Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr2
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: 50190067
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Warning! 915496 characters in sequence are not A, C, G, or T
File 16 of 161
Found at i:5469322 original size:16 final size:16
Alignment explanation
Indices: 5469301--5469332 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
5469291 CTAAATGTTA
5469301 GTATATGTTATTTGAT
1 GTATATGTTATTTGAT
5469317 GTATATGTTATTTGAT
1 GTATATGTTATTTGAT
5469333 AAATTATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.00, G:0.19, T:0.56
Consensus pattern (16 bp):
GTATATGTTATTTGAT
Found at i:5474801 original size:13 final size:13
Alignment explanation
Indices: 5474783--5474821 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
5474773 ACCCAAAACC
5474783 GACCCAATAAGCT
1 GACCCAATAAGCT
5474796 GACCCAATAAGCT
1 GACCCAATAAGCT
5474809 GACCCAATAAGCT
1 GACCCAATAAGCT
5474822 TATTTAGCTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.38, C:0.31, G:0.15, T:0.15
Consensus pattern (13 bp):
GACCCAATAAGCT
Found at i:5476307 original size:22 final size:22
Alignment explanation
Indices: 5476279--5476322 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
5476269 GAGTAAACTC
5476279 GGCGTACTATACCTATTGACGA
1 GGCGTACTATACCTATTGACGA
5476301 GGCGTACTATACCTATTGACGA
1 GGCGTACTATACCTATTGACGA
5476323 TAACTCAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (22 bp):
GGCGTACTATACCTATTGACGA
Found at i:5483022 original size:138 final size:138
Alignment explanation
Indices: 5482774--5483057 Score: 489
Period size: 138 Copynumber: 2.1 Consensus size: 138
5482764 TATAAAATAG
5482774 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCAAATTTATT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCAAATTTATT
* *
5482839 AATATAAACAGTTATATTAATTAATTTCGGCCAATATAGAAAAGACATGAAAATTAATATTATTT
66 AATATAAACAGTTATATTAATTAATTTCGGCCAAAATAGAAAAGACATAAAAATTAATATTATTT
*
5482904 TGGAAAGA
131 TGAAAAGA
*
5482912 ATATAATTAATATATGAATTTTATTCATACAAAATATTAATTGTATATAGTTTT-CCAAATTTAT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATA-TTTTACCAAATTTAT
* * *
5482976 TAATATAAACAGTTATATTAATTAATTTCGGTCAAAATATAAAAGACATAAAAATTAATATTCTT
65 TAATATAAACAGTTATATTAATTAATTTCGGCCAAAATAGAAAAGACATAAAAATTAATATTATT
5483041 TTGAAAAGA
130 TTGAAAAGA
5483050 ATATAATT
1 ATATAATT
5483058 CTTTTCCTAA
Statistics
Matches: 138, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
138 134 0.97
139 4 0.03
ACGTcount: A:0.46, C:0.06, G:0.07, T:0.40
Consensus pattern (138 bp):
ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCAAATTTATT
AATATAAACAGTTATATTAATTAATTTCGGCCAAAATAGAAAAGACATAAAAATTAATATTATTT
TGAAAAGA
Found at i:5483121 original size:20 final size:20
Alignment explanation
Indices: 5483096--5483164 Score: 111
Period size: 20 Copynumber: 3.4 Consensus size: 20
5483086 ATAATCCTAT
*
5483096 ATTCTTTTAAAAAGAATATA
1 ATTCTTTTAAAAAGTATATA
5483116 ATTCTTTTAAAAAGTATATA
1 ATTCTTTTAAAAAGTATATA
*
5483136 ATTCTTTTAAAAAGTATGTA
1 ATTCTTTTAAAAAGTATATA
5483156 ATTCCTTTT
1 ATT-CTTTT
5483165 TTTAACTTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
20 41 0.89
21 5 0.11
ACGTcount: A:0.41, C:0.07, G:0.06, T:0.46
Consensus pattern (20 bp):
ATTCTTTTAAAAAGTATATA
Found at i:5483269 original size:75 final size:75
Alignment explanation
Indices: 5483136--5483282 Score: 179
Period size: 75 Copynumber: 2.0 Consensus size: 75
5483126 AAAGTATATA
* * * ** *
5483136 ATTCTTTTAAAAAGTATGTAATTCCTTTTTTTAACTTTTTATTTATCTTACCTATTAATAAGGCA
1 ATTCTTTTAAAAAGAATATAATTCCTTTTTCTAACTTTCCATTTACCTTACCTATTAATAAGGCA
5483201 ATAATCCTAT
66 ATAATCCTAT
** * * *
5483211 ATTCTTTTGGAAAGAATATAATTCCTTTTTCTAACTTTCCATTTGCCTT-CTCTGTTAATAAGGG
1 ATTCTTTTAAAAAGAATATAATTCCTTTTTCTAACTTTCCATTTACCTTAC-CTATTAATAAGGC
5483275 AATAATCC
65 AATAATCC
5483283 GTTCCTTATG
Statistics
Matches: 60, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
74 1 0.02
75 59 0.98
ACGTcount: A:0.30, C:0.16, G:0.08, T:0.46
Consensus pattern (75 bp):
ATTCTTTTAAAAAGAATATAATTCCTTTTTCTAACTTTCCATTTACCTTACCTATTAATAAGGCA
ATAATCCTAT
Found at i:5488850 original size:15 final size:15
Alignment explanation
Indices: 5488830--5488859 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
5488820 TGGTTCGATC
5488830 AATGATGAGTCATGT
1 AATGATGAGTCATGT
5488845 AATGATGAGTCATGT
1 AATGATGAGTCATGT
5488860 TGATCTTCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.07, G:0.27, T:0.33
Consensus pattern (15 bp):
AATGATGAGTCATGT
Found at i:5493052 original size:25 final size:25
Alignment explanation
Indices: 5493024--5493072 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
5493014 TTGTCACATT
5493024 AATTAATTTAATTTGATAGTTAAAC
1 AATTAATTTAATTTGATAGTTAAAC
5493049 AATTAATTTAATTTGATAGTTAAA
1 AATTAATTTAATTTGATAGTTAAA
5493073 TATTAAACAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.45, C:0.02, G:0.08, T:0.45
Consensus pattern (25 bp):
AATTAATTTAATTTGATAGTTAAAC
Found at i:5493283 original size:138 final size:138
Alignment explanation
Indices: 5493135--5493407 Score: 417
Period size: 138 Copynumber: 2.0 Consensus size: 138
5493125 TACAATGCAA
* *
5493135 ATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCAAATTTATTAATATAAACAG
1 ATATGAATTTGATTCATACAAAATATTAAGTGTATATATTCTACCAAATTTATTAATATAAACAG
** * *
5493200 TTATATTAATTAA-TTCT-GGTCAAAATATAAAAGGCT-TGAAAATTTATATTCTTTTGGAAATA
66 TTATATTAATTAACTT-TAGGT-AAAATATAAAA-AATATGAAAATTAATATTCTTTTGGAAAAA
5493262 ATATAATTAAT
128 ATATAATTAAT
* *
5493273 ATATGAATTTGATTCATACAAAATATTAAGTGTATATATTCTACCGAATTTATTAATATAAATAG
1 ATATGAATTTGATTCATACAAAATATTAAGTGTATATATTCTACCAAATTTATTAATATAAACAG
*
5493338 TTATATTAATTAACTTTAGGTAAAATATAAAAAATATGGAAATTAATATTCTTTTGGAAAAAATA
66 TTATATTAATTAACTTTAGGTAAAATATAAAAAATATGAAAATTAATATTCTTTTGGAAAAAATA
5493403 TAATT
131 TAATT
5493408 CTTTTTCTAA
Statistics
Matches: 123, Mismatches: 9, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
137 1 0.01
138 117 0.95
139 5 0.04
ACGTcount: A:0.45, C:0.06, G:0.08, T:0.41
Consensus pattern (138 bp):
ATATGAATTTGATTCATACAAAATATTAAGTGTATATATTCTACCAAATTTATTAATATAAACAG
TTATATTAATTAACTTTAGGTAAAATATAAAAAATATGAAAATTAATATTCTTTTGGAAAAAATA
TAATTAAT
Found at i:5493468 original size:73 final size:75
Alignment explanation
Indices: 5493385--5493530 Score: 233
Period size: 74 Copynumber: 2.0 Consensus size: 75
5493375 GGAAATTAAT
5493385 ATTCTTTTGGAAAAAATATAATTC-TTTTTCTAACTTTCCATTTGCCTTCTC-ATTAATAAAGGA
1 ATTCTTTTGGAAAAAATATAATTCATTTTTCTAACTTTCCATTTGCCTTCTCTATTAATAAAGGA
5493448 ATAATCCTAG
66 ATAATCCTAG
* * * * *
5493458 ATTCTTTTGGAAAGAATATAATTCATTTTTCTAATTTTTCATTTGCCTTCTCTATTAGTAAGGGA
1 ATTCTTTTGGAAAAAATATAATTCATTTTTCTAACTTTCCATTTGCCTTCTCTATTAATAAAGGA
5493523 ATAATCCT
66 ATAATCCT
5493531 TGTTTTCCTT
Statistics
Matches: 66, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
73 23 0.35
74 25 0.38
75 18 0.27
ACGTcount: A:0.31, C:0.15, G:0.10, T:0.45
Consensus pattern (75 bp):
ATTCTTTTGGAAAAAATATAATTCATTTTTCTAACTTTCCATTTGCCTTCTCTATTAATAAAGGA
ATAATCCTAG
Found at i:5506216 original size:24 final size:27
Alignment explanation
Indices: 5506181--5506231 Score: 81
Period size: 24 Copynumber: 2.0 Consensus size: 27
5506171 GACGGTTATC
5506181 TTATTAATGTTATTTA-AAT-TGAATG
1 TTATTAATGTTATTTATAATGTGAATG
5506206 TTATT-ATGTTATTTATAATGTGAATG
1 TTATTAATGTTATTTATAATGTGAATG
5506232 GATCGATGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
24 10 0.42
25 8 0.33
26 6 0.25
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (27 bp):
TTATTAATGTTATTTATAATGTGAATG
Found at i:5506240 original size:26 final size:24
Alignment explanation
Indices: 5506187--5506240 Score: 56
Period size: 24 Copynumber: 2.2 Consensus size: 24
5506177 TATCTTATTA
* *
5506187 ATGTTATTTAAATTGAATGTTATT
1 ATGTTATTTAAATTGAATGTGATG
5506211 ATGTTATTTATAATGTGAATG-GATCG
1 ATGTTATTTA-AAT-TGAATGTGAT-G
5506237 ATGT
1 ATGT
5506241 ATAAATATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
24 10 0.40
25 5 0.20
26 10 0.40
ACGTcount: A:0.31, C:0.02, G:0.19, T:0.48
Consensus pattern (24 bp):
ATGTTATTTAAATTGAATGTGATG
Found at i:5509518 original size:26 final size:26
Alignment explanation
Indices: 5509466--5509518 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
5509456 CACTAATATC
* *
5509466 GCAGCATAGCTGCCAGTAGTAATAAT
1 GCAGCAGAGCTGCCAGTAGTAAGAAT
*
5509492 GCAGCAGAGCTGCCAGTAGTCAGAAT
1 GCAGCAGAGCTGCCAGTAGTAAGAAT
5509518 G
1 G
5509519 GCTAAGAGCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.32, C:0.21, G:0.28, T:0.19
Consensus pattern (26 bp):
GCAGCAGAGCTGCCAGTAGTAAGAAT
Found at i:5509629 original size:32 final size:32
Alignment explanation
Indices: 5509593--5509834 Score: 197
Period size: 32 Copynumber: 7.6 Consensus size: 32
5509583 TAATCTGAGT
**
5509593 GGCACAAAGCCATCAGTAGTAGTGATATGATC
1 GGCACAAAGCCATCAGTAACAGTGATATGATC
* * *
5509625 GGCACACAA-CCATCAGTAAC-GATAACATTATC
1 GGCACA-AAGCCATCAGTAACAG-TGATATGATC
* * **
5509657 GACACAAAACCATCAGTAGTAGTGATATGATC
1 GGCACAAAGCCATCAGTAACAGTGATATGATC
* *
5509689 GGCACACAA-CCATCAGTAACAGTGAAATGATT
1 GGCACA-AAGCCATCAGTAACAGTGATATGATC
* * * * * *
5509721 GGCACACATCCTTCGGTAACAATAATATGATC
1 GGCACAAAGCCATCAGTAACAGTGATATGATC
* * *
5509753 AGTACAAAGCCATCAGTAACGGT-ACTATGATC
1 GGCACAAAGCCATCAGTAACAGTGA-TATGATC
* *
5509785 GGCACAAAGCCATCAGTAACGGT-ACTGTGATC
1 GGCACAAAGCCATCAGTAACAGTGA-TATGATC
*
5509817 GGTACAAAGCCATCAGTA
1 GGCACAAAGCCATCAGTA
5509835 GTATCGCAGC
Statistics
Matches: 168, Mismatches: 35, Indels: 14
0.77 0.16 0.06
Matches are distributed among these distances:
31 5 0.03
32 158 0.94
33 5 0.03
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.21
Consensus pattern (32 bp):
GGCACAAAGCCATCAGTAACAGTGATATGATC
Found at i:5509760 original size:96 final size:96
Alignment explanation
Indices: 5509593--5509804 Score: 241
Period size: 96 Copynumber: 2.2 Consensus size: 96
5509583 TAATCTGAGT
** * * *
5509593 GGCACAAAGCCATCAGTAGTAGTGATATGATCGGCACACAACCATCAGTAACGATAACATTATCG
1 GGCACAAAGCCATCAGTAACAGTGAAATGATCGGCACACAACCATCAGTAACAATAACATGATCG
**
5509658 ACACAAAACCATCAGTAGTAGTGA-TATGATC
66 ACACAAAACCATCAGTAACAGT-ACTATGATC
* * * * *
5509689 GGCACACAA-CCATCAGTAACAGTGAAATGATTGGCACACATCCTTCGGTAACAATAATATGATC
1 GGCACA-AAGCCATCAGTAACAGTGAAATGATCGGCACACAACCATCAGTAACAATAACATGATC
* * *
5509753 -AGTACAAAGCCATCAGTAACGGTACTATGATC
65 GA-CACAAAACCATCAGTAACAGTACTATGATC
5509785 GGCACAAAGCCATCAGTAAC
1 GGCACAAAGCCATCAGTAAC
5509805 GGTACTGTGA
Statistics
Matches: 97, Mismatches: 15, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
95 4 0.04
96 91 0.94
97 2 0.02
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.20
Consensus pattern (96 bp):
GGCACAAAGCCATCAGTAACAGTGAAATGATCGGCACACAACCATCAGTAACAATAACATGATCG
ACACAAAACCATCAGTAACAGTACTATGATC
Found at i:5509865 original size:26 final size:26
Alignment explanation
Indices: 5509836--5509907 Score: 99
Period size: 26 Copynumber: 2.8 Consensus size: 26
5509826 CCATCAGTAG
5509836 TATCGCAGCAAAGCTGCCAGCAACAA
1 TATCGCAGCAAAGCTGCCAGCAACAA
* * *
5509862 TATCACAGCAAAGCTGCGAGCAACAG
1 TATCGCAGCAAAGCTGCCAGCAACAA
* *
5509888 TATCGAAGCAAAGCTTCCAG
1 TATCGCAGCAAAGCTGCCAG
5509908 TAGTAGTATA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.38, C:0.28, G:0.21, T:0.14
Consensus pattern (26 bp):
TATCGCAGCAAAGCTGCCAGCAACAA
Found at i:5510033 original size:24 final size:23
Alignment explanation
Indices: 5510006--5510087 Score: 92
Period size: 24 Copynumber: 3.5 Consensus size: 23
5509996 CCATGTTTAG
*
5510006 AATCAGTCATTCAAATCATAGACA
1 AATCAGTCATTCAAA-CACAGACA
*
5510030 AATCAGTCATAGCAAACACAGACA
1 AATCAGTCAT-TCAAACACAGACA
* *
5510054 AATCAGTCATTTAACCACAGACA
1 AATCAGTCATTCAAACACAGACA
* *
5510077 AAACAATCATT
1 AATCAGTCATT
5510088 TGACCTCGAA
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
23 19 0.38
24 27 0.54
25 4 0.08
ACGTcount: A:0.48, C:0.23, G:0.09, T:0.21
Consensus pattern (23 bp):
AATCAGTCATTCAAACACAGACA
Found at i:5510162 original size:27 final size:27
Alignment explanation
Indices: 5510109--5510397 Score: 271
Period size: 27 Copynumber: 10.8 Consensus size: 27
5510099 GGCAAAAATA
5510109 GTCA-TTTACCC-ACCA-GGGCATTACG
1 GTCATTTTACCCTA-CAGGGGCATTACG
*
5510134 GTTATTTTACCCTACAGGGGCATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
* ** * *
5510161 GTAATTTTACAGTACACGGGTATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
* * *
5510188 GTCATTTTACCTTACAGGGCCATTATG
1 GTCATTTTACCCTACAGGGGCATTACG
* * *
5510215 GTTATTTTACCATACTGGGGCATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
** * **
5510242 GTCATTTTACCCTACAAAGGTATTATA
1 GTCATTTTACCCTACAGGGGCATTACG
* * *
5510269 GTTATTTCACCCTACAGGGGTATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
*
5510296 GTCATTTTACCCTACAGGGGCATTACA
1 GTCATTTTACCCTACAGGGGCATTACG
* * * *
5510323 GTTATTTTACTCTATAGGGGTATTA-G
1 GTCATTTTACCCTACAGGGGCATTACG
* * *
5510349 AGTCATTTTACCCTACTGGGGTAATACG
1 -GTCATTTTACCCTACAGGGGCATTACG
*
5510377 GTCATTTTACCCTATAGGGGC
1 GTCATTTTACCCTACAGGGGC
5510398 TTTTGCTGTT
Statistics
Matches: 210, Mismatches: 49, Indels: 8
0.79 0.18 0.03
Matches are distributed among these distances:
25 3 0.01
26 9 0.04
27 197 0.94
28 1 0.00
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.34
Consensus pattern (27 bp):
GTCATTTTACCCTACAGGGGCATTACG
Found at i:5510677 original size:27 final size:27
Alignment explanation
Indices: 5510635--5510694 Score: 104
Period size: 27 Copynumber: 2.2 Consensus size: 27
5510625 AACAATAGTG
5510635 ATTTTACCTTTCGAGGGTATTTTGGTC
1 ATTTTACCTTTCGAGGGTATTTTGGTC
5510662 ATTTTACCCTTT-GAGGGTATTTTGGTC
1 ATTTTA-CCTTTCGAGGGTATTTTGGTC
5510689 ATTTTA
1 ATTTTA
5510695 GGCCCATTAC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
27 27 0.84
28 5 0.16
ACGTcount: A:0.17, C:0.13, G:0.20, T:0.50
Consensus pattern (27 bp):
ATTTTACCTTTCGAGGGTATTTTGGTC
Found at i:5511414 original size:15 final size:16
Alignment explanation
Indices: 5511389--5511418 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
5511379 TTTGACCCAC
5511389 AGAGAAGAGAAGAGGG
1 AGAGAAGAGAAGAGGG
5511405 AGAG-AGAGAAGAGG
1 AGAGAAGAGAAGAGG
5511419 ATTCAATCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (16 bp):
AGAGAAGAGAAGAGGG
Found at i:5514281 original size:15 final size:16
Alignment explanation
Indices: 5514261--5514290 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5514251 TGGTGCCTTG
5514261 TTGAT-ATGTGTTAAT
1 TTGATAATGTGTTAAT
5514276 TTGATAATGTGTTAA
1 TTGATAATGTGTTAA
5514291 AGCATGTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.30, C:0.00, G:0.20, T:0.50
Consensus pattern (16 bp):
TTGATAATGTGTTAAT
Found at i:5518198 original size:20 final size:20
Alignment explanation
Indices: 5518160--5518202 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
5518150 AAATGAAGAA
* * *
5518160 GTGCCCCTGTTTGCTCTTCG
1 GTGCCCCTGTATACACTTCG
5518180 GTGCCCCTGTATACACTTCG
1 GTGCCCCTGTATACACTTCG
5518200 GTG
1 GTG
5518203 TCATTGTTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.07, C:0.33, G:0.26, T:0.35
Consensus pattern (20 bp):
GTGCCCCTGTATACACTTCG
Found at i:5518253 original size:60 final size:60
Alignment explanation
Indices: 5518160--5518426 Score: 178
Period size: 60 Copynumber: 4.5 Consensus size: 60
5518150 AAATGAAGAA
** * * * * * *
5518160 GTGCCCCTGTTTGCTCTTCGGTGCCCCTGTATACACTTCGGTGTCATTGTTTGCACAACT
1 GTGCCCCTGTTCACACTTTGGTACCCCTATATACACTTCGGTGTCACTATTTGCACAACT
* * * * *
5518220 GTGCCCCTGTTCATACTTTGGTACCCCTATATACACTTTGGTGTCCCTATTTGCACGATT
1 GTGCCCCTGTTCACACTTTGGTACCCCTATATACACTTCGGTGTCACTATTTGCACAACT
* * * * * * * *
5518280 GTGCCCTTGTTCGCACTTTGGTGCCCCTATGTACACCTT-AGTGTCCCTATTTGCACGATT
1 GTGCCCCTGTTCACACTTTGGTACCCCTATATACA-CTTCGGTGTCACTATTTGCACAACT
** * ** * * * * * * ***
5518340 GTGCCTTTGTTCACACTTCGGCGCACCTATATAAACTTCAGTATCCCTGTTTGCATGTC-
1 GTGCCCCTGTTCACACTTTGGTACCCCTATATACACTTCGGTGTCACTATTTGCACAACT
* *
5518399 GTGCCCCTGTTCGCACTTTGGTGCCCCT
1 GTGCCCCTGTTCACACTTTGGTACCCCT
5518427 GACTACACAT
Statistics
Matches: 168, Mismatches: 37, Indels: 5
0.80 0.18 0.02
Matches are distributed among these distances:
59 25 0.15
60 140 0.83
61 3 0.02
ACGTcount: A:0.14, C:0.30, G:0.19, T:0.36
Consensus pattern (60 bp):
GTGCCCCTGTTCACACTTTGGTACCCCTATATACACTTCGGTGTCACTATTTGCACAACT
Found at i:5522095 original size:42 final size:42
Alignment explanation
Indices: 5522048--5522280 Score: 393
Period size: 42 Copynumber: 5.6 Consensus size: 42
5522038 GAGCATTGGA
5522048 ATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGAT
1 ATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGAT
5522090 ATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGAT
1 ATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGAT
5522132 ATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGAT
1 ATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGAT
5522174 ATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG--
1 ATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGAT
* * *
5522214 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG--
1 ATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGAT
* *
5522254 ATATGTCCGGGTTAAGACCCGAAGGCA
1 ATATATCCGGGCTAAGACCCGAAGGCA
5522281 AATGTGTTTG
Statistics
Matches: 186, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
40 62 0.33
42 124 0.67
ACGTcount: A:0.27, C:0.20, G:0.28, T:0.24
Consensus pattern (42 bp):
ATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGAT
Found at i:5532343 original size:40 final size:40
Alignment explanation
Indices: 5532254--5532517 Score: 360
Period size: 40 Copynumber: 6.7 Consensus size: 40
5532244 TTGAATGATG
* *
5532254 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGAC-AATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAA-A
* * *
5532293 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
5532333 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
5532372 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
5532412 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
5532452 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
5532493 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
5532518 AACGAGGAGC
Statistics
Matches: 206, Mismatches: 12, Indels: 13
0.89 0.05 0.06
Matches are distributed among these distances:
39 53 0.26
40 143 0.69
41 10 0.05
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:5532535 original size:120 final size:118
Alignment explanation
Indices: 5532254--5532550 Score: 338
Period size: 119 Copynumber: 2.5 Consensus size: 118
5532244 TTGAATGATG
* *
5532254 TCCGGGCTAAGTCCCGAAGGC-TTGTG--CTAAGTGAC-AATATCCGGACTAAGAT-CCGAAGGC
1 TCCGGGCTAAGTCCCGAAGGCATT-TGAAC-GAGTGACTAA-ATCCGG-TTAA-ATCCCGAAGGC
* *
5532314 ATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAA
61 ATTTGTGCGAGATACTAAATCCGGGCTAAGCCCGAAGGCATTTGTGCGAATTACTAAA
* ** * *
5532372 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCATTTGAACGAGTGACTAAATCC-GGTTAAATCCCGAAGGCATTT
* *
5532437 GTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTATAA
65 GTGCGAGATACTAAATCCGGGCTAAG-CCCGAAGGCATTTGTGCGAATTACTA-AA
* * *
5532493 -CCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGCTATATCCGGTTAAATTCCGAAGG
1 TCCGGGCTAAGTCCCGAAGGCATTTGAACGAGTGA-CTAAATCCGGTTAAATCCCGAAGG
5532551 TACGTGATTT
Statistics
Matches: 153, Mismatches: 17, Indels: 17
0.82 0.09 0.09
Matches are distributed among these distances:
118 23 0.15
119 64 0.42
120 64 0.42
121 2 0.01
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (118 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGAACGAGTGACTAAATCCGGTTAAATCCCGAAGGCATTTG
TGCGAGATACTAAATCCGGGCTAAGCCCGAAGGCATTTGTGCGAATTACTAAA
Found at i:5535679 original size:19 final size:19
Alignment explanation
Indices: 5535655--5535740 Score: 61
Period size: 19 Copynumber: 4.4 Consensus size: 19
5535645 GATATTGAAT
5535655 ATATTTATAATTTTAATAA
1 ATATTTATAATTTTAATAA
* *
5535674 ATATTTATTATTAAATT-ATTA
1 ATATTTATAATT---TTAATAA
* *
5535695 ATATTTA-ATATAATTAATAT
1 ATATTTATA-AT-TTTAATAA
5535715 A-ATTTATAATTTTAATAA
1 ATATTTATAATTTTAATAA
5535733 AGTATTTA
1 A-TATTTA
5535741 ATATTTCAAT
Statistics
Matches: 50, Mismatches: 8, Indels: 17
0.67 0.11 0.23
Matches are distributed among these distances:
18 7 0.14
19 20 0.40
20 9 0.18
21 12 0.24
22 2 0.04
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (19 bp):
ATATTTATAATTTTAATAA
Found at i:5535717 original size:21 final size:20
Alignment explanation
Indices: 5535667--5535744 Score: 58
Period size: 21 Copynumber: 3.9 Consensus size: 20
5535657 ATTTATAATT
*
5535667 TTAATAAATATTTATTATTAAA
1 TTAATAAATATTTAATA-T-AA
*
5535689 TT-ATTAATATTTAATATAA
1 TTAATAAATATTTAATATAA
5535708 TTAATATAAT-TTATAAT-T--
1 TTAATA-AATATT-TAATATAA
5535726 TTAATAAAGTATTTAATAT
1 TTAATAAA-TATTTAATAT
5535745 TTCAATTTTA
Statistics
Matches: 47, Mismatches: 3, Indels: 15
0.72 0.05 0.23
Matches are distributed among these distances:
17 2 0.04
18 11 0.23
19 7 0.15
20 6 0.13
21 19 0.40
22 2 0.04
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (20 bp):
TTAATAAATATTTAATATAA
Found at i:5535780 original size:16 final size:16
Alignment explanation
Indices: 5535759--5535789 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
5535749 ATTTTATTTT
5535759 AATAATAATTTTAAAA
1 AATAATAATTTTAAAA
5535775 AATAATAATTTTAAA
1 AATAATAATTTTAAA
5535790 TATTTCTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
AATAATAATTTTAAAA
Found at i:5535783 original size:59 final size:59
Alignment explanation
Indices: 5535661--5535788 Score: 140
Period size: 59 Copynumber: 2.2 Consensus size: 59
5535651 GAATATATTT
* * *
5535661 ATAATTTTAATAAATATTTATTATTAAATTATTAATATTTAATATAATTAATATAATTT
1 ATAATTTTAATAAATATTTAATATTAAATTATTAATATTTAATATAATTAATATAAATA
*
5535720 ATAATTTTAATAAAGTATTTAATATTTCAATT-TT-AT-TTTAATAATAATTTTAA-A-AAATA
1 ATAATTTTAATAAA-TATTTAATA-TTAAATTATTAATATTTAAT-ATAA--TTAATATAAATA
5535779 ATAATTTTAA
1 ATAATTTTAA
5535789 ATATTTCTTC
Statistics
Matches: 60, Mismatches: 4, Indels: 10
0.81 0.05 0.14
Matches are distributed among these distances:
58 6 0.10
59 33 0.55
60 11 0.18
61 10 0.17
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.51
Consensus pattern (59 bp):
ATAATTTTAATAAATATTTAATATTAAATTATTAATATTTAATATAATTAATATAAATA
Found at i:5540618 original size:20 final size:19
Alignment explanation
Indices: 5540593--5540630 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
5540583 TACAACCAAT
5540593 ATGCCATATAGGCACTTTAA
1 ATGCCATATAGGCA-TTTAA
5540613 ATGCCATATAGGCATTTA
1 ATGCCATATAGGCATTTA
5540631 GTAACTAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (19 bp):
ATGCCATATAGGCATTTAA
Found at i:5542440 original size:361 final size:362
Alignment explanation
Indices: 5541775--5542497 Score: 1394
Period size: 361 Copynumber: 2.0 Consensus size: 362
5541765 AGCAGTTTGC
* *
5541775 ATACATATAGATACATCATTTATCACATAAAACCTTTTATTACATTATAATACATCCCAATTTTG
1 ATACATATAAATACATCATTTATCACATAAAACCTTTAATTACATTATAATACATCCCAATTTTG
5541840 TACTTACCATTTCATTCTCTTTTCTTACCCGTTTCATATGCATAGTACAAGCATAATCACAAATA
66 TACTTACCATTTCATTCTCTTTTCTTACCCGTTTCATATGCATAGTACAAGCATAATCACAAATA
*
5541905 TAACTCATATCCACAAGCTTGGCATAAGCCTAAGCACATCAACAACACTTGTTAGTTCAGTTAAA
131 TAACTCATATCCACAAGCTTAGCATAAGCCTAAGCACATCAACAACACTTGTTAGTTCAGTTAAA
5541970 CATGATTTATATGAATTTGACATGGATAACCATTGTACTTGAGAATAATTCAATTGGATATATCA
196 CATGATTTATATGAATTTGACATGGATAACCATTGTACTTGAGAATAATTCAATTGGATATATCA
* *
5542035 TCCATCTCAACATAACATATTTTCCATGTAGTTCACCATTTCAAAGTTTTTCATACATACATGTC
261 TCCATCTCAACATAACATATTTTCCATGTAGTTCACCATTTCAAAATGTTTCATACATACATGTC
5542100 TTGGTTTATATAGAACACTTACCATATTCTTGTAAAT
326 TTGGTTTATATAGAACACTTACCATATTCTTGTAAAT
5542137 ATACATATAAATACATCATTTATCACATAAAACCTTTAATTACATTATAATACATCCCAATTTTG
1 ATACATATAAATACATCATTTATCACATAAAACCTTTAATTACATTATAATACATCCCAATTTTG
5542202 TACTTACCATTTCATTCTCTTTTCTTACCCGTTTCATATGCATAGTA-AAGCATAATCACAAATA
66 TACTTACCATTTCATTCTCTTTTCTTACCCGTTTCATATGCATAGTACAAGCATAATCACAAATA
5542266 TAACTCATATCCACAAGCTTAGCATAAGCCTAAGCACATCAACAACACTTGTTAGTTCAGTTAAA
131 TAACTCATATCCACAAGCTTAGCATAAGCCTAAGCACATCAACAACACTTGTTAGTTCAGTTAAA
5542331 CATGATTTATATGAATTTGACATGGATAACCATTGTACTTGAGAATAATTCAATTGGATATATCA
196 CATGATTTATATGAATTTGACATGGATAACCATTGTACTTGAGAATAATTCAATTGGATATATCA
5542396 TCCATCTCAACATAACATATTTTCCATGTAGTTCACCATTTCAAAATGTTTCATACATACATGTC
261 TCCATCTCAACATAACATATTTTCCATGTAGTTCACCATTTCAAAATGTTTCATACATACATGTC
5542461 TTGGTTTATATAGAACACTTACCATATTCTTGTAAAT
326 TTGGTTTATATAGAACACTTACCATATTCTTGTAAAT
5542498 TCATGCTCGT
Statistics
Matches: 356, Mismatches: 5, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
361 246 0.69
362 110 0.31
ACGTcount: A:0.35, C:0.20, G:0.09, T:0.36
Consensus pattern (362 bp):
ATACATATAAATACATCATTTATCACATAAAACCTTTAATTACATTATAATACATCCCAATTTTG
TACTTACCATTTCATTCTCTTTTCTTACCCGTTTCATATGCATAGTACAAGCATAATCACAAATA
TAACTCATATCCACAAGCTTAGCATAAGCCTAAGCACATCAACAACACTTGTTAGTTCAGTTAAA
CATGATTTATATGAATTTGACATGGATAACCATTGTACTTGAGAATAATTCAATTGGATATATCA
TCCATCTCAACATAACATATTTTCCATGTAGTTCACCATTTCAAAATGTTTCATACATACATGTC
TTGGTTTATATAGAACACTTACCATATTCTTGTAAAT
Found at i:5545647 original size:17 final size:17
Alignment explanation
Indices: 5545627--5545659 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
5545617 TAGCAATCGA
5545627 AACGAAACAAAAATCAT
1 AACGAAACAAAAATCAT
*
5545644 AACGGAACAAAAATCA
1 AACGAAACAAAAATCA
5545660 ATTGTAAACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.64, C:0.18, G:0.09, T:0.09
Consensus pattern (17 bp):
AACGAAACAAAAATCAT
Found at i:5548804 original size:12 final size:12
Alignment explanation
Indices: 5548779--5548817 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
5548769 ACTCGCTTTT
* *
5548779 TTACTTACTCAC
1 TTACTTGCTTAC
*
5548791 TTACTTGTTTAC
1 TTACTTGCTTAC
5548803 TTACTTGCTTAC
1 TTACTTGCTTAC
5548815 TTA
1 TTA
5548818 AATAACTCAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.21, C:0.23, G:0.05, T:0.51
Consensus pattern (12 bp):
TTACTTGCTTAC
Found at i:5549141 original size:50 final size:50
Alignment explanation
Indices: 5549084--5549258 Score: 226
Period size: 50 Copynumber: 3.5 Consensus size: 50
5549074 TATCCCAAAT
** * *
5549084 ATGGTCTTACATGGGAGTTCTCATATCGGTGCTC-ATGCCATGTCCCATAC
1 ATGGTCTTACATGGGACCTCTCATATCGGTGC-CAACGCCATGTCCCAGAC
** * *
5549134 ATGGTCTTACGGGGGACCTCTCATCTCGGTTCCAACGCCATGTCCCAGAC
1 ATGGTCTTACATGGGACCTCTCATATCGGTGCCAACGCCATGTCCCAGAC
* * * *
5549184 ATAGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATATCCTAGAC
1 ATGGTCTTACATGGGACCTCTCATATCGGTGCCAACGCCATGTCCCAGAC
5549234 ATGGTCTTACATGGGACCTCTCATA
1 ATGGTCTTACATGGGACCTCTCATA
5549259 ATCTCAATAG
Statistics
Matches: 108, Mismatches: 16, Indels: 2
0.86 0.13 0.02
Matches are distributed among these distances:
49 1 0.01
50 107 0.99
ACGTcount: A:0.21, C:0.30, G:0.21, T:0.28
Consensus pattern (50 bp):
ATGGTCTTACATGGGACCTCTCATATCGGTGCCAACGCCATGTCCCAGAC
Found at i:5555840 original size:8 final size:8
Alignment explanation
Indices: 5555827--5555851 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
5555817 TTTTAAAACA
5555827 TATTTTAT
1 TATTTTAT
5555835 TATTTTAT
1 TATTTTAT
5555843 TATTTTAT
1 TATTTTAT
5555851 T
1 T
5555852 TAGTATATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TATTTTAT
Found at i:5558388 original size:50 final size:50
Alignment explanation
Indices: 5558329--5558961 Score: 815
Period size: 50 Copynumber: 12.7 Consensus size: 50
5558319 AATATGTGAG
*
5558329 CCATGTAAGACCATGTCTGGGACATGGCGTTGGCACTGAGATGAGAGGTC
1 CCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTC
*
5558379 CCATGTAAGACCATGTCTGGGACTTGGCGTTGGCACCGAGATGAGAGGTC
1 CCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTC
* * * *
5558429 CCATGTAAGATCATGTCTGCGATATAGCGTTGGCACCGAGATGAGAGGTC
1 CCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTC
* *
5558479 CCACGTAAGACCATGTTTGGGACATGGCGTTGGCACCGAGATGAGAGGTC
1 CCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTC
* ** *
5558529 CCATGTAAGACCATGTTTGGGACACAGCGTTGGCATCGAGATGAGAGGTC
1 CCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTC
* * *
5558579 CCATGTAAGAGCATGTTTGGGACATGGCATTGGCACCGAGATGAGAGGTC
1 CCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTC
* * *
5558629 TCATGTAAGACCATGTCTGGGACATGGCGTTGGCGCTGAGATGAGAGGTC
1 CCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTC
5558679 CC-TGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTC
1 CCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTC
* *
5558728 CCATGGAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTC
1 CCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTC
* * * * *
5558778 TCATGTAAGACTATGTTTGGGACGTGGCATTGGCACCGAGATGAGAGGTC
1 CCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTC
** ** * * * * **
5558828 CCCCGTAAGACCATGTCTTTGACATGGCATGGGCACTGATATGAGAACTC
1 CCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTC
* * * * * * * **
5558878 CCATGTAAGACCATATCTGGAATATGGCATTGGAAATAC-AGA--AAACATC
1 CCATGTAAGACCATGTCTGGGACATGGCGTTGG-CA-CCGAGATGAGAGGTC
*
5558927 CCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 CCATGTAAGACCATGTCTGGGACATGGCGTTGGCA
5558962 TGTTATTATC
Statistics
Matches: 509, Mismatches: 71, Indels: 8
0.87 0.12 0.01
Matches are distributed among these distances:
48 1 0.00
49 80 0.16
50 425 0.83
51 3 0.01
ACGTcount: A:0.26, C:0.21, G:0.31, T:0.22
Consensus pattern (50 bp):
CCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTC
Found at i:5558936 original size:249 final size:249
Alignment explanation
Indices: 5558333--5558961 Score: 717
Period size: 249 Copynumber: 2.5 Consensus size: 249
5558323 TGTGAGCCAT
* * * * ** *
5558333 GTAAGACCATGTCTGGGACATGGCGTTGGCACTGAGATGAGAGGTCCCATGTAAGACCATGTCTG
1 GTAAGACCATGTTTGGGACATGGCATGGGCACCGAGATGAGAACTCCCATGTAAGACCATATCTG
* * * * * * ** * * * *
5558398 GGACTTGGCGTTGG-CACCGAGATGAGAGGTCCCATGTAAGATCATGTCTGCGATATAGCGTTGG
66 GAACATGGCATTGGAAATC-AGA-GAAACATCCCATGTAAGACCATGTCTGGGACATGGCGTTGG
* * *
5558462 CACCGAGATGAGAGGTCCCACGTAAGACCATGTTTGGGACATGGCGTTGGCACCGAGATGAGAGG
129 CACCGAGATGAGAGGTCCCACGGAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
* * *
5558527 TCCCATGTAAGACCATGTTTGGGACACAGCGTTGGCATCGAGATGAGAGGTCCCAT
194 TCCCATGTAAGACCATGTTTGGGACACAGCATTGGCACCGAGATGAGAGGTCCCAC
* * ** * *
5558583 GTAAGAGCATGTTTGGGACATGGCATTGGCACCGAGATGAGAGGTCTCATGTAAGACCATGTCTG
1 GTAAGACCATGTTTGGGACATGGCATGGGCACCGAGATGAGAACTCCCATGTAAGACCATATCTG
* * *** * * **
5558648 GGACATGGCGTTGGCGCTGAGATGAGAGGTCCC-TGTAAGACCATGTCTGGGACATGGCGTTGGC
66 GAACATGGCATTGGAAATCAGA-GAAACATCCCATGTAAGACCATGTCTGGGACATGGCGTTGGC
*
5558712 ACCGAGATGAGAGGTCCCATGGAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGT
130 ACCGAGATGAGAGGTCCCACGGAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGT
* * *** *
5558777 CTCATGTAAGACTATGTTTGGGACGTGGCATTGGCACCGAGATGAGAGGTCCCCC
195 CCCATGTAAGACCATGTTTGGGACACAGCATTGGCACCGAGATGAGAGGTCCCAC
* * *
5558832 GTAAGACCATGTCTT-TGACATGGCATGGGCACTGATATGAGAACTCCCATGTAAGACCATATCT
1 GTAAGACCATGT-TTGGGACATGGCATGGGCACCGAGATGAGAACTCCCATGTAAGACCATATCT
* *
5558896 GGAATATGGCATTGGAAATACAGA-AAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGG
65 GGAACATGGCATTGGAAAT-CAGAGAAACATCCCATGTAAGACCATGTCTGGGACATGGCGTTGG
5558960 CA
129 CA
5558962 TGTTATTATC
Statistics
Matches: 328, Mismatches: 47, Indels: 9
0.85 0.12 0.02
Matches are distributed among these distances:
248 6 0.02
249 230 0.70
250 92 0.28
ACGTcount: A:0.26, C:0.20, G:0.32, T:0.22
Consensus pattern (249 bp):
GTAAGACCATGTTTGGGACATGGCATGGGCACCGAGATGAGAACTCCCATGTAAGACCATATCTG
GAACATGGCATTGGAAATCAGAGAAACATCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA
CCGAGATGAGAGGTCCCACGGAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTC
CCATGTAAGACCATGTTTGGGACACAGCATTGGCACCGAGATGAGAGGTCCCAC
Found at i:5559404 original size:17 final size:17
Alignment explanation
Indices: 5559382--5559415 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
5559372 GTCGAAATGA
5559382 ACATGATGATCTTTTCT
1 ACATGATGATCTTTTCT
5559399 ACATGATGATCTTTTCT
1 ACATGATGATCTTTTCT
5559416 GGATATTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.18, G:0.12, T:0.47
Consensus pattern (17 bp):
ACATGATGATCTTTTCT
Found at i:5563284 original size:50 final size:50
Alignment explanation
Indices: 5563222--5563504 Score: 300
Period size: 50 Copynumber: 5.7 Consensus size: 50
5563212 AATATGTAAG
*
5563222 CCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGATGAGAGGTC
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGATGAGAGGTC
* *
5563272 CCATGTAGGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTC
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGATGAGAGGTC
** * *
5563322 CCATGTAAGACCATGTCTGGGACATGGTGTTCGCACCCAGATGAGAGGTC
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGATGAGAGGTC
** * * * * * **
5563372 CCCCGTAAGACCATGTCTGGGAGATAGCATGGGCACCGATATGAGAAATC
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGATGAGAGGTC
* * * * ** * **
5563422 CTATGTAAGACCATATCTAGGATATGGCATTGGCAATACAGA--AAACATC
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCACCA-AGATGAGAGGTC
* *
5563471 CCATGTAAGACCATGTCTGGCACATGGCTTTGGC
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGC
5563505 TTTTTATTAT
Statistics
Matches: 192, Mismatches: 40, Indels: 3
0.82 0.17 0.01
Matches are distributed among these distances:
49 33 0.17
50 157 0.82
51 2 0.01
ACGTcount: A:0.28, C:0.23, G:0.28, T:0.22
Consensus pattern (50 bp):
CCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGATGAGAGGTC
Found at i:5565461 original size:50 final size:50
Alignment explanation
Indices: 5565404--5565567 Score: 229
Period size: 50 Copynumber: 3.3 Consensus size: 50
5565394 TTCCAGATAA
** * * *
5565404 GGTCTTACATGGGAGTTCTCATATCGGAGCCTATGCCATGTCCCAGACAT
1 GGTCTTACATGGGACCTCTCATCTCGGTGCCTACGCCATGTCCCAGACAT
** * *
5565454 GGTCTTACGGGGGACCTCTCATCTTGGTGCCAACGCCATGTCCCAGACAT
1 GGTCTTACATGGGACCTCTCATCTCGGTGCCTACGCCATGTCCCAGACAT
**
5565504 GGTCTTACATGGGACCTCTCATCTCGGTGCCTACGCCATGTCCCAGAGTT
1 GGTCTTACATGGGACCTCTCATCTCGGTGCCTACGCCATGTCCCAGACAT
5565554 GGTCTTACATGGGA
1 GGTCTTACATGGGA
5565568 TCTCATTCCC
Statistics
Matches: 99, Mismatches: 15, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
50 99 1.00
ACGTcount: A:0.19, C:0.29, G:0.26, T:0.27
Consensus pattern (50 bp):
GGTCTTACATGGGACCTCTCATCTCGGTGCCTACGCCATGTCCCAGACAT
Found at i:5579238 original size:40 final size:40
Alignment explanation
Indices: 5579194--5579455 Score: 337
Period size: 39 Copynumber: 6.7 Consensus size: 40
5579184 GCTCCTCGTT
* *
5579194 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
5579234 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
5579274 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
5579313 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
5579352 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* *
5579391 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGT-ATC-TCGCA
5579432 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
5579456 CATCATTCAA
Statistics
Matches: 205, Mismatches: 9, Indels: 17
0.89 0.04 0.07
Matches are distributed among these distances:
38 2 0.01
39 128 0.62
40 64 0.31
41 11 0.05
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:5586558 original size:83 final size:83
Alignment explanation
Indices: 5586419--5586584 Score: 314
Period size: 83 Copynumber: 2.0 Consensus size: 83
5586409 GCTGTCAGCA
5586419 TCTGCCTTTAAGGTAGACTTTACCTATTTCATAGTTTCCATGATTCAACTAGCCCTTTTAGCATA
1 TCTGCCTTTAAGGTAGACTTTACCTATTTCATAGTTTCCATGATTCAACTAGCCCTTTTAGCATA
5586484 AATAGCACAATTTATGAT
66 AATAGCACAATTTATGAT
*
5586502 TCTGCCTTTAAGGTAGACTTTACCTATTTCATAGTTTCCATGATTCAACTAGCCCTTTTTGCATA
1 TCTGCCTTTAAGGTAGACTTTACCTATTTCATAGTTTCCATGATTCAACTAGCCCTTTTAGCATA
*
5586567 AGTAGCACAATTTATGAT
66 AATAGCACAATTTATGAT
5586585 AGTGATTAAC
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
83 81 1.00
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.39
Consensus pattern (83 bp):
TCTGCCTTTAAGGTAGACTTTACCTATTTCATAGTTTCCATGATTCAACTAGCCCTTTTAGCATA
AATAGCACAATTTATGAT
Found at i:5587006 original size:113 final size:113
Alignment explanation
Indices: 5586844--5587070 Score: 427
Period size: 113 Copynumber: 2.0 Consensus size: 113
5586834 CAAAATCCCG
5586844 AGTCCGATAGCTGGAGAACCAAAATCTATAAAACAGAGGATCAAAGAAACGGAGTAAGCAATTTA
1 AGTCCGATAGCTGGAGAACCAAAATCTATAAAACAGAGGATCAAAGAAACGGAGTAAGCAATTTA
*
5586909 TGCTTAGTATGTTTTGAGCAAGGAATTCCAGCACAACAAAAGTATAGC
66 TGCTTAGTAAGTTTTGAGCAAGGAATTCCAGCACAACAAAAGTATAGC
*
5586957 AGTCCGATAGCTGGAGAACCAAAATCTATAAAATAGAGGATCAAAGAAACGGAGTAAGCAATTTA
1 AGTCCGATAGCTGGAGAACCAAAATCTATAAAACAGAGGATCAAAGAAACGGAGTAAGCAATTTA
*
5587022 TGCTTAGTAAGTTTTGAGCAAGGAATTCCAGCACAGCAAAAGTATAGC
66 TGCTTAGTAAGTTTTGAGCAAGGAATTCCAGCACAACAAAAGTATAGC
5587070 A
1 A
5587071 TTCATATAGC
Statistics
Matches: 111, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
113 111 1.00
ACGTcount: A:0.42, C:0.15, G:0.22, T:0.21
Consensus pattern (113 bp):
AGTCCGATAGCTGGAGAACCAAAATCTATAAAACAGAGGATCAAAGAAACGGAGTAAGCAATTTA
TGCTTAGTAAGTTTTGAGCAAGGAATTCCAGCACAACAAAAGTATAGC
Found at i:5587460 original size:79 final size:81
Alignment explanation
Indices: 5587359--5587543 Score: 218
Period size: 79 Copynumber: 2.3 Consensus size: 81
5587349 GCTACTCGTT
* * *
5587359 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAATTGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
5587422 GAATTTAGTAAC-TCGCA
64 GAATATAGTAACTTAGCA
* ** *
5587439 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGA
* *
5587503 ATATGGTCACTTAGCA
66 ATATAGTAACTTAGCA
5587519 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
5587544 CATCATTCAA
Statistics
Matches: 90, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
78 3 0.03
79 53 0.59
80 34 0.38
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGA
ATATAGTAACTTAGCA
Found at i:5587543 original size:40 final size:40
Alignment explanation
Indices: 5587340--5587543 Score: 220
Period size: 40 Copynumber: 5.1 Consensus size: 40
5587330 CGGAATTTAA
** *
5587340 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
5587380 CCGGTTATAGTAACTCGCACAATTGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
5587420 CCGAATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
5587459 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
5587499 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
5587539 CCGGA
1 CCGGA
5587544 CATCATTCAA
Statistics
Matches: 137, Mismatches: 20, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
38 2 0.01
39 32 0.23
40 91 0.66
41 12 0.09
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:5596285 original size:3 final size:3
Alignment explanation
Indices: 5596277--5596301 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
5596267 CTCACAGAAG
5596277 GAT GAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT G
5596302 GTTGTTATTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.36, T:0.32
Consensus pattern (3 bp):
GAT
Found at i:5596320 original size:15 final size:15
Alignment explanation
Indices: 5596302--5596331 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
5596292 GATGATGATG
5596302 GTTGTTATTGTTATT
1 GTTGTTATTGTTATT
5596317 GTTGTTATTGTTATT
1 GTTGTTATTGTTATT
5596332 ATTTTTATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.00, G:0.20, T:0.67
Consensus pattern (15 bp):
GTTGTTATTGTTATT
Found at i:5596333 original size:3 final size:3
Alignment explanation
Indices: 5596306--5596371 Score: 78
Period size: 3 Copynumber: 22.0 Consensus size: 3
5596296 ATGATGGTTG
* * * * * *
5596306 TTA TTG TTA TTG TTG TTA TTG TTA TTA TTT TTA TTA TTG TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
5596354 TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA
5596372 CCTGAACATG
Statistics
Matches: 53, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:5601370 original size:12 final size:12
Alignment explanation
Indices: 5601353--5601381 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
5601343 GATCAAAGTA
5601353 AAGGAAATGAAG
1 AAGGAAATGAAG
5601365 AAGGAAATGAAG
1 AAGGAAATGAAG
5601377 AAGGA
1 AAGGA
5601382 CGATTAAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.34, T:0.07
Consensus pattern (12 bp):
AAGGAAATGAAG
Found at i:5609921 original size:51 final size:52
Alignment explanation
Indices: 5609788--5609927 Score: 178
Period size: 51 Copynumber: 2.7 Consensus size: 52
5609778 GATGAACATG
* * *
5609788 TGTGTAGTACTGTGTGAAGGCTACTACATGAATC-AATAAATGATGGTCACA
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTATCGAATAAATGATGGTCACA
* * * * *
5609839 TGTGTAGTACTAAGTGAAGGCTACTATGTGTATCGAA-AAGCT-TTGGTCACT
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTATCGAATAA-ATGATGGTCACA
5609890 TGTGTAGTACTATGTGAAGGCTACTACGTGTATCGAAT
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTATCGAAT
5609928 GATAAAAGTA
Statistics
Matches: 76, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
51 73 0.96
52 3 0.04
ACGTcount: A:0.29, C:0.14, G:0.25, T:0.32
Consensus pattern (52 bp):
TGTGTAGTACTATGTGAAGGCTACTACGTGTATCGAATAAATGATGGTCACA
Found at i:5609948 original size:51 final size:50
Alignment explanation
Indices: 5609782--5609958 Score: 140
Period size: 51 Copynumber: 3.4 Consensus size: 50
5609772 GGTATCGATG
* * * *
5609782 AACATGTGTGTAGTACTGTGTGAAGGCTACTACATGAATC-AATAAATGATGGT
1 AACATG-G-GTAGTACTATGTGAAGGCTACTACGTGTATCGAAT-GAT-ATGGT
* * * * * * *
5609835 CACATGTGTAGTACTAAGTGAAGGCTACTATGTGTATCGAAAAGCTTTGGT
1 AACATGGGTAGTACTATGTGAAGGCTACTACGTGTATCG-AATGATATGGT
* * * **
5609886 CACTTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGAATGATAAAAGT
1 AACATGGGTAGTACTATGTGAAGGCTACTACGTGTATCGAATGAT-ATGGT
*
5609937 AACATGGGTAGTACTGTGTGAA
1 AACATGGGTAGTACTATGTGAA
5609959 AAACCCCAAA
Statistics
Matches: 98, Mismatches: 23, Indels: 8
0.76 0.18 0.06
Matches are distributed among these distances:
50 4 0.04
51 86 0.88
52 1 0.01
53 7 0.07
ACGTcount: A:0.32, C:0.12, G:0.25, T:0.31
Consensus pattern (50 bp):
AACATGGGTAGTACTATGTGAAGGCTACTACGTGTATCGAATGATATGGT
Found at i:5610186 original size:37 final size:38
Alignment explanation
Indices: 5610117--5610189 Score: 94
Period size: 37 Copynumber: 1.9 Consensus size: 38
5610107 ATGTGTGGAA
** **
5610117 TTGAATTGAATATTGACTTGAAAATGGCAAAGTGAATT
1 TTGAATTGAATAGAGACTTGAAAATGAAAAAGTGAATT
*
5610155 TTGAATTGAATAGAGA-TTGAAAGTGAAAAAGTGAA
1 TTGAATTGAATAGAGACTTGAAAATGAAAAAGTGAA
5610190 ATTATGAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
37 16 0.53
38 14 0.47
ACGTcount: A:0.44, C:0.03, G:0.23, T:0.30
Consensus pattern (38 bp):
TTGAATTGAATAGAGACTTGAAAATGAAAAAGTGAATT
Found at i:5619686 original size:25 final size:25
Alignment explanation
Indices: 5619657--5619721 Score: 94
Period size: 25 Copynumber: 2.6 Consensus size: 25
5619647 GACATACCAT
5619657 AGCTCGCATGAGCTTCCCGTTATTC
1 AGCTCGCATGAGCTTCCCGTTATTC
* *
5619682 AGCTCGCATGAGCTTCCTGTTATTT
1 AGCTCGCATGAGCTTCCCGTTATTC
* *
5619707 TGCTCGTATGAGCTT
1 AGCTCGCATGAGCTT
5619722 ACTAATTACA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.15, C:0.26, G:0.22, T:0.37
Consensus pattern (25 bp):
AGCTCGCATGAGCTTCCCGTTATTC
Found at i:5621837 original size:15 final size:15
Alignment explanation
Indices: 5621817--5621847 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
5621807 AGTATGCATA
5621817 TCAATAAATTAAGTC
1 TCAATAAATTAAGTC
5621832 TCAATAAATTAAGTC
1 TCAATAAATTAAGTC
5621847 T
1 T
5621848 GAGCATTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.45, C:0.13, G:0.06, T:0.35
Consensus pattern (15 bp):
TCAATAAATTAAGTC
Found at i:5622454 original size:20 final size:18
Alignment explanation
Indices: 5622407--5622455 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
5622397 CAAGATAAAC
5622407 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
5622424 ATTAAGA-TAATCACTTTAAT
1 ATTAA-ATTAAT-A-TTTAAT
5622444 ATTAAATTAATA
1 ATTAAATTAATA
5622456 AAATACTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
17 8 0.30
18 1 0.04
19 3 0.11
20 15 0.56
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:5624451 original size:12 final size:12
Alignment explanation
Indices: 5624434--5624460 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
5624424 TTCGTGAATT
5624434 AAAAAAAAAGAG
1 AAAAAAAAAGAG
5624446 AAAAAAAAAGAG
1 AAAAAAAAAGAG
5624458 AAA
1 AAA
5624461 GTGTTTATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAGAG
Found at i:5626553 original size:19 final size:19
Alignment explanation
Indices: 5626509--5626553 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
5626499 ATGAAAACTC
5626509 AAAAGAAAAGAAAAATGAGA
1 AAAAG-AAAGAAAAATGAGA
*
5626529 AGAAGAAAGAAAAATTGA-A
1 AAAAGAAAGAAAAA-TGAGA
5626548 AAAAGA
1 AAAAGA
5626554 GAGTGAAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.73, C:0.00, G:0.20, T:0.07
Consensus pattern (19 bp):
AAAAGAAAGAAAAATGAGA
Found at i:5633994 original size:171 final size:171
Alignment explanation
Indices: 5633704--5634021 Score: 503
Period size: 171 Copynumber: 1.9 Consensus size: 171
5633694 GAATACCACC
*
5633704 TTTTTTCCTTTATATGCTTATAAACACAAGGTTCATCAACGTTTGGCTCAAATCCAAAAGTCTCG
1 TTTTGTCCTTTATATGCTTATAAACACAAGGTTCATCAACGTTTGGCTCAAATCCAAAAGTCTCG
* * *
5633769 AGTGTTTGATCAATTTTTTTATTCAATGAGCGAGACGCCTGCTTAAGTCCATAAATGGATCTTAG
66 AGTGTTTGATCAAATCTTTTATTCAATGAGCGAGACGCCTGCTTAAGACCATAAATGGATCTTAG
5633834 CAGTTTGCAAACTTTCTATCCTTTATTCACTTATAAAAAAA
131 CAGTTTGCAAACTTTCTATCCTTTATTCACTTATAAAAAAA
* * * * * *
5633875 TTTTGTCCTTTATATGCTTATAAACACAAGGTTCATCAATGTTTTGTTCATATCTAAAAGTCTTG
1 TTTTGTCCTTTATATGCTTATAAACACAAGGTTCATCAACGTTTGGCTCAAATCCAAAAGTCTCG
* * *
5633940 A-TCGTTTGATCAAATCTTTTATTCCATGAGCGTGATGCCTGCTTAAGACCATAAATGGATCTTA
66 AGT-GTTTGATCAAATCTTTTATTCAATGAGCGAGACGCCTGCTTAAGACCATAAATGGATCTTA
5634004 GCAGTTTGCAAACTTTCT
130 GCAGTTTGCAAACTTTCT
5634022 GCACTTTTCC
Statistics
Matches: 133, Mismatches: 13, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
170 1 0.01
171 132 0.99
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (171 bp):
TTTTGTCCTTTATATGCTTATAAACACAAGGTTCATCAACGTTTGGCTCAAATCCAAAAGTCTCG
AGTGTTTGATCAAATCTTTTATTCAATGAGCGAGACGCCTGCTTAAGACCATAAATGGATCTTAG
CAGTTTGCAAACTTTCTATCCTTTATTCACTTATAAAAAAA
Found at i:5634327 original size:15 final size:15
Alignment explanation
Indices: 5634307--5634335 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
5634297 TCCTTTCCTC
5634307 ATGGGTTTAATCCCT
1 ATGGGTTTAATCCCT
5634322 ATGGGTTTAATCCC
1 ATGGGTTTAATCCC
5634336 AATCGATAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (15 bp):
ATGGGTTTAATCCCT
Found at i:5638726 original size:39 final size:39
Alignment explanation
Indices: 5638672--5638751 Score: 135
Period size: 39 Copynumber: 2.1 Consensus size: 39
5638662 CAACTTTCTA
5638672 TTGAATTCAAGTGTATGTAAATAATGACCCA-AGACTCTC
1 TTGAATTCAAGTGTATGTAAATAATGACCCAGAG-CTCTC
*
5638711 TTGAATTCCAGTGTATGTAAATAATGACCCAGAGCTCTC
1 TTGAATTCAAGTGTATGTAAATAATGACCCAGAGCTCTC
5638750 TT
1 TT
5638752 TATATAGGAA
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
39 37 0.95
40 2 0.05
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.33
Consensus pattern (39 bp):
TTGAATTCAAGTGTATGTAAATAATGACCCAGAGCTCTC
Found at i:5638910 original size:62 final size:59
Alignment explanation
Indices: 5638804--5638920 Score: 171
Period size: 62 Copynumber: 1.9 Consensus size: 59
5638794 ATCACTTTAA
* * *
5638804 TATTAAATTAATATAATATTTACCAAGATAAATATTAGATTAAATTTAATATTAAATTT
1 TATTAAAATAATATAATATTTACCAAGATAAACATTAAATTAAATTTAATATTAAATTT
*
5638863 TATTAAAATAATATAATGTTTATCTACAAGATAAACATTAAATTAAATTTAATATTAA
1 TATTAAAATAATATAATATTTA-C--CAAGATAAACATTAAATTAAATTTAATATTAA
5638921 GATAATCACT
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
59 20 0.39
60 1 0.02
62 30 0.59
ACGTcount: A:0.50, C:0.04, G:0.03, T:0.42
Consensus pattern (59 bp):
TATTAAAATAATATAATATTTACCAAGATAAACATTAAATTAAATTTAATATTAAATTT
Found at i:5638946 original size:20 final size:18
Alignment explanation
Indices: 5638899--5639005 Score: 60
Period size: 20 Copynumber: 5.8 Consensus size: 18
5638889 CAAGATAAAC
5638899 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
5638916 ATTAAGA-TAATCACTTTAAT
1 ATTAA-ATTAAT-A-TTTAAT
** *
5638936 ATTAAATTAATAAAATACT
1 ATTAAATTAAT-ATTTAAT
* *
5638955 ATTTAGATAAATA-TTAA-
1 A-TTAAATTAATATTTAAT
*
5638972 ATTAAATTTAATATTAAACT
1 ATTAAA-TTAATATTTAA-T
*
5638992 ATTAAAATAATATT
1 ATTAAATTAATATT
5639006 ATTTCTGGAA
Statistics
Matches: 68, Mismatches: 12, Indels: 18
0.69 0.12 0.18
Matches are distributed among these distances:
16 4 0.06
17 14 0.21
18 6 0.09
19 14 0.21
20 30 0.44
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:5638993 original size:37 final size:37
Alignment explanation
Indices: 5638891--5638994 Score: 89
Period size: 37 Copynumber: 3.0 Consensus size: 37
5638881 TTTATCTACA
* *
5638891 AGATAAACATTAAATTAAATTTAATATT-AA-GA--T
1 AGATAAATATTAAATTAAATTTAATATTAAACTATTT
* * *
5638924 A-ATCACT-TTAATATTAAA-TTAATA-AAATACTATTT
1 AGATAAATATTAA-ATTAAATTTAATATTAA-ACTATTT
5638959 AGATAAATATTAAATTAAATTTAATATTAAACTATT
1 AGATAAATATTAAATTAAATTTAATATTAAACTATT
5638995 AAAATAATAT
Statistics
Matches: 53, Mismatches: 8, Indels: 16
0.69 0.10 0.21
Matches are distributed among these distances:
31 11 0.21
32 10 0.19
33 2 0.04
35 2 0.04
36 10 0.19
37 16 0.30
38 2 0.04
ACGTcount: A:0.52, C:0.05, G:0.03, T:0.40
Consensus pattern (37 bp):
AGATAAATATTAAATTAAATTTAATATTAAACTATTT
Found at i:5647744 original size:19 final size:18
Alignment explanation
Indices: 5647718--5647761 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
5647708 ATGCTTTAGG
*
5647718 TTAATTAATTATA-TTTAA
1 TTAATTAAGTA-AGTTTAA
5647736 TTAAGTTAAGTAAGTTTAA
1 TTAA-TTAAGTAAGTTTAA
5647755 TTAATTA
1 TTAATTA
5647762 TTTATCTAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 8 0.35
19 15 0.65
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (18 bp):
TTAATTAAGTAAGTTTAA
Found at i:5650916 original size:22 final size:23
Alignment explanation
Indices: 5650865--5650917 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 23
5650855 TTTTTATACA
* *
5650865 ATTATAATTATAATTTTAGTTAT
1 ATTATAATTAAAATTTTAATTAT
*
5650888 ATT-TAATTAAAATTTTAATTGT
1 ATTATAATTAAAATTTTAATTAT
5650910 -TTATAATT
1 ATTATAATT
5650918 CAGTACAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 2 0.08
22 21 0.81
23 3 0.12
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.57
Consensus pattern (23 bp):
ATTATAATTAAAATTTTAATTAT
Found at i:5653478 original size:17 final size:18
Alignment explanation
Indices: 5653456--5653490 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
5653446 TTTTTTATAA
*
5653456 TATTTTTTAATA-ACTTT
1 TATTTTATAATAGACTTT
5653473 TATTTTATAATAGACTTT
1 TATTTTATAATAGACTTT
5653491 CAAAAGTCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.31, C:0.06, G:0.03, T:0.60
Consensus pattern (18 bp):
TATTTTATAATAGACTTT
Found at i:5675210 original size:44 final size:44
Alignment explanation
Indices: 5675089--5675377 Score: 145
Period size: 44 Copynumber: 6.3 Consensus size: 44
5675079 TCCCTAAGCA
* *** * *
5675089 ACAGCGGAGCAGATCGAAGCCAGAAACCTTATCTCCCTGAGATT
1 ACAGCGGAGCAGATTGAAAATAAAAATCTTATCTCCCTGAGATT
** ** *
5675133 ACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATT
1 ACAGCGGAGCAGATTGAAAATAAAAATCTTATCTCCCTGAGATT
* * * * *
5675177 ATAGTGGAGCGGATT-AAAATAAAAGATCTTATCTCTCT-AAAGTT
1 ACAGCGGAGCAGATTGAAAATAAAA-ATCTTATCTCCCTGAGA-TT
* ** *
5675221 ACAGTGGAGTAGATCGCATCAGATTGAAACCAAAAATCTTATCTCCCTGATATT
1 ACA---GCG--GA--G---CAGATTGAAAATAAAAATCTTATCTCCCTGAGATT
** ** *
5675275 ACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATT
1 ACAGCGGAGCAGATTGAAAATAAAAATCTTATCTCCCTGAGATT
* * * * *
5675319 ACAGTGGAACGGATT-AAAATAAAGGATCTTATCTCTCTGA-AGTT
1 ACAGCGGAGCAGATTGAAAATAAA-AATCTTATCTCCCTGAGA-TT
*
5675363 ACAGCGGAGTAGATT
1 ACAGCGGAGCAGATT
5675378 ACATCAGATT
Statistics
Matches: 186, Mismatches: 43, Indels: 32
0.71 0.16 0.12
Matches are distributed among these distances:
43 12 0.06
44 133 0.72
47 3 0.02
49 4 0.02
51 3 0.02
54 22 0.12
55 9 0.05
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26
Consensus pattern (44 bp):
ACAGCGGAGCAGATTGAAAATAAAAATCTTATCTCCCTGAGATT
Found at i:5675354 original size:142 final size:142
Alignment explanation
Indices: 5675098--5675425 Score: 512
Period size: 142 Copynumber: 2.3 Consensus size: 142
5675088 AACAGCGGAG
* *
5675098 CAGATCGAAGCCAGAAACCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCT
1 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCT
* * *
5675163 ATCTCCCTGAGATTATAGTGGAGCGGATTAAAATAAAAGATCTTATCTCTCTAAAGTTACAGTGG
66 ATCTCCCTGAGATTACAGTGGAACGGATTAAAATAAAAGATCTTATCTCTCTAAAGTTACAGCGG
*
5675228 AGTAGATCGCAT
131 AGTAGATCACAT
* * *
5675240 CAGATTGAAACCAAAAATCTTATCTCCCTGATATTACAGCGGAGCAGATTGAAGCTAGTAATCCT
1 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCT
* *
5675305 ATCTCCCTGAGATTACAGTGGAACGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGCGG
66 ATCTCCCTGAGATTACAGTGGAACGGATTAAAATAAAAGATCTTATCTCTCTAAAGTTACAGCGG
*
5675370 AGTAGATTACAT
131 AGTAGATCACAT
* * * *
5675382 CAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAG
1 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAG
5675426 TGGATTAAAA
Statistics
Matches: 167, Mismatches: 19, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
142 167 1.00
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (142 bp):
CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCT
ATCTCCCTGAGATTACAGTGGAACGGATTAAAATAAAAGATCTTATCTCTCTAAAGTTACAGCGG
AGTAGATCACAT
Found at i:5675378 original size:44 final size:44
Alignment explanation
Indices: 5675330--5675647 Score: 153
Period size: 44 Copynumber: 6.8 Consensus size: 44
5675320 CAGTGGAACG
5675330 GATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGCGGAGTA
1 GATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGCGGAGTA
* * * * *
5675374 GATTACATCAGATTGAAGCTAGTAATCCTATCTCCCTG-AGATTACAGTGGAGTG
1 GATTA-A--A-A-T-AA---AG-GATCTTATCTCTCTGAAG-TTACAGCGGAGTA
*
5675428 GATTAAAATAAAGGATTTTATCTCTCTGAAGTTACAGCGGAGTA
1 GATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGCGGAGTA
* * * * * *
5675472 GATCGTATCAGATTGAAGCTAGTAATCCTATCTCCCTG-AGATTACAGTGGAGCA
1 GAT--TA--A-AAT-AA---AG-GATCTTATCTCTCTGAAG-TTACAGCGGAGTA
* * *
5675526 GATTAAAGTAAAGGATCTTATCTCTCTGAAGTTACAACGGAGCA
1 GATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGCGGAGTA
** * * **
5675570 GATTGAAGCT--AGTAATCCTATCTC-CTTG-AGATTACAAAGGAGTA
1 GATT-AAAATAAAG-GATCTTATCTCTC-TGAAG-TTACAGCGGAGTA
* *
5675614 GATTAAGATAAAGGATTTTATCTCTCTGAAGTTA
1 GATTAAAATAAAGGATCTTATCTCTCTGAAGTTA
5675648 TAGTAGAGTA
Statistics
Matches: 208, Mismatches: 34, Indels: 64
0.68 0.11 0.21
Matches are distributed among these distances:
43 9 0.04
44 96 0.46
45 17 0.08
46 2 0.01
47 1 0.00
48 6 0.03
49 6 0.03
50 6 0.03
51 1 0.00
52 2 0.01
53 9 0.04
54 53 0.25
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.30
Consensus pattern (44 bp):
GATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGCGGAGTA
Found at i:5675397 original size:98 final size:95
Alignment explanation
Indices: 5675284--5675647 Score: 508
Period size: 98 Copynumber: 3.8 Consensus size: 95
5675274 TACAGCGGAG
* *
5675284 CAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAACGGATTAAAATAAAGGATCTT
1 CAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCAGATTAAAATAAAGGATCTT
5675349 ATCTCTCTGAAGTTACAGCGGAGTAGATTACAT
66 ATCTCTCTGAAGTTACAGCGGAGTAGA-T--AT
** *
5675382 CAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGTGGATTAAAATAAAGGATTTT
1 CAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCAGATTAAAATAAAGGATCTT
5675447 ATCTCTCTGAAGTTACAGCGGAGTAGATCGTAT
66 ATCTCTCTGAAGTTACAGCGGAGTAGA---TAT
*
5675480 CAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCAGATTAAAGTAAAGGATCTT
1 CAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCAGATTAAAATAAAGGATCTT
*
5675545 ATCTCTCTGAAGTTACAAC-G-G-AG----
66 ATCTCTCTGAAGTTACAGCGGAGTAGATAT
* ** * * *
5675568 CAGATTGAAGCTAGTAATCCTATCTCCTTGAGATTACAAAGGAGTAGATTAAGATAAAGGATTTT
1 CAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCAGATTAAAATAAAGGATCTT
5675633 ATCTCTCTGAAGTTA
66 ATCTCTCTGAAGTTA
5675648 TAGTAGAGTA
Statistics
Matches: 248, Mismatches: 16, Indels: 14
0.89 0.06 0.05
Matches are distributed among these distances:
88 73 0.29
95 2 0.01
96 1 0.00
97 1 0.00
98 170 0.69
100 1 0.00
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30
Consensus pattern (95 bp):
CAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCAGATTAAAATAAAGGATCTT
ATCTCTCTGAAGTTACAGCGGAGTAGATAT
Found at i:5675589 original size:88 final size:88
Alignment explanation
Indices: 5675480--5675647 Score: 275
Period size: 88 Copynumber: 1.9 Consensus size: 88
5675470 TAGATCGTAT
**
5675480 CAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCAGATTAA-AGTAAAGGATCT
1 CAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAAAGGAGCAGATTAAGA-TAAAGGATCT
5675544 TATCTCTCTGAAGTTACAACGGAG
65 TATCTCTCTGAAGTTACAACGGAG
* * *
5675568 CAGATTGAAGCTAGTAATCCTATCTCCTTGAGATTACAAAGGAGTAGATTAAGATAAAGGATTTT
1 CAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAAAGGAGCAGATTAAGATAAAGGATCTT
5675633 ATCTCTCTGAAGTTA
66 ATCTCTCTGAAGTTA
5675648 TAGTAGAGTA
Statistics
Matches: 74, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
88 73 0.99
89 1 0.01
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (88 bp):
CAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAAAGGAGCAGATTAAGATAAAGGATCTT
ATCTCTCTGAAGTTACAACGGAG
Found at i:5675614 original size:240 final size:239
Alignment explanation
Indices: 5675142--5675618 Score: 588
Period size: 240 Copynumber: 2.0 Consensus size: 239
5675132 TACAGCGGAG
*
5675142 CAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTATAGTGGAGCGGATTAAAATAAAAGATCTT
1 CAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAAGATCTT
* * *
5675207 ATCTCTCTAAAGTTACAGTGGAGTAGATCGCATCAGATTGAAACCAAAAATCTTATCTCCCTGAT
66 ATCTCTCTAAAGTTACAGCGGAGTAGATCGCATCAGATTGAAACCAAAAATCCTATCTCCCTGAG
* ** *
5675272 ATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAACGGATTAAA
131 ATTACAGCGGAGCAGATTAAAGCTAGTAATCCTATCTCCCTGAGATTACAACGGAACAGATTAAA
* * **
5675337 ATAAAGGATCTTATCTCTCTGAAGTTACAGCGGAGTAGATTACAT
196 AT-AAGAATCCTATCTCTCTGAAGTTACAAAGGAGTAGATTACAT
* * *
5675382 CAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGTGGATTAAAATAAAGGATTTT
1 CAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAAGATCTT
* * * * **
5675447 ATCTCTCTGAAGTTACAGCGGAGTAGATCGTATCAGATTGAAGCTAGTAATCCTATCTCCCTGAG
66 ATCTCTCTAAAGTTACAGCGGAGTAGATCGCATCAGATTGAAACCAAAAATCCTATCTCCCTGAG
* * * * *
5675512 ATTACAGTGGAGCAGATTAAAG-TAAAG-GATCTTATCTCTCTGA-AGTTACAACGGAGCAGATT
131 ATTACAGCGGAGCAGATTAAAGCT--AGTAATCCTATCTCCCTGAGA-TTACAACGGAACAGATT
**
5675574 GAAGCT-AGTAATCCTATCTC-CTTG-AGATTACAAAGGAGTAGATTA
193 -AAAATAAG-AATCCTATCTCTC-TGAAG-TTACAAAGGAGTAGATTA
5675619 AGATAAAGGA
Statistics
Matches: 202, Mismatches: 28, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
239 7 0.03
240 190 0.94
241 5 0.02
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.29
Consensus pattern (239 bp):
CAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAAGATCTT
ATCTCTCTAAAGTTACAGCGGAGTAGATCGCATCAGATTGAAACCAAAAATCCTATCTCCCTGAG
ATTACAGCGGAGCAGATTAAAGCTAGTAATCCTATCTCCCTGAGATTACAACGGAACAGATTAAA
ATAAGAATCCTATCTCTCTGAAGTTACAAAGGAGTAGATTACAT
Found at i:5677261 original size:25 final size:28
Alignment explanation
Indices: 5677221--5677279 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 28
5677211 TAATATTAAT
5677221 TTATTATTATTTGTT-ATTTTC-ATTA-
1 TTATTATTATTTGTTAATTTTCGATTAC
5677246 TTATTA-TATTTGGTTACATTTTCGATTAC
1 TTATTATTATTT-GTTA-ATTTTCGATTAC
5677275 TTATT
1 TTATT
5677280 CTTAAATTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
24 5 0.17
25 9 0.31
27 6 0.21
28 4 0.14
29 5 0.17
ACGTcount: A:0.24, C:0.07, G:0.07, T:0.63
Consensus pattern (28 bp):
TTATTATTATTTGTTAATTTTCGATTAC
Found at i:5677358 original size:17 final size:18
Alignment explanation
Indices: 5677336--5677370 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
5677326 TTTTTTATAA
*
5677336 TATTTTTTAATA-ACTTT
1 TATTTTATAATAGACTTT
5677353 TATTTTATAATAGACTTT
1 TATTTTATAATAGACTTT
5677371 CAAAAGCCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.31, C:0.06, G:0.03, T:0.60
Consensus pattern (18 bp):
TATTTTATAATAGACTTT
Found at i:5679603 original size:22 final size:22
Alignment explanation
Indices: 5679560--5679602 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
5679550 TAAAATGCAG
**
5679560 GTACCGATATTTTGGGAAAAAT
1 GTACCGATATTTTAAGAAAAAT
5679582 GTACCGATATTTGTAAGAAAA
1 GTACCGATATTT-TAAGAAAA
5679603 TCGGTACCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.40, C:0.09, G:0.21, T:0.30
Consensus pattern (22 bp):
GTACCGATATTTTAAGAAAAAT
Found at i:5681344 original size:18 final size:18
Alignment explanation
Indices: 5681302--5681344 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
5681292 GCCCATTCCG
*
5681302 AAGTATATATATATACAT
1 AAGTATGTATATATACAT
5681320 ATA-TATGTATATATACAT
1 A-AGTATGTATATATACAT
5681338 AAGTATG
1 AAGTATG
5681345 CCCATTCGTG
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 1 0.05
18 20 0.91
19 1 0.05
ACGTcount: A:0.47, C:0.05, G:0.09, T:0.40
Consensus pattern (18 bp):
AAGTATGTATATATACAT
Found at i:5681950 original size:27 final size:28
Alignment explanation
Indices: 5681812--5681937 Score: 200
Period size: 28 Copynumber: 4.5 Consensus size: 28
5681802 TAAATTGTAC
* *
5681812 AGCACTAAGTGTGCAAGCTTGATTATGT
1 AGCACTAAGTGTGCGAGCTTGATTATAT
*
5681840 AGCACTAAGTGTGCGAGCTTGATTATGT
1 AGCACTAAGTGTGCGAGCTTGATTATAT
*
5681868 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGAGCTTGATTATAT
5681896 AGCACTAAGTGTGCGAG-TTGATTATAT
1 AGCACTAAGTGTGCGAGCTTGATTATAT
*
5681923 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
5681938 GACTTAATAT
Statistics
Matches: 94, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
27 24 0.26
28 70 0.74
ACGTcount: A:0.27, C:0.13, G:0.28, T:0.32
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGCTTGATTATAT
Found at i:5683713 original size:43 final size:43
Alignment explanation
Indices: 5683652--5683735 Score: 150
Period size: 43 Copynumber: 2.0 Consensus size: 43
5683642 AATATAAGAA
5683652 AGGCATACACTCGGAACATAGGATAGGGGTTTAGGCTATTCTT
1 AGGCATACACTCGGAACATAGGATAGGGGTTTAGGCTATTCTT
* *
5683695 AGGCATACACTTGGAACATAGGATAGGGGTTTAGGTTATTC
1 AGGCATACACTCGGAACATAGGATAGGGGTTTAGGCTATTC
5683736 CTAAGCTCCT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.29, C:0.14, G:0.29, T:0.29
Consensus pattern (43 bp):
AGGCATACACTCGGAACATAGGATAGGGGTTTAGGCTATTCTT
Found at i:5688072 original size:18 final size:19
Alignment explanation
Indices: 5688038--5688073 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
5688028 AATTTGGATT
*
5688038 AATTTAATAGTTTTAATTA
1 AATTTAATAGTTATAATTA
5688057 AATTTAAT-GTTATAATT
1 AATTTAATAGTTATAATT
5688074 TGTGTGAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.53
Consensus pattern (19 bp):
AATTTAATAGTTATAATTA
Found at i:5690625 original size:21 final size:22
Alignment explanation
Indices: 5690572--5690627 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 22
5690562 GTGTCATAGT
* *
5690572 CACACGGTCGTGTGCCTACTTT
1 CACACGGGCGTGTGCCTACTTC
5690594 CACACGGGCGTGTGCCT-CTTC
1 CACACGGGCGTGTGCCTACTTC
* *
5690615 CATATGGGCGTGT
1 CACACGGGCGTGT
5690628 TGACCCCACA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
21 14 0.47
22 16 0.53
ACGTcount: A:0.12, C:0.30, G:0.29, T:0.29
Consensus pattern (22 bp):
CACACGGGCGTGTGCCTACTTC
Found at i:5694141 original size:24 final size:22
Alignment explanation
Indices: 5694105--5694149 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
5694095 ACGAGCTGTC
5694105 CACACGGCTATGTGTGCCTCCTTT
1 CACACGGCTA--TGTGCCTCCTTT
5694129 CACACGAGC-ATGTGCCTCCTT
1 CACACG-GCTATGTGCCTCCTT
5694150 CATATGTGCG
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 11 0.55
24 7 0.35
25 2 0.10
ACGTcount: A:0.16, C:0.36, G:0.20, T:0.29
Consensus pattern (22 bp):
CACACGGCTATGTGCCTCCTTT
Found at i:5694941 original size:12 final size:11
Alignment explanation
Indices: 5694933--5694963 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
5694923 GCTTCTTACA
5694933 TTTTCTCTTAG
1 TTTTCTCTTAG
*
5694944 TTTTCCCTTAG
1 TTTTCTCTTAG
5694955 TTTTCTCTT
1 TTTTCTCTT
5694964 TCAGGTACTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.06, C:0.23, G:0.06, T:0.65
Consensus pattern (11 bp):
TTTTCTCTTAG
Found at i:5697726 original size:25 final size:25
Alignment explanation
Indices: 5697698--5697751 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
5697688 TGCTTACTCA
*
5697698 AGCTATAGATCAATATGCTCTCACG
1 AGCTATAAATCAATATGCTCTCACG
** *
5697723 AGCTATAAATCGGTATGCTCTTACG
1 AGCTATAAATCAATATGCTCTCACG
5697748 AGCT
1 AGCT
5697752 GTGGGTAGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.30
Consensus pattern (25 bp):
AGCTATAAATCAATATGCTCTCACG
Found at i:5700001 original size:16 final size:16
Alignment explanation
Indices: 5699980--5700022 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
5699970 CTGAGTTTAG
5699980 TTTTGTTTGATGGAAT
1 TTTTGTTTGATGGAAT
* *
5699996 TTTTGTTT-TTTGAAT
1 TTTTGTTTGATGGAAT
5700011 TTTTGGTTTGAT
1 TTTT-GTTTGAT
5700023 TTGTTATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
15 9 0.41
16 12 0.55
17 1 0.05
ACGTcount: A:0.14, C:0.00, G:0.21, T:0.65
Consensus pattern (16 bp):
TTTTGTTTGATGGAAT
Found at i:5704489 original size:18 final size:19
Alignment explanation
Indices: 5704466--5704504 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
5704456 ATTAATTTTG
5704466 ATCAAGTAAATT-AAATTA
1 ATCAAGTAAATTAAAATTA
*
5704484 ATCAAGTTAATTAAAATTA
1 ATCAAGTAAATTAAAATTA
5704503 AT
1 AT
5704505 ATCATATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.36
Consensus pattern (19 bp):
ATCAAGTAAATTAAAATTA
Found at i:5707189 original size:45 final size:44
Alignment explanation
Indices: 5707091--5707390 Score: 170
Period size: 45 Copynumber: 6.7 Consensus size: 44
5707081 AGGAAATGAT
* *
5707091 TAAGACCATAGTTGAAAGACACTATGTCACTATACCG-GAAA-TAAA
1 TAAGACCATAGTTGAAAGACACTATGGCAC-ATA-CGAAAAACT-AA
* * *
5707136 TAAAACCATAGTTGAAAGACACTATGGCACCATACCAAAAACTAG
1 TAAGACCATAGTTGAAAGACACTATGGCA-CATACGAAAAACTAA
* *** ** * * *
5707181 TAAGACCATAGCTGAAAGATGTTAT-G-ACATCACGATTCTATCGAG
1 TAAGACCATAGTTGAAAGACACTATGGCACAT-ACGA--AAAACTAA
* *
5707226 TAAGACCATAGCTGAAAGACACTAT-G-ACATCACGAATCAAACGAA
1 TAAGACCATAGTTGAAAGACACTATGGCACAT-ACGAA--AAACTAA
*
5707271 TAAGACCATAGTTGAAAGACACTATGGCAACACGACGAAAAA-TGAA
1 TAAGACCATAGTTGAAAGACACTATGGC-ACA-TACGAAAAACT-AA
* * * *
5707317 TAAGACCGTGGTTGAAAGACATTATGGCATCA-AGTCG-AGAA-TAAA
1 TAAGACCATAGTTGAAAGACACTATGGCA-CATA--CGAAAAACT-AA
* *
5707362 TAAGACCATGGTTGAAAGACACCATGGCA
1 TAAGACCATAGTTGAAAGACACTATGGCA
5707391 TCCTCCAATT
Statistics
Matches: 206, Mismatches: 33, Indels: 32
0.76 0.12 0.12
Matches are distributed among these distances:
42 3 0.01
43 4 0.02
44 3 0.01
45 151 0.73
46 37 0.18
48 8 0.04
ACGTcount: A:0.43, C:0.19, G:0.19, T:0.20
Consensus pattern (44 bp):
TAAGACCATAGTTGAAAGACACTATGGCACATACGAAAAACTAA
Found at i:5707335 original size:46 final size:46
Alignment explanation
Indices: 5707226--5707392 Score: 178
Period size: 45 Copynumber: 3.7 Consensus size: 46
5707216 TTCTATCGAG
* * * * *
5707226 TAAGACCATAGCTGAAAGACACTATGACATCACGA--ATCAAACGAA
1 TAAGACCATGGTTGAAAGACACTATGGCATCACGACGA-AAAATGAA
* *
5707271 TAAGACCATAGTTGAAAGACACTATGGCAACACGACGAAAAATGAA
1 TAAGACCATGGTTGAAAGACACTATGGCATCACGACGAAAAATGAA
* * * * * *
5707317 TAAGACCGTGGTTGAAAGACATTATGGCATCAAGTCG-AGAATAAA
1 TAAGACCATGGTTGAAAGACACTATGGCATCACGACGAAAAATGAA
*
5707362 TAAGACCATGGTTGAAAGACACCATGGCATC
1 TAAGACCATGGTTGAAAGACACTATGGCATC
5707393 CTCCAATTAT
Statistics
Matches: 104, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
45 66 0.63
46 37 0.36
47 1 0.01
ACGTcount: A:0.43, C:0.19, G:0.20, T:0.18
Consensus pattern (46 bp):
TAAGACCATGGTTGAAAGACACTATGGCATCACGACGAAAAATGAA
Found at i:5707616 original size:41 final size:41
Alignment explanation
Indices: 5707557--5707673 Score: 126
Period size: 41 Copynumber: 2.9 Consensus size: 41
5707547 TGATGTTGTG
* * * *
5707557 GTGTATTGTATCAAGCTTTGTGCCTAGCAGGCTTTATGCCA
1 GTGTATTATATCAGGCTTTGTGCCTAGTAGGCTTCATGCCA
* * * * *
5707598 GTGTATTATATCAGGCTTTATGCATAGTAGGCTTCGTGTCG
1 GTGTATTATATCAGGCTTTGTGCCTAGTAGGCTTCATGCCA
* * *
5707639 GTGTGTCATATCAGGCTTTGAGCCTAGTAGGCTTC
1 GTGTATTATATCAGGCTTTGTGCCTAGTAGGCTTC
5707674 GTGTCGGTGT
Statistics
Matches: 62, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
41 62 1.00
ACGTcount: A:0.19, C:0.18, G:0.26, T:0.37
Consensus pattern (41 bp):
GTGTATTATATCAGGCTTTGTGCCTAGTAGGCTTCATGCCA
Found at i:5707674 original size:41 final size:41
Alignment explanation
Indices: 5707605--5707683 Score: 133
Period size: 41 Copynumber: 1.9 Consensus size: 41
5707595 CCAGTGTATT
5707605 ATATCAGGCTTTATGCATAGTAGGCTTCGTGTCGGTGTGTC
1 ATATCAGGCTTTATGCATAGTAGGCTTCGTGTCGGTGTGTC
*
5707646 ATATCAGGCTTTGA-GCCTAGTAGGCTTCGTGTCGGTGT
1 ATATCAGGCTTT-ATGCATAGTAGGCTTCGTGTCGGTGT
5707684 ATTGTACCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
41 35 0.97
42 1 0.03
ACGTcount: A:0.16, C:0.18, G:0.30, T:0.35
Consensus pattern (41 bp):
ATATCAGGCTTTATGCATAGTAGGCTTCGTGTCGGTGTGTC
Found at i:5726466 original size:44 final size:44
Alignment explanation
Indices: 5726409--5726496 Score: 140
Period size: 44 Copynumber: 2.0 Consensus size: 44
5726399 AGATCAATTG
* **
5726409 AAGGGTGGTTACATCAAAGACATTTCCAACCACAGTGTTTGAAA
1 AAGGGTGGTTACATCAAAGACATTGCCAACCACAACGTTTGAAA
*
5726453 AAGGGTGGTTACATCAAAGGCATTGCCAACCACAACGTTTGAAA
1 AAGGGTGGTTACATCAAAGACATTGCCAACCACAACGTTTGAAA
5726497 GACTAGTATA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.23
Consensus pattern (44 bp):
AAGGGTGGTTACATCAAAGACATTGCCAACCACAACGTTTGAAA
Found at i:5727067 original size:22 final size:21
Alignment explanation
Indices: 5727037--5727099 Score: 65
Period size: 22 Copynumber: 3.0 Consensus size: 21
5727027 TTATTGTGAA
**
5727037 TATAA-AAAATTATTTTTACAT
1 TATAATAAAATTAAATTTA-AT
5727058 TATAATAAAATTAAATTTAAT
1 TATAATAAAATTAAATTTAAT
* *
5727079 TATAAATTAAATTAAAATTAA
1 TAT-AATAAAATTAAATTTAA
5727100 AATTTGATTA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
21 10 0.28
22 26 0.72
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (21 bp):
TATAATAAAATTAAATTTAAT
Found at i:5739263 original size:26 final size:25
Alignment explanation
Indices: 5739200--5739263 Score: 58
Period size: 25 Copynumber: 2.5 Consensus size: 25
5739190 TTTATTATTA
*
5739200 TTTTAATTCCATTTCAAGTTTTTCC
1 TTTTAATTCAATTTCAAGTTTTTCC
* * *
5739225 TTTTATTTTAATTTCTAA-TTTTTACT
1 TTTTAATTCAATTTC-AAGTTTTT-CC
*
5739251 TTTTAATTGAATT
1 TTTTAATTCAATT
5739264 AATTCATATT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
25 17 0.55
26 14 0.45
ACGTcount: A:0.23, C:0.11, G:0.03, T:0.62
Consensus pattern (25 bp):
TTTTAATTCAATTTCAAGTTTTTCC
Found at i:5739420 original size:20 final size:19
Alignment explanation
Indices: 5739390--5739431 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
5739380 TATAAATAAA
*
5739390 ATAATAAATATGTAATTAT
1 ATAATAAATATATAATTAT
*
5739409 ATAATAAAATATATATTTAT
1 ATAAT-AAATATATAATTAT
5739429 ATA
1 ATA
5739432 TATTATTATG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (19 bp):
ATAATAAATATATAATTAT
Found at i:5739433 original size:24 final size:24
Alignment explanation
Indices: 5739374--5739434 Score: 63
Period size: 24 Copynumber: 2.5 Consensus size: 24
5739364 ACAATTATTT
*
5739374 TATTTATATAAATAAAATAATAAA
1 TATTTATATATATAAAATAATAAA
* *
5739398 TATGTA-ATTATATAATAA-AATATA
1 TATTTATA-TATATAA-AATAATAAA
5739422 TATTTATATATAT
1 TATTTATATATAT
5739435 TATTATGTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
23 1 0.03
24 26 0.87
25 3 0.10
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (24 bp):
TATTTATATATATAAAATAATAAA
Found at i:5742278 original size:4 final size:4
Alignment explanation
Indices: 5742269--5742305 Score: 65
Period size: 4 Copynumber: 9.2 Consensus size: 4
5742259 AACTTGAAAA
*
5742269 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAC ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
5742306 ATGAAATTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.51, C:0.27, G:0.00, T:0.22
Consensus pattern (4 bp):
ACAT
Found at i:5747871 original size:126 final size:126
Alignment explanation
Indices: 5747646--5748598 Score: 1669
Period size: 126 Copynumber: 7.6 Consensus size: 126
5747636 CTGGCCATCN
5747646 GCTTCAAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGTGCCCACGTGGACGCGCTTTTGCT
1 GCTTCAAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGTGCCCACGTGGACGCGCTTTTGCT
5747711 ACAGTAGCTCGTGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTTTAAAAAAAC
66 ACAGTAGCTCGTGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTTTAAAAAAAC
5747772 GCTTCAAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGTGCCCACGTGGACGCGCTTTTGCT
1 GCTTCAAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGTGCCCACGTGGACGCGCTTTTGCT
5747837 ACAGTAGCTCGTGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTTTAAAAAAAC
66 ACAGTAGCTCGTGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTTTAAAAAAAC
5747898 GCTTCAAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGTGCCCACGTGGACGCGCTTTTGCT
1 GCTTCAAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGTGCCCACGTGGACGCGCTTTTGCT
5747963 ACAGTAGCTCGTGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTTTAAAAAAAC
66 ACAGTAGCTCGTGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTTTAAAAAAAC
5748024 GCTTCAAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGTGCCCACGTGGACGCGCTTTTGCT
1 GCTTCAAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGTGCCCACGTGGACGCGCTTTTGCT
5748089 ACAGTAGCTCGTGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTTTAAAAAAAC
66 ACAGTAGCTCGTGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTTTAAAAAAAC
5748150 GCTTCAAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGTGCCCACGTGGACGCGCTTTTGCT
1 GCTTCAAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGTGCCCACGTGGACGCGCTTTTGCT
5748215 ACAGTAGCTCGTGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTTTAAAAAAAC
66 ACAGTAGCTCGTGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTTTAAAAAAAC
5748276 GCTTCAAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGTGCCCACGTGGACGCGCTTTTGCT
1 GCTTCAAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGTGCCCACGTGGACGCGCTTTTGCT
* *
5748341 ACAGTAGCTCGTGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAACAAC
66 ACAGTAGCTCGTGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTTTAAAAAAAC
* ** *
5748402 GCTGCAAGCAGGATGCTATT-TGAGAAGAATTTGTGAAATCGCACCCTCGTGGACGCGCTTTTGC
1 GCTTCAAGCAGGATGCT-TTATGAGAAGAATTTGTGAAATCGTGCCCACGTGGACGCGCTTTTGC
* * * * * * * **
5748466 TACAGTAGGTCCTGGAAAAATAATTTCGACTTGACGTTTTTGAGCAAACAG--TATAAAGTC
65 TACAGTAGCTCGTGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTTTAAAAAAAC
* * * ** * *
5748526 GCTTCTAGCAGGATGTTTTATGAGAAGAATTTATGAAATCGCACCCACGTGGACGCGTTTTTACT
1 GCTTCAAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGTGCCCACGTGGACGCGCTTTTGCT
*
5748591 ACAATAGC
66 ACAGTAGC
5748599 ATGTTTGGGC
Statistics
Matches: 800, Mismatches: 25, Indels: 6
0.96 0.03 0.01
Matches are distributed among these distances:
123 2 0.00
124 66 0.08
126 730 0.91
127 2 0.00
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (126 bp):
GCTTCAAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGTGCCCACGTGGACGCGCTTTTGCT
ACAGTAGCTCGTGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTTTAAAAAAAC
Found at i:5751450 original size:10 final size:10
Alignment explanation
Indices: 5751427--5751460 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
5751417 ATTGTTAGTT
5751427 TATTAT-TA-
1 TATTATATAG
5751435 TATTATATAG
1 TATTATATAG
5751445 TATTATATAG
1 TATTATATAG
5751455 TATTAT
1 TATTAT
5751461 TATTGTATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 6 0.25
9 2 0.08
10 16 0.67
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (10 bp):
TATTATATAG
Found at i:5751842 original size:24 final size:25
Alignment explanation
Indices: 5751788--5751870 Score: 71
Period size: 24 Copynumber: 3.2 Consensus size: 25
5751778 ATAGTTTTTT
*
5751788 TATATACATTTATATTTTTATAATG
1 TATATACATTTATATTTTTATAATC
*
5751813 TTTATAC-TTTCATA-TTTTATAATC
1 TATATACATTT-ATATTTTTATAATC
** *
5751837 TATATATGTTTATACATTCTTTATAATA
1 TATATACATTTAT--ATT-TTTATAATC
5751865 TATATA
1 TATATA
5751871 TATGTACTTT
Statistics
Matches: 47, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
24 19 0.40
25 12 0.26
26 1 0.02
27 1 0.02
28 14 0.30
ACGTcount: A:0.35, C:0.07, G:0.02, T:0.55
Consensus pattern (25 bp):
TATATACATTTATATTTTTATAATC
Found at i:5755941 original size:1 final size:1
Alignment explanation
Indices: 5755935--5756021 Score: 57
Period size: 1 Copynumber: 87.0 Consensus size: 1
5755925 GATTCAATGC
* * ** * * * * * *
5755935 AAAAAAAAAAGAAAAAAGAAAAGGAAAAAAAAGAAGAAGAAAAAAAGAAAAAAAGAAAAAAAAAC
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * *
5756000 AAAAACAAAAAGAAACAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAA
5756022 CCTCCACTGG
Statistics
Matches: 62, Mismatches: 24, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
1 62 1.00
ACGTcount: A:0.85, C:0.03, G:0.11, T:0.00
Consensus pattern (1 bp):
A
Found at i:5755965 original size:22 final size:21
Alignment explanation
Indices: 5755937--5756021 Score: 93
Period size: 22 Copynumber: 3.9 Consensus size: 21
5755927 TTCAATGCAA
*
5755937 AAAAAAAAGAAAAAAGAAAAGG
1 AAAAAAAAGAAAAAA-AAAAAG
5755959 AAAAAAAAGAAGAAGAAAAAAAG
1 AAAAAAAAGAA-AA-AAAAAAAG
5755982 -AAAAAAAGAAAAAAAAACAA-
1 AAAAAAAAGAAAAAAAAA-AAG
*
5756002 AAACAAAAAGAAACAAAAAA
1 AAA-AAAAAGAAAAAAAAAA
5756022 CCTCCACTGG
Statistics
Matches: 56, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
20 5 0.09
21 7 0.12
22 35 0.62
23 7 0.12
24 2 0.04
ACGTcount: A:0.85, C:0.04, G:0.12, T:0.00
Consensus pattern (21 bp):
AAAAAAAAGAAAAAAAAAAAG
Found at i:5756004 original size:16 final size:16
Alignment explanation
Indices: 5755934--5756020 Score: 79
Period size: 16 Copynumber: 5.4 Consensus size: 16
5755924 AGATTCAATG
5755934 CAAAAA-AAAAAGAAAA
1 CAAAAAGAAAAA-AAAA
* *
5755950 AAGAAAAGGAAAAAAAA
1 CA-AAAAGAAAAAAAAA
* *
5755967 GAAGAAGAAAAAAAGAA
1 CAAAAAGAAAAAAA-AA
5755984 -AAAAAGAAAAAAAAA
1 CAAAAAGAAAAAAAAA
* *
5755999 CAAAAACAAAAAGAAA
1 CAAAAAGAAAAAAAAA
5756015 CAAAAA
1 CAAAAA
5756021 ACCTCCACTG
Statistics
Matches: 59, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
15 2 0.03
16 42 0.71
17 11 0.19
18 4 0.07
ACGTcount: A:0.84, C:0.05, G:0.11, T:0.00
Consensus pattern (16 bp):
CAAAAAGAAAAAAAAA
Found at i:5756547 original size:7 final size:7
Alignment explanation
Indices: 5756530--5756578 Score: 66
Period size: 7 Copynumber: 7.0 Consensus size: 7
5756520 AAAGATGTGA
5756530 AAAAATG
1 AAAAATG
5756537 -AAAATG
1 AAAAATG
5756543 AAAAATG
1 AAAAATG
5756550 AAAAATG
1 AAAAATG
5756557 AAAAATGG
1 AAAAAT-G
5756565 AAAAA-G
1 AAAAATG
5756571 TAAAAATG
1 -AAAAATG
5756579 GAGAGGCTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
6 7 0.18
7 24 0.63
8 7 0.18
ACGTcount: A:0.69, C:0.00, G:0.16, T:0.14
Consensus pattern (7 bp):
AAAAATG
Found at i:5756580 original size:15 final size:14
Alignment explanation
Indices: 5756530--5756578 Score: 57
Period size: 15 Copynumber: 3.5 Consensus size: 14
5756520 AAAGATGTGA
*
5756530 AAAAATGAAAATG-
1 AAAAATGAAAAAGT
5756543 AAAAATGAAAAA-T
1 AAAAATGAAAAAGT
5756556 GAAAAATGGAAAAAGT
1 -AAAAAT-GAAAAAGT
5756572 AAAAATG
1 AAAAATG
5756579 GAGAGGCTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
13 11 0.35
14 7 0.23
15 12 0.39
16 1 0.03
ACGTcount: A:0.69, C:0.00, G:0.16, T:0.14
Consensus pattern (14 bp):
AAAAATGAAAAAGT
Found at i:5756813 original size:44 final size:44
Alignment explanation
Indices: 5756750--5756834 Score: 134
Period size: 44 Copynumber: 1.9 Consensus size: 44
5756740 CTGAATCAGT
* *
5756750 AGGAAAGGGTACGCGACATCTTGGAGCTTCGATAGAGTATTAGC
1 AGGAAAGGGTACGCGACATCTTGGAGCATCGACAGAGTATTAGC
* *
5756794 AGGAAATGGTACGCGACATCTTGGAGCATGGACAGAGTATT
1 AGGAAAGGGTACGCGACATCTTGGAGCATCGACAGAGTATT
5756835 GTAGATCTCC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 37 1.00
ACGTcount: A:0.31, C:0.15, G:0.32, T:0.22
Consensus pattern (44 bp):
AGGAAAGGGTACGCGACATCTTGGAGCATCGACAGAGTATTAGC
Found at i:5758132 original size:50 final size:50
Alignment explanation
Indices: 5758074--5758551 Score: 261
Period size: 50 Copynumber: 9.6 Consensus size: 50
5758064 GCAATTTAAA
*
5758074 AGATTGAAGCCACAACGGCAGATCTTACTTCCCTGGCGGTGCAGTGGAGC
1 AGATTGAAGCCACAACGGCAGATCTTACTTCCCTGGCGGTGCAGTGGAAC
* * * *** * *** * * ** *
5758124 AGATTGAAGTCACAACTGTAGATCTGGTTTCCCCGATAGCGCAATTAAAA
1 AGATTGAAGCCACAACGGCAGATCTTACTTCCCTGGCGGTGCAGTGGAAC
*
5758174 AGATTGAAGCCACAACGGCAGATCTTACTTCCCTGGCGGTGCAGTGGAGC
1 AGATTGAAGCCACAACGGCAGATCTTACTTCCCTGGCGGTGCAGTGGAAC
* * * *** * *** * * ** *
5758224 AGATTGAAGTCACAACTGTAGATCTGGTTTCCCCGATAGCGCAATTAAAA
1 AGATTGAAGCCACAACGGCAGATCTTACTTCCCTGGCGGTGCAGTGGAAC
** * * *
5758274 AGATTGAAGCCACAACGGTGGATCTTACTTCCCGGGCGATGCAGTGGAGC
1 AGATTGAAGCCACAACGGCAGATCTTACTTCCCTGGCGGTGCAGTGGAAC
* ** * * * * * * *
5758324 AGATTGAAGTCACAACGGCAGAT-TTGGTTTCCCCGACAGCGCAACT-AAAA
1 AGATTGAAGCCACAACGGCAGATCTT-ACTTCCCTGGCGGTGC-AGTGGAAC
* *
5758374 AGATTGAAGCCACAACGGCGGATCTTACTTCCCTGGCGGTGCAGTGGAGC
1 AGATTGAAGCCACAACGGCAGATCTTACTTCCCTGGCGGTGCAGTGGAAC
* * * *** * *
5758424 AGATTGAAGTCACAACCGCGGATCTGGTTTCCCT---GATAGC-GT--AATT
1 AGATTGAAGCCACAACGGCAGATCTTACTTCCCTGGCGGT-GCAGTGGAA-C
* * * * * *
5758470 AAATTGAAGCCACAACGGCGGATCTTACCTCCTTAGCGGTGCAGTTGAAC
1 AGATTGAAGCCACAACGGCAGATCTTACTTCCCTGGCGGTGCAGTGGAAC
* * * *
5758520 AGATTGAAGCTACGACGGCGGATCTTATTTCC
1 AGATTGAAGCCACAACGGCAGATCTTACTTCC
5758552 TCGACATTGT
Statistics
Matches: 302, Mismatches: 114, Indels: 24
0.69 0.26 0.05
Matches are distributed among these distances:
45 1 0.00
46 26 0.09
47 4 0.01
48 4 0.01
49 8 0.03
50 253 0.84
51 6 0.02
ACGTcount: A:0.28, C:0.24, G:0.26, T:0.23
Consensus pattern (50 bp):
AGATTGAAGCCACAACGGCAGATCTTACTTCCCTGGCGGTGCAGTGGAAC
Found at i:5758189 original size:100 final size:100
Alignment explanation
Indices: 5758064--5758528 Score: 713
Period size: 100 Copynumber: 4.7 Consensus size: 100
5758054 CTTTGACATT
* *
5758064 GCAATTTAAAAGATTGAAGCCACAACGGCAGATCTTACTTCCCTGGCGGTGCAGTGGAGCAGATT
1 GCAATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTGGCGGTGCAGTGGAGCAGATT
*
5758129 GAAGTCACAACTGTAGATCTGGTTTCCCCGATAGC
66 GAAGTCACAACTGCAGATCTGGTTTCCCCGATAGC
*
5758164 GCAATTAAAAAGATTGAAGCCACAACGGCAGATCTTACTTCCCTGGCGGTGCAGTGGAGCAGATT
1 GCAATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTGGCGGTGCAGTGGAGCAGATT
*
5758229 GAAGTCACAACTGTAGATCTGGTTTCCCCGATAGC
66 GAAGTCACAACTGCAGATCTGGTTTCCCCGATAGC
* * *
5758264 GCAATTAAAAAGATTGAAGCCACAACGGTGGATCTTACTTCCCGGGCGATGCAGTGGAGCAGATT
1 GCAATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTGGCGGTGCAGTGGAGCAGATT
* * *
5758329 GAAGTCACAACGGCAGATTTGGTTTCCCCGACAGC
66 GAAGTCACAACTGCAGATCTGGTTTCCCCGATAGC
*
5758364 GCAACTAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTGGCGGTGCAGTGGAGCAGATT
1 GCAATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTGGCGGTGCAGTGGAGCAGATT
* * *
5758429 GAAGTCACAACCGCGGATCTGGTTTCCCTGATAGC
66 GAAGTCACAACTGCAGATCTGGTTTCCCCGATAGC
* * * * * *
5758464 GTAATT---AA-ATTGAAGCCACAACGGCGGATCTTACCTCCTTAGCGGTGCAGTTGAACAGATT
1 GCAATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTGGCGGTGCAGTGGAGCAGATT
5758525 GAAG
66 GAAG
5758529 CTACGACGGC
Statistics
Matches: 340, Mismatches: 25, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
96 52 0.15
97 2 0.01
100 286 0.84
ACGTcount: A:0.29, C:0.23, G:0.26, T:0.23
Consensus pattern (100 bp):
GCAATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTGGCGGTGCAGTGGAGCAGATT
GAAGTCACAACTGCAGATCTGGTTTCCCCGATAGC
Found at i:5760096 original size:10 final size:10
Alignment explanation
Indices: 5760073--5760106 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
5760063 ATTTTTAGTT
5760073 TATTAT-TA-
1 TATTATATAG
5760081 TATTATATAG
1 TATTATATAG
5760091 TATTATATAG
1 TATTATATAG
5760101 TATTAT
1 TATTAT
5760107 TATTGTATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 6 0.25
9 2 0.08
10 16 0.67
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (10 bp):
TATTATATAG
Found at i:5760440 original size:17 final size:16
Alignment explanation
Indices: 5760420--5760485 Score: 62
Period size: 17 Copynumber: 4.0 Consensus size: 16
5760410 TTCATAGTTT
*
5760420 TTTTATATATATTTATA
1 TTTT-TATATGTTTATA
5760437 TTTTTATAATGTTTATA
1 TTTTTAT-ATGTTTATA
*
5760454 TTTTCATAT-TTTATAA
1 TTTTTATATGTTTAT-A
* *
5760470 TCTATATATGTTTATA
1 TTTTTATATGTTTATA
5760486 CATTCTTTAT
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
15 5 0.12
16 13 0.32
17 23 0.56
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (16 bp):
TTTTTATATGTTTATA
Found at i:5760477 original size:24 final size:25
Alignment explanation
Indices: 5760423--5760508 Score: 86
Period size: 24 Copynumber: 3.4 Consensus size: 25
5760413 ATAGTTTTTT
*
5760423 TATATATATTTATATTTTTATAATG
1 TATATATATTTATATTTTTATAATC
*
5760448 TTTATAT-TTTCATA-TTTTATAATC
1 TATATATATTT-ATATTTTTATAATC
* *
5760472 TATATATGTTTATACATTCTTTATAATA
1 TATATATATTTAT--ATT-TTTATAATC
5760500 TATATATAT
1 TATATATAT
5760509 GTACTTTCTA
Statistics
Matches: 50, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
24 20 0.40
25 12 0.24
26 1 0.02
27 1 0.02
28 16 0.32
ACGTcount: A:0.35, C:0.05, G:0.02, T:0.58
Consensus pattern (25 bp):
TATATATATTTATATTTTTATAATC
Found at i:5763086 original size:22 final size:21
Alignment explanation
Indices: 5762893--5763470 Score: 726
Period size: 21 Copynumber: 27.0 Consensus size: 21
5762883 TCAAATTATA
5762893 TTTAAGTTAAGGGTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTT
* *
5762914 TTTAAGTTAAGTGTTAGAGTT
1 TTTAAGTTAAGGGTTAGGGTT
* * * *
5762935 TTTTATTTAAGGGTTATGATT
1 TTTAAGTTAAGGGTTAGGGTT
* **
5762956 TTAAAGTTAAGGGTTACAGTT
1 TTTAAGTTAAGGGTTAGGGTT
*
5762977 TTTAAGTTAAGGGTTAGAGTT
1 TTTAAGTTAAGGGTTAGGGTT
* *
5762998 TTAAAGTTAAGTGTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTT
* * *
5763019 TTT-ATTTAAGGGTTACGATT
1 TTTAAGTTAAGGGTTAGGGTT
* * *
5763039 TTAAAGTTAAGGGTTACGATT
1 TTTAAGTTAAGGGTTAGGGTT
*
5763060 TTAAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGG-TTAGGGTT
* *
5763082 TTAAAGTTAAGGGTTAGAGTT
1 TTTAAGTTAAGGGTTAGGGTT
*
5763103 TTTAAGTTAAAGGTTTAGGGTT
1 TTTAAGTT-AAGGGTTAGGGTT
*
5763125 TTTAAGTTAAGAGTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTT
*
5763146 TTTAAGTTAAGGTTTTAGGGTT
1 TTTAAGTTAAGG-GTTAGGGTT
5763168 TTTAAGTTAAGGGTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTT
*
5763189 TTTAAGTTAAGGGTTTAAGGTT
1 TTTAAGTTAAGGG-TTAGGGTT
* *
5763211 TTAAATTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGG-TTAGGGTT
5763233 TTTAAGTTAAGGGTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTT
* * *
5763254 TTGAAGTTAATGGTTTAGGGGT
1 TTTAAGTTAA-GGGTTAGGGTT
5763276 TTTAAGTTAAGGGGTTAGGGTT
1 TTTAAGTTAA-GGGTTAGGGTT
5763298 TTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGG-TTAGGGTT
5763320 TTTAAGTTAAGGGGTTAGGGTT
1 TTTAAGTTAA-GGGTTAGGGTT
*
5763342 TTTAAGTTAAGGGTTTATGGTT
1 TTTAAGTTAAGGG-TTAGGGTT
5763364 TTTAAGTTAAGGGTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTT
* *
5763385 TTTAGGTTAAGGGTTTATGGTT
1 TTTAAGTTAAGGG-TTAGGGTT
*
5763407 TTTAAGTTAATGGTTTAGGGTT
1 TTTAAGTTAA-GGGTTAGGGTT
*
5763429 TTTAATTTAAGGGTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTT
5763450 TTTAAGTTAAGGGTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTT
5763471 AGGATTTTTA
Statistics
Matches: 486, Mismatches: 60, Indels: 22
0.86 0.11 0.04
Matches are distributed among these distances:
20 15 0.03
21 246 0.51
22 220 0.45
23 5 0.01
ACGTcount: A:0.26, C:0.01, G:0.29, T:0.45
Consensus pattern (21 bp):
TTTAAGTTAAGGGTTAGGGTT
Found at i:5763090 original size:43 final size:42
Alignment explanation
Indices: 5762893--5763470 Score: 726
Period size: 43 Copynumber: 13.5 Consensus size: 42
5762883 TCAAATTATA
* *
5762893 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGTGTTAGAGTT
1 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTAGGGTT
* * * * * **
5762935 TTTTATTTAAGGGTTATGATTTTAAAGTTAAGGGTTACAGTT
1 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTAGGGTT
* * *
5762977 TTTAAGTTAAGGGTTAGAGTTTTAAAGTTAAGTGTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTAGGGTT
* * * * * *
5763019 TTT-ATTTAAGGGTTACGATTTTAAAGTTAAGGGTTACGATT
1 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTAGGGTT
* * *
5763060 TTAAAGTTAAGGGTTTAGGGTTTTAAAGTTAAGGGTTAGAGTT
1 TTTAAGTTAAGGG-TTAGGGTTTTTAAGTTAAGGGTTAGGGTT
* *
5763103 TTTAAGTTAAAGGTTTAGGGTTTTTAAGTTAAGAGTTAGGGTT
1 TTTAAGTT-AAGGGTTAGGGTTTTTAAGTTAAGGGTTAGGGTT
*
5763146 TTTAAGTTAAGGTTTTAGGGTTTTTAAGTTAAGGGTTAGGGTT
1 TTTAAGTTAAGG-GTTAGGGTTTTTAAGTTAAGGGTTAGGGTT
* * *
5763189 TTTAAGTTAAGGGTTTAAGGTTTTAAATTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGG-TTAGGGTTTTTAAGTTAAGGG-TTAGGGTT
* * *
5763233 TTTAAGTTAAGGGTTAGGGTTTTGAAGTTAATGGTTTAGGGGT
1 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAA-GGGTTAGGGTT
5763276 TTTAAGTTAAGGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAA-GGGTTAGGGTTTTTAAGTTAAGGG-TTAGGGTT
*
5763320 TTTAAGTTAAGGGGTTAGGGTTTTTAAGTTAAGGGTTTATGGTT
1 TTTAAGTTAA-GGGTTAGGGTTTTTAAGTTAAGGG-TTAGGGTT
* *
5763364 TTTAAGTTAAGGGTTAGGGTTTTTAGGTTAAGGGTTTATGGTT
1 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGG-TTAGGGTT
* *
5763407 TTTAAGTTAATGGTTTAGGGTTTTTAATTTAAGGGTTAGGGTT
1 TTTAAGTTAA-GGGTTAGGGTTTTTAAGTTAAGGGTTAGGGTT
5763450 TTTAAGTTAAGGGTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTT
5763471 AGGATTTTTA
Statistics
Matches: 472, Mismatches: 54, Indels: 20
0.86 0.10 0.04
Matches are distributed among these distances:
41 33 0.07
42 94 0.20
43 217 0.46
44 128 0.27
ACGTcount: A:0.26, C:0.01, G:0.29, T:0.45
Consensus pattern (42 bp):
TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTAGGGTT
Found at i:5763469 original size:27 final size:27
Alignment explanation
Indices: 5763438--5763491 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
5763428 TTTTAATTTA
*
5763438 AGGGTTAGGGTTTTTAAGTTAAGGGTT
1 AGGGTTAGGATTTTTAAGTTAAGGGTT
*
5763465 AGGGTTAGGATTTTTAGGTTAAGGGTT
1 AGGGTTAGGATTTTTAAGTTAAGGGTT
5763492 TAAGGTTTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.22, C:0.00, G:0.37, T:0.41
Consensus pattern (27 bp):
AGGGTTAGGATTTTTAAGTTAAGGGTT
Found at i:5763762 original size:21 final size:21
Alignment explanation
Indices: 5763738--5763786 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
5763728 CTTTGTCCAG
*
5763738 CTTCCGGCGAAGG-TTGTGGTT
1 CTTCCGGCG-AGGATTCTGGTT
*
5763759 CTTCCGGCGGGGATTCTGGTT
1 CTTCCGGCGAGGATTCTGGTT
5763780 CTTCCGG
1 CTTCCGG
5763787 TAGGGCATCT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 2 0.08
21 23 0.92
ACGTcount: A:0.06, C:0.24, G:0.37, T:0.33
Consensus pattern (21 bp):
CTTCCGGCGAGGATTCTGGTT
Found at i:5763797 original size:21 final size:21
Alignment explanation
Indices: 5763754--5763800 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
5763744 GCGAAGGTTG
* *
5763754 TGGTTCTTCCGGCGGGGATTC
1 TGGTTCTTCCGGAGGGCATTC
5763775 TGGTTCTTCCGGTAGGGCA-TC
1 TGGTTCTTCCGG-AGGGCATTC
5763796 TGGTT
1 TGGTT
5763801 GTCGGAGTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.06, C:0.21, G:0.36, T:0.36
Consensus pattern (21 bp):
TGGTTCTTCCGGAGGGCATTC
Found at i:5764741 original size:7 final size:7
Alignment explanation
Indices: 5764731--5764756 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
5764721 TTATATACAT
5764731 AATACTA
1 AATACTA
5764738 AATACTA
1 AATACTA
5764745 AATACTA
1 AATACTA
5764752 AATAC
1 AATAC
5764757 CAATCGACAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.15, G:0.00, T:0.27
Consensus pattern (7 bp):
AATACTA
Found at i:5765941 original size:51 final size:51
Alignment explanation
Indices: 5765897--5765996 Score: 139
Period size: 51 Copynumber: 2.0 Consensus size: 51
5765887 AATTATTTAA
*
5765897 AAATAGGGATTTAAGAGAAATTTA-AGAGGAACTTGAGAGCAAATTGAGATT
1 AAATAGGGATTTAAGAGAAATTTAGA-AGGAACTTGAAAGCAAATTGAGATT
* * * *
5765948 AAATATGGATTTGAGAGAAATTTGGAAGGAATTTGAAAGCAAATTGAGA
1 AAATAGGGATTTAAGAGAAATTTAGAAGGAACTTGAAAGCAAATTGAGA
5765997 GGAAATTTAG
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
51 42 0.98
52 1 0.02
ACGTcount: A:0.45, C:0.03, G:0.26, T:0.26
Consensus pattern (51 bp):
AAATAGGGATTTAAGAGAAATTTAGAAGGAACTTGAAAGCAAATTGAGATT
Found at i:5765970 original size:11 final size:11
Alignment explanation
Indices: 5765956--5766032 Score: 54
Period size: 11 Copynumber: 6.9 Consensus size: 11
5765946 TTAAATATGG
5765956 ATTTGAGAGAA
1 ATTTGAGAGAA
*
5765967 ATTTG-GAAGGA
1 ATTTGAG-AGAA
*
5765978 ATTTGAAAGCAA
1 ATTTGAGAG-AA
5765990 A-TTGAGAGGAA
1 ATTTGAGA-GAA
5766001 ATTT-AGAGGAA
1 ATTTGAGA-GAA
*
5766012 A-TTGAGAGGAG
1 ATTTGAGA-GAA
5766023 ATTTGAGAGA
1 ATTTGAGAGA
5766033 GGATTAGTTT
Statistics
Matches: 54, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
10 3 0.06
11 40 0.74
12 11 0.20
ACGTcount: A:0.43, C:0.01, G:0.31, T:0.25
Consensus pattern (11 bp):
ATTTGAGAGAA
Found at i:5765981 original size:22 final size:21
Alignment explanation
Indices: 5765956--5766032 Score: 77
Period size: 22 Copynumber: 3.5 Consensus size: 21
5765946 TTAAATATGG
5765956 ATTTGAGAGAAATTTG-GAAGGA
1 ATTTGAGAGAAA-TTGAG-AGGA
*
5765978 ATTTGAAAGCAAATTGAGAGGAA
1 ATTTGAGAG-AAATTGAGAGG-A
5766001 ATTT-AGAGGAAATTGAGAGGA
1 ATTTGAGA-GAAATTGAGAGGA
5766022 GATTTGAGAGA
1 -ATTTGAGAGA
5766033 GGATTAGTTT
Statistics
Matches: 47, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
21 1 0.02
22 33 0.70
23 13 0.28
ACGTcount: A:0.43, C:0.01, G:0.31, T:0.25
Consensus pattern (21 bp):
ATTTGAGAGAAATTGAGAGGA
Found at i:5769051 original size:26 final size:26
Alignment explanation
Indices: 5769021--5769175 Score: 134
Period size: 26 Copynumber: 6.0 Consensus size: 26
5769011 AACCTTGAAC
*
5769021 CAGTGGTTATTTAGCAGGCTTTAAGT
1 CAGTGGTTATTTAGCAGGCTTTGAGT
* * *
5769047 CAGTGATTATTTAGCAGGCCTCGAG-
1 CAGTGGTTATTTAGCAGGCTTTGAGT
* ** * *
5769072 CTAATGGTTATTTAGCAAACATTGAGA
1 C-AGTGGTTATTTAGCAGGCTTTGAGT
* *
5769099 C-GATGTTTATTTAGCAGGCTTTGAGC
1 CAG-TGGTTATTTAGCAGGCTTTGAGT
* * *
5769125 CAGTGTTTATTTAGCAGACCTTGAGT
1 CAGTGGTTATTTAGCAGGCTTTGAGT
**
5769151 TTGTGGTTATTTAGCAGGCTTTGAG
1 CAGTGGTTATTTAGCAGGCTTTGAG
5769176 CCGGTGTATA
Statistics
Matches: 101, Mismatches: 24, Indels: 8
0.76 0.18 0.06
Matches are distributed among these distances:
25 1 0.01
26 98 0.97
27 2 0.02
ACGTcount: A:0.24, C:0.14, G:0.26, T:0.37
Consensus pattern (26 bp):
CAGTGGTTATTTAGCAGGCTTTGAGT
Done.