Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 ID=Chr06-JGI_221_v2.0
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: 51074515
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 971674 characters in sequence are not A, C, G, or T
File 106 of 168
Found at i:31385169 original size:19 final size:19
Alignment explanation
Indices: 31385145--31385185 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
31385135 CAAGCTGGCG
31385145 TAAACACTAACA-AATAATA
1 TAAACA-TAACATAATAATA
*
31385164 TAAACATAATATAATAATA
1 TAAACATAACATAATAATA
31385183 TAA
1 TAA
31385186 TTTTAAACAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.63, C:0.10, G:0.00, T:0.27
Consensus pattern (19 bp):
TAAACATAACATAATAATA
Found at i:31385220 original size:20 final size:20
Alignment explanation
Indices: 31385174--31385226 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
31385164 TAAACATAAT
* *
31385174 ATAATAATAT-AATTTTAAAC
1 ATAA-AATATAAATATTAAAA
*
31385194 ATTAAATATAAATATTAAAA
1 ATAAAATATAAATATTAAAA
31385214 ATAAAATATAAAT
1 ATAAAATATAAAT
31385227 GTATAATATA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 5 0.18
20 23 0.82
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (20 bp):
ATAAAATATAAATATTAAAA
Found at i:31385237 original size:20 final size:20
Alignment explanation
Indices: 31385169--31385237 Score: 52
Period size: 20 Copynumber: 3.5 Consensus size: 20
31385159 TAATATAAAC
* *
31385169 ATAATATAATAATATAATTTT
1 ATAATATAA-AATATAAATAT
* *
31385190 A-AACATTAAATATAAATAT
1 ATAATATAAAATATAAATAT
* *
31385209 -TAAAAATAAAATATAAATGT
1 AT-AATATAAAATATAAATAT
31385229 ATAATATAA
1 ATAATATAA
31385238 GCTAAGAAAG
Statistics
Matches: 37, Mismatches: 8, Indels: 7
0.71 0.15 0.13
Matches are distributed among these distances:
19 9 0.24
20 26 0.70
21 2 0.05
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.36
Consensus pattern (20 bp):
ATAATATAAAATATAAATAT
Found at i:31385950 original size:10 final size:11
Alignment explanation
Indices: 31385935--31385961 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
31385925 CAAAAGGAGT
31385935 GAAAAACAAGC
1 GAAAAACAAGC
31385946 GAAAAACAAGC
1 GAAAAACAAGC
31385957 GAAAA
1 GAAAA
31385962 TCGAAAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.67, C:0.15, G:0.19, T:0.00
Consensus pattern (11 bp):
GAAAAACAAGC
Found at i:31390343 original size:15 final size:15
Alignment explanation
Indices: 31390323--31390373 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
31390313 TACCCATATC
31390323 TTTGATTTTCCAATA
1 TTTGATTTTCCAATA
**
31390338 TTTGA-TACCCATATA
1 TTTGATTTTCCA-ATA
* *
31390353 TTTGACTTTCCATTA
1 TTTGATTTTCCAATA
31390368 TTTGAT
1 TTTGAT
31390374 AACCATATAT
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
14 4 0.14
15 20 0.71
16 4 0.14
ACGTcount: A:0.25, C:0.16, G:0.08, T:0.51
Consensus pattern (15 bp):
TTTGATTTTCCAATA
Found at i:31390347 original size:30 final size:30
Alignment explanation
Indices: 31390301--31390392 Score: 121
Period size: 30 Copynumber: 3.0 Consensus size: 30
31390291 ATTTCTTATG
* *
31390301 CCAATATCTCGATACCCATATCTTTGATTTT
1 CCAATAT-TTGATACCCATATATTTGATTTT
*
31390332 CCAATATTTGATACCCATATATTTGACTTT
1 CCAATATTTGATACCCATATATTTGATTTT
* *
31390362 CCATTATTTGATAACCATATATTTGAATTTT
1 CCAATATTTGATACCCATATATTTG-ATTTT
31390393 TATAAATACG
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
30 43 0.80
31 11 0.20
ACGTcount: A:0.29, C:0.20, G:0.07, T:0.45
Consensus pattern (30 bp):
CCAATATTTGATACCCATATATTTGATTTT
Found at i:31390384 original size:15 final size:15
Alignment explanation
Indices: 31390335--31390387 Score: 63
Period size: 15 Copynumber: 3.5 Consensus size: 15
31390325 TGATTTTCCA
*
31390335 ATATTTGATACCCAT
1 ATATTTGATAACCAT
**
31390350 ATATTTGACTTTCCAT
1 ATATTTGA-TAACCAT
31390366 -TATTTGATAACCAT
1 ATATTTGATAACCAT
31390380 ATATTTGA
1 ATATTTGA
31390388 ATTTTTATAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
14 5 0.16
15 22 0.69
16 5 0.16
ACGTcount: A:0.32, C:0.15, G:0.08, T:0.45
Consensus pattern (15 bp):
ATATTTGATAACCAT
Found at i:31400409 original size:22 final size:22
Alignment explanation
Indices: 31400349--31400406 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 22
31400339 AATCTTCAAG
31400349 GATATGCAATCTT---AGATAT
1 GATATGCAATCTTAGAAGATAT
31400368 GATATGCAATCTTAGAAGATAT
1 GATATGCAATCTTAGAAGATAT
* *
31400390 GATTTTGTAATCTTAGA
1 GA-TATGCAATCTTAGA
31400407 GATTTAATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.39
22 8 0.24
23 12 0.36
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.38
Consensus pattern (22 bp):
GATATGCAATCTTAGAAGATAT
Found at i:31407051 original size:24 final size:24
Alignment explanation
Indices: 31407019--31407076 Score: 107
Period size: 24 Copynumber: 2.4 Consensus size: 24
31407009 ATGTCCCAAA
*
31407019 ATTACAGTGGATTGAACCTTGAAG
1 ATTACAGTGGATTAAACCTTGAAG
31407043 ATTACAGTGGATTAAACCTTGAAG
1 ATTACAGTGGATTAAACCTTGAAG
31407067 ATTACAGTGG
1 ATTACAGTGG
31407077 GGGGCAATCA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.34, C:0.12, G:0.24, T:0.29
Consensus pattern (24 bp):
ATTACAGTGGATTAAACCTTGAAG
Found at i:31407566 original size:72 final size:72
Alignment explanation
Indices: 31407457--31407593 Score: 168
Period size: 72 Copynumber: 1.9 Consensus size: 72
31407447 CAGTGGAACA
* * * ** *
31407457 GATTAAAGCTAAAGGTAGCGAATCTTGTTTCCCTGGCGTTGCAGTGGCATAGATTAAAGCTGAAA
1 GATTAAAGCTAAAGGTAGCGAATCCTATTTCCCTGGCGTTACAGTGAAACAGATTAAAGCTGAAA
31407522 TGGAGCG
66 TGGAGCG
* * * *
31407529 GATTAAAGCTGAAGGTAGTGAATCCTATCTT-CTTGGCGTTATAGTGAAACAGATTAAAGCTGAA
1 GATTAAAGCTAAAGGTAGCGAATCCTAT-TTCCCTGGCGTTACAGTGAAACAGATTAAAGCTGAA
31407593 A
65 A
31407594 GTAGCGAATC
Statistics
Matches: 54, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
72 52 0.96
73 2 0.04
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (72 bp):
GATTAAAGCTAAAGGTAGCGAATCCTATTTCCCTGGCGTTACAGTGAAACAGATTAAAGCTGAAA
TGGAGCG
Found at i:31407635 original size:123 final size:122
Alignment explanation
Indices: 31407414--31407644 Score: 306
Period size: 123 Copynumber: 1.9 Consensus size: 122
31407404 GGCGTTAAGA
* * *
31407414 CTGAAGGCAGTGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCTAAAGGTAGCGAA
1 CTGAAGGCAGTGAATCCTATTTCCCTGGCGTTACAGTGAAACAGATTAAAGCTAAAGGTAGCGAA
* * *
31407479 TCTTGTTTCCCTGGCGTTGCAGTGGCATAGATTAAAGCTGAAATGGAGCGGATTAAAG
66 TCTTGTTTCCCTAGCATTGCAGCGGCA-AGATTAAAGCTGAAATGGAGCGGATTAAAG
* * *
31407537 CTGAAGGTAGTGAATCCTATCTT-CTTGGCGTTATAGTGAAACAGATTAAAGCTGAAA-GTAGCG
1 CTGAAGGCAGTGAATCCTAT-TTCCCTGGCGTTACAGTGAAACAGATTAAAGCT-AAAGGTAGCG
*
31407600 AATCTTGTTTCCCTAGCATTGCAGCGAAGC-GGATTAAAGCTGAAA
64 AATCTTGTTTCCCTAGCATTGCAGCG--GCAAGATTAAAGCTGAAA
31407645 GCATCGAATC
Statistics
Matches: 94, Mismatches: 10, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
123 87 0.93
124 5 0.05
125 2 0.02
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.27
Consensus pattern (122 bp):
CTGAAGGCAGTGAATCCTATTTCCCTGGCGTTACAGTGAAACAGATTAAAGCTAAAGGTAGCGAA
TCTTGTTTCCCTAGCATTGCAGCGGCAAGATTAAAGCTGAAATGGAGCGGATTAAAG
Found at i:31408252 original size:170 final size:171
Alignment explanation
Indices: 31407880--31408348 Score: 597
Period size: 170 Copynumber: 2.7 Consensus size: 171
31407870 AAAGATGGCG
* * * **
31407880 AATCTTATCTTCCTGAAATTGTAGTGGAGTAGATTAAAGCCAAT--AATCCTATCTCTTTAAAGT
1 AATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAG--AATCCAATCCTATCTCCCTAAAGT
* * * * * * *
31407943 TACAATGGAGCGGGTTAAAATCACAGATCTTATCTCTCTAAAGTTGCAGAGAGCAGATCGTATCC
64 TGCAGTGGAGCGGATTAAAATCACAGATCTTATCTCTTTGAAGTTGCAAAGAGCAGATCGCAT-C
*
31408008 AGTCTTATCTCCCTGAAGTTGCAGCGAAGCAGACTGAATAAACC
128 AGTCTTATCTCCCTGAAGTTACAGCGAAGCAGACTGAATAAACC
* * *
31408052 AATCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTAAAGAATCCAATCCTATCTCCCTAAATTTG
1 AATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAGAATCCAATCCTATCTCCCTAAAGTTG
* * *
31408117 TAGTGGAGCGGATTAAAATCATAGATCTTATCTCTTTGAAGTTGCAAAGAGTAGATCGCAT-AGT
66 CAGTGGAGCGGATTAAAATCACAGATCTTATCTCTTTGAAGTTGCAAAGAGCAGATCGCATCAGT
* *
31408181 CTTATCTCCCTGAAGTTACAGCGGAGCAGACTGAATAAATC
131 CTTATCTCCCTGAAGTTACAGCGAAGCAGACTGAATAAACC
* * * * *
31408222 AATCTTATCTCCCTGAAGTTATAGTGGAGCATATTAAAGAAACCAACCCTATCTCCCTGAAGTTG
1 AATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAGAATCCAATCCTATCTCCCTAAAGTTG
* * *
31408287 CAGTGGAGTGGATTAAAATCACAGATCTTATCT-TTCTGAAGTTGTAGTAGAGCA-ATCGCATC
66 CAGTGGAGCGGATTAAAATCACAGATCTTATCTCTT-TGAAGTTGCA-AAGAGCAGATCGCATC
31408349 CAGCCTAGCC
Statistics
Matches: 257, Mismatches: 35, Indels: 11
0.85 0.12 0.04
Matches are distributed among these distances:
169 2 0.01
170 147 0.57
171 5 0.02
172 103 0.40
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (171 bp):
AATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAGAATCCAATCCTATCTCCCTAAAGTTG
CAGTGGAGCGGATTAAAATCACAGATCTTATCTCTTTGAAGTTGCAAAGAGCAGATCGCATCAGT
CTTATCTCCCTGAAGTTACAGCGAAGCAGACTGAATAAACC
Found at i:31408319 original size:44 final size:44
Alignment explanation
Indices: 31407881--31408340 Score: 197
Period size: 44 Copynumber: 10.7 Consensus size: 44
31407871 AAGATGGCGA
* * * * ** *
31407881 ATCTTATCTTCCTGAAATTGTAGTGGAGTAGATTAAAGCCA-ATA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCACA-G
* ** * * * * *
31407925 ATCCTATCTCTTTAAAGTTACAATGGAGCGGGTTAAAATCACAG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCACAG
* * * ***
31407969 ATCTTATCTCTCTAAAGTTGCAG-AGAGCAGA-TCGTATC-CAG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCACAG
* * * *
31408010 -TCTTATCTCCCTGAAGTTGCAGCGAAGCAGACTGAATAAAC-CA-
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TTAA-AATCACAG
*
31408053 ATCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTAAAGAATC-CA-
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT-AA-AATCACAG
* * * * * *
31408097 ATCCTATCTCCCTAAATTTGTAGTGGAGCGGATTAAAATCATAG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCACAG
** * * * *
31408141 ATCTTATCTCTTTGAAGTTGCA----A--AGAGT-AGATCGCAT
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCACAG
* * *
31408178 AGTCTTATCTCCCTGAAGTTACAGCGGAGCAGACTGAATAA--ATCA-
1 A-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TTAA-AATCA-CAG
** * *
31408223 ATCTTATCTCCCTGAAGTTATAGTGGAGCATATTAAAGA-AACCA-
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAA-ATCA-CAG
* * **
31408267 ACCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAATCACAG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCACAG
** * *
31408311 ATCTTATCTTTCTGAAGTTGTAGTAGAGCA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCA
31408341 ATCGCATCCA
Statistics
Matches: 305, Mismatches: 87, Indels: 48
0.69 0.20 0.11
Matches are distributed among these distances:
37 6 0.02
38 21 0.07
40 21 0.07
41 9 0.03
42 10 0.03
43 16 0.05
44 216 0.71
45 2 0.01
46 3 0.01
47 1 0.00
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (44 bp):
ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCACAG
Found at i:31408507 original size:89 final size:89
Alignment explanation
Indices: 31408348--31408576 Score: 323
Period size: 89 Copynumber: 2.6 Consensus size: 89
31408338 GCAATCGCAT
* * * * * **
31408348 CCAGCCTAGCCTCCCTGAGTATGCAGCGGAGTAGACTGACGATAGCAGATCTTGTCTTTTTGTAT
1 CCAGCCTTGCCTCCCTGAGTTTGTAGCGGAGCAGACTGAAGATAGCAGATCTTGTCTTCCTGTAT
*
31408413 TGGCAGCGAAGCAGATCGAAGACA
66 TGGCAGCGAAACAGATCGAAGACA
* * * * *
31408437 CTATCCTTGCCTCCCTGAGTTTGTAGCAGAGCAGAATGAATATAGCAGATCTTGTCTTCCTGTAT
1 CCAGCCTTGCCTCCCTGAGTTTGTAGCGGAGCAGACTGAAGATAGCAGATCTTGTCTTCCTGTAT
*
31408502 TGGCAGCGAAATAGATCGAAGACA
66 TGGCAGCGAAACAGATCGAAGACA
*
31408526 CCAGCCTTGCCTCCCTGATTTTGTAGCGGAGCAGACTGAAGATAGCAGATC
1 CCAGCCTTGCCTCCCTGAGTTTGTAGCGGAGCAGACTGAAGATAGCAGATC
31408577 GAAAACACCA
Statistics
Matches: 120, Mismatches: 20, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
89 120 1.00
ACGTcount: A:0.26, C:0.24, G:0.25, T:0.25
Consensus pattern (89 bp):
CCAGCCTTGCCTCCCTGAGTTTGTAGCGGAGCAGACTGAAGATAGCAGATCTTGTCTTCCTGTAT
TGGCAGCGAAACAGATCGAAGACA
Found at i:31408634 original size:58 final size:58
Alignment explanation
Indices: 31408513--31408634 Score: 145
Period size: 58 Copynumber: 2.1 Consensus size: 58
31408503 GGCAGCGAAA
* * * *
31408513 TAGATCGAAGACACCAGCCTTGCCTCCCTGATTTTGTAGCGGAGCAGACTGAAGATAG
1 TAGATCGAAAACACCAACCTTGCCTCCCTGAGTTTGCAGCGGAGCAGACTGAAGATAG
* * * * ** *
31408571 CAGATCGAAAACACCAACCTTGCCTCTCTGAGTTTGCAGTGGAGTAGGTTGAAGATTG
1 TAGATCGAAAACACCAACCTTGCCTCCCTGAGTTTGCAGCGGAGCAGACTGAAGATAG
31408629 TAGATC
1 TAGATC
31408635 TTGTCTTCCT
Statistics
Matches: 52, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
58 52 1.00
ACGTcount: A:0.28, C:0.22, G:0.25, T:0.25
Consensus pattern (58 bp):
TAGATCGAAAACACCAACCTTGCCTCCCTGAGTTTGCAGCGGAGCAGACTGAAGATAG
Found at i:31408757 original size:87 final size:87
Alignment explanation
Indices: 31408648--31408820 Score: 206
Period size: 87 Copynumber: 2.0 Consensus size: 87
31408638 TCTTCCTAAT
* * *
31408648 TAGTAGTGGAGTAGATCAAAGATGGCGA-ATCTTATCTTCCCAATGTAGTAG-GAAGCAGATTTA
1 TAGTAGTGGAGTAGATCAAAGATGG-GATATCCTATCTCCCCAA-GCAGTAGTGAAGCAGATTTA
31408711 AGCCACCAGCCCTATCTCCCTGAG
64 AGCCACCAGCCCTATCTCCCTGAG
* ** * * *
31408735 TAGTAGTGGAGTAGGTTGAAGATTGTATATCCTATCTCCCCAAGCAGTAGTGGAGCAGATTTAAG
1 TAGTAGTGGAGTAGATCAAAGATGGGATATCCTATCTCCCCAAGCAGTAGTGAAGCAGATTTAAG
* * *
31408800 TCATCAGCCTTATCTCCCTGA
66 CCACCAGCCCTATCTCCCTGA
31408821 AGTTGCAGTG
Statistics
Matches: 72, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
86 7 0.10
87 65 0.90
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (87 bp):
TAGTAGTGGAGTAGATCAAAGATGGGATATCCTATCTCCCCAAGCAGTAGTGAAGCAGATTTAAG
CCACCAGCCCTATCTCCCTGAG
Found at i:31409315 original size:22 final size:22
Alignment explanation
Indices: 31409255--31409312 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 22
31409245 AATCTTCAAG
31409255 GATATGCAATCTT---AGATAT
1 GATATGCAATCTTAGAAGATAT
*
31409274 GATATGCAATTTTAGAAGATAT
1 GATATGCAATCTTAGAAGATAT
* *
31409296 GATTTTGTAATCTTAGA
1 GA-TATGCAATCTTAGA
31409313 GATTTAATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
19 12 0.39
22 8 0.26
23 11 0.35
ACGTcount: A:0.36, C:0.07, G:0.17, T:0.40
Consensus pattern (22 bp):
GATATGCAATCTTAGAAGATAT
Found at i:31413589 original size:50 final size:47
Alignment explanation
Indices: 31413530--31413690 Score: 155
Period size: 47 Copynumber: 3.3 Consensus size: 47
31413520 CAGTGAGTGT
* *
31413530 GCCAGTGTAAGACTATGTCTGGGGCATGGCATCGGCACG-GACTAAGGAGA
1 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACGAGA-T---GAGA
* * * * *
31413580 GCCAGTGTAAAACCATGTTTGGGACATGGCATCGGCTCGAGATGCGC
1 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACGAGATGAGA
* * *
31413627 GCCAGTGTAAGACCATGTCTGGGACATGGCATTGGCACCGATATGTGA
1 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCA-CGAGATGAGA
*
31413675 TCCCA-TGTAAGACCAT
1 -GCCAGTGTAAGACCAT
31413691 ATATAGGATA
Statistics
Matches: 93, Mismatches: 15, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
47 35 0.38
48 18 0.19
49 3 0.03
50 35 0.38
51 2 0.02
ACGTcount: A:0.25, C:0.22, G:0.31, T:0.21
Consensus pattern (47 bp):
GCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACGAGATGAGA
Found at i:31413642 original size:47 final size:48
Alignment explanation
Indices: 31413530--31413664 Score: 157
Period size: 47 Copynumber: 2.8 Consensus size: 48
31413520 CAGTGAGTGT
* *
31413530 GCCAGTGTAAGACTATGTCTGGGGCATGGCATCGGCACGGACTAAGGAGA
1 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACGGACT-A-GAGA
* * * * *
31413580 GCCAGTGTAAAACCATGTTTGGGACATGGCATCGGCTCGAGA-T-GCGC
1 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACG-GACTAGAGA
*
31413627 GCCAGTGTAAGACCATGTCTGGGACATGGCATTGGCAC
1 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCAC
31413665 CGATATGTGA
Statistics
Matches: 73, Mismatches: 11, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
47 36 0.49
50 35 0.48
51 2 0.03
ACGTcount: A:0.24, C:0.22, G:0.33, T:0.20
Consensus pattern (48 bp):
GCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACGGACTAGAGA
Found at i:31416496 original size:20 final size:19
Alignment explanation
Indices: 31416473--31416515 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
31416463 AATTTAGTCT
*
31416473 TTTTTATTTTTATTTTAATA
1 TTTTTATTTTTAATTTAA-A
*
31416493 TTTTTGTTTTTAATTTAAA
1 TTTTTATTTTTAATTTAAA
31416512 TTTT
1 TTTT
31416516 ACATTCTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.74
Consensus pattern (19 bp):
TTTTTATTTTTAATTTAAA
Found at i:31421793 original size:42 final size:42
Alignment explanation
Indices: 31421713--31421794 Score: 112
Period size: 42 Copynumber: 2.0 Consensus size: 42
31421703 CATTTTCTCT
* **
31421713 ATGCCATAGTCCAACTATGGTCTTACACATATTTACATATTG
1 ATGCCATAGCCCAACTATGGTCTTACACATATGCACATATTG
*
31421755 ATGCCATAGCCCAGCTATGGTCTTACACAGTA-GCACATAT
1 ATGCCATAGCCCAACTATGGTCTTACACA-TATGCACATAT
31421795 CACACCAATG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
42 33 0.94
43 2 0.06
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.30
Consensus pattern (42 bp):
ATGCCATAGCCCAACTATGGTCTTACACATATGCACATATTG
Found at i:31428117 original size:11 final size:11
Alignment explanation
Indices: 31428101--31428125 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
31428091 GTCAAAAAAT
31428101 TTATTTTAATA
1 TTATTTTAATA
31428112 TTATTTTAATA
1 TTATTTTAATA
31428123 TTA
1 TTA
31428126 AAGCATGATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
TTATTTTAATA
Found at i:31432032 original size:21 final size:22
Alignment explanation
Indices: 31432005--31432069 Score: 80
Period size: 21 Copynumber: 3.0 Consensus size: 22
31431995 ATGTTTTAGG
31432005 TTCAGGCACTATATGTGTCGTA
1 TTCAGGCACTATATGTGTCGTA
* **
31432027 TT-AGGCACCACGTGTGTCGT-
1 TTCAGGCACTATATGTGTCGTA
*
31432047 TTCAGGCACTTTATGTGTCGTA
1 TTCAGGCACTATATGTGTCGTA
31432069 T
1 T
31432070 ACTGCTTCTG
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
20 2 0.06
21 29 0.85
22 3 0.09
ACGTcount: A:0.18, C:0.20, G:0.25, T:0.37
Consensus pattern (22 bp):
TTCAGGCACTATATGTGTCGTA
Found at i:31432325 original size:23 final size:23
Alignment explanation
Indices: 31432299--31432376 Score: 120
Period size: 23 Copynumber: 3.4 Consensus size: 23
31432289 GGCTTTGCCG
*
31432299 ATCAGGCACTTTATGTGTCATAT
1 ATCAGGCACTTTATGTGTCGTAT
31432322 ATCAGGCACTTTATGTGTCGTAT
1 ATCAGGCACTTTATGTGTCGTAT
* *
31432345 ATCATGCGCTTTATGTGTCGTAT
1 ATCAGGCACTTTATGTGTCGTAT
*
31432368 TTCAGGCAC
1 ATCAGGCAC
31432377 CTCGTGCGTC
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 49 1.00
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.38
Consensus pattern (23 bp):
ATCAGGCACTTTATGTGTCGTAT
Found at i:31432387 original size:23 final size:22
Alignment explanation
Indices: 31432361--31432411 Score: 77
Period size: 21 Copynumber: 2.3 Consensus size: 22
31432351 CGCTTTATGT
31432361 GTCGTATTTCAGGCACCTCGTGC
1 GTCGTA-TTCAGGCACCTCGTGC
*
31432384 GTCGTA-TCAGGCACCTCGTGT
1 GTCGTATTCAGGCACCTCGTGC
31432405 GTCGTAT
1 GTCGTAT
31432412 ATTGATCAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 20 0.77
23 6 0.23
ACGTcount: A:0.14, C:0.27, G:0.27, T:0.31
Consensus pattern (22 bp):
GTCGTATTCAGGCACCTCGTGC
Found at i:31441949 original size:224 final size:224
Alignment explanation
Indices: 31441513--31441949 Score: 510
Period size: 224 Copynumber: 2.0 Consensus size: 224
31441503 CAATACAACC
* *
31441513 CTAAAAAGCTAATATACTAAAAAGACTTAAACTAGTACACTTGGTTCAAATAGGCTCTTATGTTT
1 CTAAAAAGCTAATATACTAAAAAGACTTAAACTAGTACACTTGGTTCAAATAAGCCCTTATGTTT
* * * * * **
31441578 TTTTTGGTAACTAAATAACTCCTAAACTTTTATTTTTATTCATGTAAACCCTTAGTTTTAACTAA
66 TTTGTGATAACTAAATAACTCCTAAACTTTGATATTTATTCATGTAAACCCTTAGCTAAAACTAA
* *
31441643 AAATACTTTCGGAGAAACTCAATACCAAGTTACAATCAATATTCTAGAGATATTAAGTTATCAAT
131 AAATACTTTCGGAGAAACCCAATACCAAGTTACAATCAATATTCTAGAGATATTAAGCTATCAAT
* *
31441708 ATTCGATTTTTGTTTTTTCTATTATAGAG
196 ATTCGATCTTGGTTTTTTCTATTATAGAG
* * * * *
31441737 CTAAAAGGCTAATGTACTAAAGAAGGCCTTAAACTAGTACACTTTGTTTAAATAAGCCCTTATG-
1 CTAAAAAGCTAATATACTAAA-AA-GACTTAAACTAGTACACTTGGTTCAAATAAGCCCTTATGT
* * * *
31441801 TTTTTGT-ATAACTAAATAAGTCCTATACTTTGATATTTATTCATGTAAGCCCTTA-CTAAAAGT
64 TTTTTGTGATAACTAAATAACTCCTAAACTTTGATATTTATTCATGTAAACCCTTAGCTAAAACT
* * * * *
31441864 AAAACT-CTTTTTGGAGAAACCCAAATACCAAGTTACAA-CTACTGTTC-ATGAGATATTCAGCT
129 AAAAATAC-TTTCGGAGAAACCC-AATACCAAGTTACAATC-AATATTCTA-GAGATATTAAGCT
*
31441926 GTCAATATT-GAATCTTGGTTTTTT
190 ATCAATATTCG-ATCTTGGTTTTTT
31441950 TTTTTAATTT
Statistics
Matches: 178, Mismatches: 28, Indels: 14
0.81 0.13 0.06
Matches are distributed among these distances:
222 1 0.01
223 24 0.13
224 111 0.62
225 8 0.04
226 34 0.19
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (224 bp):
CTAAAAAGCTAATATACTAAAAAGACTTAAACTAGTACACTTGGTTCAAATAAGCCCTTATGTTT
TTTGTGATAACTAAATAACTCCTAAACTTTGATATTTATTCATGTAAACCCTTAGCTAAAACTAA
AAATACTTTCGGAGAAACCCAATACCAAGTTACAATCAATATTCTAGAGATATTAAGCTATCAAT
ATTCGATCTTGGTTTTTTCTATTATAGAG
Found at i:31443733 original size:13 final size:13
Alignment explanation
Indices: 31443717--31443742 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
31443707 TTTTTAATTT
31443717 TCTATAATTTATA
1 TCTATAATTTATA
31443730 TCTATAATTTATA
1 TCTATAATTTATA
31443743 ACATAATATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (13 bp):
TCTATAATTTATA
Found at i:31444058 original size:5 final size:5
Alignment explanation
Indices: 31444010--31444042 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
31444000 AATAAATAAA
*
31444010 TAATT TAATT TAATT TAATT TAATT TATTT TAA
1 TAATT TAATT TAATT TAATT TAATT TAATT TAA
31444043 AAAACTATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TAATT
Found at i:31444704 original size:21 final size:20
Alignment explanation
Indices: 31444666--31444705 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
31444656 TTTTGTCTTA
*
31444666 TATAGTTTTAATATATTAAT
1 TATAGTTTTAACATATTAAT
31444686 TATAGTTTTAAACATATTAA
1 TATAGTTTT-AACATATTAA
31444706 GCATATATAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (20 bp):
TATAGTTTTAACATATTAAT
Found at i:31452292 original size:15 final size:16
Alignment explanation
Indices: 31452257--31452295 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
31452247 TAAAGGACTT
*
31452257 AAGGATTAGTGCATGAA
1 AAGG-TTAGTGCATAAA
31452274 AAGGTTAGT-CATAAA
1 AAGGTTAGTGCATAAA
31452289 AAGGTTA
1 AAGGTTA
31452296 TGTCGAATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 12 0.57
16 5 0.24
17 4 0.19
ACGTcount: A:0.44, C:0.05, G:0.26, T:0.26
Consensus pattern (16 bp):
AAGGTTAGTGCATAAA
Found at i:31456769 original size:43 final size:43
Alignment explanation
Indices: 31456713--31456835 Score: 194
Period size: 43 Copynumber: 2.9 Consensus size: 43
31456703 ATTTCATGTC
*
31456713 AGACCAT-GCCTGGGCTATTGGCATTGATTTGAGATTTCGTATA
1 AGACCATAG-CTGGGCTATTGGCATCGATTTGAGATTTCGTATA
*
31456756 AGACCATAGCTGGGCTATTGGCATCGATTTGAGATTTCGTGTA
1 AGACCATAGCTGGGCTATTGGCATCGATTTGAGATTTCGTATA
**
31456799 AGACCATAGCTGGGCTATTGGCATCGATACGAGATTT
1 AGACCATAGCTGGGCTATTGGCATCGATTTGAGATTT
31456836 GGCATCGATA
Statistics
Matches: 75, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
43 74 0.99
44 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.32
Consensus pattern (43 bp):
AGACCATAGCTGGGCTATTGGCATCGATTTGAGATTTCGTATA
Found at i:31456839 original size:18 final size:18
Alignment explanation
Indices: 31456816--31456853 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
31456806 AGCTGGGCTA
31456816 TTGGCATCGATACGAGAT
1 TTGGCATCGATACGAGAT
31456834 TTGGCATCGATACGAGAT
1 TTGGCATCGATACGAGAT
31456852 TT
1 TT
31456854 TCATGTAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32
Consensus pattern (18 bp):
TTGGCATCGATACGAGAT
Found at i:31458220 original size:3 final size:3
Alignment explanation
Indices: 31458214--31458259 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
31458204 ATTAATCAAT
31458214 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
31458260 CATTGTATAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:31461779 original size:18 final size:18
Alignment explanation
Indices: 31461743--31461780 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
31461733 CTTTAACATT
*
31461743 TTTTTTTCCTTCTTTTTC
1 TTTTTTTCCTCCTTTTTC
31461761 TTTTTTTCC-CCTTTCTTC
1 TTTTTTTCCTCCTTT-TTC
31461779 TT
1 TT
31461781 CCTTTTATCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTTTTTCCTCCTTTTTC
Found at i:31463812 original size:27 final size:27
Alignment explanation
Indices: 31463762--31463814 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
31463752 TTTTTATATC
* *
31463762 ATAAAATTAAAATTAATTATAAATTAA
1 ATAAAAATAAAATTAATTAGAAATTAA
31463789 ATAAAAATAAAATTTAATT-GAAATTA
1 ATAAAAATAAAA-TTAATTAGAAATTA
31463815 TACTTTTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 17 0.74
28 6 0.26
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (27 bp):
ATAAAAATAAAATTAATTAGAAATTAA
Found at i:31464539 original size:8 final size:8
Alignment explanation
Indices: 31464528--31464554 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
31464518 CTTTTATTAA
31464528 TTTAAAAT
1 TTTAAAAT
31464536 TTTAAAAT
1 TTTAAAAT
31464544 TTTAAAAT
1 TTTAAAAT
31464552 TTT
1 TTT
31464555 TTAAAGAGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (8 bp):
TTTAAAAT
Found at i:31465944 original size:15 final size:15
Alignment explanation
Indices: 31465924--31465952 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
31465914 ATTAAAAATG
31465924 TTATTAAATTATATA
1 TTATTAAATTATATA
31465939 TTATTAAATTATAT
1 TTATTAAATTATAT
31465953 TTAATAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TTATTAAATTATATA
Found at i:31465982 original size:26 final size:27
Alignment explanation
Indices: 31465909--31465982 Score: 66
Period size: 26 Copynumber: 2.8 Consensus size: 27
31465899 TAAAAACATT
* *
31465909 ATTATATTAAAA-ATG-TTATTAAATT
1 ATTATATTAAAATATGATTAATAAATA
*
31465934 ATATATTATTAAATTAT-ATTTAAT-AATA
1 AT-TA-TATTAAAATATGA-TTAATAAATA
31465962 ATTATATTAAAATATGATTAA
1 ATTATATTAAAATATGATTAA
31465983 ATTATTTATT
Statistics
Matches: 39, Mismatches: 4, Indels: 11
0.72 0.07 0.20
Matches are distributed among these distances:
25 2 0.05
26 16 0.41
27 10 0.26
28 7 0.18
29 4 0.10
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (27 bp):
ATTATATTAAAATATGATTAATAAATA
Found at i:31466200 original size:16 final size:16
Alignment explanation
Indices: 31466176--31466210 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
31466166 TGAATTACTG
* *
31466176 ATTATAGCTCTATTTC
1 ATTACAGCTCTATTCC
31466192 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCC
31466208 ATT
1 ATT
31466211 TCAACCCTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.26, C:0.23, G:0.06, T:0.46
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:31466912 original size:19 final size:18
Alignment explanation
Indices: 31466866--31466915 Score: 59
Period size: 16 Copynumber: 2.8 Consensus size: 18
31466856 TGAGATTCTA
*
31466866 ATATTTAAATTTACTAAT
1 ATATTTAAATTTAGTAAT
*
31466884 ATA--GAAATTTAGTAAT
1 ATATTTAAATTTAGTAAT
31466900 ATAATTTAAATTTAGT
1 AT-ATTTAAATTTAGT
31466916 GAACCTAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
16 13 0.50
17 1 0.04
18 3 0.12
19 9 0.35
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.46
Consensus pattern (18 bp):
ATATTTAAATTTAGTAAT
Found at i:31467281 original size:3 final size:3
Alignment explanation
Indices: 31467275--31467300 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
31467265 AATAATAAAA
31467275 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
31467301 TAATCTTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:31474281 original size:16 final size:16
Alignment explanation
Indices: 31474260--31474295 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
31474250 TTTGGTTCGC
31474260 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
31474276 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
31474292 TGTA
1 TGTA
31474296 ATAGCAAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.25, C:0.00, G:0.36, T:0.39
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:31474551 original size:18 final size:17
Alignment explanation
Indices: 31474530--31474564 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
31474520 TTATTATTAA
*
31474530 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
31474548 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
31474565 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:31487462 original size:28 final size:28
Alignment explanation
Indices: 31487429--31487494 Score: 114
Period size: 28 Copynumber: 2.4 Consensus size: 28
31487419 GTTTTTTGGT
**
31487429 ATATTTTGGTAAATAAAAAAATTTTATA
1 ATATTTTGGTAAATAAAAAAAAGTTATA
31487457 ATATTTTGGTAAATAAAAAAAAGTTATA
1 ATATTTTGGTAAATAAAAAAAAGTTATA
31487485 ATATTTTGGT
1 ATATTTTGGT
31487495 TATTTTTTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.47, C:0.00, G:0.11, T:0.42
Consensus pattern (28 bp):
ATATTTTGGTAAATAAAAAAAAGTTATA
Found at i:31487691 original size:32 final size:31
Alignment explanation
Indices: 31487655--31487723 Score: 95
Period size: 32 Copynumber: 2.2 Consensus size: 31
31487645 TGCCTATAAG
*
31487655 TATTTAATTGGTATCAT-AATTTATTTAGAAAA
1 TATTTAATTGGTA-CATGAATTTATCTA-AAAA
31487687 TATTTAATTGGTACATGAATTTATCTAAAAA
1 TATTTAATTGGTACATGAATTTATCTAAAAA
*
31487718 AATTTA
1 TATTTA
31487724 TATATATATA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
31 12 0.35
32 22 0.65
ACGTcount: A:0.42, C:0.04, G:0.09, T:0.45
Consensus pattern (31 bp):
TATTTAATTGGTACATGAATTTATCTAAAAA
Found at i:31488598 original size:15 final size:15
Alignment explanation
Indices: 31488543--31488599 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
31488533 TTTATACTAC
31488543 AAAATATTTATTATT
1 AAAATATTTATTATT
* * *
31488558 AATATATGTATAATTGTA
1 AAAATAT-T-T-ATTATT
31488576 ATAAATATTTATTATT
1 A-AAATATTTATTATT
31488592 AAAATATT
1 AAAATATT
31488600 AATATTGAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
15 13 0.41
16 6 0.19
17 2 0.06
18 6 0.19
19 5 0.16
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (15 bp):
AAAATATTTATTATT
Found at i:31489634 original size:27 final size:27
Alignment explanation
Indices: 31489603--31489655 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
31489593 ACCACCACCA
31489603 TACCCACCACGCCCTCCGTATCCTCCG
1 TACCCACCACGCCCTCCGTATCCTCCG
*
31489630 TACCCACCGCGCCCTCCGTATCCTCC
1 TACCCACCACGCCCTCCGTATCCTCC
31489656 ATAACCTCCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.13, C:0.57, G:0.11, T:0.19
Consensus pattern (27 bp):
TACCCACCACGCCCTCCGTATCCTCCG
Found at i:31490817 original size:32 final size:32
Alignment explanation
Indices: 31490747--31490820 Score: 96
Period size: 32 Copynumber: 2.3 Consensus size: 32
31490737 CTAACTAATT
*
31490747 TTTAATTTAATCAATTTAATCTATCAATCAGA
1 TTTAATTTAATCAATTTAATCGATCAATCAGA
* * *
31490779 TCTAATTTAATCAATTTAATCGGTTAATCTA-A
1 TTTAATTTAATCAATTTAATCGATCAATC-AGA
31490811 TTTAATTTAA
1 TTTAATTTAA
31490821 AGAAAAATTA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
32 35 0.97
33 1 0.03
ACGTcount: A:0.39, C:0.11, G:0.04, T:0.46
Consensus pattern (32 bp):
TTTAATTTAATCAATTTAATCGATCAATCAGA
Found at i:31493670 original size:22 final size:23
Alignment explanation
Indices: 31493647--31493693 Score: 76
Period size: 25 Copynumber: 2.0 Consensus size: 23
31493637 ATTAGCTCAA
31493647 TTTTTATTATTTCATTTAACAATT
1 TTTTTATTATTTCATTTAACAA-T
31493671 GTTTTTATTATTTCATTTAACAA
1 -TTTTTATTATTTCATTTAACAA
31493694 AATCCTGCCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.30, C:0.09, G:0.02, T:0.60
Consensus pattern (23 bp):
TTTTTATTATTTCATTTAACAAT
Found at i:31494511 original size:22 final size:22
Alignment explanation
Indices: 31494486--31494529 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
31494476 TGTGCTGCTG
*
31494486 TTTGCAATTTTTGGATT-ATTTA
1 TTTGCAAATTTT-GATTAATTTA
*
31494508 TTTGTAAATTTTGATTAATTTA
1 TTTGCAAATTTTGATTAATTTA
31494530 ATTATATGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.27, C:0.02, G:0.11, T:0.59
Consensus pattern (22 bp):
TTTGCAAATTTTGATTAATTTA
Found at i:31496066 original size:12 final size:12
Alignment explanation
Indices: 31496049--31496079 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
31496039 TTAAGTTGTA
31496049 AATGGAGTCGAG
1 AATGGAGTCGAG
*
31496061 AATGGAGTTGAG
1 AATGGAGTCGAG
31496073 AATGGAG
1 AATGGAG
31496080 CATGCTTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.35, C:0.03, G:0.42, T:0.19
Consensus pattern (12 bp):
AATGGAGTCGAG
Found at i:31496525 original size:72 final size:72
Alignment explanation
Indices: 31496436--31496667 Score: 234
Period size: 72 Copynumber: 3.2 Consensus size: 72
31496426 ATTAATTATC
* * **
31496436 AAGTAAAATCGTTTATTTAATTATGTGTTTTTAAAAAGGTTAATTTAGTTCAATTTATTAAGTTT
1 AAGTGAAACCGTTTATTTAATTATGAATTTTTAAAAAGGTTAATTTAGTTCAATTTATTAAGTTT
31496501 TGATATT
66 TGATATT
* * * * * ** **
31496508 AAGCGAAACCGTTTATTTAGTTAT-ACA-TTTTCAGAAGCTTAATTTAGTTTGATTTATTAAAAT
1 AAGTGAAACCGTTTATTTAATTATGA-ATTTTTAAAAAGGTTAATTTAGTTCAATTTATTAAGTT
31496571 TTGATATT
65 TTGATATT
* * * * * * * *
31496579 AAGTAAAAACGCTTGTTCAATTATGAATTTTAAAAAAGGTTAATTTAGTTCAACTTATTGAGTTT
1 AAGTGAAACCGTTTATTTAATTATGAATTTTTAAAAAGGTTAATTTAGTTCAATTTATTAAGTTT
31496644 TGATATT
66 TGATATT
* *
31496651 AAGTGGAACCATTTATT
1 AAGTGAAACCGTTTATT
31496668 CTGTTATACA
Statistics
Matches: 121, Mismatches: 36, Indels: 6
0.74 0.22 0.04
Matches are distributed among these distances:
71 55 0.45
72 66 0.55
ACGTcount: A:0.35, C:0.06, G:0.13, T:0.45
Consensus pattern (72 bp):
AAGTGAAACCGTTTATTTAATTATGAATTTTTAAAAAGGTTAATTTAGTTCAATTTATTAAGTTT
TGATATT
Found at i:31499291 original size:13 final size:14
Alignment explanation
Indices: 31499267--31499300 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
31499257 ATGGTGGTAG
*
31499267 GATTCTGTATATCT
1 GATTCTGCATATCT
31499281 G-TTCTGCATATCT
1 GATTCTGCATATCT
31499294 GATTCTG
1 GATTCTG
31499301 TTCTCTGTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.18, C:0.18, G:0.18, T:0.47
Consensus pattern (14 bp):
GATTCTGCATATCT
Found at i:31499970 original size:9 final size:9
Alignment explanation
Indices: 31499956--31500144 Score: 81
Period size: 9 Copynumber: 21.6 Consensus size: 9
31499946 AACATTGGAT
31499956 CATAACTTA
1 CATAACTTA
*
31499965 CATAACTTG
1 CATAACTTA
*
31499974 TATAA--TA
1 CATAACTTA
*
31499981 CATAA-ATA
1 CATAACTTA
* * *
31499989 TATATCATA
1 CATAACTTA
*
31499998 TCATAAATTA
1 -CATAACTTA
*
31500008 CATAATTTA
1 CATAACTTA
31500017 CATAACTTA
1 CATAACTTA
*
31500026 CATAA-ATA
1 CATAACTTA
* * *
31500034 TATATCATA
1 CATAACTTA
31500043 TCATAACTTA
1 -CATAACTTA
31500053 CATAACTTA
1 CATAACTTA
31500062 CATAA--TA
1 CATAACTTA
***
31500069 CATAAAAAA
1 CATAACTTA
*
31500078 CAT--CATA
1 CATAACTTA
31500085 TCATAACTTA
1 -CATAACTTA
*
31500095 CATAATTTA
1 CATAACTTA
*
31500104 CATAATTTA
1 CATAACTTA
*
31500113 CATAA-ATA
1 CATAACTTA
* * *
31500121 TATATCATA
1 CATAACTTA
31500130 TCATAACTTA
1 -CATAACTTA
31500140 CATAA
1 CATAA
31500145 AACTTTGGAT
Statistics
Matches: 139, Mismatches: 29, Indels: 24
0.72 0.15 0.12
Matches are distributed among these distances:
7 14 0.10
8 18 0.13
9 87 0.63
10 20 0.14
ACGTcount: A:0.49, C:0.15, G:0.01, T:0.35
Consensus pattern (9 bp):
CATAACTTA
Found at i:31500043 original size:45 final size:43
Alignment explanation
Indices: 31499954--31500144 Score: 276
Period size: 45 Copynumber: 4.4 Consensus size: 43
31499944 AAAACATTGG
**
31499954 ATCATAACTTACATAACTTGTATAATACATAAATATATATCAT
1 ATCATAACTTACATAACTTACATAATACATAAATATATATCAT
* *
31499997 ATCATAAATTACATAATTTACATAACTTACATAAATATATATCAT
1 ATCATAACTTACATAACTTACATAA--TACATAAATATATATCAT
* *
31500042 ATCATAACTTACATAACTTACATAATACATAAA-AAACATCAT
1 ATCATAACTTACATAACTTACATAATACATAAATATATATCAT
*
31500084 ATCATAACTTACATAATTTACATAATTTACATAAATATATATCAT
1 ATCATAACTTACATAACTTACATAA--TACATAAATATATATCAT
31500129 ATCATAACTTACATAA
1 ATCATAACTTACATAA
31500145 AACTTTGGAT
Statistics
Matches: 132, Mismatches: 11, Indels: 8
0.87 0.07 0.05
Matches are distributed among these distances:
42 31 0.23
43 29 0.22
44 8 0.06
45 64 0.48
ACGTcount: A:0.49, C:0.15, G:0.01, T:0.36
Consensus pattern (43 bp):
ATCATAACTTACATAACTTACATAATACATAAATATATATCAT
Found at i:31500114 original size:87 final size:88
Alignment explanation
Indices: 31499954--31500144 Score: 321
Period size: 87 Copynumber: 2.2 Consensus size: 88
31499944 AAAACATTGG
** * *
31499954 ATCATAACTTACATAACTTGTATAATACATAAATATATATCATATCATAAATTACATAATTTACA
1 ATCATAACTTACATAACTTACATAATACATAAATAAACATCATATCATAAATTACATAATTTACA
31500019 TAACTTACATAAATATATATCAT
66 TAACTTACATAAATATATATCAT
*
31500042 ATCATAACTTACATAACTTACATAATACATAAA-AAACATCATATCATAACTTACATAATTTACA
1 ATCATAACTTACATAACTTACATAATACATAAATAAACATCATATCATAAATTACATAATTTACA
*
31500106 TAATTTACATAAATATATATCAT
66 TAACTTACATAAATATATATCAT
31500129 ATCATAACTTACATAA
1 ATCATAACTTACATAA
31500145 AACTTTGGAT
Statistics
Matches: 97, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
87 66 0.68
88 31 0.32
ACGTcount: A:0.49, C:0.15, G:0.01, T:0.36
Consensus pattern (88 bp):
ATCATAACTTACATAACTTACATAATACATAAATAAACATCATATCATAAATTACATAATTTACA
TAACTTACATAAATATATATCAT
Found at i:31508994 original size:43 final size:41
Alignment explanation
Indices: 31508880--31509022 Score: 119
Period size: 43 Copynumber: 3.4 Consensus size: 41
31508870 CTAAACCGTT
* * *
31508880 GCTAAAGATAATGTTATTTAGCGGTGTTTGTGGGGAAAGCGCC
1 GCTAAAG-TCATGTTCTTTAGC-GTGTTTGTGGGGAAAGCACC
* * * *
31508923 GCT-AA-TCATATTCTTTAGTGGAGTTTGTGGGGAAAGCACT
1 GCTAAAGTCATGTTCTTTAG-CGTGTTTGTGGGGAAAGCACC
* **
31508963 GTTAAAGGTCATGTTCTTTAGCGTCGTTTGTGGAAAAAGCACC
1 GCTAAA-GTCATGTTCTTTAGCGT-GTTTGTGGGGAAAGCACC
*
31509006 GCTAAATGTTATGTTCT
1 GCTAAA-GTCATGTTCT
31509023 ATAGTGGCGT
Statistics
Matches: 78, Mismatches: 17, Indels: 10
0.74 0.16 0.10
Matches are distributed among these distances:
40 29 0.37
41 2 0.03
42 3 0.04
43 44 0.56
ACGTcount: A:0.25, C:0.13, G:0.27, T:0.34
Consensus pattern (41 bp):
GCTAAAGTCATGTTCTTTAGCGTGTTTGTGGGGAAAGCACC
Found at i:31509034 original size:43 final size:43
Alignment explanation
Indices: 31508905--31509069 Score: 140
Period size: 43 Copynumber: 3.9 Consensus size: 43
31508895 ATTTAGCGGT
* * * * *
31508905 GTTTGTGGGGAAAGCGCCGCT-AA--TCATATTCTTTAGTGGA
1 GTTTGTGGAGAAAGCACCGCTAAATGTCATGTTCTATAGTGGC
* * * * * * *
31508945 GTTTGTGGGGAAAGCACTGTTAAAGGTCATGTTCTTTAGCGTC
1 GTTTGTGGAGAAAGCACCGCTAAATGTCATGTTCTATAGTGGC
* *
31508988 GTTTGTGGAAAAAGCACCGCTAAATGTTATGTTCTATAGTGGC
1 GTTTGTGGAGAAAGCACCGCTAAATGTCATGTTCTATAGTGGC
* * *
31509031 GTTTTTGTGAGAAA-CGCCGCTAAATGTCATGTTTTATAG
1 GTTTGTG-GAGAAAGCACCGCTAAATGTCATGTTCTATAG
31509070 CGGCATTTTC
Statistics
Matches: 100, Mismatches: 21, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
40 18 0.18
41 2 0.02
43 75 0.75
44 5 0.05
ACGTcount: A:0.24, C:0.14, G:0.27, T:0.35
Consensus pattern (43 bp):
GTTTGTGGAGAAAGCACCGCTAAATGTCATGTTCTATAGTGGC
Found at i:31510929 original size:17 final size:16
Alignment explanation
Indices: 31510873--31510930 Score: 50
Period size: 16 Copynumber: 3.6 Consensus size: 16
31510863 AAATTATTTG
31510873 TAAAAT-TAATGATAAA
1 TAAAATATAATGAT-AA
31510889 TAAAATATTAA--ATAA
1 TAAAATA-TAATGATAA
**
31510904 TTTAATATAATGATACA
1 TAAAATATAATGATA-A
31510921 TAAAATATAA
1 TAAAATATAA
31510931 ATTAATCTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 9
0.72 0.09 0.20
Matches are distributed among these distances:
14 3 0.09
15 7 0.21
16 11 0.33
17 9 0.27
18 3 0.09
ACGTcount: A:0.60, C:0.02, G:0.03, T:0.34
Consensus pattern (16 bp):
TAAAATATAATGATAA
Found at i:31510949 original size:49 final size:48
Alignment explanation
Indices: 31510801--31510951 Score: 134
Period size: 49 Copynumber: 3.2 Consensus size: 48
31510791 TTAAATGATG
* * *
31510801 TTTAAATAGTTTAATATTATGATACATGAAATATAAATT--TTAAATA
1 TTTAAATAATTTAATATAATGATACATAAAATATAAATTAATTAAATA
* *** * *
31510847 TTTTAAA-AA-TTAATATAAATTATTTGTAAAAT-TAATGATAAATAAAATA
1 -TTTAAATAATTTAATAT-AATGATACATAAAATATAA--ATTAATTAAATA
31510896 -TTAAATAATTTAATATAATGATACATAAAATATAAATTAATCTAAATA
1 TTTAAATAATTTAATATAATGATACATAAAATATAAATTAAT-TAAATA
31510944 TTTAAATA
1 TTTAAATA
31510952 CCTTTTAAAC
Statistics
Matches: 79, Mismatches: 15, Indels: 18
0.71 0.13 0.16
Matches are distributed among these distances:
45 10 0.13
46 10 0.13
47 18 0.23
48 18 0.23
49 23 0.29
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.41
Consensus pattern (48 bp):
TTTAAATAATTTAATATAATGATACATAAAATATAAATTAATTAAATA
Found at i:31511172 original size:16 final size:16
Alignment explanation
Indices: 31511151--31511186 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
31511141 TTTGGTTCGC
31511151 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
31511167 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
31511183 TGTA
1 TGTA
31511187 ATAGTAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.25, C:0.00, G:0.36, T:0.39
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:31524991 original size:18 final size:18
Alignment explanation
Indices: 31524964--31525013 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
31524954 GACCATATCT
*
31524964 CCATCCTCATACACCAT-A
1 CCATCATCAT-CACCATCA
*
31524982 CCATCATCATCATCATCA
1 CCATCATCATCACCATCA
31525000 CCATCATCATCACC
1 CCATCATCATCACC
31525014 TGTATTAACC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
17 5 0.18
18 23 0.82
ACGTcount: A:0.32, C:0.44, G:0.00, T:0.24
Consensus pattern (18 bp):
CCATCATCATCACCATCA
Found at i:31525426 original size:2 final size:2
Alignment explanation
Indices: 31525413--31525447 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
31525403 TGTCATCCCC
*
31525413 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
31525448 GTGATGACAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:31527922 original size:72 final size:72
Alignment explanation
Indices: 31527831--31527978 Score: 165
Period size: 72 Copynumber: 2.1 Consensus size: 72
31527821 CAACGACGCT
** * *
31527831 GTTTCCAAGCTTTTGGGGATTTACC-GACGTTTTTAATTAAGCGCCACTAATAATCCTAAGCCAA
1 GTTTCCAAGCTTTTGGGGATTTACCAG-CGTTTTTAAGGAAGCGCCACTAAAAACCCTAAGCCAA
31527895 ACGGTGCC
65 ACGGTGCC
* * ** * *
31527903 GTTTCCATAG-TTTTTGGGATTTAGCAGCGTTTTTGGGGAAGCGTCGCTAAAAACCCTAAGCCAA
1 GTTTCCA-AGCTTTTGGGGATTTACCAGCGTTTTTAAGGAAGCGCCACTAAAAACCCTAAGCCAA
*
31527967 ACGGTGTC
65 ACGGTGCC
31527975 GTTT
1 GTTT
31527979 TCTCAGTTTT
Statistics
Matches: 63, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
72 60 0.95
73 3 0.05
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.32
Consensus pattern (72 bp):
GTTTCCAAGCTTTTGGGGATTTACCAGCGTTTTTAAGGAAGCGCCACTAAAAACCCTAAGCCAAA
CGGTGCC
Found at i:31528176 original size:74 final size:76
Alignment explanation
Indices: 31528077--31528219 Score: 200
Period size: 74 Copynumber: 1.9 Consensus size: 76
31528067 AAACATATGT
* * *
31528077 CCAACGGCACCGTTTTCAGATCTTTC-GAGGCCTTAGCGGCGTTTT-TAATGAAGCGCCGCTAAT
1 CCAACGGCACCGTTTTCAGAACTTTCAGAGGCCTTAGCAGCGTTTTCTAATAAAGCGCCGCTAAT
31528140 GCTTGGGGTGC
66 GCTTGGGGTGC
** * * *
31528151 CCAACGGCACCGTTTTCTTAACTTTCAGTGGCGTTAGCAGCGTTTTCTAGTAAAGCGCCGCTAAT
1 CCAACGGCACCGTTTTCAGAACTTTCAGAGGCCTTAGCAGCGTTTTCTAATAAAGCGCCGCTAAT
31528216 GCTT
66 GCTT
31528220 ACTTTAGTGG
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
74 23 0.39
75 16 0.27
76 20 0.34
ACGTcount: A:0.19, C:0.26, G:0.25, T:0.30
Consensus pattern (76 bp):
CCAACGGCACCGTTTTCAGAACTTTCAGAGGCCTTAGCAGCGTTTTCTAATAAAGCGCCGCTAAT
GCTTGGGGTGC
Found at i:31528625 original size:23 final size:21
Alignment explanation
Indices: 31528574--31528636 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
31528564 AGATTTAAAG
* * *
31528574 TTTAGGGGTTAGGTGTTATGC
1 TTTAGGGGTTAGGGGTTAGGA
31528595 TTTAGGGGTTAGGGGTTAAGGGA
1 TTTAGGGGTTAGGGGTT-A-GGA
*
31528618 TTTAGGGGTTA-CGGTTAGG
1 TTTAGGGGTTAGGGGTTAGG
31528637 GTTTCAACGC
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
20 2 0.06
21 17 0.47
22 5 0.14
23 12 0.33
ACGTcount: A:0.17, C:0.03, G:0.43, T:0.37
Consensus pattern (21 bp):
TTTAGGGGTTAGGGGTTAGGA
Found at i:31529094 original size:21 final size:19
Alignment explanation
Indices: 31529062--31529143 Score: 65
Period size: 21 Copynumber: 3.9 Consensus size: 19
31529052 CAAAAAATAT
31529062 GGTTTAGGTTTACGGTTTAG
1 GGTTTAGGTTTA-GGTTTAG
31529082 GGTTTACGGTTTAGAGTTTAG
1 GGTTTA-GGTTTAG-GTTTAG
* *
31529103 AGTTTTAGGTTTGGGGTTTAG
1 -GGTTTAGGTTT-AGGTTTAG
* *
31529124 GATTTATGATTTAAGGTTTA
1 GGTTTA-GGTTT-AGGTTTA
31529144 TGGTATATTG
Statistics
Matches: 51, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
20 12 0.24
21 33 0.65
22 6 0.12
ACGTcount: A:0.20, C:0.02, G:0.32, T:0.46
Consensus pattern (19 bp):
GGTTTAGGTTTAGGTTTAG
Found at i:31529100 original size:7 final size:6
Alignment explanation
Indices: 31529062--31529143 Score: 56
Period size: 7 Copynumber: 12.0 Consensus size: 6
31529052 CAAAAAATAT
31529062 GGTTTA GGTTTA CGGTTTA GGGTTTA CGGTTTA GAGTTTA GAGTTTTA
1 GGTTTA GGTTTA -GGTTTA -GGTTTA -GGTTTA G-GTTTA G-G-TTTA
* *
31529110 GGTTTGG GGTTTA GGATTTA TGATTTAA GGTTTA
1 GGTTT-A GGTTTA GG-TTTA -GGTTT-A GGTTTA
31529144 TGGTATATTG
Statistics
Matches: 63, Mismatches: 6, Indels: 14
0.76 0.07 0.17
Matches are distributed among these distances:
6 13 0.21
7 43 0.68
8 7 0.11
ACGTcount: A:0.20, C:0.02, G:0.32, T:0.46
Consensus pattern (6 bp):
GGTTTA
Found at i:31529107 original size:14 final size:13
Alignment explanation
Indices: 31529062--31529143 Score: 67
Period size: 14 Copynumber: 5.9 Consensus size: 13
31529052 CAAAAAATAT
31529062 GGTTTAGGTTTAC
1 GGTTTAGGTTTAC
31529075 GGTTTAGGGTTTAC
1 GGTTTA-GGTTTAC
31529089 GGTTTAGAGTTTA-
1 GGTTTAG-GTTTAC
**
31529102 GAGTTTTAGGTTTGG
1 G-G-TTTAGGTTTAC
*
31529117 GGTTTAGGATTTAT
1 GGTTTAGG-TTTAC
*
31529131 GATTTAAGGTTTA
1 GGTTT-AGGTTTA
31529144 TGGTATATTG
Statistics
Matches: 58, Mismatches: 4, Indels: 13
0.77 0.05 0.17
Matches are distributed among these distances:
13 14 0.24
14 35 0.60
15 9 0.16
ACGTcount: A:0.20, C:0.02, G:0.32, T:0.46
Consensus pattern (13 bp):
GGTTTAGGTTTAC
Found at i:31529798 original size:115 final size:114
Alignment explanation
Indices: 31529596--31529833 Score: 390
Period size: 115 Copynumber: 2.1 Consensus size: 114
31529586 TGCTTCATAA
* *
31529596 AAAAACGCCGCTAAAGGTGATATATTACCGGCGTCTTCTAAAGAAACGCCGCAAATTTCCTTTAA
1 AAAAACGCCGCTAAAAGTGATATATTACCGGCGTCTTCTAAAGAAACGCCACAAATTTCCTTTAA
*
31529661 CTGTAACAAAGACGGTGCCGTTTTGTTGTTTTCCTTTAGTGGCGCATTT
66 CTGTAACAAAGACGGTGCCGTTTTGTTGTTTTCCTTTAGTGGCGAATTT
*
31529710 GAAAAACGCCGCTAAAAGTGATATTTTACCGGCGT-TT-TACGAAGAAACGCCACAAATTTCCTT
1 -AAAAACGCCGCTAAAAGTGATATATTACCGGCGTCTTCTA--AAGAAACGCCACAAATTTCCTT
*
31529773 TAACTGTAACAAAGACGGTGCCGTTTTGTTGTTTTCTTTTAGTGGCGAATTT
63 TAACTGTAACAAAGACGGTGCCGTTTTGTTGTTTTCCTTTAGTGGCGAATTT
31529825 AAAAACGCC
1 AAAAACGCC
31529834 ACAAATATTT
Statistics
Matches: 116, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
113 2 0.02
114 11 0.09
115 103 0.89
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (114 bp):
AAAAACGCCGCTAAAAGTGATATATTACCGGCGTCTTCTAAAGAAACGCCACAAATTTCCTTTAA
CTGTAACAAAGACGGTGCCGTTTTGTTGTTTTCCTTTAGTGGCGAATTT
Found at i:31530146 original size:261 final size:260
Alignment explanation
Indices: 31529696--31530225 Score: 880
Period size: 261 Copynumber: 2.0 Consensus size: 260
31529686 TTGTTTTCCT
* *
31529696 TTAGTGGCGCATTTGAAAAACGCCGCTAAAAGTGATATTTTACCGGCGTTTTACGAAGAAACGCC
1 TTAGTGGCGCATATGAAAAACGCCGCTAAAAGTGATATATTACCGGCGTTTTACGAAGAAACGCC
31529761 ACAAATTTCCTTTAACTGTAACAAAGACGGTGCCGTTTTGTTGTTTTCTTTTAGTGGCGAATTTA
66 ACAAATTTCCTTTAACTGTAACAAAGACGGTGCCGTTTTGTTGTTTTCTTTTAGTGGCGAATTTA
* * *
31529826 AAAACGCCACAAATATTTATTACGAGCTGAGGAAACGGTGTCGTTTCCTATTTTTATTAGTGGCG
131 AAAACGCCACAAATATTTACTACGAGCTGAGGAAACGGCGCCGTTTCCTATTTTTATTAGTGGCG
* * *
31529891 CTTTAGCTAAAGCGCCGCAAAAATGTTTAATGTTACCTTATAACGGTGCCGTTTTGTCCTTGTTA
196 CTTTAGATAAAGCGCCGCAAAAATGTTTAATGTTACCTTATAACGATGCCGTTTTGTCCGTGTTA
* *
31529956 TTAGTGGCGCATATGAAAAACGCCGCTAAAGGTGATATATTACTGGCGTTTTACGAAGAAACGCC
1 TTAGTGGCGCATATGAAAAACGCCGCTAAAAGTGATATATTACCGGCGTTTTACGAAGAAACGCC
* * ** * *
31530021 ACAAATTTCGTTTAACTGTAACGAAGACGGTGTTGTTTTGTTTTTTTCTTTTAGTGGCGCATTTT
66 ACAAATTTCCTTTAACTGTAACAAAGACGGTGCCGTTTTGTTGTTTTCTTTTAGTGGCG-AATTT
*
31530086 AAAAACGCCACAAATATTTACTACGAGCTGAGGAAATGGCGCCGTTTCCTATTTTTATTAGTGGC
130 AAAAACGCCACAAATATTTACTACGAGCTGAGGAAACGGCGCCGTTTCCTATTTTTATTAGTGGC
* *
31530151 GCTTTAGATAAAGCGCCGCAAAAATGTTTAATGTTATCTTATGACGATGCCGTTTTGTCCGTGTT
195 GCTTTAGATAAAGCGCCGCAAAAATGTTTAATGTTACCTTATAACGATGCCGTTTTGTCCGTGTT
31530216 A
260 A
31530217 TTAGTGGCG
1 TTAGTGGCG
31530226 TTTTTACTCT
Statistics
Matches: 250, Mismatches: 19, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
260 115 0.46
261 135 0.54
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.34
Consensus pattern (260 bp):
TTAGTGGCGCATATGAAAAACGCCGCTAAAAGTGATATATTACCGGCGTTTTACGAAGAAACGCC
ACAAATTTCCTTTAACTGTAACAAAGACGGTGCCGTTTTGTTGTTTTCTTTTAGTGGCGAATTTA
AAAACGCCACAAATATTTACTACGAGCTGAGGAAACGGCGCCGTTTCCTATTTTTATTAGTGGCG
CTTTAGATAAAGCGCCGCAAAAATGTTTAATGTTACCTTATAACGATGCCGTTTTGTCCGTGTTA
Found at i:31531567 original size:23 final size:23
Alignment explanation
Indices: 31531540--31531587 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
31531530 TAACTTGCAT
*
31531540 AATTTGAGCATTATTTTATGATA
1 AATTTGAGCATTACTTTATGATA
* *
31531563 AATTTGAGCTTTGCTTTATGATA
1 AATTTGAGCATTACTTTATGATA
31531586 AA
1 AA
31531588 AGTTGCAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.33, C:0.06, G:0.15, T:0.46
Consensus pattern (23 bp):
AATTTGAGCATTACTTTATGATA
Found at i:31533024 original size:9 final size:9
Alignment explanation
Indices: 31533010--31533439 Score: 322
Period size: 9 Copynumber: 49.2 Consensus size: 9
31533000 CACAAATTAA
31533010 ATAACTTAC
1 ATAACTTAC
31533019 ATAACTTAC
1 ATAACTTAC
* * *
31533028 AAAAATTAA
1 ATAACTTAC
31533037 ATAACTTAC
1 ATAACTTAC
31533046 ATAACTTAC
1 ATAACTTAC
* *
31533055 ATAAATTAA
1 ATAACTTAC
31533064 ATAACTTAC
1 ATAACTTAC
31533073 ATAACTTAC
1 ATAACTTAC
*
31533082 ATAAATTA-
1 ATAACTTAC
* *
31533090 AGTAAATTAA
1 A-TAACTTAC
*
31533100 ATAAGTTAC
1 ATAACTTAC
31533109 ATAACTTAC
1 ATAACTTAC
*
31533118 ATAAATTA-
1 ATAACTTAC
* *
31533126 AGTAAATTAA
1 A-TAACTTAC
*
31533136 ATAAGTTAC
1 ATAACTTAC
31533145 ATAACTTAC
1 ATAACTTAC
* *
31533154 ATAAATTAA
1 ATAACTTAC
31533163 ATAACTTAC
1 ATAACTTAC
31533172 ATAACTTAC
1 ATAACTTAC
*
31533181 ATAAATTA-
1 ATAACTTAC
* *
31533189 AGTAAATTAA
1 A-TAACTTAC
31533199 ATAACTTAC
1 ATAACTTAC
31533208 ATAACTTAC
1 ATAACTTAC
*
31533217 ATAAATTAC
1 ATAACTTAC
31533226 ATAACTTAC
1 ATAACTTAC
* *
31533235 ATAAATTAA
1 ATAACTTAC
31533244 ATAACTTAC
1 ATAACTTAC
31533253 ATAACTTAC
1 ATAACTTAC
*
31533262 ATAAATTA-
1 ATAACTTAC
31533270 AGTAACTTAC
1 A-TAACTTAC
*
31533280 ATTA--TAC
1 ATAACTTAC
31533287 ATAACCTT-C
1 ATAA-CTTAC
*
31533296 TTAACTTAC
1 ATAACTTAC
31533305 ATAA--TAC
1 ATAACTTAC
*
31533312 ATTACTTAC
1 ATAACTTAC
*
31533321 ATAGCTTAC
1 ATAACTTAC
*
31533330 ATTACTTAC
1 ATAACTTAC
*
31533339 ATTA--TAC
1 ATAACTTAC
31533346 ATAACCTT-C
1 ATAA-CTTAC
*
31533355 TTAACTTAC
1 ATAACTTAC
*
31533364 ATTA--TAC
1 ATAACTTAC
* *
31533371 ACAACTCAC
1 ATAACTTAC
* *
31533380 ATAA-TGAT
1 ATAACTTAC
* *
31533388 GT-A-GTAC
1 ATAACTTAC
*
31533395 ACAACTTAC
1 ATAACTTAC
31533404 ATAA--TAC
1 ATAACTTAC
*
31533411 ATTACTTAC
1 ATAACTTAC
31533420 ATAACTTAC
1 ATAACTTAC
*
31533429 ATTACTTAC
1 ATAACTTAC
31533438 AT
1 AT
31533440 GGGGCATACA
Statistics
Matches: 334, Mismatches: 63, Indels: 48
0.75 0.14 0.11
Matches are distributed among these distances:
7 31 0.09
8 14 0.04
9 283 0.85
10 6 0.02
ACGTcount: A:0.47, C:0.16, G:0.02, T:0.34
Consensus pattern (9 bp):
ATAACTTAC
Found at i:31535263 original size:21 final size:21
Alignment explanation
Indices: 31535211--31535268 Score: 80
Period size: 21 Copynumber: 2.8 Consensus size: 21
31535201 CTACAACTTA
* *
31535211 AAGCAGAGGCGGAAGCGAGGG
1 AAGCAGAGGCTGCAGCGAGGG
*
31535232 AAGCAGCGGCTGCAGCGAGGG
1 AAGCAGAGGCTGCAGCGAGGG
*
31535253 AAGCGGAGGCTGCAGC
1 AAGCAGAGGCTGCAGC
31535269 AAGAGAAGTA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.28, C:0.21, G:0.48, T:0.03
Consensus pattern (21 bp):
AAGCAGAGGCTGCAGCGAGGG
Found at i:31535771 original size:42 final size:42
Alignment explanation
Indices: 31535600--31535916 Score: 433
Period size: 42 Copynumber: 7.5 Consensus size: 42
31535590 ATTTTTGTAT
* *
31535600 AAAAGCGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAA
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGAGGCGCTTAGAA
* *
31535642 AAAAGACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAG-A
1 AAAA-ACGCCGCTAAAGAACATGTTCTTTAGAGGCGCTTAGAA
* * *
31535684 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCATAGAAA
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGAGGCGCTTAG-AA
* *
31535727 AAAAACGCCACTAAAGAACATGCTCTTTAGAGGCGCTTAGAA
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGAGGCGCTTAGAA
* *
31535769 AAAAACGCAGCTAAAGAACATGTTCTTTAGAGGCGTTTAGAA
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGAGGCGCTTAGAA
* **
31535811 AAAAACGCCGTTAAAGAACATGTTCTTTAGAGGCGCACA-AA
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGAGGCGCTTAGAA
**
31535852 CAAAAACGCCGCTAAAGAACATGTTCTTTAGAGGCGCACA-AA
1 -AAAAACGCCGCTAAAGAACATGTTCTTTAGAGGCGCTTAGAA
31535894 CAAAAACGCCGCTAAAGAACATG
1 -AAAAACGCCGCTAAAGAACATG
31535917 GTATTTAGCG
Statistics
Matches: 253, Mismatches: 18, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
41 37 0.15
42 146 0.58
43 70 0.28
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.19
Consensus pattern (42 bp):
AAAAACGCCGCTAAAGAACATGTTCTTTAGAGGCGCTTAGAA
Found at i:31538283 original size:16 final size:16
Alignment explanation
Indices: 31538258--31538291 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
31538248 ATGAATATAT
* *
31538258 ATGTGTAAATGTGATA
1 ATGTGCAAATATGATA
31538274 ATGTGCAAATATGATA
1 ATGTGCAAATATGATA
31538290 AT
1 AT
31538292 TGGATATTGG
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:0.41, C:0.03, G:0.21, T:0.35
Consensus pattern (16 bp):
ATGTGCAAATATGATA
Found at i:31539719 original size:18 final size:18
Alignment explanation
Indices: 31539692--31539737 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
31539682 GTACAACTAT
31539692 TATA-TATATACTATCAA
1 TATATTATATACTATCAA
*
31539709 TATATTATATACTATTAA
1 TATATTATATACTATCAA
31539727 TATATTATATA
1 TATATTATATA
31539738 TTATATGATA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
17 4 0.15
18 23 0.85
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.48
Consensus pattern (18 bp):
TATATTATATACTATCAA
Found at i:31539769 original size:5 final size:5
Alignment explanation
Indices: 31539710--31539772 Score: 56
Period size: 5 Copynumber: 12.6 Consensus size: 5
31539700 TACTATCAAT
* * * * * *
31539710 ATATT ATATA CTATTA ATATA TTAT- ATATT ATATG ATATA ATATA ATATT
1 ATATA ATATA ATA-TA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
31539760 ATATA ATATA ATA
1 ATATA ATATA ATA
31539773 GGAGGGTTAG
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
4 3 0.06
5 40 0.85
6 4 0.09
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.48
Consensus pattern (5 bp):
ATATA
Found at i:31539769 original size:15 final size:15
Alignment explanation
Indices: 31539710--31539772 Score: 67
Period size: 15 Copynumber: 4.2 Consensus size: 15
31539700 TACTATCAAT
*
31539710 ATATTATATACTATTA
1 ATATTATATAATA-TA
*
31539726 ATA-TAT-TATATATT
1 ATATTATATA-ATATA
*
31539740 ATATGATATAATATA
1 ATATTATATAATATA
31539755 ATATTATATAATATA
1 ATATTATATAATATA
31539770 ATA
1 ATA
31539773 GGAGGGTTAG
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
14 6 0.15
15 28 0.72
16 5 0.13
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.48
Consensus pattern (15 bp):
ATATTATATAATATA
Found at i:31541579 original size:31 final size:32
Alignment explanation
Indices: 31541517--31541581 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 32
31541507 GGCAAATTAC
*
31541517 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAAACACTTTA
31541549 AAGAGTAATTGAATCCTAAT-AAAACACTTTA
1 AAGAGTAATTGAATCCTAATAAAAACACTTTA
31541580 AA
1 AA
31541582 ATTATCTAAG
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 12 0.38
32 20 0.62
ACGTcount: A:0.49, C:0.12, G:0.09, T:0.29
Consensus pattern (32 bp):
AAGAGTAATTGAATCCTAATAAAAACACTTTA
Found at i:31548572 original size:12 final size:12
Alignment explanation
Indices: 31548555--31548580 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
31548545 TGATCAACTC
31548555 GAGCAATTATTT
1 GAGCAATTATTT
31548567 GAGCAATTATTT
1 GAGCAATTATTT
31548579 GA
1 GA
31548581 AGTGTTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.08, G:0.19, T:0.38
Consensus pattern (12 bp):
GAGCAATTATTT
Found at i:31551327 original size:2 final size:2
Alignment explanation
Indices: 31551320--31551372 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
31551310 ATAACTCTTA
31551320 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31551362 AT AT AT AT AT A
1 AT AT AT AT AT A
31551373 GAAANNNNNN
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:31558388 original size:14 final size:15
Alignment explanation
Indices: 31558371--31558399 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
31558361 ATTTAATAAA
31558371 ATTTTTATG-ATTTT
1 ATTTTTATGAATTTT
31558385 ATTTTTATGAATTTT
1 ATTTTTATGAATTTT
31558400 TAATTATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (15 bp):
ATTTTTATGAATTTT
Found at i:31561760 original size:2 final size:2
Alignment explanation
Indices: 31561755--31561780 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
31561745 GAGATGTATC
31561755 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
31561781 GTTCCACAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:31563822 original size:7 final size:7
Alignment explanation
Indices: 31563812--31563838 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
31563802 AGGTAGGAGG
31563812 TGGGATA
1 TGGGATA
31563819 TGGGATA
1 TGGGATA
31563826 TGGGATA
1 TGGGATA
31563833 TGGGAT
1 TGGGAT
31563839 CGAGTTGGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.26, C:0.00, G:0.44, T:0.30
Consensus pattern (7 bp):
TGGGATA
Found at i:31564022 original size:46 final size:46
Alignment explanation
Indices: 31563914--31564025 Score: 111
Period size: 46 Copynumber: 2.3 Consensus size: 46
31563904 TTTATAATTT
* * *
31563914 ATAAAATTTTAAATTAGTAATAATAAAATTATATTTTATTTTTTTAAAATA
1 ATAAAATTTT-AATT--TAAT--TAAAATTATATTTTATATTATAAAAATA
31563965 ATAAAATTTTAATTTAATTAAAATTATATTTTTACTATTATAAAAAT-
1 ATAAAATTTTAATTTAATTAAAATTATA-TTTTA-TATTATAAAAATA
*
31564012 ATACAA-TTTAATTT
1 ATAAAATTTTAATTT
31564026 TGTCCTTAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
46 18 0.33
47 10 0.18
48 13 0.24
50 4 0.07
51 10 0.18
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.49
Consensus pattern (46 bp):
ATAAAATTTTAATTTAATTAAAATTATATTTTATATTATAAAAATA
Found at i:31564757 original size:43 final size:42
Alignment explanation
Indices: 31564639--31564806 Score: 255
Period size: 42 Copynumber: 4.0 Consensus size: 42
31564629 AAACAAAAAC
* **
31564639 GCCGCTAAAGAACATGTTCTTTAGCGGCATTTTTTTACAAGC
1 GCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTTACAAAT
31564681 GCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTTACAAAT
1 GCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTTACAAAT
*
31564723 GCCGCTAAAGAACATGTTATTTAGCGGCGTTTTTTTTACAAAT
1 GCCGCTAAAGAACATGTTCTTTAGCGGCG-TTTTTTTACAAAT
* * * *
31564766 GCCGCTAAAGAACATATTCTTTAGTGGCGCTTTTATACAAA
1 GCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTTACAAA
31564807 AACGCCACTA
Statistics
Matches: 116, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
42 77 0.66
43 39 0.34
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (42 bp):
GCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTTACAAAT
Found at i:31564789 original size:85 final size:84
Alignment explanation
Indices: 31564639--31564806 Score: 255
Period size: 85 Copynumber: 2.0 Consensus size: 84
31564629 AAACAAAAAC
* * *
31564639 GCCGCTAAAGAACATGTTCTTTAGCGGCATTTTTTTACAAGCGCCGCTAAAGAACATGTTCTTTA
1 GCCGCTAAAGAACATGTTATTTAGCGGCATTTTTTTACAAACGCCGCTAAAGAACATATTCTTTA
* *
31564704 GCGGCGTTTTTTTACAAAT
66 GCGGCGCTTTTATACAAAT
* *
31564723 GCCGCTAAAGAACATGTTATTTAGCGGCGTTTTTTTTACAAATGCCGCTAAAGAACATATTCTTT
1 GCCGCTAAAGAACATGTTATTTAGCGGC-ATTTTTTTACAAACGCCGCTAAAGAACATATTCTTT
*
31564788 AGTGGCGCTTTTATACAAA
65 AGCGGCGCTTTTATACAAA
31564807 AACGCCACTA
Statistics
Matches: 75, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
84 27 0.36
85 48 0.64
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (84 bp):
GCCGCTAAAGAACATGTTATTTAGCGGCATTTTTTTACAAACGCCGCTAAAGAACATATTCTTTA
GCGGCGCTTTTATACAAAT
Found at i:31565210 original size:21 final size:21
Alignment explanation
Indices: 31565146--31565212 Score: 82
Period size: 21 Copynumber: 3.2 Consensus size: 21
31565136 GCTCTGCTCC
*
31565146 GCTTCTCTCGCTGCAGCCTCCT
1 GCTTCCCTCGCTGCAGCCT-CT
*
31565168 -CTTCCCTCGCTGCAGCCGCT
1 GCTTCCCTCGCTGCAGCCTCT
* *
31565188 GCTTCCCTCGCTTCCGCCTCT
1 GCTTCCCTCGCTGCAGCCTCT
31565209 GCTT
1 GCTT
31565213 TAAGTTGTAG
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
20 2 0.05
21 37 0.95
ACGTcount: A:0.03, C:0.48, G:0.18, T:0.31
Consensus pattern (21 bp):
GCTTCCCTCGCTGCAGCCTCT
Found at i:31569969 original size:9 final size:9
Alignment explanation
Indices: 31569955--31570192 Score: 172
Period size: 9 Copynumber: 27.3 Consensus size: 9
31569945 TAACTATGAA
31569955 TTATGTAAG
1 TTATGTAAG
*
31569964 TTATGTACG
1 TTATGTAAG
31569973 TGTA--TAAG
1 T-TATGTAAG
*
31569981 TTAAGTAAG
1 TTATGTAAG
31569990 TTATGT-A-
1 TTATGTAAG
*
31569997 TTAAGTAAG
1 TTATGTAAG
31570006 TTATGTAAG
1 TTATGTAAG
*
31570015 TTATGAAAG
1 TTATGTAAG
* *
31570024 TAATGTATG
1 TTATGTAAG
*
31570033 TAATGTAAG
1 TTATGTAAG
31570042 -T-TGTAAG
1 TTATGTAAG
*
31570049 TTAT-TATG
1 TTATGTAAG
31570057 TATTATGTAAG
1 --TTATGTAAG
31570068 TTATGTAAG
1 TTATGTAAG
31570077 TTATGTAAG
1 TTATGTAAG
31570086 TTAAATGT-A-
1 TT--ATGTAAG
31570095 TTATGTAAG
1 TTATGTAAG
31570104 -T-TGTAAG
1 TTATGTAAG
31570111 TTAAATGT-A-
1 TT--ATGTAAG
31570120 TTATGTAAG
1 TTATGTAAG
31570129 TTATGTAAG
1 TTATGTAAG
31570138 TTAAATGT-A-
1 TT--ATGTAAG
31570147 TTATGTAAG
1 TTATGTAAG
31570156 TTATGTAAG
1 TTATGTAAG
31570165 TTAAATGT-A-
1 TT--ATGTAAG
31570174 TTATGTAAG
1 TTATGTAAG
31570183 -T-TGTAAG
1 TTATGTAAG
31570190 TTA
1 TTA
31570193 AATNNNNNNN
Statistics
Matches: 186, Mismatches: 13, Indels: 60
0.72 0.05 0.23
Matches are distributed among these distances:
7 41 0.22
8 18 0.10
9 99 0.53
10 10 0.05
11 18 0.10
ACGTcount: A:0.36, C:0.00, G:0.20, T:0.44
Consensus pattern (9 bp):
TTATGTAAG
Found at i:31570032 original size:22 final size:24
Alignment explanation
Indices: 31569955--31570083 Score: 77
Period size: 22 Copynumber: 5.7 Consensus size: 24
31569945 TAACTATGAA
*
31569955 TTATGTAAGTTATGTACGTGTA-TAAG
1 TTATGTAAGTTATGTA--T-AAGTAAG
*
31569981 TTAAGTAAGTTATGTATTAAGTAAG
1 TTATGTAAGTTATGTA-TAAGTAAG
31570006 TTATGTAAGTTATG-A-AAGTAA-
1 TTATGTAAGTTATGTATAAGTAAG
*
31570027 TGTATGTAA-TGTAAGT-T--GTAAG
1 T-TATGTAAGT-TATGTATAAGTAAG
*
31570049 TTAT-TATG-TAT-TAT--GTAAG
1 TTATGTAAGTTATGTATAAGTAAG
31570068 TTATGTAAGTTATGTA
1 TTATGTAAGTTATGTA
31570084 AGTTAAATGT
Statistics
Matches: 84, Mismatches: 8, Indels: 26
0.71 0.07 0.22
Matches are distributed among these distances:
18 1 0.01
19 12 0.14
20 5 0.06
21 12 0.14
22 19 0.23
24 2 0.02
25 18 0.21
26 15 0.18
ACGTcount: A:0.35, C:0.01, G:0.21, T:0.43
Consensus pattern (24 bp):
TTATGTAAGTTATGTATAAGTAAG
Found at i:31570061 original size:62 final size:62
Alignment explanation
Indices: 31569990--31570140 Score: 236
Period size: 62 Copynumber: 2.5 Consensus size: 62
31569980 GTTAAGTAAG
*
31569990 TTATGTATTAAGTAAGTTATGTAAGTTATGAAAG-T-AATGTATGTAATGTAAGTTGTAAGTTA
1 TTATGTATTATGTAAGTTATGTAAGTTATGAAAGTTAAATGTAT-T-ATGTAAGTTGTAAGTTA
*
31570052 TTATGTATTATGTAAGTTATGTAAGTTATGTAAGTTAAATGTATTATGTAAGTTGTAAGTTA
1 TTATGTATTATGTAAGTTATGTAAGTTATGAAAGTTAAATGTATTATGTAAGTTGTAAGTTA
*
31570114 -AATGTATTATGTAAGTTATGTAAGTTA
1 TTATGTATTATGTAAGTTATGTAAGTTA
31570141 AATGTATTAT
Statistics
Matches: 84, Mismatches: 3, Indels: 5
0.91 0.03 0.05
Matches are distributed among these distances:
61 26 0.31
62 49 0.58
63 2 0.02
64 7 0.08
ACGTcount: A:0.36, C:0.00, G:0.20, T:0.44
Consensus pattern (62 bp):
TTATGTATTATGTAAGTTATGTAAGTTATGAAAGTTAAATGTATTATGTAAGTTGTAAGTTA
Found at i:31570133 original size:52 final size:54
Alignment explanation
Indices: 31570068--31570195 Score: 228
Period size: 52 Copynumber: 2.4 Consensus size: 54
31570058 ATTATGTAAG
31570068 TTATGTAAGTTATGTAAGTTAAATGTATTATGTAAG-T-TGTAAGTTAAATGTA
1 TTATGTAAGTTATGTAAGTTAAATGTATTATGTAAGTTATGTAAGTTAAATGTA
31570120 TTATGTAAGTTATGTAAGTTAAATGTATTATGTAAGTTATGTAAGTTAAATGTA
1 TTATGTAAGTTATGTAAGTTAAATGTATTATGTAAGTTATGTAAGTTAAATGTA
31570174 TTATGTAAG-T-TGTAAGTTAAAT
1 TTATGTAAGTTATGTAAGTTAAAT
31570196 NNNNNNNNNN
Statistics
Matches: 74, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
52 48 0.65
53 2 0.03
54 24 0.32
ACGTcount: A:0.37, C:0.00, G:0.19, T:0.45
Consensus pattern (54 bp):
TTATGTAAGTTATGTAAGTTAAATGTATTATGTAAGTTATGTAAGTTAAATGTA
Found at i:31570330 original size:25 final size:25
Alignment explanation
Indices: 31570296--31570450 Score: 232
Period size: 25 Copynumber: 6.4 Consensus size: 25
31570286 NNNNNNNNNN
31570296 ATTATGTAAGTTGTAAGTTAAATGT
1 ATTATGTAAGTTGTAAGTTAAATGT
31570321 ATTATGTAAG-T-T-A-TT--ATGT
1 ATTATGTAAGTTGTAAGTTAAATGT
31570340 ATTATGTAAGTTGTAAGTTAAATGT
1 ATTATGTAAGTTGTAAGTTAAATGT
*
31570365 ATTATGTAAGTTGTAAGTTAAGTGT
1 ATTATGTAAGTTGTAAGTTAAATGT
*
31570390 ATTATGTAAGTTGTAAGTTATTATGT
1 ATTATGTAAGTTGTAAGTTA-AATGT
31570416 ATTATGTAAGTTGTAAGTTAAATGT
1 ATTATGTAAGTTGTAAGTTAAATGT
*
31570441 ATTGTGTAAG
1 ATTATGTAAG
31570451 CGCCACTAAA
Statistics
Matches: 118, Mismatches: 5, Indels: 14
0.86 0.04 0.10
Matches are distributed among these distances:
19 14 0.12
20 1 0.01
21 3 0.03
22 2 0.02
23 3 0.03
24 1 0.01
25 71 0.60
26 23 0.19
ACGTcount: A:0.34, C:0.00, G:0.21, T:0.46
Consensus pattern (25 bp):
ATTATGTAAGTTGTAAGTTAAATGT
Found at i:31570359 original size:44 final size:48
Alignment explanation
Indices: 31570296--31570450 Score: 210
Period size: 51 Copynumber: 3.2 Consensus size: 48
31570286 NNNNNNNNNN
31570296 ATTATGTAAGTTGTAAGTTAAATGTATTATGTAAGTT-A-TT-A-TGT
1 ATTATGTAAGTTGTAAGTTAAATGTATTATGTAAGTTAAGTTAAGTGT
31570340 ATTATGTAAGTTGTAAGTTAAATGTATTATGTAAGTTGTAAGTTAAGTGT
1 ATTATGTAAGTTGTAAGTTAAATGTATTATGTAAG-T-TAAGTTAAGTGT
* *
31570390 ATTATGTAAGTTGTAAGTTATTATGTATTATGTAAGTTGTAAGTTAAATGT
1 ATTATGTAAGTTGTAAGTTA-AATGTATTATGTAAG-T-TAAGTTAAGTGT
*
31570441 ATTGTGTAAG
1 ATTATGTAAG
31570451 CGCCACTAAA
Statistics
Matches: 101, Mismatches: 3, Indels: 7
0.91 0.03 0.06
Matches are distributed among these distances:
44 35 0.35
45 1 0.01
46 1 0.01
47 1 0.01
48 2 0.02
49 1 0.01
50 23 0.23
51 37 0.37
ACGTcount: A:0.34, C:0.00, G:0.21, T:0.46
Consensus pattern (48 bp):
ATTATGTAAGTTGTAAGTTAAATGTATTATGTAAGTTAAGTTAAGTGT
Found at i:31570996 original size:39 final size:40
Alignment explanation
Indices: 31570928--31571008 Score: 119
Period size: 39 Copynumber: 2.0 Consensus size: 40
31570918 CCTAACCCAT
**
31570928 AACCCCTAAATCCCCCTTAACCTTTAAAGCATAAACCCTA
1 AACCCCTAAATCCCCCTTAACCCCTAAAGCATAAACCCTA
* *
31570968 AACCCCTAAAT-CTCCTTAACCCCTAAAGCATAACCCCTA
1 AACCCCTAAATCCCCCTTAACCCCTAAAGCATAAACCCTA
31571007 AA
1 AA
31571009 TAATTTTATT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
39 26 0.70
40 11 0.30
ACGTcount: A:0.38, C:0.38, G:0.02, T:0.21
Consensus pattern (40 bp):
AACCCCTAAATCCCCCTTAACCCCTAAAGCATAAACCCTA
Found at i:31571765 original size:39 final size:40
Alignment explanation
Indices: 31571691--31571767 Score: 104
Period size: 39 Copynumber: 1.9 Consensus size: 40
31571681 ACCCATAACC
* *
31571691 CCTAAATCCCCCTTAACCCTTAAGGCATAAACCCTAAACT
1 CCTAAATCCCCCTTAACCCCTAAAGCATAAACCCTAAACT
*
31571731 CCTAAATCTCCC-TAACCCCTAAAGCA-AAACCCCTAAA
1 CCTAAATCCCCCTTAACCCCTAAAGCATAAA-CCCTAAA
31571768 AAAATTTTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
38 3 0.09
39 19 0.58
40 11 0.33
ACGTcount: A:0.38, C:0.39, G:0.04, T:0.19
Consensus pattern (40 bp):
CCTAAATCCCCCTTAACCCCTAAAGCATAAACCCTAAACT
Found at i:31571946 original size:15 final size:16
Alignment explanation
Indices: 31571921--31571952 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
31571911 TAAAATAATA
31571921 TAAACTATATTAAATT
1 TAAACTATATTAAATT
31571937 TAAA-TATATTAAATT
1 TAAACTATATTAAATT
31571952 T
1 T
31571953 CTTATTAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (16 bp):
TAAACTATATTAAATT
Found at i:31572094 original size:15 final size:15
Alignment explanation
Indices: 31572044--31572087 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
31572034 AAACTCTAAA
31572044 CCCTAAATCCTTAAC
1 CCCTAAATCCTTAAC
* *
31572059 CCCTAAACCCTAAAC
1 CCCTAAATCCTTAAC
31572074 CCCTAAATCCTTAA
1 CCCTAAATCCTTAA
31572088 TTCCTAACTC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.36, C:0.41, G:0.00, T:0.23
Consensus pattern (15 bp):
CCCTAAATCCTTAAC
Found at i:31572689 original size:113 final size:110
Alignment explanation
Indices: 31572383--31572825 Score: 410
Period size: 113 Copynumber: 3.9 Consensus size: 110
31572373 TTTAAATCCT
** * *
31572383 TGAGCATTAGCGGCGCTTTTTTAAAAACGCCGCTAAAACCCCTAAAGCTAAGAAAACGACGTCGT
1 TGAGCATTAGCGGCGC-TTTCAAAAAACGCCGCTAAAACCCCGAAAGCTCAG-AAACGACGTCGT
* * * *
31572448 TGGGTTTAGGTTTTTAGCGGCGCTTTTACAAAAAACGCCGCTAAAAACC
64 TGCG-CTAGGTTTTTAGCGGCGC-TTTCCCAAAAACGCCGCTAAAAACC
* * * *
31572497 TGAGCATTAGCGGCGCTTT-ATATAAAGCGCCACTAAAACCCTGAAAGCTGGC-GAGACGACGTC
1 TGAGCATTAGCGGCGCTTTCA-A-AAAACGCCGCTAAAACCCCGAAAGCT--CAGAAACGACGTC
* * * *
31572560 GTTGCGCTAGATTTTTTTGCGGCGCTTTCCCATAAACGCCGCTAAAAGACA
62 GTTGCGCTAG-GTTTTTAGCGGCGCTTTCCCAAAAACGCCGCTAAAA-ACC
* * *
31572611 TGAGCATTAGCGGCGCTTTCAAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGCCGTT
1 TGAGCATTAGCGGCGCTTTCAAAAAACGCCGCTAAAACCCCGAAAGCTCAG-AAACGACGTCGTT
*
31572676 G-GCCTTAGGTTTTTAGCGGCGC-TTCCTTAAAAACGCCGCTAAAAACC
65 GCG-C-TAGGTTTTTAGCGGCGCTTTCC-CAAAAACGCCGCTAAAAACC
* * * * * * * *
31572723 TGAGCACTAGCTGCGCTTACTTAAAAACGCCGCTAAATCACC-AAATGCTCTTGAAACGGCGTCG
1 TGAGCATTAGCGGCGCTTTC-AAAAAACGCCGCTAAAACCCCGAAA-GCTC-AGAAACGACGTCG
* * * *
31572787 TTGCGCTAGGTTTTTTGAGGTGCTTTCCCGAAAACGCCG
63 TTGCGCTAGGTTTTTAGCGGCGCTTTCCCAAAAACGCCG
31572826 GTCATGTTTA
Statistics
Matches: 273, Mismatches: 39, Indels: 36
0.78 0.11 0.10
Matches are distributed among these distances:
111 1 0.00
112 51 0.19
113 128 0.47
114 91 0.33
115 2 0.01
ACGTcount: A:0.28, C:0.26, G:0.23, T:0.24
Consensus pattern (110 bp):
TGAGCATTAGCGGCGCTTTCAAAAAACGCCGCTAAAACCCCGAAAGCTCAGAAACGACGTCGTTG
CGCTAGGTTTTTAGCGGCGCTTTCCCAAAAACGCCGCTAAAAACC
Found at i:31573362 original size:25 final size:25
Alignment explanation
Indices: 31573317--31573365 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
31573307 ATATAGTTTT
*
31573317 TATATTAATTATAAATGTTATAATA
1 TATATTAATTATAAATATTATAATA
31573342 TATATTATATTAT-AATATTATAAT
1 TATATTA-ATTATAAATATTATAAT
31573366 TAAACAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 17 0.77
26 5 0.23
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (25 bp):
TATATTAATTATAAATATTATAATA
Found at i:31574647 original size:41 final size:41
Alignment explanation
Indices: 31574519--31574649 Score: 149
Period size: 41 Copynumber: 3.2 Consensus size: 41
31574509 TCTGATTTAT
* * * *
31574519 TGCCAGTGAA-ATAATTCAGACTTTATGTCTAGCAGGCTTTA
1 TGCCGGTGAACAT-ATTCAGACTATAAGTCTAGCAGGCTTAA
* *
31574560 TGCCGGTGAACTTATTCAGACTATACGTCTAGCAGGCTTAA
1 TGCCGGTGAACATATTCAGACTATAAGTCTAGCAGGCTTAA
* *
31574601 TGCCGGTGATACAT-TTCGGACTATAAGTCTAGCAGGCTAAA
1 TGCCGGTGA-ACATATTCAGACTATAAGTCTAGCAGGCTTAA
*
31574642 AGCCGGTG
1 TGCCGGTG
31574650 TACCGAATCA
Statistics
Matches: 78, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
41 74 0.95
42 4 0.05
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (41 bp):
TGCCGGTGAACATATTCAGACTATAAGTCTAGCAGGCTTAA
Found at i:31574851 original size:13 final size:13
Alignment explanation
Indices: 31574835--31574859 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31574825 ATATTAAATA
31574835 TATATGCATTTGG
1 TATATGCATTTGG
31574848 TATATGCATTTG
1 TATATGCATTTG
31574860 ATAAGCAATT
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:0.24, C:0.08, G:0.20, T:0.48
Consensus pattern (13 bp):
TATATGCATTTGG
Found at i:31580743 original size:36 final size:37
Alignment explanation
Indices: 31580673--31580745 Score: 98
Period size: 36 Copynumber: 2.0 Consensus size: 37
31580663 AGTGGGCGGC
*
31580673 ATGTGTATAATATATATAGTTTTTATATTAATTATAA
1 ATGTGTATAATATATATAGTTTTTATAATAATTATAA
31580710 ATGT-TATAATATATATA-TTATATTATAAT-ATTATAA
1 ATGTGTATAATATATATAGTT-T-TTATAATAATTATAA
31580746 TTAAACAAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
35 2 0.06
36 21 0.64
37 10 0.30
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (37 bp):
ATGTGTATAATATATATAGTTTTTATAATAATTATAA
Found at i:31580748 original size:14 final size:14
Alignment explanation
Indices: 31580701--31580748 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
31580691 GTTTTTATAT
*
31580701 TAATTATAAATGTTA
1 TAATTAT-AATATTA
31580716 TAA-TATATATATTA
1 TAATTATA-ATATTA
31580730 T-ATTATAATATTA
1 TAATTATAATATTA
31580743 TAATTA
1 TAATTA
31580749 AACAAATAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
13 9 0.31
14 17 0.59
15 3 0.10
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (14 bp):
TAATTATAATATTA
Found at i:31581946 original size:2 final size:2
Alignment explanation
Indices: 31581934--31581971 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
31581924 TTAGGTTCGA
*
31581934 AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31581972 GAATAAACTC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31582447 original size:41 final size:42
Alignment explanation
Indices: 31582384--31582468 Score: 118
Period size: 41 Copynumber: 2.0 Consensus size: 42
31582374 ACTAATCTGA
* *
31582384 TTTATTGCCAGTGAAATAATTCAGACTTTATGTCTAGCAGGC
1 TTTATTGCCAGTGAAATAATTCAGACTATACGTCTAGCAGGC
* * *
31582426 TTTA-TGCCGGTGAAATTATTCAGACTATACGTCTCGCAGGC
1 TTTATTGCCAGTGAAATAATTCAGACTATACGTCTAGCAGGC
31582467 TT
1 TT
31582469 AATGGTGATA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
41 34 0.89
42 4 0.11
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.35
Consensus pattern (42 bp):
TTTATTGCCAGTGAAATAATTCAGACTATACGTCTAGCAGGC
Found at i:31585137 original size:102 final size:102
Alignment explanation
Indices: 31585016--31585353 Score: 603
Period size: 102 Copynumber: 3.4 Consensus size: 102
31585006 ATAGCCGAAT
*
31585016 TATATATATATTTTTGTTATACATTGAAATGAATTAATCTATAGCTGAATGTATATGTAATTGTT
1 TATATATATATATTTGTTATACATTGAAATGAATTAATCTATAGCTGAATGTATATGTAATTGTT
31585081 ATGCAGAGAAATGAATTAAACTATGGCCGAATGTATA
66 ATGCAGAGAAATGAATTAAACTATGGCCGAATGTATA
31585118 TATATATATATATTTGTTATACATTGAAATGAATTAATCTATAGCTGAATGTATATGTAATTGTT
1 TATATATATATATTTGTTATACATTGAAATGAATTAATCTATAGCTGAATGTATATGTAATTGTT
* *
31585183 ATGCAGAGAAATAAATTAAACTATGGTCGAATGTATA
66 ATGCAGAGAAATGAATTAAACTATGGCCGAATGTATA
31585220 TATATATATATATTTGTTATACATTGAAATGAATTAATCTATAGCTGAATGTATATGTAATTGTT
1 TATATATATATATTTGTTATACATTGAAATGAATTAATCTATAGCTGAATGTATATGTAATTGTT
31585285 ATGCAGAGAAATGAATTAAACTATGGCCGAATG----
66 ATGCAGAGAAATGAATTAAACTATGGCCGAATGTATA
* *
31585318 TATATATATATATTTGTTATGCATTGAAATAAATTA
1 TATATATATATATTTGTTATACATTGAAATGAATTA
31585354 TTTGAAGTTA
Statistics
Matches: 229, Mismatches: 7, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
98 34 0.15
102 195 0.85
ACGTcount: A:0.39, C:0.06, G:0.15, T:0.40
Consensus pattern (102 bp):
TATATATATATATTTGTTATACATTGAAATGAATTAATCTATAGCTGAATGTATATGTAATTGTT
ATGCAGAGAAATGAATTAAACTATGGCCGAATGTATA
Found at i:31585147 original size:55 final size:52
Alignment explanation
Indices: 31585016--31585353 Score: 278
Period size: 47 Copynumber: 6.7 Consensus size: 52
31585006 ATAGCCGAAT
* * * *
31585016 TATATATATATTTTTGTTATACATTGAAATGAATTAATCTATAGC---TGAA
1 TATATATATATATTTGTTATGCATTGAAATGAATTAAACTATGGCGAATGAA
* * **
31585065 TGTATATGTA-A-TTGTTATGCAGAGAAATGAATTAAACTATGGCCGAATGTATA
1 TATATATATATATTTGTTATGCATTGAAATGAATTAAACTATGG-CGAATG-A-A
* * *
31585118 TATATATATATATTTGTTATACATTGAAATGAATTAATCTATAGC---TGAA
1 TATATATATATATTTGTTATGCATTGAAATGAATTAAACTATGGCGAATGAA
* * ** *
31585167 TGTATATGTA-A-TTGTTATGCAGAGAAATAAATTAAACTATGGTCGAATGTATA
1 TATATATATATATTTGTTATGCATTGAAATGAATTAAACTATGG-CGAATG-A-A
* * *
31585220 TATATATATATATTTGTTATACATTGAAATGAATTAATCTATAGC---TGAA
1 TATATATATATATTTGTTATGCATTGAAATGAATTAAACTATGGCGAATGAA
* * **
31585269 TGTATATGTA-A-TTGTTATGCAGAGAAATGAATTAAACTATGGCCGAATG--
1 TATATATATATATTTGTTATGCATTGAAATGAATTAAACTATGG-CGAATGAA
*
31585318 TATATATATATATTTGTTATGCATTGAAATAAATTA
1 TATATATATATATTTGTTATGCATTGAAATGAATTA
31585354 TTTGAAGTTA
Statistics
Matches: 224, Mismatches: 43, Indels: 42
0.72 0.14 0.14
Matches are distributed among these distances:
47 77 0.34
48 5 0.02
49 34 0.15
50 3 0.01
51 30 0.13
52 2 0.01
53 18 0.08
54 4 0.02
55 51 0.23
ACGTcount: A:0.39, C:0.06, G:0.15, T:0.40
Consensus pattern (52 bp):
TATATATATATATTTGTTATGCATTGAAATGAATTAAACTATGGCGAATGAA
Found at i:31585514 original size:41 final size:41
Alignment explanation
Indices: 31585459--31585613 Score: 238
Period size: 41 Copynumber: 3.8 Consensus size: 41
31585449 TTGTAAGTTT
* * *
31585459 GGGCTTTATGCCTAGCAGGCTTTGTGCCGATGAAATGTATT
1 GGGCTTTATGCCTAGCAGGCTCTGTGCCGGTGAAATGTATC
31585500 GGGCTTTATGCCTAGCAGGCTCTGTGCCGGTGAAATGTATC
1 GGGCTTTATGCCTAGCAGGCTCTGTGCCGGTGAAATGTATC
*
31585541 AGGCTTTATGCCTAGCAGGCTCTGTGCCGGTGAAATGTATC
1 GGGCTTTATGCCTAGCAGGCTCTGTGCCGGTGAAATGTATC
* * * *
31585582 GGGCTTTGTGTCTAGCAGGCTTTATGCCGGTG
1 GGGCTTTATGCCTAGCAGGCTCTGTGCCGGTG
31585614 TTTTATATAA
Statistics
Matches: 105, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 105 1.00
ACGTcount: A:0.17, C:0.20, G:0.32, T:0.32
Consensus pattern (41 bp):
GGGCTTTATGCCTAGCAGGCTCTGTGCCGGTGAAATGTATC
Found at i:31585627 original size:82 final size:82
Alignment explanation
Indices: 31585460--31585632 Score: 229
Period size: 82 Copynumber: 2.1 Consensus size: 82
31585450 TGTAAGTTTG
* * *
31585460 GGCTTTATGCCTAGCAGGCTTTGTGCCGATGAAATGTATTGGGCTTTATGCCTAGCAGGCTCTGT
1 GGCTTTATGCCTAGCAGGCTCTGTGCCGATGAAATGTATCGGGCTTTATGCCTAGCAGGCTCTAT
* *
31585525 GCCGGTGAAATGTATCA
66 GCCGGTGAAATATATAA
* * * *
31585542 GGCTTTATGCCTAGCAGGCTCTGTGCCGGTGAAATGTATCGGGCTTTGTGTCTAGCAGGCTTTAT
1 GGCTTTATGCCTAGCAGGCTCTGTGCCGATGAAATGTATCGGGCTTTATGCCTAGCAGGCTCTAT
***
31585607 GCCGGTGTTTTATATAA
66 GCCGGTGAAATATATAA
*
31585624 GGCTCTATG
1 GGCTTTATG
31585633 TTTAATAAGT
Statistics
Matches: 78, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
82 78 1.00
ACGTcount: A:0.18, C:0.19, G:0.29, T:0.34
Consensus pattern (82 bp):
GGCTTTATGCCTAGCAGGCTCTGTGCCGATGAAATGTATCGGGCTTTATGCCTAGCAGGCTCTAT
GCCGGTGAAATATATAA
Found at i:31594264 original size:49 final size:49
Alignment explanation
Indices: 31594142--31594244 Score: 140
Period size: 49 Copynumber: 2.1 Consensus size: 49
31594132 AGCCCTTAAG
* *
31594142 TTGAAAACCATTGTTGTC-GAGCTATCTGGGATGGTAAGATATGTCTATA
1 TTGAAAACAATCGTTGTCAG-GCTATCTGGGATGGTAAGATATGTCTATA
31594191 TTGAAAACAATCGTTGTCAGGCTATCTGGGATGGT-AGAATAT-TCATATA
1 TTGAAAACAATCGTTGTCAGGCTATCTGGGATGGTAAG-ATATGTC-TATA
31594240 TTGAA
1 TTGAA
31594245 TGCCATCTTT
Statistics
Matches: 49, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
48 4 0.08
49 44 0.90
50 1 0.02
ACGTcount: A:0.31, C:0.12, G:0.23, T:0.34
Consensus pattern (49 bp):
TTGAAAACAATCGTTGTCAGGCTATCTGGGATGGTAAGATATGTCTATA
Found at i:31600991 original size:72 final size:71
Alignment explanation
Indices: 31600835--31600994 Score: 173
Period size: 72 Copynumber: 2.2 Consensus size: 71
31600825 GGATTTCATG
** * * * *
31600835 ATCGATGGCTTGAGATCCAACATTTGTTGCGGATTCTCTGAAGCTTGTGTGAGCAGCATTAAATC
1 ATCGATGGCTTGAGATCCAACACGTGTTACGGATTCTCTGAAGCTTGTATGAGCAACATGAAATC
31600900 CTTGATT
66 CTT-ATT
* * *
31600907 ATCGATGACTTGAGATCCAGCACGTGTTACGGATTCTTTGAAGCTTGTATGAGCAACATCGAATT
1 ATCGATGGCTTGAGATCCAACACGTGTTACGGATTCTCTGAAGCTTGTATGAGCAACAT-GAA--
31600972 ATCC-T-TT
63 ATCCTTATT
31600979 A-CTGATGGCTTGAGAT
1 ATC-GATGGCTTGAGAT
31600995 TTGGCACGTG
Statistics
Matches: 74, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
71 1 0.01
72 66 0.89
73 2 0.03
74 1 0.01
75 4 0.05
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.34
Consensus pattern (71 bp):
ATCGATGGCTTGAGATCCAACACGTGTTACGGATTCTCTGAAGCTTGTATGAGCAACATGAAATC
CTTATT
Found at i:31615039 original size:15 final size:15
Alignment explanation
Indices: 31615001--31615041 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
31614991 TACATAATAG
31615001 TAAAAAAATT-AAAA
1 TAAAAAAATTCAAAA
* *
31615015 T-TACAAATTCAAAA
1 TAAAAAAATTCAAAA
31615029 TAAAAAAATTCAA
1 TAAAAAAATTCAA
31615042 TTTTTAATAC
Statistics
Matches: 21, Mismatches: 4, Indels: 3
0.75 0.14 0.11
Matches are distributed among these distances:
13 6 0.29
14 6 0.29
15 9 0.43
ACGTcount: A:0.68, C:0.07, G:0.00, T:0.24
Consensus pattern (15 bp):
TAAAAAAATTCAAAA
Found at i:31622543 original size:25 final size:25
Alignment explanation
Indices: 31622509--31622560 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
31622499 ATGGTCATAA
31622509 CATGACCCATTTACAAACCCAAATC
1 CATGACCCATTTACAAACCCAAATC
31622534 CATGACCCATTTACAAACCCAAATC
1 CATGACCCATTTACAAACCCAAATC
31622559 CA
1 CA
31622561 AATACCTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.40, C:0.37, G:0.04, T:0.19
Consensus pattern (25 bp):
CATGACCCATTTACAAACCCAAATC
Found at i:31623804 original size:23 final size:23
Alignment explanation
Indices: 31623778--31623823 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
31623768 GATTTAAACG
*
31623778 GTTGTTAAATTATGTTTTA-AATA
1 GTTGTT-AACTATGTTTTACAATA
*
31623801 GTTGTTGACTATGTTTTACAATA
1 GTTGTTAACTATGTTTTACAATA
31623824 TCATTATAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.30, C:0.04, G:0.15, T:0.50
Consensus pattern (23 bp):
GTTGTTAACTATGTTTTACAATA
Found at i:31624050 original size:20 final size:20
Alignment explanation
Indices: 31624027--31624065 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
31624017 TATTTTTAAA
*
31624027 ATTTAAAATATATTTTATAT
1 ATTTAAAATAAATTTTATAT
*
31624047 ATTTAAATTAAATTTTATA
1 ATTTAAAATAAATTTTATA
31624066 AACAATTCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
ATTTAAAATAAATTTTATAT
Found at i:31626061 original size:39 final size:37
Alignment explanation
Indices: 31625994--31626127 Score: 110
Period size: 39 Copynumber: 3.5 Consensus size: 37
31625984 ACCAGAATGG
* *
31625994 CACCCAGTGTCTCATCGGATAGTTCGAAGCAATAGTTGA
1 CACCCAGTGTCTCATCGGA-AATCCGAAG-AATAGTTGA
*
31626033 CACCCAGTGTCTCATCGGCAAATCCGAAGAA-AGTTGG
1 CACCCAGTGTCTCATCGG-AAATCCGAAGAATAGTTGA
* ** *
31626070 TACCCAGTACCTCATCGAAACTATCCGAAGAAATAAAG-TGA
1 CACCCAGTGTCTCATCGGAA--ATCCGAAG-AAT--AGTTGA
*
31626111 CATCCAGTGTCTCATCG
1 CACCCAGTGTCTCATCG
31626128 ACTCGAGGTC
Statistics
Matches: 76, Mismatches: 12, Indels: 12
0.76 0.12 0.12
Matches are distributed among these distances:
36 2 0.03
37 19 0.25
38 10 0.13
39 27 0.36
40 1 0.01
41 15 0.20
42 2 0.03
ACGTcount: A:0.31, C:0.26, G:0.20, T:0.22
Consensus pattern (37 bp):
CACCCAGTGTCTCATCGGAAATCCGAAGAATAGTTGA
Found at i:31626290 original size:37 final size:36
Alignment explanation
Indices: 31626219--31626291 Score: 101
Period size: 37 Copynumber: 2.0 Consensus size: 36
31626209 GTCTCCAAAT
* *
31626219 TCACATTTCAATTCAATTTCACTTTTTCACTTTCAA
1 TCACATTTCAATTCAAATTCACTTTTCCACTTTCAA
* *
31626255 TCACATTTCGATTCAAAATTCACTTTTCCATTTTCAA
1 TCACATTTCAATTC-AAATTCACTTTTCCACTTTCAA
31626292 GTCAATATTC
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
36 13 0.41
37 19 0.59
ACGTcount: A:0.29, C:0.25, G:0.01, T:0.45
Consensus pattern (36 bp):
TCACATTTCAATTCAAATTCACTTTTCCACTTTCAA
Found at i:31626547 original size:3 final size:3
Alignment explanation
Indices: 31626539--31626586 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
31626529 AATCTCACTC
31626539 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
31626587 CTTACCTCAC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Done.