCGTGC
*
14550879 TAATAACATGTTACGAAATATAACTTGAAAGAACAATTATGAGAGAAAAACAATTAATTCTGAAA
65 TAATAACATGTTACGAAATATAACTTGAAAGAACAACTATGAGAGAAAAACAATTAATTCTGAAA
* * *
14550944 TTTGACTCATTATAGATTGGTAAAATATGAGTAAAACAATAAAGGACAATAGACAATAATTGAAT
130 TTTAACTCATTATAAATTGGTAAAATATGAGCAAAACAATAAAGGACAATAGACAATAATTGAAT
* * * *
14551009 TAGAAAAAATAACCTGAAGAAAAATTAAAC
195 TAAAAAAAAAAACCTAAACAAAAATTAAAC
* * ** *
14551039 -TTCGACTTTGGGATAACATGAAAATTAAATAATATTAAAGCTTGAGAGATTAGAGATTCGTGCT
1 TTTCGACTTTGGGATAAAATGAAAACTAAATAATACCAAAGCTTGAGAGATTAGAGAATCGTGCT
* * *
14551103 AATAACGTGTTATGAAATATAACTTGAAAGAATAACTATGAGAGAAAAACAATTAATTCTGAAAT
66 AATAACATGTTACGAAATATAACTTGAAAGAACAACTATGAGAGAAAAACAATTAATTCTGAAAT
*
14551168 TTAACTCATTATAAATTGGT-AAATATGGGCAAAACAATAAAGTGACAATAGACAATAATTGAAT
131 TTAACTCATTATAAATTGGTAAAATATGAGCAAAACAATAAAG-GACAATAGACAATAATTGAAT
14551232 TAAAAAAAAAAACCTAAACAAAAATTAAAC
195 TAAAAAAAAAAACCTAAACAAAAATTAAAC
* *
14551262 TTTTCGACTTTGGGATAATATTGAAAACTAAATGATAC
1 -TTTCGACTTTGGGATAA-AATGAAAACTAAATAATAC
14551300 ACTTTGACTT
Statistics
Matches: 232, Mismatches: 25, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
222 20 0.09
223 167 0.72
224 15 0.06
225 16 0.07
226 14 0.06
ACGTcount: A:0.48, C:0.10, G:0.14, T:0.28
Consensus pattern (224 bp):
TTTCGACTTTGGGATAAAATGAAAACTAAATAATACCAAAGCTTGAGAGATTAGAGAATCGTGCT
AATAACATGTTACGAAATATAACTTGAAAGAACAACTATGAGAGAAAAACAATTAATTCTGAAAT
TTAACTCATTATAAATTGGTAAAATATGAGCAAAACAATAAAGGACAATAGACAATAATTGAATT
AAAAAAAAAAACCTAAACAAAAATTAAAC
Found at i:14551608 original size:17 final size:17
Alignment explanation
Indices: 14551570--14551610 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
14551560 TCGATGGATT
14551570 AAATCTTAATCTTAACCC
1 AAATC-TAATCTTAACCC
14551588 -AATCTAAT-TTACACCC
1 AAATCTAATCTTA-ACCC
14551604 AAATCTA
1 AAATCTA
14551611 GATACACATA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 3 0.14
16 8 0.38
17 10 0.48
ACGTcount: A:0.41, C:0.27, G:0.00, T:0.32
Consensus pattern (17 bp):
AAATCTAATCTTAACCC
Found at i:14556700 original size:47 final size:47
Alignment explanation
Indices: 14556643--14557015 Score: 325
Period size: 47 Copynumber: 8.0 Consensus size: 47
14556633 CGTCATGTTA
* * * * * *
14556643 GGAATGTGTGACACGGCATCGCTCAGAGTTGGTGAGACACCATGGAG
1 GGAATCTGTGACACGCCAGCGTTAAGAGTTGGTGAGACGCCATGGAG
* * * ** * * *
14556690 GAAATCTGTGAGACACCAAAGTTAAGAGTTGATGACACGCCATGGTG
1 GGAATCTGTGACACGCCAGCGTTAAGAGTTGGTGAGACGCCATGGAG
* * ** * * *
14556737 GGAATCTATGACATGGTAGCGTTCAGAGTTAGTGAGACGCCATTGAG
1 GGAATCTGTGACACGCCAGCGTTAAGAGTTGGTGAGACGCCATGGAG
* * * * * *
14556784 AGAATCTGTGATATGCCAG-ATTAAGAGTTGGTGACACGACATGGAG
1 GGAATCTGTGACACGCCAGCGTTAAGAGTTGGTGAGACGCCATGGAG
* * * *
14556830 GGAATCTGTGACACGCCAGCGTTTAGAGTTAGTGAGATGCCATGGAT
1 GGAATCTGTGACACGCCAGCGTTAAGAGTTGGTGAGACGCCATGGAG
* * * ** *
14556877 TGAATCTGTGAGATGCCAAAGTTAAGAGTTGGTGACACGCCATGGAG
1 GGAATCTGTGACACGCCAGCGTTAAGAGTTGGTGAGACGCCATGGAG
* * * * *
14556924 GGAATCTATGATACGTCAGCGTTTAGAGTTGGTGAGACGCCATTGAG
1 GGAATCTGTGACACGCCAGCGTTAAGAGTTGGTGAGACGCCATGGAG
* * * *
14556971 GGAATCTGTGACAAGCCAGAGTTTAGAGTTGGTGACACGCCATGG
1 GGAATCTGTGACACGCCAGCGTTAAGAGTTGGTGAGACGCCATGG
14557016 TCATGTTTAG
Statistics
Matches: 249, Mismatches: 76, Indels: 2
0.76 0.23 0.01
Matches are distributed among these distances:
46 37 0.15
47 212 0.85
ACGTcount: A:0.28, C:0.16, G:0.32, T:0.24
Consensus pattern (47 bp):
GGAATCTGTGACACGCCAGCGTTAAGAGTTGGTGAGACGCCATGGAG
Found at i:14556790 original size:94 final size:92
Alignment explanation
Indices: 14556665--14557015 Score: 391
Period size: 94 Copynumber: 3.8 Consensus size: 92
14556655 ACGGCATCGC
* * * *
14556665 TCAGAGTTGGTGAGACACCATGGAGGAAATCTGTGAGACACCAAAGTTAAGAGTTGATGACACGC
1 TCAGAGTTAGTGAGACGCCATGGAGG-AATCTGTGAGATACCAAAGTTAAGAGTTGGTGACACGC
*
14556730 CATGGTGGGAATCTATGACATGGTAGCGT
65 CATGGAGGGAATCTATGACA-GGTAGCGT
* * * * *
14556759 TCAGAGTTAGTGAGACGCCATTGAGAGAATCTGTGATATGCCAGA-TTAAGAGTTGGTGACACGA
1 TCAGAGTTAGTGAGACGCCATGGAG-GAATCTGTGAGATACCAAAGTTAAGAGTTGGTGACACGC
* **
14556823 CATGGAGGGAATCTGTGACACGCCAGCGT
65 CATGGAGGGAATCTATGACA-GGTAGCGT
* * * *
14556852 TTAGAGTTAGTGAGATGCCATGGATTGAATCTGTGAGATGCCAAAGTTAAGAGTTGGTGACACGC
1 TCAGAGTTAGTGAGACGCCATGGA-GGAATCTGTGAGATACCAAAGTTAAGAGTTGGTGACACGC
* *
14556917 CATGGAGGGAATCTATGATACGTCAGCGT
65 CATGGAGGGAATCTATGACAGGT-AGCGT
* * * * * *
14556946 TTAGAGTTGGTGAGACGCCATTGAGGGAATCTGTGACA-AGCCAGAGTTTAGAGTTGGTGACACG
1 TCAGAGTTAGTGAGACGCCATGGA-GGAATCTGTGAGATA-CCAAAGTTAAGAGTTGGTGACACG
14557010 CCATGG
64 CCATGG
14557016 TCATGTTTAG
Statistics
Matches: 217, Mismatches: 35, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
93 79 0.36
94 137 0.63
95 1 0.00
ACGTcount: A:0.29, C:0.16, G:0.32, T:0.24
Consensus pattern (92 bp):
TCAGAGTTAGTGAGACGCCATGGAGGAATCTGTGAGATACCAAAGTTAAGAGTTGGTGACACGCC
ATGGAGGGAATCTATGACAGGTAGCGT
Found at i:14556964 original size:187 final size:188
Alignment explanation
Indices: 14556643--14557015 Score: 509
Period size: 187 Copynumber: 2.0 Consensus size: 188
14556633 CGTCATGTTA
* * * *
14556643 GGAATGTGTGACACGGCATCGCTCAGAGTTGGTGAGACACCATGGAGGAAATCTGTGAGACACCA
1 GGAATCTGTGACACGCCAGCGCTCAGAGTTAGTGAGACACCATGGAGGAAATCTGTGAGACACCA
* *
14556708 AAGTTAAGAGTTGATGACACGCCATGGTGGGAATCTATGACATGGTAGCGTTCAGAGTTAGTGAG
66 AAGTTAAGAGTTGATGACACGCCATGGAGGGAATCTATGACATCGTAGCGTTCAGAGTTAGTGAG
* *
14556773 ACGCCATTGAGAGAATCTGTGATATGCCAGA-TTAAGAGTTGGTGACACGACATGGAG
131 ACGCCATTGAGAGAATCTGTGACAAGCCAGAGTTAAGAGTTGGTGACACGACATGGAG
* * ** * **
14556830 GGAATCTGTGACACGCCAGCGTTTAGAGTTAGTGAGATGCCATGGATTG-AATCTGTGAGATGCC
1 GGAATCTGTGACACGCCAGCGCTCAGAGTTAGTGAGACACCATGGA-GGAAATCTGTGAGACACC
* * * *
14556894 AAAGTTAAGAGTTGGTGACACGCCATGGAGGGAATCTATGATA-CGTCAGCGTTTAGAGTTGGTG
65 AAAGTTAAGAGTTGATGACACGCCATGGAGGGAATCTATGACATCGT-AGCGTTCAGAGTTAGTG
* * *
14556958 AGACGCCATTGAGGGAATCTGTGACAAGCCAGAGTTTAGAGTTGGTGACACGCCATGG
129 AGACGCCATTGAGAGAATCTGTGACAAGCCAGAGTTAAGAGTTGGTGACACGACATGG
14557016 TCATGTTTAG
Statistics
Matches: 161, Mismatches: 22, Indels: 5
0.86 0.12 0.03
Matches are distributed among these distances:
186 2 0.01
187 136 0.84
188 23 0.14
ACGTcount: A:0.28, C:0.16, G:0.32, T:0.24
Consensus pattern (188 bp):
GGAATCTGTGACACGCCAGCGCTCAGAGTTAGTGAGACACCATGGAGGAAATCTGTGAGACACCA
AAGTTAAGAGTTGATGACACGCCATGGAGGGAATCTATGACATCGTAGCGTTCAGAGTTAGTGAG
ACGCCATTGAGAGAATCTGTGACAAGCCAGAGTTAAGAGTTGGTGACACGACATGGAG
Found at i:14556999 original size:141 final size:140
Alignment explanation
Indices: 14556667--14557015 Score: 355
Period size: 140 Copynumber: 2.5 Consensus size: 140
14556657 GGCATCGCTC
* * * * *
14556667 AGAGTTGGTGAGAC-ACCATGGAGGAAATCTGTGAGACA-CCAAAGTTAAGAGTT-GATGACACG
1 AGAGTTGGTGACACGA-CATGGAGGGAATCTGTGACA-AGCCAGAGTTTAGAGTTAG-TGACACG
* * * ** ** * * * *
14556729 CCATGG-TGGGAATCTATGACATGGTAGCGTTCAGAGTTAGTGAGACGCCATTGAGAGAATCTGT
63 CCATGGAT-TGAATCTGTGAGATGCCAAAGTTAAGAGTTAGTGACACGCCATGGAGAGAATCTAT
*
14556793 GATATGCCAGATTA
127 GATACGCCAGATTA
* * * *
14556807 AGAGTTGGTGACACGACATGGAGGGAATCTGTGACACGCCAGCGTTTAGAGTTAGTGAGATGCCA
1 AGAGTTGGTGACACGACATGGAGGGAATCTGTGACAAGCCAGAGTTTAGAGTTAGTGACACGCCA
* *
14556872 TGGATTGAATCTGTGAGATGCCAAAGTTAAGAGTTGGTGACACGCCATGGAGGGAATCTATGATA
66 TGGATTGAATCTGTGAGATGCCAAAGTTAAGAGTTAGTGACACGCCATGGAGAGAATCTATGATA
* * *
14556937 CGTCAGCGTTT
131 CGCCAG-ATTA
* * * *
14556948 AGAGTTGGTGAGACGCCATTGAGGGAATCTGTGACAAGCCAGAGTTTAGAGTTGGTGACACGCCA
1 AGAGTTGGTGACACGACATGGAGGGAATCTGTGACAAGCCAGAGTTTAGAGTTAGTGACACGCCA
14557013 TGG
66 TGG
14557016 TCATGTTTAG
Statistics
Matches: 170, Mismatches: 34, Indels: 9
0.80 0.16 0.04
Matches are distributed among these distances:
140 105 0.62
141 65 0.38
ACGTcount: A:0.29, C:0.15, G:0.32, T:0.24
Consensus pattern (140 bp):
AGAGTTGGTGACACGACATGGAGGGAATCTGTGACAAGCCAGAGTTTAGAGTTAGTGACACGCCA
TGGATTGAATCTGTGAGATGCCAAAGTTAAGAGTTAGTGACACGCCATGGAGAGAATCTATGATA
CGCCAGATTA
Found at i:14557102 original size:53 final size:52
Alignment explanation
Indices: 14557003--14557102 Score: 157
Period size: 53 Copynumber: 1.9 Consensus size: 52
14556993 TTAGAGTTGG
* *
14557003 TGACACGCCATGGTCATGTTTAGAGTGTGTGACACGACATTGCTTGAAAAGC
1 TGACACGCCATGGTCATGTTTAGAGTGTGTGACACGACAGTACTTGAAAAGC
14557055 TGACACGCCATGGTCATGGTTTAGAGTGTGTGACACTG-CAGTACTTGA
1 TGACACGCCATGGTCAT-GTTTAGAGTGTGTGACAC-GACAGTACTTGA
14557103 GCAGCTAACA
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
52 17 0.39
53 26 0.59
54 1 0.02
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (52 bp):
TGACACGCCATGGTCATGTTTAGAGTGTGTGACACGACAGTACTTGAAAAGC
Found at i:14557120 original size:53 final size:52
Alignment explanation
Indices: 14557005--14557121 Score: 137
Period size: 53 Copynumber: 2.2 Consensus size: 52
14556995 AGAGTTGGTG
* * * *
14557005 ACACGCCATGGTCATGTTTAGAGTGTGTGACACGACATTGCTTGAAAAGCTG
1 ACACACCATGGTCATGTTTAGAGTGTGTGACACGACAGTACTTGAAAAGCTA
* **
14557057 ACACGCCATGGTCATGGTTTAGAGTGTGTGACACTG-CAGTACTTGAGCAGCTA
1 ACACACCATGGTCAT-GTTTAGAGTGTGTGACAC-GACAGTACTTGAAAAGCTA
*
14557110 ACACATCATGGT
1 ACACACCATGGT
14557122 TTGAAATAGA
Statistics
Matches: 56, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
52 15 0.27
53 40 0.71
54 1 0.02
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.26
Consensus pattern (52 bp):
ACACACCATGGTCATGTTTAGAGTGTGTGACACGACAGTACTTGAAAAGCTA
Found at i:14557685 original size:31 final size:31
Alignment explanation
Indices: 14557591--14557794 Score: 223
Period size: 31 Copynumber: 6.6 Consensus size: 31
14557581 AGTTAGTTAT
* *
14557591 TGGCGTGTGACAGCATTTTACTTGATATGCA
1 TGGCGTGTCACAACATTTTACTTGATATGCA
* * * * * *
14557622 TAGCATGTGATAGCATTTCACTTGATATGCA
1 TGGCGTGTCACAACATTTTACTTGATATGCA
*
14557653 TGGCGTGTGACAACATTTTACTTGATATGCA
1 TGGCGTGTCACAACATTTTACTTGATATGCA
* * * * *
14557684 TGGCGTGTCATAACGTTTAACTTGTTCTGCA
1 TGGCGTGTCACAACATTTTACTTGATATGCA
*
14557715 TGGCGTGTCACAACATTTTACTTGTTATGCA
1 TGGCGTGTCACAACATTTTACTTGATATGCA
*
14557746 TGGCGTGTCACAACATTTTGA-TT-ACAATGCA
1 TGGCGTGTCACAACATTTT-ACTTGA-TATGCA
*
14557777 TGGTGTGTCACAACATTT
1 TGGCGTGTCACAACATTT
14557795 ATTCCTTATT
Statistics
Matches: 149, Mismatches: 22, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
31 148 0.99
32 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.36
Consensus pattern (31 bp):
TGGCGTGTCACAACATTTTACTTGATATGCA
Found at i:14559629 original size:156 final size:156
Alignment explanation
Indices: 14559440--14559922 Score: 660
Period size: 156 Copynumber: 3.1 Consensus size: 156
14559430 CACAGTAATT
* * * * * *
14559440 TATGTAATTGCAGTTTACGAAAGCCACGACAGGTCCTCAAGCACCGATCGGTCTAGCTCAATCAC
1 TATGTAATTGCAGTTTACGGAAGCGACGACAGGTCCTGAAGCACTGATCGGTCTAGCTCCATCGC
* *
14559505 AGACAGCTAACGAGCTGGCGGTAAGGATATTAAAGTTGTAACGGTTAATGTTCAACAATTTCATA
66 AGACAGCTAACGAGCTAGCGGTAAGGATATTAAAGTTGTAACGGTTAATGTTCAACAATTCCATA
14559570 CATGATTATTGAATAACACAATTATA
131 CATGATTATTGAATAACACAATTATA
* * * *
14559596 TATGTAATTACAGTTTATGGAAGCGACGACAGGTCTTGAAGCACTGATCGGTCCAGCTCCATCGC
1 TATGTAATTGCAGTTTACGGAAGCGACGACAGGTCCTGAAGCACTGATCGGTCTAGCTCCATCGC
* * * * * *
14559661 AAACAGCTAACAAGCCAGCGGTAATGATATTAAAGTTATAACAGTTAATGTTCAACAATTCCATA
66 AGACAGCTAACGAGCTAGCGGTAAGGATATTAAAGTTGTAACGGTTAATGTTCAACAATTCCATA
14559726 CATGATTATTGAATAACACAATTATA
131 CATGATTATTGAATAACACAATTATA
* * * * * *
14559752 TATGTAAGTGTAGTATACGGAAGTGACGACAGGTCCTGAAGCACTGATCGGTCTGGCTCCACCGC
1 TATGTAATTGCAGTTTACGGAAGCGACGACAGGTCCTGAAGCACTGATCGGTCTAGCTCCATCGC
** * * * *
14559817 AGATTGCTAACGAGCTACCGGTTAGGATATTAAAGTTGTAATGGTTAATGTTCAATAATTCCATA
66 AGACAGCTAACGAGCTAGCGGTAAGGATATTAAAGTTGTAACGGTTAATGTTCAACAATTCCATA
* *
14559882 TATGATTATTGAATAACACAGTTATA
131 CATGATTATTGAATAACACAATTATA
* *
14559908 TATGTTATTGTAGTT
1 TATGTAATTGCAGTT
14559923 GACCCAATCG
Statistics
Matches: 282, Mismatches: 45, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
156 282 1.00
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (156 bp):
TATGTAATTGCAGTTTACGGAAGCGACGACAGGTCCTGAAGCACTGATCGGTCTAGCTCCATCGC
AGACAGCTAACGAGCTAGCGGTAAGGATATTAAAGTTGTAACGGTTAATGTTCAACAATTCCATA
CATGATTATTGAATAACACAATTATA
Found at i:14560315 original size:31 final size:31
Alignment explanation
Indices: 14560277--14560671 Score: 386
Period size: 31 Copynumber: 12.8 Consensus size: 31
14560267 GTCAGCTTTA
*
14560277 GCGTGTCACAACATTTTACTTGTTATTCATG
1 GCGTGTCACAACATTTTACTTGTTATGCATG
* * * **
14560308 GCGTGTCACAACGTTTGATTTAATATGCATG
1 GCGTGTCACAACATTTTACTTGTTATGCATG
* * * * *
14560339 GTGTGTCAGAACATTTTGCTTGTTATCCTTG
1 GCGTGTCACAACATTTTACTTGTTATGCATG
* * * *
14560370 GCATGTCACCA-AGTTTACATTATTATGCATG
1 GCGTGTCACAACATTTTAC-TTGTTATGCATG
* *
14560401 GCGTGTCACAACATTTTAATTGTTTTGCATG
1 GCGTGTCACAACATTTTACTTGTTATGCATG
* * * *
14560432 GCGTGTCACAACATTTTCCTCGTTATCCTTG
1 GCGTGTCACAACATTTTACTTGTTATGCATG
* * *
14560463 GCATGTCACCA-AGTTTATCTTGTTATGCATG
1 GCGTGTCACAACATTTTA-CTTGTTATGCATG
* *
14560494 GCGTGTCACAACATTTTAATTGTTTTGCATG
1 GCGTGTCACAACATTTTACTTGTTATGCATG
* * * *
14560525 GCGTGTCACAACATTTTCCTCGTTATCCTTG
1 GCGTGTCACAACATTTTACTTGTTATGCATG
* *
14560556 GCGTGTCACCA-AGTTTATCTTGTTATGCATG
1 GCGTGTCACAACATTTTA-CTTGTTATGCATG
* * *
14560587 GCATGTCACGACATTTTACTTGTTTTGCATG
1 GCGTGTCACAACATTTTACTTGTTATGCATG
*
14560618 GCGTGTCACAACATTTTACTTGGTATGCACT-
1 GCGTGTCACAACATTTTACTTGTTATGCA-TG
*
14560649 ACGTGTCACAACATTTTA-TTGTT
1 GCGTGTCACAACATTTTACTTGTT
14560672 TATGGTTTGT
Statistics
Matches: 286, Mismatches: 71, Indels: 15
0.77 0.19 0.04
Matches are distributed among these distances:
30 17 0.06
31 253 0.88
32 16 0.06
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.40
Consensus pattern (31 bp):
GCGTGTCACAACATTTTACTTGTTATGCATG
Found at i:14560439 original size:93 final size:93
Alignment explanation
Indices: 14560291--14560634 Score: 521
Period size: 93 Copynumber: 3.7 Consensus size: 93
14560281 GTCACAACAT
* * * * ** * * *
14560291 TTTA-CTTGTTATTCATGGCGTGTCACAACGTTTGATTTAATATGCATGGTGTGTCAGAACATTT
1 TTTATCTTGTTATGCATGGCGTGTCACAACATTTTAATTGTTTTGCATGGCGTGTCACAACATTT
* *
14560355 TGCTTGTTATCCTTGGCATGTCACCAAG
66 TCCTCGTTATCCTTGGCATGTCACCAAG
*
14560383 TTTA-CATTATTATGCATGGCGTGTCACAACATTTTAATTGTTTTGCATGGCGTGTCACAACATT
1 TTTATC-TTGTTATGCATGGCGTGTCACAACATTTTAATTGTTTTGCATGGCGTGTCACAACATT
14560447 TTCCTCGTTATCCTTGGCATGTCACCAAG
65 TTCCTCGTTATCCTTGGCATGTCACCAAG
14560476 TTTATCTTGTTATGCATGGCGTGTCACAACATTTTAATTGTTTTGCATGGCGTGTCACAACATTT
1 TTTATCTTGTTATGCATGGCGTGTCACAACATTTTAATTGTTTTGCATGGCGTGTCACAACATTT
*
14560541 TCCTCGTTATCCTTGGCGTGTCACCAAG
66 TCCTCGTTATCCTTGGCATGTCACCAAG
* * *
14560569 TTTATCTTGTTATGCATGGCATGTCACGACATTTTACTTGTTTTGCATGGCGTGTCACAACATTT
1 TTTATCTTGTTATGCATGGCGTGTCACAACATTTTAATTGTTTTGCATGGCGTGTCACAACATTT
14560634 T
66 T
14560635 ACTTGGTATG
Statistics
Matches: 233, Mismatches: 17, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
92 5 0.02
93 227 0.97
94 1 0.00
ACGTcount: A:0.21, C:0.20, G:0.19, T:0.40
Consensus pattern (93 bp):
TTTATCTTGTTATGCATGGCGTGTCACAACATTTTAATTGTTTTGCATGGCGTGTCACAACATTT
TCCTCGTTATCCTTGGCATGTCACCAAG
Found at i:14562194 original size:16 final size:16
Alignment explanation
Indices: 14562147--14562199 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 16
14562137 CAGAAATTTT
* * *
14562147 TATATACAATTCATTT
1 TATACACAATTTATTG
* *
14562163 TATACA-TATTTTTTG
1 TATACACAATTTATTG
14562178 TATACACAATTTATTG
1 TATACACAATTTATTG
14562194 TATACA
1 TATACA
14562200 ATTCATTGTA
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
15 11 0.38
16 18 0.62
ACGTcount: A:0.36, C:0.11, G:0.04, T:0.49
Consensus pattern (16 bp):
TATACACAATTTATTG
Found at i:14562207 original size:14 final size:14
Alignment explanation
Indices: 14562149--14562209 Score: 59
Period size: 14 Copynumber: 4.1 Consensus size: 14
14562139 GAAATTTTTA
*
14562149 TATACAATTCATTT
1 TATACAATTCATTG
**
14562163 TATACATATTTTTTG
1 TATACA-ATTCATTG
*
14562178 TATACACAATTTATTG
1 TAT--ACAATTCATTG
14562194 TATACAATTCATTG
1 TATACAATTCATTG
14562208 TA
1 TA
14562210 AACAGATATA
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
14 18 0.46
15 8 0.21
16 10 0.26
17 3 0.08
ACGTcount: A:0.34, C:0.11, G:0.05, T:0.49
Consensus pattern (14 bp):
TATACAATTCATTG
Found at i:14562269 original size:15 final size:15
Alignment explanation
Indices: 14562230--14562275 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
14562220 ATTCTTTCTG
*
14562230 TATACACAATATACTT
1 TATACACAAT-TATTT
14562246 TAT--ACAATTATTT
1 TATACACAATTATTT
14562259 TATACACAATTAATTT
1 TATACACAATT-ATTT
14562275 T
1 T
14562276 TTTGCCTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
13 7 0.27
14 5 0.19
15 6 0.23
16 8 0.31
ACGTcount: A:0.41, C:0.13, G:0.00, T:0.46
Consensus pattern (15 bp):
TATACACAATTATTT
Found at i:14563333 original size:31 final size:31
Alignment explanation
Indices: 14563295--14563651 Score: 368
Period size: 31 Copynumber: 11.6 Consensus size: 31
14563285 ACATCAGAAC
* *
14563295 TTGTTATGCATGGCGGGTCAGAACAATTTAA
1 TTGTTATGCATGGCGTGTCACAACAATTTAA
14563326 TTGTTATGCATGGCGTGTCA-ACACAATTTAA
1 TTGTTATGCATGGCGTGTCACA-ACAATTTAA
*
14563357 TTGTTATGCATGGCGTGTCA-ACACAATTTAC
1 TTGTTATGCATGGCGTGTCACA-ACAATTTAA
* *
14563388 TTGTTATGCATGGCGTGTCACAACATTTTAC
1 TTGTTATGCATGGCGTGTCACAACAATTTAA
* * *
14563419 TTGTTATGCATGGAGGGTCAGAACAATTTAA
1 TTGTTATGCATGGCGTGTCACAACAATTTAA
* *
14563450 TTGTTATGTATGGCGTGTCACAAC-GTTTAA
1 TTGTTATGCATGGCGTGTCACAACAATTTAA
*
14563480 CTTGTTTTGCATGGCGTGTCAGC-ACAATTT-A
1 -TTGTTATGCATGGCGTGTCA-CAACAATTTAA
* * *
14563511 --CTTATGCATGGCGTGTCACAACATTTTAC
1 TTGTTATGCATGGCGTGTCACAACAATTTAA
*** * **
14563540 TTGTTATGCATGGCGTGTCATTTCATTTTTC
1 TTGTTATGCATGGCGTGTCACAACAATTTAA
* * *
14563571 TTGTTATGCATGGCGTGTCACAATATTTTAT
1 TTGTTATGCATGGCGTGTCACAACAATTTAA
* * * * *
14563602 TTGATATGCACGGCATGTCACAACATTTTAC
1 TTGTTATGCATGGCGTGTCACAACAATTTAA
*
14563633 TTGTTATGCATGACGTGTC
1 TTGTTATGCATGGCGTGTC
14563652 TCATATTTAT
Statistics
Matches: 277, Mismatches: 40, Indels: 18
0.83 0.12 0.05
Matches are distributed among these distances:
27 1 0.00
28 22 0.08
30 6 0.02
31 243 0.88
32 5 0.02
ACGTcount: A:0.24, C:0.17, G:0.21, T:0.38
Consensus pattern (31 bp):
TTGTTATGCATGGCGTGTCACAACAATTTAA
Found at i:14566805 original size:135 final size:134
Alignment explanation
Indices: 14566562--14566831 Score: 531
Period size: 135 Copynumber: 2.0 Consensus size: 134
14566552 ATGCACATTC
14566562 TGATCGGAATTGTGCAGCCAACTGTTCTGTGAATGTCGTTTGTCTATCGGGCTGCACAAACTCTT
1 TGATCGGAATTGTGCAGCCAACTGTTCTGTGAATGTCGTTTGTCTATCGGGCTGCACAAACTCTT
14566627 GTGCGTACCTCAATTGCCATTGTTGTGGGTTACGGACCAAATGCTGTGGTATATGTGAAGCATTG
66 GTGCGTACCTCAATTGCCATTGTTGTGGGTTACGGACCAAATGCTGTGGTATATGTGAAGCATTG
14566692 TAAA
131 TAAA
14566696 TNGATCGGAATTGTGCAGCCAACTGTTCTGTGAATGTCGTTTGTCTATCGGGCTGCACAAACTCT
1 T-GATCGGAATTGTGCAGCCAACTGTTCTGTGAATGTCGTTTGTCTATCGGGCTGCACAAACTCT
14566761 TGTGCGTACCTCAATTGCCATTGTTGTGGGTTACGGACCAAATGCTGTGGTATATGTGAAGCATT
65 TGTGCGTACCTCAATTGCCATTGTTGTGGGTTACGGACCAAATGCTGTGGTATATGTGAAGCATT
14566826 GTAAA
130 GTAAA
14566831 T
1 T
14566832 CTCATTTTGA
Statistics
Matches: 135, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
134 1 0.01
135 134 0.99
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.33
Consensus pattern (134 bp):
TGATCGGAATTGTGCAGCCAACTGTTCTGTGAATGTCGTTTGTCTATCGGGCTGCACAAACTCTT
GTGCGTACCTCAATTGCCATTGTTGTGGGTTACGGACCAAATGCTGTGGTATATGTGAAGCATTG
TAAA
Found at i:14567306 original size:30 final size:31
Alignment explanation
Indices: 14567265--14567345 Score: 103
Period size: 30 Copynumber: 2.6 Consensus size: 31
14567255 TTGTTAGTCG
*
14567265 TGTTGTTACACGCCATGCATAT-AATGT-AAA
1 TGTTGTAACACGCCATGCATATCAA-GTCAAA
*
14567295 TGTTGTAACACGTCATGCATATCAAGTCAAA
1 TGTTGTAACACGCCATGCATATCAAGTCAAA
* *
14567326 TGTCGTGACACGCCATGCAT
1 TGTTGTAACACGCCATGCAT
14567346 CAGTATCATT
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
30 22 0.50
31 22 0.50
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.30
Consensus pattern (31 bp):
TGTTGTAACACGCCATGCATATCAAGTCAAA
Found at i:14567337 original size:31 final size:30
Alignment explanation
Indices: 14567272--14567345 Score: 96
Period size: 31 Copynumber: 2.4 Consensus size: 30
14567262 TCGTGTTGTT
*
14567272 ACACGCCATGCATATAATGTAAATGTTGTA
1 ACACGCCATGCATATAATGTAAATGTCGTA
* *
14567302 ACACGTCATGCATATCAA-GTCAAATGTCGTG
1 ACACGCCATGCATAT-AATGT-AAATGTCGTA
14567333 ACACGCCATGCAT
1 ACACGCCATGCAT
14567346 CAGTATCATT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
30 16 0.42
31 22 0.58
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.26
Consensus pattern (30 bp):
ACACGCCATGCATATAATGTAAATGTCGTA
Found at i:14567382 original size:23 final size:23
Alignment explanation
Indices: 14567326--14567382 Score: 78
Period size: 23 Copynumber: 2.5 Consensus size: 23
14567316 TCAAGTCAAA
*
14567326 TGTCGTGACACGCCATGCATCAG
1 TGTCGTGACACGCCATGCATCAC
* * *
14567349 TATCATTACACGCCATGCATCAC
1 TGTCGTGACACGCCATGCATCAC
14567372 TGTCGTGACAC
1 TGTCGTGACAC
14567383 ACCAACAACC
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.25
Consensus pattern (23 bp):
TGTCGTGACACGCCATGCATCAC
Found at i:14569566 original size:28 final size:29
Alignment explanation
Indices: 14569525--14569584 Score: 68
Period size: 30 Copynumber: 2.1 Consensus size: 29
14569515 GTCTATGGGC
*
14569525 AATTTTTCAATTTT-TGGGGCAAAAATGT
1 AATTTTTCAATTTTAGGGGGCAAAAATGT
* * *
14569553 AATTTTTGACTTTTACGGGGGCAAAAGTGT
1 AATTTTTCAATTTTA-GGGGGCAAAAATGT
14569583 AA
1 AA
14569585 ATTTCAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 12 0.46
30 14 0.54
ACGTcount: A:0.32, C:0.08, G:0.22, T:0.38
Consensus pattern (29 bp):
AATTTTTCAATTTTAGGGGGCAAAAATGT
Found at i:14572703 original size:21 final size:20
Alignment explanation
Indices: 14572678--14572737 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
14572668 AGATGTCTAA
*
14572678 AATAATTATTTGAAATGAAAT
1 AATAATTATTTG-AATAAAAT
* *
14572699 TATAATTGTTTGAATAAAAT
1 AATAATTATTTGAATAAAAT
14572719 AATAA-TATTT-AATAAAAT
1 AATAATTATTTGAATAAAAT
14572737 A
1 A
14572738 TTTTATTTTC
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
18 9 0.26
19 4 0.12
20 11 0.32
21 10 0.29
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (20 bp):
AATAATTATTTGAATAAAAT
Found at i:14574654 original size:11 final size:11
Alignment explanation
Indices: 14574627--14574670 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
14574617 CCTAGGGTTC
14574627 TTGTTCTT-C-
1 TTGTTCTTCCT
14574636 TT-TTCTTCCT
1 TTGTTCTTCCT
14574646 TTGTTCTTCCTT
1 TTGTTCTTCC-T
14574658 TTGTT-TTCCT
1 TTGTTCTTCCT
14574668 TTG
1 TTG
14574671 GCCGGCCATA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
8 5 0.16
9 3 0.10
10 6 0.19
11 11 0.35
12 6 0.19
ACGTcount: A:0.00, C:0.23, G:0.09, T:0.68
Consensus pattern (11 bp):
TTGTTCTTCCT
Found at i:14575812 original size:17 final size:18
Alignment explanation
Indices: 14575779--14575813 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
14575769 GAACCAAACA
14575779 AAAGAATAAGGAAGGAAT
1 AAAGAATAAGGAAGGAAT
*
14575797 AAAGAAT-AGGATGGAAT
1 AAAGAATAAGGAAGGAAT
14575814 GAAATAATCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.57, C:0.00, G:0.29, T:0.14
Consensus pattern (18 bp):
AAAGAATAAGGAAGGAAT
Found at i:14576946 original size:23 final size:23
Alignment explanation
Indices: 14576916--14576970 Score: 83
Period size: 23 Copynumber: 2.4 Consensus size: 23
14576906 TTATGTTCTT
**
14576916 GATTTCTCTCTCCCGTATTTTCA
1 GATTTCTCTCTCCCACATTTTCA
*
14576939 GATTTCTCTCTCCTACATTTTCA
1 GATTTCTCTCTCCCACATTTTCA
14576962 GATTTCTCT
1 GATTTCTCT
14576971 TTTCTGCGCT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.15, C:0.29, G:0.07, T:0.49
Consensus pattern (23 bp):
GATTTCTCTCTCCCACATTTTCA
Found at i:14577488 original size:45 final size:45
Alignment explanation
Indices: 14577439--14577578 Score: 131
Period size: 45 Copynumber: 3.1 Consensus size: 45
14577429 AATAATTTTT
* *
14577439 TTTTTCAATATGGCATGTAACAACCTAACCATGGTGTGTCACATG
1 TTTTTCAATATGGCGTGTAACAACCTAACCATGATGTGTCACATG
** * * *
14577484 TTTTTGTATATGACGTGTAACAACCTAATCATGACT-TGTCACATA
1 TTTTTCAATATGGCGTGTAACAACCTAACCATGA-TGTGTCACATG
* * * * * *
14577529 TTTTTGTAA-ATGGTGTATAACAATCTAACCATGACGTGTCATATG
1 TTTTT-CAATATGGCGTGTAACAACCTAACCATGATGTGTCACATG
14577574 TTTTT
1 TTTTT
14577579 GTATATGACA
Statistics
Matches: 75, Mismatches: 17, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
45 73 0.97
46 2 0.03
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.39
Consensus pattern (45 bp):
TTTTTCAATATGGCGTGTAACAACCTAACCATGATGTGTCACATG
Found at i:14577579 original size:45 final size:45
Alignment explanation
Indices: 14577456--14577595 Score: 163
Period size: 45 Copynumber: 3.1 Consensus size: 45
14577446 ATATGGCATG
** * *
14577456 TAACAACCTAACCATGGTGTGTCACATGTTTTTGTATATGACGTG
1 TAACAACCTAACCATGACGTGTCACATGTTTTTGTAAATGACGTA
* * * **
14577501 TAACAACCTAATCATGACTTGTCACATATTTTTGTAAATGGTGTA
1 TAACAACCTAACCATGACGTGTCACATGTTTTTGTAAATGACGTA
* * * *
14577546 TAACAATCTAACCATGACGTGTCATATGTTTTTGTATATGACATA
1 TAACAACCTAACCATGACGTGTCACATGTTTTTGTAAATGACGTA
14577591 TAACA
1 TAACA
14577596 TGTTTTTGTA
Statistics
Matches: 77, Mismatches: 18, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
45 77 1.00
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.36
Consensus pattern (45 bp):
TAACAACCTAACCATGACGTGTCACATGTTTTTGTAAATGACGTA
Found at i:14577679 original size:24 final size:24
Alignment explanation
Indices: 14577643--14577689 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
14577633 GTGTCATATA
*
14577643 TTTTTGTATATGGCATATAACATG
1 TTTTTGTACATGGCATATAACATG
* *
14577667 TTTTTGTACATGGCGTGTAACAT
1 TTTTTGTACATGGCATATAACAT
14577690 TCTAACCATG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.26, C:0.11, G:0.19, T:0.45
Consensus pattern (24 bp):
TTTTTGTACATGGCATATAACATG
Found at i:14577722 original size:45 final size:45
Alignment explanation
Indices: 14577662--14577761 Score: 119
Period size: 45 Copynumber: 2.2 Consensus size: 45
14577652 ATGGCATATA
* * * * ** *
14577662 ACATGTTTTTGTACATGGCGTGTAACATTCTAACCATGGGGTGTC
1 ACATATTTTTATACATGGCATGAAACAACCTAACCATGAGGTGTC
* *
14577707 ACATATTTTTATACATGGCATGAAACAACCTAATCATGATGTGTC
1 ACATATTTTTATACATGGCATGAAACAACCTAACCATGAGGTGTC
14577752 ACATATTTTT
1 ACATATTTTT
14577762 TTATATGGAA
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.37
Consensus pattern (45 bp):
ACATATTTTTATACATGGCATGAAACAACCTAACCATGAGGTGTC
Found at i:14577725 original size:69 final size:69
Alignment explanation
Indices: 14577524--14577727 Score: 300
Period size: 69 Copynumber: 3.0 Consensus size: 69
14577514 ATGACTTGTC
* * * *
14577524 ACATATTTTTGTAAATGGTGTATAACAATCTAACCATGACGTGTCATATGTTTTTGTATATGACA
1 ACATGTTTTTGTACATGGTGTATAACAATCTAACCATGACGTGTCATATATTTTTGTATATGGCA
14577589 TATA
66 TATA
14577593 ACATGTTTTTGTACATGGTGTATAACAATCTAACCATGACGTGTCATATATTTTTGTATATGGCA
1 ACATGTTTTTGTACATGGTGTATAACAATCTAACCATGACGTGTCATATATTTTTGTATATGGCA
14577658 TATA
66 TATA
* * * ** * * *
14577662 ACATGTTTTTGTACATGGCGTGTAACATTCTAACCATGGGGTGTCACATATTTTTATACATGGCA
1 ACATGTTTTTGTACATGGTGTATAACAATCTAACCATGACGTGTCATATATTTTTGTATATGGCA
14577727 T
66 T
14577728 GAAACAACCT
Statistics
Matches: 123, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
69 123 1.00
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.40
Consensus pattern (69 bp):
ACATGTTTTTGTACATGGTGTATAACAATCTAACCATGACGTGTCATATATTTTTGTATATGGCA
TATA
Found at i:14580930 original size:23 final size:23
Alignment explanation
Indices: 14580904--14580950 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
14580894 GTTATGAAAA
14580904 ATAACTTAAAAGAACAAATAAAG
1 ATAACTTAAAAGAACAAATAAAG
* * *
14580927 ATAACTTGAAAGAATAATTAAAG
1 ATAACTTAAAAGAACAAATAAAG
14580950 A
1 A
14580951 GAAGAAAGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.62, C:0.06, G:0.11, T:0.21
Consensus pattern (23 bp):
ATAACTTAAAAGAACAAATAAAG
Found at i:14584788 original size:13 final size:13
Alignment explanation
Indices: 14584770--14584794 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
14584760 AGAGAAATTG
14584770 TGATTTTATAAAA
1 TGATTTTATAAAA
14584783 TGATTTTATAAA
1 TGATTTTATAAA
14584795 TTTTTTGAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:14589830 original size:19 final size:19
Alignment explanation
Indices: 14589803--14589844 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
14589793 AGGAGACAAG
14589803 ATAAGATTTT-TAGAATAAA
1 ATAAGATTTTAT-GAATAAA
* *
14589822 ATAATATTTTATTAATAAA
1 ATAAGATTTTATGAATAAA
14589841 ATAA
1 ATAA
14589845 AATTAAGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 19 0.95
20 1 0.05
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (19 bp):
ATAAGATTTTATGAATAAA
Found at i:14590294 original size:20 final size:20
Alignment explanation
Indices: 14590251--14590288 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
14590241 TTTTGGCCCC
14590251 ATTTAACTTATTGGAGTATA
1 ATTTAACTTATTGGAGTATA
14590271 ATTTAACTTATTGGAGTA
1 ATTTAACTTATTGGAGTA
14590289 AGATTTGAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.34, C:0.05, G:0.16, T:0.45
Consensus pattern (20 bp):
ATTTAACTTATTGGAGTATA
Found at i:14596330 original size:10 final size:10
Alignment explanation
Indices: 14596302--14596330 Score: 51
Period size: 9 Copynumber: 3.0 Consensus size: 10
14596292 TAAATCCATT
14596302 TTTCATAAAA
1 TTTCATAAAA
14596312 TTT-ATAAAA
1 TTTCATAAAA
14596321 TTTCATAAAA
1 TTTCATAAAA
14596331 ACTACCTTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.50
10 9 0.50
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (10 bp):
TTTCATAAAA
Found at i:14598245 original size:28 final size:28
Alignment explanation
Indices: 14598211--14598393 Score: 215
Period size: 28 Copynumber: 6.5 Consensus size: 28
14598201 TTGTATTTTC
* *
14598211 ATTATTCATCCACTTTTGGTGGGTTAAA
1 ATTATTCATCCACTTCTGGTGGGTTGAA
* *
14598239 AGTATTCATCCACTTCTAGTGGGTTGAA
1 ATTATTCATCCACTTCTGGTGGGTTGAA
* *
14598267 AGTATTCATCCACATCTGGTGGGTTGAA
1 ATTATTCATCCACTTCTGGTGGGTTGAA
* * *
14598295 ATTA-TCTATCAACATCTGGCGGGTTGAA
1 ATTATTC-ATCCACTTCTGGTGGGTTGAA
* * * *
14598323 ATTATCCATACACATCTAGTGGGTTGAA
1 ATTATTCATCCACTTCTGGTGGGTTGAA
*
14598351 ATTATCCATCCACTTCTGGTGGGTTGAA
1 ATTATTCATCCACTTCTGGTGGGTTGAA
*
14598379 ATTATCCATCCACTT
1 ATTATTCATCCACTT
14598394 ATGTTGGCAA
Statistics
Matches: 136, Mismatches: 17, Indels: 4
0.87 0.11 0.03
Matches are distributed among these distances:
27 2 0.01
28 133 0.98
29 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.36
Consensus pattern (28 bp):
ATTATTCATCCACTTCTGGTGGGTTGAA
Found at i:14598413 original size:26 final size:26
Alignment explanation
Indices: 14598321--14598471 Score: 117
Period size: 28 Copynumber: 5.7 Consensus size: 26
14598311 TGGCGGGTTG
* * * *
14598321 AAATTATCCATACACATCTAGTGGGTTG
1 AAATTATCCATCCACTTCT-GTTGG-TA
* *
14598349 AAATTATCCATCCACTTCTGGTGGGTTG
1 AAATTATCCATCCACTTCT-GTTGG-TA
* *
14598377 AAATTATCCATCCACTTATGTTGGCA
1 AAATTATCCATCCACTTCTGTTGGTA
*
14598403 AAATTATCCATCCACTTCTGATGGTA
1 AAATTATCCATCCACTTCTGTTGGTA
* * ** *
14598429 AAATTATTCTTAGA-TTCTGATGGTA
1 AAATTATCCATCCACTTCTGTTGGTA
*
14598454 AAATTAT-TATCCACTTCT
1 AAATTATCCATCCACTTCT
14598472 TTCATATCCA
Statistics
Matches: 104, Mismatches: 18, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
24 2 0.02
25 22 0.21
26 33 0.32
27 4 0.04
28 43 0.41
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (26 bp):
AAATTATCCATCCACTTCTGTTGGTA
Found at i:14598471 original size:25 final size:26
Alignment explanation
Indices: 14598349--14598471 Score: 124
Period size: 26 Copynumber: 4.7 Consensus size: 26
14598339 TAGTGGGTTG
* *
14598349 AAATTATCCATCCACTTCTGGTGGGTTG
1 AAATTATCCATCCACTTCTGAT-GG-TA
* * *
14598377 AAATTATCCATCCACTTATGTTGGCA
1 AAATTATCCATCCACTTCTGATGGTA
14598403 AAATTATCCATCCACTTCTGATGGTA
1 AAATTATCCATCCACTTCTGATGGTA
* * **
14598429 AAATTATTCTTAGA-TTCTGATGGTA
1 AAATTATCCATCCACTTCTGATGGTA
*
14598454 AAATTAT-TATCCACTTCT
1 AAATTATCCATCCACTTCT
14598472 TTCATATCCA
Statistics
Matches: 79, Mismatches: 15, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
24 2 0.03
25 22 0.28
26 33 0.42
27 2 0.03
28 20 0.25
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (26 bp):
AAATTATCCATCCACTTCTGATGGTA
Found at i:14599045 original size:23 final size:23
Alignment explanation
Indices: 14599018--14599062 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
14599008 TATGAAAAAG
14599018 AACTTAAAAGAACAAATAAAGAT
1 AACTTAAAAGAACAAATAAAGAT
* * *
14599041 AACTTGAAAGAATAATTAAAGA
1 AACTTAAAAGAACAAATAAAGA
14599063 GAAGAAAGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.62, C:0.07, G:0.11, T:0.20
Consensus pattern (23 bp):
AACTTAAAAGAACAAATAAAGAT
Found at i:14600656 original size:20 final size:20
Alignment explanation
Indices: 14600631--14600676 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
14600621 TTTTGGCCCC
14600631 ATTTGACTTATTGGAGTATA
1 ATTTGACTTATTGGAGTATA
*
14600651 ATTTGACTTATTGGAGTATG
1 ATTTGACTTATTGGAGTATA
14600671 ATTTGA
1 ATTTGA
14600677 GGTTTAGGAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.28, C:0.04, G:0.22, T:0.46
Consensus pattern (20 bp):
ATTTGACTTATTGGAGTATA
Found at i:14612665 original size:24 final size:25
Alignment explanation
Indices: 14612614--14612663 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
14612604 CCAAACAAAT
14612614 AGAGTGGAAACGGCTGAAAAAAAAA
1 AGAGTGGAAACGGCTGAAAAAAAAA
*
14612639 AGAGTGGAAACGGCTGGAAAAAAAA
1 AGAGTGGAAACGGCTGAAAAAAAAA
14612664 GAAAGGGAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.54, C:0.08, G:0.30, T:0.08
Consensus pattern (25 bp):
AGAGTGGAAACGGCTGAAAAAAAAA
Found at i:14613904 original size:180 final size:180
Alignment explanation
Indices: 14613642--14613967 Score: 494
Period size: 180 Copynumber: 1.8 Consensus size: 180
14613632 GAAAGCAGTT
* * *
14613642 CAGCTCACTGTTATGACATGAATTTCAGTTTTAATTAAGAAGAAAGTCTTGGAAATTAATTCTGA
1 CAGCTCACTGTTATGACATGAATTTCAGTTTTAATTAACAAGAAACTCTTGAAAATTAATTCTGA
* * *
14613707 AAAATTCCAAGAAAATTATCTTTATTAAAATGTTCAAT-AAGGATTATTTCTGGAAAATATCATG
66 AAAATTCCAAGAAAATTATCCTTATTAAAATGTCCAATGAA-GATTAGTTCTGGAAAATATCATG
** *
14613771 GTCAAACATGCTGATTTCGAGCAAGAAAATTTGTGCAAATATAAATCTGTC
130 ACCAAACAAGCTGATTTCGAGCAAGAAAATTTGTGCAAATATAAATCTGTC
* * *
14613822 CAGCTCACTGTTTTGGCATGAATTTCAGTTTTAATTGACAAGAAACTCTTGAAAATTAATTCTGA
1 CAGCTCACTGTTATGACATGAATTTCAGTTTTAATTAACAAGAAACTCTTGAAAATTAATTCTGA
* *
14613887 AAAATTCC-AGAAAAATTATCCTTATTAAAATGTCCAATGAAGATTAGTTCTGGAAATTTTCATG
66 AAAATTCCAAG-AAAATTATCCTTATTAAAATGTCCAATGAAGATTAGTTCTGGAAAATATCATG
14613951 ACCAAACAAGCTGATTT
130 ACCAAACAAGCTGATTT
14613968 AAGCTATTAA
Statistics
Matches: 130, Mismatches: 14, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
179 2 0.02
180 126 0.97
181 2 0.02
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.34
Consensus pattern (180 bp):
CAGCTCACTGTTATGACATGAATTTCAGTTTTAATTAACAAGAAACTCTTGAAAATTAATTCTGA
AAAATTCCAAGAAAATTATCCTTATTAAAATGTCCAATGAAGATTAGTTCTGGAAAATATCATGA
CCAAACAAGCTGATTTCGAGCAAGAAAATTTGTGCAAATATAAATCTGTC
Found at i:14619056 original size:23 final size:26
Alignment explanation
Indices: 14618999--14619052 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
14618989 CTAAACAAAT
14618999 AGAGTGGAAACGACTGAAAAAAAAAA
1 AGAGTGGAAACGACTGAAAAAAAAAA
*
14619025 AGAGTGGAAACGGCT-AAAAAAAGAAA
1 AGAGTGGAAACGACTGAAAAAAA-AAA
14619051 AG
1 AG
14619053 GGAATGAACG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 7 0.27
26 19 0.73
ACGTcount: A:0.59, C:0.07, G:0.26, T:0.07
Consensus pattern (26 bp):
AGAGTGGAAACGACTGAAAAAAAAAA
Found at i:14620747 original size:2 final size:2
Alignment explanation
Indices: 14620734--14620778 Score: 58
Period size: 2 Copynumber: 23.5 Consensus size: 2
14620724 NNNNNNNNNN
* *
14620734 TA TA TA TT TA TA TA TA -A TA TA TA TA T- TT TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
14620774 TA TA T
1 TA TA T
14620779 GTGTAATTGA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
1 2 0.05
2 36 0.95
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (2 bp):
TA
Found at i:14620758 original size:11 final size:10
Alignment explanation
Indices: 14620734--14620778 Score: 58
Period size: 9 Copynumber: 4.7 Consensus size: 10
14620724 NNNNNNNNNN
*
14620734 TATATATTTA
1 TATATATATA
14620744 TATATA-ATA
1 TATATATATA
*
14620753 TATATAT-TT
1 TATATATATA
14620762 TATATATATA
1 TATATATATA
14620772 TATATAT
1 TATATAT
14620779 GTGTAATTGA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
9 16 0.53
10 14 0.47
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (10 bp):
TATATATATA
Found at i:14620758 original size:13 final size:13
Alignment explanation
Indices: 14620737--14620775 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
14620727 NNNNNNNTAT
*
14620737 ATATTTATATATA
1 ATATATATATATA
* *
14620750 ATATATATATTTT
1 ATATATATATATA
14620763 ATATATATATATA
1 ATATATATATATA
14620776 TATGTGTAAT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
ATATATATATATA
Found at i:14620758 original size:19 final size:19
Alignment explanation
Indices: 14620734--14620778 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
14620724 NNNNNNNNNN
14620734 TATATA-TTTATATATAATA
1 TATATATTTTATATAT-ATA
14620753 TATATATTTTATATATATA
1 TATATATTTTATATATATA
14620772 TATATAT
1 TATATAT
14620779 GTGTAATTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 16 0.64
20 9 0.36
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TATATATTTTATATATATA
Found at i:14621366 original size:5 final size:5
Alignment explanation
Indices: 14621356--14621398 Score: 68
Period size: 5 Copynumber: 8.6 Consensus size: 5
14621346 GGTGGGAGAG
**
14621356 AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AGGGA AAAGA AAA
1 AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAA
14621399 TAACAAGATA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
5 34 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (5 bp):
AAAGA
Found at i:14621429 original size:26 final size:26
Alignment explanation
Indices: 14621400--14621479 Score: 92
Period size: 26 Copynumber: 3.1 Consensus size: 26
14621390 AAAAGAAAAT
14621400 AACAAGATAGAAAATGGGCATGGCCC
1 AACAAGATAGAAAATGGGCATGGCCC
**
14621426 AACAAGATAGAAAATTGAACATGGCCC
1 AACAAGATAGAAAA-TGGGCATGGCCC
* *
14621453 AATAA-A-GGAAGAATGGGCATGGCCC
1 AACAAGATAGAA-AATGGGCATGGCCC
14621478 AA
1 AA
14621480 TTAAAAAGAA
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
25 15 0.33
26 17 0.37
27 14 0.30
ACGTcount: A:0.45, C:0.17, G:0.25, T:0.12
Consensus pattern (26 bp):
AACAAGATAGAAAATGGGCATGGCCC
Found at i:14621492 original size:25 final size:24
Alignment explanation
Indices: 14621445--14621494 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 24
14621435 GAAAATTGAA
14621445 CATGGCCCAATAAAGGAAGAATGGG
1 CATGGCCCAATAAA-GAAGAATGGG
14621470 CATGGCCCAATTAAA-AAGAAATGGG
1 CATGGCCCAA-TAAAGAAG-AATGGG
14621495 AGAAGTTCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 3 0.13
25 16 0.70
26 4 0.17
ACGTcount: A:0.42, C:0.16, G:0.28, T:0.14
Consensus pattern (24 bp):
CATGGCCCAATAAAGAAGAATGGG
Found at i:14629029 original size:20 final size:20
Alignment explanation
Indices: 14629004--14629049 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
14628994 CTTCTAAACC
14629004 TCAAATCATACTCCAATAAG
1 TCAAATCATACTCCAATAAG
*
14629024 TCAAATTATACTCCAATAAG
1 TCAAATCATACTCCAATAAG
14629044 TCAAAT
1 TCAAAT
14629050 GAGGACAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.46, C:0.22, G:0.04, T:0.28
Consensus pattern (20 bp):
TCAAATCATACTCCAATAAG
Found at i:14632385 original size:19 final size:19
Alignment explanation
Indices: 14632361--14632405 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
14632351 CCAAGGAGAC
14632361 AAAATAAAATTTT-TAAAAT
1 AAAATAAAATTTTAT-AAAT
* *
14632380 AAAATAATATTTTATTAAT
1 AAAATAAAATTTTATAAAT
14632399 AAAATAA
1 AAAATAA
14632406 TATTAAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 22 0.96
20 1 0.04
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
AAAATAAAATTTTATAAAT
Found at i:14632779 original size:23 final size:23
Alignment explanation
Indices: 14632731--14632779 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
14632721 AAATTAATGA
* * *
14632731 AAAAAATAAAATGAACATAGAGT
1 AAAAAATAAAATAAAAATAGAAT
14632754 AAAAAATAATAATAAAAATA-AAT
1 AAAAAATAA-AATAAAAATAGAAT
14632777 AAA
1 AAA
14632780 TATATTAGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 14 0.64
24 8 0.36
ACGTcount: A:0.73, C:0.02, G:0.06, T:0.18
Consensus pattern (23 bp):
AAAAAATAAAATAAAAATAGAAT
Found at i:14633257 original size:34 final size:34
Alignment explanation
Indices: 14633214--14633304 Score: 137
Period size: 34 Copynumber: 2.7 Consensus size: 34
14633204 CCATTTAAGA
* *
14633214 GCTGGTTTTGAAGGCTAAAAAGTGCCACTTTTTT
1 GCTGATTTTGAAGGCCAAAAAGTGCCACTTTTTT
* *
14633248 GCTGATTTTGGAGGCCAAAAAGTGCCATTTTTTT
1 GCTGATTTTGAAGGCCAAAAAGTGCCACTTTTTT
*
14633282 GCTGATTTTAAAGGCCAAAAAGT
1 GCTGATTTTGAAGGCCAAAAAGT
14633305 ACAAATTTTT
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 51 1.00
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.35
Consensus pattern (34 bp):
GCTGATTTTGAAGGCCAAAAAGTGCCACTTTTTT
Found at i:14633481 original size:34 final size:34
Alignment explanation
Indices: 14633399--14633482 Score: 91
Period size: 34 Copynumber: 2.4 Consensus size: 34
14633389 GGAAAAAGTA
*
14633399 CAGCTTAGCTGCTGAATTTTTGAGGAAAAACAGAG
1 CAGCTTAGCTGCTG-ATTTTTGAGCAAAAACAGAG
* * *
14633434 CAGCATAGATGCTGA-TTTTGAAGCAAAAATA-AG
1 CAGCTTAGCTGCTGATTTTTG-AGCAAAAACAGAG
14633467 CAGCCTTAGCTGCTGA
1 CAG-CTTAGCTGCTGA
14633483 AAAATTAAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
33 10 0.24
34 19 0.46
35 12 0.29
ACGTcount: A:0.35, C:0.17, G:0.24, T:0.25
Consensus pattern (34 bp):
CAGCTTAGCTGCTGATTTTTGAGCAAAAACAGAG
Found at i:14633631 original size:5 final size:5
Alignment explanation
Indices: 14633613--14633658 Score: 69
Period size: 5 Copynumber: 9.6 Consensus size: 5
14633603 GGTGGGAGAG
*
14633613 AAAG- AAAG- AAAGA AAAGA AAAGA AAAGA AAAGA AAGGA AAAGA AAA
1 AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAA
14633659 TAACAAGATA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
4 8 0.21
5 31 0.79
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (5 bp):
AAAGA
Found at i:14633693 original size:26 final size:26
Alignment explanation
Indices: 14633663--14633740 Score: 97
Period size: 25 Copynumber: 3.0 Consensus size: 26
14633653 AGAAAATAAC
14633663 AAGATAGAAAATGGGCATGGCCCAAT
1 AAGATAGAAAATGGGCATGGCCCAAT
*
14633689 AAGATAGAAAATTGGACATGGCCCAAT
1 AAGATAGAAAA-TGGGCATGGCCCAAT
* *
14633716 AA-A-GGAAGAATGGGCATAGCCCAAT
1 AAGATAGAA-AATGGGCATGGCCCAAT
14633741 TAAAAAGAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
25 16 0.35
26 14 0.30
27 16 0.35
ACGTcount: A:0.44, C:0.15, G:0.26, T:0.15
Consensus pattern (26 bp):
AAGATAGAAAATGGGCATGGCCCAAT
Found at i:14633716 original size:27 final size:26
Alignment explanation
Indices: 14633663--14633717 Score: 92
Period size: 27 Copynumber: 2.1 Consensus size: 26
14633653 AGAAAATAAC
*
14633663 AAGATAGAAAATGGGCATGGCCCAAT
1 AAGATAGAAAATGGACATGGCCCAAT
14633689 AAGATAGAAAATTGGACATGGCCCAAT
1 AAGATAGAAAA-TGGACATGGCCCAAT
14633716 AA
1 AA
14633718 AGGAAGAATG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
26 11 0.41
27 16 0.59
ACGTcount: A:0.45, C:0.15, G:0.24, T:0.16
Consensus pattern (26 bp):
AAGATAGAAAATGGACATGGCCCAAT
Found at i:14633752 original size:25 final size:24
Alignment explanation
Indices: 14633671--14633754 Score: 80
Period size: 25 Copynumber: 3.3 Consensus size: 24
14633661 ACAAGATAGA
*
14633671 AAATGGGCATGGCCCAATAAGATAG
1 AAATGGGCATGGCCCAATAA-AAAG
*
14633696 AAAATTGGACATGGCCCAATAAAGGAAG
1 -AAA-TGGGCATGGCCCAATAAA--AAG
*
14633724 -AATGGGCATAGCCCAATTAAAAAG
1 AAATGGGCATGGCCCAA-TAAAAAG
14633748 AAATGGG
1 AAATGGG
14633755 AGAAGTCCAT
Statistics
Matches: 49, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
24 3 0.06
25 18 0.37
26 10 0.20
27 16 0.33
28 2 0.04
ACGTcount: A:0.44, C:0.14, G:0.26, T:0.15
Consensus pattern (24 bp):
AAATGGGCATGGCCCAATAAAAAG
Found at i:14637847 original size:12 final size:12
Alignment explanation
Indices: 14637832--14637856 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
14637822 ACAAAATTTT
14637832 TTAAAAAAAAGC
1 TTAAAAAAAAGC
14637844 TTAAAAAAAAGC
1 TTAAAAAAAAGC
14637856 T
1 T
14637857 CCAAGGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.64, C:0.08, G:0.08, T:0.20
Consensus pattern (12 bp):
TTAAAAAAAAGC
Found at i:14638652 original size:20 final size:20
Alignment explanation
Indices: 14638627--14638672 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
14638617 TTTTGACCCC
14638627 ATTTGACTTATT-AGAGTATA
1 ATTTGACTTATTGA-AGTATA
*
14638647 ATTTGACTTATTGAAGTATG
1 ATTTGACTTATTGAAGTATA
14638667 ATTTGA
1 ATTTGA
14638673 GGTTTAGAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 23 0.96
21 1 0.04
ACGTcount: A:0.33, C:0.04, G:0.17, T:0.46
Consensus pattern (20 bp):
ATTTGACTTATTGAAGTATA
Found at i:14638748 original size:28 final size:27
Alignment explanation
Indices: 14638717--14638769 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
14638707 TTTGGAGTAT
*
14638717 AGGGGTAAAATGGTAATTTTGCCACCTC
1 AGGGGCAAAATGGTAATTTT-CCACCTC
*
14638745 AGGGGCAAAATTGTAATTTTCCACC
1 AGGGGCAAAATGGTAATTTTCCACC
14638770 ACCAGGATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (27 bp):
AGGGGCAAAATGGTAATTTTCCACCTC
Found at i:14638775 original size:28 final size:28
Alignment explanation
Indices: 14638717--14638775 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
14638707 TTTGGAGTAT
* *
14638717 AGGGGTAAAATGGTAATTTTGCCACCTC
1 AGGGGCAAAATGGTAATTTTGCCACCCC
*
14638745 AGGGGCAAAATTGTAATTTT-CCACCACC
1 AGGGGCAAAATGGTAATTTTGCCACC-CC
14638773 AGG
1 AGG
14638776 ATATTTTTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 5 0.19
28 22 0.81
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (28 bp):
AGGGGCAAAATGGTAATTTTGCCACCCC
Found at i:14643447 original size:23 final size:24
Alignment explanation
Indices: 14643400--14643447 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
14643390 TTTGAGTTGA
*
14643400 AAGAACTCATAAAGGAAAAATTTG
1 AAGAACTCATAAAGGAAAAACTTG
* *
14643424 AAGAACTCATGAA-GAAAAGCTTG
1 AAGAACTCATAAAGGAAAAACTTG
14643447 A
1 A
14643448 TATTTGCTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.52, C:0.10, G:0.19, T:0.19
Consensus pattern (24 bp):
AAGAACTCATAAAGGAAAAACTTG
Found at i:14643710 original size:2 final size:2
Alignment explanation
Indices: 14643705--14643751 Score: 85
Period size: 2 Copynumber: 23.0 Consensus size: 2
14643695 ATATGTGTGC
14643705 AT AT AT AGT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
14643748 AT AT
1 AT AT
14643752 GTGAGGGAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 42 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:14646090 original size:14 final size:14
Alignment explanation
Indices: 14646062--14646096 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
14646052 TTATAAAAAA
*
14646062 ATATTA-TATTTTT
1 ATATTATTAATTTT
14646075 ATATTATTAATTTT
1 ATATTATTAATTTT
14646089 ATATTATT
1 ATATTATT
14646097 CTGTTTGTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 6 0.30
14 14 0.70
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
ATATTATTAATTTT
Found at i:14647178 original size:22 final size:22
Alignment explanation
Indices: 14647137--14647180 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
14647127 TCTTTCTCTC
*
14647137 TCTTTTTTTGTCTTTTTCTATT
1 TCTTTTTTTGCCTTTTTCTATT
14647159 TCTTTTTTT-CCTTTTCTCTATT
1 TCTTTTTTTGCCTTTT-TCTATT
14647181 CTATTTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.05, C:0.18, G:0.02, T:0.75
Consensus pattern (22 bp):
TCTTTTTTTGCCTTTTTCTATT
Found at i:14647182 original size:21 final size:22
Alignment explanation
Indices: 14647129--14647187 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 22
14647119 GAGCTGTTTC
* *
14647129 TTTCTCT-CTCTTTTTTTGTCT
1 TTTCTCTATTCTTTTTTTGCCT
14647150 TTT-TCTATTTCTTTTTTT-CCT
1 TTTCTCTA-TTCTTTTTTTGCCT
*
14647171 TTTCTCTATTCTATTTT
1 TTTCTCTATTCTTTTTT
14647188 ATTTCTTTGT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
20 3 0.09
21 16 0.50
22 13 0.41
ACGTcount: A:0.05, C:0.20, G:0.02, T:0.73
Consensus pattern (22 bp):
TTTCTCTATTCTTTTTTTGCCT
Found at i:14647887 original size:23 final size:23
Alignment explanation
Indices: 14647836--14647890 Score: 92
Period size: 23 Copynumber: 2.4 Consensus size: 23
14647826 GTTTAGAGTT
* *
14647836 TGTGAAACGACATGTTGGGAATG
1 TGTGACACGACATGGTGGGAATG
14647859 TGTGACACGACATGGTGGGAATG
1 TGTGACACGACATGGTGGGAATG
14647882 TGTGACACG
1 TGTGACACG
14647891 GCTATGACAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.27, C:0.13, G:0.36, T:0.24
Consensus pattern (23 bp):
TGTGACACGACATGGTGGGAATG
Found at i:14647984 original size:47 final size:47
Alignment explanation
Indices: 14647917--14648274 Score: 428
Period size: 47 Copynumber: 7.6 Consensus size: 47
14647907 GTTTAGAGTT
* * **** *
14647917 TGACACGCCATGGAGGGAATCTGTGACATGGTAGCGTTCAGAGTTTG
1 TGACACGGCATGGAGAGAATCTGTGACACACCAGCATTCAGAGTTTG
* * *
14647964 TAACACGGTATGGAGAGAATCTGTGAAACACCAGCATTCAGAGTTTG
1 TGACACGGCATGGAGAGAATCTGTGACACACCAGCATTCAGAGTTTG
14648011 TGACACGGCATGGAGAGAATCTGTGACACACCAGCATTCAGAGTTTG
1 TGACACGGCATGGAGAGAATCTGTGACACACCAGCATTCAGAGTTTG
*
14648058 TGACATGGCATGGAGAGAATCTGTGACACACCAGCATTCAGAGTTTG
1 TGACACGGCATGGAGAGAATCTGTGACACACCAGCATTCAGAGTTTG
* * * ** * *
14648105 TGACACGACATGGAGGGAATTTGTGACATGCCAGCTTTCAAAGTTTG
1 TGACACGGCATGGAGAGAATCTGTGACACACCAGCATTCAGAGTTTG
** * * * *
14648152 TGACACTCCATGGAGGGAATCTGTGATACGCCAGCATTTAGAGTTTG
1 TGACACGGCATGGAGAGAATCTGTGACACACCAGCATTCAGAGTTTG
* * * *
14648199 TGACATGCCATGGAGGGAATCTGTGACACACCAGTATTCAGAGTTTG
1 TGACACGGCATGGAGAGAATCTGTGACACACCAGCATTCAGAGTTTG
** * *
14648246 TGACACACCATGGAGGGAATCTTTGACAC
1 TGACACGGCATGGAGAGAATCTGTGACAC
14648275 GACAGGGTTT
Statistics
Matches: 272, Mismatches: 39, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
47 272 1.00
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.25
Consensus pattern (47 bp):
TGACACGGCATGGAGAGAATCTGTGACACACCAGCATTCAGAGTTTG
Found at i:14648110 original size:24 final size:24
Alignment explanation
Indices: 14647985--14648110 Score: 84
Period size: 24 Copynumber: 5.3 Consensus size: 24
14647975 GGAGAGAATC
*
14647985 TGTGAAACACCAGCATTCAGAGTT
1 TGTGACACACCAGCATTCAGAGTT
* ** *
14648009 TGTG--ACA-CGGCATGGAGAGAATC
1 TGTGACACACCAGCATTCAGAG--TT
14648032 TGTGACACACCAGCATTCAGAGTT
1 TGTGACACACCAGCATTCAGAGTT
** ** *
14648056 TGTG--ACA-TGGCATGGAGAGAATC
1 TGTGACACACCAGCATTCAGAG--TT
14648079 TGTGACACACCAGCATTCAGAGTT
1 TGTGACACACCAGCATTCAGAGTT
14648103 TGTGACAC
1 TGTGACAC
14648111 GACATGGAGG
Statistics
Matches: 74, Mismatches: 18, Indels: 20
0.66 0.16 0.18
Matches are distributed among these distances:
21 17 0.23
22 6 0.08
23 10 0.14
24 18 0.24
25 6 0.08
26 17 0.23
ACGTcount: A:0.30, C:0.21, G:0.26, T:0.23
Consensus pattern (24 bp):
TGTGACACACCAGCATTCAGAGTT
Found at i:14648365 original size:23 final size:23
Alignment explanation
Indices: 14648335--14648378 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
14648325 GTTTAGAGTG
*
14648335 TGTGACACGGCATGGCTTGAACA
1 TGTGACACGACATGGCTTGAACA
*
14648358 TGTGACACGACATGGTTTGAA
1 TGTGACACGACATGGCTTGAA
14648379 AAAGGAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.25
Consensus pattern (23 bp):
TGTGACACGACATGGCTTGAACA
Found at i:14651026 original size:18 final size:19
Alignment explanation
Indices: 14651003--14651039 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
14650993 CTGCTAAACC
*
14651003 CTCAAATTATACT-CAATA
1 CTCAAATCATACTCCAATA
14651021 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
14651040 AGTTAAATGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.43, C:0.27, G:0.00, T:0.30
Consensus pattern (19 bp):
CTCAAATCATACTCCAATA
Found at i:14651952 original size:31 final size:30
Alignment explanation
Indices: 14651914--14651990 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 30
14651904 TCAGTGTTGG
14651914 CGTGTTACAATATTTGACTTGATACGCATAA
1 CGTGTTACAATATTT-ACTTGATACGCATAA
* * * **
14651945 CGTGTTACAACAATTTACTTTATATGCATGG
1 CGTGTTACAA-TATTTACTTGATACGCATAA
*
14651976 TGTGTTACAATATTT
1 CGTGTTACAATATTT
14651991 TACGTTATAT
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
30 4 0.11
31 30 0.79
32 4 0.11
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.40
Consensus pattern (30 bp):
CGTGTTACAATATTTACTTGATACGCATAA
Found at i:14651993 original size:31 final size:31
Alignment explanation
Indices: 14651946--14652082 Score: 213
Period size: 31 Copynumber: 4.4 Consensus size: 31
14651936 TACGCATAAC
*
14651946 GTGTTACAACAATTTACTTTATATGCATGGT
1 GTGTTACAACATTTTACTTTATATGCATGGT
* *
14651977 GTGTTACAATATTTTACGTTATATGCATGGT
1 GTGTTACAACATTTTACTTTATATGCATGGT
14652008 GTGTTACAACATTTTA-TGTTATATGCATGGT
1 GTGTTACAACATTTTACT-TTATATGCATGGT
* *
14652039 GTGTTACAACATTTTACGTTATATGCATGGC
1 GTGTTACAACATTTTACTTTATATGCATGGT
14652070 GTGTTACAACATT
1 GTGTTACAACATT
14652083 ATGGGTTAAC
Statistics
Matches: 97, Mismatches: 7, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
31 97 1.00
ACGTcount: A:0.27, C:0.12, G:0.18, T:0.42
Consensus pattern (31 bp):
GTGTTACAACATTTTACTTTATATGCATGGT
Found at i:14652013 original size:62 final size:62
Alignment explanation
Indices: 14651915--14652080 Score: 237
Period size: 62 Copynumber: 2.7 Consensus size: 62
14651905 CAGTGTTGGC
* * **
14651915 GTGTTACAATATTTGAC-TTGATACGCATAACGTGTTACAACAATTTACT-TTATATGCATGGT
1 GTGTTACAATATTTTACGTT-ATATGCATGGCGTGTTACAACAATTTA-TGTTATATGCATGGT
* *
14651977 GTGTTACAATATTTTACGTTATATGCATGGTGTGTTACAACATTTTATGTTATATGCATGGT
1 GTGTTACAATATTTTACGTTATATGCATGGCGTGTTACAACAATTTATGTTATATGCATGGT
*
14652039 GTGTTACAACATTTTACGTTATATGCATGGCGTGTTACAACA
1 GTGTTACAATATTTTACGTTATATGCATGGCGTGTTACAACA
14652081 TTATGGGTTA
Statistics
Matches: 94, Mismatches: 8, Indels: 4
0.89 0.08 0.04
Matches are distributed among these distances:
61 1 0.01
62 91 0.97
63 2 0.02
ACGTcount: A:0.28, C:0.13, G:0.18, T:0.40
Consensus pattern (62 bp):
GTGTTACAATATTTTACGTTATATGCATGGCGTGTTACAACAATTTATGTTATATGCATGGT
Found at i:14653727 original size:145 final size:145
Alignment explanation
Indices: 14653500--14653761 Score: 398
Period size: 145 Copynumber: 1.8 Consensus size: 145
14653490 GTTCGCACGA
* *
14653500 TTTGTGTTCAACAATTTCATATATGATTATCGAATAACATATCTGTGTTTGTAGTTGGACCATGC
1 TTTGTGTTCAACAATTCCATATATGATTATCGAATAACATATCTGTGTTTGCAGTTGGACCATGC
* * * *
14653565 GACGACAACTCCACAACCACCAAGAGGTCCTCTTTAGACTCACAATGCTAACGATGAGTCGGTAA
66 GACGACAACTCCACAACCACCAAGAGGTCATCCTCAGACACACAATGCTAACGATGAGTCGGTAA
14653630 AGACGGTTATAACGG
131 AGACGGTTATAACGG
* *
14653645 TTTGTGTTCAACAATTCCATATGTGATTATTGAATAACATATCTGTGTTTGCAGTTGGACCATGC
1 TTTGTGTTCAACAATTCCATATATGATTATCGAATAACATATCTGTGTTTGCAGTTGGACCATGC
* * * ** *
14653710 GACGATAGCTCCTCAACCACTGAGAGGTCATCCTCAGACACATAATGCTAAC
66 GACGACAACTCCACAACCACCAAGAGGTCATCCTCAGACACACAATGCTAAC
14653762 AGCCCATCGG
Statistics
Matches: 103, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
145 103 1.00
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (145 bp):
TTTGTGTTCAACAATTCCATATATGATTATCGAATAACATATCTGTGTTTGCAGTTGGACCATGC
GACGACAACTCCACAACCACCAAGAGGTCATCCTCAGACACACAATGCTAACGATGAGTCGGTAA
AGACGGTTATAACGG
Found at i:14653794 original size:145 final size:145
Alignment explanation
Indices: 14653496--14653828 Score: 384
Period size: 145 Copynumber: 2.3 Consensus size: 145
14653486 GACAGTTCGC
* *
14653496 ACGATTTGTGTTCAACAATTTCATATATGATTATCGAATAACATATCTGTGTTTGTAGTTGGACC
1 ACGATTTGTGTTCAACAATTCCATATATGATTATCGAATAACATATCTGTGTTTGCAGTTGGACC
* * * * **
14653561 ATGCGACGACAACTCCACAACCACCAAGAGGTCCTCTTTAGACTCACAATGCTAACGATGAGTCG
66 ATGCGACGACAACTCCACAACCACCAAGAGGTCATCCTCAGACACACAATGCTAACGACCAGTCG
14653626 GTAAAGACGGTTATA
131 GTAAAGACGGTTATA
* * *
14653641 ACGGTTTGTGTTCAACAATTCCATATGTGATTATTGAATAACATATCTGTGTTTGCAGTTGGACC
1 ACGATTTGTGTTCAACAATTCCATATATGATTATCGAATAACATATCTGTGTTTGCAGTTGGACC
* * * ** * *
14653706 ATGCGACGATAGCTCCTCAACCACTGAGAGGTCATCCTCAGACACATAATGCTAACAGCCCA-TC
66 ATGCGACGACAACTCCACAACCACCAAGAGGTCATCCTCAGACACACAATGCTAAC-GACCAGTC
*
14653770 GGT-AAGATCGGTTTTA
130 GGTAAAGA-CGGTTATA
** * * * * *
14653786 ATTATTTGTGTAT-AGCATTTCCACATATGTTTATCGAGTAACA
1 ACGATTTGTGT-TCAACAATTCCATATATGATTATCGAATAACA
14653829 CGATAATTTT
Statistics
Matches: 156, Mismatches: 29, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
144 4 0.03
145 149 0.96
146 3 0.02
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Consensus pattern (145 bp):
ACGATTTGTGTTCAACAATTCCATATATGATTATCGAATAACATATCTGTGTTTGCAGTTGGACC
ATGCGACGACAACTCCACAACCACCAAGAGGTCATCCTCAGACACACAATGCTAACGACCAGTCG
GTAAAGACGGTTATA
Found at i:14656044 original size:31 final size:31
Alignment explanation
Indices: 14655947--14656045 Score: 85
Period size: 31 Copynumber: 3.2 Consensus size: 31
14655937 GGGCATGGAG
14655947 TGTCACCCCTA-AATACTGCAACAAGTCAGCA
1 TGTCACCCC-ACAATACTGCAACAAGTCAGCA
* * * ** * * * *
14655978 TGTCACGCCAC-GTATCTCCTTCCACTTAGCG
1 TGTCACCCCACAATA-CTGCAACAAGTCAGCA
14656009 TGTCACCCCACAATACTGCAACAAGTCAGCA
1 TGTCACCCCACAATACTGCAACAAGTCAGCA
14656040 TGTCAC
1 TGTCAC
14656046 GTCATAAATC
Statistics
Matches: 47, Mismatches: 18, Indels: 6
0.66 0.25 0.08
Matches are distributed among these distances:
30 3 0.06
31 42 0.89
32 2 0.04
ACGTcount: A:0.28, C:0.35, G:0.14, T:0.22
Consensus pattern (31 bp):
TGTCACCCCACAATACTGCAACAAGTCAGCA
Found at i:14656062 original size:62 final size:62
Alignment explanation
Indices: 14655946--14656075 Score: 181
Period size: 62 Copynumber: 2.1 Consensus size: 62
14655936 GGGGCATGGA
** * * *
14655946 GTGTCACCCCTAAATACTGCAACAAGTCAGCATGTCACGCCACGTATCTCCTTCCACTTAGC
1 GTGTCACCCCTAAATACTGCAACAAGTCAGCATGTCACGCCACAAATCTACTTCCACTCAAC
* *
14656008 GTGTCACCCC-ACAATACTGCAACAAGTCAGCATGTCACGTCATAAATCTACTTCCACTCAAC
1 GTGTCACCCCTA-AATACTGCAACAAGTCAGCATGTCACGCCACAAATCTACTTCCACTCAAC
14656070 GTGTCA
1 GTGTCA
14656076 ACACAATTGG
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
61 1 0.02
62 59 0.98
ACGTcount: A:0.28, C:0.34, G:0.14, T:0.24
Consensus pattern (62 bp):
GTGTCACCCCTAAATACTGCAACAAGTCAGCATGTCACGCCACAAATCTACTTCCACTCAAC
Found at i:14656152 original size:86 final size:86
Alignment explanation
Indices: 14656006--14656339 Score: 454
Period size: 86 Copynumber: 3.9 Consensus size: 86
14655996 CTTCCACTTA
* * *
14656006 GCGTGTCACCCCACAATACTGCAACAAGTCAGCATGTCACGTCATAAATCTACTTCCACTCAACG
1 GCGTGTCACCCCACAATACTGCAACAAGTCAACGTGTCACGCCATAAATCTACTTCCACTCAACG
14656071 TGTCAACACAATTGGGGCGTG
66 TGTCAACACAATTGGGGCGTG
* * * *
14656092 ACGTGTCACCTCACAATACTGCAACAAGTCAACGTGTCACGCCATAAATTTGCTTCCACTC-ACG
1 GCGTGTCACCCCACAATACTGCAACAAGTCAACGTGTCACGCCATAAATCTACTTCCACTCAACG
*** *
14656156 TGTCAACACAATTGGTATTGGG
66 TGTCAACACAATTGG-GGCGTG
* * * * *
14656178 GCATGTCACCCCACAATACTGTAATAAGTCAGCGTGTCACGCCATAAATCTACTTCCACTCAACT
1 GCGTGTCACCCCACAATACTGCAACAAGTCAACGTGTCACGCCATAAATCTACTTCCACTCAACG
14656243 TGTCAACACAATTGGGGCGTG
66 TGTCAACACAATTGGGGCGTG
* * * * *
14656264 GCGTGTCACCCCACAATACTGCAACCAGTTAATGTGTCACGTCATAAATCTACTTCCACTCAGCG
1 GCGTGTCACCCCACAATACTGCAACAAGTCAACGTGTCACGCCATAAATCTACTTCCACTCAACG
*
14656329 TGTCACCACAA
66 TGTCAACACAA
14656340 GATGTCATTG
Statistics
Matches: 211, Mismatches: 35, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
85 18 0.09
86 176 0.83
87 17 0.08
ACGTcount: A:0.29, C:0.30, G:0.17, T:0.24
Consensus pattern (86 bp):
GCGTGTCACCCCACAATACTGCAACAAGTCAACGTGTCACGCCATAAATCTACTTCCACTCAACG
TGTCAACACAATTGGGGCGTG
Found at i:14656209 original size:172 final size:173
Alignment explanation
Indices: 14656009--14656339 Score: 529
Period size: 172 Copynumber: 1.9 Consensus size: 173
14655999 CCACTTAGCG
*
14656009 TGTCACCCCACAATACTGCAACAAGTCAGCATGTCACGTCATAAATCTACTTCCACTCAACGTGT
1 TGTCACCCCACAATACTGCAACAAGTCAGCATGTCACGCCATAAATCTACTTCCACTCAACGTGT
*
14656074 CAACACAATTGGGGCGTGACGTGTCACCTCACAATACTGCAACAAGTCAACGTGTCACGCCATAA
66 CAACACAATTGGGGCGTGACGTGTCACCCCACAATACTGCAACAAGTCAACGTGTCACGCCATAA
* *
14656139 ATTTGCTTCCACTCA-CGTGTCAACACAATTGGTATTGGGGCA
131 ATCTACTTCCACTCAGCGTGTCAACACAATTGGTATTGGGGCA
* * * *
14656181 TGTCACCCCACAATACTGTAATAAGTCAGCGTGTCACGCCATAAATCTACTTCCACTCAACTTGT
1 TGTCACCCCACAATACTGCAACAAGTCAGCATGTCACGCCATAAATCTACTTCCACTCAACGTGT
* * * * *
14656246 CAACACAATTGGGGCGTGGCGTGTCACCCCACAATACTGCAACCAGTTAATGTGTCACGTCATAA
66 CAACACAATTGGGGCGTGACGTGTCACCCCACAATACTGCAACAAGTCAACGTGTCACGCCATAA
*
14656311 ATCTACTTCCACTCAGCGTGTCACCACAA
131 ATCTACTTCCACTCAGCGTGTCAACACAA
14656340 GATGTCATTG
Statistics
Matches: 144, Mismatches: 14, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
172 132 0.92
173 12 0.08
ACGTcount: A:0.29, C:0.30, G:0.17, T:0.24
Consensus pattern (173 bp):
TGTCACCCCACAATACTGCAACAAGTCAGCATGTCACGCCATAAATCTACTTCCACTCAACGTGT
CAACACAATTGGGGCGTGACGTGTCACCCCACAATACTGCAACAAGTCAACGTGTCACGCCATAA
ATCTACTTCCACTCAGCGTGTCAACACAATTGGTATTGGGGCA
Found at i:14656642 original size:22 final size:22
Alignment explanation
Indices: 14656614--14656705 Score: 184
Period size: 22 Copynumber: 4.2 Consensus size: 22
14656604 GTCATTTTAT
14656614 ATTATTTTTGTAAAAATGATAA
1 ATTATTTTTGTAAAAATGATAA
14656636 ATTATTTTTGTAAAAATGATAA
1 ATTATTTTTGTAAAAATGATAA
14656658 ATTATTTTTGTAAAAATGATAA
1 ATTATTTTTGTAAAAATGATAA
14656680 ATTATTTTTGTAAAAATGATAA
1 ATTATTTTTGTAAAAATGATAA
14656702 ATTA
1 ATTA
14656706 ATTTACATAT
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 70 1.00
ACGTcount: A:0.46, C:0.00, G:0.09, T:0.46
Consensus pattern (22 bp):
ATTATTTTTGTAAAAATGATAA
Found at i:14660088 original size:63 final size:63
Alignment explanation
Indices: 14660010--14660133 Score: 176
Period size: 63 Copynumber: 2.0 Consensus size: 63
14660000 ACCACGGCCC
* * * *
14660010 GATGACGATGGTGCTCAATAGAGAGTTGACAGAGCTCATACAGTTCAAAGAGTTGAGAGAGCT
1 GATGACAATGGTGCTCAACAAAGAGTTGACAGAGCTCAGACAGTTCAAAGAGTTGAGAGAGCT
* * * *
14660073 GATGACAATGGTGCTCAACAAAGAGTTGACAGAGTTGAGACAGTTTAGAGAGTTGAGAGAG
1 GATGACAATGGTGCTCAACAAAGAGTTGACAGAGCTCAGACAGTTCAAAGAGTTGAGAGAG
14660134 AAAGATGAGC
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
63 53 1.00
ACGTcount: A:0.35, C:0.12, G:0.31, T:0.22
Consensus pattern (63 bp):
GATGACAATGGTGCTCAACAAAGAGTTGACAGAGCTCAGACAGTTCAAAGAGTTGAGAGAGCT
Found at i:14660108 original size:9 final size:9
Alignment explanation
Indices: 14660094--14660133 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
14660084 TGCTCAACAA
*
14660094 AGAGTTGAC
1 AGAGTTGAG
14660103 AGAGTTGAG
1 AGAGTTGAG
* *
14660112 ACAGTTTAG
1 AGAGTTGAG
14660121 AGAGTTGAG
1 AGAGTTGAG
14660130 AGAG
1 AGAG
14660134 AAAGATGAGC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.35, C:0.05, G:0.38, T:0.23
Consensus pattern (9 bp):
AGAGTTGAG
Found at i:14660474 original size:19 final size:19
Alignment explanation
Indices: 14660450--14660505 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 19
14660440 TAACAAAATG
*
14660450 AATAAAAAATAAAAATAAA
1 AATAAAAAAGAAAAATAAA
*
14660469 AATAAAAAAGATAAAT--A
1 AATAAAAAAGAAAAATAAA
* *
14660486 AATAAATAAGAAAATTAAA
1 AATAAAAAAGAAAAATAAA
14660505 A
1 A
14660506 CTCATATAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
17 14 0.47
19 16 0.53
ACGTcount: A:0.79, C:0.00, G:0.04, T:0.18
Consensus pattern (19 bp):
AATAAAAAAGAAAAATAAA
Found at i:14660504 original size:17 final size:17
Alignment explanation
Indices: 14660445--14660500 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
14660435 CAAAGTAACA
* * *
14660445 AAATGAATAAAAAATAA
1 AAATAAATAAAAAAGAT
14660462 AAATAAAAATAAAAAAGAT
1 AAAT--AAATAAAAAAGAT
*
14660481 AAATAAATAAATAAGA-
1 AAATAAATAAAAAAGAT
14660497 AAAT
1 AAAT
14660501 TAAAACTCAT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
16 4 0.12
17 15 0.45
19 14 0.42
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.18
Consensus pattern (17 bp):
AAATAAATAAAAAAGAT
Found at i:14660767 original size:50 final size:49
Alignment explanation
Indices: 14660634--14660956 Score: 319
Period size: 50 Copynumber: 6.4 Consensus size: 49
14660624 TACCATTTGA
** * *
14660634 AAAAT-AATTTTGAAAAAGATAAA-AACTCCTCACCCAAGGCTCCACCACTCT
1 AAAATCAA-TTTG-AAAA-ATAAACAACTCCTCATTCAAGGCT-TACCACTTT
** * * *
14660685 AAAATCAATTAAATAAAATAAACAACTCCTCATTCGAGGCTCTATCAGTTT
1 AAAATCAATTTGA-AAAATAAACAACTCCTCATTCAAGGCT-TACCACTTT
* * *
14660736 AAAATCAATTTGAAAAATAAACAACTCCTCATTCAAGGCTCTTCTACTTA
1 AAAATCAATTTGAAAAATAAACAACTCCTCATTCAAGGCT-TACCACTTT
* *
14660786 AAAATCAATTTGAAAAATAAACAACTCCTCATCCAAAGCTTTACCACTTT
1 AAAATCAATTTGAAAAATAAACAACTCCTCATTCAAGGC-TTACCACTTT
* *
14660836 AAAATCAATTTGAAAAATAAACCATTCCTCA-TCTAAGGCTTAACCACTTT
1 AAAATCAATTTGAAAAATAAACAACTCCTCATTC-AAGGCTT-ACCACTTT
* * * * *
14660886 AAAATCAATTTGACAAATAAACAACTCCTTATTCGAGGCTTAAACAACGTT
1 AAAATCAATTTGAAAAATAAACAACTCCTCATTCAAGGCTT--ACCACTTT
*
14660937 AAAATCAATTTGAAACATAA
1 AAAATCAATTTGAAAAATAA
14660957 TAGTAATTAT
Statistics
Matches: 229, Mismatches: 35, Indels: 16
0.82 0.12 0.06
Matches are distributed among these distances:
49 3 0.01
50 154 0.67
51 70 0.31
52 2 0.01
ACGTcount: A:0.44, C:0.22, G:0.07, T:0.28
Consensus pattern (49 bp):
AAAATCAATTTGAAAAATAAACAACTCCTCATTCAAGGCTTACCACTTT
Found at i:14660875 original size:150 final size:152
Alignment explanation
Indices: 14660633--14660925 Score: 373
Period size: 150 Copynumber: 1.9 Consensus size: 152
14660623 TTACCATTTG
*
14660633 AAAAATAATTTTGAAAAAGATAAAAACTCCTCACCCAAGGCTCCACCACTCTAAAATCAATTAAA
1 AAAAATAATTTTGAAAAAGATAAAAACTCCTCACCCAAAGCTCCACCACTCTAAAATCAATTAAA
* * *
14660698 TAAAATAAACAACTCCTCATTCGAGGCTCT-ATCAGTTTAAAATCAATTTGAAAAATAAACAACT
66 TAAAATAAACAACTCCTCATTCAAGGCT-TAACCACTTTAAAATCAATTTGAAAAATAAACAACT
14660762 CCTCATTCAAGGCTCTTCTACTT
130 CCTCATTCAAGGCTCTTCTACTT
* ** * *
14660785 AAAAATCAA-TTTG-AAAA-ATAAACAACTCCTCATCCAAAGCTTTACCACTTTAAAATCAATTT
1 AAAAAT-AATTTTGAAAAAGATAAA-AACTCCTCACCCAAAGCTCCACCACTCTAAAATCAATTA
* * * *
14660847 GA-AAAATAAACCATTCCTCA-TCTAAGGCTTAACCACTTTAAAATCAATTTGACAAATAAACAA
64 AATAAAATAAACAACTCCTCATTC-AAGGCTTAACCACTTTAAAATCAATTTGAAAAATAAACAA
* *
14660910 CTCCTTATTCGAGGCT
128 CTCCTCATTCAAGGCT
14660926 TAAACAACGT
Statistics
Matches: 122, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
149 3 0.02
150 69 0.57
151 38 0.31
152 10 0.08
153 2 0.02
ACGTcount: A:0.43, C:0.23, G:0.07, T:0.28
Consensus pattern (152 bp):
AAAAATAATTTTGAAAAAGATAAAAACTCCTCACCCAAAGCTCCACCACTCTAAAATCAATTAAA
TAAAATAAACAACTCCTCATTCAAGGCTTAACCACTTTAAAATCAATTTGAAAAATAAACAACTC
CTCATTCAAGGCTCTTCTACTT
Found at i:14661376 original size:2 final size:2
Alignment explanation
Indices: 14661371--14661403 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
14661361 AAAGTATTAG
14661371 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
14661404 GTAATTATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:14662239 original size:51 final size:51
Alignment explanation
Indices: 14662163--14662469 Score: 463
Period size: 51 Copynumber: 6.0 Consensus size: 51
14662153 CCATTGATAA
* *
14662163 CCTTATCCAAGGCCTAAACAACTTAAAAATCAATTTGAAACATAAACAACT
1 CCTTATCCGAGGCTTAAACAACTTAAAAATCAATTTGAAACATAAACAACT
* *
14662214 CCTTATCGGAGGCCTAAACAACTTAAAAATCAATTTGAAACATAAACAACT
1 CCTTATCCGAGGCTTAAACAACTTAAAAATCAATTTGAAACATAAACAACT
*
14662265 -CTTCATCCGAGGCTTAAACAACTTTAAAATCAATTTGAAACATAAACAACT
1 CCTT-ATCCGAGGCTTAAACAACTTAAAAATCAATTTGAAACATAAACAACT
* *
14662316 CCTAATCCGAGGCTTAAACAACTTTAAAAATCAATTTGAAACATAAACAACC
1 CCTTATCCGAGGCTTAAACAAC-TTAAAAATCAATTTGAAACATAAACAACT
* ** * *
14662368 CCTCATTTGTGGCTTAAACAACTTTAAAATCAATTTGAAACATAAACAACT
1 CCTTATCCGAGGCTTAAACAACTTAAAAATCAATTTGAAACATAAACAACT
*
14662419 CCTCATCCGAGGCTTAAACAACTTTAAAAATCAATTTGAAACATAAACAAC
1 CCTTATCCGAGGCTTAAACAAC-TTAAAAATCAATTTGAAACATAAACAAC
14662470 ATTAAGGTTT
Statistics
Matches: 234, Mismatches: 18, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
50 3 0.01
51 157 0.67
52 74 0.32
ACGTcount: A:0.45, C:0.22, G:0.08, T:0.25
Consensus pattern (51 bp):
CCTTATCCGAGGCTTAAACAACTTAAAAATCAATTTGAAACATAAACAACT
Found at i:14662383 original size:103 final size:103
Alignment explanation
Indices: 14662167--14662469 Score: 491
Period size: 103 Copynumber: 3.0 Consensus size: 103
14662157 TGATAACCTT
* * * * * *
14662167 ATCCAAGGCCTAAACAACTTAAAAATCAATTTGAAACATAAACAACTCCTTATCGGAGGCCTAAA
1 ATCCGAGGCTTAAACAACTTTAAAATCAATTTGAAACATAAACAACTCCTAATCCGAGGCTTAAA
* *
14662232 CAAC-TTAAAAATCAATTTGAAACATAAACAACTCTTC
66 CAACTTTAAAAATCAATTTGAAACATAAACAACCCCTC
14662269 ATCCGAGGCTTAAACAACTTTAAAATCAATTTGAAACATAAACAACTCCTAATCCGAGGCTTAAA
1 ATCCGAGGCTTAAACAACTTTAAAATCAATTTGAAACATAAACAACTCCTAATCCGAGGCTTAAA
14662334 CAACTTTAAAAATCAATTTGAAACATAAACAACCCCTC
66 CAACTTTAAAAATCAATTTGAAACATAAACAACCCCTC
** * *
14662372 ATTTGTGGCTTAAACAACTTTAAAATCAATTTGAAACATAAACAACTCCTCATCCGAGGCTTAAA
1 ATCCGAGGCTTAAACAACTTTAAAATCAATTTGAAACATAAACAACTCCTAATCCGAGGCTTAAA
14662437 CAACTTTAAAAATCAATTTGAAACATAAACAAC
66 CAACTTTAAAAATCAATTTGAAACATAAACAAC
14662470 ATTAAGGTTT
Statistics
Matches: 188, Mismatches: 12, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
102 63 0.34
103 125 0.66
ACGTcount: A:0.45, C:0.22, G:0.08, T:0.25
Consensus pattern (103 bp):
ATCCGAGGCTTAAACAACTTTAAAATCAATTTGAAACATAAACAACTCCTAATCCGAGGCTTAAA
CAACTTTAAAAATCAATTTGAAACATAAACAACCCCTC
Done.