Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr4
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: 30015117
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1306243 characters in sequence are not A, C, G, or T
File 37 of 85
Found at i:12287980 original size:16 final size:16
Alignment explanation
Indices: 12287959--12287989 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
12287949 TAGGTTAGAT
12287959 TTTCTTTCTCTTTTCC
1 TTTCTTTCTCTTTTCC
*
12287975 TTTCTTTTTCTTTTC
1 TTTCTTTCTCTTTTC
12287990 ATTTTTAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTCTTTCTCTTTTCC
Found at i:12293514 original size:16 final size:16
Alignment explanation
Indices: 12293493--12293523 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
12293483 CTTGTTTTAT
12293493 TATTATAATAATATAA
1 TATTATAATAATATAA
12293509 TATTATAATAATATA
1 TATTATAATAATATA
12293524 CTATAACAAT
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:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TATTATAATAATATAA
Found at i:12293684 original size:22 final size:21
Alignment explanation
Indices: 12293655--12293701 Score: 85
Period size: 22 Copynumber: 2.2 Consensus size: 21
12293645 TTTGGTCCTT
12293655 TTAACTTTCTTTAATCTATAA
1 TTAACTTTCTTTAATCTATAA
12293676 TTAAGCTTTCTTTAATCTATAA
1 TTAA-CTTTCTTTAATCTATAA
12293698 TTAA
1 TTAA
12293702 ATTTTTATCC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 4 0.16
22 21 0.84
ACGTcount: A:0.34, C:0.13, G:0.02, T:0.51
Consensus pattern (21 bp):
TTAACTTTCTTTAATCTATAA
Found at i:12295586 original size:217 final size:217
Alignment explanation
Indices: 12295210--12295645 Score: 721
Period size: 217 Copynumber: 2.0 Consensus size: 217
12295200 CACCACAATA
* * * *
12295210 CTCTATCGCCAAAAATAGAACTAGAAGAGAGATTAAACCTCTAAAGAAGTATGTCGAAGCTGATC
1 CTCTATCGCCAAAAACAAAACTAGAAGAGAGATTAAACCTCCAAAGAAGTATGTCAAAGCTGATC
*
12295275 TAGTTGCTTATACTTTAAATGTGGCTGAAGATATAGATACAAACCAAGAGCCATCTAATTATTCT
66 TAGTTGCTTATACTTTAAATGTAGCTGAAGATATAGATACAAACCAAGAGCCATCTAATTATTCT
* *
12295340 AAGGCAATTAGTTGTGAAGACTTAGAAAAGTAGATATTTGCTATGCAAGAGGAGATGGAATCACT
131 AAGGCAATTAGCTGTGAAGACTCAGAAAAGTAGATATTTGCTATGCAAGAGGAGATGGAATCACT
12295405 CCACAAAAATC-GAACATGGGAT
196 CCACAAAAA-CAGAACATGGGAT
* *
12295427 CTCTATCGCCAAAAGCAAAACTAGAAGAGAGATTAAACCTCCAAAGAAGTATGTCAAAGTTGATC
1 CTCTATCGCCAAAAACAAAACTAGAAGAGAGATTAAACCTCCAAAGAAGTATGTCAAAGCTGATC
* *
12295492 TAGTTGCTTATGCTTTAAATGTAGCTGAAGATATAGATGCAAACCAAGAGCCATCTAATTATTCT
66 TAGTTGCTTATACTTTAAATGTAGCTGAAGATATAGATACAAACCAAGAGCCATCTAATTATTCT
* * * *
12295557 AAGGCGATTAGCTGTGAAGACTCAGAAAAGTGGATATTTTCTATGCAAGAGGAGATGGAATCATT
131 AAGGCAATTAGCTGTGAAGACTCAGAAAAGTAGATATTTGCTATGCAAGAGGAGATGGAATCACT
12295622 CCACAAAAACAGAACATGGGAT
196 CCACAAAAACAGAACATGGGAT
12295644 CT
1 CT
12295646 TGTGAAACTT
Statistics
Matches: 203, Mismatches: 15, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
216 1 0.00
217 202 1.00
ACGTcount: A:0.39, C:0.16, G:0.20, T:0.25
Consensus pattern (217 bp):
CTCTATCGCCAAAAACAAAACTAGAAGAGAGATTAAACCTCCAAAGAAGTATGTCAAAGCTGATC
TAGTTGCTTATACTTTAAATGTAGCTGAAGATATAGATACAAACCAAGAGCCATCTAATTATTCT
AAGGCAATTAGCTGTGAAGACTCAGAAAAGTAGATATTTGCTATGCAAGAGGAGATGGAATCACT
CCACAAAAACAGAACATGGGAT
Found at i:12302414 original size:21 final size:21
Alignment explanation
Indices: 12302384--12302424 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
12302374 GCCTAAAACC
* *
12302384 TAGAACCCCAGACCCTAAATT
1 TAGAACCCCAAACCCAAAATT
*
12302405 TAGAATCCCAAACCCAAAAT
1 TAGAACCCCAAACCCAAAAT
12302425 CCAATAGTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.44, C:0.32, G:0.07, T:0.17
Consensus pattern (21 bp):
TAGAACCCCAAACCCAAAATT
Found at i:12305053 original size:18 final size:18
Alignment explanation
Indices: 12305030--12305078 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
12305020 TTTCGGGTAA
12305030 AACCGAATTAATTCGGTT
1 AACCGAATTAATTCGGTT
***
12305048 AACCGACCGAATTCGGTT
1 AACCGAATTAATTCGGTT
*
12305066 AACCAAATTAATT
1 AACCGAATTAATT
12305079 TGGTCAGGGG
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.37, C:0.20, G:0.14, T:0.29
Consensus pattern (18 bp):
AACCGAATTAATTCGGTT
Found at i:12307365 original size:220 final size:221
Alignment explanation
Indices: 12306972--12307412 Score: 875
Period size: 220 Copynumber: 2.0 Consensus size: 221
12306962 AAAATATTAA
12306972 AATTAAATTATAAAATTTTGAATGTTAAAGCATAAATTTATAATTATGTTCACTTAAAATTTTCA
1 AATTAAATTATAAAATTTTGAATGTTAAAGCATAAATTTATAATTATGTTCACTTAAAATTTTCA
12307037 TTTTTAAAGAGTTTTTTCCTTTTGTCATTTATGGAGTCCAAGGCCCTACCTCTCTTAAGGTGCGT
66 TTTTTAAAGAGTTTTTTCCTTTTGTCATTTATGGAGTCCAAGGCCCTACCTCTCTTAAGGTGCGT
12307102 TTGGTTAGGTGAAAAAGATGATAGATGGAAAGAGGGAGTGAAAAAGTAAAAAGAAAATAAATTTG
131 TTGGTTAGGTGAAAAAGATGATAGATGGAAAGAGGGAGTGAAAAAGTAAAAAGAAAATAAATTTG
12307167 GAGTGTGCTTGGTGGGAGAGAAAAGT
196 GAGTGTGCTTGGTGGGAGAGAAAAGT
12307193 AATTAAATTA-AAAATTTTGAATGTTAAAGCATAAATTTATAATTATGTTCACTTAAAATTTTCA
1 AATTAAATTATAAAATTTTGAATGTTAAAGCATAAATTTATAATTATGTTCACTTAAAATTTTCA
12307257 TTTTTAAAGAGTTTTTTCCTTTTGTCATTTATGGAGTCCAAGGCCCTACCTCTCTTAAGGTGCGT
66 TTTTTAAAGAGTTTTTTCCTTTTGTCATTTATGGAGTCCAAGGCCCTACCTCTCTTAAGGTGCGT
12307322 TTGGTTAGGTGAAAAAGATGATAGATGGAAAGAGGGAGTGAAAAAGTAAAAAGAAAATAAATTTG
131 TTGGTTAGGTGAAAAAGATGATAGATGGAAAGAGGGAGTGAAAAAGTAAAAAGAAAATAAATTTG
12307387 GAGTGTGCTTGGTGGGAGAGAAAAGT
196 GAGTGTGCTTGGTGGGAGAGAAAAGT
12307413 GAGGAAAAAA
Statistics
Matches: 220, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
220 210 0.95
221 10 0.05
ACGTcount: A:0.36, C:0.08, G:0.21, T:0.34
Consensus pattern (221 bp):
AATTAAATTATAAAATTTTGAATGTTAAAGCATAAATTTATAATTATGTTCACTTAAAATTTTCA
TTTTTAAAGAGTTTTTTCCTTTTGTCATTTATGGAGTCCAAGGCCCTACCTCTCTTAAGGTGCGT
TTGGTTAGGTGAAAAAGATGATAGATGGAAAGAGGGAGTGAAAAAGTAAAAAGAAAATAAATTTG
GAGTGTGCTTGGTGGGAGAGAAAAGT
Found at i:12309992 original size:73 final size:74
Alignment explanation
Indices: 12309887--12310039 Score: 299
Period size: 73 Copynumber: 2.1 Consensus size: 74
12309877 AAATTTATAA
12309887 TGTAAATATTAGTAGTATATTAAGTTATTTATATTTAAAATTTAATAAAAATAATTAAAAATAAT
1 TGTAAATATTAGTAGTATATTAAGTTATTTATATTTAAAATTTAATAAAAATAATTAAAAATAAT
12309952 ATAAATGTT
66 ATAAATGTT
12309961 TGTAAATATTAGTA-TATATTAAGTTATTTATATTTAAAATTTAATAAAAATAATTAAAAATAAT
1 TGTAAATATTAGTAGTATATTAAGTTATTTATATTTAAAATTTAATAAAAATAATTAAAAATAAT
12310025 ATAAATGTT
66 ATAAATGTT
12310034 TGTAAA
1 TGTAAA
12310040 AGAAATATAA
Statistics
Matches: 79, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
73 65 0.82
74 14 0.18
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (74 bp):
TGTAAATATTAGTAGTATATTAAGTTATTTATATTTAAAATTTAATAAAAATAATTAAAAATAAT
ATAAATGTT
Found at i:12310374 original size:24 final size:23
Alignment explanation
Indices: 12310331--12310382 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
12310321 TGAGATATAT
* *
12310331 AATTTATATTTACTTAATACTTA
1 AATTTATATTTAATTAATACCTA
* *
12310354 ATATTTTTATTTAATTGATACCTA
1 A-ATTTATATTTAATTAATACCTA
12310378 AATTT
1 AATTT
12310383 GAAAACAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
23 5 0.21
24 19 0.79
ACGTcount: A:0.37, C:0.08, G:0.02, T:0.54
Consensus pattern (23 bp):
AATTTATATTTAATTAATACCTA
Found at i:12313005 original size:98 final size:98
Alignment explanation
Indices: 12312835--12313129 Score: 554
Period size: 98 Copynumber: 3.0 Consensus size: 98
12312825 GTGCAATAAA
12312835 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATT
1 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATT
*
12312900 CCACTAAAATCCCAAACTCGGAATATTTCCTTT
66 CCTCTAAAATCCCAAACTCGGAATATTTCCTTT
* *
12312933 ACTTTAAAAGAACATCCACTTATCAAAGATTTAAGGAATCACACCCAATACGTTAGGGCACGATT
1 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATT
*
12312998 CCTCTAAAATCCCAAACTTGGAATATTTCCTTT
66 CCTCTAAAATCCCAAACTCGGAATATTTCCTTT
12313031 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATT
1 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATT
12313096 CCTCTAAAATCCCAAACTCGGAATATTTCCTTT
66 CCTCTAAAATCCCAAACTCGGAATATTTCCTTT
12313129 A
1 A
12313130 TTATTTTTAG
Statistics
Matches: 190, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
98 190 1.00
ACGTcount: A:0.37, C:0.25, G:0.11, T:0.27
Consensus pattern (98 bp):
ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATT
CCTCTAAAATCCCAAACTCGGAATATTTCCTTT
Found at i:12315284 original size:44 final size:44
Alignment explanation
Indices: 12315235--12315579 Score: 165
Period size: 44 Copynumber: 7.8 Consensus size: 44
12315225 AAGATTCGCC
*
12315235 GTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTATA
1 GTCTTCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTATA
* * * * * * *
12315279 ATCTTCAACCTTC-CCAGCTGCTGCTCAGGGAGATAAG-GCT-TG
1 GTCTTCAATCTGCTCCA-CTACTGCTTAGGGAGATAAGATCTATA
* ** * *
12315321 GTGGCTTAAATCTGCTTCCCACTA-T-CTTAGAAATATAAGAT-TCATC
1 GT--CTTCAATCTGC-T-CCACTACTGCTTAGGGAGATAAGATCT-ATA
* * *
12315367 GTCTTCGATCTACTCCACTATTGCTTAGGGAGATAAGATCTATA
1 GTCTTCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTATA
* * * * * * *
12315411 ATCTTCAACCTTC-CCAGCTGCTGCTCAGGGAGATAAG-GCT-TG
1 GTCTTCAATCTGCTCCA-CTACTGCTTAGGGAGATAAGATCTATA
* ** * *
12315453 GTGGCTTAAATCTGCTTCCCACTA-T-CTTAGAAATATAAGAT-TCATC
1 GT--CTTCAATCTGC-T-CCACTACTGCTTAGGGAGATAAGATCT-ATA
* * *
12315499 GTCTTCGATCTACTCCACTATTGCTTAGGGAGATAAGATCTATA
1 GTCTTCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTATA
* * * * * *
12315543 ATCTTCAACCTTCTCCGCTATTGCTCAGGGAGATAAG
1 GTCTTCAATCTGCTCCACTACTGCTTAGGGAGATAAG
12315580 GCTTGGTGGC
Statistics
Matches: 218, Mismatches: 59, Indels: 48
0.67 0.18 0.15
Matches are distributed among these distances:
42 16 0.07
43 14 0.06
44 168 0.77
45 4 0.02
46 10 0.05
47 6 0.03
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.32
Consensus pattern (44 bp):
GTCTTCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTATA
Found at i:12315401 original size:132 final size:132
Alignment explanation
Indices: 12315164--12315672 Score: 777
Period size: 132 Copynumber: 3.8 Consensus size: 132
12315154 TGTAGCTTCA
* * *
12315164 CTGCTGCTCAGGGAGATAAGGCTTGGTGGCTTTAATCTGTTTCCCACTATCTTGGAAAGATAAGA
1 CTGCTGCTCAGGGAGATAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTAGAAAGATAAGA
* *
12315229 TTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTATAATCTTCAACCTTCCC
66 TTCACCGTCTTCGATCTACTCCACTACTGCTTAGGGAGATAAGATCTATAATCTTCAACCTTCCC
12315294 AG
131 AG
*
12315296 CTGCTGCTCAGGGAGATAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTAGAAATATAAGA
1 CTGCTGCTCAGGGAGATAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTAGAAAGATAAGA
* *
12315361 TTCATCGTCTTCGATCTACTCCACTATTGCTTAGGGAGATAAGATCTATAATCTTCAACCTTCCC
66 TTCACCGTCTTCGATCTACTCCACTACTGCTTAGGGAGATAAGATCTATAATCTTCAACCTTCCC
12315426 AG
131 AG
*
12315428 CTGCTGCTCAGGGAGATAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTAGAAATATAAGA
1 CTGCTGCTCAGGGAGATAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTAGAAAGATAAGA
* *
12315493 TTCATCGTCTTCGATCTACTCCACTATTGCTTAGGGAGATAAGATCTATAATCTTCAACCTTCTC
66 TTCACCGTCTTCGATCTACTCCACTACTGCTTAGGGAGATAAGATCTATAATCTTCAACCTTC-C
12315558 C-G
130 CAG
** *
12315560 CTATTGCTCAGGGAGATAAGGCTTGGTGGCTTAAATCTACTTCCCCTGCTTCCCACTATCTTGGA
1 CTGCTGCTCAGGGAGATAAGGCTTGGTGGCTT-AA---A--T---CTGCTTCCCACTATCTTAGA
* *
12315625 AAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGA
57 AAGATAAGATTCACCGTCTTCGATCTACTCCACTACTGCTTAGGGAGA
12315673 CAAGGCTTGG
Statistics
Matches: 351, Mismatches: 16, Indels: 11
0.93 0.04 0.03
Matches are distributed among these distances:
132 283 0.81
133 4 0.01
136 1 0.00
138 1 0.00
141 62 0.18
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.31
Consensus pattern (132 bp):
CTGCTGCTCAGGGAGATAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTAGAAAGATAAGA
TTCACCGTCTTCGATCTACTCCACTACTGCTTAGGGAGATAAGATCTATAATCTTCAACCTTCCC
AG
Found at i:12315694 original size:229 final size:220
Alignment explanation
Indices: 12315431--12315876 Score: 696
Period size: 229 Copynumber: 2.0 Consensus size: 220
12315421 TTCCCAGCTG
* *
12315431 CTGCTCAGGGAGATAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTAGAAATATAAGATTC
1 CTGCTCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTAGAAAGATAAGATTC
* *
12315496 -ATCGTCTTCGATCTACTCCACTATTGCTTAGGGAGATAAGATCTATAATCTTCAACCTTCTCCG
66 GCT-GTCTTCGATCTACTCCACTACTGCTTAGGGAGATAAGATCTATAATCTTCAACCTTCTCCG
* *
12315560 CTATTGCTCAGGGAGATAAGGCTTGGTGGCTTAAATCTACTTCCCCTGCTTCCCACTATCTTGGA
130 CTACTGCTCAGGGAGACAAGGCTTGGTGGCTTAAA--T-C-T----T-CTTCCCACTATCTTGGA
*
12315625 AAGATAAGATTCGCCGTCTTCGATCTGCTCCACTA
186 AAGATAAGATTCACCGTCTTCGATCTGCTCCACTA
* *
12315660 CTGCTTAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTC
1 CTGCTCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTAGAAAGATAAGATTC
* *
12315725 GCTGTCTTCGATCTGCTCTACTACTGCTTAGGGAGATAAGATCTATAATCTTCAACCTTCTCCGC
66 GCTGTCTTCGATCTACTCCACTACTGCTTAGGGAGATAAGATCTATAATCTTCAACCTTCTCCGC
12315790 TACTGCTCAGGGAGACAAGGCTTGGTGGCTTAAATCTTCTTCCCACTATCTTGGAAAGATAAGAT
131 TACTGCTCAGGGAGACAAGGCTTGGTGGCTTAAATCTTCTTCCCACTATCTTGGAAAGATAAGAT
12315855 TCACCGTCTTCGATCTGCTCCA
196 TCACCGTCTTCGATCTGCTCCA
12315877 TTGCAATTTC
Statistics
Matches: 205, Mismatches: 11, Indels: 11
0.90 0.05 0.05
Matches are distributed among these distances:
220 48 0.23
221 1 0.00
225 1 0.00
226 1 0.00
227 1 0.00
229 152 0.74
230 1 0.00
ACGTcount: A:0.24, C:0.25, G:0.20, T:0.31
Consensus pattern (220 bp):
CTGCTCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTAGAAAGATAAGATTC
GCTGTCTTCGATCTACTCCACTACTGCTTAGGGAGATAAGATCTATAATCTTCAACCTTCTCCGC
TACTGCTCAGGGAGACAAGGCTTGGTGGCTTAAATCTTCTTCCCACTATCTTGGAAAGATAAGAT
TCACCGTCTTCGATCTGCTCCACTA
Found at i:12315695 original size:44 final size:44
Alignment explanation
Indices: 12315647--12315826 Score: 111
Period size: 44 Copynumber: 4.1 Consensus size: 44
12315637 GCCGTCTTCG
12315647 ATCTGCTCCACTACTGCTTAGGGAGACAAGGCTTGGTGGCTTAA
1 ATCTGCTCCACTACTGCTTAGGGAGACAAGGCTTGGTGGCTTAA
* * * * * **
12315691 ATCTGCTTCCCACTA-T-CTT-GGAAAGATAA-GATTCGCTGTCTTCG
1 ATCTGC-T-CCACTACTGCTTAGG-GAGACAAGGCTT-GGTGGCTTAA
* * * ** *
12315735 ATCTGCTCTACTACTGCTTAGGGAGATAAGATCTATAAT--CTTCA
1 ATCTGCTCCACTACTGCTTAGGGAGACAAG-GCT-TGGTGGCTTAA
* * * *
12315779 ACCTTCTCCGCTACTGCTCAGGGAGACAAGGCTTGGTGGCTTAA
1 ATCTGCTCCACTACTGCTTAGGGAGACAAGGCTTGGTGGCTTAA
12315823 ATCT
1 ATCT
12315827 TCTTCCCACT
Statistics
Matches: 99, Mismatches: 25, Indels: 24
0.67 0.17 0.16
Matches are distributed among these distances:
42 7 0.07
43 9 0.09
44 70 0.71
45 4 0.04
46 8 0.08
47 1 0.01
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.31
Consensus pattern (44 bp):
ATCTGCTCCACTACTGCTTAGGGAGACAAGGCTTGGTGGCTTAA
Found at i:12317121 original size:44 final size:45
Alignment explanation
Indices: 12317057--12317146 Score: 173
Period size: 44 Copynumber: 2.0 Consensus size: 45
12317047 GATTCGAAAG
12317057 ATTTTTGCCATCTATTTCACTCAAAATCAAAGCGCCTCCGGAGAA
1 ATTTTTGCCATCTATTTCACTCAAAATCAAAGCGCCTCCGGAGAA
12317102 ATTTTTGCCA-CTATTTCACTCAAAATCAAAGCGCCTCCGGAGAA
1 ATTTTTGCCATCTATTTCACTCAAAATCAAAGCGCCTCCGGAGAA
12317146 A
1 A
12317147 GCCTTTTTAA
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
44 35 0.78
45 10 0.22
ACGTcount: A:0.32, C:0.27, G:0.13, T:0.28
Consensus pattern (45 bp):
ATTTTTGCCATCTATTTCACTCAAAATCAAAGCGCCTCCGGAGAA
Found at i:12322440 original size:134 final size:134
Alignment explanation
Indices: 12322200--12322466 Score: 500
Period size: 134 Copynumber: 2.0 Consensus size: 134
12322190 CTGGATTTCA
12322200 TGTCCCTCATCGTGATGGAACTCACAGTAATTTTCCACCCTTTCGAAGCTTCTCTCTGAACTCGG
1 TGTCCCTCATCGTGATGGAACTCACAGTAATTTTCCACCCTTTCGAAGCTTCTCTCTGAACTCGG
12322265 GACGATCAATCCCCTTCTTACCATATTTTTCCAGACCCACCTCAAAGGAATTTTCACCTCTGATA
66 GACGATCAATCCCCTTCTTACCATATTTTTCCAGACCCACCTCAAAGGAATTTTCACCTCTGATA
12322330 TGTC
131 TGTC
*
12322334 TGTCCCTCATCCGTGATGGAA-TCACAGTAATTTTCCACCCTTTCGAAGCTTCTCTCTGAATTCG
1 TGTCCCTCAT-CGTGATGGAACTCACAGTAATTTTCCACCCTTTCGAAGCTTCTCTCTGAACTCG
*
12322398 GGACGATCAATCCCCTTTTTACCATATTTTTCCAGACCCACCTCAAAGGAATTTTCACCTCTGAT
65 GGACGATCAATCCCCTTCTTACCATATTTTTCCAGACCCACCTCAAAGGAATTTTCACCTCTGAT
12322463 ATGT
130 ATGT
12322467 ATTCCTTGAT
Statistics
Matches: 130, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
134 120 0.92
135 10 0.08
ACGTcount: A:0.23, C:0.30, G:0.13, T:0.33
Consensus pattern (134 bp):
TGTCCCTCATCGTGATGGAACTCACAGTAATTTTCCACCCTTTCGAAGCTTCTCTCTGAACTCGG
GACGATCAATCCCCTTCTTACCATATTTTTCCAGACCCACCTCAAAGGAATTTTCACCTCTGATA
TGTC
Found at i:12327444 original size:98 final size:98
Alignment explanation
Indices: 12327275--12327471 Score: 349
Period size: 98 Copynumber: 2.0 Consensus size: 98
12327265 GTGCAATAAA
*
12327275 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATT
1 ACTTTAAAAGAACATCCACTTATCCAAAATTTAAGAAATCACACCCAATACGTTAGGGCACGATT
**
12327340 CCTCTAAAATCCCAAACTCGGAATATTCCCTTT
66 CCTCTAAAATCCCAAACTAAGAATATTCCCTTT
*
12327373 ACTTTAAAAGAACATCCATTTATCCAAAATTTAAGAAATCACACCCAATACGTTAGGGCACGATT
1 ACTTTAAAAGAACATCCACTTATCCAAAATTTAAGAAATCACACCCAATACGTTAGGGCACGATT
*
12327438 CCTCTAAAATCCCAAACTAAGAATATTTCCTTT
66 CCTCTAAAATCCCAAACTAAGAATATTCCCTTT
12327471 A
1 A
12327472 TTATTTTTAG
Statistics
Matches: 94, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
98 94 1.00
ACGTcount: A:0.39, C:0.25, G:0.09, T:0.27
Consensus pattern (98 bp):
ACTTTAAAAGAACATCCACTTATCCAAAATTTAAGAAATCACACCCAATACGTTAGGGCACGATT
CCTCTAAAATCCCAAACTAAGAATATTCCCTTT
Found at i:12333760 original size:26 final size:26
Alignment explanation
Indices: 12333721--12333811 Score: 121
Period size: 26 Copynumber: 3.5 Consensus size: 26
12333711 TGGTTATCCG
12333721 GAGC-TCCTGATTAAAGGCTCTTCGT
1 GAGCTTCCTGATTAAAGGCTCTTCGT
*
12333746 GAGCTTCCTGTTTAAAGGCTCTTCGT
1 GAGCTTCCTGATTAAAGGCTCTTCGT
* * * *
12333772 GAGCTTCCTAATTAAAAGTTCTTTGT
1 GAGCTTCCTGATTAAAGGCTCTTCGT
*
12333798 GAACTTCCTGATTA
1 GAGCTTCCTGATTA
12333812 TGGCTATTAT
Statistics
Matches: 57, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
25 4 0.07
26 53 0.93
ACGTcount: A:0.22, C:0.21, G:0.20, T:0.37
Consensus pattern (26 bp):
GAGCTTCCTGATTAAAGGCTCTTCGT
Found at i:12340551 original size:18 final size:18
Alignment explanation
Indices: 12340505--12340551 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
12340495 CTTTTTTTTA
*
12340505 TTTCTTTC-TTTTTCTCT
1 TTTCTTTCATTTTTCTCG
*
12340522 TTTCTTTTATTTTTCTTCG
1 TTTCTTTCATTTTTC-TCG
12340541 TTT-TTTCATTT
1 TTTCTTTCATTT
12340552 ACTAGTTGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
17 7 0.28
18 13 0.52
19 5 0.20
ACGTcount: A:0.04, C:0.17, G:0.02, T:0.77
Consensus pattern (18 bp):
TTTCTTTCATTTTTCTCG
Found at i:12357311 original size:45 final size:45
Alignment explanation
Indices: 12357247--12357340 Score: 143
Period size: 45 Copynumber: 2.1 Consensus size: 45
12357237 AACAGATACT
* *
12357247 CGGTGGATTCAGCACATAGCAACCACCTTATTAACCAATGATGTC
1 CGGTGGAATCAGCACATAGCAACCACCTTACTAACCAATGATGTC
** *
12357292 CGGTGGAATCAGCACATAGCAACCACCTTACTAATTAATGATGTT
1 CGGTGGAATCAGCACATAGCAACCACCTTACTAACCAATGATGTC
12357337 CGGT
1 CGGT
12357341 TCACATAGTA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (45 bp):
CGGTGGAATCAGCACATAGCAACCACCTTACTAACCAATGATGTC
Found at i:12357424 original size:51 final size:50
Alignment explanation
Indices: 12357346--12357531 Score: 162
Period size: 51 Copynumber: 3.7 Consensus size: 50
12357336 TCGGTTCACA
* * *
12357346 TAGTAGCCTGCACAAAGTACTATACATGTAACCATTATCATCTGATACACG
1 TAGTAGCCTGCACATAGTACTACACATGTAACCA-TATCATCCGATACACG
* * * * * * *
12357397 TAGTAGCTTGTACATAGTACTACACATGTGATCGA-AACTATCCGGA-ACCCA
1 TAGTAGCCTGCACATAGTACTACACATGT-AACCATATC-ATCC-GATACACG
* * ** *
12357448 CAGTAGCTTGCACATAGTACTACACATGCGACC-TATCATTCCGGTACACG
1 TAGTAGCCTGCACATAGTACTACACATGTAACCATATCA-TCCGATACACG
*
12357498 TAGTAGCCTGCACATAGTACTACACACGTAACCA
1 TAGTAGCCTGCACATAGTACTACACATGTAACCA
12357532 CCAGTTCCAC
Statistics
Matches: 103, Mismatches: 25, Indels: 14
0.73 0.18 0.10
Matches are distributed among these distances:
49 2 0.02
50 39 0.38
51 57 0.55
52 5 0.05
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.25
Consensus pattern (50 bp):
TAGTAGCCTGCACATAGTACTACACATGTAACCATATCATCCGATACACG
Found at i:12362951 original size:23 final size:22
Alignment explanation
Indices: 12362908--12362951 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
12362898 TTCTAAGTCG
12362908 ATATTCAATTCAATTCCACACCT
1 ATATTCAATTCAATT-CACACCT
12362931 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
12362952 TTAGTCAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.36, C:0.25, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACCT
Found at i:12368483 original size:45 final size:45
Alignment explanation
Indices: 12368418--12368507 Score: 144
Period size: 45 Copynumber: 2.0 Consensus size: 45
12368408 GGAAACCTTG
* * *
12368418 ACTCTTTGAGTGCCATGAAACTGGTAGATCAATCTCCATCGATTA
1 ACTCTTTGAGTGCCACGAAACTAGCAGATCAATCTCCATCGATTA
*
12368463 ACTCTTTGAGTGCCACGAAACTAGCAGATTAATCTCCATCGATTA
1 ACTCTTTGAGTGCCACGAAACTAGCAGATCAATCTCCATCGATTA
12368508 TCAATATTGA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (45 bp):
ACTCTTTGAGTGCCACGAAACTAGCAGATCAATCTCCATCGATTA
Found at i:12370030 original size:27 final size:27
Alignment explanation
Indices: 12369981--12370034 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
12369971 TGAACTTTTG
*
12369981 AGAATTGGGACTGCCCACAACCCTCTA
1 AGAATTGGGACTACCCACAACCCTCTA
* * *
12370008 AGAATTGGGGCTACTCACGACCCTCTA
1 AGAATTGGGACTACCCACAACCCTCTA
12370035 GTAATTGAAG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.28, C:0.31, G:0.20, T:0.20
Consensus pattern (27 bp):
AGAATTGGGACTACCCACAACCCTCTA
Found at i:12371951 original size:24 final size:24
Alignment explanation
Indices: 12371904--12371951 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
12371894 AGATTTTATG
* *
12371904 CTAATAAATGCTAAATATATTATA
1 CTAATAAATACTAAATATACTATA
12371928 CTAATAAATACTAAATCAT-CTATA
1 CTAATAAATACTAAAT-ATACTATA
12371952 AAGAAAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 19 0.90
25 2 0.10
ACGTcount: A:0.50, C:0.12, G:0.02, T:0.35
Consensus pattern (24 bp):
CTAATAAATACTAAATATACTATA
Found at i:12375534 original size:178 final size:180
Alignment explanation
Indices: 12375225--12375584 Score: 521
Period size: 178 Copynumber: 2.0 Consensus size: 180
12375215 AAGTTTTGAG
** * * * *
12375225 TCTAAACTCAAAAAAAAAAAATCTTATTTGTTTTAGAATAAAAAAGTAAATCAATTAAATTAAGT
1 TCTAAACTCAAAAAAAAAAAATCTTATTTACTTAAAAATAAAAAAGTAAAACAAGTAAATTAAGT
* * * *
12375290 TCAGATCATGTTGATGTCGTGTCTCCTATTAAATTTTGCTTTCGGAATGGATTTACTTTTCTTAA
66 TCAGATCATGTCGAAGTCGGGTCTCCTATTAAATTTTGATTTCGGAATGGATTTACTTTTCTTAA
* *
12375355 GAGTCGGGGCCAGGTGGGGCA-GATTAGTCAAGCTTCGAGTTGAGCAAAAA
131 GAGTCGGGACCAGGTGGGG-AGGATTAGTCAAGCTTCGAGTCGAGCAAAAA
* *
12375405 TCTAAACT-AAAAAAAAACAATTTTATTTACTTAAAAATAAAAAA-TAAAACAAGTAAATTAAGT
1 TCTAAACTCAAAAAAAAAAAATCTTATTTACTTAAAAATAAAAAAGTAAAACAAGTAAATTAAGT
*
12375468 TCAGATCATGTCGAAGTCGGGTCTCCTATTAAATTTTGATTTCAGG-ATGGATTTATTTTTCTTA
66 TCAGATCATGTCGAAGTCGGGTCTCCTATTAAATTTTGATTTC-GGAATGGATTTACTTTTCTTA
* *
12375532 AGAGTCGGGATCATGTGGGGAGGATTAGTCAAGCTTCGAGTCGAGCAAAAA
130 AGAGTCGGGACCAGGTGGGGAGGATTAGTCAAGCTTCGAGTCGAGCAAAAA
12375583 TC
1 TC
12375585 CACTCTGTCC
Statistics
Matches: 161, Mismatches: 17, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
177 1 0.01
178 120 0.75
179 32 0.20
180 8 0.05
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.33
Consensus pattern (180 bp):
TCTAAACTCAAAAAAAAAAAATCTTATTTACTTAAAAATAAAAAAGTAAAACAAGTAAATTAAGT
TCAGATCATGTCGAAGTCGGGTCTCCTATTAAATTTTGATTTCGGAATGGATTTACTTTTCTTAA
GAGTCGGGACCAGGTGGGGAGGATTAGTCAAGCTTCGAGTCGAGCAAAAA
Found at i:12376784 original size:27 final size:25
Alignment explanation
Indices: 12376732--12376787 Score: 67
Period size: 27 Copynumber: 2.2 Consensus size: 25
12376722 TAAAACGGTA
**
12376732 ATTTTACCCTAGGGGTATTTTGGTC
1 ATTTTACCCTAGGGGTATTTAAGTC
*
12376757 ATTTTACCCTTCGAGGGTATTTAAGTC
1 ATTTTACCC-TAG-GGGTATTTAAGTC
12376784 ATTT
1 ATTT
12376788 AACAACCTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 9 0.35
26 2 0.08
27 15 0.58
ACGTcount: A:0.20, C:0.16, G:0.20, T:0.45
Consensus pattern (25 bp):
ATTTTACCCTAGGGGTATTTAAGTC
Found at i:12378764 original size:3 final size:3
Alignment explanation
Indices: 12378756--12378780 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
12378746 AGCTTTCCTT
12378756 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
12378781 AGCTTTAACC
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:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:12385801 original size:29 final size:29
Alignment explanation
Indices: 12385764--12385828 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 29
12385754 CTGTCGACGC
* *
12385764 CACACGGCCATGTGCCAGGCCGTGTGTGA
1 CACACGGCCATGTACCAGGACGTGTGTGA
* *
12385793 CACATGGCCATGTACGAGGACGTGTGTGA
1 CACACGGCCATGTACCAGGACGTGTGTGA
12385822 CACACGG
1 CACACGG
12385829 TCTAGGCCAG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.22, C:0.28, G:0.34, T:0.17
Consensus pattern (29 bp):
CACACGGCCATGTACCAGGACGTGTGTGA
Found at i:12385939 original size:28 final size:28
Alignment explanation
Indices: 12385846--12385947 Score: 80
Period size: 28 Copynumber: 3.5 Consensus size: 28
12385836 CAGTTTTGTT
* *
12385846 TGTGTGGACCACACGAGAGTGTGTGGGC
1 TGTGTGGACCACACGAGGGTGTGTGGTC
* * * *
12385874 CGTGTGTGACACACAGTCTAGGCTAGTTTGGT-
1 TGTGTG-GAC-CACA--CGAGGGT-GTGTGGTC
12385906 TCGTGTGGACCACACGAGGGTGTGTGGTC
1 T-GTGTGGACCACACGAGGGTGTGTGGTC
*
12385935 TGTGTGGGCCACA
1 TGTGTGGACCACA
12385948 TGGGGAAGCC
Statistics
Matches: 56, Mismatches: 11, Indels: 14
0.69 0.14 0.17
Matches are distributed among these distances:
28 22 0.39
29 9 0.16
30 4 0.07
31 4 0.07
32 7 0.12
33 10 0.18
ACGTcount: A:0.17, C:0.20, G:0.38, T:0.25
Consensus pattern (28 bp):
TGTGTGGACCACACGAGGGTGTGTGGTC
Found at i:12385940 original size:61 final size:61
Alignment explanation
Indices: 12385813--12385932 Score: 195
Period size: 61 Copynumber: 2.0 Consensus size: 61
12385803 TGTACGAGGA
* * *
12385813 CGTGTGTGACACACGGTCTAGGCCAGTTTTGTTTGTGTGGACCACACGAGAGTGTGTGGGC
1 CGTGTGTGACACACAGTCTAGGCCAGTTTGGTTCGTGTGGACCACACGAGAGTGTGTGGGC
* *
12385874 CGTGTGTGACACACAGTCTAGGCTAGTTTGGTTCGTGTGGACCACACGAGGGTGTGTGG
1 CGTGTGTGACACACAGTCTAGGCCAGTTTGGTTCGTGTGGACCACACGAGAGTGTGTGG
12385933 TCTGTGTGGG
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
61 54 1.00
ACGTcount: A:0.17, C:0.19, G:0.37, T:0.28
Consensus pattern (61 bp):
CGTGTGTGACACACAGTCTAGGCCAGTTTGGTTCGTGTGGACCACACGAGAGTGTGTGGGC
Found at i:12408557 original size:18 final size:18
Alignment explanation
Indices: 12408513--12408564 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
12408503 CAGCAACTTT
12408513 TTCTTCTTCAGCAACAAC
1 TTCTTCTTCAGCAACAAC
**
12408531 TTCCGCTTC-GACAACAAC
1 TTCTTCTTCAG-CAACAAC
*
12408549 TTCTTCTTCTGCAACA
1 TTCTTCTTCAGCAACA
12408565 TCAATTTCTT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
17 1 0.04
18 26 0.93
19 1 0.04
ACGTcount: A:0.25, C:0.35, G:0.08, T:0.33
Consensus pattern (18 bp):
TTCTTCTTCAGCAACAAC
Found at i:12423429 original size:174 final size:175
Alignment explanation
Indices: 12423130--12423478 Score: 673
Period size: 174 Copynumber: 2.0 Consensus size: 175
12423120 CCAGCGGCTT
12423130 CCAAAATTAAATCTGTACTTGCGTCAATTAGCATCATGCCAATTAATCATCACCAGTTCTAAGTG
1 CCAAAATTAAATCTGTACTTGCGTCAATTAGCATCATGCCAATTAATCATCACCAGTTCTAAGTG
12423195 AAATTAAGAAATTCGATTACTCAGTTGCACTTAGATGATTATGAGAAAAATCCTAAATTGAATAG
66 AAATTAAGAAATTCGATTACTCAGTTGCACTTAGATGATTATGAGAAAAATCCTAAATTGAATAG
* *
12423260 GTGATCAATCTAATTAATTTAGAAAAATTCCTTGAACGATAAAAC
131 GTGATCAATCTAATTAATTTAGAAAAATTCCTTAAAAGATAAAAC
12423305 CCAAAATT-AATCTGTACTTGCGTCAATTAGCATCATGCCAATTAATCATCACCAGTTCTAAGTG
1 CCAAAATTAAATCTGTACTTGCGTCAATTAGCATCATGCCAATTAATCATCACCAGTTCTAAGTG
12423369 AAATTAAGAAATTCGATTACTCAGTTGCACTTAGATGATTATGAGAAAAATCCTAAATTGAATAG
66 AAATTAAGAAATTCGATTACTCAGTTGCACTTAGATGATTATGAGAAAAATCCTAAATTGAATAG
12423434 GTGATCAATCTAATTAATTTAGAAAAATTCCTTAAAAGATAAAAC
131 GTGATCAATCTAATTAATTTAGAAAAATTCCTTAAAAGATAAAAC
12423479 TTAGCAATTT
Statistics
Matches: 172, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
174 164 0.95
175 8 0.05
ACGTcount: A:0.40, C:0.16, G:0.13, T:0.31
Consensus pattern (175 bp):
CCAAAATTAAATCTGTACTTGCGTCAATTAGCATCATGCCAATTAATCATCACCAGTTCTAAGTG
AAATTAAGAAATTCGATTACTCAGTTGCACTTAGATGATTATGAGAAAAATCCTAAATTGAATAG
GTGATCAATCTAATTAATTTAGAAAAATTCCTTAAAAGATAAAAC
Found at i:12442915 original size:19 final size:19
Alignment explanation
Indices: 12442875--12442915 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
12442865 TTGAACTTGA
* *
12442875 AAATTGGACCTGAGATCGT
1 AAATTGGACCTGAGAGCCT
*
12442894 AAATTGGACCTGGGAGCCT
1 AAATTGGACCTGAGAGCCT
12442913 AAA
1 AAA
12442916 ACCAATACCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.34, C:0.17, G:0.27, T:0.22
Consensus pattern (19 bp):
AAATTGGACCTGAGAGCCT
Found at i:12443264 original size:17 final size:17
Alignment explanation
Indices: 12443242--12443337 Score: 67
Period size: 17 Copynumber: 5.6 Consensus size: 17
12443232 ATTTTAATAG
12443242 TTTAATATTTAATTTAA
1 TTTAATATTTAATTTAA
12443259 TTTAATATTT-ATCTTAA
1 TTTAATATTTAAT-TTAA
* *
12443276 --TAGTATTTTA-TTAA
1 TTTAATATTTAATTTAA
* *
12443290 TTTAGTATTAAAGTGATT-A
1 TTTAATATTTAA-T--TTAA
*
12443309 TCTTAATATTAAATTTAA
1 T-TTAATATTTAATTTAA
12443327 TTTAATATTTA
1 TTTAATATTTA
12443338 CCTTGTAGAT
Statistics
Matches: 64, Mismatches: 5, Indels: 20
0.72 0.06 0.22
Matches are distributed among these distances:
14 4 0.06
15 7 0.11
16 11 0.17
17 25 0.39
18 2 0.03
19 3 0.05
20 12 0.19
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (17 bp):
TTTAATATTTAATTTAA
Found at i:12443417 original size:23 final size:24
Alignment explanation
Indices: 12443376--12443422 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
12443366 ATAAGATTTA
12443376 ATATTAAATTTAAGATAAA-TGTT
1 ATATTAAATTTAAGATAAAGTGTT
*
12443399 ATATT-AATTTAATATTAAAGTGTT
1 ATATTAAATTTAAGA-TAAAGTGTT
12443423 TAAGTTCAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 8 0.38
23 9 0.43
24 4 0.19
ACGTcount: A:0.45, C:0.00, G:0.09, T:0.47
Consensus pattern (24 bp):
ATATTAAATTTAAGATAAAGTGTT
Found at i:12445782 original size:87 final size:86
Alignment explanation
Indices: 12445620--12445782 Score: 231
Period size: 87 Copynumber: 1.9 Consensus size: 86
12445610 AACATGCATA
* *
12445620 AGGTTGAGTTCTTACCCTTAATGAATTCATATCCCAAGTTTTAGATGGTCCTATTGAAATGAACT
1 AGGTTGAGTTATTACCCTTAATGAATTCATATCCCAAGTTTTAGATGGTCCTAGTGAAATGAACT
12445685 TGATGAATTCACCAACCTGTG
66 TGATGAATTCACCAACCTGTG
* * * *
12445706 AGGTTGAGTTTATTACTCTTAATGAGTTCATATCCCAAAG-TTTGGGTGGTCCTAGTGAAAT-AG
1 AGGTTGAG-TTATTACCCTTAATGAATTCATATCCC-AAGTTTTAGATGGTCCTAGTGAAATGA-
12445769 ACTTGATGAATTCA
63 ACTTGATGAATTCA
12445783 TCGATTTTAA
Statistics
Matches: 68, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
86 9 0.13
87 56 0.82
88 3 0.04
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.36
Consensus pattern (86 bp):
AGGTTGAGTTATTACCCTTAATGAATTCATATCCCAAGTTTTAGATGGTCCTAGTGAAATGAACT
TGATGAATTCACCAACCTGTG
Found at i:12448504 original size:6 final size:7
Alignment explanation
Indices: 12448470--12448502 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
12448460 TTTGAACTAG
12448470 AAAAAAT
1 AAAAAAT
12448477 AAAAAAT
1 AAAAAAT
12448484 AAAAAAT
1 AAAAAAT
12448491 AAAAAAT
1 AAAAAAT
12448498 AAAAA
1 AAAAA
12448503 TAGAATTAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAAAT
Found at i:12454918 original size:36 final size:36
Alignment explanation
Indices: 12454877--12454950 Score: 103
Period size: 36 Copynumber: 2.1 Consensus size: 36
12454867 TCAAATGTTC
*
12454877 TTTTAGTACCTGAAATAGACCAAAACTTGCTTGGTG
1 TTTTAGTACCTGAAATAGACCAAAACTTGCTTAGTG
*** *
12454913 TTTTAGTGTTTGAAATAGACCAAAACTTTCTTAGTG
1 TTTTAGTACCTGAAATAGACCAAAACTTGCTTAGTG
12454949 TT
1 TT
12454951 GGCTAACTAC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.39
Consensus pattern (36 bp):
TTTTAGTACCTGAAATAGACCAAAACTTGCTTAGTG
Found at i:12461335 original size:12 final size:12
Alignment explanation
Indices: 12461318--12461342 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12461308 ATTATTCTGT
12461318 AAAAATAAAATA
1 AAAAATAAAATA
12461330 AAAAATAAAATA
1 AAAAATAAAATA
12461342 A
1 A
12461343 GCTTGAACAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (12 bp):
AAAAATAAAATA
Found at i:12466187 original size:813 final size:813
Alignment explanation
Indices: 12464621--12466247 Score: 3254
Period size: 813 Copynumber: 2.0 Consensus size: 813
12464611 CAACTAGTTG
12464621 TAATATCACTGTAGTAGATTTCATGTGACCAATTCCCAACTTTCTGAAAGTAGATAGTGGCATTA
1 TAATATCACTGTAGTAGATTTCATGTGACCAATTCCCAACTTTCTGAAAGTAGATAGTGGCATTA
12464686 GGTTGATGCTAGCTCTCAAGTTGCATAAAGCCTTACCCAAATAATGATTTCCAATTGAACATGGA
66 GGTTGATGCTAGCTCTCAAGTTGCATAAAGCCTTACCCAAATAATGATTTCCAATTGAACATGGA
12464751 AGAGTAAAGCTCCCAGGATCTTTCATTTTGGGGGCCAACTTATTTGTCAAAACAGCACTACAGCC
131 AGAGTAAAGCTCCCAGGATCTTTCATTTTGGGGGCCAACTTATTTGTCAAAACAGCACTACAGCC
12464816 TTCTATAAGTGTAATAGATTCCATATCACTAAGCTTCTTCTTCTTGGACCTGAGCTCCTTCATAA
196 TTCTATAAGTGTAATAGATTCCATATCACTAAGCTTCTTCTTCTTGGACCTGAGCTCCTTCATAA
12464881 ATTTCCCATAATTCAGAATTTTCACAAGAGCGTCTACTAAAAGAATATTAACCTGAAGTTGCTTT
261 ATTTCCCATAATTCAGAATTTTCACAAGAGCGTCTACTAAAAGAATATTAACCTGAAGTTGCTTT
12464946 AATGTCTTCAAGAACTATTGGTACTGCTTATCCTGCTCATTCTTCCTGAATCTTTGTGAAAAAAA
326 AATGTCTTCAAGAACTATTGGTACTGCTTATCCTGCTCATTCTTCCTGAATCTTTGTGAAAAAAA
12465011 GGTAAAGGTGGAGATACATCTGATTACGCCGAAACATTTGATTACGTTGACAGTTTCGAAGGTTG
391 GGTAAAGGTGGAGATACATCTGATTACGCCGAAACATTTGATTACGTTGACAGTTTCGAAGGTTG
12465076 GACATTAAGCATATGAGTGACAATTTGTGGAACTTCTATGTTCAAATTCAACATTCTCACCAAGG
456 GACATTAAGCATATGAGTGACAATTTGTGGAACTTCTATGTTCAAATTCAACATTCTCACCAAGG
12465141 ATCACTTCACAGTATCTTAAGGTGTTACAGTAGAGTCTATAGTTAGCTCACCAGTTTGGTTACCA
521 ATCACTTCACAGTATCTTAAGGTGTTACAGTAGAGTCTATAGTTAGCTCACCAGTTTGGTTACCA
12465206 CTCCTAAGCGTGATAGCTTTGTAGTGTTCTTTCCCCCTCGGACTGGGATTTTCTATGTCACTAGG
586 CTCCTAAGCGTGATAGCTTTGTAGTGTTCTTTCCCCCTCGGACTGGGATTTTCTATGTCACTAGG
12465271 TAGTGTGTCCGGTGGTCGAGTATTCAGATTCAAAGCAAGTTTCCATAATTGTGCCTCCAATGCCC
651 TAGTGTGTCCGGTGGTCGAGTATTCAGATTCAAAGCAAGTTTCCATAATTGTGCCTCCAATGCCC
12465336 GAATACAAGATGAATTCCCTTACACAATAACTTCTGTGCGAGTCATATGCTCATGCATTAAAGCC
716 GAATACAAGATGAATTCCCTTACACAATAACTTCTGTGCGAGTCATATGCTCATGCATTAAAGCC
12465401 TCAAAAGCTGCTAATGGGTTAGAAGTAGAAGCA
781 TCAAAAGCTGCTAATGGGTTAGAAGTAGAAGCA
12465434 TAATATCACTGTAGTAGATTTCATGTGACCAATTCCCAACTTTCTGAAAGTAGATAGTGGCATTA
1 TAATATCACTGTAGTAGATTTCATGTGACCAATTCCCAACTTTCTGAAAGTAGATAGTGGCATTA
12465499 GGTTGATGCTAGCTCTCAAGTTGCATAAAGCCTTACCCAAATAATGATTTCCAATTGAACATGGA
66 GGTTGATGCTAGCTCTCAAGTTGCATAAAGCCTTACCCAAATAATGATTTCCAATTGAACATGGA
12465564 AGAGTAAAGCTCCCAGGATCTTTCATTTTGGGGGCCAACTTATTTGTCAAAACAGCACTACAGCC
131 AGAGTAAAGCTCCCAGGATCTTTCATTTTGGGGGCCAACTTATTTGTCAAAACAGCACTACAGCC
12465629 TTCTATAAGTGTAATAGATTCCATATCACTAAGCTTCTTCTTCTTGGACCTGAGCTCCTTCATAA
196 TTCTATAAGTGTAATAGATTCCATATCACTAAGCTTCTTCTTCTTGGACCTGAGCTCCTTCATAA
12465694 ATTTCCCATAATTCAGAATTTTCACAAGAGCGTCTACTAAAAGAATATTAACCTGAAGTTGCTTT
261 ATTTCCCATAATTCAGAATTTTCACAAGAGCGTCTACTAAAAGAATATTAACCTGAAGTTGCTTT
12465759 AATGTCTTCAAGAACTATTGGTACTGCTTATCCTGCTCATTCTTCCTGAATCTTTGTGAAAAAAA
326 AATGTCTTCAAGAACTATTGGTACTGCTTATCCTGCTCATTCTTCCTGAATCTTTGTGAAAAAAA
12465824 GGTAAAGGTGGAGATACATCTGATTACGCCGAAACATTTGATTACGTTGACAGTTTCGAAGGTTG
391 GGTAAAGGTGGAGATACATCTGATTACGCCGAAACATTTGATTACGTTGACAGTTTCGAAGGTTG
12465889 GACATTAAGCATATGAGTGACAATTTGTGGAACTTCTATGTTCAAATTCAACATTCTCACCAAGG
456 GACATTAAGCATATGAGTGACAATTTGTGGAACTTCTATGTTCAAATTCAACATTCTCACCAAGG
12465954 ATCACTTCACAGTATCTTAAGGTGTTACAGTAGAGTCTATAGTTAGCTCACCAGTTTGGTTACCA
521 ATCACTTCACAGTATCTTAAGGTGTTACAGTAGAGTCTATAGTTAGCTCACCAGTTTGGTTACCA
12466019 CTCCTAAGCGTGATAGCTTTGTAGTGTTCTTTCCCCCTCGGACTGGGATTTTCTATGTCACTAGG
586 CTCCTAAGCGTGATAGCTTTGTAGTGTTCTTTCCCCCTCGGACTGGGATTTTCTATGTCACTAGG
12466084 TAGTGTGTCCGGTGGTCGAGTATTCAGATTCAAAGCAAGTTTCCATAATTGTGCCTCCAATGCCC
651 TAGTGTGTCCGGTGGTCGAGTATTCAGATTCAAAGCAAGTTTCCATAATTGTGCCTCCAATGCCC
12466149 GAATACAAGATGAATTCCCTTACACAATAACTTCTGTGCGAGTCATATGCTCATGCATTAAAGCC
716 GAATACAAGATGAATTCCCTTACACAATAACTTCTGTGCGAGTCATATGCTCATGCATTAAAGCC
12466214 TCAAAAGCTGCTAATGGGTTAGAAGTAGAAGCA
781 TCAAAAGCTGCTAATGGGTTAGAAGTAGAAGCA
12466247 T
1 T
12466248 GTGTGTACTG
Statistics
Matches: 814, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
813 814 1.00
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (813 bp):
TAATATCACTGTAGTAGATTTCATGTGACCAATTCCCAACTTTCTGAAAGTAGATAGTGGCATTA
GGTTGATGCTAGCTCTCAAGTTGCATAAAGCCTTACCCAAATAATGATTTCCAATTGAACATGGA
AGAGTAAAGCTCCCAGGATCTTTCATTTTGGGGGCCAACTTATTTGTCAAAACAGCACTACAGCC
TTCTATAAGTGTAATAGATTCCATATCACTAAGCTTCTTCTTCTTGGACCTGAGCTCCTTCATAA
ATTTCCCATAATTCAGAATTTTCACAAGAGCGTCTACTAAAAGAATATTAACCTGAAGTTGCTTT
AATGTCTTCAAGAACTATTGGTACTGCTTATCCTGCTCATTCTTCCTGAATCTTTGTGAAAAAAA
GGTAAAGGTGGAGATACATCTGATTACGCCGAAACATTTGATTACGTTGACAGTTTCGAAGGTTG
GACATTAAGCATATGAGTGACAATTTGTGGAACTTCTATGTTCAAATTCAACATTCTCACCAAGG
ATCACTTCACAGTATCTTAAGGTGTTACAGTAGAGTCTATAGTTAGCTCACCAGTTTGGTTACCA
CTCCTAAGCGTGATAGCTTTGTAGTGTTCTTTCCCCCTCGGACTGGGATTTTCTATGTCACTAGG
TAGTGTGTCCGGTGGTCGAGTATTCAGATTCAAAGCAAGTTTCCATAATTGTGCCTCCAATGCCC
GAATACAAGATGAATTCCCTTACACAATAACTTCTGTGCGAGTCATATGCTCATGCATTAAAGCC
TCAAAAGCTGCTAATGGGTTAGAAGTAGAAGCA
Found at i:12472190 original size:18 final size:18
Alignment explanation
Indices: 12472167--12472205 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
12472157 CATATGAGAT
12472167 GTTATGATTGTGCTATGA
1 GTTATGATTGTGCTATGA
12472185 GTTATGATTGTGCTATGA
1 GTTATGATTGTGCTATGA
12472203 GTT
1 GTT
12472206 TATGTTGATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.21, C:0.05, G:0.28, T:0.46
Consensus pattern (18 bp):
GTTATGATTGTGCTATGA
Found at i:12476181 original size:23 final size:24
Alignment explanation
Indices: 12476155--12476202 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
12476145 GACCACCTCA
*
12476155 AATTGCC-ATTCATTTTTTTAATC
1 AATTGCCTATTCAATTTTTTAATC
* *
12476178 AATTTCCTCTTCAATTTTTTAATC
1 AATTGCCTATTCAATTTTTTAATC
12476202 A
1 A
12476203 GTACAGTAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 6 0.29
24 15 0.71
ACGTcount: A:0.27, C:0.19, G:0.02, T:0.52
Consensus pattern (24 bp):
AATTGCCTATTCAATTTTTTAATC
Found at i:12493877 original size:19 final size:19
Alignment explanation
Indices: 12493835--12493877 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
12493825 ATGCAAGCAA
*
12493835 CAAGCTTAACCGAATTCTC
1 CAAGCTTAACCGAATGCTC
* *
12493854 TAAGCTTAATCGAATGCTC
1 CAAGCTTAACCGAATGCTC
12493873 CAAGC
1 CAAGC
12493878 CTTTTTTAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.33, C:0.28, G:0.14, T:0.26
Consensus pattern (19 bp):
CAAGCTTAACCGAATGCTC
Found at i:12505150 original size:23 final size:24
Alignment explanation
Indices: 12505124--12505176 Score: 90
Period size: 23 Copynumber: 2.2 Consensus size: 24
12505114 GCATGATTAG
12505124 TAATTAGTTAAGTTAATT-AAATA
1 TAATTAGTTAAGTTAATTAAAATA
*
12505147 TAATTAGTTAAGTTAATTAAAATT
1 TAATTAGTTAAGTTAATTAAAATA
12505171 TAATTA
1 TAATTA
12505177 ACCATAAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
23 18 0.64
24 10 0.36
ACGTcount: A:0.47, C:0.00, G:0.08, T:0.45
Consensus pattern (24 bp):
TAATTAGTTAAGTTAATTAAAATA
Found at i:12526698 original size:24 final size:24
Alignment explanation
Indices: 12526671--12526719 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
12526661 CGCAAGGCCA
*
12526671 TGTGGTCGCCCGTGCGGTAAGCCG
1 TGTGGTCGCCCGTGCGATAAGCCG
* *
12526695 TGTGGTCGCCTGTGCGATAGGCCG
1 TGTGGTCGCCCGTGCGATAAGCCG
12526719 T
1 T
12526720 ATGGCTGAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.08, C:0.27, G:0.41, T:0.24
Consensus pattern (24 bp):
TGTGGTCGCCCGTGCGATAAGCCG
Found at i:12527645 original size:13 final size:13
Alignment explanation
Indices: 12527627--12527651 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12527617 TATTTTAATA
12527627 TTATTTTGTGTGT
1 TTATTTTGTGTGT
12527640 TTATTTTGTGTG
1 TTATTTTGTGTG
12527652 CATTTGATTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.00, G:0.24, T:0.68
Consensus pattern (13 bp):
TTATTTTGTGTGT
Found at i:12529324 original size:331 final size:332
Alignment explanation
Indices: 12528849--12529513 Score: 1233
Period size: 331 Copynumber: 2.0 Consensus size: 332
12528839 CGAATATGTA
12528849 TGAGTATTCAGGTATATGTTCTTGTTTCGAAAATAAGTATAGAGTAATATATGGTTGTTAGATTC
1 TGAGTATTCAGGTATATGTTCTTGTTTCGAAAATAAGTATAGAGTAATATATGGTTGTTAGATTC
12528914 GAATATGCATATATGTACATGCATAAGATTTTGCATTGAAATGGTATATGAAATTATATAGGTAT
66 GAATATGCATATATGTACATGCATAAGATTTTGCATTGAAATGGTATATGAAATTATATAGGTAT
12528979 ATAGAGAATTCAAATGTTTAAGGTACCTAGTATATTATAAGTTAAATTTTATGATATTAGAAGTG
131 ATAGAGAATTCAAATGTTTAAGGTACCTAGTATATTATAAGTTAAATTTTATGATATTAGAAGTG
* *
12529044 GAATCTATAGTATGA-GGTTATATATACAGAAATATGTTTCAGTTGAATCATTGAATTATTTAAG
196 GAATCTATAGTATGATGGTTATATATACAGAAATATGTTTCAGTTGAACCATTGAATTATTTAAA
* *
12529108 CTAGATTTGATGATTAGGATTTATATCTATCCATGTGTTTTAAAGATATAAGTTATGAATATTGA
261 CTAGATTTGATGATTAGGATCTATACCTATCCATGTGTTTTAAAGATATAAGTTATGAATATTGA
12529173 GCTGAAT
326 GCTGAAT
*
12529180 TGAGTATTCAGGTATATGTTCTTGTTTCGAAAATAAGTATAGAGTAATATATGGTTGTTATATTC
1 TGAGTATTCAGGTATATGTTCTTGTTTCGAAAATAAGTATAGAGTAATATATGGTTGTTAGATTC
12529245 GAATATGCATATATGTACATGCATAAGATTTTGCATTGAAATGGTATATGAAATTATATAGGTAT
66 GAATATGCATATATGTACATGCATAAGATTTTGCATTGAAATGGTATATGAAATTATATAGGTAT
12529310 ATAGAGAATTCAAATGTTTAAGGTACCTAGTATATTATAAGTTAAATTTTATGATATTAGAAGTG
131 ATAGAGAATTCAAATGTTTAAGGTACCTAGTATATTATAAGTTAAATTTTATGATATTAGAAGTG
* * * *
12529375 GAATCTATAGTGTGATGGTTATATATACATAAATGTGTTTCGGTTGAACCATTGAATTATTTAAA
196 GAATCTATAGTATGATGGTTATATATACAGAAATATGTTTCAGTTGAACCATTGAATTATTTAAA
*
12529440 CTAGATTTGATGATTGGGATCTATACCTATCCATGTGTTTTAAAGATATAAGTTATGAATATTGA
261 CTAGATTTGATGATTAGGATCTATACCTATCCATGTGTTTTAAAGATATAAGTTATGAATATTGA
12529505 GCTGAAT
326 GCTGAAT
12529512 TG
1 TG
12529514 TATGTGGATT
Statistics
Matches: 323, Mismatches: 10, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
331 208 0.64
332 115 0.36
ACGTcount: A:0.35, C:0.06, G:0.19, T:0.40
Consensus pattern (332 bp):
TGAGTATTCAGGTATATGTTCTTGTTTCGAAAATAAGTATAGAGTAATATATGGTTGTTAGATTC
GAATATGCATATATGTACATGCATAAGATTTTGCATTGAAATGGTATATGAAATTATATAGGTAT
ATAGAGAATTCAAATGTTTAAGGTACCTAGTATATTATAAGTTAAATTTTATGATATTAGAAGTG
GAATCTATAGTATGATGGTTATATATACAGAAATATGTTTCAGTTGAACCATTGAATTATTTAAA
CTAGATTTGATGATTAGGATCTATACCTATCCATGTGTTTTAAAGATATAAGTTATGAATATTGA
GCTGAAT
Found at i:12529673 original size:41 final size:42
Alignment explanation
Indices: 12529616--12529731 Score: 182
Period size: 41 Copynumber: 2.8 Consensus size: 42
12529606 AAATTATTCA
*
12529616 GACTATATGTCTAGCAGGCTAAGTGTCGGTGAACTAAATC-G
1 GACTATATGTCTAGCAGGCTAAGTGCCGGTGAACTAAATCAG
*
12529657 GACTATATGTCTAGCAGGCTAAGTGCCGGTGAACTGAATCAG
1 GACTATATGTCTAGCAGGCTAAGTGCCGGTGAACTAAATCAG
* *
12529699 G-CTATAGGCCTAGCAGGCTAAGTGCCGGTGAAC
1 GACTATATGTCTAGCAGGCTAAGTGCCGGTGAAC
12529732 GAAACTAGAC
Statistics
Matches: 70, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
41 68 0.97
42 2 0.03
ACGTcount: A:0.28, C:0.20, G:0.29, T:0.23
Consensus pattern (42 bp):
GACTATATGTCTAGCAGGCTAAGTGCCGGTGAACTAAATCAG
Found at i:12529745 original size:41 final size:41
Alignment explanation
Indices: 12529615--12529751 Score: 170
Period size: 41 Copynumber: 3.3 Consensus size: 41
12529605 AAAATTATTC
* *
12529615 AGACTATATGTCTAGCAGGCTAAGTGTCGGTGAACTAAA-T
1 AGACTATATGTCTAGCAGGCTAAGTGCCGGTGAACGAAACT
* *
12529655 CGGACTATATGTCTAGCAGGCTAAGTGCCGGTGAACTGAATC-
1 -AGACTATATGTCTAGCAGGCTAAGTGCCGGTGAAC-GAAACT
* * *
12529697 AGGCTATAGGCCTAGCAGGCTAAGTGCCGGTGAACGAAACT
1 AGACTATATGTCTAGCAGGCTAAGTGCCGGTGAACGAAACT
*
12529738 AGACTATAAGTCTA
1 AGACTATATGTCTA
12529752 TTAGGTGAAG
Statistics
Matches: 81, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
40 4 0.05
41 75 0.93
42 2 0.02
ACGTcount: A:0.31, C:0.19, G:0.27, T:0.23
Consensus pattern (41 bp):
AGACTATATGTCTAGCAGGCTAAGTGCCGGTGAACGAAACT
Found at i:12532096 original size:155 final size:154
Alignment explanation
Indices: 12531802--12532114 Score: 459
Period size: 155 Copynumber: 2.0 Consensus size: 154
12531792 GAGAGAGCCT
*** *
12531802 AATTTGACGTATCAAATTACGGTAGATCATATACACAATTATGCAGTTCGTCACAAGTATTAGAA
1 AATTTGACGTATCAAATTACAACAAATCATATACACAATTATGCAGTTCGTCACAAGTATTAGAA
* **
12531867 TATTAAACAATTAATTATTTAATTATTCTAATTGACAAGGCAAATATTCTAAGTTATTAAATACC
66 TATTAAACAATTAATTATTTAATTATTCTAATAGACAAAACAAATATTCTAAGTTATTAAATACC
*
12531932 TGTCAAATATTTAACAAACCGGAAC
131 TGTCAAATATCTAAC-AACCGGAAC
* * *
12531957 AATTTGACGTATCAAATTATAACAAATCGTATACACAATTATGTAGTTCGTCACAAGTATTAGAA
1 AATTTGACGTATCAAATTACAACAAATCATATACACAATTATGCAGTTCGTCACAAGTATTAGAA
* *
12532022 TATTAAACAATTACA-TATTTAATTATTCTGATAGACAAAACAAATATTCTAAGTTATTAAAT-T
66 TATTAAACAATTA-ATTATTTAATTATTCTAATAGACAAAACAAATATTCTAAGTTATTAAATAC
*
12532085 CTAGTCGAATATCTAACAACCGGAAC
130 CT-GTCAAATATCTAACAACCGGAAC
12532111 AATT
1 AATT
12532115 GTAATTCAAA
Statistics
Matches: 142, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
154 15 0.11
155 126 0.89
156 1 0.01
ACGTcount: A:0.42, C:0.14, G:0.10, T:0.34
Consensus pattern (154 bp):
AATTTGACGTATCAAATTACAACAAATCATATACACAATTATGCAGTTCGTCACAAGTATTAGAA
TATTAAACAATTAATTATTTAATTATTCTAATAGACAAAACAAATATTCTAAGTTATTAAATACC
TGTCAAATATCTAACAACCGGAAC
Found at i:12533354 original size:158 final size:158
Alignment explanation
Indices: 12533178--12533648 Score: 703
Period size: 158 Copynumber: 3.0 Consensus size: 158
12533168 CTAACTCCAT
* *
12533178 TGTGCAACAATTCACTCTCACATATGTAATATATGTAA-GTCAAATTAAGTTTTAATTAAGGAAT
1 TGTGCAACTATCCACTCTCACATATGTAATATATGTAAGGTCAAATTAAGTTTTAATTAA-GAAT
12533242 TTTTTATTATTAAGATTATATAAGATATTAATTATTATAAAATATGATCTTATTATAAAATAAAT
65 TTTTTATTATTAAGATTATATAAGATATTAATTATTATAAAATATGATCTTATTATAAAATAAAT
12533307 TTCGGTTGCCACAACGAAATACTTCTATA
130 TTCGGTTGCCACAACGAAATACTTCTATA
12533336 TGTGCAACTATCCACTCTCACATATGTAATATATGTAAGGTCAAATTAAGTTTTAATTAAGAATT
1 TGTGCAACTATCCACTCTCACATATGTAATATATGTAAGGTCAAATTAAGTTTTAATTAAGAATT
* * *
12533401 TTTTATTATTAACATTATATACGATATTATTTATTATAAAATATGATCTTATTATAAAATAAATT
66 TTTTATTATTAAGATTATATAAGATATTAATTATTATAAAATATGATCTTATTATAAAATAAATT
* * ** * *
12533466 CCAGTTATCGCAAGGAAATACTTCTATA
131 TCGGTTGCCACAACGAAATACTTCTATA
** * * *
12533494 TGTGCTGCTATCTACTCTCACATATGTAATATATGTAAGGTCAAATTAAGTTTTAATTAA-TAGT
1 TGTGCAACTATCCACTCTCACATATGTAATATATGTAAGGTCAAATTAAGTTTTAATTAAGAATT
* * * *
12533558 TTTTATTATTAAGTTTATATAATATATTAATTATTATAAAATATGACCTTATTATGAAATAAATT
66 TTTTATTATTAAGATTATATAAGATATTAATTATTATAAAATATGATCTTATTATAAAATAAATT
* * * *
12533623 TCGATTGCTACAATGGAATACTTCTA
131 TCGGTTGCCACAACGAAATACTTCTA
12533649 CAATATCTTA
Statistics
Matches: 280, Mismatches: 32, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
157 77 0.28
158 182 0.65
159 21 0.08
ACGTcount: A:0.39, C:0.10, G:0.10, T:0.41
Consensus pattern (158 bp):
TGTGCAACTATCCACTCTCACATATGTAATATATGTAAGGTCAAATTAAGTTTTAATTAAGAATT
TTTTATTATTAAGATTATATAAGATATTAATTATTATAAAATATGATCTTATTATAAAATAAATT
TCGGTTGCCACAACGAAATACTTCTATA
Found at i:12534526 original size:12 final size:12
Alignment explanation
Indices: 12534509--12534538 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
12534499 TTGTGGAATG
12534509 GTTTCAGATTGA
1 GTTTCAGATTGA
12534521 GTTTCAGATTGA
1 GTTTCAGATTGA
12534533 GTTTCA
1 GTTTCA
12534539 TAAGTGTGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.23, C:0.10, G:0.23, T:0.43
Consensus pattern (12 bp):
GTTTCAGATTGA
Found at i:12535329 original size:13 final size:13
Alignment explanation
Indices: 12535313--12535362 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
12535303 GGGGGTAGGA
12535313 TTCTGTATATTTG
1 TTCTGTATATTTG
*
12535326 TTCTGCATATTTG
1 TTCTGTATATTTG
* *
12535339 TATCTGTATATGTA
1 T-TCTGTATATTTG
12535353 TT-TGTATATT
1 TTCTGTATATT
12535363 AAAGGATTTG
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
12 7 0.23
13 14 0.45
14 10 0.32
ACGTcount: A:0.20, C:0.08, G:0.14, T:0.58
Consensus pattern (13 bp):
TTCTGTATATTTG
Found at i:12547712 original size:17 final size:18
Alignment explanation
Indices: 12547686--12547725 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
12547676 ATTAAGAATA
* *
12547686 TATAATATATTAT-TTAT
1 TATAAAATATGATCTTAT
12547703 TATAAAATATGATCTTAT
1 TATAAAATATGATCTTAT
12547721 TATAA
1 TATAA
12547726 CATAAATTCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (18 bp):
TATAAAATATGATCTTAT
Found at i:12547868 original size:155 final size:157
Alignment explanation
Indices: 12547610--12547916 Score: 469
Period size: 155 Copynumber: 2.0 Consensus size: 157
12547600 TCCAATGTGT
*
12547610 TACTATCCACTCTCACATATGAAATATATAAAGGTCAAATTAAGTTTTAATTAAGAATTTTTTAT
1 TACTATCCACTCTCACATATGAAATATATAAAGGTCAAATTAAGCTTTAATTAAGAATTTTTTAT
* * * *
12547675 TATTAAGAATATATAATATATTATTTATTATAAAATATGATCTTATTATAACATAAAT-TCCGAT
66 TATTAAGAATATATAAGATATTAATTATTATAAAATATGATCTTATTATAAAATAAATCT-CGAC
*
12547739 TGCCGCAATGAAATACTTCTATATGTAC
130 CGCCGCAATGAAATACTTCTATATGTAC
* *
12547767 TACTATCCACTCTCACATATGTAATATATATAAGGTCAAATTAAGCTTTAATTAA-TA-TTTTT-
1 TACTATCCACTCTCACATATGAAATATATA-AAGGTCAAATTAAGCTTTAATTAAGAATTTTTTA
** *
12547829 TTATTAAGTTTATATAAGATATTAATTATTATAAAATATGATCTTGTTATAAAATAAATCTCGAC
65 TTATTAAGAATATATAAGATATTAATTATTATAAAATATGATCTTATTATAAAATAAATCTCGAC
12547894 CGCCGCAATGAAATACTTCTATA
130 CGCCGCAATGAAATACTTCTATA
12547917 ATATTTTATA
Statistics
Matches: 137, Mismatches: 11, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
155 78 0.57
156 6 0.04
157 30 0.22
158 23 0.17
ACGTcount: A:0.40, C:0.12, G:0.08, T:0.40
Consensus pattern (157 bp):
TACTATCCACTCTCACATATGAAATATATAAAGGTCAAATTAAGCTTTAATTAAGAATTTTTTAT
TATTAAGAATATATAAGATATTAATTATTATAAAATATGATCTTATTATAAAATAAATCTCGACC
GCCGCAATGAAATACTTCTATATGTAC
Found at i:12548933 original size:12 final size:12
Alignment explanation
Indices: 12548916--12548949 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
12548906 AGGGGAAAAC
12548916 AGGCATAGGCCT
1 AGGCATAGGCCT
* *
12548928 AGGCATAAGCGT
1 AGGCATAGGCCT
12548940 AGGCATAGGC
1 AGGCATAGGC
12548950 ATAAGGAGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.29, C:0.21, G:0.35, T:0.15
Consensus pattern (12 bp):
AGGCATAGGCCT
Found at i:12552411 original size:18 final size:17
Alignment explanation
Indices: 12552388--12552445 Score: 54
Period size: 18 Copynumber: 3.5 Consensus size: 17
12552378 ATAATCATAT
12552388 ATTTTAATGA-TATAATAA
1 ATTTTAAT-ATTATAAT-A
12552406 ATTTTAATATTTATAATA
1 ATTTTAATA-TTATAATA
12552424 ATTTTAA-ATT-T-A-A
1 ATTTTAATATTATAATA
12552437 ATTTTAATA
1 ATTTTAATA
12552446 GTCTTAACAT
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
13 8 0.22
14 2 0.05
15 1 0.03
16 2 0.05
17 2 0.05
18 16 0.43
19 6 0.16
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (17 bp):
ATTTTAATATTATAATA
Found at i:12552422 original size:19 final size:17
Alignment explanation
Indices: 12552398--12552435 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 17
12552388 ATTTTAATGA
12552398 TATAATAAATTTTAATATT
1 TATAAT-AATTTTAA-ATT
12552417 TATAATAATTTTAAATT
1 TATAATAATTTTAAATT
12552434 TA
1 TA
12552436 AATTTTAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 5 0.26
18 8 0.42
19 6 0.32
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TATAATAATTTTAAATT
Found at i:12552573 original size:23 final size:23
Alignment explanation
Indices: 12552517--12552566 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
12552507 TTAGTATTAA
*
12552517 ATTTTA-TAGTATAAAATATGAAT
1 ATTTTACTAATAT-AAATATGAAT
*
12552540 ATTTTACTAATATAAATATGAGT
1 ATTTTACTAATATAAATATGAAT
12552563 ATTT
1 ATTT
12552567 GTTTAATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 19 0.79
24 5 0.21
ACGTcount: A:0.44, C:0.02, G:0.08, T:0.46
Consensus pattern (23 bp):
ATTTTACTAATATAAATATGAAT
Found at i:12552716 original size:17 final size:18
Alignment explanation
Indices: 12552690--12552729 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
12552680 ATTAAGAATA
* *
12552690 TATAATATATTAT-TTAT
1 TATAAAATATGATCTTAT
12552707 TATAAAATATGATCTTAT
1 TATAAAATATGATCTTAT
12552725 TATAA
1 TATAA
12552730 CATAAATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (18 bp):
TATAAAATATGATCTTAT
Found at i:12552832 original size:157 final size:158
Alignment explanation
Indices: 12552604--12553081 Score: 705
Period size: 157 Copynumber: 3.0 Consensus size: 158
12552594 CTTTTCTAAC
* *
12552604 TCTA-ATGTGCTACTATCCACTCCCACATATGTAGTATATGT-AGGTCAAATTAAGTTTTAATTA
1 TCTATATGTGCTACTATCCACTCTCACATATGTAATATATGTAAGGTCAAATTAAGTTTTAATTA
* * *
12552667 AGATTTTTTTATTATTAAGAATATATAATATATTATTTATTATAAAATATGATCTTATTATAACA
66 AGATTTTTTTATTATTAAGATTATATAAGATATTATTTATTATAAAATATGATCTTATTATAAAA
* * *
12552732 TAAATTTTGGTTGTCACAATGAAATACT
131 TAAATTTCGGTTGCCGCAATGAAATACT
* *** *
12552760 TCTATATGTGCTACTATCCACTCTCACATATGTAATGTATGTAACACCAAATTAAGTTTTAAATA
1 TCTATATGTGCTACTATCCACTCTCACATATGTAATATATGTAAGGTCAAATTAAGTTTTAATTA
* *
12552825 AGA-TTTTTTATTATTAAGATTATATAAGATTATGA-TTATTATAAAATATGATCTCATTATAAA
66 AGATTTTTTTATTATTAAGATTATATAAGA-TATTATTTATTATAAAATATGATCTTATTATAAA
12552888 ATAAATTTCGGTTGCCGCAATGAAATACT
130 ATAAATTTCGGTTGCCGCAATGAAATACT
* *
12552917 TCTATATGTGCTACTATCCACTCTTACATATGTAATATATGTAAGGTCAAATTAAGCTTTAATTA
1 TCTATATGTGCTACTATCCACTCTCACATATGTAATATATGTAAGGTCAAATTAAGTTTTAATTA
* *
12552982 ATATTTTTATTATTATTAAGTTTATATAAGATATTAATTT-TTATAAAATATGATCTTATTATAA
66 AGATTTTT-TTATTATTAAGATTATATAAGATATT-ATTTATTATAAAATATGATCTTATTATAA
* *
12553046 AATAAATTTCGATTGCCGCAATGAAATTCT
129 AATAAATTTCGGTTGCCGCAATGAAATACT
12553076 TCTATA
1 TCTATA
12553082 ACATTTTATA
Statistics
Matches: 287, Mismatches: 28, Indels: 11
0.88 0.09 0.03
Matches are distributed among these distances:
156 4 0.01
157 170 0.59
158 32 0.11
159 79 0.28
160 2 0.01
ACGTcount: A:0.37, C:0.11, G:0.09, T:0.42
Consensus pattern (158 bp):
TCTATATGTGCTACTATCCACTCTCACATATGTAATATATGTAAGGTCAAATTAAGTTTTAATTA
AGATTTTTTTATTATTAAGATTATATAAGATATTATTTATTATAAAATATGATCTTATTATAAAA
TAAATTTCGGTTGCCGCAATGAAATACT
Found at i:12552874 original size:16 final size:16
Alignment explanation
Indices: 12552842--12552890 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 16
12552832 TTATTATTAA
*
12552842 GATTA-TATAAGATTAT
1 GATTATTATAA-AATAT
12552858 GATTATTATAAAATAT
1 GATTATTATAAAATAT
12552874 GATCTCATTATAAAATA
1 GAT-T-ATTATAAAATA
12552891 AATTTCGGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
16 12 0.41
17 6 0.21
18 11 0.38
ACGTcount: A:0.47, C:0.04, G:0.08, T:0.41
Consensus pattern (16 bp):
GATTATTATAAAATAT
Found at i:12553032 original size:17 final size:18
Alignment explanation
Indices: 12552995--12553032 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
12552985 TTTTTATTAT
*
12552995 TATTAAGTTTATATAAGA
1 TATTAAGTTTATATAAAA
*
12553013 TATTAA-TTTTTATAAAA
1 TATTAAGTTTATATAAAA
12553030 TAT
1 TAT
12553033 GATCTTATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (18 bp):
TATTAAGTTTATATAAAA
Found at i:12555959 original size:27 final size:26
Alignment explanation
Indices: 12555940--12556378 Score: 443
Period size: 27 Copynumber: 16.4 Consensus size: 26
12555930 GGGTATAATA
12555940 GTCATTTTACCCTATGGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTT-G
* *
12555967 GTCATTTTATCATAT-GGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTA-TTTG
*
12555993 GTCATTTTACCCTATGGGGGTATTTCA
1 GTCATTTTACCCTATGGGGGTATTT-G
* * * *
12556020 ATCATTTTATCCTATAGGGGTAATTAG
1 GTCATTTTACCCTATGGGGGT-ATTTG
*
12556047 GTCATTTTACCCTATAGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTT-G
*
12556074 GTCATTTTACCCTATGAGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTT-G
* *
12556101 ATCATTTTACCCTATAGGGGTATTTAG
1 GTCATTTTACCCTATGGGGGTATTT-G
* * * *
12556128 TTCATTTTACCCTCTAGGGGTATTTCA
1 GTCATTTTACCCTATGGGGGTATTT-G
*
12556155 GTCA-TTTACCATATGGGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTA-TTTG
* *
12556181 GTCATTTTATCTTAT-GGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTT-G
* * *
12556207 GCCATTTTACCCTATGAGGGTATTTCA
1 GTCATTTTACCCTATGGGGGTATTT-G
*
12556234 GTCATTTTACCCTATTGGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTA-TTTG
* *
12556261 GTCATTTTACCTTATGGGCGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTT-G
* *
12556288 GTCATTTTACCTTATCGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTT-G
* *
12556315 ATCATTTTACCCTATGAGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTT-G
* *
12556342 GTTATTTTACCCTATGAGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTA-TTTG
12556369 GTCATTTTAC
1 GTCATTTTAC
12556379 TTATTTTGGG
Statistics
Matches: 349, Mismatches: 51, Indels: 24
0.82 0.12 0.06
Matches are distributed among these distances:
25 3 0.01
26 66 0.19
27 271 0.78
28 9 0.03
ACGTcount: A:0.19, C:0.16, G:0.21, T:0.44
Consensus pattern (26 bp):
GTCATTTTACCCTATGGGGGTATTTG
Found at i:12556067 original size:54 final size:52
Alignment explanation
Indices: 12555940--12556378 Score: 495
Period size: 54 Copynumber: 8.2 Consensus size: 52
12555930 GGGTATAATA
* * *
12555940 GTCATTTTACCCTATGGGGGTATTTCGGTCATTTTATCATATGGGGTATTTTG
1 GTCATTTTACCCTAT-GGGGTATTTCGGTCATTTTACCCTATGGGGTATTTAG
** * *
12555993 GTCATTTTACCCTATGGGGGTATTTCAATCATTTTATCCTATAGGGGTAATTAG
1 GTCATTTTACCCTAT-GGGGTATTTCGGTCATTTTACCCTAT-GGGGTATTTAG
*
12556047 GTCATTTTACCCTATAGGGGTATTTCGGTCATTTTACCCTATGAGGGTATTTCG
1 GTCATTTTACCCTAT-GGGGTATTTCGGTCATTTTACCCTATG-GGGTATTTAG
* * * *
12556101 ATCATTTTACCCTATAGGGGTATTTAGTTCATTTTACCCTCTAGGGGTATTTCA-
1 GTCATTTTACCCTAT-GGGGTATTTCGGTCATTTTACCCTAT-GGGGTATTT-AG
* * * * *
12556155 GTCA-TTTACCATATGGGGGTATTTTGGTCATTTTATCTTATGGGGTATTTCG
1 GTCATTTTACCCTAT-GGGGTATTTCGGTCATTTTACCCTATGGGGTATTTAG
* * *
12556207 GCCATTTTACCCTATGAGGGTATTTCAGTCATTTTACCCTATTGGGGTATTTTG
1 GTCATTTTACCCTATG-GGGTATTTCGGTCATTTTACCCTA-TGGGGTATTTAG
* * *
12556261 GTCATTTTACCTTATGGGCGTATTTCGGTCATTTTACCTTATCGGGGTATTTCG
1 GTCATTTTACCCTATGGG-GTATTTCGGTCATTTTACCCTAT-GGGGTATTTAG
* * *
12556315 ATCATTTTACCCTATGAGGGTATTTCGGTTATTTTACCCTATGAGGGTATTTTG
1 GTCATTTTACCCTATG-GGGTATTTCGGTCATTTTACCCTATG-GGGTATTTAG
12556369 GTCATTTTAC
1 GTCATTTTAC
12556379 TTATTTTGGG
Statistics
Matches: 331, Mismatches: 43, Indels: 23
0.83 0.11 0.06
Matches are distributed among these distances:
52 13 0.04
53 103 0.31
54 212 0.64
55 3 0.01
ACGTcount: A:0.19, C:0.16, G:0.21, T:0.44
Consensus pattern (52 bp):
GTCATTTTACCCTATGGGGTATTTCGGTCATTTTACCCTATGGGGTATTTAG
Found at i:12556095 original size:81 final size:80
Alignment explanation
Indices: 12555940--12556378 Score: 528
Period size: 81 Copynumber: 5.5 Consensus size: 80
12555930 GGGTATAATA
* * * *
12555940 GTCATTTTACCCTATGGGGGTATTTCGGTCATTTTATCATATGGGGTATTTTGGTCATTTTACCC
1 GTCATTTTACCCTATAGGGGTATTTCGGTCATTTTACCCTATGGGGTATTTCGGTCATTTTACCC
* *
12556005 TATGGGGGTATTTCA
66 TATGAGGGTATTTCG
* * * *
12556020 ATCATTTTATCCTATAGGGGTAATTAGGTCATTTTACCCTATAGGGGTATTTCGGTCATTTTACC
1 GTCATTTTACCCTATAGGGGTATTTCGGTCATTTTACCCTAT-GGGGTATTTCGGTCATTTTACC
12556085 CTATGAGGGTATTTCG
65 CTATGAGGGTATTTCG
* * * * *
12556101 ATCATTTTACCCTATAGGGGTATTTAGTTCATTTTACCCTCTAGGGGTATTTCAGTCA-TTTACC
1 GTCATTTTACCCTATAGGGGTATTTCGGTCATTTTACCCTAT-GGGGTATTTCGGTCATTTTACC
* * *
12556165 ATATGGGGGTATTTTG
65 CTATGAGGGTATTTCG
* * * *
12556181 GTCATTTTATCTTAT-GGGGTATTTCGGCCATTTTACCCTATGAGGGTATTTCAGTCATTTTACC
1 GTCATTTTACCCTATAGGGGTATTTCGGTCATTTTACCCTATG-GGGTATTTCGGTCATTTTACC
*
12556245 CTATTG-GGGTATTTTG
65 CTA-TGAGGGTATTTCG
* * *
12556261 GTCATTTTACCTTAT-GGGCGTATTTCGGTCATTTTACCTTATCGGGGTATTTCGATCATTTTAC
1 GTCATTTTACCCTATAGGG-GTATTTCGGTCATTTTACCCTAT-GGGGTATTTCGGTCATTTTAC
12556325 CCTATGAGGGTATTTCG
64 CCTATGAGGGTATTTCG
* *
12556342 GTTATTTTACCCTAT-GAGGGTATTTTGGTCATTTTAC
1 GTCATTTTACCCTATAG-GGGTATTTCGGTCATTTTAC
12556379 TTATTTTGGG
Statistics
Matches: 316, Mismatches: 35, Indels: 15
0.86 0.10 0.04
Matches are distributed among these distances:
78 1 0.00
79 36 0.11
80 103 0.33
81 173 0.55
82 3 0.01
ACGTcount: A:0.19, C:0.16, G:0.21, T:0.44
Consensus pattern (80 bp):
GTCATTTTACCCTATAGGGGTATTTCGGTCATTTTACCCTATGGGGTATTTCGGTCATTTTACCC
TATGAGGGTATTTCG
Found at i:12556321 original size:214 final size:215
Alignment explanation
Indices: 12555926--12556354 Score: 636
Period size: 214 Copynumber: 2.0 Consensus size: 215
12555916 ATTTAATCTC
*
12555926 CTAGGGGTATAATAGTCATTTTACCCTATGGGGGTATTTCGGTCATTTTATCATATGGGGTATTT
1 CTAGGGGTATAATAGTCATTTTACCATATGGGGGTATTTCGGTCATTTTATCATATGGGGTATTT
* * * *
12555991 TGGTCATTTTACCCTATGGGGGTATTTCAATCATTTTATCCTATAGGGGTAATTAGGTCATTTTA
66 CGGCCATTTTACCCTATGAGGGTATTTCAATCATTTTACCCTATAGGGGTAATTAGGTCATTTTA
12556056 CCCTATAGGGGTATTTCGGTCATTTTACCCTATGAGGGTATTTCGATCATTTTACCCTAT-AGGG
131 CCCTATAGGGGTATTTCGGTCATTTTACCCTATGAGGGTATTTCGATCATTTTACCCTATGA-GG
12556120 GTATTT-AGTTCATTTTACCCT
195 GTATTTCAGTT-ATTTTACCCT
* * *
12556141 CTAGGGGTAT-TTCAGTCA-TTTACCATATGGGGGTATTTTGGTCATTTTATCTTATGGGGTATT
1 CTAGGGGTATAAT-AGTCATTTTACCATATGGGGGTATTTCGGTCATTTTATCATATGGGGTATT
* * * *
12556204 TCGGCCATTTTACCCTATGAGGGTATTTCAGTCATTTTACCCTATTGGGGTATTTTGGTCATTTT
65 TCGGCCATTTTACCCTATGAGGGTATTTCAATCATTTTACCCTATAGGGGTAATTAGGTCATTTT
* *
12556269 ACCTTAT-GGGCGTATTTCGGTCATTTTACCTTATCG-GGGTATTTCGATCATTTTACCCTATGA
130 ACCCTATAGGG-GTATTTCGGTCATTTTACCCTAT-GAGGGTATTTCGATCATTTTACCCTATGA
*
12556332 GGGTATTTCGGTTATTTTACCCT
193 GGGTATTTCAGTTATTTTACCCT
12556355 ATGAGGGTAT
Statistics
Matches: 194, Mismatches: 15, Indels: 11
0.88 0.07 0.05
Matches are distributed among these distances:
213 3 0.02
214 171 0.88
215 20 0.10
ACGTcount: A:0.20, C:0.16, G:0.21, T:0.43
Consensus pattern (215 bp):
CTAGGGGTATAATAGTCATTTTACCATATGGGGGTATTTCGGTCATTTTATCATATGGGGTATTT
CGGCCATTTTACCCTATGAGGGTATTTCAATCATTTTACCCTATAGGGGTAATTAGGTCATTTTA
CCCTATAGGGGTATTTCGGTCATTTTACCCTATGAGGGTATTTCGATCATTTTACCCTATGAGGG
TATTTCAGTTATTTTACCCT
Found at i:12559136 original size:27 final size:26
Alignment explanation
Indices: 12559080--12559136 Score: 60
Period size: 27 Copynumber: 2.2 Consensus size: 26
12559070 GTTAACACTT
* *
12559080 AAAACCTAAAGAATTTAAAGTTCATC
1 AAAACCTAAAGAAATTAAAGTGCATC
* * *
12559106 AAAACACTAAATAAATTAATGTGCATG
1 AAAAC-CTAAAGAAATTAAAGTGCATC
12559133 AAAA
1 AAAA
12559137 ATGTATGAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
26 5 0.20
27 20 0.80
ACGTcount: A:0.54, C:0.12, G:0.09, T:0.25
Consensus pattern (26 bp):
AAAACCTAAAGAAATTAAAGTGCATC
Found at i:12574905 original size:267 final size:266
Alignment explanation
Indices: 12574425--12574984 Score: 832
Period size: 267 Copynumber: 2.1 Consensus size: 266
12574415 CTTATCGCCT
* ** * *
12574425 CAACGTTGCAATGGAAAAGATTGAAGCCACAACGACGAATCTTATTTTCCTGGCGTTGTAGCGGA
1 CAACATTGCAATTTAAAAGAATGAAGCCACAACGACGAATCTTATTTTCCTGGCATTGTAGCGGA
* * * * *
12574490 GCAGATTGAAGCCACAACAACGAATCTTATCTCCCTGGCGTTAAGGCTTGGATTAGCTGAACTGG
66 GCAAATTAAAGCCACAACAACGAATCTTATCTCCCTGGCGTTAAGGCTTGGATTAGCTAAAATAG
** * *
12574555 AGCGGATTAAAGCTGTGGGCAGTGAATCCTATCTCTTTGGCATTACAGTGGAGCAGATTGAAACC
131 AGCGGATTAAAGCTGTGGGCAGCAAATCCTATCTCTTTGGCATTACAATAGAGCAGATTGAAACC
* * * *
12574620 ACGACGGTGAATCTTACTCCCCTGGCGATGTAGTGGAACAAATTGAAGCTACGACGGCGATTCTT
196 ACGACAGTGAATCTTACTCCCCTGGCGATGTAGTAGAACAAATTAAAGCTACGACGGCGAATCTT
12574685 GTTTCC
261 GTTTCC
* *
12574691 ACAACATTGCAATTTAAAAGAATGAAGCCACAACGGCGAATCTTATTTTCCTGGTATTGTAGCGG
1 -CAACATTGCAATTTAAAAGAATGAAGCCACAACGACGAATCTTATTTTCCTGGCATTGTAGCGG
***
12574756 AGCAAATTAAAGCCACAACGGTGAATCTTATCTCCCTGGCGTTAAGGCTTGGATTAGCTAAAATA
65 AGCAAATTAAAGCCACAACAACGAATCTTATCTCCCTGGCGTTAAGGCTTGGATTAGCTAAAATA
*
12574821 GTGCGGATTAAAGCTGTGGGCAGCAAATCCTATCTCTTTGGCATTACAATAGAGCAGATTGAAAC
130 GAGCGGATTAAAGCTGTGGGCAGCAAATCCTATCTCTTTGGCATTACAATAGAGCAGATTGAAAC
* * * *
12574886 CACGGCAGTGAATCTTACTCCCCTGGCGGTGTAGTAGAACAGATTAAAGCTACGATGGCGAATCT
195 CACGACAGTGAATCTTACTCCCCTGGCGATGTAGTAGAACAAATTAAAGCTACGACGGCGAATCT
12574951 TGTTTCC
260 TGTTTCC
* *
12574958 CTAACATTGCAATTTGAAAGACTGAAG
1 C-AACATTGCAATTTAAAAGAATGAAG
12574985 ATGGCAAATC
Statistics
Matches: 262, Mismatches: 30, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
266 1 0.00
267 261 1.00
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.26
Consensus pattern (266 bp):
CAACATTGCAATTTAAAAGAATGAAGCCACAACGACGAATCTTATTTTCCTGGCATTGTAGCGGA
GCAAATTAAAGCCACAACAACGAATCTTATCTCCCTGGCGTTAAGGCTTGGATTAGCTAAAATAG
AGCGGATTAAAGCTGTGGGCAGCAAATCCTATCTCTTTGGCATTACAATAGAGCAGATTGAAACC
ACGACAGTGAATCTTACTCCCCTGGCGATGTAGTAGAACAAATTAAAGCTACGACGGCGAATCTT
GTTTCC
Found at i:12575049 original size:44 final size:44
Alignment explanation
Indices: 12574989--12575111 Score: 151
Period size: 44 Copynumber: 2.8 Consensus size: 44
12574979 CTGAAGATGG
*
12574989 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCA
* ** *
12575033 -ATAATCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAATCA
1 CA-AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCA
* * *
12575077 CAGATCTTATCTCTCTGAAGTTGCAG-AGAGCAGAT
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGAT
12575112 CGCATCTAGT
Statistics
Matches: 66, Mismatches: 11, Indels: 5
0.80 0.13 0.06
Matches are distributed among these distances:
43 7 0.11
44 58 0.88
45 1 0.02
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (44 bp):
CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCA
Found at i:12575141 original size:78 final size:78
Alignment explanation
Indices: 12575054--12575223 Score: 322
Period size: 78 Copynumber: 2.2 Consensus size: 78
12575044 TCCCTGAAGT
*
12575054 TGCAGTGGAGTGGATTAAAATCACAGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCT
1 TGCAGTGGAGTGGATTAAAATCACAGATCTTATCTATCTGAAGTTGCAGAGAGCAGATCGCATCT
12575119 AGTCTTATCTCCC
66 AGTCTTATCTCCC
*
12575132 TGCAGTGGAGTAGATTAAAATCACAGATCTTATCTATCTGAAGTTGCAGAGAGCAGATCGCATCT
1 TGCAGTGGAGTGGATTAAAATCACAGATCTTATCTATCTGAAGTTGCAGAGAGCAGATCGCATCT
12575197 AGTCTTATCTCCC
66 AGTCTTATCTCCC
12575210 TGCAGTGGAGTGGA
1 TGCAGTGGAGTGGA
12575224 GTAGACTAAG
Statistics
Matches: 89, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
78 89 1.00
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.29
Consensus pattern (78 bp):
TGCAGTGGAGTGGATTAAAATCACAGATCTTATCTATCTGAAGTTGCAGAGAGCAGATCGCATCT
AGTCTTATCTCCC
Found at i:12575204 original size:40 final size:40
Alignment explanation
Indices: 12575081--12575207 Score: 129
Period size: 40 Copynumber: 3.2 Consensus size: 40
12575071 AAATCACAGA
12575081 TCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCTAG
1 TCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCTAG
* * * ** *
12575121 TCTTATCTCCCTGCAG-TGGAGTAGATTAAAAT--CA-C-AG
1 TCTTATCTCTCTGAAGTTGCAG-AGA-GCAGATCGCATCTAG
*
12575158 ATCTTATCTATCTGAAGTTGCAGAGAGCAGATCGCATCTAG
1 -TCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCTAG
12575199 TCTTATCTC
1 TCTTATCTC
12575208 CCTGCAGTGG
Statistics
Matches: 65, Mismatches: 14, Indels: 16
0.68 0.15 0.17
Matches are distributed among these distances:
37 5 0.08
38 17 0.26
39 12 0.18
40 26 0.40
41 5 0.08
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (40 bp):
TCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCTAG
Found at i:12575301 original size:45 final size:44
Alignment explanation
Indices: 12575197--12575313 Score: 125
Period size: 45 Copynumber: 2.7 Consensus size: 44
12575187 GATCGCATCT
* *
12575197 AGTCTTATCTCCCTGCAG-TGGAGTGGAGTAGACTAAGTAAGCA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGACTAAGTAAGCA
* *
12575240 AGTCTTATC-CCTCTGAAGTTGCAGTGGTGTAGACTGAAG-ATGGCGA
1 AGTCTTATCTCC-CTGAAGTTGCAGTGGAGTAGACT-AAGTA-AGC-A
*
12575286 A-TCTTATCTCCCTGAAGTTGCAGCGGAG
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAG
12575314 CAGATTAAAG
Statistics
Matches: 62, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
42 2 0.03
43 14 0.23
44 15 0.24
45 27 0.44
46 4 0.06
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (44 bp):
AGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGACTAAGTAAGCA
Found at i:12576158 original size:17 final size:16
Alignment explanation
Indices: 12576126--12576166 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 16
12576116 AAGGTTGATA
*
12576126 TTTGTTTTGTTTCTTT
1 TTTGTTTTGATTCTTT
12576142 TTTGTTGTTGATTCTTT
1 TTTGTT-TTGATTCTTT
*
12576159 TTTATTTT
1 TTTGTTTT
12576167 CGTTTTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 8 0.36
17 14 0.64
ACGTcount: A:0.05, C:0.05, G:0.12, T:0.78
Consensus pattern (16 bp):
TTTGTTTTGATTCTTT
Found at i:12585249 original size:18 final size:19
Alignment explanation
Indices: 12585226--12585264 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
12585216 AACTTATCCT
*
12585226 TAAATTAATTT-TTTTATA
1 TAAATTAATTTGTTGTATA
*
12585244 TAAATTTATTTGTTGTATA
1 TAAATTAATTTGTTGTATA
12585263 TA
1 TA
12585265 TTTTTCACTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (19 bp):
TAAATTAATTTGTTGTATA
Found at i:12586140 original size:20 final size:18
Alignment explanation
Indices: 12586103--12586154 Score: 59
Period size: 20 Copynumber: 2.7 Consensus size: 18
12586093 TATGGTTCGA
12586103 GTTTGAGGTTTAGGATTTAAG
1 GTTT-AGGTTT-GGATTT-AG
*
12586124 GTTTAGTGTTTGGATTTAT
1 GTTTAG-GTTTGGATTTAG
12586143 GTTTAGGTTTGG
1 GTTTAGGTTTGG
12586155 GGTTTGGGGT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 6 0.21
19 7 0.24
20 8 0.28
21 8 0.28
ACGTcount: A:0.17, C:0.00, G:0.33, T:0.50
Consensus pattern (18 bp):
GTTTAGGTTTGGATTTAG
Found at i:12586470 original size:119 final size:119
Alignment explanation
Indices: 12586259--12586496 Score: 476
Period size: 119 Copynumber: 2.0 Consensus size: 119
12586249 TCAACCCAAA
12586259 AAATGGAATTGGATTTATTTTTGAAAGTTCTTTTATTATTCCCTTTAGAAATAGAATGTTTTGAG
1 AAATGGAATTGGATTTATTTTTGAAAGTTCTTTTATTATTCCCTTTAGAAATAGAATGTTTTGAG
12586324 TGATCTATTTTTTTGTTTCTTTTGAAGCTTTTCGAAACAATTTAGTTTTTTTTC
66 TGATCTATTTTTTTGTTTCTTTTGAAGCTTTTCGAAACAATTTAGTTTTTTTTC
12586378 AAATGGAATTGGATTTATTTTTGAAAGTTCTTTTATTATTCCCTTTAGAAATAGAATGTTTTGAG
1 AAATGGAATTGGATTTATTTTTGAAAGTTCTTTTATTATTCCCTTTAGAAATAGAATGTTTTGAG
12586443 TGATCTATTTTTTTGTTTCTTTTGAAGCTTTTCGAAACAATTTAGTTTTTTTTC
66 TGATCTATTTTTTTGTTTCTTTTGAAGCTTTTCGAAACAATTTAGTTTTTTTTC
12586497 TTTTAAAATT
Statistics
Matches: 119, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
119 119 1.00
ACGTcount: A:0.25, C:0.08, G:0.14, T:0.52
Consensus pattern (119 bp):
AAATGGAATTGGATTTATTTTTGAAAGTTCTTTTATTATTCCCTTTAGAAATAGAATGTTTTGAG
TGATCTATTTTTTTGTTTCTTTTGAAGCTTTTCGAAACAATTTAGTTTTTTTTC
Found at i:12598064 original size:6 final size:6
Alignment explanation
Indices: 12598055--12598085 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
12598045 CTTGTGCTTG
*
12598055 TTCTTA TTCTTA TTCTTA TTCGTA TTCTTA T
1 TTCTTA TTCTTA TTCTTA TTCTTA TTCTTA T
12598086 ACTTGTACTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.16, C:0.16, G:0.03, T:0.65
Consensus pattern (6 bp):
TTCTTA
Found at i:12598528 original size:13 final size:14
Alignment explanation
Indices: 12598498--12598528 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
12598488 GAGCACGCAT
12598498 AAAACATAACTTTA
1 AAAACATAACTTTA
*
12598512 AAAACATAACTTGA
1 AAAACATAACTTTA
12598526 AAA
1 AAA
12598529 TAGAGTTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.61, C:0.13, G:0.03, T:0.23
Consensus pattern (14 bp):
AAAACATAACTTTA
Found at i:12599096 original size:27 final size:27
Alignment explanation
Indices: 12599066--12599140 Score: 114
Period size: 27 Copynumber: 2.8 Consensus size: 27
12599056 ATTCTAGAGT
12599066 TCGCCAAACCAACTGGTGAACCCCAAC
1 TCGCCAAACCAACTGGTGAACCCCAAC
* * **
12599093 TCGCCAAACCAATTGGCGAACCTTAAC
1 TCGCCAAACCAACTGGTGAACCCCAAC
12599120 TCGCCAAACCAACTGGTGAAC
1 TCGCCAAACCAACTGGTGAAC
12599141 ACAACTAGCA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.33, C:0.36, G:0.16, T:0.15
Consensus pattern (27 bp):
TCGCCAAACCAACTGGTGAACCCCAAC
Found at i:12600866 original size:42 final size:42
Alignment explanation
Indices: 12600782--12600866 Score: 98
Period size: 42 Copynumber: 2.0 Consensus size: 42
12600772 TGCACTTTTG
** * *
12600782 AACCACACGGCCAGGGACATGGGCATGTGCCCAGGCCGTGTA
1 AACCACACGGCCAAAGACATGGGCATGTGCACAGGCCATGTA
* * * *
12600824 AACCACACGGGCAAAGACATGGGCATGTGTATAGGTCATGTA
1 AACCACACGGCCAAAGACATGGGCATGTGCACAGGCCATGTA
12600866 A
1 A
12600867 CTTACTGGTT
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.29, C:0.25, G:0.31, T:0.15
Consensus pattern (42 bp):
AACCACACGGCCAAAGACATGGGCATGTGCACAGGCCATGTA
Found at i:12600969 original size:105 final size:104
Alignment explanation
Indices: 12600745--12600969 Score: 260
Period size: 105 Copynumber: 2.2 Consensus size: 104
12600735 GGCATTGGTG
* * *
12600745 TGTGTCTAGGCCATGTAACTCACTGTTTGCACTTTTGAACCACACGGCCAGGGACATGGGCATGT
1 TGTGTCTAGGCCATGTAACTCACTGTTTGCACTTTAGAACCACACAGCCAGGGACATAGGCATGT
12600810 GCCCAGGCCGTGTAAACCACACGGGCAAAGACATGGGCA
66 GCCCAGGCCGTGTAAACCACACGGGCAAAGACATGGGCA
* * *
12600849 TGTGTATAGGTCATGTAACTTACTGGTTATG-A-TTTAGAACCACACAAG-CAGGTGACATAGGC
1 TGTGTCTAGGCCATGTAACTCACT-GTT-TGCACTTTAGAACCACAC-AGCCAGG-GACATAGGC
* * * * * *
12600911 GTGTG-CCTGAGCCGTGTGAGCCACACGGGCAAGGACATGGGCT
62 ATGTGCCCAG-GCCGTGTAAACCACACGGGCAAAGACATGGGCA
*
12600954 TGTGTCCAGGCCATGT
1 TGTGTCTAGGCCATGT
12600970 GGCATATGAA
Statistics
Matches: 101, Mismatches: 15, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
104 40 0.40
105 59 0.58
106 2 0.02
ACGTcount: A:0.24, C:0.24, G:0.29, T:0.23
Consensus pattern (104 bp):
TGTGTCTAGGCCATGTAACTCACTGTTTGCACTTTAGAACCACACAGCCAGGGACATAGGCATGT
GCCCAGGCCGTGTAAACCACACGGGCAAAGACATGGGCA
Found at i:12604345 original size:21 final size:21
Alignment explanation
Indices: 12604304--12604343 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
12604294 TTTGTTTATT
12604304 TTAATTAATGCTTTAATTTTA
1 TTAATTAATGCTTTAATTTTA
*
12604325 TTAATTTAT-CTTTAATTTT
1 TTAATTAATGCTTTAATTTT
12604344 TAACAAAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.30, C:0.05, G:0.03, T:0.62
Consensus pattern (21 bp):
TTAATTAATGCTTTAATTTTA
Found at i:12616424 original size:45 final size:43
Alignment explanation
Indices: 12616373--12616472 Score: 119
Period size: 45 Copynumber: 2.2 Consensus size: 43
12616363 AGTCATGTTT
* * *
12616373 TTACTCATTTACATCATGACACCGTAGCATCTTTTAGCTATGGTC
1 TTACTCATTT--ATCATGACACCATAGCATCTCTCAGCTATGGTC
**
12616418 TTACTCATCCTTATCATGATGCCATAGCATCTCTCAGCTATGGTC
1 TTACTCAT--TTATCATGACACCATAGCATCTCTCAGCTATGGTC
12616463 TTACTCATTT
1 TTACTCATTT
12616473 TCAGCGTATA
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
43 2 0.04
45 44 0.92
47 2 0.04
ACGTcount: A:0.23, C:0.26, G:0.12, T:0.39
Consensus pattern (43 bp):
TTACTCATTTATCATGACACCATAGCATCTCTCAGCTATGGTC
Found at i:12619156 original size:43 final size:44
Alignment explanation
Indices: 12619004--12619161 Score: 185
Period size: 43 Copynumber: 3.6 Consensus size: 44
12618994 TGTGGCTTCG
* * * * * *
12619004 TCCATAACCTATATGGTAGCTTATCTG-CAAAATTGGTGGTTTA
1 TCCACAACCTACATGGTAGCTTGTTTGTGAATATTGGTGGTTTA
* * * *
12619047 TCCACAACCTACATGGTAACCTGTCTGTGAATATTGGTGGCTTCA
1 TCCACAACCTACATGGTAGCTTGTTTGTGAATATTGGTGG-TTTA
* *
12619092 TCCACAACCTACATGGCAGCTTGTTTGTGAGT-TTGGTGGTTTA
1 TCCACAACCTACATGGTAGCTTGTTTGTGAATATTGGTGGTTTA
12619135 TCCACAACCTACATGGTAGCTTGTTTG
1 TCCACAACCTACATGGTAGCTTGTTTG
12619162 CAAATAGTGG
Statistics
Matches: 98, Mismatches: 15, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
43 51 0.52
44 17 0.17
45 30 0.31
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.35
Consensus pattern (44 bp):
TCCACAACCTACATGGTAGCTTGTTTGTGAATATTGGTGGTTTA
Found at i:12623081 original size:22 final size:22
Alignment explanation
Indices: 12623053--12623096 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
12623043 CATCAAGATC
12623053 AAGATAAGTTTGATTTACTTTA
1 AAGATAAGTTTGATTTACTTTA
12623075 AAGATAAGTTTGATTTACTTTA
1 AAGATAAGTTTGATTTACTTTA
12623097 TGACTCTAAT
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:0.36, C:0.05, G:0.14, T:0.45
Consensus pattern (22 bp):
AAGATAAGTTTGATTTACTTTA
Found at i:12623113 original size:30 final size:30
Alignment explanation
Indices: 12623079--12623139 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
12623069 ACTTTAAAGA
12623079 TAAGTTTGATTTACTTTATGACTCTAATTT
1 TAAGTTTGATTTACTTTATGACTCTAATTT
12623109 TAAGTTTGATTTACTTTATGACTCTAATTT
1 TAAGTTTGATTTACTTTATGACTCTAATTT
12623139 T
1 T
12623140 TACTAGAAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.26, C:0.10, G:0.10, T:0.54
Consensus pattern (30 bp):
TAAGTTTGATTTACTTTATGACTCTAATTT
Found at i:12623351 original size:26 final size:25
Alignment explanation
Indices: 12623306--12623359 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 25
12623296 ATTCCATCTC
12623306 TTTATTTTTACTTTCTTCTCTCTTTT
1 TTTATTTTTACTTTCTTCTCT-TTTT
*
12623332 TTTATTTTTA-TTTTTATCTCTTTTT
1 TTTATTTTTACTTTCT-TCTCTTTTT
12623357 TTT
1 TTT
12623360 CTATAAATGG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 11 0.42
26 15 0.58
ACGTcount: A:0.09, C:0.13, G:0.00, T:0.78
Consensus pattern (25 bp):
TTTATTTTTACTTTCTTCTCTTTTT
Found at i:12623356 original size:24 final size:26
Alignment explanation
Indices: 12623306--12623358 Score: 83
Period size: 24 Copynumber: 2.1 Consensus size: 26
12623296 ATTCCATCTC
*
12623306 TTTATTTTTACTTTCTTCTCTCTTTT
1 TTTATTTTTACTTTCTTATCTCTTTT
12623332 TTTATTTTTA-TTT-TTATCTCTTTT
1 TTTATTTTTACTTTCTTATCTCTTTT
12623356 TTT
1 TTT
12623359 TCTATAAATG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
24 13 0.50
25 3 0.12
26 10 0.38
ACGTcount: A:0.09, C:0.13, G:0.00, T:0.77
Consensus pattern (26 bp):
TTTATTTTTACTTTCTTATCTCTTTT
Found at i:12624103 original size:21 final size:20
Alignment explanation
Indices: 12624066--12624104 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
12624056 AATATAAATC
* *
12624066 TATTTATTAAATGTTATTTT
1 TATTTATAAAATATTATTTT
12624086 TATTTAATAAAATATTATT
1 TATTT-ATAAAATATTATT
12624105 AATAATTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (20 bp):
TATTTATAAAATATTATTTT
Found at i:12627220 original size:31 final size:28
Alignment explanation
Indices: 12627157--12627224 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 28
12627147 AATACAATTC
* *
12627157 TTTATTATTATTTTTTTCTTTTTTTTCT
1 TTTATTCTTATTTTTTTCTTTTTTTTCA
12627185 TTTATTCTTACTTTTTTTCTTCTCTCTTTT-A
1 TTTATTCTTA-TTTTTTTCTT-T-T-TTTTCA
12627216 TTTATTCTT
1 TTTATTCTT
12627225 TCTTCTTTAG
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
28 9 0.26
29 10 0.29
30 1 0.03
31 10 0.29
32 4 0.12
ACGTcount: A:0.10, C:0.13, G:0.00, T:0.76
Consensus pattern (28 bp):
TTTATTCTTATTTTTTTCTTTTTTTTCA
Found at i:12628025 original size:6 final size:6
Alignment explanation
Indices: 12628014--12628058 Score: 58
Period size: 6 Copynumber: 7.7 Consensus size: 6
12628004 AAAATAAAGA
*
12628014 AAATAT AAATAT AAATAT AAATAAA AAATAT AAATA- AAATA- AAAT
1 AAATAT AAATAT AAATAT AAAT-AT AAATAT AAATAT AAATAT AAAT
12628059 TGGGTTGCCT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
5 9 0.25
6 22 0.61
7 5 0.14
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (6 bp):
AAATAT
Found at i:12628031 original size:12 final size:11
Alignment explanation
Indices: 12628007--12628058 Score: 61
Period size: 11 Copynumber: 4.5 Consensus size: 11
12627997 ATGCAAGAAA
*
12628007 ATAAAGAAAAT
1 ATAAATAAAAT
12628018 ATAAATATAAAT
1 ATAAATA-AAAT
12628030 ATAAATAAAAAAT
1 ATAAAT--AAAAT
12628043 ATAAATAAAAT
1 ATAAATAAAAT
12628054 A-AAAT
1 ATAAAT
12628059 TGGGTTGCCT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
10 4 0.11
11 12 0.32
12 10 0.27
13 10 0.27
14 1 0.03
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (11 bp):
ATAAATAAAAT
Found at i:12628034 original size:23 final size:24
Alignment explanation
Indices: 12628013--12628058 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
12628003 GAAAATAAAG
12628013 AAAATATAAATATAAATATAAATAA
1 AAAATATAAATA-AAATATAAATAA
12628038 AAAATATAAATAAAATA-AAAT
1 AAAATATAAATAAAATATAAAT
12628059 TGGGTTGCCT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 4 0.19
24 5 0.24
25 12 0.57
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (24 bp):
AAAATATAAATAAAATATAAATAA
Found at i:12628044 original size:13 final size:13
Alignment explanation
Indices: 12628013--12628052 Score: 64
Period size: 13 Copynumber: 3.2 Consensus size: 13
12628003 GAAAATAAAG
12628013 AAAATATAAAT-A
1 AAAATATAAATAA
*
12628025 TAAATATAAATAA
1 AAAATATAAATAA
12628038 AAAATATAAATAA
1 AAAATATAAATAA
12628051 AA
1 AA
12628053 TAAAATTGGG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 10 0.40
13 15 0.60
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (13 bp):
AAAATATAAATAA
Found at i:12628044 original size:19 final size:18
Alignment explanation
Indices: 12628007--12628057 Score: 68
Period size: 18 Copynumber: 2.8 Consensus size: 18
12627997 ATGCAAGAAA
* *
12628007 ATAAAGAAAAT-ATAAAT
1 ATAAATAAAATAAAAAAT
12628024 ATAAATATAAATAAAAAAT
1 ATAAATA-AAATAAAAAAT
12628043 ATAAATAAAATAAAA
1 ATAAATAAAATAAAA
12628058 TTGGGTTGCC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
17 6 0.20
18 12 0.40
19 12 0.40
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.24
Consensus pattern (18 bp):
ATAAATAAAATAAAAAAT
Found at i:12639643 original size:30 final size:31
Alignment explanation
Indices: 12639599--12639664 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 31
12639589 TAGTAAAAAT
*
12639599 AAAATTGTACTTTAATTCTTTAAAAACGATA
1 AAAATTGTAATTTAATTCTTTAAAAACGATA
* **
12639630 AAAATT-TAATTTAATTTTTTAAAAATTATA
1 AAAATTGTAATTTAATTCTTTAAAAACGATA
12639660 AAAAT
1 AAAAT
12639665 ACAAACTATT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 25 0.81
31 6 0.19
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (31 bp):
AAAATTGTAATTTAATTCTTTAAAAACGATA
Found at i:12640266 original size:1 final size:1
Alignment explanation
Indices: 12640229--12640255 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
12640219 TTGATATCCC
12640229 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
12640256 AAGCATTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:12644077 original size:69 final size:68
Alignment explanation
Indices: 12643978--12644231 Score: 305
Period size: 69 Copynumber: 3.7 Consensus size: 68
12643968 TTTACAGTTA
* * **
12643978 GAGCTTTACTCTCG-TCAACTATGTTGGAGGTCGCGGTTCTTCACCTAAGAACAATGATTTTACA
1 GAGCTTTGCTCTCGCT-AACTATGTTGGAGGTCGCGGCTCTTCACCTAAGAACCTTGATTTTACA
12644042 ACTG
65 ACTG
* * *
12644046 GAAGCTTTGCTCTCGCTAACTGTGTTGGAGGTTGCGGCTCTTCACCTGTA-AACCTTGATTTTAC
1 G-AGCTTTGCTCTCGCTAACTATGTTGGAGGTCGCGGCTCTTCACCT-AAGAACCTTGATTTTAC
12644110 AACTAG
64 AACT-G
* * * ** * *
12644116 GAGCTTTGCTCTTGCTAACTATGTTGGAGGTTGCGGCTCTTCGCCTGTGAACCTTGATTTTATAG
1 GAGCTTTGCTCTCGCTAACTATGTTGGAGGTCGCGGCTCTTCACCTAAGAACCTTGATTTTACAA
12644181 CTGG
66 CT-G
* *
12644185 GAGCTTTCCTCTCGCTAACTATGTTGGAGGTCGCGGCTCTTCGCCTA
1 GAGCTTTGCTCTCGCTAACTATGTTGGAGGTCGCGGCTCTTCACCTA
12644232 TTTTACAGCT
Statistics
Matches: 162, Mismatches: 19, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
68 1 0.01
69 157 0.97
70 4 0.02
ACGTcount: A:0.19, C:0.23, G:0.24, T:0.34
Consensus pattern (68 bp):
GAGCTTTGCTCTCGCTAACTATGTTGGAGGTCGCGGCTCTTCACCTAAGAACCTTGATTTTACAA
CTG
Found at i:12644284 original size:59 final size:59
Alignment explanation
Indices: 12644172--12644290 Score: 157
Period size: 59 Copynumber: 2.0 Consensus size: 59
12644162 GTGAACCTTG
* * ** *
12644172 ATTTTATAGCTGGGAGCTTTCCTCTCGCTAACTATGTTGGAGGTCGCGGCTCTTCGCCT
1 ATTTTACAGCTGAGAGCTTTCCTCTCGCTAACTATGTTGGAGGTCGCAACTCTTCACCT
* * * *
12644231 ATTTTACAGCTGAGAGTTTTTCTCTTGTTAACTATGTTGGAGGTCGCAACTCTTCACCT
1 ATTTTACAGCTGAGAGCTTTCCTCTCGCTAACTATGTTGGAGGTCGCAACTCTTCACCT
12644290 A
1 A
12644291 CAAATCTTAA
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
59 51 1.00
ACGTcount: A:0.18, C:0.23, G:0.22, T:0.38
Consensus pattern (59 bp):
ATTTTACAGCTGAGAGCTTTCCTCTCGCTAACTATGTTGGAGGTCGCAACTCTTCACCT
Found at i:12644345 original size:69 final size:69
Alignment explanation
Indices: 12644262--12644443 Score: 211
Period size: 69 Copynumber: 2.6 Consensus size: 69
12644252 CTCTTGTTAA
* * ** * * *
12644262 CTATGTTGGAGGTCGCAACTCTTCACCTACAAATCTTAATTTTATAGTTGGGAGCTTTGTTTTTG
1 CTATGTTGGAGGTCGCAACTCTTCACCTACAAACCTTGATTTTATAACTGGGAGCTTTGCTCTAG
12644327 CTAG
66 CTAG
* * * * * *
12644331 CTGTGTTGGAGGTCGTAGCTATTCACCTGCTAACCTTGATTTTATAACTGGGAGCTTTGCTCTAG
1 CTATGTTGGAGGTCGCAACTCTTCACCTACAAACCTTGATTTTATAACTGGGAGCTTTGCTCTAG
12644396 CTAG
66 CTAG
* * * *
12644400 CTATGTTGGAGGTCACGATTCTTCACCTACGAACCTTGATTTTA
1 CTATGTTGGAGGTCGCAACTCTTCACCTACAAACCTTGATTTTA
12644444 CAAATGATAG
Statistics
Matches: 91, Mismatches: 22, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
69 91 1.00
ACGTcount: A:0.21, C:0.20, G:0.21, T:0.38
Consensus pattern (69 bp):
CTATGTTGGAGGTCGCAACTCTTCACCTACAAACCTTGATTTTATAACTGGGAGCTTTGCTCTAG
CTAG
Found at i:12657027 original size:18 final size:17
Alignment explanation
Indices: 12656993--12657031 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
12656983 TTAAGTGAAA
**
12656993 AACTAGAAACAGGGTTT
1 AACTAGAAACAAAGTTT
12657010 AACTAGAAAACAAAGTTT
1 AACTAG-AAACAAAGTTT
12657028 AACT
1 AACT
12657032 GGTAGAAGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.49, C:0.13, G:0.15, T:0.23
Consensus pattern (17 bp):
AACTAGAAACAAAGTTT
Found at i:12674815 original size:20 final size:22
Alignment explanation
Indices: 12674779--12674819 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 22
12674769 AATGGTTTTA
12674779 ATAAAATAAATTTAAATAATAT
1 ATAAAATAAATTTAAATAATAT
12674801 ATAAAA-AAA-TTAAATAATA
1 ATAAAATAAATTTAAATAATA
12674820 ATGAAGTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.53
21 3 0.16
22 6 0.32
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (22 bp):
ATAAAATAAATTTAAATAATAT
Found at i:12677823 original size:2 final size:2
Alignment explanation
Indices: 12677816--12677844 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
12677806 AAGCTGCTTC
12677816 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
12677845 CCTTTTTGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:12697737 original size:33 final size:33
Alignment explanation
Indices: 12697692--12697762 Score: 97
Period size: 33 Copynumber: 2.2 Consensus size: 33
12697682 GCTAATGTAC
* * * * *
12697692 TCCAATGTATCTAATTTATATTACAAATTTTGT
1 TCCAATGAATCTAATTTAAATTAAAAAGTTGGT
12697725 TCCAATGAATCTAATTTAAATTAAAAAGTTGGT
1 TCCAATGAATCTAATTTAAATTAAAAAGTTGGT
12697758 TCCAA
1 TCCAA
12697763 GTTTGTTACA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.41
Consensus pattern (33 bp):
TCCAATGAATCTAATTTAAATTAAAAAGTTGGT
Found at i:12697783 original size:44 final size:44
Alignment explanation
Indices: 12697720--12697829 Score: 175
Period size: 44 Copynumber: 2.5 Consensus size: 44
12697710 TATTACAAAT
*
12697720 TTTGTTCCAATGAATCTAATTTAAATTAAAAAGTTGGTTCCAAG
1 TTTGTTACAATGAATCTAATTTAAATTAAAAAGTTGGTTCCAAG
* *
12697764 TTTGTTACAATGAATCTAATTTAAATTACATAGTTGGTTCCAAG
1 TTTGTTACAATGAATCTAATTTAAATTAAAAAGTTGGTTCCAAG
* *
12697808 TTTGGTGCAATGAATCTAATTT
1 TTTGTTACAATGAATCTAATTT
12697830 CTGCATGTAT
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
44 61 1.00
ACGTcount: A:0.34, C:0.11, G:0.15, T:0.41
Consensus pattern (44 bp):
TTTGTTACAATGAATCTAATTTAAATTAAAAAGTTGGTTCCAAG
Found at i:12703884 original size:14 final size:14
Alignment explanation
Indices: 12703848--12703886 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
12703838 GCTTAATAAA
12703848 TTATGACATATGCT
1 TTATGACATATGCT
* * *
12703862 TAATAACATATGGT
1 TTATGACATATGCT
12703876 TTATGACATAT
1 TTATGACATAT
12703887 AAACTAATGA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.36, C:0.10, G:0.13, T:0.41
Consensus pattern (14 bp):
TTATGACATATGCT
Found at i:12704117 original size:21 final size:21
Alignment explanation
Indices: 12704076--12704118 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
12704066 AATAAAGTAG
**
12704076 ATTATATATATTTTTTATAGT
1 ATTATATATATGATTTATAGT
12704097 ATTATATATTATGATTT-TAGT
1 ATTATATA-TATGATTTATAGT
12704118 A
1 A
12704119 AATTCATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.58
Consensus pattern (21 bp):
ATTATATATATGATTTATAGT
Found at i:12704171 original size:20 final size:22
Alignment explanation
Indices: 12704134--12704176 Score: 72
Period size: 20 Copynumber: 2.0 Consensus size: 22
12704124 ATATAATAAT
12704134 AATTATATTAAGAATTTTATTA
1 AATTATATTAAGAATTTTATTA
12704156 AATTATA-TAA-AATTTTATTA
1 AATTATATTAAGAATTTTATTA
12704176 A
1 A
12704177 NNNNNNNNNN
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 11 0.52
21 3 0.14
22 7 0.33
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (22 bp):
AATTATATTAAGAATTTTATTA
Found at i:12704345 original size:45 final size:44
Alignment explanation
Indices: 12704256--12704348 Score: 134
Period size: 44 Copynumber: 2.1 Consensus size: 44
12704246 ATTACAACAT
*
12704256 CATTCCATTCAACCAAACACAAGAATACTATTACAACTCTATTC
1 CATTCCATTCAACCAAACACAAGAATACTATTACAACTCCATTC
* *
12704300 CATTCCATTCAACCAAACA-ATTGAATTACTATTACAGCTCCATTC
1 CATTCCATTCAACCAAACACA-AGAA-TACTATTACAACTCCATTC
12704345 CATT
1 CATT
12704349 ACAGCTCTAT
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
43 1 0.02
44 22 0.50
45 21 0.48
ACGTcount: A:0.38, C:0.29, G:0.03, T:0.30
Consensus pattern (44 bp):
CATTCCATTCAACCAAACACAAGAATACTATTACAACTCCATTC
Found at i:12704351 original size:16 final size:16
Alignment explanation
Indices: 12704330--12704368 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
12704320 TTGAATTACT
12704330 ATTACAGCTCCATTCC
1 ATTACAGCTCCATTCC
*
12704346 ATTACAGCTCTATTCC
1 ATTACAGCTCCATTCC
12704362 ATTACAG
1 ATTACAG
12704369 TGAACCAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.28, C:0.31, G:0.08, T:0.33
Consensus pattern (16 bp):
ATTACAGCTCCATTCC
Found at i:12714393 original size:40 final size:40
Alignment explanation
Indices: 12714328--12714428 Score: 150
Period size: 40 Copynumber: 2.5 Consensus size: 40
12714318 TGACTCAGAA
* *
12714328 CACCGGCATGAAGCCTGCTAGACATTAAGTCT-ATAAAGTT
1 CACCGGCATTAAGCCTGCTAGACATTAAGTCTGA-AAAATT
* *
12714368 CACCAGCATTAAGCCTACTAGACATTAAGTCTGAAAAATT
1 CACCGGCATTAAGCCTGCTAGACATTAAGTCTGAAAAATT
12714408 CACCGGCATTAAGCCTGCTAG
1 CACCGGCATTAAGCCTGCTAG
12714429 GCACAGAACC
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
40 53 0.98
41 1 0.02
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.24
Consensus pattern (40 bp):
CACCGGCATTAAGCCTGCTAGACATTAAGTCTGAAAAATT
Found at i:12717384 original size:33 final size:33
Alignment explanation
Indices: 12717342--12717408 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
12717332 TTTATGTTCT
12717342 CTTGTAGTTTCGTTTGACACTTAGTCAAATTGG
1 CTTGTAGTTTCGTTTGACACTTAGTCAAATTGG
12717375 CTTGTAGTTTCGTTTGACACTTAGTCAAATTGG
1 CTTGTAGTTTCGTTTGACACTTAGTCAAATTGG
12717408 C
1 C
12717409 CTCAAATGTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.21, C:0.16, G:0.21, T:0.42
Consensus pattern (33 bp):
CTTGTAGTTTCGTTTGACACTTAGTCAAATTGG
Found at i:12720621 original size:21 final size:21
Alignment explanation
Indices: 12720597--12720639 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
12720587 AGAAAATAAG
12720597 TAAGATCATAAATTCATTCAT
1 TAAGATCATAAATTCATTCAT
12720618 TAAGATCATAAATTCATTCAT
1 TAAGATCATAAATTCATTCAT
12720639 T
1 T
12720640 CATATATTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.42, C:0.14, G:0.05, T:0.40
Consensus pattern (21 bp):
TAAGATCATAAATTCATTCAT
Found at i:12720648 original size:16 final size:16
Alignment explanation
Indices: 12720623--12720656 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
12720613 TTCATTAAGA
*
12720623 TCATAAATTCATTCAT
1 TCATAAATTCAATCAT
*
12720639 TCATATATTCAATCAT
1 TCATAAATTCAATCAT
12720655 TC
1 TC
12720657 TAATCATAGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.35, C:0.21, G:0.00, T:0.44
Consensus pattern (16 bp):
TCATAAATTCAATCAT
Found at i:12720841 original size:28 final size:29
Alignment explanation
Indices: 12720779--12720862 Score: 100
Period size: 28 Copynumber: 2.9 Consensus size: 29
12720769 TTTGAAGAAG
* *
12720779 AGTGGCAAAACTATAAAATTTAGAAAACA
1 AGTGGCAAAACTGTAAAATCTAGAAAACA
12720808 AGTGGCAAAACTGTAAAATCT-GAAAA-A
1 AGTGGCAAAACTGTAAAATCTAGAAAACA
* * *
12720835 TAGTGGCAGAATTGTAAAATCTATAAAA
1 -AGTGGCAAAACTGTAAAATCTAGAAAA
12720863 TGATGGTACA
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
27 1 0.02
28 24 0.50
29 23 0.48
ACGTcount: A:0.51, C:0.10, G:0.17, T:0.23
Consensus pattern (29 bp):
AGTGGCAAAACTGTAAAATCTAGAAAACA
Found at i:12721315 original size:33 final size:32
Alignment explanation
Indices: 12721251--12721321 Score: 88
Period size: 33 Copynumber: 2.2 Consensus size: 32
12721241 ATAAGAAAGA
*
12721251 TAAATTCTATTAGGATTTGAAAAGGAGTAATT
1 TAAATTCTATTAAGATTTGAAAAGGAGTAATT
* * *
12721283 TAAATTCTAGTTAAGATTTTAATAGGATTAATT
1 TAAATTCTA-TTAAGATTTGAAAAGGAGTAATT
12721316 TGAAAT
1 T-AAAT
12721322 AAATTAAGAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
32 9 0.27
33 20 0.61
34 4 0.12
ACGTcount: A:0.41, C:0.03, G:0.15, T:0.41
Consensus pattern (32 bp):
TAAATTCTATTAAGATTTGAAAAGGAGTAATT
Found at i:12727850 original size:7 final size:7
Alignment explanation
Indices: 12727834--12727866 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
12727824 TTTCAATTTC
*
12727834 ATATTAA
1 ATATTGA
12727841 ATATTGA
1 ATATTGA
12727848 ATATTGA
1 ATATTGA
12727855 ATATTGA
1 ATATTGA
12727862 ATATT
1 ATATT
12727867 TCAATTTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.45, C:0.00, G:0.09, T:0.45
Consensus pattern (7 bp):
ATATTGA
Found at i:12728361 original size:22 final size:20
Alignment explanation
Indices: 12728324--12728367 Score: 52
Period size: 22 Copynumber: 2.1 Consensus size: 20
12728314 TTGTATGGCT
*
12728324 TTCTTTTTTTTGTTTTCTTA
1 TTCTTTTTTTTGTTTTATTA
*
12728344 TTCTTTATTTTTATTTTTATTA
1 TTCTTT-TTTTT-GTTTTATTA
12728366 TT
1 TT
12728368 TTGTTTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 5 0.25
22 9 0.45
ACGTcount: A:0.11, C:0.07, G:0.02, T:0.80
Consensus pattern (20 bp):
TTCTTTTTTTTGTTTTATTA
Done.